Warn user if ranks file is unsorted.

Refs #500

Author: mikekucera

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

@@ -12,12 +12,13 @@
 import org.baderlab.csplugins.enrichmentmap.resolver.DataSetResolverTask;
 import org.baderlab.csplugins.enrichmentmap.task.CreateEMNetworkTask;
 import org.baderlab.csplugins.enrichmentmap.task.CreateEnrichmentMapTaskFactory;
+import org.baderlab.csplugins.enrichmentmap.util.DelegatingTaskMonitor;
 import org.baderlab.csplugins.enrichmentmap.util.NullTaskMonitor;
+import org.baderlab.csplugins.enrichmentmap.util.SimpleSyncTaskManager;
 import org.baderlab.csplugins.enrichmentmap.util.TaskUtil;
 import org.cytoscape.work.AbstractTask;
 import org.cytoscape.work.ContainsTunables;
 import org.cytoscape.work.ObservableTask;
-import org.cytoscape.work.SynchronousTaskManager;
 import org.cytoscape.work.TaskIterator;
 import org.cytoscape.work.TaskMonitor;
 import org.cytoscape.work.TaskMonitor.Level;
@@ -56,7 +57,6 @@ public class MastermapCommandTask extends AbstractTask implements ObservableTask
 
 
 
-	@Inject private SynchronousTaskManager<?> taskManager;
 	@Inject private CreateEnrichmentMapTaskFactory.Factory createEMTaskFactory;
 
 
@@ -77,7 +77,17 @@ public void run(TaskMonitor tm) throws Exception {
 			throw new IllegalArgumentException("rootFolder is invalid: " + rootFolder);
 		}
 
-		runTask(tm);
+		var delegatingTM = new DelegatingTaskMonitor(tm) {
+			@Override
+			public void setStatusMessage(String message) {
+				// Kind of a hack, used to suppress the flood of status messages from ComputeSimilarityTaskParallel
+				if(message != null && message.startsWith("Computing Geneset Similarity:"))
+					return;
+				super.setStatusMessage(message);
+			}
+		};
+		
+		runTask(delegatingTM);
 
 		tm.setStatusMessage("Done");
 	}
@@ -92,6 +102,8 @@ private void runTask(TaskMonitor tm) {
 			resolverTask.setPathMatcher(matcher);
 		}
 
+		var taskManager = new SimpleSyncTaskManager(tm);
+		
 		taskManager.execute(new TaskIterator(resolverTask)); // blocks
 		var dataSets = resolverTask.getDataSetResults();
 

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

@@ -57,9 +57,12 @@
 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;
 import org.cytoscape.work.TaskMonitor;
+import org.cytoscape.work.TaskMonitor.Level;
 
 /**
  * Created by User: risserlin Date: May 1, 2009 Time: 9:10:22 AM
@@ -72,53 +75,32 @@
  * rank but also have three bland columns.
  *
  */
-public class RanksFileReaderTask extends AbstractTask {
+public class RanksFileReaderTask extends AbstractTask implements ObservableTask {
 
-	private String RankFileName;
-	private EMDataSet dataset;
+	public enum UnsortedRanksStrategy {
+		LOG_WARNING,
+		FAIL_IMMEDIATELY;
+	}
+	
+	private final String RankFileName;
+	private final EMDataSet dataset;
 	private String ranks_name;
+	
+	private final UnsortedRanksStrategy unsortedRanksStrategy;
 
 
 	//distinguish between load from enrichment map input panel and heatmap interface
 	private boolean loadFromHeatmap = false;
+	private boolean sorted = true;
+	
 
 
-	/**
-	 * Class constructor
-	 *
-	 * @param rankFileName - file name of ranks file
-	 * @param dataset - which dataset is this rank file related to (dataset 1 or  dataset 2)
-	 */
-	public RanksFileReaderTask(String rankFileName, EMDataSet dataset, boolean loadFromHeatmap) {
+	public RanksFileReaderTask(String rankFileName, EMDataSet dataset, String ranks_name, boolean loadFromHeatmap, UnsortedRanksStrategy unsortedRanksStrategy) {
 		this.RankFileName = rankFileName;
-		this.dataset = dataset;
-		this.loadFromHeatmap = loadFromHeatmap;
-	}
-
-	/**
-	 * Class constructor - curent task monitor specified.
-	 *
-	 * @param rankFileName - file name of ranks file
-	 * @param dataset - which dataset is this rank file related to (dataset 1 or  dataset 2)
-	 */
-	public RanksFileReaderTask(String rankFileName, EMDataSet dataset, String ranks_name, boolean loadFromHeatmap) {
-		RankFileName = rankFileName;
 		this.ranks_name = ranks_name;
 		this.dataset = dataset;
 		this.loadFromHeatmap = loadFromHeatmap;
-	}
-
-	/**
-	 * Class constructor - for late loaded rank file that aren't specific to a dataset.
-	 *
-	 * @param params - enrichment map parameters for current map
-	 * @param rankFileName - file name of ranks file
-	 * @param ranks_name - name of rankings to be used in heat map drop down to refer to it.
-	 */
-	public RanksFileReaderTask(String rankFileName, String ranks_name, boolean loadFromHeatmap) {
-		this.RankFileName = rankFileName;
-		this.ranks_name = ranks_name;
-		this.loadFromHeatmap = loadFromHeatmap;
+		this.unsortedRanksStrategy = unsortedRanksStrategy;
 	}
 
