Move `groups` package under `resources` package

With user groups being resources that users can act on (with the
recent changes), this commit moves the `groups` module to under the
`resources` module.

It also renames the `*_resources.py` modules by dropping the
`_resources` part since the code is under the `resources` module
anyway.

1 files changed, 71 insertions, 0 deletions

diff --git a/gn_auth/auth/authorisation/resources/phenotype.py b/gn_auth/auth/authorisation/resources/phenotype.py
new file mode 100644
index 0000000..cd3f23d
--- /dev/null
+++ b/gn_auth/auth/authorisation/resources/phenotype.py
@@ -0,0 +1,71 @@
+"""Phenotype data resources functions and utilities."""
+import uuid
+from typing import Optional, Sequence
+
+import sqlite3
+
+import gn_auth.auth.db.sqlite3 as db
+
+from .groups import Group
+from .base import Resource
+from .data import __attach_data__
+
+def resource_data(
+        cursor: db.DbCursor,
+        resource_id: uuid.UUID,
+        offset: int = 0,
+        limit: Optional[int] = None) -> Sequence[sqlite3.Row]:
+    """Fetch data linked to a Phenotype resource"""
+    cursor.execute(
+        ("SELECT * FROM phenotype_resources AS pr "
+         "INNER JOIN linked_phenotype_data AS lpd "
+         "ON pr.data_link_id=lpd.data_link_id "
+         "WHERE pr.resource_id=?") + (
+             f" LIMIT {limit} OFFSET {offset}" if bool(limit) else ""),
+        (str(resource_id),))
+    return cursor.fetchall()
+
+def link_data_to_resource(
+        conn: db.DbConnection,
+        resource: Resource,
+        group: Group,
+        data_link_id: uuid.UUID) -> dict:
+    """Link Phenotype data with a resource."""
+    with db.cursor(conn) as cursor:
+        params = {
+            "group_id": str(group.group_id),
+            "resource_id": str(resource.resource_id),
+            "data_link_id": str(data_link_id)
+        }
+        cursor.execute(
+            "INSERT INTO phenotype_resources VALUES"
+            "(:group_id, :resource_id, :data_link_id)",
+            params)
+        return params
+
+def unlink_data_from_resource(
+        conn: db.DbConnection,
+        resource: Resource,
+        data_link_id: uuid.UUID) -> dict:
+    """Unlink data from Phenotype resources"""
+    with db.cursor(conn) as cursor:
+        cursor.execute("DELETE FROM phenotype_resources "
+                       "WHERE resource_id=? AND data_link_id=?",
+                       (str(resource.resource_id), str(data_link_id)))
+        return {
+            "resource_id": str(resource.resource_id),
+            "dataset_type": resource.resource_category.resource_category_key,
+            "data_link_id": str(data_link_id)
+        }
+
+def attach_resources_data(
+        cursor, resources: Sequence[Resource]) -> Sequence[Resource]:
+    """Attach linked data to Phenotype resources"""
+    placeholders = ", ".join(["?"] * len(resources))
+    cursor.execute(
+        "SELECT * FROM phenotype_resources AS pr "
+        "INNER JOIN linked_phenotype_data AS lpd "
+        "ON pr.data_link_id=lpd.data_link_id "
+        f"WHERE pr.resource_id IN ({placeholders})",
+        tuple(str(resource.resource_id) for resource in resources))
+    return __attach_data__(cursor.fetchall(), resources)