From e5fee20eaf690497232d75aacac918340ac68c73 Mon Sep 17 00:00:00 2001
From: Rick Herrick <jrherrick@wustl.edu>
Date: Wed, 11 May 2016 14:36:19 -0500
Subject: [PATCH] Removed last of XFT and other preference settings, cleaned up
some code references.
---
.../nrg/pipeline/XnatPipelineLauncher.java | 42 ++-
.../nrg/pipeline/utils/PipelineFileUtils.java | 9 +-
.../java/org/nrg/viewer/QCImageCreator.java | 26 +-
.../org/nrg/xnat/ajax/GrantProjectAccess.java | 2 +-
.../org/nrg/xnat/archive/BatchTransfer.java | 4 +-
.../java/org/nrg/xnat/archive/Transfer.java | 4 +-
.../helpers/prearchive/PrearcDatabase.java | 4 +-
.../notifications/NotifyProjectListeners.java | 4 +-
.../NotifyProjectPipelineListeners.java | 8 +-
.../org/nrg/xnat/restlet/XNATApplication.java | 11 +-
.../restlet/actions/TriggerPipelines.java | 15 +-
.../extensions/AuthenticationRestlet.java | 3 +-
.../resources/ProjectMemberResource.java | 115 +++----
.../resources/ProjtExptPipelineResource.java | 28 +-
.../restlet/resources/SecureResource.java | 4 +-
.../restlet/services/mail/MailRestlet.java | 2 +-
.../file/MoveStoredFileRequestListener.java | 2 +-
.../turbine/modules/actions/AddProject.java | 7 +-
.../modules/actions/ConfirmRegister.java | 12 +-
.../modules/actions/ManagePipeline.java | 28 +-
.../modules/actions/ManageProjectAccess.java | 6 +-
.../actions/MatchPrearchiveSessions.java | 20 +-
.../modules/actions/PipelineActions.java | 11 +-
.../modules/actions/ProcessAccessRequest.java | 12 +-
.../turbine/modules/actions/QDECAction.java | 11 +-
.../modules/actions/RequestAccess.java | 6 +-
.../turbine/modules/actions/SampleBuild.java | 11 +-
.../screens/BuildPipelineParameters.java | 5 +-
.../PipelineScreen_set_site_parameters.java | 4 +-
.../screens/XDATScreen_UpdateUser.java | 14 +-
.../xnat/turbine/utils/ArcSpecManager.java | 310 +++++++++---------
.../nrg/xnat/turbine/utils/IDGenerator.java | 6 +-
.../turbine/utils/ProjectAccessRequest.java | 4 +-
.../java/org/nrg/xnat/utils/FileUtils.java | 1 +
34 files changed, 357 insertions(+), 394 deletions(-)
diff --git a/src/main/java/org/nrg/pipeline/XnatPipelineLauncher.java b/src/main/java/org/nrg/pipeline/XnatPipelineLauncher.java
index 19dbb911..e88d15ba 100644
--- a/src/main/java/org/nrg/pipeline/XnatPipelineLauncher.java
+++ b/src/main/java/org/nrg/pipeline/XnatPipelineLauncher.java
@@ -22,9 +22,7 @@ import org.nrg.xdat.om.WrkWorkflowdata;
import org.nrg.xdat.om.XnatExperimentdata;
import org.nrg.xdat.om.XnatImagesessiondata;
import org.nrg.xdat.services.AliasTokenService;
-import org.nrg.xdat.turbine.utils.AdminUtils;
import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.XFT;
import org.nrg.xft.event.EventUtils;
import org.nrg.xft.security.UserI;
import org.nrg.xnat.turbine.utils.ArcSpecManager;
@@ -54,8 +52,8 @@ public class XnatPipelineLauncher {
private UserI user;
private String dataType;
private String host;
- private Set<String> notificationEmailIds = new HashSet<String>();
- private Map<String, List<String>> parameters = new Hashtable<String, List<String>>();
+ private Set<String> notificationEmailIds = new HashSet<>();
+ private Map<String, List<String>> parameters = new Hashtable<>();
private String startAt;
private boolean waitFor;
private boolean needsBuildDir;
@@ -136,7 +134,7 @@ public class XnatPipelineLauncher {
}
if (needsBuildDir) {
- parameters.put("builddir", Arrays.asList(path));
+ parameters.put("builddir", Collections.singletonList(path));
}
setNeedsBuildDir(false);
@@ -159,7 +157,7 @@ public class XnatPipelineLauncher {
}
public XnatPipelineLauncher(RunData data, Context context) {
- user = TurbineUtils.getUser(data);
+ user = XDAT.getUserDetails();
host = TurbineUtils.GetFullServerPath();
startAt = null;
supressNotification = false;
@@ -182,7 +180,7 @@ public class XnatPipelineLauncher {
private void addUserEmailForNotification() {
notify(user.getEmail());
- notify(AdminUtils.getAdminEmailId());
+ notify(XDAT.getSiteConfigPreferences().getAdminEmail());
}
/*
@@ -192,7 +190,7 @@ public class XnatPipelineLauncher {
*/
public boolean launch() {
- return launch(XFT.GetPipelinePath() + "bin" + File.separator + SCHEDULE);
+ return launch(XDAT.getSiteConfigPreferences().getPipelinePath() + "bin" + File.separator + SCHEDULE);
}
/*
@@ -305,7 +303,7 @@ public class XnatPipelineLauncher {
command = "";
}
- command += XFT.GetPipelinePath() + "bin" + File.separator + "XnatPipelineLauncher";
+ command += XDAT.getSiteConfigPreferences().getAdminEmail() + "bin" + File.separator + "XnatPipelineLauncher";
if (System.getProperty("os.name").toUpperCase().startsWith("WINDOWS")) {
command += ".bat";
@@ -332,7 +330,7 @@ public class XnatPipelineLauncher {
private List<String> getPipelineConfigurationArguments() {
List<String> arguments = new ArrayList<>();
try {
- String pipelinePath = new File(XFT.GetPipelinePath()).getCanonicalPath();
+ String pipelinePath = new File(XDAT.getSiteConfigPreferences().getAdminEmail()).getCanonicalPath();
boolean requiresQuotes = pipelinePath.contains(" ");
arguments.add("-config");
String configPath = pipelinePath + File.separator + "pipeline.config";
@@ -361,7 +359,7 @@ public class XnatPipelineLauncher {
private List<String> getCommandLineArguments() {
AliasToken token = XDAT.getContextService().getBean(AliasTokenService.class).issueTokenForUser(user);
- List<String> arguments = new ArrayList<String>();
+ List<String> arguments = new ArrayList<>();
arguments.add("-pipeline");
arguments.add(pipelineName);
arguments.add("-id");
@@ -437,7 +435,7 @@ public class XnatPipelineLauncher {
}
private Integer initiateWorkflowEntry() throws Exception {
- WrkWorkflowdata wrk = new WrkWorkflowdata((UserI)user);
+ WrkWorkflowdata wrk = new WrkWorkflowdata(user);
wrk.setDataType(this.getDataType());
wrk.setId(this.getId());
wrk.setExternalid(this.getExternalId());
@@ -516,7 +514,7 @@ public class XnatPipelineLauncher {
if (parameters.containsKey(name)) {
parameters.get(name).add(value);
} else {
- parameters.put(name, Arrays.asList(value));
+ parameters.put(name, Collections.singletonList(value));
}
}
@@ -528,7 +526,7 @@ public class XnatPipelineLauncher {
buildPath = buildPath.substring(0, buildPath.length() - 1);
}
if (needsBuildDir) {
- parameters.put("builddir", Arrays.asList(buildPath + File.separator + "Pipeline"));
+ parameters.put("builddir", Collections.singletonList(buildPath + File.separator + "Pipeline"));
}
}
@@ -622,11 +620,11 @@ public class XnatPipelineLauncher {
public static XnatPipelineLauncher GetLauncherForExperiment(RunData data, Context context, XnatExperimentdata imageSession) throws Exception {
XnatPipelineLauncher xnatPipelineLauncher = new XnatPipelineLauncher(data, context);
xnatPipelineLauncher.setSupressNotification(true);
- UserI user = TurbineUtils.getUser(data);
+ UserI user = XDAT.getUserDetails();
xnatPipelineLauncher.setParameter("useremail", user.getEmail());
xnatPipelineLauncher.setParameter("userfullname", XnatPipelineLauncher.getUserName(user));
- xnatPipelineLauncher.setParameter("adminemail", AdminUtils.getAdminEmailId());
- xnatPipelineLauncher.setParameter("mailhost", AdminUtils.getMailServer());
+ xnatPipelineLauncher.setParameter("adminemail", XDAT.getSiteConfigPreferences().getAdminEmail());
+ xnatPipelineLauncher.setParameter("mailhost", XDAT.getSiteConfigPreferences().getSmtpServer().get("host"));
xnatPipelineLauncher.setParameter("xnatserver", TurbineUtils.GetSystemName());
xnatPipelineLauncher.setId(imageSession.getId());
@@ -637,8 +635,8 @@ public class XnatPipelineLauncher {
xnatPipelineLauncher.setParameter("project", imageSession.getProject());
xnatPipelineLauncher.setParameter("cachepath", QCImageCreator.getQCCachePathForSession(imageSession.getProject()));
- List<String> emails = new ArrayList<String>();
- emails.add(TurbineUtils.getUser(data).getEmail());
+ List<String> emails = new ArrayList<>();
+ emails.add(XDAT.getUserDetails().getEmail());
String extraEmails = (String) TurbineUtils.GetPassedParameter("emailField", data);
if (!StringUtils.isBlank(extraEmails)) {
@@ -659,11 +657,11 @@ public class XnatPipelineLauncher {
public static XnatPipelineLauncher GetBareLauncherForExperiment(RunData data, Context context, XnatExperimentdata imageSession) throws Exception {
XnatPipelineLauncher xnatPipelineLauncher = new XnatPipelineLauncher(data, context);
xnatPipelineLauncher.setSupressNotification(true);
- UserI user = TurbineUtils.getUser(data);
+ UserI user = XDAT.getUserDetails();
xnatPipelineLauncher.setParameter("useremail", user.getEmail());
xnatPipelineLauncher.setParameter("userfullname", XnatPipelineLauncher.getUserName(user));
- xnatPipelineLauncher.setParameter("adminemail", AdminUtils.getAdminEmailId());
- xnatPipelineLauncher.setParameter("mailhost", AdminUtils.getMailServer());
+ xnatPipelineLauncher.setParameter("adminemail", XDAT.getSiteConfigPreferences().getAdminEmail());
+ xnatPipelineLauncher.setParameter("mailhost", XDAT.getSiteConfigPreferences().getSmtpServer().get("host"));
xnatPipelineLauncher.setParameter("xnatserver", TurbineUtils.GetSystemName());
xnatPipelineLauncher.setId(imageSession.getId());
diff --git a/src/main/java/org/nrg/pipeline/utils/PipelineFileUtils.java b/src/main/java/org/nrg/pipeline/utils/PipelineFileUtils.java
index 9799b168..4165fa61 100644
--- a/src/main/java/org/nrg/pipeline/utils/PipelineFileUtils.java
+++ b/src/main/java/org/nrg/pipeline/utils/PipelineFileUtils.java
@@ -15,13 +15,14 @@ import org.apache.xmlbeans.XmlException;
import org.apache.xmlbeans.XmlObject;
import org.apache.xmlbeans.XmlOptions;
import org.nrg.pipeline.xmlbeans.PipelineDocument;
+import org.nrg.xdat.XDAT;
import org.nrg.xdat.om.ArcProject;
-import org.nrg.xft.XFT;
import org.nrg.xnat.turbine.utils.ArcSpecManager;
import java.io.File;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.Calendar;
public class PipelineFileUtils {
@@ -35,7 +36,7 @@ public class PipelineFileUtils {
xopt.setErrorListener(errors);
XmlObject xo = XmlObject.Factory.parse(xmlFile, xopt);
if (errors.size() != 0) {
- throw new XmlException(errors.toArray().toString());
+ throw new XmlException(Arrays.toString(errors.toArray()));
}
//String err = XMLBeansUtils.validateAndGetErrors(xo);
//if (err != null) {
