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Diffstat (limited to 'gn_auth/auth/authorisation/groups/views.py')
| -rw-r--r-- | gn_auth/auth/authorisation/groups/views.py | 431 |
1 files changed, 0 insertions, 431 deletions
diff --git a/gn_auth/auth/authorisation/groups/views.py b/gn_auth/auth/authorisation/groups/views.py deleted file mode 100644 index 4dc17e0..0000000 --- a/gn_auth/auth/authorisation/groups/views.py +++ /dev/null @@ -1,431 +0,0 @@ -"""The views/routes for the `gn3.auth.authorisation.groups` package.""" -import uuid -import datetime -from typing import Iterable -from functools import partial - -from MySQLdb.cursors import DictCursor -from flask import request, jsonify, Response, Blueprint, current_app - -from ...db import sqlite3 as db -from ...db import mariadb as gn3db - -from ...dictify import dictify -from ...db.sqlite3 import with_db_connection - -from .data import link_data_to_group -from .models import ( - Group, user_group, all_groups, DUMMY_GROUP, GroupRole, group_by_id, - join_requests, group_role_by_id, GroupCreationError, - accept_reject_join_request, group_users as _group_users, - create_group as _create_group, add_privilege_to_group_role, - delete_privilege_from_group_role, create_group_role as _create_group_role) - -from ..roles.models import Role -from ..roles.models import user_roles - -from ..checks import authorised_p -from ..privileges import Privilege, privileges_by_ids -from ..errors import InvalidData, NotFoundError, AuthorisationError - -from ...authentication.users import User -from ...authentication.oauth2.resource_server import require_oauth - -groups = Blueprint("groups", __name__) - -@groups.route("/list", methods=["GET"]) -@require_oauth("profile group") -def list_groups(): - """Return the list of groups that exist.""" - with db.connection(current_app.config["AUTH_DB"]) as conn: - the_groups = all_groups(conn) - - return jsonify(the_groups.maybe( - [], lambda grps: [dictify(grp) for grp in grps])) - -@groups.route("/create", methods=["POST"]) -@require_oauth("profile group") -def create_group(): - """Create a new group.""" - with require_oauth.acquire("profile group") as the_token: - group_name=request.form.get("group_name", "").strip() - if not bool(group_name): - raise GroupCreationError("Could not create the group.") - - db_uri = current_app.config["AUTH_DB"] - with db.connection(db_uri) as conn: - user = the_token.user - new_group = _create_group( - conn, group_name, user, request.form.get("group_description")) - return jsonify({ - **dictify(new_group), "group_leader": dictify(user) - }) - -@groups.route("/members/<uuid:group_id>", methods=["GET"]) -@require_oauth("profile group") -def group_members(group_id: uuid.UUID) -> Response: - """Retrieve all the members of a group.""" - with require_oauth.acquire("profile group") as the_token:# pylint: disable=[unused-variable] - db_uri = current_app.config["AUTH_DB"] - ## Check that user has appropriate privileges and remove the pylint disable above - with db.connection(db_uri) as conn: - return jsonify(tuple( - dictify(user) for user in _group_users(conn, group_id))) - -@groups.route("/requests/join/<uuid:group_id>", methods=["POST"]) -@require_oauth("profile group") -def request_to_join(group_id: uuid.UUID) -> Response: - """Request to join a group.""" - def __request__(conn: db.DbConnection, user: User, group_id: uuid.UUID, - message: str): - with db.cursor(conn) as cursor: - group = user_group(conn, user).maybe(# type: ignore[misc] - False, lambda grp: grp)# type: ignore[arg-type] - if group: - error = AuthorisationError( - "You cannot request to join a new group while being a " - "member of an existing group.") - error.error_code = 400 - raise error - request_id = uuid.uuid4() - cursor.execute( - "INSERT INTO group_join_requests VALUES " - "(:request_id, :group_id, :user_id, :ts, :status, :msg)", - { - "request_id": str(request_id), - "group_id": str(group_id), - "user_id": str(user.user_id), - "ts": datetime.datetime.now().timestamp(), - "status": "PENDING", - "msg": message - }) - return { - "request_id": request_id, - "message": "Successfully sent