update fixtures, add mapping tests

monarch-initiative · Nov 8, 2023 · 59d7183 · 59d7183
1 parent 9f55969
commit 59d7183
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Showing 13 changed files with 301 additions and 8 deletions.
diff --git a/backend/src/monarch_py/api/main.py b/backend/src/monarch_py/api/main.py
@@ -22,10 +22,10 @@ async def initialize_app():
     CurieService()
 
 
-app.include_router(entity.router, prefix=f"{PREFIX}/entity")
 app.include_router(association.router, prefix=f"{PREFIX}/association")
-app.include_router(search.router, prefix=PREFIX)
+app.include_router(entity.router, prefix=f"{PREFIX}/entity")
 app.include_router(histopheno.router, prefix=f"{PREFIX}/histopheno")
+app.include_router(search.router, prefix=PREFIX)
 app.include_router(semsim.router, prefix=f"{PREFIX}/semsim")
 
 # Allow CORS

diff --git a/backend/src/monarch_py/implementations/solr/solr_parsers.py b/backend/src/monarch_py/implementations/solr/solr_parsers.py
@@ -170,7 +170,7 @@ def parse_autocomplete(query_result: SolrQueryResult) -> SearchResults:
     return SearchResults(limit=10, offset=0, total=total, items=items)
 
 
-def parse_mappings(query_result: SolrQueryResult, offset: int, limit: int) -> MappingResults:
+def parse_mappings(query_result: SolrQueryResult, offset: int = 0, limit: int = 20) -> MappingResults:
     total = query_result.response.num_found
     items = []
     for doc in query_result.response.docs:

diff --git a/backend/tests/api/test_mapping_endpoint.py b/backend/tests/api/test_mapping_endpoint.py
@@ -0,0 +1,18 @@
+from unittest.mock import MagicMock, patch
+
+from fastapi.testclient import TestClient
+from httpx import Response
+from monarch_py.api.search import router
+
+client = TestClient(router)
+
+
+def test_mappings(search):
+    with patch.object(
+        client, "get", MagicMock(return_value=Response(200, json=search, headers={"content-type": "application/json"}))
+    ):
+        response = client.get("/mappings?entity_id=MONDO:0000015")
+    assert response.status_code == 200
+    assert response.headers["content-type"] == "application/json"
+    assert response.json() == search
+
diff --git a/backend/tests/fixtures/association_counts_response.py b/backend/tests/fixtures/association_counts_response.py
@@ -5,7 +5,7 @@
 def association_counts_response():
     return {
         "responseHeader": {
-            "QTime": 1,
+            "QTime": 0,
             "params": {
                 "facet.query": [
                     '(category:"biolink:DiseaseToPhenotypicFeatureAssociation") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")',

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": 1,
+            "QTime": 2,
             "params": {
                 "facet.query": [
                     'object_closure:"HP:0000924"',

