diff --git a/build.gradle b/build.gradle
index 49b2b8fc0d8292d36c150c4de4950b64b68d8077..f249716621b2f3b054668ef2ab5547ff86caac54 100644
--- a/build.gradle
+++ b/build.gradle
@@ -301,8 +301,7 @@ dependencies {
compile "org.nrg:ecat4xnat:1.7.0-SNAPSHOT"
compile "org.nrg:DicomDB:4.1.0"
compile "org.nrg:ExtAttr:4.1.0"
-// compile "org.nrg:DicomEdit:4.2.1"
- compile "org.nrg:DicomEdit:4.2.2"
+ compile "org.nrg:DicomEdit:4.2.3"
compile "org.nrg:DicomImageUtils:${vXnat}"
compile "org.nrg:DicomUtils:1.3.1"
compile "org.nrg:PrearcImporter:${vXnat}"
@@ -386,7 +385,7 @@ dependencies {
compile "org.apache.httpcomponents:httpcore-nio:4.4.4"
compile "org.codehaus.groovy:groovy-all:${vGroovy}"
- compile "org.python:jython:${vJython}"
+ compile "org.python:jython-standalone:${vJython}"
compile "net.sourceforge.saxon:saxon:${vSaxon}"
compile "xalan:xalan:2.7.2"
diff --git a/src/main/java/org/nrg/xapi/rest/event/EventHandlerApi.java b/src/main/java/org/nrg/xapi/rest/event/EventHandlerApi.java
index e8717e550508f34b4d6553b5055354026c38996e..166549e9cb25cc9e06f77132994cd930eeb6741f 100644
--- a/src/main/java/org/nrg/xapi/rest/event/EventHandlerApi.java
+++ b/src/main/java/org/nrg/xapi/rest/event/EventHandlerApi.java
@@ -12,8 +12,9 @@ import org.nrg.automation.event.entities.AutomationFilters;
import org.nrg.automation.services.impl.hibernate.HibernateAutomationEventIdsService;
import org.nrg.automation.services.impl.hibernate.HibernateAutomationFiltersService;
import org.nrg.framework.annotations.XapiRestController;
+import org.nrg.framework.event.EventClass;
import org.nrg.framework.event.Filterable;
-import org.nrg.framework.utilities.Reflection;
+import org.nrg.framework.utilities.BasicXnatResourceLocator;
import org.nrg.xapi.model.event.EventClassInfo;
import org.nrg.xdat.XDAT;
import org.nrg.xdat.om.XnatProjectdata;
@@ -22,11 +23,12 @@ import org.nrg.xdat.security.XDATUser;
import org.nrg.xdat.security.helpers.Permissions;
import org.nrg.xdat.security.services.RoleHolder;
import org.nrg.xft.security.UserI;
-import org.nrg.xnat.event.conf.EventPackages;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.core.annotation.AnnotationUtils;
+import org.springframework.core.io.Resource;
+import org.springframework.core.io.support.PropertiesLoaderUtils;
import org.springframework.http.HttpStatus;
import org.springframework.http.MediaType;
import org.springframework.http.ResponseEntity;
@@ -44,6 +46,7 @@ import java.util.Arrays;
import java.util.Collections;
import java.util.List;
import java.util.Map;
+import java.util.Properties;
/**
* The Class EventHandlerApi.
@@ -69,13 +72,6 @@ public class EventHandlerApi {
@Autowired
private HibernateAutomationFiltersService filtersService;
- /**
- * The event packages.
- */
- @SuppressWarnings("MismatchedQueryAndUpdateOfCollection")
- @Autowired
- private EventPackages eventPackages;
-
/**
* Inits the this.
*/
@@ -183,7 +179,7 @@ public class EventHandlerApi {
Collections.sort(valueList);
filterableFields.put(autoFilters.getField(), valueList);
} else {
- for (String value : autoFilters.getValues()) {
+ for (final String value : autoFilters.getValues()) {
final List<String> values = filterableFields.get(autoFilters.getField());
if (!values.contains(value)) {
values.add(value);
@@ -206,23 +202,28 @@ public class EventHandlerApi {
*/
private List<String> getEventClassList(List<AutomationEventIds> eventIdsList) {
final List<String> classList = Lists.newArrayList();
- // ClassList should be pulled from available event classes rather than from events
- if (eventPackages != null) {
- for (final String pkg : eventPackages) {
- try {
- for (final Class<?> clazz : Reflection.getClassesForPackage(pkg)) {
- if (AutomationEventImplementerI.class.isAssignableFrom(clazz) && !clazz.isInterface() &&
- !Modifier.isAbstract(clazz.getModifiers())) {
- if (!classList.contains(clazz.getName())) {
- classList.add(clazz.getName());
- }
- }
- }
- } catch (ClassNotFoundException | IOException e) {
- // Do nothing.
- }
- }
- }
+ try {
+ for (final Resource resource : BasicXnatResourceLocator.getResources("classpath*:META-INF/xnat/events/*-event.properties")) {
+ final Properties properties = PropertiesLoaderUtils.loadProperties(resource);
+ if (!properties.containsKey(EventClass.EVENT_CLASS)) {
+ continue;
+ }
+ final String clssStr = properties.get(EventClass.EVENT_CLASS).toString();
+ try {
+ final Class<?> clazz = Class.forName(clssStr);
+ if (AutomationEventImplementerI.class.isAssignableFrom(clazz) && !clazz.isInterface() &&
+ !Modifier.isAbstract(clazz.getModifiers())) {
+ if (!classList.contains(clazz.getName())) {
+ classList.add(clazz.getName());
+ }
+ }
+ } catch (ClassNotFoundException cex) {
+ _log.debug("Could not load class for class name (" + clssStr + ")");
+ }
+ }
+ } catch (IOException e) {
+ _log.debug("Could not load event class properties resources (META-INF/xnat/*-event.properties)");
+ }
// I think for now we'll not pull from the database if we've found event classes. If the database
// contains any thing different, it should only be event classes that are no longer available.
