diff options
Diffstat (limited to 'gn_auth/auth/authorisation/resources/groups')
| -rw-r--r-- | gn_auth/auth/authorisation/resources/groups/data.py | 12 | ||||
| -rw-r--r-- | gn_auth/auth/authorisation/resources/groups/models.py | 106 | ||||
| -rw-r--r-- | gn_auth/auth/authorisation/resources/groups/views.py | 37 |
3 files changed, 131 insertions, 24 deletions
diff --git a/gn_auth/auth/authorisation/resources/groups/data.py b/gn_auth/auth/authorisation/resources/groups/data.py index 702955d..ad0dfba 100644 --- a/gn_auth/auth/authorisation/resources/groups/data.py +++ b/gn_auth/auth/authorisation/resources/groups/data.py @@ -1,7 +1,7 @@ """Handles the resource objects' data.""" +from gn_libs import mysqldb as gn3db from MySQLdb.cursors import DictCursor -from gn_auth.auth.db import mariadb as gn3db from gn_auth.auth.db import sqlite3 as authdb from gn_auth.auth.errors import NotFoundError @@ -9,7 +9,7 @@ from gn_auth.auth.authorisation.checks import authorised_p from gn_auth.auth.authorisation.resources.groups import Group def __fetch_mrna_data_by_ids__( - conn: gn3db.DbConnection, dataset_ids: tuple[str, ...]) -> tuple[ + conn: gn3db.Connection, dataset_ids: tuple[str, ...]) -> tuple[ dict, ...]: """Fetch mRNA Assay data by ID.""" with conn.cursor(DictCursor) as cursor: @@ -27,7 +27,7 @@ def __fetch_mrna_data_by_ids__( 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[ + conn: gn3db.Connection, dataset_ids: tuple[str, ...]) -> tuple[ dict, ...]: """Fetch genotype data by ID.""" with conn.cursor(DictCursor) as cursor: @@ -45,7 +45,7 @@ def __fetch_geno_data_by_ids__( 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[ + conn: gn3db.Connection, dataset_ids: tuple[str, ...]) -> tuple[ dict, ...]: """Fetch phenotype data by ID.""" with conn.cursor(DictCursor) as cursor: @@ -67,7 +67,7 @@ def __fetch_pheno_data_by_ids__( "Could not find Phenotype/Publish data with the given IDs.") def __fetch_data_by_id( - conn: gn3db.DbConnection, dataset_type: str, + conn: gn3db.Connection, dataset_type: str, dataset_ids: tuple[str, ...]) -> tuple[dict, ...]: """Fetch data from MySQL by IDs.""" fetch_fns = { @@ -83,7 +83,7 @@ def __fetch_data_by_id( "group(s)."), oauth2_scope="profile group resource") def link_data_to_group( - authconn: authdb.DbConnection, gn3conn: gn3db.DbConnection, + 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.""" diff --git a/gn_auth/auth/authorisation/resources/groups/models.py b/gn_auth/auth/authorisation/resources/groups/models.py index 3263e37..1d44ca4 100644 --- a/gn_auth/auth/authorisation/resources/groups/models.py +++ b/gn_auth/auth/authorisation/resources/groups/models.py @@ -8,14 +8,18 @@ from typing import Any, Sequence, Iterable, Optional import sqlite3 from flask import g from pymonad.maybe import Just, Maybe, Nothing +from pymonad.either import Left, Right, Either +from pymonad.tools import monad_from_none_or_value from gn_auth.auth.db import sqlite3 as db from gn_auth.auth.authentication.users import User, user_by_id from gn_auth.auth.authorisation.checks import authorised_p from gn_auth.auth.authorisation.privileges import Privilege -from gn_auth.auth.authorisation.resources.base import Resource from gn_auth.auth.authorisation.resources.errors import MissingGroupError +from gn_auth.auth.authorisation.resources.base import ( + Resource, + resource_from_dbrow) from gn_auth.auth.errors import ( NotFoundError, AuthorisationError, InconsistencyError) from gn_auth.auth.authorisation.roles.models import ( @@ -118,7 +122,7 @@ def