diff options
Diffstat (limited to 'gn3')
| -rw-r--r-- | gn3/app.py | 37 | ||||
| -rw-r--r-- | gn3/settings.py | 35 |
2 files changed, 37 insertions, 35 deletions
diff --git a/gn3/app.py b/gn3/app.py index e9a2bbe..57d9fa0 100644 --- a/gn3/app.py +++ b/gn3/app.py @@ -1,4 +1,5 @@ """Entry point from spinning up flask""" + import os import sys import logging @@ -29,6 +30,35 @@ from gn3.api.llm import gnqa 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 = { + "BCRYPT_SALT": """set BCRYPT_SALT to $2b$12$mxLvu9XRLlIaaSeDxt8Sle for local dev work + or run `python3 -c "import bcrypt; print(bcrypt.gensalt().decode())` to get a new one + """, + "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__) @@ -37,7 +67,7 @@ def create_app(config: Union[Dict, str, None] = None) -> Flask: # 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: @@ -51,6 +81,7 @@ 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 + 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")) @@ -60,7 +91,9 @@ 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") diff --git a/gn3/settings.py b/gn3/settings.py index 439d88c..2c657af 100644 --- a/gn3/settings.py +++ b/gn3/settings.py @@ -8,7 +8,7 @@ import os import uuid import tempfile -BCRYPT_SALT = "$2b$12$mxLvu9XRLlIaaSeDxt8Sle" # Change this! +BCRYPT_SALT = "" DATA_DIR = "" GEMMA_WRAPPER_CMD = os.environ.get("GEMMA_WRAPPER", "gemma-wrapper") CACHEDIR = "" @@ -29,14 +29,10 @@ LMDB_PATH = os.environ.get( SQL_URI = os.environ.get( "SQL_URI", "mysql://webqtlout:webqtlout@localhost/db_webqtl") SECRET_KEY = "password" -# gn2 results only used in fetching dataset info - # FAHAMU API TOKEN FAHAMU_AUTH_TOKEN = "" -GN2_BASE_URL = "http://www.genenetwork.org/" - # wgcna script WGCNA_RSCRIPT = "wgcna_analysis.R" # qtlreaper command @@ -83,31 +79,4 @@ ROUND_TO = 10 MULTIPROCESSOR_PROCS = 6 # Number of processes to spawn -AUTH_SERVER_URL = "https://auth.genenetwork.org" -AUTH_MIGRATIONS = "migrations/auth" -OAUTH2_SCOPE = ( - "profile", "group", "role", "resource", "user", "masquerade", - "introspect") - - -try: - # *** SECURITY CONCERN *** - # Clients with access to this privileges create a security concern. - # Be careful when adding to this configuration - OAUTH2_CLIENTS_WITH_INTROSPECTION_PRIVILEGE = tuple( - uuid.UUID(client_id) for client_id in - os.environ.get( - "OAUTH2_CLIENTS_WITH_INTROSPECTION_PRIVILEGE", "").split(",")) -except ValueError as _valerr: - OAUTH2_CLIENTS_WITH_INTROSPECTION_PRIVILEGE = tuple() - -try: - # *** SECURITY CONCERN *** - # Clients with access to this privileges create a security concern. - # Be careful when adding to this configuration - OAUTH2_CLIENTS_WITH_DATA_MIGRATION_PRIVILEGE = tuple( - uuid.UUID(client_id) for client_id in - os.environ.get( - "OAUTH2_CLIENTS_WITH_DATA_MIGRATION_PRIVILEGE", "").split(",")) -except ValueError as _valerr: - OAUTH2_CLIENTS_WITH_DATA_MIGRATION_PRIVILEGE = tuple() +AUTH_SERVER_URL = "" |