diff options
Diffstat (limited to 'gn3/app.py')
| -rw-r--r-- | gn3/app.py | 54 |
1 files changed, 46 insertions, 8 deletions
diff --git a/gn3/app.py b/gn3/app.py index c8f0c5a..9a4269c 100644 --- a/gn3/app.py +++ b/gn3/app.py @@ -1,6 +1,7 @@ """Entry point from spinning up flask""" import os import sys +import json import logging from pathlib import Path @@ -10,7 +11,7 @@ from typing import Union from flask import Flask from flask_cors import CORS # type: ignore -from gn3.loggers import setup_app_handlers +from gn3.loggers import loglevel, setup_app_logging, setup_modules_logging from gn3.api.gemma import gemma from gn3.api.rqtl import rqtl from gn3.api.general import general @@ -26,19 +27,49 @@ 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.auth import oauth2 -from gn3.case_attributes import caseattr +from gn3.api.rqtl2 import rqtl2 +from gn3.api.streaming import streaming +from gn3.api.case_attributes import caseattr +from gn3.api.lmdb_sample_data import lmdb_sample_data + + +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") + app.config.from_file( + Path(__file__).absolute().parent.joinpath("settings.json"), + load=json.load) # Load environment configuration if "GN3_CONF" in os.environ: - app.config.from_envvar('GN3_CONF') + app.config.from_envvar("GN3_CONF") # Load app specified configuration if config is not None: @@ -52,7 +83,10 @@ def create_app(config: Union[Dict, str, None] = None) -> Flask: if secrets_file and Path(secrets_file).exists(): app.config.from_envvar("GN3_SECRETS") # END: SECRETS - setup_app_handlers(app) + verify_app_config(app) + setup_app_logging(app) + setup_modules_logging(loglevel(app), ("gn3.db.menu", + "gn_libs.mysqldb")) # DO NOT log anything before this point logging.info("Guix Profile: '%s'.", os.environ.get("GUIX_PROFILE")) logging.info("Python Executable: '%s'.", sys.executable) @@ -61,7 +95,9 @@ def create_app(config: Union[Dict, str, None] = None) -> Flask: app, origins=app.config["CORS_ORIGINS"], allow_headers=app.config["CORS_HEADERS"], - supports_credentials=True, intercept_exceptions=False) + supports_credentials=True, + intercept_exceptions=False, + ) app.register_blueprint(general, url_prefix="/api/") app.register_blueprint(gemma, url_prefix="/api/gemma") @@ -76,9 +112,11 @@ def create_app(config: Union[Dict, str, None] = None) -> Flask: 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(gnqa, url_prefix="/api/llm") + app.register_blueprint(rqtl2, url_prefix="/api/rqtl2") + app.register_blueprint(streaming, url_prefix="/api/stream") + app.register_blueprint(lmdb_sample_data, url_prefix="/api/lmdb") register_error_handlers(app) return app |