diff --git a/src/main/java/org/nrg/xnat/configuration/ThemeConfig.java b/src/main/java/org/nrg/xnat/configuration/ThemeConfig.java
new file mode 100644
index 0000000000000000000000000000000000000000..f0337e268af035f1c599b72d867c55398ae0d454
--- /dev/null
+++ b/src/main/java/org/nrg/xnat/configuration/ThemeConfig.java
@@ -0,0 +1,71 @@
+/*
+ * 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) {
+ this.name = themeName;
+ }
+ 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/restlet/extensions/ThemeRestlet.java b/src/main/java/org/nrg/xnat/restlet/extensions/ThemeRestlet.java
new file mode 100644
index 0000000000000000000000000000000000000000..d072e0c0e17b9e6e64335db6262ea84dd07119ac
--- /dev/null
+++ b/src/main/java/org/nrg/xnat/restlet/extensions/ThemeRestlet.java
@@ -0,0 +1,344 @@
+/*
+ * 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 1/25/2016 1:52 PM
+ */
+
+package org.nrg.xnat.restlet.extensions;
+
+import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import org.apache.commons.fileupload.*;
+import org.apache.commons.io.FileUtils;
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+import org.nrg.action.ClientException;
+import org.nrg.xdat.security.helpers.Roles;
+import org.nrg.xnat.configuration.ThemeConfig;
+import org.nrg.xnat.restlet.XnatRestlet;
+import org.nrg.xnat.restlet.resources.SecureResource;
+import org.nrg.xnat.restlet.util.FileWriterWrapperI;
+import org.restlet.Context;
+import org.restlet.data.MediaType;
+import org.restlet.data.Request;
+import org.restlet.data.Response;
+import org.restlet.data.Status;
+import org.restlet.resource.Representation;
+import org.restlet.resource.StringRepresentation;
+import org.restlet.resource.Variant;
+
+import java.io.*;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipInputStream;
+
+/**
+ * Created by jcleve01 on 1/26/2016.
+ */
+@XnatRestlet({"/theme"})
+public class ThemeRestlet extends SecureResource {
+ private static final Log _log = LogFactory.getLog(ThemeRestlet.class);
+ private static String themesPath;
+ protected final ObjectMapper mapper = new ObjectMapper();
+ private static final int FILE_BUFFER_SIZE = 4096;
+ private File themeFile = null;
+
+ public ThemeRestlet(Context context, Request request, Response response) throws UnsupportedEncodingException {
+ super(context, request, response);
+ setModifiable(true);
+ getVariants().add(new Variant(MediaType.APPLICATION_JSON));
+ themesPath = this.getHttpSession().getServletContext().getRealPath(File.separator)+"themes";
+ themeFile = new File(themesPath + File.separator + "theme.json");
+ File checkThemesPath = new File(themesPath);
+ if (!checkThemesPath.exists()) {
+ checkThemesPath.mkdir();
+ }
+ }
+
+ @Override
+ public boolean allowDelete() {
+ return true;
+ }
+
+ /** // TODO: convert to swagger doc tags
+ * Administrator use only
+ * Deletes the entire theme package folder specified by the "theme" query parameter. If it happens to be the
+ * currently applied theme, the current theme is set to null and the default XNAT theme will be restored.
+ */
+ @Override
+ public void handleDelete() {
+ String theme = this.getQueryVariable("theme");
+ if(theme != null && !theme.isEmpty()) {
+ File f = new File(themesPath + File.separator + theme);
+ if (Roles.isSiteAdmin(user)) {
+ try {
+ FileUtils.deleteDirectory(f);
+ ThemeConfig tc = getTheme();
+ String themeName = (tc!=null)?tc.getName():null;
+ if(theme != null && theme.equals(themeName)){
+ setTheme(null);
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ getResponse().setStatus(Status.SERVER_ERROR_INTERNAL, "Theme directory deletion failed.");
+ }
+ } else {
+ getResponse().setStatus(Status.CLIENT_ERROR_UNAUTHORIZED, "Only site administrators can delete themes.");
+ }
+ }
+ }
+
+ @Override
+ public boolean allowPut() {
+ return true;
+ }
+
+ /** // TODO: convert to swagger doc tags
+ * Administrator use only
+ * Sets the currently selected global theme configuration package by updating the theme.json file under the
+ * application's theme folder and caches a copy of it in the app server's application context for reference by any
+ * other pages or servlets that may need to alter their styles and behaviors to fit the overriding theme.
