From beff6962223c1885697c5755878a0b694d210965 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Tue, 18 Jul 2023 13:39:18 +0300
Subject: Replace ORM calls with direct queries

Avoid the use of the ORM code for fetching data from the database, and
instead use direct queries that indicate easily what is being fetched
from the database.
---
 wqflask/wqflask/metadata_edits.py | 21 +++++----------------
 1 file changed, 5 insertions(+), 16 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/metadata_edits.py b/wqflask/wqflask/metadata_edits.py
index a3b7f307..9decbc16 100644
--- a/wqflask/wqflask/metadata_edits.py
+++ b/wqflask/wqflask/metadata_edits.py
@@ -52,6 +52,7 @@ from gn3.db.phenotypes import Phenotype
 from gn3.db.phenotypes import Probeset
 from gn3.db.phenotypes import Publication
 from gn3.db.phenotypes import PublishXRef
+from gn3.db.phenotypes import fetch_trait, fetch_metadata, fetch_publication
 from gn3.db.phenotypes import probeset_mapping
 from gn3.db.sample_data import delete_sample_data
 from gn3.db.sample_data import get_trait_sample_data, get_trait_csv_sample_data
@@ -92,23 +93,11 @@ def _get_diffs(diff_dir: str, redis_conn: redis.Redis):
 
 
 def edit_phenotype(conn, name, dataset_id):
-    publish_xref = fetchone(
-        conn=conn,
-        table="PublishXRef",
-        where=PublishXRef(id_=name, inbred_set_id=dataset_id),
-    )
+    publish_xref = fetch_trait(conn, dataset_id=dataset_id, trait_name=name)
     return {
         "publish_xref": publish_xref,
-        "phenotype": fetchone(
-            conn=conn,
-            table="Phenotype",
-            where=Phenotype(id_=publish_xref.phenotype_id),
-        ),
-        "publication": fetchone(
-            conn=conn,
-            table="Publication",
-            where=Publication(id_=publish_xref.publication_id),
-        ),
+        "phenotype": fetch_metadata(conn, publish_xref["phenotype_id"]),
+        "publication": fetch_publication(conn, publish_xref["publication_id"])
     }
 
 
@@ -135,7 +124,7 @@ def display_phenotype_metadata(dataset_id: str, name: str):
 
         group_name = retrieve_phenotype_group_name(conn, dataset_id)
         sample_list = retrieve_sample_list(group_name)
-        sample_data = get_trait_sample_data(conn, name, _d.get("publish_xref").phenotype_id)
+        sample_data = get_trait_sample_data(conn, name, _d["publish_xref"]["phenotype_id"])
 
         return render_template(
             "edit_phenotype.html",
-- 
cgit v1.2.3