diff --git a/README.md b/README.md
index 51d22e6d0d373937f8b85165e58b39dd7a2d3432..83165442c8a8f2bf892f53932fbe900d2ae4dd19 100644
--- a/README.md
+++ b/README.md
@@ -40,7 +40,7 @@ You can build with a simple Gradle command:
gradle clean war
```
-You may need to build the [XNAT Gradle plugin](https://bitbucket.org/xnatdev/gradle-xnat-plugin) first, although it should be available on the XNAT Maven repository.
+You may need to build the [XDAT Data Builder Gradle plugin](https://bitbucket.org/xnatdev/xdat-data-builder) and [XNAT Data Models library](https://bitbucket.org/xnatdev/xnat-data-models) first, although it should be available on the XNAT Maven repository.
This will create your deployable web application in the location:
@@ -57,10 +57,10 @@ gradle clean jar publishToMavenLocal
You can perform a build deploying to the XNAT Maven repository like this:
```bash
-gradle clean jar publishToMavenLocal publishMavenJavaPublicationToMavenRepository
+gradle clean jar publishToMavenLocal publish
```
-For this last one, the values set for **repoUsername** and **repoPassword** must be valid credentials for pushing artifacts to the Maven server.
+For this last one, the values set for **repoUsername** and **repoPassword** must be valid credentials for pushing artifacts to the Maven server. The *publish* task actually comprises a number of other tasks, which will publish all available artifacts to each repository defined in the *repositories* configuration in the *build.gradle* file. Practically speaking this means that *publish* is an alias for the *publishMavenJavaPublicationToMavenRepository* task.
You can specify the name of the generated WAR file (and thus the application context of the application within the Tomcat server) from the command line or a properties file.
@@ -85,8 +85,7 @@ Note that **gradle.properties** is in this repository's **.gitignore** file, so
You must perform a couple of configuration steps in your run-time environment (e.g. your local development workstation, a Vagrant VM, etc.) in order for XNAT to run properly:
* In your Tomcat start-up configuration, add **-Dxnat.home=<path>** where **<path>** is some writeable location. This is where XNAT will look for its configuration and logs folders, e.g. **${xnat.home}/config** and **${xnat.home}/logs**.
-* Copy **services.properties** into the **config** folder underneath the path you specified for **xnat.home**. For example, I set **xnat.home** to **~/xnat**. Under that I have the folder **config**, which contains **services.properties** (you don't have to create **logs**: log4j will create it if it doesn't exist).
-* Open **InstanceSettings.xml** and modify the settings in there to reflect your configuration. You must do this before the build. This is an annoying but temporary requirement.
+* Copy **xnat-conf.properties** into the **config** folder underneath the path you specified for **xnat.home**. For example, I set **xnat.home** to **~/xnat**. Under that I have the folder **config**, which contains **xnat-conf.properties** (you don't have to create **logs**: log4j will create it if it doesn't exist).
# Running XNAT #
diff --git a/build.gradle b/build.gradle
index 4b09cd3fa576ec7a942091539a1175956596d26a..5e30a2fb60f35e41bf8848389bc61eee625d55bf 100644
--- a/build.gradle
+++ b/build.gradle
@@ -123,6 +123,14 @@ cargo {
}
}
+if (JavaVersion.current().isJava8Compatible()) {
+ allprojects {
+ tasks.withType(Javadoc) {
+ options.addStringOption('Xdoclint:none', '-quiet')
+ }
+ }
+}
+
task sourceJar(type: Jar, dependsOn: classes) {
from sourceSets.main.allSource
}
@@ -170,7 +178,6 @@ publishing {
}
}
repositories {
- mavenLocal()
maven {
credentials {
// These properties must be set in the ~/.gradle/gradle.properties file or passed on the Gradle command
diff --git a/src/main/java/org/nrg/xnat/restlet/actions/AutomationBasedImporter.java b/src/main/java/org/nrg/xnat/restlet/actions/AutomationBasedImporter.java
index 929f86edf0e8725e786d06cfba63301aecc2a74d..b4f92dd04b4302aae130625d52f5ca13073cce3b 100644
--- a/src/main/java/org/nrg/xnat/restlet/actions/AutomationBasedImporter.java
+++ b/src/main/java/org/nrg/xnat/restlet/actions/AutomationBasedImporter.java
@@ -8,7 +8,8 @@ package org.nrg.xnat.restlet.actions;
*
* Released under the Simplified BSD.
