diff --git a/.gitignore b/.gitignore
index ce0aaf015693c03f1185e7896fb1c47cc235f43f..59586d5d406d6a479f908699febc85f3ed91659f 100644
--- a/.gitignore
+++ b/.gitignore
@@ -6,4 +6,7 @@ src/generated
gradle.properties
/out
/build
-InstanceSettings.xml
\ No newline at end of file
+InstanceSettings.xml
+/bin/
+.classpath
+.project
diff --git a/build.gradle b/build.gradle
index 63ac93f199ff13d7dc16e4fc00fa1279e9cf75b0..cb5119b4fbc7e7eaa27142066fa602917896fb48 100644
--- a/build.gradle
+++ b/build.gradle
@@ -34,7 +34,6 @@ buildscript {
jcenter()
}
dependencies {
- classpath "org.nrg.xnat.build:gradle-xnat-plugin:1.7.0-SNAPSHOT"
classpath "com.bmuschko:gradle-cargo-plugin:2.2.2"
classpath "com.bmuschko:gradle-tomcat-plugin:2.2.4"
}
@@ -62,7 +61,6 @@ repositories {
jcenter()
}
-apply plugin: 'xnat'
apply plugin: 'groovy'
apply plugin: 'java'
apply plugin: 'war'
@@ -152,6 +150,9 @@ dependencies {
compile "org.nrg:anonymize:${vXnat}"
compile "org.nrg:mail:${vXnat}"
compile "org.nrg:notify:${vXnat}"
+ compile("org.nrg.xnat:xnat-data-plugin:${vXnat}"){
+ transitive = false
+ }
compile "org.nrg:dicom-xnat-mx:1.7.0-SNAPSHOT"
compile "org.nrg:dicom-xnat-sop:1.7.0-SNAPSHOT"
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseArcArchivespecification.java b/src/main/java/org/nrg/xdat/om/base/BaseArcArchivespecification.java
deleted file mode 100644
index 836846330a196c0e52fb747d97c7006c13760082..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseArcArchivespecification.java
+++ /dev/null
@@ -1,332 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseArcArchivespecification
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.apache.commons.lang.ArrayUtils;
-import org.nrg.mail.api.NotificationSubscriberProvider;
-import org.nrg.mail.api.NotificationType;
-import org.nrg.xdat.model.ArcArchivespecificationNotificationTypeI;
-
-import org.nrg.xdat.model.ArcPathinfoI;
-import org.nrg.xdat.model.ArcProjectI;
-import org.nrg.xdat.om.ArcProject;
-import org.nrg.xdat.om.base.auto.AutoArcArchivespecification;
-import org.nrg.xdat.turbine.utils.AdminUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-import java.util.List;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseArcArchivespecification extends AutoArcArchivespecification implements NotificationSubscriberProvider {
-
- public BaseArcArchivespecification(ItemI item)
- {
- super(item);
- injectProvider();
- }
-
- public BaseArcArchivespecification(UserI user)
- {
- super(user);
- injectProvider();
- }
-
- /*
- * @deprecated Use BaseArcArchivespecification(UserI user)
- **/
- public BaseArcArchivespecification()
- {}
-
- public BaseArcArchivespecification(Hashtable properties, UserI user)
- {
- super(properties,user);
- injectProvider();
- }
-
- public String[] getSubscribers(NotificationType notificationType) {
- for (ArcArchivespecificationNotificationTypeI type : getNotificationTypes_notificationType()) {
- if (type.getNotificationType().equalsIgnoreCase(notificationType.id())) {
- String[] addresses = type.getEmailAddresses().split("[\\s]*,[\\s]*");
- if (ArrayUtils.isEmpty(addresses)) {
- return null;
- }
- return addresses;
- }
- }
-
- return null;
- }
-
- public String getGlobalArchivePath(){
- String path = null;
- ArcPathinfoI pathInfo= this.getGlobalpaths();
- if (pathInfo!=null){
- path=pathInfo.getArchivepath();
- }
- if (path==null){
- path =".";
- }
- path = path.replace('\\', '/');
- if (!path.endsWith("/")){
- path = path +"/";
- }
- return path;
- }
-
- public String getGlobalPrearchivePath(){
- String path = null;
- ArcPathinfoI pathInfo= this.getGlobalpaths();
- if (pathInfo!=null){
- path=pathInfo.getPrearchivepath();
- }
- if (path==null){
- path =".";
- }
- path = path.replace('\\', '/');
- if (!path.endsWith("/")){
- path = path +"/";
- }
- return path;
- }
-
- public String getGlobalCachePath(){
- String path = null;
- ArcPathinfoI pathInfo= this.getGlobalpaths();
- if (pathInfo!=null){
- path=pathInfo.getCachepath();
- }
- if (path==null){
- path =".";
- }
- path = path.replace('\\', '/');
- if (!path.endsWith("/")){
- path = path +"/";
- }
- return path;
- }
-
- public String getGlobalBuildPath(){
- String path = null;
- ArcPathinfoI pathInfo= this.getGlobalpaths();
- if (pathInfo!=null){
- path=pathInfo.getBuildpath();
- }
- if (path==null){
- path =".";
- }
- path = path.replace('\\', '/');
- if (!path.endsWith("/")){
- path = path +"/";
- }
- return path;
- }
-
- private String addEndingSlash(String path){
- path = path.replace('\\', '/');
- if (!path.endsWith("/")){
- path = path +"/";
- }
- return path;
- }
-
- public String getArchivePathForProject(String id){
- String path = null;
- List<ArcProjectI> projects=this.getProjects_project();
- for (ArcProjectI p : projects){
- if (p.getId().equals(id)){
- ArcPathinfoI pathInfo= p.getPaths();
- if (pathInfo!=null){
- path=pathInfo.getArchivepath();
- }
- break;
- }
- }
- if (path==null || path.trim().equals("")){
- ArcPathinfoI pathInfo= this.getGlobalpaths();
- if (pathInfo!=null){
- path=addEndingSlash(pathInfo.getArchivepath())+id;
- }
- }
- if (path==null){
- path =addEndingSlash(".")+id;
- }
- path = path.replace('\\', '/');
- if (!path.endsWith("/")){
- path = path +"/";
- }
- return path;
- }
-
- public String getCachePathForProject(String id){
- String path = null;
- List<ArcProjectI> projects=this.getProjects_project();
- for (ArcProjectI p : projects){
- if (p.getId().equals(id)){
- ArcPathinfoI pathInfo= p.getPaths();
- if (pathInfo!=null){
- path=pathInfo.getCachepath();
- }
- break;
- }
- }
- if (path==null || path.trim().equals("")){
- ArcPathinfoI pathInfo= this.getGlobalpaths();
- if (pathInfo!=null){
- path=addEndingSlash(pathInfo.getCachepath())+id;
- }
- }
- if (path==null){
- path =addEndingSlash(".")+id;
- }
- path = path.replace('\\', '/');
- if (!path.endsWith("/")){
- path = path +"/";
- }
- return path;
- }
-
- public Integer getPrearchiveCodeForProject(String id){
- List<ArcProjectI> projects=this.getProjects_project();
- for (ArcProjectI p : projects){
- if (p.getId().equals(id)){
- return p.getPrearchiveCode();
- }
- }
- return null;
- }
-
- public Integer getAutoQuarantineCodeForProject(String id){
- List<ArcProjectI> projects=this.getProjects_project();
- for (ArcProjectI p : projects){
- if (p.getId().equals(id)){
- return p.getQuarantineCode();
- }
- }
- return null;
- }
-
- public String getPrearchivePathForProject(String id){
- String path = null;
- List<ArcProjectI> projects=this.getProjects_project();
- for (ArcProjectI p : projects){
- if (p.getId().equals(id)){
- ArcPathinfoI pathInfo= p.getPaths();
- if (pathInfo!=null){
- path=pathInfo.getPrearchivepath();
- }
- break;
- }
- }
- if (path==null || path.trim().equals("")){
- ArcPathinfoI pathInfo= this.getGlobalpaths();
- if (pathInfo!=null){
- path=addEndingSlash(pathInfo.getPrearchivepath())+id;
- }
- }
- if (path==null){
- path =addEndingSlash(".")+id;
- }
- path = path.replace('\\', '/');
- if (!path.endsWith("/")){
- path = path +"/";
- }
- return path;
- }
-
- public String getBuildPathForProject(String id){
- String path = null;
- List<ArcProjectI> projects=this.getProjects_project();
- for (ArcProjectI p : projects){
- if (p.getId().equals(id)){
- ArcPathinfoI pathInfo= p.getPaths();
- if (pathInfo!=null){
- path=pathInfo.getBuildpath();
- }
- break;
- }
- }
- if (path==null || path.trim().equals("")){
- ArcPathinfoI pathInfo= this.getGlobalpaths();
- if (pathInfo!=null){
- path=pathInfo.getBuildpath();
- }
- }
- if (path==null){
- path =".";
- }
- path = path.replace('\\', '/');
- if (!path.endsWith("/")){
- path = path +"/";
- }
- return path;
- }
-
- public ArcProject getProjectArc(String id){
- List<ArcProjectI> projects=getProjects_project();
- for (ArcProjectI p : projects){
- if (p.getId().equals(id)){
- return (ArcProject)p;
- }
- }
- return null;
- }
-
- public boolean isComplete(){
- if (this.getSiteId()==null || this.getSiteId().equals("")){
- return false;
- }
-
- if (this.getSiteAdminEmail()==null || this.getSiteAdminEmail().equals("")){
- return false;
- }
-
- if (this.getGlobalpaths()==null){
- return false;
- }
-
- if (this.getGlobalpaths().getArchivepath()==null || this.getGlobalpaths().getArchivepath().equals("")){
- return false;
- }
-
- if (this.getGlobalpaths().getPrearchivepath()==null || this.getGlobalpaths().getPrearchivepath().equals("")){
- return false;
- }
-
- if (this.getGlobalpaths().getCachepath()==null || this.getGlobalpaths().getCachepath().equals("")){
- return false;
- }
-
- if (this.getGlobalpaths().getBuildpath()==null || this.getGlobalpaths().getBuildpath().equals("")){
- return false;
- }
-
- if (this.getGlobalpaths().getFtppath()==null || this.getGlobalpaths().getFtppath().equals("")){
- return false;
- }
-
- return true;
- }
-
- /**
- * This is very low-rent dependency injection.
- */
- private void injectProvider() {
- if (AdminUtils.getNotificationSubscriberProvider() == null) {
- AdminUtils.setNotificationSubscriberProvider(this);
-}
- }
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseArcArchivespecificationNotificationType.java b/src/main/java/org/nrg/xdat/om/base/BaseArcArchivespecificationNotificationType.java
deleted file mode 100644
index 40d2f31404d9eda2e8d4ce04c3be82000ed05cdf..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseArcArchivespecificationNotificationType.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseArcArchivespecificationNotificationType
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoArcArchivespecificationNotificationType;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseArcArchivespecificationNotificationType extends AutoArcArchivespecificationNotificationType {
-
- public BaseArcArchivespecificationNotificationType(ItemI item)
- {
- super(item);
- }
-
- public BaseArcArchivespecificationNotificationType(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseArcArchivespecificationNotificationType(UserI user)
- **/
- public BaseArcArchivespecificationNotificationType()
- {}
-
- public BaseArcArchivespecificationNotificationType(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseArcFieldspecification.java b/src/main/java/org/nrg/xdat/om/base/BaseArcFieldspecification.java
deleted file mode 100644
index 65f10048757d49fae5a43cf1df7cc868f5364499..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseArcFieldspecification.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseArcFieldspecification
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoArcFieldspecification;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseArcFieldspecification extends AutoArcFieldspecification {
-
- public BaseArcFieldspecification(ItemI item)
- {
- super(item);
- }
-
- public BaseArcFieldspecification(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseArcFieldspecification(UserI user)
- **/
- public BaseArcFieldspecification()
- {}
-
- public BaseArcFieldspecification(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseArcPathinfo.java b/src/main/java/org/nrg/xdat/om/base/BaseArcPathinfo.java
deleted file mode 100644
index d4b704f77fdb8fab61544ea4ba449748b700164d..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseArcPathinfo.java
+++ /dev/null
@@ -1,102 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseArcPathinfo
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoArcPathinfo;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseArcPathinfo extends AutoArcPathinfo {
-
- public BaseArcPathinfo(ItemI item)
- {
- super(item);
- }
-
- public BaseArcPathinfo(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseArcPathinfo(UserI user)
- **/
- public BaseArcPathinfo()
- {}
-
- public BaseArcPathinfo(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
- public String getArchivepath(){
- try{
- String path = super.getArchivepath();
-
- path = path.replace('\\', '/');
- if (!path.endsWith("/")){
- path = path +"/";
- }
- return path;
- } catch (Throwable e1) {logger.error(e1);return null;}
- }
- /**
- * @return Returns the prearchivePath.
- */
- public String getPrearchivepath(){
- try{
- String path = super.getPrearchivepath();
-
- path = path.replace('\\', '/');
- if (!path.endsWith("/")){
- path = path +"/";
- }
- return path;
- } catch (Throwable e1) {logger.error(e1);return null;}
- }
-
- /**
- * @return Returns the cachePath.
- */
- public String getCachepath(){
- try{
- String path = super.getCachepath();
-
- path = path.replace('\\', '/');
- if (!path.endsWith("/")){
- path = path +"/";
- }
- return path;
- } catch (Throwable e1) {logger.error(e1);return null;}
- }
-
- /**
- * @return Returns the buildPath.
- */
- public String getBuildpath(){
- try{
- String path = super.getBuildpath();
-
- path = path.replace('\\', '/');
- if (!path.endsWith("/")){
- path = path +"/";
- }
- return path;
- } catch (Throwable e1) {logger.error(e1);return null;}
- }
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseArcPipelinedata.java b/src/main/java/org/nrg/xdat/om/base/BaseArcPipelinedata.java
deleted file mode 100644
index 749adef8ab2f7e968f5f7c8ee26e80e61dfea692..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseArcPipelinedata.java
+++ /dev/null
@@ -1,96 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseArcPipelinedata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.model.ArcPipelineparameterdataI;
-import org.nrg.xdat.om.ArcPipelineparameterdata;
-import org.nrg.xdat.om.base.auto.AutoArcPipelinedata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-import org.nrg.xft.exception.ElementNotFoundException;
-import org.nrg.xft.exception.FieldNotFoundException;
-import org.nrg.xft.exception.XFTInitException;
-import org.nrg.xft.security.UserI;
-
-import java.util.ArrayList;
-import java.util.Hashtable;
-import java.util.List;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseArcPipelinedata extends AutoArcPipelinedata {
-
- public BaseArcPipelinedata(ItemI item)
- {
- super(item);
- }
-
- public BaseArcPipelinedata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseArcPipelinedata(UserI user)
- **/
- public BaseArcPipelinedata()
- {}
-
- public BaseArcPipelinedata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
- public String getCommand(XFTItem itemOfExpectedXsiType) throws ElementNotFoundException, FieldNotFoundException, XFTInitException {
- String rtn = "";
- if (getLocation() != null) {
- rtn = " -pipeline " + getLocation() + " " ;
- }
- //rtn += getName();
- List<ArcPipelineparameterdataI> parameters = this.getParameters_parameter();
- for (int i = 0; i < parameters.size(); i++) {
- ArcPipelineparameterdata param = (ArcPipelineparameterdata) parameters.get(i);
- String schemaLink = param.getSchemalink();
- String values = null;
- if (schemaLink != null) {
- Object o = itemOfExpectedXsiType.getProperty(schemaLink, true);
- if (o != null && values == null ) values = "";
- try {
- ArrayList<XFTItem> matches = (ArrayList<XFTItem>) o;
- for (int j = 0; j < matches.size(); j++) {
- values += matches.get(j) + ",";
- }
- }catch(ClassCastException cce) {
- values += o + ",";
- }
- if (values != null && values.endsWith(",")) {
- values = values.substring(0, values.length() -1);
- }
- }else {
- values = param.getCsvvalues();
- }
- if (values != null) {
- rtn += " -parameter " + param.getName() + "=" + values;
- }
- }
- return rtn;
- }
-
- public boolean hasCutomwebpage() {
- boolean rtn = false;
- if (getCustomwebpage() !=null)
- rtn = true;
- return rtn;
- }
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseArcPipelineparameterdata.java b/src/main/java/org/nrg/xdat/om/base/BaseArcPipelineparameterdata.java
deleted file mode 100644
index 50bf784e27cbafe4a643f9667930a981253d7a34..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseArcPipelineparameterdata.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseArcPipelineparameterdata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoArcPipelineparameterdata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseArcPipelineparameterdata extends AutoArcPipelineparameterdata {
-
- public BaseArcPipelineparameterdata(ItemI item)
- {
- super(item);
- }
-
- public BaseArcPipelineparameterdata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseArcPipelineparameterdata(UserI user)
- **/
- public BaseArcPipelineparameterdata()
- {}
-
- public BaseArcPipelineparameterdata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseArcProject.java b/src/main/java/org/nrg/xdat/om/base/BaseArcProject.java
deleted file mode 100644
index 26c27dc91e6e16cbdfe719321ef09d9e3c008596..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseArcProject.java
+++ /dev/null
@@ -1,317 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseArcProject
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.apache.commons.lang.StringUtils;
-import org.nrg.pipeline.PipelineRepositoryManager;
-import org.nrg.xdat.model.ArcPipelinedataI;
-import org.nrg.xdat.model.ArcProjectDescendantI;
-import org.nrg.xdat.model.ArcProjectDescendantPipelineI;
-import org.nrg.xdat.model.ArcProjectPipelineI;
-import org.nrg.xdat.om.ArcProjectDescendant;
-import org.nrg.xdat.om.ArcProjectDescendantPipeline;
-import org.nrg.xdat.om.ArcProjectPipeline;
-import org.nrg.xdat.om.base.auto.AutoArcProject;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-import org.nrg.xnat.exceptions.PipelineNotFoundException;
-
-import java.util.ArrayList;
-import java.util.Hashtable;
-import java.util.Iterator;
-import java.util.List;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseArcProject extends AutoArcProject {
-
- public BaseArcProject(ItemI item)
- {
- super(item);
- }
-
- public BaseArcProject(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseArcProject(UserI user)
- **/
- public BaseArcProject()
- {}
-
- public BaseArcProject(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
- @Override
- public Integer getPrearchiveCode() {
- Integer i= super.getPrearchiveCode();
- if(i==null){
- return new Integer(0);
- }else{
- return i;
- }
- }
-
- @Override
- public Integer getQuarantineCode() {
- Integer i= super.getQuarantineCode();
- if(i==null){
- return new Integer(0);
- }else{
- return i;
- }
- }
-
- public List<ArcProjectDescendantPipelineI> getPipelinesForDescendant(String xsiType) {
- List<ArcProjectDescendantPipelineI>rtn = new ArrayList<ArcProjectDescendantPipelineI>();
- List<ArcProjectDescendant> descendants = getPipelines_descendants_descendant();
- if (xsiType == null || descendants == null) return rtn;
- for (int i = 0; i < descendants.size(); i++) {
- if (xsiType.equals(descendants.get(i).getXsitype()) || PipelineRepositoryManager.ALL_DATA_TYPES.equals(descendants.get(i).getXsitype())) {
- List<ArcProjectDescendantPipelineI> pipelines = descendants.get(i).getPipeline();
- if (pipelines != null && pipelines.size() > 0)
- rtn.addAll(pipelines);
- }
- }
- return rtn;
- }
-
-
- public ArrayList<ArcPipelinedataI> getPipelinesForDescendantLikeStepId(String xsiType, String pipelineStep) throws PipelineNotFoundException {
- ArrayList<ArcPipelinedataI> rtn = new ArrayList<ArcPipelinedataI>();
- List<ArcProjectDescendantPipelineI> descendantPipelines = getPipelinesForDescendant(xsiType);
- for (int i = 0; i < descendantPipelines.size(); i++) {
- if (descendantPipelines.get(i).getStepid()!=null && descendantPipelines.get(i).getStepid().startsWith(pipelineStep)) {
- rtn.add(((ArcProjectDescendantPipeline)descendantPipelines.get(i)).getPipelinedata());
- }
- }
- //if (rtn.size() == 0) throw new PipelineNotFoundException("A Pipeline identified by " + pipelineStep + " could not be found for " + xsiType + " for project " + getId());
- return rtn;
- }
-
- public ArrayList<ArcPipelinedataI> getPipelinesForDescendant(String xsiType, String pipelineStep, String match) throws PipelineNotFoundException {
- ArrayList<ArcPipelinedataI> rtn = new ArrayList<ArcPipelinedataI>();
- if (match.equalsIgnoreCase("EXACT")) {
- ArcPipelinedataI pipeline = getPipelineForDescendant(xsiType, pipelineStep);
- rtn.add(pipeline);
- }else if (match.equalsIgnoreCase("LIKE")) {
- rtn = getPipelinesForDescendantLikeStepId(xsiType, pipelineStep);
- }
- //if (rtn.size() == 0) throw new PipelineNotFoundException("A Pipeline identified by " + pipelineStep + " could not be found for " + xsiType + " for project " + getId());
- return rtn;
-
- }
-
- public ArcPipelinedataI getPipelineForDescendant(String xsiType, String pipelineStep) throws PipelineNotFoundException {
- ArcPipelinedataI rtn = null;
- List<ArcProjectDescendantPipelineI> descendantPipelines = getPipelinesForDescendant(xsiType);
- for (int i = 0; i < descendantPipelines.size(); i++) {
- if (descendantPipelines.get(i).getStepid().equals(pipelineStep)) {
- rtn = ((ArcProjectDescendantPipeline)descendantPipelines.get(i)).getPipelinedata();
- break;
- }
- }
- if (rtn == null) throw new PipelineNotFoundException("A Pipeline identified by " + pipelineStep + " could not be found for " + xsiType + " for project " + getId());
- return rtn;
- }
-
- public ArcPipelinedataI getPipelineForDescendantByPath(String xsiType, String pipelinePath) throws PipelineNotFoundException {
- ArcPipelinedataI rtn = null;
- List<ArcProjectDescendantPipelineI> descendantPipelines = getPipelinesForDescendant(xsiType);
- for (int i = 0; i < descendantPipelines.size(); i++) {
- if (descendantPipelines.get(i).getLocation().equals(pipelinePath)) {
- rtn = ((ArcProjectDescendantPipeline)descendantPipelines.get(i)).getPipelinedata();
- break;
- }
- }
- if (rtn == null) throw new PipelineNotFoundException("A Pipeline identified by " + pipelinePath + " could not be found for " + xsiType + " for project " + getId());
- return rtn;
- }
-
- public ArcProjectDescendantPipeline getPipelineForDescendantEltByPath(String xsiType, String pipelinePath) throws PipelineNotFoundException {
- ArcProjectDescendantPipeline rtn = null;
- List<ArcProjectDescendantPipelineI> descendantPipelines = getPipelinesForDescendant(xsiType);
- for (int i = 0; i < descendantPipelines.size(); i++) {
- if (descendantPipelines.get(i).getLocation().equals(pipelinePath)) {
- rtn =((ArcProjectDescendantPipeline)descendantPipelines.get(i));
- break;
- }
- }
- if (rtn == null) throw new PipelineNotFoundException("A Pipeline identified by " + pipelinePath + " could not be found for " + xsiType + " for project " + getId());
- return rtn;
- }
-
- public int getPipelineForDescendantIndexByPath(String xsiType, String pipelinePath) throws PipelineNotFoundException {
- int rtn = -1;
- List<ArcProjectDescendantPipelineI> descendantPipelines = getPipelinesForDescendant(xsiType);
- for (int i = 0; i < descendantPipelines.size(); i++) {
- if (descendantPipelines.get(i).getLocation().equals(pipelinePath)) {
- rtn = i;
- break;
- }
- }
- if (rtn == -1) throw new PipelineNotFoundException("A Pipeline identified by " + pipelinePath + " could not be found for " + xsiType + " for project " + getId());
- return rtn;
- }
-
-
- public ArcPipelinedataI getPipeline(String pipelineStep) throws PipelineNotFoundException {
- ArcPipelinedataI rtn = null;
- List<ArcProjectPipelineI> pipelines =getPipelines_pipeline();
- for (int i = 0; i < pipelines.size(); i++) {
- if (pipelines.get(i).getStepid().equals(pipelineStep)) {
- rtn = ((ArcProjectPipeline)pipelines.get(i)).getPipelinedata();
- break;
- }
- }
- if (rtn == null) throw new PipelineNotFoundException("A Pipeline identified by " + pipelineStep + " could not be found for project " + getId());
- return rtn;
- }
-
- /**
- * Return root level pipeline with matching location and stepId (or null)
- * @param location
- * @param stepId
- * @return
- */
- public ArcProjectPipelineI getPipeline(String location, String stepId){
- for (ArcProjectPipelineI pipe:getPipelines_pipeline()) {
- if (StringUtils.equals(pipe.getLocation(),location) && StringUtils.equals(pipe.getStepid(),stepId)) {
- return pipe;
- }
- }
-
- return null;
- }
-
- /**
- * Return descendant pipeline with matching xsiType, location and stepId (or null)
- * @param xsiType
- * @param location
- * @param stepId
- * @return
- */
- public ArcProjectDescendantPipelineI getDescendantPipeline(String xsiType, String location, String stepId){
- for (final ArcProjectDescendantPipelineI pipe: getPipelinesForDescendant(xsiType)) {
- if (StringUtils.equals(pipe.getLocation(),location) && StringUtils.equals(pipe.getStepid(),stepId)) {
- return pipe;
- }
- }
-
- return null;
- }
-
-
- public ArcProjectPipeline getProjectPipeline(String pipelineStep) throws PipelineNotFoundException {
- ArcProjectPipeline rtn = null;
- List<ArcProjectPipelineI> pipelines =getPipelines_pipeline();
- for (int i = 0; i < pipelines.size(); i++) {
- if (pipelines.get(i).getStepid().equals(pipelineStep)) {
- return ((ArcProjectPipeline)pipelines.get(i));
- }
- }
- return null;
- }
-
-
-
- public ArcPipelinedataI getPipelineByPath(String pipelinePath) throws PipelineNotFoundException {
- ArcPipelinedataI rtn = null;
- List<ArcProjectPipelineI> pipelines =getPipelines_pipeline();
- for (int i = 0; i < pipelines.size(); i++) {
- if (pipelines.get(i).getLocation().equals(pipelinePath)) {
- rtn = ((ArcProjectPipeline)pipelines.get(i)).getPipelinedata();
- break;
- }
- }
- if (rtn == null) throw new PipelineNotFoundException("A Pipeline identified by " + pipelinePath + " could not be found for project " + getId());
- return rtn;
- }
-
- public ArcProjectPipeline getPipelineEltByPath(String pipelinePath) throws PipelineNotFoundException {
- ArcProjectPipeline rtn = null;
- List<ArcProjectPipelineI> pipelines =getPipelines_pipeline();
- for (int i = 0; i < pipelines.size(); i++) {
- if (pipelines.get(i).getLocation().equals(pipelinePath)) {
- rtn = (ArcProjectPipeline)pipelines.get(i);
- break;
- }
- }
- if (rtn == null) throw new PipelineNotFoundException("A Pipeline identified by " + pipelinePath + " could not be found for project " + getId());
- return rtn;
- }
-
- public int getPipelineIndexByPath(String pipelinePath) throws PipelineNotFoundException {
- int rtn = -1;
- List<ArcProjectPipelineI> pipelines =getPipelines_pipeline();
- for (int i = 0; i < pipelines.size(); i++) {
- if (pipelines.get(i).getLocation().equals(pipelinePath)) {
- rtn = i;
- break;
- }
- }
- if (rtn == -1) throw new PipelineNotFoundException("A Pipeline identified by " + pipelinePath + " could not be found for project " + getId());
- return rtn;
- }
-
-
- public ArcProjectDescendant getDescendant(String xsiType) {
- ArcProjectDescendant rtn = null;
- List<ArcProjectDescendantI> descendants = getPipelines_descendants_descendant();
- if (xsiType == null || descendants == null) return rtn;
- for (int i = 0; i < descendants.size(); i++) {
- if (descendants.get(i).getXsitype().equals(xsiType)) {
- rtn = (ArcProjectDescendant)descendants.get(i);
- break;
- }
- }
- return rtn;
- }
-
- public void removeAllDescendantPipelines() {
- List<ArcProjectDescendantI> descendants = getPipelines_descendants_descendant();
- if (descendants.size() > 0) {
- int i = 0;
- Iterator iter = descendants.iterator();
- while (iter.hasNext()) {
- removePipelines_descendants_descendant(i);
- descendants = getPipelines_descendants_descendant();
- iter = descendants.iterator();
- }
- }
- }
-
- public void removeAllPipelines() {
- removeAllDescendantPipelines();
- removeAllProjectPipelines();
- }
-
- public void removeAllProjectPipelines() {
- List<ArcProjectPipelineI> projPipeline = getPipelines_pipeline();
- if (projPipeline.size() > 0) {
- int i = 0;
- Iterator iter = projPipeline.iterator();
- while (iter.hasNext()) {
- this.removePipelines_pipeline(i);
- projPipeline = getPipelines_pipeline();
- iter = projPipeline.iterator();
- }
- }
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseArcProjectDescendant.java b/src/main/java/org/nrg/xdat/om/base/BaseArcProjectDescendant.java
deleted file mode 100644
index cd18839711d41117d75ec7a6a4414203a16ca340..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseArcProjectDescendant.java
+++ /dev/null
@@ -1,78 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseArcProjectDescendant
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.model.ArcProjectDescendantPipelineI;
-import org.nrg.xdat.om.ArcProjectDescendantPipeline;
-import org.nrg.xdat.om.base.auto.AutoArcProjectDescendant;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-import org.nrg.xnat.exceptions.PipelineNotFoundException;
-
-import java.util.Hashtable;
-import java.util.List;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseArcProjectDescendant extends AutoArcProjectDescendant {
-
- public BaseArcProjectDescendant(ItemI item)
- {
- super(item);
- }
-
- public BaseArcProjectDescendant(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseArcProjectDescendant(UserI user)
- **/
- public BaseArcProjectDescendant()
- {}
-
- public BaseArcProjectDescendant(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-
- public int getPipelineIndex(String pipelinePath) throws PipelineNotFoundException {
- int i = -1;
- List<ArcProjectDescendantPipelineI> pipelines = getPipeline();
- for (int j = 0; j <pipelines.size(); j++) {
- if (pipelines.get(j).getLocation().equals(pipelinePath)) {
- i = j;
- break;
- }
- }
- if (i == -1) throw new PipelineNotFoundException("Couldnt find pipelines located at " + pipelinePath + " for " + getXsitype());
- return i;
- }
-
- public ArcProjectDescendantPipeline getPipeline(String pipelinePath) throws PipelineNotFoundException {
- ArcProjectDescendantPipeline rtn = null;
- List<ArcProjectDescendantPipelineI> pipelines = getPipeline();
- for (int j = 0; j <pipelines.size(); j++) {
- if (pipelines.get(j).getLocation().equals(pipelinePath)) {
- rtn = (ArcProjectDescendantPipeline)pipelines.get(j);
- break;
- }
- }
- if (rtn == null) throw new PipelineNotFoundException("Couldnt find pipelines located at " + pipelinePath + " for " + getXsitype());
- return rtn;
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseArcProjectDescendantPipeline.java b/src/main/java/org/nrg/xdat/om/base/BaseArcProjectDescendantPipeline.java
deleted file mode 100644
index 850eb0f80bf6e4bdda3605f10299794761ef6a8b..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseArcProjectDescendantPipeline.java
+++ /dev/null
@@ -1,54 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseArcProjectDescendantPipeline
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoArcProjectDescendantPipeline;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseArcProjectDescendantPipeline extends AutoArcProjectDescendantPipeline {
-
- public BaseArcProjectDescendantPipeline(ItemI item)
- {
- super(item);
- }
-
- public BaseArcProjectDescendantPipeline(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseArcProjectDescendantPipeline(UserI user)
- **/
- public BaseArcProjectDescendantPipeline()
- {}
-
- public BaseArcProjectDescendantPipeline(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
- public boolean hasCustomwebpage() {
- boolean rtn = false;
- if (getCustomwebpage() !=null)
- rtn = true;
- return rtn;
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseArcProjectPipeline.java b/src/main/java/org/nrg/xdat/om/base/BaseArcProjectPipeline.java
deleted file mode 100644
index afe4f33412967c28b91225b938ebbfb4c396fbe2..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseArcProjectPipeline.java
+++ /dev/null
@@ -1,56 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseArcProjectPipeline
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoArcProjectPipeline;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseArcProjectPipeline extends AutoArcProjectPipeline {
-
- public BaseArcProjectPipeline(ItemI item)
- {
- super(item);
- }
-
- public BaseArcProjectPipeline(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseArcProjectPipeline(UserI user)
- **/
- public BaseArcProjectPipeline()
- {}
-
- public BaseArcProjectPipeline(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
- public boolean hasCustomwebpage() {
- boolean rtn = false;
- if (getCustomwebpage()!= null) {
- rtn = true;
- }
- return rtn;
- }
-
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseArcProperty.java b/src/main/java/org/nrg/xdat/om/base/BaseArcProperty.java
deleted file mode 100644
index d949d7067f0035c07aa7e15e490f0ba66555559d..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseArcProperty.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseArcProperty
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoArcProperty;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseArcProperty extends AutoArcProperty {
-
- public BaseArcProperty(ItemI item)
- {
- super(item);
- }
-
- public BaseArcProperty(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseArcProperty(UserI user)
- **/
- public BaseArcProperty()
- {}
-
- public BaseArcProperty(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BasePipePipelinedetails.java b/src/main/java/org/nrg/xdat/om/base/BasePipePipelinedetails.java
deleted file mode 100644
index bee5e284cfba17930f96ff9877d20e5221ca480d..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BasePipePipelinedetails.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BasePipePipelinedetails
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoPipePipelinedetails;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BasePipePipelinedetails extends AutoPipePipelinedetails {
-
- public BasePipePipelinedetails(ItemI item)
- {
- super(item);
- }
-
- public BasePipePipelinedetails(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BasePipePipelinedetails(UserI user)
- **/
- public BasePipePipelinedetails()
- {}
-
- public BasePipePipelinedetails(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BasePipePipelinedetailsElement.java b/src/main/java/org/nrg/xdat/om/base/BasePipePipelinedetailsElement.java
deleted file mode 100644
index 61c76424f4663b04bafd46c0b9339778d512b4fd..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BasePipePipelinedetailsElement.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BasePipePipelinedetailsElement
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoPipePipelinedetailsElement;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BasePipePipelinedetailsElement extends AutoPipePipelinedetailsElement {
-
- public BasePipePipelinedetailsElement(ItemI item)
- {
- super(item);
- }
-
- public BasePipePipelinedetailsElement(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BasePipePipelinedetailsElement(UserI user)
- **/
- public BasePipePipelinedetailsElement()
- {}
-
- public BasePipePipelinedetailsElement(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BasePipePipelinedetailsParameter.java b/src/main/java/org/nrg/xdat/om/base/BasePipePipelinedetailsParameter.java
deleted file mode 100644
index 7c6e2ca1142a3407fc1f513d1e29089e60af77ee..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BasePipePipelinedetailsParameter.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BasePipePipelinedetailsParameter
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoPipePipelinedetailsParameter;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BasePipePipelinedetailsParameter extends AutoPipePipelinedetailsParameter {
-
- public BasePipePipelinedetailsParameter(ItemI item)
- {
- super(item);
- }
-
- public BasePipePipelinedetailsParameter(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BasePipePipelinedetailsParameter(UserI user)
- **/
- public BasePipePipelinedetailsParameter()
- {}
-
- public BasePipePipelinedetailsParameter(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BasePipePipelinerepository.java b/src/main/java/org/nrg/xdat/om/base/BasePipePipelinerepository.java
deleted file mode 100644
index 353957d299f72f4f9533273cfeb602cc5c426d77..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BasePipePipelinerepository.java
+++ /dev/null
@@ -1,568 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BasePipePipelinerepository
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import java.io.File;
-import java.util.ArrayList;
-import java.util.Enumeration;
-import java.util.Hashtable;
-import java.util.List;
-
-import org.nrg.pipeline.PipelineRepositoryManager;
-import org.nrg.xdat.model.ArcProjectDescendantI;
-import org.nrg.xdat.model.ArcProjectDescendantPipelineI;
-import org.nrg.xdat.model.ArcProjectPipelineI;
-import org.nrg.xdat.model.PipePipelinedetailsElementI;
-import org.nrg.xdat.model.PipePipelinedetailsI;
-import org.nrg.xdat.model.PipePipelinedetailsParameterI;
-import org.nrg.xdat.om.ArcPipelinedata;
-import org.nrg.xdat.om.ArcPipelineparameterdata;
-import org.nrg.xdat.om.ArcProject;
-import org.nrg.xdat.om.ArcProjectDescendant;
-import org.nrg.xdat.om.ArcProjectDescendantPipeline;
-import org.nrg.xdat.om.ArcProjectPipeline;
-import org.nrg.xdat.om.PipePipelinedetails;
-import org.nrg.xdat.om.PipePipelinedetailsParameter;
-import org.nrg.xdat.om.XnatProjectdata;
-import org.nrg.xdat.om.base.auto.AutoPipePipelinerepository;
-import org.nrg.xdat.security.ElementSecurity;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTTable;
-import org.nrg.xft.event.EventUtils;
-import org.nrg.xft.security.UserI;
-import org.nrg.xft.utils.SaveItemHelper;
-import org.nrg.xnat.turbine.utils.ArcSpecManager;
-
-import com.google.common.collect.Lists;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BasePipePipelinerepository extends AutoPipePipelinerepository {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(BasePipePipelinerepository.class);
-
- public BasePipePipelinerepository(ItemI item)
- {
- super(item);
- }
-
- public BasePipePipelinerepository(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BasePipePipelinerepository(UserI user)
- **/
- public BasePipePipelinerepository()
- {}
-
- public BasePipePipelinerepository(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
- /**
- * Helper method to output a list of the pipelines registered to this arcProject.
- *
- * [0]: Display name of XSI type
- * [1]: Elements generated by this pipeline
- * [2]: Pipeline name
- * [3]: Pipeline description
- * [4]: Pipeline location
- * [5]: Applies To
- * [6]: xsi:type
- * [7]: stepId
- *
- * @param arcProject
- * @return
- */
- public List<String[]> listPipelines(ArcProject arcProject){
- final List<String[]> _return=Lists.newArrayList();
- if(arcProject!=null){
- final List<ArcProjectPipelineI> pipelines = arcProject.getPipelines_pipeline();
- if (pipelines.size() > 0 ) {
- for (int i = 0; i < pipelines.size(); i++) {
- final PipePipelinedetails pipeline = getPipeline(pipelines.get(i).getLocation());
- //TODO fix bug in project pipeline delete (currently is not removed correctly from projects), until then, need this check
- if (pipeline != null) {
- final String[] rowEntries = new String[8];
- rowEntries[0] = getDisplayName(XnatProjectdata.SCHEMA_ELEMENT_NAME);
- rowEntries[1] = getElementsGeneratedBy(pipeline);
- rowEntries[2] = pipelines.get(i).getName();
- rowEntries[3] = pipeline.getDescription();
- rowEntries[4] = pipelines.get(i).getLocation();
- rowEntries[5] = pipeline.getAppliesto();
- rowEntries[6] = "";
- rowEntries[7] = pipelines.get(i).getStepid();
- _return.add(rowEntries);
- }
- }
- }
-
- final List<ArcProjectDescendantI> descendants = arcProject.getPipelines_descendants_descendant();
- if (descendants.size() > 0 ) {
- for (int i = 0; i < descendants.size(); i++) {
- final List<ArcProjectDescendantPipelineI> pipelinesDesc = descendants.get(i).getPipeline();
- for (int j = 0; j < pipelinesDesc.size(); j++) {
- final PipePipelinedetails pipeline = getPipeline(pipelinesDesc.get(j).getLocation());
- final String[] rowEntries = new String[8];
- rowEntries[0] = getDisplayName(descendants.get(i).getXsitype());
- rowEntries[1] = getElementsGeneratedBy(pipeline);
- rowEntries[2] = pipelinesDesc.get(j).getName();
- rowEntries[3] = pipeline.getDescription();
- rowEntries[4] = pipelinesDesc.get(j).getLocation();
- rowEntries[5] = pipeline.getAppliesto();
- rowEntries[6] = descendants.get(i).getXsitype();
- rowEntries[7] = pipelinesDesc.get(j).getStepid();
- _return.add(rowEntries);
- }
- }
- }
- }
- return _return;
- }
-
- public XFTTable toTable(ArcProject arcProject) {
- XFTTable table = new XFTTable();
- try {
- ArrayList<String> cols = new ArrayList<String>();
- cols.add("Applies To");
- cols.add("Generates"); cols.add("Name"); cols.add("Description"); cols.add("Path");
- cols.add("Datatype");
- table.initTable(cols);
- for(String[] pipeline: listPipelines(arcProject)){
- table.insertRow(pipeline);
- }
- }catch(Exception e) {
- logger.error("Encountered exception " + e);
- }
- return table;
- }
-
- public PipePipelinedetails getPipeline(String path) {
- PipePipelinedetails rtn = null;
- List<PipePipelinedetailsI> pipelines = getPipeline();
- for (int i = 0; i < pipelines.size(); i++) {
- PipePipelinedetails pipeline = (PipePipelinedetails)pipelines.get(i);
- if (pipeline.getPath().equals(path)) {
- rtn = pipeline;
- break;
- }
- }
- return rtn;
- }
-
-
-
- private Hashtable<String, ArrayList<PipePipelinedetails>> getPipelinesPerDataType() {
- Hashtable<String, ArrayList<PipePipelinedetails>> rtn = new Hashtable<String, ArrayList<PipePipelinedetails>>();
- List<PipePipelinedetailsI> pipelines = getPipeline();
- if (pipelines.size() > 0 ) {
- for (int i = 0; i < pipelines.size(); i++) {
- PipePipelinedetails pipeline = (PipePipelinedetails)pipelines.get(i);
- if (rtn.containsKey(pipeline.getAppliesto())) {
- ArrayList<PipePipelinedetails> groupedByAppliesTo = rtn.get(pipeline.getAppliesto());
- groupedByAppliesTo.add(pipeline);
- rtn.put(pipeline.getAppliesto(),groupedByAppliesTo );
- }else {
- ArrayList<PipePipelinedetails> groupedByAppliesTo = new ArrayList<PipePipelinedetails>();
- groupedByAppliesTo.add(pipeline);
- rtn.put(pipeline.getAppliesto(), groupedByAppliesTo);
- }
- }
- }
- return rtn;
- }
-
-
- public ArrayList<PipePipelinedetails> getAllPipelines(String dataType) {
- Hashtable<String, ArrayList<PipePipelinedetails>> repository = getPipelinesPerDataType();
- return repository.get(dataType);
- }
-
-
-
- public Hashtable<String, ArrayList<ArcPipelinedata>> getPipelinesForProject(XnatProjectdata project) throws Exception {
- Hashtable<String, ArrayList<ArcPipelinedata>> rtn = new Hashtable<String,ArrayList<ArcPipelinedata>>();
- if (project == null) return rtn;
- Hashtable<String, ArrayList<PipePipelinedetails>> repository = getPipelinesPerDataType();
- if (repository == null) return rtn;
- Enumeration<String> keys = repository.keys();
- while (keys.hasMoreElements()) {
- String xsiType = keys.nextElement();
- ArrayList pipelinesForDataType = new ArrayList();
- if (xsiType.equalsIgnoreCase(XnatProjectdata.SCHEMA_ELEMENT_NAME))
- pipelinesForDataType = getArcPipelinesForProject(repository.get(xsiType));
- else
- pipelinesForDataType = getArcPipelinesForDescendant(repository.get(xsiType));
- if (pipelinesForDataType.size() > 0) {
- ArrayList<ArcPipelinedata> values = pipelinesForDataType;
- if (rtn.containsKey(xsiType)) {
- values = rtn.get(xsiType);
- values.addAll(pipelinesForDataType);
- }
- rtn.put(xsiType, values);
- }
- }
-
- return rtn;
- }
-
-
- public ArrayList<ArcProjectPipeline> getArcPipelinesForProject(ArrayList<PipePipelinedetails> pipelines) throws Exception {
- ArrayList<ArcProjectPipeline> rtn = new ArrayList<ArcProjectPipeline>();
- if (pipelines == null || pipelines.size() < 1) {
- return rtn;
- }
- for (int i = 0; i < pipelines.size(); i++) {
- PipePipelinedetails pipeline = pipelines.get(i);
- ArcProjectPipeline pBean = new ArcProjectPipeline();
- String description = pipeline.getDescription();
- if (description != null)
- description += " XNAT DATATYPE: " +pipeline.getAppliesto() + " Applies To: " + getDisplayName(pipeline.getAppliesto()) + " Generates: " + getElementsGeneratedBy(pipeline);
- else
- description = " XNAT DATATYPE: " +pipeline.getAppliesto() +" Applies To: " + getDisplayName(pipeline.getAppliesto()) + " Generates: " + getElementsGeneratedBy(pipeline);
- pBean.setDescription(description);
- String path = pipeline.getPath();
- File pipelineDescriptor = new File(path);
- //if (pipelineDescriptor.exists()) {
- pBean.setName(pipelineDescriptor.getName());
- pBean.setLocation(path);
- pBean.setDisplaytext(pipelineDescriptor.getName());
- //}
- String customwebpage = pipeline.getCustomwebpage();
- if (customwebpage != null)
- pBean.setCustomwebpage(customwebpage);
- List<PipePipelinedetailsParameterI> parameters = pipeline.getParameters_parameter();
- if (parameters != null && parameters.size() > 0 ) {
- for (int j = 0; j < parameters.size(); j++) {
- PipePipelinedetailsParameterI parameter = parameters.get(j);
- ArcPipelineparameterdata paramData = new ArcPipelineparameterdata();
- paramData.setName(parameter.getName());
- description = parameter.getDescription();
- if (description != null) {
- paramData.setDescription(description);
- }
- String value = parameter.getValues_schemalink();
- if (value != null)
- paramData.setSchemalink(value);
- else {
- value = parameter.getValues_csvvalues();
- paramData.setCsvvalues(value);
- }
- pBean.setParameters_parameter(paramData);
- }
- }
- rtn.add(pBean);
- }
- return rtn;
- }
-
- public boolean delete(ArcProject arcProject, String pathToPipeline, String dataType, UserI user) throws Exception {
- boolean success = true;
- boolean save = false;
- try {
- if (dataType.equalsIgnoreCase(XnatProjectdata.SCHEMA_ELEMENT_NAME)) {
- List<ArcProjectPipelineI> pipelines = arcProject.getPipelines_pipeline();
- for (int i = 0; i < pipelines.size(); i++) {
- ArcProjectPipeline pipeline = (ArcProjectPipeline)pipelines.get(i);
- if (pipeline.getLocation().equals(pathToPipeline)) {
- arcProject.removePipelines_pipeline(i);
- save = true;
- break;
- }
- }
- }else {
- ArcProjectDescendant descendant = arcProject.getDescendant(dataType);
- if (descendant == null) success = false;
- else {
- List<ArcProjectDescendantPipelineI> pipelines = descendant.getPipeline();
- for (int i = 0; i < pipelines.size(); i++) {
- ArcProjectDescendantPipeline pipeline = (ArcProjectDescendantPipeline)pipelines.get(i);
- if (pipeline.getLocation().equals(pathToPipeline)) {
- descendant.removePipeline(i);
- save = true;
- break;
- }
- }
- }
- }
- if (save) {
- SaveItemHelper.authorizedSave(arcProject,user, false, true,EventUtils.newEventInstance(EventUtils.CATEGORY.PROJECT_ADMIN, EventUtils.TYPE.STORE_XML, "Modified project pipelines"));
-
- }
- }catch(Exception e) {
- success = false;
- throw e;
- }
- return success;
- }
-
-
- public ArrayList<ArcProjectDescendantPipeline> getArcPipelinesForDescendant(ArrayList<PipePipelinedetails> pipelines) throws Exception {
- ArrayList<ArcProjectDescendantPipeline> rtn = new ArrayList<ArcProjectDescendantPipeline>();
- if (pipelines == null || pipelines.size() < 1) {
- return rtn;
- }
- for (int i = 0; i < pipelines.size(); i++) {
- PipePipelinedetails pipeline = pipelines.get(i);
- ArcProjectDescendantPipeline pBean = new ArcProjectDescendantPipeline();
- String description = pipeline.getDescription();
- if (description != null)
- description += " XNAT DATATYPE: " +pipeline.getAppliesto() + " Applies To: " + getDisplayName(pipeline.getAppliesto()) + " Generates: " + getElementsGeneratedBy(pipeline);
- else
- description = " XNAT DATATYPE: " +pipeline.getAppliesto() + " Applies To: " + getDisplayName(pipeline.getAppliesto()) + " Generates: " + getElementsGeneratedBy(pipeline);
- pBean.setDescription(description);
- String path = pipeline.getPath();
- File pipelineDescriptor = new File(path);
- //if (pipelineDescriptor.exists()) {
- pBean.setName(pipelineDescriptor.getName());
- pBean.setLocation(path);
- pBean.setDisplaytext(pipelineDescriptor.getName());
- //}
- String customwebpage = pipeline.getCustomwebpage();
- if (customwebpage != null)
- pBean.setCustomwebpage(customwebpage);
- List<PipePipelinedetailsParameterI> parameters = pipeline.getParameters_parameter();
- if (parameters != null && parameters.size() > 0 ) {
- for (int j = 0; j < parameters.size(); j++) {
- PipePipelinedetailsParameter parameter = (PipePipelinedetailsParameter)parameters.get(j);
- ArcPipelineparameterdata paramData = new ArcPipelineparameterdata();
- paramData.setName(parameter.getName());
- description = parameter.getDescription();
- if (description != null) {
- paramData.setDescription(description);
- }
- String value = parameter.getValues_schemalink();
- if (value != null)
- paramData.setSchemalink(value);
- else {
- value = parameter.getValues_csvvalues();
- paramData.setCsvvalues(value);
- }
- pBean.setParameters_parameter(paramData);
- }
- }
- rtn.add(pBean);
- }
- return rtn;
- }
-
- public ArcPipelineparameterdata convertToArcPipelineParameter(PipePipelinedetailsParameter parameter) {
- ArcPipelineparameterdata paramData = new ArcPipelineparameterdata();
- paramData.setName(parameter.getName());
- String description = parameter.getDescription();
- if (description != null) {
- paramData.setDescription(description);
- }
- String value = parameter.getValues_schemalink();
- if (value != null)
- paramData.setSchemalink(value);
- else {
- value = parameter.getValues_csvvalues();
- paramData.setCsvvalues(value);
- }
- return paramData;
- }
-
- public Hashtable<String, String> getGeneratedElementsByAllPipelines() {
- Hashtable<String, String> rtn = new Hashtable<String, String>();
- Hashtable<String, ArrayList<PipePipelinedetails>> repository = getPipelinesPerDataType();
- Enumeration<String> enume = repository.keys();
- while (enume.hasMoreElements()) {
- String dataType = enume.nextElement();
- ArrayList<PipePipelinedetails> pipelinesForDataType = repository.get(dataType);
- for (int i = 0; i < pipelinesForDataType.size(); i++) {
- PipePipelinedetails pipeline = pipelinesForDataType.get(i);
- List<PipePipelinedetailsElementI> generatedElements = pipeline.getGenerateselements_element();
- if (generatedElements.size() > 0) {
- for (int j = 0; j < generatedElements.size(); j++) {
- rtn.put(generatedElements.get(j).getElement().trim(), "");
- }
- }
- }
- }
- return rtn;
- }
-
-
- private boolean exists(List<ArcProjectPipelineI> pipelines, String path) {
- boolean exists = false;
- if (pipelines == null || path == null || pipelines.size() == 0) return false;
- for (int i = 0; i < pipelines.size(); i++) {
- String pipelinePath = pipelines.get(i).getLocation(); // + File.separator + pipelines.get(i).getName();
- if (pipelinePath.equals(path)) {
- exists = true;
- break;
- }
- }
- return exists;
- }
-
- private boolean existsDesc(List<ArcProjectDescendantPipelineI> pipelines, String path) {
- boolean exists = false;
- if (pipelines == null || path == null || pipelines.size() == 0 ) return exists;
- for (int i = 0; i < pipelines.size(); i++) {
- String pipelinePath = pipelines.get(i).getLocation(); // + File.separator + pipelines.get(i).getName();
- if (pipelinePath.equals(path)) {
- exists = true;
- break;
- }
- }
- return exists;
- }
-
-
-
- public String getElementsGeneratedBy(PipePipelinedetails pipeline) {
- String rtn = "";
- List<PipePipelinedetailsElementI> generatedElements = pipeline.getGenerateselements_element();
- if (generatedElements.size() > 0) {
- for (int i = 0; i < generatedElements.size(); i++) {
- rtn +=getDisplayName(generatedElements.get(i).getElement()) + ",";
- }
- }
- if (rtn.endsWith(",")) rtn = rtn.substring(0, rtn.length() - 1);
- return rtn;
- }
-
- public String getDisplayName(String dataType) {
- String rtn = dataType;
- try {
- Hashtable<String,ElementSecurity> ess = ElementSecurity.GetElementSecurities();
- rtn = ess.get(dataType).getPluralDescription();
- }catch(Exception e) {}
- return rtn;
- }
-
-
-
-
-
- public ArcProject createNewArcProject(XnatProjectdata proj) throws Exception {
- ArcProject arcProject = new ArcProject();
- if (proj == null) return arcProject;
- Hashtable<String, ArrayList<ArcPipelinedata>> pipelinesHash = PipelineRepositoryManager.GetInstance().getPipelinesForProject(proj);
- if (pipelinesHash != null && pipelinesHash.size() > 0) {
- Enumeration<String> keys = pipelinesHash.keys();
- while (keys.hasMoreElements()) {
- String dataType = keys.nextElement();
- if (dataType.equals(XnatProjectdata.SCHEMA_ELEMENT_NAME)) {
- ArrayList<ArcPipelinedata> projectPipelines = pipelinesHash.get(XnatProjectdata.SCHEMA_ELEMENT_NAME);
- if (projectPipelines != null && projectPipelines.size() > 0) {
- for (int i = 0; i < projectPipelines.size(); i++) {
- arcProject.setPipelines_pipeline(projectPipelines.get(i));
- }
- }
- }else {
- ArrayList<ArcPipelinedata> projectPipelines = pipelinesHash.get(dataType);
- if (projectPipelines != null && projectPipelines.size() > 0) {
- ArcProjectDescendant arcProjectDesc = new ArcProjectDescendant();
- arcProjectDesc.setXsitype(dataType);
- for (int i = 0; i < projectPipelines.size(); i++) {
- arcProjectDesc.setPipeline(projectPipelines.get(i));
- }
- arcProject.setPipelines_descendants_descendant(arcProjectDesc);
- }
- }
- }
- }
- return arcProject;
- }
-
- public ArcProject getAdditionalPipelines(XnatProjectdata project) throws Exception{
- //ArcProject arcProject = new ArcProject();
- ArcProject rtn = new ArcProject();
- if (project == null) return new ArcProject();
- Hashtable<String, ArrayList<ArcPipelinedata>> pipelinesHash = getPipelinesForProject(project);
- ArcProject arcProjectFromSpec = ArcSpecManager.GetFreshInstance().getProjectArc(project.getId());
- if (arcProjectFromSpec == null) return createNewArcProject(project);
- rtn.setId(arcProjectFromSpec.getId());
- //arcProject.setItem((XFTItem)arcProjectFromSpec.getItem().clone());
- //rtn.setItem((XFTItem)arcProjectFromSpec.getItem().clone());
-
- //Clear all the existing pipelines as we want only the additional pipelines that are applicable for this project
- //rtn.removeAllPipelines();
- if (pipelinesHash != null && pipelinesHash.size() > 0) { //There are some site pipelines
- List<ArcProjectPipelineI> projectSelectedPipelines = arcProjectFromSpec.getPipelines_pipeline();
- //Gather only those pipelines which have not been selected.
- ArrayList<ArcPipelinedata> additionalPipelines = new ArrayList<ArcPipelinedata>();
- ArrayList<ArcPipelinedata> pipelines = pipelinesHash.get(XnatProjectdata.SCHEMA_ELEMENT_NAME);
- if (pipelines != null && pipelines.size() > 0) {
- for (int i = 0; i < pipelines.size(); i++) {
- String id = pipelines.get(i).getLocation();
- if (!exists(projectSelectedPipelines, id)) {
- additionalPipelines.add(pipelines.get(i));
- }
- }
- for (int i = 0; i < additionalPipelines.size(); i++) {
- rtn.setPipelines_pipeline(additionalPipelines.get(i));
- }
- }
- Hashtable<String, ArrayList<ArcPipelinedata>> additionalPipelineHash = new Hashtable<String,ArrayList<ArcPipelinedata>>();
- Enumeration<String> keys = pipelinesHash.keys();
- while (keys.hasMoreElements()) {
- String xsiType = keys.nextElement();
- if (xsiType.equals(XnatProjectdata.SCHEMA_ELEMENT_NAME))
- continue;
- ArrayList<ArcPipelinedata> descpipelines = pipelinesHash.get(xsiType);
- List<ArcProjectDescendantPipelineI> projectSelectedDescPipelines = arcProjectFromSpec.getPipelinesForDescendant(xsiType);
- ArrayList<ArcPipelinedata> additionalDescPipelines = new ArrayList<ArcPipelinedata>();
- if (descpipelines != null) {
- for (int j = 0; j < descpipelines.size() ; j++) {
- String id = descpipelines.get(j).getLocation();
- if (!existsDesc(projectSelectedDescPipelines, id)) {
- additionalDescPipelines.add(descpipelines.get(j));
- }
- }
- additionalPipelineHash.put(xsiType, additionalDescPipelines);
- }
- }
- Enumeration<String> dataTypes = additionalPipelineHash.keys();
- while (dataTypes.hasMoreElements()) {
- String dataType = dataTypes.nextElement();
- ArrayList<ArcPipelinedata> additionalDescPipelines = additionalPipelineHash.get(dataType);
- ArcProjectDescendant arcProjectDesc = new ArcProjectDescendant();
- arcProjectDesc.setXsitype(dataType);
- for (int i = 0; i < additionalDescPipelines.size(); i++) {
- arcProjectDesc.setPipeline(additionalDescPipelines.get(i));
- }
- rtn.setPipelines_descendants_descendant(arcProjectDesc);
- }
- }
- return rtn;
- }
-
- public List getAdditionalPipelinesForDatatype(XnatProjectdata project, String schemaType) throws Exception{
- List rtn = new ArrayList();
- ArcProject arcProject = getAdditionalPipelines(project);
- if (arcProject == null) return rtn;
- if (schemaType.equals(XnatProjectdata.SCHEMA_ELEMENT_NAME)) {
- rtn = arcProject.getPipelines_pipeline();
- }else {
- ArcProjectDescendant desc = arcProject.getDescendant(schemaType);
- if (desc == null) {
- return rtn;
- }
- rtn = desc.getPipeline();
- }
- return rtn;
- }
-
-
-
-
-
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseProvProcess.java b/src/main/java/org/nrg/xdat/om/base/BaseProvProcess.java
deleted file mode 100644
index e0765d39c09766fc890dafc2f83d80358c416421..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseProvProcess.java
+++ /dev/null
@@ -1,44 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseProvProcess
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoProvProcess;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public class BaseProvProcess extends AutoProvProcess {
-
- public BaseProvProcess(ItemI item)
- {
- super(item);
- }
-
- public BaseProvProcess(UserI user)
- {
- super(user);
- }
-
- public BaseProvProcess()
- {}
-
- public BaseProvProcess(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseProvProcessstep.java b/src/main/java/org/nrg/xdat/om/base/BaseProvProcessstep.java
deleted file mode 100644
index f96ca43148e564fa95888c93e49d299e2d1b9c74..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseProvProcessstep.java
+++ /dev/null
@@ -1,44 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseProvProcessstep
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoProvProcessstep;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public class BaseProvProcessstep extends AutoProvProcessstep {
-
- public BaseProvProcessstep(ItemI item)
- {
- super(item);
- }
-
- public BaseProvProcessstep(UserI user)
- {
- super(user);
- }
-
- public BaseProvProcessstep()
- {}
-
- public BaseProvProcessstep(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseProvProcessstepLibrary.java b/src/main/java/org/nrg/xdat/om/base/BaseProvProcessstepLibrary.java
deleted file mode 100644
index a17a3ab23be65b38cf7f121757b1157fa64bfefe..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseProvProcessstepLibrary.java
+++ /dev/null
@@ -1,44 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseProvProcessstepLibrary
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoProvProcessstepLibrary;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public class BaseProvProcessstepLibrary extends AutoProvProcessstepLibrary {
-
- public BaseProvProcessstepLibrary(ItemI item)
- {
- super(item);
- }
-
- public BaseProvProcessstepLibrary(UserI user)
- {
- super(user);
- }
-
- public BaseProvProcessstepLibrary()
- {}
-
- public BaseProvProcessstepLibrary(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseScrScreeningassessment.java b/src/main/java/org/nrg/xdat/om/base/BaseScrScreeningassessment.java
deleted file mode 100644
index d20c50972822721814d0bb27593d855d3ef1678e..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseScrScreeningassessment.java
+++ /dev/null
@@ -1,79 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseScrScreeningassessment
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-import org.nrg.xdat.model.ScrScreeningscandataI;
-import org.nrg.xdat.om.ScrScreeningscandata;
-import org.nrg.xdat.om.base.auto.AutoScrScreeningassessment;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-import org.nrg.xnat.scanAssessors.ScanAssessorI;
-import org.nrg.xnat.scanAssessors.ScanAssessorScanI;
-
-import java.util.Hashtable;
-import java.util.List;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseScrScreeningassessment extends AutoScrScreeningassessment implements ScanAssessorI {
-
- public BaseScrScreeningassessment(ItemI item)
- {
- super(item);
- }
-
- public BaseScrScreeningassessment(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseScrScreeningassessment(UserI user)
- **/
- public BaseScrScreeningassessment()
- {}
-
- public BaseScrScreeningassessment(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
- public ScrScreeningscandata getScanScreeningAssessment(String scanId){
- ScrScreeningscandata rtn = null;
- if (scanId == null) throw new NullPointerException("Expected a non-null value for the scan id input parameter");
- List<ScrScreeningscandataI> scans = super.getScans_scan();
- if (scans != null && scans.size() > 0) {
- for (int i=0; i< scans.size(); i++) {
- ScrScreeningscandata aScan = (ScrScreeningscandata)scans.get(i);
- if (aScan.getImagescanId().equals(scanId)) {
- rtn = aScan;
- break;
- }
- }
- }
- if (rtn == null) throw new NullPointerException("Couldnt find screening assessment for scan id " + scanId);
- return rtn;
- }
-
- public ScanAssessorScanI getScanById(String id){
- return this.getScanScreeningAssessment(id);
- }
-
- public String getHeader(){
- return "Screening Assess";
- }
-
- public int getPrecedence(){
- return 1;
- }
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseScrScreeningscandata.java b/src/main/java/org/nrg/xdat/om/base/BaseScrScreeningscandata.java
deleted file mode 100644
index 8d17797a7607c3c19c4477992ff3a8b726a86505..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseScrScreeningscandata.java
+++ /dev/null
@@ -1,62 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseScrScreeningscandata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoScrScreeningscandata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-import org.nrg.xnat.scanAssessors.ScanAssessorScanI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseScrScreeningscandata extends AutoScrScreeningscandata implements ScanAssessorScanI {
-
- public BaseScrScreeningscandata(ItemI item)
- {
- super(item);
- }
-
- public BaseScrScreeningscandata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseScrScreeningscandata(UserI user)
- **/
- public BaseScrScreeningscandata()
- {}
-
- public BaseScrScreeningscandata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-
- public String getSummary(){
- String status = getPass();
- String summary = "<span>Unknown</span>";
- if(status!=null){
- if(status.equals("1")||status.equalsIgnoreCase("pass")){
- summary = "<span style=\"color:green\">Passed</span>";
- }
- else if(status.equals("0")||status.equalsIgnoreCase("fail")){
- summary = "<span style=\"color:red\">Failed</span>";
- }
- }
- return summary;
- }
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseValAdditionalval.java b/src/main/java/org/nrg/xdat/om/base/BaseValAdditionalval.java
deleted file mode 100644
index 562d5052b2e4378c7e0d6862087328c6fb07188c..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseValAdditionalval.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseValAdditionalval
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoValAdditionalval;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseValAdditionalval extends AutoValAdditionalval {
-
- public BaseValAdditionalval(ItemI item)
- {
- super(item);
- }
-
- public BaseValAdditionalval(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseValAdditionalval(UserI user)
- **/
- public BaseValAdditionalval()
- {}
-
- public BaseValAdditionalval(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseValProtocoldata.java b/src/main/java/org/nrg/xdat/om/base/BaseValProtocoldata.java
deleted file mode 100644
index ef78ac9a29e38febeed8bcfebf0e1e7353e10461..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseValProtocoldata.java
+++ /dev/null
@@ -1,80 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseValProtocoldata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.model.ValProtocoldataScanCheckI;
-import org.nrg.xdat.om.ValProtocoldataScanCheck;
-import org.nrg.xdat.om.base.auto.AutoValProtocoldata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-import org.nrg.xnat.scanAssessors.ScanAssessorI;
-import org.nrg.xnat.scanAssessors.ScanAssessorScanI;
-
-import java.util.Hashtable;
-import java.util.List;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseValProtocoldata extends AutoValProtocoldata implements ScanAssessorI{
-
- public BaseValProtocoldata(ItemI item)
- {
- super(item);
- }
-
- public BaseValProtocoldata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseValProtocolvalidationdata(UserI user)
- **/
- public BaseValProtocoldata()
- {}
-
- public BaseValProtocoldata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
- public ValProtocoldataScanCheck getScanProtocolValidation(String scanId) throws NullPointerException {
- ValProtocoldataScanCheck rtn = null;
- if (scanId == null) throw new NullPointerException("Expected a non-null value for the scan id input parameter");
- List<ValProtocoldataScanCheckI> scans = super.getScans_scanCheck();
- if (scans != null && scans.size() > 0) {
- for (int i=0; i< scans.size(); i++) {
- ValProtocoldataScanCheck aScan = (ValProtocoldataScanCheck)scans.get(i);
- if (aScan.getScanId().equals(scanId)) {
- rtn = aScan;
- break;
- }
- }
- }
- if (rtn == null) throw new NullPointerException("Couldnt find scan protocol validation for scan id " + scanId);
- return rtn;
- }
-
- public ScanAssessorScanI getScanById(String id){
- return this.getScanProtocolValidation(id);
- }
-
- public String getHeader(){
- return "Protocol Val";
- }
-
- public int getPrecedence(){
- return 0;
- }
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseValProtocoldataComment.java b/src/main/java/org/nrg/xdat/om/base/BaseValProtocoldataComment.java
deleted file mode 100644
index cb00e888d39353e328e8bc79647b17cd16cce765..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseValProtocoldataComment.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseValProtocoldataComment
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoValProtocoldataComment;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseValProtocoldataComment extends AutoValProtocoldataComment {
-
- public BaseValProtocoldataComment(ItemI item)
- {
- super(item);
- }
-
- public BaseValProtocoldataComment(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseValProtocoldataComment(UserI user)
- **/
- public BaseValProtocoldataComment()
- {}
-
- public BaseValProtocoldataComment(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseValProtocoldataCondition.java b/src/main/java/org/nrg/xdat/om/base/BaseValProtocoldataCondition.java
deleted file mode 100644
index 04511c7d153c8407142546c770ab423b3a2009ad..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseValProtocoldataCondition.java
+++ /dev/null
@@ -1,72 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseValProtocoldataCondition
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoValProtocoldataCondition;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseValProtocoldataCondition extends AutoValProtocoldataCondition {
-
- public BaseValProtocoldataCondition(ItemI item)
- {
- super(item);
- }
-
- public BaseValProtocoldataCondition(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseValProtocoldataCondition(UserI user)
- **/
- public BaseValProtocoldataCondition()
- {}
-
- public BaseValProtocoldataCondition(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
- public String getExpectedValue() {
- String rtn ="";
- String diagnosis = getDiagnosis();
- int expectedIndex = diagnosis.indexOf("Expected:");
- if (expectedIndex != -1) {
- int foundIndex = diagnosis.indexOf("Found:");
- if (foundIndex != -1) {
- rtn = diagnosis.substring(expectedIndex + 9 ,foundIndex);
- }else {
- rtn = diagnosis.substring(expectedIndex + 9);
- }
- }
- return rtn.trim();
- }
-
- public String getFoundValue() {
- String rtn ="";
- String diagnosis = getDiagnosis();
- int foundIndex = diagnosis.indexOf("Found:");
- if (foundIndex != -1) {
- rtn = diagnosis.substring(foundIndex + 6);
- }
- return rtn.trim();
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseValProtocoldataScanCheck.java b/src/main/java/org/nrg/xdat/om/base/BaseValProtocoldataScanCheck.java
deleted file mode 100644
index 9a3ed6a4bb22849349a10c6c7ba696d8c99dbbe1..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseValProtocoldataScanCheck.java
+++ /dev/null
@@ -1,62 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseValProtocoldataScanCheck
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoValProtocoldataScanCheck;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-import org.nrg.xnat.scanAssessors.ScanAssessorScanI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseValProtocoldataScanCheck extends AutoValProtocoldataScanCheck implements ScanAssessorScanI{
-
- public BaseValProtocoldataScanCheck(ItemI item)
- {
- super(item);
- }
-
- public BaseValProtocoldataScanCheck(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseValProtocoldataScanCheck(UserI user)
- **/
- public BaseValProtocoldataScanCheck()
- {}
-
- public BaseValProtocoldataScanCheck(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
- public String getSummary(){
- String status = getStatus();
- String summary = "<span>Unknown</span>";
- if(status!=null){
- if(status.equals("1")||status.equalsIgnoreCase("pass")){
- summary = "<span style=\"color:green\">Passed</span>";
- }
- else if(status.equals("0")||status.equalsIgnoreCase("fail")){
- summary = "<span style=\"color:red\">Failed</span>";
- }
- }
- return summary;
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseValProtocoldataScanCheckComment.java b/src/main/java/org/nrg/xdat/om/base/BaseValProtocoldataScanCheckComment.java
deleted file mode 100644
index c5e1ce8035ef3e84aafb9e9695a2537800e1b1be..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseValProtocoldataScanCheckComment.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseValProtocoldataScanCheckComment
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoValProtocoldataScanCheckComment;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseValProtocoldataScanCheckComment extends AutoValProtocoldataScanCheckComment {
-
- public BaseValProtocoldataScanCheckComment(ItemI item)
- {
- super(item);
- }
-
- public BaseValProtocoldataScanCheckComment(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseValProtocoldataScanCheckComment(UserI user)
- **/
- public BaseValProtocoldataScanCheckComment()
- {}
-
- public BaseValProtocoldataScanCheckComment(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseValProtocoldataScanCheckCondition.java b/src/main/java/org/nrg/xdat/om/base/BaseValProtocoldataScanCheckCondition.java
deleted file mode 100644
index 80e49e69c131338f14cd7c77e7f6c56fa0506d27..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseValProtocoldataScanCheckCondition.java
+++ /dev/null
@@ -1,73 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseValProtocoldataScanCheckCondition
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoValProtocoldataScanCheckCondition;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseValProtocoldataScanCheckCondition extends AutoValProtocoldataScanCheckCondition {
-
- public BaseValProtocoldataScanCheckCondition(ItemI item)
- {
- super(item);
- }
-
- public BaseValProtocoldataScanCheckCondition(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseValProtocoldataScanCheckCondition(UserI user)
- **/
- public BaseValProtocoldataScanCheckCondition()
- {}
-
- public BaseValProtocoldataScanCheckCondition(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
- public String getExpectedValue() {
- String rtn ="";
- String diagnosis = getDiagnosis();
- int expectedIndex = diagnosis.indexOf("Expected:");
- if (expectedIndex != -1) {
- int foundIndex = diagnosis.indexOf("Found:");
- if (foundIndex != -1) {
- rtn = diagnosis.substring(expectedIndex + 9 ,foundIndex);
- }else {
- rtn = diagnosis.substring(expectedIndex + 9);
- }
- }
- return rtn.trim();
- }
-
- public String getFoundValue() {
- String rtn ="";
- String diagnosis = getDiagnosis();
- int foundIndex = diagnosis.indexOf("Found:");
- if (foundIndex != -1) {
- rtn = diagnosis.substring(foundIndex + 6);
- }
- return rtn.trim();
- }
-
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseWrkAbstractexecutionenvironment.java b/src/main/java/org/nrg/xdat/om/base/BaseWrkAbstractexecutionenvironment.java
deleted file mode 100644
index 6f157b52a95bf4e9cc28af3bda02e0b741b0b2f3..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseWrkAbstractexecutionenvironment.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseWrkAbstractexecutionenvironment
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoWrkAbstractexecutionenvironment;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseWrkAbstractexecutionenvironment extends AutoWrkAbstractexecutionenvironment {
-
- public BaseWrkAbstractexecutionenvironment(ItemI item)
- {
- super(item);
- }
-
- public BaseWrkAbstractexecutionenvironment(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseWrkAbstractexecutionenvironment(UserI user)
- **/
- public BaseWrkAbstractexecutionenvironment()
- {}
-
- public BaseWrkAbstractexecutionenvironment(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseWrkWorkflowdata.java b/src/main/java/org/nrg/xdat/om/base/BaseWrkWorkflowdata.java
deleted file mode 100755
index 4ce46d05245d8b25db280cb6e2e67d1c036c08ae..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseWrkWorkflowdata.java
+++ /dev/null
@@ -1,406 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseWrkWorkflowdata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 8/12/13 9:39 AM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.pipeline.XnatPipelineLauncher;
-import org.nrg.xdat.model.WrkAbstractexecutionenvironmentI;
-import org.nrg.xdat.om.WrkWorkflowdata;
-import org.nrg.xdat.om.WrkXnatexecutionenvironment;
-import org.nrg.xdat.om.base.auto.AutoWrkWorkflowdata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-import org.nrg.xft.db.PoolDBUtils;
-import org.nrg.xft.event.XftEventService;
-import org.nrg.xft.event.EventMetaI;
-import org.nrg.xft.event.EventUtils.CATEGORY;
-import org.nrg.xft.event.EventUtils.TYPE;
-import org.nrg.xft.event.WorkflowStatusEvent;
-import org.nrg.xft.event.persist.PersistentWorkflowI;
-import org.nrg.xft.exception.ElementNotFoundException;
-import org.nrg.xft.exception.XFTInitException;
-import org.nrg.xft.schema.Wrappers.GenericWrapper.GenericWrapperElement;
-import org.nrg.xft.search.CriteriaCollection;
-import org.nrg.xft.security.UserI;
-import org.nrg.xft.utils.FileUtils;
-
-import java.io.File;
-import java.io.Serializable;
-import java.util.*;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public class BaseWrkWorkflowdata extends AutoWrkWorkflowdata implements PersistentWorkflowI{
-
- public static final String AWAITING_ACTION = "AWAITING ACTION";
- public static final String FAILED = "FAILED";
- public static final String RUNNING = "RUNNING";
- public static final String COMPLETE = "COMPLETE";
- public static final String ERROR = "ERROR";
- public static final String QUEUED = "QUEUED";
- public static final String FAILED_DISMISSED = "FAILED (DISMISSED)";
-
- public BaseWrkWorkflowdata(ItemI item)
- {
- super(item);
- }
-
- public BaseWrkWorkflowdata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseWrkWorkflowdata(UserI user)
- **/
- public BaseWrkWorkflowdata()
- {}
-
- public BaseWrkWorkflowdata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-
- public boolean isActive(){
- if(this.getStatus().equalsIgnoreCase(COMPLETE))
- return false;
- if(this.getStatus().equalsIgnoreCase(ERROR))
- return false;
- if(this.getStatus().equalsIgnoreCase(FAILED))
- return false;
- if(this.getStatus().equalsIgnoreCase(FAILED_DISMISSED))
- return false;
-
- return true;
- }
-
- public static ArrayList getWrkWorkflowdatasByField(org.nrg.xft.search.CriteriaCollection criteria, org.nrg.xft.security.UserI user,boolean preLoad, String sortField, String sortOrder)
- {
- ArrayList al = new ArrayList();
- try {
- org.nrg.xft.collections.ItemCollection items = org.nrg.xft.search.ItemSearch.GetItems(criteria,user,preLoad);
- Iterator iter = null;
- if (sortField != null && sortOrder != null) {
- iter = items.getItems(sortField,sortOrder).iterator();
- }else {
- iter = items.getItemIterator();
- }
- while (iter.hasNext())
- {
- WrkWorkflowdata vrc = new WrkWorkflowdata((XFTItem)iter.next());
- al.add(vrc);
- }
- } catch (Exception e) {
- logger.error("",e);
- }
-
- al.trimToSize();
- return al;
- }
-
- public String getOnlyPipelineName() {
- String rtn = getPipelineName();
- if (rtn.endsWith(File.separator)) rtn = rtn.substring(0,rtn.length());
- int lastIndexOfSlash = rtn.lastIndexOf(File.separator);
- if (lastIndexOfSlash != -1) {
- rtn = rtn.substring(lastIndexOfSlash + 1);
- }else {
- lastIndexOfSlash = rtn.lastIndexOf("/");
- if (lastIndexOfSlash != -1)
- rtn = rtn.substring(lastIndexOfSlash + 1);
- }
- int lastIndexOfDot = rtn.lastIndexOf(".");
- if (lastIndexOfDot != -1 ) {
- rtn = rtn.substring(0,lastIndexOfDot);
- }
- return rtn;
- }
-
-
- /**
- * Constructs the XnatPipelineLauncher object for the most recent pipeline entry
- *
- * @param id The id that needs to be relaunched
- * @param dataType The Datatype of the id
- * @param pipeline The pipeline which needs to be launched
- * @param user The user who needs to relaunch the pipeline
- * @return XnatPipelineLauncher to relaunch the pipeline or null if the pipeline is not waiting
- */
-
-
- public XnatPipelineLauncher getLatestLauncherByStatus(UserI user) {
- XnatPipelineLauncher rtn = null;
- //Look for the latest workflow entry for this pipeline
- //If its status is matches then construct the workflow
- String _status = getStatus();
- WrkAbstractexecutionenvironmentI absExecutionEnv = getExecutionenvironment();
- try {
- WrkXnatexecutionenvironment xnatExecutionEnv = (WrkXnatexecutionenvironment)absExecutionEnv;
- rtn = xnatExecutionEnv.getLauncher(user);
- if (_status.equalsIgnoreCase(AWAITING_ACTION)) {
- rtn.setStartAt(getNextStepId());
- }
- }catch(ClassCastException cse) {
-
- }
- return rtn;
-
- }
-
- /**
- * Constructs the XnatPipelineLauncher object to be used to restart a FAILED pipeline
- *
- * @param id The Workflow id that needs to be restarted
- * @param dataType The Datatype of the id
- * @param pipeline The pipeline which needs to be launched
- * @param user The user who needs to relaunch the pipeline
- * @return XnatPipelineLauncher to relaunch the pipeline or null if the pipeline hasnt failed
- */
-
- public XnatPipelineLauncher restartWorkflow(UserI user) {
- return getLatestLauncherByStatus(user);
- }
-
- /**
- * Constructs the XnatPipelineLauncher object to be used to resume an awaiting pipeline
- *
- * @param id The Workflow id that needs to be resumed
- * @param dataType The Datatype of the id
- * @param pipeline The pipeline which needs to be launched
- * @param user The user who needs to relaunch the pipeline
- * @return XnatPipelineLauncher to relaunch the pipeline or null if the pipeline is not waiting
- */
-
- public XnatPipelineLauncher resumeWorkflow(UserI user) {
- return getLatestLauncherByStatus(user);
- }
-
- /**
- * Returns the most recent workflow status
- * @param id
- * @param data_type
- * @param external_id
- * @param user
- * @return
- */
-
- public static String GetLatestWorkFlowStatus(String id, String data_type, String external_id,org.nrg.xft.security.UserI user) {
- ArrayList wrkFlows = GetWorkFlowsOrderByLaunchTimeDesc(id,data_type,external_id,null, user);
- String rtn = "";
- if (wrkFlows != null && wrkFlows.size() > 0) {
- rtn = ((WrkWorkflowdata)wrkFlows.get(0)).getStatus();
- }
- return rtn;
- }
-
- /**
- * Returns the most recent workflow status for a pipeline
- * @param id
- * @param data_type
- * @param external_id
- * @param user
- * @return
- */
-
- public static String GetLatestWorkFlowStatus(String id, String data_type, String external_id,String pipelineName,org.nrg.xft.security.UserI user) {
- ArrayList wrkFlows = GetWorkFlowsOrderByLaunchTimeDesc(id,data_type,external_id,pipelineName,user);
- String rtn = "";
- if (wrkFlows != null && wrkFlows.size() > 0) {
- rtn = ((WrkWorkflowdata)wrkFlows.get(0)).getStatus();
- }
- return rtn;
- }
-
- /**
- * Returns the most recent workflow status for a pipeline
- * @param id
- * @param data_type
- * @param external_id
- * @param user
- * @return
- */
-
- public static String GetLatestWorkFlowStatusByPipeline(String id, String data_type, String pipelineName, String external_id,org.nrg.xft.security.UserI user) {
- ArrayList wrkFlows = GetWorkFlowsOrderByLaunchTimeDesc(id,data_type,external_id, pipelineName,user);
- String rtn = "";
- if (wrkFlows != null && wrkFlows.size() > 0) {
- rtn = ((WrkWorkflowdata)wrkFlows.get(0)).getStatus();
- }
- return rtn;
- }
-
- public static ArrayList GetWorkFlowsOrderByLaunchTimeDesc(String id, String dataType, String externalId, String pipelineName, org.nrg.xft.security.UserI user) {
- ArrayList workflows = new ArrayList();
- org.nrg.xft.search.CriteriaCollection cc = new CriteriaCollection("AND");
- cc.addClause("wrk:workflowData.ID",id);
- cc.addClause("wrk:workflowData.data_type",dataType);
- if (externalId != null) cc.addClause("wrk:workflowData.ExternalID",externalId);
- if (pipelineName != null) cc.addClause("wrk:workflowData.pipeline_name",pipelineName);
- //Sort by Launch Time
- try {
- org.nrg.xft.collections.ItemCollection items = org.nrg.xft.search.ItemSearch.GetItems(cc,user,false);
- ArrayList workitems = items.getItems("wrk:workflowData.launch_time","DESC");
- Iterator iter = workitems.iterator();
- while (iter.hasNext())
- {
- WrkWorkflowdata vrc = new WrkWorkflowdata((XFTItem)iter.next());
- workflows.add(vrc);
- }
- }catch(Exception e) {
- logger.debug("",e);
- }
- logger.info("Workflows by Ordered by Launch Time " + workflows.size());
- return workflows;
- }
-
- public synchronized EventMetaI buildEvent(){
- Date d=Calendar.getInstance().getTime();
- return new WorkflowEvent((String)null,d,this.getUser(),this.getEventId(),FileUtils.getTimestamp(d));
- }
-
- public class WorkflowEvent implements EventMetaI, Serializable {
- private static final long serialVersionUID = 42L;
- final String message;
- final Date d;
- final UserI user;
- final Number id;
- final String timestamp;
-
- public WorkflowEvent(String message, Date d, UserI user, Number id,
- String timestamp) {
- super();
- this.message = message;
- this.d = d;
- this.user = user;
- this.id = id;
- this.timestamp = timestamp;
- }
-
- @Override
- public String getMessage() {
- return message;
- }
-
- @Override
- public Date getEventDate() {
- return d;
- }
-
- @Override
- public String getTimestamp() {
- return timestamp;
- }
-
- @Override
- public UserI getUser() {
- return user;
- }
-
- @Override
- public Number getEventId() {
- return id;
- }
-
- }
-
- public Number getEventId() {
- Number i= getWrkWorkflowdataId();
- if(i==null){
- try {
- i=(Number)getNextWorkflowID();
- setWrkWorkflowdataId(new Integer(i.intValue()));
- } catch (Exception e) {
- logger.error("",e);
- }
- }
-
- return i;
- }
-
-
- private static String __table=null;
- private static String __dbName=null;
- private static final String __pk="wrk_workflowData_id";
- private static String __sequence=null;
- private synchronized static Number getNextWorkflowID() throws Exception{
- if(__table==null){
- try {
- GenericWrapperElement element=GenericWrapperElement.GetElement(WrkWorkflowdata.SCHEMA_ELEMENT_NAME);
- __dbName=element.getDbName();
- __table=element.getSQLName();
- __sequence=element.getSequenceName();
- } catch (XFTInitException e) {
- logger.error("",e);
- } catch (ElementNotFoundException e) {
- logger.error("",e);
- }
- }
- return (Number)PoolDBUtils.GetNextID(__dbName, __table, __pk, __sequence);
- }
-
- @Override
- public Integer getWorkflowId() {
- return getWrkWorkflowdataId();
- }
-
- @Override
- public Date getLaunchTimeDate() {
- try {
- return getDateProperty("launch_time");
- } catch (Exception e) {
- logger.error("",e);
- return null;
- }
- }
-
- public String getUsername(){
- if(this.getInsertUser()!=null){
- return this.getInsertUser().getLogin();
- }else{
- return null;
- }
- }
-
- @Override
- public void setType(TYPE v) {
- this.setType(v.toString());
- }
-
- @Override
- public void setCategory(CATEGORY v) {
- this.setCategory(v.toString());
- }
-
-
- /*
- * This method is called anytime a workflow entry is saved to the database. It will trigger an event entry.
