Merge pull request #10 from scijava/batch-service

Add BatchService and integrate into search bar

Author: imagejan

pom.xml

@@ -8,7 +8,7 @@
 	<parent>
 		<groupId>org.scijava</groupId>
 		<artifactId>pom-scijava</artifactId>
-		<version>17.1.1</version>
+		<version>18.0.0</version>
 		<relativePath />
 	</parent>
 
@@ -100,17 +100,27 @@
 			<artifactId>scijava-common</artifactId>
 		</dependency>
 		<dependency>
+			<!-- TODO: remove this dependency when table support moved to SciJava -->
 			<groupId>net.imagej</groupId>
 			<artifactId>imagej</artifactId>
 		</dependency>
 		<dependency>
 			<groupId>org.scijava</groupId>
 			<artifactId>scijava-ui-swing</artifactId>
 		</dependency>
+		<dependency>
+			<groupId>org.scijava</groupId>
+			<artifactId>scijava-search</artifactId>
+		</dependency>
 		<dependency>
 			<groupId>commons-io</groupId>
 			<artifactId>commons-io</artifactId>
 			<version>2.4</version>
 		</dependency>
+		<dependency>
+			<groupId>junit</groupId>
+			<artifactId>junit</artifactId>
+			<scope>test</scope>
+		</dependency>
 	</dependencies>
 </project>

src/main/java/org/scijava/batch/BatchModuleSearchActionFactory.java

@@ -0,0 +1,34 @@
+package org.scijava.batch;
+
+import org.scijava.plugin.Parameter;
+import org.scijava.plugin.Plugin;
+import org.scijava.search.DefaultSearchAction;
+import org.scijava.search.SearchAction;
+import org.scijava.search.SearchActionFactory;
+import org.scijava.search.SearchResult;
+import org.scijava.search.module.ModuleSearchResult;
+
+/**
+ * Search action for executing a SciJava module in batch mode.
+ *
+ * @author Jan Eglinger
+ */
+@Plugin(type = SearchActionFactory.class)
+public class BatchModuleSearchActionFactory implements SearchActionFactory {
+
+	@Parameter
+	private BatchService batchService;
+
+	@Override
+	public boolean supports(final SearchResult result) {
+		return (result instanceof ModuleSearchResult)
+				&& batchService.supports(((ModuleSearchResult) result).info());
+	}
+
+	@Override
+	public SearchAction create(final SearchResult result) {
+		return new DefaultSearchAction("Batch", true, () -> {
+			batchService.run(((ModuleSearchResult) result).info());
+		});
+	}
+}

src/main/java/org/scijava/batch/BatchService.java

@@ -0,0 +1,44 @@
+package org.scijava.batch;
+
+import java.util.List;
+import java.util.stream.Collectors;
+import java.util.stream.StreamSupport;
+
+import org.scijava.module.ModuleInfo;
+import org.scijava.module.ModuleItem;
+import org.scijava.service.SciJavaService;
+
+public interface BatchService extends SciJavaService {
+	/**
+	 * Returns true if {@code moduleInfo} has at least one input item whose type
+	 * is supported by this service
+	 */
+	default public boolean supports(ModuleInfo moduleInfo) {
+		for (ModuleItem<?> input : moduleInfo.inputs()) {
+			if (supports(input.getType()))
+				return true;
+		}
+		return false;
+	}
+
+	/**
+	 * Returns true if {@code type} can be populated with batch inputs provided
+	 * by this service
+	 */
+	public boolean supports(Class<?> type);
+
+	/**
+	 * Run the module described by {@link ModuleInfo} in batch.
+	 */
+	public void run(ModuleInfo moduleInfo);
+
+	/**
+	 * A collection of input {@link ModuleItem}s of the given {@link ModuleInfo}
+	 * that are supported (i.e. can be batch-processed) by this service
+	 */
+	default public List<ModuleItem<?>> batchableInputs(ModuleInfo moduleInfo) {
+		return StreamSupport.stream(moduleInfo.inputs().spliterator(), false)
+				.filter(item -> supports(item.getType()))
+				.collect(Collectors.toList());
+	}
+}

src/main/java/org/scijava/batch/FileBatchService.java

@@ -0,0 +1,37 @@
+package org.scijava.batch;
+
+import java.io.File;
+import java.util.HashMap;
+
+import org.scijava.Priority;
+import org.scijava.command.CommandService;
+import org.scijava.module.ModuleInfo;
+import org.scijava.plugin.Parameter;
+import org.scijava.plugin.Plugin;
+import org.scijava.service.AbstractService;
+import org.scijava.service.Service;
+
+@Plugin(type = Service.class, priority = Priority.LOW)
+public final class FileBatchService extends AbstractService implements
+		BatchService {
+
+	@Parameter
+	private CommandService commandService;
+
+	/**
+	 * Returns true if {@code type} is a {@link File}.
+	 */
+	@Override
+	public boolean supports(Class<?> type) {
+		return type.isAssignableFrom(File.class);
+	}
+
+	@Override
+	public void run(ModuleInfo moduleInfo) {
+		// Call ModuleBatchProcessor with input moduleInfo
+		HashMap<String, Object> inputMap = new HashMap<>();
+		inputMap.put("moduleInfo", moduleInfo);
+		commandService.run(ModuleBatchProcessor.class, true, inputMap);
+	}
+
+}

