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 | 106 | ||||
| -rw-r--r-- | gn_auth/auth/authorisation/groups/models.py | 400 | ||||
| -rw-r--r-- | gn_auth/auth/authorisation/groups/views.py | 431 |
4 files changed, 940 insertions, 0 deletions
diff --git a/gn_auth/auth/authorisation/groups/__init__.py b/gn_auth/auth/authorisation/groups/__init__.py new file mode 100644 index 0000000..1cb0bba --- /dev/null +++ b/gn_auth/auth/authorisation/groups/__init__.py @@ -0,0 +1,3 @@ +"""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 new file mode 100644 index 0000000..ee6f70e --- /dev/null +++ b/gn_auth/auth/authorisation/groups/data.py @@ -0,0 +1,106 @@ +"""Handles the resource objects' data.""" +from MySQLdb.cursors import DictCursor + +from gn3 import db_utils as gn3db +from gn3.auth import db as authdb +from gn3.auth.authorisation.groups import Group +from gn3.auth.authorisation.checks import authorised_p +from gn3.auth.authorisation.errors import NotFoundError + +def __fetch_mrna_data_by_ids__( + conn: gn3db.Connection, 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.Connection, 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.Connection, 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.Connection, 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.Connection, + 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 new file mode 100644 index 0000000..5a3ae50 --- /dev/null +++ b/gn_auth/auth/authorisation/groups/models.py @@ -0,0 +1,400 @@ +"""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 gn3.auth import db +from gn3.auth.dictify import dictify +from gn3.auth.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.""" + 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 {})) + 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, "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 new file mode 100644 index 0000000..628df36 --- /dev/null +++ b/gn_auth/auth/authorisation/groups/views.py @@ -0,0 +1,431 @@ +"""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 gn3.auth import db +from gn3 import db_utils as gn3db + +from gn3.auth.dictify import dictify +from gn3.auth.db_utils 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.Connection, + 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" + }) |