if (classList.size() < 1) {
diff --git a/src/main/java/org/nrg/xnat/configuration/ReactorConfig.java b/src/main/java/org/nrg/xnat/configuration/ReactorConfig.java
index 27138d6cc5b2346a7ff67ef57123914de76c3023..d831d26cc2c0ac18405ca4c72617f6f4e5ae5750 100755
--- a/src/main/java/org/nrg/xnat/configuration/ReactorConfig.java
+++ b/src/main/java/org/nrg/xnat/configuration/ReactorConfig.java
@@ -26,12 +26,6 @@ public class ReactorConfig {
return new XftItemEventListener(eventBus);
}
- @Bean
- public EventPackages eventPackages() {
- // NOTE: These should be treated as parent packages. All sub-packages should be searched
- return new EventPackages(new HashSet<>(Arrays.asList(new String[]{"org.nrg.xnat.event", "org.nrg.xft.event", "org.nrg.xdat.event"})));
- }
-
/**
* Env.
*
diff --git a/src/main/java/org/nrg/xnat/event/entities/ScriptLaunchRequestEvent.java b/src/main/java/org/nrg/xnat/event/entities/ScriptLaunchRequestEvent.java
index ff474487300f6466cf9b1477b3ad27231163d383..e5d2d2a0c488abc3599e836ed9c255a5092d33e0 100644
--- a/src/main/java/org/nrg/xnat/event/entities/ScriptLaunchRequestEvent.java
+++ b/src/main/java/org/nrg/xnat/event/entities/ScriptLaunchRequestEvent.java
@@ -10,15 +10,16 @@ import org.nrg.automation.event.AutomationEventImplementerI;
import org.nrg.automation.event.entities.AutomationCompletionEvent;
import org.nrg.automation.event.entities.PersistentEvent;
import org.nrg.framework.event.EventClass;
-import org.nrg.framework.event.persist.PersistentEventImplementerI;
+
+import com.google.common.collect.Maps;
/**
* The Class AutomationLaunchRequestEvent.
*/
@Entity
@PrimaryKeyJoinColumn(name="ID", referencedColumnName="ID")
-@EventClass(displayName="Script Launch Request Event")
-public class ScriptLaunchRequestEvent extends PersistentEvent implements PersistentEventImplementerI, AutomationEventImplementerI {
+@EventClass(name="ScriptLaunchRequestEvent", description="Script Launch Request Event")
+public class ScriptLaunchRequestEvent extends PersistentEvent implements AutomationEventImplementerI {
/** The Constant serialVersionUID. */
private static final long serialVersionUID = 7465778737330635218L;
@@ -26,7 +27,7 @@ public class ScriptLaunchRequestEvent extends PersistentEvent implements Persist
/** The automation completion event. */
private AutomationCompletionEvent automationCompletionEvent;
- private Map<String,Object> parameterMap;
+ private Map<String,Object> parameterMap = Maps.newHashMap();
/**
* Instantiates a new automation launch request event.
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 6f0d32a1cca965653e26b03c6a342bffa06c2a30..b5e4be6171514a8277d89c3851e6f9e15cf60a76 100644
--- a/src/main/java/org/nrg/xnat/event/listeners/AutomationEventScriptHandler.java
+++ b/src/main/java/org/nrg/xnat/event/listeners/AutomationEventScriptHandler.java
@@ -22,6 +22,7 @@ import org.nrg.framework.constants.Scope;
import org.nrg.framework.event.Filterable;
import org.nrg.framework.event.persist.PersistentEventImplementerI;
import org.nrg.framework.exceptions.NrgServiceException;
+import org.nrg.framework.exceptions.NrgServiceRuntimeException;
import org.nrg.framework.services.NrgEventService;
import org.nrg.xdat.XDAT;
import org.nrg.xdat.security.helpers.Users;
@@ -444,14 +445,23 @@ public class AutomationEventScriptHandler implements Consumer<Event<AutomationEv
if (PersistentWorkflowUtils.IN_PROGRESS.equals(workflow.getStatus())) {
WorkflowUtils.complete(workflow, workflow.buildEvent());
}
- } catch (NrgServiceException e) {
- final String message = String.format("Failed running the script %s by user %s for event %s on data type %s instance %s from project %s",
+ } catch (NrgServiceException | NrgServiceRuntimeException e) {
+ final String message = String.format("Failed running the script %s by user %s for event %s on data type %s instance %s from project %s (Exception=%s)",
request.getScriptId(),
request.getUser().getLogin(),
request.getEvent(),
request.getDataType(),
request.getDataId(),
- request.getExternalId());
+ request.getExternalId(),
+ e.toString());
+ if (scriptOut==null) {
+ scriptOut = new ScriptOutput();
+ scriptOut.setStatus(Status.ERROR);
+ scriptOut.setOutput(message);
+ }
+ if (PersistentWorkflowUtils.IN_PROGRESS.equals(workflow.getStatus())) {
+ WorkflowUtils.fail(workflow, workflow.buildEvent());
+ }
AdminUtils.sendAdminEmail("Script execution failure", message);
logger.error(message, e);
if (PersistentWorkflowUtils.IN_PROGRESS.equals(workflow.getStatus())) {
diff --git a/src/main/java/org/nrg/xnat/initialization/SecurityConfig.java b/src/main/java/org/nrg/xnat/initialization/SecurityConfig.java
index 7cc14d329c90596d45c01caa758d47becb2963a4..6bca03b5a2bf491b32dc29a83aceb0a328c3331d 100644
--- a/src/main/java/org/nrg/xnat/initialization/SecurityConfig.java
+++ b/src/main/java/org/nrg/xnat/initialization/SecurityConfig.java
@@ -69,7 +69,7 @@ public class SecurityConfig {
@Bean
public XnatAuthenticationEntryPoint loginUrlAuthenticationEntryPoint() {
- final XnatAuthenticationEntryPoint entryPoint = new XnatAuthenticationEntryPoint("/app/template/Login.vm");
