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Bug #15358
closed
[cwl] CWL conformance test formattest2 fails with C locale
Start date:
07/03/2019
Due date:
% Done:
100%
Estimated time:
(Total: 0.00 h)
Story points:
-
Release:
Release relationship:
Auto
Description
When LANG=C instead of a UTF-8 locale like en_US.UTF-8, the CWL conformance test, v1.0/formattest2.cwl, fails with an encoding error trying to read EDAM.owl which contains UTF-8 characters, but doesn't have an XML encoding declaration in its prolog.
Test 65 failed: /home/ci/arvados-cwl-runner-with-checksum.sh --outdir=/tmp/tmp7oGCB5 --quiet v1.0/formattest2.cwl v1.0/formattest2-job.json
Test format checking against ontology using subclassOf.
Returned non-zero
URI prefix 'edam' of 'edam:format_1929' not recognized, are you missing a $namespaces section?
Could not load extension schema keep:29dc87213e125b67355699e8953d3820+62/EDAM.owl: 'ascii' codec can't decode byte 0xc3 in position 3352: ordinal not in range(128)
ERROR Workflow execution failed:
Expected value of 'input' to have format http://edamontology.org/format_2330 but
File has an incompatible format: {
"format": "http://edamontology.org/format_1929",
"basename": "ref.fasta",
"nameroot": "ref",
"nameext": ".fasta",
"location": "keep:23b1d68b203d6c75f314fe9804f50c0e+59/ref.fasta",
"class": "File",
"size": 12010
}
ERROR Workflow error, try again with --debug for more information:
Workflow did not return a result.
the offending XML snippet is:
<dc:creator>Matúš Kalaš</dc:creator>
Updated by Tom Morris 
Updated by
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