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local l4 checks #677

Merged
merged 4 commits into from
Nov 13, 2023
Merged

local l4 checks #677

merged 4 commits into from
Nov 13, 2023

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bloodearnest
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@bloodearnest bloodearnest commented Nov 10, 2023

This PR fixes local_run command to run and surface the new level 4 file checks we added

  • update black formatting
  • improve excluded outputs log formatting
  • Perform level 4 files checks in local_run
  • Add level4_excluded_files results filed to Job db

Fixes #675

Because local_run doesn't have a level 4 directory configured, the
checks were skipped.

This change move that conditional to different location, so the checks
are performed in local_run, and adds tests

Partial fix to #675:
This allows us to keep a record of how many files fail the check, for
audit purposes.

It also allows us to surface the information better in local_run, as we
can pull it from the db.
@bloodearnest bloodearnest merged commit fb80525 into main Nov 13, 2023
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@bloodearnest bloodearnest deleted the local-l4-checks branch November 13, 2023 17:05
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Warn users in local run if they have patient_id column
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