diff options
Diffstat (limited to 'gn_auth/auth/authorisation/resources')
20 files changed, 1276 insertions, 188 deletions
diff --git a/gn_auth/auth/authorisation/resources/base.py b/gn_auth/auth/authorisation/resources/base.py index ac93049..333ba0d 100644 --- a/gn_auth/auth/authorisation/resources/base.py +++ b/gn_auth/auth/authorisation/resources/base.py @@ -3,6 +3,8 @@ from uuid import UUID from dataclasses import dataclass from typing import Any, Sequence +import sqlite3 + @dataclass(frozen=True) class ResourceCategory: @@ -20,3 +22,15 @@ class Resource: resource_category: ResourceCategory public: bool resource_data: Sequence[dict[str, Any]] = tuple() + + +def resource_from_dbrow(row: sqlite3.Row): + """Convert an SQLite3 resultset row into a resource.""" + return Resource( + resource_id=UUID(row["resource_id"]), + resource_name=row["resource_name"], + resource_category=ResourceCategory( + UUID(row["resource_category_id"]), + row["resource_category_key"], + row["resource_category_description"]), + public=bool(int(row["public"]))) diff --git a/gn_auth/auth/authorisation/resources/checks.py b/gn_auth/auth/authorisation/resources/checks.py index d8e3a9f..ce2b821 100644 --- a/gn_auth/auth/authorisation/resources/checks.py +++ b/gn_auth/auth/authorisation/resources/checks.py @@ -1,14 +1,21 @@ """Handle authorisation checks for resources""" -from uuid import UUID +import uuid +import warnings from functools import reduce from typing import Sequence +from gn_libs.privileges import check + +from .base import Resource + from ...db import sqlite3 as db from ...authentication.users import User +from ..privileges.models import db_row_to_privilege + def __organise_privileges_by_resource_id__(rows): def __organise__(privs, row): - resource_id = UUID(row["resource_id"]) + resource_id = uuid.UUID(row["resource_id"]) return { **privs, resource_id: (row["privilege_id"],) + privs.get( @@ -16,14 +23,18 @@ def __organise_privileges_by_resource_id__(rows): } return reduce(__organise__, rows, {}) + def authorised_for(conn: db.DbConnection, user: User, privileges: tuple[str, ...], - resource_ids: Sequence[UUID]) -> dict[UUID, bool]: + resource_ids: Sequence[uuid.UUID]) -> dict[uuid.UUID, bool]: """ Check whether `user` is authorised to access `resources` according to given `privileges`. """ + warnings.warn(DeprecationWarning( + f"The function `{__name__}.authorised_for` is deprecated. Please use " + f"`{__name__}.authorised_for_spec`")) with db.cursor(conn) as cursor: cursor.execute( ("SELECT ur.*, rp.privilege_id FROM " @@ -45,3 +56,67 @@ def authorised_for(conn: db.DbConnection, resource_id: resource_id in authorised for resource_id in resource_ids } + + +def authorised_for2( + conn: db.DbConnection, + user: User, + resource: Resource, + privileges: tuple[str, ...] +) -> bool: + """ + Check that `user` has **ALL** the specified privileges for the resource. + """ + warnings.warn(DeprecationWarning( + f"The function `{__name__}.authorised_for2` is deprecated. Please use " + f"`{__name__}.authorised_for_spec`")) + with db.cursor(conn) as cursor: + _query = ( + "SELECT resources.resource_id, user_roles.user_id, roles.role_id, " + "privileges.* " + "FROM resources INNER JOIN user_roles " + "ON resources.resource_id=user_roles.resource_id " + "INNER JOIN roles ON user_roles.role_id=roles.role_id " + "INNER JOIN role_privileges ON roles.role_id=role_privileges.role_id " + "INNER JOIN privileges " + "ON role_privileges.privilege_id=privileges.privilege_id " + "WHERE resources.resource_id=? " + "AND user_roles.user_id=?") + cursor.execute( + _query, + (str(resource.resource_id), str(user.user_id))) + _db_privileges = tuple( + db_row_to_privilege(row) for row in cursor.fetchall()) + + str_privileges = tuple(privilege.privilege_id for privilege in _db_privileges) + return all((requested_privilege in str_privileges) + for requested_privilege in privileges) + + +def authorised_for_spec( + conn: db.DbConnection, + user_id: uuid.UUID, + resource_id: uuid.UUID, + auth_spec: str +) -> bool: + """ + Check that a user, identified with `user_id`, has a set of privileges that + satisfy the `auth_spec` for the resource identified with `resource_id`. + """ + with db.cursor(conn) as cursor: + _query = ( + "SELECT resources.resource_id, user_roles.user_id, roles.role_id, " + "privileges.* " + "FROM resources INNER JOIN user_roles " + "ON resources.resource_id=user_roles.resource_id " + "INNER JOIN roles ON user_roles.role_id=roles.role_id " + "INNER JOIN role_privileges ON roles.role_id=role_privileges.role_id " + "INNER JOIN privileges " + "ON role_privileges.privilege_id=privileges.privilege_id " + "WHERE resources.resource_id=? " + "AND user_roles.user_id=?") + cursor.execute( + _query, + (str(resource_id), str(user_id))) + _privileges = tuple(row["privilege_id"] for row in cursor.fetchall()) + return check(auth_spec, _privileges) diff --git a/gn_auth/auth/authorisation/resources/common.py b/gn_auth/auth/authorisation/resources/common.py new file mode 100644 index 0000000..fd358f1 --- /dev/null +++ b/gn_auth/auth/authorisation/resources/common.py @@ -0,0 +1,48 @@ +"""Utilities common to more than one resource.""" +import uuid + +from gn_auth.auth.db import sqlite3 as db + +def assign_resource_owner_role( + cursor: db.DbCursor, + resource_id: uuid.UUID, + user_id: uuid.UUID +) -> dict: + """Assign `user` the 'Resource Owner' role for `resource`.""" + cursor.execute("SELECT * FROM roles WHERE role_name='resource-owner'") + role = cursor.fetchone() + params = { + "user_id": str(user_id), + "role_id": role["role_id"], + "resource_id": str(resource_id) + } + cursor.execute( + "INSERT INTO user_roles " + "VALUES (:user_id, :role_id, :resource_id) " + "ON CONFLICT (user_id, role_id, resource_id) DO NOTHING", + params) + return params + + +def grant_access_to_sysadmins( + cursor: db.DbCursor, + resource_id: uuid.UUID, + system_resource_id: uuid.UUID +): + """Grant sysadmins access to resource identified by `resource_id`.""" + cursor.execute( + "SELECT role_id FROM roles WHERE role_name='system-administrator'") + sysadminroleid = cursor.fetchone()[0] + + cursor.execute(# Fetch sysadmin IDs. + "SELECT user_roles.user_id FROM roles INNER JOIN user_roles " + "ON roles.role_id=user_roles.role_id " + "WHERE role_name='system-administrator' AND resource_id=?", + (str(system_resource_id),)) + + cursor.executemany( + "INSERT INTO user_roles(user_id, role_id, resource_id) " + "VALUES (?, ?, ?) " + "ON CONFLICT (user_id, role_id, resource_id) DO NOTHING", + tuple((row["user_id"], sysadminroleid, str(resource_id)) + for row in cursor.fetchall())) diff --git a/gn_auth/auth/authorisation/resources/genotypes/__init__.py b/gn_auth/auth/authorisation/resources/genotypes/__init__.py new file mode 100644 index 0000000..f401e28 --- /dev/null +++ b/gn_auth/auth/authorisation/resources/genotypes/__init__.py @@ -0,0 +1 @@ +"""Initialise a genotypes resources package.""" diff --git a/gn_auth/auth/authorisation/resources/genotype.py b/gn_auth/auth/authorisation/resources/genotypes/models.py index 206ab61..762ee7c 100644 --- a/gn_auth/auth/authorisation/resources/genotype.py +++ b/gn_auth/auth/authorisation/resources/genotypes/models.py @@ -5,9 +5,8 @@ from typing import Optional, Sequence import sqlite3 import gn_auth.auth.db.sqlite3 as db - -from .base import Resource -from .data import __attach_data__ +from