Use namespace for attribute prefix. Refs #272

Author: mikekucera

EnrichmentMapIntegrationTest/src/test/java/org/baderlab/csplugins/enrichmentmap/integration/task/Protocol1Test.java

@@ -43,6 +43,7 @@ public void testProtocol1() throws Exception {
 		task.filterArgs.qvalue = 0.00001;
 		task.filterArgs.similaritycutoff = 0.25;
 		task.filterArgs.edgeStrategy.setSelectedValue(EdgeStrategy.COMPOUND.name());
+		task.filterArgs.attributePrefix = "EM1_";
 
 		SerialTestTaskManager taskManager = new SerialTestTaskManager();
 		taskManager.execute(new TaskIterator(task));

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/CyActivator.java

@@ -25,12 +25,15 @@
 import org.baderlab.csplugins.enrichmentmap.model.io.SessionListener;
 import org.baderlab.csplugins.enrichmentmap.rest.EnrichmentMapResource;
 import org.baderlab.csplugins.enrichmentmap.style.ChartFactoryManager;
+import org.baderlab.csplugins.enrichmentmap.style.EMStyleBuilder;
 import org.baderlab.csplugins.enrichmentmap.style.charts.radialheatmap.RadialHeatMapChartFactory;
+import org.baderlab.csplugins.enrichmentmap.view.EMColumnPresentation;
 import org.baderlab.csplugins.enrichmentmap.view.control.ControlPanelMediator;
 import org.baderlab.csplugins.enrichmentmap.view.creation.CreationDialogShowAction;
 import org.baderlab.csplugins.enrichmentmap.view.heatmap.HeatMapMediator;
 import org.baderlab.csplugins.enrichmentmap.view.legend.LegendPanelMediator;
 import org.cytoscape.application.CyApplicationConfiguration;
+import org.cytoscape.application.swing.CyColumnPresentation;
 import org.cytoscape.command.StringTunableHandlerFactory;
 import org.cytoscape.property.CyProperty;
 import org.cytoscape.service.util.AbstractCyActivator;
@@ -109,6 +112,11 @@ public void start(BundleContext bc) {
 			registerAllServices(bc, controlPanelMediator);
 			HeatMapMediator heatMapMediator = injector.getInstance(HeatMapMediator.class);
 			registerAllServices(bc, heatMapMediator);
+			
+			// column namespace
+			Properties colProps = new Properties();
+			colProps.put(CyColumnPresentation.NAMESPACE, EMStyleBuilder.Columns.NAMESPACE);
+			registerService(bc, new EMColumnPresentation(), CyColumnPresentation.class, colProps);
 		}
 
 		// If the App is updated or restarted then we want to reload the model and view from the tables

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/commands/EMGseaCommandTask.java

@@ -11,10 +11,10 @@
 import org.baderlab.csplugins.enrichmentmap.model.EMCreationParameters.EdgeStrategy;
 import org.baderlab.csplugins.enrichmentmap.model.EMCreationParameters.SimilarityMetric;
 import org.baderlab.csplugins.enrichmentmap.model.EMDataSet.Method;
-import org.baderlab.csplugins.enrichmentmap.model.EnrichmentMapManager;
 import org.baderlab.csplugins.enrichmentmap.model.EnrichmentMapParameters;
 import org.baderlab.csplugins.enrichmentmap.model.EnrichmentResultFilterParams.NESFilter;
 import org.baderlab.csplugins.enrichmentmap.model.LegacySupport;
+import org.baderlab.csplugins.enrichmentmap.style.EMStyleBuilder;
 import org.baderlab.csplugins.enrichmentmap.task.CreateEnrichmentMapTaskFactory;
 import org.cytoscape.work.AbstractTask;
 import org.cytoscape.work.TaskMonitor;
@@ -55,10 +55,11 @@ public class EMGseaCommandTask extends AbstractTask {
 	@Tunable(description="combinedconstant ", groups={"User Input","Parameters"}, gravity = 19.0, tooltip="coeffecient between 0 and 1.")
 	public Double combinedconstant ;
 
