diff --git a/src/main/java/org/nrg/xapi/rest/settings/SiteConfigApi.java b/src/main/java/org/nrg/xapi/rest/settings/SiteConfigApi.java
index f04aac762f7ff86a8be4a069b0ce402aafe74ca6..bd4957f10d1ea946e44a18c507cdb647992d46f8 100644
--- a/src/main/java/org/nrg/xapi/rest/settings/SiteConfigApi.java
+++ b/src/main/java/org/nrg/xapi/rest/settings/SiteConfigApi.java
@@ -84,7 +84,7 @@ public class SiteConfigApi extends AbstractXnatRestApi {
final Map<String, Object> values = new HashMap<>();
for (final String preference : preferences) {
- final Object value = _preferences.getValueByReference(preference);
+ final Object value = _preferences.getProperty(preference);
if (value != null) {
values.put(preference, value);
}
@@ -100,7 +100,7 @@ public class SiteConfigApi extends AbstractXnatRestApi {
if (status != null) {
return new ResponseEntity<>(status);
}
- final Object value = _preferences.getValueByReference(property);
+ final Object value = _preferences.getProperty(property);
if (_log.isDebugEnabled()) {
_log.debug("User " + getSessionUser().getUsername() + " requested the value for the site configuration property " + property + ", got value: " + value);
}
diff --git a/src/main/java/org/nrg/xnat/configuration/ApplicationConfig.java b/src/main/java/org/nrg/xnat/configuration/ApplicationConfig.java
index bf0ce3f6d7c5bd556b47ff684bf57927832c42ca..b51580982bf1df0f55c8eac7bea1ff79df75dd79 100644
--- a/src/main/java/org/nrg/xnat/configuration/ApplicationConfig.java
+++ b/src/main/java/org/nrg/xnat/configuration/ApplicationConfig.java
@@ -68,15 +68,12 @@ public class ApplicationConfig {
@Bean
public RegExpValidator regexValidator() throws SiteConfigurationException {
- final String complexityExpression = _preferences.getPasswordComplexity();
- final String complexityMessage = _preferences.getPasswordComplexityMessage();
- return new RegExpValidator(complexityExpression, complexityMessage);
+ return new RegExpValidator();
}
@Bean
public HistoricPasswordValidator historicPasswordValidator() throws SiteConfigurationException {
- final int durationInDays = _preferences.getPasswordHistoryDuration();
- return new HistoricPasswordValidator(durationInDays);
+ return new HistoricPasswordValidator();
}
@Bean
diff --git a/src/main/java/org/nrg/xnat/configuration/SchedulerConfig.java b/src/main/java/org/nrg/xnat/configuration/SchedulerConfig.java
index 36d36973c68278dc3d2f6cf52aa4a8dc0613d6cc..fd4206024839c323385e85582b1bc866b7161e7d 100644
--- a/src/main/java/org/nrg/xnat/configuration/SchedulerConfig.java
+++ b/src/main/java/org/nrg/xnat/configuration/SchedulerConfig.java
@@ -4,6 +4,7 @@ import org.nrg.config.exceptions.SiteConfigurationException;
import org.nrg.framework.exceptions.NrgServiceError;
import org.nrg.framework.exceptions.NrgServiceRuntimeException;
import org.nrg.mail.services.EmailRequestLogService;
+import org.nrg.xdat.XDAT;
import org.nrg.xdat.preferences.InitializerSiteConfiguration;
import org.nrg.xdat.preferences.SiteConfigPreferences;
import org.nrg.xnat.helpers.prearchive.SessionXMLRebuilder;
@@ -18,6 +19,8 @@ import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Lazy;
import org.springframework.jdbc.core.JdbcTemplate;
import org.springframework.jms.core.JmsTemplate;
+import org.springframework.scheduling.Trigger;
+import org.springframework.scheduling.TriggerContext;
import org.springframework.scheduling.annotation.EnableScheduling;
import org.springframework.scheduling.annotation.SchedulingConfigurer;
import org.springframework.scheduling.concurrent.ThreadPoolTaskScheduler;
@@ -28,6 +31,9 @@ import org.springframework.scheduling.support.PeriodicTrigger;
import javax.inject.Inject;
import java.sql.SQLException;
+import java.util.Calendar;
+import java.util.Date;
+import java.util.GregorianCalendar;
import java.util.List;
@Configuration
@@ -56,7 +62,24 @@ public class SchedulerConfig implements SchedulingConfigurer {
@Bean
public TriggerTask clearExpiredAliasTokens() throws SiteConfigurationException {
- return new TriggerTask(new ClearExpiredAliasTokens(_template, _preferences.getAliasTokenTimeout()), new PeriodicTrigger(3600000));
+ return new TriggerTask(new ClearExpiredAliasTokens(_template), new Trigger() {
+ @Override public Date nextExecutionTime(TriggerContext triggerContext) {
+ Calendar nextExecutionTime = new GregorianCalendar();
+ Date lastActualExecutionTime = triggerContext.lastActualExecutionTime();
+ nextExecutionTime.setTime(lastActualExecutionTime != null ? lastActualExecutionTime : new Date());
+ long expirationInterval = XDAT.getSiteConfigPreferences().getAliasTokenTimeout();
+ if(expirationInterval<120){//Check every minute if interval is 2 hours or less
+ nextExecutionTime.add(Calendar.MINUTE, 1);
+ }
+ else if(expirationInterval<2880){//Check every hour if interval is 2 days or less
+ nextExecutionTime.add(Calendar.HOUR, 1);
+ }
+ else{//Check every day
+ nextExecutionTime.add(Calendar.DAY_OF_MONTH, 1);
+ }
+ return nextExecutionTime.getTime();
+ }
+ });
}
@Bean
diff --git a/src/main/java/org/nrg/xnat/event/listeners/AutomationEventScriptHandler.java b/src/main/java/org/nrg/xnat/event/listeners/AutomationEventScriptHandler.java
index af07d88f65fce9f6dbd60229ef4ef9d82b0fba05..6f0d32a1cca965653e26b03c6a342bffa06c2a30 100644
--- a/src/main/java/org/nrg/xnat/event/listeners/AutomationEventScriptHandler.java
+++ b/src/main/java/org/nrg/xnat/event/listeners/AutomationEventScriptHandler.java
@@ -177,7 +177,8 @@ public class AutomationEventScriptHandler implements Consumer<Event<AutomationEv
*
* @param event the event
*/
- private void updateAutomationTables(Event<AutomationEventImplementerI> event) {
+ // Made this method synchronized to avoid some constraint violation exceptions that were occasionally being thrown.
+ private synchronized void updateAutomationTables(Event<AutomationEventImplementerI> event) {
final AutomationEventImplementerI eventData = event.getData();
if (eventData.getEventId() == null || eventData.getClass() == null) {
return;
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 1b359a7e4d9685ac79fe96a72975e15a96c33962..6523ee706b504559ab0d8689086162530066dce2 100644
--- a/src/main/java/org/nrg/xnat/helpers/prearchive/PrearcDatabase.java
+++ b/src/main/java/org/nrg/xnat/helpers/prearchive/PrearcDatabase.java
@@ -17,7 +17,6 @@ import org.apache.commons.lang3.StringUtils;
import org.nrg.action.ClientException;
import org.nrg.automation.entities.Script;
import org.nrg.automation.services.ScriptService;
-import org.nrg.config.exceptions.ConfigServiceException;
import org.nrg.dicomtools.filters.DicomFilterService;
import org.nrg.dicomtools.filters.SeriesImportFilter;
import org.nrg.framework.constants.PrearchiveCode;
@@ -179,12 +178,7 @@ public final class PrearcDatabase {
if (preferences != null) {
return preferences.getPrearchivePath();
}
- try {
- final Properties properties = XDAT.getSiteConfiguration();
- return properties.getProperty("prearchivePath");
- } catch (ConfigServiceException e) {
- return null;
- }
+ return XDAT.getSiteConfigPreferences().getPrearchivePath();
}
private static boolean tableExists() throws Exception {
diff --git a/src/main/java/org/nrg/xnat/initialization/XnatWebAppInitializer.java b/src/main/java/org/nrg/xnat/initialization/XnatWebAppInitializer.java
index 78901edce38b3d386a852d55685259b049e30b93..66eac2b498d7715368d0184403ee8515fc12fe62 100644
--- a/src/main/java/org/nrg/xnat/initialization/XnatWebAppInitializer.java
+++ b/src/main/java/org/nrg/xnat/initialization/XnatWebAppInitializer.java
@@ -19,7 +19,6 @@ import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.core.io.Resource;
import org.springframework.core.io.support.PropertiesLoaderUtils;
-import org.springframework.stereotype.Service;
import org.springframework.web.filter.DelegatingFilterProxy;
import org.springframework.web.servlet.support.AbstractAnnotationConfigDispatcherServletInitializer;
diff --git a/src/main/java/org/nrg/xnat/restlet/resources/UserListResource.java b/src/main/java/org/nrg/xnat/restlet/resources/UserListResource.java
index 2eda908e4c661a7100895f5198532bc2f104fe4b..97c99d4689b5e0768ce2dc308c2e4d0d51a0372b 100644
--- a/src/main/java/org/nrg/xnat/restlet/resources/UserListResource.java
+++ b/src/main/java/org/nrg/xnat/restlet/resources/UserListResource.java
@@ -81,6 +81,6 @@ public class UserListResource extends SecureResource {
* @return <b>true</b> if only site administrators can access the list of users, <b>false</b> otherwise.
*/
private boolean restrictUserListAccessToAdmins() {
- return XDAT.getBoolSiteConfigurationProperty("restrictUserListAccessToAdmins", true);
+ return XDAT.getSiteConfigPreferences().getRestrictUserListAccessToAdmins();
}
}
diff --git a/src/main/java/org/nrg/xnat/security/XnatLdapUserDetailsMapper.java b/src/main/java/org/nrg/xnat/security/XnatLdapUserDetailsMapper.java
index c0768d8673f5845ea0c409b91bd50f3480d29354..313b68e1b474210d2f5b769249ac95fa15627a6a 100644
--- a/src/main/java/org/nrg/xnat/security/XnatLdapUserDetailsMapper.java
+++ b/src/main/java/org/nrg/xnat/security/XnatLdapUserDetailsMapper.java
@@ -77,7 +77,7 @@ public class XnatLdapUserDetailsMapper extends LdapUserDetailsMapper {
try {
final UserI xdatUser = Users.getUser(userDetails.getUsername());
- if ((!XDAT.verificationOn() || xdatUser.isVerified()) && userDetails.getAuthorization().isEnabled()) {
+ if ((!XDAT.getSiteConfigPreferences().getEmailVerification() || xdatUser.isVerified()) && userDetails.getAuthorization().isEnabled()) {
return userDetails;
} else {
throw new NewLdapAccountNotAutoEnabledException(
diff --git a/src/main/java/org/nrg/xnat/security/XnatSessionEventPublisher.java b/src/main/java/org/nrg/xnat/security/XnatSessionEventPublisher.java
index 19ccdfc73c6697c8febcfabf450391473484302e..437c17d7a9d91ea4d370f246514e258231d3acbb 100644
--- a/src/main/java/org/nrg/xnat/security/XnatSessionEventPublisher.java
+++ b/src/main/java/org/nrg/xnat/security/XnatSessionEventPublisher.java
@@ -10,6 +10,7 @@
*/
package org.nrg.xnat.security;
+import org.nrg.xdat.XDAT;
import org.nrg.xft.security.UserI;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@@ -52,7 +53,7 @@ public class XnatSessionEventPublisher implements HttpSessionListener, ServletCo
}
session.setAttribute("XNAT_CSRF", UUID.randomUUID().toString());
-
+ session.setMaxInactiveInterval(XDAT.getSiteConfigPreferences().getSessionTimeout()*60);//Preference is in minutes and setMaxInactiveInterval wants seconds.
getContext(session.getServletContext()).publishEvent(e);
}
diff --git a/src/main/java/org/nrg/xnat/security/alias/ClearExpiredAliasTokens.java b/src/main/java/org/nrg/xnat/security/alias/ClearExpiredAliasTokens.java
index cb1ed6fcf20a19d5b239877e4810c370eb14fbe1..5f8d325286ad6b89d3ee3c24277e287557d4f0e4 100644
--- a/src/main/java/org/nrg/xnat/security/alias/ClearExpiredAliasTokens.java
+++ b/src/main/java/org/nrg/xnat/security/alias/ClearExpiredAliasTokens.java
@@ -10,6 +10,7 @@
*/
package org.nrg.xnat.security.alias;
+import org.nrg.xdat.XDAT;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.jdbc.core.JdbcTemplate;
@@ -18,13 +19,12 @@ import java.util.Arrays;
import java.util.List;
public class ClearExpiredAliasTokens implements Runnable {
- public ClearExpiredAliasTokens(final JdbcTemplate template, final String timeout) {
+ public ClearExpiredAliasTokens(final JdbcTemplate template) {
if (_log.isDebugEnabled()) {
- _log.debug("Initializing the alias token sweeper job with an interval of: " + timeout);
+ _log.debug("Initializing the alias token sweeper job");
}
_template = template;
- _timeout = timeout;
}
/**
@@ -35,7 +35,7 @@ public class ClearExpiredAliasTokens implements Runnable {
_log.debug("Executing alias token sweep function");
}
for (final String format : ALIAS_TOKEN_QUERIES) {
- final String query = String.format(format, _timeout);
+ final String query = String.format(format, XDAT.getSiteConfigPreferences().getAliasTokenTimeout());
if (_log.isDebugEnabled()) {
_log.debug("Executing alias token sweep query: " + query);
}
@@ -44,10 +44,9 @@ public class ClearExpiredAliasTokens implements Runnable {
}
private static final Logger _log = LoggerFactory.getLogger(ClearExpiredAliasTokens.class);
- private static final String QUERY_DELETE_TOKEN_IP_ADDRESSES = "DELETE FROM xhbm_alias_token_validipaddresses WHERE alias_token in (SELECT id FROM xhbm_alias_token WHERE created < NOW() - INTERVAL '%s')";
- private static final String QUERY_DELETE_ALIAS_TOKENS = "DELETE FROM xhbm_alias_token WHERE created < NOW() - INTERVAL '%s'";
+ private static final String QUERY_DELETE_TOKEN_IP_ADDRESSES = "DELETE FROM xhbm_alias_token_validipaddresses WHERE alias_token in (SELECT id FROM xhbm_alias_token WHERE created < NOW() - INTERVAL '%s minutes')";
+ private static final String QUERY_DELETE_ALIAS_TOKENS = "DELETE FROM xhbm_alias_token WHERE created < NOW() - INTERVAL '%s minutes'";
private static final List<String> ALIAS_TOKEN_QUERIES = Arrays.asList(QUERY_DELETE_TOKEN_IP_ADDRESSES, QUERY_DELETE_ALIAS_TOKENS);
private final JdbcTemplate _template;
- private final String _timeout;
}
diff --git a/src/main/java/org/nrg/xnat/security/provider/XnatDatabaseAuthenticationProvider.java b/src/main/java/org/nrg/xnat/security/provider/XnatDatabaseAuthenticationProvider.java
index 085bd95ec7b211d353d970e14718a4bc54c5f811..8dac7b2415dfef434d0a4e7f8abfd0775222f286 100644
--- a/src/main/java/org/nrg/xnat/security/provider/XnatDatabaseAuthenticationProvider.java
+++ b/src/main/java/org/nrg/xnat/security/provider/XnatDatabaseAuthenticationProvider.java
@@ -80,7 +80,7 @@ public class XnatDatabaseAuthenticationProvider extends DaoAuthenticationProvide
throw new AuthenticationServiceException("User details class is not of a type I know how to handle: " + userDetails.getClass());
}
final UserI xdatUserDetails = (UserI) userDetails;
- if ((XDAT.verificationOn() && !xdatUserDetails.isVerified() && xdatUserDetails.isEnabled()) || !xdatUserDetails.isAccountNonLocked()) {
+ if ((XDAT.getSiteConfigPreferences().getEmailVerification() && !xdatUserDetails.isVerified() && xdatUserDetails.isEnabled()) || !xdatUserDetails.isAccountNonLocked()) {
throw new CredentialsExpiredException("Attempted login to unverified or locked account: " + xdatUserDetails.getUsername());
}
super.additionalAuthenticationChecks(userDetails, authentication);
diff --git a/src/main/java/org/nrg/xnat/servlet/ArchiveServlet.java b/src/main/java/org/nrg/xnat/servlet/ArchiveServlet.java
new file mode 100755
index 0000000000000000000000000000000000000000..d5ebc477123d0412883739e9ad889728978fe631
--- /dev/null
+++ b/src/main/java/org/nrg/xnat/servlet/ArchiveServlet.java
@@ -0,0 +1,481 @@
+/*
+ * org.nrg.xnat.servlet.ArchiveServlet
+ * XNAT http://www.xnat.org
+ * Copyright (c) 2014, Washington University School of Medicine
+ * All Rights Reserved
+ *
+ * Released under the Simplified BSD.
+ *
+ * Last modified 7/10/13 9:04 PM
+ */
+package org.nrg.xnat.servlet;
+
+import org.apache.commons.lang.RandomStringUtils;
+import org.apache.commons.lang.StringUtils;
+import org.nrg.xdat.XDAT;
+import org.nrg.xdat.base.BaseElement;
+import org.nrg.xdat.bean.CatCatalogBean;
+import org.nrg.xdat.bean.CatEntryBean;
+import org.nrg.xdat.bean.CatEntryMetafieldBean;
+import org.nrg.xdat.om.XnatExperimentdata;
+import org.nrg.xdat.om.XnatImagesessiondata;
+import org.nrg.xdat.om.XnatProjectdata;
+import org.nrg.xdat.om.XnatSubjectdata;
+import org.nrg.xdat.security.helpers.Users;
+import org.nrg.xdat.turbine.utils.TurbineUtils;
+import org.nrg.xft.ItemI;
+import org.nrg.xft.XFTItem;
+import org.nrg.xft.db.DBAction;
+import org.nrg.xft.db.PoolDBUtils;
+import org.nrg.xft.exception.ElementNotFoundException;
+import org.nrg.xft.exception.FieldNotFoundException;
+import org.nrg.xft.exception.XFTInitException;
+import org.nrg.xft.schema.Wrappers.GenericWrapper.GenericWrapperElement;
+import org.nrg.xft.schema.Wrappers.GenericWrapper.GenericWrapperField;
+import org.nrg.xft.schema.design.SchemaElementI;
+import org.nrg.xft.search.ItemSearch;
+import org.nrg.xft.security.UserI;
+import org.nrg.xft.utils.FileUtils;
+import org.nrg.xft.utils.ResourceFile;
+import org.nrg.xft.utils.XftStringUtils;
+import org.nrg.xft.utils.zip.ZipI;
+import org.nrg.xft.utils.zip.ZipUtils;
+import org.nrg.xnat.turbine.utils.ArcSpecManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import javax.servlet.ServletConfig;
+import javax.servlet.ServletException;
+import javax.servlet.ServletOutputStream;
+import javax.servlet.http.HttpServlet;
+import javax.servlet.http.HttpServletRequest;
+import javax.servlet.http.HttpServletResponse;
+import java.io.File;
+import java.io.IOException;
+import java.io.OutputStream;
+import java.io.OutputStreamWriter;
+import java.util.ArrayList;
+import java.util.zip.ZipOutputStream;
+
+@SuppressWarnings("serial")
+public class ArchiveServlet extends HttpServlet {
+ private static final Logger logger = LoggerFactory.getLogger(ArchiveServlet.class);
+
+ /* (non-Javadoc)
+ * @see javax.servlet.http.HttpServlet#doGet(javax.servlet.http.HttpServletRequest, javax.servlet.http.HttpServletResponse)
+ */
+ @Override
+ protected void doGet(HttpServletRequest arg0, HttpServletResponse arg1) throws ServletException, IOException {
+ doGetOrPost(arg0, arg1);
+ }
+
+ /* (non-Javadoc)
+ * @see javax.servlet.http.HttpServlet#doPost(javax.servlet.http.HttpServletRequest, javax.servlet.http.HttpServletResponse)
+ */
+ @Override
+ protected void doPost(HttpServletRequest arg0, HttpServletResponse arg1) throws ServletException, IOException {
+ doGetOrPost(arg0, arg1);
+ }
+
+ @SuppressWarnings("unchecked")
+ protected void getCatalog(UserI user, String path, HttpServletRequest req, HttpServletResponse res) throws ServletException, IOException {
+ String rootElementName = path.substring(0, path.indexOf("/"));
+ path = path.substring(path.indexOf("/") + 1);
+
+ res.setContentType("text/xml");
+
+ if (rootElementName.equals("stored")) {
+ File f = Users.getUserCacheFile(user, "catalogs/" + path);
+ if (f.exists()) {
+ writeFile(f, res);
+ return;
+ } else {
+ return;
+ }
+ }
+
+ int indexOfSlash = path.indexOf("/");
+ final String value;
+ if (indexOfSlash == -1) {
+ value = path;
+ path = "";
+ } else {
+ value = path.substring(0, path.indexOf("/"));
+ path = path.substring(path.indexOf("/") + 1);
+ }
+
+ CatCatalogBean cat = new CatCatalogBean();
+
+ String server = TurbineUtils.GetFullServerPath(req);
+ if (!server.endsWith("/")) {
+ server += "/";
+ }
+
+ ArrayList<String> ids = XftStringUtils.CommaDelimitedStringToArrayList(value, true);
+
+ try {
+ final GenericWrapperElement root = GenericWrapperElement.GetElement(rootElementName);
+ final ItemSearch is = ItemSearch.GetItemSearch(root.getFullXMLName(), user);
+ int index = 0;
+ for (GenericWrapperField f : root.getAllPrimaryKeys()) {
+ is.addCriteria(f.getXMLPathString(root.getFullXMLName()), ids.get(index++));
+ }
+ final ItemI rootO = is.exec(false).getFirst();
+ final XFTItem i = (XFTItem) rootO;
+ ItemI rootOM = BaseElement.GetGeneratedItem(i);
+
+
+ String xmlPath = server + "archive/" + rootElementName + "/" + value;
+ String uri = server + "archive/cache/";
+
+ String rootPath = getRootPath(rootOM);
+ File rootDir = new File(rootPath);
+
+ final ArrayList<XFTItem> al;
+ if (!path.equals("")) {
+ al = (ArrayList<XFTItem>) i.getProperty(path, true);
+ xmlPath += "/" + path.substring(0, path.indexOf("["));
+ } else {
+ al = new ArrayList<>();
+ al.add(i);
+ }
+
+ for (XFTItem child : al) {
+ final String subString;
+ if (!path.equals("")) {
+ subString = xmlPath + "/" + child.getPKValueString() + "/";
+ } else {
+ subString = xmlPath;
+ }
+
+ BaseElement om = (BaseElement) BaseElement.GetGeneratedItem(child);
+ ArrayList<ResourceFile> rfs = om.getFileResources(rootPath);
+ for (ResourceFile rf : rfs) {
+ CatEntryBean entry = new CatEntryBean();
+
+ String relative = rf.getAbsolutePath();
+
+ Object id = cacheFileLink(subString + rf.getXdatPath(), relative, i.getDBName(), user.getLogin());
+
+ entry.setUri(uri + id);
+
+ relative = relative.replace('\\', '/');
+ String cleaned = rootPath.replace('\\', '/');
+
+ if (relative.startsWith(cleaned)) {
+ relative = relative.substring(cleaned.length());
+ } else {
+ if (relative.contains("/" + rootDir.getName() + "/")) {
+ relative = relative.substring(relative.indexOf("/" + rootDir.getName() + "/") + 1);
+ }
+ }
+
+ entry.setCachepath(relative);
+
+ CatEntryMetafieldBean meta = new CatEntryMetafieldBean();
+ meta.setMetafield(relative);
+ meta.setName("RELATIVE_PATH");
+ entry.addMetafields_metafield(meta);
+
+ meta = new CatEntryMetafieldBean();
+ meta.setMetafield(rf.getSize().toString());
+ meta.setName("SIZE");
+ entry.addMetafields_metafield(meta);
+
+
+ cat.addEntries_entry(entry);
+ }
+ }
+
+ ServletOutputStream out = res.getOutputStream();
+
+ OutputStreamWriter sw = new OutputStreamWriter(out);
+ cat.toXML(sw, false);
+ sw.flush();
+ sw.close();
+ } catch (XFTInitException e) {
+ logger.error("An error occurred initializing XFT", e);
+ } catch (ElementNotFoundException e) {
+ logger.error("Did not find the requested element on the item", e);
+ } catch (Exception e) {
+ logger.error("An unknown exception occurred", e);
+ }
+ }
+
+ public static boolean ARCHIVE_PATH_CHECKED = false;
+
+ public static Boolean CreatedArchivePathCache(String dbName, String login) throws Exception {
+ if (!ARCHIVE_PATH_CHECKED) {
+ String query = "SELECT relname FROM pg_catalog.pg_class WHERE relname=LOWER('xs_archive_path_cache');";
+ String exists = (String) PoolDBUtils.ReturnStatisticQuery(query, "relname", dbName, login);
+
+ if (exists != null) {
+ ARCHIVE_PATH_CHECKED = true;
+ } else {
+ query = "CREATE TABLE xs_archive_path_cache" +
+ "\n(" +
+ "\n id serial," +
+ "\n create_date timestamp DEFAULT now()," +
+ "\n username VARCHAR(255)," +
+ "\n url text," +
+ "\n _token VARCHAR(255)," +
+ "\n absolute_path text" +
+ "\n) " +
+ "\nWITH OIDS;";
+
+ PoolDBUtils.ExecuteNonSelectQuery(query, dbName, login);
+
+ ARCHIVE_PATH_CHECKED = true;
+ }
+ }
+ return true;
+ }
+
+ public static Object cacheFileLink(String url, String absolutePath, String dbName, String login) throws Exception {
+ CreatedArchivePathCache(dbName, login);
+ Object o = RandomStringUtils.randomAlphanumeric(64);
+ Object exists = PoolDBUtils.ReturnStatisticQuery("SELECT id FROM xs_archive_path_cache WHERE _token='" + o + "';", "id", dbName, login);
+ while (exists != null) {
+ o = RandomStringUtils.randomAlphanumeric(64);
+ exists = PoolDBUtils.ReturnStatisticQuery("SELECT id FROM xs_archive_path_cache WHERE _token='" + o + "';", "id", dbName, login);
+ }
+ String query = "INSERT INTO xs_archive_path_cache (username,url,_token,absolute_path) VALUES ('" + login + "'," + DBAction.ValueParser(url, "string", true) + ",'" + o + "'," + DBAction.ValueParser(absolutePath, "string", true) + ");";
+ PoolDBUtils.ExecuteNonSelectQuery(query, dbName, login);
+ return o;
+ }
+
+ public Object retrieveCacheFileLink(String o, String dbName, String login) throws Exception {
+ o = StringUtils.remove(o, '\'');
+ return PoolDBUtils.ReturnStatisticQuery("SELECT absolute_path FROM xs_archive_path_cache WHERE _token='" + o + "';", "absolute_path", dbName, login);
+ }
+
+ protected String getRootPath(ItemI i) {
+ if (i instanceof XnatProjectdata) {
+ return ((XnatProjectdata) i).getRootArchivePath();
+ } else if (i instanceof XnatSubjectdata) {
+ return ((XnatSubjectdata) i).getPrimaryProject(false).getRootArchivePath();
+ } else if (i instanceof XnatExperimentdata) {
+ return ((XnatExperimentdata) i).getPrimaryProject(false).getRootArchivePath();
+ }
+ return null;
+ }
+
+ protected void writeFile(File _return, HttpServletResponse res) throws IOException {
+ writeFile(_return, res, _return.getName());
+ }
+
+ protected void writeFile(File _return, HttpServletResponse res, String name) throws IOException {
+ TurbineUtils.setContentDisposition(res, name, false);
+
+ OutputStream os = res.getOutputStream();
+ java.io.FileInputStream in = new java.io.FileInputStream(_return);
+ byte[] buf = new byte[FileUtils.LARGE_DOWNLOAD];
+ int len;
+ while ((len = in.read(buf)) > 0) {
+ os.write(buf, 0, len);
+ os.flush();
+ }
+ os.flush();
+ in.close();
+ }
+
+ protected void getDataFile(UserI user, String path, HttpServletResponse response) throws ServletException, IOException {
+ String rootElementName = path.substring(0, path.indexOf("/"));
+ path = path.substring(path.indexOf("/") + 1);
+ String value = path.substring(0, path.indexOf("/"));
+ path = path.substring(path.indexOf("/") + 1);
+
+ final ArrayList<String> ids = XftStringUtils.CommaDelimitedStringToArrayList(value, true);
+
+ XFTItem session = null;
+ XFTItem project = null;
+ try {
+ final GenericWrapperElement root = GenericWrapperElement.GetElement(rootElementName);
+ SchemaElementI localE = root;
+ ItemSearch is = ItemSearch.GetItemSearch(root.getFullXMLName(), user);
+ int index = 0;
+ for (GenericWrapperField f : root.getAllPrimaryKeys()) {
+ is.addCriteria(f.getXMLPathString(root.getFullXMLName()), ids.get(index++));
+ }
+
+ final ItemI rootO = is.exec(false).getFirst();
+ XFTItem i = (XFTItem) rootO;
+
+ if (i.instanceOf("xnat:projectData")) {
+ project = i;
+ } else if (i.instanceOf("xnat:imageSessionData")) {
+ session = i;
+ }
+
+ String nextPath = null;
+ GenericWrapperField lastField = null;
+ while (path.contains("/")) {
+ final String next = path.substring(0, path.indexOf("/"));
+
+ try {
+ if (lastField == null) {
+ lastField = localE.getGenericXFTElement().getDirectField(next);
+ } else {
+ lastField = lastField.getDirectField(next);
+ }
+
+ if (nextPath == null) {
+ nextPath = next;
+ } else {
+ nextPath += "/" + next;
+ }
+
+ path = path.substring(path.indexOf("/") + 1);
+
+ if (lastField.isReference()) {
+ localE = lastField.getReferenceElement();
+ value = path.substring(0, path.indexOf("/"));
+ path = path.substring(path.indexOf("/") + 1);
+
+ ids.clear();
+ ids.addAll(XftStringUtils.CommaDelimitedStringToArrayList(value, true));
+
+ is = ItemSearch.GetItemSearch(localE.getFullXMLName(), user);
+ index = 0;
+ for (GenericWrapperField f : localE.getGenericXFTElement().getAllPrimaryKeys()) {
+ is.addCriteria(f.getXMLPathString(localE.getFullXMLName()), ids.get(index++));
+ }
+ i = (XFTItem) is.exec(false).getFirst();
+
+ lastField = null;
+ nextPath = null;
+
+ if (i.instanceOf("xnat:projectData")) {
+ project = i;
+ } else if (i.instanceOf("xnat:imageSessionData")) {
+ session = i;
+ }
+ }
+ } catch (FieldNotFoundException e) {
+ break;
+ }
+ }
+
+ System.out.println("ENDING:" + path);
+
+
+ //identify project
+ if (project == null) {
+ if (session != null) {
+ XnatImagesessiondata img = (XnatImagesessiondata) BaseElement.GetGeneratedItem(session);
+ project = img.getPrimaryProject(false).getItem();
+ } else {
+ ArrayList<XFTItem> parents = i.getParents("xnat:projectData");
+ project = parents.get(0);
+ }
+ }
+
+ XnatProjectdata p = (XnatProjectdata) BaseElement.GetGeneratedItem(project);
+ String rootPath = p.getRootArchivePath();
+
+ BaseElement om = (BaseElement) BaseElement.GetGeneratedItem(i);
+
+ ArrayList<ResourceFile> resources = om.getFileResources(rootPath);
+
+ if (path.equals("*")) {
+ response.setContentType("application/zip");
+ TurbineUtils.setContentDisposition(response, value + ".zip", false);
+ OutputStream outStream = response.getOutputStream();
+ final ZipI zip = new ZipUtils();
+ zip.setOutputStream(outStream, ZipOutputStream.DEFLATED);
+
+ for (ResourceFile rf : resources) {
+ File f = rf.getF();
+ String relative = f.getAbsolutePath();
+ if (session != null) {
+ if (relative.contains(File.separator + session.getProperty("ID"))) {
+ relative = relative.substring(relative.indexOf(File.separator + session.getProperty("ID")) + 1);
+ } else if (project != null) {
+ if (relative.contains(File.separator + project.getProperty("ID"))) {
+ relative = relative.substring(relative.indexOf(File.separator + project.getProperty("ID")) + 1);
+ }
+ }
+ } else if (project != null) {
+ if (relative.contains(File.separator + project.getProperty("ID"))) {
+ relative = relative.substring(relative.indexOf(File.separator + project.getProperty("ID")) + 1);
+ }
+ }
+ zip.write(relative, f);
+ }
+
+ // Complete the ZIP file
+ zip.close();
+ } else {
+ File _return = null;
+ for (ResourceFile rf : resources) {
+ if (rf.getF().getName().equals(path)) {
+ _return = rf.getF();
+ break;
+ }
+ }
+
+ if (_return == null) {
+ int count = Integer.parseInt(path);
+ _return = resources.get(count).getF();
+ }
+
+ if (_return != null) {
+ writeFile(_return, response);
+ }
+ }
+ } catch (XFTInitException e) {
+ logger.error("An error occurred initializing XFT", e);
+ } catch (ElementNotFoundException e) {
+ logger.error("Did not find the requested element on the item", e);
+ } catch (Exception e) {
+ logger.error("An unknown exception occurred", e);
+ }
+ }
+
