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add last debugging output via click instead of logger #694

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merged 1 commit into from
Sep 13, 2024
Merged

add last debugging output via click instead of logger #694

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5 changes: 3 additions & 2 deletions bin/validate.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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))
Expand Down Expand Up @@ -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])
Expand Down
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