*
- * Last modified 7/10/13 9:04 PM
+ * Last modified 4/25/16 9:04 PM
+ * @author Mike Hodge <hodgem@mir.wustl.edu>
*/
import java.io.File;
@@ -78,17 +79,13 @@ import org.nrg.xft.utils.zip.TarUtils;
import org.nrg.xft.utils.zip.ZipI;
import org.nrg.xft.utils.zip.ZipUtils;
-/**
- * The Class AutomationBasedImporter.
- *
- * @author Mike Hodge <hodgem@mir.wustl.edu>
- */
@ImporterHandler(handler = "automation", allowCallsWithoutFiles = true, callPartialUriWrap = false)
public class AutomationBasedImporter extends ImporterHandlerA implements Callable<List<String>> {
/** The Constant ZIP_EXT. */
static final String[] ZIP_EXT = { ".zip", ".jar", ".rar", ".ear", ".gar", ".xar" };
+ /** The Constant STATUS_COMPLETE. */
private static final String STATUS_COMPLETE = "Complete";
/** The Constant CACHE_CONSTANT. */
@@ -125,7 +122,14 @@ public class AutomationBasedImporter extends ImporterHandlerA implements Callabl
/** The configured resource. */
private String configuredResource;
- /** The send admin email. */
+ /**
+ * The send admin email.
+ *
+ * @param listenerControl the listener control
+ * @param u the u
+ * @param fw the fw
+ * @param params the params
+ */
// Is this useful? Do we want it to be configurable?
// private boolean sendAdminEmail = false;
@@ -258,6 +262,7 @@ public class AutomationBasedImporter extends ImporterHandlerA implements Callabl
/**
* Return list to html string.
*
+ * @param string the string
* @return the string
*/
/*
@@ -703,7 +708,17 @@ public class AutomationBasedImporter extends ImporterHandlerA implements Callabl
}
- private PersistentWorkflowI buildWorkflow(XnatProjectdata proj,XnatSubjectdata subj,XnatExperimentdata exp, Map<String, Object> passMap,String eventText) {
+ /**
+ * Builds the workflow.
+ *
+ * @param proj the proj
+ * @param subj the subj
+ * @param exp the exp
+ * @param passMap the pass map
+ * @param eventText the event text
+ * @return the persistent workflow i
+ */
+ private PersistentWorkflowI buildWorkflow(XnatProjectdata proj,XnatSubjectdata subj,XnatExperimentdata exp, Map<String, Object> passMap,String eventText) {
final PersistentWorkflowI wrk;
try {
returnList.add("Building workflow entry for configured resource / event handler - " + eventText);
diff --git a/src/main/java/org/nrg/xnat/restlet/resources/ScriptTriggerResource.java b/src/main/java/org/nrg/xnat/restlet/resources/ScriptTriggerResource.java
index 0b8330d3595a63e3263031b99cb4169f928293e4..16cde120fbc64aaaa3d8de3c16b97734dfe3dc86 100644
--- a/src/main/java/org/nrg/xnat/restlet/resources/ScriptTriggerResource.java
+++ b/src/main/java/org/nrg/xnat/restlet/resources/ScriptTriggerResource.java
@@ -26,8 +26,19 @@ import com.google.gson.GsonBuilder;
import java.io.IOException;
import java.util.*;
+/**
+ * The Class ScriptTriggerResource.
+ */
public class ScriptTriggerResource extends AutomationResource {
+ /**
+ * Instantiates a new script trigger resource.
