diff options
Diffstat (limited to 'gn_auth/auth/authorisation')
22 files changed, 759 insertions, 178 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/common.py b/gn_auth/auth/authorisation/resources/common.py new file mode 100644 index 0000000..5d2b72b --- /dev/null +++ b/gn_auth/auth/authorisation/resources/common.py @@ -0,0 +1,24 @@ +"""Utilities common to more than one resource.""" +import uuid + +from sqlite3 import Cursor + +def assign_resource_owner_role( + cursor: Cursor, + 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 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..e8dca9b 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( @@ -29,7 +28,7 @@ def link_data_to_resource( conn: db.DbConnection, resource: Resource, data_link_id: uuid.UUID) -> dict: - """Link Genotype data with a resource.""" + """Link Genotype data with a resource using the GUI.""" with db.cursor(conn) as cursor: params = { "resource_id": str(resource.resource_id), @@ -67,3 +66,45 @@ 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] + 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/inbredset/models.py b/gn_auth/auth/authorisation/resources/inbredset/models.py new file mode 100644 index 0000000..de1c18a --- /dev/null +++ b/gn_auth/auth/authorisation/resources/inbredset/models.py @@ -0,0 +1,96 @@ +"""Functions to handle the low-level details regarding populations auth.""" +from uuid import UUID, uuid4 + +import sqlite3 + +from gn_auth.auth.errors import NotFoundError +from gn_auth.auth.authentication.users import User +from gn_auth.auth.authorisation.resources.groups.models import Group +from gn_auth.auth.authorisation.resources.base import Resource, ResourceCategory +from gn_auth.auth.authorisation.resources.models import ( + create_resource as _create_resource) + +def create_resource( + cursor: sqlite3.Cursor, + 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( + 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.") + + +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] + 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 diff --git a/gn_auth/auth/authorisation/resources/inbredset/views.py b/gn_auth/auth/authorisation/resources/inbredset/views.py index 444c442..b559105 100644 --- a/gn_auth/auth/authorisation/resources/inbredset/views.py +++ b/gn_auth/auth/authorisation/resources/inbredset/views.py @@ -1,12 +1,22 @@ """Views for InbredSet resources.""" -from flask import jsonify, Response, Blueprint +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.requests import request_json from gn_auth.auth.db.sqlite3 import with_db_connection +from gn_auth.auth.authentication.oauth2.resource_server import require_oauth +from gn_auth.auth.authorisation.resources.groups.models import user_group + +from .models import (create_resource, + link_data_to_resource, + assign_inbredset_group_owner_role) -iset = Blueprint("inbredset", __name__) +popbp = Blueprint("populations", __name__) -@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): @@ -34,3 +44,69 @@ 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}) + + return 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..c1748f1 100644 --- a/gn_auth/auth/authorisation/resources/models.py +++ b/gn_auth/auth/authorisation/resources/models.py @@ -16,78 +16,59 @@ 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 .base import Resource, ResourceCategory, resource_from_dbrow +from .common import assign_resource_owner_role +from .groups.models import Group, is_group_leader 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] + cursor: sqlite3.Cursor, + 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 (?, ?, ?, ?)", - (str(resource.resource_id), - resource_name, - str(resource.resource_category.resource_category_id), - 1 if resource.public else 0)) - 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) + resource = Resource(uuid4(), resource_name, resource_category, public) + cursor.execute( + "INSERT INTO resources VALUES (?, ?, ?, ?)", + (str(resource.resource_id), + 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.resource_id, user.user_id) return resource @@ -152,8 +133,10 @@ 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 " 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..d4a516a --- /dev/null +++ b/gn_auth/auth/authorisation/resources/phenotypes/models.py @@ -0,0 +1,142 @@ +"""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_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) + + +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/views.py b/gn_auth/auth/authorisation/resources/views.py index 494fde9..1c4104a 100644 --- a/gn_auth/auth/authorisation/resources/views.py +++ b/gn_auth/auth/authorisation/resources/views.py @@ -40,15 +40,22 @@ 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 .