+ protected void doGetOrPost(HttpServletRequest req, HttpServletResponse res) throws ServletException, IOException {
+ System.out.println("PathInfo: " + req.getPathInfo());
+ String path = req.getPathInfo();
+ if (path.startsWith("/")) {
+ path = path.substring(1);
+ }
+
+ UserI user = XDAT.getUserDetails();
+ if (user == null) {
+ user = (UserI) req.getSession().getAttribute("user");
+ }
+
+ if (path.startsWith("catalogs/")) {
+ if (user != null)
+ getCatalog(user, path.substring(9), req, res);
+ } else if (path.startsWith("cache/")) {
+ String o = path.substring(6);
+ try {
+ String dbName = GenericWrapperElement.GetElement("xdat:user").getDbName();
+ String login = null;
+ if (user != null) {
+ login = user.getLogin();
+ }
+ String filePath = (String) retrieveCacheFileLink(o, dbName, login);
+ if (filePath != null) {
+ File f = new File(filePath);
+ if (f.exists()) {
+ writeFile(f, res);
+ }
+ }
+ } catch (Exception e) {
+ logger.error("", e);
+ }
+ } else if (user != null) {
+ getDataFile(user, path, res);
+ }
+ }
+
+ /* (non-Javadoc)
+ * @see javax.servlet.GenericServlet#init(javax.servlet.ServletConfig)
+ */
+ @Override
+ public void init(ServletConfig arg0) throws ServletException {
+ super.init(arg0);
+ ArcSpecManager.GetInstance();
+ }
+}
diff --git a/src/main/java/org/nrg/xnat/servlet/RESTServlet.java b/src/main/java/org/nrg/xnat/servlet/RESTServlet.java
deleted file mode 100644
index 471495e8c7f289cf77454f0f889803d9919c4539..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xnat/servlet/RESTServlet.java
+++ /dev/null
@@ -1,50 +0,0 @@
-/*
- * org.nrg.xnat.servlet.RESTServlet
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xnat.servlet;
-
-import java.io.IOException;
-
-import javax.servlet.ServletException;
-import javax.servlet.http.HttpServlet;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
-
-import org.apache.log4j.Logger;
-
-public class RESTServlet extends HttpServlet {
- static org.apache.log4j.Logger logger = Logger.getLogger(RESTServlet.class);
-
- @Override
- protected void doGet(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException {
-
- response.sendError(400);
- }
-
- @Override
- protected void doPost(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException {
-
- response.sendError(400);
- }
-
-
-
- @Override
- protected void doPut(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException {
-
- response.sendError(400);
- }
-
- @Override
- protected void doDelete(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException {
-
- response.sendError(400);
- }
-}
diff --git a/src/main/java/org/nrg/xnat/turbine/modules/actions/PlexiViewerSpec.java b/src/main/java/org/nrg/xnat/turbine/modules/actions/PlexiViewerSpec.java
deleted file mode 100644
index a03e05426b4280fa4853b74536654df1577ebc20..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xnat/turbine/modules/actions/PlexiViewerSpec.java
+++ /dev/null
@@ -1,32 +0,0 @@
-/*
- * org.nrg.xnat.turbine.modules.actions.PlexiViewerSpec
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-
-package org.nrg.xnat.turbine.modules.actions;
-
-import org.apache.log4j.Logger;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.plexiViewer.manager.PlexiSpecDocReader;
-import org.nrg.xdat.turbine.modules.actions.SecureAction;
-
-public class PlexiViewerSpec extends SecureAction {
-
- static Logger logger = Logger.getLogger(PlexiViewerSpec.class);
-
- public void doPerform(RunData data, Context context){
- boolean rtn = PlexiSpecDocReader.GetInstance().refresh();
- String msg = "PlexiViewerSpec file was refreshed with " + (rtn?"success":"failure");
- logger.info(msg);
- data.setMessage(msg);
- //data.getParameters().add("popup", "true");
- //data.setScreenTemplate("ClosePage.vm");
- }
-}
diff --git a/src/main/java/org/nrg/xnat/turbine/modules/actions/ShowViewerAction.java b/src/main/java/org/nrg/xnat/turbine/modules/actions/ShowViewerAction.java
deleted file mode 100644
index 0590066e63b5341f32e97f42c3b479dd84006d87..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xnat/turbine/modules/actions/ShowViewerAction.java
+++ /dev/null
@@ -1,120 +0,0 @@
-/*
- * org.nrg.xnat.turbine.modules.actions.ShowViewerAction
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xnat.turbine.modules.actions;
-
-import org.apache.log4j.Logger;
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.turbine.modules.actions.DisplaySearchAction;
-import org.nrg.xdat.turbine.modules.actions.SecureAction;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.exception.ElementNotFoundException;
-import org.nrg.xft.exception.FieldNotFoundException;
-import org.nrg.xft.exception.XFTInitException;
-import org.nrg.xft.search.TableSearch;
-
-public class ShowViewerAction extends SecureAction {
- static org.apache.log4j.Logger logger = Logger.getLogger(ShowViewerAction.class);
-
- /* (non-Javadoc)
- * @see org.apache.turbine.modules.actions.VelocityAction#doPerform(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void doPerform(RunData data, Context context) throws Exception {
- if (data.getParameters().containsKey("searchValue"))
- {
- String s = ((String)org.nrg.xdat.turbine.utils.TurbineUtils.GetPassedParameter("searchValue",data));
- if (s==null || s.equalsIgnoreCase(""))
- {
- data.setMessage("Please specify a search value.");
- data.setScreenTemplate("Index.vm");
- }else{
- s = s.toLowerCase();
- if(s.indexOf("'")>-1){
- data.setMessage("Invalid character '");
- data.setScreenTemplate("Index.vm");
- return;
- }
- if(s.indexOf("\\")>-1){
- data.setMessage("Invalid character \\");
- data.setScreenTemplate("Index.vm");
- return;
- }
- try {
- org.nrg.xft.XFTTable table =TableSearch.Execute("SELECT ID from xnat_subjectdata WHERE LOWER(ID) LIKE '%" + s + "%';",TurbineUtils.getUser(data).getDBName(),TurbineUtils.getUser(data).getLogin());
-
- if (table.size()>0)
- {
- if (table.size()==1)
- {
- String v = table.getFirstObject().toString();
- data.getParameters().setString("skipq","true");
- data.getParameters().setString("id",v);
- }else{
- DisplaySearchAction dsa = new DisplaySearchAction();
- data.getParameters().setString("ELEMENT_0","xnat:subjectData");
- data.getParameters().setString("xnat:subjectData.COMBO0_FIELDS","xnat:subjectData.SUBJECTID_equals,xnat:subjectData/label_equals,xnat:subjectData/sharing/share/label_equals");
- data.getParameters().setString("xnat:subjectData.COMBO0",s);
- dsa.doPerform(data,context);
- return;
- }
- }else{
- table =TableSearch.Execute("SELECT ID FROM xnat_mrSessionData WHERE LOWER(ID) LIKE '%" + s + "%';",TurbineUtils.getUser(data).getDBName(),TurbineUtils.getUser(data).getLogin());
-
- if (table.size()>0)
- {
- if (table.size()==1)
- {
- Object v = table.getFirstObject();
- data.getParameters().setString("search_value",v.toString());
- data.getParameters().setString("search_element","xnat:mrSessionData");
- data.getParameters().setString("search_field","xnat:mrSessionData.ID");
- }else{
- DisplaySearchAction dsa = new DisplaySearchAction();
- data.getParameters().setString("ELEMENT_0","xnat:mrSessionData");
- data.getParameters().setString("xnat:mrSessionData.SESSION_ID_equals",s);
- dsa.doPerform(data,context);
- return;
- }
- }else{
- data.setMessage("No matching items found.");
- }
- }
- } catch (ElementNotFoundException e1) {
- logger.error("",e1);
- data.setMessage(e1.getMessage());
- } catch (XFTInitException e1) {
- logger.error("",e1);
- data.setMessage(e1.getMessage());
- } catch (FieldNotFoundException e1) {
- logger.error("",e1);
- data.setMessage(e1.getMessage());
- } catch (Exception e1) {
- logger.error("",e1);
- data.setMessage(e1.getMessage());
- }
- }
- }
-
- if (data.getParameters().containsKey("skipq")) {
- context.put("skipq", "true");
- context.put("id",((String)org.nrg.xdat.turbine.utils.TurbineUtils.GetPassedParameter("id",data)));
- data.getParameters().remove("skipq");
- }else {
- String sessionId = ((String)org.nrg.xdat.turbine.utils.TurbineUtils.GetPassedParameter("session",data));
- context.put("sessionId",sessionId);
- if (((String)org.nrg.xdat.turbine.utils.TurbineUtils.GetPassedParameter("startDisplayWith",data))!=null && !((String)org.nrg.xdat.turbine.utils.TurbineUtils.GetPassedParameter("startDisplayWith",data)).equalsIgnoreCase(""))
- context.put("startDisplayWith",((String)org.nrg.xdat.turbine.utils.TurbineUtils.GetPassedParameter("startDisplayWith",data)));
- }
-
- data.setScreenTemplate("Viewer.vm");
- }
-
-}
diff --git a/src/main/java/org/nrg/xnat/turbine/modules/actions/XDATRegisterUser.java b/src/main/java/org/nrg/xnat/turbine/modules/actions/XDATRegisterUser.java
index b61c959281a8ef13a7567c88ec9bf8d04ab9862a..8db9f45c42be833aad9bf5f140c0bc07d34202ec 100644
--- a/src/main/java/org/nrg/xnat/turbine/modules/actions/XDATRegisterUser.java
+++ b/src/main/java/org/nrg/xnat/turbine/modules/actions/XDATRegisterUser.java
@@ -10,12 +10,6 @@
*/
package org.nrg.xnat.turbine.modules.actions;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Map;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
import org.apache.commons.lang3.StringUtils;
import org.apache.log4j.Logger;
import org.apache.turbine.Turbine;
@@ -25,12 +19,17 @@ import org.apache.turbine.util.RunData;
import org.apache.velocity.context.Context;
import org.nrg.xdat.XDAT;
import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.XFT;
import org.nrg.xft.security.UserI;
import org.nrg.xnat.turbine.utils.ProjectAccessRequest;
import org.springframework.security.web.savedrequest.HttpSessionRequestCache;
import org.springframework.security.web.savedrequest.SavedRequest;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
public class XDATRegisterUser extends org.nrg.xdat.turbine.modules.actions.XDATRegisterUser {
@Override
@@ -94,13 +93,13 @@ public class XDATRegisterUser extends org.nrg.xdat.turbine.modules.actions.XDATR
context.put("user", user);
action.doPerform(data, context);
} else if (!StringUtils.isEmpty(nextAction) && !nextAction.contains("XDATLoginUser") && !nextAction.equals(Turbine.getConfiguration().getString("action.login"))) {
- if (XDAT.getSiteConfigPreferences().getUserRegistration() & !XDAT.verificationOn()) {
+ if (XDAT.getSiteConfigPreferences().getUserRegistration() & !XDAT.getSiteConfigPreferences().getEmailVerification()) {
data.setAction(nextAction);
VelocityAction action = (VelocityAction) ActionLoader.getInstance().getInstance(nextAction);
action.doPerform(data, context);
}
} else if (!StringUtils.isEmpty(nextPage) && !nextPage.equals(Turbine.getConfiguration().getString("template.home"))) {
- if (XDAT.getSiteConfigPreferences().getUserRegistration() && !XDAT.verificationOn()) {
+ if (XDAT.getSiteConfigPreferences().getUserRegistration() && !XDAT.getSiteConfigPreferences().getEmailVerification()) {
data.setScreenTemplate(nextPage);
}
}
diff --git a/src/main/java/org/nrg/xnat/turbine/modules/screens/CompressedUploaderPage.java b/src/main/java/org/nrg/xnat/turbine/modules/screens/CompressedUploaderPage.java
new file mode 100644
index 0000000000000000000000000000000000000000..ab7ac9fe7b35182002a8ec09afdaf74c0c2fdc44
--- /dev/null
+++ b/src/main/java/org/nrg/xnat/turbine/modules/screens/CompressedUploaderPage.java
@@ -0,0 +1,32 @@
+/*
+ * org.nrg.xnat.turbine.modules.screens.ReportIssue
+ * XNAT http://www.xnat.org
+ * Copyright (c) 2014, Washington University School of Medicine
+ * All Rights Reserved
+ *
+ * Released under the Simplified BSD.
+ *
+ * Last modified 7/10/13 9:04 PM
+ */
+package org.nrg.xnat.turbine.modules.screens;
+
+import org.apache.turbine.util.RunData;
+import org.apache.velocity.context.Context;
+import org.nrg.xdat.om.ArcArchivespecification;
+import org.nrg.xdat.turbine.modules.screens.SecureScreen;
+import org.nrg.xnat.turbine.utils.ArcSpecManager;
+
+import java.text.SimpleDateFormat;
+import java.util.Calendar;
+
+public class CompressedUploaderPage extends SecureScreen {
+
+ @Override
+ protected void doBuildTemplate(RunData data, Context context) throws Exception {
+ final SimpleDateFormat formatter = new SimpleDateFormat("yyyyMMdd_hhmmss");
+ context.put("uploadID", formatter.format(Calendar.getInstance().getTime()));
+ final ArcArchivespecification arc = ArcSpecManager.GetInstance();
+ context.put("arc", arc);
+ }
+
+}
diff --git a/src/main/java/org/nrg/xnat/turbine/modules/screens/DICOMSCPPage.java b/src/main/java/org/nrg/xnat/turbine/modules/screens/DICOMSCPPage.java
new file mode 100644
index 0000000000000000000000000000000000000000..29b4036e7d6c58b9e60f6a53d883a9e9567b3604
--- /dev/null
+++ b/src/main/java/org/nrg/xnat/turbine/modules/screens/DICOMSCPPage.java
@@ -0,0 +1,32 @@
+/*
+ * org.nrg.xnat.turbine.modules.screens.ReportIssue
+ * XNAT http://www.xnat.org
+ * Copyright (c) 2014, Washington University School of Medicine
+ * All Rights Reserved
+ *
+ * Released under the Simplified BSD.
+ *
+ * Last modified 7/10/13 9:04 PM
+ */
+package org.nrg.xnat.turbine.modules.screens;
+
+import org.apache.turbine.util.RunData;
+import org.apache.velocity.context.Context;
+import org.nrg.xdat.om.ArcArchivespecification;
+import org.nrg.xdat.turbine.modules.screens.SecureScreen;
+import org.nrg.xnat.turbine.utils.ArcSpecManager;
+
+import java.text.SimpleDateFormat;
+import java.util.Calendar;
+
+public class DICOMSCPPage extends SecureScreen {
+
+ @Override
+ protected void doBuildTemplate(RunData data, Context context) throws Exception {
+ final SimpleDateFormat formatter = new SimpleDateFormat("yyyyMMdd_hhmmss");
+ context.put("uploadID", formatter.format(Calendar.getInstance().getTime()));
+ final ArcArchivespecification arc = ArcSpecManager.GetInstance();
+ context.put("arc", arc);
+ }
+
+}
diff --git a/src/main/java/org/nrg/xnat/turbine/modules/screens/UploadApplet.java b/src/main/java/org/nrg/xnat/turbine/modules/screens/UploadApplet.java
index c78e6e1952416dd77fbc30f17c6b9cecb113a17f..82d683f54f0b42c9775a77a0cca05792421fe9b3 100644
--- a/src/main/java/org/nrg/xnat/turbine/modules/screens/UploadApplet.java
+++ b/src/main/java/org/nrg/xnat/turbine/modules/screens/UploadApplet.java
@@ -12,8 +12,8 @@ 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.turbine.utils.TurbineUtils;
-import org.nrg.xnat.turbine.utils.ArcSpecManager;
import org.nrg.xnat.utils.AppletConfig;
import org.nrg.xnat.utils.XnatHttpUtils;
import org.slf4j.Logger;
@@ -57,9 +57,8 @@ public class UploadApplet extends UploadAppletScreen {
} else if (TurbineUtils.HasPassedParameter("no_session_date", data)) {
context.put("session_date", "no_session_date");
}
- context.put("arc", ArcSpecManager.GetInstance());
-
- org.nrg.config.entities.Configuration config = getAppletConfiguration(TurbineUtils.getUser(data), (String)context.get("project"));
+
+ org.nrg.config.entities.Configuration config = getAppletConfiguration(XDAT.getUserDetails(), (String)context.get("project"));
if(config != null) {
String json = config.getContents();
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 743912a9ac7d87995869917082b8510a853597ef..36bb43c1ceb8af03d2103116fba4f02d7f5a444d 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
@@ -50,7 +50,7 @@ public abstract class UploadAppletScreen extends SecureScreen {
scope = Scope.Site;
}
- boolean enableProjectAppletScript = XDAT.getBoolSiteConfigurationProperty("enableProjectAppletScript", false);
+ boolean enableProjectAppletScript = XDAT.getSiteConfigPreferences().getEnableProjectAppletScript();
org.nrg.config.entities.Configuration config = enableProjectAppletScript ? configService.getConfig(AppletConfig.toolName, AppletConfig.path, scope, projectId) : null;
if (config == null || org.nrg.config.entities.Configuration.DISABLED_STRING.equalsIgnoreCase(config.getStatus())) {
diff --git a/src/main/java/org/nrg/xnat/turbine/modules/screens/ViewerHelp.java b/src/main/java/org/nrg/xnat/turbine/modules/screens/UploadAssistantPage.java
similarity index 58%
rename from src/main/java/org/nrg/xnat/turbine/modules/screens/ViewerHelp.java
rename to src/main/java/org/nrg/xnat/turbine/modules/screens/UploadAssistantPage.java
index 2fea87aea58e3edc8850d7cf89dc4114ca31e8d8..25dbf7a15d597d56b128687319959fe50ebdc382 100644
--- a/src/main/java/org/nrg/xnat/turbine/modules/screens/ViewerHelp.java
+++ b/src/main/java/org/nrg/xnat/turbine/modules/screens/UploadAssistantPage.java
@@ -1,5 +1,5 @@
/*
- * org.nrg.xnat.turbine.modules.screens.ViewerHelp
+ * org.nrg.xnat.turbine.modules.screens.ReportIssue
* XNAT http://www.xnat.org
* Copyright (c) 2014, Washington University School of Medicine
* All Rights Reserved
@@ -14,13 +14,11 @@ import org.apache.turbine.util.RunData;
import org.apache.velocity.context.Context;
import org.nrg.xdat.turbine.modules.screens.SecureScreen;
-/**
- * @author Tim
- *
- */
-public class ViewerHelp extends SecureScreen {
+public class UploadAssistantPage extends SecureScreen {
- public void doBuildTemplate(RunData data, Context context)
- {
+ @Override
+ protected void doBuildTemplate(RunData data, Context context) throws Exception {
+ // doesn't currently need any context, just needed to subclass SecureScreen
}
+
}
diff --git a/src/main/java/org/nrg/xnat/turbine/modules/screens/UploadOptions.java b/src/main/java/org/nrg/xnat/turbine/modules/screens/UploadOptions.java
new file mode 100644
index 0000000000000000000000000000000000000000..bf9f2a75c84c15fdc13bb53422f3f246c0501bea
--- /dev/null
+++ b/src/main/java/org/nrg/xnat/turbine/modules/screens/UploadOptions.java
@@ -0,0 +1,41 @@
+/*
+ * org.nrg.xnat.turbine.modules.screens.ReportIssue
+ * XNAT http://www.xnat.org
+ * Copyright (c) 2014, Washington University School of Medicine
+ * All Rights Reserved
+ *
+ * Released under the Simplified BSD.
+ *
+ * Last modified 7/10/13 9:04 PM
+ */
+package org.nrg.xnat.turbine.modules.screens;
+
+import org.apache.turbine.util.RunData;
+import org.apache.velocity.context.Context;
+import org.nrg.xdat.om.ArcArchivespecification;
+import org.nrg.xdat.turbine.modules.screens.SecureScreen;
+import org.nrg.xnat.turbine.utils.ArcSpecManager;
+import org.nrg.xnat.utils.AppletConfig;
+import org.nrg.xnat.utils.XnatHttpUtils;
+import org.apache.commons.lang3.StringUtils;
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+import org.nrg.framework.utilities.Reflection;
+import org.nrg.xdat.om.XnatPvisitdata;
+import org.nrg.xdat.turbine.utils.TurbineUtils;
+
+import java.text.SimpleDateFormat;
+import java.util.Calendar;
+import java.util.List;
+
+public class UploadOptions extends SecureScreen {
+
+ @Override
+ protected void doBuildTemplate(RunData data, Context context) throws Exception {
+ final SimpleDateFormat formatter = new SimpleDateFormat("yyyyMMdd_hhmmss");
+ context.put("uploadID", formatter.format(Calendar.getInstance().getTime()));
+ final ArcArchivespecification arc = ArcSpecManager.GetInstance();
+ context.put("arc", arc);
+ }
+
+}
diff --git a/src/main/java/org/nrg/xnat/turbine/modules/screens/Viewer.java b/src/main/java/org/nrg/xnat/turbine/modules/screens/Viewer.java
deleted file mode 100644
index aec0f71c45039fa6990734d1fcda0cf7f1608caf..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xnat/turbine/modules/screens/Viewer.java
+++ /dev/null
@@ -1,86 +0,0 @@
-/*
- * org.nrg.xnat.turbine.modules.screens.Viewer
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xnat.turbine.modules.screens;
-
-import org.apache.turbine.util.RunData;
-import org.apache.velocity.context.Context;
-import org.nrg.xdat.om.XnatMrassessordata;
-import org.nrg.xdat.om.XnatMrsessiondata;
-import org.nrg.xdat.om.XnatSubjectdata;
-import org.nrg.xdat.turbine.modules.screens.SecureReport;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xnat.turbine.utils.XNATUtils;
-import org.nrg.xnat.utils.XnatHttpUtils;
-
-/**
- * @author Tim
- *
- */
-public class Viewer extends SecureReport {
-
- /* (non-Javadoc)
- * @see org.apache.turbine.modules.screens.VelocityScreen#doBuildTemplate(org.apache.turbine.util.RunData, org.apache.velocity.context.Context)
- */
- public void finalProcessing(RunData data, Context context)
- {
- if (om instanceof XnatMrsessiondata)
- {
-
- }else if (om instanceof XnatSubjectdata)
- {
- om = ((XnatSubjectdata)om).getLastSession();
- item = om.getItem();
-
- context.put("om",om);
- context.put("item",item);
- }else if (om instanceof XnatMrassessordata)
- {
- om = ((XnatMrassessordata)om).getMrSessionData();
- item = om.getItem();
-
- context.put("om",om);
- context.put("item",item);
- }
- context.put("appletPath",TurbineUtils.GetRelativeServerPath(data) + "/applet");
- context.put("jsessionid", XnatHttpUtils.getJSESSIONID(data));
- }
-
- public void noItemError(RunData data, Context context)
- {
- if (context.containsKey("skipq"))
- {
- try {
- XnatMrsessiondata mr = XNATUtils.getLastSessionForParticipant((String)context.get("id"),TurbineUtils.getUser(data));
-
- if (mr ==null)
- {
- try {
- this.doRedirect(data,"ClosePage.vm");
- } catch (Exception e) {
- }
- }else{
- context.put("item",mr.getItem());
- context.put("om",mr);
- context.put("appletPath",TurbineUtils.GetRelativeServerPath(data) + "/applet");
- context.put("jsessionid", XnatHttpUtils.getJSESSIONID(data));
- }
- } catch (Exception e){
- e.printStackTrace();
- }
- }else{
- data.setMessage("No results were found for your search.");
- try {
- this.doRedirect(data,"ClosePage.vm");
- } catch (Exception e) {
- }
- }
- }
-}
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 bbe5853cbcf632eb7aba1d6c8ccc8ffeb74eaf8e..758bf687598bcbf2a9b0c0fc726a5f0d2a96d20a 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
@@ -17,7 +17,6 @@ import org.apache.turbine.services.velocity.TurbineVelocity;
import org.apache.turbine.util.RunData;
import org.apache.velocity.context.Context;
import org.apache.velocity.tools.generic.EscapeTool;
-import org.nrg.config.exceptions.ConfigServiceException;
import org.nrg.xdat.XDAT;
import org.nrg.xdat.display.DisplayManager;
import org.nrg.xdat.security.helpers.Users;
@@ -26,7 +25,6 @@ import org.nrg.xdat.turbine.modules.screens.SecureScreen;
import org.nrg.xdat.turbine.utils.AccessLogger;
import org.nrg.xdat.turbine.utils.AdminUtils;
import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.XFT;
import org.nrg.xft.security.UserI;
import java.sql.SQLException;
@@ -54,10 +52,9 @@ public class XDATScreen_UpdateUser extends SecureScreen {
c.put("showReason", XDAT.getSiteConfigPreferences().getShowChangeJustification());
c.put("requireReason", XDAT.getSiteConfigPreferences().getRequireChangeJustification());
- try{
- c.put("siteConfig", XDAT.getSiteConfiguration());
- }catch(ConfigServiceException ignored){
- }
+
+ c.put("siteConfig", XDAT.getSiteConfigPreferences());
+
doBuildTemplate(data, c);
}
@@ -132,7 +129,7 @@ public class XDATScreen_UpdateUser extends SecureScreen {
if(!user.isEnabled()) {
throw new Exception("User is not enabled: " + user.getUsername());
}
- if (XDAT.verificationOn() && !user.isVerified()) {
+ if (XDAT.getSiteConfigPreferences().getEmailVerification() && !user.isVerified()) {
throw new Exception("User is not verified: " + user.getUsername());
}
}
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
deleted file mode 100644
index 1308f443baa5d056be40e61f5c5ddbe725541e8e..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xnat/turbine/modules/screens/XDATScreen_themes.java
+++ /dev/null
@@ -1,24 +0,0 @@
-/*
- * 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;
-
-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/resources/META-INF/xnat/spawner/site-admin-elements.yaml b/src/main/resources/META-INF/xnat/spawner/site-admin-elements.yaml
index 90ec9f5c385fe242258ffc6032ecf608ba2aa91c..96bedc629c821fcf574d230bc02972c1ddd2240a 100644
--- a/src/main/resources/META-INF/xnat/spawner/site-admin-elements.yaml
+++ b/src/main/resources/META-INF/xnat/spawner/site-admin-elements.yaml
@@ -18,22 +18,15 @@ siteId:
description: "The id used to refer to this site (also used to generate database ids). The Site ID must start with a letter and contain only letters, numbers and underscores. It should be a short, one-word name or acronym which describes your site. No spaces or non-alphanumeric characters."
siteDescriptionType:
- kind: panel.display # make this a radio button group
+ kind: panel.display
id: siteDescriptionType
name: siteDescriptionType
label: Site Description
value: Select a site description option below
- # onchange: # some javascript that toggles display of the elements below appropriately
-
-siteDescriptionOptionText:
- kind: panel.input.checkbox # make this a radio button group
- id: siteDescriptionOptionText
- label: "Text (Markdown)"
-
-siteDescriptionOptionPage:
- kind: panel.input.checkbox # make this a radio button group
- id: siteDescriptionOptionPage
- label: "Page"
+ before:
+ - "<script type=\"text/javascript\" src=\"../../scripts/xnat/admin/siteInfo.js\"></script>"
+ after:
+ - "<span style=\"position: relative; top: -15px;left: 270px;\"><input type=\"radio\" name=\"siteDescriptionType\" id=\"siteDescriptionTypePage\" value=\"Page\"> Page <input type=\"radio\" name=\"siteDescriptionType\" id=\"siteDescriptionTypeText\" value=\"Text\"> Text (Markdown)</span>"
siteDescriptionPage:
kind: panel.input.text
@@ -90,7 +83,6 @@ adminEmail:
id: adminEmail
name: adminEmail
label: Site Administrator Email Address
- value: ?? XNAT.data.siteConfig.adminEmail
fileSystemSettingsWarning:
someInfo:
@@ -101,7 +93,6 @@ fileSystemSettingsWarning:
and are seldom, if ever, changed.
style:
fontWeight: bold
-
archivePath:
kind: panel.input.text
id: archivePath
@@ -109,8 +100,6 @@ archivePath:
label: Archive Path
validation: required path
description: ""
- value: ?? XNAT.data.siteConfig.archivePath
-
cachePath:
kind: panel.input.text
id: cachePath
@@ -118,8 +107,6 @@ cachePath:
label: Cache Path
validation: required path
description: ""
- value: ?? XNAT.data.siteConfig.cachePath
-
prearchivePath:
kind: panel.input.text
id: prearchivePath
@@ -127,8 +114,6 @@ prearchivePath:
label: Prearchive Path
validation: required path
description: ""
- value: ?? XNAT.data.siteConfig.prearchivePath
-
ftpPath:
kind: panel.input.text
id: ftpPath
@@ -136,7 +121,6 @@ ftpPath:
label: FTP Path
validation: required path
description: ""
- value: ??XNAT.data.siteConfig.cachePath
buildPath:
kind: panel.input.text
id: buildPath
@@ -144,7 +128,6 @@ buildPath:
label: Build Path
validation: required id onblur
description: ""
- value: ??XNAT.data.siteConfig.cachePath
pipelinePath:
kind: panel.input.text
id: pipelinePath
@@ -152,14 +135,6 @@ pipelinePath:
label: Pipeline Path
validation: required id onblur
description: ""
- value: ??XNAT.data.siteConfig.cachePath
-dataFolders:
- kind: panel.input.text
- id: dataFolders
- name: dataFolders
- label: Data Folders
- validation: required id onblur
- description: ""
zipExtensions:
kind: panel.input.text
id: zipExtensions
@@ -171,16 +146,14 @@ siteInfo:
name: siteInfo
label: Site Information
method: POST
- action: /xapi/siteConfig/batch
- load:
- lookup: XNAT.data.siteConfig
contentType: json
+ action: /xapi/siteConfig/batch
+ load: ?? XNAT.data.siteConfig
+ refresh: /xapi/siteConfig
contents:
${siteId}
${siteUrl}
${siteDescriptionType}
- ${siteDescriptionOptionText}
- ${siteDescriptionOptionPage}
${siteDescriptionPage}
${siteDescriptionText}
${siteLoginLanding}
@@ -192,6 +165,11 @@ adminInfo:
kind: panel.form
name: adminInfo
label: Admin Information
+ method: POST
+ contentType: json
+ action: /xapi/siteConfig/batch
+ load: ?? XNAT.data.siteConfig
+ refresh: /xapi/siteConfig
contents:
${adminEmail}
@@ -199,17 +177,25 @@ generalSecuritySettings:
kind: panel.form
name: generalSecuritySettings
label: General Site Security Settings
+ method: POST
+ contentType: json
+ action: /xapi/siteConfig/batch
+ load: ?? XNAT.data.siteConfig
+ refresh: /xapi/siteConfig
contents:
securityChannel:
kind: panel.select.single
id: securityChannel
name: securityChannel
label: Security Channel
- value: https
+ value: ""
options:
- # value: label # <- simplest setup
- http: http
- https: https
+ http:
+ label: http
+ value: http
+ https:
+ label: https
+ value: https
element:
id: security-channel
title: Security Channel
@@ -226,75 +212,63 @@ userLoginsSessionControls:
label: User Logins / Session Controls
method: POST
action: /xapi/siteConfig/batch
- load:
- lookup: XNAT.data.siteConfig
- refresh: /xapi/siteConfig
+ load: ?? XNAT.data.siteConfig
+ refresh: /xapi/siteConfig
+ contentType: json
contents:
-
sessionTimeout:
kind: panel.input.number
id: sessionTimeout
- name: aliasTokenTimeout
+ name: sessionTimeout
label: Session Timeout
- value: ?? XNAT.data.siteConfig.sessionTimeout || 15
- description: >
- Interval for timing out alias tokens. Uses
- <a target="_blank" href="http://www.postgresql.org/docs/9.0/static/functions-datetime.html">PostgreSQL interval notation</a>
-
- sessionTimeoutMessage:
+ description: "Number of minutes of inactivity before users are locked out of the site. This will not affect users that are currently logged in."
