Better gene ranks error message. Some refactoring.

Refs #510

Author: mikekucera

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

@@ -57,7 +57,6 @@
 import org.baderlab.csplugins.enrichmentmap.model.EnrichmentMap;
 import org.baderlab.csplugins.enrichmentmap.model.Rank;
 import org.baderlab.csplugins.enrichmentmap.model.Ranking;
-import org.baderlab.csplugins.enrichmentmap.task.UnsortedRanksException;
 import org.baderlab.csplugins.enrichmentmap.util.NullTaskMonitor;
 import org.cytoscape.work.AbstractTask;
 import org.cytoscape.work.ObservableTask;
@@ -219,15 +218,16 @@ public void parse(TaskMonitor taskMonitor) throws IOException {
 
 		//the none of the genes are in the gene list
 		if(ranks.isEmpty()) {
-			throw new IllegalArgumentException("None of the genes in the rank file are found in the expression file.  Make sure the identifiers of the two files match.");
+			String message = "The genes in the provided rank file were not found in the enrichments file or in the GMT file.";
+			throw new RanksGeneMismatchException(RankFileName, message);
 		}
 
 		if(!sorted) {
 			String message = "The ranks file '" + RankFileName + "' is not sorted from greatest to least.";
 			if(unsortedRanksStrategy == UnsortedRanksStrategy.LOG_WARNING) {
 				taskMonitor.showMessage(Level.WARN, message);
 			} else {
-				throw new UnsortedRanksException(message, RankFileName);
+				throw new RanksUnsortedException(RankFileName, message);
 			}
 		}
 

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

@@ -0,0 +1,17 @@
+package org.baderlab.csplugins.enrichmentmap.parsers;
+
+@SuppressWarnings("serial")
+public class RanksGeneMismatchException extends RuntimeException {
+
+	private final String ranksFileName;
+	
+	public RanksGeneMismatchException(String ranksFileName, String message) {
+		super(message);
+		this.ranksFileName = ranksFileName;
+	}
+	
+	public String getRanksFileName() {
+		return ranksFileName;
+	}
+
+}

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/task/UnsortedRanksException.java renamed to EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/parsers/RanksUnsortedException.java

@@ -1,11 +1,11 @@
-package org.baderlab.csplugins.enrichmentmap.task;
+package org.baderlab.csplugins.enrichmentmap.parsers;
 
 @SuppressWarnings("serial")
-public class UnsortedRanksException extends RuntimeException {
+public class RanksUnsortedException extends RuntimeException {
 
 	private final String ranksFileName;
 
-	public UnsortedRanksException(String message, String ranksFileName) {
+	public RanksUnsortedException(String ranksFileName, String message) {
 		super(message);
 		this.ranksFileName = ranksFileName;
 	}

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

@@ -12,11 +12,11 @@
 import org.baderlab.csplugins.enrichmentmap.parsers.ParseGSEAEnrichmentException;
 import org.baderlab.csplugins.enrichmentmap.parsers.ParseGSEAEnrichmentResults.ParseGSEAEnrichmentStrategy;
 import org.baderlab.csplugins.enrichmentmap.parsers.RanksFileReaderTask.UnsortedRanksStrategy;
+import org.baderlab.csplugins.enrichmentmap.parsers.RanksUnsortedException;
 import org.baderlab.csplugins.enrichmentmap.task.CreateEnrichmentMapTaskFactory;
 import org.baderlab.csplugins.enrichmentmap.task.InitializeGenesetsOfInterestTask.MissingGenesetStrategy;
 import org.baderlab.csplugins.enrichmentmap.task.MissingGenesetsException;
 import org.baderlab.csplugins.enrichmentmap.task.TaskErrorStrategies;
-import org.baderlab.csplugins.enrichmentmap.task.UnsortedRanksException;
 import org.baderlab.csplugins.enrichmentmap.util.TaskUtil;
 import org.baderlab.csplugins.enrichmentmap.view.util.dialog.ErrorMessageDialog;
 import org.baderlab.csplugins.enrichmentmap.view.util.dialog.Message;
@@ -78,8 +78,8 @@ else if(e instanceof ParseGSEAEnrichmentException) {
 					runImpl(strategies.with(ParseGSEAEnrichmentStrategy.REPLACE_WITH_1));
 				}
 			} 
-			else if(e instanceof UnsortedRanksException) {
-				var ranksFileName = ((UnsortedRanksException)e).getRanksFileName();
+			else if(e instanceof RanksUnsortedException) {
+				var ranksFileName = ((RanksUnsortedException)e).getRanksFileName();
 				boolean retry = promptForUnsortedRanksRetry(ranksFileName);
 				if(retry) {
 					runImpl(strategies.with(UnsortedRanksStrategy.LOG_WARNING));

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/util/dialog/ErrorMessageDialog.java

@@ -134,11 +134,8 @@ public void addSection(Message message, String title, String icon) {
 	}
 
 	public void addSection(List<Message> messages, String title, String icon) {
-		final boolean hasError = messages.stream().anyMatch(Message::isError);
-		if(hasError) {
-			finishButton.setVisible(false);
-			doNotShowCheckbox.setVisible(false);
-			hasErrors = true;
+		if(messages.stream().anyMatch(Message::isError)) {
+			setError();
 		}
 
 		JLabel iconLabel = new JLabel(icon == null ? "" : " " + icon + "  ");
@@ -163,6 +160,12 @@ public void addSection(List<Message> messages, String title, String icon) {
 		}
 	}
 
+	public void setError() {
+		finishButton.setVisible(false);
+		doNotShowCheckbox.setVisible(false);
+		hasErrors = true;
+	}
+	
 	public boolean hasErrors() {
 		return hasErrors;
 	}