diff options
Diffstat (limited to 'gn_auth/auth/authorisation/groups')
| -rw-r--r-- | gn_auth/auth/authorisation/groups/__init__.py | 3 | ||||
| -rw-r--r-- | gn_auth/auth/authorisation/groups/data.py | 107 | ||||
| -rw-r--r-- | gn_auth/auth/authorisation/groups/models.py | 433 | ||||
| -rw-r--r-- | gn_auth/auth/authorisation/groups/views.py | 431 |
4 files changed, 0 insertions, 974 deletions
diff --git a/gn_auth/auth/authorisation/groups/__init__.py b/gn_auth/auth/authorisation/groups/__init__.py deleted file mode 100644 index 1cb0bba..0000000 --- a/gn_auth/auth/authorisation/groups/__init__.py +++ /dev/null @@ -1,3 +0,0 @@ -"""Initialise the `gn3.auth.authorisation.groups` package""" - -from .models import Group, GroupRole diff --git a/gn_auth/auth/authorisation/groups/data.py b/gn_auth/auth/authorisation/groups/data.py deleted file mode 100644 index 1650405..0000000 --- a/gn_auth/auth/authorisation/groups/data.py +++ /dev/null @@ -1,107 +0,0 @@ -"""Handles the resource objects' data.""" -from MySQLdb.cursors import DictCursor - -from ..groups import Group -from ..checks import authorised_p -from ..errors import NotFoundError - -from ...db import mariadb as gn3db -from ...db import sqlite3 as authdb - -def __fetch_mrna_data_by_ids__( - conn: gn3db.DbConnection, dataset_ids: tuple[str, ...]) -> tuple[ - dict, ...]: - """Fetch mRNA Assay data by ID.""" - with conn.cursor(DictCursor) as cursor: - paramstr = ", ".join(["%s"] * len(dataset_ids)) - cursor.execute( - "SELECT psf.Id, psf.Name AS dataset_name, " - "psf.FullName AS dataset_fullname, " - "ifiles.GN_AccesionId AS accession_id FROM ProbeSetFreeze AS psf " - "INNER JOIN InfoFiles AS ifiles ON psf.Name=ifiles.InfoPageName " - f"WHERE psf.Id IN ({paramstr})", - dataset_ids) - res = cursor.fetchall() - if res: - return tuple(dict(row) for row in res) - raise NotFoundError("Could not find mRNA Assay data with the given ID.") - -def __fetch_geno_data_by_ids__( - conn: gn3db.DbConnection, dataset_ids: tuple[str, ...]) -> tuple[ - dict, ...]: - """Fetch genotype data by ID.""" - with conn.cursor(DictCursor) as cursor: - paramstr = ", ".join(["%s"] * len(dataset_ids)) - cursor.execute( - "SELECT gf.Id, gf.Name AS dataset_name, " - "gf.FullName AS dataset_fullname, " - "ifiles.GN_AccesionId AS accession_id FROM GenoFreeze AS gf " - "INNER JOIN InfoFiles AS ifiles ON gf.Name=ifiles.InfoPageName " - f"WHERE gf.Id IN ({paramstr})", - dataset_ids) - res = cursor.fetchall() - if res: - return tuple(dict(row) for row in res) - raise NotFoundError("Could not find Genotype data with the given ID.") - -def __fetch_pheno_data_by_ids__( - conn: gn3db.DbConnection, dataset_ids: tuple[str, ...]) -> tuple[ - dict, ...]: - """Fetch phenotype data by ID.""" - with conn.cursor(DictCursor) as cursor: - paramstr = ", ".join(["%s"] * len(dataset_ids)) - cursor.execute( - "SELECT pxf.Id, iset.InbredSetName, pf.Id AS dataset_id, " - "pf.Name AS dataset_name, pf.FullName AS dataset_fullname, " - "ifiles.GN_AccesionId AS accession_id " - "FROM PublishXRef AS pxf " - "INNER JOIN InbredSet AS iset ON pxf.InbredSetId=iset.InbredSetId " - "INNER JOIN PublishFreeze AS pf ON iset.InbredSetId=pf.InbredSetId " - "INNER JOIN InfoFiles AS ifiles ON pf.Name=ifiles.InfoPageName " - f"WHERE pxf.Id IN ({paramstr})", - dataset_ids) - res = cursor.fetchall() - if res: - return tuple(dict(row) for row in res) - raise NotFoundError( - "Could not find Phenotype/Publish data with the given IDs.") - -def __fetch_data_by_id( - conn: gn3db.DbConnection, dataset_type: str, - dataset_ids: tuple[str, ...]) -> tuple[dict, ...]: - """Fetch data from MySQL by IDs.""" - fetch_fns = { - "mrna": __fetch_mrna_data_by_ids__, - "genotype": __fetch_geno_data_by_ids__, - "phenotype": __fetch_pheno_data_by_ids__ - } - return fetch_fns[dataset_type](conn, dataset_ids) - -@authorised_p(("system:data:link-to-group",), - error_description=( - "You do not have sufficient privileges to link data to (a) " - "group(s)."), - oauth2_scope="profile group