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Michael R. Crusoe edited this page Apr 25, 2020 · 13 revisions
  • The user interface for approving users doesn't make sense (no "activate" button; the setup button doesn't change the "activate" flag until the user logs in)
  • Export workflows+provenance as RO-Crate/CWLProv
  • Don't force users to upload public docker containers to the server, side-load them from the server and verify hashes
  • update arvados-cwl-runner to work with Python 3.8 (needs newer ruamel.yaml, I think?)
  • Can arv keep put accept a URL to directly load data from the server side (not downloading locally and then re-uploading)?
  • https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca#Provenance_graph is empty and missing the workflow that produced this collection
  • no automated install scripts/templates
  • components need official Debian packaging
    • arvados-api-server
    • arvados-controller
    • libnginx-mod-http-passenger
  • That arv:RuntimeConstraints.outputDirType.keep_output_dir was autoselected if all outputs are "streamable: True" (and that streaming "keep" writes were supported in mixed streaming setups
  • Better guidance on why jobs were killed: https://workbench.lugli.arvadosapi.com/container_requests/lugli-xvhdp-7jmagj6d9jwg9ds#Log
  • Separation of crunchstat and similar output from the stdout/stderr stream (via UI filter?)

Errors seen

Failure to upload Docker containers

$ arvados-cwl-runner Ambarish_Kumar_SOP-GATK-SAR-CoV-2.cwl Ambarish_Kumar_SOP-GATK-SAR-CoV-2_inputs.yml   
INFO /home/michael/src/2020-covid-19-bh/env3.7/bin/arvados-cwl-runner 2.0.1, arvados-python-client 2.0.1, cwltool 1.0.20190831161204
INFO Resolved 'Ambarish_Kumar_SOP-GATK-SAR-CoV-2.cwl' to 'file:///home/michael/src/2020-covid-19-bh/Ambarish_Kumar_SOP/Ambarish_Kumar_SOP-GATK-SAR-CoV-2.cwl'
WARNING Workflow checker warning:
Ambarish_Kumar_SOP-GATK-SAR-CoV-2.cwl:57:12: Source 'sequences_with_dictionary' of type "File" may
                                             be incompatible
Ambarish_Kumar_SOP-GATK-SAR-CoV-2.cwl:88:7:    with sink 'reference' of type "File"
Ambarish_Kumar_SOP-GATK-SAR-CoV-2.cwl:57:12: Source 'sequences_with_dictionary' of type "File" may
                                             be incompatible
Ambarish_Kumar_SOP-GATK-SAR-CoV-2.cwl:105:7:   with sink 'reference' of type "File"
INFO Upload local files: "ebola_mut_reads1.fq" "ebola_mut_reads2.fq" "ebola_ref.fasta"
INFO Using collection bcb759e2e40dcd91eedcded863913a7c+219 (lugli-4zz18-kk9c9rhbzq5wf4s)
INFO Downloading http://edamontology.org/EDAM_1.18.owl (2752312 bytes)
ERROR Unhandled error, try again with --debug for more information:
  <HttpError 422 when requesting https://lugli.arvadosapi.com/arvados/v1/collections?ensure_unique_name=true&alt=json returned "request failed: http://localhost:8004/arvados/v1/collections: 422 Unprocessable Entity: Name cannot contain a '/' character (req-8gddg6hazk0npc8pvpt2)">
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