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 #165

Closed inodb closed 3 years ago

inodb commented 3 years ago

Somehow the old logging configuration won't work anymore (getting some logconfiguration error). This fixes that by reverting some changes to loggin framework exclusion. In addition the the spring boot version was upgraded. Peculiarly some in memory database had to be included. Not entirely sure how the dependency tree works, but it is probably due to changes in the databaseAnnotator configuration in the new spring boot version.

inodb commented 3 years ago

Also created two PRs to see if this would break downstream pipeline inclusions:

https://github.com/knowledgesystems/cmo-pipelines/pull/828 ✅
https://github.com/knowledgesystems/pipelines/pull/413 ✅

ao508 commented 3 years ago

looking at this now

inodb commented 3 years ago

Superseded by https://github.com/genome-nexus/genome-nexus-annotation-pipeline/pull/177