create_group( cursor, group_name, ( {"group_description": group_description} if group_description else {})) - group_resource = { + _group_resource = { "group_id": str(new_group.group_id), "resource_id": str(uuid4()), "resource_name": group_name, @@ -131,17 +135,17 @@ def create_group( cursor.execute( "INSERT INTO resources VALUES " "(:resource_id, :resource_name, :resource_category_id, :public)", - group_resource) + _group_resource) cursor.execute( "INSERT INTO group_resources(resource_id, group_id) " "VALUES(:resource_id, :group_id)", - group_resource) + _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"])), + UUID(str(_group_resource["resource_id"])), "group-leader") return new_group @@ -233,15 +237,56 @@ def is_group_leader(conn: db.DbConnection, user: User, group: Group) -> bool: return "group-leader" in role_names -def all_groups(conn: db.DbConnection) -> Maybe[Sequence[Group]]: +def __build_groups_list_query__( + base: str, + search: Optional[str] = None +) -> tuple[str, tuple[Optional[str], ...]]: + """Build up the query from given search terms.""" + if search is not None and search.strip() != "": + _search = search.strip() + return ((f"{base} WHERE groups.group_name LIKE ? " + "OR groups.group_metadata LIKE ?"), + (f"%{search}%", f"%{search}%")) + return base, tuple() + + +def __limit_results_length__(base: str, start: int = 0, length: int = 0) -> str: + """Add the `LIMIT … OFFSET …` clause to query `base`.""" + if length > 0: + return f"{base} LIMIT {length} OFFSET {start}" + return base + + +def all_groups( + conn: db.DbConnection, + search: Optional[str] = None, + start: int = 0, + length: int = 0 +) -> Maybe[tuple[tuple[Group, ...], int, int]]: """Retrieve all existing groups""" with db.cursor(conn) as cursor: - cursor.execute("SELECT * FROM groups") + cursor.execute("SELECT COUNT(*) FROM groups") + _groups_total_count = int(cursor.fetchone()["COUNT(*)"]) + + _qdets = __build_groups_list_query__( + "SELECT COUNT(*) FROM groups", search) + cursor.execute(*__build_groups_list_query__( + "SELECT COUNT(*) FROM groups", search)) + _filtered_total_count = int(cursor.fetchone()["COUNT(*)"]) + + _query, _params = __build_groups_list_query__( + "SELECT * FROM groups", search) + + cursor.execute(__limit_results_length__(_query, start, length), + _params) 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 Just(( + tuple( + Group(row["group_id"], row["group_name"], + json.loads(row["group_metadata"])) for row in res), + _groups_total_count, + _filtered_total_count)) return Nothing @@ -497,3 +542,44 @@ def add_resources_to_group(conn: db.DbConnection, "group_id": str(group.group_id), "resource_id": str(rsc.resource_id) } for rsc in resources)) + + +def admin_group(conn: db.DbConnection) -> Either: + """Return a group where at least one system admin is a member.""" + query = ( + "SELECT DISTINCT g.group_id, g.group_name, g.group_metadata " + "FROM roles AS r INNER JOIN user_roles AS ur ON r.role_id=ur.role_id " + "INNER JOIN group_users AS gu ON ur.user_id=gu.user_id " + "INNER JOIN groups AS g ON gu.group_id=g.group_id " + "WHERE role_name='system-administrator'") + with db.cursor(conn) as cursor: + cursor.execute(query) + return monad_from_none_or_value( + Left("There is no group of which the system admininstrator is a " + "member."), + lambda row: Right(Group( + UUID(row["group_id"]), + row["group_name"], + json.loads(row["group_metadata"]))), + cursor.fetchone()) + + +def group_resource(conn: db.DbConnection, group_id: UUID) -> Resource: + """Retrieve the system resource.""" + with db.cursor(conn) as cursor: + cursor.execute( + "SELECT group_resources.group_id, resource_categories.