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 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") @@ -68,13 +75,20 @@ def create_resource() -> Response: resource_name = form.get("resource_name") resource_category_id = UUID(form.get("resource_category")) db_uri = app.config["AUTH_DB"] - with db.connection(db_uri) as conn: + with (db.connection(db_uri) as conn, + db.cursor(conn) as cursor): 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, + cursor, 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: @@ -397,9 +411,18 @@ 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()) + + 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 db_rows_to_roles(results) + return assigned_to_user + user_created return jsonify(with_db_connection(__roles__)) diff --git a/gn_auth/auth/authorisation/roles/models.py b/gn_auth/auth/authorisation/roles/models.py index dc1dfdc..2729b3b 100644 --- a/gn_auth/auth/authorisation/roles/models.py +++ b/gn_auth/auth/authorisation/roles/models.py @@ -133,10 +133,10 @@ def user_roles(conn: db.DbConnection, user: User) -> Sequence[dict]: return tuple() -def user_resource_roles( +def user_roles_on_resource( conn: db.DbConnection, - user: User, - resource: Resource + user_id: UUID, + resource_id: UUID ) -> tuple[Role, ...]: """Retrieve all roles assigned to a user for a particular resource.""" with db.cursor(conn) as cursor: @@ -147,12 +147,22 @@ def user_resource_roles( "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 ur.user_id=? AND ur.resource_id=?", - (str(user.user_id), str(resource.resource_id))) + (str(user_id), str(resource_id))) return db_rows_to_roles(cursor.fetchall()) return tuple() +def user_resource_roles( + conn: db.DbConnection, + user: User, + resource: Resource +) -> tuple[Role, ...]: + "Retrieve roles a user has on a particular resource." + # TODO: Temporary placeholder to prevent system from breaking. + return user_roles_on_resource(conn, user.user_id, resource.resource_id) + + def user_role(conn: db.DbConnection, user: User, role_id: UUID) -> Either: """Retrieve a specific non-resource role assigned to the user.""" with db.cursor(conn) as cursor: diff --git a/gn_auth/auth/authorisation/users/admin/ui.py b/gn_auth/auth/authorisation/users/admin/ui.py index 64e79a0..43ca0a2 100644 --- a/gn_auth/auth/authorisation/users/admin/ui.py +++ b/gn_auth/auth/authorisation/users/admin/ui.py @@ -1,6 +1,6 @@ """UI utilities for the auth system.""" from functools import wraps -from flask import flash, url_for, redirect +from flask import flash, request, url_for, redirect from gn_auth.session import logged_in, session_user, clear_session_info from gn_auth.auth.authorisation.resources.system.models import ( @@ -24,5 +24,5 @@ def is_admin(func): flash("Expected a system administrator.", "alert-danger") flash("You have been logged out of the system.", "alert-info") clear_session_info() - return redirect(url_for("oauth2.admin.login")) + return redirect(url_for("oauth2.admin.login", **dict(request.args))) return __admin__ diff --git a/gn_auth/auth/authorisation/users/admin/views.py b/gn_auth/auth/authorisation/users/admin/views.py index 85aeb50..9bc1c36 100644 --- a/gn_auth/auth/authorisation/users/admin/views.py +++ b/gn_auth/auth/authorisation/users/admin/views.py @@ -30,6 +30,7 @@ from ....authentication.oauth2.models.oauth2client import ( save_client, OAuth2Client, oauth2_clients, + update_client_attribute, client as oauth2_client, delete_client as _delete_client) from ....authentication.users import ( @@ -97,7 +98,7 @@ def login(): expires=( datetime.now(tz=timezone.utc) + timedelta(minutes=int( app.config.get("SESSION_EXPIRY_MINUTES", 10))))) - return redirect(url_for(next_uri)) + return redirect(url_for(next_uri, **dict(request.args))) raise NotFoundError(error_message) except NotFoundError as _nfe: flash(error_message, "alert-danger") @@ -196,7 +197,7 @@ def register_client(): if request.method == "GET": return render_template( "admin/register-client.html", - scope=app.config["OAUTH2_SCOPE"], + scope=app.config["OAUTH2_SCOPES_SUPPORTED"], users=with_db_connection(__list_users__), granttypes=_FORM_GRANT_TYPES_, current_user=session.session_user()) @@ -261,7 +262,7 @@ def view_client(client_id: uuid.UUID): return