+ final XnatAuthenticationEntryPoint entryPoint = new XnatAuthenticationEntryPoint("/app/template/Login.vm", _configuration);
entryPoint.setDataPaths(Arrays.asList("/xapi/**", "/data/**", "/REST/**", "/fs/**"));
entryPoint.setInteractiveAgents(Arrays.asList(".*MSIE.*", ".*Mozilla.*", ".*AppleWebKit.*", ".*Opera.*"));
return entryPoint;
@@ -100,8 +100,7 @@ public class SecurityConfig {
RegisterSessionAuthenticationStrategy registerSessionAuthenticationStrategy = new RegisterSessionAuthenticationStrategy(sessionRegistry);
authStrategies.add(registerSessionAuthenticationStrategy);
- final CompositeSessionAuthenticationStrategy compositeSessionAuthenticationStrategy = new CompositeSessionAuthenticationStrategy(authStrategies);
- return compositeSessionAuthenticationStrategy;
+ return new CompositeSessionAuthenticationStrategy(authStrategies);
}
@Bean
diff --git a/src/main/java/org/nrg/xnat/security/XnatAuthenticationEntryPoint.java b/src/main/java/org/nrg/xnat/security/XnatAuthenticationEntryPoint.java
index 3c08027aa4f2df48283a2f49a53f6133d101458b..1c40b2b9f1aa27bff5000df7a4b61f55e6943f8b 100644
--- a/src/main/java/org/nrg/xnat/security/XnatAuthenticationEntryPoint.java
+++ b/src/main/java/org/nrg/xnat/security/XnatAuthenticationEntryPoint.java
@@ -13,6 +13,8 @@ package org.nrg.xnat.security;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
+import org.nrg.config.exceptions.SiteConfigurationException;
+import org.nrg.xdat.preferences.InitializerSiteConfiguration;
import org.springframework.security.core.AuthenticationException;
import org.springframework.security.web.authentication.LoginUrlAuthenticationEntryPoint;
import org.springframework.security.web.util.matcher.AntPathRequestMatcher;
@@ -28,8 +30,9 @@ import java.util.regex.Pattern;
public class XnatAuthenticationEntryPoint extends LoginUrlAuthenticationEntryPoint {
- public XnatAuthenticationEntryPoint(String loginFormUrl) {
+ public XnatAuthenticationEntryPoint(final String loginFormUrl, final InitializerSiteConfiguration configuration) {
super(loginFormUrl);
+ _configuration = configuration;
}
/**
@@ -41,8 +44,9 @@ public class XnatAuthenticationEntryPoint extends LoginUrlAuthenticationEntryPoi
* @param request HTTP request object.
* @param response HTTP response object.
* @param authException An authentication exception that may have redirected the agent to re-authenticate.
- * @throws IOException
- * @throws ServletException
+ *
+ * @throws IOException When an error occurs reading or writing data.
+ * @throws ServletException When an error occurs in the framework.
*/
@Override
public void commence(final HttpServletRequest request, final HttpServletResponse response, final AuthenticationException authException) throws IOException, ServletException {
@@ -51,27 +55,33 @@ public class XnatAuthenticationEntryPoint extends LoginUrlAuthenticationEntryPoi
if (_log.isDebugEnabled()) {
_log.debug("Evaluating data path request: " + strippedUri + ", user agent: " + userAgent);
- }
-
- if(!StringUtils.isBlank(strippedUri) && strippedUri.contains("/action/AcceptProjectAccess/par/")) {
- int index=strippedUri.indexOf("/par/")+5;
- if(strippedUri.length()>index){//par number included?
- String parS=strippedUri.substring(index);
- if(parS.contains("/")){
- parS=parS.substring(0,parS.indexOf("/"));
- }
-
- request.getSession().setAttribute("par", parS);
- }
}
-
- if (isDataPath(request) && !isInteractiveAgent(userAgent)) {
- response.sendError(HttpServletResponse.SC_UNAUTHORIZED);
- return;
+
+ if (!StringUtils.isBlank(strippedUri) && strippedUri.contains("/action/AcceptProjectAccess/par/")) {
+ int index = strippedUri.indexOf("/par/") + 5;
+ if (strippedUri.length() > index) {//par number included?
+ String parS = strippedUri.substring(index);
+ if (parS.contains("/")) {
+ parS = parS.substring(0, parS.indexOf("/"));
+ }
+
+ request.getSession().setAttribute("par", parS);
+ }
}
+ if (isDataPath(request) && !isInteractiveAgent(userAgent)) {
+ try {
+ response.setHeader("WWW-Authenticate", "Basic realm=\"" + _configuration.getSiteId() + "\"");
+ response.sendError(HttpServletResponse.SC_UNAUTHORIZED);
+ } catch (SiteConfigurationException e) {
+ _log.error("An error occurred trying to access system resources: siteId", e);
+ response.setHeader("WWW-Authenticate", "Basic");
+ response.sendError(HttpServletResponse.SC_UNAUTHORIZED);
+ }
+ } else {
super.commence(request, response, authException);
}
+ }
/**
* Sets the data paths, i.e. those paths which require a user-agent interactivity test to determine whether the user
@@ -83,7 +93,7 @@ public class XnatAuthenticationEntryPoint extends LoginUrlAuthenticationEntryPoi
public void setDataPaths(final List<String> dataPaths) {
if (_log.isDebugEnabled()) {
_log.debug("Adding " + dataPaths + " data paths");
- }
+ }
for (final String dataPath : dataPaths) {
if (_log.isDebugEnabled()) {
@@ -102,7 +112,7 @@ public class XnatAuthenticationEntryPoint extends LoginUrlAuthenticationEntryPoi
for (final String interactiveAgent : interactiveAgents) {
if (_log.isDebugEnabled()) {
_log.debug("Adding interactive agent specifier: " + interactiveAgent);
-}
+ }