+ aliasTokenTimeout:
kind: panel.input.text
+ id: aliasTokenTimeout
+ name: aliasTokenTimeout
+ label: Alias Token Timeout
+ description: Number of minutes before alias tokens expire.
+ sessionTimeoutMessage:
+ kind: panel.textarea
id: sessionTimeoutMessage
name: sessionTimeoutMessage
label: Session Timeout Message
- value: ?? XNAT.data.siteConfig.sessionTimeoutMessage || "Your session has timed out."
- description: Alert message provided to users after a session timeout and logout.
-
+ description: Alert message provided to users after a session timeout. TIMEOUT_TIME will be replaced by the timeout time.
allowResumeOnNextLogin:
kind: panel.input.checkbox
id: allow-resume-on-next-login
name: allowResumeOnNextLogin
label: Allow Resume On Next Login?
- value: ?? XNAT.data.siteConfig.allowResumeOnNextLogin
description: Allow user to resume where they left off, if logging back in after a session timeout?
-
maximumConcurrentSessions:
kind: panel.input.number
id: maximumConcurrentSessions
- name: security.sessions.concurrent_max
+ name: sessions.concurrent_max
label: Maximum Concurrent Sessions
- value: ?? XNAT.data.siteConfig.maximumConcurrentSessions || 5
description: The maximum number of permitted sessions a user can have open simultaneously
-
loginFailureMessage:
- kind: panel.input.text
+ kind: panel.textarea
id: loginFailureMessage
name: UI.login_failure_message
label: Login Failure Message
- value: Login failed
description: Text to show when a user fails to login
-
maximumFailedLogins:
kind: panel.input.number
id: maximumFailedLogins
- name: security.max_failed_logins
+ name: maxFailedLogins
label: Maximum Failed Logins
- value: -1
description: Number of failed login attempts before accounts are temporarily locked. (-1 disables feature)
-
failedLoginLockoutDuration:
kind: panel.input.number
id: failedLoginLockoutDuration
name: maxFailedLoginsLockoutDuration
label: Failed Login Lockout Duration
- value: 0
description: Number of milliseconds to lock user accounts that have exceeded the max_failed_logins count. Select (3600000 for 1 hour, 86400000 for 24 hours)
-
userInactivityLockout:
kind: panel.input.number
id: userInactivityLockout
name: inactivityBeforeLockout
label: User Inactivity Lockout
- value: 31556926
description: Number of seconds of inactivity before an account is disabled (31556926 for 1 year)
inactivityBeforeLockoutSchedule:
kind: panel.input.text
@@ -308,36 +282,33 @@ passwords:
label: Passwords
method: POST
action: /xapi/siteConfig/batch
- load:
- lookup: XNAT.data.siteConfig
contentType: json
+ load: ?? XNAT.data.siteConfig
+ refresh: /xapi/siteConfig
contents:
passwordComplexity:
kind: panel.input.text
id: passwordComplexity
name: passwordComplexity
label: Password Complexity
- value: "^.*$"
description: Must be a valid regular expression.
passwordComplexityMessage:
- kind: panel.input.text
+ kind: panel.textarea
id: passwordComplexityMessage
name: passwordComplexityMessage
label: Password Complexity Message
- value: "Your password must contain..."
passwordHistoryDuration:
kind: panel.input.number
id: passwordHistoryDuration
name: passwordHistoryDuration
label: Password History (Duration)
- value: -1
description: "-1 to disable"
passwordExpirationType:
kind: panel.select.single
id: passwordExpirationType
name: passwordExpirationType
label: passwordExpirationType
- value: Interval
+ value: ""
options:
Interval:
label: Interval
@@ -350,7 +321,6 @@ passwords:
id: passwordExpirationInterval
name: passwordExpirationInterval
label: Password Expiration (Interval)
- value: -1
description: "-1 to disable"
passwordExpirationDate:
kind: panel.input.text
@@ -368,57 +338,39 @@ passwords:
id: requireSaltedPasswords
name: requireSaltedPasswords
label: Require Passwords To Be Salted
- value: false
csrf:
kind: panel.form
name: csrf
label: CSRF
+ method: POST
+ action: /xapi/siteConfig/batch
+ contentType: json
+ load: ?? XNAT.data.siteConfig
+ refresh: /xapi/siteConfig
contents:
enableCsrfToken:
kind: panel.input.checkbox
id: enableCsrfToken
name: enableCsrfToken
label: Require CSRF Token?
- value: true
description: Should this site require the use of a token to prevent CSRF attacks on POST, PUT, and DELETEs?
csrfEmailAlert:
kind: panel.input.checkbox
id: csrfEmailAlert
name: enable_csrf_email_alert
label: CSRF Email Alert
- value: "Should this site send an email to the site admin whenever a CSRF attack is attempted?"
-
-auditTrail:
- kind: panel.form
- name: auditTrail
- label: Audit Trail Configuration
- contents:
- enableAuditTrail:
- kind: panel.input.checkbox
- id: enableAuditTrail
- name: enableAuditTrail
- label: Enable Audit Trail?
- value: true
- allowUserJustificationForChanges:
- kind: panel.input.checkbox
- id: allowUserJustificationForChanges
- name: allowUserJustificationForChanges
- label: Allow User Justification For Changes
- value: true
- description: "Allow users to enter change justifications when modifying data"
- requireUserJustificationForChanges:
- kind: panel.input.checkbox
- id: requireUserJustificationForChanges
- name: requireUserJustificationForChanges
- label: Require User Justification For Changes
- value: false
- description: "Force users to enter change justifications when modifying data"
+ description: "Should this site send an email to the site admin whenever a CSRF attack is attempted?"
securityServices:
kind: panel.form
name: securityServices
label: Security Services
+ action: /xapi/siteConfig/batch
+ method: POST
+ contentType: json
+ load: ?? XNAT.data.siteConfig
+ refresh: /xapi/siteConfig
contents:
securityServicesFeatureDefault:
kind: panel.input.text
@@ -444,12 +396,10 @@ securityServices:
emailServerSettings:
kind: panel.form
method: POST
- action: /xapi/notifications/all
- load: # load data
- url: /xapi/siteConfig
- prop: smtpServer # which root property? gets the root object if not set
-# lookup: XNAT.data.siteConfig.smtpServer
+ action: /xapi/siteConfig/smtpServer
contentType: json
+ load: ?? XNAT.data.siteConfig.smtpServer
+ refresh: /xapi/siteConfig/smtpServer
name: emailServerSettings
label: Mail Server Settings
contents:
@@ -458,38 +408,30 @@ emailServerSettings:
id: smtpEnabled
name: smtp.enabled
label: "Enable SMTP?"
- #value: true
- checked: true
hostname:
kind: panel.input.text
name: host
label: Host
- value: localhost
+ placeholder: localhost
port:
kind: panel.input.number
name: port
label: Port
- value: ""
- element:
- placeholder: 587
+ placeholder: 587
username:
kind: panel.input.text
name: username
label: Username
- url: /xapi/notifications/username
- value: ''
- element:
- placeholder: name@host.org
+ placeholder: name@host.org
password:
kind: panel.input.password
name: password
label: Password
- value: ''
protocol:
kind: panel.input.text
name: protocol
label: Protocol
- value: ''
+ placeholder: smtp
# subhead breaks up panel items
mailServerProperties:
kind: panel.subhead
@@ -499,122 +441,147 @@ emailServerSettings:
kind: panel.input.checkbox
name: mail.smtp.auth
label: SMTP Auth?
- #value: true
- checked: true
smtpStartTls:
kind: panel.input.checkbox
name: mail.smtp.starttls.enable
label: Smart TLS?
- #value: true
- checked: true
smtpSSLTrust:
kind: panel.input.text
name: mail.smtp.ssl.trust
label: SSL Trust
- value: ''
- element:
- placeholder: localhost
+ placeholder: localhost
emailPrefix:
kind: panel.input.text
name: emailPrefix
label: Email Prefix
- element:
- placeholder: XNAT
+ placeholder: XNAT
notifications:
kind: panel.form
name: notifications
label: Notifications
+ action: /xapi/siteConfig/batch
+ method: POST
+ contentType: json
+ load: ?? XNAT.data.siteConfig
+ refresh: /xapi/siteConfig
contents:
+
helpContactInfo:
kind: panel.input.email
id: helpContactInfo
- name: helpContactInfo
+ name: notifications.helpContactInfo
label: "Help Contact Info"
+# value: "!? XNAT.data.siteConfig['notifications.helpContactInfo'] || XNAT.data.siteConfig.adminEmail"
+
+ emailMessageSubhead:
+ kind: panel.subhead
+ label: Email Messages
+
emailMessageUserRegistration:
- kind: panel.textarea # textarea
+ kind: panel.textarea
id: emailMessageUserRegistration
- name: emailMessageUserRegistration
- label: "Email Message: User Registration"
+ name: notifications.emailMessageUserRegistration
+ label: "User Registration"
description: "Text of message emailed to users upon registration. Link for email validation is auto-populated."
emailMessageForgotUsernameRequest:
- kind: panel.textarea # textarea
+ kind: panel.textarea
id: emailMessageForgotUsernameRequest
- name: emailMessageForgotUsernameRequest
- label: "Email Message: Forgot Username Request"
+ name: notifications.emailMessageForgotUsernameRequest
+ label: "Forgot Username Request"
description: "Text of message emailed to users upon lost username request."
emailMessageForgotPasswordReset:
- kind: panel.textarea # textarea
+ kind: panel.textarea
id: emailMessageForgotPasswordReset
- name: emailMessageForgotPasswordReset
- label: "Email Message: Password Reset"
+ name: notifications.emailMessageForgotPasswordReset
+ label: "Password Reset"
description: "Text of message emailed to users upon lost password reset. Link for password reset is auto-populated"
+
+ notifyAdminSubhead:
+ kind: panel.subhead
+ label: "Notify Administrator on..."
+
notifyAdminUserRegistration:
kind: panel.input.checkbox
id: notifyAdminUserRegistration
- name: notifyAdminUserRegistration
- label: "Notify Admin on User Registration"
- value: ?? XNAT.data.siteConfig.notifyAdminUserRegistration
+ name: notifications.notifyAdminUserRegistration
+# value: "?? XNAT:data:siteConfig:notifications.notifyAdminUserRegistration"
+ label: "User Registration"
description: "Whether to cc admin user on new user emails. Requires valid admin email address."
notifyAdminPipelineEmails:
kind: panel.input.checkbox
id: notifyAdminPipelineEmails
- name: notifyAdminPipelineEmails
- label: "Notify Admin on Pipeline Emails"
- value: false
+ name: notifications.notifyAdminPipelineEmails
+# value: "?? XNAT:data:siteConfig:notifications.notifyAdminPipelineEmails"
+ label: "Pipeline Emails"
description: "Whether to cc admin user on pipeline processing submit. Requires valid admin email address."
notifyAdminProjectAccessRequest:
kind: panel.input.checkbox
id: notifyAdminProjectAccessRequest
- name: notifyAdminProjectAccessRequest
- label: "Notify Admin on Project Access Request"
- value: false
+ name: notifications.notifyAdminProjectAccessRequest
+# value: "?? XNAT:data:siteConfig:notifications.notifyAdminProjectAccessRequest"
+ label: "Project Access Request"
description: "Whether to cc admin user on user project access request. Requires valid admin email address."
notifyAdminSessionTransfer:
kind: panel.input.checkbox
id: notifyAdminSessionTransfer
- name: notifyAdminSessionTransfer
- label: "Notify Admin on Session Transfer"
- value: false
+ name: notifications.notifyAdminProjectOnSessionTransfer
+# value: "?? XNAT:data:siteConfig:notifications.notifyAdminProjectOnSessionTransfer"
+ label: "Session Transfer"
description: "Whether to cc admin user on session transfer by user. Requires valid admin email address."
+
+ emailRecipientSubhead:
+ kind: panel.subhead
+ label: "Email Recipient(s) for..."
+
emailRecipientErrorMessages:
kind: panel.input.email
id: emailRecipientErrorMessages
- name: emailRecipientErrorMessages
- label: "Email Recipient: Error Messages"
+ name: notifications.emailRecipientErrorMessages
+ label: "Error Messages"
description: "What email address should receive error emails"
+ #value: "!? XNAT.data.siteConfig['notifications.emailRecipientErrorMessages'] || XNAT.data.siteConfig.adminEmail"
emailRecipientIssueReports:
kind: panel.input.email
id: emailRecipientIssueReports
- name: emailRecipientIssueReports
- label: "Email Recipient: Issue Reports"
+ name: notifications.emailRecipientIssueReports
+ label: "Issue Reports"
description: "What email address should receive issue reports"
+ #value: "!? XNAT.data.siteConfig['notifications.emailRecipientIssueReports'] || XNAT.data.siteConfig.adminEmail"
emailRecipientNewUserAlert:
kind: panel.input.email
id: emailRecipientNewUserAlert
- name: emailRecipientNewUserAlert
- label: "Email Recipient: New User Alert"
+ name: notifications.emailRecipientNewUserAlert
+ label: "New User Alert"
description: "What email address should receive New User Registration emails"
+ #value: "!? XNAT.data.siteConfig['notifications.emailRecipientNewUserAlert'] || XNAT.data.siteConfig.adminEmail"
emailRecipientUpdate:
kind: panel.input.email
id: emailRecipientUpdate
- name: emailRecipientUpdate
- label: "Email Recipient: Updates"
+ name: notifications.emailRecipientUpdate
+ label: "Updates"
description: "What email address should receive update emails"
+ #value: "!? XNAT.data.siteConfig['notifications.emailRecipientUpdate'] || XNAT.data.siteConfig.adminEmail"
+
+ otherSubhead:
+ kind: panel.subhead
+ label: "Other"
+
emailAllowNonuserSubscribers:
kind: panel.input.checkbox
id: emailAllowNonuserSubscribers
name: emailAllowNonuserSubscribers
label: "Allow Nonuser Subscribers"
- value: ?? XNAT.data.siteConfig.emailAllowNonuserSubscribers
+# value: "?? XNAT.data.siteConfig.emailAllowNonuserSubscribers"
themeManagement:
- kind: panel
+ kind: panel.form
name: themeManagement
label: Theme Management
+ action: /xapi/theme
contents:
themeScript:
- tag: script|type=text/javascript;src=../../scripts/themeManagement.js
+ tag: script|type=text/javascript;src=../../scripts/xnat/admin/themeManagement.js
themeStyle:
tag: style
element:
@@ -624,22 +591,26 @@ themeManagement:
id: currentTheme
label: Current Theme
description: The currently selected global theme.
- value: None
+ value: ""
element:
style:
color: 'red'
existingTheme:
kind: panel.select.single
id: themeSelection
+ name: themeSelection
label: Select an existing theme
description: Selected a new global theme from those available on the system.
- value: None
+ value: ""
options:
default:
label: None
value: None
after:
- - "<span style=\"position: relative; top: -49px;left: 270px;\"> <button id=\"submitThemeButton\" onclick=\"setTheme();\">Set Theme</button> <button id=\"removeThemeButton\" onclick=\"removeTheme();\">Remove Theme</button></span>"
+ - "<span style=\"position: relative; top: -49px;left: 270px;\"> <!-- <button id=\"submitThemeButton\" onclick=\"setTheme();\">Set Theme</button> --> <button id=\"removeThemeButton\" onclick=\"removeTheme();\">Remove Theme</button></span>"
+ element:
+ style:
+ min-width: 250px
uploadTheme:
kind: panel.input.upload
id: themeFileUpload
@@ -652,29 +623,36 @@ authenticationMethods:
kind: panel.form
name: authenticationMethods
label: User Authentication Methods
+ method: POST
+ action: /xapi/siteConfig/batch
+ contentType: json
+ load: ?? XNAT.data.siteConfig
+ refresh: /xapi/siteConfig
contents:
xnatInternal:
kind: panel.input.checkbox
id: xnatInternal
name: provider.providers.xnatInternal
label: XNAT (Internal)
- value: true
ldapProvider:
kind: panel.input.checkbox
id: ldapProvider
name: provider.providers.ldap
label: LDAP
- value: false
- oauthProvider:
- kind: panel.input.checkbox
- id: oauthProvider
- name: provider.providers.oauth
- label: OAuth
- value: false
+# oauthProvider:
+# kind: panel.input.checkbox
+# id: oauthProvider
+# name: provider.providers.oauth
+# label: OAuth
genericAuthenticationProvider:
kind: panel.form
name: genericAuthenticationProvider
label: Generic Authentication Provider
+ method: POST
+ action: /xapi/siteConfig/batch
+ contentType: json
+ load: ?? XNAT.data.siteConfig
+ refresh: /xapi/siteConfig
contents:
providerDbName:
kind: panel.input.text
@@ -691,10 +669,16 @@ genericAuthenticationProvider:
id: providerDbType
name: providerDbType
label: "Provider DB Type"
+
ldapAuthentication:
kind: panel.form
name: ldapAuthenticationProvider
label: LDAP Authentication Provider
+ method: POST
+ action: /xapi/siteConfig/batch
+ contentType: json
+ load: ?? XNAT.data.siteConfig
+ refresh: /xapi/siteConfig
contents:
ldapName:
kind: panel.input.text
@@ -754,123 +738,112 @@ registrationOptions:
kind: panel.form
name: registrationOptions
label: Registration Options
+ method: POST
+ action: /xapi/siteConfig/batch
+ load: ?? XNAT.data.siteConfig
+ contentType: json
contents:
requireLogin:
kind: panel.input.checkbox
id: requireLogin
name: requireLogin
label: "Require User?"
- value: true
- disabled: true
+ value: ""
requireEmailVerificationToRegister:
kind: panel.input.checkbox
id: requireEmailVerificationToRegister
name: emailVerification
label: "Require Email Verification To Register?"
- value: true
emailVerificationMessage:
- kind: panel.input.text #textarea
+ kind: panel.textarea
id: emailVerificationMessage
name: emailVerificationMessage
label: "Email Verification Message"
- value: ""
emailVerificationExpiration:
kind: panel.input.number
id: emailVerificationExpiration
name: emailVerificationExpiration
label: "Email Verification Expiration"
- value: 60000
autoEnableUserRegistration:
kind: panel.input.checkbox
id: autoEnableUserRegistration
name: userRegistration
label: "Auto-enable User Registration?"
- value: false
allowUserCommentsOnRegistration:
kind: panel.input.checkbox
id: allowUserCommentsOnRegistration
name: allowUserCommentsOnRegistration
label: "Allow User Comments on Registration?"
- value: true
restrictUserListAccessToAdmins:
kind: panel.input.checkbox
id: restrictUserListAccessToAdmins
name: restrictUserListAccessToAdmins
label: "Restrict User List Access To Admins?"
- value: true
-
-dataReporting:
- kind: panel.form
- name: dataReporting
- label: Data Reporting
- contents:
- enableAdvancedSearch:
- kind: panel.input.checkbox
- id: enableAdvancedSearch
- name: enableAdvancedSearch
- label: "Enable Advanced Search"
- value: true
manageDataTypes:
kind: panel.form
name: manageDataTypes
label: Manage Data Types
method: POST
- action: /xapi/siteConfig/batch
- load:
- lookup: XNAT.data.siteConfig
contentType: json
+ action: /xapi/siteConfig/batch
+ load: ?? XNAT.data.siteConfig
+ refresh: /xapi/siteConfig
contents:
displayNameForGenericImageSessionSingular:
kind: panel.input.text
id: displayNameForGenericImageSessionSingular
name: displayNameForGenericImageSession.singular
label: "Singular Display Name For Generic Image Session Singular"
- value: "Session"
displayNameForGenericImageSessionPlural:
kind: panel.input.text
id: displayNameForGenericImageSessionPlural
name: displayNameForGenericImageSession.plural
label: "Plural Display Name For Generic Image Session Singular"
- value: "Sessions"
anonymization:
kind: panel.form
name: Anonymization
label: "Anonymization Script (Site Wide)"
+ method: POST
+ contentType: json
+ action: /xapi/siteConfig/batch
+ load: ?? XNAT.data.siteConfig
+ refresh: /xapi/siteConfig
contents:
enableSitewideAnonymizationScript:
kind: panel.input.checkbox
id: enableSitewideAnonymizationScript
name: enableSitewideAnonymizationScript
label: "Enable Site-wide Anonymization Script"
- value: true
- editAnonymzationScript:
- kind: panel.input.text #textarea
- id: editAnonymzationScript
- name: editAnonymzationScript
- label: "Edit Anonymzation Script"
- value: true
+ editAnonymizationScript:
+ kind: panel.textarea
+ id: editAnonymizationScript
+ name: editAnonymizationScript
+ label: "Edit Anonymization Script"
seriesImportFilter:
kind: panel.form
name: seriesImportFilter
label: "Series Import Filter"
+ method: POST
+ contentType: json
+ action: /xapi/siteConfig/batch
+ load: ?? XNAT.data.siteConfig
+ refresh: /xapi/siteConfig
contents:
enableSitewideSeriesImportFilter:
kind: panel.input.checkbox
id: enableSitewideSeriesImportFilter
name: enableSitewideSeriesImportFilter
label: "Enable Site-wide Series Import Filter"
- value: false
filterMode:
kind: panel.input.checkbox
id: filterMode
name: filterMode
label: Filter Mode
- value: false
seriesImportFilter:
- kind: panel.input.text #textarea
+ kind: panel.textarea
id: seriesImportFilter
name: seriesImportFilter
label: "Edit Series Import Filter"
@@ -879,6 +852,11 @@ sessionUploadMethod:
kind: panel.form
name: sessionUploadMethod
label: "Session Upload Method"
+ method: POST
+ contentType: json
+ action: /xapi/siteConfig/batch
+ load: ?? XNAT.data.siteConfig
+ refresh: /xapi/siteConfig
contents:
selectUploadMethod:
kind: panel.select.single
@@ -887,25 +865,23 @@ sessionUploadMethod:
label: "Session Upload Method"
# options: # don't know where to populate this from
# http:
-# label: http
-# value: http
+# label:
+# value:
# https:
-# label: https
-# value: https
+# label:
+# value:
showApplet:
kind: panel.input.checkbox
id: showApplet
name: showApplet
label: Show Applet
- value: false
enableProjectAppletScript:
kind: panel.input.checkbox
id: enableProjectAppletScript
name: enableProjectAppletScript
label: Enable Project Applet Script
- value: false
appletScript:
- kind: panel.input.text #textarea
+ kind: panel.textarea
id: appletScript
name: appletScript
label: "Applet Script"
@@ -914,14 +890,11 @@ sessionUploadMethod:
id: sessionXmlRebuilderRepeat
name: sessionXmlRebuilderRepeat
label: Session Xml Rebuilder Repeat
- value: 60000
sessionXmlRebuilderInterval:
kind: panel.input.number
id: sessionXmlRebuilderInterval
name: sessionXmlRebuilderInterval
label: Session Xml Rebuilder Interval
- value: 5
-
dicomScpReceivers:
kind: panel.form
@@ -929,17 +902,14 @@ dicomScpReceivers:
label: DICOM SCP Receivers
method: POST
action: /xapi/dicomscp
- load:
- url: /xapi/dicomscp
-# prop: # Not set, so should get the root object
contentType: json
+ load: $? /xapi/dicomscp
contents:
enableDicomReceiver:
kind: panel.input.checkbox
id: enableDicomReceiver
name: enableDicomReceiver
label: DICOM Receiver Enabled?
- value: true
description: "Should the DICOM receiver listen for connections?"
someInfo:
tag: div.message
@@ -952,7 +922,6 @@ dicomScpReceivers:
id: enableDicomReceiverPropertyChangedListener
name: enableDicomReceiverPropertyChangedListener # Should this be "enableDicomReceiver.property.changed.listener"
label: "Enable Dicom Receiver Property Changed Listener"
- value: "org.nrg.dcm.DicomSCPSiteConfigurationListener"
dicomHost:
kind: panel.input.text
id: dicomHost
@@ -982,7 +951,6 @@ dicomScpReceivers:
id: receivedFileUser
name: receivedFileUser
label: "Default DICOM Receiver: User"
- value: admin
description: "User account for default DICOM receiver"
fileSystem:
@@ -990,10 +958,9 @@ fileSystem:
name: fileSystem
label: File System
method: POST
- action: /xapi/siteConfig/batch
- load:
- lookup: XNAT.data.siteConfig
contentType: json
+ action: /xapi/siteConfig/batch
+ load: ?? XNAT.data.siteConfig
contents:
${archivePath}
${cachePath}
@@ -1001,7 +968,6 @@ fileSystem:
${ftpPath}
${buildPath}
${pipelinePath}
- ${dataFolders}
${zipExtensions}
misc:
@@ -1009,30 +975,49 @@ misc:
name: misc
label: Miscellaneous
method: POST
- action: /xapi/siteConfig/batch
- load:
- lookup: XNAT.data.siteConfig
contentType: json
+ action: /xapi/siteConfig/batch
+ load: ?? XNAT.data.siteConfig
+ refresh: /xapi/siteConfig
contents:
checksums:
kind: panel.input.checkbox
id: checksums
name: checksums
label: Checksums?
- value: true
checksumsPropertyChangedListener:
kind: panel.input.text
id: checksumsPropertyChangedListener
name: checksums.property.changed.listener
label: Checksums Property Changed Listener?
- value: org.nrg.xnat.utils.ChecksumsSiteConfigurationListener
scanTypeMapping:
kind: panel.input.checkbox
id: scanTypeMapping
name: scanTypeMapping
label: Scan Type Mapping?
- value: true
-
+ development:
+ kind: panel.subhead
+ label: Development Utilities
+ spawner:
+ kind: panel.element
+ description: Manage spawner elements.
+ contents:
+ link:
+ tag: a.link
+ element:
+ href: ./page/admin/spawner/
+ target: _blank
+ html: Manage The Spawner
+ swagger:
+ kind: panel.element
+ description: View the Swagger page.
+ contents:
+ link:
+ tag: a.link
+ element:
+ href: ./xapi/swagger-ui.html
+ target: _blank
+ html: Swagger
development:
kind: panel
name: development
@@ -1081,7 +1066,6 @@ adminPage:
${userLoginsSessionControls}
${passwords}
${csrf}
- ${auditTrail}
${securityServices}
emailServer:
kind: tab
@@ -1113,14 +1097,14 @@ adminPage:
${authenticationMethods}
${genericAuthenticationProvider}
${ldapAuthentication}
-# users: # enable when users table can be re-implmented in spawner, until then use old users config?
+# users: # enable when users table can be re-implemented in spawner, until then use old users config?
# kind: tab
# name: users
# label: Users
# group: manageAccess
# contents:
# ${users}
-# userRoles: # enable when user roles table can be re-implmented in spawner, until then use old user roles config?
+# userRoles: # enable when user roles table can be re-implemented in spawner, until then use old user roles config?
