Merge pull request #196 from umccr/dev

umccr · Nov 22, 2023 · 95c3289 · 95c3289
2 parents 0fb44b4 + 1585f79
commit 95c3289
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diff --git a/deploy/cttso-ica-to-pieriandx-cdk/Changelog.md b/deploy/cttso-ica-to-pieriandx-cdk/Changelog.md
@@ -17,6 +17,12 @@ are nested under deploy/cttso-ica-to-pieriandx-cdk.
   * Resolves https://github.com/umccr/cttso-ica-to-pieriandx/issues/185
 * Use non-latest docker tag. (https://github.com/umccr/cttso-ica-to-pieriandx/pull/191) 
   * 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
+
+### Workarounds
+* Don't submit NTC samples (https://github.com/umccr/cttso-ica-to-pieriandx/pull/195)
+
 
 ## 2023-11-08
 

diff --git a/...mbdas/get_metadata_from_portal_and_defaults_and_launch_validation_workflow/lambda_code.py b/...mbdas/get_metadata_from_portal_and_defaults_and_launch_validation_workflow/lambda_code.py
@@ -188,10 +188,10 @@ def lambda_handler(event, context):
         )
     # For deidentified - we rename the external subject id as the study subject identifier
     else:
-        sample_df["study_identifier"] = sample_df["project_name"]
+        sample_df["study_id"] = sample_df["project_name"]
         sample_df = sample_df.rename(
             columns={
-                "external_subject_id": "study_subject_identifier"
+                "external_subject_id": "participant_id"
             }
         )
 

diff --git a/...k/lambdas/get_metadata_from_portal_and_redcap_and_launch_clinical_workflow/lambda_code.py b/...k/lambdas/get_metadata_from_portal_and_redcap_and_launch_clinical_workflow/lambda_code.py
@@ -303,12 +303,12 @@ def lambda_handler(event, context):
                 "external_subject_id": "mrn"
             }
         )
-    # Step 7b - for deidentified samples, use study_identified and study_subject_identifier
+    # Step 7b - for deidentified samples, use study_identified and participant_id
     else:
-        merged_df["study_identifier"] = merged_df["project_name"]
+        merged_df["study_id"] = merged_df["project_name"]
         merged_df = merged_df.rename(
             columns={
-                "external_subject_id": "study_subject_identifier"
+                "external_subject_id": "participant_id"
             }
         )
 

diff --git a/...ieriandx-cdk/lambdas/launch_available_payloads_and_update_cttso_lims_sheet/lambda_code.py b/...ieriandx-cdk/lambdas/launch_available_payloads_and_update_cttso_lims_sheet/lambda_code.py
@@ -242,7 +242,8 @@ def get_libraries_for_processing(merged_df) -> pd.DataFrame:
         "    ( "
         "      glims_needs_redcap == False "
         "    ) "
-        "  ) "
+        "  ) and "
+        "  not subject_id == 'SBJ00006' "
         ") ",
         engine="python"  # Required for the isnull bit - https://stackoverflow.com/a/54099389/6946787
     )