diff options
Diffstat (limited to 'bh20simplewebuploader/main.py')
| -rw-r--r-- | bh20simplewebuploader/main.py | 7 |
1 files changed, 5 insertions, 2 deletions
diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py index 81f2ef9..693e4fd 100644 --- a/bh20simplewebuploader/main.py +++ b/bh20simplewebuploader/main.py @@ -3,6 +3,7 @@ import tempfile import shutil import subprocess import os +import sys import re import string import yaml @@ -250,12 +251,14 @@ def receive_files(): error_message="You did not include metadata."), 403) # Try and upload files to Arvados using the sequence uploader CLI - result = subprocess.run(['bh20-seq-uploader', fasta_dest, metadata_dest], + + result = subprocess.run(['python3','bh20sequploader/main.py', fasta_dest, metadata_dest], stdout=subprocess.PIPE, stderr=subprocess.PIPE) if result.returncode != 0: # It didn't work. Complain. - error_message="Upload failed. Uploader returned {} and said:\n{}".format(result.returncode, result.stderr) + error_message="Uploader returned value {} and said:".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. |