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SDRF-PROMA-Template.html
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SDRF-PROMA-Template.html
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<!DOCTYPE html>
<html>
<head>
<base target="_top">
<script src="https://code.jquery.com/jquery-1.9.1.js"></script>
<style>
body,
html {
font-family: 'Roboto', sans-serif;
font-size: 14px;
color: #666666;
padding: 10px;
}
p {
margin: 0;
}
.branding-above {
padding: 0;
top: 0;
}
.sidebar {
width: 94%;
}
.hidden {
display: none;
}
.error {
padding-top: 10px;
color: #e74c3c;
}
.branding-below {
bottom: 56px;
position: fixed;
background-color: #fff;
top: 0;
}
.branding-text {
left: 7px;
position: relative;
font-size: .9em;
top: 3px;
}
.PROMA-header {
padding-top: 5px;
height: 75px;
}
.col-contain {
overflow: hidden;
}
h3 {
margin-left: 5px;
margin-top: 0px;
margin-bottom: 0px;
text-align: left;
font-size: 1em;
padding: 5px 6px;
border-radius: 4px;
}
.col-one {
float: left;
width: 50%;
}
.logo {
vertical-align: middle;
width: 175px;
}
.pull-left {
float: left;
}
.pull-right {
float: right;
}
.width-100 {
width: 100%;
}
#parameter {
width: 100%;
margin-bottom: 8px;
padding: 4px 6px;
border-radius: 4px;
border: 1px solid #2f3640;
}
#template {
width: 100%;
margin-bottom: 8px;
padding: 4px 6px;
border-radius: 4px;
border: 1px solid #2f3640;
}
.search-results ul {
list-style: none;
margin: 0px;
text-align: left;
}
.term-info {
float: left;
width: 70%;
margin: 3%;
}
.term-buttons {
float: right;
width: 21%;
}
.search-results ul li {
padding: 4px;
font-weight: bolder;
font-size: .9em;
}
.search-results ul li a {
color: #5A9C43;
text-decoration: none;
}
.ontology-abbr {
text-align: left;
font-weight: bolder;
font-size: 1em;
color: #414241;
}
.ontology-obo_id {
text-align: left;
font-weight: bolder;
font-size: .8em;
color: #95A5A5;
}
.term-count {
text-align: right;
padding: 7px 5px;
background-color: #4FBA6F;
color: #fff;
border-radius: 50%;
font-size: .8em;
}
.btn-green {
text-align: center;
padding: 5px 8px;
border-radius: 4px;
border: none;
background-color: #5A9C43;
width: 100%;
color: white;
display: block;
cursor: pointer;
}
.bth-green:hover {
background-color: #4FBA6F;
}
ul {
-webkit-padding-start: 5px;
}
.term-button button {
background-color: #ecf0f1;
color: #414241;
padding: 5px 8px;
border: none;
cursor: pointer;
display: block;
}
.clearfix:after {
content: " ";
/* Older browser do not support empty content */
visibility: hidden;
display: block;
height: 0;
clear: both;
}
#spinner {
margin-top: 60px;
text-align: center;
}
#spinner p {
font-weight: bolder;
color: color: #414241;
}
#search-text {
border: 1px solid #2f3640;
padding: 5px 6px;
border-radius: 4px;
}
#MT-text {
border: 1px solid #2f3640;
padding: 5px 6px;
border-radius: 4px;
}
#TA-text {
border: 1px solid #2f3640;
padding: 5px 6px;
border-radius: 4px;
.footer {
text-align: center;
position: float;
width: 242px;
bottom: 12px;
}
</style>
</head>
<body>
<div class="PROMA-header" align="center">
<img src="https://raw.githubusercontent.com/bigbio/proma/main/figures/logo_with_name.png" width="225" height="60">
</div>
<form>
<div class="block col-contain" style="margin-top:20px">
<div class="col-two">
<label style="font-size: 1em; color: #414241">Select Template</label>
<select id="template" class="width-100">
<option value="cell-line" selected>cell-line</option>
<option value="default">default</option>
<option value="human">human</option>
<option value="nonvertebrates">nonvertebrates</option>
<option value="plants">plants</option>
<option value="vertebrates">vertebrates</option>
</select>
</div>
<div>
<h style="font-size: .85em; color: #2f3640"><b>* Select a Template: </b>Selecting the template and applying it will overwrite the first line of the current sheet!
</h>
</div>
<div>
<button class="btn-green" style="width: 100%" onclick="selectTemplate(); return false;">Apply</button>
</div>
<br />
<div class="col-two">
<div id="ontomaton-search-panel">
<label for="MT-text" style="font-size: 1em; color: #414241">Modification Type [MT]</label>
<input type="text" name="MT-text" id="MT-text" value="" placeholder="e.g. Variable">
</div>
<br />
<div id="ontomaton-search-panel">
<label for="TA-text" style="font-size: 1em; color: #414241">Target Amino acid [TA]</label>
<input type="text" name="TA-text" id="TA-text" value="" placeholder="e.g. M">
</div>
<br />
<div id="ontomaton-search-panel">
<label for="search-text" style="font-size: 1em; color: #414241">Name OR Accession [NT][AC]</label>
<input type="text" name="search-text" id="search-text" value="" placeholder="e.g. Oxidation"> *
</div>
<br />
<div class="col-two">
<label style="font-size: 1em; color: #414241">Parameter Type</label>
<select id="parameter" class="width-100">
<option value="modification parameters" selected>modification parameters</option>
<option value="instrument">instrument</option>
<option value="cleavage agent details">cleavage agent details</option>
<option value="label">label</option>
</select>
</div>
</div>
</div>
<div>
<h style="font-size: .85em; color: #2f3640"><b>* Annotation: </b>When the first row is complete, search, click on the cell to determine the range and insert.
