ICGC-TCGA-PanCancer / CGP-Somatic-Docker

Dockerised and simplified version of SeqWare-CGP-SomaticCore
GNU Affero General Public License v3.0
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Feature/support new schema salad #23

Closed garyluu closed 3 years ago

garyluu commented 3 years ago

Upgrading cwltool by default installs a newer version of schema salad which prevents duplicate keys.

(venv) gluu@potato:~/CGP-Somatic-Docker$ cwltool --validate Dockstore.cwl
INFO /home/gluu/venv/bin/cwltool 3.0.20200807132242
INFO Resolved 'Dockstore.cwl' to 'file:///home/gluu/CGP-Somatic-Docker/Dockstore.cwl'
ERROR I'm sorry, I couldn't load this CWL file, try again with --debug for more information.
The error was: while constructing a mapping
  in "file:///home/gluu/CGP-Somatic-Docker/Dockstore.cwl", line 3, column 1
found duplicate key "dct:contributor" with value "ordereddict([('foaf:name', 'Denis Yuen'), ('foaf:mbox', 'mailto:denis.yuen@oicr.on.ca')])" (original value: "ordereddict([('foaf:name', "Brian O'Connor"), ('foaf:mbox', 'mailto:broconno@ucsc.edu')])")
  in "file:///home/gluu/CGP-Somatic-Docker/Dockstore.cwl", line 14, column 1

To suppress this check see:
    http://yaml.readthedocs.io/en/latest/api.html#duplicate-keys

Duplicate keys will become an error in future releases, and are errors
by default when using the new API.

This fixes the duplicate key.

Also removed the warning:

URI prefix 'foaf' of 'foaf:name' not recognized, are you missing a $namespaces section?
URI prefix 'foaf' of 'foaf:mbox' not recognized, are you missing a $namespaces section?
URI prefix 'foaf' of 'foaf:name' not recognized, are you missing a $namespaces section?
URI prefix 'foaf' of 'foaf:mbox' not recognized, are you missing a $namespaces section?
URI prefix 'foaf' of 'foaf:name' not recognized, are you missing a $namespaces section?
URI prefix 'foaf' of 'foaf:mbox' not recognized, are you missing a $namespaces section?

Also update Travis to validate