@@ -54,7 +55,7 @@ public class PipelineFileUtils {
public static String getMaxMatching(String file1, String file2, String scanId1, String scanId2) {
- String rtn = null;
+ String rtn;
if (file1 == null || file2 == null || scanId1 == null || scanId2 == null) return null;
int index = 0;
while (true) {
@@ -91,7 +92,7 @@ public class PipelineFileUtils {
public static String getBuildDir(String project, boolean postfixTimestamp) {
ArcProject arcProject = ArcSpecManager.GetFreshInstance().getProjectArc(project);
- String buildPath = XFT.GetPipelinePath() ;
+ String buildPath = XDAT.getSiteConfigPreferences().getAdminEmail() ;
if (arcProject != null) {
buildPath = arcProject.getPaths().getBuildpath();
}
diff --git a/src/main/java/org/nrg/viewer/QCImageCreator.java b/src/main/java/org/nrg/viewer/QCImageCreator.java
index fee11743..9a13829c 100644
--- a/src/main/java/org/nrg/viewer/QCImageCreator.java
+++ b/src/main/java/org/nrg/viewer/QCImageCreator.java
@@ -11,24 +11,22 @@
package org.nrg.viewer;
-import java.io.File;
-
-import org.apache.log4j.Logger;
import org.nrg.pipeline.XnatPipelineLauncher;
import org.nrg.plexiViewer.lite.xml.PlexiViewerSpecForSession;
import org.nrg.plexiViewer.manager.PlexiSpecDocReader;
+import org.nrg.xdat.XDAT;
import org.nrg.xdat.om.XnatMrsessiondata;
-import org.nrg.xdat.turbine.utils.AdminUtils;
import org.nrg.xdat.turbine.utils.TurbineUtils;
import org.nrg.xft.security.UserI;
import org.nrg.xnat.turbine.utils.ArcSpecManager;
+import java.io.File;
+
public class QCImageCreator {
XnatMrsessiondata mrSession;
UserI user;
- static Logger logger = Logger.getLogger(QCImageCreator.class);
-
+
public QCImageCreator(XnatMrsessiondata mrSession, UserI user) {
this.mrSession = mrSession;
this.user = user;
@@ -38,7 +36,7 @@ public class QCImageCreator {
public boolean createQCImagesForScans() throws Exception {
XnatPipelineLauncher xnatPipelineLauncher = new XnatPipelineLauncher(user);
- xnatPipelineLauncher.setAdmin_email(AdminUtils.getAdminEmailId());
+ xnatPipelineLauncher.setAdmin_email(XDAT.getSiteConfigPreferences().getAdminEmail());
xnatPipelineLauncher.setAlwaysEmailAdmin(ArcSpecManager.GetInstance().getEmailspecifications_pipeline());
xnatPipelineLauncher.setWaitFor(true);
String pipelineName = "images/WebBasedQCImageCreator.xml";
@@ -53,9 +51,9 @@ public class QCImageCreator {
xnatPipelineLauncher.setParameter("session", mrSession.getId() );
xnatPipelineLauncher.setParameter("notify", "0" );
xnatPipelineLauncher.setParameter("xnatserver", TurbineUtils.GetSystemName());
- xnatPipelineLauncher.setParameter("mailhost", AdminUtils.getMailServer());
+ xnatPipelineLauncher.setParameter("mailhost", XDAT.getSiteConfigPreferences().getSmtpServer().get("host"));
xnatPipelineLauncher.setParameter("useremail", user.getEmail());
- xnatPipelineLauncher.setParameter("adminemail", AdminUtils.getAdminEmailId());
+ xnatPipelineLauncher.setParameter("adminemail", XDAT.getSiteConfigPreferences().getAdminEmail());
return xnatPipelineLauncher.launch(null);
@@ -68,8 +66,7 @@ public class QCImageCreator {
public static String GetPathToQCFile(XnatMrsessiondata mrSession, String mrScanId) {
PlexiViewerSpecForSession viewerSpec = PlexiSpecDocReader.GetInstance().getSpecDoc(mrSession.getSessionType());
- String rtn = viewerSpec.getThumbnailArchiveLocation() + File.separator + mrSession.getId() +"_" + mrScanId + "_qc.gif";
- return rtn;
+ return viewerSpec.getThumbnailArchiveLocation() + File.separator + mrSession.getId() + "_" + mrScanId + "_qc.gif";
}
@@ -79,18 +76,17 @@ public class QCImageCreator {
public static String getQCThumbnailPathForSession(String project) {
- String path = null;
+ String path;
if (project!=null){
path= ArcSpecManager.GetInstance().getCachePathForProject(project);
}else{
path= ArcSpecManager.GetInstance().getGlobalCachePath();
}
- String thumb_path = path +"Thumbnail/";
- return thumb_path;
+ return path + "Thumbnail/";
}
public static String getQCCachePathForSession(String project) {
- String path = null;
+ String path;
if (project!=null){
path= ArcSpecManager.GetInstance().getCachePathForProject(project);
}else{
diff --git a/src/main/java/org/nrg/xnat/ajax/GrantProjectAccess.java b/src/main/java/org/nrg/xnat/ajax/GrantProjectAccess.java
index 43c0230e..38a16d32 100644
--- a/src/main/java/org/nrg/xnat/ajax/GrantProjectAccess.java
+++ b/src/main/java/org/nrg/xnat/ajax/GrantProjectAccess.java
@@ -55,7 +55,7 @@ public class GrantProjectAccess {
context.put("process","Transfer to the archive.");
context.put("system",TurbineUtils.GetSystemName());
context.put("access_level",level);
- context.put("admin_email",AdminUtils.getAdminEmailId());
+ context.put("admin_email",XDAT.getSiteConfigPreferences().getAdminEmail());
context.put("projectOM",project);
//SEND email to user
ProjectAccessRequest.InviteUser(context, email, user, user.getFirstname() + " " + user.getLastname()
diff --git a/src/main/java/org/nrg/xnat/archive/BatchTransfer.java b/src/main/java/org/nrg/xnat/archive/BatchTransfer.java
index c28f9d3f..d33c5638 100644
--- a/src/main/java/org/nrg/xnat/archive/BatchTransfer.java
+++ b/src/main/java/org/nrg/xnat/archive/BatchTransfer.java
@@ -409,8 +409,8 @@ public class BatchTransfer extends Thread{
}
}
- String[] to = new String[] { AdminUtils.getAdminEmailId(), user.getEmail() };
- String from = AdminUtils.getAdminEmailId();
+ String[] to = new String[] { XDAT.getSiteConfigPreferences().getAdminEmail(), user.getEmail() };
+ String from = XDAT.getSiteConfigPreferences().getAdminEmail();
String subject = system + " update: Archiving Complete.";
if (errors.size()>0)
subject += errors.size() + " errors";
diff --git a/src/main/java/org/nrg/xnat/archive/Transfer.java b/src/main/java/org/nrg/xnat/archive/Transfer.java
index f9790624..7fc86549 100644
--- a/src/main/java/org/nrg/xnat/archive/Transfer.java
+++ b/src/main/java/org/nrg/xnat/archive/Transfer.java
@@ -102,7 +102,7 @@ public class Transfer {
XnatPipelineLauncher xnatPipelineLauncher = new XnatPipelineLauncher((UserI)user);
// Modified by MR - 2010/03/11 AdminEmail is set in pipeline setup setup
- // xnatPipelineLauncher.setAdmin_email(AdminUtils.getAdminEmailId());
+ // xnatPipelineLauncher.setAdmin_email(XDAT.getSiteConfigPreferences().getAdminEmail());
//Modified bt MR - 2010/03/11 There is a setting for Site Admin to set email notification for Transfer pipeline
// xnatPipelineLauncher.setAlwaysEmailAdmin(ArcSpecManager.GetInstance().getEmailspecifications_pipeline());
String pipelineName = "xnat_tools/Transfer.xml";
@@ -131,7 +131,7 @@ public class Transfer {
xnatPipelineLauncher.setParameter("userfullname", XnatPipelineLauncher.getUserName(user));
xnatPipelineLauncher.setParameter("adminemail", admin_email);
xnatPipelineLauncher.setParameter("xnatserver", system);
- xnatPipelineLauncher.setParameter("mailhost", AdminUtils.getMailServer());
+ xnatPipelineLauncher.setParameter("mailhost", XDAT.getSiteConfigPreferences().getSmtpServer().get("host"));
xnatPipelineLauncher.setParameter("sessionType", mr.getXSIType());
xnatPipelineLauncher.setParameter("xnat_project", mr.getProject());
xnatPipelineLauncher.setParameter("logDir", XDAT.getSiteConfigPreferences().getCachePath() + "logs" + "/" + "transfer");
diff --git a/src/main/java/org/nrg/xnat/helpers/prearchive/PrearcDatabase.java b/src/main/java/org/nrg/xnat/helpers/prearchive/PrearcDatabase.java
index 457369dc..3e8b0f91 100644
--- a/src/main/java/org/nrg/xnat/helpers/prearchive/PrearcDatabase.java
+++ b/src/main/java/org/nrg/xnat/helpers/prearchive/PrearcDatabase.java
@@ -178,11 +178,11 @@ public final class PrearcDatabase {
protected static String getPrearcPath() {
final SiteConfigPreferences preferences = XDAT.getSiteConfigPreferences();
if (preferences != null) {
- return preferences.getArchiveRootPath();
+ return preferences.getPrearchivePath();
}
try {
final Properties properties = XDAT.getSiteConfiguration();
- return properties.getProperty("archiveRootPath");
+ return properties.getProperty("prearchivePath");
} catch (ConfigServiceException e) {
return null;
}
diff --git a/src/main/java/org/nrg/xnat/notifications/NotifyProjectListeners.java b/src/main/java/org/nrg/xnat/notifications/NotifyProjectListeners.java
index 9a5f0b30..cc1f3761 100644
--- a/src/main/java/org/nrg/xnat/notifications/NotifyProjectListeners.java
+++ b/src/main/java/org/nrg/xnat/notifications/NotifyProjectListeners.java
@@ -83,13 +83,13 @@ public class NotifyProjectListeners implements Callable<Boolean> {
Context context =new VelocityContext(_params);
- String from = AdminUtils.getAdminEmailId();
+ String from = XDAT.getSiteConfigPreferences().getAdminEmail();
context.put("user", _user);
context.put("expt", _expt);
context.put("username", _user.getUsername());
context.put("server", TurbineUtils.GetFullServerPath());
context.put("system", TurbineUtils.GetSystemName());
- context.put("admin_email", AdminUtils.getAdminEmailId());
+ context.put("admin_email", XDAT.getSiteConfigPreferences().getAdminEmail());
context.put("params", _params);
if(_params.get("justification")!=null){
context.put("justification",_params.get("justification"));
diff --git a/src/main/java/org/nrg/xnat/notifications/NotifyProjectPipelineListeners.java b/src/main/java/org/nrg/xnat/notifications/NotifyProjectPipelineListeners.java
index 621488d7..00ecd637 100644
--- a/src/main/java/org/nrg/xnat/notifications/NotifyProjectPipelineListeners.java
+++ b/src/main/java/org/nrg/xnat/notifications/NotifyProjectPipelineListeners.java
@@ -75,21 +75,21 @@ public class NotifyProjectPipelineListeners extends NotifyProjectListeners {
email.add(e);
}
}
- if(!email.contains(AdminUtils.getAdminEmailId())){
- email.add(AdminUtils.getAdminEmailId());
+ if(!email.contains(XDAT.getSiteConfigPreferences().getAdminEmail())){
+ email.add(XDAT.getSiteConfigPreferences().getAdminEmail());
}
if(email.size()>0){
Context context =new VelocityContext(Maps.newHashMap());
- String from = AdminUtils.getAdminEmailId();
+ String from = XDAT.getSiteConfigPreferences().getAdminEmail();
context.put("user", _user);
context.put("expt", _expt);
context.put("username", _user.getUsername());
context.put("server", TurbineUtils.GetFullServerPath());