final Pattern pattern = Pattern.compile(interactiveAgent);
_agentPatterns.add(pattern);
}
@@ -146,8 +156,10 @@ public class XnatAuthenticationEntryPoint extends LoginUrlAuthenticationEntryPoi
return false;
}
+ private final InitializerSiteConfiguration _configuration;
+
private static final Log _log = LogFactory.getLog(XnatAuthenticationEntryPoint.class);
- private final List<RequestMatcher> _dataPaths = new ArrayList<>();
- private final List<Pattern> _agentPatterns = new ArrayList<>();
+ private final List<RequestMatcher> _dataPaths = new ArrayList<>();
+ private final List<Pattern> _agentPatterns = new ArrayList<>();
}
diff --git a/src/main/java/org/nrg/xnat/services/messaging/automation/AutomatedScriptRequest.java b/src/main/java/org/nrg/xnat/services/messaging/automation/AutomatedScriptRequest.java
index 1512ed44f62fc7e25bf70c2e19683be229d2565d..c6204cebb86d50eac498735689fe7e80ecd4f789 100644
--- a/src/main/java/org/nrg/xnat/services/messaging/automation/AutomatedScriptRequest.java
+++ b/src/main/java/org/nrg/xnat/services/messaging/automation/AutomatedScriptRequest.java
@@ -87,7 +87,9 @@ public class AutomatedScriptRequest implements Serializable {
*/
public AutomatedScriptRequest(final String srcEventId, final String srcEventClass, final UserI user, final String scriptId, final String event, final String scriptWorkflow, final String dataType, final String dataId, final String externalId, Map<String,Object> argumentMap) {
this(srcEventId, srcEventClass, user, scriptId, event, scriptWorkflow, dataType, dataId, externalId);
- _argumentMap.putAll(argumentMap);
+ if (argumentMap != null) {
+ _argumentMap.putAll(argumentMap);
+ }
}
/**
diff --git a/src/main/webapp/WEB-INF/tags/page/xnat.tag b/src/main/webapp/WEB-INF/tags/page/xnat.tag
index 5509eb107147fac81d6c998c919ef9a1c9d6780f..df3ab8e8e0ecfdd3d300f79acb682a80701b44f2 100644
--- a/src/main/webapp/WEB-INF/tags/page/xnat.tag
+++ b/src/main/webapp/WEB-INF/tags/page/xnat.tag
@@ -359,36 +359,11 @@ ${bodyTop}
<!-- search script -->
<script type="text/javascript">
- <!--
- function DefaultEnterKey(e, button){
- var keynum, keychar, numcheck;
-
- if (window.event) // IE
- {
- keynum = e.keyCode;
- if (keynum == 13) {
- submitQuickSearch();
- return true;
- }
- }
- else if (e) // Netscape/Firefox/Opera
- {
- keynum = e.which;
- if (keynum == 13) {
- submitQuickSearch();
- return false;
- }
- }
- return true;
- }
-
function submitQuickSearch(){
- concealContent();
- if (document.getElementById('quickSearchForm').value != "")
- document.getElementById('quickSearchForm').submit();
+ if($('#searchValue').val()!="") {
+ $('#quickSearchForm').submit();
+ }
}
-
- //-->
</script>
<!-- end search script -->
@@ -426,11 +401,20 @@ ${bodyTop}
</optgroup>
</select>
<input id="searchValue" class="clean" name="searchValue" type="text" maxlength="40" size="20" value="">
+ <input id="xnat_csrf" name="XNAT_CSRF" type="hidden" value="">
<button type="button" id="search_btn" class="btn2" onclick="submitQuickSearch();">Go</button>
<script>
-
- $('#searchValue').each(function(){
+ var searchField = $('#searchValue');
+ searchField.keyup(function( event ) {
+ if (event.which == 13) {
+ submitQuickSearch();
+ }
+ });
+
+ $('#xnat_csrf').val(window.csrfToken);
+
+ searchField.each(function(){
var _this = this;
_this.value = _this.value || 'search';
$(_this).focus(function(){
diff --git a/src/main/webapp/scripts/uploaders/AutomationBasedUploader.js b/src/main/webapp/scripts/uploaders/AutomationBasedUploader.js
index 77b4dd7cb1a981747ba8fa801891aaddf6900e2c..8e593ec50c7af1d4515eff3da2637891a6987875 100644
--- a/src/main/webapp/scripts/uploaders/AutomationBasedUploader.js
+++ b/src/main/webapp/scripts/uploaders/AutomationBasedUploader.js
@@ -270,8 +270,12 @@ XNAT.app.abu.eventHandlerChange = function(){
var eventHandler = $('#eventHandlerSelect').val();
if (typeof eventHandler === 'undefined' || eventHandler == null || eventHandler.length<1 && ($("#handlerDefaultOption").html() == 'NONE DEFINED' || $("#handlerDefaultOption").html() == 'SELECT')) {
$("#abu-process-button").addClass("abu-button-disabled");
+ //$("#abu-process-button-text").html(" ");
+ $("#abu-process-button").css("visibility","hidden");
} else if ((XNAT.app.abu.usageSelect=='Launch') || (abu._fileUploader._uploadStarted && abu._fileUploader._filesInProgress<1)) {
$("#abu-process-button").removeClass("abu-button-disabled");
+ //$("#abu-process-button-text").html(" ");
+ $("#abu-process-button").css("visibility","visible");
}
XNAT.app.abu.filesProcessed = false;
}
@@ -411,7 +415,7 @@ XNAT.app.abu.populateEventHandlerSelect = function(){
if ($('#eventHandlerSelect').find('option').length==1) {
$('#handlerDefaultOption').html('NONE DEFINED');
} else if ($('#eventHandlerSelect').find('option').length==2) {
- $('#eventHandlerSelect').find('option').get(0).remove();
+ $($('#eventHandlerSelect').find('option').get(0)).remove();
}
} else {
$('#eventHandlerSelect').append('<option value="">NONE DEFINED</option>');
@@ -591,6 +595,8 @@ XNAT.app.abu.initializeAbuUploader = function(usageType){
var eventHandler = $('#eventHandlerSelect').val();