- */
- @Override
- public void postSave() throws Exception {
- postSave(true);
- }
-
- @Override
- public void postSave(boolean triggerEvent) throws Exception {
- super.postSave();
-
- if(getStatus()!=null){
- //status changed
- if(this.getWorkflowId()!=null && triggerEvent){
- XftEventService.getService().triggerEvent(WorkflowStatusEvent.class.getName() +
- ((this.getStatus()!=null) ? "." + this.getStatus() : ""),new WorkflowStatusEvent(this));
- }
- }
- }
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseWrkXnatexecutionenvironment.java b/src/main/java/org/nrg/xdat/om/base/BaseWrkXnatexecutionenvironment.java
deleted file mode 100644
index 73a016bab3c815891a2f8fa70d30e8651ac2cfdb..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseWrkXnatexecutionenvironment.java
+++ /dev/null
@@ -1,75 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseWrkXnatexecutionenvironment
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import java.util.Hashtable;
-import java.util.List;
-
-import org.nrg.pipeline.XnatPipelineLauncher;
-import org.nrg.xdat.model.WrkXnatexecutionenvironmentParameterI;
-import org.nrg.xdat.om.base.auto.AutoWrkXnatexecutionenvironment;
-import org.nrg.xdat.turbine.utils.AdminUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseWrkXnatexecutionenvironment extends AutoWrkXnatexecutionenvironment {
-
- public BaseWrkXnatexecutionenvironment(ItemI item)
- {
- super(item);
- }
-
- public BaseWrkXnatexecutionenvironment(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseWrkXnatexecutionenvironment(UserI user)
- **/
- public BaseWrkXnatexecutionenvironment()
- {}
-
- public BaseWrkXnatexecutionenvironment(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
- public XnatPipelineLauncher getLauncher(UserI user) {
- XnatPipelineLauncher xnatLauncher = new XnatPipelineLauncher((UserI)user);
- xnatLauncher.setPipelineName(getPipeline());
- xnatLauncher.setStartAt(getStartat());
- List parameters = getParameters_parameter();
- for (int i = 0; i < parameters.size(); i++) {
- WrkXnatexecutionenvironmentParameterI aParameter = (WrkXnatexecutionenvironmentParameterI)parameters.get(i);
- xnatLauncher.setParameter(aParameter.getName(), aParameter.getParameter());
- }
- List notified = getNotify();
- for (int i = 0; i < notified.size(); i++) {
- String notifiedEmailId = (String)notified.get(i);
- if (!notifiedEmailId.equals(user.getEmail()) && !notifiedEmailId.equals(AdminUtils.getAdminEmailId())) {
- xnatLauncher.notify(notifiedEmailId);
- }
- }
- xnatLauncher.setDataType(getDatatype());
- xnatLauncher.setId(getId());
- xnatLauncher.setSupressNotification(getSupressnotification());
- if (this.getParameterfile_path() != null) {
- xnatLauncher.setParameterFile(getParameterfile_path());
- }
- return xnatLauncher;
- }
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseWrkXnatexecutionenvironmentNotify.java b/src/main/java/org/nrg/xdat/om/base/BaseWrkXnatexecutionenvironmentNotify.java
deleted file mode 100644
index e5ff8ee63aedbaa803afc2f4d73fe659bc2d8b6f..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseWrkXnatexecutionenvironmentNotify.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseWrkXnatexecutionenvironmentNotify
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoWrkXnatexecutionenvironmentNotify;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseWrkXnatexecutionenvironmentNotify extends AutoWrkXnatexecutionenvironmentNotify {
-
- public BaseWrkXnatexecutionenvironmentNotify(ItemI item)
- {
- super(item);
- }
-
- public BaseWrkXnatexecutionenvironmentNotify(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseWrkXnatexecutionenvironmentNotify(UserI user)
- **/
- public BaseWrkXnatexecutionenvironmentNotify()
- {}
-
- public BaseWrkXnatexecutionenvironmentNotify(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseWrkXnatexecutionenvironmentParameter.java b/src/main/java/org/nrg/xdat/om/base/BaseWrkXnatexecutionenvironmentParameter.java
deleted file mode 100644
index e485f2e6e6a7b478a986b562a9244a72510448ca..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseWrkXnatexecutionenvironmentParameter.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseWrkXnatexecutionenvironmentParameter
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoWrkXnatexecutionenvironmentParameter;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseWrkXnatexecutionenvironmentParameter extends AutoWrkXnatexecutionenvironmentParameter {
-
- public BaseWrkXnatexecutionenvironmentParameter(ItemI item)
- {
- super(item);
- }
-
- public BaseWrkXnatexecutionenvironmentParameter(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseWrkXnatexecutionenvironmentParameter(UserI user)
- **/
- public BaseWrkXnatexecutionenvironmentParameter()
- {}
-
- public BaseWrkXnatexecutionenvironmentParameter(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatAbstractdemographicdata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatAbstractdemographicdata.java
deleted file mode 100644
index d2ded9523ddbf58ae4fe06b3ed6bbc3b39f994bd..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatAbstractdemographicdata.java
+++ /dev/null
@@ -1,44 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatAbstractdemographicdata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatAbstractdemographicdata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public class BaseXnatAbstractdemographicdata extends AutoXnatAbstractdemographicdata {
-
- public BaseXnatAbstractdemographicdata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatAbstractdemographicdata(UserI user)
- {
- super(user);
- }
-
- public BaseXnatAbstractdemographicdata()
- {}
-
- public BaseXnatAbstractdemographicdata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatAbstractprotocol.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatAbstractprotocol.java
deleted file mode 100644
index 69ffd4c4507dd457d501163364cc8a9af65d84c3..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatAbstractprotocol.java
+++ /dev/null
@@ -1,192 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatAbstractprotocol
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.XdatSearchField;
-import org.nrg.xdat.om.XnatAbstractprotocol;
-import org.nrg.xdat.om.XnatProjectdata;
-import org.nrg.xdat.om.base.auto.AutoXnatAbstractprotocol;
-import org.nrg.xdat.schema.SchemaElement;
-import org.nrg.xdat.security.ElementSecurity;
-import org.nrg.xdat.security.XdatStoredSearch;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.exception.ElementNotFoundException;
-import org.nrg.xft.exception.FieldNotFoundException;
-import org.nrg.xft.exception.XFTInitException;
-import org.nrg.xft.schema.Wrappers.GenericWrapper.GenericWrapperElement;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-import java.util.Iterator;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public class BaseXnatAbstractprotocol extends AutoXnatAbstractprotocol {
-
- public BaseXnatAbstractprotocol(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatAbstractprotocol(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatAbstractprotocol(UserI user)
- **/
- public BaseXnatAbstractprotocol()
- {}
-
- public BaseXnatAbstractprotocol(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-
- public String getProject()
- {
- try {
- return this.getStringProperty("xnat_projectdata_id");
- } catch (ElementNotFoundException e) {
- logger.error("",e);
- } catch (FieldNotFoundException e) {
- logger.error("",e);
- }
- return null;
- }
-
- public SchemaElement getDatatypeSchemaElement(){
- try {
- return SchemaElement.GetElement(this.getDataType());
- } catch (XFTInitException e) {
- logger.error("",e);
- } catch (ElementNotFoundException e) {
- logger.error("",e);
- }
-
- return null;
- }
-
- public XdatStoredSearch getDefaultSearch(XnatProjectdata project){
- XdatStoredSearch xss=null;
- try {
- xss=project.getDefaultSearch(this.getDataType(),this.getId());
-
- xss.setId(this.getId());
- if (this.getName()!=null)
- xss.setBriefDescription(this.getName());
- else{
- xss.setBriefDescription(ElementSecurity.GetElementSecurity(this.getDataType()).getPluralDescription());
- }
- if (this.getDescription()!=null)
- xss.setDescription(this.getDescription());
-
- xss.setSecure(true);
- xss.setAllowDiffColumns(false);
- xss.setTag(project.getId());
-
- UserI user = this.getUser();
-
- if (this.getDataType().equals("xnat:subjectData")){
- Iterator protocols2= project.getStudyprotocol().iterator();
- while(protocols2.hasNext()){
- XnatAbstractprotocol protocol2 = (XnatAbstractprotocol)protocols2.next();
- try {
- GenericWrapperElement e = GenericWrapperElement.GetElement(protocol2.getDataType());
- if (e.instanceOf("xnat:subjectAssessorData"))
- {
- XdatSearchField xsf = new XdatSearchField(user);
- xsf.setElementName("xnat:subjectData");
- xsf.setFieldId("SUB_EXPT_COUNT=" + protocol2.getDataType());
-
- xsf.setHeader(ElementSecurity.GetPluralDescription(protocol2.getDataType()));
- xsf.setType("integer");
- xsf.setSequence(xss.getSearchField().size());
- xsf.setValue(protocol2.getDataType());
- xss.setSearchField(xsf);
- }
- } catch (XFTInitException e) {
- logger.error("",e);
- } catch (ElementNotFoundException e) {
- logger.error("",e);
- } catch (Exception e) {
- logger.error("",e);
- }
- }
- }
-
- if (this.getDataType().equals("xnat:mrSessionData")){
- Iterator protocols2= project.getStudyprotocol().iterator();
- while(protocols2.hasNext()){
- XnatAbstractprotocol protocol2 = (XnatAbstractprotocol)protocols2.next();
- try {
- GenericWrapperElement e = GenericWrapperElement.GetElement(protocol2.getDataType());
- if (e.instanceOf("xnat:mrAssessorData"))
- {
- XdatSearchField xsf = new XdatSearchField(user);
- xsf.setElementName("xnat:mrSessionData");
- xsf.setFieldId("MR_EXPT_COUNT=" + protocol2.getDataType());
-
- xsf.setHeader(ElementSecurity.GetPluralDescription(protocol2.getDataType()));
- xsf.setType("integer");
- xsf.setSequence(xss.getSearchField().size());
- xsf.setValue(protocol2.getDataType());
- xss.setSearchField(xsf);
- }
- } catch (XFTInitException e) {
- logger.error("",e);
- } catch (ElementNotFoundException e) {
- logger.error("",e);
- } catch (Exception e) {
- logger.error("",e);
- }
- }
- }
-
- if (this.getDataType().equals("xnat:petSessionData")){
- Iterator protocols2= project.getStudyprotocol().iterator();
- while(protocols2.hasNext()){
- XnatAbstractprotocol protocol2 = (XnatAbstractprotocol)protocols2.next();
- try {
- GenericWrapperElement e = GenericWrapperElement.GetElement(protocol2.getDataType());
- if (e.instanceOf("xnat:petAssessorData"))
- {
- XdatSearchField xsf = new XdatSearchField(user);
- xsf.setElementName("xnat:petSessionData");
- xsf.setFieldId("PET_EXPT_COUNT=" + protocol2.getDataType());
-
- xsf.setHeader(ElementSecurity.GetPluralDescription(protocol2.getDataType()));
- xsf.setType("integer");
- xsf.setSequence(xss.getSearchField().size());
- xsf.setValue(protocol2.getDataType());
- xss.setSearchField(xsf);
- }
- } catch (XFTInitException e) {
- logger.error("",e);
- } catch (ElementNotFoundException e) {
- logger.error("",e);
- } catch (Exception e) {
- logger.error("",e);
- }
- }
- }
-
- } catch (Exception e) {
- logger.error("",e);
- }
- return xss;
- }
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatAbstractresource.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatAbstractresource.java
deleted file mode 100644
index b8c68ac22c70cb8155828fd6b6d2c6f1ba25acab..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatAbstractresource.java
+++ /dev/null
@@ -1,210 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatAbstractresource
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 11/18/13 9:35 AM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.model.XnatAbstractresourceTagI;
-import org.nrg.xdat.om.base.auto.AutoXnatAbstractresource;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.event.EventMetaI;
-import org.nrg.xft.security.UserI;
-import org.nrg.xft.utils.FileUtils;
-import org.nrg.xnat.utils.CatalogUtils;
-
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatAbstractresource extends AutoXnatAbstractresource {
-
- public BaseXnatAbstractresource(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatAbstractresource(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatAbstractresource(UserI user)
- **/
- public BaseXnatAbstractresource()
- {}
-
- public BaseXnatAbstractresource(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
- /**
- * Returns ArrayList of java.io.File objects
- * @return
- */
- public abstract ArrayList<File> getCorrespondingFiles(String rootPath);
-
-
- /**
- * Returns ArrayList of java.lang.String objects
- * @return
- */
- public abstract ArrayList getCorrespondingFileNames(String rootPath);
-
-
- Long size = null;
- public long getSize(String rootPath){
- if (size ==null){
- calculate(rootPath);
- }
- return size;
- }
-
- public String getReadableFileStats() {
- return CatalogUtils.formatFileStats(getLabel(), getFileCount(), getFileSize());
- }
-
- public String getReadableFileSize() {
- Object fileSize = getFileSize();
- if (fileSize == null) {
- return "Empty";
- }
- return CatalogUtils.formatSize((Long) fileSize);
- }
-
- public void calculate(String rootPath){
- long sizeI = 0;
- int countI = 0;
- for (File f : this.getCorrespondingFiles(rootPath)) {
- if (f.exists()){
- countI++;
- sizeI+=f.length();
- }
- }
-
- size = sizeI;
- count = countI;
- }
-
- Integer count = null;
- public Integer getCount(String rootPath){
- if (count ==null){
- calculate(rootPath);
- }
- return count;
- }
-
- /**
- * Prepends this path to the enclosed URI or path variables.
- * @param root
- */
- public abstract void prependPathsWith(String root);
-
- /**
- * Relatives this path from the first occurrence of the indexOf string.
- * @param indexOf
- */
- public abstract void relativizePaths(String indexOf, boolean caseSensitive);
-
- /**
- * Appends this path to the enclosed URI or path variables.
- * @param root
- */
- public abstract ArrayList<String> getUnresolvedPaths();
-
- public boolean isInRAWDirectory(){
- boolean hasRAW= false;
- for (String path : getUnresolvedPaths())
- {
- if (path.indexOf("RAW/")!=-1)
- {
- hasRAW=true;
- break;
- }
- if (path.indexOf("SCANS/")!=-1)
- {
- hasRAW=true;
- break;
- }
- }
- return hasRAW;
- }
-
- /**
- * Path to Files
- * @return
- */
- public String getFullPath(String rootPath){
- return "";
- }
-
- public String getContent(){
- return "";
- }
-
- public String getFormat(){
- return "";
- }
-
- public void deleteWithBackup(String rootPath, UserI user, EventMetaI c) throws Exception{
- deleteFromFileSystem(rootPath);
- }
-
- public void deleteFromFileSystem(String rootPath){
- ArrayList<File> files = this.getCorrespondingFiles(rootPath);
- for(File f: files){
- try {
- FileUtils.MoveToCache(f);
- if(FileUtils.CountFiles(f.getParentFile(),true)==0){
- FileUtils.DeleteFile(f.getParentFile());
- }
- } catch (FileNotFoundException e) {
- e.printStackTrace();
- } catch (IOException e) {
- e.printStackTrace();
- }
- }
- }
-
- public String getTagString(){
- StringBuffer sb =new StringBuffer();
- for(XnatAbstractresourceTagI tag:this.getTags_tag()){
- if(sb.length()>0){
- sb.append(",");
- }
- if(tag.getName()!=null){
- sb.append(tag.getName()).append("=");
- }
- sb.append(tag.getTag());
- }
-
- return sb.toString();
- }
-
- private String base_URI=null;
- public String getBaseURI(){return base_URI;}
- public void setBaseURI(String b){
- if(b.startsWith("/REST") || b.startsWith("/data")){
- this.base_URI=b;
- }else{
- this.base_URI="/data" +b;
- }
- }
-
-
- public abstract void moveTo(File newSessionDir, String existingSessionDir,String rootPath,UserI user,EventMetaI ci) throws IOException,Exception;
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatAbstractresourceTag.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatAbstractresourceTag.java
deleted file mode 100644
index 79fc7bfd712188daa891b9da33a7f228a273a576..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatAbstractresourceTag.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatAbstractresourceTag
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatAbstractresourceTag;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatAbstractresourceTag extends AutoXnatAbstractresourceTag {
-
- public BaseXnatAbstractresourceTag(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatAbstractresourceTag(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatAbstractresourceTag(UserI user)
- **/
- public BaseXnatAbstractresourceTag()
- {}
-
- public BaseXnatAbstractresourceTag(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatAbstractstatistics.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatAbstractstatistics.java
deleted file mode 100644
index 083cd9eece443e662aac0209a9e87ba8a69231b5..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatAbstractstatistics.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatAbstractstatistics
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatAbstractstatistics;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatAbstractstatistics extends AutoXnatAbstractstatistics {
-
- public BaseXnatAbstractstatistics(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatAbstractstatistics(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatAbstractstatistics(UserI user)
- **/
- public BaseXnatAbstractstatistics()
- {}
-
- public BaseXnatAbstractstatistics(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatAbstractsubjectmetadata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatAbstractsubjectmetadata.java
deleted file mode 100644
index 82ca7ddb64f361b2d9ea3403e89f4a4157409f30..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatAbstractsubjectmetadata.java
+++ /dev/null
@@ -1,44 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatAbstractsubjectmetadata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatAbstractsubjectmetadata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public class BaseXnatAbstractsubjectmetadata extends AutoXnatAbstractsubjectmetadata {
-
- public BaseXnatAbstractsubjectmetadata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatAbstractsubjectmetadata(UserI user)
- {
- super(user);
- }
-
- public BaseXnatAbstractsubjectmetadata()
- {}
-
- public BaseXnatAbstractsubjectmetadata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatAddfield.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatAddfield.java
deleted file mode 100644
index 858e0d9be6e83932d18092d5cdb40bc2ffb16d55..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatAddfield.java
+++ /dev/null
@@ -1,44 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatAddfield
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatAddfield;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public class BaseXnatAddfield extends AutoXnatAddfield {
-
- public BaseXnatAddfield(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatAddfield(UserI user)
- {
- super(user);
- }
-
- public BaseXnatAddfield()
- {}
-
- public BaseXnatAddfield(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatAscidresearchdata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatAscidresearchdata.java
deleted file mode 100644
index 0fc210711fea97c177b8fe8204af6ed8bdf10e17..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatAscidresearchdata.java
+++ /dev/null
@@ -1,48 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatAscidresearchdata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatAscidresearchdata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatAscidresearchdata extends AutoXnatAscidresearchdata {
-
- public BaseXnatAscidresearchdata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatAscidresearchdata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatAscidresearchdata(UserI user)
- **/
- public BaseXnatAscidresearchdata()
- {}
-
- public BaseXnatAscidresearchdata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
-
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatAsideeffectspittsburghdata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatAsideeffectspittsburghdata.java
deleted file mode 100644
index 90367eb2ac2e67386960ca25ebbe107913591529..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatAsideeffectspittsburghdata.java
+++ /dev/null
@@ -1,48 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatAsideeffectspittsburghdata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatAsideeffectspittsburghdata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatAsideeffectspittsburghdata extends AutoXnatAsideeffectspittsburghdata {
-
- public BaseXnatAsideeffectspittsburghdata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatAsideeffectspittsburghdata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatAsideeffectspittsburghdata(UserI user)
- **/
- public BaseXnatAsideeffectspittsburghdata()
- {}
-
- public BaseXnatAsideeffectspittsburghdata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
-
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatAupdrs3data.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatAupdrs3data.java
deleted file mode 100644
index b52dfb62bf74b1a4f5b956b69000078105d0abaf..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatAupdrs3data.java
+++ /dev/null
@@ -1,48 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatAupdrs3data
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatAupdrs3data;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatAupdrs3data extends AutoXnatAupdrs3data {
-
- public BaseXnatAupdrs3data(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatAupdrs3data(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatAupdrs3data(UserI user)
- **/
- public BaseXnatAupdrs3data()
- {}
-
- public BaseXnatAupdrs3data(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
-
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatAybocsdata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatAybocsdata.java
deleted file mode 100644
index 6932b83ea6b138ff210d3a2bb611ab607b19cdfe..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatAybocsdata.java
+++ /dev/null
@@ -1,48 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatAybocsdata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatAybocsdata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatAybocsdata extends AutoXnatAybocsdata {
-
- public BaseXnatAybocsdata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatAybocsdata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatAybocsdata(UserI user)
- **/
- public BaseXnatAybocsdata()
- {}
-
- public BaseXnatAybocsdata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
-
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatAygtssdata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatAygtssdata.java
deleted file mode 100644
index 037a0ae93ca44e26a479f409ea64f01c51d6ab20..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatAygtssdata.java
+++ /dev/null
@@ -1,48 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatAygtssdata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatAygtssdata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatAygtssdata extends AutoXnatAygtssdata {
-
- public BaseXnatAygtssdata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatAygtssdata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatAygtssdata(UserI user)
- **/
- public BaseXnatAygtssdata()
- {}
-
- public BaseXnatAygtssdata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
-
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatComputationdata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatComputationdata.java
deleted file mode 100644
index b082cfc108df6feb84ecdae41a5b7fcbbf262ea0..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatComputationdata.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatComputationdata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatComputationdata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public class BaseXnatComputationdata extends AutoXnatComputationdata {
-
- public BaseXnatComputationdata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatComputationdata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatComputationdata(UserI user)
- **/
- public BaseXnatComputationdata()
- {}
-
- public BaseXnatComputationdata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatContrastbolus.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatContrastbolus.java
deleted file mode 100644
index c11725683bf934d97e4bd612f1ec9de051fc5a56..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatContrastbolus.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatContrastbolus
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatContrastbolus;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatContrastbolus extends AutoXnatContrastbolus {
-
- public BaseXnatContrastbolus(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatContrastbolus(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatContrastbolus(UserI user)
- **/
- public BaseXnatContrastbolus()
- {}
-
- public BaseXnatContrastbolus(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatCrscandata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatCrscandata.java
deleted file mode 100644
index 9920efe58408d32fdeba3987715dd11cc94bb183..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatCrscandata.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatCrscandata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatCrscandata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatCrscandata extends AutoXnatCrscandata {
-
- public BaseXnatCrscandata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatCrscandata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatCrscandata(UserI user)
- **/
- public BaseXnatCrscandata()
- {}
-
- public BaseXnatCrscandata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatCrsessiondata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatCrsessiondata.java
deleted file mode 100644
index 85e69d0411c06147d57ac02f9bead854d38b5e4f..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatCrsessiondata.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatCrsessiondata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatCrsessiondata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatCrsessiondata extends AutoXnatCrsessiondata {
-
- public BaseXnatCrsessiondata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatCrsessiondata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatCrsessiondata(UserI user)
- **/
- public BaseXnatCrsessiondata()
- {}
-
- public BaseXnatCrsessiondata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatCtscandata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatCtscandata.java
deleted file mode 100644
index 0d063b3d446824db133e12cdfb139db194464a41..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatCtscandata.java
+++ /dev/null
@@ -1,48 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatCtscandata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatCtscandata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatCtscandata extends AutoXnatCtscandata {
-
- public BaseXnatCtscandata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatCtscandata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatCtscandata(UserI user)
- **/
- public BaseXnatCtscandata()
- {}
-
- public BaseXnatCtscandata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
-
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatCtscandataFocalspot.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatCtscandataFocalspot.java
deleted file mode 100644
index 08bc69a75c7ec5bee1cac8d667e13f5a68e05f28..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatCtscandataFocalspot.java
+++ /dev/null
@@ -1,48 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatCtscandataFocalspot
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatCtscandataFocalspot;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatCtscandataFocalspot extends AutoXnatCtscandataFocalspot {
-
- public BaseXnatCtscandataFocalspot(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatCtscandataFocalspot(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatCtscandataFocalspot(UserI user)
- **/
- public BaseXnatCtscandataFocalspot()
- {}
-
- public BaseXnatCtscandataFocalspot(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
-
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatCtsessiondata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatCtsessiondata.java
deleted file mode 100644
index 501f2e4856e310e158b7c005bf9583dec9cafdc6..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatCtsessiondata.java
+++ /dev/null
@@ -1,48 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatCtsessiondata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatCtsessiondata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatCtsessiondata extends AutoXnatCtsessiondata {
-
- public BaseXnatCtsessiondata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatCtsessiondata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatCtsessiondata(UserI user)
- **/
- public BaseXnatCtsessiondata()
- {}
-
- public BaseXnatCtsessiondata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
-
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatDatatypeprotocol.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatDatatypeprotocol.java
deleted file mode 100644
index dcb775cbd07d260e122ceda9632f6b5f96ae55cd..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatDatatypeprotocol.java
+++ /dev/null
@@ -1,114 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatDatatypeprotocol
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.display.DisplayField;
-import org.nrg.xdat.model.XnatFielddefinitiongroupFieldI;
-import org.nrg.xdat.model.XnatFielddefinitiongroupI;
-import org.nrg.xdat.model.XnatProjectdataI;
-import org.nrg.xdat.om.XdatSearchField;
-import org.nrg.xdat.om.XnatProjectdata;
-import org.nrg.xdat.om.base.auto.AutoXnatDatatypeprotocol;
-import org.nrg.xdat.schema.SchemaElement;
-import org.nrg.xdat.security.XdatStoredSearch;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.exception.ElementNotFoundException;
-import org.nrg.xft.exception.XFTInitException;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatDatatypeprotocol extends AutoXnatDatatypeprotocol {
-
- public BaseXnatDatatypeprotocol(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatDatatypeprotocol(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatDatatypeprotocol(UserI user)
- **/
- public BaseXnatDatatypeprotocol()
- {}
-
- public BaseXnatDatatypeprotocol(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-
- public XdatStoredSearch getDefaultSearch(XnatProjectdataI project){
- XdatStoredSearch xss = super.getDefaultSearch((XnatProjectdata)project);
-
- for(XnatFielddefinitiongroupI group : this.getDefinitions_definition()){
- for(XnatFielddefinitiongroupFieldI field : group.getFields_field()){
-
- XdatSearchField xsf = new XdatSearchField(this.getUser());
- xsf.setElementName(this.getDataType());
- String fieldID=null;
- if (field.getType().equals("custom"))
- {
- fieldID=this.getDatatypeSchemaElement().getSQLName().toUpperCase() + "_FIELD_MAP="+field.getName().toLowerCase();
-
- }else{
- try {
- SchemaElement se=SchemaElement.GetElement(this.getDataType());
-
- try {
- DisplayField df=se.getDisplayFieldForXMLPath(field.getXmlpath());
- if (df!=null){
- fieldID=df.getId();
- }
- } catch (Exception e) {
- logger.error("",e);
- }
- } catch (XFTInitException e) {
- logger.error("",e);
- } catch (ElementNotFoundException e) {
- logger.error("",e);
- }
- }
-
- if (fieldID!=null){
- xsf.setFieldId(fieldID);
-
- xsf.setHeader(field.getName());
- xsf.setType(field.getDatatype());
- xsf.setSequence(xss.getSearchField().size());
- if (field.getType().equals("custom"))xsf.setValue(field.getName().toLowerCase());
- try {
- xss.setSearchField(xsf);
- System.out.println("LOADED " + field.getXmlpath());
- } catch (Exception e) {
- logger.error("",e);
- System.out.println("FAILED to load " + field.getXmlpath());
- }
- }else{
- System.out.println("FAILED to load " + field.getXmlpath());
- }
- }
- }
-
-
-
- return xss;
- }
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatDemographicdata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatDemographicdata.java
deleted file mode 100644
index 26163e365a2796047a2bd49f89a9611f7a7c90ab..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatDemographicdata.java
+++ /dev/null
@@ -1,44 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatDemographicdata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatDemographicdata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public class BaseXnatDemographicdata extends AutoXnatDemographicdata {
-
- public BaseXnatDemographicdata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatDemographicdata(UserI user)
- {
- super(user);
- }
-
- public BaseXnatDemographicdata()
- {}
-
- public BaseXnatDemographicdata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatDeriveddata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatDeriveddata.java
deleted file mode 100644
index 9db7b9228ccad6eda24d079fa240f7fb99bf5ef0..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatDeriveddata.java
+++ /dev/null
@@ -1,44 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatDeriveddata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatDeriveddata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public class BaseXnatDeriveddata extends AutoXnatDeriveddata {
-
- public BaseXnatDeriveddata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatDeriveddata(UserI user)
- {
- super(user);
- }
-
- public BaseXnatDeriveddata()
- {}
-
- public BaseXnatDeriveddata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatDicomseries.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatDicomseries.java
deleted file mode 100644
index d7920834c1598019449f4250fb28dbb311738922..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatDicomseries.java
+++ /dev/null
@@ -1,173 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatDicomseries
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 11/18/13 9:35 AM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.model.XnatDicomseriesImageI;
-import org.nrg.xdat.om.XnatDicomseriesImage;
-import org.nrg.xdat.om.base.auto.AutoXnatDicomseries;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.event.EventMetaI;
-import org.nrg.xft.security.UserI;
-import org.nrg.xft.utils.FileUtils;
-import org.nrg.xft.utils.SaveItemHelper;
-import org.nrg.xft.utils.StringUtils;
-
-import java.io.File;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public class BaseXnatDicomseries extends AutoXnatDicomseries {
-
- public BaseXnatDicomseries(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatDicomseries(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatDicomseries(UserI user)
- **/
- public BaseXnatDicomseries()
- {}
-
- public BaseXnatDicomseries(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
- protected ArrayList files=null;
- protected ArrayList fileNames=null;
- /**
- * Returns ArrayList of java.io.File objects
- * @return
- */
- public ArrayList getCorrespondingFiles(String rootPath)
- {
- if (files==null)
- {
- files = new ArrayList();
-
- for (int i=0;i<this.getImageset_image().size();i++){
- org.nrg.xdat.om.XnatDicomseriesImage image = (org.nrg.xdat.om.XnatDicomseriesImage)this.getImageset_image().get(i);
- File f = image.getFile(rootPath);
- files.add(f);
- }
- }
- return files;
- }
-
- /**
- * Returns ArrayList of java.lang.String objects
- * @return
- */
- public ArrayList getCorrespondingFileNames(String rootPath)
- {
- if (fileNames==null)
- {
- fileNames = new ArrayList();
- for (int i=0;i<this.getImageset_image().size();i++){
- org.nrg.xdat.om.XnatDicomseriesImage image = (org.nrg.xdat.om.XnatDicomseriesImage)this.getImageset_image().get(i);
- File f = image.getFile(rootPath);
- fileNames.add(f.getName());
- }
- }
- return fileNames;
- }
-
-
- /**
- * Appends this path to the enclosed URI or path variables.
- * @param root
- */
- public void prependPathsWith(String root){
- for (int i=0;i<this.getImageset_image().size();i++){
- org.nrg.xdat.om.XnatDicomseriesImage image = (org.nrg.xdat.om.XnatDicomseriesImage)this.getImageset_image().get(i);
- image.prependPathsWith(root);
- }
- }
-
-
- /**
- * Relatives this path from the first occurrence of the indexOf string.
- * @param indexOf
- */
- public void relativizePaths(String indexOf, boolean caseSensitive){
- for (int i=0;i<this.getImageset_image().size();i++){
- org.nrg.xdat.om.XnatDicomseriesImage image = (org.nrg.xdat.om.XnatDicomseriesImage)this.getImageset_image().get(i);
- image.relativizePaths(indexOf,caseSensitive);
- }
- }
-
- /**
- * Appends this path to the enclosed URI or path variables.
- * @param root
- */
- public ArrayList<String> getUnresolvedPaths(){
- ArrayList<String> al = new ArrayList<String>();
- for (int i=0;i<this.getImageset_image().size();i++){
- org.nrg.xdat.om.XnatDicomseriesImage image = (org.nrg.xdat.om.XnatDicomseriesImage)this.getImageset_image().get(i);
- String p = image.getUri();
- p.replace('\\', '/');
- al.add(p);
- }
- return al;
- }
-
- public String getFullPath(String rootPath){
- String path = "";
-
- fileNames = new ArrayList();
- for (org.nrg.xdat.model.XnatDicomseriesImageI image:this.getImageset_image()){
- path = image.getUri();
- break;
- }
-
- String fullPath = StringUtils.ReplaceStr(FileUtils.AppendRootPath(rootPath,path),"\\","/");
- while (fullPath.indexOf("//")!=-1)
- {
- fullPath =StringUtils.ReplaceStr(fullPath,"//","/");
- }
-
- if(!fullPath.endsWith("/"))
- {
- fullPath+="/";
- }
- return fullPath;
- }
-
-
-
-
- public String getLabel(){
- if (this.getDescription().length()>15)
- {
- return this.getDescription().substring(0,14);
- }else
- return this.getDescription();
- }
-
- public void moveTo(File newSessionDir,String existingSessionDir,String rootPath,UserI user,EventMetaI ci) throws IOException,Exception{
- for(XnatDicomseriesImageI img : this.getImageset_image()){
- ((XnatDicomseriesImage)img).moveTo(newSessionDir, existingSessionDir, rootPath, user,ci);
- }
- SaveItemHelper.authorizedSave(this,user, true, false,ci);
- }
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatDicomseriesImage.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatDicomseriesImage.java
deleted file mode 100644
index 44fd166c88ebac477c95b0353cd9e64283365525..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatDicomseriesImage.java
+++ /dev/null
@@ -1,125 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatDicomseriesImage
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 11/18/13 9:35 AM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatDicomseriesImage;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.event.EventMetaI;
-import org.nrg.xft.security.UserI;
-import org.nrg.xft.utils.FileUtils;
-
-import java.io.File;
-import java.io.IOException;
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public class BaseXnatDicomseriesImage extends AutoXnatDicomseriesImage {
-
- public BaseXnatDicomseriesImage(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatDicomseriesImage(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatDicomseriesImage(UserI user)
- **/
- public BaseXnatDicomseriesImage()
- {}
-
- public BaseXnatDicomseriesImage(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
- public java.io.File getFile(String rootPath){
- java.io.File f = new java.io.File(org.nrg.xft.utils.FileUtils.AppendRootPath(rootPath,this.getUri()));
- if (!f.exists() && !getUri().endsWith(".gz"))
- {
- f = new java.io.File(org.nrg.xft.utils.FileUtils.AppendRootPath(rootPath,this.getUri()) + ".gz");
- }
- return f;
- }
-
- /**
- * Appends this path to the enclosed URI or path variables.
- * @param root
- */
- public void prependPathsWith(String root){
- if (!FileUtils.IsAbsolutePath(this.getUri())){
- try {
- this.setUri(root + this.getUri());
- } catch (Exception e) {
- logger.error("",e);
- }
- }
- }
-
- /**
- * Relatives this path from the first occurrence of the indexOf string.
- * @param indexOf
- */
- public void relativizePaths(String indexOf, boolean caseSensitive){
- String uri = this.getUri();
- uri= uri.replace('\\', '/');
- if (uri.indexOf(indexOf)==-1){
- if (!caseSensitive){
- int index = uri.toLowerCase().indexOf(indexOf.toLowerCase());
- if (index!=-1){
- this.setUri(uri.substring(index + 1));
- }
- }
- }else{
- this.setUri(uri.substring(uri.indexOf(indexOf) + 1));
- }
- }
-
- public void moveTo(File newSessionDir,String existingSessionDir,String rootPath,UserI user,EventMetaI ci) throws IOException,Exception{
- String uri = this.getUri();
-
- String relativePath=null;
- if(existingSessionDir!=null && uri.startsWith(existingSessionDir)){
- relativePath=uri.substring(existingSessionDir.length());
- }else{
- if(FileUtils.IsAbsolutePath(uri)){
- if(uri.indexOf("/")>0){
- relativePath=uri.substring(uri.indexOf("/")+1);
- }else if(uri.indexOf("\\")>0){
- relativePath=uri.substring(uri.indexOf("\\")+1);
- }else{
- relativePath=uri;
- }
- }
- }
-
- File newFile = new File(newSessionDir,relativePath);
- File parentDir=newFile.getParentFile();
- if(!parentDir.exists())
- {
- parentDir.mkdirs();
- }
-
- File f=this.getFile(rootPath);
- if(f !=null){
- FileUtils.MoveFile(f, newFile, true);
- }
-
- this.setUri(newFile.getAbsolutePath());
- }
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatDx3dcraniofacialscandata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatDx3dcraniofacialscandata.java
deleted file mode 100644
index fee86fe1ae3579813c28f6cb437e03f7a0ffd1d5..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatDx3dcraniofacialscandata.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatDx3dcraniofacialscandata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatDx3dcraniofacialscandata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatDx3dcraniofacialscandata extends AutoXnatDx3dcraniofacialscandata {
-
- public BaseXnatDx3dcraniofacialscandata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatDx3dcraniofacialscandata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatDx3dcraniofacialscandata(UserI user)
- **/
- public BaseXnatDx3dcraniofacialscandata()
- {}
-
- public BaseXnatDx3dcraniofacialscandata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatDx3dcraniofacialsessiondata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatDx3dcraniofacialsessiondata.java
deleted file mode 100644
index 6ce8a990f983ebf9205abfb4474d39c7084da439..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatDx3dcraniofacialsessiondata.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatDx3dcraniofacialsessiondata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatDx3dcraniofacialsessiondata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatDx3dcraniofacialsessiondata extends AutoXnatDx3dcraniofacialsessiondata {
-
- public BaseXnatDx3dcraniofacialsessiondata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatDx3dcraniofacialsessiondata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatDx3dcraniofacialsessiondata(UserI user)
- **/
- public BaseXnatDx3dcraniofacialsessiondata()
- {}
-
- public BaseXnatDx3dcraniofacialsessiondata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatDxscandata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatDxscandata.java
deleted file mode 100644
index bdb40f002801f849afab38d55747bfda7a131526..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatDxscandata.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatDxscandata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatDxscandata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatDxscandata extends AutoXnatDxscandata {
-
- public BaseXnatDxscandata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatDxscandata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatDxscandata(UserI user)
- **/
- public BaseXnatDxscandata()
- {}
-
- public BaseXnatDxscandata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatDxsessiondata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatDxsessiondata.java
deleted file mode 100644
index f93f7c4b83468412d481fc3f1cdd41b50952a063..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatDxsessiondata.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatDxsessiondata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatDxsessiondata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatDxsessiondata extends AutoXnatDxsessiondata {
-
- public BaseXnatDxsessiondata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatDxsessiondata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatDxsessiondata(UserI user)
- **/
- public BaseXnatDxsessiondata()
- {}
-
- public BaseXnatDxsessiondata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatEcgscandata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatEcgscandata.java
deleted file mode 100644
index 12db87eda29fbf7c6d16f76efab71c99d4fb6674..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatEcgscandata.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatEcgscandata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatEcgscandata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatEcgscandata extends AutoXnatEcgscandata {
-
- public BaseXnatEcgscandata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatEcgscandata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatEcgscandata(UserI user)
- **/
- public BaseXnatEcgscandata()
- {}
-
- public BaseXnatEcgscandata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatEcgsessiondata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatEcgsessiondata.java
deleted file mode 100644
index a8b829bc3a5385e5869fc0b955118b3dbcecc384..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatEcgsessiondata.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatEcgsessiondata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatEcgsessiondata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatEcgsessiondata extends AutoXnatEcgsessiondata {
-
- public BaseXnatEcgsessiondata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatEcgsessiondata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatEcgsessiondata(UserI user)
- **/
- public BaseXnatEcgsessiondata()
- {}
-
- public BaseXnatEcgsessiondata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatEegscandata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatEegscandata.java
deleted file mode 100644
index ef78834349dbe42226863373da737333c8cde714..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatEegscandata.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatEegscandata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatEegscandata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatEegscandata extends AutoXnatEegscandata {
-
- public BaseXnatEegscandata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatEegscandata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatEcgscandata(UserI user)
- **/
- public BaseXnatEegscandata()
- {}
-
- public BaseXnatEegscandata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatEegsessiondata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatEegsessiondata.java
deleted file mode 100644
index 9e066f83a215f7f47c444aeafa38653df431466e..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatEegsessiondata.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatEegsessiondata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatEegsessiondata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatEegsessiondata extends AutoXnatEegsessiondata {
-
- public BaseXnatEegsessiondata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatEegsessiondata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatEcgsessiondata(UserI user)
- **/
- public BaseXnatEegsessiondata()
- {}
-
- public BaseXnatEegsessiondata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatEpsscandata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatEpsscandata.java
deleted file mode 100644
index 31b58d7ee34aa40c4d08de5514115eafbc5629fe..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatEpsscandata.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatEpsscandata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatEpsscandata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatEpsscandata extends AutoXnatEpsscandata {
-
- public BaseXnatEpsscandata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatEpsscandata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatEpsscandata(UserI user)
- **/
- public BaseXnatEpsscandata()
- {}
-
- public BaseXnatEpsscandata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatEpssessiondata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatEpssessiondata.java
deleted file mode 100644
index 521f493a2696f7e9c34d9cf473744488d74b6796..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatEpssessiondata.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatEpssessiondata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatEpssessiondata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatEpssessiondata extends AutoXnatEpssessiondata {
-
- public BaseXnatEpssessiondata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatEpssessiondata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatEpssessiondata(UserI user)
- **/
- public BaseXnatEpssessiondata()
- {}
-
- public BaseXnatEpssessiondata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatEsscandata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatEsscandata.java
deleted file mode 100644
index 107ee57ec1be32d9a2a76fb49fc7574d0de85b07..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatEsscandata.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatEsscandata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatEsscandata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatEsscandata extends AutoXnatEsscandata {
-
- public BaseXnatEsscandata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatEsscandata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatEsscandata(UserI user)
- **/
- public BaseXnatEsscandata()
- {}
-
- public BaseXnatEsscandata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatEssessiondata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatEssessiondata.java
deleted file mode 100644
index fddbba3f214553b0913457efb8d3b53253e10d58..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatEssessiondata.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatEssessiondata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatEssessiondata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatEssessiondata extends AutoXnatEssessiondata {
-
- public BaseXnatEssessiondata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatEssessiondata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatEssessiondata(UserI user)
- **/
- public BaseXnatEssessiondata()
- {}
-
- public BaseXnatEssessiondata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatEsvscandata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatEsvscandata.java
deleted file mode 100644
index baa78f0ec1ccd0e9524ce57c5d12c478b26abfca..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatEsvscandata.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatEsvscandata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatEsvscandata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatEsvscandata extends AutoXnatEsvscandata {
-
- public BaseXnatEsvscandata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatEsvscandata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatEsvscandata(UserI user)
- **/
- public BaseXnatEsvscandata()
- {}
-
- public BaseXnatEsvscandata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatEsvsessiondata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatEsvsessiondata.java
deleted file mode 100644
index f09d5e0b1836209ac40ed70fbee2fe764d39f73d..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatEsvsessiondata.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatEsvsessiondata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatEsvsessiondata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatEsvsessiondata extends AutoXnatEsvsessiondata {
-
- public BaseXnatEsvsessiondata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatEsvsessiondata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatEsvsessiondata(UserI user)
- **/
- public BaseXnatEsvsessiondata()
- {}
-
- public BaseXnatEsvsessiondata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatExperimentdata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatExperimentdata.java
deleted file mode 100644
index bb32f3b9b3e57f98390439f3663d47e9ac8f5477..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatExperimentdata.java
+++ /dev/null
@@ -1,948 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatExperimentdata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 9/20/13 2:34 PM
- */
-package org.nrg.xdat.om.base;
-
-import com.google.common.collect.Lists;
-import org.apache.commons.lang.exception.ExceptionUtils;
-import org.nrg.action.ClientException;
-import org.nrg.xdat.XDAT;
-import org.nrg.xdat.base.BaseElement;
-import org.nrg.xdat.model.*;
-import org.nrg.xdat.om.*;
-import org.nrg.xdat.om.base.auto.AutoXnatExperimentdata;
-import org.nrg.xdat.schema.SchemaElement;
-import org.nrg.xdat.security.SecurityValues;
-import org.nrg.xdat.security.helpers.Permissions;
-import org.nrg.xdat.security.helpers.Users;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-import org.nrg.xft.XFTTable;
-import org.nrg.xft.db.MaterializedView;
-import org.nrg.xft.db.PoolDBUtils;
-import org.nrg.xft.event.EventDetails;
-import org.nrg.xft.event.EventMetaI;
-import org.nrg.xft.event.persist.PersistentWorkflowI;
-import org.nrg.xft.event.persist.PersistentWorkflowUtils;
-import org.nrg.xft.exception.DBPoolException;
-import org.nrg.xft.exception.ElementNotFoundException;
-import org.nrg.xft.exception.InvalidPermissionException;
-import org.nrg.xft.exception.XFTInitException;
-import org.nrg.xft.identifier.IDGeneratorFactory;
-import org.nrg.xft.identifier.IDGeneratorI;
-import org.nrg.xft.search.CriteriaCollection;
-import org.nrg.xft.security.UserI;
-import org.nrg.xft.utils.FileUtils;
-import org.nrg.xft.utils.SaveItemHelper;
-import org.nrg.xft.utils.StringUtils;
-import org.nrg.xnat.exceptions.InvalidArchiveStructure;
-import org.nrg.xnat.turbine.utils.ArcSpecManager;
-import org.nrg.xnat.turbine.utils.ArchivableItem;
-import org.nrg.xnat.utils.WorkflowUtils;
-import org.restlet.data.Status;
-
-import java.io.File;
-import java.sql.SQLException;
-import java.text.DateFormat;
-import java.text.SimpleDateFormat;
-import java.util.*;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public class BaseXnatExperimentdata extends AutoXnatExperimentdata implements ArchivableItem, MoveableI {
-
- private static final long serialVersionUID = -1237275273363081417L;
-
- public BaseXnatExperimentdata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatExperimentdata(UserI user)
- {
- super(user);
- }
-
- public BaseXnatExperimentdata()
- {}
-
- public BaseXnatExperimentdata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
- public String getArchiveDirectoryName(){
- if(this.getLabel()!=null)
- return this.getLabel();
- else
- return this.getId();
- }
-
- @SuppressWarnings("unused")
- public String getFreeFormDate(String dateParam){
- try{
- Date now = Calendar.getInstance().getTime();
- DateFormat dateFormat = new SimpleDateFormat(dateParam);
- return dateFormat.format(now);
- } catch (Exception e1) {logger.error(e1);return null;}
- }
-
- Hashtable fieldsByName = null;
- public Hashtable getFieldsByName(){
- if (fieldsByName == null){
- fieldsByName=new Hashtable();
- for(final XnatExperimentdataFieldI field: this.getFields_field()){
- fieldsByName.put(field.getName(), field);
- }
- }
-
- return fieldsByName;
- }
-
- @SuppressWarnings("unused")
- public Object getFieldByName(final String s){
- XnatExperimentdataFieldI field = (XnatExperimentdataFieldI)getFieldsByName().get(s);
- if (field!=null){
- return field.getField();
- }else{
- return null;
- }
- }
-
- public String getIdentifier(String project){
- return getIdentifier(project,false);
- }
-
- public String getIdentifier(final String project,final boolean returnNULL){
- if (project!=null){
- if (this.getProject().equals(project)){
- if (this.getLabel()!=null){
- return this.getLabel();
- }
- }
-
- for (final XnatExperimentdataShareI pp : this.getSharing_share())
- {
- if (pp.getProject().equals(project))
- {
- if (pp.getLabel()!=null){
- return pp.getLabel();
- }
- }
- }
- }
-
- if (returnNULL){
- return null;
- }else{
- return getId();
- }
- }
-
- public XnatProjectdataI getProject(final String projectID, final boolean preLoad)
- {
- XnatExperimentdataShare ep = null;
- for (final XnatExperimentdataShareI pp : this.getSharing_share())
- {
- if (pp.getProject().equals(projectID))
- {
- ep=(XnatExperimentdataShare)pp;
- break;
- }
- }
-
- try {
- if (ep!=null){
- return XnatProjectdata.getXnatProjectdatasById(ep.getProject(), this.getUser(), preLoad);
- }else if (this.getProject().equals(projectID)){
- return XnatProjectdata.getXnatProjectdatasById(this.getProject(), this.getUser(), preLoad);
- }
- } catch (RuntimeException e) {
- logger.error("",e);
- }
-
- return null;
- }
-
- public XnatProjectdata getPrimaryProject(boolean preLoad){
- if (this.getProject()!=null){
- return XnatProjectdata.getXnatProjectdatasById(getProject(), this.getUser(), preLoad);
- }else{
- return (XnatProjectdata)getFirstProject();
- }
- }
-
-
- public XnatProjectdataI getFirstProject() {
- List<XnatExperimentdataShareI> shares = getSharing_share();
- if (!shares.isEmpty()){
- for (XnatExperimentdataShareI ep : shares) {
- if (ep != null) {
- try {
- // We'll return the first non-null project, i.e. the first shared project this user can access.
- XnatProjectdata project = XnatProjectdata.getXnatProjectdatasById(ep.getProject(), this.getUser(), false);
- if (project != null) {
- return project;
- }
- } catch (RuntimeException e) {
- logger.error("",e);
- }
- }
- }
- }
-
- return null;
- }
-
-
-
- public String getIdentifiers(){
- Hashtable ids = new Hashtable();
-
- if (this.getProject()!=null){
- if (this.getLabel()!=null){
- ids.put(this.getLabel(), this.getProject());
- }else{
- ids.put(this.getId(), this.getProject());
- }
- }
-
- for (final XnatExperimentdataShareI pp : this.getSharing_share())
- {
-
- if (pp.getLabel()!=null){
- if (ids.containsKey(pp.getLabel()))
- {
- ids.put(pp.getLabel(), ids.get(pp.getLabel()) + "," + pp.getProject());
- }else{
- ids.put(pp.getLabel(), pp.getProject());
- }
- }else{
- if (ids.containsKey(this.getId()))
- {
- ids.put(this.getId(), ids.get(this.getId()) + "," + pp.getProject());
- }else{
- ids.put(this.getId(), pp.getProject());
- }
- }
- }
-
- String identifiers = "";
-
- Enumeration keys = ids.keys();
- int counter=0;
- while (keys.hasMoreElements()){
- String key =(String) keys.nextElement();
- if (counter++>0)identifiers=identifiers + ", ";
- identifiers=identifiers + key + " ("+ ids.get(key) + ")";
- }
-
- return identifiers;
- }
-
-
-
-
- public String name = null;
- public String description = null;
- public String secondaryID = null;
- private boolean initd = false;
-
- public void loadProjectDetails(){
- if (!initd)
- {
- initd=true;
- Object[] row=this.loadProjectDetails(this.getProject());
- if (row!=null)
- {
- name = (String)row[0];
- description = (String)row[1];
- secondaryID = (String)row[2];
- }
- }
- }
-
- public Object[] loadProjectDetails(String s){
- try{
- XFTTable table = XFTTable.Execute("SELECT name,description,secondary_ID FROM xnat_projectData WHERE ID ='" + s + "';", this.getDBName(), null);
-
- if (table.size()>0)
- {
- return table.rows().get(0);
- }
- } catch (SQLException | DBPoolException e) {
- logger.error("",e);
- }
-
- return null;
- }
-
- public XnatProjectdata getProjectData(){
- return XnatProjectdata.getXnatProjectdatasById(this.getProject(), this.getUser(), false);
- }
-
-
- /**
- * @return the description
- */
- public String getDescription() {
- loadProjectDetails();
- return description;
- }
-
- /**
- * @return the name
- */
- public String getProjectName() {
- loadProjectDetails();
- return name;
- }
-
- /**
- * @return the secondaryID
- */
- public String getProjectSecondaryID() {
- loadProjectDetails();
- return secondaryID;
- }
-
-
-
- /**
- * @return the secondaryID
- */
- public String getProjectDisplayID() {
- loadProjectDetails();
- if (secondaryID!=null){
- return secondaryID;
- }else{
- return getProject();
- }
- }
-
- public Hashtable<XnatProjectdataI,String> getProjectDatas(){
- Hashtable<XnatProjectdataI,String> hash = new Hashtable<>();
- for(final XnatExperimentdataShareI pp : this.getSharing_share()){
- if (pp.getLabel()==null)
- if (this.getId()!=null)
- hash.put(((XnatExperimentdataShare)pp).getProjectData(), this.getId());
- else
- hash.put(((XnatExperimentdataShare)pp).getProjectData(), "");
- else
- hash.put(((XnatExperimentdataShare)pp).getProjectData(), pp.getLabel());
- }
- return hash;
- }
-
- @SuppressWarnings("unused")
- public Collection<XnatFielddefinitiongroup> getFieldDefinitionGroups(final String dataType, final String projectID) {
- final Hashtable<String, XnatFielddefinitiongroup> groups = new Hashtable<>();
- final Hashtable<XnatProjectdataI, String> projects = getProjectDatas();
- final XnatProjectdata primaryProject = getPrimaryProject(false);
- if (primaryProject != null) {
- projects.put(primaryProject, "");
-
- for (final Map.Entry<XnatProjectdataI, String> entry : projects.entrySet()) {
- final XnatAbstractprotocol prot = ((XnatProjectdata) entry.getKey()).getProtocolByDataType(dataType);
- if ((projectID != null && !projectID.isEmpty()) && !projectID.equals(entry.getKey().getId())) {
- continue;
- }
- if (prot != null && prot instanceof XnatDatatypeprotocol) {
- final XnatDatatypeprotocol dataProt = (XnatDatatypeprotocol) prot;
- for (final XnatFielddefinitiongroupI group : dataProt.getDefinitions_definition()) {
- groups.put(group.getId(), (XnatFielddefinitiongroup) group);
- }
- }
- }
- }
- return groups.values();
- }
-
- public static XnatExperimentdata GetExptByProjectIdentifier(String project, String identifier,UserI user,boolean preLoad){
- if(StringUtils.IsEmpty(identifier)){
- return null;
- }
-
- CriteriaCollection cc=new CriteriaCollection("OR");
-
- CriteriaCollection subcc1 = new CriteriaCollection("AND");
- subcc1.addClause("xnat:experimentData/project", project);
- subcc1.addClause("xnat:experimentData/label", identifier);
-
- cc.add(subcc1);
-
- CriteriaCollection subcc2 = new CriteriaCollection("AND");
- subcc2.addClause("xnat:experimentData/sharing/share/project", project);
- subcc2.addClause("xnat:experimentData/sharing/share/label", identifier);
-
- cc.add(subcc2);
-
- ArrayList al = XnatExperimentdata.getXnatExperimentdatasByField(cc, user, preLoad);
- al = BaseElement.WrapItems(al);
- if (al.size()>0){
- return (XnatExperimentdata)al.get(0);
- }else{
- return null;
- }
-
- }
-
- public static synchronized String CreateNewID() throws Exception{
- IDGeneratorI generator = IDGeneratorFactory.GetIDGenerator("org.nrg.xnat.turbine.utils.IDGenerator");
- assert generator != null;
- generator.setTable("xnat_experimentData");
- generator.setDigits(5);
- generator.setColumn("id");
- return generator.generateIdentifier();
- }
-
- /**
- * newlabel can be null defaults to this.getLabel(), if that is null this.getId()
- * @param newProject New project to move.
- * @param newLabel New label to set.
- * @param user User moving.
- * @throws Exception
- */
- public void moveToProject(XnatProjectdata newProject,String newLabel,UserI user,EventMetaI ci,List<String> assessors) throws Exception{
-
- if(!this.getProject().equals(newProject.getId()))
- {
-
- if (!MoverMaker.check(this, user)) {
- throw new InvalidPermissionException(this.getXSIType());
- }
- String existingRootPath=this.getProjectData().getRootArchivePath();
-
- if(newLabel==null)newLabel = this.getLabel();
- if(newLabel==null)newLabel = this.getId();
-
- // newSessionDir = /ARCHIVE/proj_x/arc001
- final File newSessionDir = new File(new File(newProject.getRootArchivePath(),newProject.getCurrentArc()),newLabel);
-
- // Label defaults to this.getId()
- String current_label=this.getLabel();
- if(current_label==null)current_label=this.getId();
-
-
- for(XnatAbstractresourceI abstRes:this.getResources_resource()){
- MoverMaker.moveResource(abstRes, current_label, this, newSessionDir, existingRootPath, user,ci);
- }
-
- MoverMaker.writeDB(this, newProject, newLabel, user,ci);
- MoverMaker.setLocal(this, newProject, newLabel);
- }
- }
-
- @SuppressWarnings("unused")
- public ArrayList getCatalogSummary() throws Exception{
- String query="SELECT xnat_abstractresource_id,label,element_name ";
- query+=", 'resources'::TEXT AS category, '" + this.getId()+"'::TEXT AS cat_id";
- query+=" FROM xnat_experimentdata_resource map " +
- " LEFT JOIN xnat_abstractresource abst ON map.xnat_abstractresource_xnat_abstractresource_id=abst.xnat_abstractresource_id" +
- " LEFT JOIN xdat_meta_element xme ON abst.extension=xme.xdat_meta_element_id";
- query+= " WHERE xnat_experimentdata_id='"+this.getId() + "'";
-
- XFTTable t = XFTTable.Execute(query, this.getDBName(), "system");
-
- return t.rowHashs();
- }
-
- public boolean hasProject(String proj_id){
- if (this.getProject() == null) {
- return false;
- }
- if(this.getProject().equals(proj_id)){
- return true;
- }else{
- for(XnatExperimentdataShareI pp: this.getSharing_share()){
- if(pp.getProject().equals(proj_id)){
- return true;
- }
- }
- }
-
- return false;
- }
-
-
-
- public String canDelete(BaseXnatProjectdata proj, UserI user) {
- BaseXnatExperimentdata expt=this;
- if(this.getItem().getUser()!=null){
- expt=new XnatExperimentdata(this.getCurrentDBVersion(true));
- }
- if(!expt.hasProject(proj.getId())){
- return null;
- }else {
-
- try {
- SecurityValues values = new SecurityValues();
- values.put(this.getXSIType() + "/project", proj.getId());
- SchemaElement se= SchemaElement.GetElement(this.getXSIType());
-
- if (!Permissions.canDelete(user,se,values))
- {
- return "User cannot delete experiments for project " + proj.getId();
- }
- } catch (Exception e1) {
- return "Unable to delete subject.";
- }
-
- }
- return null;
- }
-
- public String delete(BaseXnatProjectdata proj, UserI user, boolean removeFiles,EventMetaI c){
- BaseXnatExperimentdata expt=this;
- if(this.getItem().getUser()!=null){
- expt= (BaseXnatExperimentdata)BaseElement.GetGeneratedItem(expt.getItem());
- }
-
- String msg=expt.canDelete(proj,user);
-
- if(msg!=null){
- logger.error(msg);
- return msg;
- }
-
- if(expt.getProject() != null && !expt.getProject().equals(proj.getId())){
- try {
- SecurityValues values = new SecurityValues();
- values.put(this.getXSIType() + "/project", proj.getId());
-
- if (!Permissions.canDelete(user,expt) && !Permissions.canDelete(user,this.getSchemaElement(),values))
- {
- return "User cannot delete experiments for project " + proj.getId();
- }
-
-
- //unshare children before unsharing parent
- if(expt instanceof XnatImagesessiondata){
- final List<XnatImageassessordata> expts = ((XnatImagesessiondata)expt).getAssessors_assessor();
- for (XnatImageassessordataI exptI : expts){
- final XnatImageassessordata assess = (XnatImageassessordata)exptI;
- if(assess.getProject().equals(proj.getId())){
- return "This operation would delete an experiment (rather than un-share). Please move experiment ("+expt.getId()+") to another project or manually delete.";
-
- }
- msg= assess.delete(proj,user,false,c);
- if(msg!=null){
- return msg;
- }
- }
- }
-
- int index = 0;
- int match = -1;
- for(XnatExperimentdataShareI pp : expt.getSharing_share()){
- if(pp.getProject().equals(proj.getId())){
- SaveItemHelper.authorizedRemoveChild(expt.getItem(), "xnat:experimentData/sharing/share", ((XnatExperimentdataShare)pp).getItem(), user,c);
- match=index;
- break;
- }
- index++;
- }
-
- if(match==-1)return null;
-
- this.removeSharing_share(match);
- return null;
- } catch (SQLException e) {
- logger.error("",e);
- return e.getMessage();
- } catch (Exception e) {
- logger.error("",e);
- return e.getMessage();
- }
- }else{
-
- if(XDAT.getBoolSiteConfigurationProperty("security.prevent-data-deletion", false)){
- return "User account cannot delete experiments";
- }
- try {
-
- if(!Permissions.canDelete(user,this)){
- return "User account doesn't have permission to delete this experiment.";
- }
-
- if(removeFiles){
- this.deleteFiles(user,c);
- }
-
-
- SaveItemHelper.authorizedDelete(expt.getItem().getCurrentDBVersion(), user,c);
- Users.clearCache(user);
- MaterializedView.deleteByUser(user);
-
- } catch (SQLException e) {
- logger.error("",e);
- return org.apache.commons.lang.StringUtils.isBlank(e.getMessage()) ? ExceptionUtils.getStackTrace(e) : e.getMessage();
- } catch (Exception e) {
- logger.error("",e);
- return org.apache.commons.lang.StringUtils.isBlank(e.getMessage()) ? ExceptionUtils.getStackTrace(e) : e.getMessage();
- }
- }
- return null;
- }
-
- /**
- * This method looks for an existing session directory in the archive space.s
- * @return The file for the session directory.
- */
- public File getSessionDir(){
- final File archive=new File(ArcSpecManager.GetInstance().getArchivePathForProject(this.getProject()));
- if(archive.exists()){
- final File[] files = archive.listFiles();
- if (files != null) {
- for (final File arc : files) {
- if (!arc.getName().equals("subjects") && !arc.getName().equals("resources") && arc.isDirectory()) {
- final File[] archiveFiles = arc.listFiles();
- if (archiveFiles != null) {
- for (final File dir : archiveFiles) {
- if (dir.isDirectory() && dir.getName().equals(this.getArchiveDirectoryName())) {
- return dir;
- }
- }
- }
- }
- }
- }
- }
-
- return null;
- }
-
- public void deleteFiles(UserI u, EventMetaI ci) throws Exception{
- for(XnatAbstractresourceI abstRes:this.getResources_resource()){
- ((XnatAbstractresource)abstRes).deleteWithBackup(ArcSpecManager.GetInstance().getArchivePathForProject(this.getProject()), u,ci);
- }
-
- File dir=this.getSessionDir();
- if(dir!=null){
- FileUtils.MoveToCache(dir);
- }
- }
-
-
-
- public static String cleanValue(String v){
- v= StringUtils.ReplaceStr(v, " ", "_");
- v= StringUtils.ReplaceStr(v, "`", "_");
- v= StringUtils.ReplaceStr(v, "~", "_");
- v= StringUtils.ReplaceStr(v, "@", "_");
- v= StringUtils.ReplaceStr(v, "#", "_");
- v= StringUtils.ReplaceStr(v, "$", "_");
- v= StringUtils.ReplaceStr(v, "%", "_");
- v= StringUtils.ReplaceStr(v, "^", "_");
- v= StringUtils.ReplaceStr(v, "&", "_");
- v= StringUtils.ReplaceStr(v, "*", "_");
- v= StringUtils.ReplaceStr(v, "(", "_");
- v= StringUtils.ReplaceStr(v, ")", "_");
- v= StringUtils.ReplaceStr(v, "+", "_");
- v= StringUtils.ReplaceStr(v, "=", "_");
- v= StringUtils.ReplaceStr(v, "[", "_");
- v= StringUtils.ReplaceStr(v, "]", "_");
- v= StringUtils.ReplaceStr(v, "{", "_");
- v= StringUtils.ReplaceStr(v, "}", "_");
- v= StringUtils.ReplaceStr(v, "|", "_");
- v= StringUtils.ReplaceStr(v, "\\", "_");
- v= StringUtils.ReplaceStr(v, "/", "_");
- v= StringUtils.ReplaceStr(v, "?", "_");
- v= StringUtils.ReplaceStr(v, ":", "_");
- v= StringUtils.ReplaceStr(v, ";", "_");
- v= StringUtils.ReplaceStr(v, "\"", "_");
- v= StringUtils.ReplaceStr(v, "'", "_");
- v= StringUtils.ReplaceStr(v, ",", "_");
- v= StringUtils.ReplaceStr(v, ".", "_");
- v= StringUtils.ReplaceStr(v, "<", "_");
- v= StringUtils.ReplaceStr(v, ">", "_");
-
- return v;
- }
-
- /**
- * Gets root path to the primary project's archive space.
- * @return The path to the root folder of the experiment's primary project's archive space.
- */
- public String getArchiveRootPath() throws UnknownPrimaryProjectException{
- XnatProjectdata p=getPrimaryProject(false);
- if(p!=null){
- return p.getRootArchivePath();
- }else{
- throw new UnknownPrimaryProjectException();
- }
- }
-
- public static class UnknownPrimaryProjectException extends Exception{
-
- }
-
- /**
- * Gets root path to the primary project's cache space.
- * @return The path to the root folder of the subject's primary project's cache space.
- */
- public String getCachePath(){
- final XnatProjectdata primaryProject = getPrimaryProject(false);
- return primaryProject != null ? primaryProject.getCachePath() : "";
- }
-
- /**
- * Gets root path to the primary project's prearchive space.
- * @return The path to the root folder of the subject's primary project's prearchive space.
- */
- public String getPrearchivePath(){
- final XnatProjectdata primaryProject = getPrimaryProject(false);
- return primaryProject != null ? primaryProject.getPrearchivePath() : "";
- }
-
- /**
- * This returns the current sub folder within the project archive folder for placing sessions (ie arc001).
- * @return The path to the current sub folder within the subject's primary project's archive space for session storage.
- * @throws InvalidArchiveStructure
- */
- public String getCurrentArchiveFolder() throws InvalidArchiveStructure, UnknownPrimaryProjectException {
- final String arcpath = getArchiveRootPath();
- final File f = new File(arcpath);
-
- if (!f.exists()) {
- f.mkdir();
- }
-
- final XnatProjectdata primaryProject = getPrimaryProject(false);
- if (primaryProject == null) {
- return null;
- }
-
- String curA = primaryProject.getCurrentArc();
- if (curA == null) {
- return null;
- }
-
- logger.info("CURRENT_ARC:" + curA);
- if (!curA.endsWith("\\") && !curA.endsWith("/")) {
- curA += File.separator;
- }
-
- if (FileUtils.IsAbsolutePath(curA)) {
- final File currentArc = new File(curA);
- if (!currentArc.exists()) {
- currentArc.mkdirs();
- }
-
- int index = curA.indexOf(f.getName());
- if (index == -1) {
- throw new InvalidArchiveStructure(f.getName() + " does not exist in " + curA);
- } else {
- return curA.substring(index + f.getName().length() + 1);
- }
- } else {
- final File currentArc = new File(arcpath + curA);
- if (!currentArc.exists()) {
- currentArc.mkdirs();
- }
- return curA;
- }
- }
-
- /**
- * Returns path to the current archive folder for this experiment
- * @param absolute Indicates whether the path should be returned as an absolute path or relative to the
- * {@link #getArchiveRootPath() root archive path}.
- * @return The folder location for the current session.
- * @throws InvalidArchiveStructure
- */
- public String getCurrentSessionFolder(boolean absolute) throws InvalidArchiveStructure,UnknownPrimaryProjectException{
- String session_path;
-
- final String currentarc = this.getCurrentArchiveFolder();
- if (currentarc ==null){
- session_path = this.getArchiveDirectoryName() + "/";
- }else{
- session_path = currentarc.replace('\\', '/') + this.getArchiveDirectoryName() + "/";
- }
-
- if (absolute){
- session_path= FileUtils.AppendRootPath(this.getArchiveRootPath(), session_path);
- }
-
- return session_path;
- }
-
- /**
- * This method looks for an existing session directory in the archive space. If none is found, it returns the location where said directory would be created.
- * @return The folder in which the experiment is or should be located.
