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STATIC.html
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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
<meta name="description" content="">
<meta name="author" content="">
<title>Grassroots Infrastructure</title>
<!-- Bootstrap core CSS -->
<link href="vendor/bootstrap/css/bootstrap.min.css" rel="stylesheet">
<!-- Custom fonts for this template -->
<link href="vendor/font-awesome/css/font-awesome.min.css" rel="stylesheet" type="text/css">
<!-- Custom styles for this template -->
<link href="css/site.css" rel="stylesheet">
<!-- Global site tag (gtag.js) - Google Analytics -->
<script async src="https://www.googletagmanager.com/gtag/js?id=UA-21666189-16"></script>
<script>
window.dataLayer = window.dataLayer || [];
function gtag() {
dataLayer.push(arguments);
}
gtag('js', new Date());
gtag('config', 'UA-21666189-16');
</script>
<style>
/* CSS styles here */
.tabs {
list-style-type: none;
padding: 0;
margin: 0;
display: flex;
flex-wrap: wrap;
justify-content: center; /* Centers tabs if they don't fill the entire width */
border-bottom: 2px solid #2C3E50; /* Adds a border below the tabs for better visual separation */
}
.tabs li {
display: inline-block;
margin-right: 10px;
padding: 10px 15px;
background-color: #2C3E50;
color: #fff;
cursor: pointer;
border-radius: 5px 5px 0 0; /* Rounded corners on the top */
transition: background-color 0.3s ease; /* Smooth background color transition for interaction */
}
.tabs li.active, .tabs li:hover {
background-color: #1D2E40; /* Darker shade on hover/active */
}
.tab-content div {
display: none;
padding: 20px;
border: 1px solid #ddd;
background-color: #f9f9f9; /* Light background for the content for better readability */
margin-top: -1px; /* Aligns the content box directly under the tabs */
}
.tab-content div p {
color: #2C3E50; /* Darker color for better visibility */
}
.tab-content div.active {
display: block;
}
.modal {
display: none; /* Hidden by default */
position: fixed; /* Stay in place */
z-index: 1; /* Sit on top */
left: 0;
top: 0;
width: 100%; /* Full width */
height: 100%; /* Full height */
overflow: auto; /* Enable scroll if needed */
background-color: rgba(0,0,0,0.4); /* Black w/ opacity */
}
.modal-content {
background-color: #fefefe;
margin: 15% auto; /* Adjusted for better vertical alignment */
padding: 20px;
border: 1px solid #888;
width: 90%; /* Increased width */
max-width: 1000px; /* Adjust max-width as needed */
overflow: hidden; /* Ensures the content doesn't overflow the modal box */
}
.close-button {
color: #aaa;
float: right;
font-size: 28px;
font-weight: bold;
}
.close-button:hover,
.close-button:focus {
color: black;
text-decoration: none;
cursor: pointer;
}
@media (max-width: 600px) {
.modal-content {
width: 100%;
max-width: none;
margin: 10% auto; /* Adjust margin for smaller screens */
}
}
#header-section .explanatory-text h2 {
font-size: 28px;
color: #2C3E50;
margin-bottom: 20px;
}
#header-section .explanatory-text p {
font-size: 25px;
color: #2C3E50;
margin-bottom: 30px;
}
.darker {
font-size: 18px; /* size of hyperlink text */
}
</style>
</head>
<body id="page-top">
<!-- Modal -->
<div id="resultsModal" class="modal">
<div class="modal-content">
<span class="close-button">×</span>
<div class="tabs"></div>
<div class="tab-content"></div>
</div>
</div>
<!-- Navigation -->
<nav class="navbar navbar-expand-lg navbar-light fixed-top" id="mainNav">
<div class="container">
<a class="navbar-brand js-scroll-trigger" href="#page-top"
style="text-transform: none ! important;">Grassroots
Infrastructure</a>
<button class="navbar-toggler navbar-toggler-right" type="button" data-toggle="collapse"
data-target="#navbarResponsive" aria-controls="navbarResponsive" aria-expanded="false"
aria-label="Toggle navigation">
Menu
<i class="fa fa-bars"></i>
</button>
<div class="collapse navbar-collapse" id="navbarResponsive">
<ul class="navbar-nav ml-auto">
<li class="nav-item">
<a class="nav-link js-scroll-trigger" href="#services">Services</a>
</li>
<li class="nav-item">
<a class="nav-link js-scroll-trigger" href="#data">Data</a>
</li>
<li class="nav-item">
<a class="nav-link js-scroll-trigger" href="docs/">Docs</a>
</li>
<li class="nav-item">
<a class="nav-link js-scroll-trigger" href="dfw">DFW</a>
</li>
<li class="nav-item">
<a class="nav-link js-scroll-trigger" href="service/search">Search</a>
</li>
</ul>
<img class="navbar-nav navbar-right" style="height:50px;margin-left:50px;" src="img/logo-white.png" />
</div>
</div>
</nav>
<!-- Search Box Section -->
<header id="header-section" class="masthead"
style="background-image: url('img/nature-2571086_1920_40_opac.png');background-position: center; text-align: justify ! important; padding-top: 0;">
<div class="container">
<section id="search" style="padding-top: 140px;">
<div class="explanatory-text" style="margin-bottom: 20px; color: #2C3E50;">
<p>The Grassroots Infrastructure project aims to create an easily-deployable suite of computing middleware tools to help users and developers gain access to scientific data infrastructure that can easily be interconnected.
