// Generated by CoffeeScript 1.8.0
var add_trait_data, assemble_into_json, back_to_collections, collection_click, collection_list, color_by_trait, create_trait_data_csv, get_this_trait_vals, get_trait_data, process_traits, selected_traits, submit_click, this_trait_data, trait_click,
__indexOf = [].indexOf || function(item) { for (var i = 0, l = this.length; i < l; i++) { if (i in this && this[i] === item) return i; } return -1; };
this_trait_data = null;
selected_traits = {};
$('#collections_list').attr("style", "width: 100%;");
$('#trait_table').dataTable( {
"drawCallback": function( settings ) {
$('#trait_table tr').click(function(event) {
if (event.target.type !== 'checkbox') {
$(':checkbox', this).trigger('click');
}
});
},
"columns": [
{ "type": "natural", "width": "3%" },
{ "type": "natural", "width": "8%" },
{ "type": "natural", "width": "20%" },
{ "type": "natural", "width": "25%" },
{ "type": "natural", "width": "25%" },
{ "type": "natural", "width": "15%" }
],
"columnDefs": [ {
"targets": 0,
"orderable": false
} ],
"order": [[1, "asc" ]],
"sDom": "RZtr",
"iDisplayLength": -1,
"autoWidth": true,
"bDeferRender": true,
"bSortClasses": false,
"paging": false,
"orderClasses": true
} );
if ( ! $.fn.DataTable.isDataTable( '#collection_table' ) ) {
$('#collection_table').dataTable( {
"createdRow": function ( row, data, index ) {
if ($('td', row).eq(2).text().length > 40) {
$('td', row).eq(2).text($('td', row).eq(2).text().substring(0, 40));
$('td', row).eq(2).text($('td', row).eq(2).text() + '...')
}
if ($('td', row).eq(4).text().length > 50) {
$('td', row).eq(4).text($('td', row).eq(4).text().substring(0, 50));
$('td', row).eq(4).text($('td', row).eq(4).text() + '...')
}
},
"columnDefs": [ {
"targets": 0,
"orderable": false
} ],
"order": [[1, "asc" ]],
"sDom": "ZRtr",
"iDisplayLength": -1,
"autoWidth": true,
"bSortClasses": false,
"paging": false,
"orderClasses": true
} );
}
collection_click = function() {
var this_collection_url;
this_collection_url = $(this).find('.collection_name').prop("href");
this_collection_url += "&json";
collection_list = $("#collections_holder").html();
return $.ajax({
dataType: "json",
url: this_collection_url,
success: process_traits
});
};
submit_click = function() {
var all_vals, sample, samples, scatter_matrix, this_trait_vals, trait, trait_names, trait_vals_csv, traits, _i, _j, _len, _len1, _ref;
selected_traits = {};
traits = [];
$('#collections_holder').find('input[type=checkbox]:checked').each(function() {
var this_dataset, this_trait, this_trait_url;
this_trait = $(this).parents('tr').find('.trait').text();
this_dataset = $(this).parents('tr').find('.dataset').text();
this_trait_url = "/trait/get_sample_data?trait=" + this_trait + "&dataset=" + this_dataset;
return $.ajax({
dataType: "json",
url: this_trait_url,
async: false,
success: add_trait_data
});
});
trait_names = [];
samples = $('input[name=allsamples]').val().split(" ");
all_vals = [];
this_trait_vals = get_this_trait_vals(samples);
all_vals.push(this_trait_vals);
_ref = Object.keys(selected_traits);
for (_i = 0, _len = _ref.length; _i < _len; _i++) {
trait = _ref[_i];
trait_names.push(trait);
this_trait_vals = [];
for (_j = 0, _len1 = samples.length; _j < _len1; _j++) {
sample = samples[_j];
if (__indexOf.call(Object.keys(selected_traits[trait]), sample) >= 0) {
this_trait_vals.push(parseFloat(selected_traits[trait][sample]));
} else {
this_trait_vals.push(null);
}
}
all_vals.push(this_trait_vals);
}
trait_vals_csv = create_trait_data_csv(selected_traits);
scatter_matrix = new ScatterMatrix(trait_vals_csv);
scatter_matrix.render();
return $.colorbox.close();
};
create_trait_data_csv = function(selected_traits) {
var all_vals, index, sample, sample_vals, samples, this_trait_vals, trait, trait_names, trait_vals_csv, _i, _j, _k, _l, _len, _len1, _len2, _len3, _ref;
trait_names = [];
trait_names.push($('input[name=trait_id]').val());
samples = $('input[name=allsamples]').val().split(" ");
all_vals = [];