+ */
+ @Override
+ public void handlePut() {
+ if (Roles.isSiteAdmin(user)) {
+ boolean enabled = true;
+ String name = this.getQueryVariable("theme"), path = themesPath + File.separator + name;
+ if("true".equals(this.getQueryVariable("disabled"))){
+ enabled = false;
+ }
+ setTheme(new ThemeConfig(name, themesPath, enabled));
+ } else {
+ getResponse().setStatus(Status.CLIENT_ERROR_UNAUTHORIZED, "Only site administrators can set the site theme.");
+ }
+ }
+
+ @Override
+ public boolean allowPost() {
+ return true;
+ }
+
+ /** // TODO: convert to swagger doc tags
+ * Administrator use only
+ * Accepts a multipart form with a zip file upload and extracts its contents in the theme system folder.
+ * The structure of the zipped package must have only directories at it's root
+ * If successful, the first (root) directory name (or theme name) unzipped is returned in the response.
+ * This will overwrite any other directories already existing with the same name without warning.
+ */
+ @Override
+ public void handlePost() { //Representation entity) { // Upload Theme package
+ Representation result = null;
+ if (Roles.isSiteAdmin(user)) {
+ try {
+ String firstDirName = "";
+ FileWriterWrapperI fw;
+ List<FileWriterWrapperI> fws = this.getFileWriters();
+ if (fws.size() == 0) {
+ this.getResponse().setStatus(Status.CLIENT_ERROR_BAD_REQUEST);
+ getResponse().setEntity("No valid files were uploaded.", MediaType.TEXT_PLAIN);
+ return;
+ }
+ if (fws.size() > 1) {
+ this.getResponse().setStatus(Status.CLIENT_ERROR_BAD_REQUEST);
+ getResponse().setEntity("Theme importer is limited to one uploaded theme package per request.", MediaType.TEXT_PLAIN);
+ return;
+ }
+ fw = fws.get(0); //TODO: inspect this fw object a little more for metadata
+ // TODO: validate zipped media type (fail otherwise)
+ final InputStream is = fw.getInputStream();
+ ZipInputStream zipIn = new ZipInputStream(is);
+ ZipEntry entry = zipIn.getNextEntry();
+ int dirCount = 0;
+ while (entry != null) { // iterate over entries in the zip file
+ String filePath = themesPath + 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
+ extractFile(zipIn, filePath);
+ } else { // if the entry is a directory, make the directory
+ if(dirCount == 0) {
+ firstDirName = entry.getName();
+ int slashIndex = firstDirName.indexOf('/');
+ if(slashIndex>1){
+ firstDirName = firstDirName.substring(0, slashIndex);
+ }
+ }
+ dirCount++;
+ File dir = new File(filePath);
+ dir.mkdir();
+ }
+ zipIn.closeEntry();
+ entry = zipIn.getNextEntry();
+ }
+ zipIn.close();
+ is.close();
+ getResponse().setEntity(firstDirName, MediaType.TEXT_PLAIN);
+ } catch (FileUploadBase.InvalidContentTypeException icte){
+ this.getResponse().setStatus(Status.CLIENT_ERROR_BAD_REQUEST);
+ getResponse().setEntity("Invalid Content Type: "+icte.getMessage(), MediaType.TEXT_PLAIN);
+ } catch (FileUploadException fue) {
+ this.getResponse().setStatus(Status.CLIENT_ERROR_BAD_REQUEST);
+ getResponse().setEntity("File Upload Exception: " + fue.getMessage(), MediaType.TEXT_PLAIN);
+ } catch (ClientException e) {
+ e.printStackTrace();
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+ } else {
+ getResponse().setStatus(Status.CLIENT_ERROR_UNAUTHORIZED, "Only site administrators can upload new themes.");
+ }
+ }
+
+ /**
+ * Extracts a zip entry (file entry)
+ * @param zip
+ * @param path
+ * @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 = 0;
+ while ((length = zip.read(bytes)) != -1) {
+ os.write(bytes, 0, length);
+ }
+ os.close();
+ }
+
+ /** // TODO: convert to swagger doc tags
+ * Reports the currently selected global theme (if there is one), whether or not it's enabled, and a list of
+ * available themes on the system in a JSON string.
