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"^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 8d44e8f..ef0f198 100644 --- a/src/geneweaver/api/controller/genesets.py +++ b/src/geneweaver/api/controller/genesets.py @@ -340,3 +340,33 @@ def get_geneset_ontology_terms( raise HTTPException(status_code=403, detail=api_message.ACCESS_FORBIDDEN) return terms_resp + + +@router.put("/{geneset_id}/ontologies", status_code=204) +def put_geneset_ontology_term( + geneset_id: Annotated[ + int, Path(format="int64", minimum=0, maxiumum=9223372036854775807) + ], + ontology_ref_term_id: str, + user: UserInternal = Security(deps.full_user), + cursor: Optional[deps.Cursor] = Depends(deps.cursor), +) -> None: + """Set geneset threshold for geneset owner.""" + response = genset_service.add_geneset_ontology_term( + cursor=cursor, + geneset_id=geneset_id, + ref_term_id=ontology_ref_term_id, + user=user, + ) + + if "error" in response: + if response.get("message") == api_message.ACCESS_FORBIDDEN: + raise HTTPException(status_code=403, detail=api_message.ACCESS_FORBIDDEN) + + if response.get("message") == api_message.RECORD_NOT_FOUND_ERROR: + raise HTTPException( + status_code=404, detail=api_message.RECORD_NOT_FOUND_ERROR + ) + + if response.get("message") == api_message.RECORD_EXISTS: + raise HTTPException(status_code=412, detail=api_message.RECORD_EXISTS) diff --git a/src/geneweaver/api/services/geneset.py b/src/geneweaver/api/services/geneset.py index dc677f5..c275cd5 100644 --- a/src/geneweaver/api/services/geneset.py +++ b/src/geneweaver/api/services/geneset.py @@ -5,7 +5,7 @@ from fastapi.logger import logger from geneweaver.api.controller import message from geneweaver.api.core.exceptions import UnauthorizedException -from geneweaver.api.schemas.auth import User +from geneweaver.api.schemas.auth import AppRoles, User from geneweaver.core.enum import GeneIdentifier, GenesetTier, Species from geneweaver.core.schema.score import GenesetScoreType from geneweaver.db import gene as db_gene @@ -13,7 +13,9 @@ from geneweaver.db import geneset_value as db_geneset_value from geneweaver.db import ontology as db_ontology from geneweaver.db import threshold as db_threshold -from psycopg import Cursor +from psycopg import Cursor, errors + +ONTO_GSO_REF_TYPE = "GeneWeaver Primary Annotation" def determine_geneset_access( @@ -434,3 +436,55 @@ def get_geneset_ontology_terms( except Exception as err: logger.error(err) raise err + + +def add_geneset_ontology_term( + cursor: Cursor, + geneset_id: int, + ref_term_id: str, + user: User, + gso_ref_type: str = ONTO_GSO_REF_TYPE, +) -> dict: + """Get geneset ontology terms by geneset id. + + :param cursor: DB cursor + :param geneset_id: geneset identifier + :param ref_term_id ref term identifier + :param user: GW user + :param limit: Limit the number of results. + :param offset: Offset the results. + @return: persisted record (geneset id, ontology term id). + """ + try: + if user is None or user.id is None: + return {"error": True, "message": message.ACCESS_FORBIDDEN} + + owner = db_geneset.user_is_owner( + cursor=cursor, user_id=user.id, geneset_id=geneset_id + ) + curator = user.role is AppRoles.curator + + if not owner and not curator: + return {"error": True, "message": message.ACCESS_FORBIDDEN} + + onto_term = db_ontology.by_ontology_term( + cursor=cursor, onto_ref_term_id=ref_term_id + ) + + if onto_term is None: + return {"error": True, "message": message.RECORD_NOT_FOUND_ERROR} + + results = db_ontology.add_ontology_term_to_geneset( + cursor=cursor, + geneset_id=geneset_id, + ontology_term_id=onto_term.get("onto_id"), + gso_ref_type=gso_ref_type, + ) + return {"data": results} + + except errors.UniqueViolation: + return {"error": True, "message": message.RECORD_EXISTS} + + except Exception as err: + logger.error(err) + raise err diff --git a/tests/controllers/test_genesets.py b/tests/controllers/test_genesets.py index 32c4745..eb3bd60 100644 --- a/tests/controllers/test_genesets.py +++ b/tests/controllers/test_genesets.py @@ -310,3 +310,40 @@ def test_get_geneset_ontology_terms_errors(mock_get_genenset_onto_terms, client) response = client.get("/api/genesets/1234/ontologies") assert response.status_code == 403 + + +@patch("geneweaver.api.services.geneset.add_geneset_ontology_term") +def test_add_geneset_ontology_term_response(mock_add_genenset_onto_terms, client): + """Test