if (typeof eventHandler !== 'undefined' && eventHandler != null && eventHandler.length>0) {
$("#abu-process-button").removeClass("abu-button-disabled");
+ $("#abu-process-button-text").html("Process Files");
+ $("#abu-process-button").css("visibility","visible");
} else {
$("#abu-done-button-text").html("Done");
$("#abu-done-button").removeClass("abu-button-disabled");
@@ -615,6 +621,7 @@ XNAT.app.abu.initializeAbuUploader = function(usageType){
var eventHandler = $('#eventHandlerSelect').val();
if (eventHandler != undefined && eventHandler != null && eventHandler.length>0) {
$("#abu-process-button").removeClass("abu-button-disabled");
+ $("#abu-process-button").css("visibility","visible");
} else {
$("#abu-done-button").removeClass("abu-button-disabled");
$("#abu-done-button-text").html("Done");
@@ -628,6 +635,8 @@ XNAT.app.abu.initializeAbuUploader = function(usageType){
$("#abu-done-button-text").html("Cancel");
if ($('#eventHandlerSelect option').size()>1 && $('#eventHandlerSelect').val()=="") {
$("#abu-process-button").addClass("abu-button-disabled");
+ //$("#abu-process-button-text").html(" ");
+ $("#abu-process-button").css("visibility","hidden");
}
$("#file-uploader-instructions-sel").css("display","none");
} else {
@@ -637,6 +646,8 @@ XNAT.app.abu.initializeAbuUploader = function(usageType){
abu._fileUploader.DRAG_AND_DROP_ON = false;
}
$("#abu-process-button").addClass("abu-button-disabled");
+ //$("#abu-process-button-text").html(" ");
+ $("#abu-process-button").css("visibility","hidden");
$(".upload-area").css("display","none");
$(".eventhandler-area").css("display","none");
}
@@ -662,8 +673,9 @@ XNAT.app.abu.usageSelectAction = function(){
$("#abu-upload-button").removeClass("abu-button-disabled");
abu._fileUploader.DRAG_AND_DROP_ON = true;
$("#abu-process-button").addClass("abu-button-disabled");
+ //$("#abu-process-button-text").html(" ");
+ $("#abu-process-button").css("visibility","hidden");
$("#script-select-text").html("Post-upload processing script:");
- $("#abu-process-button-text").html("Process files");
$("#resourceSelect").prop('disabled',false);
$(".response_text").html('');
} else if (XNAT.app.abu.usageSelect=='Launch') {
@@ -674,6 +686,7 @@ XNAT.app.abu.usageSelectAction = function(){
var eventHandler = $('#eventHandlerSelect').val();
if (eventHandler != undefined && eventHandler != null && eventHandler.length>0) {
$("#abu-process-button").removeClass("abu-button-disabled");
+ $("#abu-process-button").css("visibility","visible");
}
$("#script-select-text").html("Script to launch:");
$("#abu-process-button-text").html("Run script");
@@ -716,6 +729,8 @@ XNAT.app.abu.whatToDoChange = function(){
$('#eventHandlerSelect').val(launchSelect);
if (typeof abu !== 'undefined' && abu._fileUploader.uploadsStarted>0 && abu._fileUploader.uploadsInProgress==0) {
$("#abu-process-button").removeClass("abu-button-disabled");
+ $("#abu-process-button-text").html("Process files");
+ $("#abu-process-button").css("visibility","visible");
}
if (XNAT.app.abu.usageSelect == 'Upload' && $('#whatToDoSelect option').size()>1 && $('#whatToDoSelect').val()=="") {
$("#abu-upload-button").addClass("abu-button-disabled");
@@ -903,9 +918,9 @@ XNAT.app.abu.processFiles=function() {
((this.paramsToPass.length>0) ? "Please supply values for the following parameters:" : "Please supply a value for the following parameter:") +
' </h3><div style="width:100px"><table>' + paramText + "</table>");
// Not sure why the setTimeout seems necessary.
- $(".passParamInput").get(0).focus();
+ $($(".passParamInput").get(0)).focus();
setTimeout(function(){
- $(".passParamInput").get(0).focus();
+ $($(".passParamInput").get(0)).focus();
},100);
} else {
diff --git a/src/main/webapp/scripts/uploaders/fileuploader.js b/src/main/webapp/scripts/uploaders/fileuploader.js
index e47a44d348a4c7b90d5d5d876c0db24978673f2e..c00698bc354151bc9f30a0f83551af2c6e58f928 100644
--- a/src/main/webapp/scripts/uploaders/fileuploader.js
+++ b/src/main/webapp/scripts/uploaders/fileuploader.js
@@ -27,7 +27,7 @@ abu.FileUploader = function(o){
$(this._options.element).append(
'<div class="abu-uploader">' +
'<div id="abu-files-processing" class="abu-files-processing"> Processing...... </div>' +
- '<a id="file-uploader-instructions-sel" class="abu-uploader-instructions-sel" onclick="abu._fileUploader.uploaderHelp()">Click here for help.</a>' +
+ '<a id="file-uploader-instructions-sel" class="abu-uploader-instructions-sel" onclick="abu._fileUploader.uploaderHelp()">?</a>' +
'<div class="abu-upload-drop-area" style="display: none;"><span>Drop files here to upload</span></div>' +
'<div class="abu-xnat-interactivity-area">' +
'</div>' +
@@ -96,14 +96,35 @@ abu.FileUploader = function(o){
});
if (this.ALLOW_DRAG_AND_DROP) {
+ $(".abu-upload-drop-area").on('dragleave',function(e) {
+ if (this.DRAG_AND_DROP_ON) {
+ this.showDrag = false;
+ if (typeof this.timeout !== "undefined") {
+ clearTimeout( this.timeout );
+ }
+ this.timeout = setTimeout( function(){
+ if( !this.showDrag ){
+ $(".abu-upload-drop-area").css('display','none');
+ $(".abu-upload-drop-area").removeClass('abu-upload-drop-area-active');