+ */
+ @Override
+ public Representation represent(Variant variant){
+ String themeOptions = null, themeName = null;
+ boolean themeEnabled = false;
+ ThemeConfig theme = getTheme();
+ try {
+ themeOptions = mapper.writeValueAsString(loadExistingThemes().toArray());
+ } catch (JsonProcessingException e) {
+ e.printStackTrace();
+ }
+ if(theme != null) {
+ themeName="\""+theme.getName()+"\"";
+ themeEnabled=theme.isEnabled();
+ }
+ return new StringRepresentation(
+ "{\"theme\":"+themeName+", \"enabled\":"+themeEnabled+", \"themeOptions\":"+themeOptions+"}",
+ MediaType.APPLICATION_JSON);
+ }
+
+ /**
+ * Loads the system theme options
+ * @return The list of the available theme packages (folder names) available under the system themes directory
+ */
+ public ArrayList<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;
+ }
+
+ /**
+ * 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() {
+ ThemeConfig themeConfig = null, cachedTheme = (ThemeConfig) this.getHttpSession().getServletContext().getAttribute("theme");
+ if(cachedTheme != null){
+ return cachedTheme;
+ } 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 = mapper.readValue(contents, ThemeConfig.class);
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+ }
+ setTheme(themeConfig);
+ }
+ return themeConfig;
+ }
+
+ /**
+ * Sets the currently selected system theme in the theme.json file in the web application's themes folder and
+ * stores it in the application servlet context cache
+ * @param themeConfig the theme configuration object to apply
+ */
+ public void setTheme(ThemeConfig themeConfig) {
+ try {
+ if (themeConfig != null) {
+ String themeJson = mapper.writeValueAsString(themeConfig);
+ if (!themeFile.exists()) {
+ themeFile.createNewFile();
+ }
+ FileWriter writer = new FileWriter(themeFile);
+ writer.write(themeJson);
+ writer.flush();
+ writer.close();
+ } else {
+ themeFile.delete();
+ if (themeFile.exists()) { // Backup hack in case the file deletion does not
+ FileWriter writer = new FileWriter(themeFile); // succeed due to a file lock which sometimes
+ writer.write("{\"name\":null}"); // strangely happens in Windows
+ writer.flush(); // ...in that case wipe it out.
+ writer.close();
+ }
+ }
+ } catch (JsonProcessingException e) {
+ e.printStackTrace();
+ // TODO: rethrow this and respond as an internal server error
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+ this.getHttpSession().getServletContext().setAttribute("theme", themeConfig);
+ }
+
+ /**
+ * Helper class to organize the available themes for display in a select dropdown form
+ */
+ public static class TypeOption implements Comparable<TypeOption> {
+ String value, label;
+ private 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(TypeOption that) {
+ return this.label.compareToIgnoreCase(that.label);
+ }
+ }
+}
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
new file mode 100644
index 0000000000000000000000000000000000000000..54957d5e43cb9116eeb4a604a67e99f92696938b
--- /dev/null
+++ b/src/main/java/org/nrg/xnat/turbine/modules/screens/XDATScreen_themes.java
@@ -0,0 +1,30 @@
+/*
+ * 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 1/22/2016 3:20 PM
+ */
+
+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.turbine.modules.screens.SecureScreen;
+import org.nrg.xnat.restlet.extensions.ThemeRestlet;
+
+
+/**
+ * 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 {
+ }
+}
diff --git a/src/main/webapp/WEB-INF/conf/InstanceSettings.xml b/src/main/webapp/WEB-INF/conf/InstanceSettings.xml
deleted file mode 100644
index f7fff52df3be155efcf77337fbd2df6e4f09540a..0000000000000000000000000000000000000000
--- a/src/main/webapp/WEB-INF/conf/InstanceSettings.xml
+++ /dev/null
@@ -1,27 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!-- edited with XMLSPY v2004 rel. 3 U (http://www.xmlspy.com) by Tim Olsen (Washington University) -->
-<Instance_Settings xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="schemas/xdat/instance.xsd"
- site_url="http://localhost:8080" admin_email="administrator@xnat.org" archive_root_path="/data/xnat/archive"
- prearchive_path="/data/xnat/prearchive" cache_path="/data/xnat/cache"
