diff --git a/.gitignore b/.gitignore
index c84448e5b12c639424b7cb9f121fe45b127cca8f..e6be5bf7501679cf12b9e1c4adc06b23e372e38a 100644
--- a/.gitignore
+++ b/.gitignore
@@ -6,9 +6,7 @@ src/generated
gradle.properties
/out
/build
-dependencies.txt
-/webapps
-/bin/
+/bin
.classpath
.project
.settings/
diff --git a/build.gradle b/build.gradle
index b4a5e48469a209a703e0bf7fa0c6d9efb094ec8a..2e3efa7c6772f8a3c2d074fd0bdc1ab303023f74 100644
--- a/build.gradle
+++ b/build.gradle
@@ -1,7 +1,7 @@
def vXnat = '1.7.0-SNAPSHOT'
def vXnatPipeline = vXnat
-def vSpring = '4.2.4.RELEASE'
-def vSpringSecurity = '4.0.3.RELEASE'
+def vSpring = '4.2.5.RELEASE'
+def vSpringSecurity = '4.0.4.RELEASE'
def vSwagger = '2.3.1'
def vHibernate = '4.3.11.Final'
def vEhcache = '2.6.11'
@@ -34,19 +34,16 @@ 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"
}
}
-apply plugin: 'xnat'
apply plugin: 'groovy'
apply plugin: 'java'
apply plugin: 'war'
apply plugin: 'maven'
apply plugin: 'maven-publish'
-apply plugin: 'ivy-publish'
apply plugin: 'com.bmuschko.tomcat'
apply plugin: 'com.bmuschko.cargo'
apply plugin: 'idea'
@@ -238,6 +235,9 @@ configurations {
dependencies {
// NRG dependencies first.
compile "org.nrg.xnat:spawner:${vXnat}"
+ compile("org.nrg.xnat:xnat-data-models:${vXnat}"){
+ transitive = false
+ }
compile "org.nrg.xdat:core:${vXnat}"
compile "org.nrg:framework:${vXnat}"
compile "org.nrg:transaction:${vXnat}"
@@ -248,9 +248,6 @@ dependencies {
compile "org.nrg:anonymize:${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/xapi/rest/theme/ThemeApi.java b/src/main/java/org/nrg/xapi/rest/theme/ThemeApi.java
index 2abf2d607eb0254d12e5bd144ff808cdc05102a6..deea66e3e5f31938f58654b7ea812e3608f362fd 100644
--- a/src/main/java/org/nrg/xapi/rest/theme/ThemeApi.java
+++ b/src/main/java/org/nrg/xapi/rest/theme/ThemeApi.java
@@ -1,5 +1,4 @@
/*
- * org.nrg.xnat.turbine.modules.screens.ManageProtocol
* XNAT http://www.xnat.org
* Copyright (c) 2013, Washington University School of Medicine
* All Rights Reserved
@@ -16,10 +15,10 @@ import io.swagger.annotations.*;
import org.apache.commons.io.FileUtils;
import org.nrg.framework.annotations.XapiRestController;
import org.nrg.xapi.rest.NotFoundException;
+import org.nrg.xdat.entities.ThemeConfig;
import org.nrg.xdat.security.XDATUser;
import org.nrg.xft.security.UserI;
-import org.nrg.xnat.configuration.ThemeConfig;
-import org.nrg.xnat.services.ThemeService;
+import org.nrg.xdat.services.ThemeService;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
diff --git a/src/main/java/org/nrg/xnat/configuration/SerializerConfig.java b/src/main/java/org/nrg/xnat/configuration/SerializerConfig.java
index f4702c9e57e2c3e2f71ac2d2ffc3ab16919d54f8..3871859ede4960d66ad820fd82a28217b4c10d78 100644
--- a/src/main/java/org/nrg/xnat/configuration/SerializerConfig.java
+++ b/src/main/java/org/nrg/xnat/configuration/SerializerConfig.java
@@ -7,7 +7,7 @@ import com.fasterxml.jackson.core.util.DefaultPrettyPrinter;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.fasterxml.jackson.dataformat.yaml.YAMLFactory;
import org.jetbrains.annotations.NotNull;
-import org.nrg.xnat.utils.SerializerService;
+import org.nrg.framework.services.SerializerService;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
diff --git a/src/main/java/org/nrg/xnat/configuration/ThemeConfig.java b/src/main/java/org/nrg/xnat/configuration/ThemeConfig.java
deleted file mode 100644
index ca054e8cd1c35cd3dde953c0ddb2d50f01d222e2..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xnat/configuration/ThemeConfig.java
+++ /dev/null
@@ -1,68 +0,0 @@
-/*
- * org.nrg.xnat.turbine.modules.screens.ManageProtocol
- * XNAT http://www.xnat.org
- * Copyright (c) 2013, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Author: Justin Cleveland <clevelandj@wustl.edu>
- * Last modified 2/8/2016 11:29 AM
- */
-
-package org.nrg.xnat.configuration;
-
-import java.util.ArrayList;
-
-/**
- * Created by jcleve01 on 2/8/2016.
