diff options
| -rw-r--r-- | wqflask/wqflask/metadata_edits.py | 71 |
1 files changed, 56 insertions, 15 deletions
diff --git a/wqflask/wqflask/metadata_edits.py b/wqflask/wqflask/metadata_edits.py index df52fdc6..437a9cb4 100644 --- a/wqflask/wqflask/metadata_edits.py +++ b/wqflask/wqflask/metadata_edits.py @@ -35,6 +35,7 @@ from gn3.db import fetchall from gn3.db import fetchone from gn3.db import insert from gn3.db import update +from gn3.db.datasets import retrieve_sample_list, retrieve_group_name, retrieve_trait_dataset from gn3.db.metadata_audit import MetadataAudit from gn3.db.phenotypes import Phenotype from gn3.db.phenotypes import Probeset @@ -42,7 +43,7 @@ from gn3.db.phenotypes import Publication from gn3.db.phenotypes import PublishXRef from gn3.db.phenotypes import probeset_mapping from gn3.db.sample_data import delete_sample_data -from gn3.db.sample_data import get_trait_csv_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 from gn3.db.sample_data import update_sample_data @@ -131,8 +132,15 @@ def edit_probeset(conn, name): def display_phenotype_metadata(dataset_id: str, name: str): with database_connection() as conn: _d = edit_phenotype(conn=conn, name=name, dataset_id=dataset_id) + + group_name = retrieve_group_name(dataset_id, conn) + sample_list = retrieve_sample_list(group_name) + sample_data = get_trait_sample_data(conn, name, _d.get("publish_xref").phenotype_id) + return render_template( "edit_phenotype.html", + sample_list = sample_list, + sample_data = sample_data, publish_xref=_d.get("publish_xref"), phenotype=_d.get("phenotype"), publication=_d.get("publication"), @@ -171,7 +179,7 @@ def update_phenotype(dataset_id: str, name: str): or "" ) phenotype_id = str(data_.get("phenotype-id")) - if not (file_ := request.files.get("file")): + if not (file_ := request.files.get("file")) and data_.get('edited') == "false": flash("No sample-data has been uploaded", "warning") else: create_dirs_if_not_exists( @@ -189,20 +197,31 @@ def update_phenotype(dataset_id: str, name: str): diff_data = {} with database_connection() as conn: headers = ["Strain Name", "Value", "SE", "Count"] - diff_data = remove_insignificant_edits( - diff_data=csv_diff( - base_csv=( - base_csv := get_trait_csv_sample_data( - conn=conn, - trait_name=str(name), - phenotype_id=str(phenotype_id), - ) - ), - delta_csv=(delta_csv := file_.read().decode()), - tmp_dir=TMPDIR, - ), - epsilon=0.001, + base_csv = get_trait_csv_sample_data( + conn=conn, + trait_name=str(name), + phenotype_id=str(phenotype_id), ) + if not (file_) and data_.get('edited') == "true": + delta_csv = create_delta_csv(base_csv, data_) + diff_data = remove_insignificant_edits( + diff_data=csv_diff( + base_csv=base_csv, + delta_csv=delta_csv, + tmp_dir=TMPDIR, + ), + epsilon=0.001, + ) + else: + diff_data = remove_insignificant_edits( + diff_data=csv_diff( + base_csv=base_csv, + delta_csv=(delta_csv := file_.read().decode()), + tmp_dir=TMPDIR, + ), + epsilon=0.001, + ) + invalid_headers = extract_invalid_csv_headers( allowed_headers=headers, csv_text=delta_csv ) @@ -706,3 +725,25 @@ def approve_data(resource_id: str, file_name: str): "warning", ) return redirect(url_for("metadata_edit.list_diffs")) + +def create_delta_csv(base_csv, form_data): + base_csv_lines = base_csv.split("\n") + delta_csv_lines = [base_csv_lines[0]] + + for line in base_csv_lines[1:]: + sample = {} + sample['name'], sample['value'], sample['error'], sample['n_cases'] = line.split(",") + for key in form_data: + if sample['name'] in key: + new_line_items = [sample['name']] + for field in ["value", "error", "n_cases"]: + if form_data.get(field + ":" + sample['name']): + new_line_items.append(form_data.get(field + ":" + sample['name'])) + else: + new_line_items.append(sample[field]) + delta_csv_lines.append(",".join(new_line_items)) + break + else: + delta_csv_lines.append(line) + + return "\n".join(delta_csv_lines)
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