Switched using classloader to using classgraph library.

Author: Matt

pom.xml

@@ -111,7 +111,11 @@ Institute of Molecular Cell Biology and Genetics.</license.copyrightOwners>
 			<groupId>org.scijava</groupId>
 			<artifactId>scijava-common</artifactId>
 		</dependency>
-
+		<dependency>
+			<groupId>io.github.classgraph</groupId>
+			<artifactId>classgraph</artifactId>
+			<version>4.8.172</version>
+		</dependency>
 		<!-- Test dependencies -->
 		<dependency>
 			<groupId>junit</groupId>

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

@@ -31,6 +31,33 @@
 
 package org.scijava.plugins.scripting.java;
 
+import io.github.classgraph.ClassGraph;
+import org.scijava.command.CommandService;
+import org.scijava.minimaven.BuildEnvironment;
+import org.scijava.minimaven.Coordinate;
+import org.scijava.minimaven.MavenProject;
+import org.scijava.plugin.Parameter;
+import org.scijava.plugin.PluginService;
+import org.scijava.run.RunService;
+import org.scijava.script.AbstractScriptEngine;
+import org.scijava.util.FileUtils;
+import org.scijava.util.LineOutputStream;
+import org.w3c.dom.Document;
+import org.w3c.dom.Element;
+import org.xml.sax.SAXException;
+
+import javax.script.ScriptEngine;
+import javax.script.ScriptException;
+import javax.xml.parsers.DocumentBuilderFactory;
+import javax.xml.parsers.ParserConfigurationException;
+import javax.xml.transform.OutputKeys;
+import javax.xml.transform.Transformer;
+import javax.xml.transform.TransformerConfigurationException;
+import javax.xml.transform.TransformerException;
+import javax.xml.transform.TransformerFactory;
+import javax.xml.transform.TransformerFactoryConfigurationError;
+import javax.xml.transform.dom.DOMSource;
+import javax.xml.transform.stream.StreamResult;
 import java.io.BufferedReader;
 import java.io.ByteArrayInputStream;
 import java.io.ByteArrayOutputStream;
@@ -43,44 +70,13 @@
 import java.io.Reader;
 import java.io.StringReader;
 import java.io.Writer;
-import java.net.MalformedURLException;
 import java.net.URL;
 import java.net.URLClassLoader;
 import java.util.ArrayList;
 import java.util.List;
-import java.util.jar.Attributes.Name;
-import java.util.jar.JarFile;
-import java.util.jar.Manifest;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
-import javax.script.ScriptEngine;
-import javax.script.ScriptException;
-import javax.xml.parsers.DocumentBuilderFactory;
-import javax.xml.parsers.ParserConfigurationException;
-import javax.xml.transform.OutputKeys;
-import javax.xml.transform.Transformer;
-import javax.xml.transform.TransformerConfigurationException;
-import javax.xml.transform.TransformerException;
-import javax.xml.transform.TransformerFactory;
-import javax.xml.transform.TransformerFactoryConfigurationError;
-import javax.xml.transform.dom.DOMSource;
-import javax.xml.transform.stream.StreamResult;
-
-import org.scijava.command.CommandService;
-import org.scijava.minimaven.BuildEnvironment;
-import org.scijava.minimaven.Coordinate;
-import org.scijava.minimaven.MavenProject;
-import org.scijava.plugin.Parameter;
-import org.scijava.plugin.PluginService;
-import org.scijava.run.RunService;
-import org.scijava.script.AbstractScriptEngine;
-import org.scijava.util.FileUtils;
-import org.scijava.util.LineOutputStream;
-import org.w3c.dom.Document;
-import org.w3c.dom.Element;
-import org.xml.sax.SAXException;
-
 /**
  * A pseudo-{@link ScriptEngine} compiling and executing Java classes.
  * <p>
@@ -787,23 +783,14 @@ private static Element append(final Document document, final Element parent,
 		getAllDependencies(final BuildEnvironment env)
 	{
 		final List<Coordinate> result = new ArrayList<Coordinate>();
-		for (ClassLoader loader = Thread.currentThread().getContextClassLoader(); loader != null; loader =
-			loader.getParent())
-		{
-			if (loader instanceof URLClassLoader) {
-				for (final URL url : ((URLClassLoader) loader).getURLs()) {
-					if (url.getProtocol().equals("file")) {
-						final File file = new File(url.getPath());
-						if (url.toString().matches(
-							".*/target/surefire/surefirebooter[0-9]*\\.jar"))
-						{
-							getSurefireBooterURLs(file, url, env, result);
-							continue;
-						}
-						result.add(fakeDependency(env, file));
-					}
-				}
-			}
+		ClassGraph cg = new ClassGraph();
+		String cp = cg.getClasspath();
+		String[] candidates = cp.split(File.pathSeparator);
+
+		for( String candidate : candidates ){
+			File file = new File(candidate);
+			Coordinate c = fakeDependency(env, file);
+			result.add(c);
 		}
 		return result;
 	}
@@ -830,56 +817,6 @@ private static Coordinate fakeDependency(final BuildEnvironment env,
 		return dependency;
 	}
 
-	/**
-	 * Figures out the class path given a {@code .jar} file generated by the
-	 * {@code maven-surefire-plugin}.
-	 * <p>
-	 * A little-known feature of JAR files is that their manifest can specify
-	 * additional class path elements in a {@code Class-Path} entry. The
-	 * {@code maven-surefire-plugin} makes extensive use of that: the URLs of the
-	 * of the active {@link URLClassLoader} will consist of only a single
-	 * {@code .jar} file that is empty except for a manifest whose sole purpose is
-	 * to specify the dependencies.
-	 * </p>
-	 * <p>
-	 * This method can be used to discover those additional class path elements.
-	 * </p>
-	 * 
-	 * @param file the {@code .jar} file generated by the
-	 *          {@code maven-surefire-plugin}
-	 * @param baseURL the {@link URL} of the {@code .jar} file, needed for class
-	 *          path elements specified as relative paths
-	 * @param env the {@link BuildEnvironment}, to store the Maven POMs faked for
-	 *          the class path elements
-	 * @param result the list of dependencies to which the discovered dependencies
-	 *          are added
-	 */
-	private static void getSurefireBooterURLs(final File file, final URL baseURL,
-		final BuildEnvironment env, final List<Coordinate> result)
-	{
-		try {
-			final JarFile jar = new JarFile(file);
-			Manifest manifest = jar.getManifest();
-			if (manifest != null) {
-				final String classPath =
-					manifest.getMainAttributes().getValue(Name.CLASS_PATH);
-				if (classPath != null) {
-					for (final String element : classPath.split(" +"))
-						try {
-							final File dependency =
-								new File(new URL(baseURL, element).getPath());
-							result.add(fakeDependency(env, dependency));
-						}
-						catch (MalformedURLException e) {
-							e.printStackTrace();
-						}
-				}
-			}
-		}
-		catch (final IOException e) {
-			e.printStackTrace();
-		}
-	}
 
 	/**
 	 * Read complete contents of a Reader and return as String.