Quick hotfixes updates (#186, #187, #188)

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

@@ -3,6 +3,20 @@
 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.  
 
+## 2023-11-22
+
+> Author: Alexis Lucattini
+> Email: [[email protected]](mailto:[email protected])
+
+### Hotfixes
+* Update disease name to disease label (https://github.com/umccr/cttso-ica-to-pieriandx/pull/188)
+  * Resolves https://github.com/umccr/cttso-ica-to-pieriandx/issues/183
+* Coerce is_identified to boolean (https://github.com/umccr/cttso-ica-to-pieriandx/pull/187)
+  * Resolves https://github.com/umccr/cttso-ica-to-pieriandx/issues/184
+* Use comma after needs_redcap column (https://github.com/umccr/cttso-ica-to-pieriandx/pull/186)
+  * Resolves https://github.com/umccr/cttso-ica-to-pieriandx/issues/185
+
+
 ## 2023-11-08
 
 > Author: Alexis Lucattini

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

@@ -65,7 +65,7 @@ new_headers = [
     "pieriandx_case_identified",
     "pieriandx_assignee",
     "pieriandx_disease_code",
-    "pieriandx_disease_name",
+    "pieriandx_disease_label",
     "pieriandx_panel_type",
     "pieriandx_sample_type",
     "pieriandx_workflow_id",

deploy/cttso-ica-to-pieriandx-cdk/lambdas/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"]

deploy/cttso-ica-to-pieriandx-cdk/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

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

@@ -185,7 +185,7 @@ def get_libraries_for_processing(merged_df) -> pd.DataFrame:
       * pieriandx_assignee
       * pieriandx_case_identified
       * pieriandx_disease_code
-      * pieriandx_disease_name
+      * pieriandx_disease_label
       * pieriandx_panel_type
       * pieriandx_sample_type
     :return: A pandas dataframe with the following columns
@@ -276,7 +276,7 @@ def get_libraries_for_processing(merged_df) -> pd.DataFrame:
       "panel",
       "sample_type",
       "is_identified",
-      "needs_redcap"
+      "needs_redcap",
       "default_snomed_term"
     ]
 
