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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, 431 insertions, 0 deletions
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" + }) |