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recipes.html
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<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Available Data Packages — GGD documentation</title>
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" type="text/css" href="_static/style.css" />
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<script id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
<script src="_static/jquery.js"></script>
<script src="_static/underscore.js"></script>
<script src="_static/doctools.js"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="prev" title="Citing GGD" href="cite.html" />
<link href="https://fonts.googleapis.com/css?family=Lato|Raleway" rel="stylesheet">
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<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/4.3.1/css/bootstrap.min.css">
<script src="https://cdnjs.cloudflare.com/ajax/libs/datatables/1.10.21/js/jquery.dataTables.min.js"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/selectize.js/0.12.6/js/standalone/selectize.min.js"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/4.3.1/js/bootstrap.bundle.min.js"></script>
</head><body>
<div class="document">
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
<div class="sphinxsidebarwrapper">
<p class="logo">
<a href="index.html">
<img class="logo" src="_static/logo/GoGetData_name_logo.png" alt="Logo"/>
</a>
</p>
<h3>Navigation</h3>
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="quick-start.html">GGD Quick Start</a></li>
<li class="toctree-l1"><a class="reference internal" href="using-ggd.html">Using GGD</a></li>
<li class="toctree-l1"><a class="reference internal" href="GGD-CLI.html">GGD Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="meta-recipes.html">GGD meta-recipes</a></li>
<li class="toctree-l1"><a class="reference internal" href="contribute.html">Contribute</a></li>
<li class="toctree-l1"><a class="reference internal" href="private_recipes.html">Private Recipes</a></li>
<li class="toctree-l1"><a class="reference internal" href="workflows.html">Using GGD in Workflows</a></li>
<li class="toctree-l1"><a class="reference internal" href="cite.html">Citing GGD</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="#">Available Data Packages</a></li>
</ul>
<ul>
<li class="toctree-l1"><a href="https://github.com/gogetdata/ggd-recipes">ggd-recipes @ Github</a></li>
<li class="toctree-l1"><a href="https://github.com/gogetdata/ggd-cli">ggd-cli @ Github</a></li>
</ul>
<div id="searchbox" style="display: none" role="search">
<h3 id="searchlabel">Quick search</h3>
<div class="searchformwrapper">
<form class="search" action="search.html" method="get">
<input type="text" name="q" aria-labelledby="searchlabel" />
<input type="submit" value="Go" />
</form>
</div>
</div>
<script>$('#searchbox').show(0);</script>
</div>
</div>
<div class="documentwrapper">
<div class="bodywrapper">
<div class="body" role="main">
<div class="section" id="available-data-packages">
<span id="recipes"></span><h1>Available Data Packages<a class="headerlink" href="#available-data-packages" title="Permalink to this headline">¶</a></h1>
<div class="toctree-wrapper compound">
</div>
<script src="recipes.json"></script>
<body>
<hr>
<div class="container-fluid">
<div class="row">
<div class="col-sm-3">
<div class="form-group", id="channel_options">
<label for="channel_options">GGD Channel</label>
<select class="form-control" id="ggd_channel"></select>
</div>
</div>
<div class="col=sm=4">
<div class="form-group", id="species_options">
<label for="species_options">Species</label>
<select class="form-control" id="species_select"></select>
</div>
</div>
<div class="col=sm=5 pl-3">
<div class="form-group", id="build_options">
<label for="build_options">Genome Build</label>
<select class="form-control" id="build_select">
</select>
</div>
</div>
</div>
<div class="row">
<div class="col-sm-12">
<p><center><small> NOTE: A <b>GGD Channel</b> selection is required before a <b>Species</b> selection and a <b>Species</b> selection is required before a <b>Genome Build</b> selection </small></center></p>
<p><center><medium> <br> If you use GGD, please cite the <a href="https://www.nature.com/articles/s41467-021-22381-z"> Nature Communications GGD paper</a> </medium></center></p>
</div>
</div>
<hr>
<div class="row pt-3">
<div class="col-12">
<table id="recipe_table"></table>
</div>
</div>
<hr>
</div>
</body>
<script>
/*
------------------------------------------------------------------------------------------------------------------
Initiate
------------------------------------------------------------------------------------------------------------------
*/
var channel_default = "genomics"
var cur_channel = "None"
var cur_species = "None"
var cur_build = "None"
//update view based on available cookie info
$( document ).ready(function(){
getCookie()
})
/*
------------------------------------------------------------------------------------------------------------------
Populate Selectors
------------------------------------------------------------------------------------------------------------------
*/
//Add ggd channel select options
function add_channel_selection() {
$("#ggd_channel").children().remove().end()
$("#ggd_channel").append("<option>choose one</option>")
//Remove species and build info until a species is select
$("#species_select").children().remove().end()
$("#build_select").children().remove().end()
for (channel of Object.keys(recipe_data)) {
//Add region to select options
$("#ggd_channel").append("<option>" + channel + "</option>")