# kind: tab
# name: userRoles
# label: User Roles
@@ -1134,13 +1118,6 @@ adminPage:
group: manageAccess
contents:
${registrationOptions}
- dataReporting:
- kind: tab
- name: dataReporting
- label: Data Reporting
- group: manageData
- contents:
- ${dataReporting}
manageDataTypes:
kind: tab
name: manageDataTypes
@@ -1171,14 +1148,13 @@ adminPage:
group: advanced
contents:
${fileSystem}
- ${siteIdMain}
misc:
kind: tab
name: misc
label: Miscellaneous
contents:
${misc}
- ${development}
+# ${development}
###########################################
@@ -1203,7 +1179,6 @@ sitePaths:
# ${ftpPath}
# ${buildPath}
# ${pipelinePath}
- ${dataFolders}
initialSetup:
kind: panel
name: initialSetup
diff --git a/src/main/resources/META-INF/xnat/spawner/site-setup-elements.yaml b/src/main/resources/META-INF/xnat/spawner/site-setup-elements.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..4f826705412437689db0fa39b14b124f41c71290
--- /dev/null
+++ b/src/main/resources/META-INF/xnat/spawner/site-setup-elements.yaml
@@ -0,0 +1,204 @@
+# The initial setup page elements are in a separate file for now
+setupMessage:
+ tag: div.message
+ element:
+ style:
+ marginBottom: 24px
+ html: >
+ The settings below need to be configured before this XNAT system
+ can be used. Please set the properties below and submit the form to continue.
+
+# ====================
+# PANEL
+siteInfo:
+ kind: panel.form
+ name: siteInfo
+ label: Site Information
+ footer: false
+ method: POST
+ action: /xapi/siteConfig/batch
+ contentType: json
+ load: ?? XNAT.data.siteConfig
+ refresh: /xapi/siteConfig
+ contents:
+
+ siteId:
+ kind: panel.input.text
+ name: siteId
+ label: Site ID
+ value: ''
+ placeholder: XNAT
+ description: >
+ The id used to refer to this site (also used to generate ids). The Site ID must start
+ with a letter and contain only letters, numbers and underscores. It should be a short,
+ one-word name or acronym which describes your site.
+ validation: required id
+
+ siteUrl:
+ kind: panel.input.text
+ name: siteUrl
+ label: Site URL
+ value: ''
+ placeholder: localhost
+ description: >
+ The address you want visible to users in emails, and other external links. This should be a
+ functional address (i.e. if the user pasted this address in their web browser, they should
+ come to the site). localhost only works if the web browser is located on the same machine.
+ You are required to guarantee that this address is functional for reaching the site.
+ validation: required url
+
+ adminEmail:
+ kind: panel.input.email
+ name: adminEmail
+ label: Administrator Email Address
+ value: ''
+ placeholder: admin@localhost
+ description: Email address for site administrator.
+ validation: required email
+
+# ====================
+# PANEL
+dataStorage:
+ kind: panel.form
+ name: dataStorage
+ label: Data Storage
+ footer: false
+ method: POST
+ action: /xapi/siteConfig/batch
+ contentType: json
+ load: ?? XNAT.data.siteConfig
+ refresh: /xapi/siteConfig
+ contents:
+
+ archivePath:
+ kind: panel.input.text
+ name: archivePath
+ label: Archive Location
+ size: 50
+ value: ''
+ validation: required path
+
+ prearchivePath:
+ kind: panel.input.text
+ name: prearchivePath
+ label: Pre-archive Location
+ size: 50
+ value: ''
+ validation: required path
+
+ cachePath:
+ kind: panel.input.text
+ name: cachePath
+ label: Cache Location
+ size: 50
+ value: ''
+ validation: required path
+
+ buildPath:
+ kind: panel.input.text
+ name: buildPath
+ label: Build Location
+ size: 50
+ value: ''
+ validation: required path
+
+ ftpPath:
+ kind: panel.input.text
+ name: ftpPath
+ label: FTP Location
+ size: 50
+ value: ''
+ validation: required path
+
+ pipelinePath:
+ kind: panel.input.text
+ name: pipelinePath
+ label: Pipeline Installation Location
+ size: 50
+ value: ''
+ validation: required path
+
+# ====================
+# PANEL
+smtpServer:
+ kind: panel.form
+ name: smtpServer
+ label: SMTP Server Settings
+ footer: false
+ method: POST
+ action: /xapi/siteConfig/smtpServer
+ contentType: json
+ load: ?? XNAT.data.siteConfig.smtpServer
+ refresh: /xapi/siteConfig/smtpServer
+ contents:
+
+ host:
+ kind: panel.input.text
+ name: host
+ label: Host
+ #value: "?? XNAT:data:siteConfig:smtpServer:host"
+ placeholder: localhost
+ validation: required
+
+ port:
+ kind: panel.input.number
+ name: port
+ label: Port
+ #value: "?? XNAT:data:siteConfig:smtpServer:port"
+ placeholder: 25
+ validation: required number
+
+ username:
+ kind: panel.input.text
+ name: username
+ label: Username
+ #value: "?? XNAT:data:siteConfig:smtpServer:username"
+
+ password:
+ kind: panel.input.password
+ name: password
+ label: Password
+ #value: "?? XNAT:data:siteConfig:smtpServer:password"
+
+ protocol:
+ kind: panel.input.text
+ name: protocol
+ label: Protocol
+ #value: "?? XNAT:data:siteConfig:smtpServer:protocol"
+
+ mailServerProperties:
+ kind: panel.subhead
+ text: Mail Server Settings
+
+ smtpAuth:
+ kind: panel.input.checkbox
+ name: mail.smtp.auth
+ label: SMTP Auth?
+ #value: "?? XNAT:data:siteConfig:smtpServer:mail.smtp.auth"
+
+ smtpStartTls:
+ kind: panel.input.checkbox
+ name: mail.smtp.starttls.enable
+ label: Smart TLS?
+ #value: "?? XNAT:data:siteConfig:smtpServer:mail.smtp.starttls.enable"
+
+ smtpSSLTrust:
+ kind: panel.input.text
+ name: mail.smtp.ssl.trust
+ label: SSL Trust
+ #value: "?? XNAT:data:siteConfig:smtpServer:mail.smtp.ssl.trust"
+
+
+
+#################################################
+#### Root Site Setup Spawner Config Object ####
+#################################################
+setupPage:
+ kind: app.siteSetup.form
+ name: setupPage
+ label: XNAT Initial Setup
+ contents:
+ ${setupMessage}
+ ${siteInfo}
+ ${dataStorage}
+ ${smtpServer}
diff --git a/src/main/webapp/PlexiViewerSpec.xml b/src/main/webapp/PlexiViewerSpec.xml
deleted file mode 100644
index aca96331fdf79eb8feb4506e5179e3247555a87e..0000000000000000000000000000000000000000
--- a/src/main/webapp/PlexiViewerSpec.xml
+++ /dev/null
@@ -1,159 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!--
- ~ D:/Development/XNAT/1.6/xnat_builder_1_6dev/plugin-resources/project-skeletons/xnat/PlexiViewerSpec.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
- -->
-<Viewer xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="/var/lib/tomcat7/webapps/xnat17/schemas/xdat/PlexiViewer.xsd">
- <PlexiViewer sessionType="PLEXI_DEFAULT">
- <DefaultLoResType>8bit</DefaultLoResType>
- <CacheLocation>/data/xnat17/cache</CacheLocation>
- <Layout name="tal_111" voxelSize="1">
- <Coordinates originX="88" originY="84" originZ="75"/>
- </Layout>
- <Layout name="tal_222" voxelSize="2">
- <Coordinates originX="63" originY="63" originZ="34"/>
- </Layout>
- <Layout name="tal_333" voxelSize="3">
- <Coordinates originX="24" originY="29" originZ="20"/>
- </Layout>
- <Layout name="native" voxelSize="1">
- <Coordinates originX="0" originY="0" originZ="0"/>
- </Layout>
- <ViewableItem type="MPRAGE">
- <SchemaLink element="xnat:imageScanData.type" value="MPRAGE"/>
- <UserInterface selectionPriority="0" displayText="MPRAGE">
- <LinkedDropDown viewableItemType="MPRAGE_RAW"/>
- <LinkedDropDown viewableItemType="SUBJ"/>
- <LinkedDropDown viewableItemType="GFC"/>
- <LinkedDropDown viewableItemType="MASKED"/>
- <!--<LinkedDropDown viewableItemType="FSEG"/> -->
- </UserInterface>
- </ViewableItem>
- <ViewableItem type="MPRAGE_RAW" imageViewerClassName="org.nrg.plexiViewer.lite.viewer.MR.MRImage">
- <UserInterface displayText="Raw" allowedToChooseID="true"/>
- <Thumbnail format="GIF" converterClassName="org.nrg.plexiViewer.converter.CNLThumbnailConverter">
- <Slice number="79" orientation="transverse"/>
- <Slice number="80" orientation="sagittal"/>
- <Slice number="99" orientation="coronal"/>
- </Thumbnail>
- <Lo-Res type="8bit" converterClassName="org.nrg.plexiViewer.converter.DefaultConverter" format="ANALYZE 7.5">
- <MontageView scale="0.6">
- <transverse start_slice="60" end_slice="180" slice_spacing="8"/>
- <sagittal start_slice="35" end_slice="125" slice_spacing="5"/>
- <coronal start_slice="60" end_slice="180" slice_spacing="8"/>
- </MontageView>
- </Lo-Res>
- <Hi-Res format="DICOM">
- <Layer element="xnat:imageScanData.file" value="MPRAGE_RAW" num="0"/>
- <LayoutRef name="native"/>
- <MontageView scale="0.6">
- <transverse start_slice="60" end_slice="180" slice_spacing="8"/>
- <sagittal start_slice="35" end_slice="125" slice_spacing="5"/>
- <coronal start_slice="60" end_slice="180" slice_spacing="8"/>
- </MontageView>
- </Hi-Res>
- </ViewableItem>
- <ViewableItem type="GFC" imageViewerClassName="org.nrg.plexiViewer.lite.viewer.MR.MRImage">
- <UserInterface displayText="Atlas Registered"/>
- <Thumbnail format="GIF" converterClassName="org.nrg.plexiViewer.converter.CNLThumbnailConverter">
- <Slice number="79" orientation="transverse"/>
- <Slice number="80" orientation="sagittal"/>
- <Slice number="99" orientation="coronal"/>
- </Thumbnail>
- <Lo-Res type="8bit" converterClassName="org.nrg.plexiViewer.converter.DefaultConverter" format="ANALYZE 7.5">
- <MontageView scale="0.65">
- <transverse start_slice="30" end_slice="140" slice_spacing="5"/>
- <sagittal start_slice="35" end_slice="145" slice_spacing="5"/>
- <coronal start_slice="30" end_slice="165" slice_spacing="5"/>
- </MontageView>
- </Lo-Res>
- <Hi-Res format="ANALYZE 7.5">
- <Layer element="xnat:reconstructedImageData.out.file" value="T88" num="0"/>
- <LayoutRef name="tal_111"/>
- <MontageView scale="0.65">
- <transverse start_slice="30" end_slice="140" slice_spacing="5"/>
- <sagittal start_slice="35" end_slice="145" slice_spacing="5"/>
- <coronal start_slice="30" end_slice="165" slice_spacing="5"/>
- </MontageView>
- </Hi-Res>
- </ViewableItem>
- <ViewableItem type="MASKED" imageViewerClassName="org.nrg.plexiViewer.lite.viewer.MR.MRImage">
- <UserInterface displayText="Masked Atlas Reg."/>
- <Thumbnail format="GIF" converterClassName="org.nrg.plexiViewer.converter.CNLThumbnailConverter">
- <Slice number="79" orientation="transverse"/>
- <Slice number="80" orientation="sagittal"/>
- <Slice number="99" orientation="coronal"/>
- </Thumbnail>
- <Lo-Res type="8bit" converterClassName="org.nrg.plexiViewer.converter.DefaultConverter" format="ANALYZE 7.5">
- <MontageView scale="0.65">
- <transverse start_slice="30" end_slice="140" slice_spacing="5"/>
- <sagittal start_slice="30" end_slice="140" slice_spacing="5"/>
- <coronal start_slice="80" end_slice="190" slice_spacing="5"/>
- </MontageView>
- </Lo-Res>
- <Hi-Res format="ANALYZE 7.5">
- <Layer element="xnat:reconstructedImageData.out.file" value="MASKED" num="0"/>
- <LayoutRef name="tal_111"/>
- <MontageView scale="0.65">
- <transverse start_slice="30" end_slice="140" slice_spacing="5"/>
- <sagittal start_slice="30" end_slice="140" slice_spacing="5"/>
- <coronal start_slice="80" end_slice="190" slice_spacing="5"/>
- </MontageView>
- </Hi-Res>
- </ViewableItem>
- <ViewableItem type="SUBJ" imageViewerClassName="org.nrg.plexiViewer.lite.viewer.MR.MRImage">
- <UserInterface displayText="Averaged"/>
- <Thumbnail format="GIF" converterClassName="org.nrg.plexiViewer.converter.CNLThumbnailConverter">
- <Slice number="79" orientation="transverse"/>
- <Slice number="80" orientation="sagittal"/>
- <Slice number="99" orientation="coronal"/>
- </Thumbnail>
- <Lo-Res type="8bit" converterClassName="org.nrg.plexiViewer.converter.DefaultConverter" format="ANALYZE 7.5">
- <MontageView scale="0.6">
- <transverse start_slice="60" end_slice="180" slice_spacing="8"/>
- <sagittal start_slice="35" end_slice="125" slice_spacing="5"/>
- <coronal start_slice="60" end_slice="180" slice_spacing="8"/>
- </MontageView>
- </Lo-Res>
- <Hi-Res format="ANALYZE 7.5">
- <Layer element="xnat:reconstructedImageData.out.file" value="SUBJ" num="0"/>
- <LayoutRef name="native"/>
- <MontageView scale="0.6">
- <transverse start_slice="70" end_slice="180" slice_spacing="8"/>
- <sagittal start_slice="35" end_slice="145" slice_spacing="5"/>
- <coronal start_slice="70" end_slice="180" slice_spacing="8"/>
- </MontageView>
- </Hi-Res>
- </ViewableItem>
- <!-- <ViewableItem type="FSEG" imageViewerClassName="org.nrg.plexiViewer.lite.viewer.MR.MRImage">
- <UserInterface displayText="Gray/White Segmented"/>
- <Thumbnail format="GIF" converterClassName="org.nrg.plexiViewer.converter.CNLThumbnailConverter">
- <Slice number="79" orientation="transverse"/>
- <Slice number="80" orientation="sagittal"/>
- <Slice number="99" orientation="coronal"/>
- </Thumbnail>
- <Lo-Res type="8bit" converterClassName="org.nrg.plexiViewer.converter.DefaultConverter" format="ANALYZE 7.5">
- <MontageView scale="0.65">
- <transverse start_slice="30" end_slice="140" slice_spacing="5"/>
- <sagittal start_slice="35" end_slice="145" slice_spacing="5"/>
- <coronal start_slice="30" end_slice="165" slice_spacing="5"/>
- </MontageView>
- </Lo-Res>
- <Hi-Res format="ANALYZE 7.5">
- <Layer element="xnat:imageAssessorData.out.file" value="FSEG" num="0"/>
- <LayoutRef name="tal_111"/>
- <MontageView scale="0.65">
- <transverse start_slice="30" end_slice="140" slice_spacing="5"/>
- <sagittal start_slice="35" end_slice="145" slice_spacing="5"/>
- <coronal start_slice="30" end_slice="165" slice_spacing="5"/>
- </MontageView>
- </Hi-Res>
- </ViewableItem> -->
- </PlexiViewer>
-</Viewer>
diff --git a/src/main/webapp/WEB-INF/tags/page/init.tag b/src/main/webapp/WEB-INF/tags/page/init.tag
index 69236762c8603a26dee59a63b544d2ef5c32b920..e1509914c52954f2cde57c82e820379ffb7d37f3 100755
--- a/src/main/webapp/WEB-INF/tags/page/init.tag
+++ b/src/main/webapp/WEB-INF/tags/page/init.tag
@@ -16,7 +16,7 @@
<%-- REDIRECT IF NOT LOGGED IN (username will be '-') --%>
<c:if test="${username == '-'}">
- <c:redirect url="/?timeout=true"/>
+ <c:redirect url="/app/template/Login.vm"/>
</c:if>
<sec:authorize access="hasAnyRole('Administrator', 'administrator', 'Admin', 'admin', 'ADMIN')">
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index 80c36bbaba7f2f13d4dd97f20e3ad41041506178..e1fe607d9927d7a6260257b66f25aec8b18fa581 100644
Binary files a/src/main/webapp/applet/log4j-1.2.17.jar and b/src/main/webapp/applet/log4j__V1.2.17.jar differ
diff --git a/src/main/webapp/applet/log4j__V1.2.17.jar.pack.gz b/src/main/webapp/applet/log4j__V1.2.17.jar.pack.gz
new file mode 100644
index 0000000000000000000000000000000000000000..a4bc1f54d65b4cb307d349ceabca336f87d47846
Binary files /dev/null and b/src/main/webapp/applet/log4j__V1.2.17.jar.pack.gz differ
diff --git a/src/main/webapp/applet/nrgutil-2.0.0.jar b/src/main/webapp/applet/nrgutil-2.0.0.jar
deleted file mode 100644
index 61123e0fc5e419fd205051ab343ca7b08c09d3e7..0000000000000000000000000000000000000000
Binary files a/src/main/webapp/applet/nrgutil-2.0.0.jar and /dev/null differ
diff --git a/src/main/webapp/applet/nrgutil-2.0.0.jar.pack.gz b/src/main/webapp/applet/nrgutil-2.0.0.jar.pack.gz
deleted file mode 100644
index 0cee63d0b457f93f8ef8b557d5d20f279dbfe180..0000000000000000000000000000000000000000
Binary files a/src/main/webapp/applet/nrgutil-2.0.0.jar.pack.gz and /dev/null differ
diff --git a/src/main/webapp/applet/nrgutil__V1.1.0.jar b/src/main/webapp/applet/nrgutil__V1.1.0.jar
new file mode 100644
index 0000000000000000000000000000000000000000..2bb66a242f0ca6f21c8abf9ab2b29e4696343681
Binary files /dev/null and b/src/main/webapp/applet/nrgutil__V1.1.0.jar differ
diff --git a/src/main/webapp/applet/nrgutil__V1.1.0.jar.pack.gz b/src/main/webapp/applet/nrgutil__V1.1.0.jar.pack.gz
new file mode 100644
index 0000000000000000000000000000000000000000..8ffa06177378e71b198557b5f88fb02331dc055b
Binary files /dev/null and b/src/main/webapp/applet/nrgutil__V1.1.0.jar.pack.gz differ
diff --git a/src/main/webapp/applet/plexiviewer-1.6.5.jar b/src/main/webapp/applet/plexiviewer-1.6.5.jar
deleted file mode 100644
index 2ff45b15bd143a3df8c9f0414dde6c4f344ef3ca..0000000000000000000000000000000000000000
Binary files a/src/main/webapp/applet/plexiviewer-1.6.5.jar and /dev/null differ
diff --git a/src/main/webapp/applet/plexiviewer-1.6.5.jar.pack.gz b/src/main/webapp/applet/plexiviewer-1.6.5.jar.pack.gz
deleted file mode 100644
index cb55aaade245f31ced8cca302f7bca563ad6d9bd..0000000000000000000000000000000000000000
Binary files a/src/main/webapp/applet/plexiviewer-1.6.5.jar.pack.gz and /dev/null differ
diff --git a/src/main/webapp/applet/reflections__V0.9.10.jar b/src/main/webapp/applet/reflections__V0.9.10.jar
new file mode 100644
index 0000000000000000000000000000000000000000..b4df7fc82f89ef57f203fb6625c741351c9993a0
Binary files /dev/null and b/src/main/webapp/applet/reflections__V0.9.10.jar differ
diff --git a/src/main/webapp/applet/reflections__V0.9.10.jar.pack.gz b/src/main/webapp/applet/reflections__V0.9.10.jar.pack.gz
new file mode 100644
index 0000000000000000000000000000000000000000..7540addd81ce0ab08517f76b070ab997093929d2
Binary files /dev/null and b/src/main/webapp/applet/reflections__V0.9.10.jar.pack.gz differ
diff --git a/src/main/webapp/applet/slf4j-api-1.7.7.jar.pack.gz b/src/main/webapp/applet/slf4j-api-1.7.7.jar.pack.gz
deleted file mode 100644
index ce2636bbf3155c3a941ae7197a147f55aa93321c..0000000000000000000000000000000000000000
Binary files a/src/main/webapp/applet/slf4j-api-1.7.7.jar.pack.gz and /dev/null differ
diff --git a/src/main/webapp/applet/slf4j-api-1.7.7.jar b/src/main/webapp/applet/slf4j-api__V1.7.7.jar
similarity index 65%
rename from src/main/webapp/applet/slf4j-api-1.7.7.jar
rename to src/main/webapp/applet/slf4j-api__V1.7.7.jar
index c5c4612892e294a844746626197ed470b426868d..a934657518dbe60cd837402f6e765ebe83fb035a 100644
Binary files a/src/main/webapp/applet/slf4j-api-1.7.7.jar and b/src/main/webapp/applet/slf4j-api__V1.7.7.jar differ
diff --git a/src/main/webapp/applet/slf4j-api__V1.7.7.jar.pack.gz b/src/main/webapp/applet/slf4j-api__V1.7.7.jar.pack.gz
new file mode 100644
index 0000000000000000000000000000000000000000..ab6db5d7eaa227ffe8e9113b4af7a36b877ef2a4
Binary files /dev/null and b/src/main/webapp/applet/slf4j-api__V1.7.7.jar.pack.gz differ
diff --git a/src/main/webapp/applet/slf4j-log4j12-1.7.7.jar b/src/main/webapp/applet/slf4j-log4j12-1.7.7.jar
deleted file mode 100644
index 44725f13aaa1c9cf622f35125fa1d18c82802cef..0000000000000000000000000000000000000000
Binary files a/src/main/webapp/applet/slf4j-log4j12-1.7.7.jar and /dev/null differ
diff --git a/src/main/webapp/applet/slf4j-log4j12-1.7.7.jar.pack.gz b/src/main/webapp/applet/slf4j-log4j12-1.7.7.jar.pack.gz
deleted file mode 100644
index 787356dad5c376613de3b7ac908e20e35fc3b25f..0000000000000000000000000000000000000000
Binary files a/src/main/webapp/applet/slf4j-log4j12-1.7.7.jar.pack.gz and /dev/null differ
diff --git a/src/main/webapp/applet/slf4j-log4j12__V1.7.7.jar b/src/main/webapp/applet/slf4j-log4j12__V1.7.7.jar
new file mode 100644
index 0000000000000000000000000000000000000000..f736993e71b5d0c0d9b74a7e1c09f81f8ab02d14
Binary files /dev/null and b/src/main/webapp/applet/slf4j-log4j12__V1.7.7.jar differ
diff --git a/src/main/webapp/applet/slf4j-log4j12__V1.7.7.jar.pack.gz b/src/main/webapp/applet/slf4j-log4j12__V1.7.7.jar.pack.gz
new file mode 100644
index 0000000000000000000000000000000000000000..0ab331040fdf0f026216089ef83df0b6c3a93416
Binary files /dev/null and b/src/main/webapp/applet/slf4j-log4j12__V1.7.7.jar.pack.gz differ
diff --git a/src/main/webapp/applet/upload-assistant__V1.7.0-SNAPSHOT.jar b/src/main/webapp/applet/upload-assistant__V1.7.0-SNAPSHOT.jar
new file mode 100644
index 0000000000000000000000000000000000000000..a6bb3613b56e0a1747a0b4009dfe067ecfcf9c42
Binary files /dev/null and b/src/main/webapp/applet/upload-assistant__V1.7.0-SNAPSHOT.jar differ
diff --git a/src/main/webapp/applet/upload-assistant__V1.7.0-SNAPSHOT.jar.pack.gz b/src/main/webapp/applet/upload-assistant__V1.7.0-SNAPSHOT.jar.pack.gz
new file mode 100644
index 0000000000000000000000000000000000000000..5fdb05aea14e5a4aafd8c33b61c465a61c8d8b64
Binary files /dev/null and b/src/main/webapp/applet/upload-assistant__V1.7.0-SNAPSHOT.jar.pack.gz differ
diff --git a/src/main/webapp/applet/wizard-1.1.jar.pack.gz b/src/main/webapp/applet/wizard-1.1.jar.pack.gz
deleted file mode 100644
index fcf5f0e1b90c59137ea31ab4cde479ffe96e1a75..0000000000000000000000000000000000000000
Binary files a/src/main/webapp/applet/wizard-1.1.jar.pack.gz and /dev/null differ
diff --git a/src/main/webapp/applet/wizard-1.1.jar b/src/main/webapp/applet/wizard__V1.1.jar
similarity index 82%
rename from src/main/webapp/applet/wizard-1.1.jar
rename to src/main/webapp/applet/wizard__V1.1.jar
index 9ab93781af002a16307ade7dc18b7d5e1d0419d9..9bbc078b2f22df1961601757739ff968d120c1ff 100644
Binary files a/src/main/webapp/applet/wizard-1.1.jar and b/src/main/webapp/applet/wizard__V1.1.jar differ
diff --git a/src/main/webapp/applet/wizard__V1.1.jar.pack.gz b/src/main/webapp/applet/wizard__V1.1.jar.pack.gz
new file mode 100644
index 0000000000000000000000000000000000000000..67f37548e017870c18dbe3ed6c8072962b5cb1f6
Binary files /dev/null and b/src/main/webapp/applet/wizard__V1.1.jar.pack.gz differ
diff --git a/src/main/webapp/applet/xdat-beans-1.6.5.jar b/src/main/webapp/applet/xdat-beans-1.6.5.jar
deleted file mode 100644
index 923281834f06f266311ca274f1ac2a52ee146088..0000000000000000000000000000000000000000
Binary files a/src/main/webapp/applet/xdat-beans-1.6.5.jar and /dev/null differ
diff --git a/src/main/webapp/applet/xdat-beans-1.6.5.jar.pack.gz b/src/main/webapp/applet/xdat-beans-1.6.5.jar.pack.gz
deleted file mode 100644
index b0a01a241c4d928534c5e9a05c81dd93105dbd24..0000000000000000000000000000000000000000
Binary files a/src/main/webapp/applet/xdat-beans-1.6.5.jar.pack.gz and /dev/null differ
diff --git a/src/main/webapp/applet/xnat-data-models__V1.7.0-SNAPSHOT.jar b/src/main/webapp/applet/xnat-data-models__V1.7.0-SNAPSHOT.jar
new file mode 100644
index 0000000000000000000000000000000000000000..953e80b8ae689cd929382a5d1900cac288925fed
Binary files /dev/null and b/src/main/webapp/applet/xnat-data-models__V1.7.0-SNAPSHOT.jar differ
diff --git a/src/main/webapp/applet/xnat-data-models__V1.7.0-SNAPSHOT.jar.pack.gz b/src/main/webapp/applet/xnat-data-models__V1.7.0-SNAPSHOT.jar.pack.gz
new file mode 100644
index 0000000000000000000000000000000000000000..f4c80e9dad841d0b33bf307ce2a083684f32b580
Binary files /dev/null and b/src/main/webapp/applet/xnat-data-models__V1.7.0-SNAPSHOT.jar.pack.gz differ
diff --git a/src/main/webapp/page/admin/fake.jsp b/src/main/webapp/page/admin/fake.jsp
index 5d63f24f09323bea4e3e452802c48e86fb0c9e6d..18e16850573a3bd3d634a89b2f828ecfac2c7261 100644
--- a/src/main/webapp/page/admin/fake.jsp
+++ b/src/main/webapp/page/admin/fake.jsp
@@ -199,7 +199,7 @@
<label class="element-label" for="session-timeout-input">Session Timeout</label>
<div class="element-wrapper">
<input name="sessionTimeout" id="session-timeout-input" type="text" size="3" title="Session Timeout">
- <div class="description">Interval for timing out alias tokens. Uses PostgreSQL interval notation: http://www.postgresql.org/docs/9.0/static/functions-datetime.html</div>
+ <div class="description">Number of minutes of inactivity before users are locked out of the site. This will not affect users that are currently logged in.</div>
</div>
</div>
<div class="panel-element" data-name="sessionTimeoutMessage">
diff --git a/src/main/webapp/page/admin/spawner/content.jsp b/src/main/webapp/page/admin/spawner/content.jsp
index a2b46a582709ec3003c4b944406a5f44a06cdb80..e7633ba951fc41bd4bd0821660825308fc886b51 100644
--- a/src/main/webapp/page/admin/spawner/content.jsp
+++ b/src/main/webapp/page/admin/spawner/content.jsp
@@ -24,7 +24,7 @@
<%--<label class="element-label" for="!?"></label>--%>
<%--<div class="element-wrapper">--%>
- <table id="spawner-element-list" class="xnat-table alt1 clean" style="width:100%">
+ <table id="spawner-element-list" class="xnat-table alt1 clean" style="width:100%;border:none;">
<!-- list of available namespaces will show here -->
</table>
diff --git a/src/main/webapp/page/admin/spawner/spawner-admin.js b/src/main/webapp/page/admin/spawner/spawner-admin.js
index 7645623f608631cbedceec1a0a4d0e504f936c3c..b9556b8ed925c278bc0481c243776e6d86b15152 100644
--- a/src/main/webapp/page/admin/spawner/spawner-admin.js
+++ b/src/main/webapp/page/admin/spawner/spawner-admin.js
@@ -1,26 +1,26 @@
(function(){
- function showJSON(json){
- return xmodal.message({
- title: 'Site Admin JSON',
- maximize: true,
- width: '90%',
- height: '90%',
- content: spawn('pre.json', JSON.stringify(json, null, 2)).outerHTML
- })
- }
-
- spawn('button|type=button', {
- html: 'View JSON',
- onclick: function(){
- XNAT.xhr.get(XNAT.url.rootUrl('/xapi/spawner/resolve/siteAdmin/adminPage'), function(data){
- showJSON(data);
- });
- },
- $: {
- appendTo: '#view-json'
- }
- });
+ // function showJSON(json){
+ // return xmodal.message({
+ // title: 'Site Admin JSON',
+ // maximize: true,
+ // width: '90%',
+ // height: '90%',
+ // content: spawn('pre.json', JSON.stringify(json, null, 2)).outerHTML
+ // })
+ // }
+ //
+ // spawn('button|type=button', {
+ // html: 'View JSON',
+ // onclick: function(){
+ // XNAT.xhr.get(XNAT.url.rootUrl('/xapi/spawner/resolve/siteAdmin/adminPage'), function(data){
+ // showJSON(data);
+ // });
+ // },
+ // $: {
+ // appendTo: '#view-json'
+ // }
+ // });
//$('#view-json').click(function(){});
@@ -72,7 +72,7 @@ XNAT.xhr.getJSON({
}]
]]);
- var idsMenu = spawn('select#spawner-ns-ids', [['option|value=!', 'Select an Element']]);
+ var idsMenu = spawn('select.spawner-ns-ids', [['option|value=!', 'Select an Element']]);
tds.push(['td', [
@@ -84,7 +84,7 @@ XNAT.xhr.getJSON({
type: 'button',
html: 'View Selected Element',
onclick: function(){
- var getId = $('#spawner-ns-ids').val();
+ var getId = $(idsMenu).val();
if (!getId || getId === '!') {
xmodal.message('Select an Element ID');
return false;
diff --git a/src/main/webapp/scripts/search/dataTableSearch.js b/src/main/webapp/scripts/search/dataTableSearch.js
index ccef3342b157cf3562cbb47bf33be9b26164cd52..c50c2e9dff994460d3f76d038cc2bcb726fa7633 100644
--- a/src/main/webapp/scripts/search/dataTableSearch.js
+++ b/src/main/webapp/scripts/search/dataTableSearch.js
@@ -676,7 +676,7 @@ function DataTableSearch(_div_table_id,obj,_config,_options){
//insert option menu
this.renderOptions=function(obj1,obj2){
this.optionMenu=null;
- this.optionMenu=new YAHOO.widget.MenuBar(this.div_table_id +"_options",{hidedelay:750});
+ this.optionMenu=new YAHOO.widget.MenuBar(this.div_table_id +"_options",{hidedelay:300, maxheight:200, submenualignment: ["tr","br"]});
this.optionMenu.search=this;
this.optionMenu.en=this.initResults.ResultSet.rootElementName;
diff --git a/src/main/webapp/scripts/xnat/admin/siteInfo.js b/src/main/webapp/scripts/xnat/admin/siteInfo.js
new file mode 100644
index 0000000000000000000000000000000000000000..10c0ede2fe4560605ef96616e12a2cd4e97b9682
--- /dev/null
+++ b/src/main/webapp/scripts/xnat/admin/siteInfo.js
@@ -0,0 +1,31 @@
+var sdtPage, sdtText;
+setTimeout(function(){
+ sdtPage = $('#siteDescriptionTypePage');
+ sdtText = $('#siteDescriptionTypeText');
+ sdtPage.click(changeSiteDescriptionType);
+ sdtText.click(changeSiteDescriptionType);
+ changeSiteDescriptionType(XNAT.data.siteConfig.siteDescriptionType);
+}, 100);
+function changeSiteDescriptionType(eventOrValue){
+ var value = eventOrValue;
+ if(typeof eventOrValue === 'object'){
+ if(eventOrValue.target.id == "siteDescriptionTypeText"){
+ value = 'Text';
+ } else {
+ value = 'Page';
+ }
+ }
+ sdtText.val(value);
+ sdtPage.val(value);
+ var text = $('#siteDescriptionText').parent().parent();
+ var page = $('#siteDescriptionPage').parent().parent();
+ if(value == 'Text'){
+ sdtText.prop('checked',true);
+ text.show();
+ page.hide();
+ } else {
+ sdtPage.prop('checked',true);
+ page.show();
+ text.hide();
+ }
+};
\ No newline at end of file
diff --git a/src/main/webapp/scripts/xnat/admin/themeManagement.js b/src/main/webapp/scripts/xnat/admin/themeManagement.js
new file mode 100644
index 0000000000000000000000000000000000000000..930e230b9ced35ee49cde6d64c1d982e8f3d70bf
--- /dev/null
+++ b/src/main/webapp/scripts/xnat/admin/themeManagement.js
@@ -0,0 +1,128 @@
+/*
+ * org.nrg.xnat.turbine.modules.screens.ManageProtocol
+ * XNAT http://www.xnat.org
+ * Copyright (c) 2013, Washington University School of Medicine
+ * All Rights Reserved
+ *
+ * Released under the Simplified BSD.