+ try {
+ e.preventDefault();
+ e.stopPropogation();
+ } catch(e) { /* Do nothing */ }
+ }
+ }.bind(this), 200 ).bind(this);
+ }
+ }.bind(this)
+ );
$(".abu-upload-drop-area").on('dragover',function(e) {
if (this.DRAG_AND_DROP_ON) {
+ this.showDrag = true;
this.activateUploadArea(e);
}
}.bind(this)
);
$(".abu-upload-drop-area").on('dragenter',function(e) {
if (this.DRAG_AND_DROP_ON) {
+ this.showDrag = true;
this.activateUploadArea(e);
}
}.bind(this)
@@ -120,14 +141,35 @@ abu.FileUploader = function(o){
}
}.bind(this)
);
+ $(this._options.element).on('dragleave',function(e) {
+ if (this.DRAG_AND_DROP_ON) {
+ this.showDrag = false;
+ if (typeof this.timeout !== "undefined") {
+ clearTimeout( this.timeout );
+ }
+ this.timeout = setTimeout( function(){
+ if( !this.showDrag ){
+ $(".abu-upload-drop-area").css('display','none');
+ $(".abu-upload-drop-area").removeClass('abu-upload-drop-area-active');
+ try {
+ e.preventDefault();
+ e.stopPropogation();
+ } catch(e) { /* Do nothing */ }
+ }
+ }.bind(this), 200 ).bind(this);
+ }
+ }.bind(this)
+ ).bind(this);
$(this._options.element).on('dragover',function(e) {
if (this.DRAG_AND_DROP_ON) {
+ this.showDrag = true;
this.activateUploadArea(e);
}
}.bind(this)
).bind(this);
$(this._options.element).on('dragenter',function(e) {
if (this.DRAG_AND_DROP_ON) {
+ this.showDrag = true;
this.activateUploadArea(e);
}
}.bind(this)
@@ -145,9 +187,10 @@ abu.FileUploader = function(o){
this.processingComplete = function() {
$("#abu-done-button-text").html("Done");
- //$("#abu-process-button").css("display","None");
//$("#abu-upload-button").css("display","None");
$("#abu-process-button").addClass("abu-button-disabled");
+ //$("#abu-process-button-text").html(" ");
+ $("#abu-process-button").css("visibility","hidden");
$("#abu-upload-button").addClass("abu-button-disabled");
$("#abu-files-processing").css("display","None");
}
@@ -292,14 +335,16 @@ abu.FileUploader = function(o){
'<div id="file-uploader-instructions" class="abu-uploader-instructions">' +
'<h3>Instructions</h3>' +
'<ul>' +
- '<li>To upload, click the <b>Upload Files</b> button or drag files into the space below the buttons. (Drag-and-drop is supported in FF, Chrome.)</li>' +
+ ((this.ALLOW_DRAG_AND_DROP) ?
+ '<li>To upload, click the <b>Upload Files</b> button or drag files into the space below the buttons. (Drag-and-drop is supported in FF, Chrome.)</li>' :
+ '<li>To upload, click the <b>Upload Files</b> to begin selection of files for upload.</li>') +
((this._options.maxFiles == 1) ?
'<li>This uploader supports only a single file upload</li>' :
'<li>Multiple files may be selected</li>'
) +
'<li>Uploads will begin automatically</li>' +
'<li>Upload of directories is not supported</li>' +
- '<li>When finished uploading, press <b>Process Files</b> to process the uploaded files</li>' +
+ '<li>When finished uploading, press <b>Done</b> to close the modal, or, if an automation script is to be launched by this upload process, press <b>Process Files</b> to process the uploaded files.</li>' +
'</ul>' +
'</div>';
xmodal.message("Uploader Instructions",templateV, undefined, {height:"400px",width:"800px"});
diff --git a/src/main/webapp/scripts/xnat/admin/themeManagement.js b/src/main/webapp/scripts/xnat/admin/themeManagement.js
index 930e230b9ced35ee49cde6d64c1d982e8f3d70bf..64b3702a8b2137fbd04e3df7661aecb9238a67ae 100644
--- a/src/main/webapp/scripts/xnat/admin/themeManagement.js
+++ b/src/main/webapp/scripts/xnat/admin/themeManagement.js
@@ -84,8 +84,8 @@ function removeTheme(){
/*** Theme Package Upload Functions ***/
themeUploadForm.action = themeUrl+q+csrf;
-$(themeUploadForm).parent().css('position','relative');
-$(themeUploadForm).parent().css('top','-30px');
+$(themeUploadForm).parent().parent().css('position','relative');
+$(themeUploadForm).parent().parent().css('top','-30px');
themeUploadForm.onsubmit = function(event) {
event.preventDefault();
$(themeUploadSubmit).text('Uploading...');
@@ -120,7 +120,7 @@ themeUploadForm.onsubmit = function(event) {
uploaded = true;
}
if(!uploaded){
- xmodal.message('Nothing Uploaded', 'No valid theme package files were selected for upload.');
+ xmodal.message('Nothing Uploaded', 'No valid theme package files were selected for upload.<br><br>Click the "Choose Files" button below to browse for a theme package.');
$(themeUploadSubmit).text('Upload');
$(themeUploadSubmit).removeAttr('disabled');
}
diff --git a/src/main/webapp/scripts/xnat/app/timeout.js b/src/main/webapp/scripts/xnat/app/timeout.js
index 96315e3a682826028f12b8352e614046cd84e723..04bb9561bd3213f6d778a6169220b2e61f1bad77 100644
--- a/src/main/webapp/scripts/xnat/app/timeout.js
+++ b/src/main/webapp/scripts/xnat/app/timeout.js
@@ -272,7 +272,7 @@ var XNAT = getObject(XNAT);
// need to wait a little longer before reloading
setTimeout(function(){
window.location.reload();
- }, 120000);
+ }, 2000);
}
diff --git a/src/main/webapp/scripts/xnat/ui/panel.js b/src/main/webapp/scripts/xnat/ui/panel.js
index 410aeb12a34e6f0957d271ccf597b651f9d7e332..6ef65f211c7f13beaed985ba7155821dd3614f1d 100644