@@ -489,7 +489,7 @@ def append_to_cttso_lims(merged_df: pd.DataFrame, cttso_lims_df: pd.DataFrame, e
       * pieriandx_case_identified
       * pieriandx_assignee
       * pieriandx_disease_code
-      * pieriandx_disease_name
+      * pieriandx_disease_label
       * pieriandx_panel_type
       * pieriandx_sample_type
       * pieriandx_workflow_id
@@ -663,7 +663,7 @@ def get_pieriandx_incomplete_job_df_from_cttso_lims_df(cttso_lims_df: pd.DataFra
         * pieriandx_case_creation_date
         * pieriandx_case_identified
         * pieriandx_disease_code
-        * pieriandx_disease_name
+        * pieriandx_disease_label
         * pieriandx_panel_type
         * pieriandx_sample_type
         * pieriandx_workflow_id
@@ -697,7 +697,7 @@ def get_pieriandx_incomplete_job_df_from_cttso_lims_df(cttso_lims_df: pd.DataFra
         * pieriandx_case_creation_date
         * pieriandx_case_identified
         * pieriandx_disease_code
-        * pieriandx_disease_name
+        * pieriandx_disease_label
         * pieriandx_panel_type
         * pieriandx_sample_type
         * pieriandx_workflow_id
@@ -823,7 +823,7 @@ def update_pieriandx_job_status_missing_df(pieriandx_job_status_missing_df, merg
       * pieriandx_case_accession_number
       * pieriandx_case_identified
       * pieriandx_disease_code
-      * pieriandx_disease_name
+      * pieriandx_disease_label
       * pieriandx_panel_type
       * pieriandx_sample_type
       * pieriandx_workflow_id
@@ -1140,7 +1140,7 @@ def update_cttso_lims(update_df: pd.DataFrame, cttso_lims_df: pd.DataFrame, exce
       * pieriandx_case_identified
       * pieriandx_assignee
       * pieriandx_disease_code
-      * pieriandx_disease_name
+      * pieriandx_disease_label
       * pieriandx_panel_type
       * pieriandx_sample_type
       * pieriandx_workflow_id
@@ -1192,7 +1192,7 @@ def update_cttso_lims(update_df: pd.DataFrame, cttso_lims_df: pd.DataFrame, exce
             "pieriandx_assignee",
             "pieriandx_case_identified",
             "pieriandx_disease_code",
-            "pieriandx_disease_name",
+            "pieriandx_disease_label",
             "pieriandx_panel_type",
             "pieriandx_sample_type",
             "pieriandx_workflow_id",
@@ -1249,7 +1249,7 @@ def get_duplicate_case_ids(lims_df: pd.DataFrame) -> List:
       * pieriandx_case_creation_date
       * pieriandx_assignee
       * pieriandx_disease_code
-      * pieriandx_disease_name
+      * pieriandx_disease_label
       * pieriandx_panel_type
       * pieriandx_sample_type
       * pieriandx_workflow_id
@@ -1447,7 +1447,7 @@ def cleanup_duplicate_rows(merged_df: pd.DataFrame, cttso_lims_df: pd.DataFrame,
       * pieriandx_case_identified
       * pieriandx_assignee
       * pieriandx_disease_code
-      * pieriandx_disease_name
+      * pieriandx_disease_label
       * pieriandx_panel_type
       * pieriandx_sample_type
       * pieriandx_workflow_id
@@ -1511,7 +1511,7 @@ def cleanup_duplicate_rows(merged_df: pd.DataFrame, cttso_lims_df: pd.DataFrame,
         * pieriandx_case_identified
         * pieriandx_assignee
         * pieriandx_disease_code
-        * pieriandx_disease_name
+        * pieriandx_disease_label
         * pieriandx_panel_type
         * pieriandx_sample_type
         * pieriandx_workflow_id
@@ -1689,7 +1689,7 @@ def bind_pieriandx_case_submission_time_to_merged_df(merged_df: pd.DataFrame, ct
       * pieriandx_case_identified
       * pieriandx_assignee
       * pieriandx_disease_code
-      * pieriandx_disease_name
+      * pieriandx_disease_label
       * pieriandx_panel_type
       * pieriandx_sample_type
       * pieriandx_workflow_id
@@ -1722,7 +1722,7 @@ def bind_pieriandx_case_submission_time_to_merged_df(merged_df: pd.DataFrame, ct
       * pieriandx_case_creation_date
       * pieriandx_assignee
       * pieriandx_disease_code
-      * pieriandx_disease_name
+      * pieriandx_disease_label
       * pieriandx_panel_type
       * pieriandx_sample_type
       * pieriandx_workflow_id
@@ -1970,7 +1970,7 @@ def drop_to_be_deleted_cases(merged_df: pd.DataFrame, cttso_lims_df: pd.DataFram
         * pieriandx_case_identified
         * pieriandx_assignee
         * pieriandx_disease_code
-        * pieriandx_disease_name
+        * pieriandx_disease_label
         * pieriandx_panel_type
         * pieriandx_sample_type
         * pieriandx_workflow_id

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

@@ -223,7 +223,7 @@ def get_cttso_lims() -> (pd.DataFrame, pd.DataFrame):
         * pieriandx_case_identified
         * pieriandx_assignee
         * pieriandx_disease_code
-        * pieriandx_disease_name
+        * pieriandx_disease_label
         * pieriandx_panel_type
         * pieriandx_sample_type
         * pieriandx_workflow_id
@@ -302,7 +302,7 @@ def get_deleted_lims_df() -> (pd.DataFrame, pd.DataFrame):
         * pieriandx_case_identified
         * pieriandx_assignee
         * pieriandx_disease_code
-        * pieriandx_disease_name
+        * pieriandx_disease_label
         * pieriandx_panel_type
         * pieriandx_sample_type
         * pieriandx_workflow_id

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

@@ -398,7 +398,7 @@ def get_pieriandx_status_for_missing_sample(case_id: str) -> pd.Series:
       * pieriandx_case_accession_number
       * pieriandx_case_identified
       * pieriandx_disease_code
-      * pieriandx_disease_name
+      * pieriandx_disease_label
       * pieriandx_panel_type
       * pieriandx_workflow_id
       * pieriandx_workflow_status
@@ -440,7 +440,7 @@ def get_pieriandx_status_for_missing_sample(case_id: str) -> pd.Series:
             "pieriandx_case_accession_number": response.get("specimens")[0].get("accessionNumber"),
             "pieriandx_case_identified": response.get("identified", False),
             "pieriandx_disease_code": response.get("disease").get("code"),
-            "pieriandx_disease_name": response.get("disease").get("name"),
+            "pieriandx_disease_label": response.get("disease").get("label"),
             "pieriandx_panel_type": PanelType(response.get("panelName")).name,
             "pieriandx_sample_type": SampleType(response.get("sampleType")).name,
             "pieriandx_workflow_id": pd.NA,