Merge branch 'develop' for release 0.1.7

README.md

@@ -66,7 +66,17 @@ git checkout -b develop --track origin/develop
 ```
 
 ## Changelog
-**v0.1.7** [?]
+**v0.1.8** [?]
+
+**v0.1.7** [2016/03/24]
+* position saving and restoring ported from cy2sbml (saving & restoring layouts)
+* dark VisualStyle implemented (cy3sbml-dark)
+* improved visual styles & dynamic compartment colors
+* saving and restoring of full session with SBML files
+* COBRA information parsed into attributes
+* multiple bugfixes
+* first version of cofactor nodes
+* tested with Cy3.3 and Cy3.4-milestone-2
 
 **v0.1.6** [2015/08/27]
 * Testing, bug fixes and documentation

lib/local_maven_repo.sh

@@ -17,7 +17,7 @@ mvn install:install-file -DgroupId=cy3sbml-temp -DartifactId=jigsaw-dateParser -
 # JSBML (generated in build_jsbml script)
 # The registered jars have to correspond to the actual pom.xml, so changes here have to be synchronized!
 # core
-mvn install:install-file -DgroupId=cy3sbml-temp -DartifactId=jsbml -Dversion=1.1-b1 -Dfile=$DIR/jsbml-1.1-b1.jar -Dpackaging=jar -DgeneratePom=true
+mvn install:install-file -DgroupId=cy3sbml-temp -DartifactId=jsbml -Dversion=1.2-SNAPSHOT -Dfile=$DIR/jsbml-1.2-SNAPSHOT.jar -Dpackaging=jar -DgeneratePom=true
 # qual
 mvn install:install-file -DgroupId=cy3sbml-temp -DartifactId=jsbml-qual -Dversion=2.1-b1 -Dfile=$DIR/jsbml-qual-2.1-b1.jar -Dpackaging=jar -DgeneratePom=true
 # layout
@@ -26,6 +26,11 @@ mvn install:install-file -DgroupId=cy3sbml-temp -DartifactId=jsbml-layout -Dvers
 mvn install:install-file -DgroupId=cy3sbml-temp -DartifactId=jsbml-comp -Dversion=1.0-b1 -Dfile=$DIR/jsbml-comp-1.0-b1.jar -Dpackaging=jar -DgeneratePom=true
 # fbc
 mvn install:install-file -DgroupId=cy3sbml-temp -DartifactId=jsbml-fbc -Dversion=1.0-b1 -Dfile=$DIR/jsbml-fbc-1.0-b1.jar -Dpackaging=jar -DgeneratePom=true
+# groups
+mvn install:install-file -DgroupId=cy3sbml-temp -DartifactId=jsbml-groups -Dversion=0.4-b1 -Dfile=$DIR/jsbml-groups-0.4-b1.jar -Dpackaging=jar -DgeneratePom=true
 # distrib
 mvn install:install-file -DgroupId=cy3sbml-temp -DartifactId=jsbml-distrib -Dversion=0.5 -Dfile=$DIR/jsbml-distrib-0.5.jar -Dpackaging=jar -DgeneratePom=true
+# tidy SBML
+mvn install:install-file -DgroupId=cy3sbml-temp -DartifactId=jsbml-tidy -Dversion=1.2.1 -Dfile=$DIR/jsbml-tidy-1.2.1.jar -Dpackaging=jar -DgeneratePom=true
+mvn install:install-file -DgroupId=cy3sbml-temp -DartifactId=jtidy -Dversion=r938 -Dfile=$DIR/jtidy-r938.jar -Dpackaging=jar -DgeneratePom=true
 

pom.xml

@@ -229,7 +229,7 @@
 		<dependency>
       			<groupId>uk.ac.ebi.miriam</groupId>
       			<artifactId>miriam-lib</artifactId>
-      			<version>1.1.5</version>
+      			<version>1.1.6</version>
     		</dependency>
 		<dependency>
       			<groupId>uk.ac.ebi.biomodels</groupId>
@@ -241,7 +241,7 @@
   		<dependency>
   			<groupId>cy3sbml-temp</groupId>
   			<artifactId>jsbml</artifactId>
-  			<version>1.1-b1</version>
+  			<version>1.2-SNAPSHOT</version>
   		</dependency>
 
   		<!-- JSBML EXTENSION dependency -->
@@ -265,11 +265,21 @@
   			<artifactId>jsbml-fbc</artifactId>
   			<version>1.0-b1</version>
   		</dependency>
+  		<dependency>
+  			<groupId>cy3sbml-temp</groupId>
+  			<artifactId>jsbml-groups</artifactId>
+  			<version>0.4-b1</version>
+  		</dependency>
   		<dependency>
   			<groupId>cy3sbml-temp</groupId>
   			<artifactId>jsbml-distrib</artifactId>
   			<version>0.5</version>
   		</dependency>
+  		<dependency>
+  			<groupId>cy3sbml-temp</groupId>
+  			<artifactId>jsbml-tidy</artifactId>
+  			<version>1.2.1</version>
+  		</dependency>
 
   		<!-- UncertML -->
   		<!--
@@ -296,6 +306,11 @@
   			<artifactId>biojava3-ontology</artifactId>
   			<version>3.1.0</version>
   		</dependency>
+  		<dependency>
+  			<groupId>cy3sbml-temp</groupId>
+  			<artifactId>jtidy</artifactId>
+  			<version>r938</version>
+  		</dependency>
   		<!--
   		<dependency>
 	    		<groupId>junit</groupId>

src/main/java/org/cy3sbml/BundleInformation.java

@@ -1,45 +1,42 @@
 package org.cy3sbml;
 
-
 import org.osgi.framework.Bundle;
 import org.osgi.framework.BundleContext;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
 
 /**
- * Necessary to store the information interested in, because bc stops to exist at some point.
