From 414c308b8860d1b20481a2ec3b2f6381e4f6061b Mon Sep 17 00:00:00 2001
From: Adam Novak
Date: Wed, 8 Apr 2020 14:11:39 -0700
Subject: Initial commit of working frontend
---
__pycache__/main.cpython-36.pyc | Bin 0 -> 2716 bytes
main.py | 98 ++++++++++++++++++++++++++++++++++++++++
pages/index.html | 28 ++++++++++++
templates/error.html | 19 ++++++++
templates/success.html | 24 ++++++++++
5 files changed, 169 insertions(+)
create mode 100644 __pycache__/main.cpython-36.pyc
create mode 100644 main.py
create mode 100644 pages/index.html
create mode 100644 templates/error.html
create mode 100644 templates/success.html
diff --git a/__pycache__/main.cpython-36.pyc b/__pycache__/main.cpython-36.pyc
new file mode 100644
index 0000000..250c562
Binary files /dev/null and b/__pycache__/main.cpython-36.pyc differ
diff --git a/main.py b/main.py
new file mode 100644
index 0000000..630669c
--- /dev/null
+++ b/main.py
@@ -0,0 +1,98 @@
+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)
+
+
+
+
diff --git a/pages/index.html b/pages/index.html
new file mode 100644
index 0000000..2269791
--- /dev/null
+++ b/pages/index.html
@@ -0,0 +1,28 @@
+
+
+
+
+
+ Simple Web Uploader for Public SARS-CoV-2 Sequence Resource
+
+
+
Simple Web Uploader for Public SARS-CoV-2 Sequence Resource
+
+
+ This tool can be used to upload sequenced genomes of SARS-CoV-2 samples to the Public SARS-CoV-2 Sequence Resource. Your uploaded sequence will automatically be processed and incorporated into the public pangenome.
+