resource") -def link_data_to_group( - authconn: authdb.DbConnection, gn3conn: gn3db.DbConnection, - dataset_type: str, dataset_ids: tuple[str, ...], group: Group) -> tuple[ - dict, ...]: - """Link the given data to the specified group.""" - the_data = __fetch_data_by_id(gn3conn, dataset_type, dataset_ids) - with authdb.cursor(authconn) as cursor: - params = tuple({ - "group_id": str(group.group_id), "dataset_type": { - "mrna": "mRNA", "genotype": "Genotype", - "phenotype": "Phenotype" - }[dataset_type], - "dataset_or_trait_id": item["Id"], - "dataset_name": item["dataset_name"], - "dataset_fullname": item["dataset_fullname"], - "accession_id": item["accession_id"] - } for item in the_data) - 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 diff --git a/gn_auth/auth/authorisation/groups/models.py b/gn_auth/auth/authorisation/groups/models.py deleted file mode 100644 index c40adbd..0000000 --- a/gn_auth/auth/authorisation/groups/models.py +++ /dev/null @@ -1,433 +0,0 @@ -"""Handle the management of resource/user groups.""" -import json -from uuid import UUID, uuid4 -from functools import reduce -from typing import Any, Sequence, Iterable, Optional, NamedTuple - -from flask import g -from pymonad.maybe import Just, Maybe, Nothing - -from ...db import sqlite3 as db -from ...dictify import dictify -from ...authentication.users import User, user_by_id - -from ..checks import authorised_p -from ..privileges import Privilege -from ..errors import NotFoundError, AuthorisationError, InconsistencyError -from ..roles.models import ( - Role, create_role, check_user_editable, revoke_user_role_by_name, - assign_user_role_by_name) - -class Group(NamedTuple): - """Class representing a group.""" - group_id: UUID - group_name: str - group_metadata: dict[str, Any] - - def dictify(self): - """Return a dict representation of `Group` objects.""" - return { - "group_id": self.group_id, "group_name": self.group_name, - "group_metadata": self.group_metadata - } - -DUMMY_GROUP = Group( - group_id=UUID("77cee65b-fe29-4383-ae41-3cb3b480cc70"), - group_name="GN3_DUMMY_GROUP", - group_metadata={ - "group-description": "This is a dummy group to use as a placeholder" - }) - -class GroupRole(NamedTuple): - """Class representing a role tied/belonging to a group.""" - group_role_id: UUID - group: Group - role: Role - - def dictify(self) -> dict[str, Any]: - """Return a dict representation of `GroupRole` objects.""" - return { - "group_role_id": self.group_role_id, "group": dictify(self.group), - "role": dictify(self.role) - } - -class GroupCreationError(AuthorisationError): - """Raised whenever a group creation fails""" - -class MembershipError(AuthorisationError): - """Raised when there is an error with a user's membership to a group.""" - - def __init__(self, user: User, groups: Sequence[Group]): - """Initialise the `MembershipError` exception object.""" - groups_str = ", ".join(group.group_name for group in groups) - error_description = ( - f"User '{user.name} ({user.email})' is a member of {len(groups)} " - f"groups ({groups_str})") - super().__init__(f"{type(self).__name__}: {error_description}.") - -def user_membership(conn: db.DbConnection, user: User) -> Sequence[Group]: - """Returns all the groups that a member belongs to""" - query = ( - "SELECT groups.group_id, group_name, groups.group_metadata " - "FROM group_users INNER JOIN groups " - "ON group_users.group_id=groups.group_id " - "WHERE group_users.user_id=?") - with db.cursor(conn) as cursor: - cursor.execute(query, (str(user.user_id),)) - groups = tuple(Group(row[0], row[1], json.loads(row[2])) - for row in cursor.fetchall()) - - return groups - -@authorised_p( - privileges = ("system:group:create-group",), - error_description = ( - "You do not have the appropriate privileges to enable you to " - "create a new group."), - oauth2_scope = "profile group") -def create_group( - conn: db.DbConnection, group_name: str, group_leader: User, - group_description: Optional[str] = None) -> Group: - """Create a new