Change in gopubmed-ontology-generation-service-clients-jar-with-dependencies.jar stops obo2obo from printing output
Nomi Harris
I discovered that obo2obo (and presumably the other command-line obo scripts as well, though I haven't checked those) stopped printing output due to an update of one jar: runlibs/gopubmed-ontology-generation-service-clients-jar-with-dependencies.jar
This update was done on May 25 by Thomas Waechter:
http://geneontology.svn.sourceforge.net/viewvc/geneontology/java/oboedit/trunk/lib/runlibs/gopubmed-ontology-generation-service-clients-jar-with-dependencies.jar?view=log
The new jar is quite a lot bigger than the old one, so I imagine a lot of things in it have changed.
Can you help me fix this problem?
Thanks,
Nomi
Thomas Waechter
the problem with the missing output was, that I changed in my own
log4j.properties the log level to ERROR. Previously OBO-Edit was overriding
this. Now the config for log4j is set in the OBOEdit.java, so that my properties
file had effects on obo2obo.
1. Regarding the missing output in obo2obo, I removed the log4j.properties from
the jar file and added specific rules for logging apache packages to OBOEdit.java
2. Regarding the size, I reduced the dependencies for the Axis2 service clients
as much as possible to less than half the previous size. Another 1.8Mb will be
removed as soon as I managed to rewrite the Ontology Lookup with axis2 rather
than axis.
3. For removing redundancy, I added my referenced libraries as single jars,
rather than one big unpacked jar I built with Maven.
I checked these changes in, but as the test had errors already, I cannot check
whether these changes had effects on other tested components.
Best regards and have a nice weekend,
Thomas
--
Thomas Waechter, Dipl.-Inf.
Bioinformatics Group (BIOTEC)
TU Dresden
Tatzberg 47-51
01307 Dresden, Germany
Phone: +49 (351) 463 40068
Email: waechter(at)biotec.tu-dresden.de-