From 7d26be925f37b1f98cac23b018dd1a72fa506a3f Mon Sep 17 00:00:00 2001
From: Adam Novak
Date: Thu, 9 Apr 2020 15:41:29 -0700
Subject: Put back in directory
---
bh20simplewebuploader/main.py | 257 +++++++++++++++++++++++++++
bh20simplewebuploader/templates/error.html | 19 ++
bh20simplewebuploader/templates/form.html | 95 ++++++++++
bh20simplewebuploader/templates/success.html | 24 +++
4 files changed, 395 insertions(+)
create mode 100644 bh20simplewebuploader/main.py
create mode 100644 bh20simplewebuploader/templates/error.html
create mode 100644 bh20simplewebuploader/templates/form.html
create mode 100644 bh20simplewebuploader/templates/success.html
(limited to 'bh20simplewebuploader')
diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py
new file mode 100644
index 0000000..b4e8681
--- /dev/null
+++ b/bh20simplewebuploader/main.py
@@ -0,0 +1,257 @@
+import collections
+import tempfile
+import shutil
+import subprocess
+import os
+import re
+import string
+import yaml
+import urllib.request
+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)
+
+
+def type_to_heading(type_name):
+ """
+ Turn a type name like "sampleSchema" from the metadata schema into a human-readable heading.
+ """
+
+ # Remove camel case
+ decamel = re.sub('([A-Z])', r' \1', type_name)
+ # Split
+ parts = decamel.split()
+ # Capitalize words and remove unwanted components
+ filtered = [part.capitalize() for part in parts if (part.lower() != 'schema' and part != '')]
+ # Reassemble
+ return ' '.join(filtered)
+
+def name_to_label(field_name):
+ """
+ Turn a filed name like "host_health_status" from the metadata schema into a human-readable label.
+ """
+
+ return string.capwords(field_name.replace('_', ' '))
+
+def generate_form(schema):
+ """
+ Linearize the schema and send a bunch of dicts.
+ Each dict either has a 'heading' (in which case we put a heading for a
+ form section in the template) or an 'id', 'label', 'type', and 'required'
+ (in which case we make a form field in the template).
+ """
+
+ # Get the list of form components, one of which is the root
+ components = schema.get('$graph', [])
+
+ # Find the root
+ root_name = None
+ # And also index components by type name
+ by_name = {}
+ for component in components:
+ # Get the name of each
+ component_name = component.get('name', None)
+ if isinstance(component_name, str):
+ # And remember how to map back form it
+ by_name[component_name] = component
+ if component.get('documentRoot', False):
+ # Find whichever one is the root
+ root_name = component_name
+
+
+ def walk_fields(type_name, parent_keys=['metadata'], subtree_optional=False):
+ """
+ Do a traversal of the component tree.
+ Yield a bunch of form item dicts, in order.
+ Form IDs are .-separated keypaths for where they are in the structure.
+ parent_keys is the path of field names to where we are in the root record's document tree.
+ """
+
+ if len(parent_keys) > 1:
+ # First make a heading, if we aren't the very root of the form
+ yield {'heading': type_to_heading(type_name)}
+
+ for field_name, field_type in by_name.get(type_name, {}).get('fields', {}).items():
+ # For each field
+
+ ref_url = None
+ if not isinstance(field_type, str):
+ # If the type isn't a string
+ # See if it has a more info/what goes here URL
+ ref_url = field_type.get('jsonldPredicate', {}).get('_id', None)
+ # Grab out its type field
+ field_type = field_type.get('type', '')
+
+ # Decide if the field is optional (type ends in ?)
+ optional = False
+ if len(field_type) > 0 and field_type[-1] == '?':
+ # It's optional
+ optional = True
+ # Drop the ?
