Improved file inputs for scripts

pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>org.scijava</groupId>
 		<artifactId>pom-scijava</artifactId>
-		<version>13.1.0</version>
+		<version>17.0.0</version>
 		<relativePath />
 	</parent>
 

src/main/java/org/scijava/convert/FileListConverters.java

@@ -0,0 +1,162 @@
+/*
+ * #%L
+ * SciJava Common shared library for SciJava software.
+ * %%
+ * Copyright (C) 2009 - 2017 Board of Regents of the University of
+ * Wisconsin-Madison, Broad Institute of MIT and Harvard, Max Planck
+ * Institute of Molecular Cell Biology and Genetics, University of
+ * Konstanz, and KNIME GmbH.
+ * %%
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ * #L%
+ */
+
+package org.scijava.convert;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.stream.Collectors;
+
+import org.scijava.Priority;
+import org.scijava.plugin.Plugin;
+import org.scijava.util.StringUtils;
+
+/**
+ * A collection of {@link Converter} plugins for going between {@link String},
+ * {@link File} and {@code File[]}.
+ *
+ * @author Jan Eglinger
+ * @author Curtis Rueden
+ */
+public class FileListConverters {
+	// -- String to File (list) converters --
+
+	@Plugin(type = Converter.class, priority = Priority.NORMAL)
+	public static class StringToFileConverter extends
+		AbstractConverter<String, File>
+	{
+
+		@SuppressWarnings("unchecked")
+		@Override
+		public <T> T convert(final Object src, final Class<T> dest) {
+			return (T) new File((String) src);
+		}
+
+		@Override
+		public Class<File> getOutputType() {
+			return File.class;
+		}
+
+		@Override
+		public Class<String> getInputType() {
+			return String.class;
+		}
+
+	}
+
+	@Plugin(type = Converter.class, priority = Priority.NORMAL)
+	public static class StringToFileArrayConverter extends
+		AbstractConverter<String, File[]>
+	{
+
+		@SuppressWarnings("unchecked")
+		@Override
+		public <T> T convert(final Object src, final Class<T> dest) {
+			final String[] tokens = StringUtils.splitUnquoted((String) src, ",");
+			final List<File> fileList = new ArrayList<>();
+			for (final String filePath : tokens) {
+				fileList.add(new File(filePath.replaceAll("^\"|\"$", "")));
+			}
+			return (T) fileList.toArray(new File[fileList.size()]);
+		}
+
+		@Override
+		public Class<File[]> getOutputType() {
+			return File[].class;
+		}
+
+		@Override
+		public Class<String> getInputType() {
+			return String.class;
+		}
+
+	}
+
+	// TODO add StringToFileListConverter
+
+	// -- File (list) to String converters --
+
+	@Plugin(type = Converter.class, priority = Priority.NORMAL)
+	public static class FileToStringConverter extends
+		AbstractConverter<File, String>
+	{
+
+		@SuppressWarnings("unchecked")
+		@Override
+		public <T> T convert(final Object src, final Class<T> dest) {
+			return (T) ((File) src).getAbsolutePath();
+		}
+
+		@Override
+		public Class<String> getOutputType() {
+			return String.class;
+		}
+
+		@Override
+		public Class<File> getInputType() {
+			return File.class;
+		}
+
+	}
+
+	@Plugin(type = Converter.class, priority = Priority.NORMAL)
+	public static class FileArrayToStringConverter extends
+		AbstractConverter<File[], String>
+	{
+
+		@SuppressWarnings("unchecked")
+		@Override
+		public <T> T convert(final Object src, final Class<T> dest) {
+			final List<String> result = Arrays.asList((File[]) src).stream().map(
+				f -> {
+					final String path = f.getAbsolutePath();
+					return path.contains(",") ? "\"" + path + "\"" : path;
+				}).collect(Collectors.toList());
+			return (T) String.join(",", result);
+		}
+
+		@Override
+		public Class<String> getOutputType() {
+			return String.class;
+		}
+
+		@Override
+		public Class<File[]> getInputType() {
+			return File[].class;
+		}
+
+	}
+
+	// TODO add FileListToStringConverter
+}

src/main/java/org/scijava/module/DefaultModuleService.java

@@ -297,9 +297,7 @@ public <T> void save(final ModuleItem<T> item, final T value) {
 			return;
 		}
 
-		// FIXME: Convert to string, instead of just calling toString.
-		// Otherwise many things (e.g. File[]) are persisted improperly.
-		final String sValue = value == null ? "" : value.toString();
+		final String sValue = value == null ? "" : convertService.convert(value, String.class);
 
 		// do not persist if object cannot be converted back from a string
 		if (!convertService.supports(sValue, item.getType())) return;

src/main/java/org/scijava/ui/DefaultUIService.java

@@ -321,15 +321,15 @@ public File chooseFile(final File file, final String style) {
 	}
 
 	@Override
-	public File[] chooseFiles(File[] files, FileFilter filter) {
+	public File[] chooseFiles(File parent, File[] files, FileFilter filter, String style) {
 		final UserInterface ui = getDefaultUI();
-		return ui == null ? null : ui.chooseFiles(files, filter);
+		return ui == null ? null : ui.chooseFiles(parent, files, filter, style);
 	}
 