- */
-public class ThemeConfig {
- private String name = null;
- private String path = null;
- private boolean enabled = true;
- private ArrayList roles = new ArrayList();
-
- /**
- * Dummy constructor to make Jackson mapper happy. Don't explictly use this.
- */
- public ThemeConfig() {
- }
- public ThemeConfig(String themeName, String themePath, boolean enabled) {
- this.name = themeName;
- this.path = themePath;
- this.enabled = enabled;
- }
-
- public String getName() {
- return name;
- }
-
- public void setName(String name) {
- this.name = name;
- }
-
- public String getPath() {
- return path;
- }
-
- public void setPath(String path) {
- this.path = path;
- }
-
- public boolean isEnabled() {
- return enabled;
- }
-
- public void setEnabled(boolean enabled) {
- this.enabled = enabled;
- }
-
- public ArrayList getRoles() {
- return roles;
- }
-
- public void setRoles(ArrayList roles) {
- this.roles = roles;
- }
-}
diff --git a/src/main/java/org/nrg/xnat/event/listeners/PipelineEmailHandlerAbst.java b/src/main/java/org/nrg/xnat/event/listeners/PipelineEmailHandlerAbst.java
index 2a6ef18fc1091e54c4eb415de4f7a5209547ec31..30690dbe06bfbd07dd4586d768681d359639e023 100644
--- a/src/main/java/org/nrg/xnat/event/listeners/PipelineEmailHandlerAbst.java
+++ b/src/main/java/org/nrg/xnat/event/listeners/PipelineEmailHandlerAbst.java
@@ -6,6 +6,7 @@ import com.google.common.collect.Maps;
import org.apache.commons.lang3.StringEscapeUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.xmlbeans.XmlException;
+import org.nrg.framework.services.SerializerService;
import org.nrg.pipeline.xmlbeans.AllResolvedStepsDocument;
import org.nrg.pipeline.xmlbeans.ParameterData;
import org.nrg.xdat.XDAT;
@@ -19,7 +20,6 @@ import org.nrg.xdat.turbine.utils.TurbineUtils;
import org.nrg.xft.db.PoolDBUtils;
import org.nrg.xft.event.WorkflowStatusEvent;
import org.nrg.xnat.notifications.NotifyProjectPipelineListeners;
-import org.nrg.xnat.utils.SerializerService;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
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 859f28587350d4c2550d58e74244d2650e2cf44a..d24fc998c91f0adb9b095dc615647eacf16f0cb3 100644
--- a/src/main/java/org/nrg/xnat/helpers/prearchive/PrearcDatabase.java
+++ b/src/main/java/org/nrg/xnat/helpers/prearchive/PrearcDatabase.java
@@ -10,7 +10,6 @@
*/
package org.nrg.xnat.helpers.prearchive;
-import com.fasterxml.jackson.core.JsonFactory;
import com.google.common.base.Strings;
import com.google.common.collect.Maps;
import org.apache.commons.collections.CollectionUtils;
@@ -21,6 +20,7 @@ import org.nrg.automation.services.ScriptService;
import org.nrg.dicomtools.filters.DicomFilterService;
import org.nrg.dicomtools.filters.SeriesImportFilter;
import org.nrg.framework.constants.PrearchiveCode;
+import org.nrg.framework.services.SerializerService;
import org.nrg.status.ListenerUtils;
import org.nrg.status.StatusListenerI;
import org.nrg.xdat.XDAT;
@@ -41,7 +41,7 @@ import org.nrg.xnat.restlet.XNATApplication;
import org.nrg.xnat.restlet.actions.PrearcImporterA.PrearcSession;
import org.nrg.xnat.restlet.services.Archiver;
import org.nrg.xnat.turbine.utils.ArcSpecManager;
-import org.nrg.xnat.utils.SerializerService;
+
import org.nrg.xnat.utils.XnatUserProvider;
import org.restlet.data.Status;
import org.slf4j.Logger;
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 45c58132afefd1cf312754b05fd2e1a1a9abcdca..8b63e41ebdf63a6e44196954e3eef86e357340bd 100644
--- a/src/main/java/org/nrg/xnat/restlet/resources/SecureResource.java
+++ b/src/main/java/org/nrg/xnat/restlet/resources/SecureResource.java
@@ -66,7 +66,7 @@ import org.nrg.xnat.restlet.representations.*;
import org.nrg.xnat.restlet.util.FileWriterWrapperI;
import org.nrg.xnat.restlet.util.RequestUtil;
import org.nrg.xnat.turbine.utils.ArchivableItem;
-import org.nrg.xnat.utils.SerializerService;
+import org.nrg.framework.services.SerializerService;
import org.nrg.xnat.utils.WorkflowUtils;
import org.restlet.Context;
import org.restlet.data.*;
diff --git a/src/main/java/org/nrg/xnat/restlet/services/AliasTokenRestlet.java b/src/main/java/org/nrg/xnat/restlet/services/AliasTokenRestlet.java
index c7c6b2ce4da3c1417c564d0ffbd217f9e2cf0d69..e73a29c357afcfa2408c6c642e294ebd2e0b435c 100644
--- a/src/main/java/org/nrg/xnat/restlet/services/AliasTokenRestlet.java
+++ b/src/main/java/org/nrg/xnat/restlet/services/AliasTokenRestlet.java
@@ -17,7 +17,7 @@ import org.nrg.xdat.entities.AliasToken;
import org.nrg.xdat.security.helpers.Roles;
import org.nrg.xdat.services.AliasTokenService;
