Merge pull request #187 from umccr/bugfix/coerce-isidentified-to-boolean

Coerce is_identified to boolean
umccr · Nov 22, 2023 · d4df8b3 · d4df8b3
2 parents 1cc4810 + 51dad3b
commit d4df8b3
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Showing 2 changed files with 14 additions and 1 deletion.
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
@@ -90,10 +90,16 @@ def lambda_handler(event, context):
         sample_type = VALIDATION_DEFAULTS["sample_type"]
 
     # Get is identified
-    is_identified: str
+    is_identified: any  # Union[str | bool] not supported in python=3.9
     if (is_identified := event.get("is_identified", None)) is None:
         is_identified = VALIDATION_DEFAULTS["is_identified"]
 
+    # Coerce is_identified to a boolean value
+    if isinstance(is_identified, str) and is_identified == 'identified':
+        is_identified = True
+    elif isinstance(is_identified, str) and is_identified == 'deidentified':
+        is_identified = False
+
     # Check disease name
     if (disease_name := event.get("disease_name", None)) is None:
         disease_name = VALIDATION_DEFAULTS["disease_name"]

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
@@ -210,9 +210,16 @@ def lambda_handler(event, context):
     if (sample_type := event.get("sample_type", None)) is None:
         sample_type = CLINICAL_DEFAULTS["sample_type"].name.lower()
 
+    is_identified: any  # Union[str | bool] not supported in python=3.9
     if (is_identified := event.get("is_identified", None)) is None:
         is_identified = CLINICAL_DEFAULTS["is_identified"].name.lower()
 
+    # Coerce is_identified to a boolean value
+    if isinstance(is_identified, str) and is_identified == 'identified':
+        is_identified = True
+    elif isinstance(is_identified, str) and is_identified == 'deidentified':
+        is_identified = False
+
     # Set panel type (if not null)
     merged_df["panel_type"] = panel_type
     merged_df["sample_type"] = sample_type