context.put("system", TurbineUtils.GetSystemName());
- context.put("admin_email", AdminUtils.getAdminEmailId());
+ context.put("admin_email", XDAT.getSiteConfigPreferences().getAdminEmail());
context.put("workflow",_workflow);
context.put("params", _params);
for(Map.Entry<String,Object> entry : _params.entrySet()) {
diff --git a/src/main/java/org/nrg/xnat/restlet/XNATApplication.java b/src/main/java/org/nrg/xnat/restlet/XNATApplication.java
index d7567871..f297f018 100755
--- a/src/main/java/org/nrg/xnat/restlet/XNATApplication.java
+++ b/src/main/java/org/nrg/xnat/restlet/XNATApplication.java
@@ -350,9 +350,6 @@ public class XNATApplication extends Application {
"/automation/templates/{TEMPLATE_ID}",
"/projects/{PROJECT_ID}/automation/templates",
"/projects/{PROJECT_ID}/automation/templates/{TEMPLATE_ID}");
- attachURI(router, "/services/settings", SettingsRestlet.class);
- attachURI(router, "/services/settings/{PROPERTY}", SettingsRestlet.class);
- attachURI(router, "/services/settings/{PROPERTY}/{VALUE}", SettingsRestlet.class);
attachURI(router, "/status/{TRANSACTION_ID}", SQListenerRepresentation.class);
@@ -401,7 +398,7 @@ public class XNATApplication extends Application {
if (clazz.isAnnotationPresent(XnatRestlet.class)) {
XnatRestlet annotation = clazz.getAnnotation(XnatRestlet.class);
final String[] urls = annotation.value();
- if (urls == null || urls.length == 0) {
+ if (urls.length == 0) {
throw new RuntimeException("The restlet extension class " + clazz.getName() + " has no URLs configured.");
}
if (annotation.secure()) {
@@ -418,7 +415,7 @@ public class XNATApplication extends Application {
}else if (clazz.isAnnotationPresent(XnatRestlet2.class)) {
XnatRestlet2 annotation = clazz.getAnnotation(XnatRestlet2.class);
final XnatRestletURI[] urls = annotation.value();
- if (urls == null || urls.length == 0) {
+ if (urls.length == 0) {
throw new RuntimeException("The restlet extension class " + clazz.getName() + " has no URLs configured.");
}
if (annotation.secure()) {
@@ -445,7 +442,7 @@ public class XNATApplication extends Application {
private void attachPath(Router router, Class<? extends Resource> clazz, XnatRestlet annotation) {
String[] paths = annotation.value();
boolean required = annotation.required();
- if (paths == null || paths.length == 0) {
+ if (paths.length == 0) {
String message = "You must specify a value for the XnatRestlet annotation to indicate the hosting path for the restlet extension in class: " + clazz.getName();
if (required) {
throw new NrgServiceRuntimeException(message);
@@ -462,7 +459,7 @@ public class XNATApplication extends Application {
private void attachPath(Router router, Class<? extends Resource> clazz, XnatRestlet2 annotation) {
XnatRestletURI[] paths = annotation.value();
boolean required = annotation.required();
- if (paths == null || paths.length == 0) {
+ if (paths.length == 0) {
String message = "You must specify a value for the XnatRestlet annotation to indicate the hosting path for the restlet extension in class: " + clazz.getName();
if (required) {
throw new NrgServiceRuntimeException(message);
diff --git a/src/main/java/org/nrg/xnat/restlet/actions/TriggerPipelines.java b/src/main/java/org/nrg/xnat/restlet/actions/TriggerPipelines.java
index 4b58b470..e0d04488 100644
--- a/src/main/java/org/nrg/xnat/restlet/actions/TriggerPipelines.java
+++ b/src/main/java/org/nrg/xnat/restlet/actions/TriggerPipelines.java
@@ -10,24 +10,23 @@
*/
package org.nrg.xnat.restlet.actions;
-import java.util.concurrent.Callable;
-
import org.apache.log4j.Logger;
import org.nrg.pipeline.XnatPipelineLauncher;
+import org.nrg.xdat.XDAT;
import org.nrg.xdat.om.XnatExperimentdata;
-import org.nrg.xdat.turbine.utils.AdminUtils;
import org.nrg.xdat.turbine.utils.TurbineUtils;
import org.nrg.xft.security.UserI;
import org.nrg.xnat.restlet.util.XNATRestConstants;
import org.nrg.xnat.turbine.utils.ArcSpecManager;
+import java.util.concurrent.Callable;
+
/**
* @author Timothy R. Olsen <olsent@wustl.edu>
*
*/
public class TriggerPipelines implements Callable<Boolean> {
- static Logger logger = Logger.getLogger(TriggerPipelines.class);
private static final String XNAT_TOOLS_AUTO_RUN_XML = "xnat_tools/AutoRun.xml";
private final XnatExperimentdata expt;
@@ -48,7 +47,7 @@ public class TriggerPipelines implements Callable<Boolean> {
public Boolean call() {
XnatPipelineLauncher xnatPipelineLauncher = new XnatPipelineLauncher(user);
- xnatPipelineLauncher.setAdmin_email(AdminUtils.getAdminEmailId());
+ xnatPipelineLauncher.setAdmin_email(XDAT.getSiteConfigPreferences().getAdminEmail());
xnatPipelineLauncher.setAlwaysEmailAdmin(ArcSpecManager.GetInstance().getEmailspecifications_pipeline());
String pipelineName = XNAT_TOOLS_AUTO_RUN_XML;
xnatPipelineLauncher.setPipelineName(pipelineName);
@@ -59,14 +58,14 @@ public class TriggerPipelines implements Callable<Boolean> {
xnatPipelineLauncher.setDataType(expt.getXSIType());
xnatPipelineLauncher.setExternalId(expt.getProject());
xnatPipelineLauncher.setWaitFor(this.waitFor);
- xnatPipelineLauncher.setParameter(XNATRestConstants.SUPRESS_EMAIL, (new Boolean(supressEmail)).toString());
+ xnatPipelineLauncher.setParameter(XNATRestConstants.SUPRESS_EMAIL, (Boolean.valueOf(supressEmail)).toString());
xnatPipelineLauncher.setParameter("session", expt.getId());
xnatPipelineLauncher.setParameter("sessionLabel", expt.getLabel());
xnatPipelineLauncher.setParameter("useremail", user.getEmail());
xnatPipelineLauncher.setParameter("userfullname", XnatPipelineLauncher.getUserName(user));
- xnatPipelineLauncher.setParameter("adminemail", AdminUtils.getAdminEmailId());
+ xnatPipelineLauncher.setParameter("adminemail", XDAT.getSiteConfigPreferences().getAdminEmail());
xnatPipelineLauncher.setParameter("xnatserver", TurbineUtils.GetSystemName());
- xnatPipelineLauncher.setParameter("mailhost", AdminUtils.getMailServer());
+ xnatPipelineLauncher.setParameter("mailhost", XDAT.getSiteConfigPreferences().getSmtpServer().get("host"));
xnatPipelineLauncher.setParameter("sessionType", expt.getXSIType());
xnatPipelineLauncher.setParameter("xnat_project", expt.getProject());
diff --git a/src/main/java/org/nrg/xnat/restlet/extensions/AuthenticationRestlet.java b/src/main/java/org/nrg/xnat/restlet/extensions/AuthenticationRestlet.java
index cbd2dada..b7f93805 100644
--- a/src/main/java/org/nrg/xnat/restlet/extensions/AuthenticationRestlet.java
+++ b/src/main/java/org/nrg/xnat/restlet/extensions/AuthenticationRestlet.java
@@ -14,7 +14,6 @@ import org.apache.commons.lang3.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.nrg.xdat.XDAT;
-import org.nrg.xft.XFT;
import org.nrg.xnat.restlet.XnatRestlet;
import org.nrg.xnat.security.XnatProviderManager;
import org.restlet.Context;
@@ -76,7 +75,7 @@ public class AuthenticationRestlet extends Resource {
_log.debug("Passing a representation of the verify extensions restlet.");
}
- if (XFT.GetRequireLogin() && (StringUtils.isBlank(_username) || StringUtils.isBlank(_password))) {
+ if (XDAT.getSiteConfigPreferences().getRequireLogin() && (StringUtils.isBlank(_username) || StringUtils.isBlank(_password))) {
fail();
return;
}
diff --git a/src/main/java/org/nrg/xnat/restlet/resources/ProjectMemberResource.java b/src/main/java/org/nrg/xnat/restlet/resources/ProjectMemberResource.java
index 6bdefecc..3292ce80 100644
--- a/src/main/java/org/nrg/xnat/restlet/resources/ProjectMemberResource.java
+++ b/src/main/java/org/nrg/xnat/restlet/resources/ProjectMemberResource.java
@@ -14,13 +14,14 @@ import com.noelios.restlet.ext.servlet.ServletCall;
import org.apache.commons.lang3.StringUtils;
import org.apache.velocity.VelocityContext;
import org.nrg.action.ActionException;
+import org.nrg.xdat.XDAT;
import org.nrg.xdat.display.DisplayManager;
import org.nrg.xdat.om.XnatProjectdata;
import org.nrg.xdat.security.UserGroupI;
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.AdminUtils;
+import org.nrg.xdat.security.user.exceptions.UserNotFoundException;
import org.nrg.xdat.turbine.utils.TurbineUtils;
import org.nrg.xft.XFTTable;
import org.nrg.xft.event.EventMetaI;
@@ -49,8 +50,8 @@ import java.util.List;
public class ProjectMemberResource extends SecureResource {
XnatProjectdata proj=null;
UserGroupI group=null;
- ArrayList<UserI> newUsers= new ArrayList<UserI>();
- ArrayList<String> unknown= new ArrayList<String>();
+ ArrayList<UserI> newUsers= new ArrayList<>();
+ ArrayList<String> unknown= new ArrayList<>();
String gID=null;
boolean displayHiddenUsers = false;
@@ -61,12 +62,12 @@ public class ProjectMemberResource extends SecureResource {
this.getVariants().add(new Variant(MediaType.TEXT_HTML));
this.getVariants().add(new Variant(MediaType.TEXT_XML));
- String pID= (String)getUrlEncodedParameter(request,"PROJECT_ID");
+ String pID= getUrlEncodedParameter(request, "PROJECT_ID");
if(pID!=null){
proj = XnatProjectdata.getProjectByIDorAlias(pID, user, false);
}
- gID =(String)getUrlEncodedParameter(request,"GROUP_ID");
+ gID = getUrlEncodedParameter(request, "GROUP_ID");
group=Groups.getGroup(gID);
@@ -90,44 +91,44 @@ public class ProjectMemberResource extends SecureResource {
String tempValue =(String)getParameter(request,"USER_ID");
try {
- String[] ids=null;
- if(tempValue.indexOf(",")>-1){
+ String[] ids;
+ if(tempValue.contains(",")){
ids=tempValue.split(",");
}else{
ids=new String[]{tempValue};
}
-
- for(int i=0;i<ids.length;i++){
- String uID=ids[i].trim();
- Integer xdat_user_id= null;
+
+ for (final String id : ids) {
+ String uID = id.trim();
+ Integer xdat_user_id = null;
try {
- xdat_user_id=Integer.parseInt(uID);
- } catch (NumberFormatException e) {
-
+ xdat_user_id = Integer.parseInt(uID);
+ } catch (NumberFormatException ignored) {
+
}
-
-
- if (xdat_user_id==null){
+
+
+ if (xdat_user_id == null) {
//login or email
- UserI newUser=null;
+ UserI newUser = null;
try {
newUser = Users.getUser(uID);
- } catch (Exception e) {
+ } catch (UserNotFoundException ignored) {
}
- if (newUser==null){
+ if (newUser == null) {
//by email
- List<UserI> items =Users.getUsersByEmail(uID);
- if(items.size()>0){
+ List<UserI> items = Users.getUsersByEmail(uID);
+ if (items.size() > 0) {
newUsers.addAll(items);
- }else{
+ } else {
unknown.add(uID);
}
