Fetch phenotype resources by dataset name and trait name.

1 files changed, 45 insertions, 0 deletions

diff --git a/gn_auth/auth/authorisation/data/phenotypes.py b/gn_auth/auth/authorisation/data/phenotypes.py
index 788b9e7..dddd5c9 100644
--- a/gn_auth/auth/authorisation/data/phenotypes.py
+++ b/gn_auth/auth/authorisation/data/phenotypes.py
@@ -1,5 +1,7 @@
 """Handle linking of Phenotype data to the Auth(entic|oris)ation system."""
 import uuid
+import logging
+from functools import reduce
 from dataclasses import asdict
 from typing import Any, Iterable
 
@@ -20,8 +22,10 @@ from gn_auth.auth.authorisation.resources.groups.models import Group, group_reso
 from gn_auth.auth.authorisation.checks import require_json
 from gn_auth.auth.authorisation.resources.checks import authorised_for2
 
+logger = logging.getLogger(__name__)
 phenosbp = Blueprint("phenotypes", __name__)
 
+
 def linked_phenotype_data(
         authconn: authdb.DbConnection, gn3conn: gn3db.Connection,
         species: str = "") -> Iterable[dict[str, Any]]:
@@ -274,3 +278,44 @@ def delete_linked_phenotypes_data(
             "requested": len(xref_ids),
             "deleted": _deleted
         })
+
+
+def __organise_resources_data__(acc, curr) -> dict:
+    logger.debug("ORGANISING... %s", dict(curr))
+    resource_row = acc.get(curr["resource_id"], {
+        "resource_id": curr["resource_id"],
+        "resource_data": tuple(),
+    })
+    return {
+        **acc,
+        curr["resource_id"]: {
+            **resource_row,
+            "resource_data": resource_row["resource_data"] + (
+                f'{curr["dataset_name"]}::{curr["trait_id"]}',)
+        }
+    }
+
+
+def resources_by_datasets_and_traits(
+        authconn: authdb.DbConnection,
+        dsets_traits: tuple[tuple[str, str], ...]
+) -> tuple[dict, ...]:
+    """Fetch resources by their attached datasets and traits."""
+    paramstr = ", ".join(["(?, ?)"] * len(dsets_traits))
+    query = (
+        "SELECT r.*, rc.*, lpd.dataset_name, lpd.PublishXRefId AS trait_id "
+        "FROM linked_phenotype_data AS lpd "
+        "INNER JOIN phenotype_resources AS pr "
+        "ON lpd.data_link_id=pr.data_link_id "
+        "INNER JOIN resources AS r ON pr.resource_id=r.resource_id "
+        "INNER JOIN resource_categories AS rc "
+        "ON r.resource_category_id=rc.resource_category_id "
+        "WHERE (lpd.dataset_name, lpd.PublishXRefId) "
+        f"IN ({paramstr})")
+    with authdb.cursor(authconn) as cursor:
+        cursor.execute(
+            query, tuple(item for row in dsets_traits for item in row))
+        return tuple(reduce(
+            __organise_resources_data__,
+            cursor.fetchall(),
+            {}).values())