diff options
Diffstat (limited to 'bh20simplewebuploader/main.py')
| -rw-r--r-- | bh20simplewebuploader/main.py | 21 |
1 files changed, 17 insertions, 4 deletions
diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py index bfc7762..f5324a5 100644 --- a/bh20simplewebuploader/main.py +++ b/bh20simplewebuploader/main.py @@ -3,12 +3,18 @@ import tempfile import shutil import subprocess import os +import sys import re import string import yaml import urllib.request from flask import Flask, request, redirect, send_file, send_from_directory, render_template +import os.path + +if not os.path.isfile('bh20sequploader/mainx.py'): + print("WARNING: run FLASK from the root of the source repository!", file=sys.stderr) + app = Flask(__name__, static_url_path='/static', static_folder='static') # Limit file upload size. We shouldn't be working with anything over 1 MB; these are small genomes. @@ -126,6 +132,7 @@ def generate_form(schema): return list(walk_fields(root_name)) + # At startup, we need to load the current metadata schema so we can make a form for it METADATA_SCHEMA = yaml.safe_load(urllib.request.urlopen('https://raw.githubusercontent.com/arvados/bh20-seq-resource/master/bh20sequploader/bh20seq-schema.yml')) FORM_ITEMS = generate_form(METADATA_SCHEMA) @@ -184,15 +191,17 @@ def receive_files(): # We're going to work in one directory per request dest_dir = tempfile.mkdtemp() + # The uploader will happily accept a FASTQ with this name fasta_dest = os.path.join(dest_dir, 'fasta.fa') metadata_dest = os.path.join(dest_dir, 'metadata.json') try: if 'fasta' not in request.files: return (render_template('error.html', - error_message="You did not include a FASTA file."), 403) + error_message="You did not include a FASTA or FASTQ file."), 403) try: with open(fasta_dest, 'wb') as out_stream: - copy_with_limit(request.files.get('fasta').stream, out_stream) + # Use a plausible file size limit for a little FASTQ + copy_with_limit(request.files.get('fasta').stream, out_stream, limit=50*1024*1024) except FileTooBigError as e: # Delegate to the 413 error handler return handle_large_file(e) @@ -247,12 +256,16 @@ 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], + + cmd = ['python3','bh20sequploader/main.py', fasta_dest, metadata_dest] + print(" ".join(cmd),file=sys.stderr) + result = subprocess.run(cmd, 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. |