import org.nrg.xnat.restlet.resources.SecureResource;
-import org.nrg.xnat.utils.SerializerService;
+import org.nrg.framework.services.SerializerService;
import org.restlet.Context;
import org.restlet.data.MediaType;
import org.restlet.data.Request;
diff --git a/src/main/java/org/nrg/xnat/services/ThemeService.java b/src/main/java/org/nrg/xnat/services/ThemeService.java
deleted file mode 100644
index 47b61271374a434602fb88d3eb13fed31499cae5..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xnat/services/ThemeService.java
+++ /dev/null
@@ -1,141 +0,0 @@
-/*
- * org.nrg.xnat.turbine.modules.screens.ManageProtocol
- * XNAT http://www.xnat.org
- * Copyright (c) 2013, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Author: Justin Cleveland <clevelandj@wustl.edu> (jcleve01)
- * Last modified 2/29/2016 11:20 AM
- */
-package org.nrg.xnat.services;
-
-import org.jetbrains.annotations.NotNull;
-import org.nrg.xnat.configuration.ThemeConfig;
-import org.springframework.stereotype.Service;
-
-import java.io.*;
-import java.util.List;
-
-@Service
-public interface ThemeService {
-
-// abstract public void postServiceConstruction();
-
- /**
- * Returns the system theme file directory for reference by other XNAT modules.
- * @return the system theme file directory
- */
- String getThemesPath();
-
- /**
- * Gets the currently selected global system theme from a cache for a specific user role, or secondarily from the theme.json file in the themes folder.
- * @param role the name of the user role to fetch from the current global theme
- * @return The currently selected system theme configuration
- */
- ThemeConfig getTheme(String role);
-
- /**
- * Gets the currently selected global system theme from a cache, or secondarily from the theme.json file in the themes folder.
- * @return The currently selected global system theme configuration
- */
- ThemeConfig getTheme();
-
- /**
- * Searches the theme directory if a global theme is applied and returns a path string to the referenced page to redirect to.
- * If no global theme is selected or no overriding page is found the calling method should continue with it's default XNAT behavior.
- * @return a path string the referenced page if found. Otherwise returns null.
- */
- String getThemePage(String pageName);
-
- /**
- * Searches the theme directory if a global theme is applied and returns a path string to the referenced theme and matching type to redirect to.
- * If no global theme is selected or no overriding page with specified type is found the calling method should continue with it's default XNAT behavior.
- * @return a path string the referenced theme and type if found. Otherwise returns null.
- */
- String getThemePage(String pageName, String type);
-
- /**
- * Sets the currently selected system theme in the theme.json file in the web application's themes folder and caches it.
- * @param themeConfig the theme configuration object to apply
- */
- ThemeConfig setTheme(ThemeConfig themeConfig) throws ThemeNotFoundException;
-
- /**
- * Sets the currently selected system theme in the theme.json file in the web application's themes folder and caches it.
- * @param name the theme name. Creates a theme configuration object with it applying defaults
- */
- ThemeConfig setTheme(String name) throws ThemeNotFoundException;
-
- /**
- * Sets the currently selected system theme in the theme.json file in the web application's themes folder and caches it.
- * Creates a theme configuration object with it applying a defaults path
- * @param name the theme name.
- * @param enabled flag specifying whether or not the theme should be active.
- */
- ThemeConfig setTheme(String name, boolean enabled) throws ThemeNotFoundException;
-
- /**
- * Sets the currently selected system theme in the theme.json file in the web application's themes folder and caches it.
- * @param name the theme name.
- * @param path base theme directory path.
- * @param enabled flag specifying whether or not the theme should be active.
- */
- ThemeConfig setTheme(String name, String path, boolean enabled) throws ThemeNotFoundException;
-
- /**
- * Loads the system theme options
- * @return The list of the available theme packages (folder names) available under the system themes directory
- */
- List<TypeOption> loadExistingThemes();
-
- /**
- * Checks if the specified theme exists.
- * @param name the name of the theme to look for
- * @return true if it could be found in the system theme directory
- */
- boolean themeExists(String name);
-
- /**
- * Extracts a zipped theme package from an given InputStream.
