Fixture update, plus formatting

monarch-initiative · Aug 11, 2023 · f5018cf · f5018cf
1 parent 63bc5c3
commit f5018cf
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Showing 10 changed files with 88 additions and 69 deletions.
diff --git a/backend/src/monarch_py/api/entity.py b/backend/src/monarch_py/api/entity.py
@@ -51,7 +51,11 @@ def _association_table(
         title="Type of association to retrieve association table data for",
     ),
     query: str = Query(None, example="thumb", title="Query string to limit results to a subset"),
-        sort: List[str] = Query(None, example=["subject_label asc", "predicate asc", "object_label asc"], title="Sort results by a list of field + direction statements"),
+    sort: List[str] = Query(
+        None,
+        example=["subject_label asc", "predicate asc", "object_label asc"],
+        title="Sort results by a list of field + direction statements",
+    ),
     pagination: PaginationParams = Depends(),
 ) -> AssociationTableResults:
     """

diff --git a/backend/src/monarch_py/implementations/solr/solr_implementation.py b/backend/src/monarch_py/implementations/solr/solr_implementation.py
@@ -322,10 +322,10 @@ def get_association_table(
         self,
         entity: str,
         category: str,
-        q: str =None,
-        sort: List[str]=None,
-        offset: int=0,
-        limit: int =5,
+        q: str = None,
+        sort: List[str] = None,
+        offset: int = 0,
+        limit: int = 5,
     ) -> AssociationTableResults:
 
         query = build_association_table_query(

diff --git a/backend/tests/fixtures/association_table_response.py b/backend/tests/fixtures/association_table_response.py
@@ -5,7 +5,7 @@
 def association_table_response():
     return {
         "responseHeader": {
-            "QTime": 0,
+            "QTime": 1,
             "params": {
                 "mm": "100%",
                 "q": "*:*",

diff --git a/backend/tests/fixtures/autocomplete.py b/backend/tests/fixtures/autocomplete.py
@@ -8,6 +8,32 @@ def autocomplete():
         "offset": 0,
         "total": 195,
         "items": [
+            {
+                "id": "MONDO:0019391",
+                "category": "biolink:Disease",
+                "name": "Fanconi anemia",
+                "full_name": None,
+                "description": "Fanconi anemia (FA) is a hereditary DNA repair disorder characterized by progressive pancytopenia with bone marrow failure, variable congenital malformations and predisposition to develop hematological or solid tumors.",
+                "xref": [
+                    "DOID:13636",
+                    "GARD:0006425",
+                    "ICD9:284.09",
+                    "MESH:D005199",
+                    "MedDRA:10055206",
+                    "NCIT:C62505",
+                    "OMIMPS:227650",
+                    "Orphanet:84",
+                    "SCTID:30575002",
+                    "UMLS:C0015625",
+                ],
+                "provided_by": "phenio_nodes",
+                "in_taxon": None,
+                "in_taxon_label": None,
+                "symbol": None,
+                "synonym": [],
+                "highlight": None,
+                "score": None,
+            },
             {
                 "id": "MONDO:0001083",
                 "category": "biolink:Disease",
@@ -353,27 +379,6 @@ def autocomplete():
                 "highlight": None,
                 "score": None,
             },
-            {
-                "id": "MONDO:0012186",
-                "category": "biolink:Disease",
-                "name": "Fanconi anemia complementation group I",
-                "full_name": None,
-                "description": "Fanconi anemia caused by mutations in the FANCI gene, encoding Fanconi anemia group I protein.",
-                "xref": [
-                    "DOID:0111091",
-                    "MESH:C563802",
-                    "NCIT:C129026",
-                    "OMIM:609053",
-                    "UMLS:C1836861",
-                ],
-                "provided_by": "phenio_nodes",
-                "in_taxon": None,
-                "in_taxon_label": None,
-                "symbol": None,
-                "synonym": [],
-                "highlight": None,
-                "score": None,
-            },
         ],
         "facet_fields": [],
         "facet_queries": [],

diff --git a/backend/tests/fixtures/autocomplete_query.py b/backend/tests/fixtures/autocomplete_query.py
@@ -6,7 +6,7 @@ def autocomplete_query():
     return {
         "q": "fanc",
         "rows": 20,
-        "start": 1,
+        "start": 0,
         "facet": True,
         "facet_fields": [],
         "facet_queries": [],

