From 43bdf69157e0bb0270fd96d7b2a35cd9ebc219aa Mon Sep 17 00:00:00 2001 From: Alexis Lucattini Date: Wed, 22 Nov 2023 22:13:12 +1100 Subject: [PATCH 1/2] Use pd NaT when using deidentified samples --- utils/accession.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/utils/accession.py b/utils/accession.py index 6223631..c294543 100644 --- a/utils/accession.py +++ b/utils/accession.py @@ -538,7 +538,7 @@ def sanitise_data_frame(input_df: pd.DataFrame) -> pd.DataFrame: input_df["date_of_birth"] = input_df.apply( lambda x: x.date_of_birth if hasattr(x, "date_of_birth") - else pd.NAT, + else pd.NaT, axis="columns" ) input_df["first_name"] = input_df.apply( From a812aa4a5817ca0817106f3cad90f2eb6102d6ed Mon Sep 17 00:00:00 2001 From: Alexis Lucattini Date: Wed, 22 Nov 2023 22:15:59 +1100 Subject: [PATCH 2/2] Updated changelog --- deploy/cttso-ica-to-pieriandx-cdk/Changelog.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/deploy/cttso-ica-to-pieriandx-cdk/Changelog.md b/deploy/cttso-ica-to-pieriandx-cdk/Changelog.md index 046cd4d..d80020c 100644 --- a/deploy/cttso-ica-to-pieriandx-cdk/Changelog.md +++ b/deploy/cttso-ica-to-pieriandx-cdk/Changelog.md @@ -19,6 +19,8 @@ are nested under deploy/cttso-ica-to-pieriandx-cdk. * Resolves https://github.com/umccr/cttso-ica-to-pieriandx/issues/190 * Fix deidentified samples where wrong keys used for study id and participant id (https://github.com/umccr/cttso-ica-to-pieriandx/pull/194) * Resolves https://github.com/umccr/cttso-ica-to-pieriandx/issues/193 +* Fix deidentified samples where NAT instead of NaT null value was used (https://github.com/umccr/cttso-ica-to-pieriandx/pull/198) + * Resolves https://github.com/umccr/cttso-ica-to-pieriandx/issues/197 ### Workarounds * Don't submit NTC samples (https://github.com/umccr/cttso-ica-to-pieriandx/pull/195)