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-rw-r--r--gn3/auth/authorisation/data/views.py263
1 files changed, 104 insertions, 159 deletions
diff --git a/gn3/auth/authorisation/data/views.py b/gn3/auth/authorisation/data/views.py
index 03c32b3..47c3fe8 100644
--- a/gn3/auth/authorisation/data/views.py
+++ b/gn3/auth/authorisation/data/views.py
@@ -2,9 +2,11 @@
import os
import uuid
import json
+import random
+import string
import datetime
-from typing import Sequence
from functools import reduce
+from typing import Sequence, Iterable
import redis
from email_validator import validate_email, EmailNotValidError
@@ -19,9 +21,6 @@ from gn3.auth.dictify import dictify
from gn3.auth.authorisation.errors import NotFoundError
-from gn3.auth.authorisation.users.views import (
- validate_password, validate_username)
-
from gn3.auth.authorisation.roles.models import(
revoke_user_role_by_name, assign_user_role_by_name)
@@ -33,15 +32,11 @@ from gn3.auth.authorisation.resources.checks import authorised_for
from gn3.auth.authorisation.resources.models import (
user_resources, public_resources, attach_resources_data)
-from gn3.auth.authorisation.errors import ForbiddenAccess, AuthorisationError
+from gn3.auth.authorisation.errors import ForbiddenAccess
from gn3.auth.authentication.oauth2.resource_server import require_oauth
-from gn3.auth.authentication.users import User, user_by_id, set_user_password
-from gn3.auth.authentication.oauth2.models.oauth2token import (
- OAuth2Token, save_token, revoke_token)
-from gn3.auth.authentication.oauth2.models.oauth2client import (
- client_by_id_and_secret)
+from gn3.auth.authentication.users import User, user_by_email, set_user_password
data = Blueprint("data", __name__)
@@ -119,8 +114,9 @@ def migrate_user_group(conn: db.DbConnection, user: User) -> Group:
group = user_group(conn, user).maybe(# type: ignore[misc]
False, lambda grp: grp) # type: ignore[arg-type]
if not bool(group):
- group = Group(uuid.uuid4(), f"{user.name}'s Group", {
- "created": datetime.datetime.now().isoformat(),
+ now = datetime.datetime.now().isoformat()
+ group = Group(uuid.uuid4(), f"{user.name}'s Group ({now})", {
+ "created": now,
"notes": "Imported from redis"
})
with db.cursor(conn) as cursor:
@@ -160,18 +156,21 @@ def __parametrise__(group: Group, datasets: Sequence[dict],
"accession_id": dataset["accession_id"]
} for dataset in datasets)
-def user_redis_resources(rconn: redis.Redis, user_id: uuid.UUID) -> tuple[
- tuple[dict], tuple[dict], tuple[dict]]:
- """Acquire any resources from redis."""
- return reduce(# type: ignore[return-value]
- __redis_datasets_by_type__,
- (dataset for dataset in
- (dataset for _key,dataset in {
- key: json.loads(val)
- for key,val in rconn.hgetall("resources").items()
- }.items())
- if dataset["owner_id"] == str(user_id)),
- (tuple(), tuple(), tuple()))
+def __org_by_user_id__(acc, resource):
+ try:
+ user_id = uuid.UUID(resource["owner_id"])
+ return {
+ **acc,
+ user_id: acc.get(user_id, tuple()) + (resource,)
+ }
+ except ValueError as _verr:
+ return acc
+
+def redis_resources(rconn: redis.Redis) -> Iterable[dict[str, str]]:
+ """Retrieve ALL defined resources from Redis"""
+ return (
+ json.loads(resource)
+ for resource in rconn.hgetall("resources").values())
def system_admin_user(conn: db.DbConnection) -> User:
"""Return a system admin user."""
@@ -186,41 +185,45 @@ def system_admin_user(conn: db.DbConnection) -> User:
rows[0]["name"])
raise NotFoundError("Could not find a system administration user.")
-def generate_sysadmin_token() -> OAuth2Token:
- """Generate a token for a user with system administration privileges."""
- db_uri = app.config["AUTH_DB"]
- server = app.config["OAUTH2_SERVER"]
- with (require_oauth.acquire("profile") as the_token,
- db.connection(db_uri) as conn):
- admin_user = system_admin_user(conn)
- token = OAuth2Token(
- token_id = uuid.uuid4(),
- client = the_token.client,
- **server.generate_token(
- client = the_token.client,
- grant_type = "implicit",
- user = admin_user,
- scope = the_token.scope,
- expires_in = 30*60,
- include_refresh_token=False),
- refresh_token = None,
- revoked=False,
- issued_at=datetime.datetime.now(),
- user=admin_user)
- save_token(conn, token)
- return token
-
-def migrate_data(
- authconn: db.DbConnection, gn3conn: gn3db.Connection,
- redis_resources: tuple[tuple[dict], tuple[dict], tuple[dict]],
- group: Group) -> tuple[dict[str, str], ...]:
+def migrate_user(
+ conn: db.DbConnection, email: str, username: str, password: str) -> User:
+ """Migrate the user, if not already migrated."""