+ *
+ * Author: Justin Cleveland <clevelandj@wustl.edu>
+ * Last modified 3/17/2016 3:33 PM
+ */
+var themeUrl = XNAT.url.rootUrl('xapi/theme');
+var s = '/', q = '?', a = '&';
+var csrf = 'XNAT_CSRF='+window.csrfToken;
+$('#titleAppName').text(XNAT.app.siteId);
+var currentTheme = $('#currentTheme');
+var themeSelector = $('#themeSelection');
+var themeUploadForm = document.getElementById('themeFileUpload-form');
+var themeUploader = document.getElementById('themeFileUpload-input');
+var themeUploadSubmit = document.getElementById('themeFileUpload-button');
+var selectedTheme = null;
+function populateThemes(){
+ getCurrentTheme(getAvailableThemes);
+};
+function getCurrentTheme(callback){
+ var role = 'global';
+ $.get(themeUrl+s+role+q+csrf, null, function (data){
+ themeSelector.empty();
+ selectedTheme = data.name?data.name:'None';
+ currentTheme.text(selectedTheme);
+ if(typeof callback === 'function'){
+ callback(data.name);
+ }
+ }, 'json');
+};
+function getAvailableThemes(selected){
+ $.get(themeUrl+q+csrf, null, function (data){
+ themeSelector.empty();
+ addThemeOptions(data, selected);
+ }, 'json');
+};
+function addThemeOptions(newThemeOptions, selected){
+ if(Array.isArray(newThemeOptions)) {
+ $(newThemeOptions).each(function (i, opt) {
+ var select = '';
+ if (selected == opt.value) {
+ select = ' selected="selected"';
+ }
+ themeSelector.append('<option value="'+opt.value+'"'+select+'>'+opt.label+'</option>');
+ });
+ }
+};
+function selectTheme(themeToSelect){
+ if(themeToSelect && typeof themeToSelect === 'string'){
+ themeSelector.val(themeToSelect);
+ }
+};
+var themeSelectionForm = $('#themeSelection').parent().parent().parent().parent();
+themeSelectionForm.off('submit');
+themeSelectionForm.submit(function(ev){
+ ev.preventDefault();
+ 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+s+encodeURI(themeSelector.val())+q+csrf, null, function(data){
+ console.log(data);
+ populateThemes()
+ });
+ }
+ });
+})
+function removeTheme(){
+ xmodal.confirm({
+ content: 'Are you sure you wish to delete the selected theme?',
+ action: function(){
+ $.delete(themeUrl+s+encodeURI(themeSelector.val())+q+csrf, null, function(data){
+ console.log(data);
+ populateThemes();
+ });
+ }
+ });
+};
+
+/*** Theme Package Upload Functions ***/
+themeUploadForm.action = themeUrl+q+csrf;
+$(themeUploadForm).parent().css('position','relative');
+$(themeUploadForm).parent().css('top','-30px');
+themeUploadForm.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('themePackage', file, file.name); // formData.append('themes[]', file, file.name);
+ var xhr = new XMLHttpRequest();
+ xhr.open('POST', themeUploadForm.action, true);
+ xhr.onload = function () {
+ if (xhr.status !== 200) {
+ console.log(xhr.statusText);
+ console.log(xhr.responseText);
+ xmodal.message('Upload Error', 'There was a problem uploading your theme package.<br>Server responded with: '+xhr.statusText);
+ }
+ $(themeUploadSubmit).text('Upload');
+ $(themeUploadSubmit).removeAttr('disabled');
+ var newThemeOptions = $.parseJSON(xhr.responseText);
+ var selected;
+ if(newThemeOptions[0]){
+ selected = newThemeOptions[0].value;
+ }
+ addThemeOptions(newThemeOptions, selected);
+ };
+ 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"
diff --git a/src/main/webapp/scripts/xnat/app/siteSetup.js b/src/main/webapp/scripts/xnat/app/siteSetup.js
index 45915b9fe04a5457d3b4839ee9be7e45fa30c962..997b6fa9c50897208026669e99c67d932d8cc989 100644
--- a/src/main/webapp/scripts/xnat/app/siteSetup.js
+++ b/src/main/webapp/scripts/xnat/app/siteSetup.js
@@ -87,7 +87,7 @@ var XNAT = getObject(XNAT);
multiForm = spawn('form', {
name: opts.name,
- classes: 'xnat-form-panel multi-form panel panel-default',
+ classes: 'xnat-form-panel multi-form',
method: opts.method || 'POST',
action: opts.action ? XNAT.url.rootUrl(opts.action) : '#!',
onsubmit: function(e){
@@ -213,10 +213,7 @@ var XNAT = getObject(XNAT);
}
}, [
- ['div.panel-heading', [
- ['h3.panel-title', opts.title || opts.label]
- ]],
-
+
// 'inner' is where the NEXT spawned item will render
inner,
diff --git a/src/main/webapp/scripts/xnat/ui/panel.js b/src/main/webapp/scripts/xnat/ui/panel.js
index 54b24abfe724ba50669b7fd12aeff1f8a6fb1447..1f3c3c43d29751d77fa7f4f1016e8b13ce57fb46 100644
--- a/src/main/webapp/scripts/xnat/ui/panel.js
+++ b/src/main/webapp/scripts/xnat/ui/panel.js
@@ -137,16 +137,25 @@ var XNAT = getObject(XNAT || {});
// set form element values from an object map
function setValues(form, dataObj){
// find all form inputs with a name attribute
- $$(form).find(':input[name]').each(function(){
- var val = dataObj[this.name];
+ $$(form).find(':input').each(function(){
+
+ var val = dataObj[this.name||this.title];
+
if (!val) return;
+
if (Array.isArray(val)) {
val = val.join(', ');
}
else {
val = stringable(val) ? val : JSON.stringify(val);
}
- $(this).changeVal(val);
+
+ $(this).val(val);
+
+ if (/checkbox|radio/i.test(this.type)) {
+ this.checked = !!this.value;
+ }
+
});
if (xmodal && xmodal.loading && xmodal.loading.closeAll){
xmodal.loading.closeAll();
@@ -181,6 +190,7 @@ var XNAT = getObject(XNAT || {});
// if 'load' starts with '!?' do an eval()
var doEval = '!?';
+
if (obj.load && obj.load.toString().indexOf(doEval) === 0) {
obj.load = (obj.load.split(doEval)[1]||'').trim();
setValues(form, eval(obj.load));
@@ -193,23 +203,18 @@ var XNAT = getObject(XNAT || {});
// REST
//////////
+ var ajaxUrl = obj.refresh || '';
+
// if 'load' starts with $?, do ajax request
var ajaxPrefix = '$?';
- var ajaxUrl = '';
var ajaxProp = '';
-
- if (obj.refresh) {
- ajaxUrl = obj.refresh;
- }
// value: $? /path/to/data | obj:prop:name
- else if (obj.load && obj.load.toString().indexOf(ajaxPrefix) === 0) {
- ajaxUrl = obj.load;
+ if (obj.load && obj.load.toString().indexOf(ajaxPrefix) === 0) {
+ ajaxUrl = (obj.load.split(ajaxPrefix)[1]||'').trim().split('|')[0];
+ ajaxProp = ajaxUrl.split('|')[1] || '';
}
- ajaxUrl = (ajaxUrl.split(ajaxPrefix)[1]||'').trim().split('|')[0];
- ajaxProp = ajaxUrl.split('|')[1] || '';
-
// need a url to get the data
if (!ajaxUrl || !stringable(ajaxUrl)) {
xmodal.loading.close('#load-data');
@@ -268,7 +273,7 @@ var XNAT = getObject(XNAT || {});
// click 'Discard Changes' button to reload data
_resetBtn.onclick = function(){
- if (!/^#/.test($formPanel.attr('action')||'#')){
+ if (!/^#/.test($formPanel.attr('action'))){
$formPanel.triggerHandler('reload-data');
}
};
@@ -296,7 +301,7 @@ var XNAT = getObject(XNAT || {});
multiform = {};
// don't submit forms with 'action' starting with '#'
- if (/^#/.test($form.attr('action')||'#')) {
+ if (/^#/.test($form.attr('action'))) {
return false;
}
diff --git a/src/main/webapp/scripts/xnat/ui/templates.js b/src/main/webapp/scripts/xnat/ui/templates.js
index df5dadf4d40bc78fcda445acc23f3aa560752117..22fea19499da633696e49701d0560d5c7d2056e2 100644
--- a/src/main/webapp/scripts/xnat/ui/templates.js
+++ b/src/main/webapp/scripts/xnat/ui/templates.js
@@ -262,7 +262,9 @@ var XNAT = getObject(XNAT);
var hiddenInput;
// check buttons if value is true
- if (/checkbox|radio/i.test(opts.type||'')) {
+ if (/checkbox|radio/i.test(element.type||'')) {
+
+ element.checked = /true|checked/i.test((opts.checked || element.value).toString());
element.checked = /true|checked/i.test((opts.checked || element.value).toString());
@@ -320,7 +322,7 @@ var XNAT = getObject(XNAT);
// add the options
$.each(opts.options||{}, function(name, prop){
var _option = spawn('option', extend(true, {
- html: prop.label || prop.value || prop,
+ html: prop.html || prop.text || prop.label || prop.value || prop,
value: prop.value || name
}, prop.element));
// select the option if it's the select element's value
diff --git a/src/main/webapp/scripts/xnat/xhr.js b/src/main/webapp/scripts/xnat/xhr.js
index e0df7ab2fcb9b2d2efa6986dce28268c751973f6..b7e97c987bb64b30479d534b9920a8dd041b867a 100755
--- a/src/main/webapp/scripts/xnat/xhr.js
+++ b/src/main/webapp/scripts/xnat/xhr.js
@@ -483,7 +483,7 @@ var XNAT = getObject(XNAT||{}),
opts.method = opts.method || _form.method || 'GET';
if ($.isFunction(opts.validate)) {
- validation = opts.validate.apply(_form, opts);
+ validation = opts.validate.call(_form, opts);
if (!validation) {
$form.removeClass('valid').addClass('invalid');
return validation;
@@ -541,8 +541,8 @@ var XNAT = getObject(XNAT||{}),
// intercept form submissions with 'ajax' or 'json' class
// using namespaced event handler submit.json
- $('body').on('submit-json, submit-ajax', 'form.ajax, form.json', function(opts){
- return xhr.form(this, opts);
+ $('body').on('submit.json, submit.ajax', 'form.ajax, form.json', function(){
+ return xhr.form(this);
});
// special case for YUI 'GET' request
diff --git a/src/main/webapp/scripts/yui/build/assets/skins/xnat/xnat.css b/src/main/webapp/scripts/yui/build/assets/skins/xnat/xnat.css
index 4299483238dad217832d0c6728a9a9b71c44f576..82ab74682e82282f01826b0c82ad69b8b0053d83 100644
--- a/src/main/webapp/scripts/yui/build/assets/skins/xnat/xnat.css
+++ b/src/main/webapp/scripts/yui/build/assets/skins/xnat/xnat.css
@@ -2124,7 +2124,7 @@ h2.yui-editor-skipheader,h3.yui-editor-skipheader { height: 0 ; margin: 0 ; padd
.yui-skin-sam .yui-navset .yui-nav a em,
.yui-skin-sam .yui-navset .yui-navset-top .yui-nav a em {
- border: 1px solid #e0e0e0;
+ border: 1px solid #aaa;
border-bottom: none;
padding: 8px 16px;
cursor: hand;
diff --git a/src/main/webapp/style/app.css b/src/main/webapp/style/app.css
index 29caed8206049715b08329e05b9e62678b3d2be6..ee76cc001dcf71ffac5478b61acb9eca2dbdcaeb 100644
--- a/src/main/webapp/style/app.css
+++ b/src/main/webapp/style/app.css
@@ -985,6 +985,7 @@ body [type="reset"] {
font-size: 13px;
letter-spacing: 0.02em;
text-decoration: none;
+ box-shadow: 0px 1px 1px #ccc;
}
/* style for button hover */
@@ -995,6 +996,7 @@ body button:hover,
body [type="button"]:hover,
body [type="submit"]:hover,
body [type="reset"]:hover {
+ box-shadow: none;
cursor: pointer;
}
@@ -1007,8 +1009,10 @@ body input.btn1,
body .btn1[type="button"],
body [type="submit"] {
color: #fff;
- background: #1A75BB;
- border: 1px solid #096BB7;
+ background: #1A75BB linear-gradient( #3C8BC7, #1A75BB );
+ /*border: 1px solid #102040;*/
+ border: 1px solid #033E77;
+ box-shadow: 0 1px 1px #848484;
}
.btn1:hover,
@@ -1018,7 +1022,9 @@ body [type="submit"] {
body input.btn1:hover,
body .btn1[type="button"]:hover,
body [type="submit"]:hover {
- background: #096BB7;
+ /*background: #096BB7;*/
+ background: #1A75BB;
+ box-shadow: none;
}
/* btn2 gets gray background */
@@ -1028,7 +1034,7 @@ body button,
body [type="button"],
body [type="reset"] {
background: #f0f0f0 linear-gradient( #ffffff, #f0f0f0 );
- border: 1px solid #c0c0c0;
+ border: 1px solid #848484;
}
.btn:hover,
@@ -1511,6 +1517,8 @@ body.modal-popup #xnat_power {
.yui-skin-sam .yui-button button,
.yui-skin-sam .yui-button a,
.yui-skin-sam .yui-button a:visited {
+ border: none;
+ box-shadow: none;
color: #000000;
font-size: 12px;
height: 26px;
@@ -1610,7 +1618,7 @@ div.edit_title {
.yui-skin-sam .yuimenu .bd {
background-color: #fff;
- border: 1px solid #ccc;
+ border: 1px solid #aaa;
}
td.highlighted {
@@ -1789,7 +1797,9 @@ div.containerTitle.withColor {
margin-top: 0;
padding: 1px;
background: #fff;
- border: 1px solid #c0c0c0;
+ border: solid #aaa;
+ border-width: 0 1px 1px;
+ border-top: 1px solid #102040;
}
/* make sure all sub-nav menus are wide enough */
@@ -1825,14 +1835,14 @@ div.containerTitle.withColor {
display: none;
top: 0;
margin-left: -2px;
- border: 1px solid #c0c0c0;
+ border: 1px solid #aaa;
}
#main_nav ul.nav ul,
.shadowed {
- -moz-box-shadow: 0 2px 12px rgba(96, 96, 96, 0.8);
- -webkit-box-shadow: 0 2px 12px rgba(96, 96, 96, 0.8);
- box-shadow: 0 2px 12px rgba(96, 96, 96, 0.8);
+ -moz-box-shadow: 0 1px 4px rgba(132, 132, 132, 0.8);
+ -webkit-box-shadow: 0 1px 4px rgba(132, 132, 132, 0.8);
+ box-shadow: 0 1px 4px rgba(132, 132, 132, 0.8);
/* border: 2px solid rgba(204,204,204,0.5) ; */
}
diff --git a/src/main/webapp/style/app.less b/src/main/webapp/style/app.less
deleted file mode 100644
index 2c3e183ab924a2b443401151934f1c4f4cc1ce99..0000000000000000000000000000000000000000
--- a/src/main/webapp/style/app.less
+++ /dev/null
@@ -1,3280 +0,0 @@
-/* xdat.css */
-/***********************************************/
-/* Default styles */
-/***********************************************/
-body {
- margin: 0;
- padding: 0;
- font-size: 12px;
- line-height: 15px;
- font-family: Arial, Helvetica, sans-serif;
- background-color: white;
-}
-
-th {
- margin: 0;
- border-top: none;
- border-right: none;
- border-left: none;
- border-collapse: collapse;
- padding: 0 4px;
-}
-
-h2 {
- line-height: 24px;
-}
-
-h3 {
- line-height: 20px;
- margin: 0;
-}
-
-h4 {
- line-height: 18px;
-}
-
-p {
- font-size: 13px;
- line-height: 17px;
- margin: 0;
-}
-
-td {
- /* */
-}
-
-a.plainText {
- text-decoration: none;
- color: black;
-}
-
-a {
- cursor: pointer;
- text-decoration: none;
- color: #039;
-}
-
-img {
- border: none;
-}
-
-input[type="text"],
-input[type="password"],
-input[type="number"] {
- padding: 4px 5px 3px 5px;
- border: 1px solid #b0b0b0;
-}
-
-textarea {
- padding: 4px;
- font-family: Arial, Helvetica, sans-serif;
- font-size: 12px;
- border: 1px solid #b0b0b0;
-}
-
-select {
- /* */
-}
-
-/* xnat.css */
-/***********************************************/
-/* XNAT styles */
-/***********************************************/
-.withColor {
- background-color: #2d69b8;
- color: #fff;
-}
-
-.withThinBorder {
- border: 1px solid #aaa;
-}
-
-.recentDataActivity {
- cursor: default;
-}
-
-.text {
- font-size: 11px;
- line-height: 13px;
- font-family: Arial, Helvetica, sans-serif;
-}
-
-div.link {
- cursor: pointer;
- text-decoration: none;
- font-size: 11px;
- font-family: Arial, Helvetica, sans-serif;
- color: #039;
-}
-
-div.edit_title {
- font-size: 16px;
- line-height: 18px;
-}
-
-div.edit_header1 {
- font-size: 14px;
- line-height: 18px;
-}
-
-div.edit_header2 {
- font-size: 13px;
- line-height: 16px;
-}
-
-div.edit_header3 {
- font-size: 12px;
- line-height: 15px;
-}
-
-div.spacer {
- line-height: 13px;
-}
-
-.actionsBox {
- background-color: #dcdcdc;
-}
-
-.quarantine {
- background-color: #fc3;
-}
-
-#loginBox {
- top: 2px;
- position: absolute;
- text-align: right;
- right: 5px;
-}
-
-#menu1 {
- position: relative;
- top: 2px;
- left: 5px;
- width: 99%;
- height: 28px;
- border-bottom: 1px solid #aaa;
-}
-
-div.option {
- /* */
-}
-
-#tabbedList {
- margin: 10px;
-}
-
-#tabbedList li a {
- height: 20px;
- text-decoration: none;
-}
-
-#tabbedList li a:link, #tabbedList li a:visited {
- color: #000;
- display: block;
- padding: 8px 0 0 10px;
-}
-
-#tabbedList li a:hover {
- background-color: #fff;
- padding: 8px 0 0 10px;
-}
-
-td.leftBar {
- width: 170px;
- padding-top: 10px;
- padding-left: 10px;
-}
-
-/* hide leftBar if it decides to show up on a popup page */
-body.popup td.leftBar {
- width: 0;
- padding: 0;
-}
-
-body.popup td.leftBar > div {
- display: none;
-}
-
-ul.menu {
- list-style-type: none;
- text-decoration: none;
- margin: 0;
- padding: 0;
-}
-
-ul.menu li {
- float: left;
- position: relative;
- margin: 0;
- padding: 2px 6px;
-}
-
-ul.subMenu {
- margin: 0;
- padding: 1px;
- padding-top: 3px;
- display: none;
- position: absolute;
- text-decoration: none;
-}
-
-ul.subMenu li {
- list-style-type: none;
- margin: 0;
- padding: 4px 8px;
-}
-
-ul.topMenu {
- background-color: #fff;
- height: 20px;
- text-align: center;
- font-size: 11px;
- color: #4D4D4D;
- z-index: 4000;
-}
-
-ul.topMenu li {
- border: 0 solid #aaa;
- width: 124px;
-}
-
-li.topMenuHover {
- background-color: #fff;
-}
-
-ul.topSubMenu {
- text-align: center;
- color: #4D4D4D;
- z-index: 4000;
-}
-
-ul.topSubMenu li {
- border: 1px solid #aaa;
- font-size: 11px;
-}
-
-li.topSubMenuHover {
- /* */
-}
-
-div.container {
- border: 1px solid #ccc; /* width:300px; */
-}
-
-div.mainContainer {
- border: 1px solid #ccc; /* width:300px; */
-}
-
-div.containerTitle {
- border-bottom: 1px solid #ccc;
- font-size: 13px;
- font-weight: 500;
- line-height: 23px;
- padding-left: 7px !important;
- padding-right: 7px !important;
-}
-
-div.containerBody {
- overflow: auto;
- font-size: 12px;
- line-height: 15px;
- padding: 0;
-}
-
-div.containerBody a {
- font-weight: bold;
-}
-
-div.containerBody > div > div {
- padding: 5px 10px 9px;
- font-size: 12px;
-}
-
-div.containerBody #min_expt_list {
- /* */
-}
-
-div.containerBody #min_expt_list td {
- padding: 3px 6px;
-}
-
-div.containerBody h3 {
- margin: 2px 0 5px;
- font-size: 13px;
- line-height: 15px;
-}
-
-div.mainContainerBody {
- overflow: auto;
- font-size: 11px;
- line-height: 13px;
- padding: 3px;
-}
-
-div.containerItem { /* font-size: 11px ; line-height: 13px ; */
- padding: /* 3px 0 0 3px */ 8px 12px 0 12px;
-}
-
-div.projectIndex {
- font-size: 11px;
- line-height: 13px;
- padding: 3px;
- border-top: 1px solid #aaa;
-}
-
-.horizontalMenu {
- font-size: 13px;
- line-height: 15px;
- position: relative;
- padding: 3px;
-}
-
-.horizontalMenuItem {
- font-size: 11px;
- line-height: 13px;
- bottom: 0;
- display: inline;
- padding-right: 3px;
-}
-
-ul.containerMenu {
- font-size: 11px;
- padding-right: 0;
-}
-
-ul.containerMenu li {
- float: right;
- padding-right: 0;
-}
-
-ul.containerSubMenu {
- background-color: #fff;
- border: 1px solid #aaa;
-}
-
-ul.containerSubMenu li {
- float: none;
- padding-right: 0;
-}
-
-div.titleBarLink {
- text-decoration: none;
- font-size: 11px;
- color: #039;
- cursor: pointer;
- display: inline;
- height: 16px;
- border-left: 1px solid #aaa;
- border-right: 1px solid #aaa;
- border-bottom: 1px solid #aaa;
- padding-left: 5px;
- padding-right: 5px;
- margin-left: 0;
- margin-right: 0;
- background-color: #ffd;
-}
-
-div.titleBarLink:hover {
- background-color: #dedede;
-}
-
-div.titleBarText {
- text-decoration: none;
- font-size: 11px;
- color: black;
- display: inline;
- height: 16px;
- border-left: 1px solid #aaa;
- border-right: 1px solid #aaa;
- border-bottom: 1px solid #aaa;
- padding-left: 5px;
- padding-right: 5px;
- background-color: #fff;
- margin-left: 0;
- margin-right: 0;
-}
-
-div.titleBarGrey {
- text-decoration: none;
- font-weight: 500;
- font-size: 11px;
- color: black;
- display: inline;
- height: 16px;
- border-left: 1px solid #aaa;
- border-right: 1px solid #aaa;
- border-bottom: 1px solid #aaa;
- padding-left: 5px;
- padding-right: 5px;
- margin-left: 0;
- margin-right: 0;
- background-color: #fff;
-}
-
-font.titleBarComment {
- text-decoration: none;
- font-weight: 500;
- font-size: 11px;
- color: black;
-}
-
-.odd {
- background-color: #fff;
-}
-
-.even {
- background-color: #f7f7f7;
- border-top: 1px solid #ececec;
- border-bottom: 1px solid #ececec;
-}
-
-div.projectPrimary { /* font-weight: 700 ; */
-}
-
-td.highlighted {
- background-color: #ffc;
- border: 1px solid #aaa;
-}
-
-td.results {
- white-space: nowrap;
-}
-
-div.paging {
- text-align: center;
- font-size: 11px;
- z-index: 4000;
-}
-
-div.pagingTitle {
- float: left;
- position: relative;
-}
-
-table.paging {
- line-height: 11px;
- margin: 0;
- padding: 0;
- font-size: 11px;
-}
-
-tbody.paging {
- line-height: 11px;
- margin: 0;
- padding: 0;
- font-size: 11px;
-}
-
-tr.paging {
- line-height: 11px;
- margin: 0;
- padding: 0;
- font-size: 11px;
-}
-
-td.paging {
- line-height: 11px;
- margin: 0;
- font-size: 11px;
-}
-
-ul.paging {
- text-decoration: none;
- margin: 0;
- padding-left: 10px;
-}
-
-li.paging {
- list-style-type: none;
- float: left;
- position: relative;
- margin: 0;
- padding-left: 6px;
- padding-right: 6px;
- font-size: 11px;
-}
-
-a.paging {
- cursor: pointer;
- display: block;
- text-decoration: none;
- color: #039;
-}
-
-div.optionsTab {
- background-color: #fff;
- border: 1px solid #aaa;
- white-space: nowrap;
- padding: 3px;
-}
-
-div.quickSearch {
- padding: 2px;
- border: 1px solid #e8e8e8;
- white-space: nowrap;
- width: 180px;
-}
-
-td.x_rs_td {
- white-space: nowrap;
- border: 1px solid #7F7F7F;
- margin: 0;
- border-left-style: none;
- border-top-style: none;
- font-size: 12px;
- padding: 2px 6px 2px 4px;
-}
-
-td.x_rs_td a {
- font-weight: bold;
-}
-
-th.x_rs_th {
- white-space: nowrap;
- border-collapse: collapse;
- border: 1px solid #7F7F7F;
- color: #000;
- margin: 0;
- padding: 4px 10px 4px 10px;
- text-decoration: none;
- vertical-align: middle;
- border-left-style: none;
-}
-
-tr.even > td.sorted {
- background-color: #BFBFBF;
-}
-
-tr.odd > td.sorted {
- background-color: #F2F2F2;
-}
-
-th.sorted {
- /* */
-}
-
-td.first-td {
- border-left-style: solid;
-}
-
-th.first-td {
- border-left-style: solid;
-}
-
-td.ext-content {
- width: 300px;
- white-space: normal;
-}
-
-/* yellow text = NOPE */
-font[color="yellow"] {
- color: #888;
-}
-
-/* universal button style with CSS gradient */
-.button {
- display: inline-block;
- margin: 1px;
- padding: 2px 2px 4px;
- border: 1px solid #808080;
- border-radius: 3px;
- -moz-border-radius: 3px;
- -webkit-border-radius: 3px;
- -khtml-border-radius: 3px;
- font-weight: bold;
- text-align: center;
- background: #888;
- background: -moz-linear-gradient(top, #cccccc 0%, #999999 25%);
- /* FF3.6+ */
- background: -webkit-gradient(linear, left top, left bottom, color-stop(0%, #cccccc), color-stop(25%, #999999));
- /* Chrome,Safari4+ */
- background: linear-gradient(top, #cccccc 0%, #999999 25%);
- /* W3C */
- color: #fff;
-}
-
-/* width set for QC buttons */
-.QC {
- width: 4em;
-}
-
-/* styles set for QC results */
-.good {
- background: #390;
- background: -moz-linear-gradient(top, #66cc33 0%, #339900 25%);
- background: -webkit-gradient(linear, left top, left bottom, color-stop(0%, #66cc33), color-stop(25%, #339900));
- background: linear-gradient(top, #66cc33 0%, #339900 25%);
-}
-
-.acceptable {
- background: #c90;
- background: -moz-linear-gradient(top, #ffcc33 0%, #cc9900 25%);
- background: -webkit-gradient(linear, left top, left bottom, color-stop(0%, #ffcc33), color-stop(25%, #cc9900));
- background: linear-gradient(top, #ffcc33 0%, #cc9900 25%);
-}
-
-.bad {
- background: #900;
- background: -moz-linear-gradient(top, #cc3333 0%, #990000 25%);
- background: -webkit-gradient(linear, left top, left bottom, color-stop(0%, #cc3333), color-stop(25%, #990000));
- background: linear-gradient(top, #cc3333 0%, #990000 25%);
-}
-
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- vertical-align: top;
-}
-
-.xnat-table .middle {
- vertical-align: middle;
-}
-
-.xnat-table .bottom {
- vertical-align: bottom;
-}
-
-.xnat-table .left {
- text-align: left !important;
-}
-
-.xnat-table .center {
- text-align: center !important;
-}
-
-.xnat-table .right {
- text-align: right !important;
-}
-
-/* override .even and .odd styles - these are not needed in .xnat-table tables */
-.xnat-table .even,
-.xnat-table .odd {
- background: #fff;
- border: none;
-}
-
-/* alternate styling options for "xnat-table" tables */
-.xnat-table.alt1 {
- border-color: #d0d0d0;
-}
-
-.xnat-table.alt1 th {
- background: #f0f0f0;
- text-align: left;
- font-weight: bold;
-}
-
-.xnat-table.alt1 th,
-.xnat-table.alt1 td {
- border-color: #d0d0d0;
-}
-
-.xnat-table.rows-only th,
-.xnat-table.rows-only td {
- border-left: none;
- border-right: none;
-}
-
-.xnat-table.clean th {
- border-right: none;
-}
-
-.xnat-table.clean td {
- border: none;
-}
-
-.xnat-table.clean tr:hover {
- background: #e5f2ff;
-}
-
-/* overrides for Chosen menus (if used) */
-html .chosen-container-single .chosen-single {
- color: #000;
-}
-