- */
- public File getExpectedSessionDir() throws InvalidArchiveStructure,UnknownPrimaryProjectException{
- final File sessionDIR=this.getSessionDir();
-
- if(sessionDIR==null){
- return new File(this.getCurrentSessionFolder(true));
- }
-
- return sessionDIR;
- }
-
- protected void checkIsValidID(String s) throws IllegalArgumentException{
-
- if(StringUtils.IsEmpty(s)){
- throw new IllegalArgumentException();
- }
-
- if(!StringUtils.IsAlphaNumericUnderscore(s)){
- throw new IllegalArgumentException("Identifiers cannot use special characters.");
- }
- }
-
- public void checkUniqueLabel() throws Exception{
- if(!StringUtils.IsEmpty(this.getLabel())){
- Long count=(Long)PoolDBUtils.ReturnStatisticQuery(String.format("SELECT COUNT(*) FROM (SELECT label, ID FROM xnat_experimentData WHERE label='%1$s' AND ID !='%2$s' AND project='%3$s' UNION SELECT label, sharing_share_xnat_experimentda_id AS ID FROM xnat_experimentData_share WHERE label='%1$s' AND sharing_share_xnat_experimentda_id !='%2$s' AND project='%3$s') SRCH",this.getLabel(),this.getId(),this.getProject()), "count", this.getDBName(), "system");
- if(count>0){
- throw new ClientException(Status.CLIENT_ERROR_CONFLICT,"Conflict: Duplicate experiment label",new Exception());
- }
- }
- }
-
-
- @Override
- public void preSave() throws Exception{
- super.preSave();
-
- checkIsValidID(this.getId());
-
- checkIsValidID(this.getLabel());
-
- final XnatProjectdata proj = getPrimaryProject(false);
- if(proj==null){
- throw new Exception("Unable to identify project for:" + this.getProject());
- }
-
- checkUniqueLabel();
-
- final String expectedPath=this.getExpectedSessionDir().getAbsolutePath().replace('\\', '/');
-
- for(final XnatAbstractresourceI res: this.getResources_resource()){
- final String uri;
- if(res instanceof XnatResource){
- uri=((XnatResource)res).getUri();
- }else if(res instanceof XnatResourceseries){
- uri=((XnatResourceseries)res).getPath();
- }else{
- continue;
- }
-
- FileUtils.ValidateUriAgainstRoot(uri,expectedPath,"URI references data outside of the project:" + uri);
- }
- }
-
-
-
- public File getExpectedCurrentDirectory() throws InvalidArchiveStructure,UnknownPrimaryProjectException {
- return getExpectedSessionDir();
- }
-
- public String getResourceCatalogRootPathByLabel(final String label) {
- String rtn = null;
- for (final Object file : getResources_resource()) {
- if (file instanceof XnatResourcecatalog) {
- String tag = ((XnatResourcecatalog)file).getLabel();
- if (tag != null && tag.equals(label)) {
- rtn =((XnatResourcecatalog)file).getUri();
- int index = rtn.lastIndexOf("/");
- if (index != -1)
- rtn = rtn.substring(0, index);
- break;
- }
- }
- }
- return rtn;
- }
-
- public static void SaveSharedProject(XnatExperimentdataShare pp, XnatExperimentdata expt,UserI user,final EventDetails event) throws Exception{
- PersistentWorkflowI wrk= WorkflowUtils.buildOpenWorkflow(user, expt.getItem(),event);
- EventMetaI c=wrk.buildEvent();
- PersistentWorkflowUtils.save(wrk, c);
- try {
- SaveItemHelper.authorizedSave(pp,user,false,false,c);
- PersistentWorkflowUtils.complete(wrk, c);
- } catch (Exception e) {
- logger.error("",e);
- PersistentWorkflowUtils.fail(wrk, c);
- throw e;
- }
- }
-
- public static EventMetaI ChangePrimaryProject(UserI user, XnatExperimentdata assessor, XnatProjectdata newProject, String newLabel, final EventDetails event, List<String> imageAssessors) throws Exception{
- PersistentWorkflowI wrk= WorkflowUtils.buildOpenWorkflow(user, assessor.getXSIType(), assessor.getId(),assessor.getProject(),event);
- EventMetaI c=wrk.buildEvent();
- PersistentWorkflowUtils.save(wrk, c);
-
- try {
- assessor.moveToProject(newProject,newLabel,user,c,imageAssessors);
-
- PersistentWorkflowUtils.complete(wrk, c);
- } catch (Exception e) {
- logger.error("",e);
- PersistentWorkflowUtils.fail(wrk,c);
- throw e;
- }
-
- return c;
- }
-
- List<WrkWorkflowdataI> workflows=null;
- public List<WrkWorkflowdataI> getWorkflows() throws Exception{
- if(workflows==null){
- workflows = Lists.newArrayList();
-
- //search for workflow entries with a matching ID
- org.nrg.xft.search.CriteriaCollection cc = new CriteriaCollection("AND");
- cc.addClause("wrk:workflowData.ID",this.getId());
- org.nrg.xft.collections.ItemCollection items = org.nrg.xft.search.ItemSearch.GetItems(cc,null,false);
-
- //Sort by Launch Time
- final List<XFTItem> workItems = items.getItems("wrk:workflowData.launch_time","DESC");
- for (final XFTItem wrk : workItems)
- {
- workflows.add(new WrkWorkflowdata(wrk));
- }
- }
-
- return workflows;
- }
-
- public XnatExperimentdata getLightCopy() throws XFTInitException, ElementNotFoundException {
- XFTItem item = XFTItem.NewItem(this.getXSIType(), this.getUser());
- XnatExperimentdata new_expt=(XnatExperimentdata) BaseElement.GetGeneratedItem(item);
- new_expt.setId(this.getId());
- new_expt.setLabel(this.getLabel());
- new_expt.setProject(this.getProject());
- if (this instanceof XnatSubjectassessordata) {
- ((XnatSubjectassessordata) new_expt).setSubjectId(((XnatSubjectassessordata) this).getSubjectId());
- } else if (this instanceof XnatImageassessordata) {
- ((XnatImageassessordata) new_expt).setImagesessionId(((XnatImageassessordata) this).getImagesessionId());
- }
- return new_expt;
- }
-
- @Override
- public SecurityValues getSecurityTags(){
- SecurityValues projects=new SecurityValues();
- projects.getHash().put(this.getXSIType() +"/project", this.getProject());
- for (final XnatExperimentdataShareI pp:this.getSharing_share())
- {
- projects.getHash().put(this.getXSIType() +"/sharing/share/project", pp.getProject());
- }
- return projects;
-
- }
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatExperimentdataField.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatExperimentdataField.java
deleted file mode 100644
index 5d535538ae87bc75a755ee37daf14f24d87023a3..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatExperimentdataField.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatExperimentdataField
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatExperimentdataField;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public class BaseXnatExperimentdataField extends AutoXnatExperimentdataField {
-
- public BaseXnatExperimentdataField(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatExperimentdataField(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatExperimentdataField(UserI user)
- **/
- public BaseXnatExperimentdataField()
- {}
-
- public BaseXnatExperimentdataField(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatExperimentdataShare.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatExperimentdataShare.java
deleted file mode 100644
index 57220e2e39a2d11ffc2a1d071236d5f4ce12f41a..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatExperimentdataShare.java
+++ /dev/null
@@ -1,121 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatExperimentdataShare
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.model.XnatProjectdataI;
-import org.nrg.xdat.om.XnatProjectdata;
-import org.nrg.xdat.om.base.auto.AutoXnatExperimentdataShare;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTTable;
-import org.nrg.xft.exception.DBPoolException;
-import org.nrg.xft.security.UserI;
-
-import java.sql.SQLException;
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatExperimentdataShare extends AutoXnatExperimentdataShare {
-
- public BaseXnatExperimentdataShare(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatExperimentdataShare(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatExperimentdataShare(UserI user)
- **/
- public BaseXnatExperimentdataShare()
- {}
-
- public BaseXnatExperimentdataShare(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
- private String name = null;
- private String description = null;
- private String secondaryID = null;
- private boolean initd = false;
-
- public void loadProjectDetails(){
- if (!initd)
- {
- initd=true;
- try {
- XFTTable table = XFTTable.Execute("SELECT name,description,secondary_ID FROM xnat_projectData WHERE ID ='" + this.getProject() + "';", this.getDBName(), null);
-
- if (table.size()>0)
- {
- Object[] row = (Object[])table.rows().get(0);
- name = (String)row[0];
- description = (String)row[1];
- secondaryID = (String)row[2];
- }
- } catch (SQLException e) {
- logger.error("",e);
- } catch (DBPoolException e) {
- logger.error("",e);
- }
- }
- }
-
- public XnatProjectdataI getProjectData(){
- return XnatProjectdata.getXnatProjectdatasById(this.getProject(), this.getUser(), false);
- }
-
-
- /**
- * @return the description
- */
- public String getDescription() {
- loadProjectDetails();
- return description;
- }
-
- /**
- * @return the name
- */
- public String getProjectName() {
- loadProjectDetails();
- return name;
- }
-
- /**
- * @return the secondaryID
- */
- public String getProjectSecondaryID() {
- loadProjectDetails();
- return secondaryID;
- }
-
-
-
- /**
- * @return the secondaryID
- */
- public String getProjectDisplayID() {
- loadProjectDetails();
- if (secondaryID!=null){
- return secondaryID;
- }else{
- return getProject();
- }
- }
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatFielddefinitiongroup.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatFielddefinitiongroup.java
deleted file mode 100644
index f7b9887d5202a4c574fe5aad30912cf642dd1481..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatFielddefinitiongroup.java
+++ /dev/null
@@ -1,65 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatFielddefinitiongroup
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatFielddefinitiongroup;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.ArrayList;
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatFielddefinitiongroup extends AutoXnatFielddefinitiongroup {
-
- public BaseXnatFielddefinitiongroup(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatFielddefinitiongroup(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatFielddefinitiongroup(UserI user)
- **/
- public BaseXnatFielddefinitiongroup()
- {}
-
- public BaseXnatFielddefinitiongroup(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
- private ArrayList<org.nrg.xdat.om.XnatFielddefinitiongroupField> _sorted_Fields_field =null;
-
- /**
- * fields/field
- * @return Returns an ArrayList of org.nrg.xdat.om.XnatFielddefinitiongroupField
- */
- public ArrayList<org.nrg.xdat.om.XnatFielddefinitiongroupField> getFields_field() {
- try{
- if (_sorted_Fields_field==null){
- _sorted_Fields_field=org.nrg.xdat.base.BaseElement.WrapItems(getChildItemCollection("fields/field").getItems("xnat:fieldDefinitionGroup_field/sequence"));
- return _sorted_Fields_field;
- }else {
- return _sorted_Fields_field;
- }
- } catch (Exception e1) {return new ArrayList<org.nrg.xdat.om.XnatFielddefinitiongroupField>();}
- }
-}
-
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatFielddefinitiongroupField.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatFielddefinitiongroupField.java
deleted file mode 100644
index 93c7399cd21ac20a3fe9ca596df6fae305fd60bc..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatFielddefinitiongroupField.java
+++ /dev/null
@@ -1,54 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatFielddefinitiongroupField
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatFielddefinitiongroupField;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatFielddefinitiongroupField extends AutoXnatFielddefinitiongroupField {
-
- public BaseXnatFielddefinitiongroupField(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatFielddefinitiongroupField(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatFielddefinitiongroupField(UserI user)
- **/
- public BaseXnatFielddefinitiongroupField()
- {}
-
- public BaseXnatFielddefinitiongroupField(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
- public String getCleanedXMLPath(){
- String xmlPath = this.getXmlpath();
- while(xmlPath.indexOf("[")>-1){
- xmlPath= xmlPath.substring(0,xmlPath.indexOf("[")) + xmlPath.substring(xmlPath.indexOf("]")+1);
- }
- return xmlPath;
- }
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatFielddefinitiongroupFieldPossiblevalue.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatFielddefinitiongroupFieldPossiblevalue.java
deleted file mode 100644
index 2bf446675385ea20248a299acb9b74a90f133e86..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatFielddefinitiongroupFieldPossiblevalue.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatFielddefinitiongroupFieldPossiblevalue
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatFielddefinitiongroupFieldPossiblevalue;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatFielddefinitiongroupFieldPossiblevalue extends AutoXnatFielddefinitiongroupFieldPossiblevalue {
-
- public BaseXnatFielddefinitiongroupFieldPossiblevalue(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatFielddefinitiongroupFieldPossiblevalue(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatFielddefinitiongroupFieldPossiblevalue(UserI user)
- **/
- public BaseXnatFielddefinitiongroupFieldPossiblevalue()
- {}
-
- public BaseXnatFielddefinitiongroupFieldPossiblevalue(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatGenericdata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatGenericdata.java
deleted file mode 100644
index 6899564669c20f725478add573a2b80d157dbdd7..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatGenericdata.java
+++ /dev/null
@@ -1,41 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatGenericdata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatGenericdata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-
-public class BaseXnatGenericdata extends AutoXnatGenericdata{
- public BaseXnatGenericdata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatGenericdata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatHdscandata(UserI user)
- **/
- public BaseXnatGenericdata()
- {}
-
- public BaseXnatGenericdata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatGmscandata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatGmscandata.java
deleted file mode 100644
index 762b51c46d3ba0ef8829dc2eecedd4902e9d488a..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatGmscandata.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatGmscandata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatGmscandata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatGmscandata extends AutoXnatGmscandata {
-
- public BaseXnatGmscandata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatGmscandata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatGmscandata(UserI user)
- **/
- public BaseXnatGmscandata()
- {}
-
- public BaseXnatGmscandata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatGmsessiondata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatGmsessiondata.java
deleted file mode 100644
index be9d80ba5e769128d36da0cd610227b9bba7b03a..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatGmsessiondata.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatGmsessiondata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatGmsessiondata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatGmsessiondata extends AutoXnatGmsessiondata {
-
- public BaseXnatGmsessiondata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatGmsessiondata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatGmsessiondata(UserI user)
- **/
- public BaseXnatGmsessiondata()
- {}
-
- public BaseXnatGmsessiondata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatGmvscandata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatGmvscandata.java
deleted file mode 100644
index 865926837bcae907bd6d28f6881c826c0e11356e..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatGmvscandata.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatGmvscandata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatGmvscandata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatGmvscandata extends AutoXnatGmvscandata {
-
- public BaseXnatGmvscandata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatGmvscandata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatGmvscandata(UserI user)
- **/
- public BaseXnatGmvscandata()
- {}
-
- public BaseXnatGmvscandata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatGmvsessiondata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatGmvsessiondata.java
deleted file mode 100644
index 1cefd8c46ffeb0d701acfec4e90b64428ceeaf6f..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatGmvsessiondata.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatGmvsessiondata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatGmvsessiondata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatGmvsessiondata extends AutoXnatGmvsessiondata {
-
- public BaseXnatGmvsessiondata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatGmvsessiondata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatGmvsessiondata(UserI user)
- **/
- public BaseXnatGmvsessiondata()
- {}
-
- public BaseXnatGmvsessiondata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatHdscandata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatHdscandata.java
deleted file mode 100644
index 77e591bbaf21334e5527aacbe14781d8fe9f0fdd..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatHdscandata.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatHdscandata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatHdscandata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatHdscandata extends AutoXnatHdscandata {
-
- public BaseXnatHdscandata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatHdscandata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatHdscandata(UserI user)
- **/
- public BaseXnatHdscandata()
- {}
-
- public BaseXnatHdscandata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatHdsessiondata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatHdsessiondata.java
deleted file mode 100644
index f8fe3adfc9aafdf360350146bbc3211812e1e949..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatHdsessiondata.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatHdsessiondata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatHdsessiondata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatHdsessiondata extends AutoXnatHdsessiondata {
-
- public BaseXnatHdsessiondata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatHdsessiondata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatHdsessiondata(UserI user)
- **/
- public BaseXnatHdsessiondata()
- {}
-
- public BaseXnatHdsessiondata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatImageassessordata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatImageassessordata.java
deleted file mode 100644
index 3f656685a7846041576e8dfc0c1b3d990697984d..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatImageassessordata.java
+++ /dev/null
@@ -1,252 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatImageassessordata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 2/11/14 12:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.model.XnatAbstractresourceI;
-import org.nrg.xdat.om.*;
-import org.nrg.xdat.om.base.auto.AutoXnatImageassessordata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFT;
-import org.nrg.xft.XFTTable;
-import org.nrg.xft.db.PoolDBUtils;
-import org.nrg.xft.event.EventMetaI;
-import org.nrg.xft.security.UserI;
-import org.nrg.xft.utils.FileUtils;
-import org.nrg.xft.utils.StringUtils;
-import org.nrg.xnat.exceptions.InvalidArchiveStructure;
-import org.nrg.xnat.turbine.utils.ArcSpecManager;
-
-import java.io.File;
-import java.sql.SQLException;
-import java.util.ArrayList;
-import java.util.Hashtable;
-import java.util.Iterator;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatImageassessordata extends AutoXnatImageassessordata{
-
- public BaseXnatImageassessordata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatImageassessordata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatImageassessordata(UserI user)
- **/
- public BaseXnatImageassessordata()
- {}
-
- public BaseXnatImageassessordata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-
-
- private XnatImagesessiondata mr = null;
-
- public XnatImagesessiondata getImageSessionData()
- {
- if (mr==null)
- {
- ArrayList al = XnatImagesessiondata.getXnatImagesessiondatasByField("xnat:imageSessionData/ID",this.getImagesessionId(),this.getUser(),false);
- if (al.size()>0)
- {
- mr = (XnatImagesessiondata)al.get(0);
- }
- }
-
- return mr;
- }
-
- public void setImageSessionData(XnatImagesessiondata ses){
- mr=ses;
- }
-
-
- public boolean validateSessionId(){
- String session_id = this.getImagesessionId();
-
- if (session_id!=null){
- session_id=StringUtils.RemoveChar(session_id, '\'');
- String query = "SELECT ID FROM xnat_imageSessiondata WHERE ID='";
- String login =null;
- if (this.getUser()!=null){
- login = this.getUser().getUsername();
- }
-
- try {
- final String idCOUNT= (String)PoolDBUtils.ReturnStatisticQuery(query + session_id + "';", "id", this.getDBName(), login);
- if (idCOUNT!=null){
- return true;
- }
-
- final String project = this.getProject();
- if (project!=null){
- query = "SELECT id FROM xnat_experimentData WHERE label='" +
- session_id +"' AND project='" + project + "';";
- String new_session_id= (String)PoolDBUtils.ReturnStatisticQuery(query, "id", this.getDBName(), login);
- if (new_session_id!=null){
- this.setImagesessionId(new_session_id);
- return true;
- }
-
- query = "SELECT sharing_share_xnat_experimentda_id FROM xnat_experimentData_share WHERE label='" +
- session_id +"' AND project='" + project + "';";
- new_session_id= (String)PoolDBUtils.ReturnStatisticQuery(query, "sharing_share_xnat_experimentda_id", this.getDBName(), login);
- if (new_session_id!=null){
- this.setImagesessionId(new_session_id);
- return true;
- }
- }
- } catch (SQLException e) {
- logger.error("",e);
- } catch (Exception e) {
- logger.error("",e);
- }
- }
-
- return false;
- }
-
- public ArrayList getCatalogSummary() throws Exception{
- String query="SELECT xnat_abstractresource_id,label,element_name ";
- query+=", 'resources'::TEXT AS category, '" + this.getId()+"'::TEXT AS cat_id";
- query+=" FROM xnat_experimentdata_resource map " +
- " LEFT JOIN xnat_abstractresource abst ON map.xnat_abstractresource_xnat_abstractresource_id=abst.xnat_abstractresource_id" +
- " LEFT JOIN xdat_meta_element xme ON abst.extension=xme.xdat_meta_element_id";
- query+= " WHERE xnat_experimentdata_id='"+this.getId() + "'";
-
- XFTTable t = XFTTable.Execute(query, this.getDBName(), "system");
-
- return t.rowHashs();
- }
-
-
- public void deleteFiles(UserI u, EventMetaI ci) throws Exception{
- super.deleteFiles(u,ci);
-
- final String rootPath=ArcSpecManager.GetInstance().getArchivePathForProject(this.getProject());
-
- for(XnatAbstractresourceI abstRes:this.getResources_resource()){
- ((XnatAbstractresource)abstRes).deleteWithBackup(rootPath, u,ci);
- }
-
- for(XnatAbstractresourceI abstRes:this.getOut_file()){
- ((XnatAbstractresource)abstRes).deleteWithBackup(rootPath, u,ci);
- }
-
- // XNAT-1382: Delete the root Assessor Directory if it is empty.
- String assessorDir = this.getArchiveDirectoryName();
- String sessionDir = this.getExpectedSessionDir().getAbsolutePath();
- if(!StringUtils.IsEmpty(sessionDir) && !StringUtils.IsEmpty(assessorDir)){
- File f = new File(sessionDir + "/ASSESSORS/" + assessorDir);
- if(f.exists() && f.isDirectory() && f.list().length == 0){
- FileUtils.DeleteFile(f);
- }
- }
- }
-
-
- public File getExpectedSessionDir() throws InvalidArchiveStructure,UnknownPrimaryProjectException{
- return this.getImageSessionData().getExpectedSessionDir();
- }
-
- @Override
- public void preSave() throws Exception{
- if(StringUtils.IsEmpty(this.getId())){
- throw new IllegalArgumentException("Please specify an ID for your experiment.");
- }
-
- if(XFT.getBooleanProperty("security.require_image_assessor_labels", false) && StringUtils.IsEmpty(this.getLabel())){
- throw new IllegalArgumentException("Please specify a label for your experiment.");
- }
-
- if(!StringUtils.IsAlphaNumericUnderscore(getId())){
- throw new IllegalArgumentException("Identifiers cannot use special characters.");
- }
-
- if(!StringUtils.IsEmpty(this.getLabel()) && !StringUtils.IsAlphaNumericUnderscore(getLabel())){
- throw new IllegalArgumentException("Labels cannot use special characters.");
- }
-
- if(this.getImageSessionData()==null){
- throw new Exception("Unable to identify image session for:" + this.getImagesessionId());
- }
-
- final XnatProjectdata proj = this.getPrimaryProject(false);
- if(proj==null){
- throw new Exception("Unable to identify project for:" + this.getProject());
- }
-
- checkUniqueLabel();
-
- final String expectedPath=this.getExpectedSessionDir().getAbsolutePath().replace('\\', '/');
-
- for(final XnatAbstractresourceI res: this.getResources_resource()){
- final String uri;
- if(res instanceof XnatResource){
- uri=((XnatResource)res).getUri();
- }else if(res instanceof XnatResourceseries){
- uri=((XnatResourceseries)res).getPath();
- }else{
- continue;
- }
-
- FileUtils.ValidateUriAgainstRoot(uri,expectedPath,"URI references data outside of the project:" + uri);
- }
-
- for(final XnatAbstractresourceI res: this.getOut_file()){
- final String uri;
- if(res instanceof XnatResource){
- uri=((XnatResource)res).getUri();
- }else if(res instanceof XnatResourceseries){
- uri=((XnatResourceseries)res).getPath();
- }else{
- continue;
- }
-
- FileUtils.ValidateUriAgainstRoot(uri,expectedPath,"URI references data outside of the project:" + uri);
- }
- }
-
- public String getResourceCatalogRootPathByLabel( String label) {
- String rtn = super.getResourceCatalogRootPathByLabel(label);
- if (rtn == null) {
- //Check if catalog is at the out file level
- Iterator misc = this.getOut_file().iterator();
- while(misc.hasNext()) {
- Object file = misc.next();
- if (file instanceof XnatResourcecatalog) {
- String tag = ((XnatResourcecatalog)file).getLabel();
- if (tag != null && tag.equals(label)) {
- rtn =((XnatResourcecatalog)file).getUri();
- int index = rtn.lastIndexOf("/");
- if (index != -1)
- rtn = rtn.substring(0, index);
- break;
- }
- }
- }
- }
- return rtn;
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatImageresource.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatImageresource.java
deleted file mode 100644
index a1e7b18718014dee2eb2e01adc40b119cfaa70d6..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatImageresource.java
+++ /dev/null
@@ -1,48 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatImageresource
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatImageresource;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public class BaseXnatImageresource extends AutoXnatImageresource {
-
- public BaseXnatImageresource(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatImageresource(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatImageresource(UserI user)
- **/
- public BaseXnatImageresource()
- {}
-
- public BaseXnatImageresource(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatImageresourceseries.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatImageresourceseries.java
deleted file mode 100644
index 18edb36eacb33fb7bb7c52495e2ed3d9a9781a33..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatImageresourceseries.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatImageresourceseries
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatImageresourceseries;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public class BaseXnatImageresourceseries extends AutoXnatImageresourceseries {
-
- public BaseXnatImageresourceseries(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatImageresourceseries(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatImageresourceseries(UserI user)
- **/
- public BaseXnatImageresourceseries()
- {}
-
- public BaseXnatImageresourceseries(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatImagescandata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatImagescandata.java
deleted file mode 100644
index d712e56a4430ee3cf0ce1885968846a8a21130cb..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatImagescandata.java
+++ /dev/null
@@ -1,652 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatImagescandata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 12/13/13 1:12 PM
- */
-package org.nrg.xdat.om.base;
-
-import java.io.File;
-import java.util.ArrayList;
-import java.util.Comparator;
-import java.util.HashMap;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Map;
-
-import org.nrg.xdat.model.CatCatalogI;
-import org.nrg.xdat.model.CatEntryI;
-import org.nrg.xdat.model.XnatAbstractresourceI;
-import org.nrg.xdat.model.XnatQcscandataI;
-import org.nrg.xdat.model.XnatResourcecatalogI;
-import org.nrg.xdat.om.XnatAbstractresource;
-import org.nrg.xdat.om.XnatDicomseries;
-import org.nrg.xdat.om.XnatImagescandata;
-import org.nrg.xdat.om.XnatImagesessiondata;
-import org.nrg.xdat.om.XnatResource;
-import org.nrg.xdat.om.XnatResourcecatalog;
-import org.nrg.xdat.om.XnatResourceseries;
-import org.nrg.xdat.om.base.BaseXnatExperimentdata.UnknownPrimaryProjectException;
-import org.nrg.xdat.om.base.auto.AutoXnatImagescandata;
-import org.nrg.xdat.security.helpers.Permissions;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.event.EventMetaI;
-import org.nrg.xft.search.CriteriaCollection;
-import org.nrg.xft.security.UserI;
-import org.nrg.xft.utils.FileUtils;
-import org.nrg.xft.utils.StringUtils;
-import org.nrg.xnat.exceptions.InvalidArchiveStructure;
-import org.nrg.xnat.helpers.scanType.ImageScanTypeMapping;
-import org.nrg.xnat.helpers.scanType.ScanTypeMappingI;
-import org.nrg.xnat.utils.CatalogUtils;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public class BaseXnatImagescandata extends AutoXnatImagescandata {
-
- public BaseXnatImagescandata(ItemI item) {
- super(item);
- }
-
- public BaseXnatImagescandata(UserI user) {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatImagescandata(UserI user)
- **/
- public BaseXnatImagescandata()
- {}
-
- public BaseXnatImagescandata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
- public String getPreCount()
- {
- try {
- String temp = this.getId();
- if (temp != null)
- {
- if (temp.contains("-"))
- {
- return temp.substring(0,temp.indexOf("-"));
- }else{
- return temp;
- }
- }else{
- return "";
- }
- } catch (Exception e) {
- return "";
- }
- }
-
- public String getPostCount()
- {
- try {
- String temp = this.getId();
- if (temp != null)
- {
- if (temp.contains("-"))
- {
- return temp.substring(temp.indexOf("-")+1);
- }else{
- return "";
- }
- }else{
- return "";
- }
- } catch (Exception e) {
- return "";
- }
- }
-
- public Integer getPreCountI()
- {
- String s = getPreCount();
- try{
- if (s.equals(""))
- {
- return 0;
- }else{
- return new Integer(s);
- }
- } catch (NumberFormatException e) {
- return 0;
- }
- }
-
- public Integer getPostCountI()
- {
- String s = getPostCount();
- try {
- if (s.equals(""))
- {
- return 0;
- }else{
- return new Integer(s);
- }
- } catch (NumberFormatException e) {
- return 0;
- }
- }
-
- public boolean isInRAWDirectory(){
- boolean hasRAW=false;
- for (XnatAbstractresourceI xnatAbstractresourceI : getFile()) {
- XnatAbstractresource file = (XnatAbstractresource) xnatAbstractresourceI;
- if (file.isInRAWDirectory()) {
- hasRAW=true;
- break;
- }
- }
- return hasRAW;
- }
-
-
-
-
- public void deleteFilesFromFileSystem(String rootPath,UserI u, EventMetaI ci) throws Exception{
- List<XnatAbstractresourceI> files = this.getFile();
- if (!files.isEmpty())
- for (XnatAbstractresourceI resource:files){
- ((XnatAbstractresource)resource).deleteWithBackup(rootPath, u,ci);
- }
- }
-
- public ArrayList<java.io.File> getJavaFiles(String rootPath){
- ArrayList<File> jFiles = new ArrayList<File>();
- List scanFiles= this.getFile();
- if (scanFiles.size()>0)
- {
- for (Object scanFile : scanFiles) {
- XnatAbstractresource xnatFile = (XnatAbstractresource) scanFile;
- jFiles.addAll(xnatFile.getCorrespondingFiles(rootPath));
- }
- }
- return jFiles;
- }
-
- public static Comparator GetComparator() {
- return (new BaseXnatImagescandata()).getComparator();
- }
-
- public Comparator getComparator()
- {
- return new ImageScanComparator();
- }
-
- public class ImageScanComparator implements Comparator{
- public ImageScanComparator() {}
-
- public int compare(Object o1, Object o2) {
- BaseXnatImagescandata value1 = (BaseXnatImagescandata)(o1);
- BaseXnatImagescandata value2 = (BaseXnatImagescandata)(o2);
-
- if (value1 == null){
- if (value2 == null)
- {
- return 0;
- }else{
- return -1;
- }
- }
- if (value2== null) {
- return 1;
- }
-
- if (value1.getPreCountI().equals(value2.getPreCountI())) {
- return value1.getPostCountI().compareTo(value2.getPostCountI());
- }else{
- Integer i1 = value1.getPreCountI();
- Integer i2 = value2.getPreCountI();
- return i1.compareTo(i2);
- }
- }
- }
- private String scan_dir = null;
- public String deriveScanDir(){
- if (scan_dir == null) {
- String rootPath;
- try {
- rootPath = this.getImageSessionData().getArchiveRootPath();
- } catch (UnknownPrimaryProjectException e) {
- rootPath=null;
- }
- String last_dir = null;
- for (XnatAbstractresourceI xnatFile : this.getFile()) {
- if (xnatFile instanceof org.nrg.xdat.om.XnatResource){
- XnatResource resource = (XnatResource)xnatFile;
- String uri =resource.getFullPath(rootPath);
- if (last_dir==null){
- last_dir= uri;
- int index = last_dir.toUpperCase().indexOf("/RAW/");
- if (index!=-1){
- if(last_dir.toUpperCase().indexOf("/"+this.getId().toUpperCase()+"/",index)>-1){
- scan_dir = last_dir.substring(0,last_dir.toUpperCase().indexOf("/"+this.getId().toUpperCase()+"/",index)+this.getId().length()+1);
- } else {
- scan_dir = last_dir.substring(0,index+4);
- }
- return scan_dir;
- }else{
- index = last_dir.toUpperCase().indexOf("/SCANS/");
- if (index!=-1){
- if(last_dir.toUpperCase().indexOf("/"+this.getId().toUpperCase()+"/",index)>-1){
- scan_dir = last_dir.substring(0,last_dir.toUpperCase().indexOf("/"+this.getId().toUpperCase()+"/",index)+this.getId().length()+1);
- }else{
- scan_dir = last_dir.substring(0,index+6);
- }
- return scan_dir;
- }
- }
- }
- }else if(xnatFile instanceof org.nrg.xdat.om.XnatDicomseries){
- XnatDicomseries resource = (XnatDicomseries)xnatFile;
- String uri =resource.getFullPath(rootPath);
- if (last_dir==null){
- last_dir= uri;
- int index = last_dir.toUpperCase().indexOf("/RAW/");
- if (index!=-1){
- if(last_dir.toUpperCase().indexOf("/"+this.getId().toUpperCase()+"/",index)>-1){
- scan_dir = last_dir.substring(0,last_dir.toUpperCase().indexOf("/"+this.getId().toUpperCase()+"/",index)+this.getId().length()+1);
- }else{
- scan_dir = last_dir.substring(0,index+4);
- }
- return scan_dir;
- }else{
- index = last_dir.toUpperCase().indexOf("/SCANS/");
- if (index!=-1){
- if(last_dir.toUpperCase().indexOf("/"+this.getId().toUpperCase()+"/",index)>-1){
- scan_dir = last_dir.substring(0,last_dir.toUpperCase().indexOf("/"+this.getId().toUpperCase()+"/",index)+this.getId().length()+1);
- }else{
- scan_dir = last_dir.substring(0,index+6);
- }
- return scan_dir;
- }
- }
- }
- }else if(xnatFile instanceof org.nrg.xdat.om.XnatResourceseries){
- XnatResourceseries resource = (XnatResourceseries)xnatFile;
- String uri =resource.getFullPath(rootPath);
- if (last_dir==null){
- last_dir= uri;
- int index = last_dir.toUpperCase().indexOf("/RAW/");
- if (index!=-1){
- if(last_dir.toUpperCase().indexOf("/"+this.getId().toUpperCase()+"/",index)>-1){
- scan_dir = last_dir.substring(0,last_dir.toUpperCase().indexOf("/"+this.getId().toUpperCase()+"/",index)+this.getId().length()+1);
- }else{
- scan_dir = last_dir.substring(0,index+4);
- }
- return scan_dir;
- }else{
- index = last_dir.toUpperCase().indexOf("/SCANS/");
- if (index!=-1){
- if(last_dir.toUpperCase().indexOf("/"+this.getId().toUpperCase()+"/",index)>-1){
- scan_dir = last_dir.substring(0,last_dir.toUpperCase().indexOf("/"+this.getId().toUpperCase()+"/",index)+this.getId().length()+1);
- }else{
- scan_dir = last_dir.substring(0,index+6);
- }
- return scan_dir;
- }
- }
- }
- }
- }
-
- if (scan_dir == null) {
- scan_dir = this.getImageSessionData().deriveRawDir();
- }
- }
-
-
- return scan_dir;
- }
-
- private XnatImagesessiondata mr = null;
-
- public XnatImagesessiondata getImageSessionData()
- {
- if (mr==null)
- {
- ArrayList al = XnatImagesessiondata.getXnatImagesessiondatasByField("xnat:imageSessionData/ID",this.getImageSessionId(),this.getUser(),false);
- if (al.size()>0)
- {
- mr = (XnatImagesessiondata)al.get(0);
- }
- }
-
- return mr;
- }
-
- public void setImageSessionData(XnatImagesessiondata ses){
- mr=ses;
- }
-
- Snapshot snapshot=null;
- public Snapshot getSnapshot(){
- if(snapshot!=null){
- return snapshot;
- }
-
- if(this.getFile().size()>0){
- snapshot=new Snapshot();
- XnatImagesessiondata ses=this.getImageSessionData();
- String label=ses.getIdentifier(ses.getProject(),false);
- String labelImg=label + "_"+this.getId() + "_qc";
-
- String path=null;
- for(XnatAbstractresourceI res: this.getFile()){
- if(res.getLabel()!=null && res.getLabel().equalsIgnoreCase("SNAPSHOTS")){
- path="/data/experiments/"+ses.getId() + "/scans/"+this.getId() + "/resources/SNAPSHOTS/files/";
- if(res instanceof XnatResourcecatalog){
- CatCatalogI cat=((XnatResourcecatalog)res).getCleanCatalog(ses.getProjectData().getRootArchivePath(), false,null,null);
- for(CatEntryI entry:cat.getEntries_entry()){
- if(entry.getContent().equalsIgnoreCase("THUMBNAIL")){
- snapshot.setThumbnail(path + entry.getUri());
- }
- if(entry.getContent().equalsIgnoreCase("ORIGINAL")){
- snapshot.setFull(path + entry.getUri());
- }
- }
- }else{
- snapshot.setFull(path + labelImg + ".gif");
- snapshot.setThumbnail(path + labelImg + "_t.gif");
- }
- }
- }
-
- if(path==null){
- path="/app/template/QualityControl.vm?project=" + ses.getProject() + "&session_label=" + label + "&session_id=" + ses.getId() + "&scan="+ this.getId();
- snapshot.setFull(path + "&extension=.gif");
- snapshot.setThumbnail(path + "&extension=_t.gif");
- }
-
- return snapshot;
- }else{
- return null;
- }
- }
-
- public class Snapshot{
- private String thumbnail=null;
- private String full=null;
-
- public String getFull() {
- return full;
- }
- public void setFull(String full) {
- this.full = full;
- }
- public String getThumbnail() {
- return thumbnail;
- }
- public void setThumbnail(String thumbnail) {
- this.thumbnail = thumbnail;
- }
-
-
- }
-
- public void copyValuesFrom(final XnatImagescandata other) throws Exception {
- if (null != other.getType())
- this.setType(other.getType());
- if (null != other.getQuality())
- this.setQuality(other.getQuality());
- if (null != other.getNote())
- this.setNote(other.getNote());
- }
-
- public XnatQcscandataI getManualQC() {
- final XnatImagesessiondata session = getImageSessionData();
- if (session.getManualQC() != null && session.getManualQC().getScans_scan() != null) {
- for (XnatQcscandataI qc : session.getManualQC().getScans_scan()) {
- if (getId().equals(qc.getImagescanId())) {
- return qc;
- }
- }
- }
- return null;
- }
-
- public File getExpectedSessionDir() throws InvalidArchiveStructure, UnknownPrimaryProjectException{
- return this.getImageSessionData().getExpectedSessionDir();
- }
-
- @Override
- public void preSave() throws Exception{
- super.preSave();
-
- if(this.getImageSessionData()==null){
- throw new Exception("Unable to identify image session for:" + this.getImageSessionId());
- }
-
- final String expectedPath=this.getExpectedSessionDir().getAbsolutePath().replace('\\', '/');
-
- validate(expectedPath);
- }
-
- public void validate(String expectedPath) throws Exception{
-
- if(StringUtils.IsEmpty(this.getId())){
- throw new IllegalArgumentException();
- }
-
- if(!StringUtils.IsAlphaNumericUnderscore(getId())){
- throw new IllegalArgumentException("Identifiers cannot use special characters.");
- }
-
- for(final XnatAbstractresourceI res: this.getFile()){
- final String uri;
- if(res instanceof XnatResource){
- uri=((XnatResource)res).getUri();
- }else if(res instanceof XnatResourceseries){
- uri=((XnatResourceseries)res).getPath();
- }else{
- continue;
- }
-
- FileUtils.ValidateUriAgainstRoot(uri,expectedPath,"URI references data outside of the project:" + uri);
- }
- }
-
-
- public static List<XnatImagescandata> getScansByIdORType(final String scanID,
- final XnatImagesessiondata session,UserI user, boolean preLoad) {
- final CriteriaCollection cc = new CriteriaCollection("OR");
- CriteriaCollection subcc = new CriteriaCollection("AND");
- subcc.addClause("xnat:imageScanData/image_session_ID", session.getId());
- if (!(scanID.equals("*") || scanID.equals("ALL")) && !scanID.contains(",")) {
- subcc.addClause("xnat:imageScanData/ID", scanID);
- } else {
- final CriteriaCollection subsubcc = new CriteriaCollection("OR");
- for (final String s : StringUtils.CommaDelimitedStringToArrayList(
- scanID, true)) {
- subsubcc.addClause("xnat:imageScanData/ID", s);
- }
- subcc.add(subsubcc);
- }
- cc.add(subcc);
-
- subcc = new CriteriaCollection("AND");
- subcc.addClause("xnat:imageScanData/image_session_ID", session.getId());
- if (!(scanID.equals("*") || scanID.equals("ALL")) && !scanID.contains(",")) {
- if (scanID.equals("NULL")) {
- CriteriaCollection subsubcc = new CriteriaCollection("OR");
- subsubcc.addClause("xnat:imageScanData/type", "", " IS NULL ",
- true);
- subsubcc.addClause("xnat:imageScanData/type", "");
- subcc.add(subsubcc);
- } else {
- subcc.addClause("xnat:imageScanData/type", scanID);
- }
- } else {
- CriteriaCollection subsubcc = new CriteriaCollection("OR");
- for (String s : StringUtils.CommaDelimitedStringToArrayList(scanID,
- true)) {
- if (s.equals("NULL")) {
- subsubcc.addClause("xnat:imageScanData/type", "",
- " IS NULL ", true);
- subsubcc.addClause("xnat:imageScanData/type", "");
- } else {
- subsubcc.addClause("xnat:imageScanData/type", s);
- }
- }
- subcc.add(subsubcc);
- }
- cc.add(subcc);
-
- return XnatImagescandata.getXnatImagescandatasByField(cc, user,
- preLoad);
- }
-
- public ScanTypeMappingI getScanTypeMapping(String project, String dbName){
- return new ImageScanTypeMapping(project, dbName);
- }
-
-
- Map<String, Number> stats = null;
-
- public Map<String, Number> getPrearchiveFileStats(){
- if(stats==null){
- stats = new HashMap<String, Number>();
- int totalCount = 0;
- long totalSize = 0;
- for (XnatAbstractresourceI resource : this.getFile()) {
- String prearcPath = null;
- try{
- // Try to retrieve the scan path within the prearchive.
- prearcPath = this.getParent().getStringProperty("prearchivepath");
- if(null == prearcPath || prearcPath.equals("")){
- throw new Exception("Unable to determine the prearchive path for scan");
- }
- }catch(Exception e){
- // If the prearchive path is null or empty, count and size should be 0
- logger.error("Unable to retrieve file counts.", e);
- continue;
- }
-
- if(resource instanceof XnatResourcecatalogI){
- // Get the rootPath and FileStats
- final String rootPath=CatalogUtils.getCatalogFile(prearcPath, ((XnatResourcecatalogI)resource)).getParentFile().getAbsolutePath();
- CatalogUtils.Stats c_stats=CatalogUtils.getFileStats(CatalogUtils.getCleanCatalog(prearcPath, (XnatResourcecatalogI)resource, false), rootPath);
- if(null != c_stats){
- totalSize += c_stats.size;
- totalCount += c_stats.count;
- }else{
- logger.error("Unable to retrieve file counts.", new Exception("Unable to retrieve CatalogUtils.Stats for the given resource."));
- }
- }else{
- logger.error("Unable to retrieve file counts.", new Exception("Prearchive resource is not an instance of XnatResourcecatalogI. Skipping..."));
- }
- }
- stats.put("size", Long.valueOf(totalSize));
- stats.put("count", Integer.valueOf(totalCount));
- }
- return stats;
- }
-
- public List<String> getReadableFileStats() {
- List<String> stats = new ArrayList<String>();
-
- // If the scan is in the prearchive, retrieve the count & file sizes from CatalogUtils.getFileStats()
- if(this.getImageSessionId() == null){
- Map<String,Number> prearcStats = this.getPrearchiveFileStats();
- stats.add(CatalogUtils.formatFileStats("TOTAL", prearcStats.get("count").intValue(), prearcStats.get("size").longValue()));
- }else{ // If this scan is already archived, retrieve the count & file sizes from the resource
- int totalCount = 0;
- long totalSize = 0;
- for (XnatAbstractresourceI resource : getFile()) {
- // Get the label, if it is null or a snapshot skip it.
- String label = resource.getLabel();
- if (label != null && label.equals("SNAPSHOTS")) {
- continue;
- }
-
- int count;
- long size;
- Integer rawCount = resource.getFileCount();
- if (rawCount != null) {
- count = rawCount;
- } else {
- count = 0;
- }
- Object rawFileSize = resource.getFileSize();
-
- if (rawFileSize != null) {
- if (rawFileSize instanceof Integer) {
- size = (Integer) rawFileSize;
- } else if (rawFileSize instanceof Long) {
- size = (Long) rawFileSize;
- } else {
- size = Long.parseLong(rawFileSize.toString());
- }
- } else {
- size = 0;
- }
- totalSize += size;
- totalCount += count;
- stats.add(CatalogUtils.formatFileStats(label, count, size));
- }
- // Add totalCount and totalSize to the stats list
- stats.add(0, CatalogUtils.formatFileStats("TOTAL", totalCount, totalSize));
- }
-
- return stats;
- }
-
- /**
- * It's annoying to do this, but in some cases it's easier to get this formatted display directly from the scan
- * object rather than trying to manage it in the Velocity template.
- * @return A formatted string that will display the scans in a tip text format.
- */
- public String getFormattedReadableFileStats(UserI user) throws Exception {
- if (getFile().size() > 0) {
- List<String> stats = getReadableFileStats();
- if(stats == null || stats.size() == 0 || stats.get(0) == null || stats.get(0).equals("") || stats.get(0).equals("0 B in 0 files")) {
- return getEmptyResourceCount(user);
- } else if (stats.size() == 1) {
- return stats.get(0);
- } else {
- return getListAsTipText(stats);
- }
- } else {
- return getEmptyResourceCount(user);
- }
- }
-
- private String getEmptyResourceCount(UserI user) throws Exception {
- if (Permissions.canEdit(user,this)) {
- return "<a onclick=\"window.viewer.init(true);\">Show Counts</a>";
- }
- return getListAsTipText(EMPTY_RESOURCE_LIST);
- }
-
- static public String getListAsTipText(List<String> list) {
- if (list == null || list.size() == 0 || list.get(0) == null || list.get(0).trim().equals("")) {
- return "<span class=\"tip_text\">No items found.<span style=\"top:20px;white-space:nowrap;left:-10;width:auto;\" class=\"tip shadowed\">No items were found: Check your data to be sure you specified a valid system object.</span></span>";
- }
- StringBuilder buffer = new StringBuilder("<span class=\"tip_text\">").append(list.get(0)).append("<span style=\"top:20px;white-space:nowrap;left:-10;width:auto;\" class=\"tip shadowed\">");
- for (int index = 1; index < list.size(); index++) {
- buffer.append(list.get(index));
- if (index < list.size() - 1) {
- buffer.append("<br/>");
- }
- }
- buffer.append("</span></span>");
- return buffer.toString();
- }
-
- private static final List<String> EMPTY_RESOURCE_LIST = new ArrayList<String>() {{
- add("0 B in 0 files");
- add("No files were found associated with this scan. Contact a member or owner of this project to generate the file count data.");
- }};
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatImagescandataShare.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatImagescandataShare.java
deleted file mode 100644
index 9703338c23a76e0e072bd6d20adfbc1e622e6133..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatImagescandataShare.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatImagescandataShare
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatImagescandataShare;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatImagescandataShare extends AutoXnatImagescandataShare {
-
- public BaseXnatImagescandataShare(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatImagescandataShare(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatImagescandataShare(UserI user)
- **/
- public BaseXnatImagescandataShare()
- {}
-
- public BaseXnatImagescandataShare(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatImagesessiondata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatImagesessiondata.java
deleted file mode 100644
index 8fd28612c924abf8798366dcaf88fe60a67bc37b..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatImagesessiondata.java
+++ /dev/null
@@ -1,3159 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatImagesessiondata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 2/18/14 7:27 PM
- */
-package org.nrg.xdat.om.base;
-
-import com.google.common.collect.ImmutableMap;
-import com.google.common.collect.Lists;
-import com.google.common.collect.Maps;
-import com.google.common.collect.Sets;
-import edu.sdsc.grid.io.GeneralFile;
-import org.nrg.dcm.CopyOp;
-import org.nrg.transaction.OperationI;
-import org.nrg.transaction.RollbackException;
-import org.nrg.transaction.Run;
-import org.nrg.transaction.TransactionException;
-import org.nrg.xdat.XDAT;
-import org.nrg.xdat.base.BaseElement;
-import org.nrg.xdat.bean.CatCatalogBean;
-import org.nrg.xdat.bean.CatEntryBean;
-import org.nrg.xdat.bean.CatEntryMetafieldBean;
-import org.nrg.xdat.model.*;
-import org.nrg.xdat.om.*;
-import org.nrg.xdat.om.base.auto.AutoScrScreeningassessment;
-import org.nrg.xdat.om.base.auto.AutoValProtocoldata;
-import org.nrg.xdat.om.base.auto.AutoXnatImagesessiondata;
-import org.nrg.xdat.om.base.auto.AutoXnatQcassessmentdata;
-import org.nrg.xdat.schema.SchemaElement;
-import org.nrg.xdat.security.SecurityValues;
-import org.nrg.xdat.security.helpers.Permissions;
-import org.nrg.xdat.security.helpers.Users;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFT;
-import org.nrg.xft.XFTItem;
-import org.nrg.xft.XFTTable;
-import org.nrg.xft.db.MaterializedView;
-import org.nrg.xft.db.PoolDBUtils;
-import org.nrg.xft.event.EventDetails;
-import org.nrg.xft.event.EventMetaI;
-import org.nrg.xft.event.EventUtils;
-
-import org.nrg.xft.exception.*;
-import org.nrg.xft.search.CriteriaCollection;
-import org.nrg.xft.search.TableSearch;
-import org.nrg.xft.security.UserI;
-import org.nrg.xft.utils.FileTracker;
-import org.nrg.xft.utils.FileUtils;
-import org.nrg.xft.utils.SaveItemHelper;
-import org.nrg.xft.utils.StringUtils;
-import org.nrg.xnat.exceptions.InvalidArchiveStructure;
-import org.nrg.xnat.helpers.merge.ProjectAnonymizer;
-import org.nrg.xnat.helpers.scanType.ScanTypeMappingI;
-import org.nrg.xnat.scanAssessors.AssessorComparator;
-import org.nrg.xnat.scanAssessors.ScanAssessorI;
-import org.nrg.xnat.srb.XNATDirectory;
-import org.nrg.xnat.srb.XNATMetaData;
-import org.nrg.xnat.srb.XNATSrbSearch;
-import org.nrg.xnat.turbine.utils.ArcSpecManager;
-import org.nrg.xnat.turbine.utils.CatalogSet;
-import org.nrg.xnat.utils.CatalogUtils;
-
-import java.io.File;
-import java.sql.SQLException;
-import java.text.NumberFormat;
-import java.util.*;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatImagesessiondata extends AutoXnatImagesessiondata {
- public static final String SCAN_ABBR="scan";
- public static final String RECON_ABBR="recon";
- public static final String ASSESSOR_ABBR="assess";
- public static final String RESOURCES_ABBR="uploads";
- public static final String MISC_ABBR="misc";
-
- private static final Map<String,String> CUSTOM_SCAN_FIELDS =
- ImmutableMap.of("Scan Time", "startTime");
-
- private String lowerCaseSessionId = null;
-
- private FileTracker _files = new FileTracker();
- private Hashtable fileGroups=new Hashtable();
- private Map<String,String> arcFiles = null;
-
- private List<XnatImageassessordataI> assessors = null;
-
- private List<XnatImagescandataI> scans = null;
-
- protected List<XnatImageassessordataI> minLoadAssessors = null;
-
- public BaseXnatImagesessiondata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatImagesessiondata(UserI user)
- {
- super(user);
- }
-
- public BaseXnatImagesessiondata()
- {}
-
- public BaseXnatImagesessiondata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
- private String _Prearchivepath=null;
- protected XnatQcmanualassessordata manQC;
- protected XnatQcassessmentdata qc;
- protected ScrScreeningassessment scr;
-
- /**
- * @return Returns the prearchivePath.
- */
- public String getPrearchivepath(){
- try{
- if (_Prearchivepath==null){
- _Prearchivepath=getStringProperty("prearchivePath");
- return _Prearchivepath;
- }else {
- return _Prearchivepath;
- }
- } catch (Exception e1) {logger.error(e1);return null;}
- }
-
- /**
- * Sets the value for prearchivePath.
- * @param v Value to Set.
- */
- public void setPrearchivepath(String v){
- try{
- setProperty(SCHEMA_ELEMENT_NAME + "/prearchivePath",v);
- _Prearchivepath=null;
- } catch (Exception e1) {logger.error(e1);}
- }
-
- public int getAssessorCount() {
- return getAssessors().size();
- }
-
- public int getAssessorCount(String elementName) {
- return getAssessors(elementName).size();
- }
-
- public List<XnatImageassessordataI> getAssessors() {
- if (this.assessors == null) {
- try {
- assessors = this.getAssessors_assessor();
-
- } catch (Exception e) {
- logger.error("", e);
- }
- }
- return assessors;
- }
-
- public ArrayList<XnatImageassessordata> getAssessors(String elementName) {
- ArrayList<XnatImageassessordata> temp = new ArrayList<XnatImageassessordata>();
- Iterator iter = getAssessors().iterator();
- while (iter.hasNext()) {
- XnatImageassessordata o = (XnatImageassessordata) iter.next();
- if (o.getXSIType().equalsIgnoreCase(elementName)) {
- temp.add(o);
- }
- }
- return temp;
- }
-
-
- public String getArchivePath() throws UnknownPrimaryProjectException {
- return getArchivePath(getArchiveRootPath());
- }
-
- public String getArchivePath(String rootPath) throws UnknownPrimaryProjectException {
-
- String path = "";
- for(XnatImagescandataI scan : this.getScans_scan()){
- List files = scan.getFile();
- if (files.size() > 0) {
- Iterator fIter = files.iterator();
- while (fIter.hasNext()) {
- XnatAbstractresource file = (XnatAbstractresource) fIter.next();
- String filePath = file.getFullPath(rootPath);
- if (filePath != null && !filePath.equals("")) {
- try {
- String dirName = this.getArchiveDirectoryName();
- int index = filePath.indexOf(dirName);
- if (index == -1) {
- index = filePath.indexOf(dirName
- .toLowerCase());
- }
- if (index == -1) {
- index = filePath.indexOf(dirName
- .toUpperCase());
- }
-
-
- if (index<0){
- path = FileUtils.AppendRootPath("",getArchiveRootPath());
- return path;
- }
- if (index != -1) {
- path = filePath.substring(0, index);
- }
- break;
- } catch (Exception e1) {
- logger.error("", e1);
- }
-
- }
- }
-
- if (!path.equals("")) {
- break;
- }
- }
- }
-
-
- if (!path.equals("")) {
- path = FileUtils.AppendRootPath(getArchiveRootPath(),path);
- }
-
- return path;
- }
- public String getRelativeArchivePath() throws UnknownPrimaryProjectException {
- String path = "";
- for(XnatImagescandataI scan : this.getScans_scan()){
- List files = scan.getFile();
- if (files.size() > 0) {
- Iterator fIter = files.iterator();
- while (fIter.hasNext()) {
- XnatAbstractresource file = (XnatAbstractresource) fIter.next();
- for(String filePath: file.getUnresolvedPaths()){
- if (filePath != null && !filePath.equals("")) {
- try {
- String upperFilePath=filePath.toUpperCase();
-
- String dirName = this.getArchiveDirectoryName();
-
- int index = upperFilePath.indexOf(dirName.toUpperCase());
- if (index==0){
- path = getArchiveRootPath();
- return path;
- }
- if (index != -1) {
- path = filePath.substring(0, index);
- }
- break;
- } catch (Exception e1) {
- logger.error("", e1);
- }
-
- }
- }
- }
-
- if (!path.equals("")) {
- break;
- }
- }
- }
-
- if (path.equals("")){
- try {
- String currentarc = getCurrentArchiveFolder();
- if (currentarc ==null){
- path = getArchiveDirectoryName() + "/";
- }else{
- currentarc = currentarc.replace('\\', '/');
- path = currentarc + getArchiveDirectoryName() + "/";
- }
- } catch (InvalidArchiveStructure e) {
- logger.error("",e);
- }
- }else{
- path +=this.getArchiveDirectoryName() +"/";
- }
-
-
- return path;
- }
-
- /**
- * ArrayList of ArrayLists(String filename,String type, String
- * preArchiveSize, String archiveSize)
- *
- * @return
- */
- public ArrayList<ArrayList<String>> getExtraFiles() throws Exception {
- ArrayList<ArrayList<String>> extraFiles = new ArrayList<ArrayList<String>>();
- ArrayList<String> sub = new ArrayList<String>();
- sub.add("misc");
- sub.add("unknown");
- sub.add("0 Files, 0.00Mb");
- sub.add(this.getArchiveStats("misc"));
-
- extraFiles.add(sub);
- return extraFiles;
- }
-
- public ArrayList<String> getExtraFileNames() throws Exception{
- ArrayList<String> al =new ArrayList<String>();
- if (this.hasSRBData())
- {
- XNATDirectory dir = getSRBDirectory();
- XNATMetaData meta = new XNATMetaData();
- meta.setCategory("MISC"); //match operator is = by default
- XNATDirectory misc= dir.filterLocal(meta);
- al.addAll(misc.getRelativeFileNames());
- }else{
- ArrayList fileIds = (ArrayList)this.getFileGroups().get("misc");
- if (fileIds!=null){
- Iterator iter = fileIds.iterator();
- while (iter.hasNext()){
- String fID = (String)iter.next();
- al.add(this.getFileTracker().getRelativePathByID(fID));
- }
- }
- }
- return al;
- }
-
- /**
- * @return
- * @throws Exception
- */
- public Map<String,String> getArcFiles() throws Exception {
- if (arcFiles == null) {
- logger.debug("BEGIN LOAD ARC FILES");
- arcFiles = new Hashtable<String,String>();
-
- if (this.hasSRBData())
- {
- long startTime = System.currentTimeMillis();
- XNATDirectory dir = getSRBDirectory();
- if(XFT.VERBOSE)System.out.println("Time to load " + (System.currentTimeMillis()-startTime) + "ms");
- startTime = System.currentTimeMillis();
- for(XnatImagescandataI scan : this.getScans_scan()){
- int count = 0;
- long size = 0;
- try {
- XNATMetaData meta = new XNATMetaData();
- meta.setCategory("SCAN"); //match operator is = by default
- meta.setExternalId(scan.getId());
- XNATDirectory scanDIR= dir.filterLocal(meta);
- count = scanDIR.getCount();
- size = scanDIR.getSize();
-
- NumberFormat formatter = NumberFormat.getInstance();
- formatter.setMinimumFractionDigits(2);
- formatter.setMaximumFractionDigits(2);
-
- String stats= count
- + " files, "
- + formatter.format(((float) ((float)size / 1048576))) + "MB";
- arcFiles.put(scan.getId(), stats);
- } catch (RuntimeException e) {
- logger.error("",e);
- arcFiles.put(scan.getId(),"Error");
- }
- }
-
- //POPULATE EXTRA FILES
-// int count = 0;
-// long size = 0;
-// try {
-// XNATMetaData meta = new XNATMetaData();
-// meta.setCategory("MISC"); //match operator is = by default
-// XNATDirectory scanDIR= dir.filterLocal(meta);
-// count = scanDIR.getCount();
-// size = scanDIR.getSize();
-//
-// NumberFormat formatter = NumberFormat.getInstance();
-// formatter.setMinimumFractionDigits(2);
-// formatter.setMaximumFractionDigits(2);
-//
-// String stats= count
-// + " files, "
-// + formatter.format(((float) ((float)size / 1048576))) + "MB";
-// arcFiles.put("misc", stats);
-// } catch (RuntimeException e) {
-// logger.error("",e);
-// arcFiles.put("misc","Error");
-// }
- if(XFT.VERBOSE)System.out.println("Time to sort " + (System.currentTimeMillis()-startTime) + "ms");
- startTime = System.currentTimeMillis();
- }else{
- loadLocalFiles();
-
- for(XnatImagescandataI scan : this.getScans_scan()){
- int count = 0;
- long size = 0;
- try {
- String parsedScanID= StringUtils.ReplaceStr(StringUtils.ReplaceStr(scan.getId(),"-",""),"*","AST");
-
- ArrayList fileGroup = (ArrayList)getFileGroups().get(SCAN_ABBR + parsedScanID);
- if (fileGroup==null){
-
- }else{
- Iterator iter = fileGroup.iterator();
- while(iter.hasNext())
- {
- String fID = (String)iter.next();
- int idIndex = this.getFileTracker().getIDIndex(fID);
- size += this.getFileTracker().getSize(idIndex);
- }
- count = fileGroup.size();
- }
-
- NumberFormat formatter = NumberFormat.getInstance();
- formatter.setMinimumFractionDigits(2);
- formatter.setMaximumFractionDigits(2);
-
- String stats= count
- + " files, "
- + formatter.format(((float) ((float)size / 1048576))) + "MB";
- arcFiles.put(SCAN_ABBR + scan.getId(), stats);
- } catch (RuntimeException e) {
- logger.error("",e);
- arcFiles.put(SCAN_ABBR + scan.getId(),"Error");
- }
- }
-
- for(XnatReconstructedimagedataI recon : this.getReconstructions_reconstructedimage()){
- int count = 0;
- long size = 0;
- try {
- String parsedScanID= StringUtils.ReplaceStr(StringUtils.ReplaceStr(recon.getId(),"-",""),"*","AST");
-
- ArrayList fileGroup = (ArrayList)getFileGroups().get(RECON_ABBR + parsedScanID);
- if (fileGroup==null){
-
- }else{
- Iterator iter = fileGroup.iterator();
- while(iter.hasNext())
- {
- String fID = (String)iter.next();
- int idIndex = this.getFileTracker().getIDIndex(fID);
- size += this.getFileTracker().getSize(idIndex);
- }
- count = fileGroup.size();
- }
-
- NumberFormat formatter = NumberFormat.getInstance();
- formatter.setMinimumFractionDigits(2);
- formatter.setMaximumFractionDigits(2);
-
- String stats= count
- + " files, "
- + formatter.format(((float) ((float)size / 1048576))) + "MB";
- arcFiles.put(RECON_ABBR + recon.getId(), stats);
- } catch (RuntimeException e) {
- logger.error("",e);
- arcFiles.put(RECON_ABBR + recon.getId(),"Error");
- }
- }
-
- for(XnatImageassessordataI assess : this.getAssessors_assessor()){
- int count = 0;
- long size = 0;
- try {
- String parsedScanID= StringUtils.ReplaceStr(StringUtils.ReplaceStr(assess.getId(),"-",""),"*","AST");
-
- ArrayList fileGroup = (ArrayList)getFileGroups().get(ASSESSOR_ABBR + parsedScanID);
- if (fileGroup==null){
-
- }else{
- Iterator iter = fileGroup.iterator();
- while(iter.hasNext())
- {
- String fID = (String)iter.next();
- int idIndex = this.getFileTracker().getIDIndex(fID);
- size += this.getFileTracker().getSize(idIndex);
- }
- count = fileGroup.size();
- }
-
- NumberFormat formatter = NumberFormat.getInstance();
- formatter.setMinimumFractionDigits(2);
- formatter.setMaximumFractionDigits(2);
-
- String stats= count
- + " files, "
- + formatter.format(((float) ((float)size / 1048576))) + "MB";
- arcFiles.put(ASSESSOR_ABBR +assess.getId(), stats);
- } catch (RuntimeException e) {
- logger.error("",e);
- arcFiles.put(ASSESSOR_ABBR +assess.getId(),"Error");
- }
- }
-
- for(XnatAbstractresourceI res : this.getResources_resource()){
- int count = 0;
- long size = 0;
- try {
- String parsedScanID= res.getXnatAbstractresourceId().toString();
-
- ArrayList fileGroup = (ArrayList)getFileGroups().get(RESOURCES_ABBR + parsedScanID);
- if (fileGroup==null){
-
- }else{
- Iterator iter = fileGroup.iterator();
- while(iter.hasNext())
- {
- String fID = (String)iter.next();
- int idIndex = this.getFileTracker().getIDIndex(fID);
- size += this.getFileTracker().getSize(idIndex);
- }
- count = fileGroup.size();
- }
-
- NumberFormat formatter = NumberFormat.getInstance();
- formatter.setMinimumFractionDigits(2);
- formatter.setMaximumFractionDigits(2);
-
- String stats= count
- + " files, "
- + formatter.format(((float) ((float)size / 1048576))) + "MB";
- arcFiles.put(RESOURCES_ABBR +res.getXnatAbstractresourceId(), stats);
- } catch (RuntimeException e) {
- logger.error("",e);
- arcFiles.put(RESOURCES_ABBR +res.getXnatAbstractresourceId(),"Error");
- }
- }
-
- int count = 0;
- long size = 0;
- try {
- ArrayList fileGroup = (ArrayList)getFileGroups().get("misc");
- if (fileGroup!=null && !fileGroup.isEmpty()){
- Iterator iter = fileGroup.iterator();
- while(iter.hasNext())
- {
- String fID = (String)iter.next();
- size += this.getFileTracker().getSize(this.getFileTracker().getIDIndex(fID));
- }
- count = fileGroup.size();
-
- NumberFormat formatter = NumberFormat.getInstance();
- formatter.setMinimumFractionDigits(2);
- formatter.setMaximumFractionDigits(2);
-
- String stats= count
- + " files, "
- + formatter.format(((float) ((float)size / 1048576))) + "MB";
- arcFiles.put("misc", stats);
- }
- } catch (RuntimeException e) {
- logger.error("",e);
- arcFiles.put("misc","Error");
- }
-
- logger.debug("END LOAD ARC FILES");
- }
- }
- return arcFiles;
- }
-
- public String getArchiveStats(String scanId) {
- try {
- String s = (String)this.getArcFiles().get(scanId);
- if (s == null) {
- return "0 files, 0.00MB";
- } else {
- return s;
- }
- } catch (Exception e) {
- return "0 files, 0.00MB";
- }
- }
-
- public long getDateDiff(Date d) {
- try {
- Date expt = (Date) this.getDate();
-
- Calendar dobC = new GregorianCalendar();
- dobC.setTime(expt);
- Calendar acqC = new GregorianCalendar();
- acqC.setTime(d);
- long days = getDateDiff(dobC, acqC);
- return Math.round(Math.floor(days));
- } catch (Exception e) {
- return 0;
- }
- }
-
- /**
- * @param type
- * @return ArrayList of org.nrg.xdat.om.XnatMrscandata
- */
- public ArrayList<XnatImagescandata> getScansByXSIType(String type) {
- ArrayList<XnatImagescandata> _return = new ArrayList<XnatImagescandata>();
-
- for(XnatImagescandataI scan : this.getScans_scan()){
- try {
- if(((XnatImagescandata)scan).getItem().instanceOf(type)){
- _return.add((XnatImagescandata)scan);
- }
- } catch (ElementNotFoundException e) {
- e.printStackTrace();
- }
- }
- _return.trimToSize();
- return _return;
- }
-
- /**
- * @param type Scan type literal or regex of the scans to retrieve
- * @return ArrayList of org.nrg.xdat.om.XnatImagescandata
- */
- public ArrayList<XnatImagescandata> getScansByType(String type) {
- ArrayList<XnatImagescandata> _return = Lists.newArrayList();
-
- if (type == null) {
- for(XnatImagescandataI scan : this.getScans_scan()){
- if (scan.getType() == null ) {
- _return.add((XnatImagescandata)scan);
- }
- }
-
- _return.trimToSize();
- return _return;
- }
-
- Pattern p = Pattern.compile("(?i)"+type);
- Matcher m = p.matcher("");
-
- for(XnatImagescandataI scan : this.getScans_scan()){
- String scan_type = scan.getType();
-
- if (scan_type == null) {
- continue;
- }
-
- if (scan_type.equalsIgnoreCase(type)) {
- _return.add((XnatImagescandata)scan);
- }else{
- m.reset(scan_type);
- if (m.find()) {
- _return.add((XnatImagescandata)scan);
- }
- }
- }
-
- _return.trimToSize();
- return _return;
- }
-
- /**
- * @param typeList List of scan type strings (literal or regex) to retrieve from the session
- * @return ArrayList of org.nrg.xdat.om.XnatImagescandata
- */
- public ArrayList<XnatImagescandata> getScansByTypeList(List<String> typeList) {
- ArrayList<XnatImagescandata> _return = Lists.newArrayList();
- HashSet<XnatImagescandata> tempSet = Sets.newHashSet();
-
- if (typeList.size() == 0) {
- return _return;
- }
-
- for (String type : typeList) {
- tempSet.addAll(getScansByType(type));
- }
-
- _return.addAll(tempSet);
-
- Collections.sort(_return, new Comparator<XnatImagescandata>() {
- @Override
- public int compare(XnatImagescandata s1, XnatImagescandata s2) {
- String id1 = s1.getId();
- String id2 = s2.getId();
- int comp;
- try {
- comp = (new Integer(id1)).compareTo(new Integer(id2));
- } catch (NumberFormatException e) {
- comp = id1.compareTo(id2);
- }
- return comp;
- }
- });
-
- return _return;
- }
-
- /**
- * @param id The ID of the scan to retrieve.
- * @return The requested image scan data object.
- */
- public XnatImagescandata getScanById(String id) {
- for(XnatImagescandataI scan : getScans_scan()){
- if (scan.getId().equalsIgnoreCase(id)) {
- return (XnatImagescandata)scan;
- }
-
- }
- return null;
- }
-
- /**
- * @param id The ID of the assessor to retrieve.
- * @return The requested image assessor data object.
- */
- public XnatImageassessordata getAssessorById(String id) {
- for(XnatImageassessordataI scan : getAssessors()){
- if (scan.getId().equalsIgnoreCase(id)) {
- return (XnatImageassessordata) scan;
- }
-
- }
- return null;
- }
-
- /**
- * @param type
- * @return ArrayList of org.nrg.xdat.om.XnatReconstructedimagedata
- */
- public List<XnatReconstructedimagedata> getReconstructionsByType(String type) {
- ArrayList _return = new ArrayList();
- List al = this.getReconstructions_reconstructedimage();
- if (al != null) {
- for (int i = 0; i < al.size(); i++) {
- XnatReconstructedimagedata scan = (XnatReconstructedimagedata) al.get(i);
- try {
- if (scan.getBasescantype().equalsIgnoreCase(type)) {
- _return.add(scan);
- }
- }catch(NullPointerException npe) {
- if (scan.getType().equalsIgnoreCase(type)) {
- _return.add(scan);
- }
- }
- }
- }
- _return.trimToSize();
- return _return;
- }
-
- /**
- * @param type
- * @return org.nrg.xdat.om.XnatReconstructedimagedata
- */
- public XnatReconstructedimagedataI getReconstructionByID(String type) {
- List al = this.getReconstructions_reconstructedimage();
- if (al != null) {
- for (int i = 0; i < al.size(); i++) {
- XnatReconstructedimagedata scan = (XnatReconstructedimagedata) al.get(i);
- if (scan.getId().equalsIgnoreCase(type)) {
- return scan;
- }
- }
- }
- return null;
- }
-
- /**
- * @return Returns the prearchivePath.
- */
- public String getPrearchivepath(UserI user) {
- String s = super.getPrearchivepath();
- // Migration: This code was in the previous XDATUser code.
- // if (s == null || s.equalsIgnoreCase("")) {
- // s = user.getQuarantinePath();
- // }
- return s;
- }
-
- public Collection<XnatImagescandataI> getSortedScans() {
- if (null == scans) {
- try {
- scans =getScans_scan();
- Collections.sort(scans,BaseXnatImagescandata.GetComparator());
- } catch (Exception e) {
- logger.error("", e);
- return getScans_scan();
- }
- }
-
- return scans;
- }
-
-
- public int getMinimalLoadAssessorsCount(String elementName)
- {
- return getMinimalLoadAssessors(elementName).size();
- }
-
- public ArrayList getMinimalLoadAssessors(String elementName)
- {
- ArrayList al = new ArrayList();
- try {
- SchemaElement e = SchemaElement.GetElement(elementName);
- Iterator min = this.getMinimalLoadAssessors().iterator();
- while (min.hasNext())
- {
- ItemI assessor = (ItemI)min.next();
- if (assessor.getXSIType().equalsIgnoreCase(e.getFullXMLName()))
- {
- al.add(assessor);
- }
- }
-
-
-
- } catch (XFTInitException e) {
- logger.error("",e);
- } catch (ElementNotFoundException e) {
- logger.error("",e);
- }
-
- al.trimToSize();
- return al;
- }
-
- public List<XnatImageassessordataI> getMinimalLoadAssessors()
- {
- if (minLoadAssessors==null)
- {
- minLoadAssessors = new ArrayList<XnatImageassessordataI>();
- if(getItem().isPreLoaded())
- {
- minLoadAssessors=this.getAssessors();
- }else{
-
- try {
- XFTTable table = TableSearch.Execute("SELECT ex.id,ex.date,ex.project,me.element_name AS type,me.element_name,ex.note AS note,i.lastname, investigator_xnat_investigatorData_id AS invest_id,projects FROM xnat_imageAssessorData assessor LEFT JOIN xnat_experimentData ex ON assessor.ID=ex.ID LEFT JOIN xnat_experimentdata_meta_data meta ON ex.experimentdata_info=meta.meta_data_id LEFT JOIN xnat_investigatorData i ON i.xnat_investigatorData_id=ex.investigator_xnat_investigatorData_id LEFT JOIN xdat_meta_element me ON ex.extension=me.xdat_meta_element_id LEFT JOIN (SELECT xs_a_concat(project || ',') AS PROJECTS, sharing_share_xnat_experimentda_id FROM xnat_experimentData_share GROUP BY sharing_share_xnat_experimentda_id) PROJECT_SEARCH ON ex.id=PROJECT_SEARCH.sharing_share_xnat_experimentda_id WHERE assessor.imagesession_id='" + this.getId() +"' AND meta.status!='obsolete' ORDER BY ex.date ASC",getDBName(),null);
- table.resetRowCursor();
-
- while (table.hasMoreRows())
- {
- Hashtable row = table.nextRowHash();
- String element = (String)row.get("element_name");
- try {
- XFTItem child = XFTItem.NewItem(element,this.getUser());
-
- Object date = row.get("date");
- Object id = row.get("id");
- Object note = row.get("note");
- Object invest_id = row.get("invest_id");
- Object lastname = row.get("lastname");
- Object project = row.get("project");
-
- if (date!=null)
- {
- try {
- child.setProperty("date",date);
- } catch (XFTInitException e) {
- logger.error("",e);
- } catch (ElementNotFoundException e) {
- logger.error("",e);
- } catch (FieldNotFoundException e) {
- logger.error("",e);
- } catch (InvalidValueException e) {
- logger.error("",e);
- }
- }
- if (id!=null)
- {
- try {
- child.setProperty("ID",id);
- } catch (XFTInitException e) {
- logger.error("",e);
- } catch (ElementNotFoundException e) {
- logger.error("",e);
- } catch (FieldNotFoundException e) {
- logger.error("",e);
- } catch (InvalidValueException e) {
- logger.error("",e);
- }
- }
-
- if (project!=null)
- {
- try {
- child.setProperty("project",project);
- } catch (XFTInitException e) {
- logger.error("",e);
- } catch (ElementNotFoundException e) {
- logger.error("",e);
- } catch (FieldNotFoundException e) {
- logger.error("",e);
- } catch (InvalidValueException e) {
- logger.error("",e);
- }
- }
-
- if (note!=null)
- {
- try {
- child.setProperty("note",note);
- } catch (XFTInitException e) {
- logger.error("",e);
- } catch (ElementNotFoundException e) {
- logger.error("",e);
- } catch (FieldNotFoundException e) {
- logger.error("",e);
- } catch (InvalidValueException e) {
- logger.error("",e);
- }
- }
- if (lastname!=null)
- {
- try {
- child.setProperty("investigator.lastname",lastname);
- } catch (XFTInitException e) {
- logger.error("",e);
- } catch (ElementNotFoundException e) {
- logger.error("",e);
- } catch (FieldNotFoundException e) {
- logger.error("",e);
- } catch (InvalidValueException e) {
- logger.error("",e);
- }
- }
- if (invest_id!=null)
- {
- try {
- child.setProperty("investigator_xnat_investigatorData_id",invest_id);
- } catch (XFTInitException e) {
- logger.error("",e);
- } catch (ElementNotFoundException e) {
- logger.error("",e);
- } catch (FieldNotFoundException e) {
- logger.error("",e);
- } catch (InvalidValueException e) {
- logger.error("",e);
- }
- }
-
- String projects = (String)row.get("projects");
- if (projects!=null)
- {
- Iterator iter= StringUtils.CommaDelimitedStringToArrayList(projects, true).iterator();
- while(iter.hasNext())
- {
- String projectName = (String)iter.next();
- child.setProperty("sharing.share.project", projectName);
- }
- }
-
- addMinLoadAssessor(element,child,minLoadAssessors);
-
- } catch (XFTInitException e) {
- logger.error("",e);
- } catch (ElementNotFoundException e) {
- logger.error("",e);
- }
- }
- } catch (Exception e) {
- logger.error("",e);
- }
- }
- }
-
- return minLoadAssessors;
- }
-
- /**
- * Method to place minimally loaded assessors into their list.
- *
- * Some servers will want to fully load the data, others won't. Separating this into its own method allows sites to just override this method, instead of the old thing (like they used to have to).