- * @param inputStream from which to read the zipped data
- * @return List of root level directories (theme names) that were extracted
- * @throws IOException
- */
- List<String> extractTheme(InputStream inputStream) throws IOException;
-
- /**
- * Helper exception to report more specific errors
- */
- class ThemeNotFoundException extends Exception{
- private String invalidTheme;
- public ThemeNotFoundException(String invalidTheme) {
- this.invalidTheme = invalidTheme;
- }
- public String getInvalidTheme() {
- return invalidTheme;
- }
- }
-
- /**
- * Helper class to organize the available themes for display in a select dropdown form
- */
- class TypeOption implements Comparable<TypeOption> {
- String value, label;
- public TypeOption(String value, String label) {
- this.value = value;
- this.label = label;
- }
- public String getValue() {
- return value;
- }
- public String getLabel() {
- return label;
- }
- @Override
- public int compareTo(@NotNull TypeOption that) {
- return this.label.compareToIgnoreCase(that.label);
- }
- }
-}
\ No newline at end of file
diff --git a/src/main/java/org/nrg/xnat/services/impl/ThemeServiceImpl.java b/src/main/java/org/nrg/xnat/services/impl/ThemeServiceImpl.java
deleted file mode 100644
index 7673f055a8de6ccf4ee006b0d123eee3376d638f..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xnat/services/impl/ThemeServiceImpl.java
+++ /dev/null
@@ -1,325 +0,0 @@
-/*
- * org.nrg.xnat.turbine.modules.screens.ManageProtocol
- * XNAT http://www.xnat.org
- * Copyright (c) 2013, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Author: Justin Cleveland <clevelandj@wustl.edu> (jcleve01)
- * Last modified 2/30/2016 11:20 AM
- */
-package org.nrg.xnat.services.impl;
-
-import com.fasterxml.jackson.core.JsonProcessingException;
-import org.apache.commons.lang3.ArrayUtils;
-import org.apache.commons.lang3.StringUtils;
-import org.nrg.xnat.configuration.ThemeConfig;
-import org.nrg.xnat.services.ThemeService;
-import org.nrg.xnat.utils.SerializerService;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.stereotype.Service;
-
-import javax.annotation.PostConstruct;
-import javax.servlet.ServletContext;
-import java.io.*;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.zip.ZipEntry;
-import java.util.zip.ZipInputStream;
-
-@Service
-public class ThemeServiceImpl implements ThemeService {
- private static String webRelativeThemePath="themes";
- private static String themesPath;
- private static ThemeConfig themeConfig = null;
- private static File themeFile = null;
- private static final int FILE_BUFFER_SIZE = 4096;
-
- @Autowired
- private SerializerService _serializer;
-
- @Autowired
- private ServletContext servletContext;
-
- @PostConstruct
- public void postServiceConstruction(){
- themesPath = servletContext.getRealPath(File.separator)+webRelativeThemePath;
- themeFile = new File(themesPath + File.separator + "theme.json");
- File checkThemesPath = new File(themesPath);
- if (!checkThemesPath.exists()) {
- checkThemesPath.mkdir();
- }
-System.out.println("Theme Path: "+themeFile);
- servletContext.setAttribute("ThemeService", this); // This is probably a terrible way to attempt to do this. We would ideally add an instance of ThemeService to the XDAT class
- }
-
- public String getThemesPath() {
- return themesPath;
- }
-
- /**
- * Gets the currently selected system theme from an application servlet context cache, or secondarily from the
- * theme.json file in the themes folder.
- * @return The currently selected system theme configuration
- */
- public ThemeConfig getTheme(String role) {
- if(themeConfig != null){
- return themeConfig;
- } else { // Read the last saved theme selection from the theme.json file in the themes
- if (themeFile.exists()) { // directory in the event it can't be found in the application context.
- try { // (ie. the server was just started/restarted)
- BufferedReader reader = new BufferedReader(new FileReader(themeFile));
- StringBuilder sb = new StringBuilder();
- String line;
- while ((line = reader.readLine()) != null) {
- sb.append(line).append("\n");
- }
- reader.close();
- String contents = sb.toString();
- themeConfig = _serializer.deserializeJson(contents, ThemeConfig.class);
- } catch (IOException e) {
- e.printStackTrace();
- }
- }
- try {
- setTheme(themeConfig);
- } catch (ThemeNotFoundException e) {
- e.printStackTrace();
- }
- }
- if (role != null) {
- // TODO: implement search through the roles array in the ThemeConfig object for a matching ThemeConfig object for the specified role
- }
- return themeConfig;
- }
- public ThemeConfig getTheme() {
- return getTheme(null);
- }
-
- /**
- * Searches the theme directory if a global theme is applied and returns a path string to the referenced page to redirect to.
- * If no global theme is selected or no overriding page is found the calling method should continue with it's default XNAT behavior.
- * @return a path string the referenced page if found. Otherwise returns null.
- */
- public String getThemePage(String pageName) {
- return getThemePage(pageName, null);
- }
-
- /**
- * Searches the theme directory if a global theme is applied and returns a path string to the referenced theme and matching type to redirect to.
- * If no global theme is selected or no overriding page with specified type is found the calling method should continue with it's default XNAT behavior.
- * @return a path string the referenced theme and type if found. Otherwise returns null.
