refactor: move definition of auth errs and remove auth cli utils

10 files changed, 6 insertions, 160 deletions

diff --git a/example-run-dev.sh b/example-run-dev.sh
index a0c5d61..959411f 100644
--- a/example-run-dev.sh
+++ b/example-run-dev.sh
@@ -3,7 +3,6 @@
 ## Copy to run-dev.sh and update the appropriate environment variables.
 
 export SQL_URI="${SQL_URI:+${SQL_URI}}"
-export AUTH_DB="${AUTH_DB:+${AUTH_DB}}"
 export FLASK_DEBUG=1
 export FLASK_APP="main.py"
 export AUTHLIB_INSECURE_TRANSPORT=true
@@ -20,12 +19,5 @@ then
     exit 1;
 fi
 
-if [ -z "${AUTH_DB}" ]
-then
-    echo "ERROR: You need to specify the 'AUTH_DB' environment variable";
-    exit 1;
-fi
-
-
 # flask run --port=8080
 flask ${CMD_ARGS[@]}
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")
diff --git a/main.py b/main.py
index 879b344..ccbd14f 100644
--- a/main.py
+++ b/main.py
@@ -1,105 +1,9 @@
 """Main entry point for project"""
-import sys
-import uuid
-import json
-from math import ceil
-from datetime import datetime
-
-import click
 
 from gn3.app import create_app
-from gn3.auth.authorisation.users import hash_password
-
-from gn3.auth import db
 
 app = create_app()
 
-##### BEGIN: CLI Commands #####
-
-def __init_dev_users__():
-    """Initialise dev users. Get's used in more than one place"""
-    dev_users_query = "INSERT INTO users VALUES (:user_id, :email, :name)"
-    dev_users_passwd = "INSERT INTO user_credentials VALUES (:user_id, :hash)"
-    dev_users = ({
-        "user_id": "0ad1917c-57da-46dc-b79e-c81c91e5b928",
-        "email": "test@development.user",
-        "name": "Test Development User",
-        "password": "testpasswd"},)
-
-    with db.connection(app.config["AUTH_DB"]) as conn, db.cursor(conn) as cursor:
-        cursor.executemany(dev_users_query, dev_users)
-        cursor.executemany(dev_users_passwd, (
-            {**usr, "hash": hash_password(usr["password"])}
-            for usr in dev_users))
-
-@app.cli.command()
-def init_dev_users():
-    """
-    Initialise development users for OAuth2 sessions.
-
-    **NOTE**: You really should not run this in production/staging
-    """
-    __init_dev_users__()
-
-@app.cli.command()
-def init_dev_clients():
-    """
-    Initialise a development client for OAuth2 sessions.
-
-    **NOTE**: You really should not run this in production/staging
-    """
-    __init_dev_users__()
-    dev_clients_query = (
-        "INSERT INTO oauth2_clients VALUES ("
-        ":client_id, :client_secret, :client_id_issued_at, "
-        ":client_secret_expires_at, :client_metadata, :user_id"
-        ")")
-    dev_clients = ({
-        "client_id": "0bbfca82-d73f-4bd4-a140-5ae7abb4a64d",
-        "client_secret": "yadabadaboo",
-        "client_id_issued_at": ceil(datetime.now().timestamp()),
-        "client_secret_expires_at": 0,
-        "client_metadata": json.dumps({
-            "client_name": "GN2 Dev Server",
-            "token_endpoint_auth_method": [
-                "client_secret_post", "client_secret_basic"],
-            "client_type": "confidential",
-            "grant_types": ["password", "authorization_code", "refresh_token"],
-            "default_redirect_uri": "http://localhost:5033/oauth2/code",
-            "redirect_uris": ["http://localhost:5033/oauth2/code",
-                              "http://localhost:5033/oauth2/token"],
-            "response_type": ["code", "token"],
-            "scope": ["profile", "group", "role", "resource", "register-client",
-                      "user", "masquerade", "migrate-data", "introspect"]
-        }),
-        "user_id": "0ad1917c-57da-46dc-b79e-c81c91e5b928"},)
-
-    with db.connection(app.config["AUTH_DB"]) as conn, db.cursor(conn) as cursor:
-        cursor.executemany(dev_clients_query, dev_clients)
-
-
-@app.cli.command()
-@click.argument("user_id", type=click.UUID)
-def assign_system_admin(user_id: uuid.UUID):
-    """Assign user with ID `user_id` administrator role."""
-    dburi = app.config["AUTH_DB"]
-    with db.connection(dburi) as conn, db.cursor(conn) as cursor:
-        cursor.execute("SELECT * FROM users WHERE user_id=?",
-                       (str(user_id),))
-        row = cursor.fetchone()
-        if row:
-            cursor.execute(
-                "SELECT * FROM roles WHERE role_name='system-administrator'")
-            admin_role = cursor.fetchone()
-            cursor.execute("INSERT INTO user_roles VALUES (?,?)",
-                           (str(user_id), admin_role["role_id"]))
-            return 0
-        print(f"ERROR: Could not find user with ID {user_id}",
-              file=sys.stderr)
-        sys.exit(1)
-
-##### END: CLI Commands #####
-
-if __name__ == '__main__':
+if __name__ == "__main__":
     print("Starting app...")
     app.run()