Cleanup of batch code and associated tests

src/geneweaver/api/schemas/batch.py

@@ -1,65 +1,12 @@
 """Module for defining schemas for batch endpoints."""
-from typing import List, Optional
-
-from pydantic import BaseModel, validator
-from geneweaver.core.parse.score import parse_score
+from typing import List
 
 from geneweaver.api.schemas.messages import MessageResponse
-from geneweaver.api.schemas.score import GenesetScoreType
+from pydantic import BaseModel
 
 
 class BatchResponse(BaseModel):
     """Class for defining a response containing batch results."""
 
     genesets: List[int]
     messages: MessageResponse
-
-
-class Publication(BaseModel):
-    authors: str
-    title: str
-    abstract: str
-    journal: str
-    volume: str
-    pages: str
-    month: str
-    year: str
-    pubmed: str
-
-
-class GenesetValueInput(BaseModel):
-    symbol: str
-    value: float
-
-
-class GenesetValue(BaseModel):
-    ode_gene_id: str
-    value: float
-    ode_ref_id: str
-    threshold: bool
-
-
-class BatchUploadGeneset(BaseModel):
-    score: GenesetScoreType
-    # TODO: Use enum from core
-    species: str
-    gene_id_type: str
-    pubmed_id: str
-    private: bool = True
-    curation_id: Optional[int] = None
-    abbreviation: str
-    name: str
-    description: str
-    values: List[GenesetValueInput]
-
-    @validator("score", pre=True)
-    def initialize_score(cls, v):
-        return parse_score(v)
-
-    @validator("private", pre=True)
-    def private_to_bool(cls, v):
-        return v.lower() != "public"
-
-    @validator("curation_id", pre=True)
-    def curation_id_to_int(cls, v, values):
-        return 5 if values["private"] else 4

src/geneweaver/api/services/parse/batch.py

@@ -1,13 +1,17 @@
+"""Functions for processing batch files.
+
+Most of the functionality for processing batch files is contained in the
+geneweaver.core module. This module contains functions for reading the contents
+of a file and passing those contents to the core module for processing.
+"""
 from typing import List, Tuple
-from fastapi import UploadFile
 
+from fastapi import UploadFile
+from geneweaver.api.services.io import read_file_contents
 from geneweaver.core.parse import batch
 from geneweaver.core.schema.messages import SystemMessage, UserMessage
 
 
-from geneweaver.api.services.io import read_file_contents
-
-
 async def process_batch_file(
     # TODO: Add the database session to the function signature.
     # db: Session,
@@ -38,10 +42,6 @@ async def process_batch_file(
         print(geneset, "\n")
 
     # TODO: Add the genesets to the database
-    # results = [
-    #     batch_geneset_for_user(db, user_id, geneset)
-    #     for geneset in genesets
-    # ]
 
     # TODO: Return the correct values.
     return [10], [], []

tests/services/parse/batch/conftest.py

@@ -1,14 +1,16 @@
+"""Pytest fixtures for the batch parsing service tests."""
 from unittest.mock import AsyncMock
 
 import pytest
 from fastapi import UploadFile
 
-from tests.api.unit.services.parse.batch import const
+from tests.services.parse.batch import const
 
 
 # Create a pytest fixture for the mocked UploadFile
 @pytest.fixture()
 def mock_upload_file():
+    """Provide a mocked UploadFile object."""
     mock_file = AsyncMock(spec=UploadFile)
     return mock_file  # provide the mock object to the test
 
@@ -23,4 +25,5 @@ def mock_upload_file():
     ]
 )
 def example_batch_file_contents(request) -> str:
+    """Provide the contents of the example batch file."""
     return request.param

tests/services/parse/batch/const.py

@@ -1,3 +1,4 @@
+"""Constants for batch parsing tests."""
 # ruff: noqa: E501
 EXAMPLE_BATCH_FILE = """
 # This is an example batch upload file for GeneWeaver.

tests/services/parse/batch/test_parse.py

@@ -0,0 +1 @@
+"""Test for the parsing service."""