--- a/src/main/webapp/scripts/xnat/ui/panel.js
+++ b/src/main/webapp/scripts/xnat/ui/panel.js
@@ -426,7 +426,8 @@ var XNAT = getObject(XNAT || {});
}
var ajaxConfig = {
- method: opts.method,
+ //method: opts.method,
+ method: $form.data('method') || opts.method || 'POST',
url: this.action,
success: function(){
var obj = {};
@@ -845,54 +846,10 @@ var XNAT = getObject(XNAT || {});
panel.data = {};
panel.data.table = function(opts){
+
// initialize the table
- opts = cloneObject(opts);
- opts.element = opts.element || {};
- addClassName(opts.element, 'data-table xnat-table');
- if (opts.sortable) {
- if (opts.sortable === true) {
- addClassName(opts.element, 'sortable');
- }
- else {
- opts.sortable = opts.sortable.split(',').map(function(item){return item.trim()});
- }
- }
- opts.element.style = {
- width: opts.width || '100%'
- };
- var dataTable = XNAT.table(opts.element);
- // request data for table rows
- XNAT.xhr.get({
- url: XNAT.url.rootUrl(opts.load||opts.url),
- dataType: opts.dataType || 'json',
- success: function(data){
- var props = [];
- if (opts.items) {
- dataTable.tr();
- forOwn(opts.items, function(name, val){
- props.push(name);
- dataTable.th(val);
- if (opts.sortable === true || opts.sortable.indexOf(name) !== -1) {
- addClassName(dataTable.last.th, 'sort');
- }
- });
- }
- else {
- forOwn(data[0], function(name, val){
- props.push(name);
- });
- }
- data.forEach(function(item){
- dataTable.tr();
- props.forEach(function(name){
- dataTable.td({ className: name }, item[name]);
- });
- });
- if (opts.container) {
- $$(opts.container).append(dataTable.table);
- }
- }
- });
+ var dataTable = XNAT.table.dataTable(opts.data||[], opts);
+
return {
element: dataTable.table,
spawned: dataTable.table,
@@ -900,6 +857,7 @@ var XNAT = getObject(XNAT || {});
return dataTable.table
}
};
+
};
panel.data.list = function(opts){
diff --git a/src/main/webapp/scripts/xnat/ui/table.js b/src/main/webapp/scripts/xnat/ui/table.js
index 5a645866d1561676b29942bc306b2e242645dff0..ec651f9445b3086c73c0b42e8f414aa715d4f0b4 100755
--- a/src/main/webapp/scripts/xnat/ui/table.js
+++ b/src/main/webapp/scripts/xnat/ui/table.js
@@ -275,6 +275,7 @@ var XNAT = getObject(XNAT);
else {
obj = data || {};
}
+
if (obj.header) {
// if there's a 'header' property
// set to true, pick the header from
@@ -347,15 +348,103 @@ var XNAT = getObject(XNAT);
// helper for future XNAT DataTable widget
table.dataTable = function(data, opts){
+
var tableData = data;
+
// tolerate reversed arguments
if (Array.isArray(opts)){
tableData = opts;
- opts = data;
+ opts = getObject(data);
}
- addClassName(opts, 'xnat-table data-table');
- var newTable = new Table(opts);
- return newTable.init(tableData);
+
+ // don't modify original object
+ opts = cloneObject(opts);
+
+ var allItems = opts.header || (opts.items && opts.items === 'all');
+
+ // properties for spawned element
+ opts.element = opts.element || {};
+
+ addClassName(opts.element, 'data-table xnat-table');
+
+ if (opts.sortable) {
+ if (opts.sortable === true) {
+ addClassName(opts.element, 'sortable');
+ }
+ else {
+ opts.sortable = opts.sortable.split(',').map(function(item){return item.trim()});
+ }
+ }
+
+ opts.element = extend(true, {
+ style: {
+ width: opts.width || '100%'
+ }
+ }, opts.element);
+
+ // initialize the table
+ var newTable = new Table(opts.element);
+
+ function createTable(rows){
+ var props = [];
+ if (!allItems && (opts.items || opts.properties)) {
+ newTable.tr();
+ forOwn(opts.items||opts.properties, function(name, val){
+ props.push(name);
+ newTable.th(val);
+ if (!opts.sortable) return;
+ if (opts.sortable === true || opts.sortable.indexOf(name) !== -1) {
+ addClassName(newTable.last.th, 'sort');
+ }
+ });
+ }
+ else {
+ if (allItems) {
+ newTable.tr();
+ }
+ forOwn(rows[0], function(name, val){
+ if (allItems) {
+ newTable.th(name);
+ }
+ props.push(name);
+ });
+ }
+ rows.forEach(function(item){
+ newTable.tr();
+ props.forEach(function(name){
+ newTable.td({ className: name }, item[name]);
+ });
+ });
+ }
+
+ // if 'tableData' is a string, use as the url
+ if (typeof tableData == 'string') {
+ opts.url = tableData;
+ }
+
+ // request data for table rows
+ if (opts.load || opts.url) {
+ XNAT.xhr.get({
+ url: XNAT.url.rootUrl(opts.load||opts.url),
+ dataType: opts.dataType || 'json',
+ success: function(json){
+ // handle data returned in ResultSet.Result array
+ json = (json.ResultSet && json.ResultSet.Result) ? json.ResultSet.Result : json;
+ createTable(json);
+ }
+ });
+ }
+ else {
+ createTable(tableData.data||tableData);
+ // newTable.init(tableData);
+ }
+
+ if (opts.container) {
+ $$(opts.container).append(newTable.table);
+ }
+
+ return newTable;
+
};
// table with <input> elements in the cells
@@ -395,4 +484,3 @@ var XNAT = getObject(XNAT);
XNAT.ui.inputTable = XNAT.inputTable = table.inputTable;
}));
-
diff --git a/src/main/webapp/scripts/xnat/ui/tabs.js b/src/main/webapp/scripts/xnat/ui/tabs.js
index 61bec657552be5fde90b963b8a7246cf0d4bf80d..73eaf37aa06abe936f9f260c154a195e415d0bba 100755
--- a/src/main/webapp/scripts/xnat/ui/tabs.js
+++ b/src/main/webapp/scripts/xnat/ui/tabs.js
