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. +

+
+
+ +
+ +
+ +
+ +
+ +
+
+ + diff --git a/templates/error.html b/templates/error.html new file mode 100644 index 0000000..c2ab0a4 --- /dev/null +++ b/templates/error.html @@ -0,0 +1,19 @@ + + + + + + Upload Failed + + +

Upload Failed

+
+

+ Your upload has failed. {{error_message}} +

+

+ Click here to try again. +

+
+ + diff --git a/templates/success.html b/templates/success.html new file mode 100644 index 0000000..1be7861 --- /dev/null +++ b/templates/success.html @@ -0,0 +1,24 @@ + + + + + + Upload Successful + + +

Upload Successful

+
+

+ Your files have been uploaded. They should soon appear as part of the Public SARS-CoV-2 Sequence Resource. +

+

+ The upload log was: +

+ 
{{log}}
+
+

+ Click here to upload more files. +

+
+ + -- cgit v1.2.3