Add input provider plugins

This change makes batch processing extensible by allowing plugins implementing the BatchInputProvider interface to support custom script parameter inputs, such as net.imagej.Dataset which will be provided in the imagej-plugins-batch project. Because BatchService now extends HandlerService, I needed to rename the supports() methods more concisely into supportsModule() and supportsItem(), to avoid overriding supports() from HandlerService. Since we are still pre-1.0.0, we can change the API freely, but bump the version to 0.2.0-SNAPSHOT to reflect this API change.
scijava · imagejan · Aug 10, 2018 · Jul 18, 2018 · Aug 10, 2018 · c503a13ae668916c13985dbb3bbae69b83df6f7c
commit c503a13ae668916c13985dbb3bbae69b83df6f7c
diff --git a/pom.xml b/pom.xml
@@ -10,7 +10,7 @@
 	</parent>
 
 	<artifactId>batch-processor</artifactId>
-	<version>0.1.4-SNAPSHOT</version>
+	<version>0.2.0-SNAPSHOT</version>
 
 	<name>Batch Processor</name>
 	<description>A Batch Processor for SciJava Modules and Scripts</description>

diff --git a/src/main/java/org/scijava/batch/BatchModuleSearchActionFactory.java b/src/main/java/org/scijava/batch/BatchModuleSearchActionFactory.java
@@ -22,12 +22,12 @@ public class BatchModuleSearchActionFactory implements SearchActionFactory {
 	@Override
 	public boolean supports(final SearchResult result) {
 		return (result instanceof ModuleSearchResult)
-				&& batchService.supports(((ModuleSearchResult) result).info());
+				&& batchService.supportsModule(((ModuleSearchResult) result).info());
 	}
 
 	@Override
 	public SearchAction create(final SearchResult result) {
-		return new DefaultSearchAction("Batch", true, () -> {
+		return new DefaultSearchAction("Batch", () -> {
 			batchService.run(((ModuleSearchResult) result).info());
 		});
 	}

diff --git a/src/main/java/org/scijava/batch/BatchService.java b/src/main/java/org/scijava/batch/BatchService.java
@@ -4,28 +4,34 @@
 import java.util.stream.Collectors;
 import java.util.stream.StreamSupport;
 
+import org.scijava.batch.input.BatchInput;
+import org.scijava.batch.input.BatchInputProvider;
+import org.scijava.module.Module;
 import org.scijava.module.ModuleInfo;
 import org.scijava.module.ModuleItem;
+import org.scijava.plugin.HandlerService;
 import org.scijava.service.SciJavaService;
 
-public interface BatchService extends SciJavaService {
+public interface BatchService extends HandlerService<BatchInput, BatchInputProvider<?>>, 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) {
+	default public boolean supportsModule(ModuleInfo moduleInfo) {
 		for (ModuleItem<?> input : moduleInfo.inputs()) {
-			if (supports(input.getType()))
+			if (supportsItem(input))
 				return true;
 		}
 		return false;
 	}
+
+	//default public getHandler(ModuleItem)
 
 	/**
 	 * Returns true if {@code type} can be populated with batch inputs provided
 	 * by this service
 	 */
-	public boolean supports(Class<?> type);
+	public boolean supportsItem(ModuleItem<?> moduleItem);
 
 	/**
 	 * Run the module described by {@link ModuleInfo} in batch.
@@ -38,7 +44,14 @@ default public boolean supports(ModuleInfo moduleInfo) {
 	 */
 	default public List<ModuleItem<?>> batchableInputs(ModuleInfo moduleInfo) {
 		return StreamSupport.stream(moduleInfo.inputs().spliterator(), false)
-				.filter(item -> supports(item.getType()))
+				.filter(item -> supportsItem(item))
 				.collect(Collectors.toList());
 	}
+
+	/**
+	 * Fill a provided ModuleItem with a given input object
+	 * @param <I>
+	 */
+	public <I> void fillInput(Module module, ModuleItem<?> moduleItem, I inputObject);
+
 }
diff --git a/src/main/java/org/scijava/batch/FileBatchService.java b/src/main/java/org/scijava/batch/FileBatchService.java
@@ -4,30 +4,48 @@
 import java.util.HashMap;
 
 import org.scijava.Priority;
+import org.scijava.batch.input.BatchInput;
+import org.scijava.batch.input.BatchInputProvider;
 import org.scijava.command.CommandService;
 import org.scijava.log.LogService;
+import org.scijava.module.Module;
 import org.scijava.module.ModuleInfo;
+import org.scijava.module.ModuleItem;
+import org.scijava.plugin.AbstractHandlerService;
 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 {
+public final class FileBatchService extends AbstractHandlerService<BatchInput, BatchInputProvider<?>> implements BatchService {
 