the join request." - } - - with require_oauth.acquire("profile group") as the_token: - form = request.form - results = with_db_connection(partial( - __request__, user=the_token.user, group_id=group_id, message=form.get( - "message", "I hereby request that you add me to your group."))) - return jsonify(results) - -@groups.route("/requests/join/list", methods=["GET"]) -@require_oauth("profile group") -def list_join_requests() -> Response: - """List the pending join requests.""" - with require_oauth.acquire("profile group") as the_token: - return jsonify(with_db_connection(partial( - join_requests, user=the_token.user))) - -@groups.route("/requests/join/accept", methods=["POST"]) -@require_oauth("profile group") -def accept_join_requests() -> Response: - """Accept a join request.""" - with require_oauth.acquire("profile group") as the_token: - form = request.form - request_id = uuid.UUID(form.get("request_id")) - return jsonify(with_db_connection(partial( - accept_reject_join_request, request_id=request_id, - user=the_token.user, status="ACCEPTED"))) - -@groups.route("/requests/join/reject", methods=["POST"]) -@require_oauth("profile group") -def reject_join_requests() -> Response: - """Reject a join request.""" - with require_oauth.acquire("profile group") as the_token: - form = request.form - request_id = uuid.UUID(form.get("request_id")) - return jsonify(with_db_connection(partial( - accept_reject_join_request, request_id=request_id, - user=the_token.user, status="REJECTED"))) - -def unlinked_mrna_data( - conn: db.DbConnection, group: Group) -> tuple[dict, ...]: - """ - Retrieve all mRNA Assay data linked to a group but not linked to any - resource. - """ - query = ( - "SELECT lmd.* FROM linked_mrna_data lmd " - "LEFT JOIN mrna_resources mr ON lmd.data_link_id=mr.data_link_id " - "WHERE lmd.group_id=? AND mr.data_link_id IS NULL") - with db.cursor(conn) as cursor: - cursor.execute(query, (str(group.group_id),)) - return tuple(dict(row) for row in cursor.fetchall()) - -def unlinked_genotype_data( - conn: db.DbConnection, group: Group) -> tuple[dict, ...]: - """ - Retrieve all genotype data linked to a group but not linked to any resource. - """ - query = ( - "SELECT lgd.* FROM linked_genotype_data lgd " - "LEFT JOIN genotype_resources gr ON lgd.data_link_id=gr.data_link_id " - "WHERE lgd.group_id=? AND gr.data_link_id IS NULL") - with db.cursor(conn) as cursor: - cursor.execute(query, (str(group.group_id),)) - return tuple(dict(row) for row in cursor.fetchall()) - -def unlinked_phenotype_data( - authconn: db.DbConnection, gn3conn: gn3db.DbConnection, - group: Group) -> tuple[dict, ...]: - """ - Retrieve all phenotype data linked to a group but not linked to any - resource. - """ - with db.cursor(authconn) as authcur, gn3conn.cursor(DictCursor) as gn3cur: - authcur.execute( - "SELECT lpd.* FROM linked_phenotype_data AS lpd " - "LEFT JOIN phenotype_resources AS pr " - "ON lpd.data_link_id=pr.data_link_id " - "WHERE lpd.group_id=? AND pr.data_link_id IS NULL", - (str(group.group_id),)) - results = authcur.fetchall() - ids: dict[tuple[str, ...], str] = { - ( - row["SpeciesId"], row["InbredSetId"], row["PublishFreezeId"], - row["PublishXRefId"]): row["data_link_id"] - for row in results - } - if len(ids.keys()) < 1: - return tuple() - paramstr = ", ".join(["(%s, %s, %s, %s)"] * len(ids.keys())) - gn3cur.execute( - "SELECT spc.SpeciesId, spc.SpeciesName, iset.InbredSetId, " - "iset.InbredSetName, pf.Id AS PublishFreezeId, " - "pf.Name AS dataset_name, pf.FullName AS dataset_fullname, " - "pf.ShortName AS dataset_shortname, pxr.Id AS PublishXRefId, " - "pub.PubMed_ID, pub.Title, pub.Year, " - "phen.Pre_publication_description, " - "phen.Post_publication_description, phen.Original_description " - "FROM " - "Species AS spc " - "INNER JOIN InbredSet AS iset " - "ON spc.SpeciesId=iset.SpeciesId " - "INNER JOIN PublishFreeze AS pf " - "ON iset.InbredSetId=pf.InbredSetId " - "INNER JOIN PublishXRef AS pxr " - "ON pf.InbredSetId=pxr.InbredSetId " - "INNER JOIN Publication AS pub " - "ON pxr.PublicationId=pub.Id " - "INNER JOIN Phenotype AS phen " - "ON pxr.PhenotypeId=phen.Id " - "WHERE (spc.SpeciesId, iset.InbredSetId, pf.Id, pxr.Id) " - f"IN ({paramstr})", - tuple(item for sublist in ids.keys() for item in sublist)) - return tuple({ - **{key: value for key, value in row.items() if key not in - ("Post_publication_description", "Pre_publication_description", - "Original_description")}, - "description": ( - row["Post_publication_description"] or - row["Pre_publication_description"] or - row["Original_description"]), - "data_link_id": ids[tuple(str(row[key]) for key in ( - "SpeciesId", "InbredSetId", "PublishFreezeId", - "PublishXRefId"))] - } for row in gn3cur.fetchall()) - -@groups.route("/<string:resource_type>/unlinked-data") -@require_oauth("profile group resource") -def unlinked_data(resource_type: str) -> Response: - """View data linked to the group but not linked to any resource.""" - if resource_type not in ("all", "mrna", "genotype", "phenotype"): - raise AuthorisationError(f"Invalid resource type {resource_type}") - - with require_oauth.acquire("profile group resource") as the_token: - db_uri = current_app.config["AUTH_DB"] - gn3db_uri = current_app.config["SQL_URI"] - with (db.connection(db_uri) as authconn, - gn3db.database_connection(gn3db_uri) as gn3conn): - ugroup = user_group(authconn, the_token.user).maybe(# type: ignore[misc] - DUMMY_GROUP, lambda grp: grp) - if ugroup == DUMMY_GROUP: - return jsonify(tuple()) - - unlinked_fns = { - "mrna": unlinked_mrna_data, - "genotype": unlinked_genotype_data, - "phenotype": lambda conn, grp: partial( - unlinked_phenotype_data, gn3conn=gn3conn)( - authconn=conn, group=grp) - } - return jsonify(tuple( - dict(row) for row in unlinked_fns[resource_type]( - authconn, ugroup))) - - return jsonify(tuple()) - -@groups.route("/data/link", methods=["POST"]) -@require_oauth("profile group resource") -def link_data() -> Response: - """Link selected data to specified group.""" - with require_oauth.acquire("profile group resource") as _the_token: - form = request.form - group_id = uuid.UUID(form["group_id"]) - dataset_ids = form.getlist("dataset_ids") - dataset_type = form.get("dataset_type") - if dataset_type not in ("mrna", "genotype", "phenotype"): - raise InvalidData("Unexpected dataset type requested!") - def __link__(conn: db.DbConnection): - group = group_by_id(conn, group_id) - with gn3db.database_connection(current_app.config["SQL_URI"]) as gn3conn: - return link_data_to_group( - conn, gn3conn, dataset_type, dataset_ids, group) - - return jsonify(with_db_connection(__link__)) - -@groups.route("/roles", methods=["GET"]) -@require_oauth("profile group") -def group_roles(): - """Return a list of all available group roles.""" - with require_oauth.acquire("profile group role") as the_token: - def __list_roles__(conn: db.DbConnection): - ## TODO: Check that user has appropriate privileges - with db.cursor(conn) as cursor: - group = user_group(conn, the_token.user).maybe(# type: ignore[misc] - DUMMY_GROUP, lambda grp: grp) - if group == DUMMY_GROUP: - return tuple() - cursor.execute( - "SELECT gr.group_role_id, r.* " - "FROM group_roles AS gr INNER JOIN roles AS r " - "ON gr.role_id=r.role_id " - "WHERE group_id=?", - (str(group.group_id),)) - return tuple( - GroupRole(uuid.UUID(row["group_role_id"]), - group, - Role(uuid.UUID(row["role_id"]), - row["role_name"], - bool(int(row["user_editable"])), - tuple())) - for row in cursor.fetchall()) - return jsonify(tuple( - dictify(role) for role in with_db_connection(__list_roles__))) - -@groups.route("/privileges", methods=["GET"]) -@require_oauth("profile group") -def group_privileges(): - """Return a list of all available group roles.""" - with require_oauth.acquire("profile group role") as the_token: - def __list_privileges__(conn: db.DbConnection) -> Iterable[Privilege]: - ## TODO: Check that user has appropriate privileges - this_user_roles = user_roles(conn, the_token.user) - with db.cursor(conn) as cursor: - cursor.execute("SELECT * FROM privileges " - "WHERE privilege_id LIKE 'group:%'") - group_level_roles = tuple( - Privilege(row["privilege_id"], row["privilege_description"]) - for row in cursor.fetchall()) - return tuple(privilege