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"""Entry point from spinning up flask"""
import os
import sys
import logging
from pathlib import Path
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 gnqa
from gn3.api.rqtl2 import rqtl2
from gn3.case_attributes import caseattr
class ConfigurationError(Exception):
"""Raised in case of a configuration error."""
def verify_app_config(app: Flask) -> None:
"""Verify that configuration variables are as expected
It includes:
1. making sure mandatory settings are defined
2. provides examples for what to set as config variables (helps local dev)
"""
app_config = {
"AUTH_SERVER_URL": """AUTH_SERVER_URL is used for api requests that need login.
For local dev, use the running auth server url, which defaults to http://127.0.0.1:8081
""",
}
error_message = []
for setting, err in app_config.items():
print(f"{setting}: {app.config.get(setting)}")
if setting in app.config and bool(app.config[setting]):
continue
error_message.append(err)
if error_message:
raise ConfigurationError("\n".join(error_message))
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)
# BEGIN: SECRETS -- Should be the last of the settings to load
secrets_file = os.environ.get("GN3_SECRETS")
if secrets_file and Path(secrets_file).exists():
app.config.from_envvar("GN3_SECRETS")
# END: SECRETS
verify_app_config(app)
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(caseattr, url_prefix="/api/case-attribute")
app.register_blueprint(gnqa, url_prefix="/api/llm")
app.register_blueprint(rqtl2, url_prefix="/api/rqtl2")
register_error_handlers(app)
return app
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