Merge pull request #476 from openworm/development

Release 0.3.1

.gitignore

@@ -29,3 +29,18 @@ src/main/webapp/css/main.css
 /.externalToolBuilders/
 /.settings/
 .classpath
+
+#WormSim specific stuff
+*.css-e
+*.less-e
+src/main/webapp/js/components/dev/customrenderer/
+src/main/webapp/js/components/dev/wormsimbuttonbar/
+src/main/webapp/js/components/dev/wormsimlogo/
+src/main/webapp/js/components/dev/wormsimsimulationcontrols/
+src/main/webapp/js/components/dev/wormsimtutorialhandler/
+src/main/webapp/js/components/wormsim.*
+
+#other local directories that may get installed
+org.geppetto.core/
+org.geppetto.model/
+org.geppetto.simulation/

.project

@@ -5,6 +5,11 @@
 	<projects>
 	</projects>
 	<buildSpec>
+		<buildCommand>
+			<name>com.aptana.ide.core.unifiedBuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
 		<buildCommand>
 			<name>org.eclipse.wst.common.project.facet.core.builder</name>
 			<arguments>
@@ -33,5 +38,6 @@
 		<nature>org.eclipse.wst.common.modulecore.ModuleCoreNature</nature>
 		<nature>org.eclipse.jdt.core.javanature</nature>
 		<nature>org.eclipse.wst.common.project.facet.core.nature</nature>
+		<nature>com.aptana.ruby.core.rubynature</nature>
 	</natures>
 </projectDescription>

.travis.yml

@@ -2,18 +2,7 @@ language: java
 before_script:
 - npm install -g bower
 install:
-- git clone https://github.com/openworm/org.geppetto.model.git -b $TRAVIS_BRANCH
-- cd org.geppetto.model
-- mvn install
-- cd ..
-- git clone https://github.com/openworm/org.geppetto.core.git -b $TRAVIS_BRANCH
-- cd org.geppetto.core
-- mvn install
-- cd ..
-- git clone https://github.com/openworm/org.geppetto.simulation.git -b $TRAVIS_BRANCH
-- cd org.geppetto.simulation
-- mvn install
-- cd ..
+- ./travis-install.sh
 env:
   global:
     secure: EvqtUrZj3GsqzAkjZIVf2ZIze6ec72G8Dnkc0J3lKxwDTK6+KgIYgRWUWWO6tzL5Mn3Y+kkiHvyAkrHNPb2QZVBAdOdE3O308WRi64FF71nurd46zE43K/sSxcX/zCoBtxsz49oRcluPWl+nGDi/iKEysgcnQCvz23VWEYHAsOk=

Gruntfile.js

@@ -31,6 +31,7 @@ module.exports = function(grunt) {
                     'src/main/webapp/templates/dist/dashboard.vm': ['src/main/webapp/templates/dashboard.vm'],
                     'src/main/webapp/WEB-INF/web.xml': ['src/main/webapp/WEB-INF/web.xml'],
                     'src/main/webapp/templates/dist/GeppettoCoreTests.vm': ['src/main/webapp/templates/GeppettoCoreTests.vm'],
+                    'src/main/webapp/templates/dist/GeppettoComponentsTests.vm': ['src/main/webapp/templates/GeppettoComponentsTests.vm'],
                     'src/main/webapp/templates/dist/GeppettoFluidDynamicsTests.vm': ['src/main/webapp/templates/GeppettoFluidDynamicsTests.vm'],
                     'src/main/webapp/templates/dist/GeppettoNeuronalCustomTests.vm': ['src/main/webapp/templates/GeppettoNeuronalCustomTests.vm'],
                     'src/main/webapp/templates/dist/GeppettoNeuronalTests.vm': ['src/main/webapp/templates/GeppettoNeuronalTests.vm'],

pom.xml

@@ -3,12 +3,13 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>org.geppetto</groupId>
 	<artifactId>frontend</artifactId>
-	<version>0.3.0</version> 
+	<version>0.3.1</version> 
 	<name>Geppetto Frontend</name>
 	<packaging>war</packaging>
 	<properties>
 		<contextPath>org.geppetto.frontend</contextPath>
 		<spring.version>3.1.3.RELEASE</spring.version>
+	    <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
 	</properties>
 	<profiles>
 		<profile>

src/main/java/org/geppetto/frontend/controllers/Application.java

@@ -118,6 +118,12 @@ public String testNeuronalCustom()
 		return "dist/GeppettoNeuronalCustomTests";
 	}
 
