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import tempfile
import shutil
import subprocess
import os
from flask import Flask, request, redirect, send_file, send_from_directory, render_template
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.
# We will enforce the limit ourselves and set a higher safety limit here.
app.config['MAX_CONTENT_LENGTH'] = 50 * 1024 * 1024
# When a file is too big we get a 413.
@app.errorhandler(413)
def handle_large_file(e):
return (render_template('error.html',
error_message="One of your files is too large. The maximum file size is 1 megabyte."), 413)
@app.route('/')
def send_form():
"""
Send the file upload form/front page.
"""
return send_from_directory('pages', 'index.html')
class FileTooBigError(RuntimeError):
"""
Raised when the user gives a file that is too large.
"""
pass
def copy_with_limit(in_file, out_file, limit=1024*1024):
"""
Copy a file stream, and raise FileTooBigError if the file is too big.
"""
bytes_used = 0
buf_size = 65536
buf = in_file.read(buf_size)
bytes_used += len(buf)
while buf:
if bytes_used > limit:
raise FileTooBigError('Hit file length limit')
out_file.write(buf)
buf = in_file.read(buf_size)
bytes_used += len(buf)
@app.route('/submit', methods=['POST'])
def recieve_files():
"""
Recieve the uploaded files.
"""
# We're going to work in one directory per request
dest_dir = tempfile.mkdtemp()
try:
print(request)
print(request.files)
if 'fasta' not in request.files:
return (render_template('error.html',
error_message="You did not include a FASTA file."), 403)
if 'metadata' not in request.files:
return (render_template('error.html',
error_message="You did not include a metadata file."), 403)
fasta_dest = os.path.join(dest_dir, 'fasta.fa')
metadata_dest = os.path.join(dest_dir, 'metadata.json')
try:
with open(fasta_dest, 'wb') as out_stream:
copy_with_limit(request.files.get('fasta').stream, out_stream)
with open(metadata_dest, 'wb') as out_stream:
copy_with_limit(request.files.get('metadata').stream, out_stream)
except FileTooBigError as e:
# Delegate to the 413 error handler
return handle_large_file(e)
# Try and upload files to Arvados
result = subprocess.run(['bh20-seq-uploader', 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)
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'))
finally:
shutil.rmtree(dest_dir)
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