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.

1 files changed, 5 insertions, 16 deletions

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",