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Seqera Platform CLI: handle failed tasks #2286

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merged 3 commits into from Feb 2, 2024
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@ahvigil ahvigil commented Jan 30, 2024

fixes #2285 by checking for null d["complete"]

  • This comment contains a description of changes (with reason)
  • There is example tool output for tools in the https://github.com/MultiQC/test-data repository or attached to this PR
  • Code is tested and works locally (including with --strict flag)
  • docs/README.md is updated with link to below
  • docs/modulename.md is created
  • Everything that can be represented with a plot instead of a table is a plot
  • Report sections have a description and help text (with self.add_section)
  • There aren't any huge tables with > 6 columns (explain reasoning if so)
  • Each table column has a different colour scale to its neighbour, which relates to the data (eg. if high numbers are bad, they're red)
  • Module does not do any significant computational work

@@ -171,7 +171,7 @@ def _parse_data(self, d):
# "start" and "complete" are time stamps like time stamps like 2023-10-22T14:39:01Z
# parse them with a library, take the difference "complete" - "start" to get the
# wall time, and convert the wall time it to a human-readable format.
if "start" in d and "complete" in d:
if "start" in d and "complete" in d and d["complete"] is not None:
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note that due to the dict comprehension on line 162, "complete" in d is always true... but I left this in here in case the above ever changes.

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Thanks!

@vladsavelyev vladsavelyev changed the title handle failed tasks in seqera cli dump Seqera Platform CLI: handle failed tasks Feb 2, 2024
@vladsavelyev vladsavelyev merged commit 98c5bd3 into MultiQC:main Feb 2, 2024
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seqera cli files sometimes fail to load
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