this_trait_vals = get_this_trait_vals(samples);
all_vals.push(this_trait_vals);
_ref = Object.keys(selected_traits);
for (_i = 0, _len = _ref.length; _i < _len; _i++) {
trait = _ref[_i];
trait_names.push(trait);
this_trait_vals = [];
for (_j = 0, _len1 = samples.length; _j < _len1; _j++) {
sample = samples[_j];
if (__indexOf.call(Object.keys(selected_traits[trait]), sample) >= 0) {
this_trait_vals.push(parseFloat(selected_traits[trait][sample]));
} else {
this_trait_vals.push(null);
}
}
all_vals.push(this_trait_vals);
}
trait_vals_csv = trait_names.join(",");
trait_vals_csv += "\n";
for (index = _k = 0, _len2 = samples.length; _k < _len2; index = ++_k) {
sample = samples[index];
if (all_vals[0][index] === null) {
continue;
}
sample_vals = [];
for (_l = 0, _len3 = all_vals.length; _l < _len3; _l++) {
trait = all_vals[_l];
sample_vals.push(trait[index]);
}
trait_vals_csv += sample_vals.join(",");
trait_vals_csv += "\n";
}
return trait_vals_csv;
};
trait_click = function() {
var dataset, this_trait_url, trait;
trait = $(this).parent().find('.trait').text();
dataset = $(this).parent().find('.dataset').text();
this_trait_url = "/trait/get_sample_data?trait=" + trait + "&dataset=" + dataset;
$.ajax({
dataType: "json",
url: this_trait_url,
success: get_trait_data
});
return $.colorbox.close();
};
trait_row_click = function() {
var dataset, this_trait_url, trait;
trait = $(this).find('.trait').text();
dataset = $(this).find('.dataset').data("dataset");
this_trait_url = "/trait/get_sample_data?trait=" + trait + "&dataset=" + dataset;
$.ajax({
dataType: "json",
url: this_trait_url,
success: get_trait_data
});
return $.colorbox.close();
};
add_trait_data = function(trait_data, textStatus, jqXHR) {
var trait_name, trait_sample_data;
trait_name = trait_data[0];
trait_sample_data = trait_data[1];
selected_traits[trait_name] = trait_sample_data;
return console.log("selected_traits:", selected_traits);
};
populate_cofactor_info = function(trait_info) {
if ($('input[name=selecting_which_cofactor]').val() == "1"){
$('#cofactor1_trait_link').attr("href", trait_info['url'])
if (trait_info['type'] == "ProbeSet"){
$('#cofactor1_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['tissue'] + " " + trait_info['db'] + ": " + trait_info['name'])
$('#cofactor1_description').text("[" + trait_info['symbol'] + " on " + trait_info['location'] + " Mb]\n" + trait_info['description'])
} else if (trait_info['type'] == "Publish") {
$('#cofactor1_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['db'] + ": " + trait_info['name'])
if ('pubmed_link' in trait_info) {
$('#cofactor1_description').html('<a href=\"' + trait_info['pubmed_link'] + '\">PubMed: ' + trait_info['pubmed_text'] + '</a><br>' + trait_info['description'])
} else {
$('#cofactor1_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['db'] + ": " + trait_info['name'])
$('#cofactor1_description').text("[" + trait_info['name'] + " on " + trait_info['location'] + " Mb]\n" + trait_info['description'])
}
} else {
$('#cofactor1_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['db'] + ": " + trait_info['name'])
$('#cofactor1_description').text("[" + trait_info['name'] + " on " + trait_info['location'] + " Mb]\n")
}
$('#select_cofactor1').text("Change Cofactor 1");
$('#cofactor1_info_container').css("display", "inline");
$('#cofactor2_button').css("display", "inline-block");
} else if ($('input[name=selecting_which_cofactor]').val() == "2"){
$('#cofactor2_trait_link').attr("href", trait_info['url'])
if (trait_info['type'] == "ProbeSet"){
$('#cofactor2_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['tissue'] + " " + trait_info['db'] + ": " + trait_info['name'])
$('#cofactor2_description').text("[" + trait_info['symbol'] + " on " + trait_info['location'] + " Mb]\n" + trait_info['description'])
} else if (trait_info['type'] == "Publish") {
$('#cofactor2_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['db'] + ": " + trait_info['name'])
if ('pubmed_link' in trait_info) {
