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Update Gradle to 7.5.1 #8098

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merged 1 commit into from
Nov 29, 2022
Merged

Update Gradle to 7.5.1 #8098

merged 1 commit into from
Nov 29, 2022

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lbergelson
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  • gradle version 7.3.2 -> 7.5.1

@lbergelson lbergelson requested a review from droazen November 18, 2022 20:10
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@droazen droazen left a comment

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👍

@gatk-bot
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gatk-bot commented Nov 18, 2022

Github actions tests reported job failures from actions build 3499912997
Failures in the following jobs:

Test Type JDK Job ID Logs
cloud 11 3499912997.11 logs
unit 11 3499912997.13 logs
integration 11 3499912997.12 logs

@lbergelson
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Ugh, there's some wierd bug with one of our dependencies not understanding java version id's with 4 parts. The install java action must have just moved from installing 11.0.16 too 11.0.16.1 behind our back. It sounds like we have to update Jetty or something manually

java.lang.ExceptionInInitializerError
        at org.eclipse.jetty.webapp.WebInfConfiguration.findAndFilterContainerPaths(WebInfConfiguration.java:185)
        at org.eclipse.jetty.webapp.WebInfConfiguration.preConfigure(WebInfConfiguration.java:155)
        at org.eclipse.jetty.webapp.WebAppContext.preConfigure(WebAppContext.java:485)
        at org.eclipse.jetty.webapp.WebAppContext.doStart(WebAppContext.java:521)
        at org.eclipse.jetty.util.component.AbstractLifeCycle.start(AbstractLifeCycle.java:68)
        at org.eclipse.jetty.util.component.ContainerLifeCycle.start(ContainerLifeCycle.java:131)
        at org.eclipse.jetty.util.component.ContainerLifeCycle.doStart(ContainerLifeCycle.java:113)
        at org.eclipse.jetty.server.handler.AbstractHandler.doStart(AbstractHandler.java:61)
        at org.eclipse.jetty.util.component.AbstractLifeCycle.start(AbstractLifeCycle.java:68)
        at org.eclipse.jetty.util.component.ContainerLifeCycle.start(ContainerLifeCycle.java:131)
        at org.eclipse.jetty.server.Server.start(Server.java:[42](https://github.com/broadinstitute/gatk/actions/runs/3499912997/jobs/5862011952#step:10:43)7)
        at org.eclipse.jetty.util.component.ContainerLifeCycle.doStart(ContainerLifeCycle.java:105)
        at org.eclipse.jetty.server.handler.AbstractHandler.doStart(AbstractHandler.java:61)
        at org.eclipse.jetty.server.Server.doStart(Server.java:394)
        at org.eclipse.jetty.util.component.AbstractLifeCycle.start(AbstractLifeCycle.java:68)
        at org.apache.hadoop.http.HttpServer2.start(HttpServer2.java:1155)
        at org.apache.hadoop.hdfs.server.namenode.NameNodeHttpServer.start(NameNodeHttpServer.java:181)
        at org.apache.hadoop.hdfs.server.namenode.NameNode.startHttpServer(NameNode.java:885)
        at org.apache.hadoop.hdfs.server.namenode.NameNode.initialize(NameNode.java:707)
        at org.apache.hadoop.hdfs.server.namenode.NameNode.<init>(NameNode.java:953)
        at org.apache.hadoop.hdfs.server.namenode.NameNode.<init>(NameNode.java:926)
        at org.apache.hadoop.hdfs.server.namenode.NameNode.createNameNode(NameNode.java:1692)
        at org.apache.hadoop.hdfs.MiniDFSCluster.createNameNode(MiniDFSCluster.java:1314)
        at org.apache.hadoop.hdfs.MiniDFSCluster.configureNameService(MiniDFSCluster.java:1083)
        at org.apache.hadoop.hdfs.MiniDFSCluster.createNameNodesAndSetConf(MiniDFSCluster.java:958)
        at org.apache.hadoop.hdfs.MiniDFSCluster.initMiniDFSCluster(MiniDFSCluster.java:890)
        at org.apache.hadoop.hdfs.MiniDFSCluster.<init>(MiniDFSCluster.java:518)
        at org.apache.hadoop.hdfs.MiniDFSCluster$Builder.build(MiniDFSCluster.java:477)
        at org.broadinstitute.hellbender.testutils.MiniClusterUtils.getMiniCluster(MiniClusterUtils.java:30)
        at org.broadinstitute.hellbender.testutils.MiniClusterUtils.getMiniCluster(MiniClusterUtils.java:38)
        at org.broadinstitute.hellbender.metrics.MetricsUtilsTest.setupMiniCluster(MetricsUtilsTest.java:24)

        Caused by:
        java.lang.IllegalArgumentException: Invalid Java version 11.0.16.1
            at org.eclipse.jetty.util.JavaVersion.parseJDK9(JavaVersion.java:71)
            at org.eclipse.jetty.util.JavaVersion.parse(JavaVersion.java:49)
            at org.eclipse.jetty.util.JavaVersion.<clinit>(JavaVersion.java:[43](https://github.com/broadinstitute/gatk/actions/runs/3499912997/jobs/5862011952#step:10:44))
            ... 31 more

@cmnbroad
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@lbergelson FWIW I definitely saw this issue at some point in the evolution of the Java 17 branch, though I didn't associate it with the gradle upgrade part of that branch (the Java 17 branch has the same gradle upgrade). IIRC, I later had to update to a newer jetty for other reasons - I think due to some binary incompatibility - but the newer version has a different issue that surfaces only when running on the docker (I think that issue is a variant of a known jetty issue with finding resources in a jar that isn't the main jar). I think I wound up throwing SkipExceptions for 10-15 tests only when running on the docker as a workaround.

* gradle version 7.3.2 -> 7.5.1
@lbergelson lbergelson merged commit 894117c into master Nov 29, 2022
@lbergelson lbergelson deleted the lb_gradle_7.5.1 branch November 29, 2022 19:21
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4 participants