Author: rodche Date: 2011-08-11 15:35:03 -0700 (Thu, 11 Aug 2011) New Revision: 26534
Removed: csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/resources/org/cytoscape/cpathsquared/internal/plugin/ Modified: csplugins/trunk/toronto/rodche/cpathsquared-impl/pom.xml csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/task/ExecuteGetRecordByCPathId.java Log: Updated maven dependencies. Begin to update the (Pathway Commons) ws client... Modified: csplugins/trunk/toronto/rodche/cpathsquared-impl/pom.xml =================================================================== --- csplugins/trunk/toronto/rodche/cpathsquared-impl/pom.xml 2011-08-11 18:06:59 UTC (rev 26533) +++ csplugins/trunk/toronto/rodche/cpathsquared-impl/pom.xml 2011-08-11 22:35:03 UTC (rev 26534) @@ -2,13 +2,14 @@ <project xmlns="http://maven.apache.org/POM/4.0.0"; xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"; xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd";> <parent> <groupId>org.cytoscape</groupId> - <artifactId>parent</artifactId> - <version>3.0.0-alpha7</version> - <relativePath>../parent</relativePath> + <artifactId>impl-parent</artifactId> + <version>3.0.0-alpha6-SNAPSHOT</version> </parent> <properties> - <bundle.symbolicName>org.cytoscape.cpathsquared-impl</bundle.symbolicName> <bundle.namespace>org.cytoscape.cpathsquared</bundle.namespace> + <cytoscape.impl.version>3.0.0-alpha6-SNAPSHOT</cytoscape.impl.version> + <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding> + <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding> </properties> <modelVersion>4.0.0</modelVersion> <groupId>org.cytoscape</groupId> @@ -25,61 +26,55 @@ <dependency> <groupId>org.cytoscape</groupId> <artifactId>model-api</artifactId> - <version>3.0.0-alpha4</version> + <version>${cytoscape.api.version}</version> </dependency> <dependency> <groupId>org.cytoscape</groupId> <artifactId>io-api</artifactId> - <version>3.0.0-alpha3</version> + <version>${cytoscape.api.version}</version> </dependency> <dependency> <groupId>org.cytoscape</groupId> <artifactId>webservice-api</artifactId> - <version>3.0.0-alpha2</version> + <version>${cytoscape.api.version}</version> </dependency> <dependency> <groupId>org.cytoscape</groupId> <artifactId>viewmodel-api</artifactId> - <version>3.0.0-alpha4</version> - <scope>compile</scope> + <version>${cytoscape.api.version}</version> </dependency> <dependency> <groupId>org.cytoscape</groupId> <artifactId>layout-api</artifactId> - <version>3.0.0-alpha2</version> + <version>${cytoscape.api.version}</version> </dependency> <dependency> <groupId>org.cytoscape</groupId> <artifactId>presentation-api</artifactId> - <version>3.0.0-alpha4-SNAPSHOT</version> + <version>${cytoscape.api.version}</version> </dependency> <dependency> <groupId>org.cytoscape</groupId> <artifactId>swing-util-api</artifactId> - <version>3.0.0-alpha3-SNAPSHOT</version> + <version>${cytoscape.api.version}</version> </dependency> <dependency> <groupId>org.cytoscape</groupId> <artifactId>swing-application-api</artifactId> - <version>3.0.0-alpha2</version> + <version>${cytoscape.api.version}</version> </dependency> <dependency> <groupId>org.cytoscape</groupId> <artifactId>biopax-impl</artifactId> - <version>3.0.0-alpha2-SNAPSHOT</version> + <version>${parent.version}</version> </dependency> <dependency> <groupId>org.cytoscape</groupId> <artifactId>vizmap-api</artifactId> - <version>3.0.0-alpha6-SNAPSHOT</version> + <version>${cytoscape.api.version}</version> </dependency> - <dependency> - <groupId>cytoscape-temp</groupId> - <artifactId>commons-httpclient</artifactId> - <version>3.1</version> - </dependency> <dependency> <groupId>org.jdom</groupId> @@ -107,6 +102,11 @@ <version>1.8.1</version> <scope>test</scope> </dependency> + <dependency> + <groupId>org.springframework</groupId> + <artifactId>org.springframework.web</artifactId> + <version>${spring.version}</version> + </dependency> </dependencies> <repositories> @@ -173,15 +173,10 @@ </executions> </plugin> <plugin> - <groupId>org.ops4j</groupId> - <artifactId>maven-pax-plugin</artifactId> - <version>${maven-pax-plugin.version}</version> - <extensions>true</extensions> - </plugin> - <plugin> <groupId>org.apache.felix</groupId> <artifactId>maven-bundle-plugin</artifactId> <version>${maven-bundle-plugin.version}</version> + <extensions>true</extensions> <configuration> <instructions> <Bundle-SymbolicName>${bundle.symbolicName}</Bundle-SymbolicName> @@ -189,7 +184,7 @@ <_include>-osgi.bnd</_include> </instructions> </configuration> - </plugin> + </plugin> </plugins> </build> </project> Modified: csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/task/ExecuteGetRecordByCPathId.java =================================================================== --- csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/task/ExecuteGetRecordByCPathId.java 2011-08-11 18:06:59 UTC (rev 26533) +++ csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/task/ExecuteGetRecordByCPathId.java 2011-08-11 22:35:03 UTC (rev 26534) @@ -17,7 +17,6 @@ import org.biopax.paxtools.io.SimpleIOHandler; import org.biopax.paxtools.model.BioPAXElement; import org.biopax.paxtools.model.Model; -import org.biopax.paxtools.model.level2.physicalEntity; import org.biopax.paxtools.model.level3.PhysicalEntity; import org.cytoscape.biopax.BioPaxContainer; import org.cytoscape.biopax.MapBioPaxToCytoscape; @@ -55,7 +54,7 @@ /** * Controller for Executing a Get Record(s) by CPath ID(s) command. * - * @author Ethan Cerami. + * @author Ethan Cerami, Jason Montojo, Igor Rodchenkov. */ public class ExecuteGetRecordByCPathId extends AbstractTask { private CPathWebService webApi; @@ -246,7 +245,7 @@ TaskFactory tf = layoutManager.getDefaultLayout(); TaskIterator ti = tf.getTaskIterator(); Task task = ti.next(); - insertTasksAfterCurrentTask(task); + insertTasksAfterCurrentTask(new Task[] {task}); } catch (IOException e) { throw new Exception("Failed to retrieve records.", e); @@ -499,7 +498,7 @@ // Namespace ns = // Namespace.getNamespace("http://www.w3.org/1999/02/22-rdf-syntax-ns#";); // for (int j=0; j<peList.size(); j++) { - for (BioPAXElement pe : BioPaxUtil.getObjects(model, physicalEntity.class, PhysicalEntity.class)) { + for (BioPAXElement pe : model.getObjects(PhysicalEntity.class)) { // Element element = (Element) peList.get(j); // String id = element.getAttributeValue("ID", ns); String id = BioPaxUtil.getLocalPartRdfId(pe); @@ -546,51 +545,15 @@ return masterList; } - // private CyNetworkView createNetworkView (CyNetwork network, String title, - // CyLayoutAlgorithm - // layout, VisualStyle vs) { - // - // if (viewManager.viewExists((network.getSUID()))) { - // return Cytoscape.getNetworkView(network.getIdentifier()); - // } - // - // final DingNetworkView view = new DingNetworkView(network, title); - // view.setGraphLOD(new CyGraphLOD()); - // view.setIdentifier(network.getIdentifier()); - // view.setTitle(network.getTitle()); - // Cytoscape.getNetworkViewMap().put(network.getIdentifier(), view); - // Cytoscape.setSelectionMode(Cytoscape.getSelectionMode(), view); - // - // VisualMappingManager VMM = Cytoscape.getVisualMappingManager(); - // if (vs != null) { - // view.setVisualStyle(vs.getName()); - // VMM.setVisualStyle(vs); - // VMM.setNetworkView(view); - // } - // - // if (layout == null) { - // layout = CyLayouts.getDefaultLayout(); - // } - // - // Cytoscape.firePropertyChange(cytoscape.view.CytoscapeDesktop.NETWORK_VIEW_CREATED, - // null, view); - // layout.doLayout(view); - // view.fitContent(); - // view.redrawGraph(false, true); - // return view; - // } } class NullTaskMonitor implements TaskMonitor { - @Override public void setProgress(double arg0) { } - @Override public void setStatusMessage(String arg0) { } - @Override public void setTitle(String arg0) { } } -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. 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