Stian Soiland-Reyes created TAVERNA-971:
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Summary: jarcache not working through OSGi
Key: TAVERNA-971
URL: https://issues.apache.org/jira/browse/TAVERNA-971
Project: Apache Taverna
Issue Type: Bug
Components: Taverna Language
Affects Versions: language 0.15.1, commandline 3.1.0
Reporter: Stian Soiland-Reyes
Assignee: Stian Soiland-Reyes
Fix For: commandline 3.1.0, language 0.16.0
taverna-robundle includes a
[jarcache.json|https://github.com/apache/incubator-taverna-language/blob/master/taverna-robundle/src/main/resources/jarcache.json]
which specifies
[contexts/bundle.jsonld|https://github.com/apache/incubator-taverna-language/blob/master/taverna-robundle/src/main/resources/contexts/bundle.jsonld]
to be loaded from the taverna-robundle JAR instead of from
https://w3id.org/bundle/context.json
This uses [JSONLD-Java's JAR
cache|https://github.com/jsonld-ava/jsonld-java#loading-contexts-from-classpathjar]
- in order to avoiding network access when parsing the manifest JSON-LD of the
robundle.
This does however not work well under OSGi with the Taverna Command Line, as
the jarcache within the jsonld-java OSGi bundle can't access /jarcache.json in
the taverna-robundle OSGi bundle - at least not without setting
Thread.currentThread.setContextClassLoader().
This caused running of the workflow to fail with a large stack trace at the
point of closing the data bundle (this happen with or without -bundle)
Note that using Jena 3.1.0 and OpenJDK on Ubuntu, access to
https://w3id.org/bundle/context.json fails with an "internal error" SSL error,
so even with network access it can fail.
Note that in Taverna Language 0.15.1 there was also a bug that when adding the
Apache header to the bundle.json an extra } was added - this worked with
earlier versions of Jackson/JSONLD-Java but now after TAVERNA-970 upgrades this
fails - thus for the Command Line 3.1.0 I propose a workaround to add a fixed
bundle.json on its own classpath, and then set the thread context loader to its
own classloader while running the workflow.
The fix for robundle 0.16.0 would be to set the thread class loader before
parsing the manifest.json.
(Thus we can fix it properly for next Taverna Language, but can ship Command
Line 3.1.0 with existing Language 0.15.1)
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