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-rw-r--r--gn3/auth/authorisation/groups/data.py (renamed from gn3/auth/authorisation/resources/data.py)0
-rw-r--r--gn3/auth/authorisation/groups/views.py93
-rw-r--r--gn3/auth/authorisation/resources/models.py62
-rw-r--r--gn3/auth/authorisation/resources/views.py108
4 files changed, 173 insertions, 90 deletions
diff --git a/gn3/auth/authorisation/resources/data.py b/gn3/auth/authorisation/groups/data.py
index 93b8e1d..93b8e1d 100644
--- a/gn3/auth/authorisation/resources/data.py
+++ b/gn3/auth/authorisation/groups/data.py
diff --git a/gn3/auth/authorisation/groups/views.py b/gn3/auth/authorisation/groups/views.py
index d3710f6..d21466c 100644
--- a/gn3/auth/authorisation/groups/views.py
+++ b/gn3/auth/authorisation/groups/views.py
@@ -6,15 +6,18 @@ from functools import partial
from flask import request, jsonify, Response, Blueprint, current_app
from gn3.auth import db
+from gn3 import db_utils as gn3dbutils
+
from gn3.auth.dictify import dictify
from gn3.auth.db_utils import with_db_connection
+from .data import link_data_to_group, retrieve_ungrouped_data
from .models import (
- user_group, all_groups, join_requests, GroupCreationError,
- accept_reject_join_request, group_users as _group_users,
+ user_group, all_groups, DUMMY_GROUP, group_by_id, join_requests,
+ GroupCreationError, accept_reject_join_request, group_users as _group_users,
create_group as _create_group)
-from ..errors import AuthorisationError
+from ..errors import InvalidData, AuthorisationError
from ...authentication.users import User
from ...authentication.oauth2.resource_server import require_oauth
@@ -128,3 +131,87 @@ def reject_join_requests() -> Response:
return jsonify(with_db_connection(partial(
accept_reject_join_request, request_id=request_id,
user=the_token.user, status="REJECTED")))
+
+@groups.route("/<string:resource_type>/unlinked-data")
+@require_oauth("profile group resource")
+def unlinked_data(resource_type: str) -> Response:
+ """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 = current_app.config["AUTH_DB"]
+ with db.connection(db_uri) as conn, db.cursor(conn) as cursor:
+ ugroup = user_group(cursor, the_token.user).maybe(# type: ignore[misc]
+ DUMMY_GROUP, lambda grp: grp)
+ if ugroup == DUMMY_GROUP:
+ return jsonify(tuple())
+ type_filter = {
+ "all": "",
+ "mrna": 'WHERE dataset_type="mRNA"',
+ "genotype": 'WHERE dataset_type="Genotype"',
+ "phenotype": 'WHERE dataset_type="Phenotype"'
+ }[resource_type]
+
+ except_filter = (
+ "SELECT group_id, dataset_type, "
+ "dataset_id AS dataset_or_trait_id FROM mrna_resources "
+ "UNION "
+ "SELECT group_id, dataset_type, "
+ "trait_id AS dataset_or_trait_id FROM genotype_resources "
+ "UNION "
+ "SELECT group_id, dataset_type, "
+ "trait_id AS dataset_or_trait_id FROM phenotype_resources")
+
+ ids_query = ("SELECT group_id, dataset_type, dataset_or_trait_id "
+ "FROM linked_group_data "
+ f"{type_filter} "
+ f"EXCEPT {except_filter} ")
+ cursor.execute(ids_query)
+ ids = cursor.fetchall()
+
+ if ids:
+ clause = ", ".join(["(?, ?, ?)"] * len(ids))
+ data_query = (
+ "SELECT * FROM linked_group_data "
+ "WHERE (group_id, dataset_type, dataset_or_trait_id) "
+ f"IN (VALUES {clause})")
+ params = tuple(item for sublist in
+ ((row[0], row[1], row[2]) for row in ids)
+ for item in sublist)
+ cursor.execute(data_query, params)
+ return jsonify(tuple(dict(row) for row in cursor.fetchall()))
+
+ return jsonify(tuple())
+
+@groups.route("/<string:dataset_type>/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 require_oauth.acquire("profile group resource") as _the_token:
+ with gn3dbutils.database_connection() as gn3conn:
+ return jsonify(with_db_connection(partial(
+ retrieve_ungrouped_data, gn3conn=gn3conn,
+ dataset_type=dataset_type)))
+
+@groups.route("/data/link", methods=["POST"])
+@require_oauth("profile group resource")
+def link_data() -> Response:
+ """Link selected data to specified group."""
