Merge branch 'legacy-editor'

This topic branch fixes bugs identified while improving ImageJ2's script
editor with an eye to the legacy code. In particular, we need to be able
to run ImageJ 1.x plugins (with a LegacyJavaRunner contained in the
imagej-legacy project) so that Fiji can switch over to using ImageJ2's
script editor instead of its stale Script Editor (from where ImageJ2's
version was developed).

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>

Author: dscho

pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>org.scijava</groupId>
 		<artifactId>pom-scijava</artifactId>
-		<version>2.2</version>
+		<version>2.5</version>
 		<relativePath />
 	</parent>
 
@@ -97,12 +97,6 @@
 			<artifactId>junit</artifactId>
 			<scope>test</scope>
 		</dependency>
-		<dependency>
-			<groupId>org.scijava</groupId>
-			<artifactId>scijava-common</artifactId>
-			<classifier>tests</classifier>
-			<scope>test</scope>
-		</dependency>
 	</dependencies>
 
 	<build>

src/main/java/org/scijava/plugins/scripting/java/JavaEngine.java

@@ -171,6 +171,14 @@ public void compile(final File file, final Writer errorWriter) {
 		}
 	}
 
+	/**
+	 * Packages the build product into a {@code .jar} file.
+	 * 
+	 * @param file a {@code .java} or {@code pom.xml} file
+	 * @param includeSources whether to include the sources or not
+	 * @param output the {@code .jar} file to write to
+	 * @param errorWriter the destination for error messages
+	 */
 	public void makeJar(final File file, final boolean includeSources, final File output, final Writer errorWriter) {
 		try {
 			final Builder builder = new Builder(file, null, errorWriter);
@@ -288,9 +296,7 @@ private MavenProject getMavenProject(final BuildEnvironment env,
 			final File pom = new File(path, "pom.xml");
 			if (pom.exists()) return env.parse(pom, null);
 		}
-		final File rootDirectory = file.getParentFile();
-		final String artifactId = fakeArtifactId(env, file.getName());
-		return fakePOM(env, rootDirectory, artifactId, mainClass);
+		return writeTemporaryProject(env, new FileReader(file));
 	}
 
 	private static String getFullClassName(final File file) throws IOException {
@@ -361,7 +367,8 @@ private static MavenProject writeTemporaryProject(final BuildEnvironment env,
 		}
 
 		// write POM
-		return fakePOM(env, directory, fakeArtifactId(env, directory.getName()), mainClass);
+		final String artifactId = mainClass.substring(mainClass.lastIndexOf('.') + 1);
+		return fakePOM(env, directory, artifactId, mainClass, true);
 	}
 
 	private static String fakeArtifactId(final BuildEnvironment env, final String name) {
@@ -379,7 +386,7 @@ private static String fakeArtifactId(final BuildEnvironment env, final String na
 	}
 
 	private static MavenProject fakePOM(final BuildEnvironment env,
-			final File directory, final String artifactId, final String mainClass)
+			final File directory, final String artifactId, final String mainClass, boolean writePOM)
 					throws IOException, ParserConfigurationException, SAXException,
 					TransformerConfigurationException, TransformerException,
 					TransformerFactoryConfigurationError {
@@ -396,7 +403,6 @@ private static MavenProject fakePOM(final BuildEnvironment env,
 		append(pom, project, "version", DEFAULT_VERSION);
 
 		final Element build = append(pom, project, "build", null);
-		append(pom, build, "sourceDirectory", directory.getPath());
 
 		if (mainClass != null) {
 			final Element plugins = append(pom, build, "plugins", null);
@@ -428,6 +434,9 @@ private static MavenProject fakePOM(final BuildEnvironment env,
 				return env.parse(pomFile);
 			}
 		}
+		if (writePOM) {
+			transformer.transform(new DOMSource(pom), new StreamResult(new File(directory, "pom.xml")));
+		}
 		final ByteArrayOutputStream out = new ByteArrayOutputStream();
 		transformer.transform(new DOMSource(pom), new StreamResult(out));
 		return env.parse(new ByteArrayInputStream(out.toByteArray()), directory, null, null);

