From d34374f0e822edd1539ea5de6f8522f2b761de3f Mon Sep 17 00:00:00 2001 From: Peter Amstutz Date: Thu, 16 Jul 2020 14:48:22 -0400 Subject: Improve uploader reporting. Arvados-DCO-1.1-Signed-off-by: Peter Amstutz --- bh20sequploader/main.py | 22 ++++++++++------------ 1 file changed, 10 insertions(+), 12 deletions(-) (limited to 'bh20sequploader') diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py index f744a8c..6049bf9 100644 --- a/bh20sequploader/main.py +++ b/bh20sequploader/main.py @@ -29,11 +29,10 @@ def qc_stuff(metadata, sequence_p1, sequence_p2, do_qc=True): try: log.debug("Checking metadata" if do_qc else "Skipping metadata check") if do_qc and not qc_metadata(metadata.name): - log.warning("Failed metadata qc") + log.warning("Failed metadata QC") failed = True except Exception as e: - log.debug(e) - print(e) + log.exception("Failed metadata QC") failed = True target = [] @@ -45,8 +44,7 @@ def qc_stuff(metadata, sequence_p1, sequence_p2, do_qc=True): target[0] = ("reads_1."+target[0][0][6:], target[0][1]) target[1] = ("reads_2."+target[1][0][6:], target[0][1]) except Exception as e: - log.debug(e) - print(e) + log.exception("Failed sequence QC") failed = True if failed: @@ -82,7 +80,7 @@ def main(): seqlabel = target[0][1] if args.validate: - print("Valid") + log.info("Valid") exit(0) col = arvados.collection.Collection(api_client=api) @@ -91,10 +89,10 @@ def main(): if args.sequence_p2: upload_sequence(col, target[1], args.sequence_p2) - print("Reading metadata") + log.info("Reading metadata") with col.open("metadata.yaml", "w") as f: r = args.metadata.read(65536) - print(r[0:20]) + log.info(r[0:20]) while r: f.write(r) r = args.metadata.read(65536) @@ -118,7 +116,7 @@ def main(): ["portable_data_hash", "=", col.portable_data_hash()]]).execute() if dup["items"]: # This exact collection has been uploaded before. - print("Duplicate of %s" % ([d["uuid"] for d in dup["items"]])) + log.error("Duplicate of %s" % ([d["uuid"] for d in dup["items"]])) exit(1) if args.trusted: @@ -131,9 +129,9 @@ def main(): (seqlabel, properties['upload_user'], properties['upload_ip']), properties=properties, ensure_unique_name=True) - print("Saved to %s" % col.manifest_locator()) - - print("Done") + log.info("Saved to %s" % col.manifest_locator()) + log.info("Done") + exit(0) if __name__ == "__main__": main() -- cgit v1.2.3