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A couple small fixes #286

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merged 2 commits into from
Oct 30, 2023
Merged

A couple small fixes #286

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a9cdbd4
docs: fix link to source that changed after a refactor
mikix Oct 30, 2023
53d243e
fix: change overwrite detection to also allow .meta files
mikix Oct 30, 2023
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2 changes: 1 addition & 1 deletion cumulus_etl/formats/batched_files.py
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Original file line number Diff line number Diff line change
Expand Up @@ -61,7 +61,7 @@ def _confirm_no_unknown_files_exist(self, folder: str) -> None:
except FileNotFoundError:
return # folder doesn't exist, we're good!

allowed_pattern = re.compile(rf"{self.dbname}\.[0-9]+\.{self.suffix}")
allowed_pattern = re.compile(rf"{self.dbname}\.[0-9]+\.({self.suffix}|meta)")
if not all(map(allowed_pattern.fullmatch, filenames)):
errors.fatal(
f"There are unexpected files in the output folder '{folder}'.\n"
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2 changes: 1 addition & 1 deletion docs/deid.md
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Expand Up @@ -74,7 +74,7 @@ But the devil is in the details, because it can be configured to do nothing at a
or redact everything.

Cumulus ETL uses a
[custom configuration](https://github.com/smart-on-fhir/cumulus-etl/blob/main/cumulus/deid/ms-config.json),
[custom configuration](https://github.com/smart-on-fhir/cumulus-etl/blob/main/cumulus_etl/deid/ms-config.json),
designed to remove everything by default, and only allow specifically mentioned fields
(i.e. an allow-list or whitelist).

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1 change: 1 addition & 0 deletions tests/formats/test_ndjson.py
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Expand Up @@ -49,6 +49,7 @@ def store(
(None, True),
([], True),
(["condition.1234.ndjson", "condition.22.ndjson"], True),
(["condition.000.meta"], True),
(["condition.ndjson"], False),
(["condition.000.parquet"], False),
(["patient.000.ndjson"], False),
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