- */
- public String getThemePage(String pageName, String type) {
- String pagePath;
- ThemeConfig theme = getTheme();
- if(theme == null){
- return null;
- } else if (pageName == null){
- return null;
- } else { // Read the last saved theme selection from the theme.json file in the themes
- pagePath = checkThemeFileExists(theme, pageName, type);
- }
- return pagePath;
- }
-
- /**
- * Checks for the existence of a file name with a given set of accepted file extensions in the theme directory
- * and returns a relative web path string the referenced page if found.
- * @return a relative web path string prioritized by extension to the referenced page if found. Otherwise returns null.
- */
- private String checkThemeFileExists(ThemeConfig theme, String pageName) {
- return checkThemeFileExists(theme, pageName, null);
- }
-
- private String checkThemeFileExists(ThemeConfig theme, String pageName, String type) {
- String pagePath = null, typeSep = type + "s" + File.separator;
- String[] extensions = new String[]{};
- String[] pageExts = new String[]{"jsp", "vm", "htm", "html"};
- String[] scriptExts = new String[]{"js"};
- String[] styleExts = new String[]{"css"};
- if("page".equals(type)){
- extensions = (String[]) ArrayUtils.addAll(extensions, pageExts);
- }
- if("script".equals(type)){
- extensions = (String[]) ArrayUtils.addAll(extensions, scriptExts);
- }
- if("style".equals(type)){
- extensions = (String[]) ArrayUtils.addAll(extensions, styleExts);
- }
- if(type == null){
- typeSep = "";
- extensions = (String[]) ArrayUtils.addAll(extensions, pageExts);
- extensions = (String[]) ArrayUtils.addAll(extensions, scriptExts);
- extensions = (String[]) ArrayUtils.addAll(extensions, styleExts);
- }
- for (String ext : extensions) {
- File themePageFile = new File(theme.getPath() + File.separator + typeSep + pageName + "." + ext);
- if(themePageFile.exists()) {
- if(type != null){
- typeSep = type + "s/"; // This is awful and should be set once up above
- }
- pagePath = "/" + webRelativeThemePath + "/" + theme.getName() + "/" + typeSep + pageName + "." + ext;
- break;
- }
- }
- return pagePath;
- }
-
- /**
- * Sets the currently selected system theme in the theme.json file in the web application's themes folder and caches it.
- * @param themeConfig the theme configuration object to apply
- */
- public ThemeConfig setTheme(ThemeConfig themeConfig) throws ThemeNotFoundException {
- try {
- if (themeConfig == null){
- themeConfig = new ThemeConfig();
- }
- if(themeExists(themeConfig.getName())) {
- String themeJson = _serializer.toJson(themeConfig);
- if (!themeFile.exists()) {
- themeFile.createNewFile();
- }
- FileWriter writer = new FileWriter(themeFile);
- writer.write(themeJson);
- writer.flush();
- writer.close();
- ThemeServiceImpl.themeConfig = themeConfig;
- } else {
- throw new ThemeNotFoundException(themeConfig.getName());
- }
- } catch (JsonProcessingException e) {
- e.printStackTrace();
- // TODO: rethrow this and respond as an internal server error
- } catch (IOException e) {
- e.printStackTrace();
- // TODO: rethrow this and respond as an internal server error
- }
- return themeConfig;
- }
-
- /**
- * Sets the currently selected system theme in the theme.json file in the web application's themes folder and caches it.
- * @param name the theme name. Creates a theme configuration object with it applying defaults
- */
- public ThemeConfig setTheme(String name) throws ThemeNotFoundException {
- return setTheme(name, true);
- }
-
- /**
- * Sets the currently selected system theme in the theme.json file in the web application's themes folder and caches it.
- * Creates a theme configuration object with it applying a defaults path
- * @param name the theme name.
- * @param enabled flag specifying whether or not the theme should be active.
- */
- public ThemeConfig setTheme(String name, boolean enabled) throws ThemeNotFoundException {
- return setTheme(new ThemeConfig(name, themesPath + File.separator + name, enabled));
- }
-
- /**
- * Sets the currently selected system theme in the theme.json file in the web application's themes folder and caches it.
- * @param name the theme name.
- * @param path base theme directory path.
- * @param enabled flag specifying whether or not the theme should be active.
- */
- public ThemeConfig setTheme(String name, String path, boolean enabled) throws ThemeNotFoundException {
- return setTheme(new ThemeConfig(name, path, enabled));
- }
-
- /**
- * Loads the system theme options
- * @return The list of the available theme packages (folder names) available under the system themes directory
- */
- public List<TypeOption> loadExistingThemes() {
- ArrayList<TypeOption> themeOptions = new ArrayList<>();
- themeOptions.add(new TypeOption(null, "None"));
- File f = new File(themesPath); // current directory
- FileFilter directoryFilter = new FileFilter() {
- public boolean accept(File file) {
- return file.isDirectory();
- }
- };
- File[] files = f.listFiles(directoryFilter);
- if(files != null) {
- for (File file : files) {
- if (file.isDirectory()) {
- themeOptions.add(new TypeOption(file.getName(), file.getName()));
- }
- }
- }
- return themeOptions;
- }
-
- /**
- * Checks if the specified theme exists.
