Merge pull request #96 from KPMP/KPMP-5581_remove_biopsy_query

KPMP-5581: remove biopsy query, update field names
KPMP · Oct 7, 2024 · 6b3e2d9 · 6b3e2d9
2 parents f4e04a0 + 3ecab76
commit 6b3e2d9
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Showing 2 changed files with 7 additions and 17 deletions.
diff --git a/data_management/lib/spectrack_connection.py b/data_management/lib/spectrack_connection.py
@@ -72,11 +72,6 @@ def get_specimen_kit_by_specimen_kit_id(self, specimen_kit_id: str):
             self.get_url(self.SPECIMEN_KIT_URL_SUFFIX), {"kit_id": specimen_kit_id}
         )
 
-    def get_biopsy_by_redcap_id(self, redcap_id: str):
-        return self.get_results(
-            self.get_url(self.BIOPSY_URL_SUFFIX), {"redcap_record_id": redcap_id}
-        )
-
     def get_organization_by_id(self, org_id: int):
         return self.get_results(
             self.get_url(self.ORGANIZATION_URL_SUFFIX) + "/" + str(org_id)

diff --git a/data_management/services/spectrack.py b/data_management/services/spectrack.py
@@ -35,10 +35,6 @@ def get_sample_type(self, sample_type_id: int):
             self.sample_types.update({sample_type_id: sample_type})
         return sample_type
 
-    def get_biopsy(self, redcap_id: str):
-        results = self.st.get_biopsy_by_redcap_id(redcap_id)
-        return results["results"][0]
-
     def get_specimen_kit(self, specimen_kit_id: str):
         results = self.st.get_specimen_kit_by_specimen_kit_id(specimen_kit_id)
         return results["results"][0]
@@ -55,23 +51,22 @@ def convert_to_dmd_specimens(self, specimens: list):
         dmd_specimens = list()
         for specimen in specimens:
             # We don't want any records without a kit ID or Redcap ID
-            if ("specimen_kit_id" in specimen) and (
+            if ("specimen_collection__specimen_kit__kit_id" in specimen) and (
                 specimen["redcap_record_id"] is not None
             ):
-                specimen_kit = self.get_specimen_kit(specimen["specimen_kit_id"])
-                if specimen["specimen_kit_id"] and "Biopsy Kit" in specimen_kit["kit_type_name"]:
-                    biopsy = self.get_biopsy(specimen["redcap_record_id"])
-                    site = biopsy["collecting_org"]["org_name"]
-                    disease_category = biopsy["disease_category"]
-                    biopsy_date = biopsy["biopsy_date"]
+                specimen_kit = self.get_specimen_kit(specimen["specimen_collection__specimen_kit__kit_id"])
+                if specimen["specimen_collection__specimen_kit__kit_id"] and "Biopsy Kit" in specimen_kit["kit_type_name"]:
+                    site = specimen["specimen_collection__collecting_org__org_name"]
+                    disease_category = specimen["disease_category"]
+                    biopsy_date = specimen["biopsy_date"]
                 else:
                     organization = self.st.get_by_url(specimen_kit["site"])
                     site = organization["org_name"]
                     disease_category = None
                     biopsy_date = None
 
                 sample_type = self.get_sample_type(specimen["sample_type_id"])
-                kit_id = "N/A" if specimen['specimen_kit_id'] is None else specimen['specimen_kit_id']
+                kit_id = "N/A" if specimen['specimen_collection__specimen_kit__kit_id'] is None else specimen['specimen_collection__specimen_kit__kit_id']
                 dmd_specimen_tuple = (
                     specimen["id"],
                     specimen["sample_id"],