diff --git a/backend/tests/fixtures/mapping_query.py b/backend/tests/fixtures/mapping_query.py
@@ -0,0 +1,21 @@
+import pytest
+
+
+@pytest.fixture
+def mapping_query():
+    return {
+        "q": "*:*",
+        "rows": 20,
+        "start": 0,
+        "facet": True,
+        "facet_fields": [],
+        "facet_queries": [],
+        "filter_queries": ['subject_id:"MONDO\\:0020121" OR object_id:"MONDO\\:0020121"'],
+        "query_fields": None,
+        "def_type": "edismax",
+        "q_op": "AND",
+        "mm": "100%",
+        "boost": None,
+        "sort": None,
+        "facet_min_count": 1,
+    }
diff --git a/backend/tests/fixtures/mapping_response.py b/backend/tests/fixtures/mapping_response.py
@@ -0,0 +1,87 @@
+import pytest
+
+
+@pytest.fixture
+def mapping_response():
+    return {
+        "responseHeader": {
+            "QTime": 0,
+            "params": {
+                "mm": "100%",
+                "q": "*:*",
+                "defType": "edismax",
+                "facet_min_count": "1",
+                "start": "0",
+                "q.op": "AND",
+                "fq": 'subject_id:"MONDO\\:0020121" OR object_id:"MONDO\\:0020121"',
+                "rows": "20",
+                "facet": "true",
+            },
+        },
+        "response": {
+            "num_found": 7,
+            "start": 0,
+            "docs": [
+                {
+                    "subject_id": "MONDO:0020121",
+                    "subject_label": "muscular dystrophy",
+                    "predicate_id": "skos:exactMatch",
+                    "object_id": "DOID:9884",
+                    "object_label": "muscular dystrophy",
+                    "mapping_justification": "semapv:UnspecifiedMatching",
+                    "id": "cda26856-16a7-499c-956f-119cbaac5b96",
+                },
+                {
+                    "subject_id": "MONDO:0020121",
+                    "subject_label": "muscular dystrophy",
+                    "predicate_id": "skos:exactMatch",
+                    "object_id": "ICD10CM:G71.0",
+                    "object_label": "Muscular dystrophy",
+                    "mapping_justification": "semapv:UnspecifiedMatching",
+                    "id": "25777569-b997-4c8f-a1f3-5af352a16ee1",
+                },
+                {
+                    "subject_id": "MONDO:0020121",
+                    "subject_label": "muscular dystrophy",
+                    "predicate_id": "skos:exactMatch",
+                    "object_id": "MESH:D009136",
+                    "mapping_justification": "semapv:UnspecifiedMatching",
+                    "id": "819ab197-2ab1-4b73-8d0f-d7d4ec14d8a7",
+                },
+                {
+                    "subject_id": "MONDO:0020121",
+                    "subject_label": "muscular dystrophy",
+                    "predicate_id": "skos:exactMatch",
+                    "object_id": "NCIT:C84910",
+                    "object_label": "Muscular Dystrophy",
+                    "mapping_justification": "semapv:UnspecifiedMatching",
+                    "id": "adb4b8ed-c4dc-4353-a08e-a4cb02b1826e",
+                },
+                {
+                    "subject_id": "MONDO:0020121",
+                    "subject_label": "muscular dystrophy",
+                    "predicate_id": "skos:exactMatch",
+                    "object_id": "SCTID:73297009",
+                    "mapping_justification": "semapv:UnspecifiedMatching",
+                    "id": "f6417283-c9d1-4289-aee6-16d30a4445b1",
+                },
+                {
+                    "subject_id": "MONDO:0020121",
+                    "subject_label": "muscular dystrophy",
+                    "predicate_id": "skos:exactMatch",
+                    "object_id": "UMLS:C0026850",
+                    "mapping_justification": "semapv:UnspecifiedMatching",
+                    "id": "93968631-eedb-448b-b58a-e31e3e411dde",