- }else{
+ } else {
newUsers.add(newUser);
}
- }else{
+ } else {
UserI tempUser = Users.getUser(xdat_user_id);
- if (tempUser!=null){
+ if (tempUser != null) {
newUsers.add(tempUser);
}
}
@@ -167,9 +168,6 @@ public class ProjectMemberResource extends SecureResource {
}else{
getResponse().setStatus(Status.CLIENT_ERROR_FORBIDDEN);
}
- } catch (InvalidItemException e) {
- logger.error("",e);
- getResponse().setStatus(Status.SERVER_ERROR_INTERNAL);
} catch (Exception e) {
logger.error("",e);
getResponse().setStatus(Status.SERVER_ERROR_INTERNAL);
@@ -196,7 +194,7 @@ public class ProjectMemberResource extends SecureResource {
context.put("process","Transfer to the archive.");
context.put("system",TurbineUtils.GetSystemName());
context.put("access_level",gID);
- context.put("admin_email",AdminUtils.getAdminEmailId());
+ context.put("admin_email",XDAT.getSiteConfigPreferences().getAdminEmail());
context.put("projectOM",proj);
//SEND email to user
final PersistentWorkflowI wrk=PersistentWorkflowUtils.getOrCreateWorkflowData(null, user, XnatProjectdata.SCHEMA_ELEMENT_NAME, proj.getId(), proj.getId(), newEventInstance(EventUtils.CATEGORY.PROJECT_ACCESS, EventUtils.INVITE_USER_TO_PROJECT + " (" + uID + ")"));
@@ -224,31 +222,27 @@ public class ProjectMemberResource extends SecureResource {
for(UserI newUser: newUsers){
final PersistentWorkflowI wrk=PersistentWorkflowUtils.getOrCreateWorkflowData(null, user, Users.getUserDataType(),newUser.getID().toString(),proj.getId(),newEventInstance(EventUtils.CATEGORY.PROJECT_ACCESS, EventUtils.ADD_USER_TO_PROJECT));
EventMetaI c=wrk.buildEvent();
-
- try {
- proj.addGroupMember(group.getId(), newUser, user,WorkflowUtils.setStep(wrk, "Add " + newUser.getLogin()));
- WorkflowUtils.complete(wrk, c);
-
- if (sendmail){
- try {
- VelocityContext context = new VelocityContext();
-
- context.put("user",user);
- context.put("server",TurbineUtils.GetFullServerPath(request));
- context.put("process","Transfer to the archive.");
- context.put("system",TurbineUtils.GetSystemName());
- context.put("access_level","member");
- context.put("admin_email",AdminUtils.getAdminEmailId());
- context.put("projectOM",proj);
- org.nrg.xnat.turbine.modules.actions.ProcessAccessRequest.SendAccessApprovalEmail(context, newUser.getEmail(), user, TurbineUtils.GetSystemName() + " Access Granted for " + proj.getName());
- } catch (Throwable e) {
- logger.error("",e);
- }
- }
- } catch (Exception e) {
- throw e;
- }
- }
+
+ proj.addGroupMember(group.getId(), newUser, user,WorkflowUtils.setStep(wrk, "Add " + newUser.getLogin()));
+ WorkflowUtils.complete(wrk, c);
+
+ if (sendmail){
+ try {
+ VelocityContext context = new VelocityContext();
+
+ context.put("user",user);
+ context.put("server",TurbineUtils.GetFullServerPath(request));
+ context.put("process","Transfer to the archive.");
+ context.put("system",TurbineUtils.GetSystemName());
+ context.put("access_level","member");
+ context.put("admin_email", XDAT.getSiteConfigPreferences().getAdminEmail());
+ context.put("projectOM",proj);
+ org.nrg.xnat.turbine.modules.actions.ProcessAccessRequest.SendAccessApprovalEmail(context, newUser.getEmail(), user, TurbineUtils.GetSystemName() + " Access Granted for " + proj.getName());
+ } catch (Throwable e) {
+ logger.error("",e);
+ }
+ }
+ }
}
}else{
getResponse().setStatus(Status.CLIENT_ERROR_FORBIDDEN);
@@ -268,26 +262,23 @@ public class ProjectMemberResource extends SecureResource {
}
@Override
- public Representation getRepresentation(Variant variant) {
+ public Representation represent(Variant variant) {
XFTTable table=null;
if(proj!=null){
try {
- StringBuffer query = new StringBuffer("SELECT g.id AS \"GROUP_ID\", displayname,login,firstname,lastname,email FROM xdat_userGroup g RIGHT JOIN xdat_user_Groupid map ON g.id=map.groupid RIGHT JOIN xdat_user u ON map.groups_groupid_xdat_user_xdat_user_id=u.xdat_user_id WHERE tag='").append(proj.getId()).append("' ");
+ StringBuilder query = new StringBuilder("SELECT g.id AS \"GROUP_ID\", displayname,login,firstname,lastname,email FROM xdat_userGroup g RIGHT JOIN xdat_user_Groupid map ON g.id=map.groupid RIGHT JOIN xdat_user u ON map.groups_groupid_xdat_user_xdat_user_id=u.xdat_user_id WHERE tag='").append(proj.getId()).append("' ");
if(!displayHiddenUsers){
query.append(" and enabled = 1 ");
}
query.append(" ORDER BY g.id DESC;");
table = XFTTable.Execute(query.toString(), user.getDBName(), user.getLogin());
- } catch (SQLException e) {
- logger.error("",e);
- getResponse().setStatus(Status.SERVER_ERROR_INTERNAL);
- } catch (DBPoolException e) {
+ } catch (SQLException | DBPoolException e) {
logger.error("",e);
getResponse().setStatus(Status.SERVER_ERROR_INTERNAL);
}
}
- Hashtable<String,Object> params=new Hashtable<String,Object>();
+ Hashtable<String,Object> params=new Hashtable<>();
params.put("title", "Projects");
MediaType mt = overrideVariant(variant);
diff --git a/src/main/java/org/nrg/xnat/restlet/resources/ProjtExptPipelineResource.java b/src/main/java/org/nrg/xnat/restlet/resources/ProjtExptPipelineResource.java
index f82bb483..7ebc5b72 100644
--- a/src/main/java/org/nrg/xnat/restlet/resources/ProjtExptPipelineResource.java
+++ b/src/main/java/org/nrg/xnat/restlet/resources/ProjtExptPipelineResource.java
@@ -11,14 +11,6 @@
package org.nrg.xnat.restlet.resources;
-import java.io.File;
-import java.text.SimpleDateFormat;
-import java.util.ArrayList;
-import java.util.Date;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
import org.apache.commons.lang3.StringUtils;
import org.apache.xmlbeans.XmlOptions;
import org.nrg.pipeline.XnatPipelineLauncher;
@@ -27,15 +19,11 @@ import org.nrg.pipeline.xmlbeans.ParameterData;
import org.nrg.pipeline.xmlbeans.ParameterData.Values;
import org.nrg.pipeline.xmlbeans.ParametersDocument;
import org.nrg.pipeline.xmlbeans.ParametersDocument.Parameters;
+import org.nrg.xdat.XDAT;
import org.nrg.xdat.model.ArcPipelinedataI;
import org.nrg.xdat.model.ArcPipelineparameterdataI;
-import org.nrg.xdat.om.ArcPipelinedata;
-import org.nrg.xdat.om.ArcProject;
-import org.nrg.xdat.om.XnatExperimentdata;
-import org.nrg.xdat.om.XnatImagesessiondata;
-import org.nrg.xdat.om.XnatProjectdata;
+import org.nrg.xdat.om.*;
import org.nrg.xdat.security.helpers.Permissions;
-import org.nrg.xdat.turbine.utils.AdminUtils;
import org.nrg.xdat.turbine.utils.TurbineUtils;
import org.nrg.xft.XFTItem;
import org.nrg.xft.event.EventMetaI;
@@ -58,6 +46,10 @@ import org.restlet.resource.Representation;
import org.restlet.resource.Variant;
import org.xml.sax.SAXException;
+import java.io.File;
+import java.text.SimpleDateFormat;
+import java.util.*;
+
public class ProjtExptPipelineResource extends SecureResource {
XnatProjectdata proj=null;
XnatExperimentdata expt=null;
@@ -282,9 +274,9 @@ public class ProjtExptPipelineResource extends SecureResource {
hasParams.add("useremail");
xnatPipelineLauncher.setParameter("userfullname", XnatPipelineLauncher.getUserName(user));
hasParams.add("userfullname");
- xnatPipelineLauncher.setParameter("adminemail", AdminUtils.getAdminEmailId());
+ xnatPipelineLauncher.setParameter("adminemail", XDAT.getSiteConfigPreferences().getAdminEmail());
hasParams.add("adminemail");
- xnatPipelineLauncher.setParameter("mailhost", AdminUtils.getMailServer());
+ xnatPipelineLauncher.setParameter("mailhost", XDAT.getSiteConfigPreferences().getSmtpServer().get("host"));
hasParams.add("mailhost");
xnatPipelineLauncher.setParameter("xnatserver", TurbineUtils.GetSystemName());
hasParams.add("xnatserver");
@@ -396,8 +388,8 @@ public class ProjtExptPipelineResource extends SecureResource {
xnatPipelineLauncher.setSupressNotification(true);
xnatPipelineLauncher.setParameter("useremail", user.getEmail());
xnatPipelineLauncher.setParameter("userfullname", XnatPipelineLauncher.getUserName(user));
- xnatPipelineLauncher.setParameter("adminemail", AdminUtils.getAdminEmailId());
- xnatPipelineLauncher.setParameter("mailhost", AdminUtils.getMailServer());
+ xnatPipelineLauncher.setParameter("adminemail", XDAT.getSiteConfigPreferences().getAdminEmail());
+ xnatPipelineLauncher.setParameter("mailhost", XDAT.getSiteConfigPreferences().getSmtpServer().get("host"));
xnatPipelineLauncher.setParameter("xnatserver", TurbineUtils.GetSystemName());
diff --git a/src/main/java/org/nrg/xnat/restlet/resources/SecureResource.java b/src/main/java/org/nrg/xnat/restlet/resources/SecureResource.java
index 8ecce10a..b4980f64 100644
--- a/src/main/java/org/nrg/xnat/restlet/resources/SecureResource.java
+++ b/src/main/java/org/nrg/xnat/restlet/resources/SecureResource.java
@@ -151,7 +151,7 @@ public abstract class SecureResource extends Resource {
// expects that the user exists in the session (either via traditional
// session or set via the XnatSecureGuard
user = XDAT.getUserDetails();
- if(user==null && !XFT.GetRequireLogin()){
+ if(user==null && !XDAT.getSiteConfigPreferences().getRequireLogin()){
try {
user = Users.getGuest();
XDAT.setUserDetails(user);
@@ -639,7 +639,7 @@ public abstract class SecureResource extends Resource {
public FileRepresentation representFile(File f, MediaType mt) {
mt = buildMediaType(mt, f.getName());
- if (mt.getName().startsWith("APPLICATION") || !XFT.getBooleanProperty("security.allow-HTML-resource-rendering", true)) {
+ if (mt.getName().startsWith("APPLICATION") || !XDAT.getSiteConfigPreferences().getAllowHtmlResourceRendering()) {
setContentDisposition(f.getName());
}
diff --git a/src/main/java/org/nrg/xnat/restlet/services/mail/MailRestlet.java b/src/main/java/org/nrg/xnat/restlet/services/mail/MailRestlet.java
index 113758c0..b1205228 100644
--- a/src/main/java/org/nrg/xnat/restlet/services/mail/MailRestlet.java
+++ b/src/main/java/org/nrg/xnat/restlet/services/mail/MailRestlet.java
@@ -78,7 +78,7 @@ public class MailRestlet extends SecureResource {
MailMessage message = new MailMessage();
// When receiving email send requests through the REST service, the from address is always the admin, with the mail sent on behalf of the validating user.
- message.setFrom(AdminUtils.getAdminEmailId());
+ message.setFrom(XDAT.getSiteConfigPreferences().getAdminEmail());
message.setOnBehalfOf(user.getEmail());
// Handle all the addresses.
