Fix for missing directory entries in jar files.

doc/CHANGELOG.rst

@@ -5,6 +5,10 @@ This changelog *only* contains changes from the *first* pypi release (0.5.4.3) o
 
 Latest Changes:
 - **1.2.1_dev0 - 2020-11-29**
+
+  - JPype scans jar files and rebuilding missing directories to allow imports
+    from stripped and obfuscated jar files.
+
 - **1.2.0 - 2020-11-29**
 
   - Added builds for Python 3.9.  Python 3.9 on Windows is currently failing

native/java/org/jpype/JPypeContext.java

@@ -15,12 +15,16 @@
 **************************************************************************** */
 package org.jpype;
 
+import java.io.File;
 import java.lang.reflect.Array;
 import java.lang.reflect.InvocationTargetException;
 import java.lang.reflect.Method;
 import java.lang.reflect.Modifier;
 import java.nio.Buffer;
 import java.nio.ByteOrder;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
@@ -104,6 +108,8 @@ static JPypeContext createContext(long context, ClassLoader bootLoader, String n
     INSTANCE.typeFactory = new TypeFactoryNative();
     INSTANCE.typeManager = new TypeManager(context, INSTANCE.typeFactory);
     INSTANCE.initialize(interrupt);
+
+    scanExistingJars();
     return INSTANCE;
   }
 
@@ -487,7 +493,7 @@ public static void clearInterrupt(boolean x) throws InterruptedException
       {
         // Clear the flag in C++
         JPypeSignal.acknowledgePy();
-        
+
         // Clear the flag in Java
         Thread.sleep(1);
       }
@@ -637,4 +643,14 @@ public void newWrapper(long l)
     }
   }
 
+  private static void scanExistingJars()
+  {
+    // Scan existing jars for missing directory entries
+    String[] paths = System.getProperty("java.class.path").split(File.pathSeparator);
+    for (String path : paths)
+    {
+      INSTANCE.classLoader.scanJar(Paths.get(path));
+    }
+  }
+
 }

native/java/org/jpype/classloader/DynamicClassLoader.java

@@ -1,6 +1,7 @@
 package org.jpype.classloader;
 
 import java.io.ByteArrayOutputStream;
+import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.io.InputStream;
@@ -13,24 +14,32 @@
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.PathMatcher;
+import java.nio.file.Paths;
 import java.nio.file.SimpleFileVisitor;
 import java.nio.file.attribute.BasicFileAttributes;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.Enumeration;
+import java.util.HashMap;
 import java.util.LinkedList;
 import java.util.List;
+import java.util.Set;
+import java.util.jar.JarEntry;
+import java.util.jar.JarFile;
+import java.util.logging.Level;
+import java.util.logging.Logger;
 
 public class DynamicClassLoader extends ClassLoader
 {
 
   List<URLClassLoader> loaders = new LinkedList<>();
+  HashMap<String, ArrayList<URL>> map = new HashMap<>();
 
   public DynamicClassLoader(ClassLoader parent)
   {
     super(parent);
   }
-  
+
   public int getCode()
   {
     return loaders.hashCode();
@@ -85,6 +94,9 @@ public void addFile(Path path) throws FileNotFoundException
         path.toUri().toURL()
       };
       loaders.add(new URLClassLoader(urls));
+
+      // Scan the file for directory entries
+      this.scanJar(path);
     } catch (MalformedURLException ex)
     {
       // This should never happen
@@ -143,6 +155,11 @@ public URL getResource(String name)
       if (url != null)
         return url;
     }
+    // Both with and without / should generate the same result
+    if (name.endsWith("/"))
+      name = name.substring(0, name.length() - 1);
+    if (map.containsKey(name))
+      return map.get(name).get(0);
     return null;
   }
 
