1 files changed, 90 insertions, 3 deletions

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__))