$('#cofactor2_description').html('<a href=\"' + trait_info['pubmed_link'] + '\">PubMed: ' + trait_info['pubmed_text'] + '</a><br>' + trait_info['description'])
} else {
$('#cofactor2_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['db'] + ": " + trait_info['name'])
$('#cofactor2_description').text("[" + trait_info['name'] + " on " + trait_info['location'] + " Mb]\n" + trait_info['description'])
}
} else {
$('#cofactor2_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['db'] + ": " + trait_info['name'])
$('#cofactor2_description').text("[" + trait_info['name'] + " on " + trait_info['location'] + " Mb]\n")
}
$('#select_cofactor2').text("Change Cofactor 2");
$('#cofactor2_info_container').css("display", "inline");
$('#cofactor3_button').css("display", "inline-block");
} else {
$('#cofactor3_trait_link').attr("href", trait_info['url'])
if (trait_info['type'] == "ProbeSet"){
$('#cofactor3_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['tissue'] + " " + trait_info['db'] + ": " + trait_info['name'])
$('#cofactor3_description').text("[" + trait_info['symbol'] + " on " + trait_info['location'] + " Mb]\n" + trait_info['description'])
} else if (trait_info['type'] == "Publish") {
$('#cofactor3_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['db'] + ": " + trait_info['name'])
if ('pubmed_link' in trait_info) {
$('#cofactor3_description').html('<a href=\"' + trait_info['pubmed_link'] + '\">PubMed: ' + trait_info['pubmed_text'] + '</a><br>' + trait_info['description'])
} else {
$('#cofactor3_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['db'] + ": " + trait_info['name'])
$('#cofactor3_description').text("[" + trait_info['name'] + " on " + trait_info['location'] + " Mb]\n" + trait_info['description'])
}
} else {
$('#cofactor3_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['db'] + ": " + trait_info['name'])
$('#cofactor3_description').text("[" + trait_info['name'] + " on " + trait_info['location'] + " Mb]\n")
}
$('#select_cofactor3').text("Change Cofactor 3");
$('#cofactor3_info_container').css("display", "inline");
}
}
get_trait_data = function(trait_data, textStatus, jqXHR) {
var sample, samples, this_trait_vals, trait_sample_data, vals, _i, _len;
trait_sample_data = trait_data[1];
if ( $('input[name=allsamples]').length ) {
samples = $('input[name=allsamples]').val().split(" ");
} else {
samples = js_data.indIDs
}
sample_vals = [];
vals = [];
for (_i = 0, _len = samples.length; _i < _len; _i++) {
sample = samples[_i];
if (sample in trait_sample_data) {
sample_vals.push(sample + ":" + parseFloat(trait_sample_data[sample]))
vals.push(parseFloat(trait_sample_data[sample]))
} else {
sample_vals.push(null)
vals.push(null)
}
}
if ( $('input[name=allsamples]').length ) {
if ($('input[name=samples]').length < 1) {
$('#hidden_inputs').append('<input type="hidden" name="samples" value="[' + samples.toString() + ']" />');
}
$('#hidden_inputs').append('<input type="hidden" name="vals" value="[' + vals.toString() + ']" />');
this_trait_vals = get_this_trait_vals(samples);
return color_by_trait(trait_sample_data);
} else{
sorted = vals.slice().sort(function(a,b){return a-b})
ranks = vals.slice().map(function(v){ return sorted.indexOf(v)+1 });
sample_ranks = []
for (_i = 0; _i < samples.length; _i++){
if (samples[_i] in trait_sample_data){
sample_ranks.push(samples[_i] + ":" + ranks[_i])
} else {
sample_ranks.push(null)
}
}
if ($('input[name=selecting_which_cofactor]').val() == "1"){
if ($('#cofactor1_type option:selected').val() == "symbol") {
unique_vals = [...new Set(vals)]
if (unique_vals.length > 45) {
alert("If displaying cofactor as symbol, please choose a trait with 45 or fewer distinct sample values.");
return false;
}
}
$('input[name=cofactor1_vals]').val(sample_vals)
$('input[name=ranked_cofactor1_vals]').val(sample_ranks)
} else if ($('input[name=selecting_which_cofactor]').val() == "2"){
if ($('#cofactor2_type option:selected').val() == "symbol") {
unique_vals = [...new Set(vals)]