- smtp_server="irony.wusm.wustl.edu" ftp_path="/data/xnat/ftp" build_path="/data/xnat/build"
- pipeline_path="/data/xnat/pipeline" require_login="true" user_registration="false" enable_csrf_token="true">
- <Databases>
- <Database Type="POSTGRESQL" Id="xnat" Driver="org.postgresql.Driver" Url="jdbc:postgresql://localhost/xnat" User="xnat" Pass="xnat" MaxConnections="10"/>
- </Databases>
- <Models>
- <Data_Model File_Name="security.xsd" File_Location="schemas/security" DB="xnat"/>
- <Data_Model File_Name="birnprov.xsd" File_Location="schemas/birn" DB="xnat"/>
- <Data_Model File_Name="xnat.xsd" File_Location="schemas/xnat" DB="xnat"/>
- <Data_Model File_Name="workflow.xsd" File_Location="schemas/pipeline" DB="xnat"/>
- <Data_Model File_Name="repository.xsd" File_Location="schemas/pipeline" DB="xnat"/>
- <Data_Model File_Name="project.xsd" File_Location="schemas/project" DB="xnat"/>
- <Data_Model File_Name="assessments.xsd" File_Location="schemas/assessments" DB="xnat"/>
- <Data_Model File_Name="catalog.xsd" File_Location="schemas/catalog" DB="xnat"/>
- <Data_Model File_Name="protocolValidation.xsd" File_Location="schemas/validation" DB="xnat"/>
- <Data_Model File_Name="screeningAssessment.xsd" File_Location="schemas/screening" DB="xnat"/>
-
-<!--<Data_Model File_Name="ext.xsd" File_Location="schemas/ext" DB="xnat"/>-->
- <!-- Start modules schemas: Reserved for xnat_builder, don't modify anything between this line and the end modules line. -->
- <!-- End modules schemas: Reserved for xnat_builder, don't modify anything between this line and the start modules line. -->
- </Models>
-</Instance_Settings>
diff --git a/src/main/webapp/WEB-INF/web.xml b/src/main/webapp/WEB-INF/web.xml
deleted file mode 100644
index 4eb56411ccd19b6c6f6b5900afe04c7c2073677f..0000000000000000000000000000000000000000
--- a/src/main/webapp/WEB-INF/web.xml
+++ /dev/null
@@ -1,326 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!--
- ~ D:/Development/XNAT/1.6/xnat_builder_1_6dev/plugin-resources/originals/application-web.xml
- ~ XNAT http://www.xnat.org
- ~ Copyright (c) 2014, Washington University School of Medicine
- ~ All Rights Reserved
- ~
- ~ Released under the Simplified BSD.
- ~
- ~ Last modified 2/7/14 12:19 PM
- -->
-<web-app xmlns="http://java.sun.com/xml/ns/javaee" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://java.sun.com/xml/ns/javaee http://java.sun.com/xml/ns/javaee/web-app_3_0.xsd" version="3.0">
- <!-- ======================================================================== -->
- <!-- -->
- <!-- Uncomment the following block if you want to use the Session Service -->
- <!-- -->
- <!-- ======================================================================== -->
- <!--
- <listener>
- <listener-class>org.apache.turbine.services.session.SessionListener</listener-class>
- </listener>
- -->
- <!-- HttpSessionEventPublisher enables session counting for the concurrent session filter, XnatSessionEventPublisher requires the contextAttribute parameter -->
- <context-param>
- <param-name>contextAttribute</param-name>
- <param-value>org.springframework.web.servlet.FrameworkServlet.CONTEXT.spring-mvc</param-value>
- </context-param>
- <context-param>
- <param-name>org.restlet.component</param-name>
- <param-value>org.nrg.xnat.restlet.XNATComponent</param-value>
- </context-param>
- <!--
- This setting will be automatically configured according to xdat.url in build.properties.
- You can still set it manually if desired (not here - do it in xnat/projects/xnat/src/web-conf/web-projectMerge.xml).
- -->
- <context-param>
- <param-name>org.restlet.autoWire</param-name>
- <param-value>false</param-value>
- </context-param>
- <filter>
- <filter-name>springSecurityFilterChain</filter-name>
- <filter-class>org.springframework.web.filter.DelegatingFilterProxy</filter-class>
- <init-param>
- <param-name>contextAttribute</param-name>
- <param-value>org.springframework.web.servlet.FrameworkServlet.CONTEXT.spring-mvc</param-value>
- </init-param>
- </filter>
- <filter>
- <filter-name>updateExpirationCookie</filter-name>
- <filter-class>org.nrg.xnat.restlet.util.UpdateExpirationCookie</filter-class>
- </filter>
- <filter-mapping>