diff --git a/src/main/java/org/nrg/xnat/services/messaging/file/MoveStoredFileRequestListener.java b/src/main/java/org/nrg/xnat/services/messaging/file/MoveStoredFileRequestListener.java
index 25cd46d5..d25ec48d 100644
--- a/src/main/java/org/nrg/xnat/services/messaging/file/MoveStoredFileRequestListener.java
+++ b/src/main/java/org/nrg/xnat/services/messaging/file/MoveStoredFileRequestListener.java
@@ -77,7 +77,7 @@ public class MoveStoredFileRequestListener {
}
try {
- XDAT.getMailService().sendHtmlMessage(AdminUtils.getAdminEmailId(), request.getNotifyList(), subject, message);
+ XDAT.getMailService().sendHtmlMessage(XDAT.getSiteConfigPreferences().getAdminEmail(), request.getNotifyList(), subject, message);
} catch (MessagingException e) {
log.error("Failed to send email.", e);
}
diff --git a/src/main/java/org/nrg/xnat/turbine/modules/actions/AddProject.java b/src/main/java/org/nrg/xnat/turbine/modules/actions/AddProject.java
index ebf04d32..4bf7e853 100755
--- a/src/main/java/org/nrg/xnat/turbine/modules/actions/AddProject.java
+++ b/src/main/java/org/nrg/xnat/turbine/modules/actions/AddProject.java
@@ -14,16 +14,19 @@ import org.apache.commons.lang3.StringUtils;
import org.apache.turbine.modules.ScreenLoader;
import org.apache.turbine.util.RunData;
import org.apache.velocity.context.Context;
+import org.nrg.xdat.XDAT;
import org.nrg.xdat.om.ArcProject;
import org.nrg.xdat.om.XnatProjectdata;
import org.nrg.xdat.om.base.BaseXnatProjectdata;
-import org.nrg.xdat.security.helpers.*;
+import org.nrg.xdat.security.helpers.Groups;
+import org.nrg.xdat.security.helpers.Permissions;
+import org.nrg.xdat.security.helpers.Roles;
+import org.nrg.xdat.security.helpers.UserHelper;
import org.nrg.xdat.turbine.modules.actions.SecureAction;
import org.nrg.xdat.turbine.modules.screens.EditScreenA;
import org.nrg.xdat.turbine.utils.PopulateItem;
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.db.PoolDBUtils;
import org.nrg.xft.event.EventMetaI;
diff --git a/src/main/java/org/nrg/xnat/turbine/modules/actions/ConfirmRegister.java b/src/main/java/org/nrg/xnat/turbine/modules/actions/ConfirmRegister.java
index 069a156e..c56bcf28 100644
--- a/src/main/java/org/nrg/xnat/turbine/modules/actions/ConfirmRegister.java
+++ b/src/main/java/org/nrg/xnat/turbine/modules/actions/ConfirmRegister.java
@@ -10,18 +10,18 @@
*/
package org.nrg.xnat.turbine.modules.actions;
-import java.util.List;
-
import org.apache.commons.lang3.StringUtils;
import org.apache.turbine.util.RunData;
import org.apache.velocity.context.Context;
+import org.nrg.xdat.XDAT;
import org.nrg.xdat.security.helpers.Users;
import org.nrg.xdat.turbine.modules.actions.SecureAction;
import org.nrg.xdat.turbine.modules.screens.SecureScreen;
-import org.nrg.xdat.turbine.utils.AdminUtils;
import org.nrg.xdat.turbine.utils.TurbineUtils;
import org.nrg.xft.security.UserI;
+import java.util.List;
+
public class ConfirmRegister extends SecureAction {
@Override
@@ -38,7 +38,7 @@ public class ConfirmRegister extends SecureAction {
if(!StringUtils.isEmpty(par)){
context.put("par", par);
}
- if (!StringUtils.isEmpty(nextAction) && nextAction.indexOf("XDATLoginUser")==-1 && !nextAction.equals(org.apache.turbine.Turbine.getConfiguration().getString("action.login"))){
+ if (!StringUtils.isEmpty(nextAction) && !nextAction.contains("XDATLoginUser") && !nextAction.equals(org.apache.turbine.Turbine.getConfiguration().getString("action.login"))){
context.put("nextAction", nextAction);
}else if (!StringUtils.isEmpty(nextPage) && !nextPage.equals(org.apache.turbine.Turbine.getConfiguration().getString("template.home")) ) {
context.put("nextPage", nextPage);
@@ -50,7 +50,7 @@ public class ConfirmRegister extends SecureAction {
if (current==null)
{
//allowed to have multiple accounts with the admin email address
- if(!StringUtils.equals(newUser.getEmail(),AdminUtils.getAdminEmailId()))
+ if(!StringUtils.equals(newUser.getEmail(), XDAT.getSiteConfigPreferences().getAdminEmail()))
{
List<UserI> match=Users.getUsersByEmail(newUser.getEmail());
if(match.size()>0){
@@ -72,7 +72,7 @@ public class ConfirmRegister extends SecureAction {
data.setMessage("Username (" + newUser.getEmail() + ") already exists.");
data.setScreenTemplate("ForgotLogin.vm");
}
- } catch (Exception e) {
+ } catch (Exception ignored) {
}
}
diff --git a/src/main/java/org/nrg/xnat/turbine/modules/actions/ManagePipeline.java b/src/main/java/org/nrg/xnat/turbine/modules/actions/ManagePipeline.java
index aeed0589..0ac76f4e 100644
--- a/src/main/java/org/nrg/xnat/turbine/modules/actions/ManagePipeline.java
+++ b/src/main/java/org/nrg/xnat/turbine/modules/actions/ManagePipeline.java
@@ -11,12 +11,6 @@
package org.nrg.xnat.turbine.modules.actions;
-import java.io.File;
-import java.text.SimpleDateFormat;
-import java.util.ArrayList;
-import java.util.Date;
-import java.util.Hashtable;
-
import org.apache.turbine.modules.ScreenLoader;
import org.apache.turbine.util.RunData;
import org.apache.velocity.context.Context;
@@ -30,17 +24,11 @@ import org.nrg.pipeline.xmlbeans.ParameterData;
import org.nrg.pipeline.xmlbeans.ParameterData.Values;
import org.nrg.pipeline.xmlbeans.ParametersDocument;
import org.nrg.pipeline.xmlbeans.ParametersDocument.Parameters;
+import org.nrg.xdat.XDAT;
import org.nrg.xdat.model.ArcPipelinedataI;
-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.PipePipelinerepository;
-import org.nrg.xdat.om.XnatProjectdata;
+import org.nrg.xdat.om.*;
import org.nrg.xdat.turbine.modules.actions.SecureAction;
import org.nrg.xdat.turbine.modules.screens.EditScreenA;
-import org.nrg.xdat.turbine.utils.AdminUtils;
import org.nrg.xdat.turbine.utils.PopulateItem;
import org.nrg.xdat.turbine.utils.TurbineUtils;
import org.nrg.xft.XFTItem;
@@ -61,6 +49,12 @@ import org.nrg.xnat.utils.WorkflowUtils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
+import java.io.File;
+import java.text.SimpleDateFormat;
+import java.util.ArrayList;
+import java.util.Date;
+import java.util.Hashtable;
+
public class ManagePipeline extends SecureAction {
@@ -386,8 +380,8 @@ public class ManagePipeline extends SecureAction {
xnatPipelineLauncher.setSupressNotification(true);
xnatPipelineLauncher.setParameter("useremail", user.getEmail());
xnatPipelineLauncher.setParameter("userfullname", XnatPipelineLauncher.getUserName(user));
- xnatPipelineLauncher.setParameter("adminemail", AdminUtils.getAdminEmailId());
- xnatPipelineLauncher.setParameter("mailhost", AdminUtils.getMailServer());
+ xnatPipelineLauncher.setParameter("adminemail", XDAT.getSiteConfigPreferences().getAdminEmail());
+ xnatPipelineLauncher.setParameter("mailhost", XDAT.getSiteConfigPreferences().getSmtpServer().get("host"));
xnatPipelineLauncher.setParameter("xnatserver", TurbineUtils.GetSystemName());
xnatPipelineLauncher.setPipelineName(pipeline_path);
String exptLabel = item.getStringProperty("label");
@@ -433,7 +427,7 @@ public class ManagePipeline extends SecureAction {
for (int i = 0; i < totalParams; i++) {
String name = ((String)org.nrg.xdat.turbine.utils.TurbineUtils.GetPassedParameter("param[" + i + "].name",data));
int rowcount = TurbineUtils.GetPassedInteger("param[" + i + "].name.rowcount", data);
- ArrayList<String> formvalues = new ArrayList<String>();
+ ArrayList<String> formvalues = new ArrayList<>();
for (int j = 0; j < rowcount; j++) {
String formfieldname = "param[" + i + "][" + j + "].value";
if (TurbineUtils.HasPassedParameter(formfieldname, data)) //formvalues.add(data.getParameters().get(formfieldname));
diff --git a/src/main/java/org/nrg/xnat/turbine/modules/actions/ManageProjectAccess.java b/src/main/java/org/nrg/xnat/turbine/modules/actions/ManageProjectAccess.java
index feba56fc..470659ef 100644
--- a/src/main/java/org/nrg/xnat/turbine/modules/actions/ManageProjectAccess.java
+++ b/src/main/java/org/nrg/xnat/turbine/modules/actions/ManageProjectAccess.java
@@ -92,7 +92,7 @@ public class ManageProjectAccess extends SecureAction {
context.put("process", "Transfer to the archive.");
context.put("system", TurbineUtils.GetSystemName());
context.put("access_level", "owner");
- context.put("admin_email", AdminUtils.getAdminEmailId());
+ context.put("admin_email", XDAT.getSiteConfigPreferences().getAdminEmail());
context.put("projectOM", project);
org.nrg.xnat.turbine.modules.actions.ProcessAccessRequest.SendAccessApprovalEmail(context, newOwner, TurbineUtils.getUser(data), TurbineUtils.GetSystemName() + " Access Granted for " + project.getName());
}
@@ -126,7 +126,7 @@ public class ManageProjectAccess extends SecureAction {
context.put("process", "Transfer to the archive.");
context.put("system", TurbineUtils.GetSystemName());
context.put("access_level", "member");
- context.put("admin_email", AdminUtils.getAdminEmailId());
+ context.put("admin_email", XDAT.getSiteConfigPreferences().getAdminEmail());
context.put("projectOM", project);
org.nrg.xnat.turbine.modules.actions.ProcessAccessRequest.SendAccessApprovalEmail(context, newMember, TurbineUtils.getUser(data), TurbineUtils.GetSystemName() + " Access Granted for " + project.getName());
}
@@ -160,7 +160,7 @@ public class ManageProjectAccess extends SecureAction {
context.put("process", "Transfer to the archive.");
context.put("system", TurbineUtils.GetSystemName());
context.put("access_level", "collaborator");
- context.put("admin_email", AdminUtils.getAdminEmailId());
+ context.put("admin_email", XDAT.getSiteConfigPreferences().getAdminEmail());
context.put("projectOM", project);
org.nrg.xnat.turbine.modules.actions.ProcessAccessRequest.SendAccessApprovalEmail(context, newMember, TurbineUtils.getUser(data), TurbineUtils.GetSystemName() + " Access Granted for " + project.getName());
}
diff --git a/src/main/java/org/nrg/xnat/turbine/modules/actions/MatchPrearchiveSessions.java b/src/main/java/org/nrg/xnat/turbine/modules/actions/MatchPrearchiveSessions.java
index ecccb7c4..13bcaaf6 100644
--- a/src/main/java/org/nrg/xnat/turbine/modules/actions/MatchPrearchiveSessions.java
+++ b/src/main/java/org/nrg/xnat/turbine/modules/actions/MatchPrearchiveSessions.java
@@ -10,15 +10,13 @@
*/
package org.nrg.xnat.turbine.modules.actions;
-import java.io.File;
-
import org.apache.turbine.util.RunData;
import org.apache.velocity.context.Context;
+import org.nrg.xdat.XDAT;
import org.nrg.xdat.base.BaseElement;
import org.nrg.xdat.om.XnatImagescandata;
import org.nrg.xdat.om.XnatImagesessiondata;
import org.nrg.xdat.turbine.modules.actions.SecureAction;
-import org.nrg.xdat.turbine.utils.AdminUtils;
import org.nrg.xdat.turbine.utils.TurbineUtils;
import org.nrg.xft.XFTItem;
import org.nrg.xft.schema.Wrappers.XMLWrapper.SAXReader;
@@ -26,6 +24,8 @@ import org.nrg.xft.security.UserI;
import org.nrg.xnat.archive.BatchTransfer;
import org.nrg.xnat.turbine.utils.ArcSpecManager;
+import java.io.File;
+
public class MatchPrearchiveSessions extends SecureAction {
/* (non-Javadoc)
@@ -33,14 +33,14 @@ public class MatchPrearchiveSessions extends SecureAction {
*/
@Override
public void doPerform(RunData data, Context context) throws Exception {
- Integer num= ((Integer)org.nrg.xdat.turbine.utils.TurbineUtils.GetPassedInteger("num_sessions",data));
- BatchTransfer bt = new BatchTransfer(TurbineUtils.GetFullServerPath(),TurbineUtils.GetSystemName(),AdminUtils.getAdminEmailId());
