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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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Add COMPOSE_PROJECT_NAME to the readme, or else error... #48

Open andrewelamb opened 5 years ago

andrewelamb commented 5 years ago

I just restarted my instance that was running the hook. I cleared all my docker images and containers. After starting up the hook, whenever I make a submission to the queue I get this error:

workflow-hook_1 | Aug 09, 2019 5:56:09 PM org.sagebionetworks.ExponentialBackoffRunner execute workflow-hook_1 | SEVERE: Found status code 409. Will not retry: Status Code: 409 message: An entity with the name: 3360851 already exists with a parentId: syn20078502 workflow-hook_1 | 17:56:10.287 [org.sagebionetworks.WorkflowHook.main()] ERROR org.sagebionetworks.client.SynapseProfileProxy - java.lang.reflect.InvocationTargetException workflow-hook_1 | Aug 09, 2019 5:56:10 PM org.sagebionetworks.ExponentialBackoffRunner execute workflow-hook_1 | SEVERE: Found status code 409. Will not retry: Status Code: 409 message: An entity with the name: 3360851_LOCKED already exists with a parentId: syn20078502 workflow-hook_1 | [org.sagebionetworks.WorkflowHook.main()] ERROR org.sagebionetworks.WorkflowHook - Submission failed workflow-hook_1 | java.lang.RuntimeException: Cannot find value for COMPOSE_PROJECT_NAME workflow-hook_1 | at org.sagebionetworks.Utils.getProperty(Utils.java:116) workflow-hook_1 | at org.sagebionetworks.Utils.getProperty(Utils.java:87) workflow-hook_1 | at org.sagebionetworks.Utils.dockerComposeName(Utils.java:77) workflow-hook_1 | at org.sagebionetworks.WES.createDirInHostMountedSharedDir(WES.java:74) workflow-hook_1 | at org.sagebionetworks.WES.createWorkflowJob(WES.java:177) workflow-hook_1 | at org.sagebionetworks.WorkflowHook.createNewWorkflowJobs(WorkflowHook.java:263) workflow-hook_1 | at org.sagebionetworks.WorkflowHook.execute(WorkflowHook.java:201) workflow-hook_1 | at org.sagebionetworks.WorkflowHook.main(WorkflowHook.java:111) workflow-hook_1 | at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) workflow-hook_1 | at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) workflow-hook_1 | at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) workflow-hook_1 | at java.base/java.lang.reflect.Method.invoke(Method.java:566) workflow-hook_1 | at org.codehaus.mojo.exec.ExecJavaMojo$1.run(ExecJavaMojo.java:297) workflow-hook_1 | at java.base/java.lang.Thread.run(Thread.java:834) workflow-hook_1 | [WARNING] workflow-hook_1 | java.lang.reflect.InvocationTargetException workflow-hook_1 | at jdk.internal.reflect.NativeMethodAccessorImpl.invoke0 (Native Method) workflow-hook_1 | at jdk.internal.reflect.NativeMethodAccessorImpl.invoke (NativeMethodAccessorImpl.java:62) workflow-hook_1 | at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke (DelegatingMethodAccessorImpl.java:43) workflow-hook_1 | at java.lang.reflect.Method.invoke (Method.java:566) workflow-hook_1 | at org.codehaus.mojo.exec.ExecJavaMojo$1.run (ExecJavaMojo.java:297) workflow-hook_1 | at java.lang.Thread.run (Thread.java:834) workflow-hook_1 | Caused by: java.lang.RuntimeException: Cannot find value for COMPOSE_PROJECT_NAME workflow-hook_1 | at org.sagebionetworks.Utils.getProperty (Utils.java:116) workflow-hook_1 | at org.sagebionetworks.Utils.getProperty (Utils.java:87) workflow-hook_1 | at org.sagebionetworks.Utils.dockerComposeName (Utils.java:77) workflow-hook_1 | at org.sagebionetworks.WES.createDirInHostMountedSharedDir (WES.java:74) workflow-hook_1 | at org.sagebionetworks.WES.createWorkflowJob (WES.java:177) workflow-hook_1 | at org.sagebionetworks.WorkflowHook.createNewWorkflowJobs (WorkflowHook.java:263) workflow-hook_1 | at org.sagebionetworks.WorkflowHook.execute (WorkflowHook.java:201) workflow-hook_1 | at