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genome-nexus / genome-nexus-annotation-pipeline

Library and tool for annotating MAF files using Genome Nexus Webserver API
MIT License
8 stars 25 forks source link

Upgrade to java 21 #272

Closed mandawilson closed 3 months ago

mandawilson commented 5 months ago

Changes needed for running under java21 and for packaging this depenency into the pipelines codebase for cbioportal study import into msk databases.

inodb commented 4 months ago

@mandawilson @sheridancbio i noticed there's an error in the build here - are you still looking at this one? Thanks!

sheridancbio commented 4 months ago

@mandawilson @sheridancbio i noticed there's an error in the build here - are you still looking at this one? Thanks!

Yes .. we are trying to resolve conflicts with the pipelines codebase (which also packages in cbioportal-core repository). There are spring version differences between these two codebases so we may need to make the spring version of this codebase match the spring version (and boot version) in use in cbioportal-core in order for the importer to function correctly.

So consider this PR to be in flux for now.

sheridancbio commented 3 months ago

This PR seems complete now. Docker functionality has been tested. Note: the "merge" sub command mode (seen through docker build and run) is not running either in this PR or in the master branch. A new issue to repair (or delete) the merge code logic should be created (if not extant).

Studies have been annotated during import in the msk importer (which uses the annotator module as a component).

changes sets were squashed into a single changeset.

sheridancbio commented 3 months ago

Note: the merge subcommand functionality actually did succeed when executed with the proper arguments ... basically those were: java -jar {jar_filename} merge --input-mafs-list='fileA,fileB,fileC,...' --output-maf='outfilename.txt'

I am proceeding with this merge now. A description of the potential ramifications was presented to the development team in the genomenexus slack channel in the cbioportal organization and there were no objections. This included the dropping of the databaseAnnotator module, the new requirement to build and run this codebase under a java21 jdk, and the successful testing of the annotator module as a dependency in the msk importer and also in the Docker mode execution for annotating test files.