Merge pull request #868 from openworm/development

Release 0.4.2
openworm · Jan 16, 2019 · 7588ed3 · 7588ed3
2 parents d091f65 + 3f38023
commit 7588ed3
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Showing 57 changed files with 20,020 additions and 2,039 deletions.
diff --git a/.project b/.project
@@ -6,13 +6,23 @@
 	</projects>
 	<buildSpec>
 		<buildCommand>
-			<name>org.python.pydev.PyDevBuilder</name>
+			<name>org.eclipse.ui.externaltools.ExternalToolBuilder</name>
+			<triggers>full,incremental,</triggers>
 			<arguments>
+				<dictionary>
+					<key>LaunchConfigHandle</key>
+					<value>&lt;project&gt;/.externalToolBuilders/org.python.pydev.PyDevBuilder.launch</value>
+				</dictionary>
 			</arguments>
 		</buildCommand>
 		<buildCommand>
-			<name>com.aptana.ide.core.unifiedBuilder</name>
+			<name>org.eclipse.ui.externaltools.ExternalToolBuilder</name>
+			<triggers>full,incremental,</triggers>
 			<arguments>
+				<dictionary>
+					<key>LaunchConfigHandle</key>
+					<value>&lt;project&gt;/.externalToolBuilders/com.aptana.ide.core.unifiedBuilder.launch</value>
+				</dictionary>
 			</arguments>
 		</buildCommand>
 		<buildCommand>
@@ -46,5 +56,6 @@
 		<nature>com.aptana.ruby.core.rubynature</nature>
 		<nature>org.python.pydev.pythonNature</nature>
 		<nature>org.eclipse.virgo.ide.facet.core.bundlenature</nature>
+		<nature>org.eclipse.wst.jsdt.core.jsNature</nature>
 	</natures>
 </projectDescription>
diff --git a/.settings/org.eclipse.wst.common.component b/.settings/org.eclipse.wst.common.component
@@ -1,14 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?><project-modules id="moduleCoreId" project-version="1.5.0">
     <wb-module deploy-name="org.geppetto.frontend">
         <wb-resource deploy-path="/WEB-INF/classes" source-path="/src/main/java"/>
-        <wb-resource deploy-path="/js/" source-path="/src/main/webapp/js"/>
         <wb-resource deploy-path="/WEB-INF/classes" source-path="/src/main/resources"/>
-        <wb-resource deploy-path="/font/" source-path="/src/main/webapp/fonts"/>
-        <wb-resource deploy-path="/" source-path="/WebContent" tag="defaultRootSource"/>
         <wb-resource deploy-path="/" source-path="/target/m2e-wtp/web-resources"/>
-        <wb-resource deploy-path="/" source-path="/src/main/webapp"/>
+        <wb-resource deploy-path="/" source-path="/src/main/webapp" tag="defaultRootSource"/>
         <property name="context-root" value="org.geppetto.frontend"/>
-        <property name="java-output-path" value="/org.geppetto.frontend/target/classes"/>
         <property name="component.exclusion.patterns" value="node_modules/**,WEB-INF/classes/lib/*.jar,WEB-INF/lib/*.jar,node/**"/>
+        <property name="java-output-path" value="/org.geppetto.frontend/target/classes"/>
     </wb-module>
 </project-modules>
diff --git a/.settings/org.eclipse.wst.common.project.facet.core.xml b/.settings/org.eclipse.wst.common.project.facet.core.xml
@@ -1,10 +1,8 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <faceted-project>
-  <runtime name="Virgo Runtime"/>
   <fixed facet="wst.jsdt.web"/>
-  <installed facet="wst.jsdt.web" version="1.0"/>
-  <installed facet="osgi.bundle" version="4.2"/>
   <installed facet="java" version="1.7"/>
+  <installed facet="wst.jsdt.web" version="1.0"/>
   <installed facet="org.eclipse.virgo.server.bundle" version="1.0"/>
-  <installed facet="jst.web" version="2.5"/>
+  <installed facet="jst.web" version="3.0"/>
 </faceted-project>
diff --git a/.travis.yml b/.travis.yml
@@ -2,12 +2,15 @@ language: node_js
 os: linux
 sudo: required
 dist: trusty
+group: deprecated-2017Q4
 bundler_args: --retry 5
 node_js:
   - "7"
 env:
   global:
     secure: dn0FPQ5IG4M/3kdwnyI78ElQ308Vc3QnKAvkWfwMFb8QxDqxQdnTo7AV1qTMtbLrDNkeEWIgi4nc7jmXNtvGTwOfhAULVh6606Qs5B+ezTdwzajbbFMI8SKQx/pnTojOMu8dx7V4lMoR/YWcojR0VC1IWVC62TGbSB1k5BDGgH0=
+before_install:
+- sudo apt-get install -y xserver-xorg-dev libxext-dev libxi-dev 
 install:
 - npm install --silent -g phantomjs 