org.sagebionetworks.WorkflowHook.main (WorkflowHook.java:111) workflow-hook_1 | at jdk.internal.reflect.NativeMethodAccessorImpl.invoke0 (Native Method) workflow-hook_1 | at jdk.internal.reflect.NativeMethodAccessorImpl.invoke (NativeMethodAccessorImpl.java:62) workflow-hook_1 | at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke (DelegatingMethodAccessorImpl.java:43) workflow-hook_1 | at java.lang.reflect.Method.invoke (Method.java:566) workflow-hook_1 | at org.codehaus.mojo.exec.ExecJavaMojo$1.run (ExecJavaMojo.java:297) workflow-hook_1 | at java.lang.Thread.run (Thread.java:834) workflow-hook_1 | [INFO] ------------------------------------------------------------------------ workflow-hook_1 | [INFO] BUILD FAILURE workflow-hook_1 | [INFO] ------------------------------------------------------------------------ workflow-hook_1 | [INFO] Total time: 01:00 min workflow-hook_1 | [INFO] Finished at: 2019-08-09T17:56:13Z workflow-hook_1 | [INFO] ------------------------------------------------------------------------ workflow-hook_1 | [ERROR] Failed to execute goal org.codehaus.mojo:exec-maven-plugin:1.2.1:java (default-cli) on project WorkflowHook: An exception occured while executing the Java class. null: InvocationTargetException: Cannot find value for COMPOSE_PROJECT_NAME -> [Help 1] workflow-hook_1 | [ERROR] workflow-hook_1 | [ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch. workflow-hook_1 | [ERROR] Re-run Maven using the -X switch to enable full debug logging. workflow-hook_1 | [ERROR] workflow-hook_1 | [ERROR] For more information about the errors and possible solutions, please read the following articles: workflow-hook_1 | [ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException workflow-hook_1 | [Thread-1] INFO org.sagebionetworks.ShutdownHook - Shut down signal received. workflow-hook_1 | [Thread-1] INFO org.sagebionetworks.ShutdownHook - Shut down complete. compose.cli.verbose_proxy.proxy_callable: docker wait <- (u'140d45eb68c80b30f76a6efa59f3af5491cc27cd334359812770d095a4106557') compose.cli.verbose_proxy.proxy_callable: docker inspect_container <- (u'140d45eb68c80b30f76a6efa59f3af5491cc27cd334359812770d095a4106557') urllib3.connectionpool._make_request: http://localhost:None "POST /v1.25/containers/140d45eb68c80b30f76a6efa59f3af5491cc27cd334359812770d095a4106557/wait HTTP/1.1" 200 30 compose.cli.verbose_proxy.proxy_callable: docker wait -> 1 urllib3.connectionpool._make_request: http://localhost:None "GET /v1.25/containers/140d45eb68c80b30f76a6efa59f3af5491cc27cd334359812770d095a4106557/json HTTP/1.1" 200 None synapseworkflowhook_workflow-hook_1 exited with code 1 compose.cli.verbose_proxy.proxy_callable: docker inspect_container -> {u'AppArmorProfile': u'docker-default', u'Args': [u'/bin/sh', u'-c', u'exec mvn exec:java -DentryPoint=org.sagebionetworks.WorkflowHook'], u'Config': {u'ArgsEscaped': True, u'AttachStderr': False, u'AttachStdin': False, u'AttachStdout': False, u'Cmd': [u'/bin/sh', u'-c', ...

thomasyu888 commented 5 years ago

Need to add to .env: https://github.com/Sage-Bionetworks/SynapseWorkflowHook/blob/master/.envTemplate#L7

andrewelamb commented 5 years ago

I added the above field and now getting:

workflow-hook_1 | [ERROR] Failed to execute goal org.codehaus.mojo:exec-maven-plugin:1.2.1:java (default-cli) on project WorkflowHook: An exception occured while executing the Java class. null: InvocationTargetException: {"message":"get workflow_orchestrator_shared: no such volume"} -> [Help 1]

andrewelamb commented 5 years ago

I added RUN_WORKFLOW_CONTAINER_IN_PRIVILEGED_MODE=true and got the same error

andrewelamb commented 5 years ago

This was fixed by: COMPOSE_PROJECT_NAME=workfloworchestrator instead of this: COMPOSE_PROJECT_NAME=workflow_orchestrator in my .env file I noticed this volume: workfloworchestrator_shared was being created