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Sage-Bionetworks / SynapseWorkflowHook

Code for linking a workflow engine to a Synapse evaluation queue
Apache License 2.0
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Submission Status update fail #37

Closed thomasyu888 closed 5 years ago

thomasyu888 commented 5 years ago 


Submission 9684291 failed.  The workflow description is: WorkflowJobImpl [submissionId=null, containerName=workflow_job.6dd08500-f813-4559-87c7-699c29a6b364, container=com.github.dockerjava.api.model.Container@fbb82a5[command=toil-cwl-runner --defaultMemory 100M --retryCount 0 --defaultDisk 1000000 --workDir /home/ec2-user/workflow/69c0d89d-0114-4617-b6a6-5a8145367f5e --noLinkImports NCI-CPTAC-Challenge-workflowtest/workflow/docker_agent_workflow.cwl /home/ec2-user/workflow/69c0d89d-0114-4617-b6a6-5a8145367f5e/TMP7245377986362766294.yaml,created=1546917980,id=7b31bda2d55a637f48d9adc789bdc8520cb9cc55e8f2b8169e6c9510b48b1411,image=sagebionetworks/synapseworkflowhook-toil,imageId=sha256:c4703064a385f3a1f1605ad5bc186b8c54da5ca502ee22b0df0ad99bf32ccbb6,names={/workflow_job.6dd08500-f813-4559-87c7-699c29a6b364},ports={},labels={},status=Up About an hour,sizeRw=,sizeRootFs=,hostConfig=com.github.dockerjava.api.model.ContainerHostConfig@6afcae48[networkMode=default],networkSettings=com.github.dockerjava.api.model.ContainerNetworkSettings@732b386c[networks={bridge=com.github.dockerjava.api.model.ContainerNetwork@1899ac59[ipamConfig=,links=,aliases=,networkID=abc7698dfad1511313b2444dd225d5192569002844abb54752ee8db278e0df17,endpointId=a6e57d6b67130d6f96c3cb42559589af1d67b3a36253b4fb54ca6a363a149992,gateway=172.17.0.1,ipAddress=172.17.0.2,ipPrefixLen=16,ipV6Gateway=,globalIPv6Address=,globalIPv6PrefixLen=0,macAddress=02:42:ac:11:00:02]}]], submissionParameters=null]

 The message is:

    org.sagebionetworks.client.exceptions.SynapseConflictingUpdateException: Submission Status: 9684291 was updated since you last fetched it, retrieve it again and reapply the update
    at org.sagebionetworks.client.ClientUtils.throwException(ClientUtils.java:79)
    at org.sagebionetworks.client.ClientUtils.throwException(ClientUtils.java:159)
    at org.sagebionetworks.client.ClientUtils.convertResponseBodyToJSONAndThrowException(ClientUtils.java:108)
    at org.sagebionetworks.client.BaseClientImpl.putJson(BaseClientImpl.java:452)
    at org.sagebionetworks.client.BaseClientImpl.putJSONEntity(BaseClientImpl.java:561)
    at org.sagebionetworks.client.SynapseClientImpl.updateSubmissionStatus(SynapseClientImpl.java:2999)
    at jdk.internal.reflect.GeneratedMethodAccessor23.invoke(Unknown Source)
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.base/java.lang.reflect.Method.invoke(Method.java:566)
    at org.sagebionetworks.client.SynapseProfileProxy$SynapseInvocationHandler.invoke(SynapseProfileProxy.java:55)
    at com.sun.proxy.$Proxy27.updateSubmissionStatus(Unknown Source)
    at jdk.internal.reflect.GeneratedMethodAccessor23.invoke(Unknown Source)
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.base/java.lang.reflect.Method.invoke(Method.java:566)
    at org.sagebionetworks.SynapseClientFactory$1$1.execute(SynapseClientFactory.java:46)
    at org.sagebionetworks.SynapseClientFactory$1$1.execute(SynapseClientFactory.java:43)
    at org.sagebionetworks.ExponentialBackoffRunner.execute(ExponentialBackoffRunner.java:64)
    at org.sagebionetworks.SynapseClientFactory$1.invoke(SynapseClientFactory.java:43)
    at com.sun.proxy.$Proxy27.updateSubmissionStatus(Unknown Source)
    at org.sagebionetworks.SubmissionUtils$1.execute(SubmissionUtils.java:90)
    at org.sagebionetworks.SubmissionUtils$1.execute(SubmissionUtils.java:87)
    at org.sagebionetworks.ExponentialBackoffRunner.execute(ExponentialBackoffRunner.java:64)
    at org.sagebionetworks.SubmissionUtils.updateSubmissionStatus(SubmissionUtils.java:87)
    at org.sagebionetworks.WorkflowHook.updateWorkflowJobs(WorkflowHook.java:417)
    at org.sagebionetworks.WorkflowHook.execute(WorkflowHook.java:187)
    at org.sagebionetworks.WorkflowHook.main(WorkflowHook.java:105)
    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.codehaus.mojo.exec.ExecJavaMojo$1.run(ExecJavaMojo.java:297)
    at java.base/java.lang.Thread.run(Thread.java:834)```
brucehoff commented 5 years ago

Added more debug info to help sleuth this problem: https://github.com/Sage-Bionetworks/SynapseWorkflowHook/commit/9609ef30c65627d76f4c9f3fa0bf2c6069d18fac

brucehoff commented 5 years ago

No activity in 1/2 year. Please reopen if more is needed.