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authorPjotr Prins2020-04-12 12:51:24 -0500
committerGitHub2020-04-12 12:51:24 -0500
commit42ee1f77ca4a6e3a9c7dfc15e69b9de43f801c59 (patch)
treee756eb01c166ab99f00019f997c8a6a67335412a
parent0005a2544bdc48cd2ddc85e6cd6e0ddf51cc71df (diff)
parenta764f0496f47f5c93f2a6915d00c8a1e89df0712 (diff)
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Merge pull request #8 from adamnovak/ui-improvements
Clarify support for FASTQ
Diffstat
-rw-r--r--README.md8
-rw-r--r--bh20simplewebuploader/main.py6
-rw-r--r--bh20simplewebuploader/templates/form.html257
3 files changed, 194 insertions, 77 deletions
diff --git a/README.md b/README.md
index 8a5a6dd..db4fe52 100644
--- a/README.md
+++ b/README.md
@@ -59,7 +59,7 @@ sudo apt install -y virtualenv git libcurl4-openssl-dev build-essential python3-
pip3 install --user git+https://github.com/arvados/bh20-seq-resource.git@master
```
-3. **Make sure the tool is on your `PATH`.** THe `pip3` command will install the uploader in `.local/bin` inside your home directory. Your shell may not know to look for commands there by default. To fix this for the terminal you currently have open, run:
+3. **Make sure the tool is on your `PATH`.** The `pip3` command will install the uploader in `.local/bin` inside your home directory. Your shell may not know to look for commands there by default. To fix this for the terminal you currently have open, run:
```sh
export PATH=$PATH:$HOME/.local/bin
@@ -126,10 +126,10 @@ For running/developing the uploader with GNU Guix see [INSTALL.md](./doc/INSTALL
# Usage
-Run the uploader with a FASTA file and accompanying metadata file in [JSON-LD format](https://json-ld.org/):
+Run the uploader with a FASTA or FASTQ file and accompanying metadata file in JSON or YAML:
```sh
-bh20-seq-uploader example/sequence.fasta example/metadata.json
+bh20-seq-uploader example/sequence.fasta example/metadata.yaml
```
## Workflow for Generating a Pangenome
@@ -174,7 +174,7 @@ pip3 install gunicorn
gunicorn bh20simplewebuploader.main:app
```
-This runs on [http://127.0.0.1:8000/](http://127.0.0.1:8000/) by default, but can be adjusted with various [gunicorn options](http://docs.gunicorn.org/en/latest/run.html#commonly-used-arguments)
+This runs on [http://127.0.0.1:8000/](http://127.0.0.1:8000/) by default, but can be adjusted with various [gunicorn options](http://docs.gunicorn.org/en/latest/run.html#commonly-used-arguments).
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> &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()
+ 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>
generated by cgit v1.2.3 (git 2.45.2) at 2024-11-22 22:54:41 +0000