Merge pull request #98 from TheJacksonLaboratory/G3-462-add-general-s…

…earch-functions-for-geneset-search

G3 462 add general search functions for geneset search

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "geneweaver-api"
-version = "0.9.0"
+version = "0.10.0a0"
 description = "The Geneweaver API"
 authors = [
     "Alexander Berger <alexander.berger@jax.org>",
@@ -18,9 +18,9 @@ packages = [
 [tool.poetry.dependencies]
 python = "^3.9"
 geneweaver-core = "^0.10.0a3"
-fastapi = {extras = ["all"], version = "^0.111.0"}
+fastapi = {extras = ["all"], version = "^0.115.0"}
 uvicorn = {extras = ["standard"], version = "^0.30.0"}
-geneweaver-db = "0.5.0a17"
+geneweaver-db = "0.5.0a21"
 psycopg-pool = "^3.1.7"
 requests = "^2.32.3"
 python-jose = {extras = ["cryptography"], version = "^3.3.0"}

src/geneweaver/api/controller/genesets.py

@@ -8,12 +8,14 @@
 from fastapi import APIRouter, Depends, HTTPException, Path, Query, Security
 from fastapi.responses import FileResponse, StreamingResponse
 from geneweaver.api import dependencies as deps
-from geneweaver.api.schemas.apimodels import GeneValueReturn
+from geneweaver.api.schemas.apimodels import GeneValueReturn, SearchResponse
 from geneweaver.api.schemas.auth import UserInternal
+from geneweaver.api.schemas.search import GenesetSearch
 from geneweaver.api.services import geneset as genset_service
 from geneweaver.api.services import publications as publication_service
 from geneweaver.core.enum import GeneIdentifier, GenesetTier, Species
 from geneweaver.core.schema.score import GenesetScoreType, ScoreType
+from geneweaver.db import search as db_search
 from typing_extensions import Annotated
 
 from . import message as api_message
@@ -147,6 +149,22 @@ def get_visible_genesets(
     return response
 
 
+@router.get("/search")
+def search(
+    geneset_search: Annotated[GenesetSearch, Query()],
+    user: UserInternal = Security(deps.optional_full_user),
+    cursor: Optional[deps.Cursor] = Depends(deps.cursor),
+) -> SearchResponse:
+    """Search genesets."""
+    return SearchResponse(
+        db_search.genesets(
+            cursor,
+            is_readable_by=0 if user is None else user.id,
+            **geneset_search.model_dump(exclude_none=True),
+        )
+    )
+
+
 @router.get("/{geneset_id}")
 def get_geneset(
     geneset_id: Annotated[

src/geneweaver/api/controller/search.py

@@ -4,10 +4,10 @@
 
 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.apimodels import CombinedSearchResponse, GsPubSearchType
 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 geneweaver.db import search as db_search
 from typing_extensions import Annotated
 
 from . import message as api_message
@@ -41,20 +41,19 @@ def search(
             description=api_message.OFFSET,
         ),
     ] = None,
-) -> SeachResponse:
+) -> CombinedSearchResponse:
     """Search genesets and publications."""
-    data = {}
-    response = SeachResponse(data=data)
+    search_results = {}
     if "genesets" in entities:
-        geneset_response = genset_service.get_visible_genesets(
-            cursor=cursor,
-            user=user,
+        genesets = db_search.genesets(
+            cursor,
             search_text=search_text,
+            is_readable_by=0 if user is None else user.id,
             limit=limit,
             offset=offset,
         )
 
-        data["geneset"] = geneset_response.get("data")
+        search_results["genesets"] = genesets
 
     if "publications" in entities:
         pub_response = publication_service.get(
@@ -64,8 +63,8 @@ def search(
             offset=offset,
         )
 
-        data["publications"] = pub_response.get("data")
-
-    response.data = data
+        search_results["publications"] = pub_response.get("data")
 
-    return response
+    return CombinedSearchResponse(
+        object=search_results,
+    )

src/geneweaver/api/core/security.py

@@ -129,7 +129,7 @@ async def get_auth_header(
         auto_error_auth: Optional[bool] = False,
     ) -> Optional[Dict[str, str]]:
         """Get the auth header from the token."""
-        user = await self.get_user(security_scopes, creds, auto_error_auth)
+        user = await self._get_user(security_scopes, creds, auto_error_auth)
         return user.auth_header if user else None
 
     async def get_user_strict(
@@ -140,9 +140,19 @@ async def get_user_strict(
         ),
     ) -> UserInternal:
         """Get the user from the token, raise an exception if not found."""
-        return await self.get_user(security_scopes, creds, True, disallow_public=True)
+        return await self._get_user(security_scopes, creds, True, disallow_public=True)
 
-    async def get_user(  # noqa: C901
+    async def get_user(
+        self,
+        security_scopes: SecurityScopes,
+        creds: Optional[HTTPAuthorizationCredentials] = Depends(
+            Auth0HTTPBearer(auto_error=False)
+        ),
+    ) -> Optional[UserInternal]:
+        """Get the user from the token, don't error if not found."""
+        return await self._get_user(security_scopes, creds, True, disallow_public=False)
+
+    async def _get_user(  # noqa: C901
         self,
         security_scopes: SecurityScopes,
         creds: Optional[HTTPAuthorizationCredentials] = Depends(

src/geneweaver/api/schemas/apimodels.py

@@ -1,14 +1,18 @@
 """Models for API requests."""
 