+ Integer num= TurbineUtils.GetPassedInteger("num_sessions", data);
+ BatchTransfer bt = new BatchTransfer(TurbineUtils.GetFullServerPath(), TurbineUtils.GetSystemName(), XDAT.getSiteConfigPreferences().getAdminEmail());
UserI user =TurbineUtils.getUser(data);
- bt.setUser((UserI)user);
+ bt.setUser(user);
String project = (String)TurbineUtils.GetPassedParameter("project", data);
if (num !=null)
{
- for (int h=0;h<=num.intValue();h++)
+ for (int h = 0; h <= num; h++)
{
String sessionFolder = ((String)org.nrg.xdat.turbine.utils.TurbineUtils.GetPassedParameter("session" + h,data));
String match = ((String)org.nrg.xdat.turbine.utils.TurbineUtils.GetPassedParameter("match" + h,data));
@@ -82,7 +82,7 @@ public class MatchPrearchiveSessions extends SecureAction {
SAXReader reader = new SAXReader(TurbineUtils.getUser(data));
XFTItem item = reader.parse(xml.getAbsolutePath());
- XnatImagesessiondata mr = (XnatImagesessiondata)XnatImagesessiondata.getXnatImagesessiondatasById(match, user, false);
+ XnatImagesessiondata mr = XnatImagesessiondata.getXnatImagesessiondatasById(match, user, false);
int k = 0;
while(TurbineUtils.HasPassedParameter("match" + h + ".scan" + k + "_id", data)){
@@ -90,10 +90,10 @@ public class MatchPrearchiveSessions extends SecureAction {
String use = (String)TurbineUtils.GetPassedParameter("match" + h + ".scan" + k + "_use", data);
String t = (String)TurbineUtils.GetPassedParameter("match" + h + ".scan" + k + "_type", data);
- XnatImagescandata scan = (XnatImagescandata) mr.getScanById(id);
+ XnatImagescandata scan = mr.getScanById(id);
if (scan==null){
XnatImagesessiondata tempMR= (XnatImagesessiondata)BaseElement.GetGeneratedItem(item);
- scan =(XnatImagescandata)tempMR.getScanById(id);
+ scan = tempMR.getScanById(id);
if (scan!=null){
mr.setScans_scan(scan);
}
diff --git a/src/main/java/org/nrg/xnat/turbine/modules/actions/PipelineActions.java b/src/main/java/org/nrg/xnat/turbine/modules/actions/PipelineActions.java
index 942200b0..dc2d33e1 100644
--- a/src/main/java/org/nrg/xnat/turbine/modules/actions/PipelineActions.java
+++ b/src/main/java/org/nrg/xnat/turbine/modules/actions/PipelineActions.java
@@ -25,6 +25,7 @@ import org.apache.turbine.util.RunData;
import org.apache.velocity.context.Context;
import org.nrg.pipeline.PipelineManager;
import org.nrg.pipeline.XnatPipelineLauncher;
+import org.nrg.xdat.XDAT;
import org.nrg.xdat.model.ArcPipelineparameterdataI;
import org.nrg.xdat.om.WrkWorkflowdata;
import org.nrg.xdat.turbine.modules.actions.SecureAction;
@@ -108,7 +109,7 @@ public class PipelineActions extends SecureAction{
private XnatPipelineLauncher getGenericCommonParameters(RunData data, Context context, String projectId, String step, ItemI item) throws Exception {
XnatPipelineLauncher xnatPipelineLauncher = new XnatPipelineLauncher(data,context);
- xnatPipelineLauncher.setAdmin_email(AdminUtils.getAdminEmailId());
+ xnatPipelineLauncher.setAdmin_email(XDAT.getSiteConfigPreferences().getAdminEmail());
xnatPipelineLauncher.setAlwaysEmailAdmin(ArcSpecManager.GetInstance().getEmailspecifications_pipeline());
UserI user = TurbineUtils.getUser(data);
xnatPipelineLauncher.setNeedsBuildDir(true);
@@ -185,7 +186,7 @@ public class PipelineActions extends SecureAction{
}
} catch (Exception e){
logger.error("",e);
- data.setMessage("<p><img src=\"/fcon/images/error.gif\">The build process failed to launch. Please contact the <a href=\"mailto:" + AdminUtils.getAdminEmailId() + "?subject=Failed to launch build \">NRG techdesk</a>");
+ data.setMessage("<p><img src=\"/fcon/images/error.gif\">The build process failed to launch. Please contact the <a href=\"mailto:" + XDAT.getSiteConfigPreferences().getAdminEmail() + "?subject=Failed to launch build \">NRG techdesk</a>");
data.setScreenTemplate("Error.vm");
}
}
@@ -193,7 +194,7 @@ public class PipelineActions extends SecureAction{
private XnatPipelineLauncher getCommonParameters(RunData data, Context context, String projectId, String pipelineName, String step) throws Exception {
XnatPipelineLauncher xnatPipelineLauncher = new XnatPipelineLauncher(data,context);
- xnatPipelineLauncher.setAdmin_email(AdminUtils.getAdminEmailId());
+ xnatPipelineLauncher.setAdmin_email(XDAT.getSiteConfigPreferences().getAdminEmail());
xnatPipelineLauncher.setAlwaysEmailAdmin(ArcSpecManager.GetInstance().getEmailspecifications_pipeline());
xnatPipelineLauncher.setPipelineName(pipelineName);
UserI user = TurbineUtils.getUser(data);
@@ -203,9 +204,9 @@ public class PipelineActions extends SecureAction{
xnatPipelineLauncher.setDataType("xnat:mrSessionData");
xnatPipelineLauncher.setParameter("useremail", user.getEmail());
xnatPipelineLauncher.setParameter("userfullname", XnatPipelineLauncher.getUserName(user));
- xnatPipelineLauncher.setParameter("adminemail", AdminUtils.getAdminEmailId());
+ xnatPipelineLauncher.setParameter("adminemail", XDAT.getSiteConfigPreferences().getAdminEmail());
xnatPipelineLauncher.setParameter("xnatserver", TurbineUtils.GetSystemName());
- xnatPipelineLauncher.setParameter("mailhost", AdminUtils.getMailServer());
+ xnatPipelineLauncher.setParameter("mailhost", XDAT.getSiteConfigPreferences().getSmtpServer().get("host"));
String emailsStr = ((String)org.nrg.xdat.turbine.utils.TurbineUtils.GetPassedParameter("emailField",data));
if (emailsStr != null) {
diff --git a/src/main/java/org/nrg/xnat/turbine/modules/actions/ProcessAccessRequest.java b/src/main/java/org/nrg/xnat/turbine/modules/actions/ProcessAccessRequest.java
index c927eca9..73d77bda 100644
--- a/src/main/java/org/nrg/xnat/turbine/modules/actions/ProcessAccessRequest.java
+++ b/src/main/java/org/nrg/xnat/turbine/modules/actions/ProcessAccessRequest.java
@@ -89,18 +89,18 @@ public class ProcessAccessRequest extends SecureAction {
context.put("user",user);
context.put("server",TurbineUtils.GetFullServerPath());
context.put("system",TurbineUtils.GetSystemName());
- context.put("admin_email",AdminUtils.getAdminEmailId());
+ context.put("admin_email",XDAT.getSiteConfigPreferences().getAdminEmail());
context.put("projectOM",project);
StringWriter sw = new StringWriter();
Template template =Velocity.getTemplate("/screens/RequestProjectAccessDenialEmail.vm");
template.merge(context,sw);
String message= sw.toString();
- String from = AdminUtils.getAdminEmailId();
+ String from = XDAT.getSiteConfigPreferences().getAdminEmail();
String subject = TurbineUtils.GetSystemName() + " Access Request for " + project.getName() + " Denied";
try {
- XDAT.getMailService().sendHtmlMessage(from, other.getEmail(), user.getEmail(), AdminUtils.getAdminEmailId(), subject, message);
+ XDAT.getMailService().sendHtmlMessage(from, other.getEmail(), user.getEmail(), XDAT.getSiteConfigPreferences().getAdminEmail(), subject, message);
} catch (Exception e) {
logger.error("Unable to send mail",e);
throw e;
@@ -174,11 +174,11 @@ public class ProcessAccessRequest extends SecureAction {
context.put("process","Transfer to the archive.");
context.put("system",TurbineUtils.GetSystemName());
context.put("access_level",access_level);
- context.put("admin_email",AdminUtils.getAdminEmailId());
+ context.put("admin_email",XDAT.getSiteConfigPreferences().getAdminEmail());
context.put("projectOM",project);
final ArrayList<String> ownerEmails = project.getOwnerEmails();
String[] projectOwnerEmails = ownerEmails.toArray(new String[ownerEmails.size()]);
- SendAccessApprovalEmail(context,AdminUtils.getAdminEmailId(),new String[]{other.getEmail()},projectOwnerEmails,new String[]{AdminUtils.getAdminEmailId()},TurbineUtils.GetSystemName() + " Access Request for " + project.getName() + " Approved");
+ SendAccessApprovalEmail(context,XDAT.getSiteConfigPreferences().getAdminEmail(),new String[]{other.getEmail()},projectOwnerEmails,new String[]{XDAT.getSiteConfigPreferences().getAdminEmail()},TurbineUtils.GetSystemName() + " Access Request for " + project.getName() + " Approved");
}
//data.setScreenTemplate("XDATScreen_manage_xnat_projectData.vm");
//data.setScreenTemplate("/xnat_projectData/xnat_projectData_summary_management.vm");
@@ -188,7 +188,7 @@ public class ProcessAccessRequest extends SecureAction {
}
public static void SendAccessApprovalEmail(Context context, String otherEmail, UserI user, String subject) throws Exception {
- String admin = AdminUtils.getAdminEmailId();
+ String admin = XDAT.getSiteConfigPreferences().getAdminEmail();
SendAccessApprovalEmail(context, admin, new String[]{otherEmail}, new String[]{user.getEmail()}, new String[]{admin}, subject);
}
diff --git a/src/main/java/org/nrg/xnat/turbine/modules/actions/QDECAction.java b/src/main/java/org/nrg/xnat/turbine/modules/actions/QDECAction.java
index a42b5801..8d7262a6 100644
--- a/src/main/java/org/nrg/xnat/turbine/modules/actions/QDECAction.java
+++ b/src/main/java/org/nrg/xnat/turbine/modules/actions/QDECAction.java
@@ -32,6 +32,7 @@ import org.nrg.pipeline.xmlbeans.ParameterData;
import org.nrg.pipeline.xmlbeans.ParameterData.Values;
import org.nrg.pipeline.xmlbeans.ParametersDocument;
import org.nrg.pipeline.xmlbeans.ParametersDocument.Parameters;
+import org.nrg.xdat.XDAT;
import org.nrg.xdat.search.DisplaySearch;
import org.nrg.xdat.turbine.modules.actions.ListingAction;
import org.nrg.xdat.turbine.utils.AdminUtils;
@@ -106,7 +107,7 @@ public class QDECAction extends ListingAction{
//Launch the job
String pipelineName = ((String)org.nrg.xdat.turbine.utils.TurbineUtils.GetPassedParameter("hdn_pipelinename",data));
XnatPipelineLauncher xnatPipelineLauncher = new XnatPipelineLauncher(data,context);
- xnatPipelineLauncher.setAdmin_email(AdminUtils.getAdminEmailId());
+ xnatPipelineLauncher.setAdmin_email(XDAT.getSiteConfigPreferences().getAdminEmail());
xnatPipelineLauncher.setAlwaysEmailAdmin(ArcSpecManager.GetInstance().getEmailspecifications_pipeline());
xnatPipelineLauncher.setPipelineName(pipelineName);
xnatPipelineLauncher.setId(id);
@@ -122,13 +123,13 @@ public class QDECAction extends ListingAction{
data.setMessage( "<p><b>Your QDEC analysis was successfully launched. Status email will be sent to you upon its completion.</b></p>");
data.setScreenTemplate("ClosePage.vm");
}catch(Exception e) {
- data.setMessage("<p><b>The QDEC Analysis process could not be launched. Please contact <A HREF=\"mailto:"+AdminUtils.getAdminEmailId()+"?subject=Error: Performing QDEC Group Analysis" + "\">Report Error to" +TurbineUtils.GetSystemName() + " Techdesk</A></b></p>");
+ data.setMessage("<p><b>The QDEC Analysis process could not be launched. Please contact <A HREF=\"mailto:"+XDAT.getSiteConfigPreferences().getAdminEmail()+"?subject=Error: Performing QDEC Group Analysis" + "\">Report Error to" +TurbineUtils.GetSystemName() + " Techdesk</A></b></p>");
data.setScreenTemplate("Error.vm");
}
}
private ArrayList<String> removeSpaces(ArrayList<String> inList) {
- ArrayList<String> rtn = new ArrayList<String>();
+ ArrayList<String> rtn = new ArrayList<>();
for (String aStr: inList) {
rtn.add(StringUtils.deleteWhitespace(aStr));
}
@@ -200,7 +201,7 @@ public class QDECAction extends ListingAction{
param = parameters.addNewParameter();
param.setName("adminemail");
- param.addNewValues().setUnique(AdminUtils.getAdminEmailId());
+ param.addNewValues().setUnique(XDAT.getSiteConfigPreferences().getAdminEmail());
param = parameters.addNewParameter();
param.setName("xnatserver");
