monarch-initiative · kevinschaper · Aug 14, 2023 · Aug 11, 2023 · Aug 11, 2023
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/cli.py b/backend/src/monarch_py/cli.py
@@ -135,7 +135,7 @@ def associations(
 def search(
     q: str = typer.Option(None, "--query", "-q"),
     category: List[str] = typer.Option(None, "--category", "-c"),
-    in_taxon: str = typer.Option(None, "--in-taxon", "-t"),
+    in_taxon_label: str = typer.Option(None, "--in-taxon-label", "-t"),
     facet_fields: List[str] = typer.Option(None, "--facet-fields", "-ff"),
     facet_queries: List[str] = typer.Option(None, "--facet-queries"),
     limit: int = typer.Option(20, "--limit", "-l"),
@@ -155,7 +155,7 @@ def search(
     Args:
         q: The query string to search for
         category: The category of the entity
-        taxon: The taxon of the entity
+        in_taxon_label: The taxon label to filter by
         limit: The number of entities to return
         offset: The offset of the first entity to be retrieved
         fmt: The format of the output (json, yaml, tsv, table)

diff --git a/backend/src/monarch_py/datamodels/solr.py b/backend/src/monarch_py/datamodels/solr.py
@@ -37,7 +37,7 @@ class HistoPhenoKeys(Enum):
 class SolrQuery(BaseModel):
     q: str = "*:*"
     rows: int = 20
-    start: int = 1
+    start: int = 0
     facet: bool = True
     facet_min_count = 1
     facet_fields: Optional[List[str]] = Field(default_factory=list)

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/src/monarch_py/implementations/solr/solr_query_utils.py b/backend/src/monarch_py/implementations/solr/solr_query_utils.py
@@ -147,7 +147,7 @@ def build_search_query(
 
 
 def build_autocomplete_query(q: str) -> SolrQuery:
-    query = SolrQuery(q=q, limit=10, offset=0)
+    query = SolrQuery(q=q, limit=10, start=0)
     query.q = q
     # match the query fields to start with
     query.query_fields = entity_query_fields()

diff --git a/backend/src/monarch_py/service/solr_service.py b/backend/src/monarch_py/service/solr_service.py
@@ -26,6 +26,7 @@ def get(self, id):
 
     def query(self, q: SolrQuery) -> SolrQueryResult:
         url = f"{self.base_url}/{self.core.value}/select?{q.query_string()}"
+        logger.debug(f"SolrService.query: {url}")
         response = requests.get(url)
 
         data = json.loads(response.text)

diff --git a/backend/src/monarch_py/solr_cli.py b/backend/src/monarch_py/solr_cli.py
@@ -169,7 +169,7 @@ def associations(
 def search(
     q: str = typer.Option(None, "--query", "-q"),
     category: List[str] = typer.Option(None, "--category", "-c"),
-    in_taxon: str = typer.Option(None, "--in-taxon", "-t"),
+    in_taxon_label: str = typer.Option(None, "--in-taxon-label", "-t"),
     facet_fields: List[str] = typer.Option(None, "--facet-fields", "-ff"),
     facet_queries: List[str] = typer.Option(None, "--facet-queries"),
     limit: int = typer.Option(20, "--limit", "-l"),
@@ -189,7 +189,7 @@ def search(
     Optional Args:
         q: The query string to search for
         category: The category of the entity
-        taxon: The taxon of the entity
+        in_taxon_label: The taxon label to filter on
         facet_fields: The fields to facet on
         facet_queries: The queries to facet on
         limit: The number of entities to return

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": [],