Handle changes to deps in cbioportal v3.6.4

genome-nexus / genome-nexus-annotation-pipeline

Library and tool for annotating MAF files using Genome Nexus Webserver API

MIT License

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Handle changes to deps in cbioportal v3.6.4 #163

Closed inodb closed 3 years ago

inodb commented 3 years ago

Somehow the old logging configuration won't work anymore (getting some logconfiguration error). Made some changes to the logging framework. This does quite drastically change output since everything now goes to stdout for some reason. Maybe someone with more java logging experience can figure out what's really going on, but this could work as a quick fix.

ao508 commented 3 years ago

Ah, this is why we were excluding the log4j stuff from the cbioportal package

inodb commented 3 years ago

@ao508 i guess so yeah - i made some changes here: https://github.com/genome-nexus/genome-nexus-annotation-pipeline/pull/165. Which seems less invasive to the logging at least