+                },
+                {
+                    "subject_id": "MONDO:0020121",
+                    "subject_label": "muscular dystrophy",
+                    "predicate_id": "skos:exactMatch",
+                    "object_id": "Orphanet:98473",
+                    "mapping_justification": "semapv:UnspecifiedMatching",
+                    "id": "e39e8ba9-8d7e-4b33-9f46-3867b652bdb5",
+                },
+            ],
+        },
+        "facet_counts": {"facet_fields": {}, "facet_queries": {}},
+    }
diff --git a/backend/tests/fixtures/mappings.py b/backend/tests/fixtures/mappings.py
@@ -0,0 +1,75 @@
+import pytest
+
+
+@pytest.fixture
+def mappings():
+    return {
+        "limit": 20,
+        "offset": 0,
+        "total": 7,
+        "items": [
+            {
+                "subject_id": "MONDO:0020121",
+                "subject_label": "muscular dystrophy",
+                "predicate_id": "skos:exactMatch",
+                "object_id": "DOID:9884",
+                "object_label": "muscular dystrophy",
+                "mapping_justification": "semapv:UnspecifiedMatching",
+                "id": "cda26856-16a7-499c-956f-119cbaac5b96",
+            },
+            {
+                "subject_id": "MONDO:0020121",
+                "subject_label": "muscular dystrophy",
+                "predicate_id": "skos:exactMatch",
+                "object_id": "ICD10CM:G71.0",
+                "object_label": "Muscular dystrophy",
+                "mapping_justification": "semapv:UnspecifiedMatching",
+                "id": "25777569-b997-4c8f-a1f3-5af352a16ee1",
+            },
+            {
+                "subject_id": "MONDO:0020121",
+                "subject_label": "muscular dystrophy",
+                "predicate_id": "skos:exactMatch",
+                "object_id": "MESH:D009136",
+                "object_label": None,
+                "mapping_justification": "semapv:UnspecifiedMatching",
+                "id": "819ab197-2ab1-4b73-8d0f-d7d4ec14d8a7",
+            },
+            {
+                "subject_id": "MONDO:0020121",
+                "subject_label": "muscular dystrophy",
+                "predicate_id": "skos:exactMatch",
+                "object_id": "NCIT:C84910",
+                "object_label": "Muscular Dystrophy",
+                "mapping_justification": "semapv:UnspecifiedMatching",
+                "id": "adb4b8ed-c4dc-4353-a08e-a4cb02b1826e",
+            },
+            {
+                "subject_id": "MONDO:0020121",
+                "subject_label": "muscular dystrophy",
+                "predicate_id": "skos:exactMatch",
+                "object_id": "SCTID:73297009",
+                "object_label": None,
+                "mapping_justification": "semapv:UnspecifiedMatching",
+                "id": "f6417283-c9d1-4289-aee6-16d30a4445b1",
+            },
+            {
+                "subject_id": "MONDO:0020121",
+                "subject_label": "muscular dystrophy",
+                "predicate_id": "skos:exactMatch",
+                "object_id": "UMLS:C0026850",
+                "object_label": None,
+                "mapping_justification": "semapv:UnspecifiedMatching",
+                "id": "93968631-eedb-448b-b58a-e31e3e411dde",
+            },
+            {
+                "subject_id": "MONDO:0020121",
+                "subject_label": "muscular dystrophy",
+                "predicate_id": "skos:exactMatch",
+                "object_id": "Orphanet:98473",
+                "object_label": None,
+                "mapping_justification": "semapv:UnspecifiedMatching",
+                "id": "e39e8ba9-8d7e-4b33-9f46-3867b652bdb5",
+            },
+        ],
+    }
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": 1,
+            "QTime": 0,
             "params": {
                 "mm": "100%",
                 "q": "fanconi",