 - npm install --silent -g casperjs 
@@ -26,6 +29,8 @@ addons:
     - libgl1-mesa-dri
     - libglapi-mesa
     - libosmesa6
+    - net-tools
+    - lsof
 before_script:
   - "export DISPLAY=:99.0"
   - "sh -e /etc/init.d/xvfb start"
@@ -34,11 +39,11 @@ before_script:
 script:
   - npm config set registry http://registry.npmjs.org/
   - echo "Current time :$(date +"%T")"
+  - docker --version
   - cd $TRAVIS_BUILD_DIR/src/main/webapp/js/pages/tests/casperjs
   - echo "$TRAVIS_BRANCH"
-  - travis_retry docker build -t="geppetto" --build-arg frontendBranch=$TRAVIS_BRANCH https://github.com/openworm/org.geppetto.git#development:utilities/docker/geppetto/
-  - echo "Current time :$(date +"%T")"
-  - travis_retry docker run  -t -dit --name=geppetto_container -h localhost -p  28081:8080 geppetto
+  - travis_retry docker build -t="geppetto" --build-arg mainBranch=$TRAVIS_BRANCH https://github.com/openworm/org.geppetto.git#update-virgo:utilities/docker/geppetto/
+  - travis_retry docker run  -t -dit --name=geppetto_container -p 28081:8080 geppetto
   - bash $TRAVIS_BUILD_DIR/src/main/webapp/js/pages/tests/casperjs/utilities/test_geppetto_server.sh
   - sleep 30
   - http_status=$(curl -s -I $1 http://localhost:28081/org.geppetto.frontend | grep HTTP/1.1 | awk {'print $2'})
@@ -52,7 +57,7 @@ script:
       sleep 10;
       docker rm $(docker ps -a -q);
       sleep 10;
-      travis_retry docker run  -t -dit --name=geppetto_container -h localhost -p  28081:8080 geppetto;
+      travis_retry docker run  -t -dit --name=geppetto_container -p 28081:8080 geppetto;
       bash $TRAVIS_BUILD_DIR/src/main/webapp/js/pages/tests/casperjs/utilities/test_geppetto_server.sh;
       sleep 60;
       http_status=$(curl -s -I $1 http://localhost:28081/org.geppetto.frontend | grep HTTP/1.1 | awk {'print $2'});
@@ -63,8 +68,8 @@ script:
   - travis_retry xvfb-run -a --server-args="-screen 0 1024x768x24"  casperjs test --includes=utilities/TestsUtility.js UIComponentsTests.js --host=http://localhost:28081/ --engine=slimerjs  
   - travis_retry xvfb-run -a --server-args="-screen 0 1024x768x24"  casperjs test --includes=utilities/TestsUtility.js GeppettoModelTests.js --host=http://localhost:28081/ --engine=slimerjs 
   - travis_retry xvfb-run -a --server-args="-screen 0 1024x768x24"  casperjs test --includes=utilities/TestsUtility.js,NeuronalTestsLogic.js DefaultProjectsTests.js --host=http://localhost:28081/ --engine=slimerjs  
+  - docker ps -a;
   - sudo docker cp geppetto_container:/home/developer/virgo/serviceability/logs/log.log /etc
   - tail /etc/log.log -n 200
-  - echo "Current time :$(date +"%T")"
   - docker stop $(docker ps -a -q)
-  - docker rm $(docker ps -a -q)
+  - docker rm $(docker ps -a -q)
diff --git a/pom.xml b/pom.xml
@@ -3,12 +3,12 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>org.geppetto</groupId>
 	<artifactId>frontend</artifactId>
-	<version>0.4.1</version>
+	<version>0.4.2</version>
 	<name>Geppetto Frontend</name>
 	<packaging>war</packaging>
 	<properties>
 		<contextPath>org.geppetto.frontend</contextPath>
-		<spring.version>3.1.3.RELEASE</spring.version>
+		<spring.version>4.3.9.RELEASE</spring.version>
 		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
 	</properties>
 	<profiles>
@@ -132,129 +132,38 @@
 			<artifactId>simulation</artifactId>
 			<version>${project.version}</version>
 		</dependency>
-		<dependency>
-			<groupId>com.fasterxml.jackson.core</groupId>
-			<artifactId>jackson-core</artifactId>
-			<version>2.1.0</version>
-		</dependency>
-		<dependency>
-			<groupId>com.fasterxml.jackson.core</groupId>
-			<artifactId>jackson-databind</artifactId>
-			<version>2.1.0</version>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.commons</groupId>
-			<artifactId>com.springsource.org.apache.commons.logging</artifactId>
-			<version>1.1.1</version>
-		</dependency>
 		<dependency>
 			<groupId>org.apache.tomcat</groupId>
 			<artifactId>tomcat-catalina</artifactId>
-			<version>7.0.29</version>