if (unique_vals.length > 45) {
alert("If displaying cofactor as symbol, please choose a trait with 45 or fewer distinct sample values.");
return false;
}
}
$('input[name=cofactor2_vals]').val(sample_vals)
$('input[name=ranked_cofactor2_vals]').val(sample_ranks)
} else{
if ($('#cofactor3_type option:selected').val() == "symbol") {
unique_vals = [...new Set(vals)]
if (unique_vals.length > 45) {
alert("If displaying cofactor as symbol, please choose a trait with 45 or fewer distinct sample values.");
return false;
}
}
$('input[name=cofactor3_vals]').val(sample_vals)
$('input[name=ranked_cofactor3_vals]').val(sample_ranks)
}
populate_cofactor_info(trait_data[0])
chartupdatedata();
return false
}
};
get_this_trait_vals = function(samples) {
var sample, this_trait_vals, this_val, this_vals_json, _i, _len;
this_trait_vals = [];
for (_i = 0, _len = samples.length; _i < _len; _i++) {
sample = samples[_i];
this_val = parseFloat($("input[name='value:" + sample + "']").val());
if (!isNaN(this_val)) {
this_trait_vals.push(this_val);
} else {
this_trait_vals.push(null);
}
}
this_vals_json = '[' + this_trait_vals.toString() + ']';
return this_trait_vals;
};
assemble_into_json = function(this_trait_vals) {
var json_data, json_ids, num_traits, samples;
num_traits = $('input[name=vals]').length;
samples = $('input[name=samples]').val();
json_ids = samples;
json_data = '[' + this_trait_vals;
$('input[name=vals]').each((function(_this) {
return function(index, element) {
return json_data += ',' + $(element).val();
};
})(this));
json_data += ']';
return [json_ids, json_data];
};
color_by_trait = function(trait_sample_data, textStatus, jqXHR) {
return root.bar_chart.color_by_trait(trait_sample_data);
};
process_traits = function(trait_data, textStatus, jqXHR) {
var the_html, trait, _i, _len;
the_html = "<button id='back_to_collections' class='btn btn-inverse btn-small'>";
the_html += "<i class='icon-white icon-arrow-left'></i> Back </button>";
the_html += " <button id='submit_cofactors' class='btn btn-primary btn-small submit'> Submit </button>";
the_html += "<table id='collection_table' style='padding-top: 10px;' class='table table-hover'>";
the_html += "<thead><tr><th></th><th>Record</th><th>Data Set</th><th>Description</th></tr></thead>";
the_html += "<tbody>";
for (_i = 0, _len = trait_data.length; _i < _len; _i++) {
trait = trait_data[_i];
the_html += "<tr class='trait_line'>";
the_html += "<td class='select_trait'><input type='checkbox' name='selectCheck' class='checkbox edit_sample_checkbox'></td>";
if ("abbreviation" in trait) {
the_html += "<td class='trait' data-display_name='" + trait.name + " - " + trait.abbreviation + "'>" + trait.name + "</td>";
} else if ("symbol" in trait) {
the_html += "<td class='trait' data-display_name='" + trait.name + " - " + trait.symbol + "'>" + trait.name + "</td>";
} else {
the_html += "<td class='trait' data-display_name='" + trait.name + "'>" + trait.name + "</td>";
}
the_html += "<td class='dataset' data-dataset='" + trait.dataset + "'>" + trait.dataset_name + "</td>";
if (trait.dataset.includes('Geno')) {
the_html += "<td class='description'>" + trait.location + "</td>";
} else {
the_html += "<td class='description'>" + trait.description + "</td>";
}
}
the_html += "</tbody>";
the_html += "</table>";
the_html += "<script type='text/javascript' src='/static/new/javascript/get_traits_from_collection.js'></script>"
$("#collections_holder").html(the_html);
return $('#collections_holder').colorbox.resize();
};
back_to_collections = function() {
$("#collections_holder").html(collection_list);
$(document).on("click", ".collection_line", collection_click);
return $('#collections_holder').colorbox.resize();
};
$(".collection_line").on("click", collection_click);
$("#submit_cofactors").on("click", submit_click);
if ($('#scatterplot2').length){
$(".trait_line").on("click", trait_row_click);
} else {
$(".trait").on("click", trait_click);
}
$("#back_to_collections").on("click", back_to_collections);