With the data-generative approaches that are increasingly common in modern life
science research, it is
vital
that the data and metadata produced by these efforts can be shared and reused. The Grassroots
Infrastructure
project wraps up industry-standard software tools with a consistent API that can be federated on a
number of
levels. This means institutions and groups can deploy a simple lightweight virtual machine, expose local
data, connect up any existing data services, and federate their instance of the Grassroots with others
out-of-the-box.</p>
</div>
<div class="container">
<div class="row">
<div class="col-lg-8 mx-auto text-center">
<!-- Explanatory Text Above the Search Box
<div class="explanatory-text" style="margin-bottom: 20px; color: #2C3E50;">
<p>Use the search box below to explore our database. You can search by keyword and refine your search by selecting a specific category.</p>
</div>-->
<!-- Search Box -->
<div class="search-box" style="border: 2px solid #2C3E50; padding: 20px; border-radius: 5px; background-color: rgba(255, 255, 255, 0.9); box-shadow: 0 4px 8px rgba(0, 0, 0, 0.1);">
<!-- Search box title and subtitle -->
<div class="search-box-title" style="text-align: left; margin-bottom: 15px;">
<h4 style="margin: 0; color: #2C3E50;">Grassroots Search</h4>
<p style="margin: 0; color: #2C3E50; font-size: 14px;">Explore our system</p>
</div>
<!-- Search fields -->
<div class="row">
<div class="col-sm-8">
<input type="text" id="searchInput" class="form-control" placeholder="Enter search keyword...">
</div>
<div class="col-sm-4">
<select id="categorySelect" class="form-control">
<option value="All">All</option>
<option value="Dataset">Dataset</option>
<option value="Service">Service</option>
<option value="Field Trial">Field Trial</option>
<option value="Study">Study</option>
<option value="Location">Location</option>
<option value="MARTi Sample">MARTi Sample</option>
<option value="Programme">Programme</option>
<option value="Publication">Publication</option>
</select>
</div>
</div>
<button onclick="sendSearchRequest()" class="btn btn-primary btn-xl js-scroll-trigger" style="margin-top: 10px; background-color: #2C3E50; border: none;">Search</button>
</div>
</div>
</div>
</div>
</section>
</div>
</header>
<script>
function sendSearchRequest() {
var keyword = document.getElementById('searchInput').value;
var category = document.getElementById('categorySelect').value;
var categoryValue = category === "All" ? "<ANY>" : category;
var searchRequest = {
"services": [{
"start_service": true,
"so:alternateName": "search",
"parameter_set": {
"level": "simple",
"parameters": [
{ "param": "SS Keyword Search", "current_value": keyword },
{ "param": "SS Facet", "current_value": categoryValue },
{ "param": "SS Results Page Number", "current_value": 0 },
{ "param": "SS Results Page Size", "current_value": 500 }
]
}
}]
};
fetch('https://grassroots.tools/beta/grassroots/public_backend', {
//fetch('http://127.0.0.1:2000/grassroots/public_backend', {
method: 'POST',
headers: {
'Content-Type': 'application/json',
},
body: JSON.stringify(searchRequest),
})
.then(response => response.json())
.then(data => {
displayResults(data);
})
.catch((error) => console.error('Error:', error));
}
function displayResults(data) {
// Adjust selectors to target elements within the modal
const tabsContainer = document.querySelector('#resultsModal .tabs');
const contentContainer = document.querySelector('#resultsModal .tab-content');
// Clear previous tabs and content
tabsContainer.innerHTML = '';
contentContainer.innerHTML = '';
if (data.results && data.results[0].results.length > 0) {
const categoriesResults = {}; // Holds the results categorized
// Group results by their type_description
data.results[0].results.forEach(result => {
const category = result.data.type_description;
if (!categoriesResults[category]) {
categoriesResults[category] = [];
}
categoriesResults[category].push(result);
});
// Create tabs and contents only for categories with results
Object.keys(categoriesResults).forEach((category, index) => {
// Create the tab
const tab = document.createElement('li');