gn_auth.auth.authorisation.resources.base import Resource +from gn_auth.auth.authorisation.resources.data import __attach_data__ def resource_data( @@ -28,14 +27,15 @@ def resource_data( def link_data_to_resource( conn: db.DbConnection, resource: Resource, - data_link_id: uuid.UUID) -> dict: - """Link Genotype data with a resource.""" + data_link_ids: tuple[uuid.UUID, ...] +) -> tuple[dict, ...]: + """Link Genotype data with a resource using the GUI.""" with db.cursor(conn) as cursor: - params = { + params = tuple({ "resource_id": str(resource.resource_id), "data_link_id": str(data_link_id) - } - cursor.execute( + } for data_link_id in data_link_ids) + cursor.executemany( "INSERT INTO genotype_resources VALUES" "(:resource_id, :data_link_id)", params) @@ -67,3 +67,45 @@ def attach_resources_data( f"WHERE gr.resource_id IN ({placeholders})", tuple(str(resource.resource_id) for resource in resources)) return __attach_data__(cursor.fetchall(), resources) + + +def insert_and_link_data_to_resource(# pylint: disable=[too-many-arguments, too-many-positional-arguments] + cursor, + resource_id: uuid.UUID, + group_id: uuid.UUID, + species_id: int, + population_id: int, + dataset_id: int, + dataset_name: str, + dataset_fullname: str, + dataset_shortname: str +) -> dict: + """Link the genotype identifier data to the genotype resource.""" + params = { + "resource_id": str(resource_id), + "group_id": str(group_id), + "data_link_id": str(uuid.uuid4()), + "species_id": species_id, + "population_id": population_id, + "dataset_id": dataset_id, + "dataset_name": dataset_name, + "dataset_fullname": dataset_fullname, + "dataset_shortname": dataset_shortname + } + cursor.execute( + "INSERT INTO linked_genotype_data " + "VALUES (" + ":data_link_id," + ":group_id," + ":species_id," + ":population_id," + ":dataset_id," + ":dataset_name," + ":dataset_fullname," + ":dataset_shortname" + ")", + params) + cursor.execute( + "INSERT INTO genotype_resources VALUES (:resource_id, :data_link_id)", + params) + return params diff --git a/gn_auth/auth/authorisation/resources/genotypes/views.py b/gn_auth/auth/authorisation/resources/genotypes/views.py new file mode 100644 index 0000000..2beed58 --- /dev/null +++ b/gn_auth/auth/authorisation/resources/genotypes/views.py @@ -0,0 +1,78 @@ +"""Genotype-resources-specific views.""" +import uuid + +from pymonad.either import Left, Right +from flask import jsonify, Blueprint, current_app as app + +from gn_auth.auth.db import sqlite3 as db +from gn_auth.auth.requests import request_json + +from gn_auth.auth.authorisation.resources.base import ResourceCategory +from gn_auth.auth.authorisation.resources.request_utils import check_form +from gn_auth.auth.authorisation.resources.groups.models import user_group + +from gn_auth.auth.authentication.oauth2.resource_server import require_oauth + +from gn_auth.auth.authorisation.resources.models import create_resource +from gn_auth.auth.authorisation.resources.common import ( + assign_resource_owner_role) + + +from .models import insert_and_link_data_to_resource + +genobp = Blueprint("genotypes", __name__) + +@genobp.route("genotypes/create", methods=["POST"]) +@require_oauth("profile group resource") +def create_geno_resource(): + """Create a new genotype resource.""" + with (require_oauth.acquire("profile group resource") as _token, + db.connection(app.config["AUTH_DB"]) as conn, + db.cursor(conn) as cursor): + cursor.execute("SELECT * FROM resource_categories " + "WHERE resource_category_key='genotype'") + row = cursor.fetchone() + + return check_form( + request_json(), + "species_id", + "population_id", + "dataset_id", + "dataset_name", + "dataset_fullname", + "dataset_shortname" + ).then( + lambda form: user_group(conn, _token.user).maybe( + Left("No user group found!"), + lambda group: Right({"formdata": form, "group": group})) + ).then( + lambda fdgrp: { + **fdgrp, + "resource": create_resource( + cursor, + f"Genotype — {fdgrp['formdata']['dataset_fullname']}", + ResourceCategory(uuid.UUID(row["resource_category_id"]), + row["resource_category_key"], + row["resource_category_description"]), + _token.user, + fdgrp["group"], + fdgrp["formdata"].get("public", "on") == "on")} + ).then( + lambda fdgrpres: { + **fdgrpres, + "owner_role": assign_resource_owner_role( + cursor, + fdgrpres["resource"].resource_id, + _token.user.user_id)} + ).then( + lambda fdgrpres: insert_and_link_data_to_resource( + cursor, + fdgrpres["resource"].resource_id, + fdgrpres["group"].group_id, + fdgrpres["formdata"]["species_id"], + fdgrpres["formdata"]["population_id"], + fdgrpres["formdata"]["dataset_id"], + fdgrpres["formdata"]["dataset_name"], + fdgrpres["formdata"]["dataset_fullname"], + fdgrpres["formdata"]["dataset_shortname"]) + ).either(lambda error: (jsonify(error), 400), jsonify) 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..a1937ce 100644 --- a/gn_auth/auth/authorisation/resources/groups/models.py +++ b/gn_auth/auth/authorisation/resources/groups/models.py @@ -8,14 +8,21 @@ 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.system.models import system_resource +from gn_auth.auth.authorisation.resources.common import ( + grant_access_to_sysadmins) +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 ( @@ -118,9 +125,10 @@ def create_group( cursor, group_name, ( {"group_description": group_description} if group_description else {})) - group_resource = { + _group_resource_id = uuid4() + _group_resource = { "group_id": str(new_group.group_id), - "resource_id": str(uuid4()), + "resource_id": str(_group_resource_id), "resource_name": group_name, "resource_category_id": str( resource_category_by_key( @@ -131,18 +139,20 @@ 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) + grant_access_to_sysadmins(cursor, + _group_resource_id, + system_resource(conn).resource_id) 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") + assign_user_role_by_name(cursor, + group_leader, + _group_resource_id, + "group-leader") return new_group @@ -233,15 +243,56 @@ 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 @@ -268,6 +319,56 @@ def add_user_to_group(cursor: db.DbCursor, the_group: Group, user: User): ("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)}) + revoke_user_role_by_name(cursor, user, "group-creator") + + +def resource_from_group(conn: db.DbConnection, the_group: Group) -> Resource: + """Get the resource object that wraps the group for auth purposes.""" + with db.cursor(conn) as cursor: + cursor.execute( + "SELECT " + "resources.resource_id, resources.resource_name, " + "resources.public, resource_categories.* " + "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=?", + (str(the_group.group_id),)) + results = tuple(resource_from_dbrow(row) for row in cursor.fetchall()) + match len(results): + case 0: + raise InconsistencyError("The group lacks a wrapper resource.") + case 1: + return results[0] + case _: + raise InconsistencyError( + "The group has more than one wrapper resource.") + + +def remove_user_from_group( + conn: db.DbConnection, + group: Group, + user: User, + grp_resource: Resource +): + """Add `user` to `group` as a member.""" + with db.cursor(conn) as cursor: + cursor.execute( + "DELETE FROM group_users " + "WHERE group_id=:group_id AND user_id=:user_id", + {"group_id": str(group.group_id), "user_id": str(user.user_id)}) + cursor.execute( + "DELETE FROM user_roles WHERE user_id=? AND resource_id=?", + (str(user.user_id), str(grp_resource.resource_id))) + assign_user_role_by_name(cursor, + user, + grp_resource.resource_id, + "group-creator") + grant_access_to_sysadmins(cursor, + grp_resource.resource_id, + system_resource(conn).resource_id) @authorised_p( @@ -497,3 +598,108 @@ 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}") + + +def data_resources( + conn: db.DbConnection, group_id: UUID) -> Iterable[Resource]: + """Fetch a group's data resources.""" + with db.cursor(conn) as cursor: + cursor.execute( + "SELECT resource_ownership.group_id, resources.resource_id, " + "resources.resource_name, resources.public, resource_categories.