Author: jgao Date: 2011-10-29 06:59:22 -0700 (Sat, 29 Oct 2011) New Revision: 27337
Modified: csplugins/trunk/soc/jgao/IDMapping/resources/plugin.props csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/CyThesaurusPlugin.java csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/IDMapperClientImplTunables.java csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/IDMapperClientManager.java csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/service/CyThesaurusNamespace.java csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/ui/IDMappingSourceConfigDialog.java Log: cythesaurus version 1.3 Modified: csplugins/trunk/soc/jgao/IDMapping/resources/plugin.props =================================================================== --- csplugins/trunk/soc/jgao/IDMapping/resources/plugin.props 2011-10-29 01:04:54 UTC (rev 27336) +++ csplugins/trunk/soc/jgao/IDMapping/resources/plugin.props 2011-10-29 13:59:22 UTC (rev 27337) @@ -13,7 +13,7 @@ pluginDescription=Provides utilities for mapping attributes of source ID types to new attributes of destination ID types. <a href="http://www.cytoscape.org/cgi-bin/moin.cgi/CyThesaurus_Plugin";>Click for more information</a>. # Plugin version number, this must be two numbers separated by a decimlal. Ex. 0.2, 14.03 -pluginVersion=1.20 +pluginVersion=1.30 # Compatible Cytoscape version. If there are more than one version, seperate by ",". cytoscapeVersion=2.8 @@ -28,4 +28,4 @@ # List of authors. Note each author and institution pair are separated by a : (colon) # each additional author institution pair must be separated from other pairs bye a ; (semicolon) -pluginAuthorsInstitutions=Jianjiong Gao:U. of Missouri +pluginAuthorsInstitutions=Jianjiong Gao:MSKCC Modified: csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/CyThesaurusPlugin.java =================================================================== --- csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/CyThesaurusPlugin.java 2011-10-29 01:04:54 UTC (rev 27336) +++ csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/CyThesaurusPlugin.java 2011-10-29 13:59:22 UTC (rev 27337) @@ -82,11 +82,47 @@ Cytoscape.getDesktop().getCyMenus().getOperationsMenu() .add(new IDMappingAction()); + +// Cytoscape.getDesktop().getCyMenus().getOperationsMenu() +// .add(new IDMappingTestAction()); // Cytoscape.getDesktop().getCyMenus().getOperationsMenu() // .add(new CyThesurrusServiceAttributeBasedIDMappingAction()); } + + + final class IDMappingTestAction extends CytoscapeAction { + + public IDMappingTestAction() { + super("CyThesaurus test"); + } + + /** + * This method is called when the user selects the menu item. + */ + @Override + public void actionPerformed(final ActionEvent ae) { + java.util.List<String> nodeIds = new java.util.ArrayList<String>(); + for (cytoscape.CyNode cn : (java.util.List<cytoscape.CyNode>) cytoscape.Cytoscape.getCurrentNetwork().nodesList()) { + nodeIds.add(cn.getIdentifier()); + } + Map<String, Object> args = new java.util.HashMap<String, Object>(); + args.put("sourceid", nodeIds); + args.put("sourcetype", "HGNC"); + args.put("targettype", "Ensembl Human"); + cytoscape.command.CyCommandResult result = null; + try { + result = cytoscape.command.CyCommandManager.execute( + "idmapping", "general mapping", args); + System.out.println("message:"+result.getMessages().get(0)); + } catch (Exception e) { + // TODO Auto-generated catch block + e.printStackTrace(); + } + } + } + private void addListeners() { PropertyChangeSupport pcs = Cytoscape.getPropertyChangeSupport(); Modified: csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/IDMapperClientImplTunables.java =================================================================== --- csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/IDMapperClientImplTunables.java 2011-10-29 01:04:54 UTC (rev 27336) +++ csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/IDMapperClientImplTunables.java 2011-10-29 13:59:22 UTC (rev 27337) @@ -226,7 +226,8 @@ } }); - if (executor.awaitTermination(1, TimeUnit.SECONDS)) { + //TODO: how to set waiting time? + if (executor.awaitTermination(5, TimeUnit.SECONDS)) { executor.shutdown(); } Modified: csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/IDMapperClientManager.java =================================================================== --- csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/IDMapperClientManager.java 2011-10-29 01:04:54 UTC (rev 27336) +++ csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/IDMapperClientManager.java 2011-10-29 13:59:22 UTC (rev 27337) @@ -588,9 +588,9 @@ if (spt) { List<DataSourceWrapper> dsws = new ArrayList<DataSourceWrapper>(2); dsws.add(DataSourceWrapper.getInstance( - src.getFullName(), DataSourceWrapper.DsAttr.DATASOURCE)); + DataSourceUtil.getName(src), DataSourceWrapper.DsAttr.DATASOURCE)); dsws.add(DataSourceWrapper.getInstance( - tgt.getFullName(), DataSourceWrapper.DsAttr.DATASOURCE)); + DataSourceUtil.getName(tgt), DataSourceWrapper.DsAttr.DATASOURCE)); supportedMapping.add(dsws); } } Modified: csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/service/CyThesaurusNamespace.java =================================================================== --- csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/service/CyThesaurusNamespace.java 2011-10-29 01:04:54 UTC (rev 27336) +++ csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/service/CyThesaurusNamespace.java 2011-10-29 13:59:22 UTC (rev 27337) @@ -198,7 +198,7 @@ if (command.equals(ADD_RESOURCE)) return addResource(command, args); if (command.equals(REMOVE_RESOURCE)) - removeResource(command, args); + return removeResource(command, args); if (command.equals(SELECT_RESOURCE)) return selectResource(command, args); if (command.equals(DESELECT_RESOURCE)) Modified: csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/ui/IDMappingSourceConfigDialog.java =================================================================== --- csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/ui/IDMappingSourceConfigDialog.java 2011-10-29 01:04:54 UTC (rev 27336) +++ csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/ui/IDMappingSourceConfigDialog.java 2011-10-29 13:59:22 UTC (rev 27337) @@ -38,6 +38,7 @@ import csplugins.id.mapping.IDMapperClient; import csplugins.id.mapping.IDMapperClientManager; +import csplugins.id.mapping.util.DataSourceUtil; import cytoscape.task.Task; import cytoscape.task.TaskMonitor; import cytoscape.task.ui.JTaskConfig; @@ -414,7 +415,7 @@ } desc.append("\t"); - String fullName = dataSource.getFullName(); + String fullName = DataSourceUtil.getName(dataSource); if (fullName!=null) { desc.append(fullName); } -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. 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