for arole in this_user_roles - for privilege in arole.privileges) + group_level_roles - return jsonify(tuple( - dictify(priv) for priv in with_db_connection(__list_privileges__))) - - - -@groups.route("/role/create", methods=["POST"]) -@require_oauth("profile group") -def create_group_role(): - """Create a new group role.""" - with require_oauth.acquire("profile group role") as the_token: - ## TODO: Check that user has appropriate privileges - @authorised_p(("group:role:create-role",), - "You do not have the privilege to create new roles", - oauth2_scope="profile group role") - def __create__(conn: db.DbConnection) -> GroupRole: - ## TODO: Check user cannot assign any privilege they don't have. - form = request.form - role_name = form.get("role_name", "").strip() - privileges_ids = form.getlist("privileges[]") - if len(role_name) == 0: - raise InvalidData("Role name not provided!") - if len(privileges_ids) == 0: - raise InvalidData( - "At least one privilege needs to be provided.") - - group = user_group(conn, the_token.user).maybe(# type: ignore[misc] - DUMMY_GROUP, lambda grp: grp) - - if group == DUMMY_GROUP: - raise AuthorisationError( - "A user without a group cannot create a new role.") - privileges = privileges_by_ids(conn, tuple(privileges_ids)) - if len(privileges_ids) != len(privileges): - raise InvalidData( - f"{len(privileges_ids) - len(privileges)} of the selected " - "privileges were not found in the database.") - - return _create_group_role(conn, group, role_name, privileges) - - return jsonify(with_db_connection(__create__)) - -@groups.route("/role/<uuid:group_role_id>", methods=["GET"]) -@require_oauth("profile group") -def view_group_role(group_role_id: uuid.UUID): - """Return the details of the given role.""" - with require_oauth.acquire("profile group role") as the_token: - def __group_role__(conn: db.DbConnection) -> GroupRole: - group = user_group(conn, the_token.user).maybe(#type: ignore[misc] - DUMMY_GROUP, lambda grp: grp) - - if group == DUMMY_GROUP: - raise AuthorisationError( - "A user without a group cannot view group roles.") - return group_role_by_id(conn, group, group_role_id) - return jsonify(dictify(with_db_connection(__group_role__))) - -def __add_remove_priv_to_from_role__(conn: db.DbConnection, - group_role_id: uuid.UUID, - direction: str, - user: User) -> GroupRole: - assert direction in ("ADD", "DELETE") - group = user_group(conn, user).maybe(# type: ignore[misc] - DUMMY_GROUP, lambda grp: grp) - - if group == DUMMY_GROUP: - raise AuthorisationError( - "You need to be a member of a group to edit roles.") - try: - privilege_id = request.form.get("privilege_id", "") - assert bool(privilege_id), "Privilege to add must be provided." - privileges = privileges_by_ids(conn, (privilege_id,)) - if len(privileges) == 0: - raise NotFoundError("Privilege not found.") - dir_fns = { - "ADD": add_privilege_to_group_role, - "DELETE": delete_privilege_from_group_role - } - return dir_fns[direction]( - conn, - group_role_by_id(conn, group, group_role_id), - privileges[0]) - except AssertionError as aerr: - raise InvalidData(aerr.args[0]) from aerr - -@groups.route("/role/<uuid:group_role_id>/privilege/add", methods=["POST"]) -@require_oauth("profile group") -def add_priv_to_role(group_role_id: uuid.UUID) -> Response: - """Add privilege to group role.""" - with require_oauth.acquire("profile group role") as the_token: - return jsonify({ - **dictify(with_db_connection(partial( - __add_remove_priv_to_from_role__, group_role_id=group_role_id, - direction="ADD", user=the_token.user))), - "description": "Privilege added successfully" - }) - -@groups.route("/role/<uuid:group_role_id>/privilege/delete", methods=["POST"]) -@require_oauth("profile group") -def delete_priv_from_role(group_role_id: uuid.UUID) -> Response: - """Delete privilege from group role.""" - with require_oauth.acquire("profile group role") as the_token: - return jsonify({ - **dictify(with_db_connection(partial( - __add_remove_priv_to_from_role__, group_role_id=group_role_id, - direction="DELETE", user=the_token.user))), - "description": "Privilege deleted successfully" - }) |