diff options
| -rw-r--r-- | wqflask/wqflask/metadata_edits.py | 44 |
1 files changed, 14 insertions, 30 deletions
diff --git a/wqflask/wqflask/metadata_edits.py b/wqflask/wqflask/metadata_edits.py index b0251f99..10da89a5 100644 --- a/wqflask/wqflask/metadata_edits.py +++ b/wqflask/wqflask/metadata_edits.py @@ -47,7 +47,7 @@ from gn3.db import fetchone from gn3.db import insert 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.metadata_audit import create_metadata_audit from gn3.db.phenotypes import Phenotype from gn3.db.probesets import Probeset, probeset_mapping, fetch_probeset_metadata_by_name from gn3.db.phenotypes import Publication @@ -350,16 +350,10 @@ View the diffs <a href='{url}' target='_blank'>here</a>", "success") } ) with database_connection(get_setting("SQL_URI")) as conn: - insert( - conn, - table="metadata_audit", - data=MetadataAudit( - dataset_id=name, - editor=author, - json_data=json.dumps(diff_data, cls=CustomJSONEncoder), - ), - ) - conn.commit() + create_metadata_audit(conn, { + "dataset_id": dataset_id, + "editor": author, + "json_data": json.dumps(diff_data, cls=CustomJSONEncoder)}) flash(f"Diff-data: \n{diff_data}\nhas been uploaded", "success") return redirect( f"/datasets/{dataset_id}/traits/{name}" @@ -436,16 +430,10 @@ def update_probeset(name: str): ) } ) - insert( - conn, - table="metadata_audit", - data=MetadataAudit( - dataset_id=data_.get("id"), - editor=author, - json_data=json.dumps(diff_data, cls=CustomJSONEncoder), - ), - ) - conn.commit() + create_metadata_audit(conn, { + "dataset_id": data_["id"], + "editor": author, + "json_data": json.dumps(diff_data, cls=CustomJSONEncoder)}) edited_values = {k: v for (k, v) in diff_data['Probeset'].items() if k not in {"id_", "timestamp", "author"}} changes = [] @@ -759,15 +747,11 @@ def approve_data(resource_id: str, file_name: str): ] ): with database_connection(get_setting("SQL_URI")) as conn: - insert( - conn, - table="metadata_audit", - data=MetadataAudit( - dataset_id=sample_data.get("trait_name"), - editor=sample_data.get("author"), - json_data=json.dumps(sample_data, cls=CustomJSONEncoder), - ), - ) + create_metadata_audit(conn, { + "dataset_id": sample_data.get("dataset_id"), + "editor": sample_data.get("author"), + "json_data": json.dumps(sample_data, cls=CustomJSONEncoder) + }) # Once data is approved, rename it! os.rename( os.path.join(f"{TMPDIR}/sample-data/diffs", file_name), |