-/* fix for #layout_content being rendered in an xmodal modal */
-div.xmodal #layout_content {
- padding-top: 0;
-}
-
-/* prearchive file list modal */
-table.file-details {
- margin-top: -5px;
-}
-
-table.file-details th,
-table.file-details td {
- padding: 3px 5px;
- white-space: nowrap;
-}
-
-/*table.file-details td { border-right: 1px solid #d0d0d0 ; }*/
-table.file-details td.scan-image-link {
- max-width: 275px;
- overflow: hidden;
-}
-
-table.file-details td.scan-image-size {
- font-family: Courier, monospace;
- font-size: 13px;
-}
-
-table.file-details td.scan-image-buttons {
- border: none;
-}
-
-/* 'Administer' pages */
-#admin-nav {
- margin: 0 0 10px 20px;
- background: #f0f0f0;
- border: 1px solid #ccc;
- border-collapse: collapse;
-}
-
-#admin-nav td {
- padding: 0;
- font-weight: bold;
-}
-
-#admin-nav td b {
- font-weight: inherit;
-}
-
-#admin-nav b,
-#admin-nav a {
- display: inline-block;
- float: left;
- padding: 6px 12px;
-}
-
-#admin-nav a:hover {
- color: #222;
- background: #e8e8e8;
-}
-
-#admin-nav .active {
- color: #fff;
- background: #1A75BB;
- border: 1px solid #293D66;
-}
-
-.admin-content {
- margin: 20px;
-}
-
-.admin-content .header {
- margin: 20px 2px 10px;
-}
-
-.admin-content .header b {
- font-size: 15px;
-}
-
-.admin-content .header i {
- margin: 0 10px;
- color: #ccc;
- font-weight: normal;
- font-style: normal;
-}
-
-.admin-content .data-table th .sortheader {
- position: relative;
- padding: 0 12px;
- color: #000;
-}
-
-.admin-content .data-table th .sortarrow[sortdir] {
- display: inline-block;
- position: absolute;
- right: 0;
- opacity: 0.3;
-}
-
-.admin-content .data-table th .sortarrow img {
- width: 9px;
-}
-
-.admin-content .data-table th .sortarrow img[src*="arrow-none"] {
- display: none;
-}
-
-.admin-content .data-table input[type="text"] {
- padding: 3px 5px;
- border: 1px solid #d0d0d0
-}
-
-#edit-user-details {
- margin: 0 10px;
-}
-
-body.popup #edit-user-details {
- margin: 0 auto;
-}
-
-#edit-user-details th {
- background: #f0f0f0;
-}
-
-#edit-user-details h3 {
- padding-left: 10px;
- font-weight: inherit;
-}
-
-#edit-user-details th,
-#edit-user-details td {
- padding: 8px 4px;
-}
-
-#edit-user-details .label {
- text-align: right;
- font-weight: bold;
-}
-
-#edit-user-details input[type="text"],
-#edit-user-details input[type="password"] {
- padding: 4px;
-}
-
-/* Data Types page */
-#data-type-table th,
-#data-type-table td {
- padding: 6px 4px;
-}
-
-#data-type-table .data-type-link {
- padding: 0 6px;
- font-weight: bold;
-}
-
-/* Advanced Search wizard pages */
-form.search-wizard {
- min-width: 720px;
- max-width: 720px;
-}
-
-/* Step-by-step numbers */
-.steps {
- padding: 0;
- list-style: none;
-}
-
-.steps > li {
- padding: 0 20px 20px 40px;
- margin-bottom: 20px;
- background: url('../images/_.gif') 0 0 no-repeat;
- border-bottom: 1px solid #ccc;
-}
-
-.steps > li > h3 {
- line-height: 30px;
- vertical-align: middle;
-}
-
-.steps > li > p {
- margin: 10px 0 15px;
-}
-
-.steps > li.step1 {
- background-image: url('../images/number_1.gif');
-}
-
-.steps > li.step2 {
- background-image: url('../images/number_2.gif');
-}
-
-.steps > li.step3 {
- background-image: url('../images/number_3.gif');
-}
-
-.steps > li.step4 {
- background-image: url('../images/number_4.gif');
-}
-
-.steps > li.step5 {
- background-image: url('../images/number_5.gif');
-}
-
-/* Advanced Search tabs */
-.advanced-search-fields {
- position: relative;
- margin: 10px;
- font-size: 13px;
- line-height: 15px;
-}
-
-.advanced-search-fields table td {
- padding: 0 8px 0 0;
- vertical-align: top;
-}
-
-.advanced-search-fields h4 {
- margin: 15px 0 5px 0;
- font-size: 13px;
- border-bottom: 1px solid #ccc;
-}
-
-.advanced-search-fields h5 {
- margin: 5px 0 2px;
- font-size: 13px;
- font-weight: normal;
-}
-
-.advanced-search-fields div.search-group {
- float: left;
- margin-bottom: 10px;
- overflow: visible;
-}
-
-.advanced-search-fields div.search-group.by-criteria {
- max-width: 60%;
-}
-
-.advanced-search-fields div.search-group.by-id {
- max-width: 30%;
-}
-
-.advanced-search-fields div.search-group.by-id > select {
- margin-top: 10px;
-}
-
-.advanced-search-fields div.search-group h3 {
- margin-bottom: 5px;
-}
-
-.advanced-search-fields div.search-group .disabled {
- opacity: 0.5;
-}
-
-.advanced-search-fields textarea.exact-ids {
- display: block;
- margin-top: 5px;
-}
-
-.advanced-search-fields .search-item {
- /* generic search item */
- display: inline-block;
- float: left;
- height: 50px;
- margin: 0 5px 0 0;
- padding: 0 10px 0 0;
- overflow: visible;
- white-space: nowrap;
-}
-
-.advanced-search-fields.autogen .search-item {
- /*min-width: 160px;*/
- max-width: 200px;
-}
-
-label.search-method-label {
- padding: 2px 12px 2px 10px;
-}
-
-/* date range input */
-.date-range {
- white-space: nowrap;
-}
-
-/* friendlyForm styles. Taken from ConnectomeDB. To be refactored / replaced in XNAT 1.7, most likely */
-fieldset,
-.friendlyForm fieldset {
- border: solid #e4efff;
- border-width: 4px 0 0;
- margin: 1em 0;
- padding: 1em 0;
-}
-
-.friendlyForm fieldset.error {
- background-color: #fffcc9;
- border-color: #cc9;
- color: #d40000;
-}
-
-.friendlyForm p {
- line-height: 1.4em !important;
- margin-bottom: 1em;
- position: relative;
-}
-
-.friendlyForm h4 {
- border-bottom: 1px solid #999;
- font-size: 14px;
- font-weight: bold;
- margin-top: 1em;
- padding-bottom: 6px;
-}
-
-.friendlyForm label {
- color: #777;
- display: block;
- font-size: 12px !important;
- font-weight: bold;
- text-transform: uppercase;
-}
-
-.friendlyForm input[type=text],
-.friendlyForm input[type=password],
-.friendlyForm input[type=file],
-.friendlyForm textarea,
-.friendlyForm select {
- font-size: 14px !important;
- padding: 6px;
- width: 96%;
-}
-
-.friendlyForm input[type=file] {
- border: 1px solid #e0e0e0;
- border-radius: 3px;
- margin: 1em 0;
- margin-bottom: inherit;
- padding: 1em;
-}
-
-.inputWrapper {
- background-color: #f0f0f0;
- border: 1px solid #ccc;
- margin-bottom: 2em;
- padding: 20px 0;
- position: relative;
-}
-
-.inputWrapper.horizontal {
- display: inline-block;
- vertical-align: top;
- width: 350px;
-}
-
-.inputWrapper.highlighted {
- background-color: #e4efff;
-}
-
-.inputWrapper.error {
- border: none;
- padding: 6px;
- position: relative;
- top: 0;
- left: 0;
- width: inherit; /* override other .error styles */
-}
-
-.inputWrapper.error,
-.inputWrapper table tr.error {
- background-color: #fde;
-}
-
-.inputWrapper.wide {
- width: 600px;
-}
-
-.inputWrapper.error h3,
-.inputWrapper.error ul {
- margin-left: 30px !important;
-}
-
-.friendlyForm p.error {
- color: #c33;
- font-size: 12px !important;
- font-weight: bold;
-}
-
-.inputWrapper label {
- color: #37c;
-}
-
-.inputWrapper input[type=text],
-.inputWrapper input[type=password],
-.inputWrapper textarea {
- width: 330px;
-}
-
-.inputWrapper.wide input[type=text],
-.inputWrapper.wide input[type=password],
-.inputWrapper.wide textarea {
- width: 600px;
-}
-
-.inputWrapper input:read-only {
- background-color: #f0f0f0;
- color: #999;
-}
-
-.inputWrapper .helptext,
-.inputWrapper .helptext-error {
- color: #888;
- font-size: 12px;
- line-height: 14px;
- position: absolute;
- bottom: 18px;
- left: 425px;
-}
-
-.inputWrapper.wide .helptext,
-.inputWrapper.wide .helptext-error {
- padding-top: 4px;
- position: inherit;
- bottom: inherit;
- left: inherit;
-}
-
-.inputWrapper table {
- border: 1px solid #ccc;
- border-collapse: collapse;
-}
-
-.inputWrapper td, .inputWrapper th {
- padding: 3px;
-}
-
-.inputWrapper td {
- border-top: 0;
-}
-
-.inputWrapper th {
- text-align: left;
- background-color: #f3f3f3;
-}
-
-p.form-submit {
- font-size: 12px !important;
- text-align: right;
-}
-
-.form-submit input,
-.request-access input,
-.overlay-action input {
- font-size: 16px !important;
- padding: 6px 12px;
-}
-
-.request-access input {
- float: right;
-}
-
-.friendlyForm .inputWrapper {
- background-color: #fff;
- border: none;
-}
-
-.friendlyForm.mini .inputWrapper {
- padding: 10px;
-}
-
-.friendlyForm.mini label {
- display: inline-block;
- width: 200px;
- text-transform: inherit;
-}
-
-.friendlyForm.mini input[type=text],
-.friendlyForm.mini input[type=password],
-.friendlyForm.mini input[type=file],
-.friendlyForm.mini textarea {
- font-size: 12px !important;
- padding: 3px;
- width: inherit;
-}
-
-.friendlyForm.mini .dataTable label {
- width: 100px;
-}
-
-label.disabled {
- color: #a0a0a0;
- font-weight: normal;
-}
-
-/* prearchives.css */
-/***********************************************/
-div.instructions {
- width: 80%;
- margin: 1em;
-}
-
-div.instructions p {
- margin-bottom: 1em;
-}
-
-div.prearcs {
- width: 85%;
- height: 400px;
- margin-top: 2em;
- margin-bottom: 2em;
-}
-
-div.inbox div.content table {
- width: 100%;
- padding: 0.5em;
- padding-top: 0;
- padding-bottom: 0;
-}
-
-div.inbox div.actions {
- padding-bottom: 0.5em;
- margin: 0.5em;
- margin-top: 0;
-}
-
-div.inbox div.actions input {
- float: right;
-}
-
-div.inbox div.importlog {
- margin: 1em;
- padding: 0.5em;
- height: 100px;
- overflow: auto;
- border: 2px solid green;
-}
-
-div.inbox div.importlog p {
- margin-left: 1em;
- margin-right: 1em;
- margin-top: 0.25em;
- margin-bottom: 0.25em;
-}
-
-div.inbox div.importlog p.header {
- font-size: larger;
- font-weight: bolder;
-}
-
-div.inbox div.importlog p.processing {
- /* */
-}
-
-div.inbox div.importlog p.warning {
- background: #ccccff;
-}
-
-div.inbox div.importlog p.failed {
- background: #ff6666;
-}
-
-div.inbox div.importlog p.completed {
- background: #ccffcc;
-}
-
-div.prearc-select {
- text-align: center;
-}
-
-div.prearc-select select {
- margin: 1em;
-}
-
-div.prearc {
- width: 100%;
- height: 100%;
- border: 1px solid #000000;
- padding: 0.5em;
- overflow: auto;
-}
-
-table.prearc {
- width: 100%;
- padding: 0.5em;
- padding-top: 0;
-}
-
-div.match-op {
- width: 80%;
- padding: 1em;
- text-align: right;
-}
-
-/* Sessions get background color indicating status */
-div.instructions div.colorkey {
- width: 100%;
- text-align: center
-}
-
-div.instructions div.colorkey span {
- text-align: center;
- padding-left: 1em;
- padding-right: 1em;
-}
-
-table.prearc tr.RECEIVING {
- background: #ccccff;
-}
-
-div.colorkey span.RECEIVING {
- background: #ccccff;
-}
-
-table.prearc tr.BUILDING {
- background: #ffccff;
-}
-
-div.colorkey span.BUILDING {
- background: #ffccff;
-}
-
-/* table.prearc tr.READY { } */
-table.prearc tr.ARCHIVING {
- background: #ccffff;
-}
-
-div.colorkey span.ARCHIVING {
- background: #ccffff;
-}
-
-table.prearc tr.ERROR {
- background: #ff6666;
-}
-
-div.colorkey span.ERROR {
- background: #ff6666;
-}
-
-/* scans.css */
-/***********************************************/
-td.quality-usable {
- color: green;
- font-weight: 700
-}
-
-td.quality-questionable {
- color: orange;
- font-weight: 700
-}
-
-td.quality-unusable {
- color: red;
- font-weight: 700
-}
-
-/* uploaded.css */
-/***********************************************/
-div.submit div.actions {
- text-align: center;
-}
-
-hr {
- margin: 2em 0;
-}
diff --git a/src/main/webapp/xnat-templates/screens/Basic.vm b/src/main/webapp/xnat-templates/screens/Basic.vm
index 98eb09a9107efaa28f6ac5016efb7c652a00d4d0..a1babb6560413d36190b2911d157b678ba67c25c 100644
--- a/src/main/webapp/xnat-templates/screens/Basic.vm
+++ b/src/main/webapp/xnat-templates/screens/Basic.vm
@@ -1,10 +1,5 @@
## There's not a Java class file for this template yet.
-###* @vtlvariable name="displayManager" type="org.nrg.xdat.display.DisplayManager" *#
-###* @vtlvariable name="par_count" type="java.lang.Integer" *#
###* @vtlvariable name="data" type="org.apache.turbine.util.RunData" *#
-###* @vtlvariable name="turbineUtils" type="org.nrg.xdat.turbine.utils.TurbineUtils" *#
-###* @vtlvariable name="siteConfig" type="java.util.Properties" *#
-###* @vtlvariable name="content" type="org.apache.turbine.services.pull.tools.ContentTool" *#
#set ($template = $data.getTemplateInfo())
$!template.setLayoutTemplate("Basic.vm")
<head>
diff --git a/src/main/webapp/xnat-templates/screens/CompressedUploaderPage.vm b/src/main/webapp/xnat-templates/screens/CompressedUploaderPage.vm
new file mode 100644
index 0000000000000000000000000000000000000000..cdb8ad38200732062534a8120c6c8c2fd2226569
--- /dev/null
+++ b/src/main/webapp/xnat-templates/screens/CompressedUploaderPage.vm
@@ -0,0 +1,579 @@
+<script type="text/javascript">
+ function disableForm(theform) {
+ if (document.getElementById) {
+ document.getElementById('progressBar').style.display = 'block';
+ }
+ else if (document.all) {
+ document.all['progressBar'].style.display = 'block';
+ }
+
+ if (document.all || document.getElementById) {
+ for (i = 0; i < theform.length; i++) {
+ var tempobj = theform.elements[i];
+ if (tempobj.type.toLowerCase() == "submit" || tempobj.type.toLowerCase() == "reset" || tempobj.type.toLowerCase() == "button")
+ tempobj.disabled = true;
+ }
+ return true;
+ }
+ else {
+ return true;
+ }
+ }
+
+ function enableForm() {
+ var theform;
+ if (document.getElementById) {
+ theform = document.getElementById('uploadFORM');
+ }
+ else if (document.all) {
+ theform = document.all['uploadFORM'];
+ }
+
+ if (document.all || document.getElementById) {
+ for (i = 0; i < theform.length; i++) {
+ var tempobj = theform.elements[i];
+ if (tempobj.type.toLowerCase() == "submit" || tempobj.type.toLowerCase() == "reset" || tempobj.type.toLowerCase() == "button")
+ tempobj.disabled = false;
+ }
+ return true;
+ } else {
+ return true;
+ }
+ }
+</script>
+<script type="text/javascript">
+ var i;
+ var req;
+
+ var uploadCount = 0;
+ var extractCount = 0;
+ var progressBar;
+ var progressPercent;
+ var uploadID = "$uploadID";
+ var started = 0;
+ var extractTimeOut = 300;
+
+ function setUploadProgress(i) {
+ if (i == 0) {
+ document.getElementById("uploadPercent").innerHTML = "";
+ document.getElementById("uploadBar").style.width = 0 + "px";
+ } else {
+ if (i > 100) {
+
+ } else {
+ var pixels = i * 3;
+ if (i > 10) {
+ document.getElementById("uploadPercent").innerHTML = parseInt(i) + "%";
+ }
+ else {
+ document.getElementById('preparing').innerHTML = "";
+ }
+ document.getElementById("uploadBar").style.width = pixels + "px";
+ document.getElementById('preparing').innerHTML = "Loading File... ";
+ }
+ }
+ }
+
+ function setExtractSummary(jsonobj) {
+ var messages = "";
+ try {
+ var respPos = jsonobj.msgs[0].length - 1;
+ for (i = 0; i <= respPos; i++) {
+ var level = jsonobj.msgs[0][i].status;
+ var message = jsonobj.msgs[0][i].msg;
+ if (level == "COMPLETED") {
+ message = "<tr bgcolor='#CCFFCC'><td>" + message;
+ } else if (level == "PROCESSING") {
+ message = "<tr bgcolor='#CCFFFF'><td>" + message;
+ } else if (level == "WARNING") {
+ message = "<tr bgcolor='#FFCCC'><td>" + message;
+ } else if (level == "FAILED") {
+ message = "<tr bgcolor='#FF99CC'><td>" + message;
+ } else {
+ message = "<tr bgcolor='#CCCCCC'><td>" + message;
+ }
+ messages = messages + message + "</td></tr>";
+ }
+ } catch (e) {
+ }
+ document.getElementById("extractSummary").innerHTML =
+ "<table width='100%' cellpadding='2' cellspacing='0'><tr><th>Extraction / Review summary:</th></tr>" +
+ messages +
+ "</table>";
+ }
+
+ function toggleExtractSummary() {
+ if (document.getElementById("extractSummary").style.display == "none") {
+ document.getElementById("extractSummaryTable").border = "1";
+ document.getElementById("extractSummary").style.display = "block";
+ } else {
+ document.getElementById("extractSummaryTable").border = "0";
+ document.getElementById("extractSummary").style.display = "none";
+ }
+ }
+
+ function setExtractProgress(i) {
+ if (i == 0) {
+ document.getElementById("extractPercent").innerHTML = "";
+ document.getElementById("extractBar").style.width = 0 + "px";
+ } else {
+ if (i > 100) {
+
+ } else {
+ var pixels = i * 3;
+ if (i > 10) {
+ document.getElementById("extractPercent").innerHTML = parseInt(i) + "%";
+ }
+ document.getElementById("extractBar").style.width = pixels + "px";
+ }
+ }
+ }
+
+ function evaluateDestination(ele) {
+ if (ele.value == '2') {
+ document.getElementById("auto-archive").value = 'true';
+ document.getElementById("quarantine").value = 'true';
+ } else if (ele.value == '1') {
+ document.getElementById("auto-archive").value = 'true';
+ document.getElementById("quarantine").value = 'false';
+ } else if (ele.value == '0') {
+ document.getElementById("auto-archive").value = 'false';
+ document.getElementById("quarantine").value = 'false';
+ }
+ }
+
+ var checkProgressFinal = 0;
+
+ function prog(theform) {
+ var imageArchive = document.getElementById("image_archive");
+ if (!imageArchive.value) {
+ xModalMessage('Upload Action', 'Please select an archive to upload.');
+ return false;
+ }
+ if (!(imageArchive.value.endsWith(".gz") || imageArchive.value.endsWith(".tgz") || imageArchive.value.endsWith(".zip"))) {
+ xModalMessage('Upload Action', 'Please select a tar or zip archive to upload.');
+ return false;
+ }
+ if (document.getElementById("project").selectedIndex == 0) {
+ xModalMessage('Upload Action', 'Please select a $displayManager.getSingularDisplayNameForProject().toLowerCase().');
+ return false;
+ }
+ disableForm(theform);
+ document.getElementById("iframe").src = "";
+ started = 0;
+ checkProgressFinal = 0;
+ progressBar = document.getElementById("uploadBar");
+ progressPercent = document.getElementById("uploadPercent");
+
+ document.getElementById('preparing').style.display = 'block';
+ document.getElementById('preparing').innerHTML = "Loading File... ";
+ setUploadProgress(0);
+ setExtractProgress(0);
+ setExtractSummary("");
+ resetProgress();
+ checkProgress();
+
+ return true;
+ }
+
+ function callback() {
+ if (req.readyState == 4) {
+ if (req.status == 200) {
+ started = 1;
+ // handle response
+ var respDat = YAHOO.lang.JSON.parse(req.responseText);
+ var respPos = respDat.msgs[0].length - 1;
+ var uploadI = 0;
+ var extractI = 0;
+ var statusCount = 0;
+ if (respDat.msgs[0].length > 0) {
+ if (respDat.msgs[0].length > 0) {
+ var level = respDat.msgs[0][respPos].status;
+ var message = respDat.msgs[0][respPos].msg;
+ }
+ }
+
+ if (req.responseText.indexOf("file uploaded") >= 0) {
+ uploadI = 100;
+ }
+ if (req.responseText.indexOf("Successfully uploaded") >= 0) {
+ extractI = 100;
+ }
+ if (req.responseText.indexOf("archiving operation complete") >= 0) {
+ extractI = 100;
+ }
+ setExtractSummary(respDat);
+ setCurrentStep(message);
+
+ //alert("Upload(" + uploadI + "); Extract(" + extractI + ");\r\n" + statusText + "\r\n" + req.responseText);
+
+ if (uploadI == -1) {
+ document.getElementById('preparing').innerHTML = " <font color=red><B>Error: Upload Failed. Please retry at a later time or contact technical support.</B></font>";
+ document.getElementById('preparing').style.display = 'block';
+ } else if (extractI == -1) {
+ document.getElementById('preparing').innerHTML = " <font color=red><B>Error: Extraction/Review Failed. Please verify the integrity of the zipped file and the contained image files.</B></font>";
+ document.getElementById('preparing').style.display = 'block';
+ } else if (uploadI != 100) {
+ //upload complete
+
+ if (uploadCount != 98) {
+ uploadCount = uploadCount + 1;
+ }
+
+ if (uploadCount > 40) {
+ extractTimeOut = 600;
+ }
+ if (uploadCount > 50) {
+ extractTimeOut = 800;
+ }
+ if (uploadCount > 60) {
+ extractTimeOut = 1000;
+ }
+ if (uploadCount > 70) {
+ extractTimeOut = 2000;
+ }
+ if (uploadCount > 80) {
+ extractTimeOut = 3000;
+ }
+ if (uploadCount > 85) {
+ extractTimeOut = 6000;
+ }
+ if (uploadCount > 88) {
+ extractTimeOut = 9000;
+ }
+
+ setUploadProgress(uploadCount);
+ setExtractProgress(0);
+
+ setTimeout("checkProgress();", extractTimeOut);
+ } else if (extractI == 100) {
+ //extract complete
+ setUploadProgress(100);
+ setExtractProgress(100);
+
+ setExtractSummary(respDat);
+ setCurrentStep(message);
+ if (checkProgressFinal == 0) {
+ checkProgressFinal = 1;
+ //check progress one final time to capture final step summary
+ setTimeout("checkProgress();", 200);
+ }
+ } else {
+ //extract in progress
+ setUploadProgress(100);
+
+ if (extractCount != 98) {
+ extractCount = extractCount + 1;
+ }
+ if (extractCount < 10) {
+ extractTimeOut = 500;
+ }
+ if (extractCount > 10) {
+ extractTimeOut = 100;
+ }
+ if (extractCount > 20) {
+ extractTimeOut = 1500;
+ }
+ if (extractCount > 30) {
+ extractTimeOut = 2000;
+ }
+ if (extractCount > 50) {
+ extractTimeOut = 2800;
+ }
+ if (extractCount > 60) {
+ extractTimeOut = 3300;
+ }
+ if (extractCount > 70) {
+ extractTimeOut = 4000;
+ }
+ if (extractCount > 80) {
+ extractTimeOut = 5000;
+ }
+ if (extractCount > 85) {
+ extractTimeOut = 6000;
+ }
+ if (extractCount > 88) {
+ extractTimeOut = 9000;
+ }
+
+ setExtractProgress(extractCount);
+
+ if (statusCount > 0) {
+ setExtractSummary(respDat);
+ setCurrentStep(message);
+ }
+ setTimeout("checkProgress();", extractTimeOut);
+ }
+ }
+ }
+ }
+
+
+ function setCurrentStep(message) {
+ if (message != null && message != undefined) {
+ document.getElementById("current_step").innerHTML = "<A href='' ONCLICK='toggleExtractSummary();return false;'>" + message + "...</A>";
+ }
+ }
+
+ function resetProgress() {
+ var url = "$content.getURI("servlet/AjaxServlet")?remote-class=org.nrg.xnat.ajax.UploadProgress";
+ url = url + "&remote-method=start";
+ url = url + "&ID=" + uploadID;
+ if (window.XMLHttpRequest) {
+ req = new XMLHttpRequest();
+ } else if (window.ActiveXObject) {
+ req = new ActiveXObject("Microsoft.XMLHTTP");
+ }
+ req.open("GET", url, true);
+ req.send(null);
+ }
+
+ function checkProgress() {
+ //var url = "$content.getURI("/REST/status/$uploadID")?format=json";
+ var url = "$content.getURI("/REST/status/$uploadID")?format=json&stamp=" + (new Date()).getTime();
+ if (window.XMLHttpRequest) {
+ req = new XMLHttpRequest();
+ } else if (window.ActiveXObject) {
+ req = new ActiveXObject("Microsoft.XMLHTTP");
+ }
+ req.open("GET", url, true);
+ req.onreadystatechange = callback;
+ req.send(null);
+ }
+ function makeTheFormGo() {
+ var form = document.getElementById("uploadFORM");
+ prog(form);
+ form.submit();
+ }
+</script>
+
+<table border="0" cellpadding="5" cellspacing="0">
+ <tr>
+ <td>
+ <h4>
+ Compressed upload</h4></td>
+ </tr>
+ <tr>
+ <td valign="top" align="left">
+ <div style="width:500px">Raw image files can be zipped (.zip or .tar.gz) and uploaded using the form. This
+ tool currently supports DICOM and ECAT files. Selecting 'Prearchive' will place your images into a
+ temporary holding space. You will then have the ability to review the details and match the data to the
+ proper $displayManager.getSingularDisplayNameForSubject().toLowerCase() & $displayManager.getSingularDisplayNameForImageSession().toLowerCase() ID. If you are confident the data will be mapped properly, you can directly
+ 'Archive' the files and specify whether the resulting $displayManager.getSingularDisplayNameForImageSession().toLowerCase() should go into a quarantine state.
+ </div>
+ <div class="alert" style="margin:15px 0;max-width:696px;min-width:400px;">
+ The compressed uploader does not yet support splitting PET/MR sessions based on the site-wide or
+ project-specific settings for handling PET/MR data. If you are uploading PET/MR data and need to have
+ the data split into separate PET and MR sessions or created as a PET session rather than a PET/MR
+ session, you should use either the <a href="$link.setPage("LaunchUploadApplet.vm")">upload applet</a> or the
+ DICOM C-STORE receiver as described below.