render_template( "admin/view-oauth2-client.html", client=with_db_connection(partial(oauth2_client, client_id=client_id)), - scope=app.config["OAUTH2_SCOPE"], + scope=app.config["OAUTH2_SCOPES_SUPPORTED"], granttypes=_FORM_GRANT_TYPES_) @@ -321,3 +322,37 @@ def delete_client(): "successfully."), "alert-success") return redirect(url_for("oauth2.admin.list_clients")) + + +@admin.route("/clients/<uuid:client_id>/change-secret", methods=["GET", "POST"]) +@is_admin +def change_client_secret(client_id: uuid.UUID): + """Enable changing of a client's secret.""" + def __no_client__(): + # Calling the function causes the flash to be evaluated + # flash("No such client was found!", "alert-danger") + return redirect(url_for("oauth2.admin.list_clients")) + + with db.connection(app.config["AUTH_DB"]) as conn: + if request.method == "GET": + return oauth2_client( + conn, client_id=client_id + ).maybe(__no_client__(), lambda _client: render_template( + "admin/confirm-change-client-secret.html", + client=_client + )) + + _raw = random_string() + return oauth2_client( + conn, client_id=client_id + ).then( + lambda _client: save_client( + conn, + update_client_attribute( + _client, "client_secret", hash_password(_raw))) + ).then( + lambda _client: render_template( + "admin/registered-client.html", + client=_client, + client_secret=_raw) + ).maybe(__no_client__(), lambda resp: resp) diff --git a/gn_auth/auth/authorisation/users/collections/models.py b/gn_auth/auth/authorisation/users/collections/models.py index b4a24f3..f0a7fa2 100644 --- a/gn_auth/auth/authorisation/users/collections/models.py +++ b/gn_auth/auth/authorisation/users/collections/models.py @@ -205,8 +205,10 @@ def add_traits(rconn: Redis, mod_col = tuple(coll for coll in ucolls if coll["id"] == collection_id) __raise_if_not_single_collection__(user, collection_id, mod_col) new_members = tuple(set(tuple(mod_col[0]["members"]) + traits)) + now = datetime.utcnow() new_coll = { **mod_col[0], + "changed": now, "members": new_members, "num_members": len(new_members) } @@ -233,8 +235,10 @@ def remove_traits(rconn: Redis, __raise_if_not_single_collection__(user, collection_id, mod_col) new_members = tuple( trait for trait in mod_col[0]["members"] if trait not in traits) + now = datetime.utcnow() new_coll = { **mod_col[0], + "changed": now, "members": new_members, "num_members": len(new_members) } diff --git a/gn_auth/auth/authorisation/users/collections/views.py b/gn_auth/auth/authorisation/users/collections/views.py index eeae91d..f619c3d 100644 --- a/gn_auth/auth/authorisation/users/collections/views.py +++ b/gn_auth/auth/authorisation/users/collections/views.py @@ -113,6 +113,7 @@ def import_anonymous() -> Response: anon_id = UUID(request.json.get("anon_id"))#type: ignore[union-attr] anon_colls = user_collections(redisconn, User( anon_id, "anon@ymous.user", "Anonymous User")) + anon_colls = tuple(coll for coll in anon_colls if coll['num_members'] > 0) save_collections( redisconn, token.user, diff --git a/gn_auth/auth/authorisation/users/masquerade/models.py b/gn_auth/auth/authorisation/users/masquerade/models.py index 8ac1a68..a155899 100644 --- a/gn_auth/auth/authorisation/users/masquerade/models.py +++ b/gn_auth/auth/authorisation/users/masquerade/models.py @@ -1,5 +1,4 @@ """Functions for handling masquerade.""" -import uuid from functools import wraps from datetime import datetime from authlib.jose import jwt @@ -10,12 +9,16 @@ from flask import current_app as app from gn_auth.auth.errors import ForbiddenAccess from gn_auth.auth.jwks import newest_jwk_with_rotation, jwks_directory +from gn_auth.auth.authentication.oauth2.grants.refresh_token_grant import ( + RefreshTokenGrant) +from gn_auth.auth.authentication.oauth2.models.jwtrefreshtoken import ( + JWTRefreshToken, + save_refresh_token) from ...roles.models import user_roles from ....db import sqlite3 as db from ....authentication.users import User -from ....authentication.oauth2.models.oauth2token import ( - OAuth2Token, save_token) +from ....authentication.oauth2.models.oauth2token import OAuth2Token __FIVE_HOURS__ = (60 * 60 * 5) @@ -53,28 +56,30 @@ def masquerade_as( original_token: OAuth2Token, masqueradee: User) -> OAuth2Token: """Get a token that enables `masquerader` to act as `masqueradee`.""" - token_details = app.config["OAUTH2_SERVER"].generate_token( + scope = original_token.get_scope().replace( + # Do not allow more than one level of masquerading + "masquerade", "").strip() + new_token = app.config["OAUTH2_SERVER"].generate_token( client=original_token.client, - grant_type="authorization_code", + grant_type="urn:ietf:params:oauth:grant-type:jwt-bearer", user=masqueradee, - expires_in=__FIVE_HOURS__, - include_refresh_token=True) - + expires_in=original_token.get_expires_in(), + include_refresh_token=True, + scope=scope) _jwt = jwt.decode( - original_token.access_token, + new_token["access_token"], newest_jwk_with_rotation( jwks_directory(app), int(app.config["JWKS_ROTATION_AGE_DAYS"]))) - new_token = OAuth2Token( - token_id=uuid.UUID(_jwt["jti"]), + save_refresh_token(conn, JWTRefreshToken( + token=new_token["refresh_token"], client=original_token.client, - token_type=token_details["token_type"], - access_token=token_details["access_token"], - refresh_token=token_details.get("refresh_token"), - scope=original_token.scope, + user=masqueradee, + issued_with=_jwt["jti"], + issued_at=datetime.fromtimestamp(_jwt["iat"]), + expires=datetime.fromtimestamp( + int(_jwt["iat"]) + RefreshTokenGrant.DEFAULT_EXPIRES_IN), + scope=scope, revoked=False, - issued_at=datetime.now(), - expires_in=token_details["expires_in"], - user=masqueradee) - save_token(conn, new_token) + parent_of=None)) return new_token diff --git a/gn_auth/auth/authorisation/users/masquerade/views.py b/gn_auth/auth/authorisation/users/masquerade/views.py index 68f19ee..8b897f2 100644 --- a/gn_auth/auth/authorisation/users/masquerade/views.py +++ b/gn_auth/auth/authorisation/users/masquerade/views.py @@ -28,22 +28,17 @@ def masquerade() -> Response: masq_user = with_db_connection(partial( user_by_id, user_id=masqueradee_id)) + def __masq__(conn): new_token = masquerade_as(conn, original_token=token, masqueradee=masq_user) return new_token - def __dump_token__(tok): - return { - key: value for key, value in asdict(tok).items() - if key in ("access_token", "refresh_token", "expires_in", - "token_type") - } + return jsonify({ "original": { - "user": asdict(token.user), - "token": __dump_token__(token) + "user": asdict(token.user) }, "masquerade_as": { "user": asdict(masq_user), - "token": __dump_token__(with_db_connection(__masq__)) + "token": with_db_connection(__masq__) } }) diff --git a/gn_auth/auth/authorisation/users/views.py b/gn_auth/auth/authorisation/users/views.py index 4cd498c..7adcd06 100644 --- a/gn_auth/auth/authorisation/users/views.py +++ b/gn_auth/auth/authorisation/users/views.py @@ -152,8 +152,8 @@ def send_verification_email( timedelta( minutes=expiration_minutes)).timestamp()) }) - send_message(smtp_user=current_app.config["SMTP_USER"], - smtp_passwd=current_app.config["SMTP_PASSWORD"], + send_message(smtp_user=current_app.config.get("SMTP_USER", ""), + smtp_passwd=current_app.config.get("SMTP_PASSWORD", ""), message=build_email_message( from_address=current_app.config["EMAIL_ADDRESS"], to_addresses=(user_address(user),), @@ -435,8 +435,7 @@ def forgot_password(): flash("You MUST provide an email.", "alert-danger") return redirect(url_for("oauth2.users.forgot_password")) - with (db.connection(current_app.config["AUTH_DB"]) as conn, - db.cursor(conn) as cursor): + with db.connection(current_app.config["AUTH_DB"]) as conn: user = user_by_email(conn, form["email"]) if not bool(user): flash("We could not find an account with that email.", @@ -467,8 +466,8 @@ def change_password(forgot_password_token): "SELECT fpt.*, u.email FROM forgot_password_tokens AS fpt " "INNER JOIN users AS u ON fpt.user_id=u.user_id WHERE token=?", (forgot_password_token,)) + token = cursor.fetchone() if request.method == "GET": - token = cursor.fetchone() if bool(token): return render_template( "users/change-password.html", @@ -480,4 +479,28 @@ def change_password(forgot_password_token): flash("Invalid Token: We cannot change your password!", "alert-danger") return login_page - return "Do actual password change..." + + password = request.form["password"] + confirm_password = request.form["confirm-password"] + change_password_page = redirect(url_for( + "oauth2.users.change_password", + client_id=request.args["client_id"], + redirect_uri=request.args["redirect_uri"], + response_type=request.args["response_type"], + forgot_password_token=forgot_password_token)) + if bool(password) and bool(confirm_password): + if password == confirm_password: + _user, _hashed_password = set_user_password( + cursor, user_by_email(conn, token["email"]), password) + cursor.execute( + "DELETE FROM forgot_password_tokens WHERE token=?", + (forgot_password_token,)) + flash("Password changed successfully!", "alert-success") + return login_page + + flash("Passwords do not match!", "alert-danger") + return change_password_page + + flash("Both the password and its confirmation MUST be provided!", + "alert-danger") + return change_password_page |