@@ -209,7 +210,7 @@ public class QDECAction extends ListingAction{
param = parameters.addNewParameter();
param.setName("mailhost");
- param.addNewValues().setUnique( AdminUtils.getMailServer());
+ param.addNewValues().setUnique( XDAT.getSiteConfigPreferences().getSmtpServer().get("host"));
return parameters;
diff --git a/src/main/java/org/nrg/xnat/turbine/modules/actions/RequestAccess.java b/src/main/java/org/nrg/xnat/turbine/modules/actions/RequestAccess.java
index 8d6165a4..a769213b 100644
--- a/src/main/java/org/nrg/xnat/turbine/modules/actions/RequestAccess.java
+++ b/src/main/java/org/nrg/xnat/turbine/modules/actions/RequestAccess.java
@@ -49,7 +49,7 @@ public class RequestAccess extends SecureAction {
context.put("server",TurbineUtils.GetFullServerPath());
context.put("process","Transfer to the archive.");
context.put("system",TurbineUtils.GetSystemName());
- context.put("admin_email",AdminUtils.getAdminEmailId());
+ context.put("admin_email",XDAT.getSiteConfigPreferences().getAdminEmail());
context.put("projectOM",project);
context.put("access_level",access_level);
context.put("comments",comments);
@@ -81,10 +81,10 @@ public class RequestAccess extends SecureAction {
String[] bcc = null;
if(ArcSpecManager.GetInstance().getEmailspecifications_projectAccess()){
- bcc = new String[] { AdminUtils.getAdminEmailId() };
+ bcc = new String[] { XDAT.getSiteConfigPreferences().getAdminEmail() };
}
- String from = AdminUtils.getAdminEmailId();
+ String from = XDAT.getSiteConfigPreferences().getAdminEmail();
String subject = TurbineUtils.GetSystemName() + " Access Request for " + project.getName();
try {
diff --git a/src/main/java/org/nrg/xnat/turbine/modules/actions/SampleBuild.java b/src/main/java/org/nrg/xnat/turbine/modules/actions/SampleBuild.java
index aae9fcdb..79eef6cd 100644
--- a/src/main/java/org/nrg/xnat/turbine/modules/actions/SampleBuild.java
+++ b/src/main/java/org/nrg/xnat/turbine/modules/actions/SampleBuild.java
@@ -15,9 +15,9 @@ import org.apache.log4j.Logger;
import org.apache.turbine.util.RunData;
import org.apache.velocity.context.Context;
import org.nrg.pipeline.XnatPipelineLauncher;
+import org.nrg.xdat.XDAT;
import org.nrg.xdat.om.XnatMrsessiondata;
import org.nrg.xdat.turbine.modules.actions.SecureAction;
-import org.nrg.xdat.turbine.utils.AdminUtils;
import org.nrg.xdat.turbine.utils.TurbineUtils;
import org.nrg.xft.ItemI;
import org.nrg.xnat.turbine.utils.ArcSpecManager;
@@ -37,17 +37,18 @@ public class SampleBuild extends SecureAction
}
String xnat = ((String)org.nrg.xdat.turbine.utils.TurbineUtils.GetPassedParameter("xnat",data));
XnatPipelineLauncher pipelineLauncher = new XnatPipelineLauncher(data,context);
- pipelineLauncher.setAdmin_email(AdminUtils.getAdminEmailId());
+ pipelineLauncher.setAdmin_email(XDAT.getSiteConfigPreferences().getAdminEmail());
pipelineLauncher.setAlwaysEmailAdmin(ArcSpecManager.GetInstance().getEmailspecifications_pipeline());
pipelineLauncher.setId(mr.getId());
pipelineLauncher.setDataType("xnat:mrSessionData");
pipelineLauncher.setPipelineName(pipelineName);
pipelineLauncher.setParameter("sessionId",mr.getId());
pipelineLauncher.setParameter("xnat",xnat);
- String emailsStr = TurbineUtils.getUser(data).getEmail() + "," + ((String)org.nrg.xdat.turbine.utils.TurbineUtils.GetPassedParameter("emailField",data));
+ String emailsStr = XDAT.getUserDetails().getEmail() + "," + TurbineUtils.GetPassedParameter("emailField", data);
String[] emails = emailsStr.trim().split(",");
- for (int i = 0 ; i < emails.length; i++)
- pipelineLauncher.notify(emails[i]);
+ for (final String email : emails) {
+ pipelineLauncher.notify(email);
+ }
boolean success = pipelineLauncher.launch();
if (success) {
data.setMessage("Build was launched successfully");
diff --git a/src/main/java/org/nrg/xnat/turbine/modules/screens/BuildPipelineParameters.java b/src/main/java/org/nrg/xnat/turbine/modules/screens/BuildPipelineParameters.java
index 9a4d267f..709dd0bb 100644
--- a/src/main/java/org/nrg/xnat/turbine/modules/screens/BuildPipelineParameters.java
+++ b/src/main/java/org/nrg/xnat/turbine/modules/screens/BuildPipelineParameters.java
@@ -13,14 +13,13 @@ package org.nrg.xnat.turbine.modules.screens;
import org.apache.turbine.util.RunData;
import org.apache.velocity.context.Context;
+import org.nrg.xdat.XDAT;
import org.nrg.xdat.om.XnatMrsessiondata;
import org.nrg.xdat.turbine.modules.screens.SecureReport;
import org.nrg.xdat.turbine.utils.TurbineUtils;
import org.nrg.xft.XFT;
-public class BuildPipelineParameters extends SecureReport
-{
-
+public class BuildPipelineParameters extends SecureReport {
public void preProcessing(RunData data, Context context)
{
TurbineUtils.InstanciatePassedItemForScreenUse(data,context);
diff --git a/src/main/java/org/nrg/xnat/turbine/modules/screens/PipelineScreen_set_site_parameters.java b/src/main/java/org/nrg/xnat/turbine/modules/screens/PipelineScreen_set_site_parameters.java
index de09fe62..d53b11b3 100644
--- a/src/main/java/org/nrg/xnat/turbine/modules/screens/PipelineScreen_set_site_parameters.java
+++ b/src/main/java/org/nrg/xnat/turbine/modules/screens/PipelineScreen_set_site_parameters.java
@@ -19,12 +19,12 @@ import org.nrg.pipeline.xmlbeans.PipelineData.Documentation.InputParameters;
import org.nrg.pipeline.xmlbeans.PipelineData.Documentation.InputParameters.Parameter;
import org.nrg.pipeline.xmlbeans.PipelineData.Documentation.InputParameters.Parameter.Values;
import org.nrg.pipeline.xmlbeans.PipelineDocument;
+import org.nrg.xdat.XDAT;
import org.nrg.xdat.om.PipePipelinedetails;
import org.nrg.xdat.om.PipePipelinedetailsParameter;
import org.nrg.xdat.om.PipePipelinerepository;
import org.nrg.xdat.turbine.modules.screens.AdminEditScreenA;
import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.XFT;
import org.nrg.xft.event.EventUtils;
import org.nrg.xft.security.UserI;
import org.nrg.xft.utils.SaveItemHelper;
@@ -88,7 +88,7 @@ public class PipelineScreen_set_site_parameters extends AdminEditScreenA{
}catch(Exception e) {
logger.error(e);
e.printStackTrace();
- data.setMessage("The pipeline could not be added to the repository. Please contact " + XDAT.getSiteConfigPreferences().getAdminEmail() );
+ data.setMessage("The pipeline could not be added to the repository. Please contact " + XDAT.getSiteConfigPreferences().getAdminEmail());
data.setScreenTemplate("Error.vm");
}
}
diff --git a/src/main/java/org/nrg/xnat/turbine/modules/screens/XDATScreen_UpdateUser.java b/src/main/java/org/nrg/xnat/turbine/modules/screens/XDATScreen_UpdateUser.java
index c524493f..bbe5853c 100644
--- a/src/main/java/org/nrg/xnat/turbine/modules/screens/XDATScreen_UpdateUser.java
+++ b/src/main/java/org/nrg/xnat/turbine/modules/screens/XDATScreen_UpdateUser.java
@@ -46,22 +46,14 @@ public class XDATScreen_UpdateUser extends SecureScreen {
}
c.put("user", XDAT.getUserDetails());
- if (TurbineUtils.GetPassedParameter("popup", data) != null) {
- if (((String) TurbineUtils.GetPassedParameter("popup", data)).equalsIgnoreCase("true")) {
- c.put("popup", "true");
- } else {
- c.put("popup", "false");
- }
- } else {
- c.put("popup", "false");
- }
+ checkForPopup(data, c);
c.put("displayManager", DisplayManager.GetInstance());
c.put("systemName", TurbineUtils.GetSystemName());
c.put("esc", new EscapeTool());
- c.put("showReason", XFT.getShowChangeJustification());
- c.put("requireReason", XFT.getRequireChangeJustification());
+ c.put("showReason", XDAT.getSiteConfigPreferences().getShowChangeJustification());
+ c.put("requireReason", XDAT.getSiteConfigPreferences().getRequireChangeJustification());
try{
c.put("siteConfig", XDAT.getSiteConfiguration());
}catch(ConfigServiceException ignored){
diff --git a/src/main/java/org/nrg/xnat/turbine/utils/ArcSpecManager.java b/src/main/java/org/nrg/xnat/turbine/utils/ArcSpecManager.java
index cc5c76f6..c39e1289 100644
--- a/src/main/java/org/nrg/xnat/turbine/utils/ArcSpecManager.java
+++ b/src/main/java/org/nrg/xnat/turbine/utils/ArcSpecManager.java
@@ -61,131 +61,129 @@ public class ArcSpecManager {
logger.info("Initializing ArcSpec...");
arcSpec = GetFreshInstance();
- if (arcSpec!=null){
-
- if (arcSpec.getSiteAdminEmail()!=null && !arcSpec.getSiteAdminEmail().equals("")){
- XFT.SetAdminEmail(arcSpec.getSiteAdminEmail());
- }else{
- arcSpec.setSiteAdminEmail(XDAT.getSiteConfigPreferences().getAdminEmail());
- }
-
- if (arcSpec.getSiteUrl()!=null && !arcSpec.getSiteUrl().equals("")){
- XFT.SetSiteURL(arcSpec.getSiteUrl());
- }else{
- arcSpec.setSiteUrl(XDAT.getSiteConfigPreferences().getSiteUrl());
- }
-
- if (arcSpec.getSiteId()!=null && !arcSpec.getSiteId().equals("")){
- XFT.SetSiteID(arcSpec.getSiteId());
- }else{
- arcSpec.setSiteId("");
- }
-
- if (arcSpec.getSmtpHost()!=null && !arcSpec.getSmtpHost().equals("")){
- XFT.SetAdminEmailHost(arcSpec.getSmtpHost());
- }else{
- arcSpec.setSmtpHost(XFT.GetAdminEmailHost());
- }
-
- if (arcSpec.getEnableNewRegistrations()!=null){
- XFT.SetUserRegistration(arcSpec.getEnableNewRegistrations().toString());
- }else{
- arcSpec.setEnableNewRegistrations(XDAT.getSiteConfigPreferences().getUserRegistration());
- }
-
- if (arcSpec.getRequireLogin()!=null){
- XFT.SetRequireLogin(arcSpec.getRequireLogin().toString());
- }else{
- arcSpec.setRequireLogin(XDAT.getSiteConfigPreferences().getRequireLogin());
- }
-
- if (arcSpec.getGlobalpaths()!=null && arcSpec.getGlobalpaths().getPipelinepath()!=null){
- XFT.SetPipelinePath(arcSpec.getGlobalpaths().getPipelinepath());
- }else{
- if (arcSpec.getGlobalpaths()!=null){
- arcSpec.getGlobalpaths().setPipelinepath(XFT.GetPipelinePath());
- }
- }
-
- if (arcSpec.getGlobalpaths()!=null && arcSpec.getGlobalpaths().getArchivepath()!=null){
- XFT.SetArchiveRootPath(arcSpec.getGlobalpaths().getArchivepath());
- }else{
- if (arcSpec.getGlobalpaths()!=null && XFT.GetArchiveRootPath()!=null){
- arcSpec.getGlobalpaths().setArchivepath(XFT.GetArchiveRootPath());
- }
- }
-
- if (arcSpec.getGlobalpaths()!=null && arcSpec.getGlobalpaths().getCachepath()!=null){
- XFT.SetCachePath(arcSpec.getGlobalpaths().getCachepath());
- }else{
- if (arcSpec.getGlobalpaths()!=null && XDAT.getSiteConfigPreferences().getCachePath()!=null){
- arcSpec.getGlobalpaths().setCachepath(XDAT.getSiteConfigPreferences().getCachePath());
- }
- }
-
- if (arcSpec.getGlobalpaths()!=null && arcSpec.getGlobalpaths().getFtppath()!=null){
- XFT.setFtpPath(arcSpec.getGlobalpaths().getFtppath());
- }else{
- if (arcSpec.getGlobalpaths()!=null && XFT.getFtpPath()!=null){
- arcSpec.getGlobalpaths().setFtppath(XFT.getFtpPath());
- }
- }
-
- if (arcSpec.getGlobalpaths()!=null && arcSpec.getGlobalpaths().getBuildpath()!=null){
- XFT.setFtpPath(arcSpec.getGlobalpaths().getBuildpath());
- }else{
- if (arcSpec.getGlobalpaths()!=null && XFT.getBuildPath()!=null){
- arcSpec.getGlobalpaths().setBuildpath(XFT.getBuildPath());
- }
- }
-
- if (arcSpec.getGlobalpaths()!=null && arcSpec.getGlobalpaths().getPrearchivepath()!=null){
- XFT.SetPrearchivePath(arcSpec.getGlobalpaths().getPrearchivepath());
- }else{
- if (arcSpec.getGlobalpaths()!=null && XFT.GetPrearchivePath()!=null){
- arcSpec.getGlobalpaths().setPrearchivepath(XFT.GetPrearchivePath());
- }
- }
-
-
- //set email defaults
- if (arcSpec.getEmailspecifications_newUserRegistration()==null){
- arcSpec.setEmailspecifications_newUserRegistration(true);
- }
