Bug #13766


[API] bug in libyaml / Pysch used by API server to parse yaml

Added by Peter Amstutz about 6 years ago. Updated 5 months ago.

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Since 0.13.11 ruamel.yaml produces files like this:

  - id: #main/x
    type: File
    default: {class: File, location: keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt,
      size: 16, basename: blorp.txt, nameroot: blorp, nameext: .txt}

The issue comes up from keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt in "flow style" has an embedded ':' character.

Relevant changelog:

(0.13.11) 2017-01-23:
  - allow ':' in flow style scalars if not followed by space. Also don't
    quote such scalar as this is no longer necessary.
  - add python 3.6 manylinux wheel to PyPI

This is explicitly allowed by the YAML spec, however the API server rejects it:

<HttpError 422 when requesting returned "Definition is not valid yaml abc: (<unknown>): found unexpected ':' while scanning a plain scalar at line 22 column 38">

This seems to be a bug in libyaml, which is used by Pysch (the Ruby YAML engine). It was recently fixed:

However at the time of this writing there is no stable release of libyaml with this bugfix, only a prerelease 0.2.2-pre1

Pysch is part of the standard library. I don't know if it is tied to a particular libyaml, and how to upgrade which libyaml gets used.


  • Wait for stable releases of libyaml / pysch (unknown amount of time)
  • Downgrade ruamel.yaml (messy)
  • Some kind of regex output fixup in a-c-r to ensure these values are quoted
  • Some kind of regex input fixup on api server to ensure these values are quoted
  • Emit plain block style yaml, not "round trip" (breaks tests, tedious but fixable)
  • Emit plain json (breaks tests, tedious but fixable)

Subtasks 2 (1 open1 closed)

Task #13769: Review 13766-libyaml-workaroundResolvedPeter Amstutz07/09/2018Actions
Task #13848: Monitor dependencies for release of updateIn Progress07/09/2018Actions

Related issues

Related to Arvados - Bug #13681: [CWL] Cannot set submit-runner-ram when running from WorkbenchResolvedPeter Amstutz07/05/2018Actions

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