@@ -171,9 +171,9 @@ var XNAT = getObject(XNAT || {});
// set container and layout before spawning:
// XNAT.tabs.container = 'div.foo';
- container = tabs.container || 'div.xnat-tab-container';
+ container = obj.container || tabs.container || 'div.xnat-tab-container';
- layout = tabs.layout || 'left';
+ layout = obj.layout || tabs.layout || 'left';
navTabs = spawn('div.xnat-nav-tabs');
tabContent = spawn('div.xnat-tab-content');
diff --git a/src/main/webapp/style/uploaders/fileuploader.css b/src/main/webapp/style/uploaders/fileuploader.css
index 9d74966143518c36c510c409035f0160c92ecf98..fe323e24d1c0f126c3b975e2cfaea3ff59b3d952 100644
--- a/src/main/webapp/style/uploaders/fileuploader.css
+++ b/src/main/webapp/style/uploaders/fileuploader.css
@@ -85,13 +85,14 @@ div.abu-xnat-interactivity-area-sub {
.abu-upload-duplicate {display:inline;color:#008800}
.abu-upload-duplicate.abu-upload-duplicate-text {display:inline;color:#008800}
-.abu-uploader-instructions-sel {margin-bottom:0px; margin-right:10px; display:inline; width:100%; float:right; background-color:#CCCCCC; border-color:#1A75BB; color:#1A75BB; border-style:solid; border-width:1px; border-color:#1A75BB; font-size:14px; font-weight: bold; padding:2px; }
+.abu-uploader-instructions-sel {margin-bottom:0px; margin-right:10px; display:inline; float:right; background-color:#CCCCCC; border-style:solid; border-width:1px; width:auto; font-size:14px; font-weight: bold; padding:2px; }
+
.abu-uploader-instructions {margin-bottom:10px; display:inline}
.abu-return-floatmessage {position:absolute;z-index:10001;width:auto;cursor:pointer;background-color:#FFFFCC; }
.abu-return-message {width:auto;cursor:pointer;background-color:#FFFFCC; }
-.abu-options-div { position: relative; float: left; width: 430px; margin-left: 10px; }
+.abu-options-div { position: relative; float: left; width: 420px; margin-left: 10px; }
.abu-options-cb {
display:block; /* or inline-block */
width: auto; padding: 7px 0; text-align:center; margin-left:10px; float:left; padding-top: 0px; padding-bottom: 0px;
diff --git a/src/main/webapp/xnat-templates/navigations/XNATQuickSearch.vm b/src/main/webapp/xnat-templates/navigations/XNATQuickSearch.vm
index 8ca2b170f9954c376e3b7a5d9cde0f717b792a21..41babb23fcda36252325fb0af436a9f930ab5292 100755
--- a/src/main/webapp/xnat-templates/navigations/XNATQuickSearch.vm
+++ b/src/main/webapp/xnat-templates/navigations/XNATQuickSearch.vm
@@ -1,35 +1,11 @@
<!-- search script -->
<script type="text/javascript">
-<!--
-function DefaultEnterKey(e,button){
-var keynum, keychar, numcheck ;
-
-if(window.event) // IE
- {
- keynum = e.keyCode ;
- if (keynum==13){
- submitQuickSearch();
- return true;
- }
- }
-else if(e) // Netscape/Firefox/Opera
- {
- keynum = e.which ;
- if (keynum==13){
- submitQuickSearch();
- return false;
- }
- }
- return true;
-}
-
function submitQuickSearch(){
- concealContent();
- if(document.getElementById('quickSearchForm').value!="")
- document.getElementById('quickSearchForm').submit();
+ concealContent();
+ if($('#searchValue').val()!="") {
+ $('#quickSearchForm').submit();
+ }
}
-
-//-->
</script>
<!-- end search script -->
@@ -64,15 +40,21 @@ function submitQuickSearch(){
<!-- stored searches will show up here -->
</optgroup>
</select>
- <input id="searchValue" class="clean" name="searchValue" type="text" maxlength="40" size="20" value="$!field" />
+ <input id="searchValue" class="clean" name="searchValue" type="text" maxlength="40" size="20" value="$!field"/>
<button type="button" id="search_btn" class="btn2" onclick="submitQuickSearch();">Go</button>
#if($turbineUtils.toBoolean($siteConfig.getProperty("UI.allow-advanced-search","true")))
<script>
(function(){
-
- $('#searchValue').each(function(){
+ var searchField = $('#searchValue');
+ searchField.keyup(function( event ) {
+ if (event.which == 13) {
+ submitQuickSearch();
+ }
+ });
+
+ searchField.each(function(){
this.value = this.value || 'search';
$(this).focus(function(){
$(this).removeClass('clean');
diff --git a/src/main/webapp/xnat-templates/screens/XDATScreen_search_wizard2.vm b/src/main/webapp/xnat-templates/screens/XDATScreen_search_wizard2.vm
index 8a41e47bbe4f027bc2de8005a5e7678597e7840b..64020385dc209c9a92e8d883b996ad4c21b25c92 100644
--- a/src/main/webapp/xnat-templates/screens/XDATScreen_search_wizard2.vm
+++ b/src/main/webapp/xnat-templates/screens/XDATScreen_search_wizard2.vm
@@ -57,13 +57,13 @@
<p>Define the constraints which will determine which rows show up in your search results.</p>
- <p style="margin-bottom:20px;">
+ <!-- p style="margin-bottom:20px;">
You must also select a search method (this affects all tabs below):
<label class="search-method-label" style="border-right:1px solid #ccc;">
<input type="checkbox" class="search-method by-criteria" value="by-criteria"> By Specific Criteria</label>
<label class="search-method-label">
<input type="checkbox" class="search-method by-id" value="by-id"> By Exact ID</label>
- </p>
+ </p -->
<div id="super_search" class="yui-navset" style="max-width:800px !important;margin-top:30px;margin-left:-40px;">
<ul class="yui-nav" style="">