Add pattern argument to mastermap command. Refs #374

Author: mikekucera

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

@@ -1,6 +1,8 @@
 package org.baderlab.csplugins.enrichmentmap.commands;
 
 import java.io.File;
+import java.nio.file.FileSystems;
+import java.nio.file.PathMatcher;
 import java.util.Arrays;
 import java.util.List;
 
@@ -40,6 +42,9 @@ public class MastermapCommandTask extends AbstractTask implements ObservableTask
 	@Inject
 	public FilterTunables filterArgs;
 
+	@Tunable(description="A glob-style path filter. Sub-folders inside the root folder that do not match the pattern will be ignored. "
+			+ "For more details on syntax see https://docs.oracle.com/javase/8/docs/api/java/nio/file/FileSystem.html#getPathMatcher-java.lang.String-")
+	public String pattern;
 
 	@Inject private SynchronousTaskManager<?> taskManager;
 	@Inject private CreateEnrichmentMapTaskFactory.Factory taskFactoryFactory;
@@ -60,6 +65,12 @@ public void run(TaskMonitor tm) throws Exception {
 
 		// Scan root folder (note: throws exception if no data sets were found)
 		ResolverTask resolverTask = new ResolverTask(rootFolder);
+		
+		if(pattern != null) {
+			PathMatcher matcher = FileSystems.getDefault().getPathMatcher("glob:" + pattern);
+			resolverTask.setPathMatcher(matcher);
+		}
+		
 		taskManager.execute(new TaskIterator(resolverTask)); // blocks
 		List<DataSetParameters> dataSets = resolverTask.getDataSetResults();
 

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

@@ -1,6 +1,8 @@
 package org.baderlab.csplugins.enrichmentmap.commands;
 
 import java.io.File;
+import java.nio.file.FileSystems;
+import java.nio.file.PathMatcher;
 import java.util.Arrays;
 import java.util.List;
 
@@ -25,6 +27,10 @@ public class MastermapListCommandTask extends AbstractTask implements Observable
 			+ "The files will be scanned and automatically grouped into data sets. Sub-folders will be scanned up to one level deep.")
 	public File rootFolder;
 
+	@Tunable(description="A glob-style path filter. Sub-folders inside the root folder that do not match the pattern will be ignored. "
+			+ "For more details on syntax see https://docs.oracle.com/javase/8/docs/api/java/nio/file/FileSystem.html#getPathMatcher-java.lang.String-")
+	public String pattern;
+	
 	@Inject private SynchronousTaskManager<?> taskManager;
 
 	private List<DataSetParameters> results;
@@ -40,8 +46,13 @@ public void run(TaskMonitor tm) throws Exception {
 			throw new IllegalArgumentException("rootFolder is invalid: " + rootFolder);
 		}
 
-		// Scan root folder (note: throws exception if no data sets were found)
 		ResolverTask resolverTask = new ResolverTask(rootFolder);
+		
+		if(pattern != null) {
+			PathMatcher matcher = FileSystems.getDefault().getPathMatcher("glob:" + pattern);
+			resolverTask.setPathMatcher(matcher);
+		}
+		
 		taskManager.execute(new TaskIterator(resolverTask)); // blocks
 		results = resolverTask.getDataSetResults();
 

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/resolver/CancelStatus.java

@@ -1,16 +1,13 @@
 package org.baderlab.csplugins.enrichmentmap.resolver;
 
+@FunctionalInterface
 public interface CancelStatus {
 
-	public void cancel();
-	
 	public boolean isCancelled();
 
-	
 	public static CancelStatus notCancelable() {
 		return new CancelStatus() {
 			@Override public boolean isCancelled() { return false; }
-			@Override public void cancel() { }
 		};
 	}
 }

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/resolver/ResolverTask.java

@@ -3,6 +3,7 @@
 import java.io.File;
 import java.nio.file.Files;
 import java.nio.file.Path;
+import java.nio.file.PathMatcher;
 import java.util.ArrayList;
 import java.util.List;
 
@@ -11,11 +12,14 @@
 import org.cytoscape.work.ObservableTask;
 import org.cytoscape.work.TaskMonitor;
 
-public class ResolverTask extends AbstractTask implements ObservableTask, CancelStatus {
+public class ResolverTask extends AbstractTask implements ObservableTask {
 
 	private final List<Path> paths = new ArrayList<>();
 	private final List<DataSetParameters> results = new ArrayList<>();
 
+	private PathMatcher matcher = null;
+	
+	
 	public ResolverTask(Path root) {
 		paths.add(root);
 	}
@@ -29,6 +33,11 @@ public ResolverTask(List<File> files) {
 			paths.add(file.toPath());
 	}
 
+	public void setPathMatcher(PathMatcher matcher) {
+		this.matcher = matcher;
+	}
+	
+	
 	@Override
 	public void run(TaskMonitor tm) {
 		tm.setTitle("EnrichmentMap");
@@ -39,19 +48,24 @@ public void run(TaskMonitor tm) {
 			Path path = paths.get(0);
 			if(Files.isDirectory(path)) {
 				for(File subdirectory : path.toFile().listFiles(File::isDirectory)) {
-					paths.add(subdirectory.toPath());
+					Path subDirPath = subdirectory.toPath();
+					if(matcher == null || matcher.matches(subDirPath.getFileName())) {
+						paths.add(subDirPath);
+					}
 				}
 			}
 		}
 
 		List<Path> miscFiles = new ArrayList<>();
 
 		for(Path path : paths) {
-			if(cancelled)
-				break;
+			if(cancelled) {
+				results.clear();
+				return;
+			}
 			try {
 				if(Files.isDirectory(path)) {
-					List<DataSetParameters> dataSets = DataSetResolver.guessDataSets(path, this);
+					List<DataSetParameters> dataSets = DataSetResolver.guessDataSets(path, () -> cancelled);
 					results.addAll(dataSets);
 				} else {
 					miscFiles.add(path);
@@ -62,8 +76,12 @@ public void run(TaskMonitor tm) {
 		}
 
 		try {
+			if(cancelled) {
+				results.clear();
+				return;
+			}
 			if(!miscFiles.isEmpty()) {
-				List<DataSetParameters> dataSets = DataSetResolver.guessDataSets(miscFiles, this);
+				List<DataSetParameters> dataSets = DataSetResolver.guessDataSets(miscFiles, () -> cancelled);
 				results.addAll(dataSets);
 			}
 		} catch(Exception e) {
@@ -83,9 +101,4 @@ public List<DataSetParameters> getDataSetResults() {
 		return results;
 	}
 
-	@Override
-	public boolean isCancelled() {
-		return cancelled;
-	}
-	
 }