Better error reporting from expression task.

Refs #185

Author: mikekucera

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

@@ -20,6 +20,7 @@
 import org.cytoscape.work.SynchronousTaskManager;
 import org.cytoscape.work.TaskIterator;
 import org.cytoscape.work.TaskMonitor;
+import org.cytoscape.work.TaskMonitor.Level;
 import org.cytoscape.work.Tunable;
 import org.cytoscape.work.util.ListSingleSelection;
 
@@ -56,10 +57,10 @@ public class MastermapCommandTask extends AbstractTask implements ObservableTask
 
 
 	@Inject private SynchronousTaskManager<?> taskManager;
-	@Inject private CreateEnrichmentMapTaskFactory.Factory taskFactoryFactory;
+	@Inject private CreateEnrichmentMapTaskFactory.Factory createEMTaskFactory;
 
 
-	private Long[] result = { null };
+	private Long[] resultNetworkSUID = { null };
 
 
 	public MastermapCommandTask() {
@@ -76,6 +77,13 @@ public void run(TaskMonitor tm) throws Exception {
 			throw new IllegalArgumentException("rootFolder is invalid: " + rootFolder);
 		}
 
+		runTask(tm);
+		
+		tm.setStatusMessage("Done");
+	}
+	
+	
+	private void runTask(TaskMonitor tm) {
 		// Scan root folder (note: throws exception if no data sets were found)
 		var resolverTask = new DataSetResolverTask(rootFolder);
 
@@ -104,14 +112,12 @@ public void run(TaskMonitor tm) throws Exception {
 			params.setNetworkName(filterArgs.networkName);
 		}
 
-		var taskFactory = taskFactoryFactory.create(params, dataSets);
-		var tasks = taskFactory.createTaskIterator();
-		
-		taskManager.execute(tasks, TaskUtil.taskFinished(CreateEMNetworkTask.class, networkTask -> {
-			result[0] = networkTask.getResults(Long.class); // get SUID of created network
-		}));
+		var tasks = createEMTaskFactory.create(params, dataSets).createTaskIterator();
 
-		tm.setStatusMessage("Done");
+		taskManager.execute(tasks, TaskUtil.taskFinished(CreateEMNetworkTask.class,
+			(task)  -> resultNetworkSUID[0] = task.getResults(Long.class),
+			(error) -> tm.showMessage(Level.ERROR, "Failed to create EnrichmentMap network. Check task log for details.")
+		));
 	}
 
 
@@ -156,11 +162,12 @@ public List<Class<?>> getResultClasses() {
 
 	@Override
 	public <R> R getResults(Class<? extends R> type) {
+		Long suid = resultNetworkSUID[0];
 		if(String.class.equals(type)) {
-			return type.cast(String.valueOf(result[0]));
+			return type.cast(String.valueOf(suid));
 		}
 		if(Long.class.equals(type)) {
-			return type.cast(result[0]);
+			return type.cast(suid);
 		}
 		return null;
 	}

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

@@ -45,8 +45,6 @@
 
 import java.util.Arrays;
 
-import org.apache.commons.math3.util.Precision;
-
 
 /**
  * Class representing the expression of one gene/protein
@@ -57,7 +55,7 @@ public class GeneExpression {
 	private String description;
 	private float[] expression;
 
-	public GeneExpression(String name, String description) {
+	private GeneExpression(String name, String description) {
 		this.name = name;
 		this.description = description;
 	}
@@ -72,37 +70,6 @@ public GeneExpression(String name, String description, float dummyVal) {
 		this.expression = new float[] { dummyVal };
 	}
 
-	/**
-	 * Create an array of the expression values.
-	 */
-	public void setExpression(String[] expres) {
-		// ignore the first two cells --> only if there are at least 3 cells
-		int size = expres.length;
-
-		if (size > 2) {
-			expression = new float[size - 2];
-			for (int i = 2; i < size; i++) {
-				expression[i - 2] = parseAndRound(expres[i]);
-			}
-		} else {
-			expression = new float[1];
-			try {
-				expression[0] = parseAndRound(expres[1]);
-			} catch (NumberFormatException e) {
-				// if the column doesn't contain doubles then just assume that the expression file is empty
-				expression[0] = 0.0f;
-			}
-		}
-	}
-	
-	
-	private float parseAndRound(String exp) {
-		float f = Float.parseFloat(exp);
-		float r = Precision.round(f, 4);
-		return r;
-	}
-
-
 	/**
 	 * Row normalize the current gene expression set. Row normalization involved
 	 * subtracting the mena of the row from each expression value in the row and

