Fixtures and formatting

monarch-initiative · Oct 21, 2023 · 6b0128b · 6b0128b
1 parent 1d1b2e1
commit 6b0128b
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Showing 22 changed files with 6,168 additions and 12,125 deletions.
diff --git a/backend/src/monarch_py/api/main.py b/backend/src/monarch_py/api/main.py
@@ -3,7 +3,7 @@
 from fastapi.middleware.cors import CORSMiddleware
 from fastapi.responses import RedirectResponse
 from monarch_py.api import association, entity, histopheno, search, semsim
-from monarch_py.api.config import oak, solr
+from monarch_py.api.config import oak
 from monarch_py.api.middleware.logging_middleware import LoggingMiddleware
 from monarch_py.service.curie_service import CurieService
 
@@ -38,6 +38,7 @@ async def initialize_app():
 )
 app.add_middleware(LoggingMiddleware)
 
+
 @app.get("/")
 async def _root():
     return RedirectResponse(url="/v3/docs")

diff --git a/backend/src/monarch_py/api/middleware/logging_middleware.py b/backend/src/monarch_py/api/middleware/logging_middleware.py
@@ -37,4 +37,4 @@ async def dispatch(self, request: Request, call_next):
         # request._body = body
 
         response = await call_next(request)
-        return response
+        return response
diff --git a/backend/src/monarch_py/api/semsim.py b/backend/src/monarch_py/api/semsim.py
@@ -1,6 +1,4 @@
-from typing import List
-
-from fastapi import APIRouter, Path, Query
+from fastapi import APIRouter, Path
 
 from monarch_py.api.additional_models import CompareRequest
 from monarch_py.api.config import oak

diff --git a/backend/src/monarch_py/datamodels/model.py b/backend/src/monarch_py/datamodels/model.py
diff --git a/backend/tests/fixtures/association_counts_query.py b/backend/tests/fixtures/association_counts_query.py
@@ -18,6 +18,8 @@ def association_counts_query():
             '(category:"biolink:GeneToGeneHomologyAssociation") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")',
             '(category:"biolink:ChemicalToPathwayAssociation") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")',
             '(category:"biolink:MacromolecularMachineToMolecularActivityAssociation") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")',
+            '(category:"biolink:MacromolecularMachineToCellularComponentAssociation") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")',
+            '(category:"biolink:MacromolecularMachineToBiologicalProcessAssociation") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")',
             '(category:"biolink:CausalGeneToDiseaseAssociation") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")',
             '(category:"biolink:CorrelatedGeneToDiseaseAssociation") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")',
             '(category:"biolink:DiseaseToPhenotypicFeatureAssociation") AND (object:"MONDO:0020121" OR object_closure:"MONDO:0020121")',
@@ -28,6 +30,8 @@ def association_counts_query():
             '(category:"biolink:GeneToGeneHomologyAssociation") AND (object:"MONDO:0020121" OR object_closure:"MONDO:0020121")',
             '(category:"biolink:ChemicalToPathwayAssociation") AND (object:"MONDO:0020121" OR object_closure:"MONDO:0020121")',
             '(category:"biolink:MacromolecularMachineToMolecularActivityAssociation") AND (object:"MONDO:0020121" OR object_closure:"MONDO:0020121")',
+            '(category:"biolink:MacromolecularMachineToCellularComponentAssociation") AND (object:"MONDO:0020121" OR object_closure:"MONDO:0020121")',
+            '(category:"biolink:MacromolecularMachineToBiologicalProcessAssociation") AND (object:"MONDO:0020121" OR object_closure:"MONDO:0020121")',
             '(category:"biolink:CausalGeneToDiseaseAssociation") AND (object:"MONDO:0020121" OR object_closure:"MONDO:0020121")',
             '(category:"biolink:CorrelatedGeneToDiseaseAssociation") AND (object:"MONDO:0020121" OR object_closure:"MONDO:0020121")',
         ],