 	@Parameter
 	private LogService log;
-	
+
 	@Parameter
 	private CommandService commandService;
 
 	/**
 	 * Returns true if {@code type} is a {@link File}.
 	 */
 	@Override
-	public boolean supports(Class<?> type) {
-		return type.isAssignableFrom(File.class);
+	public boolean supportsItem(ModuleItem<?> moduleItem) {
+		BatchInputProvider<?> handler = getHandler(new BatchInput(File.class, moduleItem));
+		if (handler == null) {
+			return false;
+		}
+		return handler.canProvide(mo
10000
duleItem);
+	}
+
+	@SuppressWarnings("unchecked")
+	@Override
+	public <I> void fillInput(Module module, ModuleItem<?> moduleItem, I inputObject) {
+		BatchInputProvider<File> handler = (BatchInputProvider<File>) getHandler(new BatchInput(File.class, moduleItem));
+		if (handler == null) {
+			log.error("No handler found for input: " + moduleItem.getName());
+			return;
+		}
+		handler.populateInput(module, moduleItem, (File) inputObject);
 	}
 
 	@Override
@@ -37,10 +55,30 @@ public void run(ModuleInfo moduleInfo) {
 			log.error("No compatible inputs (of type File) found.");
 			return;
 		}
+
+		// 1) get input ModuleItems
+		// 2) choose ModuleItem
+		// 3) get suitable BatchInputProvider
+		// 4) get Iterator for ModuleItem
+
+		//for (getHandler(new BatchInput(File.class, moduleItem)).iterate(fileList)) {
+		//}
+
 		// Call ModuleBatchProcessor with input moduleInfo
 		HashMap<String, Object> inputMap = new HashMap<>();
 		inputMap.put("moduleInfo", moduleInfo);
 		commandService.run(ModuleBatchProcessor.class, true, inputMap);
 	}
 
+	@SuppressWarnings({ "unchecked", "rawtypes" })
+	@Override
+	public Class<BatchInputProvider<?>> getPluginType() {
+		return (Class) BatchInputProvider.class;
+	}
+
+	@Override
+	public Class<BatchInput> getType() {
+		return BatchInput.class;
+	}
+
 }
diff --git a/src/main/java/org/scijava/batch/ModuleBatchProcessor.java b/src/main/java/org/scijava/batch/ModuleBatchProcessor.java
@@ -27,7 +27,7 @@
 import org.scijava.widget.FileWidget;
 
 @Plugin(type = Command.class, label = "Choose batch processing parameters", initializer = "initInputChoice")
-public class ModuleBatchProcessor extends DynamicCommand {
+public class ModuleBatchProcessor<T> extends DynamicCommand {
 	@Parameter
 	private ModuleService moduleService;
 
@@ -66,6 +66,8 @@ protected void initInputChoice() {
 		} else if (compatibleInputs.size() > 1) {
 			choiceInput.setChoices(compatibleInputs.stream()
 					.map(ModuleItem::getName).collect(Collectors.toList()));
+		} else {
+			log.error("No compatible inputs found. Unable to initialize input choice.");
 		}
 	}
 
@@ -74,7 +76,7 @@ protected void initInputChoice() {
 	@Override
 	public void run() {
 		// mark inputChoice as resolved, then harvest script parameters (i.e. run)
-		ModuleItem<File> fileInput = moduleInfo.getInput(inputChoice, File.class);
+		ModuleItem<?> inputModuleItem = moduleInfo.getInput(inputChoice);
 		// TODO check if conversion needed?
 		Module scriptModule = moduleService.createModule(moduleInfo);
 		scriptModule.resolveInput(inputChoice);
@@ -89,8 +91,8 @@ public void run() {
 			scriptModule.resolveOutput(outputKey);
 		}
 
-		for (File file: inputFileList) {
-			if(!processFile(scriptModule, fileInput, file)) {
+		for (File file : inputFileList) {
+			if(!processFile(scriptModule, inputModuleItem, file)) {
 				log.warn("Terminating batch process.");
 				break; // end for loop
 			}
@@ -105,8 +107,9 @@ public void run() {
 	// -- Helper methods --
 
 	@SuppressWarnings("unchecked")
-	private boolean processFile(Module module, ModuleItem<File> fileInput, File file) {
-		fileInput.setValue(module, file);
+	private boolean processFile(Module module, ModuleItem<?> inputModuleItem, File file) {
+		batchService.fillInput(module, inputModuleItem, file);
+		//fileInput.setValue(module, file);
 		outputTable.appendRow(file.getName());
 