- *
- * @param xsiType
- * @param child
- * @param minLoadAssessors
- * @throws InvalidItemException
- * @throws Exception
- */
- public void addMinLoadAssessor(String xsiType,XFTItem child, List<XnatImageassessordataI> minLoadAssessors) throws InvalidItemException, Exception{
- XnatImageassessordata assessor= (XnatImageassessordata)BaseElement.GetGeneratedItem(child);
-
- if (xsiType.equalsIgnoreCase(XnatQcmanualassessordata.SCHEMA_ELEMENT_NAME))
- {
- if (Permissions.canRead(this.getUser(), child))
- {
- this.manQC = new XnatQcmanualassessordata(child.getCurrentDBVersion(false));
- minLoadAssessors.add(this.manQC);
- }else{
- minLoadAssessors.add(new XnatQcmanualassessordata(child));
- }
- }else if (xsiType.equalsIgnoreCase(XnatQcassessmentdata.SCHEMA_ELEMENT_NAME))
- {
- if (this.qc == null)
- {
- if (Permissions.canRead(this.getUser(), child))
- {
- this.qc = new XnatQcassessmentdata(child.getCurrentDBVersion(false));
- minLoadAssessors.add(this.qc);
- }else{
- minLoadAssessors.add(new XnatQcassessmentdata(child));
- }
- }else{
- this.qc = new XnatQcassessmentdata(child.getCurrentDBVersion(false));
- minLoadAssessors.add(this.qc);
- }
- }else if(assessor instanceof ScanAssessorI){
- minLoadAssessors.add( (XnatImageassessordata)BaseElement.GetGeneratedItem(child.getCurrentDBVersion(false)));
- }else{
- minLoadAssessors.add(assessor);
- }
- }
-
- public void loadSRBFiles()
- {
- if (this.fileGroups.size()==0)
- {
- long startTime = System.currentTimeMillis();
- XNATDirectory dir = getSRBDirectory();
- System.out.println("Time to load " + (System.currentTimeMillis()-startTime) + "ms");
- startTime = System.currentTimeMillis();
-
- for(XnatImagescandataI scan : this.getSortedScans()){
- XNATMetaData meta = new XNATMetaData();
- meta.setCategory("SCAN"); //match operator is = by default
- meta.setExternalId(scan.getId());
- String parsedScanID= StringUtils.ReplaceStr(StringUtils.ReplaceStr(scan.getId(),"-",""),"*","AST");
- fileGroups.put(SCAN_ABBR +parsedScanID,dir.filterLocal(meta));
- }
-
- Iterator reconIter= this.getReconstructions_reconstructedimage().iterator();
- while (reconIter.hasNext())
- {
- XnatReconstructedimagedata recon = (XnatReconstructedimagedata)reconIter.next();
-
- XNATMetaData meta = new XNATMetaData();
- meta.setCategory("RECON"); //match operator is = by default
- meta.setExternalId(recon.getId());
- String parsedScanID= StringUtils.ReplaceStr(StringUtils.ReplaceStr(recon.getId(),"-",""),"*","AST");
- fileGroups.put(RECON_ABBR +parsedScanID,dir.filterLocal(meta));
-
- }
-
- for(XnatImageassessordataI assess : this.getAssessors_assessor()){
-
- XNATMetaData meta = new XNATMetaData();
- meta.setCategory("ASSESSOR"); //match operator is = by default
- meta.setExternalId(assess.getId());
- String parsedScanID= StringUtils.ReplaceStr(StringUtils.ReplaceStr(assess.getId(),"-",""),"*","AST");
- fileGroups.put("assess" +parsedScanID,dir.filterLocal(meta));
-
- }
-
- XNATMetaData meta = new XNATMetaData();
- meta.setCategory("MISC"); //match operator is = by default
- fileGroups.put("misc0",dir.filterLocal(meta));
- startTime = System.currentTimeMillis();
- System.out.println("Time to sort " + (System.currentTimeMillis()-startTime) + "ms");
- }
- }
-
- private void loadDefinedFiles(String rootPath)
- {
- if (!rootPath.startsWith("srb:"))
- {
- rootPath =FileUtils.AppendSlash(rootPath);
- }
- for(XnatImagescandataI scan : this.getSortedScans()){
- final ArrayList fileGrouping = new ArrayList();
- if (!scan.getFile().isEmpty())
- {
- for (XnatAbstractresourceI xnatFile:scan.getFile())
- {
- for (File f:((XnatAbstractresource)xnatFile).getCorrespondingFiles(rootPath))
- {
- if (f.exists())
- {
- String fileID = this._files.addFile(f.getPath(),f,FileTracker.KNOWN);
- fileGrouping.add(fileID);
- }
- }
-
- if (xnatFile instanceof XnatResourcecatalog){
- File f = ((XnatResourcecatalog)xnatFile).getCatalogFile(rootPath);
- if (f.exists())
- {
- String fileID = this._files.addFile(f.getPath(),f,FileTracker.KNOWN);
- fileGrouping.add(fileID);
- }
- }
- }
- if (fileGrouping.size()>0){
- String parsedScanID= StringUtils.ReplaceStr(StringUtils.ReplaceStr(scan.getId(),"-",""),"*","AST");
- fileGroups.put(SCAN_ABBR + parsedScanID,fileGrouping);
- }
- }
- }
-
- Iterator reconIter= this.getReconstructions_reconstructedimage().iterator();
- while (reconIter.hasNext())
- {
- XnatReconstructedimagedata recon = (XnatReconstructedimagedata)reconIter.next();
- ArrayList fileGrouping = new ArrayList();
- List outFiles = recon.getOut_file();
- if (outFiles.size()>0)
- {
- Iterator files =outFiles.iterator();
- while (files.hasNext())
- {
- XnatAbstractresource xnatFile = (XnatAbstractresource) files.next();
- ArrayList jFiles = xnatFile.getCorrespondingFiles(rootPath);
-
- Iterator iter = jFiles.iterator();
- while (iter.hasNext())
- {
- File f = (File)iter.next();
- if (f.exists())
- {
- String fileID = this._files.addFile(f.getPath(),f,FileTracker.KNOWN);
- fileGrouping.add(fileID);
- }
-
- }
-
- if (xnatFile instanceof XnatResourcecatalog){
- File f = ((XnatResourcecatalog)xnatFile).getCatalogFile(rootPath);
- if (f.exists())
- {
- String fileID = this._files.addFile(f.getPath(),f,FileTracker.KNOWN);
- fileGrouping.add(fileID);
- }
- }
- }
-
- if (fileGrouping.size()>0){
- if (recon.getId()!=null)
- {
- String parsedScanID= StringUtils.ReplaceStr(StringUtils.ReplaceStr(recon.getId(),"-",""),"*","AST");
- fileGroups.put(RECON_ABBR + parsedScanID,fileGrouping);
- }
- }
-
- }
- }
-
- for(XnatImageassessordataI assess : this.getAssessors_assessor()){
- ArrayList fileGrouping = new ArrayList();
- List outFiles = assess.getOut_file();
- if (outFiles.size()>0)
- {
- Iterator files =outFiles.iterator();
- while (files.hasNext())
- {
- XnatAbstractresource xnatFile = (XnatAbstractresource) files.next();
- ArrayList jFiles = xnatFile.getCorrespondingFiles(rootPath);
-
- Iterator iter = jFiles.iterator();
- while (iter.hasNext())
- {
- File f = (File)iter.next();
- if (f.exists())
- {
- String fileID = this._files.addFile(f.getPath(),f,FileTracker.KNOWN);
- fileGrouping.add(fileID);
- }
- }
-
- if (xnatFile instanceof XnatResourcecatalog){
- File f = ((XnatResourcecatalog)xnatFile).getCatalogFile(rootPath);
- if (f.exists())
- {
- String fileID = this._files.addFile(f.getPath(),f,FileTracker.KNOWN);
- fileGrouping.add(fileID);
- }
- }
- }
- if (fileGrouping.size()>0){
- String parsedScanID= StringUtils.ReplaceStr(StringUtils.ReplaceStr(assess.getId(),"-",""),"*","AST");
- fileGroups.put(ASSESSOR_ABBR + parsedScanID,fileGrouping);
- }
- }
- }
-
- Iterator resourceIter= this.getResources_resource().iterator();
- while (resourceIter.hasNext())
- {
- XnatAbstractresource xnatFile = (XnatAbstractresource)resourceIter.next();
- ArrayList fileGrouping = new ArrayList();
- ArrayList jFiles = xnatFile.getCorrespondingFiles(rootPath);
-
- Iterator iter = jFiles.iterator();
- while (iter.hasNext())
- {
- File f = (File)iter.next();
- if (f.exists())
- {
- String fileID = this._files.addFile(f.getPath(),f,FileTracker.KNOWN);
- fileGrouping.add(fileID);
- }
- }
-
- if (xnatFile instanceof XnatResourcecatalog){
- File f = ((XnatResourcecatalog)xnatFile).getCatalogFile(rootPath);
- if (f.exists())
- {
- String fileID = this._files.addFile(f.getPath(),f,FileTracker.KNOWN);
- fileGrouping.add(fileID);
- }
- }
-
- if (fileGrouping.size()>0){
- String parsedScanID= xnatFile.getXnatAbstractresourceId().toString();
- fileGroups.put(RESOURCES_ABBR + parsedScanID,fileGrouping);
- }
- }
- }
-
- /**
- */
- public void loadLocalFiles()
- {
- loadLocalFiles(true);
- }
-
- /**
- */
- public void loadLocalFiles(boolean loadMISCFiles)
- {
- if (_files.getSize()==0)
- {
- String s;
- try {
- s = this.getArchiveRootPath();
- } catch (UnknownPrimaryProjectException e) {
- s=null;
- }
-
- loadDefinedFiles(s);
-
- if (loadMISCFiles)
- {
- String rawdir = this.deriveSessionDir();
- if (rawdir!=null){
- File misc = new File(rawdir);
- if (misc.exists())
- loadDirectoryFiles(misc,"",false,new ArrayList());
- }
- }
-
-
- _files.syncToFS() ;
- }
- }
-
- /**
- */
- public void loadLocalRAWFiles()
- {
- if (_files.getSize()==0)
- {
- String s;
- try {
- s = this.getArchiveRootPath();
- } catch (UnknownPrimaryProjectException e) {
- s=null;
- }
- loadDefinedFiles(s);
-
- String rawdir = this.deriveRawDir();
- if (rawdir!=null){
- File misc = new File(rawdir);
- if (misc.exists())
- loadDirectoryFiles(misc,"",false,new ArrayList());
- }
-
-
- _files.syncToFS() ;
- }
- }
-
- public void loadDirectoryFiles(File dir,String parents,boolean raw,ArrayList miscRaw)
- {
- if (dir.exists())
- {
- parents += dir.getName() + "/";
-
- if (!raw){
- if (dir.getName().equalsIgnoreCase("RAW") || dir.getName().equalsIgnoreCase("SCANS")){
- raw = true;
- }
- }
- File[] children = dir.listFiles();
- for (int i=0;i<children.length;i++)
- {
- File child = children[i];
- if (child.isDirectory())
- {
- loadDirectoryFiles(child,parents,raw,miscRaw);
- }else{
- if (_files.indexOf(child)==-1)
- {
- if (!child.getName().equalsIgnoreCase("dcmtoxnat.log") && !child.getName().equalsIgnoreCase("dcmtoxnat.log.gz"))
- {
- String fileID = this._files.addFile(parents + child.getName(),child,FileTracker.MISC);
- if (raw){
- miscRaw.add(fileID);
- }
- }
- }
- }
- }
-
- if (dir.getName().equalsIgnoreCase("RAW") || dir.getName().equalsIgnoreCase("SCANS")){
- fileGroups.put("misc", miscRaw);
- }
-
- }
- }
-
-
-
- public String listArchiveToHTML(String server)
- {
- String rootPath;
- try {
- rootPath = this.getArchiveRootPath();
- } catch (UnknownPrimaryProjectException e2) {
- rootPath=null;
- }
- String miscDir = null;
- File achive = new File(rootPath);
- StringBuffer sb = new StringBuffer();
- StringBuffer allFiles = new StringBuffer();
- int fileCount=0;
-
- allFiles.append("<script type=\"text/javascript\" language=\"JavaScript1.3\">\n");
- allFiles.append(" function allFilesCheckAll(checkAll)\n");
- allFiles.append(" {\n");
- allFiles.append(" var change=null;\n");
- allFiles.append(" var node=null;\n");
-
- sb.append(" <TR>");
- sb.append(" <TD VALIGN=\"top\" ALIGN=\"left\"><b>SCANS</b></TD><TD>");
- for(XnatImagescandataI scan : this.getSortedScans()){
- ArrayList fileGrouping = new ArrayList();
- List scanFiles= scan.getFile();
- if (scanFiles.size()>0)
- {
- Iterator files = scanFiles.iterator();
- boolean hasContent= false;
- boolean hasFunctionText=false;
- StringBuffer scanLinkBuffer = new StringBuffer();
- while (files.hasNext())
- {
- XnatAbstractresource xnatFile = (XnatAbstractresource) files.next();
- ArrayList jFiles = xnatFile.getCorrespondingFiles(rootPath);
- if (miscDir==null){
- miscDir=xnatFile.getFullPath(rootPath);
- int mrIndex = miscDir.toLowerCase().indexOf("/" + getArchiveDirectoryName().toLowerCase() +"/");
- if (mrIndex==-1){
- String sPath = rootPath.replace('\\', '/');
- sPath = sPath.replace("//", "/");
- if (miscDir.startsWith(sPath)){
- int index =miscDir.indexOf(File.separator,sPath.length()+1);
- if (index==-1){
- index =miscDir.indexOf("/",sPath.length()+1);
- if (index==-1){
- index =miscDir.indexOf("\\",sPath.length()+1);
- }
- if (index==-1){
- index =miscDir.indexOf("\\",sPath.length()+1);
- }else{
- miscDir = null;
- }
- }else{
- miscDir = miscDir.substring(0,index);
- }
- }else{
- int index = miscDir.indexOf(achive.getName());
- if (index==-1){
- miscDir=null;
- }else{
- index += achive.getName().length()+1;
- miscDir = miscDir.substring(0,index);
- }
- }
- }else{
- mrIndex += getArchiveDirectoryName().length()+2;
- miscDir = miscDir.substring(0,mrIndex);
- }
- }
-
- Iterator iter = jFiles.iterator();
- while (iter.hasNext())
- {
- File f = (File)iter.next();
- if (f.exists())
- {
- String fileID = this._files.addFile(f.getAbsolutePath(),f,FileTracker.KNOWN);
- scanLinkBuffer.append("<b>").append(f.getName()).append("</b><BR>");
- fileGrouping.add(fileID);
- hasContent=true;
- hasFunctionText=true;
- fileCount++;
- }else{
- scanLinkBuffer.append("\n").append(f.getName()).append(" (File off-line)<BR>");
- hasContent=true;
- }
- }
-
- if (xnatFile instanceof XnatResourcecatalog){
- File f = ((XnatResourcecatalog)xnatFile).getCatalogFile(rootPath);
- if (f.exists())
- {
- String fileID = this._files.addFile(f.getAbsolutePath(),f,FileTracker.KNOWN);
- scanLinkBuffer.append("<b>").append(f.getName()).append("</b><BR>");
- fileGrouping.add(fileID);
- hasContent=true;
- hasFunctionText=true;
- fileCount++;
- }else{
- scanLinkBuffer.append("\n").append(f.getName()).append(" (File off-line)<BR>");
- hasContent=true;
- }
- }
- }
- String parsedScanID= StringUtils.ReplaceStr(StringUtils.ReplaceStr(scan.getId(),"-",""),"*","AST");
- if (hasContent){
- sb.append("\n");
- if (hasFunctionText)
- {
- sb.append("<INPUT type=\"checkbox\" id=\"scan").append(parsedScanID).append("\" name=\"scan").append(parsedScanID).append("\" CHECKED/> ");
- this.fileGroups.put("scan" +parsedScanID,fileGrouping);
- }
- sb.append("<span class=\"trigger\" onClick=\"blocking('scan").append(parsedScanID).append("');\">");
- sb.append("<img ID=\"IMGscan").append(parsedScanID).append("\" src=\"").append(server).append("/images/plus.jpg\" border=0/> ");
- sb.append("<b>").append(scan.getId()).append("</b> ");
- if (scan.getType()!=null)
- {
- sb.append("(" + scan.getType() + ")");
- }
- sb.append("</span>");
- sb.append("<BR><span class=\"branch\" ID=\"spanscan").append(parsedScanID).append("\">");
- sb.append(scanLinkBuffer);
- sb.append("</span><BR>");
-
- if (hasFunctionText){
- allFiles.append(" \n");
- allFiles.append(" change = \"scan").append(parsedScanID).append("\";\n");
- allFiles.append(" node = document.getElementById(change);\n");
- allFiles.append(" node.checked=checkAll.checked;\n");
- }
- }else{
- sb.append("<span class=\"trigger\"><b>"+ scan.getId() + "</b> (" + scan.getType() + ")</span><br><span class=\"branch\" style=\"display: block;\">No files found for this scan.</span><BR>");
- }
- }else{
- sb.append("<span class=\"trigger\"><b>"+ scan.getId() + "</b> (" + scan.getType() + ")</span><br><span class=\"branch\" style=\"display: block;\">No files defined for this scan.</span><br>");
- }
- }
- sb.append("</TD></TR>");
-
- sb.append("<TR><TD> </TD></TR>");
-
- sb.append(" <TR>");
- int c=0;
- sb.append(" <TD VALIGN=\"top\" ALIGN=\"left\">");
- Iterator reconIter= this.getReconstructions_reconstructedimage().iterator();
- while (reconIter.hasNext())
- {
- XnatReconstructedimagedata recon = (XnatReconstructedimagedata)reconIter.next();
- ArrayList fileGrouping = new ArrayList();
- List outFiles = recon.getOut_file();
- if (outFiles.size()>0)
- {
- Iterator files =outFiles.iterator();
- boolean hasContent= false;
- boolean hasFunctionText=false;
- StringBuffer scanLinkBuffer = new StringBuffer();
- while (files.hasNext())
- {
- XnatAbstractresource xnatFile = (XnatAbstractresource) files.next();
- ArrayList jFiles = xnatFile.getCorrespondingFiles(rootPath);
-
- Iterator iter = jFiles.iterator();
- while (iter.hasNext())
- {
- File f = (File)iter.next();
- if (f.exists())
- {
- String fileID = this._files.addFile(f.getAbsolutePath(),f,FileTracker.KNOWN);
- scanLinkBuffer.append("<b>").append(f.getName()).append("</b><BR>");
- fileGrouping.add(fileID);
- hasContent=true;
- hasFunctionText=true;
- fileCount++;
- }else{
- scanLinkBuffer.append("\n").append(f.getName()).append(" (File off-line)<BR>");
- hasContent=true;
- }
- }
-
- if (xnatFile instanceof XnatResourcecatalog){
- File f = ((XnatResourcecatalog)xnatFile).getCatalogFile(rootPath);
- if (f.exists())
- {
- String fileID = this._files.addFile(f.getAbsolutePath(),f,FileTracker.KNOWN);
- scanLinkBuffer.append("<b>").append(f.getName()).append("</b><BR>");
- fileGrouping.add(fileID);
- hasContent=true;
- hasFunctionText=true;
- fileCount++;
- }else{
- scanLinkBuffer.append("\n").append(f.getName()).append(" (File off-line)<BR>");
- hasContent=true;
- }
- }
- }
- String parsedScanID= StringUtils.ReplaceStr(StringUtils.ReplaceStr(recon.getId(),"-",""),"*","AST");
- if (hasContent){
- if(c++==0)
- sb.append("<b>RECONSTRUCTIONS</b></TD><TD>");
- sb.append("\n");
- if (hasFunctionText){
- sb.append("<INPUT type=\"checkbox\" id=\"recon").append(parsedScanID).append("\" name=\"recon").append(parsedScanID).append("\" CHECKED/> ");
- this.fileGroups.put("recon" +parsedScanID,fileGrouping);
- }
- sb.append("<span class=\"trigger\" onClick=\"blocking('recon").append(parsedScanID).append("');\">");
- sb.append("<img ID=\"IMGrecon").append(parsedScanID).append("\" src=\"").append(server).append("/images/plus.jpg\" border=0/> <b>").append(recon.getId()).append("</b> ");
- if (recon.getType()!=null)
- sb.append("(" + recon.getType() + ")");
- sb.append("</span>");
- sb.append("<BR><span class=\"branch\" ID=\"spanrecon").append(parsedScanID).append("\">");
- sb.append(scanLinkBuffer);
-
- sb.append("</span><BR>");
-
- if (hasFunctionText){
- allFiles.append(" \n");
- allFiles.append(" change = \"recon").append(parsedScanID).append("\";\n");
- allFiles.append(" node = document.getElementById(change);\n");
- allFiles.append(" node.checked=checkAll.checked;\n");
- }
- }else{
- if(c++==0)
- sb.append("<b>RECONSTRUCTIONS</b></TD><TD>");
- sb.append("<span class=\"trigger\"><b>"+ recon.getId() + "</b> (" + recon.getType() + ")</span><br><span class=\"branch\" style=\"display: block;\">No files found for this reconstruction.</span><BR>");
- }
- }else{
- if(c++==0)
- sb.append("<b>RECONSTRUCTIONS</b></TD><TD>");
- sb.append("<span class=\"trigger\"><b>"+ recon.getId() + "</b> (" + recon.getType() + ")</span><br><span class=\"branch\" style=\"display: block;\">No files defined for this reconstruction.</span><BR>");
- }
- }
- sb.append("</TD></TR>");
-
- try {
- sb.append("<TR><TD> </TD></TR>");
-
- sb.append(" <TR>");
- sb.append(" <TD VALIGN=\"top\" ALIGN=\"left\">");
- c=0;
- for(XnatImageassessordataI assess : this.getAssessors_assessor()){
- ArrayList fileGrouping = new ArrayList();
- List outFiles = assess.getOut_file();
- if (outFiles.size()>0)
- {
- Iterator files =outFiles.iterator();
-
- boolean hasContent= false;
- boolean hasFunctionText=false;
- StringBuffer scanLinkBuffer = new StringBuffer();
- while (files.hasNext())
- {
- XnatAbstractresource xnatFile = (XnatAbstractresource) files.next();
- ArrayList jFiles = xnatFile.getCorrespondingFiles(rootPath);
-
- Iterator iter = jFiles.iterator();
- while (iter.hasNext())
- {
- File f = (File)iter.next();
- if (f.exists())
- {
- String fileID = this._files.addFile(f.getAbsolutePath(),f,FileTracker.KNOWN);
- scanLinkBuffer.append("<b>").append(f.getName()).append("</b><BR>");
- fileGrouping.add(fileID);
- hasContent=true;
- hasFunctionText=true;
- fileCount++;
- }else{
- scanLinkBuffer.append("\n").append(f.getName()).append(" (File off-line)<BR>");
- hasContent=true;
- }
- }
-
- if (xnatFile instanceof XnatResourcecatalog){
- File f = ((XnatResourcecatalog)xnatFile).getCatalogFile(rootPath);
- if (f.exists())
- {
- String fileID = this._files.addFile(f.getAbsolutePath(),f,FileTracker.KNOWN);
- scanLinkBuffer.append("<b>").append(f.getName()).append("</b><BR>");
- fileGrouping.add(fileID);
- hasContent=true;
- hasFunctionText=true;
- fileCount++;
- }else{
- scanLinkBuffer.append("\n").append(f.getName()).append(" (File off-line)<BR>");
- hasContent=true;
- }
- }
- }
- String parsedScanID= StringUtils.ReplaceStr(StringUtils.ReplaceStr(assess.getId(),"-",""),"*","AST");
- if (hasContent){
- if(c++==0)
- sb.append("<b>ASSESSMENTS</b></TD><TD>");
-
- sb.append("\n");
- if (hasFunctionText){
- sb.append("<INPUT type=\"checkbox\" id=\"assess").append(parsedScanID).append("\" name=\"assess").append(parsedScanID).append("\" checked/> ");
- this.fileGroups.put("assess" +parsedScanID,fileGrouping);
- }
- sb.append("<span class=\"trigger\" onClick=\"blocking('assess").append(parsedScanID).append("');\">");
- sb.append("<img ID=\"IMGassess").append(parsedScanID).append("\" src=\"").append(server).append("/images/plus.jpg\" border=0/> <b>").append(assess.getId()).append("</b> ");
- sb.append("(" + ((XnatImageassessordata)assess).getItem().getProperName() + ")");
- sb.append("</span>");
- sb.append("<BR>\n<span class=\"branch\" ID=\"spanassess").append(parsedScanID).append("\">");
- sb.append(scanLinkBuffer);
- sb.append("</span><BR>");
-
- if (hasFunctionText)
- {
- allFiles.append(" \n");
- allFiles.append(" change = \"assess").append(parsedScanID).append("\";\n");
- allFiles.append(" node = document.getElementById(change);\n");
- allFiles.append(" node.checked=checkAll.checked;\n");
- }
- }else{
- if(c++==0)
- sb.append("<b>ASSESSMENTS</b></TD><TD>");
- sb.append("<span class=\"trigger\"><b>"+ assess.getId() + "</b> (" + ((XnatImageassessordata)assess).getItem().getProperName() + ")</span><br><span class=\"branch\" style=\"display: block;\">No files found for this assessment.</span><BR>");
- }
- }else{
- if(c++==0)
- sb.append("<b>ASSESSMENTS</b></TD><TD>");
- sb.append("<span class=\"trigger\"><b>"+ assess.getId() + "</b> (" + ((XnatImageassessordata)assess).getItem().getProperName() + ")</span><br><span class=\"branch\" style=\"display: block;\">No files defined for this assessment.</span><BR>");
- }
- }
- sb.append("</TD></TR>");
- } catch (ElementNotFoundException e1) {
- logger.error("",e1);
- }
-
- sb.append("<TR><TD> </TD></TR>");
-
- sb.append(" <TR>");
- sb.append(" <TD VALIGN=\"top\" ALIGN=\"left\">");
- c=0;
- Iterator uploadsIter= this.getResources_resource().iterator();
- while (uploadsIter.hasNext())
- {
- XnatAbstractresource xnatFile = (XnatAbstractresource)uploadsIter.next();
- ArrayList fileGrouping = new ArrayList();
- ArrayList jFiles = xnatFile.getCorrespondingFiles(rootPath);
-
- boolean hasContent= false;
- boolean hasFunctionText=false;
- StringBuffer scanLinkBuffer = new StringBuffer();
-
- Iterator iter = jFiles.iterator();
- while (iter.hasNext())
- {
- File f = (File)iter.next();
- if (f.exists())
- {
- String fileID = this._files.addFile(f.getAbsolutePath(),f,FileTracker.KNOWN);
- scanLinkBuffer.append("<b>").append(f.getName()).append("</b><BR>");
- fileGrouping.add(fileID);
- hasContent=true;
- hasFunctionText=true;
- fileCount++;
- }else{
- scanLinkBuffer.append("\n").append(f.getName()).append(" (File off-line)<BR>");
- hasContent=true;
- }
- }
-
- if (xnatFile instanceof XnatResourcecatalog){
- File f = ((XnatResourcecatalog)xnatFile).getCatalogFile(rootPath);
- if (f.exists())
- {
- String fileID = this._files.addFile(f.getAbsolutePath(),f,FileTracker.KNOWN);
- scanLinkBuffer.append("<b>").append(f.getName()).append("</b><BR>");
- fileGrouping.add(fileID);
- hasContent=true;
- hasFunctionText=true;
- fileCount++;
- }else{
- scanLinkBuffer.append("\n").append(f.getName()).append(" (File off-line)<BR>");
- hasContent=true;
- }
- }
-
- String label = xnatFile.getLabel();
- if (label==null){
- label = xnatFile.getXnatAbstractresourceId().toString();
- }
- if(xnatFile instanceof XnatResourcecatalog){
- if (((XnatResourcecatalog)xnatFile).getTags_tag().size()>0){
- int counter =0;
- label +=" Tags: ";
- for(XnatAbstractresourceTagI tag : xnatFile.getTags_tag()){
- if (counter++>0)label+=", ";
- label+=tag.getTag();
- }
- }
- }
-
- String parsedScanID= xnatFile.getXnatAbstractresourceId().toString();
- if (hasContent){
- if(c++==0)
- sb.append("<b>ADDITIONAL RESOURCES</b></TD><TD>");
-
- sb.append("\n");
- if (hasFunctionText){
- sb.append("<INPUT type=\"checkbox\" id=\"uploads").append(parsedScanID).append("\" name=\"uploads").append(parsedScanID).append("\" CHECKED/> ");
- this.fileGroups.put("uploads" +parsedScanID,fileGrouping);
- }
- sb.append("<span class=\"trigger\" onClick=\"blocking('uploads").append(parsedScanID).append("');\">");
- sb.append("<img ID=\"IMGuploads").append(parsedScanID).append("\" src=\"").append(server).append("/images/plus.jpg\" border=0/> <b>").append(label).append("</b> ");
- sb.append("");
- sb.append("</span>");
- sb.append("<BR>\n<span class=\"branch\" ID=\"spanuploads").append(parsedScanID).append("\">");
- sb.append(scanLinkBuffer);
- sb.append("</span><BR>");
-
- if (hasFunctionText)
- {
- allFiles.append(" \n");
- allFiles.append(" change = \"uploads").append(parsedScanID).append("\";\n");
- allFiles.append(" node = document.getElementById(change);\n");
- allFiles.append(" node.checked=checkAll.checked;\n");
- }
- }else{
- if(c++==0)
- sb.append("<b>ADDITIONAL RESOURCES</b></TD><TD>");
- sb.append("<span class=\"trigger\"><b>"+ label + "</b> </span><br><span class=\"branch\" style=\"display: block;\">No files found for this upload.</span><BR>");
- }
- }
- sb.append("</TD></TR>");
-
- if (miscDir!=null){
- File misc = new File(miscDir);
- if(misc.exists()){
- sb.append("<TR><TD> </TD></TR>");
-
- sb.append(" <TR>");
- sb.append(" <TD VALIGN=\"top\" ALIGN=\"left\"><b>MISC FILES</b></TD><TD>");
- String dirListing = listDirectoryToHTML(misc,server,"",0).toString();
- sb.append(dirListing);
- sb.append("</TD></TR>");
- sb.append("</TABLE>");
-
- if (dirListing.length()>0){
- fileCount++;
- allFiles.append(" \n");
- allFiles.append(" f").append(misc.getName() + "0").append("CheckAll(checkAll);\n");
- allFiles.append(" change = \"dir_").append(misc.getName() + "/").append("\";\n");
- allFiles.append(" node = document.getElementById(change);\n");
- allFiles.append(" node.checked=checkAll.checked;\n");
- }
- }
- }
-
-
- allFiles.append(" }");
- allFiles.append(" </script>");
-
- sb.insert(0," </TH></TR>");
- sb.insert(0," <TD></TD><TH VALIGN=\"top\" ALIGN=\"left\">");
-
- if (fileCount>0)
- {
- sb.insert(0,"<input type=\"checkbox\" id=\"all_files\" name=\"all_files\" checked onclick=\"allFilesCheckAll(this);\"/><label for=\"all_files\"> Select All</label>");
- }
- sb.insert(0," <TR>");
- sb.insert(0,"<TABLE>");
- return allFiles.toString() + "<BR>" + sb.toString();
- }
-
- /**
- * @return Returns the fileGroups.
- */
- public Hashtable getFileGroups() {
- return fileGroups;
- }
-
- public StringBuffer listDirectoryToHTML(File dir,String server,String parents,int count)
- {
- StringBuffer sb = new StringBuffer();
- StringBuffer function = new StringBuffer();
-
- int fileCount=0;
-
- if (dir.exists())
- {
- int local_count=count;
- parents += dir.getName() + "/";
- function.append("<script type=\"text/javascript\" language=\"JavaScript1.3\">\n");
- function.append(" function f").append(dir.getName() + local_count).append("CheckAll(checkAll)\n");
- function.append(" {\n");
- function.append(" var change=null;\n");
- function.append(" var node=null;\n");
-
- sb.append("<INPUT type=\"checkbox\" id=\"dir_").append(parents).append("\" name=\"dir_").append(parents).append("\" ONCLICK=\"f").append(dir.getName()).append(local_count + "CheckAll(this)\" CHECKED/>");
- sb.append(" <span class=\"trigger\" onClick=\"blocking('").append(dir.getName() + local_count).append("');\">");
- sb.append("<img ID=\"IMG").append(dir.getName() + local_count).append("\" src=\"").append(server).append("/images/plus.jpg\" border=0/> <b>").append(dir.getName()).append("</b></span>");
- sb.append("<span class=\"branch\" ID=\"span").append(dir.getName() + local_count).append("\">");
- File[] children = dir.listFiles();
- for (int i=0;i<children.length;i++)
- {
- File child = children[i];
- if (child.isDirectory())
- {
- count++;
- StringBuffer functionTemp = new StringBuffer();
- functionTemp.append(" \n");
- functionTemp.append(" f").append(child.getName() + count).append("CheckAll(checkAll);\n");
- functionTemp.append(" change = \"dir_").append(parents + child.getName()+ "/").append("\";\n");
- functionTemp.append(" node = document.getElementById(change);\n");
- functionTemp.append(" node.checked=checkAll.checked;\n");
- StringBuffer temp =listDirectoryToHTML(child,server,parents,count);
- if (temp.length()>0){
- sb.append("\n").append(temp).append("<BR>");
- function.append(functionTemp);
- fileCount++;
- }
- }else{
- if (_files.indexOf(child)==-1)
- {
- if (!child.getName().equalsIgnoreCase("dcmtoxnat.log") && !child.getName().equalsIgnoreCase("dcmtoxnat.log.gz"))
- {
- String fileID = this._files.addFile(parents + child.getName(),child,FileTracker.MISC);
- function.append(" \n");
- function.append(" change = \"dir_file_").append(fileID).append("\";\n");
- function.append(" node = document.getElementById(change);\n");
- function.append(" node.checked=checkAll.checked;\n");
- sb.append("<INPUT type=\"checkbox\" id=\"dir_file_").append(fileID).append("\" name=\"dir_file_").append(fileID).append("\" CHECKED/> ").append(child.getName()).append("<BR>");
- fileCount++;
- }
- }
- }
- }
- function.append(" }");
- function.append(" </script>");
- sb.append("</span>");
-
- }
-
- if (fileCount>0){
- function.append(sb);
- return function;
- }else{
- return new StringBuffer();
- }
- }
-
- public ArrayList getAllFilePaths()
- {
- return this._files.getAbsolutePaths();
- }
-
- /**
- * @return Returns the _files.
- */
- public FileTracker getFileTracker() {
- return _files;
- }
-
-
- /**
- * @return Returns the lowerCaseSessionId.
- */
- public String getLowerCaseSessionId() {
- if (lowerCaseSessionId==null)
- lowerCaseSessionId = getId().toLowerCase();
- return lowerCaseSessionId;
- }
-
- XNATDirectory srbDIR = null;
- public XNATDirectory getSRBDirectory()
- {
- if (srbDIR==null)
- {
- String sessionDIR = deriveSessionDir();
-
- int index = sessionDIR.indexOf("/home/");
- sessionDIR= sessionDIR.substring(index);
-
- //LOAD ALL RAW IMAGES
- srbDIR = XNATSrbSearch.getFilteredFiles(sessionDIR,null);
- }
-
- return srbDIR;
- }
-
- public boolean hasSRBData(){
- String rootPath;
- try {
- rootPath = getArchiveRootPath();
- } catch (UnknownPrimaryProjectException e) {
- rootPath=null;
- }
- for(XnatImagescandataI scan : this.getSortedScans()){
- List scanFiles= scan.getFile();
- Iterator files = scanFiles.iterator();
- while (files.hasNext())
- {
- XnatAbstractresource xnatFile = (XnatAbstractresource) files.next();
- if (xnatFile instanceof org.nrg.xdat.om.XnatResource){
- XnatResource resource = (XnatResource)xnatFile;
- String uri =resource.getFullPath(rootPath);
- if (uri.startsWith("srb:"))
- return true;
- }else if(xnatFile instanceof org.nrg.xdat.om.XnatDicomseries){
- XnatDicomseries resource = (XnatDicomseries)xnatFile;
- String uri =resource.getFullPath(rootPath);
- if (uri.startsWith("srb:"))
- return true;
- }else if(xnatFile instanceof org.nrg.xdat.om.XnatResourceseries){
- XnatResourceseries resource = (XnatResourceseries)xnatFile;
- String uri =resource.getFullPath(rootPath);
- if (uri.startsWith("srb:"))
- return true;
- }
- }
- }
-
- return false;
- }
-
- private String raw_dir = null;
- public String deriveRawDir(){
- if (raw_dir==null)
- {
- String rootPath;
- try {
- rootPath = getArchiveRootPath();
- } catch (UnknownPrimaryProjectException e) {
- rootPath=null;
- }
- String last_dir = null;
- for(XnatImagescandataI scan : this.getSortedScans()){
- for (XnatAbstractresourceI xnatFile:scan.getFile())
- {
- if (xnatFile instanceof org.nrg.xdat.om.XnatResource){
- XnatResource resource = (XnatResource)xnatFile;
- String uri =resource.getFullPath(rootPath);
- if (last_dir==null){
- last_dir= uri;
- int index = last_dir.toUpperCase().indexOf("/RAW/");
- if (index!=-1){
- raw_dir = last_dir.substring(0,index+4);
- return raw_dir;
- }else{
- index = last_dir.toUpperCase().indexOf("/SCANS/");
- if (index!=-1){
- raw_dir = last_dir.substring(0,index+6);
- return raw_dir;
- }
- }
- }else{
-
- }
- }else if(xnatFile instanceof org.nrg.xdat.om.XnatDicomseries){
- XnatDicomseries resource = (XnatDicomseries)xnatFile;
- String uri =resource.getFullPath(rootPath);
- if (last_dir==null){
- last_dir= uri;
- int index = last_dir.toUpperCase().indexOf("/RAW/");
- if (index!=-1){
- raw_dir = last_dir.substring(0,index+4);
- return raw_dir;
- }else{
- index = last_dir.toUpperCase().indexOf("/SCANS/");
- if (index!=-1){
- raw_dir = last_dir.substring(0,index+6);
- return raw_dir;
- }
- }
- }else{
-
- }
- }else if(xnatFile instanceof org.nrg.xdat.om.XnatResourceseries){
- XnatResourceseries resource = (XnatResourceseries)xnatFile;
- String uri =resource.getFullPath(rootPath);
- if (last_dir==null){
- last_dir= uri;
- int index = last_dir.toUpperCase().indexOf("/RAW/");
- if (index!=-1){
- raw_dir = last_dir.substring(0,index+4);
- return raw_dir;
- }else{
- index = last_dir.toUpperCase().indexOf("/SCANS/");
- if (index!=-1){
- raw_dir = last_dir.substring(0,index+6);
- return raw_dir;
- }
- }
- }else{
-
- }
- }
- }
- }
-
- if (raw_dir ==null)
- {
- raw_dir = deriveSessionDir();
- }
- }
-
-
- return raw_dir;
- }
-
- private String session_dir=null;
- public String deriveSessionDir(){
- if (session_dir==null)
- {
- String rootPath;
- try {
- rootPath = getArchiveRootPath();
- } catch (UnknownPrimaryProjectException e) {
- rootPath=null;
- }
- for(XnatImagescandataI scan : this.getSortedScans()){
- logger.debug("CHECKING SCAN: "+scan.getId());
- List scanFiles= scan.getFile();
- Iterator files = scanFiles.iterator();
- while (files.hasNext())
- {
- XnatAbstractresource xnatFile = (XnatAbstractresource) files.next();
- if (xnatFile instanceof org.nrg.xdat.om.XnatResource){
- XnatResource resource = (XnatResource)xnatFile;
- String uri =resource.getFullPath(rootPath);
- logger.debug("CHECKING RESOURCE: " + uri);
- String last_dir = null;
- if (last_dir==null){
- last_dir= uri;
- String UPPER_dir=last_dir.toUpperCase();
- int index = UPPER_dir.indexOf("/" + getArchiveDirectoryName().toUpperCase() + "/");
- if (index!=-1){
- session_dir = last_dir.substring(0,index+(2+getArchiveDirectoryName().length()));
-
- logger.debug("MATCHED BY getArchiveDirectoryName():" + session_dir);
- return session_dir;
- }else{
- index = UPPER_dir.indexOf(getArchiveDirectoryName().toUpperCase());
- if (index!=-1){
- int unixSepIndex = last_dir.indexOf("/", index);
- int winSepIndex = last_dir.indexOf("\\", index);
- if (unixSepIndex ==-1 && winSepIndex==-1)
- {
- session_dir= last_dir + File.separator;
- }else if(unixSepIndex ==-1){
- session_dir = last_dir.substring(0,winSepIndex+1);
- }else if(winSepIndex ==-1){
- session_dir = last_dir.substring(0,unixSepIndex+1);
- }else if(winSepIndex < unixSepIndex){
- session_dir = last_dir.substring(0,winSepIndex+1);
- }else if(winSepIndex > unixSepIndex){
- session_dir = last_dir.substring(0,unixSepIndex+1);
- }
- }else{
- logger.debug("MOT MATCHED");
- }
- }
- }
- }else if(xnatFile instanceof org.nrg.xdat.om.XnatDicomseries){
- XnatDicomseries resource = (XnatDicomseries)xnatFile;
- String uri =resource.getFullPath(rootPath);
- String last_dir = null;
- if (last_dir==null){
- last_dir= uri;
- String UPPER_dir=last_dir.toUpperCase();
- int index = UPPER_dir.indexOf("/" + getArchiveDirectoryName().toUpperCase() + "/");
- if (index!=-1){
- session_dir = last_dir.substring(0,index+(2+getArchiveDirectoryName().length()));
- return session_dir;
- }else{
- index = UPPER_dir.indexOf(getArchiveDirectoryName().toUpperCase());
- if (index!=-1){
- int unixSepIndex = last_dir.indexOf("/", index);
- int winSepIndex = last_dir.indexOf("\\", index);
- if (unixSepIndex ==-1 && winSepIndex==-1)
- {
- session_dir= last_dir + File.separator;
- }else if(unixSepIndex ==-1){
- session_dir = last_dir.substring(0,winSepIndex+1);
- }else if(winSepIndex ==-1){
- session_dir = last_dir.substring(0,unixSepIndex+1);
- }else if(winSepIndex < unixSepIndex){
- session_dir = last_dir.substring(0,winSepIndex+1);
- }else if(winSepIndex > unixSepIndex){
- session_dir = last_dir.substring(0,unixSepIndex+1);
- }
- }
- }
- }
- }else if(xnatFile instanceof org.nrg.xdat.om.XnatResourceseries){
- XnatResourceseries resource = (XnatResourceseries)xnatFile;
- String uri =resource.getFullPath(rootPath);
- String last_dir = null;
- if (last_dir==null){
- last_dir= uri;
- String UPPER_dir=last_dir.toUpperCase();
- int index = UPPER_dir.indexOf("/" + getArchiveDirectoryName().toUpperCase() + "/");
- if (index!=-1){
- session_dir = last_dir.substring(0,index+(2+getArchiveDirectoryName().length()));
- return session_dir;
- }else{
- index = UPPER_dir.indexOf(getArchiveDirectoryName().toUpperCase());
- if (index!=-1){
- int unixSepIndex = last_dir.indexOf("/", index);
- int winSepIndex = last_dir.indexOf("\\", index);
- if (unixSepIndex ==-1 && winSepIndex==-1)
- {
- session_dir= last_dir + File.separator;
- }else if(unixSepIndex ==-1){
- session_dir = last_dir.substring(0,winSepIndex+1);
- }else if(winSepIndex ==-1){
- session_dir = last_dir.substring(0,unixSepIndex+1);
- }else if(winSepIndex < unixSepIndex){
- session_dir = last_dir.substring(0,winSepIndex+1);
- }else if(winSepIndex > unixSepIndex){
- session_dir = last_dir.substring(0,unixSepIndex+1);
- }
- }
- }
- }
- }
- }
- }
- }
-
- return session_dir;
- }
-
-
-
- /**
- * @param c The condition.
- * @return ArrayList of org.nrg.xdat.om.XnatImagescandataI
- */
- public List<XnatImagescandataI> getScansByCondition(String c) {
- List _return = new ArrayList();
- for(XnatImagescandataI scan : this.getSortedScans()){
- String condition = scan.getCondition();
- if (condition ==null)
- {
- if (c==null)
- {
- _return.add(scan);
- }
- }else{
- if (condition.equalsIgnoreCase(c)) {
- _return.add(scan);
- }
- }
- }
- return _return;
- }
-
-
- public List<XnatAbstractresourceI> getAllResources(){
- List<XnatAbstractresourceI> resources = new ArrayList<XnatAbstractresourceI>();
- for(XnatImagescandataI scan : this.getSortedScans()){
- Iterator files = scan.getFile().iterator();
- while (files.hasNext()){
- XnatAbstractresource file = (XnatAbstractresource)files.next();
- resources.add(file);
- }
- }
-
- Iterator recons = getReconstructions_reconstructedimage().iterator();
- while(recons.hasNext())
- {
- XnatReconstructedimagedata scan = (XnatReconstructedimagedata)recons.next();
- Iterator outfiles = scan.getOut_file().iterator();
- while (outfiles.hasNext()){
- XnatAbstractresource file = (XnatAbstractresource)outfiles.next();
- resources.add(file);
- }
-
- Iterator infiles = scan.getIn_file().iterator();
- while (infiles.hasNext()){
- XnatAbstractresource file = (XnatAbstractresource)infiles.next();
- resources.add(file);
- }
- }
-
- for(XnatImageassessordataI assess : this.getAssessors_assessor()){
- Iterator outfiles = assess.getOut_file().iterator();
- while (outfiles.hasNext()){
- XnatAbstractresource file = (XnatAbstractresource)outfiles.next();
- resources.add(file);
- }
-
- Iterator infiles = assess.getIn_file().iterator();
- while (infiles.hasNext()){
- XnatAbstractresource file = (XnatAbstractresource)infiles.next();
- resources.add(file);
- }
- }
-
- Iterator misc = getResources_resource().iterator();
- while(misc.hasNext())
- {
- XnatAbstractresource file = (XnatAbstractresource)misc.next();
- resources.add(file);
- }
- return resources;
- }
-
- /**
- * Appends this path to the enclosed URI or path variables.
- * @param session_path The path to the session.
- */
- public void prependPathsWith(String session_path){
- Iterator files= getAllResources().iterator();
- while(files.hasNext())
- {
- XnatAbstractresource file = (XnatAbstractresource)files.next();
- file.prependPathsWith(session_path);
- }
- }
-
-
-
-
- /**
- * Relatives this path from the first occurrence of the indexOf string.
- * @param indexOf
- */
- public void relativePaths(String indexOf){
- Iterator files= getAllResources().iterator();
- while(files.hasNext())
- {
- XnatAbstractresource file = (XnatAbstractresource)files.next();
- file.relativizePaths(indexOf,false);
- }
- }
-
- public void preLoadFiles(){
- if(this.hasSRBData()){
- this.loadSRBFiles();
- }else{
- this.loadLocalFiles();
- }
- }
-
- public CatalogSet getCatalogBean(String url){
- XnatProjectdata project = this.getPrimaryProject(false);
-
- this.preLoadFiles();
-
- Hashtable<String,Object> fileMap = new Hashtable<String,Object>();
- CatCatalogBean catalog = new CatCatalogBean();
-
- catalog.setId(this.getId());
-
- if (hasSRBData()){
-
- Hashtable fileGroups = getFileGroups();
- for (Enumeration e = fileGroups.keys(); e.hasMoreElements();) {
- String key = (String)e.nextElement();
-
- ArrayList groupFiles = (ArrayList)fileGroups.get(key);
- int counter=0;
- for(Iterator iter=groupFiles.iterator();iter.hasNext();){
- Object o = iter.next();
- if (o instanceof String){
-
- String id = (String)o;
-
- int index = getFileTracker().getIDIndex(id);
- File f = getFileTracker().getFile(index);
- String identifier = "/file/" + id;
- CatEntryBean entry = new CatEntryBean();
- entry.setUri(url + identifier);
-
- fileMap.put(identifier, f);
-
- String path = f.getAbsolutePath();
- if (path.indexOf(File.separator + project.getId())!=-1){
- path = path.substring(path.indexOf(File.separator + project.getId()) + 1);
- }else{
- if (path.indexOf(File.separator + getArchiveDirectoryName())!=-1){
- path = path.substring(path.indexOf(File.separator + getArchiveDirectoryName()) + 1);
- }
- }
-
- entry.setCachepath(path);
- entry.setName(f.getName());
-
- CatEntryMetafieldBean meta = new CatEntryMetafieldBean();
- meta.setMetafield(path);
- meta.setName("RELATIVE_PATH");
- entry.addMetafields_metafield(meta);
-
-
- meta = new CatEntryMetafieldBean();
- meta.setMetafield(key);
- meta.setName("GROUP");
- entry.addMetafields_metafield(meta);
-
- meta = new CatEntryMetafieldBean();
- meta.setMetafield(new Long(f.length()).toString());
- meta.setName("SIZE");
- entry.addMetafields_metafield(meta);
-
- catalog.addEntries_entry(entry);
- }else{
- XNATDirectory dir = (XNATDirectory)o;
-
-
- for (Map.Entry<String,GeneralFile> entryF: dir.getRelativeFiles().entrySet()) {
-
- String relative = entryF.getKey();
-
- if(relative.indexOf(getArchiveDirectoryName())!=-1)
- {
- relative = relative.substring(relative.indexOf(getArchiveDirectoryName()));
- }
-
- String identifier = "/file/" + counter++;
- CatEntryBean entry = new CatEntryBean();
- entry.setUri(url + identifier);
-
- fileMap.put(identifier, entryF.getValue());
-
- entry.setCachepath(relative);
- entry.setName(entryF.getValue().getName());
-
- CatEntryMetafieldBean meta = new CatEntryMetafieldBean();
- meta.setMetafield(relative);
- meta.setName("RELATIVE_PATH");
- entry.addMetafields_metafield(meta);
-
- meta = new CatEntryMetafieldBean();
- meta.setMetafield(key);
- meta.setName("GROUP");
- entry.addMetafields_metafield(meta);
-
- meta = new CatEntryMetafieldBean();
- meta.setMetafield(new Long(entryF.getValue().length()).toString());
- meta.setName("SIZE");
- entry.addMetafields_metafield(meta);
-
- catalog.addEntries_entry(entry);
- }
- }
- }
- }
- }else{
- FileTracker ft =getFileTracker();
- for(String id: ft.getIds()){
- int index = getFileTracker().getIDIndex(id);
- File f = getFileTracker().getFile(index);
- String identifier = "/file/" + id;
- CatEntryBean entry = new CatEntryBean();
- entry.setUri(url + identifier);
-
- fileMap.put(identifier, f);
-
- String path = f.getAbsolutePath();
- if (path.indexOf(File.separator + project.getId())!=-1){
- path = path.substring(path.indexOf(File.separator + project.getId()) + 1);
- }else{
- if (path.indexOf(File.separator + getArchiveDirectoryName())!=-1){
- path = path.substring(path.indexOf(File.separator + getArchiveDirectoryName()) + 1);
- }
- }
-
- entry.setCachepath(path);
- entry.setName(f.getName());
-
- CatEntryMetafieldBean meta = new CatEntryMetafieldBean();
- meta.setMetafield(path);
- meta.setName("RELATIVE_PATH");
- entry.addMetafields_metafield(meta);
-
- meta = new CatEntryMetafieldBean();
- meta.setMetafield(new Long(f.length()).toString());
- meta.setName("SIZE");
- entry.addMetafields_metafield(meta);
-
- catalog.addEntries_entry(entry);
- }
- }
-
- return new CatalogSet(catalog,fileMap);
- }
-
-
-
- public void fixScanTypes(){
- Map<String,ScanTypeMappingI> mappers = new Hashtable<String,ScanTypeMappingI>();
-
- String project=this.getProject();
-
- List al = this.getScans_scan();
- if (al != null) {
- for (int i = 0; i < al.size(); i++) {
- XnatImagescandata scan = (XnatImagescandata) al.get(i);
-
- if(!mappers.containsKey(scan.getXSIType())){
- mappers.put(scan.getXSIType(), scan.getScanTypeMapping(project, this.getDBName()));
- }
-
-
- mappers.get(scan.getXSIType()).setType(scan);
-
- if(scan.getFile().size()>0){
- XnatAbstractresourceI abstRes=scan.getFile().get(0);
- if(abstRes instanceof XnatResource){
- if(((XnatResource)abstRes).getContent()==null || ((XnatResource)abstRes).getContent().equals("")){
- ((XnatResource)abstRes).setContent("RAW");
- }
- if(abstRes.getLabel()!=null && ((XnatResource)abstRes).getFormat()==null){
- ((XnatResource)abstRes).setFormat(abstRes.getLabel());
- }
- }
- }
- }
- }
- }
-
- public void defaultQuality(String s){
- for(XnatImagescandataI scan:this.getScans_scan()){
- if(scan.getQuality()==null)
- ((XnatImagescandata)scan).setQuality(s);
- }
- }
-
- public String getDefaultIdentifier(){
- return null;
- }
-
- /**
- * Copies assigned field values from the indicated image session object to
- * this one, potentially overwriting existing values.
- * @param other object from which assigned values will be copied
- * @throws Exception from XnatExperimentdata.setProjects_project()
- */
- public void copyValuesFrom(final XnatImagesessiondata other) throws Exception {
-
- if (null != other.getSessionType()){
- this.setSessionType(other.getSessionType());
- }
-
- if (null != other.getScanner()){
- this.setScanner(other.getScanner());
- }
-
- if (null != other.getOperator()){
- this.setOperator(other.getOperator());
- }
-
- if (null != other.getDate()){
- this.setDate(other.getDate());
- }
-
- if (null != other.getAcquisitionSite()){
- this.setAcquisitionSite(other.getAcquisitionSite());
- }
-
- if (null != other.getNote()){
- this.setNote(other.getNote());
- }
-
- if (null != other.getInvestigatorFK()){
- this.setInvestigatorFK(other.getInvestigatorFK());
- }
-
- if (null != other.getSubjectId()){
- this.setSubjectId(other.getSubjectId());
- }
-
- while (this.getSharing_share().size()>0){
- this.removeSharing_share(0);
- }
-
- for (final XnatExperimentdataShareI project : other.getSharing_share()) {
- this.setSharing_share((XnatExperimentdataShare)project);
- }
-
- if (null != other.getProject()){
- this.setProject(other.getProject());
- }
-
- if (null != other.getLabel()){
- this.setLabel(other.getLabel());
- }else{
- if(this.getLabel()!=null){
- this.setLabel("NULL");
- }
- }
-
- for(final XnatExperimentdataFieldI otherField : other.getFields_field()){
- final XnatExperimentdataField field=new XnatExperimentdataField(this.getUser());
- if (otherField.getName() != null){
- field.setName(otherField.getName());
- field.setField(otherField.getField());
- this.setFields_field(field);
- }
- }
-
- int scancounter = 0;
- for (final XnatImagescandataI scan : this.getScans_scan()){
- final XnatImagescandata otherScan = other.getScanById(scan.getId());
- if (null != otherScan){
- if (null != otherScan.getType())
- ((XnatImagescandata)scan).setType(otherScan.getType());
- if (null != otherScan.getQuality())
- ((XnatImagescandata)scan).setQuality(otherScan.getQuality());
- if (null != otherScan.getNote())
- ((XnatImagescandata)scan).setNote(otherScan.getNote());
- }
- scancounter++;
- }
- }
-//
-// /**
-// * Generates assessor id to be used for xnat_imageAssessorData.
-// * @return
-// * @throws SQLException
-// */
-// public String createNewAssessorId(String type) throws SQLException{
-// String newID= "";
-// String prefix= "";
-// int i = this.getAssessors(type).size()+1;
-// prefix +=this.getId();
-//
-// String code =ElementSecurity.GetCode(type);
-// if(code!=null && !code.equals(""))
-// prefix+="_" + code;
-//
-// newID=prefix + "_"+ i;
-// String query = "SELECT count(ID) AS id_count FROM xnat_experimentdata WHERE ID='";
-//
-// String login = null;
-// if (this.getUser()!=null){
-// login=this.getUser().getUsername();
-// }
-// try {
-// Long idCOUNT= (Long)PoolDBUtils.ReturnStatisticQuery(query + newID + "';", "id_count", this.getDBName(), login);
-// while (idCOUNT > 0){
-// i++;
-// newID=prefix + "_"+ i;
-// idCOUNT= (Long)PoolDBUtils.ReturnStatisticQuery(query + newID + "';", "id_count", this.getDBName(), login);
-// }
-// } catch (Exception e) {
-// logger.error("",e);
-// }
-//
-// return newID;
-// }
-
-
-// /**
-// * Generates assessor id to be used for xnat_imageAssessorData.
-// * @return
-// * @throws SQLException
-// */
-// public String createNewAssessorId(String visitNum) throws SQLException{
-// String newID= "";
-// int i = this.getAssessorCount()+1;
-// newID=this.getId() + "_"+ visitNum + "_"+ i;
-// String query = "SELECT count(ID) AS id_count FROM xnat_experimentdata WHERE ID='";
-//
-// String login = null;
-// if (this.getUser()!=null){
-// login=this.getUser().getUsername();
-// }
-// try {
-// Long idCOUNT= (Long)PoolDBUtils.ReturnStatisticQuery(query + newID + "';", "id_count", this.getDBName(), this.getUser().getUsername());
-// while (idCOUNT > 0){
-// i++;
-// newID=this.getId() + "_"+ visitNum + "_"+ i;
-// idCOUNT= (Long)PoolDBUtils.ReturnStatisticQuery(query + newID + "';", "id_count", this.getDBName(), this.getUser().getUsername());
-// }
-// } catch (Exception e) {
-// logger.error("",e);
-// }
-//
-// return newID;
-// }
-
- public boolean validateSubjectId(){
- String subjectid = this.getSubjectId();
- if (subjectid!=null){
- subjectid=StringUtils.RemoveChar(subjectid, '\'');
- String query = "SELECT ID FROM xnat_subjectdata WHERE ID='";
- String login =null;
- if (this.getUser()!=null){
- login = this.getUser().getUsername();
- }
-
- try {
- final String idCOUNT= (String)PoolDBUtils.ReturnStatisticQuery(query + subjectid + "';", "id", this.getDBName(), login);
- if (idCOUNT!=null){
- return true;
- }
-
- final String project = this.getProject();
- if (project!=null){
- //CHECK by primary label
- query = "SELECT id FROM xnat_subjectdata WHERE label='" +
- subjectid +"' AND project='" + project + "';";
- String new_subjectid= (String)PoolDBUtils.ReturnStatisticQuery(query, "id", this.getDBName(), login);
- if (new_subjectid!=null){
- this.setSubjectId(new_subjectid);
- return true;
- }
-
- //CHECK by secondary labels
- query = "SELECT subject_id FROM xnat_projectParticipant WHERE label='" +
- subjectid +"' AND project='" + project + "';";
- new_subjectid= (String)PoolDBUtils.ReturnStatisticQuery(query, "subject_id", this.getDBName(), login);
- if (new_subjectid!=null){
- this.setSubjectId(new_subjectid);
- return true;
- }
- }
- } catch (SQLException e) {
- logger.error("",e);
- } catch (Exception e) {
- logger.error("",e);
- }
- }
-
- return false;
- }
-
- public List<String> getSessionReadableScanStats() {
- return getSessionReadableScanStats(false);
- }
-
- public String getFormattedSessionReadableScanStats(){
- List<String> stats = this.getSessionReadableScanStats();
- if (stats.size() == 1) {
- return stats.get(0);
- } else {
- return BaseXnatImagescandata.getListAsTipText(stats);
- }
- }
-
- public static List<String> getPrearchiveSessionReadableScanStats(Collection <XnatImagescandataI> scans){
- List<String> stats = new ArrayList<String>();
- int count = 0;
- long size = 0;
- for (XnatImagescandataI scan : scans){
- if(scan instanceof BaseXnatImagescandata){
- Map<String,Number> prearcStats = ((BaseXnatImagescandata)scan).getPrearchiveFileStats();
- count += prearcStats.get("count").intValue();
- size += prearcStats.get("size").longValue();
- }else{
- logger.error("Unable to retrieve file counts.", new Exception("Prearchive scan is not an instance of BaseXnatImagescandata. Skipping..."));
- }
- }
- stats.add(CatalogUtils.formatFileStats("TOTAL", count, size));
- return stats;
- }
-
-
- public List<String> getSessionReadableScanStats(boolean useLabel) {
- List<String> stats = new ArrayList<String>();
- // Use the TreeMap so that the keys are sorted
- Map<String, List<Long>> accumulator = new TreeMap<String, List<Long>>();
-
- if(this.getId() == null){
- // If the session is in the prearchive
- stats = this.getPrearchiveSessionReadableScanStats(this.getSortedScans());
- }else{
- // The session is in the archive
- int count = 0;
- long size = 0;
- for (XnatImagescandataI scan : this.getSortedScans()){
- for (XnatAbstractresourceI resource : scan.getFile()) {
- String fileLabel = resource.getLabel();
- if (fileLabel != null && fileLabel.equals("SNAPSHOTS")) {
- continue;
- }
- if (fileLabel == null || fileLabel.trim().equals("")) {
- fileLabel = "Unknown";
- }
-
- Integer fileCount = resource.getFileCount();
- Object rawFileSize = resource.getFileSize();
-
- List<Long> data;
- if (accumulator.containsKey(fileLabel)) {
- data = accumulator.get(fileLabel);
- } else {
- data = new ArrayList<Long>() {{ add(0L); add(0L); }};
- accumulator.put(fileLabel, data);
- }
-
- if (fileCount != null) {
- count += fileCount;
- Long aggregate = data.get(0);
- data.set(0, aggregate + fileCount);
- }
- if (rawFileSize != null) {
- long fileSize;
- if (rawFileSize instanceof Integer) {
- fileSize = (Integer) rawFileSize;
- } else if (rawFileSize instanceof Long) {
- fileSize = (Long) rawFileSize;
- } else {
- fileSize = Long.parseLong(rawFileSize.toString());
- }
- size += fileSize;
- data.set(1, data.get(1) + fileSize);
- }
- }
- }
- stats.add(CatalogUtils.formatFileStats(useLabel ? getLabel() : "TOTAL", count, size));
- }
- if (accumulator.containsKey("DICOM")) {
- List<Long> values = accumulator.get("DICOM");
- stats.add(CatalogUtils.formatFileStats("DICOM", values.get(0), values.get(1)));
- accumulator.remove("DICOM");
- }
- for (String modality : accumulator.keySet()) {
- List<Long> values = accumulator.get(modality);
- stats.add(CatalogUtils.formatFileStats(modality, values.get(0), values.get(1)));
- }
- return stats;
- }
-
- public void correctArchivePaths() throws InvalidArchiveStructure, UnknownPrimaryProjectException{
- this.correctArchivePaths(true);
- }
-
-
- public void correctArchivePaths(boolean relativePaths)
- throws InvalidArchiveStructure, UnknownPrimaryProjectException {
- final String session_path = getCurrentSessionFolder(false);
- for (final XnatImagescandataI scan : scans) {
- final List<XnatAbstractresource> files=scan.getFile();
- for (final XnatAbstractresource file : files) {
- file.prependPathsWith(session_path);
-
- try {
- if (files.size()==1 || (file.getContent()!=null && file.getContent().endsWith("_RAW")))
- file.setProperty("content", "RAW");
- } catch (Throwable e) {
- logger.error("",e);
-
- }
- }
- }
- }
-
- public Map<String,String> getCustomScanFields(String project){
- return Maps.newLinkedHashMap(CUSTOM_SCAN_FIELDS);
- }
-
- public void moveToProject(final XnatProjectdata newProject, final String label , final UserI user,final EventMetaI c, final List<String> assessorsToMove) throws Exception{
- if(!this.getProject().equals(newProject.getId()))
- {
- if (!MoverMaker.check(this, user)) {
- throw new InvalidPermissionException(this.getXSIType());
- }
-
- final File rootBackup=MoverMaker.createPrimaryBackupDirectory("move",this.getProject(),getId());
- final String existingRootPath=this.getProjectData().getRootArchivePath();
- //FIXME: Is this correct?
- final String newLabel = label == null? (this.getLabel() == null ? this.getId() : this.getLabel()) : label;
- final File newSessionDir = new File(new File(newProject.getRootArchivePath(),newProject.getCurrentArc()),newLabel);
- final String current_label=this.getLabel() == null ? this.getId() : this.getLabel();
- final BaseXnatImagesessiondata base = this;
-
- Map<String,File> fs = new HashMap<String,File>();
- fs.put("src", this.getSessionDir());
- CopyOp scanOp = new CopyOp(new OperationI<Map<String,File>>(){
- public void run(Map<String,File> fs) throws Exception {
- new ProjectAnonymizer(base,newProject.getId(), base.getArchivePath(existingRootPath)).call();
- for(XnatImagescandataI scan: getScans_scan()){
- for(XnatAbstractresourceI abstRes: scan.getFile()){
- MoverMaker.Mover m = MoverMaker.moveResource(abstRes, current_label, base, newSessionDir, existingRootPath, user,c);
- m.setResource((XnatAbstractresource)abstRes);
- m.call();
- }
- }
-
- for(XnatReconstructedimagedataI recon:base.getReconstructions_reconstructedimage()){
- for(XnatAbstractresourceI abstRes: recon.getOut_file()){
- MoverMaker.Mover m = MoverMaker.moveResource(abstRes, current_label, base, newSessionDir, existingRootPath, user,c);
- m.setResource((XnatAbstractresource)abstRes);
- m.call();
- }
- }
-
- for(XnatImageassessordataI assessor:base.getAssessors_assessor()){
- // assessors need to be updated
- if (assessorsToMove != null && assessorsToMove.contains(assessor.getId())) {
- EventDetails event = EventUtils.newEventInstance(EventUtils.CATEGORY.DATA, EventUtils.TYPE.WEB_SERVICE, "Moved assessor to new project.");
- XnatImageassessordata.ChangePrimaryProject(user, (XnatImageassessordata)assessor, newProject, null, event, null);
- }
-
- for(XnatAbstractresourceI abstRes: assessor.getOut_file()){
- MoverMaker.Mover m = MoverMaker.moveResource(abstRes, current_label, base, newSessionDir, existingRootPath, user,c);
- m.setResource((XnatAbstractresource)abstRes);
- m.call();
- }
- for(XnatAbstractresourceI abstRes: assessor.getResources_resource()){
- MoverMaker.Mover m = MoverMaker.moveResource(abstRes, current_label, base, newSessionDir, existingRootPath, user,c);
- m.setResource((XnatAbstractresource)abstRes);
- m.call();
- }
- }
- BaseXnatImagesessiondata.super.moveToProject(newProject, newLabel, user,c,assessorsToMove);
- }
- }, new File(rootBackup, "src_backup"), fs);
-
- try {
- Run.runTransaction(scanOp);
- }
- catch (TransactionException e) {
- throw new Exception(e);
- }
- catch (RollbackException e) {
- throw new Exception(e);
- }
- }
- }
-
- public ArrayList getCatalogSummary() throws Exception{
- String query="SELECT * FROM (SELECT xnat_abstractresource_id,label,element_name, 'resources'::TEXT AS category, NULL::TEXT AS cat_id"+
- " FROM xnat_experimentdata_resource res_map"+
- " JOIN xnat_abstractresource abst ON res_map.xnat_abstractresource_xnat_abstractresource_id=abst.xnat_abstractresource_id" +
- " JOIN xdat_meta_element xme ON abst.extension=xme.xdat_meta_element_id"+
- " WHERE res_map.xnat_experimentdata_id='"+this.getId() + "'"+
- " UNION"+
- " SELECT xnat_abstractresource_id,label,element_name, 'scans'::TEXT,isd.id"+
- " FROM xnat_imagescanData isd "+
- " JOIN xnat_abstractresource abst ON isd.xnat_imagescandata_id=abst.xnat_imagescandata_xnat_imagescandata_id"+
- " JOIN xdat_meta_element xme ON abst.extension=xme.xdat_meta_element_id"+
- " WHERE isd.image_session_id='"+this.getId() + "'"+
- " UNION"+
- " SELECT xnat_abstractresource_id,label,element_name, 'reconstructions'::TEXT,recon.id"+
- " FROM xnat_reconstructedimagedata recon"+
- " JOIN recon_out_resource map ON recon.xnat_reconstructedimagedata_id=map.xnat_reconstructedimagedata_xnat_reconstructedimagedata_id"+
- " JOIN xnat_abstractresource abst ON map.xnat_abstractresource_xnat_abstractresource_id=abst.xnat_abstractresource_id"+
- " JOIN xdat_meta_element xme ON abst.extension=xme.xdat_meta_element_id"+
- " WHERE image_session_id='"+this.getId() + "'"+
- " UNION"+
- " SELECT xnat_abstractresource_id,label,element_name, 'assessments'::TEXT,iad.id"+
- " FROM xnat_imageAssessorData iad"+
- " JOIN img_assessor_out_resource map ON iad.id=map.xnat_imageassessordata_id"+
- " JOIN xnat_abstractresource abst ON map.xnat_abstractresource_xnat_abstractresource_id=abst.xnat_abstractresource_id"+
- " JOIN xdat_meta_element xme ON abst.extension=xme.xdat_meta_element_id"+
- " WHERE imagesession_id='"+this.getId() + "'"+
- " UNION"+
- " SELECT xnat_abstractresource_id,label,element_name, 'assessments'::TEXT,iad.id"+
- " FROM xnat_imageAssessorData iad"+
- " JOIN xnat_experimentdata_resource map ON iad.id=map.xnat_experimentdata_id"+
- " JOIN xnat_abstractresource abst ON map.xnat_abstractresource_xnat_abstractresource_id=abst.xnat_abstractresource_id" +
- " JOIN xdat_meta_element xme ON abst.extension=xme.xdat_meta_element_id"+
- " WHERE imagesession_id='"+this.getId() + "') all_resources";
-
- XFTTable t = XFTTable.Execute(query, this.getDBName(), "system");
-
- return t.rowHashs();
- }
-
-
-
- public String canDelete(XnatProjectdata proj, UserI user){
-
- BaseXnatImagesessiondata expt=this;
- if(this.getItem().getUser()!=null){
- expt=new XnatImagesessiondata(this.getCurrentDBVersion(true));
- }
- if(!expt.hasProject(proj.getId())){
- return null;
- }else {
-
- try {
- SecurityValues values = new SecurityValues();
- values.put(this.getXSIType() + "/project", proj.getId());
- SchemaElement se= SchemaElement.GetElement(this.getXSIType());
-
- if (!Permissions.canDelete(user,se,values))
- {
- return "User cannot delete experiments for project " + proj.getId();
- }
- } catch (Exception e1) {
- return "Unable to delete subject.";
- }
-
- for(XnatImageassessordataI sad: expt.getAssessors_assessor()){
- String msg=((XnatImageassessordata)sad).canDelete(proj,user);
- if(msg!=null){
- return msg;
- }
- }
- }
- return null;
- }
-
-
-
- public String delete(XnatProjectdata proj, UserI user, boolean removeFiles,EventMetaI c){
- BaseXnatImagesessiondata expt=this;
- if(this.getItem().getUser()!=null){
- expt=new XnatImagesessiondata(this.getCurrentDBVersion(true));
- }
-
- String msg=expt.canDelete(proj,user);
-
- if(msg!=null){
- logger.error(msg);
- return msg;
- }
-
- if(!expt.getProject().equals(proj.getId())){
- try {
- SecurityValues values = new SecurityValues();
- values.put(this.getXSIType() + "/project", proj.getId());
-
- if (!Permissions.canDelete(user,expt) && !Permissions.canDelete(user,this.getSchemaElement(),values))
- {
- return "User cannot delete experiments for project " + proj.getId();
- }
-
-
- //unshare children before unsharing parent
- final List<XnatImageassessordata> expts = (expt).getAssessors_assessor();
- for (XnatImageassessordataI exptI : expts){
- final XnatImageassessordata assess = (XnatImageassessordata)exptI;
- if(assess.getProject().equals(proj.getId())){
- return "This operation would delete an experiment (rather than un-share). Please move experiment ("+expt.getId()+") to another project or manually delete.";
-
- }
- msg= assess.delete(proj,user,false,c);
- if(msg!=null){
- return msg;
- }
- }
-
- int index = 0;
- int match = -1;
- for(XnatExperimentdataShareI pp : expt.getSharing_share()){
- if(pp.getProject().equals(proj.getId())){
- SaveItemHelper.authorizedRemoveChild(expt.getItem(), "xnat:experimentData/sharing/share", ((XnatExperimentdataShare)pp).getItem(), user,c);
- match=index;
- break;
- }
- index++;
- }
-
- if(match==-1)return null;
-
- this.removeSharing_share(match);
-
- return null;
- } catch (SQLException e) {
- logger.error("",e);
- return e.getMessage();
- } catch (Exception e) {
- logger.error("",e);
- return e.getMessage();
- }
- }else{
-
- if(XDAT.getBoolSiteConfigurationProperty("security.prevent-data-deletion", false)){
- return "User account cannot delete experiments";
- }
-
- try {
-
- if(!Permissions.canDelete(user,this)){
- return "User account doesn't have permission to delete this experiment.";
- }
-
- if(removeFiles){
- this.deleteFiles(user,c);
- }
-
- final List<XnatImageassessordata> expts = expt.getAssessors_assessor();
- for (XnatImageassessordata iad : expts){
- msg=iad.delete(proj,user,removeFiles,c);
- if(msg!=null)return msg;
- }
-
- SaveItemHelper.authorizedDelete(expt.getItem().getCurrentDBVersion(), user,c);
-
- Users.clearCache(user);
- MaterializedView.deleteByUser(user);
- } catch (SQLException e) {
- logger.error("",e);
- return e.getMessage();
- } catch (Exception e) {
- logger.error("",e);
- return e.getMessage();
- }
- }
- return null;
- }
-
- public void deleteFiles(UserI user, EventMetaI ci) throws Exception{
- for(XnatAbstractresourceI abstRes:this.getResources_resource()){
- ((XnatAbstractresource)abstRes).deleteWithBackup(ArcSpecManager.GetInstance().getArchivePathForProject(this.getProject()), user,ci);
- }
-
- String rootPath=ArcSpecManager.GetInstance().getArchivePathForProject(this.getProject());
-
- for(final XnatImagescandataI scan: this.getScans_scan()){
- for(XnatAbstractresourceI abstRes:scan.getFile()){
- ((XnatAbstractresource)abstRes).deleteWithBackup(rootPath, user, ci);
- }
- }
-
- for(XnatReconstructedimagedataI scan: this.getReconstructions_reconstructedimage()){
- for(XnatAbstractresourceI abstRes:scan.getOut_file()){
- ((XnatAbstractresource)abstRes).deleteWithBackup(rootPath, user, ci);
- }
- }
-
- for(XnatImageassessordataI scan: this.getAssessors_assessor()){
- for(XnatAbstractresourceI abstRes:scan.getResources_resource()){
- ((XnatAbstractresource)abstRes).deleteWithBackup(rootPath, user, ci);
- }
-
- for(XnatAbstractresourceI abstRes:scan.getOut_file()){
- ((XnatAbstractresource)abstRes).deleteWithBackup(rootPath, user, ci);
- }
- }
-
- File dir=this.getSessionDir();
- if(dir!=null){
- FileUtils.MoveToCache(dir);
- }
- }
-
- public int getAssessmentCount(String project){
- int count=0;
- for(int i=0;i<this.getMinimalLoadAssessors().size();i++){
- XnatExperimentdata expt=(XnatExperimentdata)this.getMinimalLoadAssessors().get(i);
- if(expt.getProject().equals(project)){
- count++;
- }
- }
- return count;
- }
-
-
- public XnatQcmanualassessordataI getManualQC() {
- final List<XnatImageassessordata> assessors = getMinimalLoadAssessors(XnatQcmanualassessordata.SCHEMA_ELEMENT_NAME);
- if (assessors != null && assessors.size() > 0) {
- return (XnatQcmanualassessordata) assessors.get(assessors.size()-1);
- }
- return null;
- }
-
- public XnatQcassessmentdataI getQCByType(String type) {
- final List<XnatImageassessordata> assessors = getMinimalLoadAssessors(XnatQcassessmentdata.SCHEMA_ELEMENT_NAME);
- final List<XnatImageassessordata> qcassessorOfType = new ArrayList<XnatImageassessordata>();
- for (int i = 0; i < assessors.size(); i++) {
- if (((AutoXnatQcassessmentdata)assessors.get(i)).getType().equals(type)) {
- qcassessorOfType.add(assessors.get(i));
- }
- }
- if (qcassessorOfType != null && qcassessorOfType.size() > 0) {
- return (XnatQcassessmentdata) qcassessorOfType.get(qcassessorOfType.size()-1);
- }
- return null;
- }
-
- public ValProtocoldataI getProtocolValidation() {
- final List<XnatImageassessordata> protocolData = getMinimalLoadAssessors(AutoValProtocoldata.SCHEMA_ELEMENT_NAME);
- if (protocolData != null && protocolData.size() > 0) {
- return (ValProtocoldataI) protocolData.get(protocolData.size()-1);
- }
- return null;
- }
-
- public ScrScreeningassessmentI getScreeningAssessment() {
- final List<XnatImageassessordata> screeningAssessment = getMinimalLoadAssessors(AutoScrScreeningassessment.SCHEMA_ELEMENT_NAME);
- if (screeningAssessment != null && screeningAssessment.size() > 0) {
- return (ScrScreeningassessmentI) screeningAssessment.get(screeningAssessment.size()-1);
- }
- return null;
- }
-
- public List<ScanAssessorI> getScanAssessors(){
- List al = new ArrayList();
- Iterator min = this.getMinimalLoadAssessors().iterator();
- while (min.hasNext())
- {
- ItemI assessor = (ItemI)min.next();
- if (assessor instanceof ScanAssessorI)
- {
- al.add(assessor);
- }
- }
- Collections.sort(al, new AssessorComparator());
- return al;
- }
-
- @Override
- public void preSave() throws Exception{
- super.preSave();
-
- final String expectedPath=this.getExpectedSessionDir().getAbsolutePath().replace('\\', '/');
-
- for(final XnatImagescandataI scan:this.getScans_scan()){
- ((XnatImagescandata)scan).setImageSessionData((XnatImagesessiondata)this);
- ((XnatImagescandata)scan).validate(expectedPath);
-
- }
-
- for(final XnatReconstructedimagedataI recon:this.getReconstructions_reconstructedimage()){
- ((XnatReconstructedimagedata)recon).setImageSessionData((XnatImagesessiondata)this);
- ((XnatReconstructedimagedata)recon).validate(expectedPath);
- }
-
- for(final XnatImageassessordataI assess:this.getAssessors_assessor()){
- ((XnatImageassessordata)assess).setImageSessionData((XnatImagesessiondata)this);
- ((XnatImageassessordata)assess).preSave();
- }
- }
-
- List<WrkWorkflowdataI> workflows=null;
- public List<WrkWorkflowdataI> getWorkflows() throws Exception{
- if(workflows==null){
- workflows = Lists.newArrayList();
-
- //search for workflow entries with a matching ID
- org.nrg.xft.search.CriteriaCollection cc = new CriteriaCollection("AND");
- cc.addClause("wrk:workflowData.ID",this.getId());
- org.nrg.xft.collections.ItemCollection items = org.nrg.xft.search.ItemSearch.GetItems(cc,null,false);
-
- //Sort by Launch Time
- List<XFTItem> workitems = items.getItems("wrk:workflowData.launch_time","DESC");
- for (XFTItem wrk:workitems)
- {
- workflows.add(new WrkWorkflowdata(wrk));
- }
- }
-
- return workflows;
- }
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatInvestigatordata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatInvestigatordata.java
deleted file mode 100644
index 4e10ba6a9fbef3b4df8bf42828956446a797555d..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatInvestigatordata.java
+++ /dev/null
@@ -1,44 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatInvestigatordata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatInvestigatordata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public class BaseXnatInvestigatordata extends AutoXnatInvestigatordata {
-
- public BaseXnatInvestigatordata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatInvestigatordata(UserI user)
- {
- super(user);
- }
-
- public BaseXnatInvestigatordata()
- {}
-
- public BaseXnatInvestigatordata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatIoscandata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatIoscandata.java
deleted file mode 100644
index f38758c0a64e2dfefb8ccdbf82828d29c5092711..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatIoscandata.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatIoscandata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatIoscandata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatIoscandata extends AutoXnatIoscandata {
-
- public BaseXnatIoscandata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatIoscandata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatIoscandata(UserI user)
- **/
- public BaseXnatIoscandata()
- {}
-
- public BaseXnatIoscandata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatIosessiondata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatIosessiondata.java
deleted file mode 100644
index 973171a595bd111a14936746f2bff389355dc920..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatIosessiondata.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatIosessiondata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatIosessiondata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatIosessiondata extends AutoXnatIosessiondata {
-
- public BaseXnatIosessiondata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatIosessiondata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatIosessiondata(UserI user)
- **/
- public BaseXnatIosessiondata()
- {}
-
- public BaseXnatIosessiondata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatMegscandata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatMegscandata.java
deleted file mode 100644
index 6c8522b3f9b8dfd3b1b874f9542810bda3723508..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatMegscandata.java
+++ /dev/null
@@ -1,37 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatMegscandata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatMegscandata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-@SuppressWarnings({"unchecked","rawtypes"})
-public class BaseXnatMegscandata extends AutoXnatMegscandata {
-
- public BaseXnatMegscandata(ItemI item) {
- super(item);
- }
-
- public BaseXnatMegscandata(UserI user) {
- super(user);
- }
-
- public BaseXnatMegscandata() {
- }
-
- public BaseXnatMegscandata(Hashtable properties, UserI user) {
- super(properties, user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatMegsessiondata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatMegsessiondata.java
deleted file mode 100644
index e8c5d530b7b585b438139d3f229d6d507cf38bb5..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatMegsessiondata.java
+++ /dev/null
@@ -1,37 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatMegsessiondata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatMegsessiondata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-@SuppressWarnings({"unchecked","rawtypes"})
-public class BaseXnatMegsessiondata extends AutoXnatMegsessiondata {
-
- public BaseXnatMegsessiondata(ItemI item) {
- super(item);
- }
-
- public BaseXnatMegsessiondata(UserI user) {
- super(user);
- }
-
- public BaseXnatMegsessiondata() {
- }
-
- public BaseXnatMegsessiondata(Hashtable properties, UserI user) {
- super(properties, user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatMgscandata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatMgscandata.java
deleted file mode 100644
index 0f86deb176e3cfb8ea52972820164a61f81e1e08..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatMgscandata.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatMgscandata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatMgscandata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatMgscandata extends AutoXnatMgscandata {
-
- public BaseXnatMgscandata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatMgscandata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatMgscandata(UserI user)
- **/
- public BaseXnatMgscandata()
- {}
-
- public BaseXnatMgscandata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatMgsessiondata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatMgsessiondata.java
deleted file mode 100644
index dc20a52df8f6db771d4f4cea508c042293171b29..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatMgsessiondata.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatMgsessiondata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatMgsessiondata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatMgsessiondata extends AutoXnatMgsessiondata {
-
- public BaseXnatMgsessiondata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatMgsessiondata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatMgsessiondata(UserI user)
- **/
- public BaseXnatMgsessiondata()
- {}
-
- public BaseXnatMgsessiondata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatMrassessordata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatMrassessordata.java
deleted file mode 100644
index 1df63a40c2eb380665d27e1d9323d25d54d2c921..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatMrassessordata.java
+++ /dev/null
@@ -1,74 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatMrassessordata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.model.XnatAddfieldI;
-import org.nrg.xdat.om.XnatMrsessiondata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-import java.util.Iterator;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public class BaseXnatMrassessordata extends org.nrg.xdat.om.base.auto.AutoXnatMrassessordata {
-
- public BaseXnatMrassessordata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatMrassessordata(UserI user)
- {
- super(user);
- }
-
- public BaseXnatMrassessordata()
- {}
-
- public BaseXnatMrassessordata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-
- public XnatMrsessiondata getMrSessionData()
- {
- return (XnatMrsessiondata)this.getImageSessionData();
- }
-
- Hashtable parametersByName = null;
- public Hashtable getAddParametersByName(){
- if (parametersByName == null){
- parametersByName=new Hashtable();
- Iterator iter = this.getParameters_addparam().iterator();
- while (iter.hasNext()){
- XnatAddfieldI field = (XnatAddfieldI)iter.next();
- parametersByName.put(field.getName(), field);
- }
- }
-
- return parametersByName;
- }
-
- public Object getAddParameterByName(String s){
- XnatAddfieldI field = (XnatAddfieldI)getAddParametersByName().get(s);
- if (field!=null){
- return field.getAddfield();
- }else{
- return null;
- }
- }
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatMrqcscandata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatMrqcscandata.java
deleted file mode 100644
index e2e33e092105c80eb86d2a76058afaf14ab31cb5..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatMrqcscandata.java
+++ /dev/null
@@ -1,35 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatMrqcscandata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatMrqcscandata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatMrqcscandata extends AutoXnatMrqcscandata {
- public BaseXnatMrqcscandata(ItemI item) {
- super(item);
- }
-
- public BaseXnatMrqcscandata(UserI user) {
- super(user);
- }
-
- public BaseXnatMrqcscandata() {
- }
-
- public BaseXnatMrqcscandata(Hashtable properties, UserI user) {
- super(properties, user);
- }
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatMrscandata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatMrscandata.java
deleted file mode 100644
index 534707a732ab6a7121caeb42592923ca5a391e5a..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatMrscandata.java
+++ /dev/null
@@ -1,177 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatMrscandata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import com.google.common.base.Strings;
-import com.google.common.collect.Lists;
-import org.nrg.xdat.model.XnatImagescandataI;
-import org.nrg.xdat.model.XnatMrqcscandataI;
-import org.nrg.xdat.model.XnatMrscandataI;
-import org.nrg.xdat.om.base.auto.AutoXnatMrscandata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-import org.nrg.xnat.helpers.scanType.AbstractScanTypeMapping;
-import org.nrg.xnat.helpers.scanType.ScanTypeMappingI;
-
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Map;
-
-@SuppressWarnings({"unchecked","rawtypes"})
-public class BaseXnatMrscandata extends AutoXnatMrscandata {
-
- public BaseXnatMrscandata(ItemI item) {
- super(item);
- }
-
- public BaseXnatMrscandata(UserI user) {
- super(user);
- }
-
- public BaseXnatMrscandata() {
- }
-
- public BaseXnatMrscandata(Hashtable properties, UserI user) {
- super(properties, user);
- }
-
- public XnatMrqcscandataI getManualQC() {
- return (XnatMrqcscandataI) super.getManualQC();
- }
-
- public ScanTypeMappingI getScanTypeMapping(final String project, final String dbName){
- return new MRScanTypeMapping(project,dbName);
- }
-
- private static class ScanTypeHistory{
- private final List<ScanType> types = Lists.newArrayList();
-
- public void add(String t, String it, Integer f){
- types.add(new ScanType(t,it,f));
- }
-
- public String match(String desc,String imgtype,Integer frames){
- if(types.size()==1){
- return types.get(0).getType();
- }
- //match by imgtype
- if(imgtype!=null && !imgtype.equals("")){
- for(ScanType st: types){
- if(imgtype.equalsIgnoreCase(st.getImgtype())){
- return st.getType();
- }
- }
- }
-
- //match by frames
- if(frames!=null){
- for(ScanType st: types){
- if(frames.equals(st.getFrames())){
- return st.getType();
- }
- }
- }
-
- if(imgtype==null){
- ScanType candidate = null;
- for (ScanType scanType : types) {
- if (scanType.getImgtype() == null) {
- if (candidate == null || (candidate.getType() == null && scanType.getType() != null)) {
- candidate = scanType;
- }
- }
- }
- if (candidate != null) {
- return candidate.getType();
- }
- }
-
- if(frames==null){
- for(ScanType st: types){
- if(st.getFrames()==null){
- return st.getType();
- }
- }
- }
-
- return types.get(0).getType();
- }
- }
-
- private static class ScanType{
- private final String _type;
- private final String _imgtype;
- private final Integer _frames;
-
- public ScanType(final String t, final String it, final Integer f) {
- _type=t;
- _imgtype=it;
- _frames=f;
- }
-
- public Integer getFrames() {
- return _frames;
- }
-
- public String getImgtype() {
- return _imgtype;
- }
-
- public String getType() {
- return _type;
- }
- }
-
- /**
- * For MR, we also use the DICOM image type parameters for matching scan types.