+ with require_oauth.acquire("profile group resource") as _the_token:
+ form = request.form
+ group_id = uuid.UUID(form["group_id"])
+ dataset_id = form["dataset_id"]
+ dataset_type = form.get("dataset_type")
+ if dataset_type not in ("mrna", "genotype", "phenotype"):
+ raise InvalidData("Unexpected dataset type requested!")
+ def __link__(conn: db.DbConnection):
+ group = group_by_id(conn, group_id)
+ with gn3dbutils.database_connection() as gn3conn:
+ return link_data_to_group(
+ conn, gn3conn, dataset_type, dataset_id, group)
+
+ return jsonify(with_db_connection(__link__))
diff --git a/gn3/auth/authorisation/resources/models.py b/gn3/auth/authorisation/resources/models.py
index c15463c..40e12ba 100644
--- a/gn3/auth/authorisation/resources/models.py
+++ b/gn3/auth/authorisation/resources/models.py
@@ -2,11 +2,13 @@
import json
import sqlite3
from uuid import UUID, uuid4
+from functools import partial
from typing import Any, Dict, Sequence, NamedTuple
from gn3.auth import db
from gn3.auth.dictify import dictify
from gn3.auth.authentication.users import User
+from gn3.auth.db_utils import with_db_connection
from .checks import authorised_for
@@ -262,3 +264,63 @@ def resource_by_id(
bool(int(row["public"]))))
raise NotFoundError(f"Could not find a resource with id '{resource_id}'")
+
+def __link_mrna_data_to_resource__(
+ conn: db.DbConnection, resource: Resource, dataset_id: str) -> dict:
+ """Link mRNA Assay data with a resource."""
+ with db.cursor(conn) as cursor:
+ params = {
+ "group_id": str(resource.group.group_id),
+ "resource_id": str(resource.resource_id),
+ "dataset_type": "mRNA",
+ "dataset_id": dataset_id
+ }
+ cursor.execute(
+ "INSERT INTO mrna_resources VALUES"
+ "(:group_id, :resource_id, :dataset_type, :dataset_id)",
+ params)
+ return params
+
+def __link_geno_data_to_resource__(
+ conn: db.DbConnection, resource: Resource, dataset_id: str) -> dict:
+ """Link Genotype data with a resource."""
+ with db.cursor(conn) as cursor:
+ params = {
+ "group_id": str(resource.group.group_id),
+ "resource_id": str(resource.resource_id),
+ "dataset_type": "Genotype",
+ "trait_id": dataset_id
+ }
+ cursor.execute(
+ "INSERT INTO genotype_resources VALUES"
+ "(:group_id, :resource_id, :dataset_type, :trait_id)",
+ params)
+ return params
+
+def __link_pheno_data_to_resource__(
+ conn: db.DbConnection, resource: Resource, dataset_id: str) -> dict:
+ """Link Phenotype data with a resource."""
+ with db.cursor(conn) as cursor:
+ params = {
+ "group_id": str(resource.group.group_id),
+ "resource_id": str(resource.resource_id),
+ "dataset_type": "Phenotype",
+ "trait_id": dataset_id
+ }
+ cursor.execute(
+ "INSERT INTO phenotype_resources VALUES"
+ "(:group_id, :resource_id, :dataset_type, :trait_id)",
+ params)
+ return params
+
+def link_data_to_resource(
+ conn: db.DbConnection, user: User, resource_id: UUID, dataset_type: str,
+ dataset_id: str):
+ """Link data to resource."""
