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a/pyproject.toml +++ b/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 ", @@ -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"} diff --git a/src/geneweaver/api/controller/genesets.py b/src/geneweaver/api/controller/genesets.py index 29a51b3..33d36fe 100644 --- a/src/geneweaver/api/controller/genesets.py +++ b/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[ diff --git a/src/geneweaver/api/controller/search.py b/src/geneweaver/api/controller/search.py index a821d53..aaf22d6 100644 --- a/src/geneweaver/api/controller/search.py +++ b/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, + ) diff --git a/src/geneweaver/api/core/security.py b/src/geneweaver/api/core/security.py index 5be4162..bb65dcc 100644 --- a/src/geneweaver/api/core/security.py +++ b/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( diff --git a/src/geneweaver/api/schemas/apimodels.py b/src/geneweaver/api/schemas/apimodels.py index e6f7377..16ca9c0 100644 --- a/src/geneweaver/api/schemas/apimodels.py +++ b/src/geneweaver/api/schemas/apimodels.py @@ -1,7 +1,9 @@ """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 @@ -9,6 +11,8 @@ 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) diff --git a/src/geneweaver/api/schemas/search.py b/src/geneweaver/api/schemas/search.py new file mode 100644 index 0000000..b503554 --- /dev/null +++ b/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 diff --git a/tests/controllers/test_search.py b/tests/controllers/test_search.py index 3c6919a..6fee62f 100644 --- a/tests/controllers/test_search.py +++ b/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 diff --git a/tests/core/test_security.py b/tests/core/test_security.py index bc600e5..6466072 100644 --- a/tests/core/test_security.py +++ b/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,