- *
- */
- public static class MRScanTypeMapping extends AbstractScanTypeMapping<ScanTypeHistory> implements ScanTypeMappingI {
- public MRScanTypeMapping(String project,String dbName){
- super(project, dbName, buildSelectSql(project));
- }
-
- private static final String buildSelectSql(final String project) {
- if (Strings.isNullOrEmpty(project)) {
- return null;
- } else {
- return "SELECT DISTINCT REPLACE(REPLACE(REPLACE(REPLACE(UPPER(scan.series_description),' ',''),'_',''),'-',''),'*','') AS series_description,scan.type,UPPER(parameters_imagetype) AS parameters_imagetype,frames FROM xnat_imagescandata scan LEFT JOIN xnat_mrscandata mr ON scan.xnat_imagescandata_id=mr.xnat_imagescandata_id LEFT JOIN xnat_experimentData isd ON scan.image_session_id=isd.id WHERE scan.series_description IS NOT NULL AND isd.project='" + project + "';";
- }
- }
-
- /*
- * (non-Javadoc)
- * @see org.nrg.xnat.helpers.scanType.AbstractScanTypeMapping#getMappedType(org.nrg.xdat.model.XnatImagescandataI, java.util.Map)
- */
- protected String getMappedType(XnatImagescandataI scan, Map<String,ScanTypeHistory> histories) {
- final String seriesDescription = scan.getSeriesDescription();
- final String formatted = AbstractScanTypeMapping.standardizeFormat(seriesDescription);
- final String imgType = ((XnatMrscandataI)scan).getParameters_imagetype();
-
- final ScanTypeHistory history = histories.get(formatted);
- return null == history ? null : history.match(seriesDescription, imgType, scan.getFrames());
- }
-
- /*
- * (non-Javadoc)
- * @see org.nrg.xnat.helpers.scanType.AbstractScanTypeMapping#newScanHistory()
- */
- protected ScanTypeHistory newScanHistory() { return new ScanTypeHistory(); }
-
- /*
- * (non-Javadoc)
- * @see org.nrg.xnat.helpers.scanType.AbstractScanTypeMapping#update(java.lang.Object, java.util.Hashtable)
- */
- protected void update(final ScanTypeHistory h, final Hashtable<?,?> row) {
- h.add((String)row.get("type"),(String)row.get("parameters_imagetype"),(Integer)row.get("frames"));
- }
- }
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatMrsessiondata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatMrsessiondata.java
deleted file mode 100644
index a09f1b670b29fa44f624d418db2e06e80e8e764d..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatMrsessiondata.java
+++ /dev/null
@@ -1,239 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatMrsessiondata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.model.XnatImagescandataI;
-import org.nrg.xdat.om.WrkWorkflowdata;
-import org.nrg.xdat.om.XnatImagesessiondata;
-import org.nrg.xdat.om.XnatMrsessiondata;
-import org.nrg.xdat.om.base.auto.AutoXnatMrsessiondata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.search.CriteriaCollection;
-import org.nrg.xft.security.UserI;
-
-import java.util.ArrayList;
-import java.util.Comparator;
-import java.util.Hashtable;
-import java.util.Map;
-
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public class BaseXnatMrsessiondata extends AutoXnatMrsessiondata {
-
- public BaseXnatMrsessiondata(ItemI item) {
- super(item);
- }
-
- public BaseXnatMrsessiondata(UserI user) {
- super(user);
- }
-
- public BaseXnatMrsessiondata() {
- }
-
- public BaseXnatMrsessiondata(Hashtable properties, UserI user) {
- super(properties, user);
- }
-
- public static Comparator GetScannerDelayComparator()
- {
- return (new BaseXnatMrsessiondata()).getScannerDelayComparator();
- }
-
- public Comparator getScannerDelayComparator()
- {
- return new ScannerDelayComparator();
- }
-
- public class ScannerDelayComparator implements Comparator{
- public ScannerDelayComparator()
- {
- }
- public int compare(Object o1, Object o2) {
- BaseXnatMrsessiondata value1 = (BaseXnatMrsessiondata)(o1);
- BaseXnatMrsessiondata value2 = (BaseXnatMrsessiondata)(o2);
-
- if (value1 == null){
- if (value2 == null)
- {
- return 0;
- }else{
- return -1;
- }
- }
- if (value2== null)
- {
- return 1;
- }
-
- int i = Compare(value1.getScanner(),value2.getScanner());
-
- if (i == 0)
- {
- return Compare(value1.getDelay(),value2.getDelay());
- }else{
- return i;
- }
- }
- }
-
- private static int Compare(final Comparable o1, final Comparable o2) {
- if (o1 == null) {
- return null == o2 ? 0 : -1;
- } else {
- return null == o2 ? 1 : o1.compareTo(o2);
- }
- }
-
- public String getWorkflowStatus()
- {
- WrkWorkflowdata wkdata = null;
-
- CriteriaCollection cc= new CriteriaCollection("AND");
- cc.addClause("wrk:workFlowData.ID",getId());
- ArrayList al =WrkWorkflowdata.getWrkWorkflowdatasByField(cc, getUser(), false);
- if (al.size()>0){
- wkdata= (WrkWorkflowdata)al.get(al.size()-1);
- if (wkdata.getPipelineName().toLowerCase().indexOf("transfer")!=-1){
- if(wkdata.getStatus().equalsIgnoreCase("In Progress"))
- {
- if (wkdata.getCurrentStepId().equalsIgnoreCase("Store"))
- return "storing";
- else
- return "archiving";
- }if(wkdata.getStatus().equalsIgnoreCase("Running"))
- {
- if (wkdata.getCurrentStepId().equalsIgnoreCase("Store"))
- return "storing";
- else
- return "archiving";
- }else if (wkdata.getStatus().equalsIgnoreCase("Complete")){
- return "uploaded";
- }else if (wkdata.getStatus().equalsIgnoreCase("Queued")){
- return "queued";
- }else{
- return wkdata.getPipelineName() + " " + wkdata.getStatus();
- }
- }else{
- if(wkdata.getStatus().equalsIgnoreCase("Running"))
- {
- return "processing";
- }else if (wkdata.getStatus().equalsIgnoreCase("Complete")){
- return "processed";
- }else if (wkdata.getStatus().equalsIgnoreCase("Awaiting Action")){
- return "waiting";
- }else if (wkdata.getStatus().equalsIgnoreCase("Queued")){
- return "queued";
- }else{
- return wkdata.getPipelineName() + " " + wkdata.getStatus();
- }
- }
- }
-
- if (this.getScanner()!=null)
- {
- return "uploading";
- }else{
- return "";
- }
-
-
- }
-
- /**
- *
- * @param otherImageSession
- * @throws Exception
- */
- public void copyValuesFrom(final XnatImagesessiondata otherImageSession) throws Exception {
- super.copyValuesFrom(otherImageSession);
-
- if(otherImageSession instanceof XnatMrsessiondata){
- final XnatMrsessiondata otherMR = (XnatMrsessiondata)otherImageSession;
-
- if (null != otherMR.getStabilization()){
- this.setStabilization(otherMR.getStabilization());
- }
-
- if (null != otherMR.getMarker()){
- this.setMarker(otherMR.getMarker());
- }
-
- if (null != otherMR.getCoil()){
- this.setCoil(otherMR.getCoil());
- }
- }
- }
-
- public String getDefaultIdentifier(){
- return this.getDcmpatientname();
- }
-
- public ArrayList getUnionOfScansByType(String csvType) {
- ArrayList _return = new ArrayList();
- String[] types = csvType.split(",");
- if (types != null && types.length > 0) {
- for(int i = 0; i < types.length; i++) {
- ArrayList rtn = getScansByType(types[i].trim());
- if (rtn.size() > 0 )_return.addAll(rtn);
- }
- }
- _return.trimToSize();
- return _return;
- }
-
- public ArrayList getUnionOfScansByType(String csvType, boolean chronological) {
- ArrayList _return = new ArrayList();
- if (chronological) {
- String[] types = csvType.split(",");
- Hashtable scanTypes = new Hashtable();
- if (types != null && types.length > 0) {
- for(int i = 0; i < types.length; i++) {
- scanTypes.put(types[i].trim(), "");
- }
- }
- for(XnatImagescandataI scan : this.getScans_scan()){
- if (scan.getType() != null && scanTypes.containsKey(scan.getType())) {
- _return.add(scan);
- }
- }
- _return.trimToSize();
- return _return;
- }else
- return getUnionOfScansByType(csvType);
- }
-
- public ArrayList getUnionOfScansByType(String csvType, String chronological) {
- return getUnionOfScansByType(csvType, new Boolean(chronological).booleanValue());
- }
-
- public Map<String,String> getCustomScanFields(String project){
- Map<String,String> customheaders= super.getCustomScanFields(project);
-
- customheaders.put("parameters/tr","");
- customheaders.put("parameters/te","");
- customheaders.put("parameters/ti","");
- customheaders.put("parameters/flip","");
- customheaders.put("parameters/sequence","");
- customheaders.put("parameters/imageType","");
- customheaders.put("parameters/scanSequence","");
- customheaders.put("parameters/seqVariant","");
- customheaders.put("parameters/scanOptions","");
- customheaders.put("parameters/acqType","");
-
- return customheaders;
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatMrsscandata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatMrsscandata.java
deleted file mode 100644
index 642ea115818ed6b65777349c0b35ba3f37609883..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatMrsscandata.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatMrsscandata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatMrsscandata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatMrsscandata extends AutoXnatMrsscandata {
-
- public BaseXnatMrsscandata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatMrsscandata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatMrsscandata(UserI user)
- **/
- public BaseXnatMrsscandata()
- {}
-
- public BaseXnatMrsscandata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatNmscandata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatNmscandata.java
deleted file mode 100644
index 09fa2892db0f1e10b1a78788525793ddbfc89ec9..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatNmscandata.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatNmscandata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatNmscandata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatNmscandata extends AutoXnatNmscandata {
-
- public BaseXnatNmscandata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatNmscandata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatNmscandata(UserI user)
- **/
- public BaseXnatNmscandata()
- {}
-
- public BaseXnatNmscandata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatNmsessiondata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatNmsessiondata.java
deleted file mode 100644
index d86d0ac399b2032988c23abdfabcc79c95ab8209..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatNmsessiondata.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatNmsessiondata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatNmsessiondata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatNmsessiondata extends AutoXnatNmsessiondata {
-
- public BaseXnatNmsessiondata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatNmsessiondata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatNmsessiondata(UserI user)
- **/
- public BaseXnatNmsessiondata()
- {}
-
- public BaseXnatNmsessiondata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatOpscandata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatOpscandata.java
deleted file mode 100644
index 96e4a2b1f905daebe05a1f6777744b0befc7cee7..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatOpscandata.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatOpscandata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatOpscandata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatOpscandata extends AutoXnatOpscandata {
-
- public BaseXnatOpscandata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatOpscandata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatOpscandata(UserI user)
- **/
- public BaseXnatOpscandata()
- {}
-
- public BaseXnatOpscandata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatOpsessiondata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatOpsessiondata.java
deleted file mode 100644
index e968c31293916c41dd3a307d86465ed84ae5f3d4..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatOpsessiondata.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatOpsessiondata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatOpsessiondata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatOpsessiondata extends AutoXnatOpsessiondata {
-
- public BaseXnatOpsessiondata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatOpsessiondata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatOpsessiondata(UserI user)
- **/
- public BaseXnatOpsessiondata()
- {}
-
- public BaseXnatOpsessiondata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatOptscandata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatOptscandata.java
deleted file mode 100644
index bd15941a07d0904dda12651f84508bd08711da6f..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatOptscandata.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatOptscandata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatOptscandata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatOptscandata extends AutoXnatOptscandata {
-
- public BaseXnatOptscandata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatOptscandata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatOptscandata(UserI user)
- **/
- public BaseXnatOptscandata()
- {}
-
- public BaseXnatOptscandata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatOptsessiondata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatOptsessiondata.java
deleted file mode 100644
index 97b9373e24dd742fdc03607043b8745c72909dc3..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatOptsessiondata.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatOptsessiondata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatOptsessiondata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatOptsessiondata extends AutoXnatOptsessiondata {
-
- public BaseXnatOptsessiondata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatOptsessiondata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatOptsessiondata(UserI user)
- **/
- public BaseXnatOptsessiondata()
- {}
-
- public BaseXnatOptsessiondata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatOtherdicomscandata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatOtherdicomscandata.java
deleted file mode 100644
index 7e6ea76778b5d3454d107fb1d76fa7e8e7e47b34..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatOtherdicomscandata.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatOtherdicomscandata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatOtherdicomscandata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatOtherdicomscandata extends AutoXnatOtherdicomscandata {
-
- public BaseXnatOtherdicomscandata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatOtherdicomscandata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatOtherdicomscandata(UserI user)
- **/
- public BaseXnatOtherdicomscandata()
- {}
-
- public BaseXnatOtherdicomscandata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatOtherdicomsessiondata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatOtherdicomsessiondata.java
deleted file mode 100644
index 30a76791cb993fbd0f2f985076ed338755d6bbaa..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatOtherdicomsessiondata.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatOtherdicomsessiondata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatOtherdicomsessiondata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatOtherdicomsessiondata extends AutoXnatOtherdicomsessiondata {
-
- public BaseXnatOtherdicomsessiondata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatOtherdicomsessiondata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatOtherdicomsessiondata(UserI user)
- **/
- public BaseXnatOtherdicomsessiondata()
- {}
-
- public BaseXnatOtherdicomsessiondata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatOtherqcscandata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatOtherqcscandata.java
deleted file mode 100644
index 66663b4efd75346053489278495685bb55f0dd81..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatOtherqcscandata.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatOtherqcscandata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatOtherqcscandata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatOtherqcscandata extends AutoXnatOtherqcscandata {
-
- public BaseXnatOtherqcscandata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatOtherqcscandata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatOtherqcscandata(UserI user)
- **/
- public BaseXnatOtherqcscandata()
- {}
-
- public BaseXnatOtherqcscandata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatPetassessordata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatPetassessordata.java
deleted file mode 100644
index 0e4e364aa034b72ad572a0fd65508b87a6961745..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatPetassessordata.java
+++ /dev/null
@@ -1,54 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatPetassessordata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.XnatPetsessiondata;
-import org.nrg.xdat.om.base.auto.AutoXnatPetassessordata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public class BaseXnatPetassessordata extends AutoXnatPetassessordata {
-
- public BaseXnatPetassessordata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatPetassessordata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatPetassessordata(UserI user)
- **/
- public BaseXnatPetassessordata()
- {}
-
- public BaseXnatPetassessordata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-
-
- public XnatPetsessiondata getPetSessionData()
- {
- return (XnatPetsessiondata)this.getImageSessionData();
- }
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatPetmrsessiondata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatPetmrsessiondata.java
deleted file mode 100644
index dfcaaa0ec4cdba0344c7cde4351b195f5da0ee94..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatPetmrsessiondata.java
+++ /dev/null
@@ -1,87 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatPetmrsessiondata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.model.XnatImagescandataI;
-import org.nrg.xdat.om.base.auto.AutoXnatPetmrsessiondata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.ArrayList;
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatPetmrsessiondata extends AutoXnatPetmrsessiondata {
-
- public BaseXnatPetmrsessiondata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatPetmrsessiondata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatPetmrsessiondata(UserI user)
- **/
- public BaseXnatPetmrsessiondata()
- {}
-
- public BaseXnatPetmrsessiondata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
- public ArrayList getUnionOfScansByType(String csvType) {
- ArrayList _return = new ArrayList();
- String[] types = csvType.split(",");
- if (types != null && types.length > 0) {
- for(int i = 0; i < types.length; i++) {
- ArrayList rtn = getScansByType(types[i].trim());
- if (rtn.size() > 0 )_return.addAll(rtn);
- }
- }
- _return.trimToSize();
- return _return;
- }
-
- public ArrayList getUnionOfScansByType(String csvType, boolean chronological) {
- ArrayList _return = new ArrayList();
- if (chronological) {
- String[] types = csvType.split(",");
- Hashtable scanTypes = new Hashtable();
- if (types != null && types.length > 0) {
- for(int i = 0; i < types.length; i++) {
- scanTypes.put(types[i].trim(), "");
- }
- }
- for(XnatImagescandataI scan : this.getScans_scan()){
- if (scan.getType() != null && scanTypes.containsKey(scan.getType())) {
- _return.add(scan);
- }
- }
- _return.trimToSize();
- return _return;
- }else
- return getUnionOfScansByType(csvType);
- }
-
- public ArrayList getUnionOfScansByType(String csvType, String chronological) {
- return getUnionOfScansByType(csvType, new Boolean(chronological).booleanValue());
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatPetqcscandata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatPetqcscandata.java
deleted file mode 100644
index b67679709ad6d6bf541fb6432974ec52e936f074..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatPetqcscandata.java
+++ /dev/null
@@ -1,35 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatPetqcscandata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatPetqcscandata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatPetqcscandata extends AutoXnatPetqcscandata {
- public BaseXnatPetqcscandata(ItemI item) {
- super(item);
- }
-
- public BaseXnatPetqcscandata(UserI user) {
- super(user);
- }
-
- public BaseXnatPetqcscandata() {
- }
-
- public BaseXnatPetqcscandata(Hashtable properties, UserI user) {
- super(properties, user);
- }
-}
\ No newline at end of file
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatPetqcscandataProcessingerror.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatPetqcscandataProcessingerror.java
deleted file mode 100644
index 5cd1d6a9c2f985a202ab19e8a0e6d12345ed3d27..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatPetqcscandataProcessingerror.java
+++ /dev/null
@@ -1,39 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatPetqcscandataProcessingerror
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatPetqcscandataProcessingerror;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-@SuppressWarnings({"unchecked","rawtypes"})
-public class BaseXnatPetqcscandataProcessingerror extends AutoXnatPetqcscandataProcessingerror {
- public BaseXnatPetqcscandataProcessingerror(ItemI item) {
- super(item);
- }
-
- public BaseXnatPetqcscandataProcessingerror(UserI user) {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatPetqcscandataProcessingerror(UserI user)
- */
- public BaseXnatPetqcscandataProcessingerror() {
- }
-
- public BaseXnatPetqcscandataProcessingerror(Hashtable properties, UserI user) {
- super(properties, user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatPetscandata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatPetscandata.java
deleted file mode 100644
index f854cc98b5a0fe1a1266aed2b05eb86ca0c461cd..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatPetscandata.java
+++ /dev/null
@@ -1,62 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatPetscandata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.XnatAbstractresource;
-import org.nrg.xdat.om.base.auto.AutoXnatPetscandata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-import java.util.Iterator;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public class BaseXnatPetscandata extends AutoXnatPetscandata {
- public BaseXnatPetscandata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatPetscandata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatPetscandata(UserI user)
- **/
- public BaseXnatPetscandata()
- {}
-
- public BaseXnatPetscandata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-
- public boolean isInRAWDirectory(){
- boolean hasRAW=false;
- Iterator files = getFile().iterator();
- while (files.hasNext()){
- XnatAbstractresource file = (XnatAbstractresource)files.next();
- if (file.isInRAWDirectory())
- {
- hasRAW=true;
- break;
- }
- }
- return hasRAW;
- }
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatPetscandataFrame.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatPetscandataFrame.java
deleted file mode 100644
index 9f6d82d06eb24abb70220d6c7d429940aa02e4f3..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatPetscandataFrame.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatPetscandataFrame
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatPetscandataFrame;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public class BaseXnatPetscandataFrame extends AutoXnatPetscandataFrame {
-
- public BaseXnatPetscandataFrame(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatPetscandataFrame(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatPetscandataFrame(UserI user)
- **/
- public BaseXnatPetscandataFrame()
- {}
-
- public BaseXnatPetscandataFrame(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatPetsessiondata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatPetsessiondata.java
deleted file mode 100644
index a4621dbb161798d03a561944bf5d7aab8d15a244..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatPetsessiondata.java
+++ /dev/null
@@ -1,225 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatPetsessiondata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.model.XnatImagescandataI;
-import org.nrg.xdat.model.XnatPetscandataI;
-import org.nrg.xdat.om.XnatImagesessiondata;
-import org.nrg.xdat.om.XnatPetsessiondata;
-import org.nrg.xdat.om.base.auto.AutoXnatPetsessiondata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.ArrayList;
-import java.util.Hashtable;
-import java.util.Map;
-
-/**
- * @author XDAT
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public class BaseXnatPetsessiondata extends AutoXnatPetsessiondata {
- public BaseXnatPetsessiondata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatPetsessiondata(UserI user)
- {
- super(user);
- }
-
- /**
- * @deprecated Use BaseXnatPetsessiondata(UserI user)
- **/
- public BaseXnatPetsessiondata()
- {}
-
- public BaseXnatPetsessiondata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-
- public XnatPetscandataI getDynamicEmissionScan()
- {
- ArrayList scans = this.getScansByType("Dynamic emission");
-
- if (scans.size()>0)
- {
- return (XnatPetscandataI)scans.get(0);
- }else{
- return null;
- }
- }
-
-
- public XnatPetscandataI getTransmissionScan()
- {
- ArrayList scans = this.getScansByType("Transmission");
-
- if (scans.size()>0)
- {
- return (XnatPetscandataI)scans.get(0);
- }else{
- return null;
- }
- }
-
-
-
- public String getDefaultIdentifier(){
- return this.getPatientname();
- }
-
-
- public void copyValuesFrom(XnatImagesessiondata otherImage) throws Exception {
- super.copyValuesFrom(otherImage);
- if(otherImage instanceof XnatPetsessiondata){
- final XnatPetsessiondata tempPET = (XnatPetsessiondata)otherImage;
- if (null != tempPET.getTracer_dose())
- this.setTracer_dose(tempPET.getTracer_dose());
- if (null != tempPET.getTracer_dose_units())
- this.setTracer_dose_units(tempPET.getTracer_dose_units());
- if (null != tempPET.getTracer_intermediate_units())
- this.setTracer_intermediate_units(tempPET.getTracer_intermediate_units());
- if (null != tempPET.getTracer_intermediate())
- this.setTracer_intermediate(tempPET.getTracer_intermediate());
- if (null != tempPET.getTracer_isotope_halfLife())
- this.setTracer_isotope_halfLife(tempPET.getTracer_isotope_halfLife());
- if (null != tempPET.getTracer_isotope())
- this.setTracer_isotope(tempPET.getTracer_isotope());
- if (null != tempPET.getTracer_name())
- this.setTracer_name(tempPET.getTracer_name());
- if (null != tempPET.getTracer_specificactivity())
- this.setTracer_specificactivity(tempPET.getTracer_specificactivity());
- if (null != tempPET.getTracer_transmissions())
- this.setTracer_transmissions(tempPET.getTracer_transmissions());
- if (null != tempPET.getTracer_totalmass())
- this.setTracer_totalmass(tempPET.getTracer_totalmass());
- if (null != tempPET.getTracer_totalmass_units())
- this.setTracer_totalmass_units(tempPET.getTracer_totalmass_units());
- if (null != tempPET.getStartTimeInjection())
- this.setStartTimeInjection(tempPET.getStartTimeInjection());
- if (null != tempPET.getStartTimeScan())
- this.setStartTimeScan(tempPET.getStartTimeScan());
- }
-
- }
-
- public Map<String,String> getCustomScanFields(String project){
- Map<String,String> customheaders= super.getCustomScanFields(project);
-
- customheaders.put("Original File Name","parameters/originalFileName");
- customheaders.put("System Type","parameters/systemType");
- customheaders.put("File Type","parameters/fileType");
- customheaders.put("Transaxial FOV","parameters/transaxialFOV");
- customheaders.put("Acq Type","parameters/acqType");
- customheaders.put("Facility","parameters/facility");
- customheaders.put("Num Planes","parameters/numPlanes");
- customheaders.put("Num Gates","parameters/numGates");
- customheaders.put("Plane Separation","parameters/planeSeparation");
- customheaders.put("Bin Size","parameters/binSize");
- customheaders.put("Data Type","parameters/dataType");
- customheaders.put("Dimensions x","parameters/dimensions/x");
- customheaders.put("Dimensions y","parameters/dimensions/y");
- customheaders.put("Dimensions z","parameters/dimensions/z");
- customheaders.put("Dimensions num","parameters/dimensions/num");
- customheaders.put("Offset x","parameters/offset/x");
- customheaders.put("Offset y","parameters/offset/y");
- customheaders.put("Offset z","parameters/offset/z");
- customheaders.put("Recon Zoom","parameters/reconZoom");
- customheaders.put("Pixel Size x","parameters/pixelSize/x");
- customheaders.put("Pixel Size y","parameters/pixelSize/y");
- customheaders.put("Pixel Size z","parameters/pixelSize/z");
- customheaders.put("Filter Code","parameters/filterCode");
- customheaders.put("Resolution x","parameters/resolution/x");
- customheaders.put("Resolution y","parameters/resolution/y");
- customheaders.put("Resolution z","parameters/resolution/z");
- customheaders.put("Num RElements","parameters/numRElements");
- customheaders.put("Num Angles","parameters/numAngles");
- customheaders.put("ZRotation Angle","parameters/ZRotationAngle");
- customheaders.put("Processing Code","parameters/processingCode");
- customheaders.put("Gate Duration","parameters/gateDuration");
- customheaders.put("rWave Offset","parameters/rWaveOffset");
- customheaders.put("Num Accepted Beats","parameters/numAcceptedBeats");
- customheaders.put("Filter cutoff","parameters/filter/cutoff");
- customheaders.put("Annotation","parameters/annotation");
- customheaders.put("MT_1_1","parameters/MT_1_1");
- customheaders.put("MT_1_2","parameters/MT_1_2");
- customheaders.put("MT_1_3","parameters/MT_1_3");
- customheaders.put("MT_1_4","parameters/MT_1_4");
- customheaders.put("MT_2_1","parameters/MT_2_1");
- customheaders.put("MT_2_2","parameters/MT_2_2");
- customheaders.put("MT_2_3","parameters/MT_2_3");
- customheaders.put("MT_2_4","parameters/MT_2_4");
- customheaders.put("MT_3_1","parameters/MT_3_1");
- customheaders.put("MT_3_2","parameters/MT_3_2");
- customheaders.put("MT_3_3","parameters/MT_3_3");
- customheaders.put("MT_3_4","parameters/MT_3_4");
- customheaders.put("RFilter cutoff","parameters/RFilter/cutoff");
- customheaders.put("RFilter resolution","parameters/RFilter/resolution");
- customheaders.put("RFilter code","parameters/RFilter/code");
- customheaders.put("RFilter order","parameters/RFilter/order");
- customheaders.put("ZFilter cutoff","parameters/ZFilter/cutoff");
- customheaders.put("ZFilter resolution","parameters/ZFilter/resolution");
- customheaders.put("ZFilter code","parameters/ZFilter/code");
- customheaders.put("ZFilter order","parameters/ZFilter/order");
- customheaders.put("scatter Type","parameters/scatterType");
- customheaders.put("recon Type","parameters/reconType");
- customheaders.put("recon Views","parameters/reconViews");
- customheaders.put("bed Position","parameters/bedPosition");
- customheaders.put("ecat Calibration Factor","parameters/ecatCalibrationFactor");
- customheaders.put("ecat Validation","ecatValidation");
- customheaders.put("ecat Validation status","ecatValidation/status");
-
-
- return customheaders;
- }
-
- public ArrayList getUnionOfScansByType(String csvType) {
- ArrayList _return = new ArrayList();
- String[] types = csvType.split(",");
- if (types != null && types.length > 0) {
- for(int i = 0; i < types.length; i++) {
- ArrayList rtn = getScansByType(types[i].trim());
- if (rtn.size() > 0 )_return.addAll(rtn);
- }
- }
- _return.trimToSize();
- return _return;
- }
-
- public ArrayList getUnionOfScansByType(String csvType, boolean chronological) {
- ArrayList _return = new ArrayList();
- if (chronological) {
- String[] types = csvType.split(",");
- Hashtable scanTypes = new Hashtable();
- if (types != null && types.length > 0) {
- for(int i = 0; i < types.length; i++) {
- scanTypes.put(types[i].trim(), "");
- }
- }
- for(XnatImagescandataI scan : this.getScans_scan()){
- if (scan.getType() != null && scanTypes.containsKey(scan.getType())) {
- _return.add(scan);
- }
- }
- _return.trimToSize();
- return _return;
- }else
- return getUnionOfScansByType(csvType);
- }
-
- public ArrayList getUnionOfScansByType(String csvType, String chronological) {
- return getUnionOfScansByType(csvType, new Boolean(chronological).booleanValue());
- }
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatProjectdata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatProjectdata.java
deleted file mode 100755
index dd67968ffad7a2a5e82d07b5c49d30df452f3ade..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatProjectdata.java
+++ /dev/null
@@ -1,1731 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatProjectdata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 2/18/14 1:28 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.action.ActionException;
-import org.nrg.action.ClientException;
-import org.nrg.action.ServerException;
-import org.nrg.automation.entities.ScriptTrigger;
-import org.nrg.automation.entities.ScriptTriggerTemplate;
-import org.nrg.automation.services.ScriptTriggerService;
-import org.nrg.automation.services.ScriptTriggerTemplateService;
-import org.nrg.config.entities.Configuration;
-import org.nrg.config.exceptions.ConfigServiceException;
-import org.nrg.config.services.ConfigService;
-import org.nrg.framework.constants.Scope;
-import org.nrg.framework.utilities.Reflection;
-import org.nrg.xdat.XDAT;
-import org.nrg.xdat.base.BaseElement;
-import org.nrg.xdat.display.DisplayField;
-import org.nrg.xdat.display.DisplayManager;
-import org.nrg.xdat.model.*;
-import org.nrg.xdat.om.*;
-import org.nrg.xdat.om.base.auto.AutoXnatProjectdata;
-import org.nrg.xdat.schema.SchemaElement;
-import org.nrg.xdat.search.CriteriaCollection;
-import org.nrg.xdat.search.DisplaySearch;
-import org.nrg.xdat.security.ElementSecurity;
-import org.nrg.xdat.security.SecurityValues;
-import org.nrg.xdat.security.UserGroupI;
-import org.nrg.xdat.security.XdatStoredSearch;
-import org.nrg.xdat.security.helpers.Groups;
-import org.nrg.xdat.security.helpers.Permissions;
-import org.nrg.xdat.security.helpers.Users;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFT;
-import org.nrg.xft.XFTItem;
-import org.nrg.xft.XFTTable;
-import org.nrg.xft.db.MaterializedView;
-import org.nrg.xft.db.PoolDBUtils;
-import org.nrg.xft.event.*;
-import org.nrg.xft.event.persist.PersistentWorkflowI;
-import org.nrg.xft.event.persist.PersistentWorkflowUtils;
-import org.nrg.xft.event.persist.PersistentWorkflowUtils.EventRequirementAbsent;
-import org.nrg.xft.exception.*;
-import org.nrg.xft.schema.Wrappers.GenericWrapper.GenericWrapperElement;
-import org.nrg.xft.search.ItemSearch;
-import org.nrg.xft.security.UserI;
-import org.nrg.xft.utils.FileUtils;
-import org.nrg.xft.utils.SaveItemHelper;
-import org.nrg.xft.utils.StringUtils;
-import org.nrg.xft.utils.ValidationUtils.ValidationResults;
-import org.nrg.xnat.exceptions.InvalidArchiveStructure;
-import org.nrg.xnat.helpers.prearchive.PrearcUtils;
-import org.nrg.xnat.restlet.resources.SecureResource;
-import org.nrg.xnat.turbine.utils.ArcSpecManager;
-import org.nrg.xnat.turbine.utils.ArchivableItem;
-import org.nrg.xnat.utils.WorkflowUtils;
-import org.restlet.data.Status;
-
-import java.io.File;
-import java.sql.SQLException;
-import java.text.NumberFormat;
-import java.util.*;
-
-/**
- * @author XDAT
- */
-@SuppressWarnings({"unchecked", "rawtypes"})
-public class BaseXnatProjectdata extends AutoXnatProjectdata implements ArchivableItem {
- public final static String MEMBER_GROUP = "member";
- public final static String COLLABORATOR_GROUP = "collaborator";
- public final static String OWNER_GROUP = "owner";
-
- public BaseXnatProjectdata(ItemI item) {
- super(item);
- }
-
- public BaseXnatProjectdata(UserI user) {
- super(user);
- }
-
- public BaseXnatProjectdata() {
- }
-
- public BaseXnatProjectdata(Hashtable properties, UserI user) {
- super(properties, user);
- }
-
- public int getSubjectCount() {
- try {
- XFTTable table = XFTTable.Execute("SELECT COUNT(*) FROM (SELECT DISTINCT subject_id,project FROM (SELECT pp.subject_id,pp.project FROM xnat_projectparticipant pp LEFT JOIN xnat_subjectData sub ON pp.subject_id=sub.id WHERE sub.id IS NOT NULL UNION SELECT ID,project FROM xnat_subjectdata )SEARCH )SEARCH WHERE project='" + getId() + "';", getDBName(), null);
-
- Long i = (Long) table.getFirstObject();
- if (i != null) {
- return i.intValue();
- }
- } catch (SQLException e) {
- logger.error("", e);
- } catch (DBPoolException e) {
- logger.error("", e);
- }
- return -1;
- }
-
- public Hashtable<String, Long> getExperimentCountByName() {
- Hashtable<String, Long> hash = new Hashtable<String, Long>();
- try {
- XFTTable table = XFTTable.Execute("SELECT COUNT(*) AS expt_count,element_name FROM (SELECT DISTINCT project,sharing_share_xnat_experimentda_id,extension FROM (SELECT exs.project, sharing_share_xnat_experimentda_id,extension FROM xnat_experimentdata_share exs LEFT JOIN xnat_experimentData ex ON exs.sharing_share_xnat_experimentda_id=ex.id WHERE ex.id IS NOT NULL UNION SELECT project,ID,extension FROM xnat_experimentdata) SEARCH )SEARCH LEFT JOIN xdat_meta_element ON SEARCH.extension=xdat_meta_element.xdat_meta_element_id WHERE project='" + getId() + "' GROUP BY element_name;", getDBName(), null);
-
- table.resetRowCursor();
- while (table.hasMoreRows()) {
- Object[] row = table.nextRow();
- Long count = (Long) row[0];
- String elementN = (String) row[1];
- try {
- SchemaElement se = SchemaElement.GetElement(elementN);
- elementN = se.getProperName();
- } catch (XFTInitException e) {
- logger.error("", e);
- } catch (ElementNotFoundException e) {
- logger.error("", e);
- }
- hash.put(elementN, count);
- }
- } catch (SQLException e) {
- logger.error("", e);
- } catch (DBPoolException e) {
- logger.error("", e);
- }
-
- return hash;
- }
-
- Hashtable<String, Long> exptCountsByType = null;
-
- public Hashtable<String, Long> getExperimentCountByXSIType() {
- if (exptCountsByType == null) {
- exptCountsByType = new Hashtable<String, Long>();
- try {
- XFTTable table = XFTTable.Execute("SELECT COUNT(*) AS expt_count,element_name FROM (SELECT DISTINCT project,sharing_share_xnat_experimentda_id,extension FROM (SELECT exs.project, sharing_share_xnat_experimentda_id,extension FROM xnat_experimentdata_share exs LEFT JOIN xnat_experimentData ex ON exs.sharing_share_xnat_experimentda_id=ex.id WHERE ex.id IS NOT NULL UNION SELECT project,ID,extension FROM xnat_experimentdata) SEARCH )SEARCH LEFT JOIN xdat_meta_element ON SEARCH.extension=xdat_meta_element.xdat_meta_element_id WHERE project='" + getId() + "' GROUP BY element_name;", getDBName(), null);
-
- table.resetRowCursor();
- while (table.hasMoreRows()) {
- Object[] row = table.nextRow();
- Long count = (Long) row[0];
- String elementN = (String) row[1];
- exptCountsByType.put(elementN, count);
- }
- } catch (SQLException e) {
- logger.error("", e);
- } catch (DBPoolException e) {
- logger.error("", e);
- }
- }
-
- return exptCountsByType;
- }
-
- public ArrayList<org.nrg.xdat.om.XnatPublicationresource> getPublicationsByType(String t) {
- ArrayList<org.nrg.xdat.om.XnatPublicationresource> pubs = new ArrayList<org.nrg.xdat.om.XnatPublicationresource>();
-
- List<XnatPublicationresourceI> allPubs = getPublications_publication();
- for (int i = 0; i < allPubs.size(); i++) {
- org.nrg.xdat.om.XnatPublicationresource res = (org.nrg.xdat.om.XnatPublicationresource) allPubs.get(i);
- if (res.getType().equals(t)) {
- pubs.add(res);
- }
- }
-
- return pubs;
-
- }
-
- public String getShortenedDescription() {
- if (getDescription() == null) {
- return "";
- }
- if (getDescription().length() > 500) {
- return getDescription().substring(0, 499) + "...";
- } else {
- return getDescription();
- }
- }
-
- public String createID(String base, int digits) throws Exception {
- String identifier = "";
-
- if (base != null) {
- identifier = base;
- identifier = StringUtils.ReplaceStr(identifier, " ", "");
- identifier = StringUtils.ReplaceStr(identifier, "-", "_");
- identifier = StringUtils.ReplaceStr(identifier, "\"", "");
- identifier = StringUtils.ReplaceStr(identifier, "'", "");
-
- identifier = incrementID(identifier, digits);
- }
-
- return identifier;
- }
-
- public String createID(String base) throws Exception {
- return createID(base, -1);
- }
-
- private String incrementID(String s, int digits) throws Exception {
- String temp_id = null;
-
- if (s == null) {
- throw new NullPointerException();
- }
-
- XFTTable table = org.nrg.xft.search.TableSearch.Execute("SELECT id FROM xnat_projectdata WHERE id LIKE '" + s + "%';", this.getSchemaElement().getDbName(), null);
- ArrayList al = table.convertColumnToArrayList("id");
-
- NumberFormat nf = NumberFormat.getIntegerInstance();
- nf.setMinimumIntegerDigits(digits);
- if (al.size() > 0) {
- int count = al.size() + 1;
- String full = StringUtils.ReplaceStr(nf.format(count), ",", "");
- temp_id = s + full;
-
- while (al.contains(temp_id)) {
- count++;
- full = StringUtils.ReplaceStr(nf.format(count), ",", "");
- temp_id = s + full;
- }
-
- return temp_id;
- } else {
- int count = 1;
- String full = nf.format(count);
- temp_id = s + full;
- return temp_id;
- }
- }
-
- public String setId(XnatInvestigatordataI i) throws Exception {
-
- if (i == null) {
- throw new NullPointerException();
- }
- String temp_id = createID(i.getLastname());
-
- this.setId(temp_id);
-
- return temp_id;
- }
-
- private ArrayList<XnatSubjectdata> _participants = null;
-
- public ArrayList<XnatSubjectdata> getParticipants_participant() {
- if (_participants == null) {
- final UserI user = this.getUser();
- final CriteriaCollection cc = new CriteriaCollection("OR");
- cc.addClause("xnat:subjectData/project", this.getId());
- cc.addClause("xnat:subjectData/sharing/share/project", this.getId());
- _participants = XnatSubjectdata.getXnatSubjectdatasByField(cc, user, false);
- }
-
- return _participants;
- }
-
- private ArrayList<XnatExperimentdata> _experiments = null;
-
- public ArrayList<XnatExperimentdata> getExperiments() {
- if (_experiments == null) {
- final UserI user = this.getUser();
- final CriteriaCollection cc = new CriteriaCollection("OR");
- cc.addClause("xnat:experimentData/project", this.getId());
- cc.addClause("xnat:experimentData/sharing/share/project", this.getId());
- _experiments = XnatExperimentdata.getXnatExperimentdatasByField(cc, user, false);
- }
-
- return _experiments;
- }
-
- public ArrayList getExperimentsByXSIType(String type) {
- ArrayList<XnatExperimentdata> typed = new ArrayList<XnatExperimentdata>();
- for (final XnatExperimentdata expt : this.getExperiments()) {
- if (expt.getXSIType().equals(type)) {
- typed.add(expt);
- }
- }
- return typed;
- }
-
-
- Hashtable<String, XnatProjectdataField> fieldsByName = null;
-
- public Hashtable getFieldsByName() {
- if (fieldsByName == null) {
- fieldsByName = new Hashtable<String, XnatProjectdataField>();
- for (final XnatProjectdataFieldI field : this.getFields_field()) {
- fieldsByName.put(field.getName(), (XnatProjectdataField) field);
- }
- }
-
- return fieldsByName;
- }
-
- public Object getFieldByName(String s) {
- final XnatProjectdataFieldI field = (XnatProjectdataFieldI) getFieldsByName().get(s);
- if (field != null) {
- return field.getField();
- } else {
- return null;
- }
- }
-
- public ArrayList<String> getOwnerEmails() throws Exception {
- return this.getOwners();
- }
-
-
- public ArrayList<String> getOwners() throws Exception {
- final XFTTable table2 = XFTTable.Execute("SELECT DISTINCT email FROM xdat_element_access ea LEFT JOIN xdat_field_mapping_set fms ON ea.xdat_element_access_id=fms.permissions_allow_set_xdat_elem_xdat_element_access_id LEFT JOIN xdat_field_mapping fm ON fms.xdat_field_mapping_set_id=fm.xdat_field_mapping_set_xdat_field_mapping_set_id LEFT JOIN xdat_userGroup ug ON ea.xdat_usergroup_xdat_usergroup_id=ug.xdat_usergroup_id LEFT JOIN xdat_user_groupid map ON ug.id=map.groupid LEFT JOIN xdat_user u ON map.groups_groupid_xdat_user_xdat_user_id=u.xdat_user_id WHERE read_element=1 AND delete_element=1 AND login !='guest' AND element_name='xnat:subjectData' AND field_value='" + getId() + "' ORDER BY email;", getDBName(), null);
- return table2.convertColumnToArrayList("email");
- }
-//
-// public ArrayList<XnatProjectparticipant> getParticipants(String field, Object value){
-// final ArrayList<XnatProjectparticipant> matches = new ArrayList<XnatProjectparticipant>();
-//
-// ArrayList<XnatProjectparticipant> participants = this.getSharing_sh();
-// if (participants.size()>0)
-// {
-// for (XnatProjectparticipant pp: participants){
-// try {
-// if (pp.hasProperty(field, value)){
-// matches.add(pp);
-// }
-// } catch (XFTInitException e) {
-// logger.error("",e);
-// } catch (ElementNotFoundException e) {
-// logger.error("",e);
-// } catch (FieldNotFoundException e) {
-// logger.error("",e);
-// }
-// }
-// }
-//
-// return matches;
-// }
-
- public String getSubjectSummary() {
- final StringBuffer sb = new StringBuffer();
- sb.append(this.getSubjectCount());
- sb.append(" Subjects ");
-
- return sb.toString();
- }
-
- public String getRootArchivePath() {
- String path = null;
-
- final ArcProject arcProj = this.getArcSpecification();
- if (arcProj != null) {
- ArcPathinfo pathInfo = arcProj.getPaths();
- if (pathInfo != null) {
- path = pathInfo.getArchivepath();
- }
- }
-
- if (path == null) {
- path = ArcSpecManager.GetInstance().getGlobalArchivePath() + "/" + this.getId();
- }
-
- path = path.replace('\\', '/');
- if (!path.endsWith("/")) {
- path = path + "/";
- }
-
- return path;
- }
-
- public String getCachePath() {
- String path = null;
-
- final ArcProject arcProj = this.getArcSpecification();
- if (arcProj != null) {
- ArcPathinfoI pathInfo = arcProj.getPaths();
- if (pathInfo != null) {
- path = pathInfo.getCachepath();
- }
- }
-
- if (path == null) {
- path = ArcSpecManager.GetInstance().getGlobalCachePath() + "/" + this.getId();
- }
-
- path = path.replace('\\', '/');
- if (!path.endsWith("/")) {
- path = path + "/";
- }
-
- return path;
- }
-
- public String getPrearchivePath() {
- String path = null;
-
- final ArcProject arcProj = this.getArcSpecification();
- if (arcProj != null) {
- ArcPathinfoI pathInfo = arcProj.getPaths();
- if (pathInfo != null) {
- path = pathInfo.getPrearchivepath();
- }
- }
-
- if (path == null) {
- path = ArcSpecManager.GetInstance().getGlobalPrearchivePath() + "/" + this.getId();
- }
-
- path = path.replace('\\', '/');
- if (!path.endsWith("/")) {
- path = path + "/";
- }
-
- return path;
- }
-
- public String getBuildPath() {
- String path = null;
-
- final ArcProject arcProj = this.getArcSpecification();
- if (arcProj != null) {
- ArcPathinfoI pathInfo = arcProj.getPaths();
- if (pathInfo != null) {
- path = pathInfo.getBuildpath();
- }
- }
-
- if (path == null) {
- path = ArcSpecManager.GetInstance().getGlobalBuildPath() + "/" + this.getId();
- }
-
- path = path.replace('\\', '/');
- if (!path.endsWith("/")) {
- path = path + "/";
- }
-
- return path;
- }
-
- public String getCurrentArc() {
- String path = null;
-
- final ArcProject arcProj = this.getArcSpecification();
-
- if (arcProj == null) return "arc001";
-
- path = arcProj.getCurrentArc();
- if (path == null || path.equals("")) {
- path = "arc001";
- }
-
- return path;
- }
-
- public ArrayList<String> getGroupMembers(String level) {
- try {
- final XFTTable table = XFTTable.Execute("SELECT DISTINCT email FROM xdat_user RIGHT JOIN xdat_user_groupid xug ON xdat_user.xdat_user_id=xug.groups_groupid_xdat_user_xdat_user_id WHERE groupid='" + this.getId() + "_" + level + "';", this.getDBName(), null);
- return table.convertColumnToArrayList("email");
- } catch (SQLException e) {
- logger.error("", e);
- } catch (DBPoolException e) {
- logger.error("", e);
-
- }
-
- return null;
- }
-
- public ArrayList<String> getGroupMembersByGroupID(String groupid) {
- try {
- final XFTTable table = XFTTable.Execute("SELECT DISTINCT email FROM xdat_user RIGHT JOIN xdat_user_groupid xug ON xdat_user.xdat_user_id=xug.groups_groupid_xdat_user_xdat_user_id WHERE groupid='" + groupid + "';", this.getDBName(), null);
- return table.convertColumnToArrayList("email");
- } catch (SQLException e) {
- logger.error("", e);
- } catch (DBPoolException e) {
- logger.error("", e);
-
- }
-
- return null;
- }
-
- public List<UserGroupI> getGroups() throws Exception {
- return Groups.getGroupsByTag(this.getId());
- }
-
- public ArrayList<List> getGroupIDs() {
- try {
- final XFTTable groups = XFTTable.Execute("SELECT id,displayname FROM xdat_usergroup WHERE tag='" + this.getId() + "' ORDER BY displayname DESC", this.getDBName(), null);
- return groups.toArrayListOfLists();
- } catch (Exception e) {
- logger.error("", e);
- return new ArrayList();
- }
- }
-
- public UserGroupI addGroupMember(String group_id, UserI newUser, UserI currentUser, EventMetaI ci) throws Exception {
- if (!Permissions.canDelete(currentUser, this) && !currentUser.getLogin().equals(newUser.getLogin())) {//equal user skips security here.
- throw new InvalidPermissionException("User cannot modify project " + this.getId());
- }
- return Groups.addUserToGroup(group_id, newUser, currentUser, ci);
- }
-
- public void removeGroupMember(String group_id, UserI newUser, UserI currentUser, EventDetails ci) throws Exception {
- if (!Permissions.canDelete(currentUser, this)) {
- throw new InvalidPermissionException("User cannot modify project " + this.getId());
- }
-
- if (Groups.isMember(newUser, group_id)) {
- PersistentWorkflowI wrk = PersistentWorkflowUtils.buildOpenWorkflow(currentUser, Users.getUserDataType(), newUser.getID().toString(), this.getId(), ci);
- try {
- Groups.removeUserFromGroup(newUser, group_id, wrk.buildEvent());
-
- PersistentWorkflowUtils.complete(wrk, wrk.buildEvent());
- } catch (Exception e) {
- PersistentWorkflowUtils.fail(wrk, wrk.buildEvent());
- throw e;
- }
- }
- }
-
-
- private List<ElementSecurity> getSecuredElements() {
-
- final ArrayList<ElementSecurity> ess = new ArrayList<ElementSecurity>();
- try {
- ess.addAll(ElementSecurity.GetElementSecurities().values());
- } catch (Exception e2) {
- logger.error("", e2);
- }
-
- for (final ElementSecurity es : (ArrayList<ElementSecurity>) ess.clone()) {
- try {
- if (es.isSecure() && (es.getSchemaElement().getGenericXFTElement().instanceOf("xnat:subjectData") || es.getSchemaElement().getGenericXFTElement().instanceOf("xnat:experimentData"))) {
-
- es.initPSF(es.getElementName() + "/project", EventUtils.DEFAULT_EVENT(getUser(), null));
- es.initPSF(es.getElementName() + "/sharing/share/project", EventUtils.DEFAULT_EVENT(getUser(), null));
- } else {
- ess.remove(es);
- }
- } catch (Exception e) {
- logger.error("", e);
- }
- }
- return ess;
- }
-
- public boolean initGroups() throws Exception {
- boolean modified = false;
- final long startTime = Calendar.getInstance().getTimeInMillis();
-
- if (XFT.VERBOSE)
- System.out.println("Group init() BEGIN: " + (Calendar.getInstance().getTimeInMillis() - startTime) + "ms");
- List<ElementSecurity> ess = getSecuredElements();
-
- Groups.createOrUpdateGroup(getId() + "_" + OWNER_GROUP, "Owners", Boolean.TRUE, Boolean.TRUE, Boolean.TRUE, Boolean.TRUE, Boolean.TRUE, Boolean.TRUE, ess, this.getId(), this.getUser());
-
-
- Groups.createOrUpdateGroup(getId() + "_" + MEMBER_GROUP, "Members", Boolean.TRUE, Boolean.TRUE, Boolean.FALSE, Boolean.TRUE, Boolean.TRUE, Boolean.TRUE, ess, this.getId(), this.getUser());
-
-
- Groups.createOrUpdateGroup(getId() + "_" + COLLABORATOR_GROUP, "Collaborators", Boolean.FALSE, Boolean.TRUE, Boolean.FALSE, Boolean.FALSE, Boolean.TRUE, Boolean.TRUE, ess, this.getId(), this.getUser());
- return modified;
- }
-
- public static void quickSave(XnatProjectdata project, UserI user, boolean allowDataDeletion, boolean overrideSecurity, EventMetaI ci) throws Exception {
- project.initNewProject(user, allowDataDeletion, true, ci);
-
- SaveItemHelper.authorizedSave(project, user, overrideSecurity, false, ci);
- XFTItem item = project.getItem().getCurrentDBVersion(false);
-
- XnatProjectdata postSave = new XnatProjectdata(item);
- postSave.getItem().setUser(user);
-
- postSave.initGroups();
-
- Groups.reloadGroupForUser(user, postSave.getId() + "_" + BaseXnatProjectdata.OWNER_GROUP);
-
- postSave.initArcProject(null, user, ci);
-
- Users.clearCache(user);
- MaterializedView.deleteByUser(user);
- ElementSecurity.refresh();
- }
-
- public XnatAbstractprotocol getProtocolByDataType(String elementName) {
- Iterator iter = this.getStudyprotocol().iterator();
- while (iter.hasNext()) {
- XnatAbstractprotocol protocol = (XnatAbstractprotocol) iter.next();
- if (protocol.getDataType().equals(elementName)) {
- return protocol;
- }
- }
-
- return null;
- }
-
-
- public ArrayList<XdatStoredSearch> getBundles() {
- ArrayList<XdatStoredSearch> searches = XdatStoredSearch.GetSearches("xdat:stored_search/tag", this.getId(), true);
-
- Hashtable<String, Long> counts = this.getExperimentCountByXSIType();
-
- boolean matched = false;
- for (XdatStoredSearch xss : searches) {
- if (xss.getRootElementName().equalsIgnoreCase("xnat:subjectData") &&
- xss.getBriefDescription().equalsIgnoreCase(DisplayManager.GetInstance().getPluralDisplayNameForSubject())) {
- matched = true;
- break;
- }
- }
-
- if (!matched) {
- XnatAbstractprotocol protocol = this.getProtocolByDataType("xnat:subjectData");
- XdatStoredSearch xss = null;
- if (protocol != null) {
- xss = protocol.getDefaultSearch((XnatProjectdata) this);
- } else {
- xss = this.getDefaultSearch("xnat:subjectData");
- }
- xss.setId("@xnat:subjectData");
- searches.add(xss);
- }
-
- for (String key : counts.keySet()) {
- matched = false;
- for (XdatStoredSearch xss : searches) {
- if (xss.getRootElementName().equalsIgnoreCase(key) &&
- xss.getBriefDescription().equalsIgnoreCase(DisplayManager.GetInstance().getPluralDisplayNameForElement(key))) {
- matched = true;
- break;
- }
- }
-
- if (!matched) {
- XnatAbstractprotocol protocol = this.getProtocolByDataType(key);
- try {
- if (ElementSecurity.IsBrowseableElement(key)) {
- XdatStoredSearch xss = null;
- if (protocol != null) {
- xss = protocol.getDefaultSearch((XnatProjectdata) this);
- } else {
- xss = this.getDefaultSearch(key);
- }
- xss.setId("@" + key);
- searches.add(xss);
- } else {
- logger.error("Erroneous data (rows=" + counts.get(key) + ") of type '" + key + "' in project '" + this.getId() + "'.");
- }
- } catch (Exception e) {
- logger.error("Error while accessing data (rows=" + counts.get(key) + ") of type '" + key + "' in project '" + this.getId() + "'.", e);
- }
- }
- }
- try {
- dynamicSearchAdd(this.getUser(), searches, this);
- } catch (Exception e) {
- e.printStackTrace(); //TODO fix this
- }
-
- return searches;
- }
-
- public interface AddBundlesI {
- public void execute(UserI user, List<XdatStoredSearch> storedSearches, BaseXnatProjectdata proj) throws Exception;
- }
-
- private void dynamicSearchAdd(UserI user, List<XdatStoredSearch> storedSearches, BaseXnatProjectdata proj) throws Exception {
- List<Class<?>> classes = Reflection.getClassesForPackage("org.nrg.xnat.project.getBundles.extensions");
-
- if (classes != null && classes.size() > 0) {
- for (Class<?> clazz : classes) {
- if (AddBundlesI.class.isAssignableFrom(clazz)) {
- AddBundlesI action = (AddBundlesI) clazz.newInstance();
- action.execute(user, storedSearches, proj);
- }
- }
- }
- }
-
- public XdatStoredSearch getDefaultSearch(String elementName) {
- XdatStoredSearch xss = null;
- try {
- xss = this.getDefaultSearch(elementName, this.getId() + "_" + elementName);
-
- xss.setId(this.getId() + "_" + elementName);
-
- ElementSecurity es = ElementSecurity.GetElementSecurity(elementName);
-
- if (es != null)
- xss.setBriefDescription(es.getPluralDescription());
- else {
- xss.setBriefDescription(elementName);
- }
- xss.setSecure(false);
- xss.setAllowDiffColumns(false);
- xss.setTag(this.getId());
-
- UserI user = this.getUser();
-
- XnatAbstractprotocol protocol = this.getProtocolByDataType(elementName);
- if (protocol != null) {
- if (protocol instanceof XnatDatatypeprotocol)
- for (XnatFielddefinitiongroupI group : ((XnatDatatypeprotocol) protocol).getDefinitions_definition()) {
- for (XnatFielddefinitiongroupFieldI field : group.getFields_field()) {
-
- XdatSearchField xsf = new XdatSearchField(this.getUser());
- xsf.setElementName(((XnatDatatypeprotocol) protocol).getDataType());
- String fieldID = null;
- if (field.getType().equals("custom")) {
- fieldID = ((XnatDatatypeprotocol) protocol).getDatatypeSchemaElement().getSQLName().toUpperCase() + "_FIELD_MAP=" + field.getName().toLowerCase();
-
- } else {
- try {
- SchemaElement se = SchemaElement.GetElement(((XnatDatatypeprotocol) protocol).getDataType());
-
- try {
- DisplayField df = se.getDisplayFieldForXMLPath(field.getXmlpath());
- if (df != null) {
- fieldID = df.getId();
- }
- } catch (Exception e) {
- logger.error("", e);
- }
- } catch (XFTInitException e) {
- logger.error("", e);
- } catch (ElementNotFoundException e) {
- logger.error("", e);
- }
- }
-
- if (fieldID != null) {
- xsf.setFieldId(fieldID);
-
- xsf.setHeader(field.getName());
- xsf.setType(field.getDatatype());
- xsf.setSequence(xss.getSearchField().size());
- if (field.getType().equals("custom")) xsf.setValue(field.getName().toLowerCase());
- try {
- xss.setSearchField(xsf);
- System.out.println("LOADED " + field.getXmlpath());
- } catch (Exception e) {
- logger.error("", e);
- System.out.println("FAILED to load " + field.getXmlpath());
- }
- } else {
- System.out.println("FAILED to load " + field.getXmlpath());
- }
- }
- }
- }
-
- SchemaElement root = SchemaElement.GetElement(elementName);
-
- if (elementName.equals("xnat:subjectData")) {
- for (String xsiType : this.getExperimentCountByXSIType().keySet()) {
- try {
- final GenericWrapperElement e = GenericWrapperElement.GetElement(xsiType);
- if (e.instanceOf("xnat:subjectAssessorData")) {
- SchemaElement se = SchemaElement.GetElement(xsiType);
- if (se != null) {
- //generate a project specific count column
- DisplayField df = root.getSQLQueryField("CNT_" + se.getSQLName().toUpperCase(), ElementSecurity.GetPluralDescription(xsiType), true, false, "integer", "sub_project_count", "SELECT COUNT(*) as sub_project_count, subject_id FROM xnat_subjectAssessorData sad LEFT JOIN xnat_experimentData ex ON sad.ID=ex.ID LEFT JOIN xnat_experimentData_meta_data inf ON ex.experimentData_info=inf.meta_data_id JOIN xdat_meta_element xme ON ex.extension=xme.xdat_meta_element_id LEFT JOIN xnat_experimentdata_share sp ON ex.id=sp.sharing_share_xnat_experimentda_id AND sp.project='@WHERE' WHERE xme.element_name='" + xsiType + "' AND (ex.project='@WHERE' OR sp.project='@WHERE') AND (inf.status = 'active' OR inf.status = 'locked' OR inf.status = 'quarantine') GROUP BY subject_id", "xnat:subjectData.ID", "subject_id");
-
- XdatSearchField xsf = new XdatSearchField(user);
- xsf.setElementName("xnat:subjectData");
-
- xsf.setFieldId(df.getId() + "=" + this.getId());
- xsf.setHeader(ElementSecurity.GetPluralDescription(xsiType));
- xsf.setValue(this.getId());
-
- xsf.setType("integer");
- xsf.setSequence(xss.getSearchField().size());
- xss.setSearchField(xsf);
- }
- }
- } catch (XFTInitException e) {
- logger.error("", e);
- } catch (ElementNotFoundException e) {
- logger.error("", e);
- } catch (Exception e) {
- logger.error("", e);
- }
- }
- }
-
- if (root.getGenericXFTElement().instanceOf("xnat:imageSessionData")) {
- for (String xsiType : this.getExperimentCountByXSIType().keySet()) {
- try {
- final GenericWrapperElement e = GenericWrapperElement.GetElement(xsiType);
- if (e.instanceOf("xnat:imageAssessorData")) {
- SchemaElement se = SchemaElement.GetElement(xsiType);
- if (se != null) {
- //generate a project specific count column
- DisplayField df = root.getSQLQueryField("CNT_" + se.getSQLName().toUpperCase(), ElementSecurity.GetPluralDescription(xsiType), true, false, "integer", "mr_project_count", "SELECT COUNT(*) as mr_project_count, imagesession_id FROM xnat_imageAssessorData iad LEFT JOIN xnat_experimentData ex ON iad.ID=ex.ID LEFT JOIN xnat_experimentData_meta_data inf ON ex.experimentData_info=inf.meta_data_id JOIN xdat_meta_element xme ON ex.extension=xme.xdat_meta_element_id LEFT JOIN xnat_experimentdata_share sp ON ex.id=sp.sharing_share_xnat_experimentda_id AND sp.project='@WHERE' WHERE xme.element_name='" + xsiType + "' AND (ex.project='@WHERE' OR sp.project='@WHERE') AND (inf.status = 'active' OR inf.status = 'locked' OR inf.status = 'quarantine') GROUP BY imagesession_id", elementName + ".ID", "imagesession_id");
-
- XdatSearchField xsf = new XdatSearchField(user);
- xsf.setElementName(elementName);
-
- xsf.setFieldId(df.getId() + "=" + this.getId());
- xsf.setHeader(ElementSecurity.GetPluralDescription(xsiType));
- xsf.setValue(this.getId());
-
- xsf.setType("integer");
- xsf.setSequence(xss.getSearchField().size());
- xss.setSearchField(xsf);
- }
- }
- } catch (XFTInitException e) {
- logger.error("", e);
- } catch (ElementNotFoundException e) {
- logger.error("", e);
- } catch (Exception e) {
- logger.error("", e);
- }
- }
- }
-
- } catch (Exception e) {
- logger.error("", e);
- }
-
- return xss;
- }
-
- public String getPublicAccessibility() throws Exception {
- UserI guest = Users.getGuest();
- if (Permissions.canRead(guest, "xnat:subjectData/project", this.getId())) {
- return "public";
- } else if (Permissions.canRead(guest, "xnat:projectData/ID", this.getId())) {
- return "protected";
- } else {
- return "private";
- }
- }
-
- /* (non-Javadoc)
- * @see org.nrg.xft.ItemWrapper#save(org.nrg.xft.security.UserI, boolean, boolean)
- */
- @Override
- public boolean save(UserI user, boolean overrideSecurity, boolean allowItemRemoval, EventMetaI c) throws Exception {
-
- UserGroupI ownerG = Groups.getGroup(getId() + "_" + OWNER_GROUP);
- if (ownerG == null) {
- //if there is no owner group, then this must be a new project.
- //projects are secured. Thus, you can't just create a project. In order to create a project, you have to be an owner of the project.
- //So, before we actually save the project, we create the owner group and add the user to it.