* " + "FROM resource_ownership INNER JOIN resources " + "ON resource_ownership.resource_id=resources.resource_id " + "INNER JOIN resource_categories " + "ON resources.resource_category_id=resource_categories.resource_category_id " + "WHERE group_id=?", + (str(group_id),)) + yield from (resource_from_dbrow(row) for row in cursor.fetchall()) + + +def group_leaders(conn: db.DbConnection, group_id: UUID) -> Iterable[User]: + """Fetch all of a group's group leaders.""" + with db.cursor(conn) as cursor: + cursor.execute( + "SELECT users.* FROM group_users INNER JOIN group_resources " + "ON group_users.group_id=group_resources.group_id " + "INNER JOIN user_roles " + "ON group_resources.resource_id=user_roles.resource_id " + "INNER JOIN roles " + "ON user_roles.role_id=roles.role_id " + "INNER JOIN users " + "ON user_roles.user_id=users.user_id " + "WHERE group_users.group_id=? " + "AND roles.role_name='group-leader'", + (str(group_id),)) + yield from (User.from_sqlite3_row(row) for row in cursor.fetchall()) + + +def delete_group(conn: db.DbConnection, group_id: UUID): + """ + Delete the group with the given ID + + Parameters: + conn (db.DbConnection): an open connection to an SQLite3 database. + group_id (uuid.UUID): The identifier for the group to delete. + + Returns: + None: It does not return a value. + + Raises: + sqlite3.IntegrityError: if the group has members or linked resources, or + both. + """ + rsc = group_resource(conn, group_id) + with db.cursor(conn) as cursor: + cursor.execute("DELETE FROM group_join_requests WHERE group_id=?", + (str(group_id),)) + cursor.execute("DELETE FROM user_roles WHERE resource_id=?", + (str(rsc.resource_id),)) + cursor.execute( + "DELETE FROM group_resources WHERE group_id=? AND resource_id=?", + (str(group_id), str(rsc.resource_id))) + cursor.execute("DELETE FROM resources WHERE resource_id=?", + (str(rsc.resource_id),)) + cursor.execute("DELETE FROM groups WHERE group_id=?", + (str(group_id),)) diff --git a/gn_auth/auth/authorisation/resources/groups/views.py b/gn_auth/auth/authorisation/resources/groups/views.py index 920f504..2aa115a 100644 --- a/gn_auth/auth/authorisation/resources/groups/views.py +++ b/gn_auth/auth/authorisation/resources/groups/views.py @@ -6,28 +6,44 @@ import datetime from functools import partial from dataclasses import asdict +import sqlite3 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 from gn_auth.auth.errors import InvalidData, NotFoundError, AuthorisationError -from gn_auth.auth.authentication.users import User +from gn_auth.auth.authentication.users import User, user_by_id from gn_auth.auth.authentication.oauth2.resource_server import require_oauth +from gn_auth.auth.authorisation.resources.checks import authorised_for_spec +from gn_auth.auth.authorisation.resources.groups.models import (resource_from_group, + remove_user_from_group) + 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) +from .models import (Group, + GroupRole, + user_group, + all_groups, + DUMMY_GROUP, + group_by_id, + group_leaders, + join_requests, + data_resources, + group_role_by_id, + GroupCreationError, + accept_reject_join_request, + add_privilege_to_group_role, + group_users as _group_users, + create_group as _create_group, + delete_group as _delete_group, + delete_privilege_from_group_role) groups = Blueprint("groups", __name__) @@ -35,11 +51,31 @@ 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 +205,7 @@ 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 +271,7 @@ 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 +289,8 @@ 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]( @@ -347,3 +384,111 @@ def delete_priv_from_role(group_role_id: uuid.UUID) -> Response: direction="DELETE", user=the_token.user))), "description": "Privilege deleted successfully" }) + + +@groups.route("/<uuid:group_id>", methods=["GET"]) +@require_oauth("profile group") +def view_group(group_id: uuid.UUID) -> Response: + """View a particular group's details.""" + # TODO: do authorisation checks here… + with (require_oauth.acquire("profile group") as _token, + db.connection(current_app.config["AUTH_DB"]) as conn): + return jsonify(group_by_id(conn, group_id)) + + +@groups.route("/<uuid:group_id>/data-resources", methods=["GET"]) +@require_oauth("profile group") +def view_group_data_resources(group_id: uuid.UUID) -> Response: + """View data resources linked to the group.""" + # TODO: do authorisation checks here… + with (require_oauth.acquire("profile group") as _token, + db.connection(current_app.config["AUTH_DB"]) as conn): + return jsonify(tuple(data_resources(conn, group_id))) + + +@groups.route("/<uuid:group_id>/leaders", methods=["GET"]) +@require_oauth("profile group") +def view_group_leaders(group_id: uuid.UUID) -> Response: + """View a group's leaders.""" + # TODO: do authorisation checks here… + with (require_oauth.acquire("profile group") as _token, + db.connection(current_app.config["AUTH_DB"]) as conn): + return jsonify(tuple(group_leaders(conn, group_id))) + + +@groups.route("/<uuid:group_id>/remove-member", methods=["POST"]) +@require_oauth("profile group") +def remove_group_member(group_id: uuid.UUID): + """Remove a user as member of this group.""" + with (require_oauth.acquire("profile group") as _token, + db.connection(current_app.config["AUTH_DB"]) as conn): + group = group_by_id(conn, group_id) + grp_resource = resource_from_group(conn, group) + if not authorised_for_spec( + conn, + _token.user.user_id, + grp_resource.resource_id, + "(OR group:user:remove-group-member system:group:remove-group-member)"): + raise AuthorisationError( + "You do not have appropriate privileges to remove a user from this " + "group.") + + form = request_json() + if not bool(form.get("user_id")): + response = jsonify({ + "error": "MissingUserId", + "error-description": ( + "Expected 'user_id' value/parameter was not provided.") + }) + response.status_code = 400 + return response + + try: + user = user_by_id(conn, uuid.UUID(form["user_id"])) + remove_user_from_group(conn, group, user, grp_resource) + success_msg = ( + f"User '{user.name} ({user.email})' is no longer a member of " + f"group '{group.group_name}'.