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/parsers/ExpressionFileReaderTask.java

@@ -47,13 +47,15 @@
 import java.util.List;
 import java.util.Map;
 
+import org.apache.commons.math3.util.Precision;
 import org.baderlab.csplugins.enrichmentmap.model.EMDataSet;
 import org.baderlab.csplugins.enrichmentmap.model.EnrichmentMap;
 import org.baderlab.csplugins.enrichmentmap.model.GeneExpression;
 import org.baderlab.csplugins.enrichmentmap.model.GeneExpressionMatrix;
 import org.baderlab.csplugins.enrichmentmap.util.NullTaskMonitor;
 import org.cytoscape.work.AbstractTask;
 import org.cytoscape.work.TaskMonitor;
+import org.cytoscape.work.TaskMonitor.Level;
 
 /**
  * Parse expression file. The user can also use a rank file instead of an
@@ -114,7 +116,7 @@ public GeneExpressionMatrix parse(TaskMonitor taskMonitor) throws IOException {
 		int expressionUniverse = 0;
 		boolean twoColumns = false;
 
-		taskMonitor.setStatusMessage("Parsing GCT file - " + maxValue + " rows");
+		taskMonitor.setStatusMessage("Parsing Expression file - " + maxValue + " rows");
 
 		for(int i = 0; i < lines.size(); i++) {
 			String line = lines.get(i);
@@ -193,8 +195,8 @@ public GeneExpressionMatrix parse(TaskMonitor taskMonitor) throws IOException {
 					description = tokens[1];
 				}
 
-				GeneExpression expres = new GeneExpression(Name, description);
-				expres.setExpression(tokens);
+				float[] expressionsAsFloat = parseExpressions(tokens);
+				GeneExpression expres = new GeneExpression(Name, description, expressionsAsFloat);
 				expression.put(genekey, expres);
 			}
 			expressionUniverse++;
@@ -211,10 +213,49 @@ public GeneExpressionMatrix parse(TaskMonitor taskMonitor) throws IOException {
 		return expressionMatrix;
 	}
 
+	
+	public static float[] parseExpressions(String[] expres) {
+		// ignore the first two cells --> only if there are at least 3 cells
+		int size = expres.length;
+		float[] expression;
+		
+		if (size > 2) {
+			expression = new float[size - 2];
+			for (int i = 2; i < size; i++) {
+				try {
+					expression[i - 2] = parseAndRound(expres[i]);
+				} catch(NumberFormatException e) {
+					throw new NumberFormatException("The expression file contains the text '" + expres[i] + "' where a number was expected.");
+				}
+			}
+		} else {
+			expression = new float[1];
+			try {
+				expression[0] = parseAndRound(expres[1]);
+			} catch (NumberFormatException e) {
+				// if the column doesn't contain doubles then just assume that the expression file is empty
+				expression[0] = 0.0f;
+			}
+		}
+		return expression;
+	}
+	
+	
+	private static float parseAndRound(String exp) {
+		float f = Float.parseFloat(exp);
+		float r = Precision.round(f, 4);
+		return r;
+	}
+	
 
 	@Override
 	public void run(TaskMonitor taskMonitor) throws Exception {
-		taskMonitor.setTitle("Parsing GCT file");
-		parse(taskMonitor);
+		taskMonitor.setTitle("Parsing Expression file");
+		try {
+			parse(taskMonitor);
+		} catch(NumberFormatException e) {
+			taskMonitor.showMessage(Level.ERROR, e.getMessage());
+			throw e;
+		}
 	}
 }

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/util/TaskUtil.java

@@ -65,6 +65,23 @@ public void allFinished(FinishStatus finishStatus) { }
 		};
 	}
 
+	public static <T> TaskObserver taskFinished(Class<T> taskType, Consumer<T> finishConsumer, Consumer<FinishStatus> failConsumer) {
+		return new TaskObserver() {
+			@Override
+			public void taskFinished(ObservableTask task) {
+				if(taskType.isInstance(task)) {
+					finishConsumer.accept(taskType.cast(task));
+				}
+			}
+			@Override
+			public void allFinished(FinishStatus finishStatus) { 
+				if(finishStatus.getType() == Type.FAILED) {
+					failConsumer.accept(finishStatus);
+				}
+			}
+		};
+	}
+	
 	public static ListSingleSelection<String> lssFromEnum(Enum<?> ... values) {
 		List<String> names = new ArrayList<>(values.length);
 		for(Enum<?> value : values) {