REST API access to stdout and stderr files
open | Created 2017-11-21 | Last updated 2019-02-07| Posted by antonkulaga | See in Github


User Requested Improvement


Currently when I ask for metadata or for logs, I get something like:

{
  "calls": {
    "annotate_de_novo.transdecoder": [
      {
        "stderr": "/pipelines/cromwell_1/cromwell-executions/annotate_de_novo/e64a866e-d5c1-4779-8f9d-75457f22f43e/call-transdecoder/execution/stderr",
        "stdout": "/pipelines/cromwell_1/cromwell-executions/annotate_de_novo/e64a866e-d5c1-4779-8f9d-75457f22f43e/call-transdecoder/execution/stdout",
        "attempt": 1,
        "shardIndex": -1
      }
    ]
  },
  "id": "e64a866e-d5c1-4779-8f9d-75457f22f43e"
}

All the details about what really happened (stderr and stdout of the tools that failed) are not accessible via REST API and I have to ssh to the server to read those files. What can be useful is to have a way to get stdout/stderr content for each call with Cromwell REST API, that can save a lot of time on ssh-ing.


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