Class cannot be created (missing no-arg constructor): nextflow.file.http.XPath #5208

nvnieuwk · 2024-08-06T19:03:41Z

Bug report

Expected behavior and actual behavior

We encountered this error when debugging a PR in nf-core/demultiplex. This issue only occurs with the last version of Nextflow edge (24.07.0-edge)

Error traceback

com.esotericsoftware.kryo.KryoException: Class cannot be created (missing no-arg constructor): nextflow.file.http.XPath
	at com.esotericsoftware.kryo.Kryo$DefaultInstantiatorStrategy.newInstantiatorOf(Kryo.java:1228)
	at nextflow.util.InstantiationStrategy.newInstantiatorOf(SerializationHelper.groovy:247)
	at com.esotericsoftware.kryo.Kryo.newInstantiator(Kryo.java:1049)
	at com.esotericsoftware.kryo.Kryo.newInstance(Kryo.java:1058)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.create(FieldSerializer.java:547)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.read(FieldSerializer.java:523)
	at com.esotericsoftware.kryo.Kryo.readClassAndObject(Kryo.java:761)
	at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
	at nextflow.util.KryoHelper.deserialize(SerializationHelper.groovy:181)
	at nextflow.util.KryoHelper.deserialize(SerializationHelper.groovy)
	at nextflow.file.SortFileCollector.saveFile(SortFileCollector.groovy:315)
	at nextflow.file.FileCollector.saveTo0(FileCollector.groovy:228)
	at nextflow.file.FileCollector.saveTo(FileCollector.groovy:251)
	at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
	at nextflow.extension.CollectFileOp.emitItems(CollectFileOp.groovy:187)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:568)
	at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
	at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
	at groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1333)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088)
	at groovy.lang.MetaClassImpl.invokeMethodClosure(MetaClassImpl.java:1017)
	at groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1207)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
	at groovy.lang.Closure.call(Closure.java:433)
	at groovy.lang.Closure.call(Closure.java:422)
	at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
	at nextflow.extension.DataflowHelper$3.afterStop(DataflowHelper.groovy:257)
	at groovyx.gpars.dataflow.operator.DataflowProcessor.fireAfterStop(DataflowProcessor.java:324)
	at groovyx.gpars.dataflow.operator.DataflowProcessorActor.afterStop(DataflowProcessorActor.java:59)
	at jdk.internal.reflect.GeneratedMethodAccessor75.invoke(Unknown Source)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:568)
	at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
	at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
	at groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1333)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
	at org.codehaus.groovy.runtime.InvokerHelper.invokePojoMethod(InvokerHelper.java:633)
	at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:624)
	at groovyx.gpars.actor.Actor.callDynamic(Actor.java:369)
	at groovyx.gpars.actor.Actor.handleTermination(Actor.java:320)
	at groovyx.gpars.actor.AbstractLoopingActor.terminate(AbstractLoopingActor.java:204)
	at groovyx.gpars.dataflow.operator.DataflowProcessor.terminate(DataflowProcessor.java:147)
	at groovyx.gpars.dataflow.operator.DataflowProcessorActor.checkPoison(DataflowProcessorActor.java:115)
	at groovyx.gpars.dataflow.operator.DataflowOperatorActor.onMessage(DataflowOperatorActor.java:83)
	at groovyx.gpars.actor.impl.SDAClosure$1.call(SDAClosure.java:43)
	at groovyx.gpars.actor.AbstractLoopingActor.runEnhancedWithoutRepliesOnMessages(AbstractLoopingActor.java:293)
	at groovyx.gpars.actor.AbstractLoopingActor.access$400(AbstractLoopingActor.java:30)
	at groovyx.gpars.actor.AbstractLoopingActor$1.handleMessage(AbstractLoopingActor.java:93)
	at groovyx.gpars.util.AsyncMessagingCore.run(AsyncMessagingCore.java:132)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
	at java.base/java.lang.Thread.run(Thread.java:840)

Steps to reproduce the problem

(Provide a test case that reproduce the problem either with a self-contained script or GitHub repository)

Program output

(Copy and paste here output produced by the failing execution. Please highlight it as a code block. Whenever possible upload the .nextflow.log file.)

Environment

Nextflow version: 24.07.0-edge
Java version: 17.0.11
Operating system: Linux

Additional context

(Add any other context about the problem here)

The text was updated successfully, but these errors were encountered:

bentsherman · 2024-08-07T13:19:13Z

Indeed there is no empty XPath constructor, though it's curious why this issue only appeared now

pditommaso · 2024-09-09T13:15:57Z

It would be nice to a test case to replicate the error

nvnieuwk · 2024-09-09T13:33:01Z

@atrigila do you remember what the issue was here?

atrigila · 2024-09-09T15:43:35Z

nf-tests failed due to unknown reason after simply updating modules and a directory path, we can see the results from those nf-tests in CI here: https://github.com/nf-core/demultiplex/actions/runs/10271920060/job/28422982280 for this commit

Assertion failed: 
  
  8 of 8 assertions failed
  
  Nextflow stdout:
  
  ERROR ~ Class cannot be created (missing no-arg constructor): nextflow.file.http.XPath
  