+ *
+ * @param context the context
+ * @param request the request
+ * @param response the response
+ * @throws ResourceException the resource exception
+ */
public ScriptTriggerResource(Context context, Request request, Response response) throws ResourceException {
super(context, request, response);
@@ -103,26 +114,41 @@ public class ScriptTriggerResource extends AutomationResource {
}
}
+ /* (non-Javadoc)
+ * @see org.nrg.xnat.restlet.resources.AutomationResource#getResourceType()
+ */
@Override
protected String getResourceType() {
return ScriptTrigger.class.getSimpleName();
}
+ /* (non-Javadoc)
+ * @see org.nrg.xnat.restlet.resources.AutomationResource#getResourceId()
+ */
@Override
protected String getResourceId() {
return _trigger == null ? null : _trigger.getEvent();
}
+ /* (non-Javadoc)
+ * @see org.restlet.resource.Resource#allowPut()
+ */
@Override
public boolean allowPut() {
return true;
}
+ /* (non-Javadoc)
+ * @see org.restlet.resource.Resource#allowDelete()
+ */
@Override
public boolean allowDelete() {
return true;
}
+ /* (non-Javadoc)
+ * @see org.restlet.resource.Resource#represent(org.restlet.resource.Variant)
+ */
@Override
public Representation represent(Variant variant) throws ResourceException {
final MediaType mediaType = overrideVariant(variant);
@@ -140,6 +166,9 @@ public class ScriptTriggerResource extends AutomationResource {
}
}
+ /* (non-Javadoc)
+ * @see org.restlet.resource.Resource#handlePut()
+ */
@Override
public void handlePut() {
try {
@@ -152,6 +181,9 @@ public class ScriptTriggerResource extends AutomationResource {
}
}
+ /* (non-Javadoc)
+ * @see org.restlet.resource.Resource#handleDelete()
+ */
@Override
public void handleDelete() {
if (_log.isDebugEnabled()) {
@@ -163,6 +195,12 @@ public class ScriptTriggerResource extends AutomationResource {
recordAutomationEvent(triggerId, containerId, "Delete", ScriptTrigger.class);
}
+ /**
+ * Map trigger.
+ *
+ * @param trigger the trigger
+ * @return the map
+ */
private Map<String, String> mapTrigger(final ScriptTrigger trigger) {
final Map<String, String> association = Scope.decode(trigger.getAssociation());
@@ -181,6 +219,7 @@ public class ScriptTriggerResource extends AutomationResource {
/**
* Lists the script triggers with the specified scope and entity ID and event.
*
+ * @param mediaType the media type
* @return A representation of the script triggers available for the specified scope, entity ID (if specified), and event.
*/
private Representation listScriptTriggers(final MediaType mediaType) {
@@ -245,6 +284,12 @@ public class ScriptTriggerResource extends AutomationResource {
return representTable(table, mediaType, params);
}
+ /**
+ * Put script trigger.
+ *
+ * @throws ClientException the client exception
+ * @throws ServerException the server exception
+ */
private void putScriptTrigger() throws ClientException, ServerException {
// TODO: this needs to properly handle a PUT to an existing script as well as an existing but disabled script.
final Representation entity = getRequest().getEntity();
@@ -357,6 +402,12 @@ public class ScriptTriggerResource extends AutomationResource {
}
}
+ /**
+ * Gets the event filters.
+ *
+ * @param filters the filters
+ * @return the event filters
+ */
@SuppressWarnings("unused")
private Set<EventFilters> getEventFilters(Map<String, List<String>> filters) {
final Set<EventFilters> eventSet = Sets.newHashSet();
@@ -367,6 +418,11 @@ public class ScriptTriggerResource extends AutomationResource {
return eventSet;
}
+ /**
+ * Format scope entity id and event.
+ *
+ * @return the string
+ */
private String formatScopeEntityIdAndEvent() {
final StringBuilder buffer = new StringBuilder();
if (_trigger != null) {
@@ -396,64 +452,137 @@ public class ScriptTriggerResource extends AutomationResource {
return buffer.toString();
}
+ /**
+ * The Class JsonResults.
