Hi I'm trying to setup a workflow orchestrator for a challenge I'm setting up. I have been trying to follow the instructions found at https://help.synapse.org/docs/Running-a-Challenge.2163409505.html but occasionally found some of them unclear so it's likely I've messed something up but given the nature of the error I have no context to debug this myself. The error occurs in the logs of the docker container after step 13.
See full logs below. Any help would be appreciated.
```
workflow-orchestrator_1 | [INFO] Building WorkflowOrchestrator 1.0-SNAPSHOT
workflow-orchestrator_1 | [INFO] --------------------------------[ jar ]---------------------------------
workflow-orchestrator_1 | [INFO]
workflow-orchestrator_1 | [INFO] >>> exec-maven-plugin:1.2.1:java (default-cli) > validate @ WorkflowOrchestrator >>>
workflow-orchestrator_1 | [INFO]
workflow-orchestrator_1 | [INFO] <<< exec-maven-plugin:1.2.1:java (default-cli) < validate @ WorkflowOrchestrator <<<
workflow-orchestrator_1 | [INFO]
workflow-orchestrator_1 | [INFO]
workflow-orchestrator_1 | [INFO] --- exec-maven-plugin:1.2.1:java (default-cli) @ WorkflowOrchestrator ---
workflow-orchestrator_1 | [org.sagebionetworks.WorkflowOrchestrator.main()] INFO org.sagebionetworks.WorkflowOrchestrator - Precheck completed successfully.
workflow-orchestrator_1 | 19:46:18.553 [org.sagebionetworks.WorkflowOrchestrator.main()] ERROR org.sagebionetworks.client.SynapseProfileProxy - java.lang.reflect.InvocationTargetException
workflow-orchestrator_1 | Nov 17, 2023 7:46:18 PM org.sagebionetworks.ExponentialBackoffRunner execute
workflow-orchestrator_1 | SEVERE: Will not retry: Object syn52966293 does not have a file handle associated with it.
workflow-orchestrator_1 | [WARNING]
workflow-orchestrator_1 | java.lang.reflect.InvocationTargetException
workflow-orchestrator_1 | at jdk.internal.reflect.NativeMethodAccessorImpl.invoke0 (Native Method)
workflow-orchestrator_1 | at jdk.internal.reflect.NativeMethodAccessorImpl.invoke (NativeMethodAccessorImpl.java:62)
workflow-orchestrator_1 | at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke (DelegatingMethodAccessorImpl.java:43)
workflow-orchestrator_1 | at java.lang.reflect.Method.invoke (Method.java:566)
workflow-orchestrator_1 | at org.codehaus.mojo.exec.ExecJavaMojo$1.run (ExecJavaMojo.java:297)
workflow-orchestrator_1 | at java.lang.Thread.run (Thread.java:829)
workflow-orchestrator_1 | Caused by: org.sagebionetworks.client.exceptions.SynapseNotFoundException: Object syn52966293 does not have a file handle associated with it.