+	@RequestMapping(value = "/GeppettoComponentsTests.html", method = RequestMethod.GET)
+	public String testComponents()
+	{
+		return "dist/GeppettoComponentsTests";
+	}
+
 	@RequestMapping(value = "/GeppettoCoreTests.html", method = RequestMethod.GET)
 	public String testCore()
 	{

src/main/java/org/geppetto/frontend/controllers/ConnectionHandler.java

@@ -65,6 +65,7 @@
 import org.geppetto.core.utilities.URLReader;
 import org.geppetto.core.utilities.Zipper;
 import org.geppetto.frontend.Resources;
+import org.geppetto.frontend.controllers.WebsocketConnection.RunnableQueryParameters;
 import org.geppetto.frontend.messages.OutboundMessages;
 import org.geppetto.model.ExperimentState;
 import org.geppetto.model.GeppettoModel;
@@ -81,6 +82,7 @@
 import com.google.gson.JsonDeserializationContext;
 import com.google.gson.JsonDeserializer;
 import com.google.gson.JsonElement;
+import com.google.gson.JsonObject;
 import com.google.gson.JsonParseException;
 
 /**
@@ -231,6 +233,31 @@ public void newExperiment(String requestID, long projectId)
 
 	}
 
+	/**
+	 * @param projectId
+	 */
+	public void cloneExperiment(String requestID, long projectId, long experimentID)
+	{
+
+		IGeppettoProject project = retrieveGeppettoProject(projectId);
+
+		try
+		{
+			IExperiment originalExperiment = retrieveExperiment(experimentID, project);
+			IExperiment cloneExperiment = geppettoManager.cloneExperiment(requestID, project, originalExperiment);
+
+			Gson gson = new Gson();
+			String json = gson.toJson(cloneExperiment);
+			websocketConnection.sendMessage(requestID, OutboundMessages.EXPERIMENT_CREATED, json);
+
+		}
+		catch(GeppettoExecutionException | GeppettoAccessException e)
+		{
+			error(e, "Error creating a new experiment");
+		}
+
+	}
+
 	/**
 	 * @param requestID
 	 * @param experimentID
@@ -311,14 +338,13 @@ public void runExperiment(String requestID, long experimentID, long projectId)
 	 * @param dataSourceId
 	 * @param variableId
 	 */
-	public void fetchVariable(String requestID, Long projectId, Long experimentId, String dataSourceId, String variableId)
+	public void fetchVariable(String requestID, Long projectId, String dataSourceId, String variableId)
 	{
 		IGeppettoProject geppettoProject = retrieveGeppettoProject(projectId);
-		IExperiment experiment = retrieveExperiment(experimentId, geppettoProject);
 		try
 		{
-			GeppettoModel geppettoModel = geppettoManager.fetchVariable(dataSourceId, variableId, experiment, geppettoProject);
-			
+			GeppettoModel geppettoModel = geppettoManager.fetchVariable(dataSourceId, variableId, geppettoProject);
+
 			String serializedModel = GeppettoSerializer.serializeToJSON(geppettoModel, true);
 
 			websocketConnection.sendMessage(requestID, OutboundMessages.VARIABLE_FETCHED, serializedModel);
@@ -348,28 +374,56 @@ public void fetchVariable(String requestID, Long projectId, Long experimentId, S
 	 * @param experimentId
 	 * @param dataSourceServiceId
 	 * @param variableId
-	 * @throws GeppettoExecutionException 
+	 * @throws GeppettoExecutionException
 	 */
-	public void resolveImportType(String requestID, Long projectId, Long experimentId, String typePath)
+	public void resolveImportType(String requestID, Long projectId, List<String> typePaths)
 	{
 		IGeppettoProject geppettoProject = retrieveGeppettoProject(projectId);
-		IExperiment experiment = retrieveExperiment(experimentId, geppettoProject);
 		try
 		{
-			GeppettoModel geppettoModel = geppettoManager.resolveImportType(typePath, experiment, geppettoProject);
+			GeppettoModel geppettoModel = geppettoManager.resolveImportType(typePaths, geppettoProject);
 			websocketConnection.sendMessage(requestID, OutboundMessages.IMPORT_TYPE_RESOLVED, GeppettoSerializer.serializeToJSON(geppettoModel, true));
 		}
 		catch(IOException e)
 		{
-			error(e, "Error importing type " + typePath);
+			error(e, "Error importing type " + typePaths);
 		}
 		catch(GeppettoExecutionException e)
 		{
-			error(e, "Error importing type " + typePath);
+			error(e, "Error importing type " + typePaths);
 		}
 