\n" + "They could, however, still have access to resources owned by " + "the group.") + return jsonify({ + "description": success_msg, + "message": success_msg + }) + except ValueError as _verr: + response = jsonify({ + "error": "InvalidUserId", + "error-description": "The 'user_id' provided was invalid" + }) + response.status_code = 400 + return response + + +@groups.route("/<uuid:group_id>/delete", methods=["DELETE"]) +@require_oauth("profile group") +def delete_group(group_id: uuid.UUID) -> Response: + """Delete group with the specified `group_id`.""" + with (require_oauth.acquire("profile group") as _token, + db.connection(current_app.config["AUTH_DB"]) as conn): + group = group_by_id(conn, group_id) + grp_resource = resource_from_group(conn, group) + if not authorised_for_spec( + conn, + _token.user.user_id, + grp_resource.resource_id, + "(AND system:group:delete-group)"): + raise AuthorisationError( + "You do not have appropriate privileges to delete this group.") + try: + _delete_group(conn, group.group_id) + return Response(status=204) + except sqlite3.IntegrityError as _s3ie: + response = jsonify({ + "error": "IntegrityError", + "error-description": ( + "A group that has members, linked resources, or both, " + "cannot be deleted from the system. Remove any members and " + "unlink any linked resources, and try again.") + }) + response.status_code = 400 + return response diff --git a/gn_auth/auth/authorisation/resources/inbredset/models.py b/gn_auth/auth/authorisation/resources/inbredset/models.py new file mode 100644 index 0000000..2626f3e --- /dev/null +++ b/gn_auth/auth/authorisation/resources/inbredset/models.py @@ -0,0 +1,85 @@ +"""Functions to handle the low-level details regarding populations auth.""" +from uuid import UUID, uuid4 +from typing import Sequence, Optional + +import sqlite3 + +import gn_auth.auth.db.sqlite3 as db +from gn_auth.auth.authentication.users import User +from gn_auth.auth.authorisation.resources.base import Resource + + +def assign_inbredset_group_owner_role( + cursor: sqlite3.Cursor, + resource: Resource, + user: User +) -> Resource: + """ + Assign `user` as `InbredSet Group Owner` is resource category is + 'inbredset-group'. + """ + if resource.resource_category.resource_category_key == "inbredset-group": + cursor.execute( + "SELECT * FROM roles WHERE role_name='inbredset-group-owner'") + role = cursor.fetchone() + cursor.execute( + "INSERT INTO user_roles " + "VALUES(:user_id, :role_id, :resource_id) " + "ON CONFLICT (user_id, role_id, resource_id) DO NOTHING", + { + "user_id": str(user.user_id), + "role_id": str(role["role_id"]), + "resource_id": str(resource.resource_id) + }) + + return resource + + +def link_data_to_resource(# pylint: disable=[too-many-arguments, too-many-positional-arguments] + cursor: sqlite3.Cursor, + resource_id: UUID, + species_id: int, + population_id: int, + population_name: str, + population_fullname: str +) -> dict: + """Link a species population to a resource for auth purposes.""" + params = { + "resource_id": str(resource_id), + "data_link_id": str(uuid4()), + "species_id": species_id, + "population_id": population_id, + "population_name": population_name, + "population_fullname": population_fullname + } + cursor.execute( + "INSERT INTO linked_inbredset_groups " + "VALUES(" + " :data_link_id," + " :species_id," + " :population_id," + " :population_name," + " :population_fullname" + ")", + params) + cursor.execute( + "INSERT INTO inbredset_group_resources " + "VALUES (:resource_id, :data_link_id)", + params) + return params + + +def resource_data( + cursor: db.DbCursor, + resource_id: UUID, + offset: int = 0, + limit: Optional[int] = None) -> Sequence[sqlite3.Row]: + """Fetch data linked to a inbred-set resource""" + cursor.execute( + ("SELECT * FROM inbredset_group_resources AS igr " + "INNER JOIN linked_inbredset_groups AS lig " + "ON igr.data_link_id=lig.data_link_id " + "WHERE igr.resource_id=?") + ( + f" LIMIT {limit} OFFSET {offset}" if bool(limit) else ""), + (str(resource_id),)) + return cursor.fetchall() diff --git a/gn_auth/auth/authorisation/resources/inbredset/views.py b/gn_auth/auth/authorisation/resources/inbredset/views.py index 444c442..9603b5b 100644 --- a/gn_auth/auth/authorisation/resources/inbredset/views.py +++ b/gn_auth/auth/authorisation/resources/inbredset/views.py @@ -1,12 +1,56 @@ """Views for InbredSet resources.""" -from flask import jsonify, Response, Blueprint +import uuid + +from pymonad.either import Left, Right, Either +from flask import jsonify, Response, Blueprint, current_app as app + from gn_auth.auth.db import sqlite3 as db -from gn_auth.auth.db.sqlite3 import with_db_connection +from gn_auth.auth.errors import NotFoundError +from gn_auth.auth.requests import request_json +from gn_auth.auth.authentication.users import User +from gn_auth.auth.authentication.oauth2.resource_server import require_oauth +from gn_auth.auth.authorisation.resources.base import Resource, ResourceCategory +from gn_auth.auth.authorisation.resources.groups.models import (Group, + user_group, + admin_group) +from gn_auth.auth.authorisation.resources.models import ( + create_resource as _create_resource) + +from .models import (link_data_to_resource, + assign_inbredset_group_owner_role) + +popbp = Blueprint("populations", __name__) + -iset = Blueprint("inbredset", __name__) +def create_resource( + cursor: db.DbCursor, + resource_name: str, + user: User, + group: Group, + public: bool +) -> Resource: + """Convenience function to create a resource of type 'inbredset-group'.""" + cursor.execute("SELECT * FROM resource_categories " + "WHERE resource_category_key='inbredset-group'") + category = cursor.fetchone() + if category: + return _create_resource(cursor, + resource_name, + ResourceCategory( + resource_category_id=uuid.UUID( + category["resource_category_id"]), + resource_category_key="inbredset-group", + resource_category_description=category[ + "resource_category_description"]), + user, + group, + public) + raise NotFoundError("Could not find a 'inbredset-group' resource category.") -@iset.route("/resource-id/<int:speciesid>/<int:inbredsetid>") + +@popbp.route("/populations/resource-id/<int:speciesid>/<int:inbredsetid>", + methods=["GET"]) def resource_id_by_inbredset_id(speciesid: int, inbredsetid: int) -> Response: """Retrieve the resource ID for resource attached to the inbredset.""" def __res_by_iset_id__(conn): @@ -20,7 +64,7 @@ def resource_id_by_inbredset_id(speciesid: int, inbredsetid: int) -> Response: (speciesid, inbredsetid)) return cursor.fetchone() - res = with_db_connection(__res_by_iset_id__) + res = db.with_db_connection(__res_by_iset_id__) if res: resp = jsonify({"status": "success", "resource-id": res["resource_id"]}) else: @@ -34,3 +78,76 @@ def resource_id_by_inbredset_id(speciesid: int, inbredsetid: int) -> Response: resp.status_code = 404 return resp + + +@popbp.route("/populations/create", methods=["POST"]) +@require_oauth("profile group resource") +def create_population_resource(): + """Create a resource of type 'inbredset-group'.""" + with (require_oauth.acquire("profile group resource") as _token, + db.connection(app.config["AUTH_DB"]) as conn, + db.cursor(conn) as cursor): + + def __check_form__(form, usergroup) -> Either: + """Check form for errors.""" + errors: tuple[str, ...] = tuple() + + species_id = form.get("species_id") + if not bool(species_id): + errors = errors + ("Missing `species_id` value.",) + + population_id = form.get("population_id") + if not bool(population_id): + errors = errors + ("Missing `population_id` value.",) + + population_name = form.get("population_name") + if not bool(population_name): + errors = errors + ("Missing `population_name` value.",) + + population_fullname = form.get("population_fullname") + if not bool(population_fullname): + errors = errors + ("Missing `population_fullname` value.",) + + if bool(errors): + error_messages = "\n\t - ".join(errors) + return Left({ + "error": "Invalid Request Data!", + "error_description": error_messages + }) + + return Right({"formdata": form, "group": usergroup}) + + def __default_group_if_none__(group) -> Either: + if group.is_nothing(): + return admin_group(conn) + return Right(group.value) + + return __default_group_if_none__( + user_group(conn, _token.user) + ).then( + lambda group: __check_form__(request_json(), group) + ).then( + lambda formdata: { + **formdata, + "resource": create_resource( + cursor, + f"Population — {formdata['formdata']['population_name']}", + _token.user, + formdata["group"], + formdata["formdata"].get("public", "on") == "on")} + ).then( + lambda resource: { + **resource, + "resource": assign_inbredset_group_owner_role( + cursor, resource["resource"], _token.user)} + ).then( + lambda resource: link_data_to_resource( + cursor, + resource["resource"].resource_id, + resource["formdata"]["species_id"], + resource["formdata"]["population_id"], + resource["formdata"]["population_name"], + resource["formdata"]["population_fullname"]) + ).either( + lambda error: (jsonify(error), 400), + jsonify) diff --git a/gn_auth/auth/authorisation/resources/models.py b/gn_auth/auth/authorisation/resources/models.py index c7c8352..31371fd 100644 --- a/gn_auth/auth/authorisation/resources/models.py +++ b/gn_auth/auth/authorisation/resources/models.py @@ -4,8 +4,6 @@ from uuid import UUID, uuid4 from functools import reduce, partial from typing import Dict, Sequence, Optional -import sqlite3 - from gn_auth.auth.db import sqlite3 as db from gn_auth.auth.authentication.users import User from gn_auth.auth.db.sqlite3 import with_db_connection @@ -15,68 +13,42 @@ from gn_auth.auth.authorisation.privileges import Privilege from gn_auth.auth.authorisation.checks import authorised_p from gn_auth.auth.errors import NotFoundError, AuthorisationError -from .checks import authorised_for -from .base import Resource, ResourceCategory -from .groups.models import Group, user_group, is_group_leader +from .system.models import system_resource +from .checks import authorised_for, authorised_for_spec +from .base import Resource, ResourceCategory, resource_from_dbrow +from .common import assign_resource_owner_role, grant_access_to_sysadmins +from .groups.models import Group, is_group_leader +from .inbredset.models import resource_data as inbredset_resource_data from .mrna import ( resource_data as mrna_resource_data, attach_resources_data as mrna_attach_resources_data, link_data_to_resource as mrna_link_data_to_resource, unlink_data_from_resource as mrna_unlink_data_from_resource) -from .genotype import ( +from .genotypes.models import ( resource_data as genotype_resource_data, attach_resources_data as genotype_attach_resources_data, link_data_to_resource as genotype_link_data_to_resource, unlink_data_from_resource as genotype_unlink_data_from_resource) -from .phenotype import ( +from .phenotypes.models import ( resource_data as phenotype_resource_data, attach_resources_data as phenotype_attach_resources_data, link_data_to_resource as phenotype_link_data_to_resource, unlink_data_from_resource as phenotype_unlink_data_from_resource) -from .errors import MissingGroupError - -def __assign_resource_owner_role__(cursor, resource, user): - """Assign `user` the 'Resource Owner' role for `resource`.""" - cursor.execute("SELECT * FROM roles WHERE role_name='resource-owner'") - role = cursor.fetchone() - cursor.execute( - "INSERT INTO user_roles " - "VALUES (:user_id, :role_id, :resource_id) " - "ON CONFLICT (user_id, role_id, resource_id) DO NOTHING", - { - "user_id": str(user.user_id), - "role_id": role["role_id"], - "resource_id": str(resource.resource_id) - }) - - -def resource_from_dbrow(row: sqlite3.Row): - """Convert an SQLite3 resultset row into a resource.""" - return Resource( - resource_id=UUID(row["resource_id"]), - resource_name=row["resource_name"], - resource_category=ResourceCategory( - UUID(row["resource_category_id"]), - row["resource_category_key"], - row["resource_category_description"]), - public=bool(int(row["public"]))) - @authorised_p(("group:resource:create-resource",), error_description="Insufficient privileges to create a resource", oauth2_scope="profile resource") -def create_resource( - conn: db.DbConnection, resource_name: str, - resource_category: ResourceCategory, user: User, - public: bool) -> Resource: +def create_resource(# pylint: disable=[too-many-arguments, too-many-positional-arguments] + conn: db.DbConnection, + resource_name: str, + resource_category: ResourceCategory, + user: User, + group: Group, + public: bool +) -> Resource: """Create a resource item.""" with db.cursor(conn) as cursor: - group = user_group(conn, user).maybe( - False, lambda grp: grp)# type: ignore[misc, arg-type] - if not group: - raise MissingGroupError(# Not all resources require an owner group - "User with no group cannot create a resource.") resource = Resource(uuid4(), resource_name, resource_category, public) cursor.execute( "INSERT INTO resources VALUES (?, ?, ?, ?)", @@ -84,12 +56,40 @@ def create_resource( resource_name, str(resource.resource_category.resource_category_id), 1 if resource.public else 0)) + # TODO: @fredmanglis,@rookie101 + # 1. Move the actions below into a (the?) hooks system + # 2. Do more checks: A resource can have varying hooks depending on type + # e.g. if mRNA, pheno or geno resource, assign: + # - "resource-owner" + # if inbredset-group, assign: + # - "resource-owner", + # - "inbredset-group-owner" etc. + # if resource is of type "group", assign: + # - group-leader cursor.execute("INSERT INTO resource_ownership (group_id, resource_id) " "VALUES (?, ?)", (str(group.group_id), str(resource.resource_id))) - __assign_resource_owner_role__(cursor, resource, user) + assign_resource_owner_role(cursor, resource.resource_id, user.user_id) + grant_access_to_sysadmins( + cursor, resource.resource_id, system_resource(conn).resource_id) + + return resource + + +def delete_resource(conn: db.DbConnection, resource_id: UUID): + """Delete a resource.""" + with db.cursor(conn) as cursor: + cursor.execute("DELETE FROM user_roles WHERE resource_id=?", + (str(resource_id),)) + cursor.execute("DELETE FROM resource_roles WHERE resource_id=?", + (str(resource_id),)) + cursor.execute("DELETE FROM group_resources WHERE resource_id=?", + (str(resource_id),)) + cursor.execute("DELETE FROM resource_ownership WHERE resource_id=?", + (str(resource_id),)) + cursor.execute("DELETE FROM resources WHERE resource_id=?", + (str(resource_id),)) - return resource def resource_category_by_id( conn: db.DbConnection, category_id: UUID) -> ResourceCategory: @@ -152,8 +152,10 @@ def user_resources(conn: db.DbConnection, user: User) -> Sequence[Resource]: """List the resources available to the user""" with db.cursor(conn) as cursor: cursor.execute( - ("SELECT r.