+	@Tunable(description="Prefix added to all column names. In older versions of EnrichmentMap this was typically 'EM1_'.")
+	public String attributePrefix = EMStyleBuilder.Columns.NAMESPACE_PREFIX;
+	
 
 	@Inject private CreateEnrichmentMapTaskFactory.Factory taskFactoryFactory;
-	@Inject private EnrichmentMapManager emManager;
-	@Inject private LegacySupport legacySupport;
 
 	public EMGseaCommandTask() {
 		similaritymetric = new ListSingleSelection<String>(EnrichmentMapParameters.SM_OVERLAP, EnrichmentMapParameters.SM_JACCARD, EnrichmentMapParameters.SM_COMBINED);
@@ -79,9 +80,8 @@ private void buildEnrichmentMap(){
 
 		SimilarityMetric metric = EnrichmentMapParameters.stringToSimilarityMetric(similaritymetric.getSelectedValue());
 
-		String prefix = legacySupport.getNextAttributePrefix();
 		EMCreationParameters creationParams = 
-				new EMCreationParameters(prefix, pvalue, qvalue, NESFilter.ALL, Optional.empty(), true,
+				new EMCreationParameters(attributePrefix, pvalue, qvalue, NESFilter.ALL, Optional.empty(), true,
 						metric, overlap, combinedconstant, EdgeStrategy.AUTOMATIC);
 
 		CreateEnrichmentMapTaskFactory taskFactory = taskFactoryFactory.create(creationParams, dataSets);

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/commands/tunables/FilterTunables.java

@@ -14,11 +14,10 @@
 import org.baderlab.csplugins.enrichmentmap.model.EMCreationParameters.SimilarityMetric;
 import org.baderlab.csplugins.enrichmentmap.model.EnrichmentResultFilterParams.NESFilter;
 import org.baderlab.csplugins.enrichmentmap.model.LegacySupport;
+import org.baderlab.csplugins.enrichmentmap.style.EMStyleBuilder;
 import org.cytoscape.work.Tunable;
 import org.cytoscape.work.util.ListSingleSelection;
 
-import com.google.inject.Inject;
-
 
 /**
  * Use with the @ContainsTunables annotation.
@@ -56,8 +55,8 @@ public class FilterTunables {
 	@Tunable
 	public String networkName = null;
 
-	
-	@Inject private LegacySupport legacySupport;
+	@Tunable(description="Prefix added to all column names. In older versions of EnrichmentMap this was typically 'EM1_'.")
+	public String attributePrefix = EMStyleBuilder.Columns.NAMESPACE_PREFIX;
 
 
 	public FilterTunables() {
@@ -72,8 +71,7 @@ public FilterTunables() {
 
 
 	public EMCreationParameters getCreationParameters() throws IllegalArgumentException {
-		String prefix = legacySupport.getNextAttributePrefix();
-		return new EMCreationParameters(prefix, pvalue, qvalue, getNesFilter(), 
+		return new EMCreationParameters(attributePrefix, pvalue, qvalue, getNesFilter(), 
 					Optional.ofNullable(minExperiments), filterByExpressions,
 					getSimilarityMetric(), similaritycutoff, combinedConstant, 
 					getEdgeStrategy());

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/model/EMCreationParameters.java

@@ -19,7 +19,7 @@ public static enum EdgeStrategy {
 		AUTOMATIC, DISTINCT, COMPOUND
 	}
 
-	private String attributePrefix; // MKTODO this shouldn't be here
+	private String attributePrefix;
 
 	// Node filtering (gene-sets)
 	private double pvalue;

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/style/EMStyleBuilder.java

@@ -84,6 +84,9 @@ public class EMStyleBuilder {
 	private static final NodeShape SIGNATURE_NODE_SHAPE = DIAMOND;
 
 	public static class Columns {
+		public static final String NAMESPACE = "EnrichmentMap";
+		public static final String NAMESPACE_PREFIX = NAMESPACE + "::"; // added in Cytoscape 3.7
+		
 		// Common attributes that apply to the entire network
 		public static final ColumnDescriptor<String> NODE_NAME = new ColumnDescriptor<>("Name", String.class);
 		public static final ColumnDescriptor<String> NODE_GS_DESCR = new ColumnDescriptor<>("GS_DESCR", String.class);

