From 9fdeca0b0ce4d82a1dc178d67ff0eb2b0ed09498 Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Fri, 13 Sep 2024 15:10:05 -0700 Subject: [PATCH] add last debugging output --- bin/validate.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/bin/validate.py b/bin/validate.py index 535e1ebb..abb479fc 100755 --- a/bin/validate.py +++ b/bin/validate.py @@ -281,7 +281,7 @@ def produce_gaf(dataset, source_gaf, ontology_graph, gpipaths=None, paint=False, report_json_path = os.path.join(os.path.split(source_gaf)[0], "{}.report.json".format(dataset)) click.echo("About to write json report to {}".format(report_json_path)) with open(report_json_path, "w") as report_json: - logger.click.echo("Opened for writing {}".format(report_json_path)) + click.echo("Opened for writing {}".format(report_json_path)) report_json.write(json.dumps(parser.report.to_report_json(), indent=4)) click.echo("json {} written out".format(report_markdown_path)) @@ -760,12 +760,13 @@ def produce(ctx, group, metadata_dir, gpad, gpad_gpi_output_version, ttl, target ontology_graph, gpipaths=gpi_list, base_download_url=base_download_url, rule_metadata=rule_metadata, replace_existing_files=not skip_existing_files, gaf_output_version=gaf_output_version) + click.echo("Merged mixin datasets into the final GAF...{}".format(end_gaf)) click.echo("Pre-isoform fix gaf file...{}".format(end_gaf)) click.echo("Executing the isoform fixing step in validate.produce...") # run the resulting gaf through one last parse and replace, to handle the isoforms # see: https://github.com/geneontology/go-site/issues/2291 - click.echo("path to end gaf _temp.gaf") + click.echo("path to end gaf _temp.gaf: {}".format(end_gaf)) click.echo(os.path) click.echo(os.path.split(end_gaf)[0])