tab.textContent = category;
tab.dataset.target = `tab-${index}`;
tabsContainer.appendChild(tab);
// Create the content for this tab
const tabContent = document.createElement('div');
tabContent.id = `tab-${index}`;
categoriesResults[category].forEach(result => {
const item = document.createElement('p');
item.innerHTML = result.title; // Use innerHTML in case titles have HTML content
tabContent.appendChild(item);
});
contentContainer.appendChild(tabContent);
// Add click event listener to the tab
tab.addEventListener('click', function() {
document.querySelectorAll('.tab-content div').forEach(div => div.classList.remove('active'));
document.querySelectorAll('.tabs li').forEach(li => li.classList.remove('active'));
tab.classList.add('active');
document.getElementById(this.dataset.target).classList.add('active');
});
// Automatically activate the first tab
if (index === 0) {
tab.classList.add('active');
tabContent.classList.add('active');
}
});
// Open the modal after populating it with results
openModal();
} else {
// If no results are found, show a message inside the modal and open it
contentContainer.textContent = 'No results found.';
openModal();
}
}
// Function to open the modal
function openModal() {
var modal = document.getElementById("resultsModal");
modal.style.display = "block";
}
// Function to close the modal
function setupModalClose() {
// Get the <span> element that closes the modal
var span = document.querySelector('.close-button');
// When the user clicks on <span> (x), close the modal
span.onclick = function() {
var modal = document.getElementById("resultsModal");
modal.style.display = "none";
};
// Optionally, close the modal when clicking outside of it
window.onclick = function(event) {
var modal = document.getElementById("resultsModal");
if (event.target == modal) {
modal.style.display = "none";
}
};
}
// Ensure modal close functionality is setup after the document has loaded
document.addEventListener('DOMContentLoaded', setupModalClose);
// Get the modal
var modal = document.getElementById("resultsModal");
// Get the <span> element that closes the modal
var span = document.getElementsByClassName("close-button")[0];
// When the user clicks on the button, open the modal
function openModal() {
modal.style.display = "block";
}
// When the user clicks on <span> (x), close the modal
span.onclick = function() {
modal.style.display = "none";
}
</script>
<!-- Portfolio Grid Section -->
<section class="success" id="services">
<div class="container">
<h2 class="text-center">Services</h2>
<hr class="star-light">
<p style="text-align: justify;">
<p> The Grassroots Infrastructure has been developed to expose a number of important
and powerful technologies
that can benefit
researchers and developers to realise their data management needs.</p>
<p>Existing services:</p>
<ul>
<li><a class="darker" href="service/search" target="_blank">Search Grassroots</a></li>
<li><a class="darker" href="fieldtrial" target="_blank">Field Trials</a></li>
<li><a class="darker" href="docs/user/services/field_trial/" target="_blank">Submitting Field Trials</a></li>
<li><a class="darker" href="service/blast-blastn" target="_blank">Blast searches</a>
</li>
<li><a class="darker" href="https://opendata.earlham.ac.uk/wheat/under_license/toronto/" target="_blank">Grassroots Data Portal</a></li>
<li><a class="darker" href="yellowrust-map/" target="_blank">Yellow Rust Field Pathogenomics</a></li>
<li><a class="darker" href="service/" target="_blank">List of all public services</a></li>
</ul>
</div>
</section>
<!-- Portfolio Grid Section -->
<section id="data">
<div class="container">
<h2 class="text-center">Data</h2>
<hr class="star-primary">
<p style="text-align: justify;">As well as providing services, the Grassroots infrastructure also has the
ability to host data. Building upon <a href="https://irods.org/" target="_blank">iRODS</a> as a data
management solution, we have added a number of features
such as a search service and a fully featured web interface, using <a
href="https://github.com/billyfish/eirods-dav">mod_eirods_dav</a>, for accessing the data