- UserGroupI group = Groups.createOrUpdateGroup(getId() + "_" + OWNER_GROUP, "Owners", Boolean.TRUE, Boolean.TRUE, Boolean.TRUE, Boolean.TRUE, Boolean.TRUE, Boolean.TRUE, getSecuredElements(), this.getId(), this.getUser());
-
- if (!Groups.getGroupsForUser(user).containsKey(group.getId())) {
- Groups.updateUserForGroup(user, group.getId(), group);
-
- this.addGroupMember(this.getId() + "_" + OWNER_GROUP, user, user, c);
- }
- }
-
- return super.save(user, overrideSecurity, allowItemRemoval, c);
- }
-
- public String getDisplayName() {
- if (this.getSecondaryId() == null)
- return this.getId();
- else
- return this.getSecondaryId();
- }
-
- public String getDisplayID() {
- if (this.getSecondaryId() == null)
- return this.getId();
- else
- return this.getSecondaryId();
- }
-
- public ArcProject getArcSpecification() {
- return ArcSpecManager.GetInstance().getProjectArc(getId());
- }
-
-
- public static Comparator GetComparator() {
- return (new BaseXnatProjectdata()).getComparator();
- }
-
- public Comparator getComparator() {
- return new ProjectIDComparator();
- }
-
- public class ProjectIDComparator implements Comparator {
- public ProjectIDComparator() {
- }
-
- public int compare(Object o1, Object o2) {
- BaseXnatProjectdata value1 = (BaseXnatProjectdata) (o1);
- BaseXnatProjectdata value2 = (BaseXnatProjectdata) (o2);
-
- if (value1 == null) {
- if (value2 == null) {
- return 0;
- } else {
- return -1;
- }
- }
- if (value2 == null) {
- return 1;
- }
-
- return value1.getId().compareTo(value2.getId());
-
- }
- }
-
- public void initNewProject(UserI user, boolean allowDataDeletion, boolean allowMatchingID, EventMetaI c) throws Exception {
- if (this.getId() == null) {
- String secondaryID = this.getSecondaryId();
- if (secondaryID == null) {
- throw new ClientException(Status.CLIENT_ERROR_BAD_REQUEST, new Exception("Please define a project abbreviation."));
- } else {
- setId(secondaryID);
-
- XFTItem db = getCurrentDBVersion();
- if (db != null) {
- String msg = "Project '" + getId() + "' already exists.";
- this.setId("");
- throw new ClientException(Status.CLIENT_ERROR_CONFLICT, new Exception(msg));
- }
- }
- } else {
- XFTItem db = getCurrentDBVersion();
- if (!allowMatchingID) {
- if (db != null) {
- String msg = "Project '" + getId() + "' already exists.";
- this.setId("");
- throw new ClientException(Status.CLIENT_ERROR_CONFLICT, new Exception(msg));
- }
- } else if (db != null) {
- if (!Permissions.canEdit(user, db)) {
- String msg = "Project '" + getId() + "' already exists.";
- this.setId("");
- throw new ClientException(Status.CLIENT_ERROR_CONFLICT, new Exception(msg));
- }
- }
- }
-
- if (this.getSecondaryId() == null) {
- this.setSecondaryId(this.getId());
- }
-
- if (this.getName() == null) {
- this.setName(this.getId());
- }
-
- if (this.getStudyprotocol().size() > 0) {
- Hashtable<String, ElementSecurity> ess = ElementSecurity.GetElementSecurities();
-
- int index = 0;
- for (XnatAbstractprotocolI protocolT : this.getStudyprotocol()) {
- XnatAbstractprotocol protocol = (XnatAbstractprotocol) protocolT;
- if (protocol.getProperty("data-type") == null) {
- if (allowDataDeletion) {
- //NOT REQUESTED
- if (protocol.getProperty("xnat_abstractProtocol_id") != null) {
- try {
- getItem().getCurrentDBVersion().removeChildFromDB("xnat:projectData/studyProtocol", protocol.getCurrentDBVersion(), user, c);
- //This may need to use a authorized call instead of the unauthorized call that's inside removeChildFromDB
- } catch (SQLException e) {
- logger.error("", e);
- } catch (Exception e) {
- logger.error("", e);
- }
- }
-
- getItem().removeChild("xnat:projectData/studyProtocol", getItem().getChildItems("xnat:projectData/studyProtocol").indexOf(protocol));
- }
- } else {
- //REQUESTED
- GenericWrapperElement e = GenericWrapperElement.GetElement((String) protocol.getProperty("data-type"));
- if (protocol.getProperty("ID") == null) {
- try {
- protocol.setProperty("ID", getItem().getProperty("ID") + "_" + e.getSQLName());
- } catch (InvalidValueException e1) {
- logger.error("", e1);
- }
- }
- if (protocol.getProperty("name") == null) {
- protocol.setProperty("name", ess.get(e.getFullXMLName()).getPluralDescription());
- }
-
- if (protocol.getXSIType().equals("xnat:datatypeProtocol")) {
- protocol.setProperty("xnat:datatypeProtocol/definitions/definition[ID=default]/data-type", protocol.getProperty("data-type"));
- protocol.setProperty("xnat:datatypeProtocol/definitions/definition[ID=default]/project-specific", "false");
- }
- }
- index++;
- }
- }
-
- for (XnatInvestigatordataI inv : this.getInvestigators_investigator()) {
- if (inv.getFirstname() == null) {
- XFTItem temp = ((XnatInvestigatordata) inv).getCurrentDBVersion();
- ((XnatInvestigatordata) inv).setFirstname(temp.getStringProperty("firstname"));
- ((XnatInvestigatordata) inv).setLastname(temp.getStringProperty("lastname"));
- }
- }
-
- for (XnatInvestigatordataI inv : this.getInvestigators_investigator()) {
- if (inv.getFirstname() == null) {
- XFTItem temp = ((XnatInvestigatordata) inv).getCurrentDBVersion();
- ((XnatInvestigatordata) inv).setFirstname(temp.getStringProperty("firstname"));
- ((XnatInvestigatordata) inv).setLastname(temp.getStringProperty("lastname"));
- }
- }
- }
-
- public void initArcProject(ArcProject arcP, UserI user, EventMetaI c) throws Exception {
- if (!Permissions.canDelete(user, this)) {
- throw new InvalidPermissionException("User cannot modify project " + this.getId());
- }
-
- if (arcP == null) {
- XFTItem item = XFTItem.NewItem("arc:project", user);
- arcP = new ArcProject(item);
- arcP.setCurrentArc("arc001");
- }
- arcP.setProperty("projects_project_arc_archivespe_arc_archivespecification_id", ArcSpecManager.GetInstance().getArcArchivespecificationId());
- arcP.setId(getId());
-
- arcP.setProperty("arc:project/paths/archivePath", ArcSpecManager.GetInstance().getGlobalArchivePath() + getId() + "/");
- arcP.setProperty("arc:project/paths/prearchivePath", ArcSpecManager.GetInstance().getGlobalPrearchivePath() + getId() + "/");
- arcP.setProperty("arc:project/paths/cachePath", ArcSpecManager.GetInstance().getGlobalCachePath() + getId() + "/");
- arcP.setProperty("arc:project/paths/buildPath", ArcSpecManager.GetInstance().getGlobalBuildPath() + getId() + "/");
- arcP.setPrearchiveCode(4);
-
- SaveItemHelper.authorizedSave(arcP, user, true, false, c);
- ArcSpecManager.Reset();
- }
-
- public XdatStoredSearch getDefaultSearch(String dataType, String id) {
- XdatStoredSearch xss = null;
- try {
- DisplaySearch search = new DisplaySearch();
- search.setDisplay("project_bundle");
- search.setRootElement(dataType);
- CriteriaCollection cc = new CriteriaCollection("OR");
- cc.addClause(dataType + "/sharing/share/project", "=", getId());
- cc.addClause(dataType + ".PROJECT", "=", getId());
-
- search.addCriteria(cc);
-
- xss = search.convertToStoredSearch(id);
-
- Iterator fields = xss.getSearchFields().iterator();
- while (fields.hasNext()) {
- XdatSearchField f = (XdatSearchField) fields.next();
- if (f.getFieldId().endsWith("_PROJECT_IDENTIFIER")) {
- f.setValue(getId());
- f.setFieldId(f.getFieldId() + "=" + getId());
- }
- }
- } catch (XFTInitException e) {
- logger.error("", e);
- } catch (ElementNotFoundException e) {
- logger.error("", e);
- } catch (FieldNotFoundException e) {
- logger.error("", e);
- } catch (Exception e) {
- logger.error("", e);
- }
- return xss;
- }
-
- public static String CleanID(String s) {
- s = s.replace('`', '_');
- s = s.replace('~', '_');
- s = s.replace('!', '_');
- s = s.replace('@', '_');
- s = s.replace('#', '_');
- s = s.replace('$', '_');
- s = s.replace('%', '_');
- s = s.replace('^', '_');
- s = s.replace('&', '_');
- s = s.replace('*', '_');
- s = s.replace('(', '_');
- s = s.replace(')', '_');
- s = s.replace('+', '_');
- s = s.replace('=', '_');
- s = s.replace('|', '_');
- s = s.replace('\\', '_');
- s = s.replace('{', '_');
- s = s.replace('[', '_');
- s = s.replace('}', '_');
- s = s.replace(']', '_');
- s = s.replace(':', '_');
- s = s.replace(';', '_');
- s = s.replace('"', '_');
- s = s.replace('\'', '_');
- s = s.replace('<', '_');
- s = s.replace('>', '_');
- s = s.replace('?', '_');
- s = s.replace(',', '_');
- s = s.replace('.', '_');
- s = s.replace('/', '_');
- return s;
- }
-
-
- public String checkDelete(UserI user) {
- try {
- if (!Permissions.canDelete(user, this.getItem())) {
- return "Invalid delete permissions for this project.";
- }
- } catch (Exception e) {
- e.printStackTrace();
- return "Invalid delete permissions for this project.";
- }
-
- for (XnatSubjectdata sub : this.getParticipants_participant()) {
- String msg = sub.canDelete(this, user);
- if (msg != null) {
- return msg;
- }
- }
-
- return null;
- }
-
- public void deleteFiles(UserI user, EventMetaI ci) throws Exception {
- String archive = this.getRootArchivePath();
- File dir = new File(archive);
- if (dir.exists()) {
- FileUtils.MoveToCache(dir);
- }
-
- for (XnatAbstractresourceI abstRes : this.getResources_resource()) {
- ((XnatAbstractresource) abstRes).deleteWithBackup(archive, user, ci);
- }
- }
-
- public void delete(boolean removeFiles, UserI user, EventMetaI ci) throws SQLException, Exception {
- boolean preventProjectDelete = false;
- boolean preventProjectDeleteByP = false;
-
- if (!Permissions.canDelete(user, this)) {
- throw new InvalidPermissionException("User cannot delete project:" + getId());
- }
-
- if (XDAT.getBoolSiteConfigurationProperty("security.prevent-data-deletion", false)) {
- throw new InvalidPermissionException("User cannot delete project:" + getId());
- }
-
- for (XnatSubjectdata subject : getParticipants_participant()) {
- if (subject != null) {
- boolean preventSubjectDelete = false;
- boolean preventSubjectDeleteByP = false;
- final List<XnatSubjectassessordataI> expts = subject.getExperiments_experiment();
-
- if (!(preventSubjectDelete || preventSubjectDeleteByP) && expts.size() != subject.getSubjectAssessorCount()) {
- preventSubjectDelete = true;
- }
-
- for (XnatSubjectassessordataI exptI : expts) {
- final XnatSubjectassessordata expt = (XnatSubjectassessordata) exptI;
-
- if (expt.getProject().equals(getId())) {
- if (Permissions.canDelete(user, expt)) {
- if (removeFiles) {
- final List<XFTItem> hash = expt.getItem().getChildrenOfType("xnat:abstractResource");
-
- for (XFTItem resource : hash) {
- ItemI om = BaseElement.GetGeneratedItem((XFTItem) resource);
- if (om instanceof XnatAbstractresource) {
- XnatAbstractresource resourceA = (XnatAbstractresource) om;
- resourceA.deleteWithBackup(getRootArchivePath(), user, ci);
- }
- }
- }
-
- SaveItemHelper.authorizedDelete(expt.getItem().getCurrentDBVersion(), user, ci);
- } else {
- preventSubjectDeleteByP = true;
- }
- } else {
- preventSubjectDelete = true;
- for (XnatExperimentdataShareI pp : expt.getSharing_share()) {
- if (pp.getProject().equals(getId())) {
- SaveItemHelper.authorizedDelete(((XnatExperimentdataShare) pp).getItem(), user, ci);
- }
- }
- }
-
- }
-
-
- if (!subject.getProject().equals(getId())) {
- for (XnatProjectparticipantI pp : subject.getSharing_share()) {
- if (pp.getProject().equals(getId())) {
- SaveItemHelper.authorizedDelete(((XnatProjectparticipant) pp).getItem(), user, ci);
- }
- }
- } else {
- if (preventSubjectDelete) {
- preventProjectDelete = true;
- } else if (preventSubjectDeleteByP) {
- preventProjectDeleteByP = true;
- } else {
- if (Permissions.canDelete(user, subject)) {
- if (removeFiles) {
- final List<XFTItem> hash = subject.getItem().getChildrenOfType("xnat:abstractResource");
-
- for (XFTItem resource : hash) {
- ItemI om = BaseElement.GetGeneratedItem((XFTItem) resource);
- if (om instanceof XnatAbstractresource) {
- XnatAbstractresource resourceA = (XnatAbstractresource) om;
- resourceA.deleteFromFileSystem(getRootArchivePath());
- }
- }
- }
- SaveItemHelper.authorizedDelete(subject.getItem().getCurrentDBVersion(), user, ci);
- } else {
- preventProjectDeleteByP = true;
- }
- }
- }
- }
- }
-
- Users.clearCache(user);
- MaterializedView.deleteByUser(user);
-
- if (!preventProjectDelete && !preventProjectDeleteByP) {
- final File arc = new File(this.getRootArchivePath());
-
- PrearcUtils.deleteProject(this.getId());
- SaveItemHelper.authorizedDelete(getItem().getCurrentDBVersion(), user, ci);
-
- Groups.deleteGroupsByTag(getId(), user, ci);
-
- //DELETE any other field mappings (i.e. guest settings)
- ItemSearch is = ItemSearch.GetItemSearch("xdat:field_mapping", user);
- is.addCriteria("xdat:field_mapping.field_value", getId());
- Iterator items = is.exec(false).iterator();
- while (items.hasNext()) {
- XFTItem item = (XFTItem) items.next();
- SaveItemHelper.authorizedDelete(item, user, ci);
- }
-
- //DELETE storedSearches
- for (final ItemI bundle : getBundles()) {
- try {
- SaveItemHelper.authorizedDelete(bundle.getItem(), user, ci);
- } catch (Throwable e) {
- logger.error("", e);
- }
- }
-
- ArcProject p = getArcSpecification();
- try {
- if (p != null) SaveItemHelper.authorizedDelete(p.getItem(), user, ci);
- } catch (Throwable e) {
- logger.error("", e);
- }
-
- try {
- if (arc.exists() && removeFiles) FileUtils.MoveToCache(arc);
- } catch (Exception e) {
- logger.error("", e);
- }
-
- final ScriptTriggerTemplateService templateService = XDAT.getContextService().getBean(ScriptTriggerTemplateService.class);
- final List<ScriptTriggerTemplate> templates = templateService.getTemplatesForEntity(getId());
- if (templates != null) {
- for (ScriptTriggerTemplate template : templates) {
- if (logger.isDebugEnabled()) {
- logger.debug("Deleting script trigger template association between template " + template.getTemplateId() + " and project " + getId());
- }
- template.getAssociatedEntities().remove(getId());
- templateService.update(template);
- }
- }
- final ScriptTriggerService triggerService = XDAT.getContextService().getBean(ScriptTriggerService.class);
- final List<ScriptTrigger> triggers = triggerService.getByScope(Scope.Project, getId());
- if (triggers != null) {
- for (ScriptTrigger trigger : triggers) {
- if (logger.isDebugEnabled()) {
- logger.debug("Deleting script trigger " + trigger.getTriggerId() + " with script ID " + trigger.getScriptId() + " and event " + trigger.getEvent() + " while deleting project " + getId());
- }
- triggerService.delete(trigger);
- }
- }
-
- try {
- XftEventService.getService().triggerEvent(new XftItemEvent(Groups.getGroupDatatype(), XftItemEvent.UPDATE));
- } catch (Exception e1) {
- logger.error("", e1);
- }
- }
- }
-
-
- @Override
- public void preSave() throws Exception {
- super.preSave();
-
- if (StringUtils.IsEmpty(this.getId())) {
- throw new IllegalArgumentException();
- }
-
- if (!StringUtils.IsAlphaNumericUnderscore(getId())) {
- throw new IllegalArgumentException("Identifiers cannot use special characters.");
- }
-
- // Validate project fields. If there are conflicts, throw a new exception
- this.trimProjectFields();
- Collection<String> conflicts = this.validateProjectFields();
- if (!conflicts.isEmpty()) {
- StringBuilder conflictStr = new StringBuilder();
- for (String conflict : conflicts) {
- conflictStr.append(conflict).append("\n");
- }
- throw new IllegalArgumentException(conflictStr.toString());
- }
-
- final String expectedPath = getExpectedCurrentDirectory().getAbsolutePath().replace('\\', '/');
-
- for (final XnatAbstractresourceI res : this.getResources_resource()) {
- final String uri;
- if (res instanceof XnatResource) {
- uri = ((XnatResource) res).getUri();
- } else if (res instanceof XnatResourceseries) {
- uri = ((XnatResourceseries) res).getPath();
- } else {
- continue;
- }
-
- FileUtils.ValidateUriAgainstRoot(uri, expectedPath, "URI references data outside of the project:" + uri);
- }
-
- XFTItem existing = this.getCurrentDBVersion();
- if (existing == null) {
- Long count = (Long) PoolDBUtils.ReturnStatisticQuery("SELECT COUNT(ID) FROM xnat_projectdata_history WHERE ID='" + this.getId() + "';", "COUNT", null, null);
- if (count > 0) {
- throw new Exception("Project '" + this.getId() + "' was used in a previously deleted project and cannot be reused.");
- }
- }
-
- UserGroupI ownerG = Groups.getGroup(getId() + "_" + OWNER_GROUP);
- if (ownerG == null) {
- PersistentWorkflowI wrk = PersistentWorkflowUtils.getOrCreateWorkflowData(null, this.getUser(), this.getXSIType(), this.getId(), PersistentWorkflowUtils.ADMIN_EXTERNAL_ID, EventUtils.newEventInstance(EventUtils.CATEGORY.PROJECT_ADMIN, EventUtils.TYPE.WEB_SERVICE, "Initialized permissions"));
-
- EventMetaI ci = wrk.buildEvent();
- try {
- UserI u = this.getUser();
-
- UserGroupI group = Groups.createOrUpdateGroup(getId() + "_" + OWNER_GROUP, "Owners", Boolean.TRUE, Boolean.TRUE, Boolean.TRUE, Boolean.TRUE, Boolean.TRUE, Boolean.TRUE, getSecuredElements(), this.getId(), this.getUser());
-
- wrk.setDataType(Groups.getGroupDatatype());
- wrk.setId(group.getPK().toString());
- wrk.setExternalid(this.getId());
-
- if (!Groups.isMember(u, group.getId())) {
- this.addGroupMember(this.getId() + "_" + OWNER_GROUP, u, u, ci);
-
- Groups.updateUserForGroup(u, group.getId(), group);
-
- //add a workflow entry for the user audit trail
- PersistentWorkflowI wrk2 = PersistentWorkflowUtils.getOrCreateWorkflowData(null, u, "xdat:user", u.getID().toString(), PersistentWorkflowUtils.ADMIN_EXTERNAL_ID, EventUtils.newEventInstance(EventUtils.CATEGORY.PROJECT_ADMIN, EventUtils.TYPE.WEB_SERVICE, "Initialized permissions"));
- PersistentWorkflowUtils.complete(wrk2, wrk2.buildEvent());
- }
-
- PersistentWorkflowUtils.complete(wrk, ci);
- } catch (Exception e) {
- PersistentWorkflowUtils.fail(wrk, ci);
- throw e;
- }
- }
- }
-
-
- public String getArchiveDirectoryName() {
- return this.getId();
- }
-
- public File getExpectedCurrentDirectory() throws InvalidArchiveStructure {
- return new File(getRootArchivePath(), "resources");
- }
-
- @SuppressWarnings("unused")
- public boolean isAutoArchive() {
- Integer i = ArcSpecManager.GetInstance().getAutoQuarantineCodeForProject(this.getId());
- return !(i == null || i < 4);
- }
-
- public static XnatProjectdata getProjectByIDorAlias(String pID, UserI user, boolean preLoad) {
- XnatProjectdata proj = null;
- if (pID != null) {
- proj = XnatProjectdata.getXnatProjectdatasById(pID, user, preLoad);
- }
-
- if (proj == null && pID != null) {
- final ArrayList<XnatProjectdata> matches = XnatProjectdata
- .getXnatProjectdatasByField(
- "xnat:projectData/aliases/alias/alias", pID,
- user, preLoad);
- if (matches.size() == 1) {
- proj = matches.get(0);
- }
- }
-
- return proj;
- }
-
- @Override
- public String getProject() {
- return getId();
- }
-
- @Override
- public String getArchiveRootPath() {
- return this.getRootArchivePath();
- }
-
- public static String createProject(XnatProjectdata project, UserI user, boolean allowDataDeletion, boolean allowMatchingID, EventDetails event, String accessibility) throws ActionException {
- PersistentWorkflowI wrk;
- try {
- wrk = PersistentWorkflowUtils.getOrCreateWorkflowData(null, user, XnatProjectdata.SCHEMA_ELEMENT_NAME, project.getId(), project.getId(), event);
- } catch (EventRequirementAbsent e1) {
- throw new ClientException(Status.CLIENT_ERROR_FORBIDDEN, e1);
- }
- EventMetaI c = wrk.buildEvent();
-
- try {
- String id = createProject(project, user, allowDataDeletion, allowMatchingID, c, accessibility);
-
- Users.clearCache(user);
- ElementSecurity.refresh();
- try {
- WorkflowUtils.complete(wrk, c);
- } catch (Exception e) {
- throw new ServerException(e);
- }
- return id;
- } catch (ActionException e) {
- try {
- WorkflowUtils.fail(wrk, c);
- } catch (Exception e1) {
- logger.error("", e1);
- }
- throw e;
- }
- }
-
- public static String createProject(XnatProjectdata project, UserI user, boolean allowDataDeletion, boolean allowMatchingID, EventMetaI event, String accessibility) throws ActionException {
- try {
- project.initNewProject(user, allowDataDeletion, allowMatchingID, event);
-
- final ValidationResults vr = project.validate();
-
- if (vr != null && !vr.isValid()) {
- throw new ClientException(Status.CLIENT_ERROR_BAD_REQUEST, vr.toFullString(), null);
- }
-
- project.save(user, true, false, event);
- } catch (ClientException e) {
- throw e;
- } catch (Exception e) {
- SecureResource.logger.error("", e);
- throw new ServerException(Status.SERVER_ERROR_INTERNAL, e);
- }
- try {
- XFTItem item = project.getItem().getCurrentDBVersion(false);
-
- XnatProjectdata postSave = new XnatProjectdata(item);
- postSave.getItem().setUser(user);
-
- postSave.initGroups();
-
- if (accessibility == null) {
- accessibility = "protected";
- }
-
- if (!accessibility.equals("private"))
- Permissions.setDefaultAccessibility(project.getId(), accessibility, true, user, event);
-
- Groups.reloadGroupForUser(user, postSave.getId() + "_" + OWNER_GROUP);
-
- postSave.initArcProject(null, user, event);
-
- return postSave.getId();
- } catch (Exception e) {
- throw new ServerException(e);
- }
- }
-
-
- public Integer getMetaId() {
- return ((XFTItem) this.getItem()).getMetaDataId();
- }
-
- /**
- * Return the project info ID (meta data id) for this project ID.
- *
- * @param project
- * @return
- */
- public static Long getProjectInfoIdFromStringId(String project) {
- if (project != null) {
- XnatProjectdata p = XnatProjectdata.getXnatProjectdatasById(project, null, false);
- if (p != null) {
- return Long.parseLong(p.getItem().getProps().get("projectdata_info").toString());
- }
- }
- return null;
- }
-
- /**
- * Function removes excess whitespace from the project id, secondary id, name and alias fields.
- */
- public void trimProjectFields() throws Exception {
- String trim; //Temporary variable to store trimmed variables.
-
- //Trim excess white space from the project id
- String id = this.getId();
- if (!StringUtils.IsEmpty(id)) {
- trim = id.trim();
- if (!trim.equals(id)) {
- this.setId(trim);
- }
- }
-
- // Trim excess white space from the secondary id
- String secondaryId = this.getSecondaryId();
- if (!StringUtils.IsEmpty(secondaryId)) {
- trim = secondaryId.trim();
- if (!trim.equals(secondaryId)) {
- this.setSecondaryId(trim);
- }
- }
-
- // Trim excess white space from the project name
- String name = this.getName();
- if (!StringUtils.IsEmpty(name)) {
- trim = name.trim();
- if (!trim.equals(name)) {
- this.setName(trim);
- }
- }
-
- // Trim excess white space from each alias
- for (XnatProjectdataAliasI a : this.getAliases_alias()) {
- String newA = a.getAlias().trim();
- if (!newA.equals(a)) {
- a.setAlias(newA);
- }
- }
- }
-
- /**
- * Function validates a project's id, secondary id, name and aliases
- * to make sure they will not conflict with any existing projects within the database.
- * See: XNAT-2801, XNAT-2934, XNAT-2813, XNAT-2551, XNAT-2628, XNAT-2780
- *
- * @return - A list of conflict errors. If the list is empty, all elements passed validation.
- */
- public Collection<String> validateProjectFields() throws Exception {
-
- // Make sure the Id isn't null or empty
- if (StringUtils.IsEmpty(this.getId())) {
- return Arrays.asList("Missing required field: Project Id.");
- }
-
- // Add all the elements that require validation to a Map.
- Map<String, String> elements = new HashMap<String, String>();
- elements.put("Project Id", TurbineUtils.escapeParam(this.getId().toLowerCase())); // Add the Project Id.
-
- if (!StringUtils.IsEmpty(this.getName())) { // Add the Project Title.
- elements.put("Project Title", TurbineUtils.escapeParam(this.getName().toLowerCase()));
- }
-
- if (!StringUtils.IsEmpty(this.getSecondaryId())) { // Add the Running Title.
- elements.put("Running Title", TurbineUtils.escapeParam(this.getSecondaryId().toLowerCase()));
- }
-
- return validateElements(elements, getNewProjectAliasStrings());
- }
-
- /**
- * Validates a collection of elements and aliases that we wish to insert into the database.
- * Elements are validated against all
- *
- * @param elements - The Collection elements we wish to validate.
- * @param aliases - The Collection of aliases we wish to validate.
- * @return - A list of conflict errors. If the list is empty, all elements passed validation.
- * @throws Exception
- */
- private Collection<String> validateElements(Map<String, String> elements, Collection<String> aliases) throws Exception {
-
- // Get a list of the aliases the user wishes to add and validate them.
- Collection<String> conflicts = validateAliases(aliases);
-
- // Create a query and find all possible matches in the database
- String inClause = collectionToCommaDelimitedString(elements.values());
- Collection<String> matches = getMatchingElements("SELECT LOWER(a.id) as id, LOWER(a.secondary_id) as secondary_id, LOWER(a.name) as name, LOWER(b.alias) as alias FROM (SELECT id,secondary_id,name FROM xnat_projectdata WHERE LOWER(id) != '" + this.getId().toLowerCase() + "') a FULL OUTER JOIN ( SELECT aliases_alias_xnat_projectdata_id as id, alias FROM xnat_projectdata_alias) b ON a.id = b.id WHERE (LOWER(a.secondary_id) IN (" + inClause + ") OR LOWER(a.name) IN (" + inClause + ") OR LOWER(b.alias) IN (" + inClause + ") OR LOWER(a.id) IN (" + inClause + "));");
-
- // For each element, check to see if it is contained within the collection of possible matches. If so, add a conflict.
- for (Map.Entry<String, String> entry : elements.entrySet()) {
- if (matches.contains(entry.getValue())) {
- conflicts.add("Invalid " + entry.getKey() + ": '" + entry.getValue() + "' is already being used.");
- }
- if (aliases.contains(entry.getValue())) { // element cannot be an alias as well as a project id, secondary id or title.
- conflicts.add("Invalid " + entry.getKey() + ": '" + entry.getValue() + "' cannot be used as the " + entry.getKey() + " and an alias.");
- }
- }
- return conflicts;
- }
-
- /**
- * Validates any Aliases the user is trying to add to this project.
- *
- * @return - A list of conflict errors. If the list is empty, all elements passed validation.
- * @throws Exception
- */
- private Collection<String> validateAliases(Collection<String> aliases) throws Exception {
- Collection<String> conflicts = new ArrayList<String>();
- if (null == aliases || aliases.isEmpty()) {
- return conflicts;
- }
-
- // Create a query and find all possible matches in the database
- String inClause = collectionToCommaDelimitedString(aliases);
- Collection<String> matches = getMatchingElements("SELECT LOWER(a.id) as id, LOWER(a.secondary_id) as secondary_id, LOWER(a.name) as name, LOWER(b.alias) as alias FROM (SELECT id,secondary_id,name FROM xnat_projectdata) a FULL OUTER JOIN ( SELECT aliases_alias_xnat_projectdata_id as id, alias FROM xnat_projectdata_alias WHERE LOWER(aliases_alias_xnat_projectdata_id) != '" + this.getId().toLowerCase() + "') b ON a.id = b.id WHERE (LOWER(a.secondary_id) IN (" + inClause + ") OR LOWER(a.name) IN (" + inClause + ") OR LOWER(b.alias) IN (" + inClause + ") OR LOWER(a.id) IN (" + inClause + "));");
-
- // For each alias, check to see if it is contained within the collection of possible matches. If so, add a conflict.
- for (String entry : aliases) {
- if (matches.contains(entry)) {
- conflicts.add("Invalid Alias: '" + entry + "' is already being used.");
- }
- }
- return conflicts;
- }
-
- /**
- * Function executes a query and returns all results in one Set of strings.
- *
- * @param query - the query to execute
- * @return A set of any strings that are returned from the database
- * @throws Exception
- */
- private Collection<String> getMatchingElements(String query) throws Exception {
- XFTTable t = new PoolDBUtils().executeSelectQuery(query, null, this.getUser().getUsername());
- ArrayList<ArrayList<String>> l = t.convertColumnsToArrayList(new ArrayList(Arrays.asList(t.getColumns())));
-
- // Convert the ArrayList<ArrayList<String>> into a one Set<String> so it's easy to manage.
- // We don't care about duplicate values or the column names anymore.
- Collection<String> retSet = new HashSet<String>();
- for (Collection<String> e : l) {
- retSet.addAll(e);
- }
- return retSet;
- }
-
- /**
- * Function gets the string form of each alias the user is trying to add to this project.
- *
- * @return - List of Alias Strings
- */
- public Collection<String> getNewProjectAliasStrings() {
- Collection<String> retList = new ArrayList<String>();
- for (org.nrg.xdat.model.XnatProjectdataAliasI a : this.getAliases_alias()) {
- retList.add(TurbineUtils.escapeParam(a.getAlias().toLowerCase()));
- }
- return retList;
- }
-
- /**
- * Converts a collection of strings into a single comma delimited string.
- *
- * @param elements - A collection of strings
- * @return a comma delimited string. e.g. "'element_1', 'element_2', 'element_3' ... 'element_n'"
- */
- private String collectionToCommaDelimitedString(Collection<String> elements) {
- StringBuilder q = new StringBuilder().append("'");
- Iterator<String> it = elements.iterator();
- while (it.hasNext()) {
- q.append(it.next());
- if (it.hasNext()) {
- q.append("','");
- }
- }
- return q.append("'").toString();
- }
-
- @Override
- public SecurityValues getSecurityTags() {
- SecurityValues projects = new SecurityValues();
- projects.getHash().put("xnat:projectData/ID", this.getId());
- return projects;
- }
-
- public boolean getUseScanTypeMapping() {
- ConfigService configService = XDAT.getConfigService();
-
- // check project config
- Configuration config = configService.getConfig("project", "scanTypeMapping", new Long((Integer) this.getProps().get("projectdata_info")));
- if (config != null && config.getStatus().equals("enabled")) {
- return Boolean.valueOf(config.getContents());
- }
-
- // if nothing there, check site config
- return XDAT.getBoolSiteConfigurationProperty("scanTypeMapping", true);
- }
-
- public void setUseScanTypeMapping(boolean newValue) {
- ConfigService configService = XDAT.getConfigService();
- try {
- configService.replaceConfig(getUser().getUsername(), "", "project", "scanTypeMapping", String.valueOf(newValue), new Long((Integer) this.getProps().get("projectdata_info")));
- } catch (ConfigServiceException exception) {
- logger.error("Configuration service error replacing config for user " + getUser().getUsername() + " and project " + getId());
- }
- }
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatProjectdataAlias.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatProjectdataAlias.java
deleted file mode 100644
index cb7b392cc866dff33d579d950a60c5eaea5a3549..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatProjectdataAlias.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatProjectdataAlias
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatProjectdataAlias;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatProjectdataAlias extends AutoXnatProjectdataAlias {
-
- public BaseXnatProjectdataAlias(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatProjectdataAlias(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatProjectdataAlias(UserI user)
- **/
- public BaseXnatProjectdataAlias()
- {}
-
- public BaseXnatProjectdataAlias(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatProjectdataField.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatProjectdataField.java
deleted file mode 100644
index b7bbfee1b7d3bb02019262d7a6c80bb3227f063c..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatProjectdataField.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatProjectdataField
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatProjectdataField;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatProjectdataField extends AutoXnatProjectdataField {
-
- public BaseXnatProjectdataField(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatProjectdataField(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatProjectdataField(UserI user)
- **/
- public BaseXnatProjectdataField()
- {}
-
- public BaseXnatProjectdataField(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatProjectparticipant.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatProjectparticipant.java
deleted file mode 100644
index 8e5f6f78d6dad2f545a3522d669028fcf2880318..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatProjectparticipant.java
+++ /dev/null
@@ -1,120 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatProjectparticipant
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.model.XnatProjectdataI;
-import org.nrg.xdat.om.XnatProjectdata;
-import org.nrg.xdat.om.base.auto.AutoXnatProjectparticipant;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTTable;
-import org.nrg.xft.exception.DBPoolException;
-import org.nrg.xft.security.UserI;
-
-import java.sql.SQLException;
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatProjectparticipant extends AutoXnatProjectparticipant {
-
- public BaseXnatProjectparticipant(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatProjectparticipant(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatProjectparticipant(UserI user)
- **/
- public BaseXnatProjectparticipant()
- {}
-
- public BaseXnatProjectparticipant(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
- private String name = null;
- private String description = null;
- private String secondaryID = null;
- private boolean initd = false;
-
- public void loadProjectDetails(){
- if (!initd)
- {
- initd=true;
- try {
- XFTTable table = XFTTable.Execute("SELECT name,description,secondary_ID FROM xnat_projectData WHERE ID ='" + this.getProject() + "';", this.getDBName(), null);
-
- if (table.size()>0)
- {
- Object[] row = (Object[])table.rows().get(0);
- name = (String)row[0];
- description = (String)row[1];
- secondaryID = (String)row[2];
- }
- } catch (SQLException e) {
- logger.error("",e);
- } catch (DBPoolException e) {
- logger.error("",e);
- }
- }
- }
-
- public XnatProjectdataI getProjectData(){
- return XnatProjectdata.getXnatProjectdatasById(this.getProject(), this.getUser(), false);
- }
-
- /**
- * @return the description
- */
- public String getProjectDescription() {
- loadProjectDetails();
- return description;
- }
-
- /**
- * @return the name
- */
- public String getProjectName() {
- loadProjectDetails();
- return name;
- }
-
- /**
- * @return the secondaryID
- */
- public String getProjectSecondaryID() {
- loadProjectDetails();
- return secondaryID;
- }
-
-
-
- /**
- * @return the secondaryID
- */
- public String getProjectDisplayID() {
- loadProjectDetails();
- if (secondaryID!=null){
- return secondaryID;
- }else{
- return getProject();
- }
- }
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatPublicationresource.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatPublicationresource.java
deleted file mode 100644
index 2ff375b34c4c9141a5dfff9917c4541f31d5a94d..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatPublicationresource.java
+++ /dev/null
@@ -1,293 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatPublicationresource
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 11/18/13 9:35 AM
- */
-package org.nrg.xdat.om.base;
-
-import edu.sdsc.grid.io.GeneralFile;
-import edu.sdsc.grid.io.srb.SRBFile;
-import org.nrg.xdat.om.base.auto.AutoXnatPublicationresource;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.event.EventMetaI;
-import org.nrg.xft.security.UserI;
-import org.nrg.xft.utils.FileUtils;
-import org.nrg.xft.utils.SaveItemHelper;
-import org.nrg.xft.utils.StringUtils;
-import org.nrg.xnat.srb.XNATDirectory;
-import org.nrg.xnat.srb.XNATSrbSearch;
-
-import java.io.File;
-import java.io.FilenameFilter;
-import java.io.IOException;
-import java.net.URI;
-import java.util.ArrayList;
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public class BaseXnatPublicationresource extends AutoXnatPublicationresource {
-
- public BaseXnatPublicationresource(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatPublicationresource(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatPublicationresource(UserI user)
- **/
- public BaseXnatPublicationresource()
- {}
-
- public BaseXnatPublicationresource(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-
- protected ArrayList files=null;
- protected ArrayList fileNames=null;
- /**
- * Returns ArrayList of java.io.File objects
- * @return
- */
- public ArrayList<File> getCorrespondingFiles(String rootPath)
- {
- if (files==null)
- {
- String fullPath = getFullPath(rootPath);
- if (fullPath.endsWith("\\")) {
- fullPath = fullPath.substring(0,fullPath.length() -1);
- }
- if (fullPath.endsWith("/")) {
- fullPath = fullPath.substring(0,fullPath.length() -1);
- }
- /* files = new ArrayList();
- File f = new File(org.nrg.xft.utils.FileUtils.AppendRootPath(rootPath,this.getUri()));
- if (!f.getPath().startsWith("srb:") && !f.getPath().startsWith("http:")){
- if (!f.exists() && !getUri().endsWith(".gz"))
- {
- f = new java.io.File(org.nrg.xft.utils.FileUtils.AppendRootPath(rootPath,this.getUri()) + ".gz");
- }
- }
- files.add(f); */
- files = getAssociatedFilesOnLocalFileSystem(fullPath);
- }
- return files;
- }
-
- /**
- * Returns ArrayList of java.lang.String objects
- * @return
- */
- public ArrayList getCorrespondingFileNames(String rootPath)
- {
- if (fileNames==null)
- {
- fileNames = new ArrayList();
- File f = new File(org.nrg.xft.utils.FileUtils.AppendRootPath(rootPath,this.getUri()));
- if (!f.exists() && !getUri().endsWith(".gz"))
- {
- f = new java.io.File(org.nrg.xft.utils.FileUtils.AppendRootPath(rootPath,this.getUri()) + ".gz");
- }
- fileNames.add(f.getName());
- }
- return fileNames;
- }
- /**
- * Appends this path to the enclosed URI or path variables.
- * @param root
- */
- public void prependPathsWith(String root){
- if (!FileUtils.IsAbsolutePath(this.getUri())){
- try {
- this.setUri(root + this.getUri());
- } catch (Exception e) {
- logger.error("",e);
- }
- }
- }
-
- /**
- * Relatives this path from the first occurrence of the indexOf string.
- * @param indexOf
- */
- public void relativizePaths(String indexOf, boolean caseSensitive){
- String uri = this.getUri();
- if (uri.indexOf(indexOf)==-1){
- if (!caseSensitive){
- int index = uri.toLowerCase().indexOf(indexOf.toLowerCase());
- if (index!=-1){
- this.setUri(uri.substring(index));
- }
- }
- }else{
- this.setUri(uri.substring(uri.indexOf(indexOf)));
- }
- }
-
-
- /**
- * Appends this path to the enclosed URI or path variables.
- * @param root
- */
- public ArrayList<String> getUnresolvedPaths(){
- ArrayList<String> al = new ArrayList<String>();
- String p = getUri();
- p.replace('\\', '/');
- al.add(p);
- return al;
- }
-
- public String getFullPath(String rootPath){
-
- String fullPath = StringUtils.ReplaceStr(FileUtils.AppendRootPath(rootPath,this.getUri()),"\\","/");
- while (fullPath.indexOf("//")!=-1)
- {
- fullPath =StringUtils.ReplaceStr(fullPath,"//","/");
- }
-
- if(!fullPath.endsWith("/"))
- {
- fullPath+="/";
- }
-
- return fullPath;
- }
-
-
- /**
- * Gets the files associated with an image.
- * For an uri which is say like: /data/a.img
- * This method will return all files which match the pattern /data/a.*
- *
- * @return
- */
-
-
- public ArrayList<File> getAssociatedFiles(String rootPath, File tempDir) {
- String fullPath = getFullPath(rootPath);
- if (fullPath.endsWith(File.separator)) {
- fullPath = fullPath.substring(0,fullPath.length() -1);
- }
- if (fullPath.startsWith("srb:"))
- return getAssociatedFilesFromRemoteFileSystem(fullPath,tempDir);
- else
- return getAssociatedFilesOnLocalFileSystem(fullPath);
- }
-
- protected ArrayList<File> getAssociatedFilesFromRemoteFileSystem(String fullPath,File tempDir) {
- ArrayList<File> associatedFiles = new ArrayList();
- int lastIndexOfSlash = fullPath.lastIndexOf(SRBFile.PATH_SEPARATOR);
- if (lastIndexOfSlash != -1) {
- String path = fullPath.substring(0,lastIndexOfSlash);
- try {
- URI uri = new URI(path);
- XNATDirectory srbDir = XNATSrbSearch.getFilesAssociatedWith(uri.getPath(),fullPath.substring(lastIndexOfSlash+1));
- srbDir.importFiles(tempDir);
- ArrayList srbAssociatedFiles = srbDir.getFiles();
- for (int i = 0; i < srbAssociatedFiles.size(); i++) {
- associatedFiles.add(new File(tempDir.getAbsolutePath() + File.separator + ((GeneralFile)srbAssociatedFiles.get(i)).getName()));
- }
- }catch(Exception e) {
- logger.error("Couldnt get Files for " + fullPath,e);
- }
-
- }
- return associatedFiles;
- }
-
- protected ArrayList<File> getAssociatedFilesOnLocalFileSystem(String fullPath) {
- ArrayList<File> associatedFiles = new ArrayList();
- if (!new File(fullPath).exists()) return associatedFiles;
- int lastSlash = fullPath.lastIndexOf("/");
- if (lastSlash==-1){
- lastSlash = fullPath.lastIndexOf("\\");
- }
- String path = "";
- String fileroot = fullPath;
- if (lastSlash != -1) {
- path = fullPath.substring(0, lastSlash);
- fileroot = fullPath.substring(lastSlash+1);
- }
- int indexOfDot = fileroot.lastIndexOf(".");
- if (indexOfDot != -1) {
- fileroot = fileroot.substring(0,indexOfDot);
- }
- final String fileRoot = fileroot;
- File dir = new File(path);
- if (dir.exists() && dir.isDirectory()) {
- FilenameFilter filter = new FilenameFilter() {
- public boolean accept(File dir, String name) {
- return (name.startsWith(fileRoot));
- }
- };
- String[] associatedFileNames = dir.list(filter);
- if (associatedFileNames == null) {
- return associatedFiles;
- }
- for (int i = 0; i < associatedFileNames.length; i++) {
- associatedFiles.add(new File(dir.getAbsolutePath() + File.separator + associatedFileNames[i]));
- }
- }
- return associatedFiles;
- }
-
-
-
- public String getLabel(){
- if (this.getTitle().length()>15)
- {
- return this.getTitle().substring(0,14);
- }else
- return this.getTitle();
- }
-
- public void moveTo(File newSessionDir,String existingSessionDir,String rootPath,UserI user,EventMetaI c) throws IOException,Exception{
- String uri = this.getUri();
-
- String relativePath=null;
- if(existingSessionDir!=null && uri.startsWith(existingSessionDir)){
- relativePath=uri.substring(existingSessionDir.length());
- }else{
- if(FileUtils.IsAbsolutePath(uri)){
- if(uri.indexOf("/")>0){
- relativePath=uri.substring(uri.indexOf("/")+1);
- }else if(uri.indexOf("\\")>0){
- relativePath=uri.substring(uri.indexOf("\\")+1);
- }else{
- relativePath=uri;
- }
- }else{
- relativePath=uri;
- }
- }
-
- File newFile = new File(newSessionDir,relativePath);
- File parentDir=newFile.getParentFile();
- if(!parentDir.exists())
- {
- parentDir.mkdirs();
- }
-
- for(File f: this.getCorrespondingFiles(rootPath)){
- FileUtils.MoveFile(f, new File(parentDir,f.getName()), true, true);
- }
-
- this.setUri(newFile.getAbsolutePath());
- SaveItemHelper.authorizedSave(this,user, true, false,c);
- }
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatPvisitdata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatPvisitdata.java
deleted file mode 100644
index e9910d634cb64fb00fb6ef63d6e34ae6ef18e858..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatPvisitdata.java
+++ /dev/null
@@ -1,306 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatPvisitdata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import java.sql.SQLException;
-import java.util.ArrayList;
-import java.util.Hashtable;
-
-import org.apache.commons.lang.builder.CompareToBuilder;
-import org.apache.commons.lang.builder.EqualsBuilder;
-import org.apache.commons.lang.builder.HashCodeBuilder;
-import org.nrg.xdat.base.BaseElement;
-import org.nrg.xdat.model.XnatExperimentdataShareI;
-import org.nrg.xdat.om.*;
-import org.nrg.xdat.om.base.auto.AutoXnatPvisitdata;
-import org.nrg.xdat.security.SecurityValues;
-import org.nrg.xdat.security.helpers.Permissions;
-import org.nrg.xdat.security.helpers.Users;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-import org.nrg.xft.XFTTable;
-import org.nrg.xft.db.MaterializedView;
-import org.nrg.xft.db.ViewManager;
-import org.nrg.xft.event.EventMetaI;
-import org.nrg.xft.exception.DBPoolException;
-import org.nrg.xft.exception.ElementNotFoundException;
-import org.nrg.xft.exception.XFTInitException;
-import org.nrg.xft.identifier.IDGeneratorFactory;
-import org.nrg.xft.identifier.IDGeneratorI;
-import org.nrg.xft.search.CriteriaCollection;
-import org.nrg.xft.search.QueryOrganizer;
-import org.nrg.xft.security.UserI;
-import org.nrg.xft.utils.SaveItemHelper;
-import org.nrg.xft.utils.StringUtils;
-
-public class BaseXnatPvisitdata extends AutoXnatPvisitdata implements Comparable {
-
- public ArrayList<ItemI> getVisits()
- {
- return null;
-
- }
-
- public BaseXnatPvisitdata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatPvisitdata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatHdscandata(UserI user)
- **/
- public BaseXnatPvisitdata()
- {}
-
- public BaseXnatPvisitdata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-
- public static XnatPvisitdata GetVisitByProjectIdentifier(String project, String identifier,UserI user,boolean preLoad){
- if(StringUtils.IsEmpty(identifier)){
- return null;
- }
-
- CriteriaCollection cc=new CriteriaCollection("OR");
-
- CriteriaCollection subcc1 = new CriteriaCollection("AND");
- subcc1.addClause("xnat:pvisitData/project", project);
- subcc1.addClause("xnat:pvisitData/label", identifier);
-
- cc.add(subcc1);
-
- CriteriaCollection subcc2 = new CriteriaCollection("AND");
- subcc2.addClause("xnat:pvisitData/sharing/share/project", project);
- subcc2.addClause("xnat:pvisitData/sharing/share/label", identifier);
-
- cc.add(subcc2);
-
- ArrayList al = XnatPvisitdata.getXnatPvisitdatasByField(cc, user, preLoad);
- al = BaseElement.WrapItems(al);
- if (al.size()>0){
- return (XnatPvisitdata)al.get(0);
- }else{
- return null;
- }
-
- }
-
- public XnatSubjectdata getSubjectData()
- {
- XnatSubjectdata subject = null;
-
- if (getSubjectId()!=null)
- {
- ArrayList al = XnatSubjectdata.getXnatSubjectdatasByField("xnat:subjectData/ID",this.getSubjectId(),this.getUser(),false);
- if (al.size()>0)
- {
- subject = (XnatSubjectdata)al.get(0);
- }
- }
-
- return subject;
- }
-
- public static synchronized String CreateNewID() throws Exception{
- IDGeneratorI generator = IDGeneratorFactory.GetIDGenerator("org.nrg.xnat.turbine.utils.IDGenerator");
- generator.setTable("xnat_pvisitData");
- generator.setDigits(5);
- generator.setColumn("id");
- return generator.generateIdentifier();
- }
-
- public String delete(BaseXnatProjectdata proj, UserI user, boolean removeFiles,EventMetaI c){
- BaseXnatPvisitdata visit=this;
- if(this.getItem().getUser()!=null){
- visit=new BaseXnatPvisitdata(this.getCurrentDBVersion(true));
- }
-
- String msg=visit.canDelete(proj,user);
-
- if(msg!=null){
- logger.error(msg);
- return msg;
- }
-
- if(visit.getProject() != null && !visit.getProject().equals(proj.getId())){
- try {
- SecurityValues values = new SecurityValues();
- values.put(this.getXSIType() + "/project", proj.getId());
-
- if (!Permissions.canDelete(user,visit) && !Permissions.canDelete(user,this.getSchemaElement(),values))
- {
- return "User cannot delete experiments for project " + proj.getId();
- }
-
- int index = 0;
- int match = -1;
- for(XnatExperimentdataShareI pp : visit.getSharing_share()){
- if(pp.getProject().equals(proj.getId())){
- SaveItemHelper.authorizedRemoveChild(visit.getItem(), "xnat:experimentData/sharing/share", ((XnatExperimentdataShare)pp).getItem(), user,c);
- match=index;
- break;
- }
- index++;
- }
-
- if(match==-1)return null;
-
- //TODO:at this point, retrieve all experiments associated with this visit and disassociate them.
-
- this.removeSharing_share(match);
- return null;
- } catch (SQLException e) {
- logger.error("",e);
- return e.getMessage();
- } catch (Exception e) {
- logger.error("",e);
- return e.getMessage();
- }
- }else{
- try {
-
- if(!Permissions.canDelete(user,this)){
- return "User account doesn't have permission to delete this experiment.";
- }
-
- if(removeFiles){
- this.deleteFiles(user,c);
- }
-
- String visitId=visit.getId();
-
- //find any experiments that reference this visit and delete the reference.
- try {
-
- final QueryOrganizer qo = new QueryOrganizer("xnat:experimentdata",user,ViewManager.ALL);
- qo.addField("xnat:experimentdata/ID");
-
- CriteriaCollection where=new CriteriaCollection("AND");
-
- CriteriaCollection cc= new CriteriaCollection("OR");
-
- CriteriaCollection cc2=new CriteriaCollection("AND");
- cc2.addClause("xnat:experimentdata/sharing/share/project", proj.getId());
- cc2.addClause("xnat:experimentdata/sharing/share/visit", visit.getId());
-
- CriteriaCollection cc3=new CriteriaCollection("AND");
- cc3.addClause("xnat:experimentdata/project", proj.getId());
- cc3.addClause("xnat:experimentdata/visit", visit.getId());
-
- cc.addClause(cc2);
- cc.addClause(cc3);
-
- where.addClause(cc);
- qo.setWhere(where);
-
- String query=qo.buildQuery();
-
- String exptIdColumn= qo.getFieldAlias("xnat:experimentdata/ID");
-
- XFTTable table=XFTTable.Execute(query, user.getDBName(), user.getUsername());
- //TODO: these are the visits we're going to have to disassociate.
- table.resetRowCursor();
- while (table.hasMoreRows())
- {
- final Hashtable row = table.nextRowHash();
-
- try {
- final Object exptID = row.get(exptIdColumn.toLowerCase()); //fun, we have to do a toLowerCase because getFieldAlias returns a different case than Execute creates. Hopefully, it will always lowercase it. I am guessing.
- //grab the experiment, clear out visit and save...
- XnatExperimentdata frank = XnatExperimentdata.getXnatExperimentdatasById(exptID.toString(), user, true);
- if(org.apache.commons.lang.StringUtils.equalsIgnoreCase(frank.getVisit(), visitId)){
- XnatExperimentdata new_expt = frank.getLightCopy();
- new_expt.setProperty("xnat:experimentdata/visit", "NULL");
- SaveItemHelper.authorizedSave(new_expt, user, false, false, c);
- } else {
- //the visit must be in the shared project, then. So, we need to clear that out...
- //TODO: implement this.
- throw new Exception("Unable to delete a shared project's visit from an experiment because the feature is not implemented.");
- }
- } catch (XFTInitException e) {
- logger.error("",e);
- } catch (ElementNotFoundException e) {
- logger.error("",e);
- }
- }
-
- } catch (SQLException e) {
- e.printStackTrace();
- } catch (DBPoolException e) {
- e.printStackTrace();
- } catch (Exception e) {
- e.printStackTrace();
- }
-
-
- SaveItemHelper.authorizedDelete(visit.getItem().getCurrentDBVersion(), user,c);
-
- Users.clearCache(user);
- MaterializedView.deleteByUser(user);
-
- } catch (SQLException e) {
- logger.error("",e);
- return e.getMessage();
- } catch (Exception e) {
- logger.error("",e);
- return e.getMessage();
- }
- }
- return null;
- }
-
- public int hashCode() {
- return new HashCodeBuilder(11, 37). // two randomly chosen prime numbers
- // if deriving: appendSuper(super.hashCode()).
- append(this.getVisitName()).
- append(this.getSubjectId()).
- append(this.getVisitType()).
-
- toHashCode();
- }
-
- public boolean equals(Object obj) {
- if (obj == null)
- return false;
- if (obj == this)
- return true;
- if (obj.getClass() != getClass())
- return false;
-
- BaseXnatPvisitdata rhs = (BaseXnatPvisitdata) obj;
- return new EqualsBuilder().
- // if deriving: appendSuper(super.equals(obj)).
- append(this.getVisitName(), rhs.getVisitName()).
- append(this.getSubjectId(), rhs.getSubjectId()).
- append(this.getVisitType(), rhs.getVisitType()).
-
- isEquals();
- }
-
- @Override
- public int compareTo(Object obj) {
- BaseXnatPvisitdata rhs = (BaseXnatPvisitdata) obj;
-
- return new CompareToBuilder().
- //if deriving: .appendSuper(super.compareTo(o)).
- append(this.getVisitName(), rhs.getVisitName()).
- append(this.getSubjectId(), rhs.getSubjectId()).
- append(this.getVisitType(), rhs.getVisitType()).
- toComparison();
- }
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatQcassessmentdata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatQcassessmentdata.java
deleted file mode 100644
index b270a1e387519cbc24168df538e7fce276a90ccf..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatQcassessmentdata.java
+++ /dev/null
@@ -1,75 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatQcassessmentdata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.XnatQcassessmentdataScan;
-import org.nrg.xdat.om.base.auto.AutoXnatQcassessmentdata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-import org.nrg.xnat.scanAssessors.ScanAssessorI;
-import org.nrg.xnat.scanAssessors.ScanAssessorScanI;
-
-import java.util.Hashtable;
-import java.util.List;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatQcassessmentdata extends AutoXnatQcassessmentdata implements ScanAssessorI{
-
- public BaseXnatQcassessmentdata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatQcassessmentdata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatQcassessmentdata(UserI user)
- **/
- public BaseXnatQcassessmentdata()
- {}
-
- public BaseXnatQcassessmentdata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
- public ScanAssessorScanI getScanById(String scanId){
- XnatQcassessmentdataScan rtn = null;
- if (scanId == null) throw new NullPointerException("Expected a non-null value for the scan id input parameter");
- List<XnatQcassessmentdataScan> scans = super.getScans_scan();
- if (scans != null && scans.size() > 0) {
- for (int i=0; i< scans.size(); i++) {
- XnatQcassessmentdataScan aScan = (XnatQcassessmentdataScan)scans.get(i);
- if (aScan.getId().equals(scanId)) {
- rtn = aScan;
- break;
- }
- }
- }
- if (rtn == null) throw new NullPointerException("Couldnt find QC assessment for scan id " + scanId);
- return rtn;
- }
-
- public String getHeader(){
- return this.getType();
- }
-
- public int getPrecedence(){
- return 3;
- }
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatQcassessmentdataScan.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatQcassessmentdataScan.java
deleted file mode 100644
index d5a3f76a3469087fab87282d2d99ea853b289665..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatQcassessmentdataScan.java
+++ /dev/null
@@ -1,52 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatQcassessmentdataScan
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatQcassessmentdataScan;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-import org.nrg.xnat.scanAssessors.ScanAssessorScanI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatQcassessmentdataScan extends AutoXnatQcassessmentdataScan implements ScanAssessorScanI{
-
- public BaseXnatQcassessmentdataScan(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatQcassessmentdataScan(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatQcassessmentdataScan(UserI user)
- **/
- public BaseXnatQcassessmentdataScan()
- {}
-
- public BaseXnatQcassessmentdataScan(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
- public String getSummary(){
- return "Present";
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatQcassessmentdataScanSlice.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatQcassessmentdataScanSlice.java
deleted file mode 100644
index cb31dcd6f2db5f875baf95e72cef5519862c37cb..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatQcassessmentdataScanSlice.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatQcassessmentdataScanSlice
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatQcassessmentdataScanSlice;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatQcassessmentdataScanSlice extends AutoXnatQcassessmentdataScanSlice {
-
- public BaseXnatQcassessmentdataScanSlice(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatQcassessmentdataScanSlice(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatQcassessmentdataScanSlice(UserI user)
- **/
- public BaseXnatQcassessmentdataScanSlice()
- {}
-
- public BaseXnatQcassessmentdataScanSlice(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatQcmanualassessordata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatQcmanualassessordata.java
deleted file mode 100644
index f193d814c9cbee7ceea0adcb30a9317fb5f9e741..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatQcmanualassessordata.java
+++ /dev/null
@@ -1,67 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatQcmanualassessordata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.XnatQcscandata;
-import org.nrg.xdat.om.base.auto.AutoXnatQcmanualassessordata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-import org.nrg.xnat.scanAssessors.ScanAssessorI;
-import org.nrg.xnat.scanAssessors.ScanAssessorScanI;
-
-import java.util.Hashtable;
-import java.util.List;
-
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatQcmanualassessordata extends AutoXnatQcmanualassessordata implements ScanAssessorI{
- public BaseXnatQcmanualassessordata(ItemI item) {
- super(item);
- }
-
- public BaseXnatQcmanualassessordata(UserI user) {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatQcmanualassessordata(UserI user)
- */
- public BaseXnatQcmanualassessordata() {
- }
-
- public BaseXnatQcmanualassessordata(Hashtable properties, UserI user) {
- super(properties, user);
- }
-
- public ScanAssessorScanI getScanById(String scanId){
- XnatQcscandata rtn = null;
- if (scanId == null) throw new NullPointerException("Expected a non-null value for the scan id input parameter");
- List<XnatQcscandata> scans = super.getScans_scan();
- if (scans != null && scans.size() > 0) {
- for (int i=0; i< scans.size(); i++) {
- XnatQcscandata aScan = (XnatQcscandata)scans.get(i);
- if (aScan.getImagescanId().equals(scanId)) {
- rtn = aScan;
- break;
- }
- }
- }
- if (rtn == null) throw new NullPointerException("Couldnt find manual QC assessment for scan id " + scanId);
- return rtn;
- }
-
- public String getHeader(){
- return "Manual QC";
- }
-
- public int getPrecedence(){
- return 2;
- }
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatQcscandata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatQcscandata.java
deleted file mode 100644
index e3470e660d9cbca5c02d4c19a96f08ca0a7ce630..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatQcscandata.java
+++ /dev/null
@@ -1,52 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatQcscandata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatQcscandata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-import org.nrg.xnat.scanAssessors.ScanAssessorScanI;
-
-import java.util.Hashtable;
-
-
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatQcscandata extends AutoXnatQcscandata implements ScanAssessorScanI{
- public BaseXnatQcscandata(ItemI item) {
- super(item);
- }
-
- public BaseXnatQcscandata(UserI user) {
- super(user);
- }
-
- public BaseXnatQcscandata() {
- }
-
- public BaseXnatQcscandata(Hashtable properties, UserI user) {
- super(properties, user);
- }
-
- public String getSummary(){
- String status = getPass();
- String summary = "<span>Unknown</span>";
- if(status!=null){
- if(status.equals("1")||status.equalsIgnoreCase("pass")){
- summary = "<span style=\"color:green\">Passed</span>";
- }
- else if(status.equals("0")||status.equalsIgnoreCase("fail")){
- summary = "<span style=\"color:red\">Failed</span>";
- }
- }
- return summary;
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatQcscandataField.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatQcscandataField.java
deleted file mode 100644
index 61384bc23c5eeb5dd8aaa0938f60c3be3ec84c3b..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatQcscandataField.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatQcscandataField
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatQcscandataField;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatQcscandataField extends AutoXnatQcscandataField {
-
- public BaseXnatQcscandataField(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatQcscandataField(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatQcscandataField(UserI user)
- **/
- public BaseXnatQcscandataField()
- {}
-
- public BaseXnatQcscandataField(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatReconstructedimagedata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatReconstructedimagedata.java
deleted file mode 100644
index d99ae4c64cce8487c6aab7d966e65081d84c578f..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatReconstructedimagedata.java
+++ /dev/null
@@ -1,186 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatReconstructedimagedata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.model.XnatAbstractresourceI;
-import org.nrg.xdat.om.*;
-import org.nrg.xdat.om.base.BaseXnatExperimentdata.UnknownPrimaryProjectException;
-import org.nrg.xdat.om.base.auto.AutoXnatReconstructedimagedata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-import org.nrg.xft.utils.FileUtils;
-import org.nrg.xft.utils.StringUtils;
-import org.nrg.xnat.exceptions.InvalidArchiveStructure;
-
-import java.io.File;
-import java.util.ArrayList;
-import java.util.Hashtable;
-import java.util.List;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public class BaseXnatReconstructedimagedata extends AutoXnatReconstructedimagedata {
-
- public BaseXnatReconstructedimagedata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatReconstructedimagedata(UserI user)
- {
- super(user);
- }
-
- public BaseXnatReconstructedimagedata()
- {}
-
- public BaseXnatReconstructedimagedata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
- private XnatImagesessiondata mr = null;
-
- public XnatImagesessiondata getImageSessionData()
- {
- if (mr==null)
- {
- ArrayList al = XnatImagesessiondata.getXnatImagesessiondatasByField("xnat:imageSessionData/ID",this.getImageSessionId(),this.getUser(),false);
- if (al.size()>0)
- {
- mr = (XnatImagesessiondata)al.get(0);
- }
- }
-
- return mr;
- }
-
- public void setImageSessionData(XnatImagesessiondata ses){
- mr=ses;
- }
-
- public ArrayList getOutFileByContent(String content) {
-
- ArrayList files = new ArrayList();
-
- List outFiles = getOut_file();
-
- if (outFiles == null || outFiles.size() == 0) return files;
-
- for (int i = 0 ; i < outFiles.size(); i++) {
-
- XnatAbstractresource absrsc = (XnatAbstractresource) outFiles.get(i);
-
- String rcontent = null;
-
- if (absrsc instanceof XnatResource) {
-
- XnatResource resource = (XnatResource)outFiles.get(i);
-
- rcontent = resource.getContent();
-
- }
-
- if (rcontent != null && content != null && rcontent.equals(content)) {
-
- files.add(absrsc);
-
- }
-
- }
-
- return files;
-
- }
-
- public ArrayList getComputationByName(String name) {
-
- ArrayList rtn = new ArrayList();
-
- List datums = this.getComputations_datum();
-
- if (datums == null || datums.size() == 0) {
-
- return rtn;
-
- }
-
- for (int i = 0; i < datums.size(); i++) {
-
- XnatComputationdata aDatum = (XnatComputationdata)datums.get(i);
-
- if (aDatum.getName().equals(name)) {
-
- rtn.add(datums.get(i));
-
- }
-
- }
-
- return rtn;
-
- }
-
-
- public File getExpectedSessionDir() throws InvalidArchiveStructure, UnknownPrimaryProjectException{
- return this.getImageSessionData().getExpectedSessionDir();
- }
- @Override
- public void preSave() throws Exception{
- super.preSave();
- if(this.getImageSessionData()==null){
- throw new Exception("Unable to identify image session for:" + this.getImageSessionId());
- }
- final String expectedPath=this.getExpectedSessionDir().getAbsolutePath().replace('\\', '/');
-
- validate(expectedPath);
- }
-
- public void validate(String expectedPath) throws Exception{
-
- if(StringUtils.IsEmpty(this.getId())){
- throw new IllegalArgumentException();
- }
-
- if(!StringUtils.IsAlphaNumericUnderscore(getId())){
- throw new IllegalArgumentException("Identifiers cannot use special characters.");
- }
-
- for(final XnatAbstractresourceI res: this.getOut_file()){
- final String uri;
- if(res instanceof XnatResource){
- uri=((XnatResource)res).getUri();
- }else if(res instanceof XnatResourceseries){
- uri=((XnatResourceseries)res).getPath();
- }else{
- continue;
- }
-
- FileUtils.ValidateUriAgainstRoot(uri,expectedPath,"URI references data outside of the project:" + uri);
- }
-
- for(final XnatAbstractresourceI res: this.getIn_file()){
- final String uri;
- if(res instanceof XnatResource){
- uri=((XnatResource)res).getUri();
- }else if(res instanceof XnatResourceseries){
- uri=((XnatResourceseries)res).getPath();
- }else{
- continue;
- }
-
- FileUtils.ValidateUriAgainstRoot(uri,expectedPath,"URI references data outside of the project:" + uri);
-}
- }
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatReconstructedimagedataScanid.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatReconstructedimagedataScanid.java
deleted file mode 100644
index 698cd72a6be0f6e4cc0222239684b1a3e3563e23..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatReconstructedimagedataScanid.java
+++ /dev/null
@@ -1,44 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatReconstructedimagedataScanid
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatReconstructedimagedataScanid;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public class BaseXnatReconstructedimagedataScanid extends AutoXnatReconstructedimagedataScanid {
-
- public BaseXnatReconstructedimagedataScanid(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatReconstructedimagedataScanid(UserI user)
- {
- super(user);
- }
-
- public BaseXnatReconstructedimagedataScanid()
- {}
-
- public BaseXnatReconstructedimagedataScanid(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatRegionresource.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatRegionresource.java
deleted file mode 100644
index f067ef410d1451ba11ceda62c4efc6c477f02318..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatRegionresource.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatRegionresource
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatRegionresource;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public class BaseXnatRegionresource extends AutoXnatRegionresource {
-
- public BaseXnatRegionresource(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatRegionresource(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatRegionresource(UserI user)
- **/
- public BaseXnatRegionresource()
- {}
-
- public BaseXnatRegionresource(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatRegionresourceLabel.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatRegionresourceLabel.java
deleted file mode 100644
index 4e5da4588bae9357e0800fc5c44066dcc74c2467..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatRegionresourceLabel.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatRegionresourceLabel
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatRegionresourceLabel;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public class BaseXnatRegionresourceLabel extends AutoXnatRegionresourceLabel {
-
- public BaseXnatRegionresourceLabel(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatRegionresourceLabel(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatRegionresourceLabel(UserI user)
- **/
- public BaseXnatRegionresourceLabel()
- {}
-
- public BaseXnatRegionresourceLabel(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatResource.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatResource.java
deleted file mode 100644
index 25b272b0279fc81263be19a4b4a9ba82db65301b..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatResource.java
+++ /dev/null
@@ -1,336 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatResource
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 11/18/13 9:35 AM
- */
-package org.nrg.xdat.om.base;
-
-import java.io.File;
-import java.io.FilenameFilter;
-import java.io.IOException;
-import java.net.URI;
-import java.util.ArrayList;
-import java.util.Hashtable;
-
-import org.nrg.xdat.om.base.auto.AutoXnatResource;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.event.EventMetaI;
-import org.nrg.xft.security.UserI;
-import org.nrg.xft.utils.FileUtils;
-import org.nrg.xft.utils.SaveItemHelper;
-import org.nrg.xft.utils.StringUtils;
-import org.nrg.xnat.srb.XNATDirectory;
-import org.nrg.xnat.srb.XNATSrbSearch;
-
-import edu.sdsc.grid.io.GeneralFile;
-import edu.sdsc.grid.io.srb.SRBFile;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public class BaseXnatResource extends AutoXnatResource {
-
- public BaseXnatResource(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatResource(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatResource(UserI user)
- **/
- public BaseXnatResource()
- {}
-
- public BaseXnatResource(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-
- protected ArrayList files=null;
- protected ArrayList fileNames=null;
- /**
- * Returns ArrayList of java.io.File objects
- * @return
- */
- public ArrayList<File> getCorrespondingFiles(String rootPath)
- {
- if (files==null)
- {
- String fullPath = getFullPath(rootPath);
- if (fullPath.endsWith("\\")) {
- fullPath = fullPath.substring(0,fullPath.length() -1);
- }
- if (fullPath.endsWith("/")) {
- fullPath = fullPath.substring(0,fullPath.length() -1);
- }
- files = getAssociatedFilesOnLocalFileSystem(fullPath);
- }
- return files;
- }
-
- public ArrayList<File> getCorrespondingFiles()
- {
- if (files==null || files.size()==0)
- {
- if (getUri().startsWith("file:")) {
- try {
- URI uri = new URI(getUri());
- File file = new File(uri);
- files = getAssociatedFilesOnLocalFileSystem(file.getAbsolutePath());
- }catch(Exception e) {
-
- }
- }
- }
- return files;
- }
-
- /**
- * Returns ArrayList of java.lang.String objects
- * @return
- */
- public ArrayList getCorrespondingFileNames(String rootPath)
- {
- if (fileNames==null)
- {
- fileNames = new ArrayList();
- File f = new File(org.nrg.xft.utils.FileUtils.AppendRootPath(rootPath,this.getUri()));
- if (!f.exists() && !getUri().endsWith(".gz"))
- {
- f = new java.io.File(org.nrg.xft.utils.FileUtils.AppendRootPath(rootPath,this.getUri()) + ".gz");
- }
- fileNames.add(f.getName());
- }
- return fileNames;
- }
- /**
- * Prepends this path to the enclosed URI or path variables.
- * @param root
- */
- public void prependPathsWith(String root){
- if (!FileUtils.IsAbsolutePath(this.getUri())){
- try {
- this.setUri(root + this.getUri());
- } catch (Exception e) {
- logger.error("",e);
- }
- }
- }
-
- /**
- * Relatives this path from the first occurrence of the indexOf string.
- * @param indexOf
- */
- public void relativizePaths(String indexOf, boolean caseSensitive){
- String uri = this.getUri();
- uri= uri.replace('\\', '/');
- if (uri.indexOf(indexOf)==-1){
- if (!caseSensitive){
- int index = uri.toLowerCase().indexOf(indexOf.toLowerCase());
- if (index!=-1){
- this.setUri(uri.substring(index + 1));
- }
- }
- }else{
- this.setUri(uri.substring(uri.indexOf(indexOf) + 1));
- }
- }
-
-
- /**
- * Appends this path to the enclosed URI or path variables.
- * @param root
- */
- public ArrayList<String> getUnresolvedPaths(){
- ArrayList<String> al = new ArrayList<String>();
- String p = getUri();
- p.replace('\\', '/');
- al.add(p);
- return al;
- }
-
- public String getFullPath(String rootPath){
-
- String fullPath = StringUtils.ReplaceStr(FileUtils.AppendRootPath(rootPath,this.getUri()),"\\","/");
- while (fullPath.indexOf("//")!=-1)
- {
- fullPath =StringUtils.ReplaceStr(fullPath,"//","/");
- }
-
- if(!fullPath.endsWith("/"))
- {
- fullPath+="/";
- }
-
- return fullPath;
- }
-
- /**
- * Gets the files associated with an image.
- * For an uri which is say like: /data/a.img
- * This method will return all files which match the pattern /data/a.*
- *
- * @return
- */
-
-
- public ArrayList<File> getAssociatedFiles(String rootPath, File tempDir) {
- String fullPath = getFullPath(rootPath);
- if (fullPath.endsWith(File.separator)) {
- fullPath = fullPath.substring(0,fullPath.length() -1);
- }
- if (fullPath.startsWith("srb:"))
- return getAssociatedFilesFromRemoteFileSystem(fullPath,tempDir);
- else
- return getAssociatedFilesOnLocalFileSystem(fullPath);
- }
-
- protected ArrayList<File> getAssociatedFilesFromRemoteFileSystem(String fullPath,File tempDir) {
- ArrayList<File> associatedFiles = new ArrayList();
- int lastIndexOfSlash = fullPath.lastIndexOf(SRBFile.PATH_SEPARATOR);
- if (lastIndexOfSlash != -1) {
- String path = fullPath.substring(0,lastIndexOfSlash);
- try {
- URI uri = new URI(path);
- XNATDirectory srbDir = XNATSrbSearch.getFilesAssociatedWith(uri.getPath(),fullPath.substring(lastIndexOfSlash+1));
- srbDir.importFiles(tempDir);
- ArrayList srbAssociatedFiles = srbDir.getFiles();
- for (int i = 0; i < srbAssociatedFiles.size(); i++) {
- associatedFiles.add(new File(tempDir.getAbsolutePath() + File.separator + ((GeneralFile)srbAssociatedFiles.get(i)).getName()));
- }
- }catch(Exception e) {
- logger.error("Couldnt get Files for " + fullPath,e);
- }
-
- }
- return associatedFiles;
- }
-
- protected File getFileOnLocalFileSystem(String fullPath) {
- File f = new File(fullPath);
- if (!f.exists()){
- if (!fullPath.endsWith(".gz")){
- f= new File(fullPath + ".gz");
- if (!f.exists()){
- logger.debug("Unable to find file:" + fullPath);
- return null;
- }
- }else{
- return null;
- }
- }
-
- return f;
- }
-
- protected ArrayList<File> getAssociatedFilesOnLocalFileSystem(String fullPath) {
- ArrayList<File> associatedFiles = new ArrayList();
- if (!new File(fullPath).exists()){
- if (!fullPath.endsWith(".gz")){
- if (!new File(fullPath +".gz").exists())return associatedFiles;
- }else{
- return associatedFiles;
- }
- }
- int lastSlash = fullPath.lastIndexOf("/");
- if (lastSlash==-1){
- lastSlash = fullPath.lastIndexOf("\\");
- }
- String path = "";
- String fileroot = fullPath;
- if (lastSlash != -1) {
- path = fullPath.substring(0, lastSlash);
- fileroot = fullPath.substring(lastSlash+1);
- }
- int indexOfDot = (fileroot.toLowerCase().lastIndexOf(".ima")!=-1 ?fileroot.toLowerCase().lastIndexOf(".ima") : fileroot.toLowerCase().lastIndexOf(".img"));
- if (indexOfDot != -1) {
- fileroot = fileroot.substring(0,indexOfDot);
- final String fileRoot = fileroot;
- File dir = new File(path);
- if (dir.exists() && dir.isDirectory()) {
- FilenameFilter filter = new FilenameFilter() {
- public boolean accept(File dir, String name) {
- return (name.startsWith(fileRoot));
- }
- };
- String[] associatedFileNames = dir.list(filter);
- if (associatedFileNames == null) {
- return associatedFiles;
- }
- for (int i = 0; i < associatedFileNames.length; i++) {
- associatedFiles.add(new File(dir.getAbsolutePath() + File.separator + associatedFileNames[i]));
- }
- }
- }else{
- if (!new File(fullPath).exists()){
- if (!fullPath.endsWith(".gz")){
- if (new File(fullPath +".gz").exists()){
- associatedFiles.add(new File(fullPath +".gz"));
- }
- }
- }else{
- associatedFiles.add(new File(fullPath));
- }
- }
- return associatedFiles;
- }
-
- public void moveTo(File newSessionDir,String existingSessionDir,String rootPath,UserI user,EventMetaI ci) throws IOException,Exception{
- String uri = this.getUri();
-
- String relativePath=null;
- if(existingSessionDir!=null && uri.startsWith(existingSessionDir)){
- relativePath=uri.substring(existingSessionDir.length());
- }else{
- if(FileUtils.IsAbsolutePath(uri)){
- if(uri.indexOf("/")>0){
- relativePath=uri.substring(uri.indexOf("/")+1);
- }else if(uri.indexOf("\\")>0){
- relativePath=uri.substring(uri.indexOf("\\")+1);
- }else{
- relativePath=uri;
- }
- }else{
- relativePath=uri;
- }
- }
-
- File newFile = new File(newSessionDir,relativePath);
- File parentDir=newFile.getParentFile();
- if(!parentDir.exists())
- {
- parentDir.mkdirs();
- }
-
- for(File f: this.getCorrespondingFiles(rootPath)){
- FileUtils.MoveFile(f, new File(parentDir,f.getName()), true, true);
- }
-
- this.setUri(newFile.getAbsolutePath());
- SaveItemHelper.authorizedSave(this,user, true, false,ci);
- }
-
- @Override
- public String getUri() {
- if( super.getUri()!=null){
- return super.getUri().replace('\\', '/');
- }else{
- return null;
- }
- }
-
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatResourcecatalog.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatResourcecatalog.java
deleted file mode 100644
index 12ef36b7f44acbe8d8f04f8c98db94b3bc8a921f..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatResourcecatalog.java
+++ /dev/null
@@ -1,359 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatResourcecatalog
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 10/14/13 5:42 PM
- */
-package org.nrg.xdat.om.base;
-
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.io.InputStream;
-import java.util.ArrayList;
-import java.util.Hashtable;
-import java.util.Iterator;
-import java.util.zip.GZIPInputStream;
-
-import org.nrg.xdat.bean.CatCatalogBean;
-import org.nrg.xdat.bean.CatEntryBean;
-import org.nrg.xdat.bean.base.BaseElement;
-import org.nrg.xdat.bean.reader.XDATXMLReader;
-import org.nrg.xdat.model.CatCatalogI;
-import org.nrg.xdat.model.CatEntryI;
-import org.nrg.xdat.om.base.auto.AutoXnatResourcecatalog;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.event.EventMetaI;
-import org.nrg.xft.event.EventUtils;
-import org.nrg.xft.security.UserI;
-import org.nrg.xft.utils.FileUtils;
-import org.nrg.xft.utils.SaveItemHelper;
-import org.nrg.xft.utils.StringUtils;
-import org.nrg.xnat.utils.CatalogUtils;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatResourcecatalog extends AutoXnatResourcecatalog {
-
- public BaseXnatResourcecatalog(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatResourcecatalog(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatResourcecatalog(UserI user)
- **/
- public BaseXnatResourcecatalog()
- {}
-
- public BaseXnatResourcecatalog(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
- /**
- * Returns ArrayList of java.io.File objects
- * @return
- */
- public ArrayList getCorrespondingFiles(String rootPath)
- {
- if (files==null)
- {
- files = new ArrayList<File>();
-
- final File catFile = this.getCatalogFile(rootPath);
- final String parentPath=catFile.getParent();
- final CatCatalogBean cat=CatalogUtils.getCatalog(rootPath, this);
-
- if (cat!=null){
- for(CatEntryI entry: cat.getEntries_entry()){
- String entryPath = StringUtils.ReplaceStr(FileUtils.AppendRootPath(parentPath,entry.getUri()),"\\","/");
- File temp=getFileOnLocalFileSystem(entryPath);
- if(temp!=null)
- files.add(temp);
- }
- }
-
- }
- return files;
- }
-
- public void clearFiles() {
- files = null;
- }
-
-
- /**
- * Returns ArrayList of java.lang.String objects
- * @return
- */
- public ArrayList getCorrespondingFileNames(String rootPath)
- {
- if (fileNames==null)
- {
- fileNames = new ArrayList();
- ArrayList files = getCorrespondingFiles(rootPath);
- for (int i=0;i<files.size();i++){
- File f = (File)files.get(i);
- fileNames.add(f.getName());
- }
- }
- return fileNames;
- }
-
- /**
- * Appends this path to the enclosed URI or path variables.
- * @param root
- */
- public void prependPathsWith(String root){
- if (!FileUtils.IsAbsolutePath(this.getUri())){
- try {
- this.setUri(root + this.getUri());
- } catch (Exception e) {
- logger.error("",e);
- }
- }
- }
-
- public File getCatalogFile(String rootPath){
- return CatalogUtils.getCatalogFile(rootPath, this);
- }
-
- public CatCatalogBean getCatalog(String rootPath){
- return CatalogUtils.getCatalog(rootPath, this);
- }
-
- public static void backupEntry(String parentPath,CatCatalogBean cat,UserI user, EventMetaI c, String timestamp) throws FileNotFoundException, IOException{
- if (cat!=null){
- for(CatEntryI entry: cat.getEntries_entry()){
- final File f = new File(parentPath,entry.getUri());
- final File newFile=FileUtils.CopyToHistory(f,timestamp);
- entry.setUri(newFile.getAbsolutePath());
- ((CatEntryBean)entry).setModifiedtime(EventUtils.getEventDate(c, false));
- if(user!=null){
- entry.setModifiedby(user.getUsername());
- }
-
- if(c!=null && c.getEventId()!=null){
- entry.setModifiedeventid(Integer.valueOf(c.getEventId().intValue()));
- }
- }
- }
- }
-
- public void backupToHistory(String rootPath,UserI user, EventMetaI c) throws Exception{
- final File f = this.getCatalogFile(rootPath);
- final String parentPath=f.getParentFile().getAbsolutePath();
- final CatCatalogBean cat=CatalogUtils.getCatalog(rootPath,this);
-
- if(cat!=null){
- String timestamp=EventUtils.getTimestamp(c);
- backupEntry(parentPath, cat, user, c,timestamp);
- CatalogUtils.writeCatalogToFile(cat, FileUtils.BuildHistoryFile(f,timestamp));
- }
- }
-
-
-
- public void deleteWithBackup(String rootPath, UserI user, EventMetaI c) throws Exception{
- if(CatalogUtils.maintainFileHistory()){
- backupToHistory(rootPath, user, c);
- }
-
- deleteFromFileSystem(rootPath);
- }
-
- public void deleteFromFileSystem(String rootPath){
- super.deleteFromFileSystem(rootPath);
-
- final File f = this.getCatalogFile(rootPath);
-
- if (f.exists()){
- try {
- FileUtils.MoveToCache(f);
- if(FileUtils.CountFiles(f.getParentFile(),true)==0){
- FileUtils.DeleteFile(f.getParentFile());
- }
- } catch (FileNotFoundException e) {
- logger.error("",e);
- } catch (IOException e) {
- logger.error("",e);
- }
- }
- }
-
- public int entryCount =0;
- public boolean formalizeCatalog(CatCatalogI cat, String catPath,UserI user, EventMetaI now){
- return CatalogUtils.formalizeCatalog(cat,catPath,user,now);
- }
-
- public CatCatalogBean getCleanCatalog(String rootPath,boolean includeFullPaths,UserI user, EventMetaI c){
- return CatalogUtils.getCleanCatalog(rootPath, this, includeFullPaths,user,c);
- }
-
- public void clearCountAndSize() {
- count = null;
- size = null;
- }
-
- Integer count = null;
- public Integer getCount(String rootPath){
- if (count ==null){
- long sizeI = 0;
- int countI = 0;
- Iterator files = this.getCorrespondingFiles(rootPath).iterator();
- while (files.hasNext()){
- File f = (File)files.next();
-
- if (f!=null && f.exists() && !f.getName().endsWith("catalog.xml")){
- countI++;
- sizeI+=f.length();
- }
- }
-
- size = new Long(sizeI);
- count = new Integer(countI);
- }
- return count;
- }
-
- Long size = null;
- public long getSize(String rootPath){
- if (size ==null){
- long sizeI = 0;
- int countI = 0;
- Iterator files = this.getCorrespondingFiles(rootPath).iterator();
- while (files.hasNext()){
- File f = (File)files.next();
- if (!f.getName().endsWith("catalog.xml")){
- countI++;
- sizeI+=f.length();
- }
- }
-
- size = new Long(sizeI);
- count = new Integer(countI);
- }
- return size.longValue();
- }
-
- public void moveTo(File newSessionDir,String existingSessionDir,String rootPath,UserI user,EventMetaI ci) throws IOException,Exception{
- String uri = this.getUri();
-
- String relativePath=null;
- if(existingSessionDir!=null && uri.startsWith(existingSessionDir)){
- relativePath=uri.substring(existingSessionDir.length());
- }else{
- if(FileUtils.IsAbsolutePath(uri)){
- if(uri.indexOf("/")>0){
- relativePath=uri.substring(uri.indexOf("/")+1);
- }else if(uri.indexOf("\\")>0){
- relativePath=uri.substring(uri.indexOf("\\")+1);
- }else{
- relativePath=uri;
- }
- }else{
- relativePath=uri;
- }
- }
-
- File newFile = new File(newSessionDir,relativePath);
- File parentDir=newFile.getParentFile();
- if(!parentDir.exists())
- {
- parentDir.mkdirs();
- }
-
- File catalog =this.getCatalogFile(rootPath);
-
- InputStream fis = new FileInputStream(catalog);
- if (catalog.getName().endsWith(".gz"))
- {
- fis = new GZIPInputStream(fis);
- }
- XDATXMLReader reader = new XDATXMLReader();
- BaseElement base = reader.parse(fis);
-
- if (base instanceof CatCatalogBean){
- moveCatalogEntries((CatCatalogBean)base,catalog.getParent(),newFile.getParent());
- }
-
- try {
- FileWriter fw = new FileWriter(catalog);
- base.toXML(fw, true);
- fw.close();
- } catch (IOException e) {
- logger.error("",e);
- }
-
- FileUtils.MoveFile(catalog, newFile, true, true);
-
- this.setUri(newFile.getAbsolutePath());
- SaveItemHelper.authorizedSave(this,user, true, false,ci);
- }
-
- public void moveCatalogEntries(CatCatalogI cat,String existingRootPath,String newRootPath) throws IOException{
- for(CatEntryI entry: cat.getEntries_entry()){
- File existingLocation=null;
- String relativePath=null;
-
- String uri= entry.getUri();
- if(FileUtils.IsAbsolutePath(entry.getUri())){
- existingLocation=new File(entry.getUri());
- if(entry.getUri().startsWith(existingRootPath)){
- relativePath=uri.substring(existingRootPath.length());
- }else{
- if(FileUtils.IsAbsolutePath(entry.getUri())){
- if(entry.getUri().indexOf("/")>0){
- relativePath=uri.substring(entry.getUri().indexOf("/")+1);
- }else if(uri.indexOf("\\")>0){
- relativePath=uri.substring(entry.getUri().indexOf("\\")+1);
- }else{
- relativePath=uri;
- }
- }else{
- relativePath=uri;
- }
- }
- ((CatEntryBean)entry).setUri(relativePath);
- }else{
- existingLocation=new File(existingRootPath,uri);
- relativePath=uri;
- }
-
-
-
- File newFile = new File(newRootPath,relativePath);
- File parentDir=newFile.getParentFile();
- if(!parentDir.exists())
- {
- parentDir.mkdirs();
- }
-
- if(!existingLocation.exists())
- existingLocation=getFileOnLocalFileSystem(existingLocation.getAbsolutePath());
-
- if(existingLocation!=null && existingLocation.exists()){
- FileUtils.MoveFile(existingLocation, newFile, true, true);
- }
- }
-
- for(CatCatalogI subset: cat.getSets_entryset()){
- moveCatalogEntries(subset, existingRootPath, newRootPath);
- }
- }
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatResourceseries.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatResourceseries.java
deleted file mode 100644
index 2544fb1d145799e046e2804d7b31a0afa8094a3f..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatResourceseries.java
+++ /dev/null
@@ -1,292 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatResourceseries
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 11/18/13 9:35 AM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatResourceseries;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.event.EventMetaI;
-import org.nrg.xft.event.EventUtils;
-import org.nrg.xft.security.UserI;
-import org.nrg.xft.utils.FileUtils;
-import org.nrg.xft.utils.FileUtils.OldFileHandlerI;
-import org.nrg.xft.utils.SaveItemHelper;
-import org.nrg.xft.utils.StringUtils;
-
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FilenameFilter;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Hashtable;
-import java.util.regex.Pattern;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public class BaseXnatResourceseries extends AutoXnatResourceseries {
-
- public BaseXnatResourceseries(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatResourceseries(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatResourceseries(UserI user)
- **/
- public BaseXnatResourceseries()
- {}
-
- public BaseXnatResourceseries(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
- protected ArrayList files=null;
- protected ArrayList fileNames=null;
-
- private String fullPath = null;
-
-
- public String getFullPath(String rootpath){
- if (fullPath==null)
- {
- fullPath = StringUtils.ReplaceStr(FileUtils.AppendRootPath(rootpath,this.getPath()),"\\","/");
- while (fullPath.indexOf("//")!=-1)
- {
- fullPath =StringUtils.ReplaceStr(fullPath,"//","/");
- }
-
- if(!fullPath.endsWith("/"))
- {
- fullPath+="/";
- }
- }
- return fullPath;
- }
-
- /**
- * Returns ArrayList of java.io.File objects
- * @return
- */
- public ArrayList<File> getCorrespondingFiles(String rootPath)
- {
- if (files==null)
- {
- files = new ArrayList();
- String fullPath = getFullPath(rootPath);
- if (!fullPath.endsWith(File.separator))
- {
- fullPath += File.separator;
- }
- File dir = new File(fullPath);
- if (dir.exists())
- {
- String pattern = this.getPattern();
- if (pattern==null)
- {
- files = new ArrayList(Arrays.asList(dir.listFiles()));
- }else{
- XNATFileFilter filter= new XNATFileFilter();
- filter.setPattern(pattern);
- files = new ArrayList(Arrays.asList(dir.listFiles(filter)));
- }
- }
- }
- return files;
- }
-
- /**
- * Returns ArrayList of java.lang.String objects
- * @return
- */
- public ArrayList getCorrespondingFileNames(String rootPath)
- {
- if (fileNames==null)
- {
- fileNames = new ArrayList();
- String fullPath = getFullPath(rootPath);
- if (!fullPath.endsWith(File.separator))
- {
- fullPath += File.separator;
- }
- File dir = new File(fullPath);
- if (dir.exists())
- {
- String pattern = this.getPattern();
- if (pattern==null)
- {
- fileNames = new ArrayList(Arrays.asList(dir.list()));
- }else{
- XNATFileNameFilter filter= new XNATFileNameFilter();
- filter.setPattern(pattern);
- fileNames = new ArrayList(Arrays.asList(dir.list(filter)));
- }
- }
- }
- return fileNames;
- }
-
- public class XNATFileFilter implements java.io.FileFilter {
- private Pattern _pattern=null;
- public XNATFileFilter()
- {
- }
-
- public void setPattern(String pattern){
- _pattern=java.util.regex.Pattern.compile(pattern);
- }
-
- public boolean accept(File f)
- {
- if (_pattern.matcher(f.getName()).find())
- {
- return true;
- }else{
- return false;
- }
-
- }
- }
-
- public class XNATFileNameFilter implements FilenameFilter {
- private Pattern _pattern=null;
- public XNATFileNameFilter()
- {
- }
-
- public void setPattern(String pattern){
- _pattern=java.util.regex.Pattern.compile(pattern);
- }
-
- public boolean accept(File dir,String name)
- {
- if (_pattern.matcher(name).find())
- {
- return true;
- }else{
- return false;
- }
- }
- }
-
- /**
- * Prepends this path to the enclosed URI or path variables.