group.""" - def resource_category_by_key( - cursor: db.DbCursor, category_key: str): - """Retrieve a resource category by its key.""" - cursor.execute( - "SELECT * FROM resource_categories WHERE " - "resource_category_key=?", - (category_key,)) - results = cursor.fetchone() - if results: - return dict(results) - raise NotFoundError( - f"Could not find a ResourceCategory with key '{category_key}'") - - user_groups = user_membership(conn, group_leader) - if len(user_groups) > 0: - raise MembershipError(group_leader, user_groups) - - with db.cursor(conn) as cursor: - new_group = save_group( - cursor, group_name,( - {"group_description": group_description} - if group_description else {})) - group_resource = { - "group_id": str(new_group.group_id), - "resource_id": str(uuid4()), - "resource_name": group_name, - "resource_category_id": str( - resource_category_by_key(cursor, "group")["resource_category_id"]), - "public": 0 - } - cursor.execute( - "INSERT INTO resources VALUES " - "(:resource_id, :resource_name, :resource_category_id, :public)", - group_resource) - cursor.execute( - "INSERT INTO group_resources(resource_id, group_id) " - "VALUES(:resource_id, :group_id)", - group_resource) - add_user_to_group(cursor, new_group, group_leader) - revoke_user_role_by_name(cursor, group_leader, "group-creator") - assign_user_role_by_name( - cursor, - group_leader, - UUID(str(group_resource["resource_id"])), - "group-leader") - return new_group - -@authorised_p(("group:role:create-role",), - error_description="Could not create the group role") -def create_group_role( - conn: db.DbConnection, group: Group, role_name: str, - privileges: Iterable[Privilege]) -> GroupRole: - """Create a role attached to a group.""" - with db.cursor(conn) as cursor: - group_role_id = uuid4() - role = create_role(cursor, role_name, privileges) - cursor.execute( - ("INSERT INTO group_roles(group_role_id, group_id, role_id) " - "VALUES(?, ?, ?)"), - (str(group_role_id), str(group.group_id), str(role.role_id))) - - return GroupRole(group_role_id, group, role) - -def authenticated_user_group(conn) -> Maybe: - """ - Returns the currently authenticated user's group. - - Look into returning a Maybe object. - """ - user = g.user - with db.cursor(conn) as cursor: - cursor.execute( - ("SELECT groups.* FROM group_users " - "INNER JOIN groups ON group_users.group_id=groups.group_id " - "WHERE group_users.user_id = ?"), - (str(user.user_id),)) - groups = tuple(Group(UUID(row[0]), row[1], json.loads(row[2] or "{}")) - for row in cursor.fetchall()) - - if len(groups) > 1: - raise MembershipError(user, groups) - - if len(groups) == 1: - return Just(groups[0]) - - return Nothing - -def user_group(conn: db.DbConnection, user: User) -> Maybe[Group]: - """Returns the given user's group""" - with db.cursor(conn) as cursor: - cursor.execute( - ("SELECT groups.group_id, groups.group_name, groups.group_metadata " - "FROM group_users " - "INNER JOIN groups ON group_users.group_id=groups.group_id " - "WHERE group_users.user_id = ?"), - (str(user.user_id),)) - groups = tuple( - Group(UUID(row[0]), row[1], json.loads(row[2] or "{}")) - for row in cursor.fetchall()) - - if len(groups) > 1: - raise MembershipError(user, groups) - - if len(groups) == 1: - return Just(groups[0]) - - return Nothing - -def is_group_leader(conn: db.DbConnection, user: User, group: Group) -> bool: - """Check whether the given `user` is the leader of `group`.""" - - ugroup = user_group(conn, user).maybe( - False, lambda val: val) # type: ignore[arg-type, misc] - if not group: - # User cannot be a group leader if not a member of ANY group - return False - - if not ugroup == group: - # User cannot be a group leader if not a member of THIS group - return False - - with db.cursor(conn) as cursor: - cursor.execute( - ("SELECT roles.role_name FROM user_roles LEFT JOIN roles " - "ON user_roles.role_id = roles.role_id WHERE user_id = ?"), - (str(user.user_id),)) - role_names = tuple(row[0] for row in cursor.fetchall()) - - return "group-leader" in role_names - -def all_groups(conn: db.DbConnection) -> Maybe[Sequence[Group]]: - """Retrieve all existing groups""" - with db.cursor(conn) as cursor: - cursor.execute("SELECT * FROM groups") - res = cursor.fetchall() - if res: - return Just(tuple( - Group(row["group_id"], row["group_name"], - json.loads(row["group_metadata"])) for row in res)) - - return Nothing - -def save_group( - cursor: db.DbCursor, group_name: str, - group_metadata: dict[str, Any]) -> Group: - """Save a group to db""" - the_group = Group(uuid4(), group_name, group_metadata) - cursor.execute( - ("INSERT INTO groups " - "VALUES(:group_id, :group_name, :group_metadata) " - "ON CONFLICT (group_id) DO UPDATE SET " - "group_name=:group_name, group_metadata=:group_metadata"), - {"group_id": str(the_group.group_id), "group_name": the_group.group_name, - "group_metadata": json.dumps(the_group.group_metadata)}) - return the_group - -def add_user_to_group(cursor: db.DbCursor, the_group: Group, user: User): - """Add `user` to `the_group` as a member.""" - cursor.execute( - ("INSERT INTO group_users VALUES (:group_id, :user_id) " - "ON CONFLICT (group_id, user_id) DO NOTHING"), - {"group_id": str(the_group.group_id), "user_id": str(user.user_id)}) - -@authorised_p( - privileges = ("system:group:view-group",), - error_description = ( - "You do not have the appropriate privileges to access the list of users" - " in the group.")) -def group_users(conn: db.DbConnection, group_id: UUID) -> Iterable[User]: - """Retrieve all users that are members of group with id `group_id`.""" - with db.cursor(conn) as cursor: - cursor.execute( - "SELECT u.* FROM group_users AS gu INNER JOIN users AS u " - "ON gu.user_id = u.user_id WHERE gu.group_id=:group_id", - {"group_id": str(group_id)}) - results = cursor.fetchall() - - return (User(UUID(row["user_id"]), row["email"], row["name"]) - for row in results) - -@authorised_p( - privileges = ("system:group:view-group",), - error_description = ( - "You do not have the appropriate privileges to access the group.")) -def group_by_id(conn: db.DbConnection, group_id: UUID) -> Group: - """Retrieve a group by its ID""" - with db.cursor(conn) as cursor: - cursor.execute("SELECT * FROM groups WHERE group_id=:group_id", - {"group_id": str(group_id)}) - row = cursor.fetchone() - if row: - return Group( - UUID(row["group_id"]), - row["group_name"], - json.loads(row["group_metadata"])) - - raise NotFoundError(f"Could not find group with ID '{group_id}'.") - -@authorised_p(("system:group:view-group", "system:group:edit-group"), - error_description=("You do not have the appropriate authorisation" - " to act upon the join requests."), - oauth2_scope="profile group") -def join_requests(conn: db.DbConnection, user: User): - """List all the join requests for the user's group.""" - with db.cursor(conn) as cursor: - group = user_group(conn, user).maybe(DUMMY_GROUP, lambda grp: grp)# type: ignore[misc] - if group != DUMMY_GROUP and is_group_leader(conn, user, group): - cursor.execute( - "SELECT gjr.*, u.email, u.name FROM group_join_requests AS gjr " - "INNER JOIN users AS u ON gjr.requester_id=u.user_id " - "WHERE gjr.group_id=? AND gjr.status='PENDING'", - (str(group.group_id),)) - return tuple(dict(row)for row in cursor.fetchall()) - - raise AuthorisationError( - "You do not have the appropriate authorisation to access the " - "group's join requests.") - -@authorised_p(("system:group:view-group", "system:group:edit-group"), - error_description=("You do not have the appropriate authorisation" - " to act upon the join requests."), - oauth2_scope="profile group") -def accept_reject_join_request( - conn: db.DbConnection, request_id: UUID, user: User, status: str) -> dict: - """Accept/Reject a join request.""" - assert status in ("ACCEPTED", "REJECTED"), f"Invalid status '{status}'." - with db.cursor(conn) as cursor: - group = user_group(conn, user).maybe(DUMMY_GROUP, lambda grp: grp) # type: ignore[misc] - cursor.execute("SELECT * FROM group_join_requests