+ try:
+ return user_by_email(conn, email)
+ except NotFoundError as _nfe:
+ user = User(uuid.uuid4(), email, username)
+ with db.cursor(conn) as cursor:
+ cursor.execute(
+ "INSERT INTO users(user_id, email, name) "
+ "VALUES (?, ?, ?)",
+ (str(user.user_id), user.email, user.name))
+ set_user_password(cursor, user, password)
+ return user
+
+def __generate_random_password__(length: int = 25):
+ """Generate a random password string"""
+ return "".join(random.choices(
+ string.ascii_letters + string.punctuation + string.digits,
+ k=length))
+
+def migrate_data(# pylint: disable=[too-many-locals]
+ authconn: db.DbConnection,
+ gn3conn: gn3db.Connection,
+ rconn: redis.Redis,
+ redis_user_id: uuid.UUID,
+ redisresources: tuple[dict[str, str], ...]) -> tuple[
+ User, Group, tuple[dict[str, str], ...]]:
"""Migrate data attached to the user to the user's group."""
- redis_mrna, redis_geno, redis_pheno = redis_resources
- ## BEGIN: Escalate privileges temporarily to enable fetching of data
- ## =====================================
- new_token = generate_sysadmin_token()
- with app.test_request_context(headers={
- "Authorization": f"Bearer {new_token.access_token}"}):
+ try:
+ user_details = json.loads(rconn.hget("users", str(redis_user_id)))
+ email = validate_email(user_details["email_address"])
+ user = migrate_user(authconn, email["email"],
+ user_details.get("full_name") or "NOT SET",
+ __generate_random_password__())
+ group = migrate_user_group(authconn, user)
+ redis_mrna, redis_geno, redis_pheno = reduce(#type: ignore[var-annotated]
+ __redis_datasets_by_type__, redisresources,
+ (tuple(), tuple(), tuple()))
mrna_datasets = __unmigrated_data__(
retrieve_ungrouped_data(authconn, gn3conn, "mrna"), redis_mrna)
geno_datasets = __unmigrated_data__(
@@ -228,79 +231,27 @@ def migrate_data(
pheno_datasets = __unmigrated_data__(
retrieve_ungrouped_data(authconn, gn3conn, "phenotype"), redis_pheno)
- save_token(authconn, revoke_token(new_token))
- ## =====================================
- ## END: Escalate privileges temporarily to enable fetching of data
-
- params = (
- __parametrise__(group, mrna_datasets, "mRNA") +
- __parametrise__(group, geno_datasets, "Genotype") +
- __parametrise__(group, pheno_datasets, "Phenotype"))
- if len(params) > 0:
- with db.cursor(authconn) as cursor:
- cursor.executemany(
- "INSERT INTO linked_group_data VALUES"
- "(:group_id, :dataset_type, :dataset_or_trait_id, "
- ":dataset_name, :dataset_fullname, :accession_id)",
- params)
-
- return params
-
-@data.route("/user/migrate", methods=["POST"])
-# @require_oauth("migrate-data")
-def migrate_user() -> Response:
- """Migrate the user"""
- def __migrate_user__(conn: db.DbConnection, user_id: uuid.UUID, email: str,
- username: str, password: str) -> User:
- """Migrate the user, if not already migrated."""
- try:
- return user_by_id(conn, user_id)
- except NotFoundError as _nfe:
- user = User(user_id, email, username)
- with db.cursor(conn) as cursor:
- cursor.execute(
- "INSERT INTO users(user_id, email, name) "
- "VALUES (?, ?, ?)",
- (str(user.user_id), user.email, user.name))
- set_user_password(cursor, user, password)
- return user
- try:
- db_uri = app.config.get("AUTH_DB", "").strip()
- with (db.connection(db_uri) as authconn,
- redis.Redis(decode_responses=True) as rconn):
- client_id = uuid.UUID(request.form.get("client_id"))
- client_secret = request.form.get("client_secret", "NOTASECRET")
- client = client_by_id_and_secret(authconn, client_id, client_secret)
- authorised_clients = app.config.get(
- "OAUTH2_CLIENTS_WITH_DATA_MIGRATION_PRIVILEGE", [])
- if client.client_id not in authorised_clients:
- raise ForbiddenAccess("You cannot access this endpoint.")