- * Access to full manifest information and registered services is possible via the bundle.
+ * The BundleInformation provides runtime information on the bundle.
+ * 
+ * Important things like 
+ * - name
+ * - version
+ * - dependencies
+ * can be accessed and used programmatically.
+ * 
+ * All String generation using names and versions should use the 
+ * BundleInformation directly.
  */
 public class BundleInformation {
-	private static final Logger logger = LoggerFactory.getLogger(BundleInformation.class);
-
 	private String name;
 	private String version;
 
-	private static BundleInformation uniqueInstance;
-
-	public static synchronized BundleInformation getInstance(BundleContext bc){
-		if (uniqueInstance == null){
-			uniqueInstance = new BundleInformation(bc);
-		}
-		return uniqueInstance;
-	}
-	public static synchronized BundleInformation getInstance(){
-		return uniqueInstance;
-	}
-
+	/** Constructor. */
 	public BundleInformation(BundleContext bc){
 		Bundle bundle = bc.getBundle();
 		name = bundle.getSymbolicName();
 		version = bundle.getVersion().toString();
 	}
 
+	/** {name}-v{version} of bundle. */
 	public String getInfo(){
 		return getName() + "-v" + getVersion();
 	}
+
+	/** Name of bundle. */
 	public String getName(){
 		return name;
 	}
+
+	/** Version of bundle. */
 	public String getVersion(){
 		return version;
 	}

src/main/java/org/cy3sbml/ConnectionProxy.java

@@ -13,23 +13,22 @@
 
 /**
  * Handling the system proxy settings required to use the web services (SOAP, REST).
- * Listening to changes in the cytoscape properties which are used for 
+ * Listens to changes in Cytoscape properties which are used for 
  * updating the system proxy settings.
  * 
  * Proxy authentication is currently not supported.
- * Will be supported if requested. 
- * 
- * TODO: listen to changes in settings
  */
 public class ConnectionProxy implements PropertyUpdatedListener{
 	private static final Logger logger = LoggerFactory.getLogger(ConnectionProxy.class);
 
 	private CyProperty<Properties> cyProperties;
 
+	/** Constructor. */
 	public ConnectionProxy(CyProperty<Properties> cyProperties){
 		this.cyProperties = cyProperties;
 	}
 
+	/** Get proxy information. */
 	public Proxy getProxy() {
 		Properties properties = cyProperties.getProperties();
 		final String proxyType = properties.getProperty("proxy.server.type");
@@ -56,7 +55,7 @@ public Proxy getProxy() {
 		return Proxy.NO_PROXY;
 	}
 
-	/** Set Cytoscape proxy settings for system. */
+	/** Sets Cytoscape proxy settings. */
 	public void setSystemProxyFromCyProperties(){
 		String type = getProxyType();
 		String host = getProxyHost();
@@ -67,15 +66,17 @@ public void setSystemProxyFromCyProperties(){
 	public String getProxyType() {
 		return cyProperties.getProperties().getProperty("proxy.server.type");
 	}
+
 	public String getProxyHost() {
 		return cyProperties.getProperties().getProperty("proxy.server");
 	}
+
 	public String getProxyPort() {
 		return cyProperties.getProperties().getProperty("proxy.server.port");
 	}
 
 	public void setSystemProxy(String type, String host, String port) {
-		logger.info("set proxy: "+ type + " " + host + ":" + port);
+		logger.debug("set proxy: "+ type + " " + host + ":" + port);
 		if ("direct".equals(type)){
 			System.setProperty("http.proxyHost", "");
 		    System.setProperty("http.proxyPort", "");
@@ -95,8 +96,9 @@ public void handleEvent(PropertyUpdatedEvent event) {
 		// TODO: currently bug in change of properties in cytoscape
 		// as a consequence there is no way to listen to these changes.
 
+		@SuppressWarnings("rawtypes")
 		CyProperty property = event.getSource();
 		String name = property.getName();
-		logger.info("PropertyUpdatedEvent: " + name);
+		logger.debug("PropertyUpdatedEvent: " + name);
 	}
 }