- * @param root
- */
- public void prependPathsWith(String root){
- if (!FileUtils.IsAbsolutePath(this.getPath())){
- try {
- this.setPath(root + this.getPath());
- } catch (Exception e) {
- logger.error("",e);
- }
- }
- }
-
- /**
- * Relatives this path from the first occurrence of the indexOf string.
- * @param indexOf
- */
- public void relativizePaths(String indexOf, boolean caseSensitive){
- String uri = this.getPath();
- uri= uri.replace('\\', '/');
- if (uri.indexOf(indexOf)==-1){
- if (!caseSensitive){
- int index = uri.toLowerCase().indexOf(indexOf.toLowerCase());
- if (index!=-1){
- this.setPath(uri.substring(index + 1));
- }
- }
- }else{
- this.setPath(uri.substring(uri.indexOf(indexOf)+ 1));
- }
- }
-
- /**
- * Appends this path to the enclosed URI or path variables.
- * @param root
- */
- public ArrayList<String> getUnresolvedPaths(){
- ArrayList<String> al = new ArrayList<String>();
- String p = getPath();
- p.replace('\\', '/');
- if (!p.endsWith("/"))
- {
- p +="/";
- }
- al.add(p + getPattern());
- return al;
- }
-
-
- public void moveTo(File newSessionDir,String existingSessionDir,String rootPath,UserI user,final EventMetaI ci) throws IOException,Exception{
- String uri = this.getPath();
-
- String relativePath=null;
- if(existingSessionDir!=null && uri.startsWith(existingSessionDir)){
- relativePath=uri.substring(existingSessionDir.length());
- }else{
- if(FileUtils.IsAbsolutePath(uri)){
- if(uri.indexOf("/")>0){
- relativePath=uri.substring(uri.indexOf("/")+1);
- }else if(uri.indexOf("\\")>0){
- relativePath=uri.substring(uri.indexOf("\\")+1);
- }else{
- relativePath=uri;
- }
- }
- }
-
- File newFile = new File(newSessionDir,relativePath);
- if(!newFile.exists())
- {
- newFile.mkdirs();
- }
-
- for(File f: this.getCorrespondingFiles(rootPath)){
- FileUtils.MoveFile(f, new File(newFile,f.getName()), true, true,new OldFileHandlerI(){
- @Override
- public boolean handle(File f) {
- try {
- FileUtils.MoveToHistory(f, EventUtils.getTimestamp(ci));
- } catch (FileNotFoundException e) {
- logger.error("",e);
- return false;
- } catch (IOException e) {
- logger.error("",e);
- return false;
- }
- return true;
- }});
- }
-
- this.setPath(newFile.getAbsolutePath());
- SaveItemHelper.authorizedSave(this,user, true, false,ci);
- }
-
-
- @Override
- public String getPath() {
- if( super.getPath()!=null){
- return super.getPath().replace('\\', '/');
- }else{
- return null;
- }
- }
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatRfscandata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatRfscandata.java
deleted file mode 100644
index 5c44d5ff2db84f887de6dd49f555149c32419140..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatRfscandata.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatRfscandata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatRfscandata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatRfscandata extends AutoXnatRfscandata {
-
- public BaseXnatRfscandata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatRfscandata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatRfscandata(UserI user)
- **/
- public BaseXnatRfscandata()
- {}
-
- public BaseXnatRfscandata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatRfsessiondata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatRfsessiondata.java
deleted file mode 100644
index d5de3c4379eb97be0965aa571bf311cca84e4d49..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatRfsessiondata.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatRfsessiondata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatRfsessiondata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatRfsessiondata extends AutoXnatRfsessiondata {
-
- public BaseXnatRfsessiondata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatRfsessiondata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatRfsessiondata(UserI user)
- **/
- public BaseXnatRfsessiondata()
- {}
-
- public BaseXnatRfsessiondata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatRtimagescandata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatRtimagescandata.java
deleted file mode 100644
index c6de9feda522aeb57f67d107a5983b22993bd929..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatRtimagescandata.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatRtimagescandata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatRtimagescandata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatRtimagescandata extends AutoXnatRtimagescandata {
-
- public BaseXnatRtimagescandata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatRtimagescandata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatRtimagescandata(UserI user)
- **/
- public BaseXnatRtimagescandata()
- {}
-
- public BaseXnatRtimagescandata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatRtsessiondata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatRtsessiondata.java
deleted file mode 100644
index 9828e20320e292cf135bd3dcdc04774774f25f79..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatRtsessiondata.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatRtsessiondata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatRtsessiondata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatRtsessiondata extends AutoXnatRtsessiondata {
-
- public BaseXnatRtsessiondata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatRtsessiondata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatRtsessiondata(UserI user)
- **/
- public BaseXnatRtsessiondata()
- {}
-
- public BaseXnatRtsessiondata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatScscandata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatScscandata.java
deleted file mode 100644
index 2a85bdd922e5112b7e87def8446b63a9a13f54ab..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatScscandata.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatScscandata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatScscandata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatScscandata extends AutoXnatScscandata {
-
- public BaseXnatScscandata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatScscandata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatScscandata(UserI user)
- **/
- public BaseXnatScscandata()
- {}
-
- public BaseXnatScscandata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatSegscandata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatSegscandata.java
deleted file mode 100644
index 07f043bc95bf75833f726b14869454b376120e6c..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatSegscandata.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatSegscandata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatSegscandata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatSegscandata extends AutoXnatSegscandata {
-
- public BaseXnatSegscandata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatSegscandata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatSegscandata(UserI user)
- **/
- public BaseXnatSegscandata()
- {}
-
- public BaseXnatSegscandata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatSmscandata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatSmscandata.java
deleted file mode 100644
index 68cfd004a566c76059496164d1fc75cdf878072c..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatSmscandata.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatSmscandata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatSmscandata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatSmscandata extends AutoXnatSmscandata {
-
- public BaseXnatSmscandata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatSmscandata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatSmscandata(UserI user)
- **/
- public BaseXnatSmscandata()
- {}
-
- public BaseXnatSmscandata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatSmsessiondata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatSmsessiondata.java
deleted file mode 100644
index 37ecea83eeb857a51d0deabfd0e43cdf47717f74..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatSmsessiondata.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatSmsessiondata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatSmsessiondata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatSmsessiondata extends AutoXnatSmsessiondata {
-
- public BaseXnatSmsessiondata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatSmsessiondata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatSmsessiondata(UserI user)
- **/
- public BaseXnatSmsessiondata()
- {}
-
- public BaseXnatSmsessiondata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatSrscandata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatSrscandata.java
deleted file mode 100644
index 4bdeebd9b5381dc74122345c91f919edb4f6cb48..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatSrscandata.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatSrscandata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatSrscandata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatSrscandata extends AutoXnatSrscandata {
-
- public BaseXnatSrscandata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatSrscandata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatSrscandata(UserI user)
- **/
- public BaseXnatSrscandata()
- {}
-
- public BaseXnatSrscandata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatSrsessiondata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatSrsessiondata.java
deleted file mode 100644
index eee1d7a4a42e2e8982cf8f034626a2341fdde964..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatSrsessiondata.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatSrsessiondata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatSrsessiondata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatSrsessiondata extends AutoXnatSrsessiondata {
-
- public BaseXnatSrsessiondata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatSrsessiondata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatSrsessiondata(UserI user)
- **/
- public BaseXnatSrsessiondata()
- {}
-
- public BaseXnatSrsessiondata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatStatisticsdata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatStatisticsdata.java
deleted file mode 100644
index 6674c465f03e3b90b3cae10183624f91a1c07695..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatStatisticsdata.java
+++ /dev/null
@@ -1,77 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatStatisticsdata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.model.XnatStatisticsdataAddfieldI;
-import org.nrg.xdat.model.XnatStatisticsdataAdditionalstatisticsI;
-import org.nrg.xdat.om.XnatStatisticsdataAddfield;
-import org.nrg.xdat.om.XnatStatisticsdataAdditionalstatistics;
-import org.nrg.xdat.om.base.auto.AutoXnatStatisticsdata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-import java.util.List;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatStatisticsdata extends AutoXnatStatisticsdata {
-
- public BaseXnatStatisticsdata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatStatisticsdata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatStatisticsdata(UserI user)
- **/
- public BaseXnatStatisticsdata()
- {}
-
- public BaseXnatStatisticsdata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
- public XnatStatisticsdataAdditionalstatistics getAdditionalstatistics(String name) {
- XnatStatisticsdataAdditionalstatistics rtn = null;
- List<XnatStatisticsdataAdditionalstatisticsI> additionalStats = getAdditionalstatistics() ;
- for (int i = 0; i < additionalStats.size(); i++) {
- if (additionalStats.get(i).getName().equals(name)) {
- rtn = (XnatStatisticsdataAdditionalstatistics)additionalStats.get(i);
- break;
- }
- }
- return rtn;
- }
-
- public XnatStatisticsdataAddfield getAddfield(String name) {
- XnatStatisticsdataAddfield rtn = null;
- List<XnatStatisticsdataAddfieldI> additionalFields = getAddfield() ;
- for (int i = 0; i < additionalFields.size(); i++) {
- if (additionalFields.get(i).getName().equals(name)) {
- rtn = (XnatStatisticsdataAddfield)additionalFields.get(i);
- break;
- }
- }
- return rtn;
- }
-
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatStatisticsdataAddfield.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatStatisticsdataAddfield.java
deleted file mode 100644
index 63f6e628d096a2ef1e7930e2c41546fd45739d6f..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatStatisticsdataAddfield.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatStatisticsdataAddfield
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatStatisticsdataAddfield;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatStatisticsdataAddfield extends AutoXnatStatisticsdataAddfield {
-
- public BaseXnatStatisticsdataAddfield(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatStatisticsdataAddfield(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatStatisticsdataAddfield(UserI user)
- **/
- public BaseXnatStatisticsdataAddfield()
- {}
-
- public BaseXnatStatisticsdataAddfield(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatStatisticsdataAdditionalstatistics.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatStatisticsdataAdditionalstatistics.java
deleted file mode 100644
index ae6c846f93d7c8f42f139f6dc25e46fa2687e2e2..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatStatisticsdataAdditionalstatistics.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatStatisticsdataAdditionalstatistics
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatStatisticsdataAdditionalstatistics;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatStatisticsdataAdditionalstatistics extends AutoXnatStatisticsdataAdditionalstatistics {
-
- public BaseXnatStatisticsdataAdditionalstatistics(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatStatisticsdataAdditionalstatistics(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatStatisticsdataAdditionalstatistics(UserI user)
- **/
- public BaseXnatStatisticsdataAdditionalstatistics()
- {}
-
- public BaseXnatStatisticsdataAdditionalstatistics(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatStudyprotocol.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatStudyprotocol.java
deleted file mode 100644
index 4bc9e3d5f3b68bb717863b8138def0c0c15b6a06..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatStudyprotocol.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatStudyprotocol
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatStudyprotocol;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public class BaseXnatStudyprotocol extends AutoXnatStudyprotocol {
-
- public BaseXnatStudyprotocol(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatStudyprotocol(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatStudyprotocol(UserI user)
- **/
- public BaseXnatStudyprotocol()
- {}
-
- public BaseXnatStudyprotocol(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatStudyprotocolCondition.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatStudyprotocolCondition.java
deleted file mode 100644
index 79999cb33b6f633d9aa112686a6fe0fcb686b502..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatStudyprotocolCondition.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatStudyprotocolCondition
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatStudyprotocolCondition;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public class BaseXnatStudyprotocolCondition extends AutoXnatStudyprotocolCondition {
-
- public BaseXnatStudyprotocolCondition(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatStudyprotocolCondition(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatStudyprotocolCondition(UserI user)
- **/
- public BaseXnatStudyprotocolCondition()
- {}
-
- public BaseXnatStudyprotocolCondition(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatStudyprotocolGroup.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatStudyprotocolGroup.java
deleted file mode 100644
index b3d68bc26dea4e59640912353678b6c2f5068528..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatStudyprotocolGroup.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatStudyprotocolGroup
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatStudyprotocolGroup;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public class BaseXnatStudyprotocolGroup extends AutoXnatStudyprotocolGroup {
-
- public BaseXnatStudyprotocolGroup(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatStudyprotocolGroup(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatStudyprotocolGroup(UserI user)
- **/
- public BaseXnatStudyprotocolGroup()
- {}
-
- public BaseXnatStudyprotocolGroup(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatStudyprotocolSession.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatStudyprotocolSession.java
deleted file mode 100644
index 2471ae689fa629bb6cfdcc192af41720c2469890..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatStudyprotocolSession.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatStudyprotocolSession
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatStudyprotocolSession;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public class BaseXnatStudyprotocolSession extends AutoXnatStudyprotocolSession {
-
- public BaseXnatStudyprotocolSession(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatStudyprotocolSession(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatStudyprotocolSession(UserI user)
- **/
- public BaseXnatStudyprotocolSession()
- {}
-
- public BaseXnatStudyprotocolSession(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatStudyprotocolVariable.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatStudyprotocolVariable.java
deleted file mode 100644
index 3f980f70bf6f7c7175cdf4fed0d7a6d52e3121e4..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatStudyprotocolVariable.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatStudyprotocolVariable
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatStudyprotocolVariable;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public class BaseXnatStudyprotocolVariable extends AutoXnatStudyprotocolVariable {
-
- public BaseXnatStudyprotocolVariable(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatStudyprotocolVariable(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatStudyprotocolVariable(UserI user)
- **/
- public BaseXnatStudyprotocolVariable()
- {}
-
- public BaseXnatStudyprotocolVariable(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatSubjectassessordata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatSubjectassessordata.java
deleted file mode 100644
index 8956238d51985cbaf0a8addda2282ce3dad56999..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatSubjectassessordata.java
+++ /dev/null
@@ -1,131 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatSubjectassessordata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 1/30/14 11:48 AM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.dcm.CopyOp;
-import org.nrg.transaction.OperationI;
-import org.nrg.transaction.TransactionException;
-import org.nrg.xdat.om.XnatImagesessiondata;
-import org.nrg.xdat.om.XnatSubjectdata;
-import org.nrg.xdat.om.base.auto.AutoXnatSubjectassessordata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-import org.nrg.xft.utils.DateUtils;
-import org.nrg.xnat.helpers.merge.ProjectAnonymizer;
-
-import java.io.File;
-import java.text.NumberFormat;
-import java.util.ArrayList;
-import java.util.Date;
-import java.util.Hashtable;
-import java.util.Map;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public class BaseXnatSubjectassessordata extends AutoXnatSubjectassessordata {
-
- public BaseXnatSubjectassessordata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatSubjectassessordata(UserI user)
- {
- super(user);
- }
-
- public BaseXnatSubjectassessordata()
- {}
-
- public BaseXnatSubjectassessordata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
- private XnatSubjectdata subject = null;
- public XnatSubjectdata getSubjectData()
- {
- if (subject==null)
- {
- if (getSubjectId()!=null)
- {
- ArrayList al = XnatSubjectdata.getXnatSubjectdatasByField("xnat:subjectData/ID",this.getSubjectId(),this.getUser(),false);
- if (al.size()>0)
- {
- subject = (XnatSubjectdata)al.get(0);
- }
- }
- }
- return subject;
- }
-
-
- public String getSubjectAge() {
- if (this.getAge()!=null){
- Double d = getAge();
- NumberFormat formatter = NumberFormat.getInstance();
- formatter.setGroupingUsed(false);
- formatter.setMaximumFractionDigits(2);
- formatter.setMinimumFractionDigits(2);
- return formatter.format(d);
- }
-
- XnatSubjectdata s = this.getSubjectData();
- if (s == null) {
- return "--";
- } else {
- try {
- Object o = this.getDate();
- if (o instanceof String)
- {
- Date expt_date = DateUtils.parseDateTime((String)o);
- return s.getAge(expt_date);
- }else{
- Date expt_date = (Date) this.getDate();
- return s.getAge(expt_date);
- }
- } catch (Exception e) {
- logger.error("", e);
- if (s.getAge()!=null)
- {
- return s.getAge().toString();
- }else
- return "--";
-
- }
- }
- }
-
- @Override
- public void preSave() throws Exception{
- super.preSave();
-
- if(this.getSubjectData()==null){
- throw new Exception("Unable to identify subject for:" + this.getSubjectId());
- }
- }
-
- public void applyAnonymizationScript(final ProjectAnonymizer anonymizer) throws TransactionException{
- if(this instanceof XnatImagesessiondata){
- final BaseXnatSubjectassessordata expt = this;
- File tmpDir = new File(System.getProperty("java.io.tmpdir"), "anon_backup");
- new CopyOp(new OperationI<Map<String,File>>() {
- @Override
- public void run(Map<String, File> a) throws Throwable {
- anonymizer.call();
- }
- }, tmpDir,expt.getSessionDir()).run();
- }
- }
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatSubjectdata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatSubjectdata.java
deleted file mode 100644
index 8ba4df86d327058ba95b54c35d33f2c125689764..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatSubjectdata.java
+++ /dev/null
@@ -1,1507 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatSubjectdata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 2/18/14 5:54 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.action.ClientException;
-import org.nrg.xdat.XDAT;
-import org.nrg.xdat.base.BaseElement;
-import org.nrg.xdat.model.*;
-import org.nrg.xdat.om.*;
-import org.nrg.xdat.om.base.auto.AutoXnatSubjectdata;
-import org.nrg.xdat.schema.SchemaElement;
-import org.nrg.xdat.security.SecurityValues;
-import org.nrg.xdat.security.helpers.Permissions;
-import org.nrg.xdat.security.helpers.Users;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-import org.nrg.xft.XFTTable;
-import org.nrg.xft.db.MaterializedView;
-import org.nrg.xft.db.PoolDBUtils;
-import org.nrg.xft.event.EventDetails;
-import org.nrg.xft.event.EventMetaI;
-import org.nrg.xft.event.persist.PersistentWorkflowI;
-import org.nrg.xft.event.persist.PersistentWorkflowUtils;
-import org.nrg.xft.exception.*;
-import org.nrg.xft.identifier.IDGeneratorFactory;
-import org.nrg.xft.identifier.IDGeneratorI;
-import org.nrg.xft.search.CriteriaCollection;
-import org.nrg.xft.search.TableSearch;
-import org.nrg.xft.security.UserI;
-import org.nrg.xft.utils.FileUtils;
-import org.nrg.xft.utils.SaveItemHelper;
-import org.nrg.xft.utils.StringUtils;
-import org.nrg.xnat.exceptions.InvalidArchiveStructure;
-import org.nrg.xnat.turbine.utils.ArchivableItem;
-import org.nrg.xnat.turbine.utils.XNATUtils;
-import org.nrg.xnat.utils.WorkflowUtils;
-import org.restlet.data.Status;
-
-import java.io.File;
-import java.sql.SQLException;
-import java.text.DateFormat;
-import java.text.NumberFormat;
-import java.util.*;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public class BaseXnatSubjectdata extends AutoXnatSubjectdata implements ArchivableItem, MoveableI{
- protected ArrayList<ItemI> minLoadAssessors = null;
-
- public BaseXnatSubjectdata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatSubjectdata(UserI user)
- {
- super(user);
- }
-
- public BaseXnatSubjectdata()
- {}
-
- public BaseXnatSubjectdata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
- public String getArchiveDirectoryName(){
- if(this.getLabel()!=null)
- return this.getLabel();
- else
- return this.getId();
- }
-
- @SuppressWarnings("unused")
- public String getAddIdString(){
- StringBuilder sb = new StringBuilder();
- for(int j=0;j<getAddid().size();j++)
- {
- XnatSubjectdataAddid addid =(XnatSubjectdataAddid) getAddid().get(j);
- if (j==0)
- {
- sb.append(addid.getAddid()).append(" (").append(addid.getName()).append(")");
- }else{
- sb.append(", ").append(addid.getAddid()).append(" (").append(addid.getName()).append(")");
- }
- }
- return sb.toString();
- }
-
- public String getGenderText()
- {
- String s = null;
- try {
- XnatAbstractdemographicdataI ame = this.getDemographics();
- if (ame instanceof XnatDemographicdata)
- {
- s= ((XnatDemographicdata)ame).getGender();
- }
- } catch (Exception e) {
- logger.error("",e);
- }
- if (s==null)
- {
- return "";
- }else{
- if (s.equalsIgnoreCase("m"))
- {
- return "Male";
- }else if (s.equalsIgnoreCase("f"))
- {
- return "Female";
- }else if (s.equalsIgnoreCase("o"))
- {
- return "Other";
- }else if (s.equalsIgnoreCase("u"))
- {
- return "Unknown";
- }else{
- return StringUtils.CapitalFirstLetter(s.toLowerCase());
- }
- }
- }
-
- public Date getDOB()
- {
- XnatAbstractdemographicdataI ame = this.getDemographics();
- if (ame instanceof XnatDemographicdata)
- {
- return (Date)((XnatDemographicdata)ame).getDob();
- }
- return null;
- }
-
- public String getGender()
- {
- XnatAbstractdemographicdataI ame = this.getDemographics();
- if (ame instanceof XnatDemographicdata)
- {
- return ((XnatDemographicdata)ame).getGender();
- }
- return null;
- }
-
- public String getHandedness()
- {
- XnatAbstractdemographicdataI ame = this.getDemographics();
- if (ame instanceof XnatDemographicdata)
- {
- return ((XnatDemographicdata)ame).getHandedness();
- }
- return null;
- }
-
- public Integer getYOB()
- {
- XnatAbstractdemographicdataI ame = this.getDemographics();
- if (ame instanceof XnatDemographicdata)
- {
- return ((XnatDemographicdata)ame).getYob();
- }
- return null;
- }
-
- public String getHandedText()
- {
- String s = null;
- try {
- XnatAbstractdemographicdataI ame = this.getDemographics();
- if (ame instanceof XnatDemographicdata)
- {
- s= ((XnatDemographicdata)ame).getHandedness();
- }
- } catch (Exception e) {
- logger.error("",e);
- }
- if (s==null)
- {
- return "";
- }else{
- if (s.equalsIgnoreCase("l"))
- {
- return "Left";
- }else if (s.equalsIgnoreCase("r"))
- {
- return "Right";
- }else if (s.equalsIgnoreCase("a"))
- {
- return "Ambidextrous";
- }else if (s.equalsIgnoreCase("u"))
- {
- return "Unknown";
- }else{
- return StringUtils.CapitalFirstLetter(s.toLowerCase());
- }
- }
- }
-
- @SuppressWarnings({"deprecation", "unused"})
- public String getDOBDisplay()
- {
- try {
- if (this.getYOB()!=null)
- {
- return (getYOB()) + "";
- }else if(this.getDOB()!=null){
- return (this.getDOB().getYear() + 1900) + "";
- }else{
- return "--";
- }
- } catch (Exception e) {
- logger.error("",e);
- return "--";
- }
- }
-
- public String getLongCreateTime()
- {
- if (this.getItem().getInsertDate() == null)
- {
- return "--";
- }else
- {
- Date date = this.getItem().getInsertDate();
- return DateFormat.getDateInstance(DateFormat.LONG).format(date);
- }
- }
-
- public String getAge(Date experimentDate) {
- if (experimentDate == null) {
- return failSafeAge();
- }
- try {
- Date dob = getDOB();
- if (dob != null) {
- return formatAge(calculateAge(experimentDate, dob));
- } else {
- Integer year = getYOB();
- if (year == null) {
- return failSafeAge();
- } else {
- Calendar cal = Calendar.getInstance();
- cal.set(year, Calendar.JANUARY, 1);
- dob = cal.getTime();
- return formatAge(calculateAge(experimentDate, dob));
- }
- }
- } catch (Exception e) {
- logger.error("",e);
- return failSafeAge();
- }
- }
-
- private Calendar makeCalendar(Date date) {
- Calendar calendar = new GregorianCalendar();
- calendar.setTime(date);
- return calendar;
- }
-
- private int calculateAge(Date current, Date dob) {
- Calendar currentCalendar = makeCalendar(current);
- Calendar dobCalendar = makeCalendar(dob);
- int age = currentCalendar.get(Calendar.YEAR) - dobCalendar.get(Calendar.YEAR);
- if (currentCalendar.get(Calendar.DAY_OF_YEAR) < dobCalendar.get(Calendar.DAY_OF_YEAR)) {
- age--;
- }
- return age;
- }
-
- private String formatAge(double age) {
- NumberFormat formatter = NumberFormat.getInstance();
- formatter.setGroupingUsed(false);
- formatter.setMaximumFractionDigits(2);
- formatter.setMinimumFractionDigits(2);
- return formatter.format(age);
- }
-
- private String failSafeAge() {
- if (getAge() != null) {
- return getAge().toString();
- } else {
- return "--";
- }
- }
-
- public String getRace(){
- try {
- XnatAbstractdemographicdataI ame = this.getDemographics();
- if (ame instanceof XnatDemographicdata)
- {
- return ((XnatDemographicdata)ame).getRace();
- }
- } catch (Exception e) {
- logger.error("",e);
- }
- return null;
- }
-
- public String getEthnicity(){
- try {
- XnatAbstractdemographicdataI ame = this.getDemographics();
- if (ame instanceof XnatDemographicdata)
- {
- return ((XnatDemographicdata)ame).getEthnicity();
- }
- } catch (Exception e) {
- logger.error("",e);
- }
- return null;
- }
-
- public Integer getAge(){
- try {
- XnatAbstractdemographicdataI ame = this.getDemographics();
- if (ame instanceof XnatDemographicdata)
- {
- return ((XnatDemographicdata)ame).getAge();
- }
- } catch (Exception e) {
- logger.error("",e);
- }
- return null;
- }
-
- public Integer getEducation(){
- try {
- XnatAbstractdemographicdataI ame = this.getDemographics();
- if (ame instanceof XnatDemographicdata)
- {
- return ((XnatDemographicdata)ame).getEducation();
- }
- } catch (Exception e) {
- logger.error("",e);
- }
- return null;
- }
-
- public String getEducationDesc(){
- try {
- XnatAbstractdemographicdataI ame = this.getDemographics();
- if (ame instanceof XnatDemographicdata)
- {
- return ((XnatDemographicdata)ame).getEducationdesc();
- }
- } catch (Exception e) {
- logger.error("",e);
- }
- return null;
- }
-
- public Integer getSes(){
- try {
- XnatAbstractdemographicdataI ame = this.getDemographics();
- if (ame instanceof XnatDemographicdata)
- {
- return ((XnatDemographicdata)ame).getSes();
- }
- } catch (Exception e) {
- logger.error("",e);
- }
- return null;
- }
-
- public String getCohort(){
- try {
- XnatAbstractsubjectmetadataI ame = this.getMetadata();
- if (ame instanceof XnatSubjectmetadata)
- {
- return ((XnatSubjectmetadata)ame).getCohort();
- }
- } catch (Exception e) {
- logger.error("",e);
- }
- return null;
- }
-
-
- public ArrayList<ItemI> getMinimalLoadAssessors()
- {
- if (minLoadAssessors==null)
- {
- minLoadAssessors = new ArrayList<>();
-
- try {
- XFTTable table = TableSearch.Execute("SELECT ex.id,ex.date,me.element_name AS type,ex.project,me.element_name,ex.note AS note,projects,label,visit as visit, protocol as protocol FROM xnat_subjectAssessorData assessor LEFT JOIN xnat_experimentData ex ON assessor.ID=ex.ID LEFT JOIN xnat_experimentdata_meta_data meta ON ex.experimentdata_info=meta.meta_data_id LEFT JOIN xdat_meta_element me ON ex.extension=me.xdat_meta_element_id LEFT JOIN (SELECT xs_a_concat(project || ':' || label || ',') AS PROJECTS, sharing_share_xnat_experimentda_id FROM xnat_experimentData_share GROUP BY sharing_share_xnat_experimentda_id) PROJECT_SEARCH ON ex.id=PROJECT_SEARCH.sharing_share_xnat_experimentda_id WHERE assessor.subject_id='" + this.getId() +"' AND meta.status!='obsolete' ORDER BY ex.date ASC",getDBName(),null);
- table.resetRowCursor();
- while (table.hasMoreRows())
- {
- final Hashtable row = table.nextRowHash();
- final String element = (String)row.get("element_name");
- try {
- final XFTItem child = XFTItem.NewItem(element,this.getUser());
-
- final Object date = row.get("date");
- final Object id = row.get("id");
- final Object note = row.get("note");
- final Object project = row.get("project");
- final Object label = row.get("label");
- final Object visit = row.get("visit");
- final Object protocol = row.get("protocol");
-
- if (date!=null)
- {
- try {
- child.setProperty("date",date);
- } catch (XFTInitException | ElementNotFoundException | InvalidValueException | FieldNotFoundException e) {
- logger.error("",e);
- }
- }
- if (id!=null)
- {
- try {
- child.setProperty("ID",id);
- } catch (XFTInitException | ElementNotFoundException | InvalidValueException | FieldNotFoundException e) {
- logger.error("",e);
- }
- }
- if (label!=null)
- {
- try {
- child.setProperty("label",label);
- } catch (XFTInitException | ElementNotFoundException | InvalidValueException | FieldNotFoundException e) {
- logger.error("",e);
- }
- }
- if (visit!=null)
- {
- try {
- child.setProperty("visit",visit);
- } catch (XFTInitException | ElementNotFoundException | InvalidValueException | FieldNotFoundException e) {
- logger.error("",e);
- }
- }
- if (protocol!=null)
- {
- try {
- child.setProperty("protocol",protocol);
- } catch (XFTInitException | ElementNotFoundException | InvalidValueException | FieldNotFoundException e) {
- logger.error("",e);
- }
- }
- if (note!=null)
- {
- try {
- child.setProperty("note",note);
- } catch (XFTInitException | ElementNotFoundException | InvalidValueException | FieldNotFoundException e) {
- logger.error("",e);
- }
- }
- if (project!=null)
- {
- try {
- child.setProperty("project",project);
- } catch (XFTInitException | ElementNotFoundException | InvalidValueException | FieldNotFoundException e) {
- logger.error("",e);
- }
- }
-
- final String projects = (String)row.get("projects");
- if (projects!=null)
- {
- for(final String projectName:StringUtils.CommaDelimitedStringToArrayList(projects, true))
- {
- if(projectName.contains(":")){
- XnatExperimentdataShare es = new XnatExperimentdataShare(this.getUser());
- es.setProject(projectName.substring(0,projectName.indexOf(":")));
- if(!projectName.endsWith(":")){
- es.setLabel(projectName.substring(projectName.indexOf(":")+1));
- }
- child.setChild("xnat:experimentData/sharing/share",es.getItem(),false);
- }else{
- child.setProperty("sharing.share.project", projectName);
- }
- }
- }
-
-
- if (child.instanceOf("xnat:imageSessionData"))
- {
- minLoadAssessors.add(BaseElement.GetGeneratedItem(child));
- try {
- XFTTable table2 = TableSearch.Execute("SELECT ex.id,ex.date,me.element_name AS type,ex.project,me.element_name,ex.note AS note,projects,label,assessor.imagesession_id,visit as visit, protocol as protocol FROM xnat_imageAssessorData assessor LEFT JOIN xnat_experimentData ex ON assessor.ID=ex.ID LEFT JOIN xnat_experimentdata_meta_data meta ON ex.experimentdata_info=meta.meta_data_id LEFT JOIN xdat_meta_element me ON ex.extension=me.xdat_meta_element_id LEFT JOIN (SELECT xs_a_concat(project || ':' || label || ',') AS PROJECTS, sharing_share_xnat_experimentda_id FROM xnat_experimentData_share GROUP BY sharing_share_xnat_experimentda_id) PROJECT_SEARCH ON ex.id=PROJECT_SEARCH.sharing_share_xnat_experimentda_id WHERE assessor.imagesession_id='" + id +"' AND meta.status!='obsolete' ORDER BY ex.date ASC",getDBName(),null);
- table2.resetRowCursor();
- while (table2.hasMoreRows())
- {
- final Hashtable row2 = table2.nextRowHash();
- final String element2 = (String)row2.get("element_name");
- try {
- final XFTItem child2 = XFTItem.NewItem(element2,this.getUser());
-
- final Object date2 = row2.get("date");
- final Object id2 = row2.get("id");
- final Object project2 = row2.get("project");
- final Object note2 = row2.get("note");
- final Object label2 = row2.get("label");
- final Object visit2 = row2.get("visit");
- final Object protocol2 = row2.get("protocol");
- final Object imgsession2 = row2.get("imagesession_id");
-
-
- if (imgsession2!=null)
- {
- try {
- child2.setProperty("imageSession_ID",imgsession2);
- } catch (XFTInitException | ElementNotFoundException | InvalidValueException | FieldNotFoundException e) {
- logger.error("",e);
- }
- }
- if (date2!=null)
- {
- try {
- child2.setProperty("date",date2);
- } catch (XFTInitException | ElementNotFoundException | InvalidValueException | FieldNotFoundException e) {
- logger.error("",e);
- }
- }
- if (id2!=null)
- {
- try {
- child2.setProperty("ID",id2);
- } catch (XFTInitException | ElementNotFoundException | InvalidValueException | FieldNotFoundException e) {
- logger.error("",e);
- }
- }
- if (label2!=null)
- {
- try {
- child2.setProperty("label",label2);
- } catch (XFTInitException | ElementNotFoundException | InvalidValueException | FieldNotFoundException e) {
- logger.error("",e);
- }
- }
- if (visit2!=null)
- {
- try {
- child2.setProperty("visit_id",visit2);
- } catch (XFTInitException | ElementNotFoundException | InvalidValueException | FieldNotFoundException e) {
- logger.error("",e);
- }
- }
- if (protocol2!=null)
- {
- try {
- child2.setProperty("protocol",protocol2);
- } catch (XFTInitException | ElementNotFoundException | InvalidValueException | FieldNotFoundException e) {
- logger.error("",e);
- }
- }
- if (note2!=null)
- {
- try {
- child2.setProperty("note",note2);
- } catch (XFTInitException | ElementNotFoundException | InvalidValueException | FieldNotFoundException e) {
- logger.error("",e);
- }
- }
- if (project2!=null)
- {
- try {
- child2.setProperty("project",project2);
- } catch (XFTInitException | ElementNotFoundException | InvalidValueException | FieldNotFoundException e) {
- logger.error("",e);
- }
- }
-
- final String projects2 = (String)row2.get("projects");
- if (projects2!=null)
- {
- for(final String projectName:StringUtils.CommaDelimitedStringToArrayList(projects2, true))
- {
- if(projectName.contains(":")){
- final XnatExperimentdataShare es = new XnatExperimentdataShare(this.getUser());
- es.setProject(projectName.substring(0,projectName.indexOf(":")));
- if(!projectName.endsWith(":")){
- es.setLabel(projectName.substring(projectName.indexOf(":")+1));
- }
- child2.setChild("xnat:experimentData/sharing/share",es.getItem(),false);
- }else{
- child2.setProperty("sharing.share.project", projectName);
- }
- }
- }
-
- minLoadAssessors.add(BaseElement.GetGeneratedItem(child2));
- } catch (XFTInitException | ElementNotFoundException e) {
- logger.error("",e);
- }
- }
- } catch (Exception e) {
- logger.error("",e);
- }
- }else{
- minLoadAssessors.add(BaseElement.GetGeneratedItem(child));
- }
- } catch (XFTInitException | ElementNotFoundException e) {
- logger.error("",e);
- }
- }
- } catch (Exception e) {
- logger.error("",e);
- }
- }
-
- return minLoadAssessors;
- }
-
- @SuppressWarnings("unused")
- public int getMinimalLoadAssessorsCount(String elementName)
- {
- return getMinimalLoadAssessors(elementName).size();
- }
-
- @SuppressWarnings("unused")
- public Map<String,List<MinLoadExptByP>> getMinimalLoadAssessorsByProject()
- {
- final Map<String,List<MinLoadExptByP>> al = new TreeMap<>();
- final Map<String,String> projects= new Hashtable<>();
- for (final ItemI assessor:this.getMinimalLoadAssessors())
- {
- try{
- final XnatExperimentdata expt=(XnatExperimentdata)assessor;
- if(projects.get(expt.getProject())==null){
- final String pAlias=expt.getProjectDisplayID();
- projects.put(expt.getProject(), pAlias);
- al.put(pAlias, new ArrayList<MinLoadExptByP>());
- }
-
- al.get(projects.get(expt.getProject())).add(new MinLoadExptByP(expt.getProject(), expt.getIdentifier(expt.getProject()),expt));
-
- for(final XnatExperimentdataShareI share:expt.getSharing_share()){
- if(projects.get(share.getProject())==null){
- final String pAlias=((XnatExperimentdataShare)share).getProjectDisplayID();
- projects.put(share.getProject(), pAlias);
- al.put(pAlias, new ArrayList<MinLoadExptByP>());
- }
-
- al.get(projects.get(share.getProject())).add(new MinLoadExptByP(share.getProject(), expt.getIdentifier(share.getProject()),expt));
- }
- }catch (Throwable e){
- logger.error("", e);
- }
- }
-
- return al;
- }
-
- public class MinLoadExptByP{
- String project=null;
- String label=null;
- ItemI item =null;
-
- public MinLoadExptByP(String p, String l, ItemI i){
- project=p;
- label=l;
- item=i;
- }
-
- public ItemI getItem() {
- return item;
- }
-
- public void setItem(ItemI item) {
- this.item = item;
- }
-
- public String getLabel() {
- return label;
- }
-
- public void setLabel(String label) {
- this.label = label;
- }
-
- public String getProject() {
- return project;
- }
-
- public void setProject(String project) {
- this.project = project;
- }
-
-
- }
-
- public ArrayList getMinimalLoadAssessors(String elementName)
- {
- ArrayList al = new ArrayList();
- try {
- SchemaElement e = SchemaElement.GetElement(elementName);
- for (final ItemI assessor : this.getMinimalLoadAssessors()) {
- if (assessor.getXSIType().equalsIgnoreCase(e.getFullXMLName())) {
- al.add(assessor);
- }
- }
- } catch (XFTInitException | ElementNotFoundException e) {
- logger.error("",e);
- }
-
- al.trimToSize();
- return al;
- }
-
-
- public ArrayList<XnatSubjectassessordata> getExperiments_experiment(String type)
- {
- ArrayList<XnatSubjectassessordata> al = new ArrayList<>();
- for (final XnatSubjectassessordataI o : getExperiments_experiment()) {
- XnatSubjectassessordata expt = (XnatSubjectassessordata) o;
- try {
- if (expt.getItem().instanceOf(type)) {
- al.add(expt);
- }
- } catch (ElementNotFoundException e) {
- logger.error("",e);
- }
- }
-
- return al;
- }
-
- @SuppressWarnings("unused")
- public ArrayList getSessionsByType(String type) {
- ArrayList al = new ArrayList();
- for (final XnatSubjectassessordata assessor : getExperiments_experiment("xnat:mrSessionData")) {
- XnatMrsessiondata expt = (XnatMrsessiondata) assessor;
- if (expt.getSessionType()!=null){
- if (expt.getSessionType().equalsIgnoreCase(type)) {
- al.add(expt);
- }
- }else{
- if(type==null)
- al.add(expt);
- }
- }
- return al;
- }
-
- @SuppressWarnings("unused")
- public int getExperiments_experiment_Count(String type)
- {
- return getExperiments_experiment(type).size();
- }
-
- @SuppressWarnings("unused")
- public boolean isMrAssessor(ItemI i) {
- return i instanceof BaseXnatMrassessordata;
- }
-
- public boolean isImageAssessor(ItemI i)
- {
- return i instanceof BaseXnatImageassessordata;
- }
-
- public XnatMrsessiondata getLastSession()
- {
- return XNATUtils.getLastSessionForParticipant(getId(), getUser());
- }
-
- @SuppressWarnings("unused")
- public ArrayList getScannerSortedSessions()
- {
- ArrayList al = this.getExperiments_experiment("xnat:mrSessionData");
- Collections.sort(al,BaseXnatMrsessiondata.GetScannerDelayComparator());
- return al;
- }
-
- @SuppressWarnings("unused")
- public String getAddFieldValueByName(String name)
- {
- return (String)this.getFieldByName(name);
- }
-
- // XNAT-2865 - Function performs case insensitive search for subject
- public static XnatSubjectdata GetSubjectByProjectIdentifierCaseInsensitive(String project, String identifier, UserI user, boolean preLoad){
- try{
- String id = (String)PoolDBUtils.ReturnStatisticQuery("SELECT id, label, project FROM xnat_subjectdata WHERE LOWER(project) = '" + project.toLowerCase() + "' AND LOWER(label) = '" + identifier.toLowerCase() + "';", "id", null, null);
- return XnatSubjectdata.getXnatSubjectdatasById(id, user, preLoad);
- }catch(Exception e){
- logger.debug("Unable to find subject.",e);
- return null;
- }
- }
-
- public static XnatSubjectdata GetSubjectByProjectIdentifier(String project, String identifier,UserI user,boolean preLoad){
- CriteriaCollection cc=new CriteriaCollection("OR");
-
- CriteriaCollection subcc1 = new CriteriaCollection("AND");
- subcc1.addClause("xnat:subjectData/project", project);
- subcc1.addClause("xnat:subjectData/label", identifier);
-
- cc.add(subcc1);
-
- CriteriaCollection subcc2 = new CriteriaCollection("AND");
- subcc2.addClause("xnat:subjectData/sharing/share/project", project);
- subcc2.addClause("xnat:subjectData/sharing/share/label", identifier);
-
- cc.add(subcc2);
-
- ArrayList al = XnatSubjectdata.getXnatSubjectdatasByField(cc, user, preLoad);
- if (al.size()>0){
- return new XnatSubjectdata((ItemI)al.get(0));
- }else{
- return null;
- }
-
- }
-
- public String getIdentifier(String project){
- return this.getIdentifier(project, true);
- }
-
- public String getIdentifiers(){
- final Hashtable<String,String> ids = new Hashtable<>();
-
- if (this.getProject()!=null){
- if (this.getLabel()!=null){
- ids.put(this.getLabel(), this.getProject());
- }else{
- ids.put(this.getId(), this.getProject());
- }
- }
- for (final XnatProjectparticipantI pp:this.getSharing_share())
- {
- if (pp.getLabel()!=null){
- if (ids.containsKey(pp.getLabel()))
- {
- ids.put(pp.getLabel(), ids.get(pp.getLabel()) + "," + pp.getProject());
- }else{
- ids.put(pp.getLabel(), pp.getProject());
- }
- }else{
- if (ids.containsKey(this.getId()))
- {
- ids.put(this.getId(), ids.get(this.getId()) + "," + pp.getProject());
- }else{
- ids.put(this.getId(), pp.getProject());
- }
- }
- }
-
- StringBuilder identifiers = new StringBuilder();
-
- int counter=0;
- for (String key: ids.keySet()){
- if (counter++>0) {
- identifiers.append(", ");
- }
- identifiers.append(key).append(" (").append(ids.get(key)).append(")");
- }
-
- return identifiers.toString();
- }
-
- public Hashtable<XnatProjectdataI,String> getProjectDatas(){
- final Hashtable<XnatProjectdataI,String> hash = new Hashtable<>();
- for (final XnatProjectparticipantI pp:this.getSharing_share())
- {
- if (pp.getLabel()==null)
- hash.put(((XnatProjectparticipant)pp).getProjectData(), this.getId());
- else
- hash.put(((XnatProjectparticipant)pp).getProjectData(), pp.getLabel());
- }
- return hash;
- }
-
- Hashtable fieldsByName = null;
- public Hashtable getFieldsByName(){
- if (fieldsByName == null){
- fieldsByName=new Hashtable();
- for (final XnatSubjectdataFieldI field : this.getFields_field()){
- fieldsByName.put(field.getName(), field);
- }
- }
-
- return fieldsByName;
- }
-
- public Object getFieldByName(String s){
- final XnatSubjectdataFieldI field = (XnatSubjectdataFieldI)getFieldsByName().get(s);
- if (field!=null){
- return field.getField();
- }else{
- return null;
- }
- }
-
-
- public XnatProjectdataI getProject(String projectID, boolean preLoad)
- {
- XnatProjectparticipant ep = null;
- for (final XnatProjectparticipantI tempep: this.getSharing_share())
- {
- if (tempep.getProject().equals(projectID))
- {
- ep=(XnatProjectparticipant)tempep;
- break;
- }
- }
-
- try {
- if (ep!=null){
- return XnatProjectdata.getXnatProjectdatasById(ep.getProject(), this.getUser(), preLoad);
- }else if (this.getProject().equals(projectID)){
- return XnatProjectdata.getXnatProjectdatasById(this.getProject(), this.getUser(), preLoad);
- }
- } catch (RuntimeException e) {
- logger.error("",e);
- }
-
- return null;
- }
-
-
-
- public XnatProjectdata getPrimaryProject(boolean preLoad){
- if (this.getProject()!=null){
- return XnatProjectdata.getXnatProjectdatasById(getProject(), this.getUser(), preLoad);
- }else{
- return (XnatProjectdata)getFirstProject();
- }
- }
-
-
- public XnatProjectdataI getFirstProject()
- {
- XnatProjectparticipant ep = null;
- if (!this.getSharing_share().isEmpty()){
- ep = (XnatProjectparticipant)this.getSharing_share().get(0);
- }
-
- try {
- if (ep!=null){
- return XnatProjectdata.getXnatProjectdatasById(ep.getProject(), this.getUser(), false);
- }
- } catch (RuntimeException e) {
- logger.error("",e);
- }
-
- return null;
- }
-
- public String getIdentifier(String project,boolean returnNULL){
- if (project!=null){
- if (this.getProject().equals(project)){
- if (this.getLabel()!=null){
- return this.getLabel();
- }
- }
-
- for (final XnatProjectparticipantI pp: this.getSharing_share())
- {
- if (pp.getProject().equals(project))
- {
- if (pp.getLabel()!=null){
- return pp.getLabel();
- }
- }
- }
- }
-
- if (returnNULL){
- return null;
- }else{
- return getId();
- }
- }
-
- public int getSubjectAssessorCount(){
- try {
- final XFTTable table = XFTTable.Execute("SELECT COUNT(*) FROM xnat_subjectassessordata WHERE subject_id='" + getId() + "';", getDBName(), null);
-
- Long i = (Long)table.getFirstObject();
- if (i!=null){
- return i.intValue();
- }
- } catch (SQLException | DBPoolException e) {
- logger.error("",e);
- }
- return -1;
- }
-
-
-// public String createNewAssessorId(String xsiType) throws SQLException{
-// String newID= "";
-// String prefix= "";
-// long i = this.getExperiments_experiment_Count(xsiType)+1;
-// prefix+=this.getId();
-//
-// NumberFormat nf = NumberFormat.getInstance();
-// nf.setMinimumIntegerDigits(3);
-//
-// String code =ElementSecurity.GetCode(xsiType);
-// if(code!=null && !code.equals(""))
-// prefix+="_" + code;
-//
-// newID+=prefix +"_"+ StringUtils.ReplaceStr(nf.format(i), ",", "");
-//
-// String query = "SELECT count(ID) AS id_count FROM xnat_experimentdata WHERE ID='";
-//
-// String login = null;
-// if (this.getUser()!=null){
-// login=this.getUser().getUsername();
-// }
-// try {
-// Long idCOUNT= (Long)PoolDBUtils.ReturnStatisticQuery(query + newID + "';", "id_count", this.getDBName(), login);
-// while (idCOUNT > 0){
-// i++;
-// newID=prefix + "_"+ StringUtils.ReplaceStr(nf.format(i), ",", "");
-// idCOUNT= (Long)PoolDBUtils.ReturnStatisticQuery(query + newID + "';", "id_count", this.getDBName(), login);
-// }
-// } catch (Exception e) {
-// logger.error("",e);
-// }
-//
-// return newID;
-// }
-
- private String name = null;
- private String description = null;
- private String secondaryID = null;
- private boolean initd = false;
-
- public void loadProjectDetails(){
- if (!initd)
- {
- initd=true;
- try {
- XFTTable table = XFTTable.Execute("SELECT name,description,secondary_ID FROM xnat_projectData WHERE ID ='" + this.getProject() + "';", this.getDBName(), null);
-
- if (table.size()>0)
- {
- final Object[] row = table.rows().get(0);
- name = (String)row[0];
- description = (String)row[1];
- secondaryID = (String)row[2];
- }
- } catch (SQLException | DBPoolException e) {
- logger.error("",e);
- }
- }
- }
-
- public XnatProjectdata getProjectData(){
- return XnatProjectdata.getXnatProjectdatasById(this.getProject(), this.getUser(), false);
- }
-
-
- /**
- * @return the description
- */
- public String getDescription() {
- loadProjectDetails();
- return description;
- }
-
- /**
- * @return the name
- */
- public String getProjectName() {
- loadProjectDetails();
- return name;
- }
-
- /**
- * @return the secondaryID
- */
- public String getProjectSecondaryID() {
- loadProjectDetails();
- return secondaryID;
- }
-
-
-
- /**
- * @return the secondaryID
- */
- public String getProjectDisplayID() {
- loadProjectDetails();
- if (secondaryID!=null){
- return secondaryID;
- }else{
- return getProject();
- }
- }
-
- @SuppressWarnings("unused")
- public Collection<XnatFielddefinitiongroup> getFieldDefinitionGroups(final String dataType, final String projectID) {
- final Hashtable<String, XnatFielddefinitiongroup> groups = new Hashtable<>();
- final Hashtable<XnatProjectdataI, String> projects = getProjectDatas();
- final XnatProjectdata primaryProject = getPrimaryProject(false);
- if (primaryProject != null) {
- projects.put(primaryProject, "");
-
- for (final Map.Entry<XnatProjectdataI, String> entry : projects.entrySet()) {
- final XnatAbstractprotocol prot = ((XnatProjectdata) entry.getKey()).getProtocolByDataType(dataType);
- if((projectID != null && !projectID.isEmpty()) && !projectID.equals(entry.getKey().getId())){
- continue;
- }
- if (prot!=null && prot instanceof XnatDatatypeprotocol){
- final XnatDatatypeprotocol dataProt = (XnatDatatypeprotocol) prot;
- for (final XnatFielddefinitiongroupI group : dataProt.getDefinitions_definition()) {
- groups.put(group.getId(), (XnatFielddefinitiongroup)group);
- }
- }
- }
- }
- return groups.values();
- }
-
- public static String CreateNewID() throws Exception{
- IDGeneratorI generator = IDGeneratorFactory.GetIDGenerator("org.nrg.xnat.turbine.utils.IDGenerator");
- assert generator != null;
- generator.setTable("xnat_subjectData");
- generator.setDigits(5);
- generator.setColumn("id");
- return generator.generateIdentifier();
- }
-
- public void moveToProject(XnatProjectdata newProject,String newLabel,UserI user,EventMetaI ci) throws Exception{
- if(!this.getProject().equals(newProject.getId()))
- {
- if (!MoverMaker.check(this, user)) {
- throw new InvalidPermissionException(this.getXSIType());
- }
-
- String existingRootPath=this.getProjectData().getRootArchivePath();
-
- if(newLabel==null)newLabel = this.getLabel();
- if(newLabel==null)newLabel = this.getId();
-
- File newSessionDir = new File(new File(newProject.getRootArchivePath(),newProject.getCurrentArc()),newLabel);
-
- String current_label=this.getLabel();
-
- if(current_label==null)current_label=this.getId();
- for(XnatAbstractresourceI abstRes:this.getResources_resource()){
- MoverMaker.Mover m = MoverMaker.moveResource(abstRes, current_label, this, newSessionDir, existingRootPath, user,ci);
- m.setResource((XnatAbstractresource) abstRes);
- m.call();
- }
-
- MoverMaker.writeDB(this, newProject, newLabel, user,ci);
- MoverMaker.setLocal(this, newProject, newLabel);
- }
- }
-
- public boolean hasProject(String proj_id){
- if(this.getProject().equals(proj_id)){
- return true;
- }else{
- for(XnatProjectparticipantI pp: this.getSharing_share()){
- if(pp.getProject().equals(proj_id)){
- return true;
- }
- }
- }
-
- return false;
- }
-
- public String canDelete(BaseXnatProjectdata proj, UserI user) {
- BaseXnatSubjectdata subj=this;
- if(this.getItem().getUser()!=null){
- subj=new XnatSubjectdata(this.getCurrentDBVersion(true));
- }
- if(!subj.hasProject(proj.getId())){
- return "Subject is not assigned to specified project " + proj.getId();
- }else {
-
- try {
- SecurityValues values = new SecurityValues();
- values.put(this.getXSIType() + "/project", proj.getId());
-
- if (!Permissions.canDelete(user, this.getSchemaElement(), values))
- {
- return "User cannot delete subjects for project " + proj.getId();
- }
- } catch (Exception e1) {
- return "Unable to delete subject.";
- }
-
- for(XnatSubjectassessordataI sad: subj.getExperiments_experiment()){
- String msg=((XnatSubjectassessordata)sad).canDelete(proj,user);
- if(msg!=null){
- return msg;
- }
- }
-
- return null;
- }
- }
-
- public String delete(BaseXnatProjectdata proj, UserI user, boolean removeFiles,final EventMetaI c){
- BaseXnatSubjectdata sub=this;
- if(this.getItem().getUser()!=null){
- sub=new XnatSubjectdata(this.getCurrentDBVersion(true));
- }
-
- String msg=sub.canDelete(proj,user);
- if(msg!=null){
- logger.error(msg);
- return msg;
- }
-
- if(!sub.getProject().equals(proj.getId())){
- try {
- SecurityValues values = new SecurityValues();
- values.put(this.getXSIType() + "/project", proj.getId());
-
- if (!Permissions.canDelete(user, sub) && !Permissions.canDelete(user,this.getSchemaElement(),values))
- {
- return null;
- }
-
- //unshare children before unsharing parent
- final List<XnatSubjectassessordataI> expts = sub.getExperiments_experiment();
- for (XnatSubjectassessordataI exptI : expts){
- final XnatSubjectassessordata expt = (XnatSubjectassessordata)exptI;
- if(expt.getProject().equals(proj.getId())){
- return "This operation would delete an experiment (rather than un-share). Please modify experiment ("+expt.getId()+").";
-
- }
- msg=expt.delete(proj,user,false,c);
- if(msg!=null){
- return msg;
- }
- }
-
- int index = 0;
- int match = -1;
- for(XnatProjectparticipantI pp : sub.getSharing_share()){
- if(pp.getProject().equals(proj.getId())){
- SaveItemHelper.authorizedRemoveChild(sub.getItem(), "xnat:subjectData/sharing/share", ((XnatProjectparticipant)pp).getItem(), user,c);
- match=index;
- break;
- }
- index++;
- }
-
- if(match==-1)return null;
-
- this.removeSharing_share(match);
-
- return null;
- } catch (SQLException e) {
- logger.error("",e);
- return e.getMessage();
- } catch (Exception e) {
- logger.error("",e);
- return e.getMessage();
- }
- }else{
-
- if(XDAT.getBoolSiteConfigurationProperty("security.prevent-data-deletion", false)){
- return "User account cannot delete experiments";
- }
-
- try {
-
- if(!Permissions.canDelete(user, this)){
- return "User account doesn't have permission to delete this subject.";
- }
-
- if(removeFiles){
- this.deleteFiles(user,c);
- }
-
- final List<XnatSubjectassessordataI> expts = sub.getExperiments_experiment();
- for (XnatSubjectassessordataI exptI : expts){
- final XnatSubjectassessordata expt = (XnatSubjectassessordata)exptI;
- msg=expt.delete(proj,user,removeFiles,c);
- if(msg!=null)return msg;
- }
-
- SaveItemHelper.authorizedDelete(sub.getItem().getCurrentDBVersion(), user,c);
-
- Users.clearCache(user);
- MaterializedView.deleteByUser(user);
- } catch (SQLException e) {
- logger.error("",e);
- return e.getMessage();
- } catch (Exception e) {
- logger.error("",e);
- return e.getMessage();
- }
- }
- return null;
- }
-
- public void deleteFiles(UserI user, EventMetaI ci) throws Exception{
- final XnatProjectdata project = this.getPrimaryProject(false);
- if (project != null) {
- String archive=project.getRootArchivePath();
- File dir=new File(archive,"subjects/"+ this.getArchiveDirectoryName());
- if(dir.exists()){
- FileUtils.MoveToCache(dir);
- }
-
- for(XnatAbstractresourceI abstRes:this.getResources_resource()){
- ((XnatAbstractresource)abstRes).deleteWithBackup(archive,user,ci);
- }
- } else {
- logger.warn("User " + user.getUsername() + " tried to delete the files for the primary project for subject " + getLabel() + ", but there was no primary project found.");
- }
- }
-
- public int getAssessmentCount(String project){
- int count=0;
- for(int i=0;i<this.getMinimalLoadAssessors().size();i++){
- XnatExperimentdata expt=(XnatExperimentdata)this.getMinimalLoadAssessors().get(i);
- if(expt.getProject().equals(project)){
- count++;
- }
- }
- return count;
- }
-
- public static String cleanValue(String v){
- v= StringUtils.ReplaceStr(v, " ", "_");
- v= StringUtils.ReplaceStr(v, "`", "_");
- v= StringUtils.ReplaceStr(v, "~", "_");
- v= StringUtils.ReplaceStr(v, "@", "_");
- v= StringUtils.ReplaceStr(v, "#", "_");
- v= StringUtils.ReplaceStr(v, "$", "_");
- v= StringUtils.ReplaceStr(v, "%", "_");
- v= StringUtils.ReplaceStr(v, "^", "_");
- v= StringUtils.ReplaceStr(v, "&", "_");
- v= StringUtils.ReplaceStr(v, "*", "_");
- v= StringUtils.ReplaceStr(v, "(", "_");
- v= StringUtils.ReplaceStr(v, ")", "_");
- v= StringUtils.ReplaceStr(v, "+", "_");
- v= StringUtils.ReplaceStr(v, "=", "_");
- v= StringUtils.ReplaceStr(v, "[", "_");
- v= StringUtils.ReplaceStr(v, "]", "_");
- v= StringUtils.ReplaceStr(v, "{", "_");
- v= StringUtils.ReplaceStr(v, "}", "_");
- v= StringUtils.ReplaceStr(v, "|", "_");
- v= StringUtils.ReplaceStr(v, "\\", "_");
- v= StringUtils.ReplaceStr(v, "/", "_");
- v= StringUtils.ReplaceStr(v, "?", "_");
- v= StringUtils.ReplaceStr(v, ":", "_");
- v= StringUtils.ReplaceStr(v, ";", "_");
- v= StringUtils.ReplaceStr(v, "\"", "_");
- v= StringUtils.ReplaceStr(v, "'", "_");
- v= StringUtils.ReplaceStr(v, ",", "_");
- v= StringUtils.ReplaceStr(v, ".", "_");
- v= StringUtils.ReplaceStr(v, "<", "_");
- v= StringUtils.ReplaceStr(v, ">", "_");
-
- return v;
- }
-
- public void checkUniqueLabel() throws Exception{
- if(!StringUtils.IsEmpty(this.getLabel())){
- Long count=(Long)PoolDBUtils.ReturnStatisticQuery(String.format("SELECT COUNT(*) FROM (SELECT label,id FROM xnat_subjectData WHERE label='%1$s' AND ID !='%2$s' AND project='%3$s' UNION SELECT label, subject_id as ID FROM xnat_projectParticipant WHERE label='%1$s' AND subject_id !='%2$s' AND project='%3$s')SRCH",this.getLabel(),this.getId(),this.getProject()), "count", this.getDBName(), "system");
- if(count>0){
- throw new ClientException(Status.CLIENT_ERROR_CONFLICT,"Conflict: Duplicate subject label",new Exception());
- }
- }
- }
-
-
- @Override
- public void preSave() throws Exception{
- super.preSave();
-
- if(StringUtils.IsEmpty(this.getId())){
- throw new IllegalArgumentException();
- }
-
- if(StringUtils.IsEmpty(this.getLabel())){
- throw new IllegalArgumentException();
- }
-
- if(!StringUtils.IsAlphaNumericUnderscore(getId())){
- throw new IllegalArgumentException("Identifiers cannot use special characters.");
- }
-
- if(!StringUtils.IsAlphaNumericUnderscore(getLabel())){
- throw new IllegalArgumentException("Labels cannot use special characters.");
- }
-
-
- final XnatProjectdata proj = this.getPrimaryProject(false);
- if(proj==null){
- throw new Exception("Unable to identify project for:" + this.getProject());
- }
-
- checkUniqueLabel();
-
- final String expectedPath=getExpectedCurrentDirectory().getAbsolutePath().replace('\\', '/');
-
- for(final XnatAbstractresourceI res: this.getResources_resource()){
- final String uri;
- if(res instanceof XnatResource){
- uri=((XnatResource)res).getUri();
- }else if(res instanceof XnatResourceseries){
- uri=((XnatResourceseries)res).getPath();
- }else{
- continue;
- }
-
- File u = new File(uri);
- if (u.isFile()) {
- FileUtils.ValidateUriAgainstRoot(u.getParent(),expectedPath,"URI references data outside of the project: " + uri);
- }
- else {
- FileUtils.ValidateUriAgainstRoot(uri,expectedPath,"URI references data outside of the project: " + uri);
- }
- }
-
- for(final XnatSubjectassessordataI expt:this.getExperiments_experiment()){
- ((XnatSubjectassessordata)expt).preSave();
- }
- }
-
- public File getExpectedCurrentDirectory() throws InvalidArchiveStructure {
- final XnatProjectdata primaryProject = this.getPrimaryProject(false);
- return primaryProject == null ? null : new File(primaryProject.getRootArchivePath(),"subjects/"+ this.getArchiveDirectoryName());
- }
-
- public static void save(XnatSubjectdata subject,boolean overrideSecurity, boolean allowItemRemoval, UserI user,EventDetails event) throws Exception{
- PersistentWorkflowI wrk= WorkflowUtils.buildOpenWorkflow(user, subject.getXSIType(), subject.getId(),subject.getProject(),event);
- EventMetaI c=wrk.buildEvent();
-
- try {
- SaveItemHelper.authorizedSave(subject,user, overrideSecurity, allowItemRemoval,c);
- WorkflowUtils.complete(wrk, c);
- } catch (Exception e) {
- WorkflowUtils.fail(wrk, c);
- throw e;
- }
- }
-
- public static void SaveSharedProject(XnatProjectparticipant pp, XnatSubjectdata expt,UserI user,EventDetails event) throws Exception{
- PersistentWorkflowI wrk= WorkflowUtils.buildOpenWorkflow(user, expt.getItem(), event);
- EventMetaI c=wrk.buildEvent();
- PersistentWorkflowUtils.save(wrk, c);
- try {
- SaveItemHelper.authorizedSave(pp, user, false,false,c);
- PersistentWorkflowUtils.complete(wrk, c);
- } catch (Exception e) {
- logger.error("",e);
- PersistentWorkflowUtils.fail(wrk, c);
- throw e;
- }
- }
-
- public static EventMetaI ChangePrimaryProject(UserI user, XnatSubjectdata assessor, XnatProjectdata newProject, String newLabel,EventDetails event) throws Exception{
- PersistentWorkflowI wrk= WorkflowUtils.buildOpenWorkflow(user, assessor.getXSIType(), assessor.getId(),assessor.getProject(),event);
- wrk.setDetails("Move subject from project " + assessor.getProject() + " to " + newProject.getId());
- EventMetaI c=wrk.buildEvent();
- PersistentWorkflowUtils.save(wrk, c);
-
- try {
- assessor.moveToProject(newProject,newLabel,user,c);
-
- PersistentWorkflowUtils.complete(wrk, c);
- } catch (Exception e) {
- logger.error("",e);
- PersistentWorkflowUtils.fail(wrk,c);
- throw e;
- }
-
- return c;
- }
-
- /**
- * Gets root path to the primary project's archive space.
- * @return The path to the root folder of the subject's primary project's archive space.