workflow-orchestrator_1 | at org.sagebionetworks.client.ClientUtils.throwException (ClientUtils.java:94)
workflow-orchestrator_1 | at org.sagebionetworks.client.ClientUtils.convertResponseBodyToJSONAndThrowException (ClientUtils.java:127)
workflow-orchestrator_1 | at org.sagebionetworks.client.BaseClientImpl.getJson (BaseClientImpl.java:511)
workflow-orchestrator_1 | at org.sagebionetworks.client.BaseClientImpl.getJSONEntity (BaseClientImpl.java:744)
workflow-orchestrator_1 | at org.sagebionetworks.client.SynapseClientImpl.getEntityFileHandlesForCurrentVersion (SynapseClientImpl.java:2086)
workflow-orchestrator_1 | at jdk.internal.reflect.NativeMethodAccessorImpl.invoke0 (Native Method)
workflow-orchestrator_1 | at jdk.internal.reflect.NativeMethodAccessorImpl.invoke (NativeMethodAccessorImpl.java:62)
workflow-orchestrator_1 | at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke (DelegatingMethodAccessorImpl.java:43)
workflow-orchestrator_1 | at java.lang.reflect.Method.invoke (Method.java:566)
workflow-orchestrator_1 | at org.sagebionetworks.client.SynapseProfileProxy$SynapseInvocationHandler.invoke (SynapseProfileProxy.java:55)
workflow-orchestrator_1 | at com.sun.proxy.$Proxy27.getEntityFileHandlesForCurrentVersion (Unknown Source)
workflow-orchestrator_1 | at jdk.internal.reflect.NativeMethodAccessorImpl.invoke0 (Native Method)
workflow-orchestrator_1 | at jdk.internal.reflect.NativeMethodAccessorImpl.invoke (NativeMethodAccessorImpl.java:62)
workflow-orchestrator_1 | at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke (DelegatingMethodAccessorImpl.java:43)
workflow-orchestrator_1 | at java.lang.reflect.Method.invoke (Method.java:566)
workflow-orchestrator_1 | at org.sagebionetworks.SynapseClientFactory$1$1.execute (SynapseClientFactory.java:46)
workflow-orchestrator_1 | at org.sagebionetworks.SynapseClientFactory$1$1.execute (SynapseClientFactory.java:43)
workflow-orchestrator_1 | at org.sagebionetworks.ExponentialBackoffRunner.execute (ExponentialBackoffRunner.java:62)
workflow-orchestrator_1 | at org.sagebionetworks.SynapseClientFactory$1.invoke (SynapseClientFactory.java:43)
workflow-orchestrator_1 | at com.sun.proxy.$Proxy27.getEntityFileHandlesForCurrentVersion (Unknown Source)
workflow-orchestrator_1 | at org.sagebionetworks.WorkflowOrchestrator.getWorkflowURLAndEntrypoint (WorkflowOrchestrator.java:181)
workflow-orchestrator_1 | at org.sagebionetworks.WorkflowOrchestrator.execute (WorkflowOrchestrator.java:225)
workflow-orchestrator_1 | at org.sagebionetworks.WorkflowOrchestrator.main (WorkflowOrchestrator.java:119)
workflow-orchestrator_1 | at jdk.internal.reflect.NativeMethodAccessorImpl.invoke0 (Native Method)
workflow-orchestrator_1 | at jdk.internal.reflect.NativeMethodAccessorImpl.invoke (NativeMethodAccessorImpl.java:62)
workflow-orchestrator_1 | at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke (DelegatingMethodAccessorImpl.java:43)
workflow-orchestrator_1 | at java.lang.reflect.Method.invoke (Method.java:566)
workflow-orchestrator_1 | at org.codehaus.mojo.exec.ExecJavaMojo$1.run (ExecJavaMojo.java:297)
workflow-orchestrator_1 | at java.lang.Thread.run (Thread.java:829)
workflow-orchestrator_1 | [INFO] ------------------------------------------------------------------------
workflow-orchestrator_1 | [INFO] BUILD FAILURE
workflow-orchestrator_1 | [INFO] ------------------------------------------------------------------------
workflow-orchestrator_1 | [INFO] Total time: 5.834 s
workflow-orchestrator_1 | [INFO] Finished at: 2023-11-17T19:46:18Z
workflow-orchestrator_1 | [INFO] ------------------------------------------------------------------------
workflow-orchestrator_1 | [ERROR] Failed to execute goal org.codehaus.mojo:exec-maven-plugin:1.2.1:java (default-cli) on project WorkflowOrchestrator: An exception occured while executing the Java class. null: InvocationTargetException: Object syn52966293 does not have a file handle associated with it. -> [Help 1]
workflow-orchestrator_1 | [ERROR]
workflow-orchestrator_1 | [ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
workflow-orchestrator_1 | [ERROR] Re-run Maven using the -X switch to enable full debug logging.