+ */
@SuppressWarnings("unused")
private class JsonResults {
- private String event;
+
+ /** The event. */
+ private String event;
+
+ /** The event class. */
private String eventClass;
+
+ /** The script id. */
private String scriptId;
+
+ /** The description. */
private String description;
- private Map<String,List<String>> filters;
- public String getEvent() {
+ /** The filters. */
+ private Map<String,List<String>> filters;
+
+ /**
+ * Gets the event.
+ *
+ * @return the event
+ */
+ public String getEvent() {
return event;
}
+ /**
+ * Sets the event.
+ *
+ * @param event the new event
+ */
public void setEvent(String event) {
this.event = event;
}
- public String getEventClass() {
+ /**
+ * Gets the event class.
+ *
+ * @return the event class
+ */
+ public String getEventClass() {
return eventClass;
}
+ /**
+ * Sets the event class.
+ *
+ * @param eventClass the new event class
+ */
public void setEventClass(String eventClass) {
this.eventClass = eventClass;
}
+ /**
+ * Gets the script id.
+ *
+ * @return the script id
+ */
public String getScriptId() {
return scriptId;
}
+ /**
+ * Sets the script id.
+ *
+ * @param scriptId the new script id
+ */
public void setScriptId(String scriptId) {
this.scriptId = scriptId;
}
- public String getDescription() {
+ /**
+ * Gets the description.
+ *
+ * @return the description
+ */
+ public String getDescription() {
return description;
}
+ /**
+ * Sets the description.
+ *
+ * @param description the new description
+ */
public void setDescription(String description) {
this.description = description;
}
+ /**
+ * Gets the filters.
+ *
+ * @return the filters
+ */
public Map<String, List<String>> getFilters() {
return filters;
}
+ /**
+ * Sets the filters.
+ *
+ * @param filters the filters
+ */
public void setFilters(Map<String, List<String>> filters) {
this.filters = filters;
}
}
+ /** The Constant _log. */
private static final Logger _log = LoggerFactory.getLogger(ScriptTriggerResource.class);
+ /** The Constant EVENT_ID. */
private static final String EVENT_ID = "EVENT_ID";
+
+ /** The Constant TRIGGER_ID. */
private static final String TRIGGER_ID = "TRIGGER_ID";
+
+ /** The Constant ID. */
private static final String ID = "ID";
+ /** The _script trigger service. */
private final ScriptTriggerService _scriptTriggerService;
+ /** The _event id. */
private final String _eventId;
+
+ /** The _trigger. */
private final ScriptTrigger _trigger;
}
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 3937cfadfe8d3af9a7b2e68fcc1b8c2f8371ee41..1512ed44f62fc7e25bf70c2e19683be229d2565d 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
@@ -8,21 +8,57 @@ import com.google.common.collect.Maps;
import java.io.Serializable;
import java.util.Map;
+/**
+ * The Class AutomatedScriptRequest.
+ */
public class AutomatedScriptRequest implements Serializable {
+ /** The Constant serialVersionUID. */
private static final long serialVersionUID = -5425712284737600869L;
+ /** The _src event id. */
private final String _srcEventId;
+
+ /** The _src event class. */
private final String _srcEventClass;
+
+ /** The _user. */
private final UserI _user;
+
+ /** The _script id. */
private final String _scriptId;
+
+ /** The _event. */
private final String _event;
+
+ /** The _script workflow id. */
private final String _scriptWorkflowId;
+
+ /** The _external id. */
private final String _externalId;
+
+ /** The _data type. */
private final String _dataType;
+
+ /** The _data id. */
private final String _dataId;
+
+ /** The _argument map. */
private final Map<String,Object> _argumentMap = Maps.newHashMap();
+ /**
+ * Instantiates a new automated script request.
+ *
+ * @param srcEventId the src event id
+ * @param srcEventClass the src event class
+ * @param user the user
+ * @param scriptId the script id
+ * @param event the event
+ * @param scriptWorkflow the script workflow
+ * @param dataType the data type
+ * @param dataId the data id
+ * @param externalId the external id
+ */
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) {
_srcEventId = srcEventId;
_srcEventClass = srcEventClass;
@@ -35,51 +71,120 @@ public class AutomatedScriptRequest implements Serializable {
_externalId = externalId;
}
+ /**
+ * Instantiates a new automated script request.
