diff options
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/wqflask/metadata_edits.py | 90 |
1 files changed, 16 insertions, 74 deletions
diff --git a/wqflask/wqflask/metadata_edits.py b/wqflask/wqflask/metadata_edits.py index c9af0467..9d99f4da 100644 --- a/wqflask/wqflask/metadata_edits.py +++ b/wqflask/wqflask/metadata_edits.py @@ -465,83 +465,25 @@ def reject_data(resource_id: str, file_name: str): @login_required def approve_data(resource_id:str, file_name: str): sample_data = {file_name: str} - with database_connection() as conn: - TMPDIR = current_app.config.get("TMPDIR") - with open(os.path.join(f"{TMPDIR}/sample-data/diffs", - file_name), 'r') as myfile: - sample_data = json.load(myfile) - for modification in ( - modifications := [d for d in sample_data.get("Modifications")]): - if modification.get("Current"): - (strain_name, - value, se, count) = modification.get("Current").split(",") - update_sample_data( - conn=conn, - trait_name=sample_data.get("trait_name"), - strain_name=strain_name, - phenotype_id=int(sample_data.get("phenotype_id")), - value=value, - error=se, - count=count) - - n_deletions = 0 - for deletion in (deletions := [d for d in sample_data.get("Deletions")]): - strain_name, _, _, _ = deletion.split(",") - __deletions, _, _ = delete_sample_data( + conn = MySQLdb.Connect(db=current_app.config.get("DB_NAME"), + user=current_app.config.get("DB_USER"), + passwd=current_app.config.get("DB_PASS"), + host=current_app.config.get("DB_HOST")) + TMPDIR = current_app.config.get("TMPDIR") + with open(os.path.join(f"{TMPDIR}/sample-data/diffs", + file_name), 'r') as myfile: + sample_data = json.load(myfile) + for modification in ( + modifications := [d for d in sample_data.get("Modifications")]): + if modification.get("Current"): + update_sample_data( conn=conn, trait_name=sample_data.get("trait_name"), - strain_name=strain_name, + original_data=modification.get("Original"), + updated_data=modification.get("Current"), + csv_header=sample_data.get("Columns", + "Strain Name,Value,SE,Count"), phenotype_id=int(sample_data.get("phenotype_id"))) - if __deletions: - n_deletions += 1 - # Remove any data that already exists from sample_data deletes - else: - sample_data.get("Deletions").remove(deletion) - - n_insertions = 0 - for insertion in ( - insertions := [d for d in sample_data.get("Additions")]): - (strain_name, - value, se, count) = insertion.split(",") - __insertions, _, _ = insert_sample_data( - conn=conn, - trait_name=sample_data.get("trait_name"), - strain_name=strain_name, - phenotype_id=int(sample_data.get("phenotype_id")), - value=value, - error=se, - count=count) - if __insertions: - n_insertions += 1 - # Remove any data that already exists from sample_data inserts - else: - sample_data.get("Additions").remove(insertion) - if any([sample_data.get("Additions"), - sample_data.get("Modifications"), - sample_data.get("Deletions")]): - 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))) - # Once data is approved, rename it! - os.rename(os.path.join(f"{TMPDIR}/sample-data/diffs", file_name), - os.path.join(f"{TMPDIR}/sample-data/diffs", - f"{file_name}.approved")) - message = "" - if n_deletions: - flash(f"# Deletions: {n_deletions}", "success") - if n_insertions: - flash("# Additions: {len(modifications)", "success") - if len(modifications): - flash("# Modifications: {len(modifications)}", "success") - else: # Edge case where you need to automatically reject the file - os.rename(os.path.join(f"{TMPDIR}/sample-data/diffs", file_name), - os.path.join(f"{TMPDIR}/sample-data/diffs", - f"{file_name}.rejected")) - flash(("Automatically rejecting this file since no " - "changes could be applied."), "warning") n_deletions = 0 for data in [d for d in sample_data.get("Deletions")]: |