 
@@ -153,6 +135,9 @@ public void parse(TaskMonitor taskMonitor) throws IOException {
 		 */
 
 		int nScores = 0; //number of found scores
+		double prevScore = Double.MAX_VALUE;
+		boolean sorted = true;
+		
 		for(int i = 0; i < lines.size(); i++) {
 			String line = lines.get(i);
 
@@ -225,12 +210,25 @@ public void parse(TaskMonitor taskMonitor) throws IOException {
 			int percentComplete = (int) (((double) currentProgress / maxValue) * 100);
 			taskMonitor.setProgress(percentComplete);
 			currentProgress++;
-
+			
+			if(score > prevScore) {
+				sorted = false;
+			}
+			prevScore = score;
 		}
 
 		//the none of the genes are in the gene list
 		if(ranks.isEmpty()) {
-			throw new IllegalThreadStateException("None of the genes in the rank file are found in the expression file.  Make sure the identifiers of the two files match.");
+			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.");
+		}
+		
+		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);
+			}
 		}
 
 		//remove Null values from collector
@@ -300,4 +298,13 @@ public void run(TaskMonitor taskMonitor) throws Exception {
 		taskMonitor.setTitle("Parsing Ranks file");
 		parse(taskMonitor);
 	}
+
+	public boolean isSorted() {
+		return sorted;
+	}
+	
+	@Override
+	public <R> R getResults(Class<? extends R> type) {
+		return null;
+	}
 }

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/task/CreateEnrichmentMapTaskFactory.java

@@ -34,7 +34,6 @@
 import org.baderlab.csplugins.enrichmentmap.parsers.ParseGenericEnrichmentResults;
 import org.baderlab.csplugins.enrichmentmap.parsers.RanksFileReaderTask;
 import org.baderlab.csplugins.enrichmentmap.resolver.DataSetResolver;
-import org.baderlab.csplugins.enrichmentmap.task.InitializeGenesetsOfInterestTask.MissingGenesetStrategy;
 import org.baderlab.csplugins.enrichmentmap.util.Baton;
 import org.cytoscape.service.util.CyServiceRegistrar;
 import org.cytoscape.work.AbstractTask;
@@ -66,25 +65,24 @@ public CreateEnrichmentMapTaskFactory(@Assisted EMCreationParameters params, @As
 		this.params = params;
 	}
 
-	
 	public TaskIterator createTaskIterator() {
-		return createTaskIterator(MissingGenesetStrategy.FAIL_IMMEDIATELY, ParseGSEAEnrichmentStrategy.FAIL_IMMEDIATELY);
+		return createTaskIterator(TaskErrorStrategies.commandDefaults());
 	}
 
-	public TaskIterator createTaskIterator(MissingGenesetStrategy genesetStrategy, ParseGSEAEnrichmentStrategy gseaStrategy) {
+	public TaskIterator createTaskIterator(TaskErrorStrategies strategies) {
 		TaskIterator tasks = new TaskIterator();
 		if(dataSets.isEmpty())
 			return tasks;
 		tasks.append(new TitleTask("Building EnrichmentMap"));
 
 		EnrichmentMap map = new EnrichmentMap(params, serviceRegistrar);
-		createTasks(map, tasks, genesetStrategy, gseaStrategy);
+		createTasks(map, tasks, strategies);
 
 		return tasks;
 	}
 
 
-	private void createTasks(EnrichmentMap map, TaskIterator tasks, MissingGenesetStrategy genesetStrategy, ParseGSEAEnrichmentStrategy gseaStrategy) {
+	private void createTasks(EnrichmentMap map, TaskIterator tasks, TaskErrorStrategies strategies) {
 		for(DataSetParameters dataSetParameters : dataSets) {
 			String datasetName = dataSetParameters.getName();
 			Method method = dataSetParameters.getMethod();
@@ -120,7 +118,7 @@ private void createTasks(EnrichmentMap map, TaskIterator tasks, MissingGenesetSt
 					tasks.append(new GMTFileReaderTask(dataset));
 
 				// Load the enrichments 
-				tasks.append(getEnrichmentParserTasks(dataset, gseaStrategy));
+				tasks.append(getEnrichmentParserTasks(dataset, strategies.getGseaStrategy()));
 
 				// Load expression file if specified in the dataset.
 				// If there is no expression file then create a dummy file to associate with this dataset so we can still use the expression viewer (heat map)
@@ -132,15 +130,15 @@ private void createTasks(EnrichmentMap map, TaskIterator tasks, MissingGenesetSt
 				// Load ranks if present
 				String ranksName = dataset.getMethod() == Method.GSEA ? Ranking.GSEARanking : datasetName;
 				if(dataset.getRanksByName(ranksName) != null)
-					tasks.append(new RanksFileReaderTask(files.getRankedFile(), dataset, ranksName, false));
+					tasks.append(new RanksFileReaderTask(files.getRankedFile(), dataset, ranksName, false, strategies.getRanksStrategy()));
 
 				if(!Strings.isNullOrEmpty(dataset.getDataSetFiles().getClassFile()))
 					tasks.append(new ClassFileReaderTask(dataset));
 			}
 		}
 
