diff options
| -rw-r--r-- | bh20sequploader/main.py | 22 | ||||
| -rw-r--r-- | bh20simplewebuploader/main.py | 4 | ||||
| -rw-r--r-- | bh20simplewebuploader/templates/error.html | 2 | ||||
| -rw-r--r-- | bh20simplewebuploader/templates/success.html | 2 |
4 files changed, 14 insertions, 16 deletions
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() diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py index 62b68d9..c814f30 100644 --- a/bh20simplewebuploader/main.py +++ b/bh20simplewebuploader/main.py @@ -445,12 +445,12 @@ def receive_files(): if result.returncode != 0: # It didn't work. Complain. - error_message="Uploader returned value {} and said:".format(result.returncode) + str(result.stderr.decode('utf-8')) + error_message="Uploader returned value {} and said:\n".format(result.returncode) + str(result.stderr.decode('utf-8')) print(error_message, file=sys.stderr) return (render_template('error.html', error_message=error_message), 403) else: # It worked. Say so. - return render_template('success.html', log=result.stdout.decode('utf-8', errors='replace')) + return render_template('success.html', log=result.stderr.decode('utf-8', errors='replace')) finally: shutil.rmtree(dest_dir) diff --git a/bh20simplewebuploader/templates/error.html b/bh20simplewebuploader/templates/error.html index b1d9402..fc08aed 100644 --- a/bh20simplewebuploader/templates/error.html +++ b/bh20simplewebuploader/templates/error.html @@ -15,7 +15,7 @@ </pre> </p> <p> - <a href="/">Click here to try again.</a> + <a href="/upload">Click here to try again.</a> </p> <hr> </body> diff --git a/bh20simplewebuploader/templates/success.html b/bh20simplewebuploader/templates/success.html index 9f0987c..c2302fa 100644 --- a/bh20simplewebuploader/templates/success.html +++ b/bh20simplewebuploader/templates/success.html @@ -9,7 +9,7 @@ <h1>Upload Successful</h1> <hr> <p> - Your files have been uploaded. They should soon appear as output of the <a href="/download">Public SARS-CoV-2 Sequence Resource</a>. + Your files have been uploaded. You can track their <a href="/status">QC status</a>, once validated they will be part of the <a href="/download">Public SARS-CoV-2 Sequence Resource</a>. </p> <p> The upload log was: |