+ </div>
+ </td>
+ </tr>
+ <tr>
+ <td> </td>
+ </tr>
+ <tr id="option1">
+ <td>
+ <input type="hidden" name="popup" value="true"/>
+ <form id="uploadFORM" class="noHide" target="iframe" enctype="multipart/form-data" method="POST"
+ action="$content.getURI("/REST/services/import?http-session-listener=$uploadID&format=html&XNAT_CSRF=$!XNAT_CSRF")">
+ <input type="hidden" name="threshhold" value="51516279"/>
+
+ #if($session)
+ <input type="hidden" name="EXPT_LABEL" value="$!session.getLabel()"/>
+ <input type="hidden" name="SUBJECT_ID" value="$!session.getSubjectData().getLabel()"/>
+ #end
+
+ <table border=0 cellpadding="5" cellspacing="0">
+ <tr>
+ <th align="left">$displayManager.getSingularDisplayNameForProject()</th>
+ <td>
+ #if(!$session)
+ <select id="project" name="project" disabled=true></select>
+ #else
+ <input type="hidden" name="project" id="project"
+ value="$session.getProject()"/>$session.getProject()
+ #end
+ </td>
+ </tr>
+
+ #if($session)
+ <tr>
+ <th align="left">$displayManager.getSingularDisplayNameForImageSession()</th>
+ <td>$!session.getLabel()</td>
+ </tr>
+ #end
+ <tr>
+ <th align="left">Destination</th>
+ <td>
+ <label><input id="pc_0" type='radio' name='prearchive_code' value='0'
+ #if(!$session)CHECKED#end onchange="evaluateDestination(this)"/>
+ Prearchive</label>
+ <label><input id="pc_2" type='radio' name='prearchive_code' value='1'
+ #if($session)CHECKED#end onchange="evaluateDestination(this)"/>
+ Archive</label>
+ #if($session)
+ <input type="hidden" name="overwrite" value="append"/>
+ <input type="hidden" id="auto-archive" name='auto-archive' value='TRUE'/>
+ #else
+ <input type="hidden" id="auto-archive" name='auto-archive' value='FALSE'/>
+ #end
+ <input type="hidden" id="quarantine" name='quarantine' value='FALSE'/>
+ </td>
+ </tr>
+ <tr>
+ <th align="left">File</th>
+ <td><input type="file" id="image_archive" name="image_archive" size="60"
+ accept="application/zip, application/x-gzip, application/x-tgz"/></td>
+ </tr>
+ #auditBoxes("3" "" "Standard Upload" "Upload Images")
+ #hideFormJustification()
+ <tr>
+ <td> </td>
+ <td><input id="directButton" type="button" name="eventSubmit_doPerform" value="Begin Upload" onclick="makeTheFormGo();"/>
+ </td>
+ </tr>
+ </table>
+ </form>
+
+<span id="progressBar" style="position:relative; display:none;">
+<div id="ex" style="position:relative;width:468px;background:#eeeeee;border:3px double #000000;">
+ <table width="100%">
+ <tr>
+ <td colspan=2 align="left">
+ <div id="preparing">Loading File... </div>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div id="uploadLabel">Upload: </div>
+ </td>
+ <td align="center">
+ <div id="emptyUpload"
+ style="background-color:#cccccc;border:1px solid black;height:22px;width:300px;padding:0;"
+ align="left">
+ <div id="uploadBar"
+ style="position:relative;top:0;left:0;background-color:#333333;height:22px;width:0;padding-top:5px;padding:0;">
+ <div id="uploadPercent"
+ style="position:relative;top:0;left:0;color:#f0ffff;height:22px;text-align:center;font:bold;padding:0;padding-top:5px;">
+ </div>
+ </div>
+ </div>
+ </td>
+ </tr>
+ <tr>
+ <td> </td>
+ </tr>
+ <tr>
+ <td>
+ <div id="extractLabel">Extract/Review: </div>
+ </td>
+ <td align="center">
+ <div id="emptyExtract"
+ style="background-color:#cccccc;border:1px solid black;height:22px;width:300px;padding:0;"
+ align="left">
+ <div id="extractBar"
+ style="position:relative;top:0;left:0;background-color:#333333;height:22px;width:0;padding-top:5px;padding:0;">
+ <div id="extractPercent"
+ style="position:relative;top:0;left:0;color:#f0ffff;height:22px;text-align:center;font:bold;padding:0;padding-top:5px;">
+ </div>
+ </div>
+ </div>
+ </td>
+ </tr>
+ <tr>
+ <td colspan=2 align="center">
+ <div id="current_step"></div>
+ </td>
+ </tr>
+ </table>
+</div>
+<br>
+<table id="extractSummaryTable" border=0 style="border-collapse: collapse;">
+ <tr>
+ <td>
+ <span id="extractSummary"
+ style="position:relative;width:468px;height:100px;display:none;overflow:auto; "></span>
+ </td>
+ </tr>
+</table>
+<br>
+<iframe id="iframe" name="iframe" src="" width="468" height="80" frameborder="0">
+ PROGRESS BAR DISABLED. <br>Try using a more recent web browser.
+</iframe>
+</span>
+ <script type="text/javascript">
+ progressBar = document.getElementById("uploadBar");
+ progressPercent = document.getElementById("uploadPercent");
+ </script>
+ </td>
+ </tr>
+ <tr>
+ <td> </td>
+ </tr>
+ <script type="text/javascript">
+ // Adapted from Sun Java Web Start Auto-Install Demo
+ // http://java.sun.com/developer/technicalArticles/JavaLP/javawebstart/AutoInstallDemo.html
+ var detect = navigator.userAgent.toLowerCase();
+ var windowsIE = (checkPlatform("msie") && checkPlatform("win"));
+
+ function checkPlatform(string) {
+ place = detect.indexOf(string) + 1;
+ thestring = string;
+ return place;
+ }
+ </script>
+</table>
+
+#if(!$session)
+<script type="text/javascript" src="$content.getURI('scripts/subjectAssessorData/proj_tools.js')"></script>
+
+<script type="text/javascript">
+ //load projects
+ window.defaultProject = "$!project";
+
+ window.projectLoader = new ProjectLoader();
+
+ window.projectLoader.onLoadComplete.subscribe(function () {
+ renderProjects(document.getElementById("project"), window.projectLoader.list, window.defaultProject);
+ });
+
+ document.getElementById("project").onchange = function (o) {
+ if (this.selectedIndex > 0) {
+ var s = this.options[this.selectedIndex];
+ var pc = document.getElementById("pc_0");
+ if (pc != undefined && pc != null) {
+ if (s.pc == "4") {
+ if (s.qc == "0") {
+ document.getElementById("pc_2").click();
+ } else {
+ document.getElementById("pc_1").click();
+ }
+ } else {
+ document.getElementById("pc_0").click();
+ }
+ }
+ }
+ };
+
+ window.projectLoader.init();
+
+ function prepApplet(_form) {
+ return true;
+ }
+
+ //build breadcrumb
+ var breadcrumbs = document.getElementById('breadcrumbs');
+
+ if (breadcrumbs != null) {
+ var bread = "";
+ #if($project)
+ bread = bread + "<a href='$link.setAction("DisplayItemAction").addPathInfo("search_element","xnat:projectData").addPathInfo("search_field","xnat:projectData.ID").addPathInfo("search_value","$project")'>$displayManager.getSingularDisplayNameForProject().toUpperCase(): $!project</a>";
+ bread = bread + " > Upload Images";
+ #end
+ breadcrumbs.innerHTML = bread;
+ }
+
+</script>
+#end
\ No newline at end of file
diff --git a/src/main/webapp/xnat-templates/screens/DICOMSCPPage.vm b/src/main/webapp/xnat-templates/screens/DICOMSCPPage.vm
new file mode 100644
index 0000000000000000000000000000000000000000..e40241f0258ab0614c33340fccb828eea73f8304
--- /dev/null
+++ b/src/main/webapp/xnat-templates/screens/DICOMSCPPage.vm
@@ -0,0 +1,24 @@
+<table>
+<tr>
+ <td>
+ <h4>DICOM C-STORE Service Class User</h4>
+ </td>
+</tr>
+<tr>
+ <td valign="top" align="left">
+ <div style="width:500px">Any DICOM C-STORE SCU, including scanner consoles or DICOM applications like
+ <a href="http://www.osirix-viewer.com">OsiriX</a> or <a href="http://nrg.wustl.edu/software/dicom-browser">DicomBrowser</a>,
+ can send files directly to this server.
+ </div>
+</tr>
+<tr id="option4">
+ <td>
+ <br><b>DICOM C-STORE receiver (SCP) Specifications</b>
+ <ul>
+ <li>Host Name: $!arc.getDcm_dcmHost()</li>
+ <li>Port: $!arc.getDcm_dcmPort()</li>
+ <li>AE Title(s): $!arc.getDcm_dcmAe()</li>
+ </ul>
+ </td>
+</tr>
+ </table>
\ No newline at end of file
diff --git a/src/main/webapp/xnat-templates/screens/Index.vm b/src/main/webapp/xnat-templates/screens/Index.vm
index b3be92bbd689868928d6ea0410084925eb9df6b5..e2ed210c971241742bd3b68897fb84779807f09e 100644
--- a/src/main/webapp/xnat-templates/screens/Index.vm
+++ b/src/main/webapp/xnat-templates/screens/Index.vm
@@ -3,7 +3,7 @@
#* @vtlvariable name="par_count" type="java.lang.Integer" *#
#* @vtlvariable name="data" type="org.apache.turbine.util.RunData" *#
#* @vtlvariable name="turbineUtils" type="org.nrg.xdat.turbine.utils.TurbineUtils" *#
-#* @vtlvariable name="siteConfig" type="java.util.Properties" *#
+#* @vtlvariable name="siteConfig" type="org.nrg.xdat.preferences.SiteConfigPreferences" *#
#* @vtlvariable name="content" type="org.apache.turbine.services.pull.tools.ContentTool" *#
#set ($template = $data.getTemplateInfo())
#if($data.getParameters().getString("login").equals("true"))
diff --git a/src/main/webapp/xnat-templates/screens/Login.vm b/src/main/webapp/xnat-templates/screens/Login.vm
index 10ddc6ef72f44ab0a4fabae3d31e660404f520c7..5dd17f54993edd06ae7481e123756854d68191a6 100644
--- a/src/main/webapp/xnat-templates/screens/Login.vm
+++ b/src/main/webapp/xnat-templates/screens/Login.vm
@@ -2,7 +2,7 @@
#* @vtlvariable name="method" type="java.lang.String" *#
#* @vtlvariable name="login_methods" type="java.util.List" *#
#* @vtlvariable name="turbineUtils" type="org.nrg.xdat.turbine.utils.TurbineUtils" *#
-#* @vtlvariable name="siteConfig" type="java.util.Properties" *#
+#* @vtlvariable name="siteConfig" type="org.nrg.xdat.preferences.SiteConfigPreferences" *#
#* @vtlvariable name="content" type="org.apache.turbine.services.pull.tools.ContentTool" *#
#* @vtlvariable name="page" type="org.apache.turbine.util.template.HtmlPageAttributes" *#
#* @vtlvariable name="ui" type="org.apache.turbine.services.pull.util.UIManager" *#
diff --git a/src/main/webapp/xnat-templates/screens/Page.vm b/src/main/webapp/xnat-templates/screens/Page.vm
index 18c7aaa7e9cb85b71e8c385677c9447e5d644287..729980183bc89bfa1daa381a0ab041c78ad3ac1b 100644
--- a/src/main/webapp/xnat-templates/screens/Page.vm
+++ b/src/main/webapp/xnat-templates/screens/Page.vm
@@ -2,7 +2,7 @@
#* @vtlvariable name="par_count" type="java.lang.Integer" *#
#* @vtlvariable name="data" type="org.apache.turbine.util.RunData" *#
#* @vtlvariable name="turbineUtils" type="org.nrg.xdat.turbine.utils.TurbineUtils" *#
-#* @vtlvariable name="siteConfig" type="java.util.Properties" *#
+#* @vtlvariable name="siteConfig" type="org.nrg.xdat.preferences.SiteConfigPreferences" *#
#* @vtlvariable name="content" type="org.apache.turbine.services.pull.tools.ContentTool" *#
<!-- start xnat-templates/screens/Page.vm -->
diff --git a/src/main/webapp/xnat-templates/screens/Register.vm b/src/main/webapp/xnat-templates/screens/Register.vm
index cdd653d1112210e654df3713442a1574590a12fd..48b117f516e715e57987b7d8a5fd940f28f5c861 100644
--- a/src/main/webapp/xnat-templates/screens/Register.vm
+++ b/src/main/webapp/xnat-templates/screens/Register.vm
@@ -1,5 +1,5 @@
<!-- BEGIN xnat-templates/screens/Register.vm -->
-#* @vtlvariable name="siteConfig" type="java.util.Properties" *#
+#* @vtlvariable name="siteConfig" type="org.nrg.xdat.preferences.SiteConfigPreferences" *#
#* @vtlvariable name="data" type="org.apache.turbine.util.RunData" *#
#* @vtlvariable name="page" type="org.apache.turbine.util.template.HtmlPageAttributes" *#
#* @vtlvariable name="ui" type="org.apache.turbine.services.pull.util.UIManager" *#
diff --git a/src/main/webapp/xnat-templates/screens/Scripts.vm b/src/main/webapp/xnat-templates/screens/Scripts.vm
index 3737ecb0a3cfdb4bf226cfdce6689a4ab634335e..decd810e2b0468c9452ee84ca960a93a9f6983d4 100644
--- a/src/main/webapp/xnat-templates/screens/Scripts.vm
+++ b/src/main/webapp/xnat-templates/screens/Scripts.vm
@@ -1,6 +1,6 @@
<!-- BEGIN plugin-resources/webapp/xnat-templates/screens/Scripts.vm -->
#* @vtlvariable name="turbineUtils" type="org.nrg.xdat.turbine.utils.TurbineUtils" *#
-#* @vtlvariable name="siteConfig" type="java.util.Properties" *#
+#* @vtlvariable name="siteConfig" type="org.nrg.xdat.preferences.SiteConfigPreferences" *#
#* @vtlvariable name="content" type="org.apache.turbine.services.pull.tools.ContentTool" *#
#* @vtlvariable name="data" type="org.apache.turbine.util.RunData" *#
#* @vtlvariable name="tabs" type="java.util.List<java.util.Properties>" *#
diff --git a/src/main/webapp/xnat-templates/screens/UploadApplet.vm b/src/main/webapp/xnat-templates/screens/UploadApplet.vm
index b74ab4ca15563f73e31fa70e6b353b6b5d9d3db9..16fdc1372ff1ae97563c719a7334272e0b84eea4 100644
--- a/src/main/webapp/xnat-templates/screens/UploadApplet.vm
+++ b/src/main/webapp/xnat-templates/screens/UploadApplet.vm
@@ -1,3 +1,9 @@
+#* @vtlvariable name="appletParams" type="java.lang.String" *#
+#* @vtlvariable name="expectedModality" type="java.lang.String" *#
+#* @vtlvariable name="protocol" type="java.lang.String" *#
+#* @vtlvariable name="visit" type="java.lang.String" *#
+#* @vtlvariable name="jsessionid" type="java.lang.String" *#
+#* @vtlvariable name="siteConfig" type="org.nrg.xdat.preferences.SiteConfigPreferences" *#
#* @vtlvariable name="session_id" type="java.lang.String" *#
#* @vtlvariable name="scan_type" type="java.lang.String" *#
#* @vtlvariable name="visit_id" type="java.lang.String" *#
@@ -5,7 +11,6 @@
#* @vtlvariable name="subject_id" type="java.lang.String" *#
#* @vtlvariable name="project" type="java.lang.String" *#
#* @vtlvariable name="content" type="org.apache.turbine.services.pull.tools.ContentTool" *#
-#* @vtlvariable name="arc" type="org.nrg.xdat.om.ArcArchivespecification" *#
<!-- UploadApplet.vm -->
<script type="text/javascript" src="https://java.com/js/deployJava.js"></script>
<p style="width:760px;margin-bottom:20px;font-size:12px;">This tool supports uploading DICOM and ECAT formatted medical imaging data. If you are unsure of the format of your data, please contact
@@ -55,7 +60,7 @@ function loadApplet() {
var attributes = { code: 'org.nrg.xnat.upload.ui.UploadAssistantApplet', codebase: '$content.getURI("applet/")', width: 800, height: 500, /* class: 'upload_applet', */ archive: 'upload-assistant__V1.7.0-SNAPSHOT.jar, DicomEdit__V4.0.0.jar, DicomUtils__V1.3.1.jar, antlr-runtime__V3.5.2.jar, commons-codec__V1.10.jar, commons-lang3__V3.4.jar, commons-lang__V2.6.jar, config__V1.7.0-SNAPSHOT.jar, dcm4che-core__V2.0.25.jar, dicom-xnat-sop__V1.7.0-20160210.212402-3.jar, dicom-xnat-util__V1.7.0-20160210.212409-3.jar, dicomtools__V1.7.0-SNAPSHOT.jar, ecat-edit__V0.2.0.jar, ecat-io__V0.1.0.jar, framework__V1.7.0-SNAPSHOT.jar, guava__V19.0.jar, jackson-annotations__V2.6.5.jar, jackson-core__V2.6.5.jar, jackson-databind__V2.6.5.jar, java-uuid-generator__V3.1.3.jar, javax.inject__V1.jar, jcalendar__V1.4.jar, joda-time__V2.1.jar, json__V20151123.jar, log4j__V1.2.17.jar, nrgutil__V1.1.0.jar, slf4j-api__V1.7.7.jar, slf4j-log4j12__V1.7.7.jar, wizard__V1.1.jar' }
- var parameters = { 'xnat-url': '$!arc.getSiteUrl()', 'xnat-admin-email': '$!arc.getSiteAdminEmail()', 'xnat-description': '$!arc.getSiteId()', 'n-upload-threads': '4', 'fixed-size-streaming': 'true', 'java_arguments': '-Djnlp.packEnabled=true', 'jsessionid': '$jsessionid'};
+ var parameters = { 'xnat-url': '$!siteConfig.getSiteUrl()', 'xnat-admin-email': '$!siteConfig.getAdminEmail()', 'xnat-description': '$!siteConfig.getSiteId()', 'n-upload-threads': '4', 'fixed-size-streaming': 'true', 'java_arguments': '-Djnlp.packEnabled=true', 'jsessionid': '$jsessionid'};
parameters['window-name'] = this.window.name;
diff --git a/src/main/webapp/xnat-templates/screens/UploadAssistantPage.vm b/src/main/webapp/xnat-templates/screens/UploadAssistantPage.vm
new file mode 100644
index 0000000000000000000000000000000000000000..20c3dc90e3a8c5c655f7ea64de3d734593615342
--- /dev/null
+++ b/src/main/webapp/xnat-templates/screens/UploadAssistantPage.vm
@@ -0,0 +1,12 @@
+<table>
+ <tr>
+ <td>
+ <h4>Download Upload Assistant application</h4>
+ </td>
+ </tr>
+ <tr>
+ <td valign="top" align="left">
+ <div style="width:500px">You can download the XNAT Upload Assistant application and use it to upload your session. If the Upload Applet does not work for you, you might want to try this. <a href="https://bitbucket.org/xnatdev/upload-assistant/downloads">Click here</a> to find the appropriate version of the XNAT Upload Assistant application for your operating system.
+ </div>
+ </tr>
+</table>
\ No newline at end of file
diff --git a/src/main/webapp/xnat-templates/screens/UploadOptions.vm b/src/main/webapp/xnat-templates/screens/UploadOptions.vm
new file mode 100644
index 0000000000000000000000000000000000000000..89b03f05ca54cb4eec243616fd7a21a27629125f
--- /dev/null
+++ b/src/main/webapp/xnat-templates/screens/UploadOptions.vm
@@ -0,0 +1,646 @@
+<script type="text/javascript">
+ function disableForm(theform) {
+ if (document.getElementById) {
+ document.getElementById('progressBar').style.display = 'block';
+ }
+ else if (document.all) {
+ document.all['progressBar'].style.display = 'block';
+ }
+
+ if (document.all || document.getElementById) {
+ for (i = 0; i < theform.length; i++) {
+ var tempobj = theform.elements[i];
+ if (tempobj.type.toLowerCase() == "submit" || tempobj.type.toLowerCase() == "reset" || tempobj.type.toLowerCase() == "button")
+ tempobj.disabled = true;
+ }
+ return true;
+ }
+ else {
+ return true;
+ }
+ }
+
+ function enableForm() {
+ var theform;
+ if (document.getElementById) {
+ theform = document.getElementById('uploadFORM');
+ }
+ else if (document.all) {
+ theform = document.all['uploadFORM'];
+ }
+
+ if (document.all || document.getElementById) {
+ for (i = 0; i < theform.length; i++) {
+ var tempobj = theform.elements[i];
+ if (tempobj.type.toLowerCase() == "submit" || tempobj.type.toLowerCase() == "reset" || tempobj.type.toLowerCase() == "button")
+ tempobj.disabled = false;
+ }
+ return true;
+ } else {
+ return true;
+ }
+ }
+</script>
+<script type="text/javascript">
+ var i;
+ var req;
+
+ var uploadCount = 0;
+ var extractCount = 0;
+ var progressBar;
+ var progressPercent;
+ var uploadID = "$uploadID";
+ var started = 0;
+ var extractTimeOut = 300;
+
+ function setUploadProgress(i) {
+ if (i == 0) {
+ document.getElementById("uploadPercent").innerHTML = "";
+ document.getElementById("uploadBar").style.width = 0 + "px";
+ } else {
+ if (i > 100) {
+
+ } else {
+ var pixels = i * 3;
+ if (i > 10) {
+ document.getElementById("uploadPercent").innerHTML = parseInt(i) + "%";
+ }
+ else {
+ document.getElementById('preparing').innerHTML = "";
+ }
+ document.getElementById("uploadBar").style.width = pixels + "px";
+ document.getElementById('preparing').innerHTML = "Loading File... ";
+ }
+ }
+ }
+
+ function setExtractSummary(jsonobj) {
+ var messages = "";
+ try {
+ var respPos = jsonobj.msgs[0].length - 1;
+ for (i = 0; i <= respPos; i++) {
+ var level = jsonobj.msgs[0][i].status;
+ var message = jsonobj.msgs[0][i].msg;
+ if (level == "COMPLETED") {
+ message = "<tr bgcolor='#CCFFCC'><td>" + message;
+ } else if (level == "PROCESSING") {
+ message = "<tr bgcolor='#CCFFFF'><td>" + message;
+ } else if (level == "WARNING") {
+ message = "<tr bgcolor='#FFCCC'><td>" + message;
+ } else if (level == "FAILED") {
+ message = "<tr bgcolor='#FF99CC'><td>" + message;
+ } else {
+ message = "<tr bgcolor='#CCCCCC'><td>" + message;
+ }
+ messages = messages + message + "</td></tr>";
+ }
+ } catch (e) {
+ }
+ document.getElementById("extractSummary").innerHTML =
+ "<table width='100%' cellpadding='2' cellspacing='0'><tr><th>Extraction / Review summary:</th></tr>" +
+ messages +
+ "</table>";
+ }
+
+ function toggleExtractSummary() {
+ if (document.getElementById("extractSummary").style.display == "none") {
+ document.getElementById("extractSummaryTable").border = "1";
+ document.getElementById("extractSummary").style.display = "block";
+ } else {
+ document.getElementById("extractSummaryTable").border = "0";
+ document.getElementById("extractSummary").style.display = "none";
+ }
+ }
+
+ function setExtractProgress(i) {
+ if (i == 0) {
+ document.getElementById("extractPercent").innerHTML = "";
+ document.getElementById("extractBar").style.width = 0 + "px";
+ } else {
+ if (i > 100) {
+
+ } else {
+ var pixels = i * 3;
+ if (i > 10) {
+ document.getElementById("extractPercent").innerHTML = parseInt(i) + "%";
+ }
+ document.getElementById("extractBar").style.width = pixels + "px";
+ }
+ }
+ }
+
+ function evaluateDestination(ele) {
+ if (ele.value == '2') {
+ document.getElementById("auto-archive").value = 'true';
+ document.getElementById("quarantine").value = 'true';
+ } else if (ele.value == '1') {
+ document.getElementById("auto-archive").value = 'true';
+ document.getElementById("quarantine").value = 'false';
+ } else if (ele.value == '0') {
+ document.getElementById("auto-archive").value = 'false';
+ document.getElementById("quarantine").value = 'false';
+ }
+ }
+
+ var checkProgressFinal = 0;
+
+ function prog(theform) {
+ var imageArchive = document.getElementById("image_archive");
+ if (!imageArchive.value) {
+ xModalMessage('Upload Action', 'Please select an archive to upload.');
+ return false;
+ }
+ if (!(imageArchive.value.endsWith(".gz") || imageArchive.value.endsWith(".tgz") || imageArchive.value.endsWith(".zip"))) {
+ xModalMessage('Upload Action', 'Please select a tar or zip archive to upload.');
+ return false;
+ }
+ if (document.getElementById("project").selectedIndex == 0) {
+ xModalMessage('Upload Action', 'Please select a $displayManager.getSingularDisplayNameForProject().toLowerCase().');
+ return false;
+ }
+ disableForm(theform);
+ document.getElementById("iframe").src = "";
+ started = 0;
+ checkProgressFinal = 0;
+ progressBar = document.getElementById("uploadBar");
+ progressPercent = document.getElementById("uploadPercent");
+
+ document.getElementById('preparing').style.display = 'block';
+ document.getElementById('preparing').innerHTML = "Loading File... ";
+ setUploadProgress(0);
+ setExtractProgress(0);
+ setExtractSummary("");
+ resetProgress();
+ checkProgress();
+
+ return true;
+ }
+
+ function callback() {
+ if (req.readyState == 4) {
+ if (req.status == 200) {
+ started = 1;
+ // handle response
+ var respDat = YAHOO.lang.JSON.parse(req.responseText);
+ var respPos = respDat.msgs[0].length - 1;
+ var uploadI = 0;
+ var extractI = 0;
+ var statusCount = 0;
+ if (respDat.msgs[0].length > 0) {
+ if (respDat.msgs[0].length > 0) {
+ var level = respDat.msgs[0][respPos].status;
+ var message = respDat.msgs[0][respPos].msg;
+ }
+ }
+
+ if (req.responseText.indexOf("file uploaded") >= 0) {
+ uploadI = 100;
+ }
+ if (req.responseText.indexOf("Successfully uploaded") >= 0) {
+ extractI = 100;
+ }
+ if (req.responseText.indexOf("archiving operation complete") >= 0) {
+ extractI = 100;
+ }
+ setExtractSummary(respDat);
+ setCurrentStep(message);
+
+ //alert("Upload(" + uploadI + "); Extract(" + extractI + ");\r\n" + statusText + "\r\n" + req.responseText);
+
+ if (uploadI == -1) {
+ document.getElementById('preparing').innerHTML = " <font color=red><B>Error: Upload Failed. Please retry at a later time or contact technical support.</B></font>";
+ document.getElementById('preparing').style.display = 'block';
+ } else if (extractI == -1) {
+ document.getElementById('preparing').innerHTML = " <font color=red><B>Error: Extraction/Review Failed. Please verify the integrity of the zipped file and the contained image files.</B></font>";
+ document.getElementById('preparing').style.display = 'block';
+ } else if (uploadI != 100) {
+ //upload complete
+
+ if (uploadCount != 98) {
+ uploadCount = uploadCount + 1;
+ }
+
+ if (uploadCount > 40) {
+ extractTimeOut = 600;
+ }
+ if (uploadCount > 50) {
+ extractTimeOut = 800;
+ }
+ if (uploadCount > 60) {
+ extractTimeOut = 1000;
+ }
+ if (uploadCount > 70) {
+ extractTimeOut = 2000;
+ }
+ if (uploadCount > 80) {
+ extractTimeOut = 3000;
+ }
+ if (uploadCount > 85) {
+ extractTimeOut = 6000;
+ }
+ if (uploadCount > 88) {
+ extractTimeOut = 9000;
+ }
+
+ setUploadProgress(uploadCount);
+ setExtractProgress(0);
+
+ setTimeout("checkProgress();", extractTimeOut);
+ } else if (extractI == 100) {
+ //extract complete
+ setUploadProgress(100);
+ setExtractProgress(100);
+
+ setExtractSummary(respDat);
+ setCurrentStep(message);
+ if (checkProgressFinal == 0) {
+ checkProgressFinal = 1;
+ //check progress one final time to capture final step summary
+ setTimeout("checkProgress();", 200);
+ }
+ } else {
+ //extract in progress
+ setUploadProgress(100);
+
+ if (extractCount != 98) {
+ extractCount = extractCount + 1;
+ }
+ if (extractCount < 10) {
+ extractTimeOut = 500;
+ }
+ if (extractCount > 10) {
+ extractTimeOut = 100;
+ }
+ if (extractCount > 20) {
+ extractTimeOut = 1500;
+ }
+ if (extractCount > 30) {
+ extractTimeOut = 2000;
+ }
+ if (extractCount > 50) {
+ extractTimeOut = 2800;
+ }
+ if (extractCount > 60) {
+ extractTimeOut = 3300;
+ }
+ if (extractCount > 70) {
+ extractTimeOut = 4000;
+ }
+ if (extractCount > 80) {
+ extractTimeOut = 5000;
+ }
+ if (extractCount > 85) {
+ extractTimeOut = 6000;
+ }
+ if (extractCount > 88) {
+ extractTimeOut = 9000;
+ }
+
+ setExtractProgress(extractCount);
+
+ if (statusCount > 0) {
+ setExtractSummary(respDat);
+ setCurrentStep(message);
+ }
+ setTimeout("checkProgress();", extractTimeOut);
+ }
+ }
+ }
+ }
+
+
+ function setCurrentStep(message) {
+ if (message != null && message != undefined) {
+ document.getElementById("current_step").innerHTML = "<A href='' ONCLICK='toggleExtractSummary();return false;'>" + message + "...</A>";
+ }
+ }
+
+ function resetProgress() {
+ var url = "$content.getURI("servlet/AjaxServlet")?remote-class=org.nrg.xnat.ajax.UploadProgress";
+ url = url + "&remote-method=start";
+ url = url + "&ID=" + uploadID;
+ if (window.XMLHttpRequest) {
+ req = new XMLHttpRequest();
+ } else if (window.ActiveXObject) {
+ req = new ActiveXObject("Microsoft.XMLHTTP");
+ }
+ req.open("GET", url, true);
+ req.send(null);
+ }
+
+ function checkProgress() {
+ //var url = "$content.getURI("/REST/status/$uploadID")?format=json";
+ var url = "$content.getURI("/REST/status/$uploadID")?format=json&stamp=" + (new Date()).getTime();
+ if (window.XMLHttpRequest) {
+ req = new XMLHttpRequest();
+ } else if (window.ActiveXObject) {
+ req = new ActiveXObject("Microsoft.XMLHTTP");
+ }
+ req.open("GET", url, true);
+ req.onreadystatechange = callback;
+ req.send(null);
+ }
+ function makeTheFormGo() {
+ var form = document.getElementById("uploadFORM");
+ prog(form);
+ form.submit();
+ }
+</script>
+
+<table border="0" cellpadding="5" cellspacing="0">
+ <tr>
+ <td> </td>
+ </tr>
+ <tr>
+ <td><h3>Options for Uploading $displayManager.getPluralDisplayNameForImageSession()</h3></td>
+ </tr>
+ <tr>
+ <td> </td>
+ </tr>
+
+
+ <tr>
+ <td>
+ <hr/>
+ <h4>Option 1: Upload Applet</h4>
+ </td>
+ </tr>
+ <tr>
+ <td valign="top" align="left">
+ <div style="width:500px">DICOM and ECAT files can be uploaded via the Upload Applet. <a href="$link.setPage("LaunchUploadApplet.vm")">Click here</a> to upload using the Upload Applet.
