Updating enum usage for consistency with geneweaver-core updates

src/geneweaver/api/controller/genesets.py

@@ -5,16 +5,14 @@
 from tempfile import TemporaryDirectory
 from typing import Optional
 
-from fastapi import APIRouter, Depends, HTTPException, Query, Security
+from fastapi import APIRouter, Depends, HTTPException, Path, Security
 from fastapi.responses import FileResponse
 from geneweaver.api import dependencies as deps
-from geneweaver.api.schemas.apimodels import gene_id_type_options
 from geneweaver.api.schemas.auth import UserInternal
 from geneweaver.api.services import geneset as genset_service
 from geneweaver.core.enum import GeneIdentifier
-from geneweaver.core.schema.geneset import GenesetUpload
 from geneweaver.db import geneset as db_geneset
-from geneweaver.db import geneset_value as db_geneset_value
+from typing_extensions import Annotated
 
 from . import message as api_message
 
@@ -33,20 +31,17 @@ def get_visible_genesets(
 
 @router.get("/{geneset_id}")
 def get_geneset(
-    geneset_id: int,
+    geneset_id: Annotated[
+        int, Path(format="int64", minimum=0, maxiumum=9223372036854775807)
+    ],
     user: UserInternal = Security(deps.full_user),
     cursor: Optional[deps.Cursor] = Depends(deps.cursor),
-    # using int type and adding doc options here as using GeneIdentifier
-    # won't produce the right docs for gene identifier options
-    gene_id_type: Optional[int] = Query(
-        None, description=f"Options: {gene_id_type_options}"
-    ),
+    gene_id_type: Optional[GeneIdentifier] = None,
 ) -> dict:
     """Get a geneset by ID. Optional filter results by gene identifier type."""
     if gene_id_type:
-        gene_identifier_type = get_gene_identifier_type(gene_id_type)
         response = genset_service.get_geneset_w_gene_id_type(
-            cursor, geneset_id, user, gene_identifier_type
+            cursor, geneset_id, user, gene_id_type
         )
     else:
         response = genset_service.get_geneset(cursor, geneset_id, user)
@@ -62,24 +57,21 @@ def get_geneset(
 
 @router.get("/{geneset_id}/file", response_class=FileResponse)
 def get_export_geneset_by_id_type(
-    geneset_id: int,
+    geneset_id: Annotated[
+        int, Path(format="int64", minimum=0, maxiumum=9223372036854775807)
+    ],
     user: UserInternal = Security(deps.full_user),
     cursor: Optional[deps.Cursor] = Depends(deps.cursor),
     temp_dir: TemporaryDirectory = Depends(deps.get_temp_dir),
-    # using int type and adding doc options here as using
-    # GeneIdentifier won't produce the right docs for gene identifier options
-    gene_id_type: Optional[int] = Query(
-        None, description=f"Options: {gene_id_type_options}"
-    ),
-) -> dict:
+    gene_id_type: Optional[GeneIdentifier] = None,
+) -> FileResponse:
     """Export geneset into JSON file. Search by ID and optional gene identifier type."""
     timestr = time.strftime("%Y%m%d-%H%M%S")
 
     # Validate gene identifier type
     if gene_id_type:
-        gene_identifier_type = get_gene_identifier_type(gene_id_type)
         response = genset_service.get_geneset_w_gene_id_type(
-            cursor, geneset_id, user, gene_identifier_type
+            cursor, geneset_id, user, gene_id_type
         )
     else:
         response = genset_service.get_geneset(cursor, geneset_id, user)
@@ -107,30 +99,3 @@ def get_export_geneset_by_id_type(
         media_type="application/octet-stream",
         filename=geneset_filename,
     )
-
-
-def upload_geneset(
-    geneset: GenesetUpload,
-    user: UserInternal = Security(deps.full_user),
-    cursor: Optional[deps.Cursor] = Depends(deps.cursor),
-) -> dict:
-    """Upload a geneset."""
-    db_geneset_value.format_geneset_values_for_file_insert(geneset.gene_list)
-    return {"geneset_id": 0}
-
-
-def get_gene_identifier_type(gene_id_type: int) -> GeneIdentifier:
-    """Get a valid GeneIdentifier object. Raise HTTP exception if invalid value.
-
-    @param gene_id_type: gene identifier type
-    @return: GeneIdentifier obj or HTTP exception if invalid id value.
-    """
-    try:
-        gene_identifier = GeneIdentifier(gene_id_type)
-    except ValueError as err:
-        raise HTTPException(
-            status_code=400,
-            detail=f"{api_message.GENE_IDENTIFIER_TYPE_VALUE_ERROR}, "
-            f"valid options= {gene_id_type_options}",
-        ) from err
-    return gene_identifier

src/geneweaver/api/schemas/apimodels.py

@@ -1,13 +1,9 @@
 """Models for API requests."""
 from typing import Iterable, Optional
 
-from fastapi import Query
 from geneweaver.core.enum import GeneIdentifier, Species
 from pydantic import BaseModel
 
-gene_id_type_options = [f"{choice.name} ({choice.value})" for choice in GeneIdentifier]
-species_type_options = [f"{choice.name} ({choice.value})" for choice in Species]
-
 
 class GeneIdMappingResp(BaseModel):
     """Model for gene id mapping."""
@@ -19,15 +15,7 @@ class GeneIdMappingReq(BaseModel):
     """Model for gene id mapping request."""
 
     source_ids: Iterable[str]
-    target_gene_id_type: GeneIdentifier = Query(
-        description=f"Options: {gene_id_type_options}"
-    )
-    source_gene_id_type: Optional[GeneIdentifier] = Query(
-        None, description=f"Options: {gene_id_type_options}"
-    )
-    target_species: Optional[Species] = Query(
-        None, description=f"Options: {species_type_options}"
-    )
-    source_species: Optional[Species] = Query(
-        None, description=f"Options: {species_type_options}"
-    )
+    target_gene_id_type: GeneIdentifier
+    source_gene_id_type: Optional[GeneIdentifier] = None
+    target_species: Optional[Species] = None
+    source_species: Optional[Species] = None

src/geneweaver/api/services/geneset.py

@@ -54,7 +54,7 @@ def get_geneset_w_gene_id_type(
         original_gene_id_type = gene_id_type
         genedb_sp_id = db_gene.gene_database_by_id(cursor, gene_id_type)[0]["sp_id"]
 
-        if genedb_sp_id != 0 and geneset["sp_id"] != genedb_sp_id:
+        if genedb_sp_id != 0 and geneset["species_id"] != genedb_sp_id:
             mapping_across_species = True
             gene_id_type = GeneIdentifier(7)
 

tests/controllers/test_genesets.py

@@ -2,7 +2,6 @@
 from unittest.mock import patch
 
 import pytest
-from geneweaver.api.controller import message
 
 from tests.data import test_geneset_data
 
@@ -78,5 +77,5 @@ def test_invalid_gene_type_id(mock_service_get_geneset_w_gene_id_type, client):
     mock_service_get_geneset_w_gene_id_type.return_value = geneset_w_gene_id_type_resp
     response = client.get("/api/genesets/1234/file?gene_id_type=25")
 
-    assert message.GENE_IDENTIFIER_TYPE_VALUE_ERROR in response.json()["detail"]
-    assert response.status_code == 400
+    assert 'ctx' in response.json()["detail"][0]
+    assert response.status_code == 422