*, rc.resource_category_key, " - "rc.resource_category_description FROM user_roles AS ur " + ("SELECT DISTINCT(r.resource_id), r.resource_name, " + "r.resource_category_id, r.public, rc.resource_category_key, " + "rc.resource_category_description " + "FROM user_roles AS ur " "INNER JOIN resources AS r ON ur.resource_id=r.resource_id " "INNER JOIN resource_categories AS rc " "ON r.resource_category_id=rc.resource_category_id " @@ -176,7 +178,8 @@ def resource_data(conn, resource, offset: int = 0, limit: Optional[int] = None) "genotype-metadata": lambda *args: tuple(), "mrna-metadata": lambda *args: tuple(), "system": lambda *args: tuple(), - "group": lambda *args: tuple() + "group": lambda *args: tuple(), + "inbredset-group": inbredset_resource_data, } with db.cursor(conn) as cursor: return tuple( @@ -204,9 +207,11 @@ def attach_resource_data(cursor: db.DbCursor, resource: Resource) -> Resource: def resource_by_id( conn: db.DbConnection, user: User, resource_id: UUID) -> Resource: """Retrieve a resource by its ID.""" - if not authorised_for( - conn, user, ("group:resource:view-resource",), - (resource_id,))[resource_id]: + if not authorised_for_spec( + conn, + user.user_id, + resource_id, + "(OR group:resource:view-resource system:resource:view)"): raise AuthorisationError( "You are not authorised to access resource with id " f"'{resource_id}'.") @@ -224,8 +229,12 @@ def resource_by_id( raise NotFoundError(f"Could not find a resource with id '{resource_id}'") def link_data_to_resource( - conn: db.DbConnection, user: User, resource_id: UUID, dataset_type: str, - data_link_id: UUID) -> dict: + conn: db.DbConnection, + user: User, + resource_id: UUID, + dataset_type: str, + data_link_ids: tuple[UUID, ...] +) -> tuple[dict, ...]: """Link data to resource.""" if not authorised_for( conn, user, ("group:resource:edit-resource",), @@ -240,7 +249,7 @@ def link_data_to_resource( "mrna": mrna_link_data_to_resource, "genotype": genotype_link_data_to_resource, "phenotype": phenotype_link_data_to_resource, - }[dataset_type.lower()](conn, resource, data_link_id) + }[dataset_type.lower()](conn, resource, data_link_ids) def unlink_data_from_resource( conn: db.DbConnection, user: User, resource_id: UUID, data_link_id: UUID): diff --git a/gn_auth/auth/authorisation/resources/mrna.py b/gn_auth/auth/authorisation/resources/mrna.py index 7fce227..66f8824 100644 --- a/gn_auth/auth/authorisation/resources/mrna.py +++ b/gn_auth/auth/authorisation/resources/mrna.py @@ -26,14 +26,15 @@ def resource_data(cursor: db.DbCursor, def link_data_to_resource( conn: db.DbConnection, resource: Resource, - data_link_id: uuid.UUID) -> dict: + data_link_ids: tuple[uuid.UUID, ...] +) -> tuple[dict, ...]: """Link mRNA Assay data with a resource.""" with db.cursor(conn) as cursor: - params = { + params = tuple({ "resource_id": str(resource.resource_id), "data_link_id": str(data_link_id) - } - cursor.execute( + } for data_link_id in data_link_ids) + cursor.executemany( "INSERT INTO mrna_resources VALUES" "(:resource_id, :data_link_id)", params) diff --git a/gn_auth/auth/authorisation/resources/phenotype.py b/gn_auth/auth/authorisation/resources/phenotype.py deleted file mode 100644 index 7005db3..0000000 --- a/gn_auth/auth/authorisation/resources/phenotype.py +++ /dev/null @@ -1,68 +0,0 @@ -"""Phenotype data resources functions and utilities.""" -import uuid -from typing import Optional, Sequence - -import sqlite3 - -import gn_auth.auth.db.sqlite3 as db - -from .base import Resource -from .data import __attach_data__ - -def resource_data( - cursor: db.DbCursor, - resource_id: uuid.UUID, - offset: int = 0, - limit: Optional[int] = None) -> Sequence[sqlite3.Row]: - """Fetch data linked to a Phenotype resource""" - cursor.execute( - ("SELECT * FROM phenotype_resources AS pr " - "INNER JOIN linked_phenotype_data AS lpd " - "ON pr.data_link_id=lpd.data_link_id " - "WHERE pr.resource_id=?") + ( - f" LIMIT {limit} OFFSET {offset}" if bool(limit) else ""), - (str(resource_id),)) - return cursor.fetchall() - -def link_data_to_resource( - conn: db.DbConnection, - resource: Resource, - data_link_id: uuid.UUID) -> dict: - """Link Phenotype data with a resource.""" - with db.cursor(conn) as cursor: - params = { - "resource_id": str(resource.resource_id), - "data_link_id": str(data_link_id) - } - cursor.execute( - "INSERT INTO phenotype_resources VALUES" - "(:resource_id, :data_link_id)", - params) - return params - -def unlink_data_from_resource( - conn: db.DbConnection, - resource: Resource, - data_link_id: uuid.UUID) -> dict: - """Unlink data from Phenotype resources""" - with db.cursor(conn) as cursor: - cursor.execute("DELETE FROM phenotype_resources " - "WHERE resource_id=? AND data_link_id=?", - (str(resource.resource_id), str(data_link_id))) - return { - "resource_id": str(resource.resource_id), - "dataset_type": resource.resource_category.resource_category_key, - "data_link_id": str(data_link_id) - } - -def attach_resources_data( - cursor, resources: Sequence[Resource]) -> Sequence[Resource]: - """Attach linked data to Phenotype resources""" - placeholders = ", ".join(["?"] * len(resources)) - cursor.execute( - "SELECT * FROM phenotype_resources AS pr " - "INNER JOIN linked_phenotype_data AS lpd " - "ON pr.data_link_id=lpd.data_link_id " - f"WHERE pr.resource_id IN ({placeholders})", - tuple(str(resource.resource_id) for resource in resources)) - return __attach_data__(cursor.fetchall(), resources) diff --git a/gn_auth/auth/authorisation/resources/phenotypes/__init__.py b/gn_auth/auth/authorisation/resources/phenotypes/__init__.py new file mode 100644 index 0000000..0d4dbfa --- /dev/null +++ b/gn_auth/auth/authorisation/resources/phenotypes/__init__.py @@ -0,0 +1 @@ +"""The phenotypes package.""" diff --git a/gn_auth/auth/authorisation/resources/phenotypes/models.py b/gn_auth/auth/authorisation/resources/phenotypes/models.py new file mode 100644 index 0000000..0ef91ab --- /dev/null +++ b/gn_auth/auth/authorisation/resources/phenotypes/models.py @@ -0,0 +1,143 @@ +"""Phenotype data resources functions and utilities.""" +import uuid +from functools import reduce +from typing import Optional, Sequence + +import sqlite3 +from pymonad.maybe import Just, Maybe, Nothing +from pymonad.tools import monad_from_none_or_value + +import gn_auth.auth.db.sqlite3 as db +from gn_auth.auth.authorisation.resources.data import __attach_data__ +from gn_auth.auth.authorisation.resources.base import Resource, resource_from_dbrow + +def resource_data( + cursor: db.DbCursor, + resource_id: uuid.UUID, + offset: int = 0, + limit: Optional[int] = None) -> Sequence[sqlite3.Row]: + """Fetch data linked to a Phenotype resource""" + cursor.execute( + ("SELECT * FROM phenotype_resources AS pr " + "INNER JOIN linked_phenotype_data AS lpd " + "ON pr.data_link_id=lpd.data_link_id " + "WHERE pr.resource_id=?") + ( + f" LIMIT {limit} OFFSET {offset}" if bool(limit) else ""), + (str(resource_id),)) + return cursor.fetchall() + +def link_data_to_resource( + conn: db.DbConnection, + resource: Resource, + data_link_ids: tuple[uuid.UUID, ...] +) -> tuple[dict, ...]: + """Link Phenotype data with a resource.""" + with db.cursor(conn) as cursor: + params = tuple({ + "resource_id": str(resource.resource_id), + "data_link_id": str(data_link_id) + } for data_link_id in data_link_ids) + cursor.executemany( + "INSERT INTO phenotype_resources VALUES" + "(:resource_id, :data_link_id)", + params) + return params + +def unlink_data_from_resource( + conn: db.DbConnection, + resource: Resource, + data_link_id: uuid.UUID) -> dict: + """Unlink data from Phenotype resources""" + with db.cursor(conn) as cursor: + cursor.execute("DELETE FROM phenotype_resources " + "WHERE resource_id=? AND data_link_id=?", + (str(resource.resource_id), str(data_link_id))) + return { + "resource_id": str(resource.resource_id), + "dataset_type": resource.resource_category.resource_category_key, + "data_link_id": str(data_link_id) + } + +def attach_resources_data( + cursor, resources: Sequence[Resource]) -> Sequence[Resource]: + """Attach linked data to Phenotype resources""" + placeholders = ", ".join(["?"] * len(resources)) + cursor.execute( + "SELECT * FROM phenotype_resources AS pr " + "INNER JOIN linked_phenotype_data AS lpd " + "ON pr.data_link_id=lpd.data_link_id " + f"WHERE pr.resource_id IN ({placeholders})", + tuple(str(resource.resource_id) for resource in resources)) + return __attach_data__(cursor.fetchall(), resources) + + +def individual_linked_resource( + conn: db.DbConnection, + species_id: int, + population_id: int, + dataset_id: int, + xref_id: str) -> Maybe: + """Given the data details, return the linked resource, if one is defined.""" + with db.cursor(conn) as cursor: + cursor.execute( + "SELECT " + "rsc.