</h>
<br />
</div>
<div class="block" id="button-bar">
<button class="btn-green" id="run-search" style="width: 100%">Search</button>
</div>
<div id="search-results" class="block form-group search-results"
style="height:50vh; width:100%; overflow: scroll; padding-top: 5px">
</div>
</form>
<br />
<div class="footer" align="center">
<img alt="Add-on logo" class="logo" src="//isa-tools.org/OntoMaton/figures/ontomaton-search.png"><br />
<span class="gray branding-text">Powered by <a href="http://isa-tools.org/OntoMaton" target="_blank">OntoMaton</a>
</span>
</div>
<script>
$(function () {
$('#run-search').click(runSearch);
});
function replaceAll(oldStr, removeStr, replaceStr, caseSenitivity) {
var cs = "gi"
if (caseSenitivity == 1) {
cs = "g";
}
var myPattern = new RegExp(removeStr, cs);
return oldStr.replace(myPattern, replaceStr);
}
function insertTerm(term_id) {
var MT = $('input[name=MT-text]').val();
var TA = $('input[name=TA-text]').val();
var parameter = $('#parameter').val();
google.script.run
.withSuccessHandler(
function (result, element) {
console.log("success")
}).withFailureHandler(
function (msg, element) {
console.log("failure")
showError(msg, $('#button-bar'));
element.disabled = false;
})
.withUserObject(this)
.handleSDRFInsertion(term_id,MT,TA,parameter);
}
function selectTemplate() {
var template = $('#template').val();
google.script.run
.withSuccessHandler(
function (result, element) {
console.log("success")
}).withFailureHandler(
function (msg, element) {
console.log("failure")
showError(msg, $('#button-bar'));
element.disabled = false;
})
.withUserObject(this)
.handleTemplateInsertion(template);
}
function runSearch() {
var term = $('input[name=search-text]').val();
var MT = $('input[name=MT-text]').val();
var TA = $('input[name=TA-text]').val();
var parameter = $('#parameter').val();
if(parameter == 'modification parameters'){
if(term == '' || TA == ''){
showError('NT and TA must be filled in!', $('#button-bar'));
return
}
}
else if(parameter == 'instrument' || parameter == 'cleavage agent details' || parameter == 'label'){
if(term == ''){
showError('NT must be filled in!.', $('#button-bar'));
return
}
else if(MT != '' || TA != ''){
showError('Only NT or AC is required!', $('#button-bar'));
return
}
}
this.disabled = true;
$('#search-results').html('<div id="spinner"><img src="//s-media-cache-ak0.pinimg.com/originals/0a/59/71/0a59718a5ee79a0558930ca9907c0659.gif" width="70px"/><p>Searching...</p></div>');
$('#error').remove();
var service = "ols";
google.script.run
.withSuccessHandler(
function (result, element) {
// process results
var html = '<div id="accordion" class="accordion">';
console.log(result);
if (result) {
Object.keys(result).sort().forEach(function(ontology_abbr) {
var ontology = result[ontology_abbr]; //ontology is the whole result that contains all the ontology_abbr
Object.keys(ontology["terms"]).forEach(function(term_idx) {
var term = ontology["terms"][term_idx];
var label = term["label"];
var MT = $('input[name=MT-text]').val();
var TA = $('input[name=TA-text]').val();
var parameter = $('#parameter').val();
if(parameter == 'modification parameters'){
if(MT == ''){
var modification = "NT=" + label + ";TA=" + TA + ";AC=" + term["ontology-obo_id"]
}
else{
var modification = "NT=" + label + ";MT=" + MT + ";TA=" + TA + ";AC=" + term["ontology-obo_id"];
}
if(ontology_abbr == "UNIMOD" || ontology_abbr == "MOD"){
html += '<h3><span class="ontology-abbr">' + ontology_abbr + '</span> - <span class="ontology-obo_id">' + term["ontology-obo_id"] + '</span></h3>' +
'<div><ul>'+
'<li>' +
'<div class="term-info">' +
'<a href="' + term["url"] + '" target="_blank">' + modification + '</a>' +
'</div>' +
'<div class="term-button"><button onclick="insertTerm(\'' + term["id"] + '\'); return false;">Insert</button></div>' +
'<div class="clearfix"></div>' +
'</li>';
}
}
if(parameter == 'instrument' || parameter == 'cleavage agent details' || parameter == 'label'){
var modification = "NT=" + label + ";AC=" + term["ontology-obo_id"];
if(ontology_abbr == "MS" || ontology_abbr == "PRIDE"){
html += '<h3><span class="ontology-abbr">' + ontology_abbr + '</span> - <span class="ontology-obo_id">' + term["ontology-obo_id"] + '</span></h3>' +
'<div><ul>'+
'<li>' +
'<div class="term-info">' +
'<a href="' + term["url"] + '" target="_blank">' + modification + '</a>' +
'</div>' +
'<div class="term-button"><button onclick="insertTerm(\'' + term["id"] + '\'); return false;">Insert</button></div>' +
'<div class="clearfix"></div>' +
'</li>';
}
}
});
html += '</ul></div>';
});
} else {
html += "<p>Sorry, no results were found matching your query...</p>";
}
html += "</div>";
$('#search-results').html(html);
element.disabled = false;
$('#spinner').addClass("hidden");
})
.withFailureHandler(
function (msg, element) {
$('#spinner').addClass("hidden");
showError(msg, $('#button-bar'));
element.disabled = false;
})
.withUserObject(this)
.runSearchSDRF(term);
return false;
}
function showError(msg, element) {
var div = $('<div id="error" class="error">' + msg + '</div>');
$(element).after(div);
}
</script>
</body>
</html>