Added snomed term to submission df

umccr · Nov 7, 2023 · 051f2d0 · 051f2d0
1 parent fba4d3f
commit 051f2d0
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Showing 3 changed files with 21 additions and 9 deletions.
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
@@ -46,7 +46,8 @@ def lambda_handler(event, context):
         "ica_workflow_run_id": "wfr.123abc",
         "panel_type": "main",
         "sample_type": "validation",
-        "is_identified": False
+        "is_identified": False | "deidentified",
+        "disease_name": ""Disseminated malignancy of unknown primary""
     }
     """
 
@@ -93,13 +94,16 @@ def lambda_handler(event, context):
     if (is_identified := event.get("is_identified", None)) is None:
         is_identified = VALIDATION_DEFAULTS["is_identified"]
 
+    # Check disease name
+    if (disease_name := event.get("disease_name", None)) is None:
+        disease_name = VALIDATION_DEFAULTS["disease_name"]
+
     # Update sample_df with validation defaults
     sample_df["sample_type"] = sample_type
     sample_df["panel_type"] = panel_type
     sample_df["is_identified"] = is_identified
+    sample_df["disease_name"] = disease_name
     sample_df["indication"] = VALIDATION_DEFAULTS["indication"]
-    sample_df["disease_id"] = VALIDATION_DEFAULTS["disease_id"]
-    sample_df["disease_name"] = VALIDATION_DEFAULTS["disease_name"]
     sample_df["requesting_physicians_first_name"] = VALIDATION_DEFAULTS["requesting_physicians_first_name"]
     sample_df["requesting_physicians_last_name"] = VALIDATION_DEFAULTS["requesting_physicians_last_name"]
     sample_df["specimen_type"] = VALIDATION_DEFAULTS["specimen_type"]

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
@@ -195,6 +195,7 @@ def get_libraries_for_processing(merged_df) -> pd.DataFrame:
       * is_identified
       * needs_redcap
       * redcap_is_complete
+      * default_snomed_term
     """
 
     # Initialise
@@ -206,7 +207,8 @@ def get_libraries_for_processing(merged_df) -> pd.DataFrame:
         "sample_type",
         "is_identified",
         "needs_redcap",
-        "redcap_is_complete"
+        "redcap_is_complete",
+        "default_snomed_term"
     ]
 
     # Processing libraries must meet the following criteria
@@ -273,6 +275,7 @@ def get_libraries_for_processing(merged_df) -> pd.DataFrame:
       "sample_type",
       "is_identified",
       "needs_redcap"
+      "default_snomed_term"
     ]
 
     for column_name in new_column_names:
@@ -284,14 +287,17 @@ 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: bool):
+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):
     """
     Submit library to pieriandx
+    :param is_identified:
+    :param sample_type:
     :param subject_id:
     :param library_id:
     :param workflow_run_id:
     :param lambda_arn:
     :param panel_type:
+    :param default_snomed_term
     :return:
     """
     lambda_client: LambdaClient = get_boto3_lambda_client()
@@ -302,7 +308,8 @@ def submit_library_to_pieriandx(subject_id: str, library_id: str, workflow_run_i
             "ica_workflow_run_id": workflow_run_id,
             "panel_type": panel_type,
             "sample_type": sample_type,
-            "is_identified": is_identified
+            "is_identified": is_identified,
+            "disease_name": default_snomed_term
     }
 
     logger.info(f"Launching lambda function {lambda_arn} with the following payload {json.dumps(lambda_payload)}")
@@ -361,6 +368,7 @@ def submit_libraries_to_pieriandx(processing_df: pd.DataFrame) -> pd.DataFrame:
       * is_identified
       * needs_redcap
       * redcap_is_complete
+      * default_snomed_term
     :return:
       A pandas dataframe with the following columns
       * subject_id
@@ -411,7 +419,8 @@ def submit_libraries_to_pieriandx(processing_df: pd.DataFrame) -> pd.DataFrame:
                 lambda_arn=row.submission_arn,
                 panel_type=row.panel,
                 sample_type=row.sample_type,
-                is_identified=row.is_identified
+                is_identified=row.is_identified,
+                default_snomed_term=row.default_snomed_term
             )
         except ValueError:
             pass

diff --git a/deploy/cttso-ica-to-pieriandx-cdk/lambdas/layers/lambda_utils/globals.py b/deploy/cttso-ica-to-pieriandx-cdk/lambdas/layers/lambda_utils/globals.py
@@ -97,7 +97,6 @@ class SampleType(Enum):
     "sample_type": "validation",
     "panel_type": PanelType.MAIN,
     "indication": "NA",
-    "disease_id": 285645000,
     "disease_name": "Disseminated malignancy of unknown primary",
     "is_identified": True,
     "requesting_physicians_first_name": "Sean",
@@ -175,7 +174,7 @@ class SampleType(Enum):
 
 EXPECTED_ATTRIBUTES = [
     "sample_type",
-    "disease_id",
+    "disease_name",
     "indication",
     "accession_number",
     "external_specimen_id",