+			<version>8.5.31</version>
 		</dependency>
 		<dependency>
 			<groupId>org.apache.tomcat</groupId>
 			<artifactId>tomcat-coyote</artifactId>
-			<version>7.0.29</version>
-		</dependency>
-		<dependency>
-			<groupId>javax.servlet</groupId>
-			<artifactId>com.springsource.javax.servlet.jsp.jstl</artifactId>
-			<version>1.1.2</version>
-			<scope>runtime</scope>
-		</dependency>
-		<dependency>
-			<groupId>com.google.code.gson</groupId>
-			<artifactId>gson</artifactId>
-			<version>2.2.2</version>
-		</dependency>
-
-		<dependency>
-			<groupId>org.springframework</groupId>
-			<artifactId>spring-core</artifactId>
-			<version>${spring.version}</version>
+			<version>8.5.31</version>
 		</dependency>
 		<dependency>
-			<groupId>org.springframework</groupId>
-			<artifactId>spring-aspects</artifactId>
-			<version>${spring.version}</version>
-		</dependency>
-		<dependency>
-			<groupId>org.springframework</groupId>
-			<artifactId>spring-context</artifactId>
-			<version>${spring.version}</version>
-		</dependency>
-		<dependency>
-			<groupId>org.springframework</groupId>
-			<artifactId>spring-context-support</artifactId>
-			<version>${spring.version}</version>
-		</dependency>
-		<dependency>
-			<groupId>org.springframework</groupId>
-			<artifactId>spring-beans</artifactId>
-			<version>${spring.version}</version>
+			<groupId>org.apache.tomcat</groupId>
+			<artifactId>tomcat-websocket</artifactId>
+			<version>8.5.31</version>
 		</dependency>
 		<dependency>
 			<groupId>org.springframework</groupId>
 			<artifactId>spring-web</artifactId>
 			<version>${spring.version}</version>
 		</dependency>
 		<dependency>
-			<groupId>org.springframework</groupId>
-			<artifactId>spring-test</artifactId>
-			<version>${spring.version}</version>
-		</dependency>
-		<dependency>
-			<groupId>org.springframework</groupId>
-			<artifactId>spring-webmvc</artifactId>
-			<version>${spring.version}</version>
-		</dependency>
-		<dependency>
-			<groupId>org.springframework.osgi</groupId>
-			<artifactId>spring-osgi-core</artifactId>
-			<version>1.2.1</version>
-		</dependency>
-		<dependency>
-			<groupId>org.springframework.osgi</groupId>
-			<artifactId>spring-osgi-web</artifactId>
-			<version>1.2.1</version>
-		</dependency>
-		<dependency>
-			<groupId>org.springframework.osgi</groupId>
-			<artifactId>spring-osgi-extender</artifactId>
-			<version>1.2.1</version>
-		</dependency>
-		<dependency>
-			<groupId>org.springframework.osgi</groupId>
-			<artifactId>spring-osgi-web-extender</artifactId>
-			<version>1.2.1</version>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.servicemix.bundles</groupId>
-			<artifactId>org.apache.servicemix.bundles.velocity</artifactId>
-			<version>1.7_6</version>
-		</dependency>
-		<dependency>
-			<groupId>org.osgi</groupId>
-			<artifactId>org.osgi.core</artifactId>
-			<version>5.0.0</version>
-		</dependency>
+   			<groupId>javax.servlet</groupId>
+   			<artifactId>javax.servlet-api</artifactId>
+   			<version>3.1.0</version>
+   			 <scope>provided</scope>
+   		</dependency>
 		<dependency>
 			<groupId>org.junit</groupId>
 			<artifactId>com.springsource.org.junit</artifactId>
 			<version>4.7.0</version>
 			<scope>test</scope>
 		</dependency>
-		<dependency>
-			<groupId>org.apache.httpcomponents</groupId>
-			<artifactId>httpcore-osgi</artifactId>
-			<version>4.3.2</version>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.httpcomponents</groupId>
-			<artifactId>httpclient-osgi</artifactId>
-			<version>4.4-alpha1</version>
-		</dependency>
 		<dependency>
 			<groupId>org.apache.shiro</groupId>
 			<artifactId>shiro-core</artifactId>
@@ -329,7 +238,6 @@
 							org.eclipse.virgo.web.dm;version="2.1.1.RELEASE",*
 						</Import-Package>
 						<Import-Library>org.springframework.spring;version="${spring.version}"</Import-Library>
-						<Import-Bundle>org.springframework.aop;version="${spring.version}"</Import-Bundle>
 					</instructions>
 				</configuration>
 				<executions>

