From c876c9f53018529fed1cb025a085b6e9d37dc3ef Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Wed, 22 Feb 2023 16:22:47 +0300 Subject: auth: List data not linked to any group. --- gn3/auth/authorisation/resources/data.py | 96 +++++++++++++++++++++++++++++++ gn3/auth/authorisation/resources/views.py | 24 +++++++- 2 files changed, 119 insertions(+), 1 deletion(-) create mode 100644 gn3/auth/authorisation/resources/data.py (limited to 'gn3/auth/authorisation/resources') diff --git a/gn3/auth/authorisation/resources/data.py b/gn3/auth/authorisation/resources/data.py new file mode 100644 index 0000000..7598f34 --- /dev/null +++ b/gn3/auth/authorisation/resources/data.py @@ -0,0 +1,96 @@ +"""Handles the resource objects' data.""" +from typing import Any, Sequence + +from MySQLdb.cursors import DictCursor + +from gn3 import db_utils as gn3db +from gn3.auth import db as authdb +from gn3.auth.authorisation.errors import InvalidData + +def __fetch_grouped_data__( + conn: authdb.DbConnection, dataset_type: str) -> Sequence[dict[str, Any]]: + """Retrieve ids for all data that are linked to groups in the auth db.""" + with authdb.cursor(conn) as cursor: + cursor.execute( + "SELECT dataset_type, dataset_or_trait_id FROM linked_group_data " + "WHERE LOWER(dataset_type)=?", + (dataset_type,)) + return tuple(dict(row) for row in cursor.fetchall()) + +def __fetch_ungrouped_mrna_data__( + conn: gn3db.Connection, grouped_data, + offset: int = 0) -> Sequence[dict]: + """Fetch ungrouped mRNA Assay data.""" + query = ("SELECT psf.Id, psf.Name, psf.FullName, " + "ifiles.GN_AccesionId AS accession_id FROM ProbeSetFreeze AS psf " + "INNER JOIN InfoFiles AS ifiles ON psf.Name=ifiles.InfoPageName") + params: tuple[Any, ...] = tuple() + if bool(grouped_data): + clause = ", ".join(["%s"] * len(grouped_data)) + query = f"{query} WHERE psf.Id NOT IN ({clause})" + params = tuple(item["dataset_or_trait_id"] for item in grouped_data) + + query = f"{query} LIMIT 100 OFFSET %s" + with conn.cursor(cursorclass=DictCursor) as cursor:# type: ignore[call-arg] + cursor.execute(query, (params + (offset,))) + return tuple(dict(row) for row in cursor.fetchall()) + +def __fetch_ungrouped_geno_data__( + conn: gn3db.Connection, grouped_data, + offset: int = 0) -> Sequence[dict]: + """Fetch ungrouped Genotype data.""" + query = ("SELECT gf.Id, gf.Name, gf.FullName, " + "ifiles.GN_AccesionId AS accession_id FROM GenoFreeze AS gf " + "INNER JOIN InfoFiles AS ifiles ON gf.Name=ifiles.InfoPageName") + params: tuple[Any, ...] = tuple() + if bool(grouped_data): + clause = ", ".join(["%s"] * len(grouped_data)) + query = f"{query} WHERE gf.Id NOT IN ({clause})" + params = tuple(item["dataset_or_trait_id"] for item in grouped_data) + + query = f"{query} LIMIT 100 OFFSET %s" + with conn.cursor(cursorclass=DictCursor) as cursor:# type: ignore[call-arg] + cursor.execute(query, (params + (offset,))) + return tuple(dict(row) for row in cursor.fetchall()) + +def __fetch_ungrouped_pheno_data__( + conn: gn3db.Connection, grouped_data, + offset: int = 0) -> Sequence[dict]: + """Fetch ungrouped Phenotype data.""" + query = ("SELECT pf.Id, pf.Name, pf.FullName, " + "ifiles.GN_AccesionId AS accession_id FROM PublishFreeze AS pf " + "INNER JOIN InfoFiles AS ifiles ON pf.Name=ifiles.InfoPageName") + params: tuple[Any, ...] = tuple() + if bool(grouped_data): + clause = ", ".join(["%s"] * len(grouped_data)) + query = f"{query} WHERE pf.Id NOT IN ({clause})" + params = tuple(item["dataset_or_trait_id"] for item in grouped_data) + + query = f"{query} LIMIT 100 OFFSET %s" + with conn.cursor(cursorclass=DictCursor) as cursor:# type: ignore[call-arg] + cursor.execute(query, (params + (offset,))) + return tuple(dict(row) for row in cursor.fetchall()) + +def __fetch_ungrouped_data__( + conn: gn3db.Connection, dataset_type: str, + ungrouped: Sequence[dict[str, Any]]) -> Sequence[dict[str, Any]]: + """Fetch any ungrouped data.""" + fetch_fns = { + "mrna": __fetch_ungrouped_mrna_data__, + "genotype": __fetch_ungrouped_geno_data__, + "phenotype": __fetch_ungrouped_pheno_data__ + } + return fetch_fns[dataset_type](conn, ungrouped) + +def retrieve_ungrouped_data( + authconn: authdb.DbConnection, + gn3conn: gn3db.Connection, + dataset_type: str) -> Sequence[dict]: + """Retrieve any data not linked to any group.""" + if dataset_type not in ("mrna", "genotype", "phenotype"): + raise InvalidData( + "Requested dataset type is invalid. Expected one of " + "'mrna', 'genotype' or 'phenotype'.") + grouped_data = __fetch_grouped_data__(authconn, dataset_type) + print(f"GROUPED DATA: {grouped_data}") + return __fetch_ungrouped_data__(gn3conn, dataset_type, grouped_data) diff --git a/gn3/auth/authorisation/resources/views.py b/gn3/auth/authorisation/resources/views.py index ad39df7..44e2c4e 100644 --- a/gn3/auth/authorisation/resources/views.py +++ b/gn3/auth/authorisation/resources/views.py @@ -1,11 +1,18 @@ """The views/routes for the resources package""" import uuid +from functools import partial + from flask import request, jsonify, Response, Blueprint, current_app as app +from gn3 import db_utils as gn3dbutils +from gn3.auth.db_utils import with_db_connection + +from .data import retrieve_ungrouped_data from .models import ( resource_by_id, resource_categories, resource_category_by_id, create_resource as _create_resource) +from ..errors import AuthorisationError from ..groups.models import user_group, DUMMY_GROUP from ... import db @@ -52,7 +59,10 @@ def view_resource(resource_id: uuid.UUID) -> Response: @resources.route("//unlinked-data") @require_oauth("profile group resource") def unlinked_data(resource_type: str) -> Response: - """View unlinked data""" + """View data linked to the group but not linked to any resource.""" + if resource_type not in ("all", "mrna", "genotype", "phenotype"): + raise AuthorisationError(f"Invalid resource type {resource_type}") + with require_oauth.acquire("profile group resource") as the_token: db_uri = app.config["AUTH_DB"] with db.connection(db_uri) as conn, db.cursor(conn) as cursor: @@ -97,3 +107,15 @@ def unlinked_data(resource_type: str) -> Response: return jsonify(tuple(dict(row) for row in cursor.fetchall())) return jsonify(tuple()) + +@resources.route("//ungrouped-data", methods=["GET"]) +@require_oauth("profile group resource") +def ungrouped_data(dataset_type: str) -> Response: + """View data not linked to any group.""" + if dataset_type not in ("all", "mrna", "genotype", "phenotype"): + raise AuthorisationError(f"Invalid dataset type {dataset_type}") + + with gn3dbutils.database_connection() as gn3conn: + return jsonify(with_db_connection(partial( + retrieve_ungrouped_data, gn3conn=gn3conn, + dataset_type=dataset_type))) -- cgit v1.2.3