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Fix resolution of nested Groovy class in v2 parser#6744

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bentsherman merged 3 commits intomasterfrom
fix-nested-groovy-class
Jan 23, 2026
Merged

Fix resolution of nested Groovy class in v2 parser#6744
bentsherman merged 3 commits intomasterfrom
fix-nested-groovy-class

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@bentsherman
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This PR fixes an issue where the v2 script parser could resolve a Groovy class like groovy.json.JsonSlurper but not a nested class like groovy.json.JsonGenerator.Options

The issue was surfaced by ongoing efforts to make nf-test work with strict syntax: askimed/nf-test#336

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
@bentsherman bentsherman requested a review from jorgee January 21, 2026 18:55
@bentsherman bentsherman requested a review from a team as a code owner January 21, 2026 18:55
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@bentsherman
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@jorgee there are some unit tests failing that seem to be related to #6733 , which is strange since they didn't fail when merged to master (24b858d)

I wonder if they are flaky tests. Can you look into this?

CmdCloneTest > testClone FAILED
    org.eclipse.jgit.api.errors.TransportException at CmdCloneTest.groovy:41
        Caused by: org.eclipse.jgit.errors.TransportException at CmdCloneTest.groovy:41

CmdInfoTest > initializationError FAILED
    org.eclipse.jgit.api.errors.TransportException at CmdInfoTest.groovy:54
        Caused by: org.eclipse.jgit.errors.TransportException at CmdInfoTest.groovy:54

CmdPluginCreateTest > should clone and create a plugin project FAILED
    nextflow.exception.AbortOperationException at CmdPluginCreateTest.groovy:49

CmdPullTest > should pull the github repository in the local folder FAILED
    org.eclipse.jgit.api.errors.TransportException at CmdPullTest.groovy:49
        Caused by: org.eclipse.jgit.errors.TransportException at CmdPullTest.groovy:49

AssetManagerTest > test download with legacy FAILED
    org.eclipse.jgit.api.errors.TransportException at AssetManagerTest.groovy:178
        Caused by: org.eclipse.jgit.errors.TransportException at AssetManagerTest.groovy:178

AssetManagerTest > test download from tag twice with multi-revision FAILED
    org.eclipse.jgit.api.errors.TransportException at AssetManagerTest.groovy:199
        Caused by: org.eclipse.jgit.errors.TransportException at AssetManagerTest.groovy:199

@jorgee
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jorgee commented Jan 22, 2026

It looks like there was a temporary failure in Github. All errors are sush as the following

org.eclipse.jgit.api.errors.TransportException: https://github.com/nextflow-io/hello.git: 500 Internal Server Error
	at app//org.eclipse.jgit.api.FetchCommand.call(FetchCommand.java:249)
	at app//org.eclipse.jgit.api.CloneCommand.fetch(CloneCommand.java:319)
	at app//org.eclipse.jgit.api.CloneCommand.call(CloneCommand.java:189)
	at app//nextflow.scm.LegacyRepositoryStrategy.download(LegacyRepositoryStrategy.groovy:89)
	at app//nextflow.scm.AssetManager.download(AssetManager.groovy:756)
	at nextflow.scm.AssetManagerTest.test download with legacy(AssetManagerTest.groovy:178)
Caused by: org.eclipse.jgit.errors.TransportException: https://github.com/nextflow-io/hello.git: 500 Internal Server Error
	at app//org.eclipse.jgit.transport.TransportHttp.connect(TransportHttp.java:728)
	at app//org.eclipse.jgit.transport.TransportHttp.openFetch(TransportHttp.java:465)
	at app//org.eclipse.jgit.transport.FetchProcess.executeImp(FetchProcess.java:153)
	at app//org.eclipse.jgit.transport.FetchProcess.execute(FetchProcess.java:105)
	at app//org.eclipse.jgit.transport.Transport.fetch(Transport.java:1458)
	at app//org.eclipse.jgit.api.FetchCommand.call(FetchCommand.java:238)
	... 5 more

@bentsherman bentsherman merged commit 10dff25 into master Jan 23, 2026
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@bentsherman bentsherman deleted the fix-nested-groovy-class branch January 23, 2026 16:11
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3 participants