Fix 'enrichmentmap build' command bogus second dataset

Author: mikekucera

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

@@ -183,6 +183,11 @@ private DataSetFiles getDataSet2Files() {
 		return dataset2files;
 	}
 
+	
+	private boolean is2DataSet() {
+		return expressionDataset2 != null || enrichmentsDataset2 != null || enrichments2Dataset2 != null;
+	}
+	
 
 	@Override
 	public void run(TaskMonitor tm) {
@@ -192,8 +197,8 @@ public void run(TaskMonitor tm) {
 		DataSetFiles dataset1files = getDataSet1Files();
 		dataSets.add(new DataSetParameters(LegacySupport.DATASET1, method, dataset1files));
 
-		DataSetFiles dataset2files = getDataSet2Files();
-		if(!dataset2files.isEmpty()) {
+		if(is2DataSet()) {
+			DataSetFiles dataset2files = getDataSet2Files();
 			dataSets.add(new DataSetParameters(LegacySupport.DATASET2, method, dataset2files));
 		}
 

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

@@ -114,16 +114,4 @@ public void copy(DataSetFiles copy) {
 		this.phenotype2 = copy.getPhenotype2();
 	}
 
-
-	public boolean isEmpty() {
-		if(this.GMTFileName != null && !this.GMTFileName.equalsIgnoreCase(""))
-			return false;
-		if(this.expressionFileName != null && !this.expressionFileName.equalsIgnoreCase(""))
-			return false;
-		if(this.enrichmentFileName1 != null && !this.enrichmentFileName1.equalsIgnoreCase(""))
-			return false;
-		if(this.enrichmentFileName2 != null && !this.enrichmentFileName2.equalsIgnoreCase(""))
-			return false;
-		return true;
-	}
 }