+ *
+ * @param srcEventId the src event id
+ * @param srcEventClass the src event class
+ * @param user the user
+ * @param scriptId the script id
+ * @param event the event
+ * @param scriptWorkflow the script workflow
+ * @param dataType the data type
+ * @param dataId the data id
+ * @param externalId the external id
+ * @param argumentMap the argument map
+ */
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);
}
+ /**
+ * Gets the src event id.
+ *
+ * @return the src event id
+ */
public String getSrcEventId() {
return _srcEventId;
}
+ /**
+ * Gets the src event class.
+ *
+ * @return the src event class
+ */
public String getSrcEventClass() {
return _srcEventClass;
}
+ /**
+ * Gets the user.
+ *
+ * @return the user
+ */
public UserI getUser() {
return _user;
}
+ /**
+ * Gets the script id.
+ *
+ * @return the script id
+ */
public String getScriptId() {
return _scriptId;
}
+ /**
+ * Gets the event.
+ *
+ * @return the event
+ */
public String getEvent() {
return _event;
}
+ /**
+ * Gets the script workflow id.
+ *
+ * @return the script workflow id
+ */
public String getScriptWorkflowId() {
return _scriptWorkflowId;
}
+ /**
+ * Gets the external id.
+ *
+ * @return the external id
+ */
public String getExternalId() {
return _externalId;
}
+ /**
+ * Gets the data type.
+ *
+ * @return the data type
+ */
public String getDataType() {
return _dataType;
}
+ /**
+ * Gets the data id.
+ *
+ * @return the data id
+ */
public String getDataId() {
return _dataId;
}
+ /**
+ * Gets the argument map.
+ *
+ * @return the argument map
+ */
public Map<String,Object> getArgumentMap() {
return _argumentMap;
}
+ /**
+ * Gets the argument json.
+ *
+ * @return the argument json
+ */
public String getArgumentJson() {
return new JSONObject(_argumentMap).toString();
}
diff --git a/src/main/java/org/nrg/xnat/services/messaging/automation/AutomatedScriptRequestListener.java b/src/main/java/org/nrg/xnat/services/messaging/automation/AutomatedScriptRequestListener.java
index 6b93b22ffba2151b0fba3e3464dff36fd30952c5..27386704d0be736bee76639627c865dae5039e6f 100644
--- a/src/main/java/org/nrg/xnat/services/messaging/automation/AutomatedScriptRequestListener.java
+++ b/src/main/java/org/nrg/xnat/services/messaging/automation/AutomatedScriptRequestListener.java
@@ -13,8 +13,25 @@ import javax.inject.Inject;
import java.util.HashMap;
import java.util.Map;
+/**
+ * The listener interface for receiving automatedScriptRequest events.
+ * The class that is interested in processing a automatedScriptRequest
+ * event implements this interface, and the object created
+ * with that class is registered with a component using the
+ * component's <code>addAutomatedScriptRequestListener<code> method. When
+ * the automatedScriptRequest event occurs, that object's appropriate
+ * method is invoked.
+ *
+ * @see AutomatedScriptRequestEvent
+ */
public class AutomatedScriptRequestListener {
+ /**
+ * On request.
+ *
+ * @param request the request
+ * @throws Exception the exception
+ */
public void onRequest(final AutomatedScriptRequest request) throws Exception {
final PersistentWorkflowI workflow = WorkflowUtils.getUniqueWorkflow(request.getUser(), request.getScriptWorkflowId());
workflow.setStatus(PersistentWorkflowUtils.IN_PROGRESS);
@@ -58,8 +75,10 @@ public class AutomatedScriptRequestListener {
}
}
+ /** The Constant logger. */
private static final Logger logger = LoggerFactory.getLogger(AutomatedScriptRequestListener.class);
+ /** The _service. */
@Inject
private ScriptRunnerService _service;
}