galaxyproject / galaxyproject/blend4j

Workflow execution throws exception

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#40 5 comments 0 reactions 0 assignees View on GitHub
Dominant language
Java
Stars
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Forks
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Description

Executing a workflow according to the example in the JavaDocs no longer seem to work correctly.
The `WorkflowsClientImpl.runWorkflow()` call results in the following Exception:

```
Exception in thread "main" GalaxyResponseException{status=500, responseBody={"err_msg": "Uncaught exception in exposed API method:", "err_code": 0}, errorMessage=Uncaught exception in exposed API method:, errorCode=0, traceback=null}
at com.github.jmchilton.blend4j.galaxy.Client.buildResponseException(Client.java:18)
at com.github.jmchilton.blend4j.BaseClient.checkResponse(BaseClient.java:138)
at com.github.jmchilton.blend4j.BaseClient.create(BaseClient.java:47)
at com.github.jmchilton.blend4j.BaseClient.create(BaseClient.java:36)
at com.github.jmchilton.blend4j.BaseClient.create(BaseClient.java:32)
at com.github.jmchilton.blend4j.galaxy.WorkflowsClientImpl.runWorkflowResponse(WorkflowsClientImpl.java:38)
at com.github.jmchilton.blend4j.galaxy.WorkflowsClientImpl.runWorkflow(WorkflowsClientImpl.java:42)
```

Despite this the workflow does start, but the particular workflow involved here does not complete fully. Some jobs simply fail to run, even though the same workflow runs fine through the GUI or with bioblend (using the same inputs). This could be a separate problem, but first need to get the `WorkflowsClientImpl.runWorkflow()` call working correctly.

Contributor guide

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Research direction

Start with the JavaDocs workflow example and reproduce the WorkflowsClientImpl.runWorkflow() call. Read WorkflowsClientImpl.java and the Client.java/BaseClient.java stack locations shown in the exception, then compare the request with the GUI or bioblend behavior. Done means the call completes without the 500 exception and the workflow runs successfully.

Written by the indexing model from the issue text.

Assessment

Tech stack
java
Domain
api
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
38/100

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