add geneset ontology_terms response.""" + mock_resp = test_ontology_data.get("geneset_ontology_terms") + mock_add_genenset_onto_terms.return_value = mock_resp + + response = client.put("/api/genesets/1234/ontologies?ontology_ref_term_id=D001921") + assert response.status_code == 204 + + +@patch("geneweaver.api.services.geneset.add_geneset_ontology_term") +def test_add_geneset_ontology_terms_errors(mock_add_genenset_onto_terms, client): + """Test add geneset ontology_terms errors.""" + mock_resp = { + "error": True, + "message": message.ACCESS_FORBIDDEN, + } + mock_add_genenset_onto_terms.return_value = mock_resp + + response = client.put("/api/genesets/1234/ontologies?ontology_ref_term_id=D001921") + assert response.status_code == 403 + + mock_add_genenset_onto_terms.return_value = { + "error": True, + "message": message.RECORD_NOT_FOUND_ERROR, + } + response = client.put("/api/genesets/1234/ontologies?ontology_ref_term_id=QEQWEWE") + assert response.status_code == 404 + + mock_add_genenset_onto_terms.return_value = { + "error": True, + "message": message.RECORD_EXISTS, + } + response = client.put("/api/genesets/1234/ontologies?ontology_ref_term_id=D001921") + assert response.status_code == 412 diff --git a/tests/data/publications.json b/tests/data/publications.json index fda0c79..a94407c 100644 --- a/tests/data/publications.json +++ b/tests/data/publications.json @@ -32,7 +32,7 @@ "volume": "3", "pages": "565-76", "month": null, - "year": 1975 + "year": "1975" }, "add_pubmed_resp": { "pubmed_id": 1234, diff --git a/tests/services/test_genset.py b/tests/services/test_genset.py index e91a4d4..f53597a 100644 --- a/tests/services/test_genset.py +++ b/tests/services/test_genset.py @@ -472,3 +472,64 @@ def test_geneset_gene_value_w_gene_id_type_none_resp2(mock_db_geneset): None, user=mock_user, geneset_id=1234, gene_id_type=GeneIdentifier(2) ) assert response == {"data": None} + + +@patch("geneweaver.api.services.geneset.db_geneset") +@patch("geneweaver.api.services.geneset.db_ontology") +def test_add_genset_ontology_term(mock_db_ontology, mock_db_geneset): + """Test geneset gene value data response.""" + mock_reponse = {"data": {"gs_id": 1234, "ont_id": 1}} + mock_db_ontology.by_ontology_term.return_value = {"onto_id": 123123} + mock_db_geneset.user_is_owner.return_value = True + mock_db_ontology.add_ontology_term_to_geneset.return_value = mock_reponse.get( + "data" + ) + + response = geneset.add_geneset_ontology_term( + cursor=None, user=mock_user, geneset_id=1234, ref_term_id="D001921" + ) + assert response == mock_reponse + + +@patch("geneweaver.api.services.geneset.db_geneset") +@patch("geneweaver.api.services.geneset.db_ontology") +def test_add_geneset_ontology_term_errors(mock_db_ontology, mock_db_geneset): + """Test geneset gene value data response.""" + mock_reponse = {"data": {"gs_id": 1234, "ont_id": 1}} + mock_db_ontology.by_ontology_term.return_value = {"onto_id": 123123} + mock_db_geneset.user_is_owner.return_value = False + mock_db_ontology.add_ontology_term_to_geneset.return_value = mock_reponse.get( + "data" + ) + + # user is not the geneset owner + response = geneset.add_geneset_ontology_term( + cursor=None, user=mock_user, geneset_id=1234, ref_term_id="D001921" + ) + assert response.get("error") is True + assert response.get("message") == message.ACCESS_FORBIDDEN + + # user is not logged-in + response = geneset.add_geneset_ontology_term( + cursor=None, user=None, geneset_id=1234, ref_term_id="D001921" + ) + assert response.get("error") is True + assert response.get("message") == message.ACCESS_FORBIDDEN + + # Ontology term is not found + mock_db_ontology.by_ontology_term.return_value = None + mock_db_geneset.user_is_owner.return_value = True + response = geneset.add_geneset_ontology_term( + cursor=None, user=mock_user, geneset_id=1234, ref_term_id="D001921" + ) + assert response.get("error") is True + assert response.get("message") == message.RECORD_NOT_FOUND_ERROR + + # db error + mock_db_geneset.user_is_owner.return_value = True + mock_db_ontology.by_ontology_term.return_value = {"onto_id": 123123} + mock_db_ontology.add_ontology_term_to_geneset.side_effect = Exception("ERROR") + with pytest.raises(expected_exception=Exception): + geneset.add_geneset_ontology_term( + cursor=None, user=mock_user, geneset_id=1234, ref_term_id="D001921" + )