diff --git a/backend/tests/fixtures/association_counts_response.py b/backend/tests/fixtures/association_counts_response.py
diff --git a/backend/tests/fixtures/association_response.py b/backend/tests/fixtures/association_response.py
diff --git a/backend/tests/fixtures/association_table.py b/backend/tests/fixtures/association_table.py
@@ -9,7 +9,7 @@ def association_table():
         "total": 4027,
         "items": [
             {
-                "id": "uuid:aafbc2e0-6c84-11ee-9c86-072f86c27f6e",
+                "id": "uuid:89aa7b9b-5d8c-11ee-9b27-2b20ed86a9d9",
                 "category": "biolink:DiseaseToPhenotypicFeatureAssociation",
                 "subject": "MONDO:0020793",
                 "original_subject": "OMIM:164310",
@@ -170,7 +170,7 @@ def association_table():
                 "aggregator_knowledge_source": ["infores:monarchinitiative"],
                 "negated": None,
                 "pathway": None,
-                "evidence_count": 4,
+                "evidence_count": 6,
                 "has_evidence": ["ECO:0000269"],
                 "has_evidence_links": [{"id": "ECO:0000269", "url": "http://purl.obolibrary.org/obo/ECO_0000269"}],
                 "provided_by": "hpoa_disease_to_phenotype_edges",
@@ -212,7 +212,7 @@ def association_table():
                 "direction": "outgoing",
             },
             {
-                "id": "uuid:aafbc2f1-6c84-11ee-9c86-072f86c27f6e",
+                "id": "uuid:89aa7bac-5d8c-11ee-9b27-2b20ed86a9d9",
                 "category": "biolink:DiseaseToPhenotypicFeatureAssociation",
                 "subject": "MONDO:0020793",
                 "original_subject": "OMIM:164310",
@@ -427,7 +427,7 @@ def association_table():
                 "aggregator_knowledge_source": ["infores:monarchinitiative"],
                 "negated": None,
                 "pathway": None,
-                "evidence_count": 4,
+                "evidence_count": 6,
                 "has_evidence": ["ECO:0000269"],
                 "has_evidence_links": [{"id": "ECO:0000269", "url": "http://purl.obolibrary.org/obo/ECO_0000269"}],
                 "provided_by": "hpoa_disease_to_phenotype_edges",
@@ -469,7 +469,7 @@ def association_table():
                 "direction": "outgoing",
             },
             {
-                "id": "uuid:a77a5b0a-6c84-11ee-9c86-072f86c27f6e",
+                "id": "uuid:862bc0d4-5d8c-11ee-9b27-2b20ed86a9d9",
                 "category": "biolink:DiseaseToPhenotypicFeatureAssociation",
                 "subject": "MONDO:0013049",
                 "original_subject": "OMIM:612937",
@@ -660,9 +660,7 @@ def association_table():
                     "entity",
                     "continuant",
                     "continuant",
-                    "occurrent",
                     "independent continuant",
-                    "process",
                     "specifically dependent continuant",
                     "material entity",
                     "gas molecular entity",
@@ -691,8 +689,6 @@ def association_table():
                     "nitrogen molecular entity",
                     "creatine kinase complex",
                     "cellular_component",
-                    "biological_process",
-                    "metabolic process",
                     "protein-containing complex",
                     "transferase complex, transferring phosphorus-containing groups",
                     "catalytic complex",
@@ -760,7 +756,7 @@ def association_table():
                 "aggregator_knowledge_source": ["infores:monarchinitiative"],
                 "negated": None,
                 "pathway": None,
-                "evidence_count": 3,
+                "evidence_count": 5,
                 "has_evidence": ["ECO:0000269"],
                 "has_evidence_links": [{"id": "ECO:0000269", "url": "http://purl.obolibrary.org/obo/ECO_0000269"}],
                 "provided_by": "hpoa_disease_to_phenotype_edges",
@@ -801,7 +797,7 @@ def association_table():
                 "direction": "outgoing",
             },
             {
-                "id": "uuid:abeb7c29-6c84-11ee-9c86-072f86c27f6e",
+                "id": "uuid:8a99d6f0-5d8c-11ee-9b27-2b20ed86a9d9",
                 "category": "biolink:DiseaseToPhenotypicFeatureAssociation",
                 "subject": "MONDO:0009681",
                 "original_subject": "OMIM:254090",
@@ -960,7 +956,7 @@ def association_table():
                 "aggregator_knowledge_source": ["infores:monarchinitiative"],
                 "negated": None,
                 "pathway": None,
-                "evidence_count": 3,
+                "evidence_count": 5,
                 "has_evidence": ["ECO:0000269"],
                 "has_evidence_links": [{"id": "ECO:0000269", "url": "http://purl.obolibrary.org/obo/ECO_0000269"}],
                 "provided_by": "hpoa_disease_to_phenotype_edges",
@@ -1001,7 +997,7 @@ def association_table():
                 "direction": "outgoing",
             },
             {
-                "id": "uuid:aa9b85eb-6c84-11ee-9c86-072f86c27f6e",
+                "id": "uuid:894ab8ce-5d8c-11ee-9b27-2b20ed86a9d9",
                 "category": "biolink:DiseaseToPhenotypicFeatureAssociation",
                 "subject": "MONDO:0009676",
                 "original_subject": "OMIM:253601",
@@ -1158,7 +1154,7 @@ def association_table():
                 "aggregator_knowledge_source": ["infores:monarchinitiative"],
                 "negated": None,
                 "pathway": None,
-                "evidence_count": 3,
+                "evidence_count": 5,
                 "has_evidence": ["ECO:0000269"],
                 "has_evidence_links": [{"id": "ECO:0000269", "url": "http://purl.obolibrary.org/obo/ECO_0000269"}],
                 "provided_by": "hpoa_disease_to_phenotype_edges",

