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| -rw-r--r-- | __pycache__/main.cpython-36.pyc | bin | 0 -> 2716 bytes | |||
| -rw-r--r-- | main.py | 98 | ||||
| -rw-r--r-- | pages/index.html | 28 | ||||
| -rw-r--r-- | templates/error.html | 19 | ||||
| -rw-r--r-- | templates/success.html | 24 |
5 files changed, 169 insertions, 0 deletions
diff --git a/__pycache__/main.cpython-36.pyc b/__pycache__/main.cpython-36.pyc new file mode 100644 index 0000000..250c562 --- /dev/null +++ b/__pycache__/main.cpython-36.pyc Binary files differdiff --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 @@ +<!DOCTYPE html> +<html> + <head> + <meta charset="UTF-8"> + <meta name="viewport" content="width=device-width, initial-scale=1"> + <title>Simple Web Uploader for Public SARS-CoV-2 Sequence Resource</title> + </head> + <body> + <h1>Simple Web Uploader for Public SARS-CoV-2 Sequence Resource</h1> + <hr> + <p> + This tool can be used to upload sequenced genomes of SARS-CoV-2 samples to the <a href="https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca">Public SARS-CoV-2 Sequence Resource</a>. Your uploaded sequence will automatically be processed and incorporated into the public pangenome. + </p> + <hr> + <form action="/submit" method="POST" enctype="multipart/form-data"> + <label for="fasta">Select FASTA file for assembled genome (max 1MB):</label> + <br> + <input type="file" id="fasta" name="fasta" accept=".fa,.fasta,.fna"> + <br> + <label for="metadata">Select JSON-LD metadata file following <a href="https://raw.githubusercontent.com/arvados/bh20-seq-resource/master/bh20sequploader/bh20seq-schema.yml">this schema</a> (max 1MB):</label> + <br> + <input type="file" id="metadata" name="metadata" accept=".json"> + <br> + <input type="submit" value="Add to Pangenome"> + </form> + <hr> + </body> +</html> 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 @@ +<!DOCTYPE html> +<html> + <head> + <meta charset="UTF-8"> + <meta name="viewport" content="width=device-width, initial-scale=1"> + <title>Upload Failed</title> + </head> + <body> + <h1>Upload Failed</h1> + <hr> + <p> + Your upload has failed. {{error_message}} + </p> + <p> + <a href="/">Click here to try again.</a> + </p> + <hr> + </body> +</html> 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 @@ +<!DOCTYPE html> +<html> + <head> + <meta charset="UTF-8"> + <meta name="viewport" content="width=device-width, initial-scale=1"> + <title>Upload Successful</title> + </head> + <body> + <h1>Upload Successful</h1> + <hr> + <p> + Your files have been uploaded. They should soon appear as part of the <a href="https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca">Public SARS-CoV-2 Sequence Resource</a>. + </p> + <p> + The upload log was: + </p> + <pre>{{log}}</pre> + <hr> + <p> + <a href="/">Click here to upload more files.</a> + </p> + <hr> + </body> +</html> |