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NPE Parsing a workflow #26

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coverbeck opened this issue Jul 20, 2022 · 4 comments
Open

NPE Parsing a workflow #26

coverbeck opened this issue Jul 20, 2022 · 4 comments

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@coverbeck
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Dockstore is failing to register this workflow from this repo: https://github.com/nebiolabs/neb-galaxy-workflows

I tried debugging it a little, and this plugin is throwing an NPE, so there's not even an error message that the end-user sees.

Here's the stack trace I see when running in the plugin locally (I added a test in my local repo, hence the testPrestoImmuneValidation method which doesn't exist in this repo:

java.lang.NullPointerException
	at org.galaxyproject.gxformat2.v19_09.utils.LoadingOptions.expandUrl(LoadingOptions.java:93)
	at org.galaxyproject.gxformat2.v19_09.utils.UriLoader.expandUrl(UriLoader.java:26)
	at org.galaxyproject.gxformat2.v19_09.utils.UriLoader.load(UriLoader.java:48)
	at org.galaxyproject.gxformat2.v19_09.utils.Loader.load(Loader.java:16)
	at org.galaxyproject.gxformat2.v19_09.utils.Loader.loadField(Loader.java:85)
	at org.galaxyproject.gxformat2.v19_09.WorkflowStepInputImpl.<init>(WorkflowStepInputImpl.java:149)
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
	at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490)
	at org.galaxyproject.gxformat2.v19_09.utils.RecordLoader.load(RecordLoader.java:23)
	at org.galaxyproject.gxformat2.v19_09.utils.RecordLoader.load(RecordLoader.java:6)
	at org.galaxyproject.gxformat2.v19_09.utils.UnionLoader.load(UnionLoader.java:26)
	at org.galaxyproject.gxformat2.v19_09.utils.Loader.load(Loader.java:16)
	at org.galaxyproject.gxformat2.v19_09.utils.Loader.loadField(Loader.java:85)
	at org.galaxyproject.gxformat2.v19_09.utils.ArrayLoader.load(ArrayLoader.java:27)
	at org.galaxyproject.gxformat2.v19_09.utils.ArrayLoader.load(ArrayLoader.java:6)
	at org.galaxyproject.gxformat2.v19_09.utils.OptionalLoader.load(OptionalLoader.java:20)
	at org.galaxyproject.gxformat2.v19_09.utils.OptionalLoader.load(OptionalLoader.java:5)
	at org.galaxyproject.gxformat2.v19_09.utils.Loader.load(Loader.java:16)
	at org.galaxyproject.gxformat2.v19_09.utils.IdMapLoader.load(IdMapLoader.java:51)
	at org.galaxyproject.gxformat2.v19_09.utils.Loader.load(Loader.java:16)
	at org.galaxyproject.gxformat2.v19_09.utils.Loader.loadField(Loader.java:85)
	at org.galaxyproject.gxformat2.v19_09.WorkflowStepImpl.<init>(WorkflowStepImpl.java:476)
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
	at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490)
	at org.galaxyproject.gxformat2.v19_09.utils.RecordLoader.load(RecordLoader.java:23)
	at org.galaxyproject.gxformat2.v19_09.utils.RecordLoader.load(RecordLoader.java:6)
	at org.galaxyproject.gxformat2.v19_09.utils.UnionLoader.load(UnionLoader.java:26)
	at org.galaxyproject.gxformat2.v19_09.utils.Loader.load(Loader.java:16)
	at org.galaxyproject.gxformat2.v19_09.utils.Loader.loadField(Loader.java:85)
	at org.galaxyproject.gxformat2.v19_09.utils.ArrayLoader.load(ArrayLoader.java:27)
	at org.galaxyproject.gxformat2.v19_09.utils.ArrayLoader.load(ArrayLoader.java:6)
	at org.galaxyproject.gxformat2.v19_09.utils.Loader.load(Loader.java:16)
	at org.galaxyproject.gxformat2.v19_09.utils.IdMapLoader.load(IdMapLoader.java:51)
	at org.galaxyproject.gxformat2.v19_09.utils.Loader.load(Loader.java:16)
	at org.galaxyproject.gxformat2.v19_09.utils.Loader.loadField(Loader.java:85)
	at org.galaxyproject.gxformat2.v19_09.GalaxyWorkflowImpl.<init>(GalaxyWorkflowImpl.java:311)
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
	at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490)
	at org.galaxyproject.gxformat2.v19_09.utils.RecordLoader.load(RecordLoader.java:23)
	at org.galaxyproject.gxformat2.v19_09.utils.RecordLoader.load(RecordLoader.java:6)
	at org.galaxyproject.gxformat2.v19_09.utils.UnionLoader.load(UnionLoader.java:26)
