diff options
Diffstat (limited to 'bh20simplewebuploader')
| -rw-r--r-- | bh20simplewebuploader/main.py | 6 | ||||
| -rw-r--r-- | bh20simplewebuploader/templates/form.html | 257 |
2 files changed, 190 insertions, 73 deletions
diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py index bfc7762..383ef84 100644 --- a/bh20simplewebuploader/main.py +++ b/bh20simplewebuploader/main.py @@ -184,15 +184,17 @@ def receive_files(): # We're going to work in one directory per request dest_dir = tempfile.mkdtemp() + # The uploader will happily accept a FASTQ with this name 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) + error_message="You did not include a FASTA or FASTQ file."), 403) try: with open(fasta_dest, 'wb') as out_stream: - copy_with_limit(request.files.get('fasta').stream, out_stream) + # Use a plausible file size limit for a little FASTQ + copy_with_limit(request.files.get('fasta').stream, out_stream, limit=50*1024*1024) except FileTooBigError as e: # Delegate to the 413 error handler return handle_large_file(e) diff --git a/bh20simplewebuploader/templates/form.html b/bh20simplewebuploader/templates/form.html index 2934a7c..986581f 100644 --- a/bh20simplewebuploader/templates/form.html +++ b/bh20simplewebuploader/templates/form.html @@ -1,95 +1,210 @@ <!DOCTYPE html> <html> + <style> + hr { + margin: auto 0; + } + + body { + color: #101010; + } + + h1, h4 { + font-family: 'Roboto Slab', serif; + } + + h1 { + text-align: center; + } + + p { + color: #505050; + font-style: italic; + } + + p, form { + font-family: 'Raleway', sans-serif; + line-height: 1.5; + } + + form h4 { + text-transform: 'uppercase'; + } + + .intro, form { + padding: 20px; + } + + .intro { + margin: 0 auto; + padding: 20px; + } + + .grid-container { + display: grid; + grid-template-columns: repeat(4, 1fr); + grid-template-rows: auto; + row-gap:5px; + grid-template-areas: + "a a b b" + "a a c c" + "a a d d" + "e e e e" + "f f f f"; + grid-auto-flow: column; + } + + .intro { + grid-area: a; + } + + .fasta-file-select { + grid-area: b; + } + + .metadata { + grid-area: c; + } + + #metadata_upload_form_spot { + grid-area: d; + } + + #metadata_fill_form_spot { + grid-area: e; + } + + #metadata_fill_form { + column-count: 4; + margin-top: 0.5em; + column-width: 250px; + } + + .record { + display: flex; + flex-direction: column; + border: solid 1px #808080; + padding: 1em; + background: #F8F8F8; + margin-bottom: 1em; + } + + .record label { + font-size: small; + margin-top: 10px; + } + + .submit { + grid-area: f; + width: 17em; + justify-self: center; + } + </style> + <head> <meta charset="UTF-8"> + <link href="https://fonts.googleapis.com/css2?family=Raleway:wght@500&family=Roboto+Slab&display=swap" rel="stylesheet"> <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> + <section> + <form action="/submit" method="POST" enctype="multipart/form-data" id="main_form" class="grid-container"> + <p class="intro"> + 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> + <div class="fasta-file-select"> + <label for="fasta">Select FASTA file of assembled genome, or FASTQ of reads (max 50MB):</label> + <br> + <input type="file" id="fasta" name="fasta" accept=".fa,.fasta,.fna,.fq" required> + <br> + </div> + + <div class="metadata"> + <label>Select metadata submission method:</label> <br> - <input type="file" id="metadata" name="metadata" accept=".json,.yml,.yaml" required> + <input type="radio" id="metadata_upload" name="metadata_type" value="upload" onchange="setMode()" checked required> + <label for="metadata_upload">Upload metadata file</label> + <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> - </div> - - <div id="metadata_fill_form_spot"> - <div id="metadata_fill_form"> - {% for record in fields %} + + <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"> + {{ record }} + {% for record in fields %} + {% if 'heading' in record %} - <h4>{{ record['heading'] }}</h4> + {% if loop.index > 1 %} + </div> + {% endif %} + <div class="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> + <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> + <input type="{{ record['type'] }}" id="{{ record['id'] }}" name="{{ record['id'] }}" {{ "required" if record['required'] else "" }}> {% endif %} + {% if loop.index == loop.length %} + </div> + {% endif %} {% endfor %} </div> - </div> - - <input type="submit" value="Add to Pangenome"> - </form> + </div> + + + <input class="submit" type="submit" value="Add to Pangenome"> + </form> + </section> <hr> <small><a href="https://github.com/arvados/bh20-seq-resource">Source</a> · 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() + 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> |