workflow-orchestrator_1 | [ERROR]
workflow-orchestrator_1 | [ERROR] For more information about the errors and possible solutions, please read the following articles:
workflow-orchestrator_1 | [ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException
workflow-orchestrator_1 | [Thread-1] INFO org.sagebionetworks.ShutdownHook - Shut down signal received.
workflow-orchestrator_1 | [Thread-1] INFO org.sagebionetworks.ShutdownHook - Shut down complete.
workflow-orchestrator_1 | [INFO] Scanning for projects...
workflow-orchestrator_1 | [WARNING]
workflow-orchestrator_1 | [WARNING] Some problems were encountered while building the effective model for org.sagebionetworks:WorkflowOrchestrator:jar:1.0-SNAPSHOT
workflow-orchestrator_1 | [WARNING] 'build.plugins.plugin.version' for org.apache.maven.plugins:maven-eclipse-plugin is missing. @ line 48, column 21
workflow-orchestrator_1 | [WARNING]
workflow-orchestrator_1 | [WARNING] It is highly recommended to fix these problems because they threaten the stability of your build.
workflow-orchestrator_1 | [WARNING]
workflow-orchestrator_1 | [WARNING] For this reason, future Maven versions might no longer support building such malformed projects.
workflow-orchestrator_1 | [WARNING]
```
Created by Seth Paulson Sarudak Ah I see! The file has it's own id. That was the missing piece. Thank you very much for your assistance. I'll see if I can create a clarifying PR when I get the chance. Please review steps 2-4 here: https://github.com/Sage-Bionetworks/SynapseWorkflowOrchestrator/tree/master#linking-your-workflow-with-evaluation-queue-manually
Did you mean
```
EVALUATION_TEMPLATES={"9615450":"syn52968024"}
```
instead of
```
EVALUATION_TEMPLATES={"9615450":"syn52966293"}
```
?
If the instructions are unclear then, once you understand them you might consider submitting a clarifying pull request to the above repo'. Thank you. Thank you for the prompt response! I'm guessing it must be a problem with my ".env" file. Does this look right? (creds removed)
```
WES_ENDPOINT=http://localhost:8082/ga4gh/wes/v1
DOCKER_ENGINE_URL=unix:///var/run/docker.sock
#WES_SHARED_DIR_PROPERTY=
SYNAPSE_USERNAME=---REMOVED---
SYNAPSE_PASSWORD=---REMOVED---
WORKFLOW_OUTPUT_ROOT_ENTITY_ID=syn52966292
EVALUATION_TEMPLATES={"9615450":"syn52966293"}
TOIL_CLI_OPTIONS=--defaultMemory 100M --retryCount 0 --defaultDisk 1000000
COMPOSE_PROJECT_NAME=workflow_orchestrator
#NOTIFICATION_PRINCIPAL_ID=
#SHARE_RESULTS_IMMEDIATELY=
#DATA_UNLOCK_SYNAPSE_PRINCIPAL_ID=
#WORKFLOW_ENGINE_DOCKER_IMAGE=
#MAX_CONCURRENT_WORKFLOWS=10
#RUN_WORKFLOW_CONTAINER_IN_PRIVILEGED_MODE=
```
The evaluation template field is the one location that points at syn52966293 instead of syn52966292 so I guess it must be the culprit? I tried to follow the instructions but found
"JSON map of evaluation IDs to the workflow repo archive, where the key is the evaluation ID and the value is the link address to the archive.
Use the evaluation IDs from Step 3 as the key(s) and the synIDs from Step 5 as the value(s)."
difficult to parse. It looks like the code failed here:
https://github.com/Sage-Bionetworks/SynapseWorkflowOrchestrator/blob/master/src/main/java/org/sagebionetworks/WorkflowOrchestrator.java#L181
when trying to access what it expected to be a file, but where you gave it not a **file** but a **project**: https://www.synapse.org/#!Synapse:syn52966293
Drop files to upload
Object syn52966293 does not have a file handle associated with it page is loading…