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": "*:*",
@@ -26,7 +26,7 @@ def association_table_response():
             "start": 0,
             "docs": [
                 {
-                    "id": "uuid:aafbc2e0-6c84-11ee-9c86-072f86c27f6e",
+                    "id": "uuid:89aa7b9b-5d8c-11ee-9b27-2b20ed86a9d9",
                     "original_subject": "OMIM:164310",
                     "predicate": "biolink:has_phenotype",
                     "category": "biolink:DiseaseToPhenotypicFeatureAssociation",
@@ -189,10 +189,10 @@ def association_table_response():
                     "frequency_qualifier_closure": ["HP:0000001", "HP:0040282", "HP:0040279"],
                     "frequency_qualifier_closure_label": ["All (HPO)", "Frequency (HPO)", "Frequent (HPO)"],
                     "frequency_qualifier_label": "Frequent (HPO)",
-                    "evidence_count": 4,
+                    "evidence_count": 6,
                 },
                 {
-                    "id": "uuid:aafbc2f1-6c84-11ee-9c86-072f86c27f6e",
+                    "id": "uuid:89aa7bac-5d8c-11ee-9b27-2b20ed86a9d9",
                     "original_subject": "OMIM:164310",
                     "predicate": "biolink:has_phenotype",
                     "category": "biolink:DiseaseToPhenotypicFeatureAssociation",
@@ -409,10 +409,10 @@ def association_table_response():
                     "frequency_qualifier_closure": ["HP:0000001", "HP:0040282", "HP:0040279"],
                     "frequency_qualifier_closure_label": ["All (HPO)", "Frequency (HPO)", "Frequent (HPO)"],
                     "frequency_qualifier_label": "Frequent (HPO)",
-                    "evidence_count": 4,
+                    "evidence_count": 6,
                 },
                 {
-                    "id": "uuid:a77a5b0a-6c84-11ee-9c86-072f86c27f6e",
+                    "id": "uuid:862bc0d4-5d8c-11ee-9b27-2b20ed86a9d9",
                     "original_subject": "OMIM:612937",
                     "predicate": "biolink:has_phenotype",
                     "category": "biolink:DiseaseToPhenotypicFeatureAssociation",
@@ -605,9 +605,7 @@ def association_table_response():
                         "entity",
                         "continuant",
                         "continuant",
-                        "occurrent",
                         "independent continuant",
-                        "process",
                         "specifically dependent continuant",
                         "material entity",
                         "gas molecular entity",
@@ -636,8 +634,6 @@ def association_table_response():
                         "nitrogen molecular entity",
                         "creatine kinase complex",
                         "cellular_component",
-                        "biological_process",
-                        "metabolic process",
                         "protein-containing complex",
                         "transferase complex, transferring phosphorus-containing groups",
                         "catalytic complex",
@@ -705,10 +701,10 @@ def association_table_response():
                     "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040280"],
                     "frequency_qualifier_closure_label": ["All (HPO)", "Frequency (HPO)", "Obligate (HPO)"],
                     "frequency_qualifier_label": "Obligate (HPO)",
-                    "evidence_count": 3,
+                    "evidence_count": 5,
                 },
                 {
-                    "id": "uuid:abeb7c29-6c84-11ee-9c86-072f86c27f6e",
+                    "id": "uuid:8a99d6f0-5d8c-11ee-9b27-2b20ed86a9d9",
                     "original_subject": "OMIM:254090",
                     "predicate": "biolink:has_phenotype",
                     "category": "biolink:DiseaseToPhenotypicFeatureAssociation",
@@ -869,10 +865,10 @@ def association_table_response():
                     "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040280"],
                     "frequency_qualifier_closure_label": ["All (HPO)", "Frequency (HPO)", "Obligate (HPO)"],
                     "frequency_qualifier_label": "Obligate (HPO)",
-                    "evidence_count": 3,
+                    "evidence_count": 5,
                 },
                 {
-                    "id": "uuid:aa9b85eb-6c84-11ee-9c86-072f86c27f6e",
+                    "id": "uuid:894ab8ce-5d8c-11ee-9b27-2b20ed86a9d9",
                     "original_subject": "OMIM:253601",
                     "predicate": "biolink:has_phenotype",
                     "category": "biolink:DiseaseToPhenotypicFeatureAssociation",
@@ -1031,7 +1027,7 @@ def association_table_response():
                     "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040280"],
                     "frequency_qualifier_closure_label": ["All (HPO)", "Frequency (HPO)", "Obligate (HPO)"],
                     "frequency_qualifier_label": "Obligate (HPO)",
-                    "evidence_count": 3,
+                    "evidence_count": 5,
                 },
             ],
         },