*, rc.*, lpd.SpeciesId AS species_id, " + "lpd.InbredSetId AS population_id, lpd.PublishXRefId AS xref_id, " + "lpd.dataset_name, lpd.dataset_fullname, lpd.dataset_shortname " + "FROM linked_phenotype_data AS lpd " + "INNER JOIN phenotype_resources AS pr " + "ON lpd.data_link_id=pr.data_link_id " + "INNER JOIN resources AS rsc ON pr.resource_id=rsc.resource_id " + "INNER JOIN resource_categories AS rc " + "ON rsc.resource_category_id=rc.resource_category_id " + "WHERE " + "(lpd.SpeciesId, lpd.InbredSetId, lpd.PublishFreezeId, lpd.PublishXRefId) = " + "(?, ?, ?, ?)", + (species_id, population_id, dataset_id, xref_id)) + return monad_from_none_or_value( + Nothing, Just, cursor.fetchone()).then(resource_from_dbrow) + + +def all_linked_resources( + conn: db.DbConnection, + species_id: int, + population_id: int, + dataset_id: int) -> Maybe: + """Given the data details, return the linked resource, if one is defined.""" + with db.cursor(conn) as cursor: + cursor.execute( + "SELECT rsc.*, rc.resource_category_key, " + "rc.resource_category_description, lpd.SpeciesId AS species_id, " + "lpd.InbredSetId AS population_id, lpd.PublishXRefId AS xref_id, " + "lpd.dataset_name, lpd.dataset_fullname, lpd.dataset_shortname " + "FROM linked_phenotype_data AS lpd " + "INNER JOIN phenotype_resources AS pr " + "ON lpd.data_link_id=pr.data_link_id INNER JOIN resources AS rsc " + "ON pr.resource_id=rsc.resource_id " + "INNER JOIN resource_categories AS rc " + "ON rsc.resource_category_id=rc.resource_category_id " + "WHERE " + "(lpd.SpeciesId, lpd.InbredSetId, lpd.PublishFreezeId) = (?, ?, ?)", + (species_id, population_id, dataset_id)) + + _rscdatakeys = ( + "species_id", "population_id", "xref_id", "dataset_name", + "dataset_fullname", "dataset_shortname") + def __organise__(resources, row): + _rscid = uuid.UUID(row["resource_id"]) + _resource = resources.get(_rscid, resource_from_dbrow(row)) + return { + **resources, + _rscid: Resource( + _resource.resource_id, + _resource.resource_name, + _resource.resource_category, + _resource.public, + _resource.resource_data + ( + {key: row[key] for key in _rscdatakeys},)) + } + results: dict[uuid.UUID, Resource] = reduce( + __organise__, cursor.fetchall(), {}) + if len(results) == 0: + return Nothing + return Just(tuple(results.values())) diff --git a/gn_auth/auth/authorisation/resources/phenotypes/views.py b/gn_auth/auth/authorisation/resources/phenotypes/views.py new file mode 100644 index 0000000..c0a5e81 --- /dev/null +++ b/gn_auth/auth/authorisation/resources/phenotypes/views.py @@ -0,0 +1,77 @@ +"""Views for the phenotype resources.""" +from pymonad.either import Left, Right +from flask import jsonify, Blueprint, current_app as app + +from gn_auth.auth.db import sqlite3 as db +from gn_auth.auth.requests import request_json +from gn_auth.auth.authorisation.resources.request_utils import check_form +from gn_auth.auth.authorisation.roles.models import user_roles_on_resource + +from gn_auth.auth.authentication.oauth2.resource_server import require_oauth + +from .models import all_linked_resources, individual_linked_resource + +phenobp = Blueprint("phenotypes", __name__) + +@phenobp.route("/phenotypes/individual/linked-resource", methods=["POST"]) +@require_oauth("profile group resource") +def get_individual_linked_resource(): + """Get the linked resource for a particular phenotype within the dataset. + + Phenotypes are a tad tricky. Each phenotype could technically be a resource + on its own, and thus a user could have access to only a subset of phenotypes + within the entire dataset.""" + with (require_oauth.acquire("profile group resource") as _token, + db.connection(app.config["AUTH_DB"]) as conn): + return check_form( + request_json(), + "species_id", + "population_id", + "dataset_id", + "xref_id" + ).then( + lambda formdata: individual_linked_resource( + conn, + int(formdata["species_id"]), + int(formdata["population_id"]), + int(formdata["dataset_id"]), + formdata["xref_id"] + ).maybe(Left("No linked resource!"), + lambda lrsc: Right({ + "formdata": formdata, + "resource": lrsc + })) + ).then( + lambda fdlrsc: { + **fdlrsc, + "roles": user_roles_on_resource( + conn, _token.user.user_id, fdlrsc["resource"].resource_id) + } + ).either(lambda error: (jsonify(error), 400), + lambda res: jsonify({ + key: value for key, value in res.items() + if key != "formdata" + })) + + +@phenobp.route("/phenotypes/linked-resources", methods=["POST"]) +@require_oauth("profile group resource") +def get_all_linked_resources(): + """Get all the linked resources for all phenotypes within a dataset. + + See `get_individual_linked_resource(…)` documentation.""" + with (require_oauth.acquire("profile group resource") as _token, + db.connection(app.config["AUTH_DB"]) as conn): + return check_form( + request_json(), + "species_id", + "population_id", + "dataset_id" + ).then( + lambda formdata: all_linked_resources( + conn, + int(formdata["species_id"]), + int(formdata["population_id"]), + int(formdata["dataset_id"])).maybe( + Left("No linked resource!"), Right) + ).either(lambda error: (jsonify(error), 400), jsonify) diff --git a/gn_auth/auth/authorisation/resources/request_utils.py b/gn_auth/auth/authorisation/resources/request_utils.py new file mode 100644 index 0000000..ade779e --- /dev/null +++ b/gn_auth/auth/authorisation/resources/request_utils.py @@ -0,0 +1,20 @@ +"""Some common utils for requests to the resources endpoints.""" +from functools import reduce + +from pymonad.either import Left, Right, Either + +def check_form(form, *fields) -> Either: + """Check form for errors""" + def __check_field__(errors, field): + if not bool(form.get(field)): + return errors + (f"Missing `{field}` value.",) + return errors + + errors: tuple[str, ...] = reduce(__check_field__, fields, tuple()) + if len(errors) > 0: + return Left({ + "error": "Invalid request data!", + "error_description": "\n\t - ".join(errors) + }) + + return Right(form) diff --git a/gn_auth/auth/authorisation/resources/system/models.py b/gn_auth/auth/authorisation/resources/system/models.py index 7c176aa..303b0ac 100644 --- a/gn_auth/auth/authorisation/resources/system/models.py +++ b/gn_auth/auth/authorisation/resources/system/models.py @@ -4,11 +4,15 @@ from functools import reduce from typing import Sequence from gn_auth.auth.db import sqlite3 as db +from gn_auth.auth.errors import NotFoundError from gn_auth.auth.authentication.users import User from gn_auth.auth.authorisation.roles import Role from gn_auth.auth.authorisation.privileges import Privilege +from gn_auth.auth.authorisation.resources.base import ( + Resource, + resource_from_dbrow) def __organise_privileges__(acc, row): role_id = UUID(row["role_id"]) @@ -24,6 +28,7 @@ def __organise_privileges__(acc, row): (Privilege(row["privilege_id"], row["privilege_description"]),))) } + def user_roles_on_system(conn: db.DbConnection, user: User) -> Sequence[Role]: """ Retrieve all roles assigned to the `user` that act on `system` resources. @@ -45,3 +50,19 @@ def user_roles_on_system(conn: db.DbConnection, user: User) -> Sequence[Role]: return tuple(reduce( __organise_privileges__, cursor.fetchall(), {}).values()) return tuple() + + +def system_resource(conn: db.DbConnection) -> Resource: + """Retrieve the system resource.""" + with db.cursor(conn) as cursor: + cursor.execute( + "SELECT resource_categories.