@@ -157,6 +174,81 @@ public Enumeration<URL> getResources(String name) throws IOException
       urls = cl.findResources(name);
       out.addAll(Collections.list(urls));
     }
+    // Both with and without / should generate the same result
+    if (name.endsWith("/"))
+      name = name.substring(0, name.length() - 1);
+    if (map.containsKey(name))
+      out.addAll(map.get(name));
     return Collections.enumeration(out);
   }
+
+  public void addResource(String name, URL url)
+  {
+    if (!this.map.containsKey(name))
+      this.map.put(name, new ArrayList<>());
+    this.map.get(name).add(url);
+  }
+
+  /**
+   * Recreate missing directory entries for Jars that lack indexing.
+   *
+   * Some jar files are missing the directory entries that prevents use from
+   * properly importing their contents. This procedure scans a jar file when
+   * loaded to build missing directories.
+   *
+   * @param p1
+   */
+  public void scanJar(Path p1)
+  {
+    if (!Files.exists(p1))
+      return;
+    if (Files.isDirectory(p1))
+      return;
+    try ( JarFile jf = new JarFile(p1.toFile()))
+    {
+      Enumeration<JarEntry> entries = jf.entries();
+      Path abs = p1.toAbsolutePath();
+      Set urls = new java.util.HashSet();
+      while (entries.hasMoreElements())
+      {
+        JarEntry next = entries.nextElement();
+        String name = next.getName();
+
+        // Skip over META-INF
+        if (name.startsWith("META-INF/"))
+          continue;
+
+        if (next.isDirectory())
+        {
+          // If we find a directory entry then the jar has directories already
+          return;
+        }
+
+        // Split on each separator in the name
+        int i = 0;
+        while (true)
+        {
+          i = name.indexOf("/", i);
+          if (i == -1)
+            break;
+          String name2 = name.substring(0, i);
+
+          i++;
+
+          // Already have an entry no problem
+          if (urls.contains(name2))
+            continue;
+
+          // Add a new entry for the missing directory
+          String jar = "jar:file:" + abs + "!/" + name2 + "/";
+          urls.add(name2);
+          this.addResource(name2, new URL(jar));
+        }
+      }
+    } catch (IOException ex)
+    {
+      // Anything goes wrong skip it
+    }
+  }
+
 }

project/jars/README

@@ -0,0 +1 @@
+This directory contains patterns for constructing special jar files used in testing.

project/jars/missing/build.sh

@@ -0,0 +1,2 @@
+javac --release 7 -d classes src/org/jpype/missing/*.java
+jar --create --file missing.jar -M -C classes META-INF/MANIFEST.MF -C classes org/jpype/missing/Test.class

project/jars/missing/classes/META-INF/MANIFEST.MF

@@ -0,0 +1,3 @@
+Manifest-Version: 1.0
+Created-By: 11.0.9.1 (Ubuntu)
+

project/jars/missing/src/org/jpype/missing/Test.java

@@ -0,0 +1,6 @@
+package org.jpype.missing;
+
+public class Test
+{
+}
+

resolve.sh

@@ -2,5 +2,5 @@
 # This is used to pull dependencies needed for this package
 
 # drill has a bunch of dependencies, so we are going to use ivy to collect it all at once.
-wget -nc "https://repo1.maven.org/maven2/org/apache/ivy/ivy/2.4.0/ivy-2.4.0.jar" -P lib
-java -jar lib/ivy-2.4.0.jar -ivy ivy.xml -retrieve 'lib/[artifact]-[revision](-[classifier]).[ext]'
+wget -nc "https://repo1.maven.org/maven2/org/apache/ivy/ivy/2.5.0/ivy-2.5.0.jar" -P lib
+java -jar lib/ivy-2.5.0.jar -ivy ivy.xml -retrieve 'lib/[artifact]-[revision](-[classifier]).[ext]'

test/jpypetest/test_imports.py

@@ -132,6 +132,10 @@ def testAddClassPath(self):
     def testStar(self):
         import importstar
 
+    def testMissing(self):
+        import org
+        self.assertTrue("missing" in dir(org.jpype))
+
 
 @subrun.TestCase
 class ImportsBeforeCase(common.unittest.TestCase):