diff options
Diffstat (limited to 'gn3')
| -rw-r--r-- | gn3/api/metadata.py | 3 | ||||
| -rw-r--r-- | gn3/app.py | 2 | ||||
| -rw-r--r-- | gn3/auth/__init__.py | 3 | ||||
| -rw-r--r-- | gn3/auth/authorisation/__init__.py | 2 | ||||
| -rw-r--r-- | gn3/auth/authorisation/errors.py | 42 | ||||
| -rw-r--r-- | gn3/case_attributes.py | 2 | ||||
| -rw-r--r-- | gn3/errors.py | 4 | ||||
| -rw-r--r-- | gn3/settings.py | 2 |
8 files changed, 5 insertions, 55 deletions
diff --git a/gn3/api/metadata.py b/gn3/api/metadata.py index 6329c69..59c25d3 100644 --- a/gn3/api/metadata.py +++ b/gn3/api/metadata.py @@ -9,7 +9,8 @@ from flask import Blueprint from flask import request from flask import current_app -from gn3.auth.authorisation.errors import AuthorisationError + +from gn3.oauth2.errors import AuthorisationError from gn3.db.datasets import (retrieve_metadata, save_metadata, get_history) diff --git a/gn3/app.py b/gn3/app.py index c8f0c5a..e9a2bbe 100644 --- a/gn3/app.py +++ b/gn3/app.py @@ -26,7 +26,6 @@ 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 @@ -76,7 +75,6 @@ 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") diff --git a/gn3/auth/__init__.py b/gn3/auth/__init__.py index cd65e9b..d9caec9 100644 --- a/gn3/auth/__init__.py +++ b/gn3/auth/__init__.py @@ -1,4 +1 @@ """Top-Level `Auth` module""" -from . import authorisation - -from .views import oauth2 diff --git a/gn3/auth/authorisation/__init__.py b/gn3/auth/authorisation/__init__.py deleted file mode 100644 index abd2747..0000000 --- a/gn3/auth/authorisation/__init__.py +++ /dev/null @@ -1,2 +0,0 @@ -"""The authorisation module.""" -from .checks import authorised_p diff --git a/gn3/auth/authorisation/errors.py b/gn3/auth/authorisation/errors.py deleted file mode 100644 index 3bc7a04..0000000 --- a/gn3/auth/authorisation/errors.py +++ /dev/null @@ -1,42 +0,0 @@ -"""Authorisation exceptions""" - -class AuthorisationError(Exception): - """ - Top-level exception for the `gn3.auth.authorisation` package. - - All exceptions in this package should inherit from this class. - """ - error_code: int = 400 - -class ForbiddenAccess(AuthorisationError): - """Raised for forbidden access.""" - error_code: int = 403 - -class UserRegistrationError(AuthorisationError): - """Raised whenever a user registration fails""" - -class NotFoundError(AuthorisationError): - """Raised whenever we try fetching (a/an) object(s) that do(es) not exist.""" - error_code: int = 404 - -class InvalidData(AuthorisationError): - """ - Exception if user requests invalid data - """ - error_code: int = 400 - -class InconsistencyError(AuthorisationError): - """ - Exception raised due to data inconsistencies - """ - error_code: int = 500 - -class PasswordError(AuthorisationError): - """ - Raise in case of an error with passwords. - """ - -class UsernameError(AuthorisationError): - """ - Raise in case of an error with a user's name. - """ diff --git a/gn3/case_attributes.py b/gn3/case_attributes.py index efc82e9..9baff1e 100644 --- a/gn3/case_attributes.py +++ b/gn3/case_attributes.py @@ -27,7 +27,7 @@ from gn3.commands import run_cmd from gn3.db_utils import Connection, database_connection from gn3.oauth2.authorisation import require_token -from gn3.auth.authorisation.errors import AuthorisationError +from gn3.oauth2.errors import AuthorisationError caseattr = Blueprint("case-attribute", __name__) diff --git a/gn3/errors.py b/gn3/errors.py index cd795e8..46483db 100644 --- a/gn3/errors.py +++ b/gn3/errors.py @@ -16,7 +16,7 @@ from authlib.oauth2.rfc6749.errors import OAuth2Error from flask import Flask, jsonify, Response, current_app from gn3.oauth2 import errors as oautherrors -from gn3.auth.authorisation.errors import AuthorisationError +from gn3.oauth2.errors import AuthorisationError from gn3.llms.errors import LLMError def add_trace(exc: Exception, jsonmsg: dict) -> dict: @@ -60,7 +60,7 @@ def handle_authorisation_error(exc: AuthorisationError): return jsonify(add_trace(exc, { "error": type(exc).__name__, "error_description": " :: ".join(exc.args) - })), exc.error_code + })), 500 def handle_oauth2_errors(exc: OAuth2Error): diff --git a/gn3/settings.py b/gn3/settings.py index 04aa129..439d88c 100644 --- a/gn3/settings.py +++ b/gn3/settings.py @@ -85,8 +85,6 @@ MULTIPROCESSOR_PROCS = 6 # Number of processes to spawn AUTH_SERVER_URL = "https://auth.genenetwork.org" AUTH_MIGRATIONS = "migrations/auth" -AUTH_DB = os.environ.get( - "AUTH_DB", f"{os.environ.get('HOME')}/genenetwork/gn3_files/db/auth.db") OAUTH2_SCOPE = ( "profile", "group", "role", "resource", "user", "masquerade", "introspect") |