+ </div>
+ </tr>
+
+
+
+ <tr>
+ <td>
+ <hr/>
+ <h4>Option 2: Download Upload Assistant application</h4>
+ </td>
+ </tr>
+ <tr>
+ <td valign="top" align="left">
+ <div style="width:500px">You can download the XNAT Upload Assistant application and use it to upload your session. If the Upload Applet does not work for you, you might want to try this. <a href="https://bitbucket.org/xnatdev/upload-assistant/downloads">Click here</a> to find the appropriate version of the XNAT Upload Assistant application for your operating system.
+ </div>
+ </tr>
+
+
+
+ <tr>
+ <td>
+ <hr/>
+ <h4>
+ Option 3: Compressed upload</h4></td>
+ </tr>
+ <tr>
+ <td valign="top" align="left">
+ <div style="width:500px">Raw image files can be zipped (.zip or .tar.gz) and uploaded using the form. This
+ tool currently supports DICOM and ECAT files. Selecting 'Prearchive' will place your images into a
+ temporary holding space. You will then have the ability to review the details and match the data to the
+ proper $displayManager.getSingularDisplayNameForSubject().toLowerCase() & $displayManager.getSingularDisplayNameForImageSession().toLowerCase() ID. If you are confident the data will be mapped properly, you can directly
+ 'Archive' the files and specify whether the resulting $displayManager.getSingularDisplayNameForImageSession().toLowerCase() should go into a quarantine state.
+ </div>
+ <div class="alert" style="margin:15px 0;max-width:696px;min-width:400px;">
+ The compressed uploader does not yet support splitting PET/MR sessions based on the site-wide or
+ project-specific settings for handling PET/MR data. If you are uploading PET/MR data and need to have
+ the data split into separate PET and MR sessions or created as a PET session rather than a PET/MR
+ session, you should use either the <a href="$link.setPage("LaunchUploadApplet.vm")">upload applet</a> or the
+ DICOM C-STORE receiver as described below.
+ </div>
+ </td>
+ </tr>
+ <tr>
+ <td> </td>
+ </tr>
+ <tr id="option3">
+ <td>
+ <input type="hidden" name="popup" value="true"/>
+ <form id="uploadFORM" class="noHide" target="iframe" enctype="multipart/form-data" method="POST"
+ action="$content.getURI("/REST/services/import?http-session-listener=$uploadID&format=html&XNAT_CSRF=$!XNAT_CSRF")">
+ <input type="hidden" name="threshhold" value="51516279"/>
+
+ #if($session)
+ <input type="hidden" name="EXPT_LABEL" value="$!session.getLabel()"/>
+ <input type="hidden" name="SUBJECT_ID" value="$!session.getSubjectData().getLabel()"/>
+ #end
+
+ <table border=0 cellpadding="5" cellspacing="0">
+ <tr>
+ <th align="left">$displayManager.getSingularDisplayNameForProject()</th>
+ <td>
+ #if(!$session)
+ <select id="project" name="project" disabled=true></select>
+ #else
+ <input type="hidden" name="project" id="project"
+ value="$session.getProject()"/>$session.getProject()
+ #end
+ </td>
+ </tr>
+
+ #if($session)
+ <tr>
+ <th align="left">$displayManager.getSingularDisplayNameForImageSession()</th>
+ <td>$!session.getLabel()</td>
+ </tr>
+ #end
+ <tr>
+ <th align="left">Destination</th>
+ <td>
+ <label><input id="pc_0" type='radio' name='prearchive_code' value='0'
+ #if(!$session)CHECKED#end onchange="evaluateDestination(this)"/>
+ Prearchive</label>
+ <label><input id="pc_2" type='radio' name='prearchive_code' value='1'
+ #if($session)CHECKED#end onchange="evaluateDestination(this)"/>
+ Archive</label>
+ #if($session)
+ <input type="hidden" name="overwrite" value="append"/>
+ <input type="hidden" id="auto-archive" name='auto-archive' value='TRUE'/>
+ #else
+ <input type="hidden" id="auto-archive" name='auto-archive' value='FALSE'/>
+ #end
+ <input type="hidden" id="quarantine" name='quarantine' value='FALSE'/>
+ </td>
+ </tr>
+ <tr>
+ <th align="left">File</th>
+ <td><input type="file" id="image_archive" name="image_archive" size="60"
+ accept="application/zip, application/x-gzip, application/x-tgz"/></td>
+ </tr>
+ #auditBoxes("3" "" "Standard Upload" "Upload Images")
+ #hideFormJustification()
+ <tr>
+ <td> </td>
+ <td><input id="directButton" type="button" name="eventSubmit_doPerform" value="Begin Upload" onclick="makeTheFormGo();"/>
+ </td>
+ </tr>
+ </table>
+ </form>
+
+<span id="progressBar" style="position:relative; display:none;">
+<div id="ex" style="position:relative;width:468px;background:#eeeeee;border:3px double #000000;">
+ <table width="100%">
+ <tr>
+ <td colspan=2 align="left">
+ <div id="preparing">Loading File... </div>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div id="uploadLabel">Upload: </div>
+ </td>
+ <td align="center">
+ <div id="emptyUpload"
+ style="background-color:#cccccc;border:1px solid black;height:22px;width:300px;padding:0;"
+ align="left">
+ <div id="uploadBar"
+ style="position:relative;top:0;left:0;background-color:#333333;height:22px;width:0;padding-top:5px;padding:0;">
+ <div id="uploadPercent"
+ style="position:relative;top:0;left:0;color:#f0ffff;height:22px;text-align:center;font:bold;padding:0;padding-top:5px;">
+ </div>
+ </div>
+ </div>
+ </td>
+ </tr>
+ <tr>
+ <td> </td>
+ </tr>
+ <tr>
+ <td>
+ <div id="extractLabel">Extract/Review: </div>
+ </td>
+ <td align="center">
+ <div id="emptyExtract"
+ style="background-color:#cccccc;border:1px solid black;height:22px;width:300px;padding:0;"
+ align="left">
+ <div id="extractBar"
+ style="position:relative;top:0;left:0;background-color:#333333;height:22px;width:0;padding-top:5px;padding:0;">
+ <div id="extractPercent"
+ style="position:relative;top:0;left:0;color:#f0ffff;height:22px;text-align:center;font:bold;padding:0;padding-top:5px;">
+ </div>
+ </div>
+ </div>
+ </td>
+ </tr>
+ <tr>
+ <td colspan=2 align="center">
+ <div id="current_step"></div>
+ </td>
+ </tr>
+ </table>
+</div>
+<br>
+<table id="extractSummaryTable" border=0 style="border-collapse: collapse;">
+ <tr>
+ <td>
+ <span id="extractSummary"
+ style="position:relative;width:468px;height:100px;display:none;overflow:auto; "></span>
+ </td>
+ </tr>
+</table>
+<br>
+<iframe id="iframe" name="iframe" src="" width="468" height="80" frameborder="0">
+ PROGRESS BAR DISABLED. <br>Try using a more recent web browser.
+</iframe>
+</span>
+ <script type="text/javascript">
+ progressBar = document.getElementById("uploadBar");
+ progressPercent = document.getElementById("uploadPercent");
+ </script>
+ </td>
+ </tr>
+
+
+ <tr>
+ <td>
+ <hr/>
+ <h4>Option 4: DICOM C-STORE Service Class User</h4>
+ </td>
+ </tr>
+ <tr>
+ <td valign="top" align="left">
+ <div style="width:500px">Any DICOM C-STORE SCU, including scanner consoles or DICOM applications like
+ <a href="http://www.osirix-viewer.com">OsiriX</a> or <a href="http://nrg.wustl.edu/software/dicom-browser">DicomBrowser</a>,
+ can send files directly to this server.
+ </div>
+ </tr>
+ <tr id="option4">
+ <td>
+ <br><b>DICOM C-STORE receiver (SCP) Specifications</b>
+ <ul>
+ <li>Host Name: $!arc.getDcm_dcmHost()</li>
+ <li>Port: $!arc.getDcm_dcmPort()</li>
+ <li>AE Title(s): $!arc.getDcm_dcmAe()</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <hr/>
+ </td>
+ </tr>
+ <script type="text/javascript">
+ // Adapted from Sun Java Web Start Auto-Install Demo
+ // http://java.sun.com/developer/technicalArticles/JavaLP/javawebstart/AutoInstallDemo.html
+ var detect = navigator.userAgent.toLowerCase();
+ var windowsIE = (checkPlatform("msie") && checkPlatform("win"));
+
+ function checkPlatform(string) {
+ place = detect.indexOf(string) + 1;
+ thestring = string;
+ return place;
+ }
+ </script>
+</table>
+
+#if(!$session)
+<script type="text/javascript" src="$content.getURI('scripts/subjectAssessorData/proj_tools.js')"></script>
+
+<script type="text/javascript">
+ //load projects
+ window.defaultProject = "$!project";
+
+ window.projectLoader = new ProjectLoader();
+
+ window.projectLoader.onLoadComplete.subscribe(function () {
+ renderProjects(document.getElementById("project"), window.projectLoader.list, window.defaultProject);
+ });
+
+ document.getElementById("project").onchange = function (o) {
+ if (this.selectedIndex > 0) {
+ var s = this.options[this.selectedIndex];
+ var pc = document.getElementById("pc_0");
+ if (pc != undefined && pc != null) {
+ if (s.pc == "4") {
+ if (s.qc == "0") {
+ document.getElementById("pc_2").click();
+ } else {
+ document.getElementById("pc_1").click();
+ }
+ } else {
+ document.getElementById("pc_0").click();
+ }
+ }
+ }
+ };
+
+ window.projectLoader.init();
+
+ function prepApplet(_form) {
+ return true;
+ }
+
+ //build breadcrumb
+ var breadcrumbs = document.getElementById('breadcrumbs');
+
+ if (breadcrumbs != null) {
+ var bread = "";
+ #if($project)
+ bread = bread + "<a href='$link.setAction("DisplayItemAction").addPathInfo("search_element","xnat:projectData").addPathInfo("search_field","xnat:projectData.ID").addPathInfo("search_value","$project")'>$displayManager.getSingularDisplayNameForProject().toUpperCase(): $!project</a>";
+ bread = bread + " > Upload Images";
+ #end
+ breadcrumbs.innerHTML = bread;
+ }
+
+</script>
+#end
\ No newline at end of file
diff --git a/src/main/webapp/xnat-templates/screens/Viewer.vm b/src/main/webapp/xnat-templates/screens/Viewer.vm
deleted file mode 100644
index 334793b5e4872d8c3aeca5e54a935454db2d9c21..0000000000000000000000000000000000000000
--- a/src/main/webapp/xnat-templates/screens/Viewer.vm
+++ /dev/null
@@ -1,89 +0,0 @@
-##Copyright 2005 Harvard University / Howard Hughes Medical Institute (HHMI) All Rights Reserved
-$page.setTitle("Viewer: $om.Id")
-
-#set ($age = $om.SubjectAge)
-#if ($age < 0)
-#set ($age = "--")
-#end
-
-#set ($qt='"')
-
-<script type="text/javascript">
- jq(document).ready(function() {
- // add "applet" class to body to support special handling for applets
- jq('body').addClass('applet');
- });
-</script>
-
-<table border="0" >
- <tr bgcolor="white">
- <td style="border-style:none;" valign="top" align="left" colspan="2">
- <applet name="plexiviewer" code="org.nrg.plexiViewer.lite.applet.PlexiViewerApplet"
- codebase="$!appletPath" archive="plexiviewer-1.6.5.jar, ij-1.49t.jar, framework-1.6.5.jar, xdat-beans-1.6.5.jar, log4j-1.2.17.jar, commons-lang-2.6.jar, nrgutil-2.0.0.jar"
- width=250 height=200>
- <param name="sessionId" value="$om.Id">
- #if ($startDisplayWith)
- <param name="startDisplayWith" value="$!startDisplayWith">
- #end
- <param name="jsessionid" value="$jsessionid">
- </applet>
- </td>
- </tr>
- <tr style="border-style:none;">
- <td style="border-style:none;" >
- <b>$displayManager.getSingularDisplayNameForImageSession() information</b>
- </td>
- <td style="border-style:none;" valign="top" align="right">
- <a class=b HREF="" onClick="return popup('$link.setPage('ViewerHelp.vm').addPathInfo('popup','true')','$om.Id')">Help</a>
- </td>
- </tr>
- <tr style="border-style:none;">
- <td style="border-style:none;" colspan="2" >
- <textarea
- rows="10"
- cols="32"
- style="font-family:'courier'; font-style:normal; font-weight:normal; font-size:12px; border-style:ridge;">$displayManager.getSingularDisplayNameForImageSession().toUpperCase() ID: $om.Label
-LAB ID: $!om.SubjectData.LabId
-MAP#: $!om.SubjectData.Map
-AGE: $age
-GENDER: $om.SubjectData.GenderText
-HANDEDNESS: $om.SubjectData.HandedText
-ACQ. DATE: $!om.Date
-SCANNER: $!om.Scanner
-STABILIZATION:$!om.Stabilization
-REF. MARKER: $!om.Marker
-INVESTIGATOR: $!om.Investigator.Firstname $!om.Investigator.Lastname
-OPERATOR: $!om.Operator
-
-#foreach ($scan in $om.Scans_scan)
-$scan.Id $!scan.Type $!scan.Quality
-#end
-
-Additional notes
-$!om.Note
-
-#foreach ($scan in $om.Scans_scan)
-SCAN NUMBER: $!scan.Id
-TYPE: $!scan.Type
-Quality: $!scan.Quality
-Vox res (mm):$!scan.Parameters_voxelres_x x $!scan.Parameters_voxelres_y x $!scan.Parameters_voxelres_z
-Rect. Fov: $!scan.Parameters_fov_x/$!scan.Parameters_fov_y
-Matrix: $!scan.Parameters_matrix_x/$!scan.Parameters_matrix_y
-Partitions: $!scan.Parameters_partitions
-Orientation: $!scan.Parameters_orientation
-TR (ms): $!scan.Parameters_tr
-TE (ms): $!scan.Parameters_te
-TI (ms): $!scan.Parameters_ti
-Flip: $!scan.Parameters_flip
-Sequence: $!scan.Parameters_sequence
-Origin: $!scan.Parameters_origin
-Time: $!scan.startTime
-Note: $!scan.Note
-
-#end
-</textarea>
- </td>
- </tr>
-</table>
-
-
diff --git a/src/main/webapp/xnat-templates/screens/ViewerHelp.vm b/src/main/webapp/xnat-templates/screens/ViewerHelp.vm
deleted file mode 100644
index 3c2a245adce2d11bd306a930bc3220700a76adee..0000000000000000000000000000000000000000
--- a/src/main/webapp/xnat-templates/screens/ViewerHelp.vm
+++ /dev/null
@@ -1,130 +0,0 @@
-##Copyright 2005 Harvard University / Howard Hughes Medical Institute (HHMI) All Rights Reserved
-<a name="#top"> Frequently Asked Questions </a>
-<UL>
-<li> <b>Adjusting an Image </b>
- <ul>
- <li> <a href="#adjustZ"> How do I zoom an Image?</a></li>
- <li> <a href="#adjustBC"> How do I adjust brightness of an Image?</a></li>
- <li> <a href="#adjustBC"> How do I adjust contrast of an Image?</a></li>
- <li> <a href="#adjustMM"> How do I adjust Max and Min intensity of an Image?</a></li>
- </ul>
-</li>
-<li><a href="#printImage"> How do I print an image?</a> </li>
-<li><a href="#saveImage"> How do I save a snapshot of an image?</a> </li>
-<li><a href="#blankScanData"> Why are Scan and Data choices blank?</a> </li>
-<li><a href="#tooSlow"> Why do some images like ASEG take more than a minute to load </a> </li>
-<li><a href="#increaseJvmMemory">How do I increase memory and avoid the error message of "Not enough memory..."? </a> </li>
-<li><b> Macintosh Issues (OS ver. 9x and earlier)</b>
- <ol>
- <li> <a href="#menuInvisible"> I do not see a menu after the image loads</a></li>
- <li> <a href="#saveMac"> When I save a snapshot, files are not saved as "GIF"</a></li>
- <li> <a href="#mrjIssue"> When I try to load ASEG images, I get an error message "read/write error..." and my machine hangs</a></li>
- </ol>
-</li>
-
-<li><a href="#contact"> Whom should I contact to report a bug? </a></li>
-</UL>
-
-
-<h3><a name="adjustZ">How do I zoom an Image? </a></h3>
-<p>
-Pressing digits 1, 2 or 3 on the keyboard will zoom an image by a factor of 1, 2 or 3.
-<p align="right"><small><a href="#top">Top</a></small></p>
-
-<h3><a name="adjustBC">How do I adjust brightness/contrast of an Image? </a></h3>
-<p>
-To adjust brighness/contrast of an image:
-<p> You can either
-<p> Under the menu item <b>Adjust</b> on the viewer, use <b>Brightness/Contrast</b>
-<p> Or
-<p> Use the combination <b>Ctrl+B</b> to pop-up the brightness/contrast adjuster window
-<p> Or
-<p> drag the mouse over the image while pressing the left or right mouse button down
-<p align="right"><small><a href="#top">Top</a></small></p>
-
-<h3><a name="adjustMM">How do I adjust max and min intensity of an Image? </a></h3>
-<p>
-To adjust max and/or min intensity of an image:
-<p> Under the menu <b>Adjust</b> on the viewer, use <b>Brightness/Contrast<b>
-<p align="right"><small><a href="#top">Top</a></small></p>
-
-<h3><a name="printImage">How do I print an image? </a></h3>
-<p>
- To print the image, <b>choose Print (Ctrl+P)</b> on the menu under <b>File</b>
-<p align="right"><small><a href="#top">Top</a></small></p>
-
-<h3><a name="saveImage">How do I save a snapshot of an image? </a></h3>
-<p>
- To save a snapshot of the image, <b>choose Save (Ctrl+S)</b> on the menu under <b>File</b>. The image files are saved as "GIF" files.
-<p align="right"><small><a href="#top">Top</a></small></p>
-
-<h3><a name="blankScanData">Why are Scan and Data choices blank? </a></h3>
-<p>
- Scan and Data Choices are displayed for built images. The $displayManager.getSingularDisplayNameForImageSession().toLowerCase() that you chose may not have been built.
-<p align="right"><small><a href="#top">Top</a></small></p>
-
-<h3> <a name="tooSlow"> Why do some images like ASEG take more than a minute to load? </a> </h3>
-<p>
- In order to display an image, a lot of the processing is handled by your machine, the delay in displaying an image could be because of slow network and less memory on your machine.
-<p align="right"><small><a href="#top">Top</a></small></p>
-
-<h3> <a name="menuInvisible"> I do not see a menu after the image loads </a> </h3>
-<p>
- On Mac machines, the menu of the viewer will be added to the main Menu bar of the browser.
-<p align="right"><small><a href="#top">Top</a></small></p>
-
-<h3> <a name="saveMac"> When I save a snapshot, files are not saved as "GIF"</a> </h3>
-<p>
- Due to the restriction of max. 31 characters for a file name, if the name of the file is more than 31 characters, the file name is truncated. The extension and/or part of the file name may be lost due this truncation. You should manually set the extension of the saved file.
-<p align="right"><small><a href="#top">Top</a></small></p>
-
-<h3> <a name="mrjIssue"> When I try to load ASEG images, I get an error message "read/write error..." and my machine hangs</a> </h3>
-<p>
- We suspect this problem is because the JAVA/MRJ version on your Mac is MRJ 2.2.5. Please upgrade MRJ to version 2.2.6 from here
- <a href="http://docs.info.apple.com/article.html?artnum=120209" target="_blank">MRJ 2.2.6</a>
-
- <p>
- In order to check the version of MRJ running on your machine, perform the following steps:
-
- <ol>
- <li>Open the System Folder in your Hard Disk</li>
- <li>Open the 'Extensions' folder</li>
- <li>Find and open the 'MRJ Libraries' folder (if there is no MRJ folder then you need to download and install MRJ Version 2.2.6)</li>
- <li>Select (highlight) the file 'MRJLib'</li>
- <li>Choose 'Get Info' from the File menu</li>
- <li>Check the version of MRJ you have</li>
- </ol> </p>
-
-<p align="right"><small><a href="#top">Top</a></small></p>
-
-<h3> <a name="increaseJvmMemory"> How do I increase memory and avoid the error message of "Not enough memory..."?</a> </h3>
-<p>
- <ul>
- <li> <b>Windows Users</b></li>
- <p> Open Control Panel
- <p> Click on Java (opens Java Control Panel)
- <p> Select Java Tab
- <p> Click on View (under Java Applet Runtime Settings)
- <p> Depending on the amount of RAM on you machine set -Xms128m -Xmx128m under the Java Runtime Parameter Column
- <p> Note: 128m above assumes that your machine has more than 128MB of physical RAM memory available.
- <p> Restart your browser
- <li> <b>Mac X Users</b></li>
- <p> Open Applications
- <p> Open Utilities
- <p> Open Java
- <p> Select Java <version number> Plugin Settings
- <p> Select the Advanced Tab
- <p> Depending on the amount of RAM on you machine set -Xms128m -Xmx128m under Java Runtime Parameter
- <p> Note: 128m above assumes that your machine has more than 128MB of physical RAM memory available.
- <p> Restart your browser
- <li> <b>Linux Users</b></li>
- </ul>
-</p>
-<p align="right"><small><a href="#top">Top</a></small></p>
-
-
-<h3> <a name="contact"> Whom should I contact to report a bug? </a></h3>
-<p>
- Email <a href="mailto:cnltech@iacmail.wustl.edu?subject=Image Viewer Assistance">CNDA Management </A>
-<p align="right"><small><a href="#top">Top</a></small></p>
-
diff --git a/src/main/webapp/xnat-templates/screens/XDATScreen_themes.vm b/src/main/webapp/xnat-templates/screens/XDATScreen_themes.vm
deleted file mode 100644
index cf8dab12ced971d3f65e7ea985117ed427d06743..0000000000000000000000000000000000000000
--- a/src/main/webapp/xnat-templates/screens/XDATScreen_themes.vm
+++ /dev/null
@@ -1,30 +0,0 @@
-<!-- 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 type="text/javascript" src="$content.getURI('scripts/themeManagement.js')"></script>
-
-<!-- End XDATScreen_themes.vm -->
\ No newline at end of file
diff --git a/src/main/webapp/xnat-templates/screens/register_box.vm b/src/main/webapp/xnat-templates/screens/register_box.vm
index c17ec1a544f95d6661c51fecffaaf2d1dae51394..1fd5adc2b37dfca0ee2b5514ac9db0acc3b9422e 100644
--- a/src/main/webapp/xnat-templates/screens/register_box.vm
+++ b/src/main/webapp/xnat-templates/screens/register_box.vm
@@ -5,7 +5,7 @@
#* @vtlvariable name="phone" type="java.lang.String" *#
#* @vtlvariable name="lab" type="java.lang.String" *#
#* @vtlvariable name="comments" type="java.lang.String" *#
-#* @vtlvariable name="siteConfig" type="java.util.Properties" *#
+#* @vtlvariable name="siteConfig" type="org.nrg.xdat.preferences.SiteConfigPreferences" *#
#* @vtlvariable name="data" type="org.apache.turbine.util.RunData" *#
#* @vtlvariable name="link" type="org.apache.turbine.services.pull.tools.TemplateLink" *#
#* @vtlvariable name="turbineUtils" type="org.nrg.xdat.turbine.utils.TurbineUtils" *#
diff --git a/src/main/webapp/xnat-templates/screens/topBar/New/Default.vm b/src/main/webapp/xnat-templates/screens/topBar/New/Default.vm
index 26ee8c3e88c9cf7a747a77c8faaabbd9457e655e..0080ac60de5fcabb8c5397e3a4fa4487b67cacbf 100644
--- a/src/main/webapp/xnat-templates/screens/topBar/New/Default.vm
+++ b/src/main/webapp/xnat-templates/screens/topBar/New/Default.vm
@@ -1,5 +1,5 @@
#* @vtlvariable name="projectString" type="java.lang.String" *#
-#* @vtlvariable name="siteConfig" type="java.util.Properties" *#
+#* @vtlvariable name="siteConfig" type="org.nrg.xdat.preferences.SiteConfigPreferences" *#
#* @vtlvariable name="data" type="org.apache.turbine.util.RunData" *#
#* @vtlvariable name="link" type="org.apache.turbine.services.pull.tools.TemplateLink" *#
#* @vtlvariable name="displayManager" type="org.nrg.xdat.display.DisplayManager" *#
diff --git a/src/main/webapp/xnat-templates/screens/xnat_ctSessionData/edit/scans.vm b/src/main/webapp/xnat-templates/screens/xnat_ctSessionData/edit/scans.vm
index 8e12c586b0c9806c601a73531bc2b8004cb266f4..714a6d849d13311e088347a4cac790c96a77cdf1 100644
--- a/src/main/webapp/xnat-templates/screens/xnat_ctSessionData/edit/scans.vm
+++ b/src/main/webapp/xnat-templates/screens/xnat_ctSessionData/edit/scans.vm
@@ -1,5 +1,5 @@
#* @vtlvariable name="content" type="org.apache.turbine.services.pull.tools.ContentTool" *#
-#* @vtlvariable name="siteConfig" type="java.util.Properties" *#
+#* @vtlvariable name="siteConfig" type="org.nrg.xdat.preferences.SiteConfigPreferences" *#
#* @vtlvariable name="turbineUtils" type="org.nrg.xdat.turbine.utils.TurbineUtils" *#
#* @vtlvariable name="user" type="org.nrg.xdat.security.XDATUser" *#
#* @vtlvariable name="om" type="org.nrg.xdat.om.XnatCtsessiondata" *#
diff --git a/src/main/webapp/xnat-templates/screens/xnat_imageSessionData/xnat_imageSessionData_scans.vm b/src/main/webapp/xnat-templates/screens/xnat_imageSessionData/xnat_imageSessionData_scans.vm
index b5de0812351fb963d717e848c0e53ed652866480..c572cf802bcfe31cdedd00f7e928e8197f461805 100644
--- a/src/main/webapp/xnat-templates/screens/xnat_imageSessionData/xnat_imageSessionData_scans.vm
+++ b/src/main/webapp/xnat-templates/screens/xnat_imageSessionData/xnat_imageSessionData_scans.vm
@@ -1,6 +1,6 @@
#* @vtlvariable name="item" type="org.nrg.xft.XFTItem" *#
#* @vtlvariable name="user" type="org.nrg.xdat.security.XDATUser" *#
-#* @vtlvariable name="siteConfig" type="java.util.Properties" *#
+#* @vtlvariable name="siteConfig" type="org.nrg.xdat.preferences.SiteConfigPreferences" *#
#* @vtlvariable name="turbineUtils" type="org.nrg.xdat.turbine.utils.TurbineUtils" *#
#* @vtlvariable name="om" type="org.nrg.xdat.om.XnatImagesessiondata" *#
#* @vtlvariable name="scan" type="org.nrg.xdat.om.XnatImagescandata" *#
diff --git a/src/main/webapp/xnat-templates/screens/xnat_projectData/xnat_projectData_actions_box.vm b/src/main/webapp/xnat-templates/screens/xnat_projectData/xnat_projectData_actions_box.vm
index ae62bd05c05567366db83c9f406bc93a615f6a31..abfc804c1b8f967e8cfcfe1ddb899d60dac81219 100644
--- a/src/main/webapp/xnat-templates/screens/xnat_projectData/xnat_projectData_actions_box.vm
+++ b/src/main/webapp/xnat-templates/screens/xnat_projectData/xnat_projectData_actions_box.vm
@@ -22,7 +22,8 @@
autosubmenudisplay: true,
scrollincrement: 5,
position: "static",
- maxheight: 150
+ maxheight: 150,
+ submenualignment: ["tr","br"] // aligns top-right (tr) corner of submenu to bottom-right (br) corner of parent item
});
// Render the MenuBar instance
actionsMenu.getItem(0).cfg.setProperty("disabled", true);
diff --git a/src/main/webapp/xnat-templates/screens/xnat_projectData/xnat_projectData_summary_manage.vm b/src/main/webapp/xnat-templates/screens/xnat_projectData/xnat_projectData_summary_manage.vm
index 29a51ff89185998c6fd6eb3a105cca383cac14e9..024af73d65d004b61a76325a90d691b8ba9392a2 100644
--- a/src/main/webapp/xnat-templates/screens/xnat_projectData/xnat_projectData_summary_manage.vm
+++ b/src/main/webapp/xnat-templates/screens/xnat_projectData/xnat_projectData_summary_manage.vm
@@ -1,5 +1,5 @@
#* @vtlvariable name="displayManager" type="org.nrg.xdat.display.DisplayManager" *#
-#* @vtlvariable name="siteConfig" type="java.util.Properties" *#
+#* @vtlvariable name="siteConfig" type="org.nrg.xdat.preferences.SiteConfigPreferences" *#
#* @vtlvariable name="content" type="org.apache.turbine.services.pull.tools.ContentTool" *#
#* @vtlvariable name="turbineUtils" type="org.nrg.xdat.turbine.utils.TurbineUtils" *#
#* @vtlvariable name="project" type="org.nrg.xdat.om.XnatProjectdata" *#
diff --git a/src/main/webapp/xnat-templates/screens/xnat_projectData/xnat_projectData_summary_management.vm b/src/main/webapp/xnat-templates/screens/xnat_projectData/xnat_projectData_summary_management.vm
index b6807c984a4e1aa91cf7ee6cf6e7d59f184718c6..8fd56e1fe413e6e88538da160280ddcc268136b2 100644
--- a/src/main/webapp/xnat-templates/screens/xnat_projectData/xnat_projectData_summary_management.vm
+++ b/src/main/webapp/xnat-templates/screens/xnat_projectData/xnat_projectData_summary_management.vm
@@ -1,4 +1,4 @@
-#* @vtlvariable name="siteConfig" type="java.util.Properties" *#
+#* @vtlvariable name="siteConfig" type="org.nrg.xdat.preferences.SiteConfigPreferences" *#
#* @vtlvariable name="data" type="org.apache.turbine.util.RunData" *#
#* @vtlvariable name="turbineUtils" type="org.nrg.xdat.turbine.utils.TurbineUtils" *#
#* @vtlvariable name="content" type="org.apache.turbine.services.pull.tools.ContentTool" *#