- <filter-name>springSecurityFilterChain</filter-name>
- <url-pattern>/*</url-pattern>
- </filter-mapping>
- <filter-mapping>
- <filter-name>updateExpirationCookie</filter-name>
- <url-pattern>/*</url-pattern>
- </filter-mapping>
- <listener>
- <listener-class>org.nrg.xnat.security.XnatSessionEventPublisher</listener-class>
- </listener>
- <listener>
- <listener-class>org.apache.axis.transport.http.AxisHTTPSessionListener</listener-class>
- </listener>
- <servlet>
- <servlet-name>xnat17</servlet-name>
- <servlet-class>org.apache.turbine.Turbine</servlet-class>
- <init-param>
- <param-name>properties</param-name>
- <param-value>WEB-INF/conf/TurbineResources.properties</param-value>
- </init-param>
- <load-on-startup>1</load-on-startup>
- </servlet>
- <!-- BEGIN XNAT CUSTOMIZATIONS -->
- <!-- ======================================================================== -->
- <!-- INSERTED FOR Spring Framework -->
- <!-- ======================================================================== -->
- <servlet>
- <servlet-name>spring-mvc</servlet-name>
- <servlet-class>org.springframework.web.servlet.DispatcherServlet</servlet-class>
- <init-param>
- <param-name>contextConfigLocation</param-name>
- <param-value>/WEB-INF/conf/root-spring-config.xml</param-value>
- </init-param>
- <load-on-startup>1</load-on-startup>
- </servlet>
- <servlet>
- <servlet-name>xdat</servlet-name>
- <servlet-class>org.nrg.xdat.servlet.XDATServlet</servlet-class>
- <load-on-startup>1</load-on-startup>
- </servlet>
- <!-- ======================================================================== -->
- <!-- INSERTED FOR RESTServlet -->
- <!-- ======================================================================== -->
- <servlet>
- <servlet-name>RestletServlet</servlet-name>
- <servlet-class>org.nrg.xnat.restlet.servlet.XNATRestletServlet</servlet-class>
- <load-on-startup>2</load-on-startup>
- </servlet>
- <!-- ======================================================================== -->
- <!-- INSERTED FOR ArchiveServlet -->
- <!-- ======================================================================== -->
- <servlet>
- <servlet-name>ArchiveServlet</servlet-name>
- <servlet-class>org.nrg.xnat.servlet.ArchiveServlet</servlet-class>
- <load-on-startup>2</load-on-startup>
- </servlet>
- <!-- ======================================================================== -->
- <!-- INSERTED FOR Ajax -->
- <!-- ======================================================================== -->
- <servlet>
- <servlet-name>XDATAjaxServlet</servlet-name>
- <servlet-class>org.nrg.xdat.servlet.XDATAjaxServlet</servlet-class>
- </servlet>
- <!-- ======================================================================== -->
- <!-- INSERTED FOR Apache Axis -->
- <!-- ======================================================================== -->
- <servlet>
- <servlet-name>AxisServlet</servlet-name>
- <servlet-class>org.apache.axis.transport.http.AxisServlet</servlet-class>
- </servlet>
- <servlet>
- <servlet-name>AdminServlet</servlet-name>
- <servlet-class>org.apache.axis.transport.http.AdminServlet</servlet-class>
- <load-on-startup>100</load-on-startup>
- </servlet>
- <servlet>
- <servlet-name>SOAPMonitorService</servlet-name>
- <servlet-class>org.apache.axis.monitor.SOAPMonitorService</servlet-class>
- <init-param>
- <param-name>SOAPMonitorPort</param-name>
- <param-value>5001</param-value>
- </init-param>
- <load-on-startup>100</load-on-startup>
- </servlet>
- <!-- ======================================================================== -->
- <!-- INSERTED FOR Image Viewer -->
- <!-- ======================================================================== -->
- <servlet>
- <servlet-name>PopulateServlet</servlet-name>
- <servlet-class>org.nrg.plexiViewer.Servlet.PopulateServlet</servlet-class>
- </servlet>
- <servlet>
- <servlet-name>ImageDistributorServlet</servlet-name>
- <servlet-class>org.nrg.plexiViewer.Servlet.ImageDistributorServlet</servlet-class>
- </servlet>
- <servlet>
- <servlet-name>ImageLoaderServlet</servlet-name>
- <servlet-class>org.nrg.plexiViewer.Servlet.ImageLoaderServlet</servlet-class>
- </servlet>
- <servlet>