and metadata. Currently it is used to host the <a href="https://opendata.earlham.ac.uk/wheat">Designing
Future Wheat Data Portal</a>.</p>
</div>
</section>
<!-- About Section -->
<section class="success" id="about">
<div class="container">
<h2 class="text-center">About</h2>
<hr class="star-light">
<h3>Designing Future Wheat:</h3>
<p style="text-align: justify;">Grassroots has traditionally been the result of an effort to produce an
interoperable data sharing platform
for the wheat community. Whilst Grassroots is by no means organism-specific, our main use cases come
from
the wheat community. We get most of our community feedback from plant researchers at the EI, JIC,
Bristol
University, and other UK institutions, as well as from various international wheat working groups such
as
the <a class="darker" href="https://www.rd-alliance.org/groups/wheat-data-interoperability-wg.html"
target="_blank">RDA Wheat Data
Interoperability maintenance group</a> and the <a class="darker"
href="http://www.wheatinitiative.org/activities/expert-working-groups/wheat-information-system"
target="_blank">Wheat
Initiative Wheat Information
System expert working group</a>. The newly awarded cross-institute programme grant,
Designing Future Wheat (DFW), is the first flagship project of its kind to bring the UK’s wheat
researchers
together to deliver new varieties relevant to the international stage, through the coordinated effort of
biologists, breeders, and informaticians. As such, Grassroots is funded by the DFW programme, enabling
us to
build a platform that can meet the needs of not only this ambitious programme, but the wider UK and
international wheat community that needs fast and openly-licenced unfettered access to the data and
experimental information arising from DFW.</p>
<h3>How to cite us:</h3>
<p style="text-align: justify;">If you have used any of the services that Grassroots provides in your own
research, we would very much
appreciate that you let us know and cite us in any publications, as follows:</p>
<p>Bian. X, Tyrrell. S, Davey R.P. <i>The Grassroots life science data infrastructure (2017).</i>
https://grassroots.tools</p>
</div>
</section>
<!-- Contact Section -->
<section id="contact">
<div class="container">
<h2 class="text-center">Contact us</h2>
<hr class="star-primary">
<p>If you have any queries, please email the <a href="mailto:[email protected]">Grassroots
Helpdesk</a></p>
<div class="row">
<div class="col-sm-4 portfolio-item mx-auto">
<a class="portfolio-link" href="#simon" data-toggle="modal">
<div class="caption">
<div class="caption-content">
<i class="fa fa-search-plus fa-3x"></i>
</div>
</div>
<img class="img-fluid" src="img/simon-tyrrell-web.jpg" alt="">
</a>
</div>
<div class="col-sm-4 portfolio-item mx-auto">
<a class="portfolio-link" href="#daniel" data-toggle="modal">
<div class="caption">
<div class="caption-content">
<i class="fa fa-search-plus fa-3x"></i>
</div>
</div>
<img class="img-fluid" src="img/daniel-olvera-web-profile2023.jpg" alt="">
</a>
</div>
</div>
</div>
</section>
<!-- Footer -->
<footer class="text-center">
<div class="footer-above">
<div class="container">
<div class="row">
<div class="footer-col col-md-4" style="text-align: left ! important;">
<h3>Earlham Institute</h3>
<p>Norwich Research Park<br />
Norwich<br />
NR4 7UZ<br />
UK</p>
</div>
<div class="footer-col col-md-4">
<h3>Project Code</h3>
<p>The project is fully open source and the source code is available on <a
href="https://github.com/TGAC?q=grassroots" target="_blank">GitHub</a>:</p>
<ul class="list-inline">
<li class="list-inline-item">
<a class="btn-social btn-outline" href="https://github.com/TGAC?q=grassroots"
target="_blank">
<i class="fa fa-fw fa-github"></i>
</a>
</li>
<!--<li class="list-inline-item">-->
<!--<a class="btn-social btn-outline" href="#">-->
<!--<i class="fa fa-fw fa-twitter"></i>-->
<!--</a>-->
<!--</li>-->
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<h3>Funding</h3>
<p>The Grassroots project is strategically funded through the BBSRC Designing Future Wheat
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