- * @param name the name of the theme to look for
- * @return true if it could be found in the system theme directory
- */
- public boolean themeExists(String name) {
- if(name == null) {
- return true;
- } else if(StringUtils.isEmpty(name)){
- return false;
- } else {
- List<TypeOption> themeList = loadExistingThemes();
- for (TypeOption to: themeList) {
- if(name.equals(to.getValue())){
- return true;
- }
- }
- }
- return false;
- }
-
- /**
- * Extracts a zipped theme package from an given InputStream.
- * @param inputStream from which to read the zipped data
- * @return List of root level directories (theme names) that were extracted
- * @throws IOException
- */
- public List<String> extractTheme(InputStream inputStream) throws IOException {
- final List<String> rootDirs = new ArrayList<>();
- ZipInputStream zipIn = new ZipInputStream(inputStream);
- ZipEntry entry = zipIn.getNextEntry();
- while (entry != null) { // iterate over entries in the zip file
- String filePath = this.getThemesPath() + File.separator + entry.getName();
- if (!entry.isDirectory()) { // if the entry is a file, extract it // TODO: Make sure we get a directory the first iteration through (fail otherwise) so that no files get dumped in the root themes directory
- this.extractFile(zipIn, filePath);
- } else { // if the entry is a directory, make the directory
- String rootDir = entry.getName();
- int slashIndex = rootDir.indexOf('/');
- if(slashIndex>1){
- int nextSlashIndex = rootDir.indexOf('/', slashIndex+1);
- if(nextSlashIndex<0) {
- rootDir = rootDir.substring(0, slashIndex);
- rootDirs.add(rootDir);
- }
- }
- File dir = new File(filePath);
- dir.mkdir();
- }
- zipIn.closeEntry();
- entry = zipIn.getNextEntry();
- }
- zipIn.close();
- inputStream.close();
- return rootDirs;
- }
-
- /**
- * Extracts a single zip entry (file entry)
- * @param zip zip input stream to extract it from
- * @param path to the file within the zip package
- * @throws IOException
- */
- private void extractFile(ZipInputStream zip, String path) throws IOException {
- BufferedOutputStream os = new BufferedOutputStream(new FileOutputStream(path));
- byte[] bytes = new byte[FILE_BUFFER_SIZE];
- int length;
- while ((length = zip.read(bytes)) != -1) {
- os.write(bytes, 0, length);
- }
- os.close();
- }
-}
\ No newline at end of file
diff --git a/src/main/java/org/nrg/xnat/turbine/modules/screens/Index.java b/src/main/java/org/nrg/xnat/turbine/modules/screens/Index.java
index 64953b9ed8e8195772189a7d17afba7b9dd3c21a..4fcc18635ad2bef853db38c058d44ad09f72f96c 100644
--- a/src/main/java/org/nrg/xnat/turbine/modules/screens/Index.java
+++ b/src/main/java/org/nrg/xnat/turbine/modules/screens/Index.java
@@ -14,7 +14,6 @@ import java.util.Date;
import org.apache.turbine.util.RunData;
import org.apache.velocity.context.Context;
-import org.nrg.xdat.XDAT;
import org.nrg.xdat.security.helpers.UserHelper;
import org.nrg.xdat.turbine.modules.screens.SecureScreen;
import org.nrg.xdat.turbine.utils.TurbineUtils;
@@ -22,32 +21,18 @@ import org.nrg.xft.db.PoolDBUtils;
import org.nrg.xft.security.UserI;
import org.nrg.xnat.helpers.prearchive.PrearcDatabase;
-import org.nrg.xnat.services.ThemeService;
+
import org.nrg.xnat.turbine.utils.ProjectAccessRequest;
public class Index extends SecureScreen {
@Override
protected void doBuildTemplate(RunData data, Context context) throws Exception {
- ThemeService themeService = XDAT.getContextService().getBean(ThemeService.class);
-// String themedLandingPath = themeService.getThemePage("Landing");
-// if(themedLandingPath != null) {
-// doRedirect(data, themedLandingPath);
-// data.setRedirectURI(themedLandingPath);
-// }
- String themedRedirect = themeService.getThemePage("Landing"); // put all this in a method in the theme service with an optional requested page parameter
+ String themedRedirect = themeService.getThemePage("Landing"); // TODO: put all this in a method in the theme service with an optional requested page parameter
if(themedRedirect != null) {
context.put("themedRedirect", themedRedirect);
return;
}