-
- user_id = uuid.UUID(request.form.get("user_id"))
- redis_dets = rconn.hget("users", str(user_id))
- user_details = json.loads(redis_dets)
- if user_details:
- email = validate_email(user_details["email_address"])
- user = __migrate_user__(
- authconn, user_id, email["email"],
- validate_username(user_details.get("full_name", "")),
- validate_password(
- request.form.get("password", ""),
- request.form.get("confirm_password", "")))
- return jsonify({
- "user": dictify(user),
- "description": "Successfully migrated user."
- })
- raise NotFoundError(
- f"No user with ID '{user_id}'")
- except EmailNotValidError as enve:
- raise AuthorisationError(f"Email Error: {str(enve)}") from enve
- except ValueError as verr:
- raise AuthorisationError(verr.args[0]) from verr
-
-@data.route("/user/<uuid:user_id>/migrate", methods=["POST"])
+ params = (
+ __parametrise__(group, mrna_datasets, "mRNA") +
+ __parametrise__(group, geno_datasets, "Genotype") +
+ __parametrise__(group, pheno_datasets, "Phenotype"))
+ if len(params) > 0:
+ with db.cursor(authconn) as cursor:
+ cursor.executemany(
+ "INSERT INTO linked_group_data VALUES"
+ "(:group_id, :dataset_type, :dataset_or_trait_id, "
+ ":dataset_name, :dataset_fullname, :accession_id)",
+ params)
+
+ return user, group, params
+ except EmailNotValidError as _enve:
+ pass
+
+ return tuple() # type: ignore[return-value]
+
+@data.route("/users/migrate", methods=["POST"])
@require_oauth("migrate-data")
-def migrate_user_data(user_id: uuid.UUID) -> Response:
+def migrate_users_data() -> Response:
"""
Special, protected endpoint to enable the migration of data from the older
system to the newer system with groups, resources and privileges.
@@ -312,30 +263,30 @@ def migrate_user_data(user_id: uuid.UUID) -> Response:
if bool(db_uri) and os.path.exists(db_uri):
authorised_clients = app.config.get(
"OAUTH2_CLIENTS_WITH_DATA_MIGRATION_PRIVILEGE", [])
- with require_oauth.acquire("migrate-data") as the_token:
+ with (require_oauth.acquire("migrate-data") as the_token,
+ db.connection(db_uri) as authconn,
+ redis.Redis(decode_responses=True) as rconn,
+ gn3db.database_connection() as gn3conn):
if the_token.client.client_id in authorised_clients:
- user = the_token.user
- if not user_id == user.user_id:
- raise AuthorisationError(
- "You cannot trigger migration of another user's data.")
- with (db.connection(db_uri) as authconn,
- redis.Redis(decode_responses=True) as rconn,
- gn3db.database_connection() as gn3conn):
- redis_resources = user_redis_resources(rconn, user.user_id)
- user_resource_data: tuple = tuple()
- if any(bool(item) for item in redis_resources):
- group = migrate_user_group(authconn, user)
- user_resource_data = migrate_data(
- authconn, gn3conn, redis_resources, group)
- ## TODO: Maybe delete user from redis...
- return jsonify({
- "description": (
- f"Migrated {len(user_resource_data)} resource data "
- "items."),
- "user": dictify(user),
- "group": dictify(group)
- })
-
+ by_user: dict[uuid.UUID, tuple[dict[str, str], ...]] = reduce(
+ __org_by_user_id__, redis_resources(rconn), {})
+ users, groups, resource_data_params = reduce(# type: ignore[var-annotated, arg-type]
+ lambda acc, ugp: (acc[0] + (ugp[0],),# type: ignore[return-value, arg-type]
+ acc[1] + (ugp[1],),
+ acc[2] + ugp[2]),
+ (
+ migrate_data(
+ authconn, gn3conn, rconn, user_id, user_resources)
+ for user_id, user_resources in by_user.items()),
+ (tuple(), tuple(), tuple()))
+ return jsonify({
+ "description": (
+ f"Migrated {len(resource_data_params)} resource data "
+ f"items for {len(users)} users into {len(groups)} "
+ "groups."),
+ "users": tuple(dictify(user) for user in users),
+ "groups": tuple(dictify(group) for group in groups)
+ })
raise ForbiddenAccess("You cannot access this endpoint.")
return app.response_class(
@@ -345,9 +296,3 @@ def migrate_user_data(user_id: uuid.UUID) -> Response:
"The data migration service is currently unavailable.")
}),
status=500, mimetype="application/json")
-
- # return jsonify({
- # "error": "Unavailable",
- # "error_description": (
- # "The data migration service is currently unavailable.")
- # }), 503
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-22 20:48:26 +0000