diff options
| -rw-r--r-- | wqflask/wqflask/metadata_edits.py | 21 |
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", |