- String themedStyle = themeService.getThemePage("theme", "style");
- if(themedStyle != null) {
- context.put("themedStyle", themedStyle);
- }
- String themedScript = themeService.getThemePage("theme", "script");
- if(themedScript != null) {
- context.put("themedScript", themedScript);
- }
UserI user = TurbineUtils.getUser(data);
diff --git a/src/main/java/org/nrg/xnat/turbine/modules/screens/Login.java b/src/main/java/org/nrg/xnat/turbine/modules/screens/Login.java
index 8b2785b2df6b22e7853a4bc3ad43b6a5adb02cc3..60e02df12b06c62f6d75659643a2aa570a8e9c42 100644
--- a/src/main/java/org/nrg/xnat/turbine/modules/screens/Login.java
+++ b/src/main/java/org/nrg/xnat/turbine/modules/screens/Login.java
@@ -1,5 +1,4 @@
/*
- * org.nrg.xnat.turbine.modules.screens.ManageProtocol
* XNAT http://www.xnat.org
* Copyright (c) 2013, Washington University School of Medicine
* All Rights Reserved
@@ -15,30 +14,25 @@ import org.apache.log4j.Logger;
import org.apache.turbine.util.RunData;
import org.apache.velocity.context.Context;
import org.nrg.xdat.XDAT;
-import org.nrg.xnat.services.ThemeService;
+import org.nrg.xdat.services.ThemeService;
public class Login extends org.nrg.xdat.turbine.modules.screens.Login {
public final static Logger logger = Logger.getLogger(XDATScreen_themes.class);
@Override
- protected void doBuildTemplate(RunData data, Context context) throws Exception {
+ protected void doBuildTemplate(RunData data, Context c) throws Exception {
ThemeService themeService = XDAT.getContextService().getBean(ThemeService.class);
-// String themedLoginPath = themeService.getThemePage("Login");
-// if(themedLoginPath != null) {
-// doRedirect(data, themedLoginPath);
-// data.setRedirectURI(themedLoginPath);
-// }
String themedRedirect = themeService.getThemePage("Login");
if(themedRedirect != null) {
- context.put("themedRedirect", themedRedirect);
+ c.put("themedRedirect", themedRedirect);
return;
}
String themedStyle = themeService.getThemePage("theme", "style");
if(themedStyle != null) {
- context.put("themedStyle", themedStyle);
+ c.put("themedStyle", themedStyle);
}
String themedScript = themeService.getThemePage("theme", "script");
if(themedScript != null) {
- context.put("themedScript", themedScript);
+ c.put("themedScript", themedScript);
}
}
}
\ No newline at end of file
diff --git a/src/main/java/org/nrg/xnat/turbine/modules/screens/UploadAppletScreen.java b/src/main/java/org/nrg/xnat/turbine/modules/screens/UploadAppletScreen.java
index 46ad360a7cc91d8c106c383877badbb8ad1f263b..743912a9ac7d87995869917082b8510a853597ef 100644
--- a/src/main/java/org/nrg/xnat/turbine/modules/screens/UploadAppletScreen.java
+++ b/src/main/java/org/nrg/xnat/turbine/modules/screens/UploadAppletScreen.java
@@ -8,7 +8,7 @@ import org.nrg.xdat.security.helpers.Permissions;
import org.nrg.xdat.turbine.modules.screens.SecureScreen;
import org.nrg.xft.security.UserI;
import org.nrg.xnat.utils.AppletConfig;
-import org.nrg.xnat.utils.SerializerService;
+import org.nrg.framework.services.SerializerService;
/**
* Contains basic methods used by upload applet screen classes.
diff --git a/src/main/java/org/nrg/xnat/turbine/modules/screens/XDATScreen_admin_options.java b/src/main/java/org/nrg/xnat/turbine/modules/screens/XDATScreen_admin_options.java
index 3bb1cb82c45c4456bcd12ebc23c1272afaa89fa2..83a7291d7c1b502a557bdfdcded13b359997c391 100644
--- a/src/main/java/org/nrg/xnat/turbine/modules/screens/XDATScreen_admin_options.java
+++ b/src/main/java/org/nrg/xnat/turbine/modules/screens/XDATScreen_admin_options.java
@@ -1,5 +1,4 @@
/*
- * org.nrg.xnat.turbine.modules.screens.ManageProtocol
* XNAT http://www.xnat.org
* Copyright (c) 2013, Washington University School of Medicine
* All Rights Reserved
@@ -15,26 +14,11 @@ package org.nrg.xnat.turbine.modules.screens;
import org.apache.log4j.Logger;
import org.apache.turbine.util.RunData;
import org.apache.velocity.context.Context;
-import org.nrg.xdat.XDAT;
import org.nrg.xdat.turbine.modules.screens.SecureScreen;
-import org.nrg.xnat.services.ThemeService;
-
-/**
- * Created by jcleve01 on 1/22/2016.
