update disease-normalizer version + fix indication tests

cancervariants · Oct 25, 2023 · 8788bb8 · 8788bb8
1 parent 62ab943
commit 8788bb8
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Showing 6 changed files with 10 additions and 18 deletions.
diff --git a/Pipfile b/Pipfile
@@ -13,7 +13,7 @@ boto3 = "*"
 
 [dev-packages]
 thera-py = {editable = true, path = "."}
-disease-normalizer = {editable = true, path = "cancervariants/disease-normalization"}
+disease-normalizer = "~=0.4.0.dev0"
 owlready2 = "*"
 rdflib = "*"
 wikibaseintegrator = ">=0.12.0"

diff --git a/setup.cfg b/setup.cfg
@@ -32,6 +32,7 @@ test =
     pytest-cov
 
 dev =
+    disease-normalizer ~= 0.4.0.dev0
     owlready2
     rdflib
     wikibaseintegrator >= 0.12.0

diff --git a/tests/data/fixtures/query_fixtures.json b/tests/data/fixtures/query_fixtures.json
@@ -356,7 +356,6 @@
               "id": "mesh:D014565",
               "type": "Disease",
               "label": "Urogenital Neoplasms",
-              "disease": null,
               "extensions": [
                 {
                   "type": "Extension",
@@ -1104,7 +1103,6 @@
               "id": "mesh:D020250",
               "type": "Disease",
               "label": "Postoperative Nausea and Vomiting",
-              "disease": null,
               "extensions": [
                 {
                   "type": "Extension",
@@ -1600,7 +1598,6 @@
               "id": "mesh:D009325",
               "type": "Disease",
               "label": "Nausea",
-              "disease": null,
               "extensions": [
                 {
                   "type": "Extension",
@@ -1991,7 +1988,6 @@
               "id": "mesh:D009362",
               "type": "Disease",
               "label": "Neoplasm Metastasis",
-              "disease": null,
               "extensions": [
                 {
                   "type": "Extension",
@@ -2214,7 +2210,6 @@
               "id": "mesh:D010996",
               "type": "Disease",
               "label": "Pleural Effusion",
-              "disease": null,
               "extensions": [
                 {
                   "type": "Extension",
@@ -2290,7 +2285,6 @@
               "id": "mesh:D014987",
               "type": "Disease",
               "label": "Xerostomia",
-              "disease": null,
               "extensions": [
                 {
                   "type": "Extension",
@@ -3364,7 +3358,6 @@
       "Spiramycin I",
       "Foromacidin A"
     ],
-    "extensions": [],
     "mappings": [
       {
         "coding": {
@@ -3472,7 +3465,6 @@
       "any_therapy",
       "treatment"
     ],
-    "extensions": [],
     "mappings": [
       {
         "coding": {

diff --git a/tests/unit/test_query.py b/tests/unit/test_query.py
@@ -180,9 +180,9 @@ def get_extension(extensions, name):
                 assert set(ratings_actual) == set(ratings_fixture)
             assert set(approv_actual.value.get("approval_year", [])) == \
                 set(approv_fixture.value.get("approval_year", []))
-            approv_inds = [json.dumps(ind) for ind
+            approv_inds = [json.dumps(ind, sort_keys=True) for ind
                            in approv_actual.value.get("has_indication", [])]
-            fixture_inds = [json.dumps(ind) for ind
+            fixture_inds = [json.dumps(ind, sort_keys=True) for ind
                             in approv_fixture.value.get("has_indication", [])]
             assert set(approv_inds) == set(fixture_inds)
 

diff --git a/therapy/etl/base.py b/therapy/etl/base.py
@@ -328,7 +328,7 @@ def _normalize_disease(self, query: str) -> Optional[str]:
         """
         response = self.disease_normalizer.normalize(query)
         if response.match_type > 0:
-            return response.disease.id
+            return response.normalized_id
         else:
             logger.warning(f"Failed to normalize disease term: {query}")
             return None

diff --git a/therapy/query.py b/therapy/query.py
@@ -500,12 +500,11 @@ def _add_therapeutic_agent(
             )
             extensions.append(approv)
 
-        for field, name in (("trade_names", "trade_names"),
-                            ("associated_with", "associated_with")):
-            values = record.get(field)
-
-            if values:
-                extensions.append(core_models.Extension(name=name, value=values))
+        trade_names = record.get("trade_names")
+        if trade_names:
+            extensions.append(
+                core_models.Extension(name="trade_names", value=trade_names)
+            )
 
         if extensions:
             therapeutic_agent_obj.extensions = extensions