src/main/java/org/scijava/batch/ModuleBatchProcessor.java

@@ -7,6 +7,7 @@
 import java.util.Map.Entry;
 import java.util.concurrent.ExecutionException;
 import java.util.concurrent.Future;
+import java.util.stream.Collectors;
 
 import net.imagej.table.Column;
 import net.imagej.table.DefaultGenericTable;
@@ -15,8 +16,7 @@
 import org.scijava.ItemIO;
 import org.scijava.command.Command;
 import org.scijava.command.DynamicCommand;
-import org.scijava.convert.ConvertService;
-import org.scijava.log.LogService;
+import org.scijava.log.Logger;
 import org.scijava.module.Module;
 import org.scijava.module.ModuleInfo;
 import org.scijava.module.ModuleItem;
@@ -29,17 +29,17 @@
 @Plugin(type = Command.class, label = "Choose batch processing parameters", initializer = "initInputChoice")
 public class ModuleBatchProcessor extends DynamicCommand {
 	@Parameter
-	private ModuleService modules;
+	private ModuleService moduleService;
 
 	@Parameter
-	private ConvertService convert;
-	
+	private BatchService batchService;
+
 	@Parameter
-	private LogService log;
-	
+	private Logger log;
+
 	@Parameter
 	private ModuleInfo moduleInfo; // to be provided at runtime!
-	
+
 	@Parameter(label = "Which input parameter to batch?", persist = false)
 	private String inputChoice;
 
@@ -57,23 +57,15 @@ public class ModuleBatchProcessor extends DynamicCommand {
 
 	protected void initInputChoice() {
 		MutableModuleItem<String> choiceInput = getInfo().getMutableInput("inputChoice", String.class);
-		// get compatible inputs from module
-		ArrayList<String> compatibleInputs = new ArrayList<>();
-		for (ModuleItem<?> input : moduleInfo.inputs()) {
-			// TODO consider replacing by isAssignableFrom
-			if (convert.supports(new File(""), input.getType())) {
-				// if we can convert a File to the given input,
-				// add it to the list of compatible inputs
-				compatibleInputs.add(input.getName());
-			}
-		}
-		// if only single input left, fill module input and resolve 'inputChoice'
+		// Get compatible inputs for moduleInfo
+		List<ModuleItem<?>> compatibleInputs = batchService
+				.batchableInputs(moduleInfo);
 		if (compatibleInputs.size() == 1) {
-			choiceInput.setValue(this, compatibleInputs.get(0));
+			choiceInput.setValue(this, compatibleInputs.get(0).getName());
 			resolveInput("inputChoice");
-		}
-		else if (compatibleInputs.size() > 1) {
-			choiceInput.setChoices(compatibleInputs);
+		} else if (compatibleInputs.size() > 1) {
+			choiceInput.setChoices(compatibleInputs.stream()
+					.map(ModuleItem::getName).collect(Collectors.toList()));
 		}
 	}
 
@@ -84,7 +76,7 @@ public void run() {
 		// mark inputChoice as resolved, then harvest script parameters (i.e. run)
 		ModuleItem<File> fileInput = moduleInfo.getInput(inputChoice, File.class);
 		// TODO check if conversion needed?
-		Module scriptModule = modules.createModule(moduleInfo);
+		Module scriptModule = moduleService.createModule(moduleInfo);
 		scriptModule.resolveInput(inputChoice);
 
 		/* Create output Table and mark all outputs as resolved */
@@ -117,7 +109,7 @@ private boolean processFile(Module module, ModuleItem<File> fileInput, File file
 		fileInput.setValue(module, file);
 		outputTable.appendRow(file.getName());
 
-		Future<Module> instance = modules.run(module, true);
+		Future<Module> instance = moduleService.run(module, true);
 		try {
 			// run the script
 			Map<String, Object> outputs = instance.get().getOutputs();

src/test/java/org/scijava/batch/BatchServiceTest.java

@@ -0,0 +1,28 @@
+package org.scijava.batch;
+
+import static org.junit.Assert.assertNotNull;
+
+import org.junit.After;
+import org.junit.Test;
+import org.scijava.Context;
+
+public class BatchServiceTest {
+	
+	private Context context;
+
+	@After
+	public void disposeContext() {
+		if (context != null) {
+			context.dispose();
+			context = null;
+		}
+	}
+
+	@Test
+	public void testContext() {
+		context = new Context(BatchService.class);
+		final BatchService batchService =
+			context.getService(BatchService.class);
+		assertNotNull(batchService);
+	}
+}