diff options
Diffstat (limited to 'gn_auth/auth/authorisation/resources/inbredset')
| -rw-r--r-- | gn_auth/auth/authorisation/resources/inbredset/models.py | 51 | ||||
| -rw-r--r-- | gn_auth/auth/authorisation/resources/inbredset/views.py | 55 |
2 files changed, 68 insertions, 38 deletions
diff --git a/gn_auth/auth/authorisation/resources/inbredset/models.py b/gn_auth/auth/authorisation/resources/inbredset/models.py index de1c18a..2626f3e 100644 --- a/gn_auth/auth/authorisation/resources/inbredset/models.py +++ b/gn_auth/auth/authorisation/resources/inbredset/models.py @@ -1,39 +1,12 @@ """Functions to handle the low-level details regarding populations auth.""" from uuid import UUID, uuid4 +from typing import Sequence, Optional import sqlite3 -from gn_auth.auth.errors import NotFoundError +import gn_auth.auth.db.sqlite3 as db 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.") +from gn_auth.auth.authorisation.resources.base import Resource def assign_inbredset_group_owner_role( @@ -62,7 +35,7 @@ def assign_inbredset_group_owner_role( return resource -def link_data_to_resource(# pylint: disable=[too-many-arguments] +def link_data_to_resource(# pylint: disable=[too-many-arguments, too-many-positional-arguments] cursor: sqlite3.Cursor, resource_id: UUID, species_id: int, @@ -94,3 +67,19 @@ def link_data_to_resource(# pylint: disable=[too-many-arguments] "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 b559105..9603b5b 100644 --- a/gn_auth/auth/authorisation/resources/inbredset/views.py +++ b/gn_auth/auth/authorisation/resources/inbredset/views.py @@ -1,20 +1,54 @@ """Views for InbredSet resources.""" +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.errors import NotFoundError from gn_auth.auth.requests import request_json -from gn_auth.auth.db.sqlite3 import with_db_connection +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.groups.models import user_group - -from .models import (create_resource, - link_data_to_resource, +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__) + +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.") + + @popbp.route("/populations/resource-id/<int:speciesid>/<int:inbredsetid>", methods=["GET"]) def resource_id_by_inbredset_id(speciesid: int, inbredsetid: int) -> Response: @@ -30,7 +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: @@ -83,7 +117,14 @@ def create_population_resource(): return Right({"formdata": form, "group": usergroup}) - return user_group(conn, _token.user).then( + 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: { |