- */
- public String getArchiveRootPath(){
- final XnatProjectdata primaryProject = getPrimaryProject(false);
- return primaryProject != null ? primaryProject.getRootArchivePath() : null;
- }
-
- public XnatSubjectdata getLightCopy() throws XFTInitException, ElementNotFoundException {
- XFTItem item = XFTItem.NewItem(this.getXSIType(), this.getUser());
- XnatSubjectdata new_expt=(XnatSubjectdata) BaseElement.GetGeneratedItem(item);
- new_expt.setId(this.getId());
- new_expt.setLabel(this.getLabel());
- new_expt.setProject(this.getProject());
- return new_expt;
- }
-
- @Override
- public SecurityValues getSecurityTags() {
- SecurityValues projects=new SecurityValues();
- projects.getHash().put(this.getXSIType() +"/project", this.getProject());
- for (final XnatProjectparticipantI pp:this.getSharing_share())
- {
- projects.getHash().put(this.getXSIType() +"/sharing/share/project", pp.getProject());
- }
- return projects;
- }
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatSubjectdataAddid.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatSubjectdataAddid.java
deleted file mode 100644
index cdb08ab084d5e1079a66b85fc3973d22426ea694..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatSubjectdataAddid.java
+++ /dev/null
@@ -1,44 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatSubjectdataAddid
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatSubjectdataAddid;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public class BaseXnatSubjectdataAddid extends AutoXnatSubjectdataAddid {
-
- public BaseXnatSubjectdataAddid(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatSubjectdataAddid(UserI user)
- {
- super(user);
- }
-
- public BaseXnatSubjectdataAddid()
- {}
-
- public BaseXnatSubjectdataAddid(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatSubjectdataField.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatSubjectdataField.java
deleted file mode 100644
index 46103999cc11a42a293aef1f5ee2f2cfd90489c2..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatSubjectdataField.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatSubjectdataField
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatSubjectdataField;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatSubjectdataField extends AutoXnatSubjectdataField {
-
- public BaseXnatSubjectdataField(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatSubjectdataField(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatSubjectdataField(UserI user)
- **/
- public BaseXnatSubjectdataField()
- {}
-
- public BaseXnatSubjectdataField(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatSubjectmetadata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatSubjectmetadata.java
deleted file mode 100644
index c0dd9cb642eb25fa9c14c45f290ec288564317fb..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatSubjectmetadata.java
+++ /dev/null
@@ -1,44 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatSubjectmetadata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatSubjectmetadata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public class BaseXnatSubjectmetadata extends AutoXnatSubjectmetadata {
-
- public BaseXnatSubjectmetadata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatSubjectmetadata(UserI user)
- {
- super(user);
- }
-
- public BaseXnatSubjectmetadata()
- {}
-
- public BaseXnatSubjectmetadata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatSubjectvariablesdata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatSubjectvariablesdata.java
deleted file mode 100644
index 2f923d386e32dd6ba81d0746e548cfd97074cf56..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatSubjectvariablesdata.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatSubjectvariablesdata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatSubjectvariablesdata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public class BaseXnatSubjectvariablesdata extends AutoXnatSubjectvariablesdata {
-
- public BaseXnatSubjectvariablesdata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatSubjectvariablesdata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatSubjectvariablesdata(UserI user)
- **/
- public BaseXnatSubjectvariablesdata()
- {}
-
- public BaseXnatSubjectvariablesdata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatSubjectvariablesdataVariable.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatSubjectvariablesdataVariable.java
deleted file mode 100644
index 65ddc9f55a19a3ce2850c103129779015527a3a6..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatSubjectvariablesdataVariable.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatSubjectvariablesdataVariable
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatSubjectvariablesdataVariable;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public class BaseXnatSubjectvariablesdataVariable extends AutoXnatSubjectvariablesdataVariable {
-
- public BaseXnatSubjectvariablesdataVariable(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatSubjectvariablesdataVariable(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatSubjectvariablesdataVariable(UserI user)
- **/
- public BaseXnatSubjectvariablesdataVariable()
- {}
-
- public BaseXnatSubjectvariablesdataVariable(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatUsscandata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatUsscandata.java
deleted file mode 100644
index 21f9269387e877bea655f6bb42bd7d68796dafe2..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatUsscandata.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatUsscandata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatUsscandata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatUsscandata extends AutoXnatUsscandata {
-
- public BaseXnatUsscandata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatUsscandata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatUsscandata(UserI user)
- **/
- public BaseXnatUsscandata()
- {}
-
- public BaseXnatUsscandata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatUssessiondata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatUssessiondata.java
deleted file mode 100644
index e779aaffbec99fce63f18c5f661fe463db52f95a..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatUssessiondata.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatUssessiondata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatUssessiondata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatUssessiondata extends AutoXnatUssessiondata {
-
- public BaseXnatUssessiondata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatUssessiondata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatUssessiondata(UserI user)
- **/
- public BaseXnatUssessiondata()
- {}
-
- public BaseXnatUssessiondata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatValidationdata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatValidationdata.java
deleted file mode 100644
index d9db6f160b59072b039a5a224680a817bbe037e6..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatValidationdata.java
+++ /dev/null
@@ -1,44 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatValidationdata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatValidationdata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public class BaseXnatValidationdata extends AutoXnatValidationdata {
-
- public BaseXnatValidationdata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatValidationdata(UserI user)
- {
- super(user);
- }
-
- public BaseXnatValidationdata()
- {}
-
- public BaseXnatValidationdata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatVoiceaudioscandata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatVoiceaudioscandata.java
deleted file mode 100644
index 7a94c522ce328fe6bc5d47588ed135f895939044..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatVoiceaudioscandata.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatVoiceaudioscandata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatVoiceaudioscandata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatVoiceaudioscandata extends AutoXnatVoiceaudioscandata {
-
- public BaseXnatVoiceaudioscandata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatVoiceaudioscandata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatVoiceaudioscandata(UserI user)
- **/
- public BaseXnatVoiceaudioscandata()
- {}
-
- public BaseXnatVoiceaudioscandata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatVolumetricregion.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatVolumetricregion.java
deleted file mode 100644
index 63ddb93651b8f7427d41c45a031c7032e7085807..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatVolumetricregion.java
+++ /dev/null
@@ -1,62 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatVolumetricregion
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.XnatVolumetricregionSubregion;
-import org.nrg.xdat.om.base.auto.AutoXnatVolumetricregion;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-import java.util.Iterator;
-import java.util.List;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public class BaseXnatVolumetricregion extends AutoXnatVolumetricregion {
-
- public BaseXnatVolumetricregion(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatVolumetricregion(UserI user)
- {
- super(user);
- }
-
- public BaseXnatVolumetricregion()
- {}
-
- public BaseXnatVolumetricregion(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
- public BaseXnatVolumetricregionSubregion getSubRegionByName(String name)
- {
- List al = this.getSubregions_subregion();
- Iterator iter = al.iterator();
- while (iter.hasNext())
- {
- XnatVolumetricregionSubregion sub = (XnatVolumetricregionSubregion)iter.next();
- if (sub.getName().equalsIgnoreCase(name))
- {
- return sub;
- }
- }
-
- return null;
- }
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatVolumetricregionSubregion.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatVolumetricregionSubregion.java
deleted file mode 100644
index 35338a6eb5a872f777381e589a513df6207dc004..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatVolumetricregionSubregion.java
+++ /dev/null
@@ -1,44 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatVolumetricregionSubregion
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatVolumetricregionSubregion;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public class BaseXnatVolumetricregionSubregion extends AutoXnatVolumetricregionSubregion {
-
- public BaseXnatVolumetricregionSubregion(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatVolumetricregionSubregion(UserI user)
- {
- super(user);
- }
-
- public BaseXnatVolumetricregionSubregion()
- {}
-
- public BaseXnatVolumetricregionSubregion(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatXa3dscandata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatXa3dscandata.java
deleted file mode 100644
index b71acce6dd03755dcf45cfe8be1d47f13677adb3..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatXa3dscandata.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatXa3dscandata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatXa3dscandata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatXa3dscandata extends AutoXnatXa3dscandata {
-
- public BaseXnatXa3dscandata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatXa3dscandata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatXa3dscandata(UserI user)
- **/
- public BaseXnatXa3dscandata()
- {}
-
- public BaseXnatXa3dscandata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatXa3dsessiondata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatXa3dsessiondata.java
deleted file mode 100644
index 90ced8f1945a93c1408fd082110cc3103137c7cf..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatXa3dsessiondata.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatXa3dsessiondata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatXa3dsessiondata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatXa3dsessiondata extends AutoXnatXa3dsessiondata {
-
- public BaseXnatXa3dsessiondata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatXa3dsessiondata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatXa3dsessiondata(UserI user)
- **/
- public BaseXnatXa3dsessiondata()
- {}
-
- public BaseXnatXa3dsessiondata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatXascandata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatXascandata.java
deleted file mode 100644
index bef2c93e1832b151643a01c896afdb1a2e1864d7..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatXascandata.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatXascandata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatXascandata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatXascandata extends AutoXnatXascandata {
-
- public BaseXnatXascandata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatXascandata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatXascandata(UserI user)
- **/
- public BaseXnatXascandata()
- {}
-
- public BaseXnatXascandata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatXasessiondata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatXasessiondata.java
deleted file mode 100644
index 9da9224955bc29551240cf6c4162f16d13749615..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatXasessiondata.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatXasessiondata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatXasessiondata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatXasessiondata extends AutoXnatXasessiondata {
-
- public BaseXnatXasessiondata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatXasessiondata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatXasessiondata(UserI user)
- **/
- public BaseXnatXasessiondata()
- {}
-
- public BaseXnatXasessiondata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatXcscandata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatXcscandata.java
deleted file mode 100644
index 333c7389336e8c43df16ce9b6e48d047b93fdc4e..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatXcscandata.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatXcscandata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatXcscandata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatXcscandata extends AutoXnatXcscandata {
-
- public BaseXnatXcscandata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatXcscandata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatXcscandata(UserI user)
- **/
- public BaseXnatXcscandata()
- {}
-
- public BaseXnatXcscandata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatXcsessiondata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatXcsessiondata.java
deleted file mode 100644
index 2a3342a0e1cb0417ab607921d30454302577fadb..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatXcsessiondata.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatXcsessiondata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatXcsessiondata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatXcsessiondata extends AutoXnatXcsessiondata {
-
- public BaseXnatXcsessiondata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatXcsessiondata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatXcsessiondata(UserI user)
- **/
- public BaseXnatXcsessiondata()
- {}
-
- public BaseXnatXcsessiondata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatXcvscandata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatXcvscandata.java
deleted file mode 100644
index bfa0cc1f028faa16f47acb277f37a88a585367ef..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatXcvscandata.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatXcvscandata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatXcvscandata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatXcvscandata extends AutoXnatXcvscandata {
-
- public BaseXnatXcvscandata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatXcvscandata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatXcvscandata(UserI user)
- **/
- public BaseXnatXcvscandata()
- {}
-
- public BaseXnatXcvscandata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/om/base/BaseXnatXcvsessiondata.java b/src/main/java/org/nrg/xdat/om/base/BaseXnatXcvsessiondata.java
deleted file mode 100644
index d98168ed024fa18ef135048cc5fb903697ed9a20..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/om/base/BaseXnatXcvsessiondata.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * org.nrg.xdat.om.base.BaseXnatXcvsessiondata
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xdat.om.base;
-
-import org.nrg.xdat.om.base.auto.AutoXnatXcvsessiondata;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.security.UserI;
-
-import java.util.Hashtable;
-
-/**
- * @author XDAT
- *
- */
-@SuppressWarnings({"unchecked","rawtypes"})
-public abstract class BaseXnatXcvsessiondata extends AutoXnatXcvsessiondata {
-
- public BaseXnatXcvsessiondata(ItemI item)
- {
- super(item);
- }
-
- public BaseXnatXcvsessiondata(UserI user)
- {
- super(user);
- }
-
- /*
- * @deprecated Use BaseXnatXcvsessiondata(UserI user)
- **/
- public BaseXnatXcvsessiondata()
- {}
-
- public BaseXnatXcvsessiondata(Hashtable properties, UserI user)
- {
- super(properties,user);
- }
-
-}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_cat_catalog.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_cat_catalog.java
deleted file mode 100644
index 95089303ff2df482e6c8402fd6c8cdb256ea1147..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_cat_catalog.java
+++ /dev/null
@@ -1,34 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:04 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_cat_catalog extends org.nrg.xdat.turbine.modules.screens.EditScreenA {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_cat_catalog.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "cat:catalog";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_cat_dcmCatalog.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_cat_dcmCatalog.java
deleted file mode 100644
index ae39c89abf3e1abd0bf0f640538126d0dd377f39..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_cat_dcmCatalog.java
+++ /dev/null
@@ -1,34 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:04 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_cat_dcmCatalog extends org.nrg.xdat.turbine.modules.screens.EditScreenA {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_cat_dcmCatalog.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "cat:dcmCatalog";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_cat_entry.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_cat_entry.java
deleted file mode 100644
index 2c210a655b939e4775c342a6cc709365d5bc71b3..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_cat_entry.java
+++ /dev/null
@@ -1,34 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:04 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_cat_entry extends org.nrg.xdat.turbine.modules.screens.EditScreenA {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_cat_entry.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "cat:entry";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_prov_process.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_prov_process.java
deleted file mode 100644
index 986f37bf7e57f8f0ee0126bd926581f23e416422..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_prov_process.java
+++ /dev/null
@@ -1,34 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:10 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_prov_process extends org.nrg.xdat.turbine.modules.screens.EditScreenA {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_prov_process.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "prov:process";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_scr_screeningAssessment.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_scr_screeningAssessment.java
deleted file mode 100644
index b0f01c535ddb8defd1d7bc36b2103485322b4d94..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_scr_screeningAssessment.java
+++ /dev/null
@@ -1,34 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:04 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_scr_screeningAssessment extends org.nrg.xnat.turbine.modules.screens.EditImageAssessorScreen {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_scr_screeningAssessment.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "scr:screeningAssessment";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_val_protocolData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_val_protocolData.java
deleted file mode 100644
index 1e4783940c5d7a4d4146969c2b90bc424f9ed9d2..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_val_protocolData.java
+++ /dev/null
@@ -1,34 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:05 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_val_protocolData extends org.nrg.xnat.turbine.modules.screens.EditImageAssessorScreen {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_val_protocolData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "val:protocolData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_wrk_workflowData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_wrk_workflowData.java
deleted file mode 100644
index 687914db4a47ed91a7089e1c5f35311cf4f0b1f1..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_wrk_workflowData.java
+++ /dev/null
@@ -1,34 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:03 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_wrk_workflowData extends org.nrg.xdat.turbine.modules.screens.EditScreenA {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_wrk_workflowData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "wrk:workflowData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_a_scidResearchData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_a_scidResearchData.java
deleted file mode 100644
index 85cc61b09edb12f72ad470fb2b485977edae1f93..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_a_scidResearchData.java
+++ /dev/null
@@ -1,35 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:10 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_a_scidResearchData extends org.nrg.xnat.turbine.modules.screens.EditSubjectAssessorScreen {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_a_scidResearchData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat_a:scidResearchData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- super.finalProcessing(data,context);
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_a_sideEffectsPittsburghData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_a_sideEffectsPittsburghData.java
deleted file mode 100644
index ff81291443f2097fb5c446e9057d7d3f4e8fed21..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_a_sideEffectsPittsburghData.java
+++ /dev/null
@@ -1,35 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:09 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_a_sideEffectsPittsburghData extends org.nrg.xnat.turbine.modules.screens.EditSubjectAssessorScreen {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_a_sideEffectsPittsburghData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat_a:sideEffectsPittsburghData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- super.finalProcessing(data,context);
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_a_updrs3Data.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_a_updrs3Data.java
deleted file mode 100644
index 49f5b0c0218b784b1afff821f3ebe329d375d8a3..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_a_updrs3Data.java
+++ /dev/null
@@ -1,35 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:10 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_a_updrs3Data extends org.nrg.xnat.turbine.modules.screens.EditSubjectAssessorScreen {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_a_updrs3Data.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat_a:updrs3Data";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- super.finalProcessing(data,context);
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_a_ybocsData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_a_ybocsData.java
deleted file mode 100644
index 923dc15c43ff065289630c010d44080bc4a0532f..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_a_ybocsData.java
+++ /dev/null
@@ -1,35 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:09 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_a_ybocsData extends org.nrg.xnat.turbine.modules.screens.EditSubjectAssessorScreen {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_a_ybocsData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat_a:ybocsData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- super.finalProcessing(data,context);
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_a_ygtssData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_a_ygtssData.java
deleted file mode 100644
index 633ed4ec610ac1753b7e6f7a600280cb17feed31..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_a_ygtssData.java
+++ /dev/null
@@ -1,35 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:09 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_a_ygtssData extends org.nrg.xnat.turbine.modules.screens.EditSubjectAssessorScreen {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_a_ygtssData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat_a:ygtssData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- super.finalProcessing(data,context);
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_crScanData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_crScanData.java
deleted file mode 100644
index 57a7b8ac6a00c1791d8bc036146edeafb8ef8e9a..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_crScanData.java
+++ /dev/null
@@ -1,34 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:06 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_crScanData extends org.nrg.xdat.turbine.modules.screens.EditScreenA {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_crScanData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:crScanData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_crSessionData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_crSessionData.java
deleted file mode 100644
index f089047abf74a687929929c131d6bc9b64c2eebe..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_crSessionData.java
+++ /dev/null
@@ -1,35 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:06 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_crSessionData extends org.nrg.xnat.turbine.modules.screens.EditSubjectAssessorScreen {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_crSessionData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:crSessionData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- super.finalProcessing(data,context);
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_ctScanData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_ctScanData.java
deleted file mode 100644
index 427ff888476e0ca99aef27a9a64cdb54fd2fbecd..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_ctScanData.java
+++ /dev/null
@@ -1,34 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:06 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_ctScanData extends org.nrg.xdat.turbine.modules.screens.EditScreenA {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_ctScanData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:ctScanData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_ctSessionData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_ctSessionData.java
deleted file mode 100644
index c2c0e5877d3a40b70c3f4af4d7a511cc061ae394..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_ctSessionData.java
+++ /dev/null
@@ -1,35 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:06 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_ctSessionData extends org.nrg.xnat.turbine.modules.screens.EditSubjectAssessorScreen {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_ctSessionData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:ctSessionData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- super.finalProcessing(data,context);
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_dx3DCraniofacialScanData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_dx3DCraniofacialScanData.java
deleted file mode 100644
index 4ee6bd2dc3b71decd670e9607f11ddb083f8ecbc..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_dx3DCraniofacialScanData.java
+++ /dev/null
@@ -1,34 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:07 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_dx3DCraniofacialScanData extends org.nrg.xdat.turbine.modules.screens.EditScreenA {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_dx3DCraniofacialScanData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:dx3DCraniofacialScanData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_dx3DCraniofacialSessionData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_dx3DCraniofacialSessionData.java
deleted file mode 100644
index 8bfd589f228fc31171277f64efab6a9c7d80a9ef..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_dx3DCraniofacialSessionData.java
+++ /dev/null
@@ -1,35 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:06 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_dx3DCraniofacialSessionData extends org.nrg.xnat.turbine.modules.screens.EditSubjectAssessorScreen {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_dx3DCraniofacialSessionData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:dx3DCraniofacialSessionData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- super.finalProcessing(data,context);
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_dxScanData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_dxScanData.java
deleted file mode 100644
index d35a8f8be78e6801802a9ec4ece7afc9d23a3bdd..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_dxScanData.java
+++ /dev/null
@@ -1,34 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:06 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_dxScanData extends org.nrg.xdat.turbine.modules.screens.EditScreenA {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_dxScanData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:dxScanData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_dxSessionData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_dxSessionData.java
deleted file mode 100644
index adc6eb5d39be8bf176e3a1ec4ce9cb9ca86e2196..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_dxSessionData.java
+++ /dev/null
@@ -1,35 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:06 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_dxSessionData extends org.nrg.xnat.turbine.modules.screens.EditSubjectAssessorScreen {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_dxSessionData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:dxSessionData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- super.finalProcessing(data,context);
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_ecgScanData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_ecgScanData.java
deleted file mode 100644
index 089e1ae3d41040d034dd3b1adfb4060a23adf77d..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_ecgScanData.java
+++ /dev/null
@@ -1,34 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:06 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_ecgScanData extends org.nrg.xdat.turbine.modules.screens.EditScreenA {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_ecgScanData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:ecgScanData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_ecgSessionData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_ecgSessionData.java
deleted file mode 100644
index 128ec375c7f19dbf7e0691ff71a304bc311fcdc8..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_ecgSessionData.java
+++ /dev/null
@@ -1,35 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:06 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_ecgSessionData extends org.nrg.xnat.turbine.modules.screens.EditSubjectAssessorScreen {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_ecgSessionData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:ecgSessionData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- super.finalProcessing(data,context);
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_eegScanData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_eegScanData.java
deleted file mode 100644
index 967c18fc04229becd1b5d26bf82ff5d25d9920cb..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_eegScanData.java
+++ /dev/null
@@ -1,34 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:09 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_eegScanData extends org.nrg.xdat.turbine.modules.screens.EditScreenA {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_eegScanData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:eegScanData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_eegSessionData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_eegSessionData.java
deleted file mode 100644
index 592a3264ff465fe26c4e3b61e06b11e74e6c0787..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_eegSessionData.java
+++ /dev/null
@@ -1,35 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:09 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_eegSessionData extends org.nrg.xnat.turbine.modules.screens.EditSubjectAssessorScreen {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_eegSessionData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:eegSessionData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- super.finalProcessing(data,context);
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_epsScanData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_epsScanData.java
deleted file mode 100644
index 71660c1c6b928ebf445686af5cae604144e2563d..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_epsScanData.java
+++ /dev/null
@@ -1,34 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:06 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_epsScanData extends org.nrg.xdat.turbine.modules.screens.EditScreenA {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_epsScanData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:epsScanData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_epsSessionData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_epsSessionData.java
deleted file mode 100644
index 81405545ac449f9b5d9ef58ede8f3411a01db91f..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_epsSessionData.java
+++ /dev/null
@@ -1,35 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:06 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_epsSessionData extends org.nrg.xnat.turbine.modules.screens.EditSubjectAssessorScreen {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_epsSessionData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:epsSessionData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- super.finalProcessing(data,context);
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_esScanData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_esScanData.java
deleted file mode 100644
index 1c1954042d00082303cb28ac5fba25cced051c90..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_esScanData.java
+++ /dev/null
@@ -1,34 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:08 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_esScanData extends org.nrg.xdat.turbine.modules.screens.EditScreenA {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_esScanData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:esScanData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_esSessionData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_esSessionData.java
deleted file mode 100644
index 1a721d58863a144ffe9015e89e99c1603912ba2d..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_esSessionData.java
+++ /dev/null
@@ -1,35 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:08 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_esSessionData extends org.nrg.xnat.turbine.modules.screens.EditSubjectAssessorScreen {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_esSessionData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:esSessionData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- super.finalProcessing(data,context);
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_esvScanData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_esvScanData.java
deleted file mode 100644
index ab44b6ff3a0be1e9ee5dc4738b98620ad832db31..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_esvScanData.java
+++ /dev/null
@@ -1,34 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:08 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_esvScanData extends org.nrg.xdat.turbine.modules.screens.EditScreenA {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_esvScanData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:esvScanData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_esvSessionData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_esvSessionData.java
deleted file mode 100644
index e888afa7d5319af524704e0be3743539705341be..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_esvSessionData.java
+++ /dev/null
@@ -1,35 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:08 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_esvSessionData extends org.nrg.xnat.turbine.modules.screens.EditSubjectAssessorScreen {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_esvSessionData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:esvSessionData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- super.finalProcessing(data,context);
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_fieldDefinitionGroup.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_fieldDefinitionGroup.java
deleted file mode 100644
index fc04385236bec36f9bd9371e39bac94e12f5dc9a..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_fieldDefinitionGroup.java
+++ /dev/null
@@ -1,34 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:06 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_fieldDefinitionGroup extends org.nrg.xdat.turbine.modules.screens.EditScreenA {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_fieldDefinitionGroup.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:fieldDefinitionGroup";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_genericData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_genericData.java
deleted file mode 100644
index d8fafaf71b9e724e79bc39f8909457f1f049b8e3..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_genericData.java
+++ /dev/null
@@ -1,34 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:05 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_genericData extends org.nrg.xdat.turbine.modules.screens.EditScreenA {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_genericData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:genericData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_gmScanData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_gmScanData.java
deleted file mode 100644
index fa957ca50c1d00444a577cdc149387a320941881..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_gmScanData.java
+++ /dev/null
@@ -1,34 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:09 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_gmScanData extends org.nrg.xdat.turbine.modules.screens.EditScreenA {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_gmScanData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:gmScanData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_gmSessionData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_gmSessionData.java
deleted file mode 100644
index 9377aab3f0b52633fa38397a95f39e57c749ed5c..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_gmSessionData.java
+++ /dev/null
@@ -1,35 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:09 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_gmSessionData extends org.nrg.xnat.turbine.modules.screens.EditSubjectAssessorScreen {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_gmSessionData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:gmSessionData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- super.finalProcessing(data,context);
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_gmvScanData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_gmvScanData.java
deleted file mode 100644
index 8f5dfdce46e25cdd4f48d706c42eb5abe5aa192a..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_gmvScanData.java
+++ /dev/null
@@ -1,34 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:09 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_gmvScanData extends org.nrg.xdat.turbine.modules.screens.EditScreenA {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_gmvScanData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:gmvScanData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_gmvSessionData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_gmvSessionData.java
deleted file mode 100644
index b96de23b2a2ab3d4e77e49082ff6d60f466a347f..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_gmvSessionData.java
+++ /dev/null
@@ -1,35 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:09 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_gmvSessionData extends org.nrg.xnat.turbine.modules.screens.EditSubjectAssessorScreen {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_gmvSessionData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:gmvSessionData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- super.finalProcessing(data,context);
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_hdScanData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_hdScanData.java
deleted file mode 100644
index b0967b40f51ded5593db2563996c85e0aa599d82..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_hdScanData.java
+++ /dev/null
@@ -1,34 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:06 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_hdScanData extends org.nrg.xdat.turbine.modules.screens.EditScreenA {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_hdScanData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:hdScanData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_hdSessionData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_hdSessionData.java
deleted file mode 100644
index b16abe922eaeb8fea1ae8269d8dd1e9d1f70875f..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_hdSessionData.java
+++ /dev/null
@@ -1,35 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:06 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_hdSessionData extends org.nrg.xnat.turbine.modules.screens.EditSubjectAssessorScreen {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_hdSessionData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:hdSessionData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- super.finalProcessing(data,context);
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_investigatorData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_investigatorData.java
deleted file mode 100644
index 7a7578ebc926e890996d55ac7c14b98a26eacc4e..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_investigatorData.java
+++ /dev/null
@@ -1,34 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:05 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_investigatorData extends org.nrg.xdat.turbine.modules.screens.EditScreenA {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_investigatorData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:investigatorData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_ioScanData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_ioScanData.java
deleted file mode 100644
index e8af894db803f45cd8d45f437ee289c5dfea40c4..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_ioScanData.java
+++ /dev/null
@@ -1,34 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:06 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_ioScanData extends org.nrg.xdat.turbine.modules.screens.EditScreenA {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_ioScanData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:ioScanData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_ioSessionData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_ioSessionData.java
deleted file mode 100644
index d95ce793dca41515697f78852aeba88608eb00f5..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_ioSessionData.java
+++ /dev/null
@@ -1,35 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:06 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_ioSessionData extends org.nrg.xnat.turbine.modules.screens.EditSubjectAssessorScreen {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_ioSessionData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:ioSessionData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- super.finalProcessing(data,context);
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_megScanData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_megScanData.java
deleted file mode 100644
index 49aadae79b7a7a414bc27d6670181d3ba72e3181..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_megScanData.java
+++ /dev/null
@@ -1,34 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:09 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_megScanData extends org.nrg.xdat.turbine.modules.screens.EditScreenA {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_megScanData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:megScanData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_megSessionData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_megSessionData.java
deleted file mode 100644
index 4f0d5d3fde62bbc627f014bf95b440552593c419..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_megSessionData.java
+++ /dev/null
@@ -1,35 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:09 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_megSessionData extends org.nrg.xnat.turbine.modules.screens.EditSubjectAssessorScreen {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_megSessionData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:megSessionData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- super.finalProcessing(data,context);
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_mgScanData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_mgScanData.java
deleted file mode 100644
index 5f56275186429ec7720bef40835b2fcb90d0f3eb..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_mgScanData.java
+++ /dev/null
@@ -1,34 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:06 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_mgScanData extends org.nrg.xdat.turbine.modules.screens.EditScreenA {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_mgScanData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:mgScanData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_mgSessionData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_mgSessionData.java
deleted file mode 100644
index 3f128ca103facc9c28112ee2ddb78a2b6f9ccafc..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_mgSessionData.java
+++ /dev/null
@@ -1,35 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:06 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_mgSessionData extends org.nrg.xnat.turbine.modules.screens.EditSubjectAssessorScreen {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_mgSessionData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:mgSessionData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- super.finalProcessing(data,context);
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_mrScanData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_mrScanData.java
deleted file mode 100644
index 2007cdee259b8a934688fa8e74c4c28f1f54d5aa..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_mrScanData.java
+++ /dev/null
@@ -1,34 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:05 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_mrScanData extends org.nrg.xdat.turbine.modules.screens.EditScreenA {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_mrScanData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:mrScanData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_mrSessionData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_mrSessionData.java
deleted file mode 100644
index 4d52f6da1263742870f473629d32ace2e155e61c..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_mrSessionData.java
+++ /dev/null
@@ -1,35 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:05 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_mrSessionData extends org.nrg.xnat.turbine.modules.screens.EditSubjectAssessorScreen {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_mrSessionData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:mrSessionData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- super.finalProcessing(data,context);
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_mrsScanData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_mrsScanData.java
deleted file mode 100644
index 43bd3de1b546250a2d27693d602664e9369768f9..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_mrsScanData.java
+++ /dev/null
@@ -1,34 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:09 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_mrsScanData extends org.nrg.xdat.turbine.modules.screens.EditScreenA {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_mrsScanData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:mrsScanData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_nmScanData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_nmScanData.java
deleted file mode 100644
index 34fdddb3573ca49dfcb53ee0b891ff4e4200ed14..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_nmScanData.java
+++ /dev/null
@@ -1,34 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:08 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_nmScanData extends org.nrg.xdat.turbine.modules.screens.EditScreenA {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_nmScanData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:nmScanData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_nmSessionData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_nmSessionData.java
deleted file mode 100644
index 5ec55be6be223b36dc53f07a3e7026c921c1a6b8..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_nmSessionData.java
+++ /dev/null
@@ -1,35 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:07 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_nmSessionData extends org.nrg.xnat.turbine.modules.screens.EditSubjectAssessorScreen {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_nmSessionData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:nmSessionData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- super.finalProcessing(data,context);
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_opScanData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_opScanData.java
deleted file mode 100644
index 006c28efba79ebfb98da50dc1cdc6ff886a27f60..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_opScanData.java
+++ /dev/null
@@ -1,34 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:09 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_opScanData extends org.nrg.xdat.turbine.modules.screens.EditScreenA {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_opScanData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:opScanData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_opSessionData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_opSessionData.java
deleted file mode 100644
index 912c430c3ff6f265b49dcf61bf2904b62fd22cd4..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_opSessionData.java
+++ /dev/null
@@ -1,35 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:09 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_opSessionData extends org.nrg.xnat.turbine.modules.screens.EditSubjectAssessorScreen {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_opSessionData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:opSessionData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- super.finalProcessing(data,context);
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_optScanData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_optScanData.java
deleted file mode 100644
index b8ed60bc694f71ac425d8aceb9ca81bde3fa9005..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_optScanData.java
+++ /dev/null
@@ -1,34 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:09 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_optScanData extends org.nrg.xdat.turbine.modules.screens.EditScreenA {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_optScanData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:optScanData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_optSessionData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_optSessionData.java
deleted file mode 100644
index d5ec871817ba5888bd7ffb964c0de5a60156b9e3..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_optSessionData.java
+++ /dev/null
@@ -1,35 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:09 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_optSessionData extends org.nrg.xnat.turbine.modules.screens.EditSubjectAssessorScreen {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_optSessionData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:optSessionData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- super.finalProcessing(data,context);
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_otherDicomScanData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_otherDicomScanData.java
deleted file mode 100644
index 59f112cb5d8cee44953642f8c41eb79e85b2b89e..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_otherDicomScanData.java
+++ /dev/null
@@ -1,34 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:09 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_otherDicomScanData extends org.nrg.xdat.turbine.modules.screens.EditScreenA {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_otherDicomScanData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:otherDicomScanData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_otherDicomSessionData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_otherDicomSessionData.java
deleted file mode 100644
index 983a363b5262b12f6f9e0192e6b35bb4673a18c5..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_otherDicomSessionData.java
+++ /dev/null
@@ -1,35 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:09 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_otherDicomSessionData extends org.nrg.xnat.turbine.modules.screens.EditSubjectAssessorScreen {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_otherDicomSessionData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:otherDicomSessionData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- super.finalProcessing(data,context);
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_pVisitData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_pVisitData.java
deleted file mode 100644
index 3c74112724672285fe0093d6893987f39f78c030..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_pVisitData.java
+++ /dev/null
@@ -1,34 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:05 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_pVisitData extends org.nrg.xdat.turbine.modules.screens.EditScreenA {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_pVisitData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:pVisitData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_petScanData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_petScanData.java
deleted file mode 100644
index 4e87e343c8f2f3048c06e956f259ba07dc9c8b67..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_petScanData.java
+++ /dev/null
@@ -1,34 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:05 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_petScanData extends org.nrg.xdat.turbine.modules.screens.EditScreenA {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_petScanData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:petScanData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_petSessionData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_petSessionData.java
deleted file mode 100644
index aaeeb59f64a76cd42527073c74dc61ff316c8b97..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_petSessionData.java
+++ /dev/null
@@ -1,35 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:05 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_petSessionData extends org.nrg.xnat.turbine.modules.screens.EditSubjectAssessorScreen {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_petSessionData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:petSessionData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- super.finalProcessing(data,context);
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_petmrSessionData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_petmrSessionData.java
deleted file mode 100644
index 272f0a87048ca3a9efdbe86786f74fd6da0154b4..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_petmrSessionData.java
+++ /dev/null
@@ -1,35 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:05 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_petmrSessionData extends org.nrg.xnat.turbine.modules.screens.EditSubjectAssessorScreen {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_petmrSessionData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:petmrSessionData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- super.finalProcessing(data,context);
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_projectData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_projectData.java
deleted file mode 100644
index d2eac129e7444a7b9454720c69d619fd7daf073d..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_projectData.java
+++ /dev/null
@@ -1,34 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:05 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_projectData extends org.nrg.xdat.turbine.modules.screens.EditScreenA {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_projectData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:projectData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_qcAssessmentData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_qcAssessmentData.java
deleted file mode 100644
index a560e4a0d8c45fb5e06fd1bfddf048d0ea3e67d5..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_qcAssessmentData.java
+++ /dev/null
@@ -1,34 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:05 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_qcAssessmentData extends org.nrg.xnat.turbine.modules.screens.EditImageAssessorScreen {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_qcAssessmentData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:qcAssessmentData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_qcManualAssessorData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_qcManualAssessorData.java
deleted file mode 100644
index c522781c2cbc21406f8bdfa1059e29c6b3326801..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_qcManualAssessorData.java
+++ /dev/null
@@ -1,34 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:09 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_qcManualAssessorData extends org.nrg.xnat.turbine.modules.screens.EditImageAssessorScreen {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_qcManualAssessorData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:qcManualAssessorData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_reconstructedImageData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_reconstructedImageData.java
deleted file mode 100644
index 55a49b204f1ad5c0426c51b6c5c8de7956d48ff5..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_reconstructedImageData.java
+++ /dev/null
@@ -1,34 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:05 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_reconstructedImageData extends org.nrg.xdat.turbine.modules.screens.EditScreenA {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_reconstructedImageData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:reconstructedImageData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_regionResource.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_regionResource.java
deleted file mode 100644
index 67ec38a40a92f790613c037ce762700ee0dc8a14..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_regionResource.java
+++ /dev/null
@@ -1,34 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:05 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_regionResource extends org.nrg.xdat.turbine.modules.screens.EditScreenA {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_regionResource.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:regionResource";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_resourceCatalog.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_resourceCatalog.java
deleted file mode 100644
index 66e00380d6d38d8d19a27ec95b55d26a01cefc7b..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_resourceCatalog.java
+++ /dev/null
@@ -1,34 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:05 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_resourceCatalog extends org.nrg.xdat.turbine.modules.screens.EditScreenA {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_resourceCatalog.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:resourceCatalog";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_rfScanData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_rfScanData.java
deleted file mode 100644
index dab9256bf3fbc159028ba619012ea1e94280eb41..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_rfScanData.java
+++ /dev/null
@@ -1,34 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:06 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_rfScanData extends org.nrg.xdat.turbine.modules.screens.EditScreenA {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_rfScanData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:rfScanData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_rfSessionData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_rfSessionData.java
deleted file mode 100644
index 7abc642ef698a35517998b3fa54f23f1341b4639..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_rfSessionData.java
+++ /dev/null
@@ -1,35 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:06 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_rfSessionData extends org.nrg.xnat.turbine.modules.screens.EditSubjectAssessorScreen {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_rfSessionData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:rfSessionData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- super.finalProcessing(data,context);
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_rtImageScanData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_rtImageScanData.java
deleted file mode 100644
index 000ee2015430d0bd90fd314cd7e8925be3885f8f..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_rtImageScanData.java
+++ /dev/null
@@ -1,34 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:09 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_rtImageScanData extends org.nrg.xdat.turbine.modules.screens.EditScreenA {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_rtImageScanData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:rtImageScanData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_rtSessionData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_rtSessionData.java
deleted file mode 100644
index 1236ae7e08e17a597c4c1e6e748fe6e2776415c2..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_rtSessionData.java
+++ /dev/null
@@ -1,35 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:09 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_rtSessionData extends org.nrg.xnat.turbine.modules.screens.EditSubjectAssessorScreen {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_rtSessionData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:rtSessionData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- super.finalProcessing(data,context);
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_scScanData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_scScanData.java
deleted file mode 100644
index d209939fca9ca25394d8801ac22dbab4564cbd26..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_scScanData.java
+++ /dev/null
@@ -1,34 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:09 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_scScanData extends org.nrg.xdat.turbine.modules.screens.EditScreenA {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_scScanData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:scScanData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_segScanData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_segScanData.java
deleted file mode 100644
index a449b0663c5727c26ce8fcdbf84e1f04df02d928..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_segScanData.java
+++ /dev/null
@@ -1,34 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:09 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_segScanData extends org.nrg.xdat.turbine.modules.screens.EditScreenA {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_segScanData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:segScanData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_smScanData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_smScanData.java
deleted file mode 100644
index 3a273d7e97b093738fba853458ab57fdbbd3079e..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_smScanData.java
+++ /dev/null
@@ -1,34 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:09 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_smScanData extends org.nrg.xdat.turbine.modules.screens.EditScreenA {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_smScanData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:smScanData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_smSessionData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_smSessionData.java
deleted file mode 100644
index 4107023a315cb225bd564f84a31a2bf10367ce6d..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_smSessionData.java
+++ /dev/null
@@ -1,35 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:09 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_smSessionData extends org.nrg.xnat.turbine.modules.screens.EditSubjectAssessorScreen {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_smSessionData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:smSessionData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- super.finalProcessing(data,context);
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_srScanData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_srScanData.java
deleted file mode 100644
index 81df9ba163638cd3d64d7d62315d501b3d0e81e7..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_srScanData.java
+++ /dev/null
@@ -1,34 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:08 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_srScanData extends org.nrg.xdat.turbine.modules.screens.EditScreenA {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_srScanData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:srScanData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_srSessionData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_srSessionData.java
deleted file mode 100644
index 970de5ab3899ed9509edd2f04539fd4666fb7fe7..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_srSessionData.java
+++ /dev/null
@@ -1,35 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:08 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_srSessionData extends org.nrg.xnat.turbine.modules.screens.EditSubjectAssessorScreen {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_srSessionData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:srSessionData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- super.finalProcessing(data,context);
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_subjectData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_subjectData.java
deleted file mode 100644
index 54e468ab287a5ef2ef87584cf8cbf045385771dd..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_subjectData.java
+++ /dev/null
@@ -1,34 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:05 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_subjectData extends org.nrg.xdat.turbine.modules.screens.EditScreenA {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_subjectData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:subjectData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_subjectVariablesData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_subjectVariablesData.java
deleted file mode 100644
index 6a43553a0f653fc46158aa122b93487b0d6fde28..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_subjectVariablesData.java
+++ /dev/null
@@ -1,35 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:05 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_subjectVariablesData extends org.nrg.xnat.turbine.modules.screens.EditSubjectAssessorScreen {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_subjectVariablesData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:subjectVariablesData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- super.finalProcessing(data,context);
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_usScanData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_usScanData.java
deleted file mode 100644
index 4062f89e1654d2418102efeaee73bf851331a878..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_usScanData.java
+++ /dev/null
@@ -1,34 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:06 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_usScanData extends org.nrg.xdat.turbine.modules.screens.EditScreenA {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_usScanData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:usScanData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_usSessionData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_usSessionData.java
deleted file mode 100644
index f18be7a468033fd2110a38e304bbac640b5ad61c..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_usSessionData.java
+++ /dev/null
@@ -1,35 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:06 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_usSessionData extends org.nrg.xnat.turbine.modules.screens.EditSubjectAssessorScreen {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_usSessionData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:usSessionData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- super.finalProcessing(data,context);
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_voiceAudioScanData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_voiceAudioScanData.java
deleted file mode 100644
index fb4c3518eb6d71b991277a24398b6b42eb602ba7..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_voiceAudioScanData.java
+++ /dev/null
@@ -1,34 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:09 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_voiceAudioScanData extends org.nrg.xdat.turbine.modules.screens.EditScreenA {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_voiceAudioScanData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:voiceAudioScanData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_xa3DScanData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_xa3DScanData.java
deleted file mode 100644
index f38d892a21b7b08156f12f2298830f9ae1940569..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_xa3DScanData.java
+++ /dev/null
@@ -1,34 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:06 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_xa3DScanData extends org.nrg.xdat.turbine.modules.screens.EditScreenA {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_xa3DScanData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:xa3DScanData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_xa3DSessionData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_xa3DSessionData.java
deleted file mode 100644
index 41664b90066f8d61f0b62a59ad961c11c74a6530..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_xa3DSessionData.java
+++ /dev/null
@@ -1,35 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:06 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_xa3DSessionData extends org.nrg.xnat.turbine.modules.screens.EditSubjectAssessorScreen {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_xa3DSessionData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:xa3DSessionData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- super.finalProcessing(data,context);
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_xaScanData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_xaScanData.java
deleted file mode 100644
index 4ad1333adb8747370077fc36ee88368003d3321b..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_xaScanData.java
+++ /dev/null
@@ -1,34 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:06 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_xaScanData extends org.nrg.xdat.turbine.modules.screens.EditScreenA {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_xaScanData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:xaScanData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_xaSessionData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_xaSessionData.java
deleted file mode 100644
index e4ad81af5e0b38425c6e030b239e994d563f7890..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_xaSessionData.java
+++ /dev/null
@@ -1,35 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:06 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_xaSessionData extends org.nrg.xnat.turbine.modules.screens.EditSubjectAssessorScreen {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_xaSessionData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:xaSessionData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- super.finalProcessing(data,context);
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_xcScanData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_xcScanData.java
deleted file mode 100644
index ff425e865ad2f3067057ddb4cd5623cb70f3be1f..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_xcScanData.java
+++ /dev/null
@@ -1,34 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:09 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_xcScanData extends org.nrg.xdat.turbine.modules.screens.EditScreenA {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_xcScanData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:xcScanData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_xcSessionData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_xcSessionData.java
deleted file mode 100644
index 9add3ddf7385ea3f23dd8cc5c44b94a6cf1ce369..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_xcSessionData.java
+++ /dev/null
@@ -1,35 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:09 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_xcSessionData extends org.nrg.xnat.turbine.modules.screens.EditSubjectAssessorScreen {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_xcSessionData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:xcSessionData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- super.finalProcessing(data,context);
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_xcvScanData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_xcvScanData.java
deleted file mode 100644
index 72d120ebd3348c5330a37f2951bdd307cd54942b..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_xcvScanData.java
+++ /dev/null
@@ -1,34 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:09 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_xcvScanData extends org.nrg.xdat.turbine.modules.screens.EditScreenA {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_xcvScanData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:xcvScanData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_xcvSessionData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_xcvSessionData.java
deleted file mode 100644
index 289dd7adb4ef283a94b3b678fca68a987c90a068..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_edit_xnat_xcvSessionData.java
+++ /dev/null
@@ -1,35 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:09 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.ItemI;
-import org.nrg.xft.XFTItem;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_edit_xnat_xcvSessionData extends org.nrg.xnat.turbine.modules.screens.EditSubjectAssessorScreen {
- static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_edit_xnat_xcvSessionData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.EditScreenA#getElementName()
- */
- public String getElementName() {
- return "xnat:xcvSessionData";
- }
-
- public ItemI getEmptyItem(RunData data) throws Exception
- {
- return super.getEmptyItem(data);
- }
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- super.finalProcessing(data,context);
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_cat_catalog.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_cat_catalog.java
deleted file mode 100644
index 1c88c2d183661e7fb4715379ab53b471935dfa7c..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_cat_catalog.java
+++ /dev/null
@@ -1,21 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:04 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_cat_catalog extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_cat_catalog.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_cat_dcmCatalog.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_cat_dcmCatalog.java
deleted file mode 100644
index fbd9af4d4fdab3a0b7bc67ac0b34cf3dace1ea00..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_cat_dcmCatalog.java
+++ /dev/null
@@ -1,21 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:04 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_cat_dcmCatalog extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_cat_dcmCatalog.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_cat_entry.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_cat_entry.java
deleted file mode 100644
index 5205052ebac7ce5635be0104a60f2dab7d354843..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_cat_entry.java
+++ /dev/null
@@ -1,21 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:04 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_cat_entry extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_cat_entry.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_prov_process.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_prov_process.java
deleted file mode 100644
index 20f1e2e02b5aca19d5d1d22a2768e8a84c4ea12e..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_prov_process.java
+++ /dev/null
@@ -1,21 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:10 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_prov_process extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_prov_process.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_scr_screeningAssessment.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_scr_screeningAssessment.java
deleted file mode 100644
index 32806698aad6941c1ce0a67ebbc55b780cfb9798..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_scr_screeningAssessment.java
+++ /dev/null
@@ -1,21 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:04 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_scr_screeningAssessment extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_scr_screeningAssessment.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_val_protocolData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_val_protocolData.java
deleted file mode 100644
index a16a907e7a6c6e2dc207c3a16efe056333f0eba5..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_val_protocolData.java
+++ /dev/null
@@ -1,21 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:05 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_val_protocolData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_val_protocolData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_wrk_workflowData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_wrk_workflowData.java
deleted file mode 100644
index d2b02bf862cecf2464ea1a4c11d7f963bc9438e5..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_wrk_workflowData.java
+++ /dev/null
@@ -1,21 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:03 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_wrk_workflowData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_wrk_workflowData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_a_scidResearchData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_a_scidResearchData.java
deleted file mode 100644
index c5de342afa570588fd893452bc4f0f29f1bd9ea3..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_a_scidResearchData.java
+++ /dev/null
@@ -1,28 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:10 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_a_scidResearchData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_a_scidResearchData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- try{
- org.nrg.xdat.om.XnatAscidresearchdata om = new org.nrg.xdat.om.XnatAscidresearchdata(item);
- context.put("om",om);
- System.out.println("Loaded om object (org.nrg.xdat.om.XnatAscidresearchdata) as context parameter 'om'.");
- context.put("subject",om.getSubjectData());
- System.out.println("Loaded subject object (org.nrg.xdat.om.XnatSubjectdata) as context parameter 'subject'.");
- } catch(Exception e){}
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_a_sideEffectsPittsburghData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_a_sideEffectsPittsburghData.java
deleted file mode 100644
index 041615e966bc22b3779dd7e40a2b6a441afb54c2..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_a_sideEffectsPittsburghData.java
+++ /dev/null
@@ -1,28 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:09 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_a_sideEffectsPittsburghData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_a_sideEffectsPittsburghData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- try{
- org.nrg.xdat.om.XnatAsideeffectspittsburghdata om = new org.nrg.xdat.om.XnatAsideeffectspittsburghdata(item);
- context.put("om",om);
- System.out.println("Loaded om object (org.nrg.xdat.om.XnatAsideeffectspittsburghdata) as context parameter 'om'.");
- context.put("subject",om.getSubjectData());
- System.out.println("Loaded subject object (org.nrg.xdat.om.XnatSubjectdata) as context parameter 'subject'.");
- } catch(Exception e){}
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_a_updrs3Data.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_a_updrs3Data.java
deleted file mode 100644
index db74e497c72420ed3168e36c7407fc65ca37b9fc..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_a_updrs3Data.java
+++ /dev/null
@@ -1,28 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:10 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_a_updrs3Data extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_a_updrs3Data.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- try{
- org.nrg.xdat.om.XnatAupdrs3data om = new org.nrg.xdat.om.XnatAupdrs3data(item);
- context.put("om",om);
- System.out.println("Loaded om object (org.nrg.xdat.om.XnatAupdrs3data) as context parameter 'om'.");
- context.put("subject",om.getSubjectData());
- System.out.println("Loaded subject object (org.nrg.xdat.om.XnatSubjectdata) as context parameter 'subject'.");
- } catch(Exception e){}
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_a_ybocsData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_a_ybocsData.java
deleted file mode 100644
index b940e5ac5618419df3af6cab04cdb3dffd97e425..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_a_ybocsData.java
+++ /dev/null
@@ -1,28 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:09 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_a_ybocsData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_a_ybocsData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- try{
- org.nrg.xdat.om.XnatAybocsdata om = new org.nrg.xdat.om.XnatAybocsdata(item);
- context.put("om",om);
- System.out.println("Loaded om object (org.nrg.xdat.om.XnatAybocsdata) as context parameter 'om'.");
- context.put("subject",om.getSubjectData());
- System.out.println("Loaded subject object (org.nrg.xdat.om.XnatSubjectdata) as context parameter 'subject'.");
- } catch(Exception e){}
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_a_ygtssData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_a_ygtssData.java
deleted file mode 100644
index 1b3347dedfbefb8d815a3096cb4976bec1e89f0f..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_a_ygtssData.java
+++ /dev/null
@@ -1,28 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:09 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_a_ygtssData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_a_ygtssData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- try{
- org.nrg.xdat.om.XnatAygtssdata om = new org.nrg.xdat.om.XnatAygtssdata(item);
- context.put("om",om);
- System.out.println("Loaded om object (org.nrg.xdat.om.XnatAygtssdata) as context parameter 'om'.");
- context.put("subject",om.getSubjectData());
- System.out.println("Loaded subject object (org.nrg.xdat.om.XnatSubjectdata) as context parameter 'subject'.");
- } catch(Exception e){}
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_crScanData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_crScanData.java
deleted file mode 100644
index e29bf7b787250708d13c93f6907f3b66a821c401..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_crScanData.java
+++ /dev/null
@@ -1,21 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:06 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_crScanData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_crScanData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_crSessionData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_crSessionData.java
deleted file mode 100644
index bc013ce6e013e0900416cec2c1bca64dab19396f..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_crSessionData.java
+++ /dev/null
@@ -1,28 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:06 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_crSessionData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_crSessionData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- try{
- org.nrg.xdat.om.XnatCrsessiondata om = new org.nrg.xdat.om.XnatCrsessiondata(item);
- context.put("om",om);
- System.out.println("Loaded om object (org.nrg.xdat.om.XnatCrsessiondata) as context parameter 'om'.");
- context.put("subject",om.getSubjectData());
- System.out.println("Loaded subject object (org.nrg.xdat.om.XnatSubjectdata) as context parameter 'subject'.");
- } catch(Exception e){}
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_ctScanData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_ctScanData.java
deleted file mode 100644
index a7f0e9f6ff9ef481c71a2563022feaca83e924f0..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_ctScanData.java
+++ /dev/null
@@ -1,21 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:06 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_ctScanData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_ctScanData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_ctSessionData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_ctSessionData.java
deleted file mode 100644
index 0dc44daa338bf2ad2c6ceb8884769f1662fbd44d..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_ctSessionData.java
+++ /dev/null
@@ -1,28 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:06 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_ctSessionData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_ctSessionData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- try{
- org.nrg.xdat.om.XnatCtsessiondata om = new org.nrg.xdat.om.XnatCtsessiondata(item);
- context.put("om",om);
- System.out.println("Loaded om object (org.nrg.xdat.om.XnatCtsessiondata) as context parameter 'om'.");
- context.put("subject",om.getSubjectData());
- System.out.println("Loaded subject object (org.nrg.xdat.om.XnatSubjectdata) as context parameter 'subject'.");
- } catch(Exception e){}
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_dx3DCraniofacialScanData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_dx3DCraniofacialScanData.java
deleted file mode 100644
index 66bea736c65fe88e98b9ac93fe3a894b00ebd1b2..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_dx3DCraniofacialScanData.java
+++ /dev/null
@@ -1,21 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:07 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_dx3DCraniofacialScanData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_dx3DCraniofacialScanData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_dx3DCraniofacialSessionData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_dx3DCraniofacialSessionData.java
deleted file mode 100644
index 93576e512f906a583ed3fb6d93aba2c9207ace07..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_dx3DCraniofacialSessionData.java
+++ /dev/null
@@ -1,28 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:06 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_dx3DCraniofacialSessionData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_dx3DCraniofacialSessionData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- try{
- org.nrg.xdat.om.XnatDx3dcraniofacialsessiondata om = new org.nrg.xdat.om.XnatDx3dcraniofacialsessiondata(item);
- context.put("om",om);
- System.out.println("Loaded om object (org.nrg.xdat.om.XnatDx3dcraniofacialsessiondata) as context parameter 'om'.");
- context.put("subject",om.getSubjectData());
- System.out.println("Loaded subject object (org.nrg.xdat.om.XnatSubjectdata) as context parameter 'subject'.");
- } catch(Exception e){}
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_dxScanData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_dxScanData.java
deleted file mode 100644
index 903f4a9747e36c627641772b67067e1dfbb7908d..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_dxScanData.java
+++ /dev/null
@@ -1,21 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:06 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_dxScanData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_dxScanData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_dxSessionData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_dxSessionData.java
deleted file mode 100644
index 65f25cb1bb51e4b89e87e34add2c365e99b520ed..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_dxSessionData.java
+++ /dev/null
@@ -1,28 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:06 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_dxSessionData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_dxSessionData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- try{
- org.nrg.xdat.om.XnatDxsessiondata om = new org.nrg.xdat.om.XnatDxsessiondata(item);
- context.put("om",om);
- System.out.println("Loaded om object (org.nrg.xdat.om.XnatDxsessiondata) as context parameter 'om'.");
- context.put("subject",om.getSubjectData());
- System.out.println("Loaded subject object (org.nrg.xdat.om.XnatSubjectdata) as context parameter 'subject'.");
- } catch(Exception e){}
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_ecgScanData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_ecgScanData.java
deleted file mode 100644
index f5f10ee12c5871b979ce4a531c975efb003b2bae..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_ecgScanData.java
+++ /dev/null
@@ -1,21 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:06 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_ecgScanData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_ecgScanData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_ecgSessionData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_ecgSessionData.java
deleted file mode 100644
index 0b3d22b11b8d02efc922fe996dc828383f4909e7..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_ecgSessionData.java
+++ /dev/null
@@ -1,28 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:06 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_ecgSessionData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_ecgSessionData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- try{
- org.nrg.xdat.om.XnatEcgsessiondata om = new org.nrg.xdat.om.XnatEcgsessiondata(item);
- context.put("om",om);
- System.out.println("Loaded om object (org.nrg.xdat.om.XnatEcgsessiondata) as context parameter 'om'.");
- context.put("subject",om.getSubjectData());
- System.out.println("Loaded subject object (org.nrg.xdat.om.XnatSubjectdata) as context parameter 'subject'.");
- } catch(Exception e){}
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_eegScanData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_eegScanData.java
deleted file mode 100644
index 898bd7809993a64f4879990d32bd5891ba40b91d..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_eegScanData.java
+++ /dev/null
@@ -1,21 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:09 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_eegScanData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_eegScanData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_eegSessionData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_eegSessionData.java
deleted file mode 100644
index 06dc353ff712f913994c25822c0d7b4c0a7cfe7c..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_eegSessionData.java
+++ /dev/null
@@ -1,28 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:09 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_eegSessionData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_eegSessionData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- try{
- org.nrg.xdat.om.XnatEegsessiondata om = new org.nrg.xdat.om.XnatEegsessiondata(item);
- context.put("om",om);
- System.out.println("Loaded om object (org.nrg.xdat.om.XnatEegsessiondata) as context parameter 'om'.");
- context.put("subject",om.getSubjectData());
- System.out.println("Loaded subject object (org.nrg.xdat.om.XnatSubjectdata) as context parameter 'subject'.");
- } catch(Exception e){}
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_epsScanData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_epsScanData.java
deleted file mode 100644
index 253a69bfb6292c6c6ec9cfc301975138dd1b5498..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_epsScanData.java
+++ /dev/null
@@ -1,21 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:06 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_epsScanData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_epsScanData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_epsSessionData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_epsSessionData.java
deleted file mode 100644
index 61e758b794a43911d4b17385396fdcb372c9ff67..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_epsSessionData.java
+++ /dev/null
@@ -1,28 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:06 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_epsSessionData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_epsSessionData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- try{
- org.nrg.xdat.om.XnatEpssessiondata om = new org.nrg.xdat.om.XnatEpssessiondata(item);
- context.put("om",om);
- System.out.println("Loaded om object (org.nrg.xdat.om.XnatEpssessiondata) as context parameter 'om'.");
- context.put("subject",om.getSubjectData());
- System.out.println("Loaded subject object (org.nrg.xdat.om.XnatSubjectdata) as context parameter 'subject'.");
- } catch(Exception e){}
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_esScanData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_esScanData.java
deleted file mode 100644
index 18e9d1f11349d57f580b163afa628087c1eb00e1..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_esScanData.java
+++ /dev/null
@@ -1,21 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:08 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_esScanData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_esScanData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_esSessionData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_esSessionData.java
deleted file mode 100644
index 374bf43fcbf0d5c26f7da7b5a810c22ea9bc109e..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_esSessionData.java
+++ /dev/null
@@ -1,28 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:08 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_esSessionData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_esSessionData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- try{
- org.nrg.xdat.om.XnatEssessiondata om = new org.nrg.xdat.om.XnatEssessiondata(item);
- context.put("om",om);
- System.out.println("Loaded om object (org.nrg.xdat.om.XnatEssessiondata) as context parameter 'om'.");
- context.put("subject",om.getSubjectData());
- System.out.println("Loaded subject object (org.nrg.xdat.om.XnatSubjectdata) as context parameter 'subject'.");
- } catch(Exception e){}
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_esvScanData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_esvScanData.java
deleted file mode 100644
index b3f058f25391e263f22763bbe75bdb971a51e66b..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_esvScanData.java
+++ /dev/null
@@ -1,21 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:08 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_esvScanData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_esvScanData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_esvSessionData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_esvSessionData.java
deleted file mode 100644
index 19e14deb4823e385065f8b1fbb175f0e4ff62c00..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_esvSessionData.java
+++ /dev/null
@@ -1,28 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:08 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_esvSessionData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_esvSessionData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- try{
- org.nrg.xdat.om.XnatEsvsessiondata om = new org.nrg.xdat.om.XnatEsvsessiondata(item);
- context.put("om",om);
- System.out.println("Loaded om object (org.nrg.xdat.om.XnatEsvsessiondata) as context parameter 'om'.");
- context.put("subject",om.getSubjectData());
- System.out.println("Loaded subject object (org.nrg.xdat.om.XnatSubjectdata) as context parameter 'subject'.");
- } catch(Exception e){}
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_fieldDefinitionGroup.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_fieldDefinitionGroup.java
deleted file mode 100644
index fa4a37c11b454b630f1e798a76e6dfefc9d24b35..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_fieldDefinitionGroup.java
+++ /dev/null
@@ -1,21 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:05 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_fieldDefinitionGroup extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_fieldDefinitionGroup.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_genericData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_genericData.java
deleted file mode 100644
index 5d01bf287d4ed872d2307dc3febd8748be1fa768..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_genericData.java
+++ /dev/null
@@ -1,21 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:05 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_genericData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_genericData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_gmScanData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_gmScanData.java
deleted file mode 100644
index 2c0a318f501cef5f575160bb4926b3cab0787dc7..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_gmScanData.java
+++ /dev/null
@@ -1,21 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:09 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_gmScanData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_gmScanData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_gmSessionData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_gmSessionData.java
deleted file mode 100644
index bc72828f303a40ef98783484ddb2a672f016c3ca..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_gmSessionData.java
+++ /dev/null
@@ -1,28 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:08 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_gmSessionData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_gmSessionData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- try{
- org.nrg.xdat.om.XnatGmsessiondata om = new org.nrg.xdat.om.XnatGmsessiondata(item);
- context.put("om",om);
- System.out.println("Loaded om object (org.nrg.xdat.om.XnatGmsessiondata) as context parameter 'om'.");
- context.put("subject",om.getSubjectData());
- System.out.println("Loaded subject object (org.nrg.xdat.om.XnatSubjectdata) as context parameter 'subject'.");
- } catch(Exception e){}
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_gmvScanData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_gmvScanData.java
deleted file mode 100644
index 4277c2a8e97405f4b982f6a1b6b9f93d4348dc69..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_gmvScanData.java
+++ /dev/null
@@ -1,21 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:09 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_gmvScanData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_gmvScanData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_gmvSessionData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_gmvSessionData.java
deleted file mode 100644
index e040013ac1f13511795c6d0ef1160cdbda2804ef..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_gmvSessionData.java
+++ /dev/null
@@ -1,28 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:09 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_gmvSessionData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_gmvSessionData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- try{
- org.nrg.xdat.om.XnatGmvsessiondata om = new org.nrg.xdat.om.XnatGmvsessiondata(item);
- context.put("om",om);
- System.out.println("Loaded om object (org.nrg.xdat.om.XnatGmvsessiondata) as context parameter 'om'.");
- context.put("subject",om.getSubjectData());
- System.out.println("Loaded subject object (org.nrg.xdat.om.XnatSubjectdata) as context parameter 'subject'.");
- } catch(Exception e){}
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_hdScanData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_hdScanData.java
deleted file mode 100644
index f1f2e03e01be6d7ca1e3b4aaf1b3d43a6450a57c..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_hdScanData.java
+++ /dev/null
@@ -1,21 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:06 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_hdScanData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_hdScanData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_hdSessionData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_hdSessionData.java
deleted file mode 100644
index 1fcecdc71b48dec1768ae4985e4b1265acdf0cfc..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_hdSessionData.java
+++ /dev/null
@@ -1,28 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:06 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_hdSessionData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_hdSessionData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- try{
- org.nrg.xdat.om.XnatHdsessiondata om = new org.nrg.xdat.om.XnatHdsessiondata(item);
- context.put("om",om);
- System.out.println("Loaded om object (org.nrg.xdat.om.XnatHdsessiondata) as context parameter 'om'.");
- context.put("subject",om.getSubjectData());
- System.out.println("Loaded subject object (org.nrg.xdat.om.XnatSubjectdata) as context parameter 'subject'.");
- } catch(Exception e){}
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_investigatorData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_investigatorData.java
deleted file mode 100644
index 5857139cbfeeccd395e146ed82a48c0a210f4c3f..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_investigatorData.java
+++ /dev/null
@@ -1,21 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:05 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_investigatorData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_investigatorData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_ioScanData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_ioScanData.java
deleted file mode 100644
index 00f49770daa8c70b56c0f474721b875fe2e689b5..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_ioScanData.java
+++ /dev/null
@@ -1,21 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:06 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_ioScanData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_ioScanData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_ioSessionData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_ioSessionData.java
deleted file mode 100644
index b2364fe54c0ae3dd22b004c98c49f4f8c59d3482..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_ioSessionData.java
+++ /dev/null
@@ -1,28 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:06 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_ioSessionData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_ioSessionData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- try{
- org.nrg.xdat.om.XnatIosessiondata om = new org.nrg.xdat.om.XnatIosessiondata(item);
- context.put("om",om);
- System.out.println("Loaded om object (org.nrg.xdat.om.XnatIosessiondata) as context parameter 'om'.");
- context.put("subject",om.getSubjectData());
- System.out.println("Loaded subject object (org.nrg.xdat.om.XnatSubjectdata) as context parameter 'subject'.");
- } catch(Exception e){}
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_megScanData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_megScanData.java
deleted file mode 100644
index c71a2c96607b8569abb18dfa34f36d09dcdab114..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_megScanData.java
+++ /dev/null
@@ -1,21 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:09 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_megScanData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_megScanData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_megSessionData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_megSessionData.java
deleted file mode 100644
index ba5becf28be573a602ca0343ed5c81967e7e40fa..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_megSessionData.java
+++ /dev/null
@@ -1,28 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:09 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_megSessionData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_megSessionData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- try{
- org.nrg.xdat.om.XnatMegsessiondata om = new org.nrg.xdat.om.XnatMegsessiondata(item);
- context.put("om",om);
- System.out.println("Loaded om object (org.nrg.xdat.om.XnatMegsessiondata) as context parameter 'om'.");
- context.put("subject",om.getSubjectData());
- System.out.println("Loaded subject object (org.nrg.xdat.om.XnatSubjectdata) as context parameter 'subject'.");
- } catch(Exception e){}
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_mgScanData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_mgScanData.java
deleted file mode 100644
index 7dd6f8f9f8243f848e1ceccfeafe7465edf18b95..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_mgScanData.java
+++ /dev/null
@@ -1,21 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:06 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_mgScanData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_mgScanData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_mgSessionData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_mgSessionData.java
deleted file mode 100644
index 1a23a6bc78cc1298868df3fd1b07ef40b9e39bd9..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_mgSessionData.java
+++ /dev/null
@@ -1,28 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:06 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_mgSessionData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_mgSessionData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- try{
- org.nrg.xdat.om.XnatMgsessiondata om = new org.nrg.xdat.om.XnatMgsessiondata(item);
- context.put("om",om);
- System.out.println("Loaded om object (org.nrg.xdat.om.XnatMgsessiondata) as context parameter 'om'.");
- context.put("subject",om.getSubjectData());
- System.out.println("Loaded subject object (org.nrg.xdat.om.XnatSubjectdata) as context parameter 'subject'.");
- } catch(Exception e){}
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_mrScanData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_mrScanData.java
deleted file mode 100644
index 39940d349ed060d13c002a71acb97560fcc0a0af..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_mrScanData.java
+++ /dev/null
@@ -1,21 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:05 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_mrScanData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_mrScanData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_mrSessionData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_mrSessionData.java
deleted file mode 100644
index 496583596fddc2e1e1a9492631c910840f870f9e..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_mrSessionData.java
+++ /dev/null
@@ -1,28 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:05 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_mrSessionData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_mrSessionData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- try{
- org.nrg.xdat.om.XnatMrsessiondata om = new org.nrg.xdat.om.XnatMrsessiondata(item);
- context.put("om",om);
- System.out.println("Loaded om object (org.nrg.xdat.om.XnatMrsessiondata) as context parameter 'om'.");
- context.put("subject",om.getSubjectData());
- System.out.println("Loaded subject object (org.nrg.xdat.om.XnatSubjectdata) as context parameter 'subject'.");
- } catch(Exception e){}
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_mrsScanData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_mrsScanData.java
deleted file mode 100644
index e107ca09a0fcccf0ea4d06e81c424112c152fd88..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_mrsScanData.java
+++ /dev/null
@@ -1,21 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:09 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_mrsScanData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_mrsScanData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_nmScanData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_nmScanData.java
deleted file mode 100644
index bc6a1ee5d7a66182879231e248925d2314f20299..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_nmScanData.java
+++ /dev/null
@@ -1,21 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:08 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_nmScanData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_nmScanData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_nmSessionData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_nmSessionData.java
deleted file mode 100644
index 79fc65b13d2cce9d8975435d7385a9ff603031b5..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_nmSessionData.java
+++ /dev/null
@@ -1,28 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:07 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_nmSessionData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_nmSessionData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- try{
- org.nrg.xdat.om.XnatNmsessiondata om = new org.nrg.xdat.om.XnatNmsessiondata(item);
- context.put("om",om);
- System.out.println("Loaded om object (org.nrg.xdat.om.XnatNmsessiondata) as context parameter 'om'.");
- context.put("subject",om.getSubjectData());
- System.out.println("Loaded subject object (org.nrg.xdat.om.XnatSubjectdata) as context parameter 'subject'.");
- } catch(Exception e){}
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_opScanData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_opScanData.java
deleted file mode 100644
index 5314dc410f57fd825ccbeae782666f06ccd973c7..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_opScanData.java
+++ /dev/null
@@ -1,21 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:09 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_opScanData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_opScanData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_opSessionData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_opSessionData.java
deleted file mode 100644
index cf7db5d19fa73ce04cabbf812d2b72350043102e..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_opSessionData.java
+++ /dev/null
@@ -1,28 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:09 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_opSessionData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_opSessionData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- try{
- org.nrg.xdat.om.XnatOpsessiondata om = new org.nrg.xdat.om.XnatOpsessiondata(item);
- context.put("om",om);
- System.out.println("Loaded om object (org.nrg.xdat.om.XnatOpsessiondata) as context parameter 'om'.");
- context.put("subject",om.getSubjectData());
- System.out.println("Loaded subject object (org.nrg.xdat.om.XnatSubjectdata) as context parameter 'subject'.");
- } catch(Exception e){}
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_optScanData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_optScanData.java
deleted file mode 100644
index 9d538777eef08c0f6bb2f0729634e89c7bea2673..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_optScanData.java
+++ /dev/null
@@ -1,21 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:09 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_optScanData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_optScanData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_optSessionData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_optSessionData.java
deleted file mode 100644
index 6575e2d024df0700f4654c4c3709e728e905c1f1..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_optSessionData.java
+++ /dev/null
@@ -1,28 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:09 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_optSessionData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_optSessionData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- try{
- org.nrg.xdat.om.XnatOptsessiondata om = new org.nrg.xdat.om.XnatOptsessiondata(item);
- context.put("om",om);
- System.out.println("Loaded om object (org.nrg.xdat.om.XnatOptsessiondata) as context parameter 'om'.");
- context.put("subject",om.getSubjectData());
- System.out.println("Loaded subject object (org.nrg.xdat.om.XnatSubjectdata) as context parameter 'subject'.");
- } catch(Exception e){}
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_otherDicomScanData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_otherDicomScanData.java
deleted file mode 100644
index 570a74d0470e940d83f7eaad4187e62813beaab7..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_otherDicomScanData.java
+++ /dev/null
@@ -1,21 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:09 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_otherDicomScanData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_otherDicomScanData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_otherDicomSessionData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_otherDicomSessionData.java
deleted file mode 100644
index e07828bf6282d9bc9e8ac97cba9375d6b9dadcb3..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_otherDicomSessionData.java
+++ /dev/null
@@ -1,28 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:09 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_otherDicomSessionData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_otherDicomSessionData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- try{
- org.nrg.xdat.om.XnatOtherdicomsessiondata om = new org.nrg.xdat.om.XnatOtherdicomsessiondata(item);
- context.put("om",om);
- System.out.println("Loaded om object (org.nrg.xdat.om.XnatOtherdicomsessiondata) as context parameter 'om'.");
- context.put("subject",om.getSubjectData());
- System.out.println("Loaded subject object (org.nrg.xdat.om.XnatSubjectdata) as context parameter 'subject'.");
- } catch(Exception e){}
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_pVisitData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_pVisitData.java
deleted file mode 100644
index fb9b410e87cb9450e0f89fd168e41de6e5d282ab..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_pVisitData.java
+++ /dev/null
@@ -1,21 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:05 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_pVisitData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_pVisitData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_petScanData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_petScanData.java
deleted file mode 100644
index b4846e09efe60139bd36fd8a71c5bd966a0efa1f..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_petScanData.java
+++ /dev/null
@@ -1,21 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:05 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_petScanData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_petScanData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_petSessionData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_petSessionData.java
deleted file mode 100644
index 8115a386794cd884a69acfb636f09efde2bdb6ce..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_petSessionData.java
+++ /dev/null
@@ -1,28 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:05 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_petSessionData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_petSessionData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- try{
- org.nrg.xdat.om.XnatPetsessiondata om = new org.nrg.xdat.om.XnatPetsessiondata(item);
- context.put("om",om);
- System.out.println("Loaded om object (org.nrg.xdat.om.XnatPetsessiondata) as context parameter 'om'.");
- context.put("subject",om.getSubjectData());
- System.out.println("Loaded subject object (org.nrg.xdat.om.XnatSubjectdata) as context parameter 'subject'.");
- } catch(Exception e){}
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_petmrSessionData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_petmrSessionData.java
deleted file mode 100644
index 8474b39851c897dccf213122984f21b64b01b4d2..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_petmrSessionData.java
+++ /dev/null
@@ -1,28 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:05 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_petmrSessionData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_petmrSessionData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- try{
- org.nrg.xdat.om.XnatPetmrsessiondata om = new org.nrg.xdat.om.XnatPetmrsessiondata(item);
- context.put("om",om);
- System.out.println("Loaded om object (org.nrg.xdat.om.XnatPetmrsessiondata) as context parameter 'om'.");
- context.put("subject",om.getSubjectData());
- System.out.println("Loaded subject object (org.nrg.xdat.om.XnatSubjectdata) as context parameter 'subject'.");
- } catch(Exception e){}
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_projectData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_projectData.java
deleted file mode 100644
index a264a8043b0002e5a697d57c16ebfa0e321391f0..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_projectData.java
+++ /dev/null
@@ -1,21 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:05 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_projectData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_projectData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_qcAssessmentData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_qcAssessmentData.java
deleted file mode 100644
index 6b6858ce0a2ac15567737cdc136bc794f2ae5521..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_qcAssessmentData.java
+++ /dev/null
@@ -1,31 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:05 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_qcAssessmentData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_qcAssessmentData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- try{
- org.nrg.xdat.om.XnatQcassessmentdata om = new org.nrg.xdat.om.XnatQcassessmentdata(item);
- org.nrg.xdat.om.XnatMrsessiondata mr = om.getMrSessionData();
- context.put("om",om);
- System.out.println("Loaded om object (org.nrg.xdat.om.XnatQcassessmentdata) as context parameter 'om'.");
- context.put("mr",mr);
- System.out.println("Loaded mr session object (org.nrg.xdat.om.XnatMrsessiondata) as context parameter 'mr'.");
- context.put("subject",mr.getSubjectData());
- System.out.println("Loaded subject object (org.nrg.xdat.om.XnatSubjectdata) as context parameter 'subject'.");
- } catch(Exception e){}
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_qcManualAssessorData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_qcManualAssessorData.java
deleted file mode 100644
index c39c305ce2667f28e97045eab51de46dc686107c..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_qcManualAssessorData.java
+++ /dev/null
@@ -1,21 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:09 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_qcManualAssessorData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_qcManualAssessorData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_reconstructedImageData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_reconstructedImageData.java
deleted file mode 100644
index 9671230e855787df540ae3eee7c0efa9ebc70e7e..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_reconstructedImageData.java
+++ /dev/null
@@ -1,21 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:05 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_reconstructedImageData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_reconstructedImageData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_regionResource.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_regionResource.java
deleted file mode 100644
index ed2fc29ef79a6010211b91d0566119b2529e43b5..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_regionResource.java
+++ /dev/null
@@ -1,21 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:05 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_regionResource extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_regionResource.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_resourceCatalog.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_resourceCatalog.java
deleted file mode 100644
index 30e877caaec6a8f7c9568cc58a2f811837f2a23d..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_resourceCatalog.java
+++ /dev/null
@@ -1,21 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:05 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_resourceCatalog extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_resourceCatalog.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_rfScanData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_rfScanData.java
deleted file mode 100644
index 385a56f850e2b0c26ad159a39a5642b05c1b8f1b..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_rfScanData.java
+++ /dev/null
@@ -1,21 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:06 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_rfScanData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_rfScanData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_rfSessionData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_rfSessionData.java
deleted file mode 100644
index dbff58f2121dfd44c4033b61492e59f354f670c2..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_rfSessionData.java
+++ /dev/null
@@ -1,28 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:06 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_rfSessionData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_rfSessionData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- try{
- org.nrg.xdat.om.XnatRfsessiondata om = new org.nrg.xdat.om.XnatRfsessiondata(item);
- context.put("om",om);
- System.out.println("Loaded om object (org.nrg.xdat.om.XnatRfsessiondata) as context parameter 'om'.");
- context.put("subject",om.getSubjectData());
- System.out.println("Loaded subject object (org.nrg.xdat.om.XnatSubjectdata) as context parameter 'subject'.");
- } catch(Exception e){}
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_rtImageScanData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_rtImageScanData.java
deleted file mode 100644
index 00788fd70f1330f234d68fe3dac2119b895cf340..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_rtImageScanData.java
+++ /dev/null
@@ -1,21 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:09 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_rtImageScanData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_rtImageScanData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_rtSessionData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_rtSessionData.java
deleted file mode 100644
index 83870e40f8dde28708d350750f96035e6d9faecd..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_rtSessionData.java
+++ /dev/null
@@ -1,28 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:09 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_rtSessionData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_rtSessionData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- try{
- org.nrg.xdat.om.XnatRtsessiondata om = new org.nrg.xdat.om.XnatRtsessiondata(item);
- context.put("om",om);
- System.out.println("Loaded om object (org.nrg.xdat.om.XnatRtsessiondata) as context parameter 'om'.");
- context.put("subject",om.getSubjectData());
- System.out.println("Loaded subject object (org.nrg.xdat.om.XnatSubjectdata) as context parameter 'subject'.");
- } catch(Exception e){}
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_scScanData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_scScanData.java
deleted file mode 100644
index e6ff71a0f752ff7fd154ad389b52320a88203169..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_scScanData.java
+++ /dev/null
@@ -1,21 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:09 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_scScanData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_scScanData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_segScanData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_segScanData.java
deleted file mode 100644
index 317cefcea26697b723ab9ec78716c7e7314790a8..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_segScanData.java
+++ /dev/null
@@ -1,21 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:09 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_segScanData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_segScanData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_smScanData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_smScanData.java
deleted file mode 100644
index 651b40626a3cd366e9486c9e3d51d81db91e40a9..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_smScanData.java
+++ /dev/null
@@ -1,21 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:09 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_smScanData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_smScanData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_smSessionData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_smSessionData.java
deleted file mode 100644
index 813f9de54c2cb42c878b8d656753d63addfc0e27..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_smSessionData.java
+++ /dev/null
@@ -1,28 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:09 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_smSessionData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_smSessionData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- try{
- org.nrg.xdat.om.XnatSmsessiondata om = new org.nrg.xdat.om.XnatSmsessiondata(item);
- context.put("om",om);
- System.out.println("Loaded om object (org.nrg.xdat.om.XnatSmsessiondata) as context parameter 'om'.");
- context.put("subject",om.getSubjectData());
- System.out.println("Loaded subject object (org.nrg.xdat.om.XnatSubjectdata) as context parameter 'subject'.");
- } catch(Exception e){}
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_srScanData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_srScanData.java
deleted file mode 100644
index b8974febea3157af219d7705439b24d3c37da862..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_srScanData.java
+++ /dev/null
@@ -1,21 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:08 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_srScanData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_srScanData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_srSessionData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_srSessionData.java
deleted file mode 100644
index a857dabf0dc78c799137297d34a79819906cc4d2..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_srSessionData.java
+++ /dev/null
@@ -1,28 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:08 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_srSessionData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_srSessionData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- try{
- org.nrg.xdat.om.XnatSrsessiondata om = new org.nrg.xdat.om.XnatSrsessiondata(item);
- context.put("om",om);
- System.out.println("Loaded om object (org.nrg.xdat.om.XnatSrsessiondata) as context parameter 'om'.");
- context.put("subject",om.getSubjectData());
- System.out.println("Loaded subject object (org.nrg.xdat.om.XnatSubjectdata) as context parameter 'subject'.");
- } catch(Exception e){}
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_subjectData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_subjectData.java
deleted file mode 100644
index 14c0b962b553c5a01c7f484223a20329542f1691..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_subjectData.java
+++ /dev/null
@@ -1,21 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:05 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_subjectData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_subjectData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_subjectVariablesData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_subjectVariablesData.java
deleted file mode 100644
index c7052b8ceefd28220bc5b32fdce5c8dc01e1a6a4..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_subjectVariablesData.java
+++ /dev/null
@@ -1,28 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:05 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_subjectVariablesData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_subjectVariablesData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- try{
- org.nrg.xdat.om.XnatSubjectvariablesdata om = new org.nrg.xdat.om.XnatSubjectvariablesdata(item);
- context.put("om",om);
- System.out.println("Loaded om object (org.nrg.xdat.om.XnatSubjectvariablesdata) as context parameter 'om'.");
- context.put("subject",om.getSubjectData());
- System.out.println("Loaded subject object (org.nrg.xdat.om.XnatSubjectdata) as context parameter 'subject'.");
- } catch(Exception e){}
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_usScanData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_usScanData.java
deleted file mode 100644
index b0708a38914f9df217f0607c687bac7e8f603ce2..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_usScanData.java
+++ /dev/null
@@ -1,21 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:06 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_usScanData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_usScanData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_usSessionData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_usSessionData.java
deleted file mode 100644
index 7223896d1b53eb97ea340bdbb06804eedd4db52d..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_usSessionData.java
+++ /dev/null
@@ -1,28 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:06 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_usSessionData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_usSessionData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- try{
- org.nrg.xdat.om.XnatUssessiondata om = new org.nrg.xdat.om.XnatUssessiondata(item);
- context.put("om",om);
- System.out.println("Loaded om object (org.nrg.xdat.om.XnatUssessiondata) as context parameter 'om'.");
- context.put("subject",om.getSubjectData());
- System.out.println("Loaded subject object (org.nrg.xdat.om.XnatSubjectdata) as context parameter 'subject'.");
- } catch(Exception e){}
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_voiceAudioScanData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_voiceAudioScanData.java
deleted file mode 100644
index 207429e781dc2d26eb195e53e14d294570b46006..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_voiceAudioScanData.java
+++ /dev/null
@@ -1,21 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:09 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_voiceAudioScanData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_voiceAudioScanData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_xa3DScanData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_xa3DScanData.java
deleted file mode 100644
index a0850141fc075be86d7b28cb077c5651c9dfa92b..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_xa3DScanData.java
+++ /dev/null
@@ -1,21 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:06 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_xa3DScanData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_xa3DScanData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_xa3DSessionData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_xa3DSessionData.java
deleted file mode 100644
index 49fb8cfa3da5c820cddf9e44226a4709fe8d8d9a..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_xa3DSessionData.java
+++ /dev/null
@@ -1,28 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:06 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_xa3DSessionData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_xa3DSessionData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- try{
- org.nrg.xdat.om.XnatXa3dsessiondata om = new org.nrg.xdat.om.XnatXa3dsessiondata(item);
- context.put("om",om);
- System.out.println("Loaded om object (org.nrg.xdat.om.XnatXa3dsessiondata) as context parameter 'om'.");
- context.put("subject",om.getSubjectData());
- System.out.println("Loaded subject object (org.nrg.xdat.om.XnatSubjectdata) as context parameter 'subject'.");
- } catch(Exception e){}
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_xaScanData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_xaScanData.java
deleted file mode 100644
index 4fd14653e16570db7eb3b79e60416dc31523c4b9..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_xaScanData.java
+++ /dev/null
@@ -1,21 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:06 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_xaScanData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_xaScanData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_xaSessionData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_xaSessionData.java
deleted file mode 100644
index e0c2a53447f79608c933a4c8a6a6168be051702d..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_xaSessionData.java
+++ /dev/null
@@ -1,28 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:06 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_xaSessionData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_xaSessionData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- try{
- org.nrg.xdat.om.XnatXasessiondata om = new org.nrg.xdat.om.XnatXasessiondata(item);
- context.put("om",om);
- System.out.println("Loaded om object (org.nrg.xdat.om.XnatXasessiondata) as context parameter 'om'.");
- context.put("subject",om.getSubjectData());
- System.out.println("Loaded subject object (org.nrg.xdat.om.XnatSubjectdata) as context parameter 'subject'.");
- } catch(Exception e){}
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_xcScanData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_xcScanData.java
deleted file mode 100644
index 481b92d93c5e92d2025baa5f64f7f8050ec81314..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_xcScanData.java
+++ /dev/null
@@ -1,21 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:09 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_xcScanData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_xcScanData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_xcSessionData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_xcSessionData.java
deleted file mode 100644
index d8270a5bcb95c797f78540fc54c96140c05b1875..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_xcSessionData.java
+++ /dev/null
@@ -1,28 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:09 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_xcSessionData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_xcSessionData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- try{
- org.nrg.xdat.om.XnatXcsessiondata om = new org.nrg.xdat.om.XnatXcsessiondata(item);
- context.put("om",om);
- System.out.println("Loaded om object (org.nrg.xdat.om.XnatXcsessiondata) as context parameter 'om'.");
- context.put("subject",om.getSubjectData());
- System.out.println("Loaded subject object (org.nrg.xdat.om.XnatSubjectdata) as context parameter 'subject'.");
- } catch(Exception e){}
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_xcvScanData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_xcvScanData.java
deleted file mode 100644
index 0844b7fa769abe64316d1bc2e653eff4ddb52158..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_xcvScanData.java
+++ /dev/null
@@ -1,21 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:09 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_xcvScanData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_xcvScanData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- }}
diff --git a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_xcvSessionData.java b/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_xcvSessionData.java
deleted file mode 100644
index b9156350013c9227bd9d1a86d015d6126d347405..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xdat/turbine/modules/screens/XDATScreen_report_xnat_xcvSessionData.java
+++ /dev/null
@@ -1,28 +0,0 @@
-/*
- * GENERATED FILE
- * Created on Thu Jan 28 18:10:09 UTC 2016
- *
- */
-package org.nrg.xdat.turbine.modules.screens;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-
-/**
- * @author XDAT
- *
- */
-public class XDATScreen_report_xnat_xcvSessionData extends SecureReport {
- public static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(XDATScreen_report_xnat_xcvSessionData.class);
- /* (non-Javadoc)
- * @see org.nrg.xdat.turbine.modules.screens.SecureReport#finalProcessing(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context) {
- try{
- org.nrg.xdat.om.XnatXcvsessiondata om = new org.nrg.xdat.om.XnatXcvsessiondata(item);
- context.put("om",om);
- System.out.println("Loaded om object (org.nrg.xdat.om.XnatXcvsessiondata) as context parameter 'om'.");
- context.put("subject",om.getSubjectData());
- System.out.println("Loaded subject object (org.nrg.xdat.om.XnatSubjectdata) as context parameter 'subject'.");
- } catch(Exception e){}
- }}