- <servlet-name>MontageImageLoaderServlet</servlet-name>
- <servlet-class>org.nrg.plexiViewer.Servlet.MontageImageLoaderServlet</servlet-class>
- </servlet>
- <servlet>
- <servlet-name>GetRecFileContents</servlet-name>
- <servlet-class>org.nrg.plexiViewer.Servlet.GetRecFileContents</servlet-class>
- </servlet>
- <servlet>
- <servlet-name>getAsegRegionVolumes</servlet-name>
- <servlet-class>org.nrg.plexiViewer.Servlet.getAsegRegionVolumes</servlet-class>
- </servlet>
- <servlet>
- <servlet-name>PublisherServlet</servlet-name>
- <servlet-class>org.nrg.plexiViewer.Servlet.PublisherServlet</servlet-class>
- </servlet>
- <servlet-mapping>
- <servlet-name>spring-mvc</servlet-name>
- <url-pattern>/admin/*</url-pattern>
- </servlet-mapping>
- <servlet-mapping>
- <servlet-name>spring-mvc</servlet-name>
- <url-pattern>/xapi/*</url-pattern>
- </servlet-mapping>
- <!-- END XNAT CUSTOMIZATIONS -->
- <servlet-mapping>
- <servlet-name>xnat17</servlet-name>
- <url-pattern>/app/*</url-pattern>
- </servlet-mapping>
- <servlet-mapping>
- <servlet-name>xdat</servlet-name>
- <url-pattern>/xdat/*</url-pattern>
- </servlet-mapping>
- <!-- ======================================================================== -->
- <!-- INSERTED FOR RESTServlet -->
- <!-- ======================================================================== -->
- <servlet-mapping>
- <servlet-name>RestletServlet</servlet-name>
- <url-pattern>/REST/*</url-pattern>
- </servlet-mapping>
- <servlet-mapping>
- <servlet-name>RestletServlet</servlet-name>
- <url-pattern>/data/*</url-pattern>
- </servlet-mapping>
- <!-- ======================================================================== -->
- <!-- INSERTED FOR Ajax -->
- <!-- ======================================================================== -->
- <servlet-mapping>
- <servlet-name>XDATAjaxServlet</servlet-name>
- <url-pattern>/ajax/*</url-pattern>
- </servlet-mapping>
- <servlet-mapping>
- <servlet-name>XDATAjaxServlet</servlet-name>
- <url-pattern>/servlet/XDATAjaxServlet</url-pattern>
- </servlet-mapping>
- <servlet-mapping>
- <servlet-name>XDATAjaxServlet</servlet-name>
- <url-pattern>/servlet/AjaxServlet</url-pattern>
- </servlet-mapping>
- <!-- ======================================================================== -->
- <!-- INSERTED FOR Apache Axis -->
- <!-- ======================================================================== -->
- <servlet-mapping>
- <servlet-name>AdminServlet</servlet-name>
- <url-pattern>/servlet/AdminServlet</url-pattern>
- </servlet-mapping>
- <servlet-mapping>
- <servlet-name>AxisServlet</servlet-name>
- <url-pattern>/servlet/AxisServlet</url-pattern>
- </servlet-mapping>
- <servlet-mapping>
- <servlet-name>AxisServlet</servlet-name>
- <url-pattern>*.jws</url-pattern>
- </servlet-mapping>
- <servlet-mapping>
- <servlet-name>AxisServlet</servlet-name>
- <url-pattern>/services/*</url-pattern>
- </servlet-mapping>
- <!-- ======================================================================== -->
- <!-- INSERTED FOR Image Viewer -->
- <!-- ======================================================================== -->
- <servlet-mapping>
- <servlet-name>SOAPMonitorService</servlet-name>
- <url-pattern>/SOAPMonitor</url-pattern>
- </servlet-mapping>
- <servlet-mapping>
- <servlet-name>PopulateServlet</servlet-name>
- <url-pattern>/servlet/PopulateServlet</url-pattern>
- </servlet-mapping>
- <servlet-mapping>
- <servlet-name>ImageDistributorServlet</servlet-name>
- <url-pattern>/servlet/ImageDistributorServlet</url-pattern>
- </servlet-mapping>
- <servlet-mapping>
- <servlet-name>ImageLoaderServlet</servlet-name>
- <url-pattern>/servlet/ImageLoaderServlet</url-pattern>
- </servlet-mapping>
- <servlet-mapping>
- <servlet-name>MontageImageLoaderServlet</servlet-name>
- <url-pattern>/servlet/MontageImageLoaderServlet</url-pattern>
- </servlet-mapping>
- <servlet-mapping>
- <servlet-name>GetRecFileContents</servlet-name>
- <url-pattern>/servlet/GetRecFileContents</url-pattern>
- </servlet-mapping>
- <servlet-mapping>
- <servlet-name>getAsegRegionVolumes</servlet-name>
- <url-pattern>/servlet/getAsegRegionVolumes</url-pattern>
- </servlet-mapping>
- <servlet-mapping>
