"""Entry point from spinning up flask""" import os import sys import logging import getpass import traceback from typing import Dict from typing import Union from flask import Flask from flask_cors import CORS # type: ignore from gn3.loggers import setup_app_handlers from gn3.api.gemma import gemma from gn3.api.rqtl import rqtl from gn3.api.general import general from gn3.api.heatmaps import heatmaps from gn3.api.correlation import correlation from gn3.api.data_entry import data_entry from gn3.api.wgcna import wgcna from gn3.api.ctl import ctl from gn3.errors import register_error_handlers from gn3.api.async_commands import async_commands from gn3.api.menu import menu from gn3.api.search import search from gn3.api.metadata import metadata from gn3.api.sampledata import sampledata from gn3.api.llm import GnQNA from gn3.auth import oauth2 from gn3.case_attributes import caseattr def create_app(config: Union[Dict, str, None] = None) -> Flask: """Create a new flask object""" app = Flask(__name__) # Load default configuration app.config.from_object("gn3.settings") # Load environment configuration if "GN3_CONF" in os.environ: app.config.from_envvar('GN3_CONF') # Load app specified configuration if config is not None: if isinstance(config, dict): app.config.update(config) elif config.endswith(".py"): app.config.from_pyfile(config) setup_app_handlers(app) # DO NOT log anything before this point logging.info("Guix Profile: '%s'.", os.environ.get("GUIX_PROFILE")) logging.info("Python Executable: '%s'.", sys.executable) CORS( app, origins=app.config["CORS_ORIGINS"], allow_headers=app.config["CORS_HEADERS"], supports_credentials=True, intercept_exceptions=False) app.register_blueprint(general, url_prefix="/api/") app.register_blueprint(gemma, url_prefix="/api/gemma") app.register_blueprint(rqtl, url_prefix="/api/rqtl") app.register_blueprint(heatmaps, url_prefix="/api/heatmaps") app.register_blueprint(correlation, url_prefix="/api/correlation") app.register_blueprint(data_entry, url_prefix="/api/dataentry") app.register_blueprint(wgcna, url_prefix="/api/wgcna") app.register_blueprint(ctl, url_prefix="/api/ctl") app.register_blueprint(async_commands, url_prefix="/api/async_commands") app.register_blueprint(menu, url_prefix="/api/menu") app.register_blueprint(search, url_prefix="/api/search") app.register_blueprint(metadata, url_prefix="/api/metadata") app.register_blueprint(sampledata, url_prefix="/api/sampledata") app.register_blueprint(oauth2, url_prefix="/api/oauth2") app.register_blueprint(caseattr, url_prefix="/api/case-attribute") app.register_blueprint(GnQNA, url_prefix="/api/llm") register_error_handlers(app) return app