diff --git a/src/geneweaver/api/controller/genesets.py b/src/geneweaver/api/controller/genesets.py index 00761a7..165dba9 100644 --- a/src/geneweaver/api/controller/genesets.py +++ b/src/geneweaver/api/controller/genesets.py @@ -10,7 +10,7 @@ from geneweaver.api import dependencies as deps 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 geneset as geneset_service from geneweaver.api.services import publications as publication_service from geneweaver.core.enum import GeneIdentifier, GenesetTier, Species from geneweaver.core.schema.geneset import GeneValue @@ -117,7 +117,7 @@ def get_visible_genesets( ] = None, ) -> CollectionResponse: """Get all visible genesets.""" - response = genset_service.get_visible_genesets( + response = geneset_service.get_visible_genesets( cursor=cursor, user=user, gs_id=gs_id, @@ -179,11 +179,11 @@ def get_geneset( ) -> Response: """Get a geneset by ID. Optional filter results by gene identifier type.""" if gene_id_type: - response = genset_service.get_geneset_w_gene_id_type( + response = geneset_service.get_geneset_w_gene_id_type( cursor, geneset_id, user, gene_id_type ) else: - response = genset_service.get_geneset( + response = geneset_service.get_geneset( cursor=cursor, geneset_id=geneset_id, user=user, in_threshold=in_threshold ) @@ -203,7 +203,7 @@ def get_geneset_values( in_threshold: Optional[bool] = None, ) -> CollectionResponse[GeneValue]: """Get geneset gene values by geneset ID.""" - response = genset_service.get_geneset_gene_values( + response = geneset_service.get_geneset_gene_values( cursor=cursor, geneset_id=geneset_id, user=user, @@ -237,11 +237,11 @@ def get_export_geneset_by_id_type( # Validate gene identifier type if gene_id_type: - response = genset_service.get_geneset_w_gene_id_type( + response = geneset_service.get_geneset_w_gene_id_type( cursor, geneset_id, user, gene_id_type ) else: - response = genset_service.get_geneset(cursor, geneset_id, user) + response = geneset_service.get_geneset(cursor, geneset_id, user) if "error" in response: raise_http_error(response) @@ -279,7 +279,7 @@ def get_geneset_metadata( include_pub_info: Optional[bool] = False, ) -> Response: """Get a geneset metadata by geneset id.""" - response = genset_service.get_geneset_metadata( + response = geneset_service.get_geneset_metadata( cursor, geneset_id, user, include_pub_info ) @@ -297,7 +297,7 @@ def get_publication_for_geneset( cursor: Optional[deps.Cursor] = Depends(deps.cursor), ) -> Response[Publication]: """Get the publication associated with the geneset.""" - geneset_resp = genset_service.get_geneset_metadata(cursor, geneset_id, user, True) + geneset_resp = geneset_service.get_geneset_metadata(cursor, geneset_id, user, True) if "error" in geneset_resp: raise_http_error(geneset_resp) @@ -329,7 +329,7 @@ def put_geneset_threshold( cursor: Optional[deps.Cursor] = Depends(deps.cursor), ) -> None: """Set geneset threshold for geneset owner.""" - response = genset_service.update_geneset_threshold( + response = geneset_service.update_geneset_threshold( cursor, geneset_id, gene_score_type, user ) @@ -363,7 +363,7 @@ def get_geneset_ontology_terms( ] = None, ) -> CollectionResponse: """Get geneset ontology terms.""" - terms_resp = genset_service.get_geneset_ontology_terms( + terms_resp = geneset_service.get_geneset_ontology_terms( cursor, geneset_id, user, limit, offset ) @@ -388,7 +388,7 @@ def put_geneset_ontology_term( cursor: Optional[deps.Cursor] = Depends(deps.cursor), ) -> None: """Set geneset threshold for geneset owner.""" - response = genset_service.add_geneset_ontology_term( + response = geneset_service.add_geneset_ontology_term( cursor=cursor, geneset_id=geneset_id, term_ref_id=ontology_id, @@ -414,7 +414,7 @@ def delete_geneset_ontology_term( cursor: Optional[deps.Cursor] = Depends(deps.cursor), ) -> None: """Set geneset threshold for geneset owner.""" - response = genset_service.delete_geneset_ontology_term( + response = geneset_service.delete_geneset_ontology_term( cursor=cursor, geneset_id=geneset_id, term_ref_id=ontology_id,