- <servlet-name>PublisherServlet</servlet-name>
- <url-pattern>/servlet/PublisherServlet</url-pattern>
- </servlet-mapping>
- <!-- ======================================================================== -->
- <!-- INSERTED FOR ArchiveServlet -->
- <!-- ======================================================================== -->
- <servlet-mapping>
- <servlet-name>ArchiveServlet</servlet-name>
- <url-pattern>/archive/*</url-pattern>
- </servlet-mapping>
- <session-config>
- <!-- Default to 15 minute session timeouts -->
- <session-timeout>15</session-timeout>
- </session-config>
- <mime-mapping>
- <extension>wsdl</extension>
- <mime-type>text/xml</mime-type>
- </mime-mapping>
- <mime-mapping>
- <extension>xsd</extension>
- <mime-type>text/xml</mime-type>
- </mime-mapping>
- <!-- ======================================================================== -->
- <!-- -->
- <!-- Redirect the home page of the application to the turbine servlet -->
- <!-- -->
- <!-- ======================================================================== -->
- <welcome-file-list>
- <welcome-file>index.jsp</welcome-file>
- <welcome-file>app</welcome-file>
- </welcome-file-list>
- <!-- ======================================================================== -->
- <!-- -->
- <!-- Mapping HTTP error codes and exceptions to custom error pages to make -->
- <!-- the display a bit more pleasant and preserve system confidentiality. -->
- <!-- -->
- <!-- ======================================================================== -->
- <error-page>
- <exception-type>java.lang.Throwable</exception-type>
- <location>/app/template/Error.vm</location>
- </error-page>
- <!-- ======================================================================== -->
- <!-- -->
- <!-- Make sure that templates, resources and logs are not available through -->
- <!-- the servlet container. Remove security constraints or add an authen- -->
- <!-- tication role if you need access to these paths. -->
- <!-- -->
- <!-- ======================================================================== -->
- <security-constraint>
- <web-resource-collection>
- <web-resource-name>templates</web-resource-name>
- <url-pattern>/templates/*</url-pattern>
- </web-resource-collection>
- <web-resource-collection>
- <web-resource-name>logs</web-resource-name>
- <url-pattern>/logs/*</url-pattern>
- </web-resource-collection>
- <web-resource-collection>
- <web-resource-name>resources</web-resource-name>
- <url-pattern>/resources/*</url-pattern>
- </web-resource-collection>
- <auth-constraint />
- </security-constraint>
-</web-app>
-
diff --git a/src/main/webapp/scripts/footer.js b/src/main/webapp/scripts/footer.js
index 177a65065693896b8f25c68ae7f7634feed7e6af..98590d8ac31767d4ba254ddc8eeb2f76a5764c07 100644
--- a/src/main/webapp/scripts/footer.js
+++ b/src/main/webapp/scripts/footer.js
@@ -544,6 +544,23 @@ $(function(){
});
jq(window).load(function(){
+ // adding shortcut methods to put and delete AJAX calls for clarity
+ jq.each(["put", "delete"], function(i, method) {
+ jq[method] = function(url, data, callback, type) {
+ if (jq.isFunction(data)) {
+ type = type || callback;
+ callback = data;
+ data = undefined;
+ }
+ return jq.ajax({
+ url: url,
+ type: method,
+ dataType: type,
+ data: data,
+ success: callback
+ });
+ };
+ });
// trying to make the text readable
jq('[style*="font-size:8px"]').addClass('smallest_text');
diff --git a/src/main/webapp/xnat-templates/screens/XDATScreen_admin_options.vm b/src/main/webapp/xnat-templates/screens/XDATScreen_admin_options.vm
index a1a2af2ffbb51a55223c8bce529a4f75ee557a02..98c311be4ebdd84fec77db45264e344d9af4cd29 100644
--- a/src/main/webapp/xnat-templates/screens/XDATScreen_admin_options.vm
+++ b/src/main/webapp/xnat-templates/screens/XDATScreen_admin_options.vm
@@ -53,6 +53,8 @@ $!template.setLayoutTemplate("DefaultExptList.vm")
<a href="$link.setPage("XDATScreen_add_xnat_projectData.vm")">Create $displayManager.getSingularDisplayNameForProject()</a>
+ <a href="$link.setPage("XDATScreen_themes.vm")">Manage Themes</a>
+
#addGlobalCustomScreens("admin/options")
</div>
diff --git a/src/main/webapp/xnat-templates/screens/XDATScreen_themes.vm b/src/main/webapp/xnat-templates/screens/XDATScreen_themes.vm