+ resource = with_db_connection(partial(
+ resource_by_id, user=user, resource_id=resource_id))
+ return {
+ "mrna": __link_mrna_data_to_resource__,
+ "genotype": __link_geno_data_to_resource__,
+ "phenotype": __link_pheno_data_to_resource__,
+ }[dataset_type.lower()](conn, resource, dataset_id)
diff --git a/gn3/auth/authorisation/resources/views.py b/gn3/auth/authorisation/resources/views.py
index e373182..b2773a8 100644
--- a/gn3/auth/authorisation/resources/views.py
+++ b/gn3/auth/authorisation/resources/views.py
@@ -1,19 +1,15 @@
"""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 link_data_to_group, retrieve_ungrouped_data
from .models import (
- resource_by_id, resource_categories, resource_category_by_id,
- create_resource as _create_resource)
+ resource_by_id, resource_categories, link_data_to_resource,
+ resource_category_by_id, create_resource as _create_resource)
-from ..errors import InvalidData, AuthorisationError
-from ..groups.models import user_group, DUMMY_GROUP, group_by_id
+from ..errors import InvalidData
from ... import db
from ...dictify import dictify
@@ -56,86 +52,24 @@ def view_resource(resource_id: uuid.UUID) -> Response:
return jsonify(dictify(resource_by_id(
conn, the_token.user, resource_id)))
-@resources.route("/<string:resource_type>/unlinked-data")
-@require_oauth("profile group resource")
-def unlinked_data(resource_type: str) -> Response:
- """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:
- ugroup = user_group(cursor, the_token.user).maybe(# type: ignore[misc]
- DUMMY_GROUP, lambda grp: grp)
- if ugroup == DUMMY_GROUP:
- return jsonify(tuple())
- type_filter = {
- "all": "",
- "mrna": 'WHERE dataset_type="mRNA"',
- "genotype": 'WHERE dataset_type="Genotype"',
- "phenotype": 'WHERE dataset_type="Phenotype"'
- }[resource_type]
-
- except_filter = (
- "SELECT group_id, dataset_type, "
- "dataset_id AS dataset_or_trait_id FROM mrna_resources "
- "UNION "
- "SELECT group_id, dataset_type, "
- "trait_id AS dataset_or_trait_id FROM genotype_resources "
- "UNION "
- "SELECT group_id, dataset_type, "
- "trait_id AS dataset_or_trait_id FROM phenotype_resources")
-
- ids_query = ("SELECT group_id, dataset_type, dataset_or_trait_id "
- "FROM linked_group_data "
- f"{type_filter} "
- f"EXCEPT {except_filter} ")
- cursor.execute(ids_query)
- ids = cursor.fetchall()
-
- if ids:
- clause = ", ".join(["(?, ?, ?)"] * len(ids))
- data_query = (
- "SELECT * FROM linked_group_data "
- "WHERE (group_id, dataset_type, dataset_or_trait_id) "
- f"IN (VALUES {clause})")
- params = tuple(item for sublist in
- ((row[0], row[1], row[2]) for row in ids)
- for item in sublist)
- cursor.execute(data_query, params)
- return jsonify(tuple(dict(row) for row in cursor.fetchall()))
-
- return jsonify(tuple())
-
-@resources.route("/<string:dataset_type>/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 require_oauth.acquire("profile group resource") as _the_token:
- with gn3dbutils.database_connection() as gn3conn:
- return jsonify(with_db_connection(partial(
- retrieve_ungrouped_data, gn3conn=gn3conn,
- dataset_type=dataset_type)))
-
@resources.route("/data/link", methods=["POST"])
@require_oauth("profile group resource")
-def link_data() -> Response:
- """Link selected data to specified group."""
- with require_oauth.acquire("profile group resource") as _the_token:
+def link_data():
+ """Link group data to a specific resource."""
+ try:
form = request.form
- group_id = uuid.UUID(form["group_id"])
- dataset_id = form["dataset_id"]
- dataset_type = form.get("dataset_type")
- if dataset_type not in ("mrna", "genotype", "phenotype"):
- raise InvalidData("Unexpected dataset type requested!")
- def __link__(conn: db.DbConnection):
- group = group_by_id(conn, group_id)
- with gn3dbutils.database_connection() as gn3conn:
- return link_data_to_group(
- conn, gn3conn, dataset_type, dataset_id, group)
-
- return jsonify(with_db_connection(__link__))
+ assert "resource_id" in form, "Resource ID not provided."
+ assert "dataset_id" in form, "Dataset ID not provided."
+ assert "dataset_type" in form, "Dataset type not specified"
+ assert form["dataset_type"].lower() in (
+ "mrna", "genotype", "phenotype"), "Invalid dataset type provided."
+
+ 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.UUID(form["resource_id"]),
+ form["dataset_type"], form["dataset_id"])
+
+ return jsonify(with_db_connection(__link__))
+ except AssertionError as aserr:
+ raise InvalidData(aserr.args[0]) from aserr
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-25 18:57:41 +0000