src/main/java/org/scijava/plugins/scripting/java/JavaScriptLanguage.java

@@ -67,6 +67,11 @@ public String getEngineName() {
 		return "MiniMaven";
 	}
 
+	@Override
+	public List<String> getNames() {
+		return Arrays.asList("Java");
+	}
+
 	@Override
 	public List<String> getMimeTypes() {
 		return Arrays.asList("application/x-java");

src/test/java/org/scijava/plugins/scripting/java/JavaEngineTest.java

@@ -97,7 +97,6 @@ public void minimalProjectFromPOM() throws Exception {
 		assertTrue(jar.exists());
 
 		System.gc();
-		assertTrue(FileUtils.deleteRecursively(dir));
 	}
 
 	@Test
@@ -134,7 +133,6 @@ public void minimalProjectFromSource() throws Exception {
 		assertTrue(jar.exists());
 
 		System.gc();
-		assertTrue(FileUtils.deleteRecursively(dir));
 	}
 
 	@Test

src/test/java/org/scijava/plugins/scripting/java/MakeJarTest.java

@@ -0,0 +1,78 @@
+/*
+ * #%L
+ * JSR-223-compliant Java scripting language plugin.
+ * %%
+ * Copyright (C) 2008 - 2014 Board of Regents of the University of
+ * Wisconsin-Madison, Broad Institute of MIT and Harvard, and Max Planck
+ * Institute of Molecular Cell Biology and Genetics.
+ * %%
+ * 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.plugins.scripting.java;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
+import java.io.File;
+import java.io.IOException;
+import java.io.StringWriter;
+import java.util.Arrays;
+import java.util.Set;
+import java.util.TreeSet;
+import java.util.jar.JarEntry;
+import java.util.jar.JarFile;
+
+import org.junit.Test;
+import org.scijava.test.TestUtils;
+import org.scijava.util.FileUtils;
+import org.scijava.util.IteratorPlus;
+
+public class MakeJarTest {
+	@Test
+	public void testSingle() throws Exception {
+		final StringWriter writer = new StringWriter();
+		final JavaEngine engine = new JavaEngine();
+		final File file = FileUtils.urlToFile(getClass().getResource("/Dummy.java"));
+		final File tmpDir = TestUtils.createTemporaryDirectory("jar-test-");
+		final File output = new File(tmpDir, "test.jar");
+		engine.makeJar(file, false, output, writer);
+		assertJarEntries(output, "META-INF/MANIFEST.MF",
+				"META-INF/maven/net.imagej/Dummy/pom.xml", "Dummy.class");
+		engine.makeJar(file, true, output, writer);
+		assertJarEntries(output, "META-INF/MANIFEST.MF",
+				"META-INF/maven/net.imagej/Dummy/pom.xml", "Dummy.class",
+				"pom.xml", "src/main/java/Dummy.java");
+	}
+
+	private void assertJarEntries(File output, String... paths) throws IOException {
+		final Set<String> set = new TreeSet<String>(Arrays.asList(paths));
+		final JarFile jar = new JarFile(output);
+		for (final JarEntry entry : new IteratorPlus<JarEntry>(jar.entries())) {
+			final String path = entry.getName();
+			assertTrue("Unexpected: " + path, set.remove(path));
+		}
+		jar.close();
+		assertEquals("Missing: " + set, 0, set.size());
+	}
+}

src/test/resources/Dummy.java

@@ -0,0 +1,41 @@
+/*
+ * #%L
+ * JSR-223-compliant Java scripting language plugin.
+ * %%
+ * Copyright (C) 2008 - 2014 Board of Regents of the University of
+ * Wisconsin-Madison, Broad Institute of MIT and Harvard, and Max Planck
+ * Institute of Molecular Cell Biology and Genetics.
+ * %%
+ * 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%
+ */
+
+/**
+ * Dummy class for testing {@code .jar} file packaging.
+ * 
+ * @author Johannes Schindelin
+ */
+public class Dummy {
+	public static void main(final String... args) {
+		throw new RuntimeException("Civilized people do not execute!");
+	}
+}