Hotfixes for type hinting error

Changelog.md

@@ -4,6 +4,16 @@ Changes in this log refer only to changes that make it to the 'main' branch. and
 
 For changes in deployment, please see the [deployment changelog](deploy/cttso-ica-to-pieriandx-cdk/Changelog.md) 
 
+## 2023-11-22
+
+> Author: Alexis Lucattini
+> Email: [[email protected]](mailto:[email protected])
+
+### Hotfixes
+* 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
+
+
 ## 2023-11-08
 
 > Author: Alexis Lucattini

deploy/cttso-ica-to-pieriandx-cdk/Changelog.md

@@ -3,6 +3,19 @@
 Changes in this log refer only to changes that make it to the 'main' branch and
 are nested under deploy/cttso-ica-to-pieriandx-cdk.  
 
+## 2023-11-27
+
+> Author: Alexis Lucattini
+> Email: [[email protected]](mailto:[email protected])
+
+### Hotfixes
+* lims maker lambda fails on type hinting for multiple types (https://github.com/umccr/cttso-ica-to-pieriandx/pull/201)
+  * Resolves https://github.com/umccr/cttso-ica-to-pieriandx/issues/200
+
+### Enhancements
+* Use global var for NTC Subject ID (https://github.com/umccr/cttso-ica-to-pieriandx/pull/202)
+
+
 ## 2023-11-22
 
 > Author: Alexis Lucattini

deploy/cttso-ica-to-pieriandx-cdk/lambdas/launch_available_payloads_and_update_cttso_lims_sheet/lambda_code.py

@@ -61,7 +61,8 @@
     REDCAP_APIS_LAMBDA_FUNCTION_ARN_SSM_PARAMETER, \
     CLINICAL_LAMBDA_FUNCTION_SSM_PARAMETER_PATH, \
     VALIDATION_LAMBDA_FUNCTION_ARN_SSM_PARAMETER_PATH, \
-    MAX_SUBMISSIONS_PER_LIMS_UPDATE_CYCLE, MAX_ATTEMPTS_WAKE_LAMBDAS, EVENT_RULE_FUNCTION_NAME_SSM_PARAMETER_PATH
+    MAX_SUBMISSIONS_PER_LIMS_UPDATE_CYCLE, MAX_ATTEMPTS_WAKE_LAMBDAS, EVENT_RULE_FUNCTION_NAME_SSM_PARAMETER_PATH, \
+    NTC_SUBJECT_ID
 
 logger = get_logger()
 
@@ -228,23 +229,23 @@ def get_libraries_for_processing(merged_df) -> pd.DataFrame:
     one_week_ago = (datetime.now() - timedelta(days=7)).date()
 
     to_process_df = merged_df.query(
-        "("
-        "  pieriandx_case_id.isnull() and "
-        "  ( pieriandx_submission_time.isnull() or pieriandx_submission_time < @one_week_ago ) and "
-        "  not in_pieriandx and "
-        "  not portal_wfr_id.isnull() and "
-        "  portal_wfr_status == 'Succeeded' and "
-        "  portal_is_failed_run == False and "
-        "  ( "
-        "    ( "
-        "      not redcap_is_complete.isnull() and redcap_is_complete.str.lower() == 'complete' "
-        "    ) or "
-        "    ( "
-        "      glims_needs_redcap == False "
-        "    ) "
-        "  ) and "
-        "  not subject_id == 'SBJ00006' "
-        ") ",
+        f"("
+        f"  pieriandx_case_id.isnull() and "
+        f"  ( pieriandx_submission_time.isnull() or pieriandx_submission_time < @one_week_ago ) and "
+        f"  not in_pieriandx and "
+        f"  not portal_wfr_id.isnull() and "
+        f"  portal_wfr_status == 'Succeeded' and "
+        f"  portal_is_failed_run == False and "
+        f"  ( "
+        f"    ( "
+        f"      not redcap_is_complete.isnull() and redcap_is_complete.str.lower() == 'complete' "
+        f"    ) or "
+        f"    ( "
+        f"      glims_needs_redcap == False "
+        f"    ) "
+        f"  ) and "
+        f"  not subject_id == '{NTC_SUBJECT_ID}' "
+        f") ",
         engine="python"  # Required for the isnull bit - https://stackoverflow.com/a/54099389/6946787
     )
 
@@ -290,7 +291,7 @@ def get_libraries_for_processing(merged_df) -> pd.DataFrame:
     ]
 
 
-def submit_library_to_pieriandx(subject_id: str, library_id: str, workflow_run_id: str, lambda_arn: str, panel_type: str, sample_type: str, is_identified: Union[bool | str], default_snomed_term: str):
+def submit_library_to_pieriandx(subject_id: str, library_id: str, workflow_run_id: str, lambda_arn: str, panel_type: str, sample_type: str, is_identified: str, default_snomed_term: str):
     """
     Submit library to pieriandx
     :param is_identified:

deploy/cttso-ica-to-pieriandx-cdk/lambdas/layers/lambda_utils/globals.py

@@ -194,3 +194,5 @@ class SampleType(Enum):
     rf"umccr__automated__{PORTAL_CTTSO_WORKFLOW_TYPE_NAME}__(SBJ\d{{5}})__(L\d{{7}})__\S+"
 )
 
+
+NTC_SUBJECT_ID = "SBJ00006"