- */
public class XDATScreen_admin_options extends SecureScreen {
public final static Logger logger = Logger.getLogger(XDATScreen_admin_options.class);
@Override
protected void doBuildTemplate(RunData data, Context context) throws Exception {
- ThemeService themeService = XDAT.getContextService().getBean(ThemeService.class);
- String themedStyle = themeService.getThemePage("theme", "style");
- if (themedStyle != null) {
- context.put("themedStyle", themedStyle);
- }
- String themedScript = themeService.getThemePage("theme", "script");
- if (themedScript != null) {
- context.put("themedScript", themedScript);
- }
}
}
diff --git a/src/main/java/org/nrg/xnat/turbine/modules/screens/XDATScreen_themes.java b/src/main/java/org/nrg/xnat/turbine/modules/screens/XDATScreen_themes.java
index 85a637e82cefc55d0ad151c935d10300c1a0e5fc..1308f443baa5d056be40e61f5c5ddbe725541e8e 100644
--- a/src/main/java/org/nrg/xnat/turbine/modules/screens/XDATScreen_themes.java
+++ b/src/main/java/org/nrg/xnat/turbine/modules/screens/XDATScreen_themes.java
@@ -1,5 +1,4 @@
/*
- * org.nrg.xnat.turbine.modules.screens.ManageProtocol
* XNAT http://www.xnat.org
* Copyright (c) 2013, Washington University School of Medicine
* All Rights Reserved
@@ -15,26 +14,11 @@ package org.nrg.xnat.turbine.modules.screens;
import org.apache.log4j.Logger;
import org.apache.turbine.util.RunData;
import org.apache.velocity.context.Context;
-import org.nrg.xdat.XDAT;
import org.nrg.xdat.turbine.modules.screens.SecureScreen;
-import org.nrg.xnat.services.ThemeService;
-
-/**
- * Created by jcleve01 on 1/22/2016.
- */
public class XDATScreen_themes extends SecureScreen {
public final static Logger logger = Logger.getLogger(XDATScreen_themes.class);
@Override
protected void doBuildTemplate(RunData data, Context context) throws Exception {
- ThemeService themeService = XDAT.getContextService().getBean(ThemeService.class);
- String themedStyle = themeService.getThemePage("theme", "style");
- if (themedStyle != null) {
- context.put("themedStyle", themedStyle);
- }
- String themedScript = themeService.getThemePage("theme", "script");
- if (themedScript != null) {
- context.put("themedScript", themedScript);
- }
}
}
diff --git a/src/main/java/org/nrg/xnat/utils/SerializerService.java b/src/main/java/org/nrg/xnat/utils/SerializerService.java
deleted file mode 100644
index 529f10b6777439e32150894975a3fb9f594621f2..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xnat/utils/SerializerService.java
+++ /dev/null
@@ -1,53 +0,0 @@
-package org.nrg.xnat.utils;
-
-import com.fasterxml.jackson.core.type.TypeReference;
-import com.fasterxml.jackson.databind.JsonNode;
-import com.fasterxml.jackson.databind.ObjectMapper;
-import org.springframework.stereotype.Service;
-
-import javax.inject.Inject;
-import javax.inject.Named;
-import java.io.IOException;
-
-@Service
-public class SerializerService {
- public JsonNode deserializeJson(final String json) throws IOException {
- return _jsonObjectMapper.readTree(json);
- }
-
- public <T> T deserializeJson(final String json, final Class<T> clazz) throws IOException {
- return _jsonObjectMapper.readValue(json, clazz);
- }
-
- public <T> T deserializeJson(final String json, final TypeReference<T> typeRef) throws IOException {
- return _jsonObjectMapper.readValue(json, typeRef);
- }
-
- public <T> String toJson(final T instance) throws IOException {
- return _jsonObjectMapper.writeValueAsString(instance);
- }
-
- public JsonNode deserializeYaml(final String yaml) throws IOException {
- return _yamlObjectMapper.readTree(yaml);
- }
-
- public <T> T deserializeYaml(final String yaml, Class<T> clazz) throws IOException {
- return _yamlObjectMapper.readValue(yaml, clazz);
- }
-
- public <T> T deserializeYaml(final String yaml, final TypeReference<T> typeRef) throws IOException {
- return _yamlObjectMapper.readValue(yaml, typeRef);
- }
-
- public <T> String toYaml(final T instance) throws IOException {
- return _yamlObjectMapper.writeValueAsString(instance);
- }
-
- @Inject
- @Named("jsonObjectMapper")
- private ObjectMapper _jsonObjectMapper;
-
- @Inject
- @Named("yamlObjectMapper")
- private ObjectMapper _yamlObjectMapper;
-}
diff --git a/src/main/webapp/xnat-templates/navigations/HeaderIncludes.vm b/src/main/webapp/xnat-templates/navigations/HeaderIncludes.vm
index d7046f0bf41af35a976d23d49adee590f8cd93d8..b370bdf5ba00ecd776143e5b91fdaf8646af31be 100755
--- a/src/main/webapp/xnat-templates/navigations/HeaderIncludes.vm
+++ b/src/main/webapp/xnat-templates/navigations/HeaderIncludes.vm
@@ -22,6 +22,12 @@
</script>
#end
+#if ($theme)
+<script type="text/javascript">
+ XNAT.theme = $theme}";
+</script>
+#end
+
<!-- load polyfills before ANY other JavaScript -->
<script type="text/javascript" src="$content.getURI('scripts/polyfills.js')"></script>