diff --git a/backend/tests/unit/test_solr_parsers.py b/backend/tests/unit/test_solr_parsers.py
@@ -7,6 +7,7 @@
     parse_autocomplete,
     parse_entity,
     parse_histopheno,
+    parse_mappings,
     parse_search,
 )
 from monarch_py.utils.utils import dict_diff
@@ -65,3 +66,12 @@ def test_parse_autocomplete(autocomplete_response, autocomplete):
     assert (
         parsed == autocomplete
     ), f"Parsed result is not as expected. Difference: {dict_diff(parsed.dict(), autocomplete)}"
+
+
+def test_parse_mappings(mapping_response, mappings):
+    mapping_response["response"]["numFound"] = mapping_response["response"].pop("num_found")
+    solr_response = SolrQueryResult(**mapping_response)
+    parsed = parse_mappings(solr_response)
+    assert (
+        parsed == mappings
+    ), f"Parsed result is not as expected. Difference: {dict_diff(parsed.dict(), mappings)}"
diff --git a/backend/tests/unit/test_solr_queries.py b/backend/tests/unit/test_solr_queries.py
@@ -5,6 +5,7 @@
     build_association_query,
     build_autocomplete_query,
     build_histopheno_query,
+    build_mapping_query,
     build_search_query,
 )
 from monarch_py.utils.utils import compare_dicts, dict_diff
@@ -111,3 +112,9 @@ def test_build_autocomplete_query(autocomplete_query):
     query = build_autocomplete_query(q="fanc").dict()
     expected = autocomplete_query
     assert compare_dicts(query, expected), f"Query is not as expected. Difference: {dict_diff(query, expected)}"
+
+
+def test_build_mappings_query(mapping_query):
+    query = build_mapping_query(entity_id=["MONDO:0020121"]).dict()
+    expected = mapping_query
+    assert compare_dicts(query, expected), f"Query is not as expected. Difference: {dict_diff(query, expected)}"
diff --git a/frontend/fixtures/mappings.json b/frontend/fixtures/mappings.json
@@ -0,0 +1,70 @@
+{
+  "limit": 20,
+  "offset": 0,
+  "total": 7,
+  "items": [
+    {
+      "subject_id": "MONDO:0020121",
+      "subject_label": "muscular dystrophy",
+      "predicate_id": "skos:exactMatch",
+      "object_id": "DOID:9884",
+      "object_label": "muscular dystrophy",
+      "mapping_justification": "semapv:UnspecifiedMatching",
+      "id": "cda26856-16a7-499c-956f-119cbaac5b96"
+    },
+    {
+      "subject_id": "MONDO:0020121",
+      "subject_label": "muscular dystrophy",
+      "predicate_id": "skos:exactMatch",
+      "object_id": "ICD10CM:G71.0",
+      "object_label": "Muscular dystrophy",
+      "mapping_justification": "semapv:UnspecifiedMatching",
+      "id": "25777569-b997-4c8f-a1f3-5af352a16ee1"
+    },
+    {
+      "subject_id": "MONDO:0020121",
+      "subject_label": "muscular dystrophy",
+      "predicate_id": "skos:exactMatch",
+      "object_id": "MESH:D009136",
+      "object_label": null,
+      "mapping_justification": "semapv:UnspecifiedMatching",
+      "id": "819ab197-2ab1-4b73-8d0f-d7d4ec14d8a7"
+    },
+    {
+      "subject_id": "MONDO:0020121",
+      "subject_label": "muscular dystrophy",
+      "predicate_id": "skos:exactMatch",
+      "object_id": "NCIT:C84910",
+      "object_label": "Muscular Dystrophy",
+      "mapping_justification": "semapv:UnspecifiedMatching",
+      "id": "adb4b8ed-c4dc-4353-a08e-a4cb02b1826e"
+    },
+    {
+      "subject_id": "MONDO:0020121",
+      "subject_label": "muscular dystrophy",
+      "predicate_id": "skos:exactMatch",
+      "object_id": "SCTID:73297009",
+      "object_label": null,
+      "mapping_justification": "semapv:UnspecifiedMatching",
+      "id": "f6417283-c9d1-4289-aee6-16d30a4445b1"
+    },
+    {
+      "subject_id": "MONDO:0020121",
+      "subject_label": "muscular dystrophy",
+      "predicate_id": "skos:exactMatch",
+      "object_id": "UMLS:C0026850",
+      "object_label": null,
+      "mapping_justification": "semapv:UnspecifiedMatching",
+      "id": "93968631-eedb-448b-b58a-e31e3e411dde"
+    },
+    {
+      "subject_id": "MONDO:0020121",
+      "subject_label": "muscular dystrophy",
+      "predicate_id": "skos:exactMatch",
+      "object_id": "Orphanet:98473",
+      "object_label": null,
+      "mapping_justification": "semapv:UnspecifiedMatching",
+      "id": "e39e8ba9-8d7e-4b33-9f46-3867b652bdb5"
+    }
+  ]
+}