+ field_type = field_type[:-1]
+
+ if field_type in by_name:
+ # This is a subrecord. We need to recurse
+ for item in walk_fields(field_type, parent_keys + [field_name], subtree_optional or optional):
+ yield item
+ else:
+ # We know how to make a string input
+ record = {}
+ record['id'] = '.'.join(parent_keys + [field_name])
+ record['label'] = name_to_label(field_name)
+ record['required'] = not optional and not subtree_optional
+ if ref_url:
+ record['ref_url'] = ref_url
+ if field_type == 'string':
+ record['type'] = 'text' # HTML input type
+ elif field_type == 'int':
+ record['type'] = 'number'
+ else:
+ raise NotImplementedError('Unimplemented field type {} in {} in metadata schema'.format(field_type, type_name))
+ yield record
+
+ 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)
+
+@app.route('/')
+def send_form():
+ """
+ Send the file upload form/front page.
+ """
+
+ return render_template('form.html', fields=FORM_ITEMS)
+
+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)
+
+def parse_input(input_string, html_type):
+ """
+ Parse an input from the given HTML input type into a useful Python type.
+
+ Raise ValueError if something does not parse.
+ Raise NotImplementedError if we forgot to implement a type.
+ """
+
+ if html_type == 'text':
+ return input_string
+ elif html_type == 'number':
+ return int(input_string)
+ else:
+ raise NotImplementedError('Unimplemented input type: {}'.format(html_type))
+
+@app.route('/submit', methods=['POST'])
+def receive_files():
+ """
+ Receive the uploaded files.
+ """
+
+ # We're going to work in one directory per request
+ dest_dir = tempfile.mkdtemp()
+ 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)
+ try:
+ with open(fasta_dest, 'wb') as out_stream:
+ copy_with_limit(request.files.get('fasta').stream, out_stream)
+ except FileTooBigError as e:
+ # Delegate to the 413 error handler
+ return handle_large_file(e)
+
+ if request.form.get('metadata_type', None) == 'upload':
+ if 'metadata' not in request.files:
+ return (render_template('error.html',
+ error_message="You did not include a metadata file."), 403)
+ try:
+ 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)
+ elif request.form.get('metadata_type', None) == 'fill':
+ # Build a metadata dict
+ metadata = {}
+
+ for item in FORM_ITEMS:
+ # Pull all the field values we wanted from the form
+ if 'heading' in item:
+ continue
+
+ if item['id'] in request.form and len(request.form[item['id']]) > 0:
+ # We have this thing. Make a place in the dict tree for it.
+ parts = item['id'].split('.')
+ key = parts[-1]
+ # Remove leading 'metadata'
+ path = parts[1:-1]
+ dest_dict = metadata
+ for parent in path:
+ if parent not in dest_dict:
+ dest_dict[parent] = {}
+ dest_dict = dest_dict[parent]
+
+ try:
+ # Now finally add the item
+ dest_dict[key] = parse_input(request.form[item['id']], item['type'])
+ except ValueError:
+ # We don't like that input
+ return (render_template('error.html',
+ error_message="You provided an unacceptable value for the metadata item {}".format(item['id'])), 403)
+ elif item['required']:
+ return (render_template('error.html',
+ error_message="You omitted the required metadata item {}".format(item['id'])), 403)
+
+ # Now serialize the file with all the items
+ with open(metadata_dest, 'w') as out_stream:
+ yaml.dump(metadata, out_stream)
+ else:
+ return (render_template('error.html',
+ 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],
+ 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/bh20simplewebuploader/templates/error.html b/bh20simplewebuploader/templates/error.html
new file mode 100644
index 0000000..c2ab0a4
--- /dev/null
+++ b/bh20simplewebuploader/templates/error.html
@@ -0,0 +1,19 @@
+
+
+
+
+
+ Upload Failed
+
+
+
+
+
+
diff --git a/bh20simplewebuploader/templates/form.html b/bh20simplewebuploader/templates/form.html
new file mode 100644
index 0000000..4ad41e2
--- /dev/null
+++ b/bh20simplewebuploader/templates/form.html
@@ -0,0 +1,95 @@
+
+
+
+
+
+ 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.
+