 		Future<Module> instance = moduleService.run(module, true);

diff --git a/src/main/java/org/scijava/batch/input/BatchInput.java b/src/main/java/org/scijava/batch/input/BatchInput.java
@@ -0,0 +1,36 @@
+package org.scijava.batch.input;
+
+import java.lang.reflect.Type;
+
+import org.scijava.module.ModuleItem;
+
+/**
+ * Currency for use with {@link BatchInputProvider} methods
+ * 
+ * 
+ * 
+ * @author Jan Eglinger
+ *
+ */
+public class BatchInput {
+	private final Type srcType;
+	private final ModuleItem<?> destItem;
+
+	public BatchInput(final Class<?> srcClass, final ModuleItem<?> destItem) {
+		this.srcType = srcClass;
+		this.destItem = destItem;
+	}
+
+	public BatchInput(final Type srcType, final ModuleItem<?> destItem) {
+		this.srcType = srcType;
+		this.destItem = destItem;
+	}
+
+	public Type sourceType() {
+		return srcType;
+	}
+
+	public ModuleItem<?> moduleItem() {
+		return destItem;
+	}
+}
diff --git a/src/main/java/org/scijava/batch/input/BatchInputProvider.java b/src/main/java/org/scijava/batch/input/BatchInputProvider.java
@@ -0,0 +1,32 @@
+
+package org.scijava.batch.input;
+
+import org.scijava.module.Module;
+import org.scijava.module.ModuleItem;
+import org.scijava.plugin.HandlerPlugin;
+
+public interface BatchInputProvider<I> extends HandlerPlugin<BatchInput> {
+
+	@Override
+	default public Class<BatchInput> getType() {
+		return BatchInput.class;
+	}
+
+	/**
+	 * Check if a given {@code ModuleItem} can be populated by this input provider.
+	 * Implementations should make sure to not only match the type of objects, but
+	 * also respect possible widget style settings, such as files, directories,
+	 * image files only, etc.
+	 *
+	 * @param moduleItem
+	 *            the input item that needs to be populated
+	 * @return true if this input provider can provide suitable objects
+	 */
+	public boolean canProvide(ModuleItem<?> moduleItem);
+
+	public void populateInput(Module module, ModuleItem<?> moduleItem, I inputObject);
+
+	public String getTargetWidgetStyle(ModuleItem<?> moduleItem);
+
+	// public Iterable<O> iterate(Collection<I> fileList);
+}
diff --git a/src/main/java/org/scijava/batch/input/FileBatchInputProvider.java b/src/main/java/org/scijava/batch/input/FileBatchInputProvider.java
@@ -0,0 +1,65 @@
+
+package org.scijava.batch.input;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.Arrays;
+
+import org.scijava.module.Module;
+import org.scijava.module.ModuleItem;
+import org.scijava.plugin.AbstractHandlerPlugin;
+import org.scijava.plugin.Plugin;
+import org.scijava.widget.FileListWidget;
+import org.scijava.widget.FileWidget;
+
+@Plugin(type = BatchInputProvider.class)
+public class FileBatchInputProvider extends AbstractHandlerPlugin<BatchInput> implements
+	BatchInputProvider<File>
+{
+	@Override
+	public boolean supports(BatchInput input) {
+		return canProvide(input.moduleItem());
+	}
+
+	@Override
+	public boolean canProvide(ModuleItem<?> item) {
+		// we can't provide inputs for saving files
+		return item.getType() == File.class && !hasStyle(item, FileWidget.SAVE_STYLE);
+	}
+
+	@SuppressWarnings("unchecked")
+	@Override
+	public void populateInput(Module module, ModuleItem<?> moduleItem, File inputObject) {
+		((ModuleItem<File>)moduleItem).setValue(module, inputObject);
+	}
+
+	@Override
+	public String getTargetWidgetStyle(ModuleItem<?> item) {
+		ArrayList<String> targetStyles = new ArrayList<>();
+
+		if (hasStyle(item, FileWidget.DIRECTORY_STYLE)) {
+			targetStyles.add(FileListWidget.DIRECTORIES_ONLY);
+		} else {
+			targetStyles.add(FileListWidget.FILES_ONLY);
+		}
+
+		// extensions?
+		String widgetStyle = item.getWidgetStyle();
+		if (widgetStyle != null) {
+			String[] styles = widgetStyle.trim().split("\\s*,\\s*");
+			for (String s : styles) {
+				if (s.startsWith("extensions")) { // TODO: use new constant from FileListWidget
+					targetStyles.add(s);
+				}
+			}			
+		}
+		return String.join(",", targetStyles);
+	}
+
+	private boolean hasStyle(ModuleItem<?> item, String style) {
+		String widgetStyle = item.getWidgetStyle();
+		if (widgetStyle == null) return false;
+		return Arrays.asList(widgetStyle.trim().split("\\s*,\\s*"))
+			.contains(style);
+	}
+}