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Feature #14322

closed

[CWL] Accept collection uuid in input

Added by Peter Amstutz over 5 years ago. Updated about 5 years ago.

Status:
Resolved
Priority:
Normal
Assigned To:
Peter Amstutz
Category:
-
Target version:
2019-03-27 Sprint
Story points:
2.0
Release:
Arvados v1.4 - Q1/Q2 2019
Release relationship:
Auto

Description

Arvados-cwl-runner should allow users to provide uuids in input documents. For example:

{
  "file1": {
    "class": "File",
    "location": "keep:zzzzz-4zz18-zzzzzzzzzzzzz/file1.txt" 
  }
}

Arvados-cwl-runner should replace the value in "location" with the portable data hash and record the UUID in the "arv:collection" field. This applies to both File and Directory objects. Implementation note: this should probably happen somewhere in upload_workflow_deps() which is responsible for updating File references for uploaded files.

{
  "file1": {
    "class": "File",
    "location": "keep:abc+123/file1.txt",
    "arv:collection": "zzzzz-4zz18-zzzzzzzzzzzzz/file1.txt" 
  }
}

Users may provide both "location" by PDH and "arv:collection" in the input. If both portable data hash and arv:collection are present, the portable data hash will take precedence. Print a warning (or error???) if the collection uuid is not readable or the does not match the PDH that was provided.

When constructing container requests, if "arv:collection" is known for a File or Directory object, include it in the mount object alongside the portable data hash.

Implementation note: code paths that test startswith("keep:") will need to be updated to distinguish keep identifiers by UUID or PDH. (Alternately, we could use a different uri scheme for uuids).

Subtasks 1 (0 open — 1 closed)

Task #14893: Review 14322-cwl-uuid-inputResolvedPeter Amstutz03/13/2019Actions

Related issues

Related to Arvados - Feature #11442: [CWL] Resolve symbolic names to collectionsNewActions
Related to Arvados - Feature #14323: [API] Accept container mounts that specify both uuid and portable_data_hashResolvedLucas Di Pentima11/07/2018Actions
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