   -- Check '/home/runner/work/demultiplex/demultiplex/.nf-test/tests/d4593e0[74](https://github.com/nf-core/demultiplex/actions/runs/10271920060/job/28422982280#step:5:75)a7ce42935e81a6ef47fa4ce/meta/nextflow.log' file for details
  ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting
  
   -- Check '/home/runner/work/demultiplex/demultiplex/.nf-test/tests/d4593e074a7ce42935e81a6ef47fa4ce/meta/nextflow.log' file for details
  Join mismatch for the following entries: key=[id:sim-data, lane:null] values=

In the following commits we changed the latest-everything to latest-stable and that solved that issue.

pditommaso · 2024-09-23T13:53:18Z

Likely it's enough to add the default constructor

pditommaso · 2024-09-26T13:23:57Z

Can anyone include the corresponding .nextflow.log file for the failed execution?

nvnieuwk · 2024-10-02T09:45:25Z

Thank you for fixing this!

atrigila · 2024-10-16T13:11:07Z

We came across this error again in nf-core/demultiplex#276

Tests are failing in latest-everything but not in 24.04.2.

Example: https://github.com/nf-core/demultiplex/actions/runs/11365226302/job/31612964417?pr=276

  ERROR ~ Class cannot be created (missing no-arg constructor): nextflow.file.http.XFileSystem
  Serialization trace:
  fs (nextflow.file.http.XPath)

cc @maxulysse

atrigila · 2024-10-16T13:12:53Z

Attaching logs for those runs
logs_29690945475.zip

maxulysse · 2024-10-16T13:24:04Z

latest-everything is 24.09.2-edge

jorgee · 2024-10-16T17:08:43Z

Attaching logs for those runs logs_29690945475.zip

Is there a wa to get the .nextflow.log file of this execution? I can't see in the logs zip file

jorgee · 2024-10-17T08:55:37Z

I have been able to reproduce the error. It is slightly different. The class that is deserializing is different. In previous issue, the class that was failing to deserialize was XPath. Now, it is failing to XFileSystem. It is failing in a collectFile operator. I think it is when collecting this file https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/sim-data/out.sample_meta.csv

maxulysse · 2024-10-17T10:01:11Z

Interesting

pditommaso · 2024-10-17T10:11:37Z

is not the default constructor solving it?

jorgee · 2024-10-17T10:17:12Z

is not the default constructor solving it?

It is failing in a different point. In the reported issue was XPath and now it is XFileSystem. I have tested adding the default constructor also to XFileSystem it fix the issue. In this case, I was able to reproduce the issue with a unit test. should I reopen the issue or create a new one.?

pditommaso · 2024-10-17T10:18:42Z

Let's use the previous one

pditommaso assigned jorgee Sep 23, 2024

bentsherman added the bug label Sep 25, 2024

jorgee linked a pull request Sep 26, 2024 that will close this issue

Add XPath default serializer #5339

Merged

jorgee mentioned this issue Sep 26, 2024

Add XPath default serializer #5339

Merged

pditommaso closed this as completed in #5339 Oct 2, 2024

jorgee reopened this Oct 17, 2024

jorgee mentioned this issue Oct 17, 2024

Fix XFileSystem serilization issue #5411

Merged

pditommaso closed this as completed in #5411 Oct 17, 2024

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Class cannot be created (missing no-arg constructor): nextflow.file.http.XPath #5208

Class cannot be created (missing no-arg constructor): nextflow.file.http.XPath #5208

nvnieuwk commented Aug 6, 2024

bentsherman commented Aug 7, 2024

pditommaso commented Sep 9, 2024

nvnieuwk commented Sep 9, 2024

atrigila commented Sep 9, 2024

pditommaso commented Sep 23, 2024

pditommaso commented Sep 26, 2024

nvnieuwk commented Oct 2, 2024

atrigila commented Oct 16, 2024

atrigila commented Oct 16, 2024

maxulysse commented Oct 16, 2024

jorgee commented Oct 16, 2024 •

edited

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jorgee commented Oct 17, 2024

maxulysse commented Oct 17, 2024

pditommaso commented Oct 17, 2024

jorgee commented Oct 17, 2024

pditommaso commented Oct 17, 2024

Class cannot be created (missing no-arg constructor): nextflow.file.http.XPath #5208

Class cannot be created (missing no-arg constructor): nextflow.file.http.XPath #5208

Comments

nvnieuwk commented Aug 6, 2024

Bug report

Expected behavior and actual behavior

Steps to reproduce the problem

Program output

Environment

Additional context

bentsherman commented Aug 7, 2024

pditommaso commented Sep 9, 2024

nvnieuwk commented Sep 9, 2024

atrigila commented Sep 9, 2024

pditommaso commented Sep 23, 2024

pditommaso commented Sep 26, 2024

nvnieuwk commented Oct 2, 2024

atrigila commented Oct 16, 2024

atrigila commented Oct 16, 2024

maxulysse commented Oct 16, 2024

jorgee commented Oct 16, 2024 • edited Loading

jorgee commented Oct 17, 2024

maxulysse commented Oct 17, 2024

pditommaso commented Oct 17, 2024

jorgee commented Oct 17, 2024

pditommaso commented Oct 17, 2024

jorgee commented Oct 16, 2024 •

edited

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