diff --git a/backend/tests/fixtures/autocomplete_response.py b/backend/tests/fixtures/autocomplete_response.py
@@ -12,16 +12,35 @@ def autocomplete_response():
                 "defType": "edismax",
                 "facet_min_count": "1",
                 "qf": "id^100 name^10 name_t^5 name_ac symbol^10 symbol_t^5 symbol_ac synonym synonym_t synonym_ac",
-                "start": "1",
+                "start": "0",
                 "boost": 'product(if(termfreq(category,"biolink:Disease"),10.0,1),if(and(termfreq(in_taxon,"NCBITaxon:9606"),termfreq(category,"biolink:Gene")),5.0,1))',
                 "rows": "20",
                 "facet": "true",
             },
         },
         "response": {
             "num_found": 195,
-            "start": 1,
+            "start": 0,
             "docs": [
+                {
+                    "id": "MONDO:0019391",
+                    "category": "biolink:Disease",
+                    "name": "Fanconi anemia",
+                    "xref": [
+                        "DOID:13636",
+                        "GARD:0006425",
+                        "ICD9:284.09",
+                        "MESH:D005199",
+                        "MedDRA:10055206",
+                        "NCIT:C62505",
+                        "OMIMPS:227650",
+                        "Orphanet:84",
+                        "SCTID:30575002",
+                        "UMLS:C0015625",
+                    ],
+                    "provided_by": "phenio_nodes",
+                    "description": "Fanconi anemia (FA) is a hereditary DNA repair disorder characterized by progressive pancytopenia with bone marrow failure, variable congenital malformations and predisposition to develop hematological or solid tumors.",
+                },
                 {
                     "id": "MONDO:0001083",
                     "category": "biolink:Disease",
@@ -235,20 +254,6 @@ def autocomplete_response():
                     "provided_by": "phenio_nodes",
                     "description": "Inherited cancer-predisposing syndrome due to biallelic BRCA2 mutations is a rare cancer-predisposing syndrome, associated with the D1 subgroup of Fanconi anemia (FA), characterized by progressive bone marrow failure, cardiac, brain, intestinal or skeletal abnormalities and predisposition to various malignancies. Bone marrow suppression and the incidence of developmental abnormalities are less frequent than in other FA, but cancer risk is very high with the spectrum of childhood cancers including Wilms tumor, brain tumor (often medulloblastoma) and ALL/AML.",
                 },
-                {
-                    "id": "MONDO:0012186",
-                    "category": "biolink:Disease",
-                    "name": "Fanconi anemia complementation group I",
-                    "xref": [
-                        "DOID:0111091",
-                        "MESH:C563802",
-                        "NCIT:C129026",
-                        "OMIM:609053",
-                        "UMLS:C1836861",
-                    ],
-                    "provided_by": "phenio_nodes",
-                    "description": "Fanconi anemia caused by mutations in the FANCI gene, encoding Fanconi anemia group I protein.",
-                },
             ],
         },
         "facet_counts": {"facet_fields": {}, "facet_queries": {}},

diff --git a/backend/tests/fixtures/histopheno_response.py b/backend/tests/fixtures/histopheno_response.py
@@ -5,7 +5,7 @@
 def histopheno_response():
     return {
         "responseHeader": {
-            "QTime": 2,
+            "QTime": 1,
             "params": {
                 "facet.query": [
                     'object_closure:"HP:0000924"',

diff --git a/backend/tests/fixtures/search_response.py b/backend/tests/fixtures/search_response.py
@@ -5,7 +5,7 @@
 def search_response():
     return {
         "responseHeader": {
-            "QTime": 0,
+            "QTime": 1,
             "params": {
                 "mm": "100%",
                 "q": "fanconi",

diff --git a/frontend/fixtures/association-table.json b/frontend/fixtures/association-table.json
@@ -63,7 +63,7 @@
         "human disease or disorder"
       ],
       "subject_taxon": null,
-      "subject_taxon_label": "test subject taxon label",
+      "subject_taxon_label": null,
       "predicate": "biolink:has_phenotype",
       "object": "HP:0002460",
       "original_object": null,
@@ -134,7 +134,7 @@
         "organ system subdivision"
       ],
       "object_taxon": null,
-      "object_taxon_label": "test object taxon label",
+      "object_taxon_label": null,
       "primary_knowledge_source": "infores:hpo-annotations",
       "aggregator_knowledge_source": ["infores:monarchinitiative"],
       "category": "biolink:DiseaseToPhenotypicFeatureAssociation",

diff --git a/frontend/fixtures/autocomplete.json b/frontend/fixtures/autocomplete.json
@@ -3,6 +3,32 @@
   "offset": 0,
   "total": 195,
   "items": [
+    {
+      "id": "MONDO:0019391",
+      "category": "biolink:Disease",
+      "name": "Fanconi anemia",
+      "full_name": null,
+      "description": "Fanconi anemia (FA) is a hereditary DNA repair disorder characterized by progressive pancytopenia with bone marrow failure, variable congenital malformations and predisposition to develop hematological or solid tumors.",
+      "xref": [
+        "DOID:13636",
+        "GARD:0006425",
+        "ICD9:284.09",
+        "MESH:D005199",
+        "MedDRA:10055206",
+        "NCIT:C62505",
+        "OMIMPS:227650",
+        "Orphanet:84",
+        "SCTID:30575002",
+        "UMLS:C0015625"
+      ],
+      "provided_by": "phenio_nodes",
+      "in_taxon": null,
+      "in_taxon_label": null,
+      "symbol": null,
+      "synonym": [],
+      "highlight": null,
+      "score": null
+    },
     {
       "id": "MONDO:0001083",
       "category": "biolink:Disease",
@@ -332,27 +358,6 @@
       "synonym": [],
       "highlight": null,
       "score": null
-    },
-    {
-      "id": "MONDO:0012186",
-      "category": "biolink:Disease",
-      "name": "Fanconi anemia complementation group I",
-      "full_name": null,
-      "description": "Fanconi anemia caused by mutations in the FANCI gene, encoding Fanconi anemia group I protein.",
-      "xref": [
-        "DOID:0111091",
-        "MESH:C563802",
-        "NCIT:C129026",
-        "OMIM:609053",
-        "UMLS:C1836861"
-      ],
-      "provided_by": "phenio_nodes",
-      "in_taxon": null,
-      "in_taxon_label": null,
-      "symbol": null,
-      "synonym": [],
-      "highlight": null,
-      "score": null
     }
   ],
   "facet_fields": [],