*, " + "resources.resource_id, resources.resource_name, resources.public " + "FROM group_resources INNER JOIN resources " + "ON group_resources.resource_id=resources.resource_id " + "INNER JOIN resource_categories " + "ON resources.resource_category_id=resource_categories.resource_category_id " + "WHERE group_resources.group_id=? " + "AND resource_categories.resource_category_key='group'", + (str(group_id),)) + row = cursor.fetchone() + if row: + return resource_from_dbrow(row) + + raise NotFoundError("Could not find a resource for group with ID " + f"{group_id}") diff --git a/gn_auth/auth/authorisation/resources/groups/views.py b/gn_auth/auth/authorisation/resources/groups/views.py index 920f504..e6c92cb 100644 --- a/gn_auth/auth/authorisation/resources/groups/views.py +++ b/gn_auth/auth/authorisation/resources/groups/views.py @@ -9,10 +9,10 @@ from dataclasses import asdict from MySQLdb.cursors import DictCursor from flask import jsonify, Response, Blueprint, current_app -from gn_auth.auth.requests import request_json +from gn_libs import mysqldb as gn3db +from gn_auth.auth.requests import request_json from gn_auth.auth.db import sqlite3 as db -from gn_auth.auth.db import mariadb as gn3db from gn_auth.auth.db.sqlite3 import with_db_connection from gn_auth.auth.authorisation.privileges import privileges_by_ids @@ -35,11 +35,31 @@ groups = Blueprint("groups", __name__) @require_oauth("profile group") def list_groups(): """Return the list of groups that exist.""" + _kwargs = request_json() + def __add_total_group_count__(groups_info): + return { + "groups": groups_info[0], + "total-groups": groups_info[1], + "total-filtered": groups_info[2] + } + with db.connection(current_app.config["AUTH_DB"]) as conn: - the_groups = all_groups(conn) + return jsonify(all_groups( + conn, + search=_kwargs.get("search"), + start=int(_kwargs.get("start", "0")), + length=int(_kwargs.get("length", "0")) + ).then( + __add_total_group_count__ + ).maybe( + { + "groups": [], + "message": "No groups found!", + "total-groups": 0, + "total-filtered": 0 + }, + lambda _grpdata: _grpdata)) - return jsonify(the_groups.maybe( - [], lambda grps: [asdict(grp) for grp in grps])) @groups.route("/create", methods=["POST"]) @require_oauth("profile group") @@ -169,7 +189,7 @@ def unlinked_genotype_data( return tuple(dict(row) for row in cursor.fetchall()) def unlinked_phenotype_data( - authconn: db.DbConnection, gn3conn: gn3db.DbConnection, + authconn: db.DbConnection, gn3conn: gn3db.Connection, group: Group) -> tuple[dict, ...]: """ Retrieve all phenotype data linked to a group but not linked to any @@ -235,7 +255,7 @@ def unlinked_data(resource_type: str) -> Response: if resource_type in ("system", "group"): return jsonify(tuple()) - if resource_type not in ("all", "mrna", "genotype", "phenotype"): + if resource_type not in ("all", "mrna", "genotype", "phenotype", "inbredset-group"): raise AuthorisationError(f"Invalid resource type {resource_type}") with require_oauth.acquire("profile group resource") as the_token: @@ -253,7 +273,8 @@ def unlinked_data(resource_type: str) -> Response: "genotype": unlinked_genotype_data, "phenotype": lambda conn, grp: partial( unlinked_phenotype_data, gn3conn=gn3conn)( - authconn=conn, group=grp) + authconn=conn, group=grp), + "inbredset-group": lambda authconn, ugroup: [] # Still need to implement this } return jsonify(tuple( dict(row) for row in unlinked_fns[resource_type]( |