1 files changed, 414 insertions, 0 deletions
diff --git a/gn2/wqflask/static/new/javascript/get_traits_from_collection.js b/gn2/wqflask/static/new/javascript/get_traits_from_collection.js
new file mode 100644
index 00000000..c115f3b0
--- /dev/null
+++ b/gn2/wqflask/static/new/javascript/get_traits_from_collection.js
@@ -0,0 +1,414 @@
+// 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);