new file mode 100644
index 0000000000000000000000000000000000000000..f9d016eda9441f8c2ea6f97ac5cd1799f05038ca
--- /dev/null
+++ b/src/main/webapp/xnat-templates/screens/XDATScreen_themes.vm
@@ -0,0 +1,112 @@
+<!-- Begin XDATScreen_themes.vm -->
+<style>
+ .bold{
+ font-weight: bold;
+ }
+</style>
+<div style="margin-left: 20px;">
+ <h2><span id="titleAppName"></span> Theme Management</h2>
+ <div id="currentThemeDiv">
+ <span class="label bold">Current theme: </span>
+ <span id="currentTheme">None</span>
+ </div>
+ <br>
+ <div id="selectThemeDiv">
+ <span class="label bold">Select an existing theme: </span>
+ <select id="themeSelection" name="theme" style="width: 270px;"></select>
+ <button id="submitThemeButton" onclick="setTheme();">Set Theme</button>
+ <button id="removeThemeButton" onclick="removeTheme();">Remove Theme</button>
+ </div>
+ <br>
+ <form id="uploadThemeForm" method="POST" class="optOutOfXnatDefaultFormValidation">
+ <span class="label bold">Upload a theme package: </span>
+ <input type="file" id="themeFileUpload" name="themeFileUpload" multiple style="width: 270px;"/>
+ <button type="submit" id="submitThemeUploadButton">Upload</button>
+ </form>
+</div>
+
+<script>
+ var themeUrl = "$content.getURI('/data/theme')";
+ var q = '?', a = '&';
+ var csrf = 'XNAT_CSRF='+window.csrfToken;
+ $('#titleAppName').text(XNAT.app.siteId);
+ var currentTheme = $('#currentTheme');
+ var themeSelector = $('#themeSelection');
+ var uploadForm = document.getElementById('uploadThemeForm');
+ var themeUploader = document.getElementById('themeFileUpload');
+ var themeUploadSubmit = document.getElementById('submitThemeUploadButton');
+ var selectedTheme = null;
+ function populateThemes(themeToSelect){
+ $.get(themeUrl+q+csrf, null, function (data){
+ themeSelector.empty();
+ $(data.themeOptions).each(function(i, opt) {
+ var selected = '', selectedTheme = null;
+ if(data.theme == opt.value){
+ selectedTheme = data.theme;
+ selected = ' selected="selected"';
+ currentTheme.text(selectedTheme?selectedTheme:'None');
+ }
+ themeSelector.append('<option value="'+opt.value+'"'+selected+'>'+opt.label+'</option>');
+ });
+ if(themeToSelect && typeof themeToSelect === 'string'){
+ themeSelector.val(themeToSelect);
+ }
+ }, 'json');
+ }
+ function setTheme(){
+ xmodal.confirm({
+ content: 'Theme selection appearances may not fully take effect until users log out, clear their browser cache and log back in.'+
+ '<br><br>Are you sure you wish to change the global theme?',
+ action: function(){
+ $.put(themeUrl+q+'theme='+encodeURI(themeSelector.val())+a+csrf, null, populateThemes);
+ }
+ });
+ }
+ function removeTheme(){
+ xmodal.confirm({
+ content: 'Are you sure you wish to delete the selected theme?',
+ action: function(){
+ $.delete(themeUrl+q+'theme='+encodeURI(themeSelector.val())+a+csrf, null, populateThemes);
+ }
+ });
+ }
+
+ /*** Theme Package Upload Functions ***/
+ uploadForm.action = themeUrl+q+csrf;
+ uploadForm.onsubmit = function(event) {
+ event.preventDefault();
+ $(themeUploadSubmit).text('Uploading...');
+ $(themeUploadSubmit).attr('disabled', 'disabled');
+ var files = themeUploader.files;
+ var formData = new FormData();
+ var uploaded = false;
+ for (var i = 0; i < files.length; i++) {
+ var file = files[i];
+ if (!file.type.match('zip.*')) {
+ continue;
+ }
+ formData.append('themes[]', file, file.name);
+ var xhr = new XMLHttpRequest();
+ xhr.open('POST', uploadForm.action, true);
+ xhr.onload = function () {
+ if (xhr.status !== 200) {
+ xmodal.message('Upload Error', xhr.responseText);
+ }
+ var uploadedTheme = xhr.responseText;
+ $(themeUploadSubmit).text('Upload');
+ $(themeUploadSubmit).removeAttr('disabled');
+ populateThemes(uploadedTheme);
+ };
+ xhr.send(formData);
+ uploaded = true;
+ }
+ if(!uploaded){
+ xmodal.message('Nothing Uploaded', 'No valid theme package files were selected for upload.');
+ $(themeUploadSubmit).text('Upload');
+ $(themeUploadSubmit).removeAttr('disabled');
+ }
+ }
+ $(populateThemes); // ...called once DOM is fully loaded "ready"
+</script>
+
+<!-- End XDATScreen_themes.vm -->
\ No newline at end of file