Java11 updates - Githubissues

genome-nexus / genome-nexus-annotation-pipeline

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

MIT License

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Java11 updates #267

Closed callachennault closed 9 months ago

callachennault commented 9 months ago

This PR contains:

Updates to build with Java 11
Check if gnResponse is null in GenomeNexusImpl.java getAnnotatedRecordsUsingPOST() function to maintain compatibility with CVR fetcher code. Without this change, we saw the following error when running the CVR fetcher:

2023-10-02 16:00:39 [main] ERROR org.cbioportal.cmo.pipelines.cvr.mutation.GMLMutationDataReader - Error annotating with POSTs
java.lang.NullPointerException
        at org.cbioportal.annotator.internal.GenomeNexusImpl.getAnnotatedRecordsUsingPOST(GenomeNexusImpl.java:659)

averyniceday commented 9 months ago

@callachennault can you look into updating circlci config to build with java11 as well