1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
|
<!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;
}
@media only screen and (max-device-width: 480px) {
.grid-container {
display: flex;
flex-direction: column;
}
}
</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>
<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 for assembled genome (max 1MB):</label>
<br>
<input type="file" id="fasta" name="fasta" accept=".fa,.fasta,.fna" required>
<br>
</div>
<div class="metadata">
<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>
<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 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 %}
{% 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>
<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 class="submit" type="submit" value="Add to Pangenome">
</form>
</section>
<hr>
<small><a href="https://github.com/adamnovak/bh20-simple-web-uploader">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()
</script>
</body>
</html>
|
