path: root/gn2/wqflask/static/new/javascript/get_traits_from_collection.js

// 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>";
    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);