*, resources.resource_id, " + "resources.resource_name, resources.public " + "FROM resource_categories INNER JOIN resources " + "ON resource_categories.resource_category_id=resources.resource_category_id " + "WHERE resource_categories.resource_category_key='system'") + row = cursor.fetchone() + if row: + return resource_from_dbrow(row) + + raise NotFoundError("Could not find a system resource!") diff --git a/gn_auth/auth/authorisation/resources/views.py b/gn_auth/auth/authorisation/resources/views.py index 494fde9..a960ca3 100644 --- a/gn_auth/auth/authorisation/resources/views.py +++ b/gn_auth/auth/authorisation/resources/views.py @@ -39,16 +39,23 @@ from gn_auth.auth.authorisation.roles.models import ( from gn_auth.auth.authentication.oauth2.resource_server import require_oauth from gn_auth.auth.authentication.users import User, user_by_id, user_by_email -from .checks import authorised_for +from .inbredset.views import popbp +from .genotypes.views import genobp +from .phenotypes.views import phenobp +from .errors import MissingGroupError +from .groups.models import Group, user_group +from .checks import authorised_for, authorised_for_spec from .models import ( Resource, resource_data, resource_by_id, public_resources, resource_categories, assign_resource_user, link_data_to_resource, unassign_resource_user, resource_category_by_id, user_roles_on_resources, unlink_data_from_resource, create_resource as _create_resource, - get_resource_id) -from .groups.models import Group + get_resource_id, delete_resource as _delete_resource) resources = Blueprint("resources", __name__) +resources.register_blueprint(popbp, url_prefix="/") +resources.register_blueprint(genobp, url_prefix="/") +resources.register_blueprint(phenobp, url_prefix="/") @resources.route("/categories", methods=["GET"]) @require_oauth("profile group resource") @@ -70,11 +77,17 @@ def create_resource() -> Response: db_uri = app.config["AUTH_DB"] with db.connection(db_uri) as conn: try: + group = user_group(conn, the_token.user).maybe( + False, lambda grp: grp)# type: ignore[misc, arg-type] + if not group: + raise MissingGroupError(# Not all resources require an owner group + "User with no group cannot create a resource.") resource = _create_resource( conn, resource_name, resource_category_by_id(conn, resource_category_id), the_token.user, + group, (form.get("public") == "on")) return jsonify(asdict(resource)) except sqlite3.IntegrityError as sql3ie: @@ -86,7 +99,9 @@ def create_resource() -> Response: f"{type(sql3ie)=}: {sql3ie=}") raise + @resources.route("/view/<uuid:resource_id>") +@resources.route("/<uuid:resource_id>/view") @require_oauth("profile group resource") def view_resource(resource_id: UUID) -> Response: """View a particular resource's details.""" @@ -123,7 +138,7 @@ def view_resource_data(resource_id: UUID) -> Response: with require_oauth.acquire("profile group resource") as the_token: db_uri = app.config["AUTH_DB"] count_per_page = __safe_get_requests_count__("count_per_page") - offset = (__safe_get_requests_page__("page") - 1) + offset = __safe_get_requests_page__("page") - 1 with db.connection(db_uri) as conn: resource = resource_by_id(conn, the_token.user, resource_id) return jsonify(resource_data( @@ -139,7 +154,7 @@ def link_data(): try: form = request_json() assert "resource_id" in form, "Resource ID not provided." - assert "data_link_id" in form, "Data Link ID not provided." + assert "data_link_ids" in form, "Data Link IDs not provided." assert "dataset_type" in form, "Dataset type not specified" assert form["dataset_type"].lower() in ( "mrna", "genotype", "phenotype"), "Invalid dataset type provided." @@ -147,8 +162,11 @@ def link_data(): with require_oauth.acquire("profile group resource") as the_token: def __link__(conn: db.DbConnection): return link_data_to_resource( - conn, the_token.user, UUID(form["resource_id"]), - form["dataset_type"], UUID(form["data_link_id"])) + conn, + the_token.user, + UUID(form["resource_id"]), + form["dataset_type"], + tuple(UUID(dlinkid) for dlinkid in form["data_link_ids"])) return jsonify(with_db_connection(__link__)) except AssertionError as aserr: @@ -397,9 +415,18 @@ def resource_roles(resource_id: UUID) -> Response: "ON rp.privilege_id=p.privilege_id " "WHERE rr.resource_id=? AND rr.role_created_by=?", (str(resource_id), str(_token.user.user_id))) - results = cursor.fetchall() + user_created = db_rows_to_roles(cursor.fetchall()) - return db_rows_to_roles(results) + cursor.execute( + "SELECT ur.user_id, ur.resource_id, r.*, p.* FROM user_roles AS ur " + "INNER JOIN roles AS r ON ur.role_id=r.role_id " + "INNER JOIN role_privileges AS rp ON r.role_id=rp.role_id " + "INNER JOIN privileges AS p ON rp.privilege_id=p.privilege_id " + "WHERE resource_id=? AND user_id=?", + (str(resource_id), str(_token.user.user_id))) + assigned_to_user = db_rows_to_roles(cursor.fetchall()) + + return assigned_to_user + user_created return jsonify(with_db_connection(__roles__)) @@ -647,3 +674,49 @@ def user_resource_roles(resource_id: UUID, user_id: UUID): return jsonify([asdict(role) for role in _user_resource_roles(conn, _token.user, _resource)]) + + +@resources.route("/delete", methods=["POST"]) +@require_oauth("profile group resource") +def delete_resource(): + """Delete the specified resource, if possible.""" + with (require_oauth.acquire("profile group resource") as the_token, + db.connection(app.config["AUTH_DB"]) as conn): + form = request_json() + try: + resource_id = UUID(form.get("resource_id")) + if not authorised_for_spec( + conn, + the_token.user.user_id, + resource_id, + "(OR group:resource:delete-resource system:resource:delete)"): + raise AuthorisationError("You do not have the appropriate " + "privileges to delete this resource.") + + data = resource_data( + conn, + resource_by_id(conn, the_token.user, resource_id), + 0, + 10) + if bool(data): + return jsonify({ + "error": "NonEmptyResouce", + "error-description": "Cannot delete a resource with linked data" + }), 400 + + _delete_resource(conn, resource_id) + return jsonify({ + "description": f"Successfully deleted resource with ID '{resource_id}'." + }) + except ValueError as _verr: + app.logger.debug("Error!", exc_info=True) + return jsonify({ + "error": "ValueError", + "error-description": "An invalid identifier was provided" + }), 400 + except TypeError as _terr: + app.logger.debug("Error!", exc_info=True) + return jsonify({ + "error": "TypeError", + "error-description": "An invalid identifier was provided" + }), 400 |