Better command validation. Fixes #222.

Author: mikekucera

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

@@ -54,7 +54,6 @@
 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;
@@ -160,7 +159,6 @@ public class EMBuildCommandTask extends AbstractTask {
 	public Boolean distinctEdges;
 
 
-	@Inject private EnrichmentMapManager emManager;
 	@Inject private CreateEnrichmentMapTaskFactory.Factory taskFactoryFactory;
 	@Inject private LegacySupport legacySupport;
 	@Inject private PropertyManager propertyManager;
@@ -239,6 +237,9 @@ else if(distinctEdges)
 				new EMCreationParameters(prefix, pvalue, qvalue, NESFilter.ALL, Optional.empty(), 
 						metric, similaritycutoff, propertyManager.getCombinedConstant(), edgeStrategy);
 
+		//System.out.println(creationParams);
+		//System.out.println(dataSets);
+		
 		CreateEnrichmentMapTaskFactory taskFactory = taskFactoryFactory.create(creationParams, dataSets);
 		insertTasksAfterCurrentTask(taskFactory.createTaskIterator());
 	}

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

@@ -27,7 +27,7 @@
 
 public class ResolverCommandTask extends AbstractTask {
 
-	@Tunable
+	@Tunable(required=true)
 	public File rootFolder;
 
 	@Tunable
@@ -91,6 +91,31 @@ public ResolverCommandTask(PropertyManager propertyManager) {
 	public void run(TaskMonitor taskMonitor) throws Exception {
 		logger.info("Running EnrichmentMap Data Set Resolver Task");
 
+		EdgeStrategy strategy;
+		try {
+			strategy = EdgeStrategy.valueOf(edgeStrategy.getSelectedValue().toUpperCase());
+		} catch(IllegalArgumentException e) {
+			throw new IllegalArgumentException("edgeStrategy is invalid: '" + edgeStrategy.getSelectedValue() + "'");
+		}
+		
+		SimilarityMetric sm;
+		try {
+			sm = SimilarityMetric.valueOf(similarityMetric.getSelectedValue().toUpperCase());
+		} catch(IllegalArgumentException e) {
+			throw new IllegalArgumentException("similarityMetric is invalid: '" + similarityMetric.getSelectedValue() + "'");
+		}
+		
+		NESFilter nesf;
+		try {
+			nesf = NESFilter.valueOf(nesFilter.getSelectedValue().toUpperCase());
+		} catch(IllegalArgumentException e) {
+			throw new IllegalArgumentException("nesFilter is invalid: '" + nesFilter.getSelectedValue() + "'");
+		}
+		
+		if(rootFolder == null || !rootFolder.exists()) {
+			throw new IllegalArgumentException("rootFolder is invalid: " + rootFolder);
+		}
+		
 		// Scan root folder (note: throws exception if no data sets were found)
 		ResolverTask resolverTask = new ResolverTask(rootFolder);
 		taskManager.execute(new TaskIterator(resolverTask)); // blocks
@@ -123,16 +148,11 @@ public void run(TaskMonitor taskMonitor) throws Exception {
 
 		// Create Enrichment Map
 		String prefix = legacySupport.getNextAttributePrefix();
-		SimilarityMetric sm = SimilarityMetric.valueOf(similarityMetric.getSelectedValue());
-		NESFilter nesf = NESFilter.valueOf(nesFilter.getSelectedValue());
-		
 		String info = String.format(
 			"prefix:%s, pvalue:%f, qvalue:%f, nesFilter:%s, minExperiments:%d, similarityMetric:%s, similarityCutoff:%f, combinedConstant:%f", 
 			prefix, pvalue, qvalue, nesf, minExperiments, sm, similarityCutoff, combinedConstant);
 		logger.info(info);
 
-		EdgeStrategy strategy = EdgeStrategy.valueOf(edgeStrategy.getSelectedValue());
-		
 		EMCreationParameters params = 
 				new EMCreationParameters(prefix, pvalue, qvalue, nesf, Optional.ofNullable(minExperiments), 
 										 sm, similarityCutoff, combinedConstant, strategy);

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

@@ -257,10 +257,24 @@ public static String similarityMetricToString(SimilarityMetric metric) {
 
 	public static Method stringToMethod(String name) {
 		switch(name) {
+			case method_generic:
+			case "GENERIC":
+				return Method.Generic;
+			case method_GSEA:        
+			case "gsea":
+				return Method.GSEA;
+			case method_Specialized: 
+			case "david":
+			case "DAVID":
+			case "bingo":
+			case "BINGO":
+			case "BiNGO":
+			case "great":
+			case "GREAT":
+			case "Great":
+				return Method.Specialized;
 			default:
-			case method_generic:     return Method.Generic;
-			case method_GSEA:        return Method.GSEA;
-			case method_Specialized: return Method.Specialized;
+				throw new IllegalArgumentException("Method '" + name + "' not recognized");
 		}
 	}