Merge pull request #73 from TheJacksonLaboratory/G3-270-search-endpoint

G3-270 search endpoint

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "geneweaver-api"
-version = "0.7.0a1"
+version = "0.7.0a2"
 description = "The Geneweaver API"
 authors = [
     "Alexander Berger <[email protected]>",

src/geneweaver/api/controller/api.py

@@ -7,7 +7,7 @@
 from fastapi import APIRouter, FastAPI, Security
 from geneweaver.api import __version__
 from geneweaver.api import dependencies as deps
-from geneweaver.api.controller import genes, genesets, publications, species
+from geneweaver.api.controller import genes, genesets, publications, search, species
 from geneweaver.api.core.config import settings
 
 app = FastAPI(
@@ -30,5 +30,6 @@
 api_router.include_router(genes.router)
 api_router.include_router(publications.router)
 api_router.include_router(species.router)
+api_router.include_router(search.router)
 
 app.include_router(api_router, prefix=settings.API_PREFIX)

src/geneweaver/api/controller/message.py

@@ -22,3 +22,7 @@
 PUBMED_ID = "Show only results with this PubMed ID"
 SEARCH_TEXT = "Return genesets that match this search text"
 WITH_PUBLICATION = "Include publication info in the return"
+GS_PUB_SEARCH_ENTITIES = "Entites to search, genesets and/or publications"
+GS_PUB_SEARCH_TEXT = (
+    "Gensets and/or publications search types ('genesets', 'publications') "
+)

src/geneweaver/api/controller/search.py

@@ -1 +1,71 @@
 """Endpoints related to searching."""
+
+from typing import List, Optional
+
+from fastapi import APIRouter, Depends, Query, Security
+from geneweaver.api import dependencies as deps
+from geneweaver.api.schemas.apimodels import GsPubSearchType, SeachResponse
+from geneweaver.api.schemas.auth import UserInternal
+from geneweaver.api.services import geneset as genset_service
+from geneweaver.api.services import publications as publication_service
+from typing_extensions import Annotated
+
+from . import message as api_message
+
+router = APIRouter(prefix="/search", tags=["search"])
+
+
+@router.get("")
+def search(
+    entities: Annotated[
+        List[GsPubSearchType], Query(description=api_message.GS_PUB_SEARCH_TEXT)
+    ],
+    search_text: Annotated[str, Query(description=api_message.SEARCH_TEXT)],
+    user: UserInternal = Security(deps.optional_full_user),
+    cursor: Optional[deps.Cursor] = Depends(deps.cursor),
+    limit: Annotated[
+        Optional[int],
+        Query(
+            format="int64",
+            minimum=0,
+            maxiumum=1000,
+            description=api_message.LIMIT,
+        ),
+    ] = 10,
+    offset: Annotated[
+        Optional[int],
+        Query(
+            format="int64",
+            minimum=0,
+            maxiumum=9223372036854775807,
+            description=api_message.OFFSET,
+        ),
+    ] = None,
+) -> SeachResponse:
+    """Search genesets and publications."""
+    data = {}
+    response = SeachResponse(data=data)
+    if "genesets" in entities:
+        geneset_response = genset_service.get_visible_genesets(
+            cursor=cursor,
+            user=user,
+            search_text=search_text,
+            limit=limit,
+            offset=offset,
+        )
+
+        data["geneset"] = geneset_response.get("data")
+
+    if "publications" in entities:
+        pub_response = publication_service.get(
+            cursor,
+            search_text=search_text,
+            limit=limit,
+            offset=offset,
+        )
+
+        data["publications"] = pub_response.get("data")
+
+    response.data = data
+
+    return response

src/geneweaver/api/schemas/apimodels.py

@@ -1,5 +1,6 @@
 """Models for API requests."""
 
+from enum import Enum
 from typing import Iterable, List, Optional
 
 from geneweaver.core.enum import GeneIdentifier, Species
@@ -89,3 +90,16 @@ class NewPubmedRecord(BaseModel):
 
     pub_id: int
     pubmed_id: int
+
+
+class GsPubSearchType(str, Enum):
+    """Enum model for genesets and publication search types."""
+
+    GENESETS = "genesets"
+    PUBLICATIONS = "publications"
+
+
+class SeachResponse(CollectionResponse):
+    """Model for search response endpoint."""
+
+    data: dict

tests/controllers/test_search.py

@@ -0,0 +1,36 @@
+"""Tests for search API."""
+
+from unittest.mock import patch
+
+from tests.data import test_geneset_data, test_publication_data
+
+get_publications = test_publication_data.get("get_publications")
+geneset_by_id_resp = test_geneset_data.get("geneset_by_id_resp")
+
+
+@patch("geneweaver.api.services.publications.get")
+def test_pub_search(mock_pub_service_call, client):
+    """Test search for publications data response."""
+    mock_pub_service_call.return_value = get_publications
+
+    response = client.get(
+        url="/api/search/", params={"entities": "publications", "search_text": "gene"}
+    )
+
+    assert response.status_code == 200
+    assert response.json().get("data").get("publications") == get_publications.get(
+        "data"
+    )
+
+
+@patch("geneweaver.api.services.geneset.get_visible_genesets")
+def test_genesets_search_response(mock_get_visible_genesets, client):
+    """Test search for geneset data response."""
+    mock_data = geneset_by_id_resp.get("geneset")
+    mock_get_visible_genesets.return_value = mock_data
+
+    response = client.get(
+        url="/api/search/", params={"entities": "genesets", "search_text": "gene"}
+    )
+    assert response.status_code == 200
+    assert response.json().get("data").get("genesets") == mock_data.get("data")