Execution from JAR files and Classpaths -- Help

Question

I am confused about how classes are resolved when running from within a JAR file, and why this is different than running a class that is not inside a JAR file.
I have an application that uses classes from a third party library stored in a JAR file (biojava.jar) . If I run the app from the class file it works as expected and is capable of finding the external classes when the path to the biojava.jar is on my classpath. It also works if biojava.jar is instead placed in the extensions folder jre/lib/ext folder without an explicit path entry in my classpath.
However when I package all my application classes up in a JAR file and try to execute the application from the JAR file it will ONLY work if I add a manifest entry to myApp.jar ... Class-Path: biojava.jar AND I place the file biojava.jar in the SAME directory as the Packaged JAR application. I would like to find a way to make this JAR file work for anyone who has biojava.jar in their classpath or ext directory. In other words I don't want my user community to have to copy the biojava.jar file when I email them myApp.jar. This community will already have biojava.jar on their CLASSPATH.
How can I make my app within a JAR recognize either the user's CLASSPATH or ext folder? I have tried reading the documentation and many experiments but the only way it works is as described above.
I am running Running Windows 2000.
java version "1.4.1_01"
Java(TM) 2 Runtime Environment, Standard Edition (build 1.4.1_01-b01)
Java HotSpot(TM) Client VM (build 1.4.1_01-b01, mixed mode)
Here are the results of my experimentations:
The following Works:
Manifest: Main-Class: org/biojava/app/SequenceSpiral
Manifest: Class-Path: biojava.jar
Place biojava.jar in the same directory as SequenceSpiral.jar
java -jar SequenceSpiral.jar
This works perfectly
NONE of the following work
0) Placing biojava.jar in my jre/lib/ext directory instead of the same dir as SequenceSpiral.jar
Exception in thread "main" java.lang.NoClassDefFoundError: org/biojava/bio/seq/FeatureFilter
(this is the first class referenced from biojava.jar)
1) Just see if it will find the proper jar on my classpath
Manifest: Main-Class: org/biojava/app/SequenceSpiral
I have biojava.jar on my classpath but not in same directory as SequenceSprial.jar
java -jar SequenceSpiral.jar
Exception in thread "main" java.lang.NoClassDefFoundError: org/biojava/bio/seq/FeatureFilter
2) Specify the name if the jar in the Manifest Classpath and see if it will find the proper jar on my classpath
Manifest: Main-Class: org/biojava/app/SequenceSpiral
Manifest: Class-Path: biojava.jar
I have biojava.jar on my classpath but not in same directory as SequenceSprial.jar
java -jar SequenceSpiral.jar
Exception in thread "main" java.lang.NoClassDefFoundError: org/biojava/bio/seq/FeatureFilter
3) Specify the path of the jar in the Manifest Classpath
Manifest: Main-Class: org/biojava/app/SequenceSpiral
Manifest: Class-Path: d:/biojava/biojava.jar
I have biojava.jar on my classpath (D;\biojava\biojava.jar) but not in same directory as SequenceSprial.jar
java -jar SequenceSpiral.jar
Exception in thread "main" java.lang.NoClassDefFoundError: org/biojava/bio/seq/FeatureFilter
(note that in this case it is not fnding my main even though the Main-Class is specified)
4) Specify current directory and biojava.jar in the Manifest Class-Path
Manifest: Main-Class: org/biojava/app/SequenceSpiral
Manifest: Class-Path: .;biojava.jar
I have biojava.jar on my classpath (D;\biojava\biojava.jar) but not in same directory as SequenceSprial.jar
java -jar SequenceSpiral.jar
Exception in thread "main" java.lang.NoClassDefFoundError: org/biojava/bio/seq/FeatureFilter
5)Specify current directory and the URL of biojava.jar in the Manifest Class-Path
Manifest: Main-Class: org/biojava/app/SequenceSpiral
Manifest: Class-Path: . d:/biojava/biojava.jar
I have biojava.jar on my classpath (D;\biojava\biojava.jar) but not in same directory as SequenceSprial.jar
java -jar SequenceSpiral.jar
Exception in thread "main" java.lang.NoClassDefFoundError: org/biojava/bio/seq/FeatureFilter.
Thank you very much for any help or suggestions,
David Maynard

Answer 1

I did some more testing and I think I now understand what is going on.
I don't like it, but at least I understand it.
The problem: I have an app packaged into a JAR file, myApp.jar. It has a dependancy upon an external JAR file extern.jar.
extern.jar is on my Classpath (and also in jre/lib/ext)
1) For some reason (bug?) java -jar myApp.jar does NOT use the classpath or the jre/lib/ext mechanisms to find .jar files needed to resolve references to external classes. This seems to be true even if you add an explicit -classpath argument on the command line!
thus
java -jar -cp c:\\absolutePathToMy\extern.jar myApp.jar
also fails as does
java -cp c:\\absolutePathToMy\extern.jar -jar myApp.jar
2) Inside the myApp Jar file you can specify a URL to an jar extension jar file but the URL IS RELATIVE TO THE PATH WHERE THE myApp.Jar is executed from! If I add the Manifest item Class-Path: ..\..\..\myexterndir\extern.jar then
java -jar myApp.jar
works correctly and resolves the external references.
This is why several people have reported that this class-path mechanism works ONLY when the extern.jar file is in the SAME DIRECTORY as the myApp.jar file when they had added a Class-Path: extern.jar to the Manifest.
However together these two items make it IMPOSSIBLE to distribute myApp.jar to others and have it work since the path names statically encoded inside the jar are relative to where the jar gets executed from. If I move myApp.jar to a different location on my hard drive it may also fail.
In my case I know all my customers already have extern.jar (5MB) installed on their classpaths and I would like to just send them the myApp.jar ( .5MB ).
However I don't see how to do this given the current specification of a JAR file, and the bug that makes all -jar file act like they have the Sealed=true property.
I tried explicity setting Sealed=false in the manifest but this didn't seem to have any effect.
I hope that this will save others the many hours of time it has taken be to determine that JARS are not well suited for deploying apps with dependenncies on external libs.
I also hope that someone can show me how execute a JAR and specify a classpath that doesn't get IGNORED my the classloader used in loading the jar classes.
This is using java version:
java version "1.4.1_01"
Java(TM) 2 Runtime Environment, Standard Edition (build 1.4.1_01-b01)
Java HotSpot(TM) Client VM (build 1.4.1_01-b01, mixed mode)
Does any one know this bug is fixed in a later release?
David Maynard