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fix: Ga4gh tes bugfixes #1127

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merged 11 commits into from Aug 12, 2021
Merged

fix: Ga4gh tes bugfixes #1127

merged 11 commits into from Aug 12, 2021

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svedziok
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@svedziok svedziok commented Aug 9, 2021

Description

This PR contains two bugfixes

  • Adds missing py-tes package, which is required for GA4GH job submission
  • Resolve bug with remote log or benchmarkfiles

QC

  • [ x] The PR contains a test case for the changes or the changes are already covered by an existing test case.
  • [ x] The documentation (docs/) is updated to reflect the changes or this is not necessary (e.g. if the change does neither modify the language nor the behavior or functionalities of Snakemake).

@svedziok svedziok changed the title Ga4gh tes bugfixes fix: Ga4gh tes bugfixes Aug 9, 2021
@svedziok svedziok marked this pull request as ready for review Aug 9, 2021
@svedziok svedziok requested a review from johanneskoester as a code owner Aug 9, 2021
setup.py Outdated
@@ -76,6 +76,7 @@
"filelock",
"stopit",
"tabulate",
"py-tes",
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@johanneskoester johanneskoester Aug 10, 2021

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I don't think this needs to be a required dependency. But the docs should probably say that py-tes needs to be installed.

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@johanneskoester johanneskoester Aug 10, 2021

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And the import statement here should be wrapped in a try-except with a WorkflowError("Unable to import Python package tes. TES backend requires py-tes to be installed. Please install py-tes, e.g. via Conda or Pip.")

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@svedziok svedziok Aug 10, 2021

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Ok, I added a try-except statement in the init function. I will also a note at the documentation

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github-actions bot commented Aug 10, 2021

Please format your code with black: black snakemake tests/*.py.

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sonarcloud bot commented Aug 10, 2021

Kudos, SonarCloud Quality Gate passed!    Quality Gate passed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 0 Code Smells

No Coverage information No Coverage information
0.0% 0.0% Duplication

@svedziok svedziok requested a review from johanneskoester Aug 11, 2021
@johanneskoester johanneskoester merged commit af21d6c into main Aug 12, 2021
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@johanneskoester johanneskoester deleted the ga4gh_tes_bugfixes branch Aug 12, 2021
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johanneskoester commented Aug 12, 2021

Thank you!

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2 participants