 	}
 
+	public void runQuery(String requestID, Long projectId, List<RunnableQueryParameters> runnableQueries)
+	{
+		IGeppettoProject geppettoProject = retrieveGeppettoProject(projectId);
+		// GeppettoModel geppettoModel = geppettoManager.runQuery(typePaths, geppettoProject);
+		// websocketConnection.sendMessage(requestID, OutboundMessages.QUERY_RESULT, GeppettoSerializer.serializeToJSON(geppettoModel, true));
+
+	}
+
+	/**
+	 * @param requestID
+	 * @param projectId
+	 * @param runnableQueries
+	 */
+	public void runQueryCount(String requestID, Long projectId, List<RunnableQueryParameters> runnableQueries)
+	{
+		IGeppettoProject geppettoProject = retrieveGeppettoProject(projectId);
+		int count;
+		try
+		{
+			count = geppettoManager.runQueryCount(null, geppettoProject);
+			// websocketConnection.sendMessage(requestID, OutboundMessages.QUERY_RESULT, GeppettoSerializer.serializeToJSON(geppettoModel, true));
+			websocketConnection.sendMessage(requestID, OutboundMessages.RETURN_QUERY_COUNT, Integer.toString(count));
+		}
+		catch(GeppettoDataSourceException | GeppettoModelException | GeppettoExecutionException e)
+		{
+			error(e, "Error running query count");
+		}
+	}
+
 	/**
 	 * Adds watch lists with variables to be watched
 	 * 
@@ -566,6 +620,40 @@ public void sendScriptData(String requestID, URL url, WebsocketConnection visito
 		}
 	}
 
+	/**
+	 * @param requestID
+	 * @param url
+	 * @param visitor
+	 */
+	public void sendDataSourceResults(String requestID, String dataSourceName, URL url, WebsocketConnection visitor)
+	{
+		try
+		{
+			String line = null;
+			StringBuilder sb = new StringBuilder();
+
+			BufferedReader br = new BufferedReader(new InputStreamReader(url.openStream()));
+
+			while((line = br.readLine()) != null)
+			{
+				sb.append(line + "\n");
+			}
+			String script = sb.toString();
+
+			JsonObject obj = new JsonObject();
+			obj.addProperty("data_source_name", dataSourceName);
+			obj.addProperty("results", script);
+
+			String message = obj.toString();
+
+			websocketConnection.sendMessage(requestID, OutboundMessages.DATASOURCE_RESULTS_FETCHED, message);
+		}
+		catch(IOException e)
+		{
+			error(e, "Error while reading the script at " + url);
+		}
+	}
+
 	/**
 	 * @param requestID
 	 * @param modelPath
@@ -1127,6 +1215,7 @@ public void saveExperimentProperties(String requestID, long projectId, long expe
 					}
 				}
 			}
+			websocketConnection.sendMessage(requestID, OutboundMessages.EXPERIMENT_PROPS_SAVED, "");
 		}
 	}
 

src/main/java/org/geppetto/frontend/controllers/ConnectionsManager.java

@@ -93,7 +93,27 @@ public void removeConnection(WebsocketConnection websocketConnection)
 	{
 		if(_connections.contains(websocketConnection))
 		{
-			_connections.remove(websocketConnection.getConnectionID());
+			if(websocketConnection.getConnectionID() != null)
+			{
+				_connections.remove(websocketConnection.getConnectionID());
+			}
+			else
+			{
+				//TODO Sometimes for some reason the websocketConnection has null as ID, need to investigate more
+				String toRemove = null;
+				for(String key : _connections.keySet())
+				{
+					if(_connections.get(key).equals(websocketConnection))
+					{
+						toRemove = key;
+						break;
+					}
+				}
+				if(toRemove != null)
+				{
+					_connections.remove(toRemove);
+				}
+			}
 			_logger.info("Websocket connection removed " + websocketConnection.getConnectionID());
 		}
 	}