	at org.galaxyproject.gxformat2.v19_09.utils.Loader.documentLoad(Loader.java:41)
	at org.galaxyproject.gxformat2.v19_09.utils.RootLoader.loadDocument(RootLoader.java:18)
	at org.galaxyproject.gxformat2.v19_09.utils.RootLoader.loadDocument(RootLoader.java:23)
	at org.galaxyproject.gxformat2.v19_09.utils.RootLoader.loadDocument(RootLoader.java:27)
	at org.galaxyproject.gxformat2.Format2Linter.lint(Format2Linter.java:10)
	at org.galaxyproject.gxformat2.Lint.lint(Lint.java:20)
	at org.galaxyproject.dockstore_galaxy_interface.language.GalaxyWorkflowPlugin$GalaxyWorkflowPluginImpl.validateWorkflowSet(GalaxyWorkflowPlugin.java:115)
	at org.galaxyproject.dockstore_galaxy_interface.language.GalaxyWorkflowLanguagePluginTest.testPrestoImmuneValidation(GalaxyWorkflowLanguagePluginTest.java:173)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:566)
	at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:50)
	at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
	at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:47)
	at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:17)
	at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:325)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:78)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:57)
	at org.junit.runners.ParentRunner$3.run(ParentRunner.java:290)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:71)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:288)
	at org.junit.runners.ParentRunner.access$000(ParentRunner.java:58)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:268)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:363)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$3.run(ParentRunner.java:290)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:71)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:288)
	at org.junit.runners.ParentRunner.access$000(ParentRunner.java:58)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:268)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:363)
	at org.junit.runner.JUnitCore.run(JUnitCore.java:137)
	at com.intellij.junit4.JUnit4IdeaTestRunner.startRunnerWithArgs(JUnit4IdeaTestRunner.java:69)
	at com.intellij.rt.junit.IdeaTestRunner$Repeater$1.execute(IdeaTestRunner.java:38)
	at com.intellij.rt.execution.junit.TestsRepeater.repeat(TestsRepeater.java:11)
	at com.intellij.rt.junit.IdeaTestRunner$Repeater.startRunnerWithArgs(IdeaTestRunner.java:35)
	at com.intellij.rt.junit.JUnitStarter.prepareStreamsAndStart(JUnitStarter.java:235)
	at com.intellij.rt.junit.JUnitStarter.main(JUnitStarter.java:54)
coverbeck added a commit that referenced this issue Jul 20, 2022
@coverbeck
Scaffolding for #26 -- test fails.
84b7d71 
Needed to update the dockstore.version for it to build;
I think we cleaned out our Maven repo.
@coverbeck
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If there's anybody from Galaxy who can take this over, I created a branch, feature/26/npe, which recreates the failure. But the fix is beyond my knowledge.

@bethsheets
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Hi @mvdbeek, we were trying to support a user sharing their Galaxy workflow written in the latest format (gx2) on Dockstore and ran into this issue. Charles from the Dockstore team wasn't sure how to fix it. Could you help us find the correct person for help? Thanks so much!

@mvdbeek
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mvdbeek commented Jul 21, 2022 •
edited
Loading

Yes, would be great if dockstore can support gxformat2, we'd like to make that move. I suppose it's either @jmchilton or I that can help you. What's the question ?

@bethsheets
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@mvdbeek the user was trying to use the GitHub app integration to register with Dockstore and it was failing. Charles was able to recreate the error, but the error code is not useful. He was hoping someone from Galaxy may have a better understanding of what is going wrong.

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@coverbeck @mvdbeek @bethsheets