WHERE request_id=?", - (str(request_id),)) - row = cursor.fetchone() - if row: - if group.group_id == UUID(row["group_id"]): - try: - the_user = user_by_id(conn, UUID(row["requester_id"])) - if status == "ACCEPTED": - add_user_to_group(cursor, group, the_user) - revoke_user_role_by_name(cursor, the_user, "group-creator") - cursor.execute( - "UPDATE group_join_requests SET status=? " - "WHERE request_id=?", - (status, str(request_id))) - return {"request_id": request_id, "status": status} - except NotFoundError as nfe: - raise InconsistencyError( - "Could not find user associated with join request." - ) from nfe - raise AuthorisationError( - "You cannot act on other groups join requests") - raise NotFoundError(f"Could not find request with ID '{request_id}'") - -def __organise_privileges__(acc, row): - role_id = UUID(row["role_id"]) - role = acc.get(role_id, False) - if role: - return { - **acc, - role_id: Role( - role.role_id, role.role_name, - bool(int(row["user_editable"])), - role.privileges + ( - Privilege(row["privilege_id"], - row["privilege_description"]),)) - } - return { - **acc, - role_id: Role( - UUID(row["role_id"]), row["role_name"], - bool(int(row["user_editable"])), - (Privilege(row["privilege_id"], row["privilege_description"]),)) - } - -# @authorised_p(("group:role:view",), -# "Insufficient privileges to view role", -# oauth2_scope="profile group role") -def group_role_by_id( - conn: db.DbConnection, group: Group, group_role_id: UUID) -> GroupRole: - """Retrieve GroupRole from id by its `group_role_id`.""" - ## TODO: do privileges check before running actual query - ## the check commented out above doesn't work correctly - with db.cursor(conn) as cursor: - cursor.execute( - "SELECT gr.group_role_id, r.*, p.* " - "FROM group_roles AS gr " - "INNER JOIN roles AS r ON gr.role_id=r.role_id " - "INNER JOIN role_privileges AS rp ON rp.role_id=r.role_id " - "INNER JOIN privileges AS p ON p.privilege_id=rp.privilege_id " - "WHERE gr.group_role_id=? AND gr.group_id=?", - (str(group_role_id), str(group.group_id))) - rows = cursor.fetchall() - if rows: - roles: tuple[Role,...] = tuple(reduce( - __organise_privileges__, rows, {}).values()) - assert len(roles) == 1 - return GroupRole(group_role_id, group, roles[0]) - raise NotFoundError( - f"Group role with ID '{group_role_id}' does not exist.") - -@authorised_p(("group:role:edit-role",), - "You do not have the privilege to edit a role.", - oauth2_scope="profile group role") -def add_privilege_to_group_role(conn: db.DbConnection, group_role: GroupRole, - privilege: Privilege) -> GroupRole: - """Add `privilege` to `group_role`.""" - ## TODO: do privileges check. - check_user_editable(group_role.role) - with db.cursor(conn) as cursor: - cursor.execute( - "INSERT INTO role_privileges(role_id,privilege_id) " - "VALUES (?, ?) ON CONFLICT (role_id, privilege_id) " - "DO NOTHING", - (str(group_role.role.role_id), str(privilege.privilege_id))) - return GroupRole( - group_role.group_role_id, - group_role.group, - Role(group_role.role.role_id, - group_role.role.role_name, - group_role.role.user_editable, - group_role.role.privileges + (privilege,))) - -@authorised_p(("group:role:edit-role",), - "You do not have the privilege to edit a role.", - oauth2_scope="profile group role") -def delete_privilege_from_group_role( - conn: db.DbConnection, group_role: GroupRole, - privilege: Privilege) -> GroupRole: - """Delete `privilege` to `group_role`.""" - ## TODO: do privileges check. - check_user_editable(group_role.role) - with db.cursor(conn) as cursor: - cursor.execute( - "DELETE FROM role_privileges WHERE " - "role_id=? AND privilege_id=?", - (str(group_role.role.role_id), str(privilege.privilege_id))) - return GroupRole( - group_role.group_role_id, - group_role.group, - Role(group_role.role.role_id, - group_role.role.role_name, - group_role.role.user_editable, - tuple(priv for priv in group_role.role.privileges - if priv != privilege))) 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" - }) |