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authorFrederick Muriuki Muriithi2023-07-19 09:52:30 +0300
committerFrederick Muriuki Muriithi2023-07-19 09:52:30 +0300
commit88006dd282fc2945cd9cd510ef336e9c077cc8ce (patch)
treee0b59c72b3ba01b4a7a21a7b7c53fe2d14119c1b
parent8b441bbbd1e073b7b2e471fda0c6f1b2a4255882 (diff)
downloadgenenetwork2-88006dd282fc2945cd9cd510ef336e9c077cc8ce.tar.gz
Replace ORM code with direct queries for ProbeSets
-rw-r--r--wqflask/wqflask/metadata_edits.py17
1 files changed, 2 insertions, 15 deletions
diff --git a/wqflask/wqflask/metadata_edits.py b/wqflask/wqflask/metadata_edits.py
index f6e74d68..47e2ae28 100644
--- a/wqflask/wqflask/metadata_edits.py
+++ b/wqflask/wqflask/metadata_edits.py
@@ -49,11 +49,10 @@ from gn3.db import update
from gn3.db.datasets import retrieve_sample_list, retrieve_phenotype_group_name
from gn3.db.metadata_audit import MetadataAudit
from gn3.db.phenotypes import Phenotype
-from gn3.db.phenotypes import Probeset
+from gn3.db.probesets import Probeset, probeset_mapping, fetch_probeset_metadata_by_name
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
from gn3.db.sample_data import insert_sample_data
@@ -101,18 +100,6 @@ def edit_phenotype(conn, name, dataset_id):
}
-def edit_probeset(conn, name):
- probeset_ = fetchone(
- conn=conn,
- table="ProbeSet",
- columns=list(probeset_mapping.values()),
- where=Probeset(name=name),
- )
- return {
- "probeset": probeset_,
- }
-
-
@metadata_edit.route("/<dataset_id>/traits/<name>")
@required_access(
("group:resource:view-resource", "group:resource:edit-resource"))
@@ -146,7 +133,7 @@ def display_phenotype_metadata(dataset_id: str, name: str):
def display_probeset_metadata(name: str):
from utility.tools import get_setting
with database_connection(get_setting("SQL_URI")) as conn:
- _d = edit_probeset(conn=conn, name=name)
+ _d = {"probeset": fetch_probeset_metadata_by_name(conn, name)}
return render_template(
"edit_probeset.html",
diff=_d.get("diff"),