diff options
| -rw-r--r-- | gn_auth/auth/authorisation/data/phenotypes.py | 36 | ||||
| -rw-r--r-- | gn_auth/auth/authorisation/data/views.py | 28 | ||||
| -rw-r--r-- | gn_auth/auth/authorisation/users/admin/views.py | 8 |
3 files changed, 0 insertions, 72 deletions
diff --git a/gn_auth/auth/authorisation/data/phenotypes.py b/gn_auth/auth/authorisation/data/phenotypes.py index dddd5c9..92cbe89 100644 --- a/gn_auth/auth/authorisation/data/phenotypes.py +++ b/gn_auth/auth/authorisation/data/phenotypes.py @@ -13,7 +13,6 @@ from flask import request, jsonify, Response, Blueprint, current_app as app from gn_auth.auth.authentication.oauth2.resource_server import require_oauth from gn_auth.auth.errors import AuthorisationError -from gn_auth.auth.authorisation.checks import authorised_p from gn_auth.auth.authorisation.resources.checks import can_delete from gn_auth.auth.authorisation.resources.system.models import system_resource from gn_auth.auth.authorisation.resources.groups.models import Group, group_resource @@ -62,41 +61,6 @@ def linked_phenotype_data( gn3cursor.execute(query, params) return (item for item in gn3cursor.fetchall()) -@authorised_p(("system:data:link-to-group",), - error_description=( - "You do not have sufficient privileges to link data to (a) " - "group(s)."), - oauth2_scope="profile group resource") -def ungrouped_phenotype_data( - authconn: authdb.DbConnection, gn3conn: gn3db.Connection): - """Retrieve phenotype data that is not linked to any user group.""" - with gn3conn.cursor() as cursor: - params = tuple( - (row["SpeciesId"], row["InbredSetId"], row["PublishFreezeId"], - row["PublishXRefId"]) - for row in linked_phenotype_data(authconn, gn3conn)) - paramstr = ", ".join(["(?, ?, ?, ?)"] * len(params)) - query = ( - "SELECT spc.SpeciesId, spc.SpeciesName, iset.InbredSetId, " - "iset.InbredSetName, pf.Id AS PublishFreezeId, " - "pf.Name AS dataset_name, pf.FullName AS dataset_fullname, " - "pf.ShortName AS dataset_shortname, pxr.Id AS PublishXRefId " - "FROM " - "Species AS spc " - "INNER JOIN InbredSet AS iset " - "ON spc.SpeciesId=iset.SpeciesId " - "INNER JOIN PublishFreeze AS pf " - "ON iset.InbredSetId=pf.InbredSetId " - "INNER JOIN PublishXRef AS pxr " - "ON pf.InbredSetId=pxr.InbredSetId") - if len(params) > 0: - query = query + ( - f" WHERE (iset.InbredSetId, pf.Id, pxr.Id) NOT IN ({paramstr})") - - cursor.execute(query, params) - return tuple(dict(row) for row in cursor.fetchall()) - - return tuple() def pheno_traits_from_db(gn3conn: gn3db.Connection, params: tuple[dict, ...]) -> tuple[dict, ...]: """An internal utility function. Don't use outside of this module.""" diff --git a/gn_auth/auth/authorisation/data/views.py b/gn_auth/auth/authorisation/data/views.py index fc1849f..584b239 100644 --- a/gn_auth/auth/authorisation/data/views.py +++ b/gn_auth/auth/authorisation/data/views.py @@ -49,34 +49,6 @@ data = Blueprint("data", __name__) data.register_blueprint(phenosbp, url_prefix="/phenotypes") -def build_trait_name(trait_fullname): - """ - Initialises the trait's name, and other values from the search data provided - - This is a copy of `gn3.db.traits.build_trait_name` function. - """ - def dataset_type(dset_name): - if dset_name.find('Temp') >= 0: - return "Temp" - if dset_name.find('Geno') >= 0: - return "Geno" - if dset_name.find('Publish') >= 0: - return "Publish" - return "ProbeSet" - - name_parts = trait_fullname.split("::") - assert len(name_parts) >= 2, f"Name format error: '{trait_fullname}'" - dataset_name = name_parts[0] - dataset_type = dataset_type(dataset_name) - return { - "db": { - "dataset_name": dataset_name, - "dataset_type": dataset_type}, - "trait_fullname": trait_fullname, - "trait_name": name_parts[1], - "cellid": name_parts[2] if len(name_parts) == 3 else "" - } - @data.route("species") def list_species() -> Response: """List all available species information.""" diff --git a/gn_auth/auth/authorisation/users/admin/views.py b/gn_auth/auth/authorisation/users/admin/views.py index 9bc1c36..62eccfd 100644 --- a/gn_auth/auth/authorisation/users/admin/views.py +++ b/gn_auth/auth/authorisation/users/admin/views.py @@ -1,6 +1,5 @@ """UI for admin stuff""" import uuid -import json import random import string from typing import Optional @@ -240,13 +239,6 @@ def register_client(): client_secret = raw_client_secret) -def __parse_client__(sqlite3_row) -> dict: - """Parse the client details into python datatypes.""" - return { - **dict(sqlite3_row), - "client_metadata": json.loads(sqlite3_row["client_metadata"]) - } - @admin.route("/list-client", methods=["GET"]) @is_admin def list_clients(): |