Put back in directory

4 files changed, 395 insertions, 0 deletions

diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py
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+++ b/bh20simplewebuploader/main.py
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+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
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+++ b/bh20simplewebuploader/templates/error.html
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+<!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/bh20simplewebuploader/templates/form.html b/bh20simplewebuploader/templates/form.html
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+++ b/bh20simplewebuploader/templates/form.html
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+<!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" id="main_form">
+            <label for="fasta">Select FASTA file for assembled genome (max 1MB):</label>
+            <br>
+            <input type="file" id="fasta" name="fasta" accept=".fa,.fasta,.fna" required>
+            <br>
+            
+            <label>Select metadata submission method:</label>
+            <br>
+            <input type="radio" id="metadata_upload" name="metadata_type" value="upload" onchange="setMode()" checked required>
+            <label for="metadata_upload">Upload metadata file</label>
+            <br>
+            <input type="radio" id="metadata_form" name="metadata_type" value="fill" onchange="setMode()" required>
+            <label for="metadata_form">Fill in metadata manually</label>
+            <br>
+            
+            <div id="metadata_upload_form_spot">
+                <div id="metadata_upload_form">
+                    <label for="metadata">Select JSON or YAML metadata file following <a href="https://github.com/arvados/bh20-seq-resource/blob/master/bh20sequploader/bh20seq-schema.yml" target="_blank">this schema</a> (<a href="https://github.com/arvados/bh20-seq-resource/blob/master/example/metadata.yaml" target="_blank">Example 1</a>, <a href="https://github.com/arvados/bh20-seq-resource/blob/master/example/minimal_example.yaml" target="_blank">Example 2</a>, max 1MB):</label>
+                    <br>
+                    <input type="file" id="metadata" name="metadata" accept=".json,.yml,.yaml" required>
+                    <br>
+                </div>
+            </div>
+            
+            <div id="metadata_fill_form_spot">
+                <div id="metadata_fill_form">
+                    {% for record in fields %}
+                        {% if 'heading' in record %}
+                            <h4>{{ record['heading'] }}</h4>
+                        {% else %}
+                            <label for="{{ record['id'] }}">
+                                {{ record['label'] }}
+                                {{ "*" if record['required'] else "" }}
+                                {% if 'ref_url' in record %}
+                                    <a href="{{ record['ref_url'] }}" title="More Info" target="_blank">?</a>
+                                {% endif %}
+                            </label>
+                            <br>
+                            <input type="{{ record['type'] }}" id="{{ record['id'] }}" name="{{ record['id'] }}" {{ "required" if record['required'] else "" }}>
+                            <br>
+                        {% endif %}
+                    {% endfor %}
+                </div>
+            </div>
+            
+            <input type="submit" value="Add to Pangenome">
+        </form>
+        <hr>
+        <small><a href="https://github.com/adamnovak/bh20-simple-web-uploader">Source</a> &middot; Made for <a href="https://github.com/virtual-biohackathons/covid-19-bh20">COVID-19-BH20</a></small>
+        <script type="text/javascript">
+            let uploadForm = document.getElementById('metadata_upload_form')
+            let uploadFormSpot = document.getElementById('metadata_upload_form_spot')
+            let fillForm = document.getElementById('metadata_fill_form')
+            let fillFormSpot = document.getElementById('metadata_fill_form_spot')
+            
+            function setUploadMode() {
+                // Make the upload form the one in use
+                uploadFormSpot.appendChild(uploadForm)
+                fillFormSpot.removeChild(fillForm)
+            }
+            
+            function setFillMode() {
+                // Make the fillable form the one in use
+                uploadFormSpot.removeChild(uploadForm)
+                fillFormSpot.appendChild(fillForm)
+            }
+            
+            function setMode() {
+                // Pick mode based on radio
+                if (document.getElementById('metadata_upload').checked) {
+                    setUploadMode()
+                } else {
+                    setFillMode()
+                }
+            }
+            
+            // Start in mode appropriate to selected form item
+            setMode()
+        </script>
+    </body>
+</html>
diff --git a/bh20simplewebuploader/templates/success.html b/bh20simplewebuploader/templates/success.html
new file mode 100644
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--- /dev/null
+++ b/bh20simplewebuploader/templates/success.html
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+<!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>