}
if (cur_channel != "None") {
//Set selected value
$("#ggd_channel").val(cur_channel)
}
}
//Add species selection options
function add_species_selector() {
//Update species selection
$("#species_select").children().remove().end()
$("#species_select").append("<option>choose one</option>")
//Remove build info until a species is select
$("#build_select").children().remove().end()
//Update selection list
if (cur_channel in recipe_data) {
for (species of Object.keys(recipe_data[cur_channel])) {
$("#species_select").append("<option>" + species + "</option>")
}
//Set selected value
if (cur_species != "None") {
$("#species_select").val(cur_species)
}
}
}
//Add build selection options
function add_build_selector() {
$("#build_select").children().remove().end()
$("#build_select").append("<option>choose one</option>")
//Update selection list
if (cur_channel in recipe_data && cur_species in recipe_data[cur_channel]) {
for (build of Object.keys(recipe_data[cur_channel][cur_species])) {
$("#build_select").append("<option>" + build + "</option>")
}
//Set selected value
if (cur_build != "None") {
$("#build_select").val(cur_build)
}
}
}
/*
------------------------------------------------------------------------------------------------------------------
Display Recipes
------------------------------------------------------------------------------------------------------------------
*/
//Method to remove recipe table
function removeRecipeTable() {
//Remove previous data table if it exists
if ($.fn.DataTable.isDataTable('#recipe_table')) {
let table = $('#recipe_table').DataTable()
table.destroy();
$('#recipe_table').empty();
};
}
//Add a jQuery data table with recipe info
function getRecipeTable(recipe_dict) {
//Remove prexisting table
removeRecipeTable()
//Get the href strings for each recipe
let hrefs = []
Object.values(recipe_dict).forEach((href,i) => {
hrefs.push([href])
});
//Create data table
jQuery("#recipe_table").DataTable({
destory: true,
data: hrefs,
columns: [{"title": "Packages", width: "20%"}],
paging: false,
scroller: true,
scrollY: '60vh',
scrollX: true,
scrollCollapse: true,
"dom": '<"pull-right"f><"pull-left"l>tip'
});
};
/*
------------------------------------------------------------------------------------------------------------------
Event Handling
------------------------------------------------------------------------------------------------------------------
*/
//Set local cookie info
function setCookie(extraMinutes = 5) {
var d = new Date();
d.setTime(d.getTime() + (extraMinutes * 60 * 1000))
document.cookie = "channel = " + cur_channel + ";"
document.cookie = "species = " + cur_species + ";"
document.cookie = "build = " + cur_build + ";"
document.cookie = "expires = " + d.toUTCString() + ";"
}
//Unset local cookie info
function unsetCookie() {
document.cookie = "channel = " + "None" + ";"
document.cookie = "species = " + "None" + ";"
document.cookie = "build = " + "None" + ";"
}
//Get Cookie info and update page
function getCookie() {
var d = new Date();
d.setTime(d.getTime())
var cookieElements = document.cookie.split(";")
//check cookie
for (item of cookieElements) {
if (item.split("=")[0].trim() == "channel") {
//check for set channel cookie. if none, set to default
if (item.split("=")[1] == "None") {
cur_channel = channel_default
} else {
cur_channel = item.split("=")[1]
}
//check species cookie
} else if (item.split("=")[0].trim() == "species") {
cur_species = item.split("=")[1]
//check build cookie
} else if (item.split("=")[0].trim() == "build") {
cur_build = item.split("=")[1]
//check cookie expires
} else if (item.split("=")[0].trim() == "expires") {
//check if the cookie has expired
if (d.toUTCString() > item.split("=")[1]) {
cur_channel = channel_default
cur_species = "None"
cur_build = "None"
unsetCookie()
break;
}
}
};
//Add Channel Selection options
add_channel_selection()
add_species_selector()
add_build_selector()
//Add Recipe Table
if (cur_build != "None") {
getRecipeTable(recipe_data[cur_channel][cur_species][cur_build])
}
}
//Select Channel
/// Add species available for that channel
$("#ggd_channel").on('change', function(e) {
var selectedValue = this.value
//Unset the Cookie
unsetCookie()
//Keep track of current channel
cur_channel = selectedValue
cur_species = "None"
cur_build = "None"
//Remove the recipe table
removeRecipeTable()
if (cur_channel == "choose one") {
//Reset Selectors
$("#species_select").children().remove().end()
$("#build_select").children().remove().end()
}
//Update selector
add_species_selector()
add_build_selector()
});
//Select Species
/// Add genome build available for that species
$("#species_select").on('change', function(e) {
var selectedValue = this.value
//Unset the Cookie
unsetCookie()
//Keep track of current species
cur_species = selectedValue
//Remove the recipe table
cur_build = "None"
removeRecipeTable()
if (cur_species == "choose one") {
//Reset build selector
$("#build_select").children().remove().end()
}
//Update selector
add_build_selector()
});
//Select build
/// Add genome build available for that species
$("#build_select").on('change', function(e) {
var selectedValue = this.value
//Keep track of current species
cur_build = selectedValue
setCookie()
if (cur_build == "choose one") {
//Remove the recipe table
removeRecipeTable()
} else {
getRecipeTable(recipe_data[cur_channel][cur_species][cur_build])
}
});
</script></div>
</div>
</div>
</div>
<div class="clearer"></div>
</div>
<div class="footer">
©2016-2021, The GoGetData team.
|
<a href="_sources/recipes.rst.txt"
rel="nofollow">Page source</a>
</div>
</body>
</html>