diff --git a/src/main/java/org/geppetto/frontend/ApplicationListenerBean.java b/src/main/java/org/geppetto/frontend/ApplicationListenerBean.java
@@ -1,13 +1,14 @@
 package org.geppetto.frontend;
 
+import org.springframework.context.ApplicationEvent;
 import org.springframework.context.ApplicationListener;
 import org.springframework.context.event.ContextRefreshedEvent;
 
-public class ApplicationListenerBean implements ApplicationListener<ContextRefreshedEvent>
+public class ApplicationListenerBean implements ApplicationListener
 {
 	@Override
-	public void onApplicationEvent(ContextRefreshedEvent event)
-	{
-		// DONT'DO ANYTHING THAT HAS TO DO WITH THE DATABASE HERE OR DATANUCLEUS BREAKS
+	public void onApplicationEvent(ApplicationEvent event) {
+		// TODO Auto-generated method stub
+
 	}
 }
diff --git a/src/main/java/org/geppetto/frontend/controllers/Application.java b/src/main/java/org/geppetto/frontend/controllers/Application.java
@@ -42,13 +42,11 @@
 @Controller
 public class Application
 {
-
 	@Autowired
 	private IGeppettoManager geppettoManager;
 
 	private static Log logger = LogFactory.getLog(Application.class);
 
-
 	private String getGeppetto(HttpServletRequest req, String page){
 		try
 		{
@@ -164,5 +162,4 @@ public String root(HttpServletRequest request, HttpServletResponse response)
 
 		return "dashboard";
 	}
-
 }
diff --git a/src/main/java/org/geppetto/frontend/controllers/ConnectionHandler.java b/src/main/java/org/geppetto/frontend/controllers/ConnectionHandler.java
@@ -151,7 +151,7 @@ public void loadProjectFromURL(String requestID, String urlString)
 		}
 		catch(IOException e)
 		{
-			error(e, "Could not load geppetto project");
+			error(e, "Could not load geppetto project from url: " + urlString );
 		}
 	}
 
@@ -519,10 +519,8 @@ public void resolveImportValue(String requestID, Long projectId, Long experiment
 		catch(IOException e)
 		{
 			error(e, "Error importing value " + path);
-		}
-		catch(GeppettoExecutionException e)
-		{
-			error(e, "Error importing value " + path);
+		} catch (GeppettoExecutionException e) {
+			error(e, "Error importing value " + path);	
 		}
 
 	}

diff --git a/src/main/java/org/geppetto/frontend/controllers/ConnectionsManager.java b/src/main/java/org/geppetto/frontend/controllers/ConnectionsManager.java
@@ -1,6 +1,5 @@
 package org.geppetto.frontend.controllers;
 
-import java.io.IOException;
 import java.nio.CharBuffer;
 import java.util.ArrayList;
 import java.util.Collection;
@@ -67,15 +66,7 @@ private void purgeLostConnections()
 		for(WebsocketConnection client : this.getConnections())
 		{
 			CharBuffer buffer = CharBuffer.wrap("ping");
-			try
-			{
-				client.getWsOutbound().writeTextMessage(buffer);
-			}
-			catch(IOException e)
-			{
-				_logger.error("Unable to communicate with client " + e.getMessage() + ". Removing connection.");
-				toBeRemoved.add(client);
-			}
+			client.getSession().getAsyncRemote().sendObject(buffer);
 		}
 		for(WebsocketConnection client : toBeRemoved)
 		{