Bug #16083: a-c-r run with workflow id doesn't work? - Arvados

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Bug #16083

closed

a-c-r run with workflow id doesn't work?

Added by Peter Amstutz about 4 years ago. Updated about 4 years ago.

Status:

Resolved

Priority:

Normal

Assigned To:

Category:

CWL

Target version:

Story points:

Description

From gitter:

dante@dante-ryzen:~/arvados/doc/user/cwl/bwa-mem$ /home/dante/arvados/sdk/cwl/bin/arvados-cwl-runner arv01-7fd4e-rpsv98hqd451ywz
2020-01-23 12:07:24 cwltool INFO: /home/dante/arvados/sdk/cwl/bin/arvados-cwl-runner 1.4.3, arvados-python-client 1.4.3, cwltool 1.0.20181217162649
2020-01-23 12:07:24 cwltool INFO: Resolved 'arv01-7fd4e-rpsv98hqd451ywz' to 'arvwf:arv01-7fd4e-rpsv98hqd451ywz#main'
2020-01-23 12:07:24 cwltool ERROR: I'm sorry, I couldn't load this CWL file, try again with --debug for more information.
The error was: expected a single document in the stream
  in "arvwf:arv01-7fd4e-rpsv98hqd451ywz", line 1, column 1
but found another document
  in "arvwf:arv01-7fd4e-rpsv98hqd451ywz", line 128, column 1
dante@dante-ryzen:~/arvados/doc/user/cwl/bwa-mem$

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Updated by Peter Amstutz about 4 years ago

Description updated (diff)

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Updated by Peter Amstutz about 4 years ago

Fixed in master.

It was adding a "label" field, but the assumption was that the yaml was in block style, but at some point we switched it to flow (JSON) style, so adding the "label" field by just tacking on an extra line became a syntax error.

Now it parses the yaml, adds the field, then dumps it again.

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