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/EMColumnPresentation.java

@@ -0,0 +1,29 @@
+package org.baderlab.csplugins.enrichmentmap.view;
+
+import java.net.URL;
+
+import javax.swing.Icon;
+import javax.swing.ImageIcon;
+
+import org.cytoscape.application.swing.CyColumnPresentation;
+
+public class EMColumnPresentation implements CyColumnPresentation {
+
+	private final Icon icon; 
+	
+	public EMColumnPresentation() {
+		URL logoURL = getClass().getClassLoader().getResource("images/enrichmentmap_logo_16.png");
+		icon = new ImageIcon(logoURL);
+	}
+	
+	@Override
+	public Icon getNamespaceIcon() {
+		return icon;
+	}
+
+	@Override
+	public String getNamespaceDescription() {
+		return null;
+	}
+
+}

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/creation/MasterDetailDialogPage.java

@@ -54,8 +54,8 @@
 import org.baderlab.csplugins.enrichmentmap.model.EMCreationParameters.SimilarityMetric;
 import org.baderlab.csplugins.enrichmentmap.model.EMDataSet.Method;
 import org.baderlab.csplugins.enrichmentmap.model.EnrichmentResultFilterParams.NESFilter;
-import org.baderlab.csplugins.enrichmentmap.model.LegacySupport;
 import org.baderlab.csplugins.enrichmentmap.resolver.ResolverTask;
+import org.baderlab.csplugins.enrichmentmap.style.EMStyleBuilder;
 import org.baderlab.csplugins.enrichmentmap.task.CreateEnrichmentMapTaskFactory;
 import org.baderlab.csplugins.enrichmentmap.view.util.CardDialogCallback;
 import org.baderlab.csplugins.enrichmentmap.view.util.CardDialogPage;
@@ -81,7 +81,6 @@ public class MasterDetailDialogPage implements CardDialogPage {
 	@Inject private Provider<JFrame> jframeProvider;
 	@Inject private FileBrowser fileBrowser;
 	@Inject private PropertyManager propertyManager;
-	@Inject private LegacySupport legacySupport;
 
 	@Inject private Provider<DetailCommonPanel> commonPanelProvider;
 	@Inject private DetailDataSetPanel.Factory dataSetPanelFactory;
@@ -120,7 +119,8 @@ public void finish() {
 		if(!validateInput())
 			return;
 
-		String prefix = legacySupport.getNextAttributePrefix();
+		String prefix = EMStyleBuilder.Columns.NAMESPACE_PREFIX;
+		
 		SimilarityMetric similarityMetric = cutoffPanel.getSimilarityMetric();
 		double pvalue = cutoffPanel.getPValue();
 		double qvalue = cutoffPanel.getQValue();

EnrichmentMapPlugin/src/test/java/org/baderlab/csplugins/enrichmentmap/task/TableLoadNetworkTest.java

@@ -83,6 +83,7 @@ public void testTableCommand(TableCommandTask command, CyNetworkManager networkM
 		command.tableArgs.nameColumn = NAME;
 		command.tableArgs.genesColumn = GENES;
 		command.tableArgs.descriptionColumn = DESCRIPTION;
+		command.filterArgs.attributePrefix = "EM1_";
 
 	   	SerialTestTaskManager testTaskManager = new SerialTestTaskManager();
 	   	testTaskManager.ignoreTask(CreateEMViewTask.class);

pom.xml

@@ -10,7 +10,7 @@
 	<properties>
 		<bundle.namespace>org.baderlab.csplugins</bundle.namespace>
 	    <project.name>EnrichmentMap</project.name>
-	    <cy3.version>3.6.0</cy3.version>
+	    <cy3.version>3.7.0</cy3.version>
 		<osgi.api.version>4.2.0</osgi.api.version>
 		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
 	</properties>