Adding in progress src and tests code

src/geneweaver/api/controller/api.py

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+"""The root API definition for the GeneWeaver API.
+
+This file defines the root API for the GeneWeaver API. It is responsible for
+defining the FastAPI application and including all other API routers.
+"""
+from fastapi import FastAPI, APIRouter, Security
+
+from geneweaver.api.core import deps
+from geneweaver.api.core.config import settings
+
+from geneweaver.api.controller import batch
+from geneweaver.api.controller import genesets
+
+app = FastAPI(
+    title="GeneWeaver API",
+    docs_url=f"{settings.API_PREFIX}/docs",
+    redoc_url=f"{settings.API_PREFIX}/redoc",
+    openapi_url=f"{settings.API_PREFIX}/openapi.json",
+    swagger_ui_oauth2_redirect_url=f"{settings.API_PREFIX}/docs/oauth2-redirect",
+    swagger_ui_init_oauth={"clientId": settings.AUTH_CLIENT_ID},
+)
+
+api_router = APIRouter(
+    tags=["api"],
+    dependencies=[
+        Security(deps.auth.implicit_scheme),
+    ],
+)
+api_router.include_router(batch.router)
+api_router.include_router(genesets.router)
+
+app.include_router(api_router, prefix=settings.API_PREFIX)

src/geneweaver/api/controller/batch.py

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+"""API Controller definition for batch processing."""
+from typing import Optional
+
+from fastapi import APIRouter, UploadFile, Security
+
+from geneweaver.api.core import deps
+from geneweaver.api.schemas.auth import UserInternal
+from geneweaver.api.schemas.batch import BatchResponse
+from geneweaver.api.services.parse.batch import process_batch_file
+
+router = APIRouter(prefix="/batch")
+
+
+@router.post(path="")
+async def batch(
+    batch_file: UploadFile,
+    curation_group_id: Optional[int] = None,
+    user: UserInternal = Security(deps.auth.get_user_strict),
+) -> BatchResponse:
+    """Submit a batch file for processing."""
+    user_id = 1  # TODO: Get user ID from session
+    genesets, user_messages, system_messages = await process_batch_file(
+        batch_file, user_id
+    )
+
+    return {
+        "genesets": genesets,
+        "messages": {
+            "user_messages": user_messages,
+            "system_messages": system_messages,
+        },
+    }

src/geneweaver/api/controller/genesets.py

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+"""Endpoints related to genesets."""
+from typing import Optional
+
+from fastapi import APIRouter, Security, Depends, HTTPException
+
+from geneweaver.api import dependencies as deps
+from geneweaver.api.schemas.auth import UserInternal
+from geneweaver.db import geneset_value as db_geneset_value
+from geneweaver.db import geneset as db_geneset
+from geneweaver.db import gene as db_gene
+from geneweaver.db.geneset import by_id, by_user_id, is_readable
+from geneweaver.db.geneset_value import by_geneset_id
+from geneweaver.db.user import by_sso_id
+from geneweaver.core.schema.geneset import GenesetUpload
+
+
+router = APIRouter(prefix="/genesets")
+
+
+@router.get("")
+def get_visible_genesets(
+    user: UserInternal = Security(deps.full_user),
+        cursor: Optional[deps.Cursor] = Depends(deps.cursor),
+):
+    """Get all visible genesets."""
+    user_genesets = db_geneset.by_user_id(cursor, user.id)
+    return {"genesets": user_genesets}
+
+
+@router.get("/{geneset_id}")
+def get_geneset(
+    geneset_id: int,
+    user: UserInternal = Security(deps.full_user),
+    cursor: Optional[deps.Cursor] = Depends(deps.cursor),
+):
+    """Get a geneset by ID."""
+    if not is_readable(cursor, user.id, geneset_id):
+        raise HTTPException(status_code=403, detail="Forbidden")
+
+    geneset = db_geneset.by_id(cursor, geneset_id)
+    geneset_values = db_geneset_value.by_geneset_id(cursor, geneset_id)
+    return {"geneset": geneset, "geneset_values": geneset_values}
+
+
+@router.post("")
+def upload_geneset(
+    geneset: GenesetUpload,
+    user: UserInternal = Security(deps.full_user),
+    cursor: Optional[deps.Cursor] = Depends(deps.cursor),
+):
+    """Upload a geneset."""
+    formatted_geneset_values = db_geneset_value.format_geneset_values_for_file_insert(
+        geneset.gene_list
+    )
+    return {"geneset_id": 0}

src/geneweaver/api/controller/search.py

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+"""Endpoints related to searching."""

