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| author | zsloan | 2023-05-10 22:17:13 +0000 |
|---|---|---|
| committer | zsloan | 2023-05-22 17:18:15 +0000 |
| commit | 88d518ed7ce05569b1204136fb314e7c101df8e1 (patch) | |
| tree | 78817e736e7e7b24bbf6fd1db17b6d96c610bbf1 /wqflask | |
| parent | 507f14a120169edbe3c1a76e15466da9d071ef19 (diff) | |
| download | genenetwork2-88d518ed7ce05569b1204136fb314e7c101df8e1.tar.gz | |
Allow for editing values of samples that don't currently have values
Deletions aren't working yet. This is dependent on a GN3 chance that allows the sample_list to be passed to get_trait_csv_sample_data
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/wqflask/metadata_edits.py | 14 |
1 files changed, 9 insertions, 5 deletions
diff --git a/wqflask/wqflask/metadata_edits.py b/wqflask/wqflask/metadata_edits.py index 437a9cb4..06eca376 100644 --- a/wqflask/wqflask/metadata_edits.py +++ b/wqflask/wqflask/metadata_edits.py @@ -196,14 +196,17 @@ def update_phenotype(dataset_id: str, name: str): ) diff_data = {} with database_connection() as conn: + group_name = retrieve_group_name(dataset_id, conn) + sample_list = retrieve_sample_list(group_name) headers = ["Strain Name", "Value", "SE", "Count"] base_csv = get_trait_csv_sample_data( conn=conn, trait_name=str(name), phenotype_id=str(phenotype_id), + sample_list=sample_list, ) if not (file_) and data_.get('edited') == "true": - delta_csv = create_delta_csv(base_csv, data_) + delta_csv = create_delta_csv(base_csv, data_, sample_list) diff_data = remove_insignificant_edits( diff_data=csv_diff( base_csv=base_csv, @@ -726,7 +729,7 @@ def approve_data(resource_id: str, file_name: str): ) return redirect(url_for("metadata_edit.list_diffs")) -def create_delta_csv(base_csv, form_data): +def create_delta_csv(base_csv, form_data, sample_list): base_csv_lines = base_csv.split("\n") delta_csv_lines = [base_csv_lines[0]] @@ -738,9 +741,10 @@ def create_delta_csv(base_csv, form_data): 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]) + if form_data.get(field + ":" + sample['name']).isnumeric(): + new_line_items.append(form_data.get(field + ":" + sample['name'])) + continue + new_line_items.append(sample[field]) delta_csv_lines.append(",".join(new_line_items)) break else: |