Clarify expected list format for sync manifest

Description

When multiple values are provided for a field in the sync manifest file, the expected format of that string is unclear — for example, multiple synIDs in the "used" field. Looking at the docs for syncToSynapse, the answer is there (semicolon-separated values), but it's not entirely obvious whether the "Example" provided ("https://github.org/; /path/to_local/code.py") is an example of a list or multiple examples.

Moreover, the docs show values separated by a semicolon AND space, but this causes an error with the client (it's possible this is a bug):

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 Validating provenance...Traceback (most recent call last): File "run_sync.py", line 21, in <module> main(sys.argv[1:]) File "run_sync.py", line 17, in main sync.syncToSynapse(syn, manifest_file, dry_run=True) File "/hpc/packages/minerva-common/py_packages/2.7/lib/python2.7/site-packages/synapseutils/sync.py", line 320, in syncToSynapse df = readManifestFile(syn, manifest_file) import sys File "/hpc/packages/minerva-common/py_packages/2.7/lib/python2.7/site-packages/synapseutils/sync.py", line 214, in readManifestFile df = _sortAndFixProvenance(syn, df) File "/hpc/packages/minerva-common/py_packages/2.7/lib/python2.7/site-packages/synapseutils/sync.py", line 153, in _sortAndFixProvenance df.set_value(path, 'used', [_checkProvenace(item, path) for item in used]) File "/hpc/packages/minerva-common/py_packages/2.7/lib/python2.7/site-packages/synapseutils/sync.py", line 146, in _checkProvenace "Specifically %s, is neither a valid URL or synapseId.") %(path, item)) synapseclient.exceptions.SynapseProvenanceError: The provenance record for file: ./1005_TCX_sailfish_out.tar.gz is incorrect. Specifically syn8621132, is neither a valid URL or synapseId.

In this case, the value "syn8619777; syn8621132" under "used" seems to be causing the error, because the space in " syn8621132" isn't getting stripped before looking up the entity.

Environment

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Status

Assignee

Unassigned

Reporter

James Eddy

Validator

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Release Version History

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Epic Link

Fix versions

Affects versions

py-1.7

Priority

Major
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