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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 logging changes for cbioportal 3.6.4 plus upgrade to 3.7.0 #176

Closed inodb closed 3 years ago

inodb commented 3 years ago

This combines #165 with the logging changes + #175 the 3.7.0 upgrade. The standalone upgrade to 3.7.0 didn't work, because it needs the logging changes

The description of https://github.com/genome-nexus/genome-nexus-annotation-pipeline/pull/165 is better, so please see the discussion there for a better explanation of the changes

Note that there is a failing test, but it is already failing in master. We should address those in a separate PR. I'm guessing they are actually server issues since we get a status of annotation failed in the MAF

This supersedes #165 and #175

inodb commented 3 years ago

superseded by https://github.com/genome-nexus/genome-nexus-annotation-pipeline/pull/177