- if (arcSpec.getEmailspecifications_pageEmail()==null){
- arcSpec.setEmailspecifications_pageEmail(true);
- }
- if (arcSpec.getEmailspecifications_pipeline()==null){
- arcSpec.setEmailspecifications_pipeline(true);
- }
- if (arcSpec.getEmailspecifications_projectAccess()==null){
- arcSpec.setEmailspecifications_projectAccess(true);
- }
- if (arcSpec.getEmailspecifications_transfer()==null){
- arcSpec.setEmailspecifications_transfer(true);
- }
- //end email defaults
-
- if (arcSpec.getEmailspecifications_newUserRegistration()!=null){
- AdminUtils.SetNewUserRegistrationsEmail(arcSpec.getEmailspecifications_newUserRegistration());
- }
-
- if (arcSpec.getEmailspecifications_pageEmail()!=null){
- AdminUtils.SetPageEmail(arcSpec.getEmailspecifications_pageEmail());
- }
-
- if (arcSpec.getDcm_appletLink()==null){
- arcSpec.setDcm_appletLink(Boolean.TRUE);
- }
-
- if (arcSpec.getEnableCsrfToken()!=null){
- XFT.SetEnableCsrfToken(arcSpec.getEnableCsrfToken().toString());
- }else{
- arcSpec.setEnableCsrfToken(XDAT.getSiteConfigPreferences().getEnableCsrfToken());
- }
-
-
- }
+// if (arcSpec!=null){
+//
+// if (arcSpec.getSiteAdminEmail()!=null && !arcSpec.getSiteAdminEmail().equals("")){
+// XFT.SetAdminEmail(arcSpec.getSiteAdminEmail());
+// }else{
+// arcSpec.setSiteAdminEmail(XDAT.getSiteConfigPreferences().getAdminEmail());
+// }
+//
+// if (arcSpec.getSiteUrl()!=null && !arcSpec.getSiteUrl().equals("")){
+// XFT.SetSiteURL(arcSpec.getSiteUrl());
+// }else{
+// arcSpec.setSiteUrl(XDAT.getSiteConfigPreferences().getSiteUrl());
+// }
+//
+// if (arcSpec.getSiteId()!=null && !arcSpec.getSiteId().equals("")){
+// XFT.SetSiteID(arcSpec.getSiteId());
+// }else{
+// arcSpec.setSiteId("");
+// }
+//
+// if (arcSpec.getSmtpHost()!=null && !arcSpec.getSmtpHost().equals("")){
+// XFT.SetAdminEmailHost(arcSpec.getSmtpHost());
+// }else{
+// arcSpec.setSmtpHost(XFT.GetAdminEmailHost());
+// }
+//
+// if (arcSpec.getEnableNewRegistrations()!=null){
+// XFT.SetUserRegistration(arcSpec.getEnableNewRegistrations().toString());
+// }else{
+// arcSpec.setEnableNewRegistrations(XDAT.getSiteConfigPreferences().getUserRegistration());
+// }
+//
+// if (arcSpec.getRequireLogin()!=null){
+// XFT.SetRequireLogin(arcSpec.getRequireLogin().toString());
+// }else{
+// arcSpec.setRequireLogin(XDAT.getSiteConfigPreferences().getRequireLogin());
+// }
+//
+// if (arcSpec.getGlobalpaths()!=null && arcSpec.getGlobalpaths().getPipelinepath()!=null){
+// XFT.SetPipelinePath(arcSpec.getGlobalpaths().getPipelinepath());
+// }else{
+// if (arcSpec.getGlobalpaths()!=null){
+// arcSpec.getGlobalpaths().setPipelinepath(XDAT.getSiteConfigPreferences().getAdminEmail());
+// }
+// }
+//
+// if (arcSpec.getGlobalpaths()!=null && arcSpec.getGlobalpaths().getArchivepath()!=null){
+// XFT.SetArchiveRootPath(arcSpec.getGlobalpaths().getArchivepath());
+// }else{
+// if (arcSpec.getGlobalpaths()!=null && XFT.GetArchiveRootPath()!=null){
+// arcSpec.getGlobalpaths().setArchivepath(XFT.GetArchiveRootPath());
+// }
+// }
+//
+// if (arcSpec.getGlobalpaths()!=null && arcSpec.getGlobalpaths().getCachepath()!=null){
+// XFT.SetCachePath(arcSpec.getGlobalpaths().getCachepath());
+// }else{
+// if (arcSpec.getGlobalpaths()!=null && XDAT.getSiteConfigPreferences().getCachePath()!=null){
+// arcSpec.getGlobalpaths().setCachepath(XDAT.getSiteConfigPreferences().getCachePath());
+// }
+// }
+//
+// if (arcSpec.getGlobalpaths()!=null && arcSpec.getGlobalpaths().getFtppath()!=null){
+// XFT.setFtpPath(arcSpec.getGlobalpaths().getFtppath());
+// }else{
+// if (arcSpec.getGlobalpaths()!=null && XFT.getFtpPath()!=null){
+// arcSpec.getGlobalpaths().setFtppath(XFT.getFtpPath());
+// }
+// }
+//
+// if (arcSpec.getGlobalpaths()!=null && arcSpec.getGlobalpaths().getBuildpath()!=null){
+// XFT.setFtpPath(arcSpec.getGlobalpaths().getBuildpath());
+// }else{
+// if (arcSpec.getGlobalpaths()!=null && XFT.getBuildPath()!=null){
+// arcSpec.getGlobalpaths().setBuildpath(XFT.getBuildPath());
+// }
+// }
+//
+// if (arcSpec.getGlobalpaths()!=null && arcSpec.getGlobalpaths().getPrearchivepath()!=null){
+// XFT.SetPrearchivePath(arcSpec.getGlobalpaths().getPrearchivepath());
+// }else{
+// if (arcSpec.getGlobalpaths()!=null && XFT.GetPrearchivePath()!=null){
+// arcSpec.getGlobalpaths().setPrearchivepath(XFT.GetPrearchivePath());
+// }
+// }
+//
+//
+// //set email defaults
+// if (arcSpec.getEmailspecifications_newUserRegistration()==null){
+// arcSpec.setEmailspecifications_newUserRegistration(true);
+// }
+// if (arcSpec.getEmailspecifications_pageEmail()==null){
+// arcSpec.setEmailspecifications_pageEmail(true);
+// }
+// if (arcSpec.getEmailspecifications_pipeline()==null){
+// arcSpec.setEmailspecifications_pipeline(true);
+// }
+// if (arcSpec.getEmailspecifications_projectAccess()==null){
+// arcSpec.setEmailspecifications_projectAccess(true);
+// }
+// if (arcSpec.getEmailspecifications_transfer()==null){
+// arcSpec.setEmailspecifications_transfer(true);
+// }
+// //end email defaults
+//
+// if (arcSpec.getEmailspecifications_newUserRegistration()!=null){
+// AdminUtils.SetNewUserRegistrationsEmail(arcSpec.getEmailspecifications_newUserRegistration());
+// }
+//
+// if (arcSpec.getEmailspecifications_pageEmail()!=null){
+// AdminUtils.SetPageEmail(arcSpec.getEmailspecifications_pageEmail());
+// }
+//
+// if (arcSpec.getDcm_appletLink()==null){
+// arcSpec.setDcm_appletLink(Boolean.TRUE);
+// }
+//
+// if (arcSpec.getEnableCsrfToken()!=null){
+// XFT.SetEnableCsrfToken(arcSpec.getEnableCsrfToken().toString());
+// }else{
+// arcSpec.setEnableCsrfToken(XDAT.getSiteConfigPreferences().getEnableCsrfToken());
+// }
+// }
try {
if (arcSpec!=null){
@@ -236,37 +234,37 @@ public class ArcSpecManager {
arcSpec.setSiteUrl(XDAT.getSiteConfigPreferences().getSiteUrl());
}
- if (XFT.GetAdminEmailHost()!=null && !XFT.GetAdminEmailHost().equals("")) {
- arcSpec.setSmtpHost(XFT.GetAdminEmailHost());
- }
-
- arcSpec.setEnableNewRegistrations(XDAT.getSiteConfigPreferences().getUserRegistration());
-
- arcSpec.setRequireLogin(XDAT.getSiteConfigPreferences().getRequireLogin());
- if (XFT.GetPipelinePath()!=null && !XFT.GetPipelinePath().equals("")) {
- arcSpec.setProperty("globalPaths/pipelinePath", XFT.GetPipelinePath());
- }
-
- if (XFT.GetArchiveRootPath()!=null && !XFT.GetArchiveRootPath().equals("")) {
- arcSpec.setProperty("globalPaths/archivePath", XFT.GetArchiveRootPath());
- }
-
- if (XFT.GetPrearchivePath()!=null && !XFT.GetPrearchivePath().equals("")) {
- arcSpec.setProperty("globalPaths/prearchivePath", XFT.GetPrearchivePath());
- }
-
- if (XDAT.getSiteConfigPreferences().getCachePath()!=null && !XDAT.getSiteConfigPreferences().getCachePath().equals("")) {
- arcSpec.setProperty("globalPaths/cachePath", XDAT.getSiteConfigPreferences().getCachePath());
- }
-
- if (XFT.getFtpPath()!=null && !XFT.getFtpPath().equals("")) {
- arcSpec.setProperty("globalPaths/ftpPath", XFT.getFtpPath());
- }
-
- if (XFT.getBuildPath()!=null && !XFT.getBuildPath().equals("")) {
- arcSpec.setProperty("globalPaths/buildPath", XFT.getBuildPath());
- }
- arcSpec.setEnableCsrfToken(XFT.GetEnableCsrfToken());
+// if (XFT.GetAdminEmailHost()!=null && !XFT.GetAdminEmailHost().equals("")) {
+// arcSpec.setSmtpHost(XFT.GetAdminEmailHost());
+// }
+//
+// arcSpec.setEnableNewRegistrations(XDAT.getSiteConfigPreferences().getUserRegistration());
+//
+// arcSpec.setRequireLogin(XDAT.getSiteConfigPreferences().getRequireLogin());
+// if (XDAT.getSiteConfigPreferences().getAdminEmail()!=null && !XDAT.getSiteConfigPreferences().getAdminEmail().equals("")) {
+// arcSpec.setProperty("globalPaths/pipelinePath", XDAT.getSiteConfigPreferences().getAdminEmail());
+// }
+//
+// if (XFT.GetArchiveRootPath()!=null && !XFT.GetArchiveRootPath().equals("")) {
+// arcSpec.setProperty("globalPaths/archivePath", XFT.GetArchiveRootPath());
+// }
+//
+// if (XFT.GetPrearchivePath()!=null && !XFT.GetPrearchivePath().equals("")) {
+// arcSpec.setProperty("globalPaths/prearchivePath", XFT.GetPrearchivePath());
+// }
+//
+// if (XDAT.getSiteConfigPreferences().getCachePath()!=null && !XDAT.getSiteConfigPreferences().getCachePath().equals("")) {
+// arcSpec.setProperty("globalPaths/cachePath", XDAT.getSiteConfigPreferences().getCachePath());
+// }
+//
+// if (XFT.getFtpPath()!=null && !XFT.getFtpPath().equals("")) {
+// arcSpec.setProperty("globalPaths/ftpPath", XFT.getFtpPath());
+// }
+//
+// if (XFT.getBuildPath()!=null && !XFT.getBuildPath().equals("")) {
+// arcSpec.setProperty("globalPaths/buildPath", XFT.getBuildPath());
+// }
+// arcSpec.setEnableCsrfToken(XFT.GetEnableCsrfToken());
return arcSpec;
}
diff --git a/src/main/java/org/nrg/xnat/turbine/utils/IDGenerator.java b/src/main/java/org/nrg/xnat/turbine/utils/IDGenerator.java
index e6b57e20..d71c1d7d 100644
--- a/src/main/java/org/nrg/xnat/turbine/utils/IDGenerator.java
+++ b/src/main/java/org/nrg/xnat/turbine/utils/IDGenerator.java
@@ -11,7 +11,7 @@
package org.nrg.xnat.turbine.utils;
import org.apache.commons.lang3.StringUtils;
-import org.nrg.xft.XFT;
+import org.nrg.xdat.XDAT;
import org.nrg.xft.XFTTable;
import org.nrg.xft.identifier.IDGeneratorI;
import org.nrg.xnat.services.impl.hibernate.HibernateHostInfoService;
@@ -53,7 +53,7 @@ public class IDGenerator implements IDGeneratorI {
}
/** The claimed i ds. */
- private static List<String> claimedIDs=new ArrayList<String>();
+ private static List<String> claimedIDs= new ArrayList<>();
/** The Constant lock. */
private static final Object lock=new Object();
@@ -80,7 +80,7 @@ public class IDGenerator implements IDGeneratorI {
site +="_V";
}
- String temp_id=null;
+ String temp_id;
XFTTable table = org.nrg.xft.search.TableSearch.Execute("SELECT DISTINCT " + column + " FROM (SELECT " + column + " FROM " + tableName + " WHERE " + column + " LIKE '" + site + "%' UNION SELECT DISTINCT " + column + " FROM " + tableName + "_history WHERE " + column + " LIKE '" + site + "%') SRCH;", null, null);
ArrayList al =table.convertColumnToArrayList(column.toLowerCase());
diff --git a/src/main/java/org/nrg/xnat/turbine/utils/ProjectAccessRequest.java b/src/main/java/org/nrg/xnat/turbine/utils/ProjectAccessRequest.java
index 08d261b0..660bb8c0 100644
--- a/src/main/java/org/nrg/xnat/turbine/utils/ProjectAccessRequest.java
+++ b/src/main/java/org/nrg/xnat/turbine/utils/ProjectAccessRequest.java
@@ -486,10 +486,10 @@ public class ProjectAccessRequest {
String bcc = null;
if (ArcSpecManager.GetInstance().getEmailspecifications_projectAccess()) {
- bcc = AdminUtils.getAdminEmailId();
+ bcc = XDAT.getSiteConfigPreferences().getAdminEmail();
}
- String from = AdminUtils.getAdminEmailId();
+ String from = XDAT.getSiteConfigPreferences().getAdminEmail();
try {
XDAT.getMailService().sendHtmlMessage(from, invitee, user.getEmail(), bcc, subject, writer.toString());
diff --git a/src/main/java/org/nrg/xnat/utils/FileUtils.java b/src/main/java/org/nrg/xnat/utils/FileUtils.java
index 7a3bf3fa..d7c11066 100644
--- a/src/main/java/org/nrg/xnat/utils/FileUtils.java
+++ b/src/main/java/org/nrg/xnat/utils/FileUtils.java
@@ -13,6 +13,7 @@ package org.nrg.xnat.utils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
+import org.nrg.xdat.XDAT;
import org.nrg.xft.XFT;
import java.io.BufferedReader;
--
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