ArvadosWishlist

• 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 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?)

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)">

• the arvados-api-server package breaks during package installation when installed on an empty system: https://gist.github.com/gijzelaerr/7faebd0d769b4707a0683dadeb6deb33 A package installation should not crash.
• When Nginx and bundle are installed the installation still crashes: https://gist.github.com/gijzelaerr/1011528df850a766855ae0aaf247bd87