+# ruff: noqa: ANN002, ANN003
+
 from enum import Enum
-from typing import Iterable, List, Optional
+from typing import Dict, Generic, Iterable, List, Optional, TypeVar
 
 from geneweaver.core.enum import GeneIdentifier, Species
 from geneweaver.core.schema.gene import Gene as GeneSchema
 from geneweaver.core.schema.geneset import GeneValue as GeneValueSchema
 from geneweaver.core.schema.species import Species as SpeciesSchema
 from pydantic import AnyUrl, BaseModel
 
+T = TypeVar("T")
+
 
 class PagingLinks(BaseModel):
     """Schema for holding paging links."""
@@ -99,7 +103,31 @@ class GsPubSearchType(str, Enum):
     PUBLICATIONS = "publications"
 
 
-class SeachResponse(CollectionResponse):
+class SearchResponse(CollectionResponse, Generic[T]):
     """Model for search response endpoint."""
 
-    data: dict
+    data: List[T]
+
+    def __init__(self, *args, **kwargs) -> None:
+        """Initialize the search response model.
+
+        First argument is assigned to `data`.
+        """
+        if args:
+            kwargs["data"] = args[0]
+        super().__init__(**kwargs)
+
+
+class CombinedSearchResponse(BaseModel, Generic[T]):
+    """Model for combined search response endpoint."""
+
+    object: Dict[str, List[T]]
+
+    def __init__(self, *args, **kwargs) -> None:
+        """Initialize the combined search response model.
+
+        First argument is assigned to `object`.
+        """
+        if args:
+            kwargs["object"] = args[0]
+        super().__init__(**kwargs)

src/geneweaver/api/schemas/search.py

@@ -0,0 +1,26 @@
+"""Schema for search API."""
+
+from datetime import date
+from typing import Optional, Set
+
+from geneweaver.core.enum import GenesetTier, ScoreType, Species
+from pydantic import BaseModel, Field
+
+
+class GenesetSearch(BaseModel):
+    """Schema for geneset search."""
+
+    search_text: str
+    publication_id: Optional[int] = None
+    pubmed_id: Optional[int] = None
+    species: Optional[Set[Species]] = None
+    curation_tier: Optional[Set[GenesetTier]] = None
+    score_type: Optional[Set[ScoreType]] = None
+    lte_count: Optional[int] = None
+    gte_count: Optional[int] = None
+    created_before: Optional[date] = None
+    created_after: Optional[date] = None
+    updated_before: Optional[date] = None
+    updated_after: Optional[date] = None
+    limit: Optional[int] = Field(25, ge=0, le=1000)
+    offset: Optional[int] = None

tests/controllers/test_search.py

@@ -18,19 +18,19 @@ def test_pub_search(mock_pub_service_call, client):
     )
 
     assert response.status_code == 200
-    assert response.json().get("data").get("publications") == get_publications.get(
+    assert response.json().get("object").get("publications") == get_publications.get(
         "data"
     )
 
 
-@patch("geneweaver.api.services.geneset.get_visible_genesets")
-def test_genesets_search_response(mock_get_visible_genesets, client):
+@patch("geneweaver.api.controller.search.db_search.genesets")
+def test_genesets_search_response(mock_geneset_search, client):
     """Test search for geneset data response."""
-    mock_data = geneset_by_id_resp.get("geneset")
-    mock_get_visible_genesets.return_value = mock_data
+    mock_data = [geneset_by_id_resp.get("geneset")]
+    mock_geneset_search.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")
+    assert response.json().get("object").get("genesets") == mock_data

tests/core/test_security.py

@@ -95,7 +95,7 @@ async def test_invalid_token_format(mock_requests, mock_security_scope):
     creds = HTTPAuthorizationCredentials(scheme="", credentials="token")
 
     with pytest.raises(expected_exception=Auth0UnauthenticatedException):
-        await auth.get_user(
+        await auth._get_user(
             security_scopes=mock_security_scope,
             creds=creds,
             auto_error_auth=True,
@@ -118,7 +118,7 @@ async def test_valid_jwt_token(
     token = create_test_token()
     creds = HTTPAuthorizationCredentials(credentials=token, scheme="")
 
-    user: UserInternal = await auth.get_user(
+    user: UserInternal = await auth._get_user(
         security_scopes=mock_security_scope,
         creds=creds,
         auto_error_auth=True,
@@ -228,7 +228,7 @@ async def test_is_user_not_public(
 ):
     """Test user is not public."""
     auth = do_auth()
-    is_public = await auth.get_user(
+    is_public = await auth._get_user(
         security_scopes=mock_security_scope, creds=None, disallow_public=False
     )
 
@@ -257,7 +257,7 @@ async def test_invalid_claim(
     creds = HTTPAuthorizationCredentials(credentials=token, scheme="")
 
     with pytest.raises(expected_exception=Auth0UnauthenticatedException):
-        await auth.get_user(
+        await auth._get_user(
             security_scopes=mock_security_scope,
             creds=creds,
             auto_error_auth=True,
@@ -289,7 +289,7 @@ async def test_missing_claim_email_error_claim(
     creds = HTTPAuthorizationCredentials(credentials=token, scheme="")
 
     with pytest.raises(expected_exception=Auth0UnauthorizedException):
-        await auth.get_user(
+        await auth._get_user(
             security_scopes=mock_security_scope,
             creds=creds,
             auto_error_auth=True,