[MOBY-guts] biomoby commit

[Paul Gordon]

gordonp
Wed Oct 29 22:33:24 EDT 2008
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/minnow
In directory dev.open-bio.org:/tmp/cvs-serv10500/src/main/ca/ucalgary/minnow

Modified Files:
	MinJarMaker.java 
Log Message:
Updates related to SAWSDL wrapping Web Service implementation
moby-live/Java/src/main/ca/ucalgary/minnow MinJarMaker.java,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/minnow/MinJarMaker.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/minnow/MinJarMaker.java	2008/02/15 07:27:47	1.4
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/minnow/MinJarMaker.java	2008/10/30 02:33:24	1.5
@@ -214,8 +214,15 @@
 	    if(classBytes != null){
 		clas = defineClass( name, classBytes, 0, classBytes.length );
 	    }
-	} catch( IOException ie ) {}
-	
+	} catch( IOException ie ) {
+	} catch(ClassFormatError cfe){ 
+	    // If the data did not contain a valid class 
+	    cfe.printStackTrace(System.err);
+	} catch(NoClassDefFoundError ncdfe){ 
+	    // If name is not equal to the binary name of the class specified by classBytes	
+	    ncdfe.printStackTrace(System.err);
+	}
+
 	// We weren't able to get the class, so
 	// use the default Classloader.
 	if (clas == null) {
@@ -327,17 +334,19 @@
 
 		    InputStream classStream = jarFile.getInputStream(je);
 		    byte[] classBytes = null;
-		    if(classSize != -1){ // We know the size of the class already
-
-			classBytes = new byte[(int) classSize]; //classes better not be bigger than 2 GB!
-			// Slurp it up in one shot
-			classStream.read(classBytes, 0, (int) classSize); 
-                        if(Boolean.getBoolean(VERBOSE)){
-                          System.err.println("[Loaded " + name + " from " + f.getCanonicalPath() + "]");
-                        }
-			return classBytes;
-		    }
-		    else{
+		    // NOTE: This if case is commented out because false file sizes are sometimes
+		    // reported, which leads to invalid class definitions
+// 		    if(classSize != -1){ // We know the size of the class already
+
+// 			classBytes = new byte[(int) classSize]; //classes better not be bigger than 2 GB!
+// 			// Slurp it up in one shot
+// 			classStream.read(classBytes, 0, (int) classSize); 
+//                         if(Boolean.getBoolean(VERBOSE)){
+//                           System.err.println("[Loaded " + name + " from " + f.getCanonicalPath() + "]");
+//                         }
+// 			return classBytes;
+// 		    }
+// 		    else{
 
 			byte[] byteBufferChunk = new byte[1024];
 			ByteArrayOutputStream byteBuffer = new ByteArrayOutputStream();
@@ -350,7 +359,7 @@
                           System.err.println("[Loaded " + name + " from " + f.getCanonicalPath() + "]");
                         }
 			return byteBuffer.toByteArray();
-		    }
+// 		    }
 		}
 		
 	    }