src/geneweaver/api/core/config.py

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+"""A namespace for the initialized Geneweaver API configuration."""
+from geneweaver.db.core.settings_class import Settings as DBSettings
+
+from geneweaver.api.core.config_class import GeneweaverAPIConfig
+
+settings = GeneweaverAPIConfig()
+
+db_settings = DBSettings()

src/geneweaver/api/core/config_class.py

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+"""Namespace for the config class for the Geneweaver API."""
+from typing import Any, Dict, Optional, List
+
+from pydantic import BaseSettings, PostgresDsn, validator
+from geneweaver.db.core.settings_class import Settings
+
+
+class GeneweaverAPIConfig(BaseSettings):
+    """Config class for the Geneweaver API."""
+
+    API_PREFIX: str = ""
+
+    POSTGRES_SERVER: str
+    POSTGRES_USER: str
+    POSTGRES_PASSWORD: str
+    POSTGRES_DB: str
+    SQLALCHEMY_DATABASE_URI: Optional[PostgresDsn] = None
+
+    @validator("SQLALCHEMY_DATABASE_URI", pre=True)
+    def assemble_db_connection(cls, v: Optional[str], values: Dict[str, Any]) -> Any:
+        if isinstance(v, str):
+            return v
+        return PostgresDsn.build(
+            scheme="postgresql",
+            user=values.get("POSTGRES_USER"),
+            password=values.get("POSTGRES_PASSWORD"),
+            host=values.get("POSTGRES_SERVER"),
+            path=f"/{values.get('POSTGRES_DB') or ''}",
+        )
+
+    AUTH_DOMAIN: str = "geneweaver.auth0.com"
+    AUTH_AUDIENCE: str = "https://api.geneweaver.org"
+    AUTH_ALGORITHMS: List[str] = ["RS256"]
+    AUTH_EMAIL_NAMESPACE: str = AUTH_AUDIENCE
+    AUTH_SCOPES = {
+        "openid profile email": "read",
+    }
+    JWT_PERMISSION_PREFIX: str = "approle"
+    AUTH_CLIENT_ID: str = "oVm9omUtLBpVyL7YfJA8gp3hHaHwyVt8"
+
+    class Config:
+        """Configuration for the BaseSettings class."""
+
+        env_file = ".env"
+        case_sensitive = True

src/geneweaver/api/core/deps.py

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+"""A module to keep track of injectable dependencies for FastAPI endpoints.
+- https://fastapi.tiangolo.com/tutorial/dependencies/
+"""
+from geneweaver.api.core.config import settings
+from geneweaver.api.core.security import Auth0
+
+auth = Auth0(
+    domain=settings.AUTH_DOMAIN,
+    api_audience=settings.AUTH_AUDIENCE,
+    scopes=settings.AUTH_SCOPES,
+    auto_error=False,
+)

src/geneweaver/api/core/exceptions.py

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+""""""
+from fastapi import HTTPException
+
+
+class Auth0UnauthenticatedException(HTTPException):
+    def __init__(self, **kwargs):
+        super().__init__(401, **kwargs)
+
+
+class Auth0UnauthorizedException(HTTPException):
+    def __init__(self, **kwargs):
+        super().__init__(403, **kwargs)
+
+
+class NotAHeaderRowError(Exception):
+    pass
+
+
+class InvalidBatchValueLine(Exception):
+    pass
+
+
+class MultiLineStringError(Exception):
+    pass
+
+
+class IgnoreLineError(Exception):
+    pass
+
+
+class MissingRequiredHeaderError(Exception):
+    pass
+
+
+class InvalidScoreThresholdException(Exception):
+    pass