 		// Filter out genesets that don't pass the p-value and q-value thresholds
-		InitializeGenesetsOfInterestTask genesetsTask = new InitializeGenesetsOfInterestTask(map, genesetStrategy);
+		InitializeGenesetsOfInterestTask genesetsTask = new InitializeGenesetsOfInterestTask(map, strategies.getGenesetStrategy());
 		tasks.append(genesetsTask);
 
 		// Trim the genesets to only contain the genes that are in the data file.

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/task/TaskErrorStrategies.java

@@ -0,0 +1,70 @@
+package org.baderlab.csplugins.enrichmentmap.task;
+
+import java.util.Objects;
+
+import org.baderlab.csplugins.enrichmentmap.parsers.ParseGSEAEnrichmentResults.ParseGSEAEnrichmentStrategy;
+import org.baderlab.csplugins.enrichmentmap.parsers.RanksFileReaderTask.UnsortedRanksStrategy;
+import org.baderlab.csplugins.enrichmentmap.task.InitializeGenesetsOfInterestTask.MissingGenesetStrategy;
+
+public class TaskErrorStrategies {
+
+	private final MissingGenesetStrategy genesetStrategy;
+	private final ParseGSEAEnrichmentStrategy gseaStrategy;
+	private final UnsortedRanksStrategy ranksStrategy;
+	
+	
+	public TaskErrorStrategies(MissingGenesetStrategy genesetStrategy, ParseGSEAEnrichmentStrategy gseaStrategy, UnsortedRanksStrategy ranksStrategy) {
+		this.genesetStrategy = Objects.requireNonNull(genesetStrategy);
+		this.gseaStrategy = Objects.requireNonNull(gseaStrategy);
+		this.ranksStrategy = Objects.requireNonNull(ranksStrategy);
+	}
+	
+	
+	public static TaskErrorStrategies dialogDefaults() {
+		return new TaskErrorStrategies(
+				MissingGenesetStrategy.FAIL_AT_END, 
+				ParseGSEAEnrichmentStrategy.FAIL_IMMEDIATELY, 
+				UnsortedRanksStrategy.FAIL_IMMEDIATELY);
+	}
+	
+	public static TaskErrorStrategies commandDefaults() {
+		return new TaskErrorStrategies(
+				MissingGenesetStrategy.FAIL_AT_END, 
+				ParseGSEAEnrichmentStrategy.FAIL_IMMEDIATELY, 
+				UnsortedRanksStrategy.LOG_WARNING);
+	}
+	
+	public static TaskErrorStrategies testDefaults() {
+		return new TaskErrorStrategies(
+				MissingGenesetStrategy.FAIL_IMMEDIATELY, 
+				ParseGSEAEnrichmentStrategy.FAIL_IMMEDIATELY, 
+				UnsortedRanksStrategy.FAIL_IMMEDIATELY);
+	}
+	
+
+	public MissingGenesetStrategy getGenesetStrategy() {
+		return genesetStrategy;
+	}
+
+	public ParseGSEAEnrichmentStrategy getGseaStrategy() {
+		return gseaStrategy;
+	}
+
+	public UnsortedRanksStrategy getRanksStrategy() {
+		return ranksStrategy;
+	}
+	
+	
+	public TaskErrorStrategies with(MissingGenesetStrategy genesetStrategy) {
+		return new TaskErrorStrategies(genesetStrategy, gseaStrategy, ranksStrategy);
+	}
+	
+	public TaskErrorStrategies with(ParseGSEAEnrichmentStrategy gseaStrategy) {
+		return new TaskErrorStrategies(genesetStrategy, gseaStrategy, ranksStrategy);
+	}
+	
+	public TaskErrorStrategies with(UnsortedRanksStrategy ranksStrategy) {
+		return new TaskErrorStrategies(genesetStrategy, gseaStrategy, ranksStrategy);
+	}
+	
+}

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/task/UnsortedRanksException.java

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

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

@@ -0,0 +1,34 @@
+package org.baderlab.csplugins.enrichmentmap.util;
+
+import org.cytoscape.work.TaskMonitor;
+
+public class DelegatingTaskMonitor implements TaskMonitor {
+
+	
+	private final TaskMonitor delegate;
+	
+	public DelegatingTaskMonitor(TaskMonitor delegate) {
+		this.delegate = delegate;
+	}
+	
+	@Override
+	public void setTitle(String title) {
+		delegate.setTitle(title);
+	}
+
+	@Override
+	public void setProgress(double progress) {
+		delegate.setProgress(progress);
+	}
+
+	@Override
+	public void setStatusMessage(String statusMessage) {
+		delegate.setStatusMessage(statusMessage);
+	}
+
+	@Override
+	public void showMessage(Level level, String message) {
+		delegate.showMessage(level, message);
+	}
+
+}