 	@Override
-	public List<File> chooseFiles(List<File> fileList, FileFilter filter) {
+	public List<File> chooseFiles(File parent, List<File> fileList, FileFilter filter, String style) {
 		final UserInterface ui = getDefaultUI();
-		return ui == null ? null : ui.chooseFiles(fileList, filter);
+		return ui == null ? null : ui.chooseFiles(parent, fileList, filter, style);
 	}
 
 	@Override

src/main/java/org/scijava/ui/FileListPreprocessor.java

@@ -56,7 +56,9 @@ public void process(final Module module) {
 		final File[] files = fileInput.getValue(module);
 
 		// show file chooser dialog box
-		final File[] result = uiService.chooseFiles(files, null);
+		// TODO decide how to create filter from style attributes
+		// TODO retrieve parent folder??
+		final File[] result = uiService.chooseFiles(null, files, null, fileInput.getWidgetStyle());
 		if (result == null) {
 			cancel("");
 			return;

src/main/java/org/scijava/ui/UIService.java

@@ -304,7 +304,7 @@ DialogPrompt.Result showDialog(String message, String title,
 	 * @param files The initial value displayed in the file chooser prompt.
 	 * @param filter A filter allowing to restrict the choice of files
 	 */
-	File[] chooseFiles(File[] files, FileFilter filter);
+	File[] chooseFiles(File parent, File[] files, FileFilter filter, String style);
 
 	/**
 	 * Prompts the user to select one or multiple files.
@@ -315,7 +315,7 @@ DialogPrompt.Result showDialog(String message, String title,
 	 * @param fileList The initial value displayed in the file chooser prompt.
 	 * @param filter A filter allowing to restrict the choice of files
 	 */
-	List<File> chooseFiles(List<File> fileList, FileFilter filter);
+	List<File> chooseFiles(File parent, List<File> fileList, FileFilter filter, String style);
 
 	/**
 	 * Displays a popup context menu for the given display at the specified

src/main/java/org/scijava/ui/UserInterface.java

@@ -191,26 +191,30 @@ default File chooseFile(String title, File file, String style) {
 	/**
 	 * Prompts the user to choose a list of files.
 	 *
+	 * @param parent Parent folder for file selection
 	 * @param files The initial value displayed in the file chooser prompt.
 	 * @param filter A filter allowing to restrict file choice.
+	 * @param style File selection style (files, directories, or both) and optional filters
 	 * @return The selected {@link File}s chosen by the user, or null if the
 	 *         user cancels the prompt.
 	 */
-	default File[] chooseFiles(File[] files, FileFilter filter) {
+	default File[] chooseFiles(File parent, File[] files, FileFilter filter, String style) {
 		throw new UnsupportedOperationException();
 	}
 
 	/**
 	 * Prompts the user to choose a list of files.
 	 *
+	 * @param parent Parent folder for file selection
 	 * @param fileList The initial value displayed in the file chooser prompt.
 	 * @param filter A filter allowing to restrict file choice.
+	 * @param style File selection style (files, directories, or both) and optional filters
 	 * @return The selected {@link File}s chosen by the user, or null if the
 	 *         user cancels the prompt.
 	 */
-	default List<File> chooseFiles(List<File> fileList, FileFilter filter) {
+	default List<File> chooseFiles(File parent, List<File> fileList, FileFilter filter, String style) {
 		final File[] initialFiles = fileList.toArray(new File[fileList.size()]);
-		final File[] chosenFiles = chooseFiles(initialFiles, filter);
+		final File[] chosenFiles = chooseFiles(parent, initialFiles, filter, style);
 		return chosenFiles == null ? null : Arrays.asList(chosenFiles);
 	}
 

src/main/java/org/scijava/util/StringUtils.java

@@ -63,6 +63,7 @@
 
 import java.io.File;
 import java.text.DecimalFormatSymbols;
+import java.util.regex.Pattern;
 
 /**
  * Useful methods for working with {@link String}s.
@@ -80,6 +81,16 @@ private StringUtils() {
 		// NB: prevent instantiation of utility class.
 	}
 
+	/**
+	 * Splits a string only at separators outside of quotation marks ({@code "}).
+	 * Does not handle escaped quotes.
+	 */
+	public static String[] splitUnquoted(final String s, final String separator) {
+		// See https://stackoverflow.com/a/1757107/1919049
+		return s.split(Pattern.quote(separator) +
+			"(?=(?:[^\"]*\"[^\"]*\")*[^\"]*$)", -1);
+	}
+
 	/** Normalizes the decimal separator for the user's locale. */
 	public static String sanitizeDouble(String value) {
 		value = value.replaceAll("[^0-9,\\.]", "");

src/main/java/org/scijava/widget/FileListWidget.java

@@ -34,5 +34,24 @@
 import java.io.File;
 
 public interface FileListWidget<U> extends InputWidget<File[], U> {
-	// NB: No changes to interface.
+	/**
+	 * Widget style to allow file selection only
+	 * 
+	 * @see org.scijava.plugin.Parameter#style()
+	 */
+	String FILES_ONLY = "files";
+
+	/**
+	 * Widget style to allow directory selection only
+	 * 
+	 * @see org.scijava.plugin.Parameter#style()
+	 */
+	String DIRECTORIES_ONLY = "directories";
+
+	/**
+	 * Widget style to allow selection of both files and directories
+	 * 
+	 * @see org.scijava.plugin.Parameter#style()
+	 */
+	String FILES_AND_DIRECTORIES = "both";
 }