GD.loadPcRedrawValidation - Code Metrics - Inspection of "fix issue of the broken filename of the expression..." - GeoDiver/GeoDiver - Measure and Improve Code Quality continuously with Scrutinizer

Completed
Push — master ( 4e0cb0...0037c0 )

by Ismail
created 2017-07-17 12:18 UTC
GD.loadPcRedrawValidation C

↳ Parent: GD.loadPcRedrawValidation
Complexity

Conditions	7
Paths	3
Size

Total Lines
Duplication

Lines	0
Ratio	0 %
Importance

Changes	2
Bugs	1	Features	0
Metric	Value
c	2
b	1
f	0
dl	0
loc	25
rs	6.7272
cc	7
nc	3
nop	2
/*
    GD - GeoDiver's JavaScript module

    Define a global GD (acronym for GeoDiver) object containing all
    GD associated methods:
*/

// define global GD object
var GD;
if (!GD) {

  GD = {};
}

// GD module
(function() {
  GD.setUpValidatorDefaults = function() {
    $.validator.addMethod('geoDb', function (value) {
        return /^G[DS][SE]\d\d?\d?\d?\d?$/i.test(value);
    }, 'Please enter a valid GEO dataset accession number (in the format GDSxxxx).');

    $.validator.addMethod('checkIfGeoExists', function(value) {
      var doesNotExist = 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      if (value.length > 3) {
        if($.inArray( parseInt( value.substring(3) ), doesNotExist) !== -1 && /^GDS\d\d?\d?\d?$/i.test(value)) {
          return false;
        } else { return true; }
      } else { return true; }
    }, 'This GEO dataset accession number does not exist.');

    $.validator.setDefaults({
      errorClass: 'invalid',
      validClass: "valid",
      errorPlacement: function (error, element) {
          $(element)
            .closest("form")
            .find("label[for='" + element.attr("id") + "']")
            .attr('data-error', error.text());
      },
    });
  };

  ///// AJAXs

  GD.loadGeoDbValidation = function() {
    'use strict';
    $('#load_geo_db').validate({
      rules: {
        geo_db: {
          geoDb: true,
          checkIfGeoExists: true,
          required: true
        },
      },
      submitHandler: function() {
        $('.card-action').remove();
        $('#results_section').empty();
        var geo_db = $('input[name=geo_db]').val().toUpperCase();
        $('#modal_header_text').text('Loading GEO Dataset: ' + geo_db);
        $('#modal_text').text('This should take a few seconds. Please leave this page open');
        $('#loading_modal').modal({ dismissible: false });
        $('#loading_modal').modal('open');
        $.ajax({
          type: 'POST',
          url: '/load_geo_db',
          data: $('#load_geo_db').serialize(),
          success: function(response) {
            $( response ).insertAfter( "#load_geo_card" );
            $('#geo_db_summary').html(response);
            $('#geo_db_summary').show();
            $('.adv_param_collapsible').collapsible();
            $("input:radio[name=factor]:first").attr('checked', true);
            $('#' + $("input:radio[name=factor]:first").attr('id') + '_select').show();
            $('#adv_params_btn').click(function(){
              if ( ! $('#adv_params_params_tabs').hasClass('tabs_initialised')) {
                setTimeout(
                  function(){
                    $('#adv_params_params_tabs').tabs();
                    $('#adv_params_params_tabs').addClass('tabs_initialised');
                  }, 1);
              }
            });
            $('select[name="groupa[]"]').on('change', function(){
              if ( $.isEmptyObject( $('select[name="groupa[]"]:enabled').val() ) ) {
                $('#groupa_params').attr('data-tooltip', 'This is Group A' );
                $('#groupa_params').tooltip({delay: 50});
              } else {
                $('#groupa_params').attr('data-tooltip', 'Group A: ' + $('select[name="groupa[]"]:enabled').val().join(", ") );
                $('#groupa_params').tooltip({delay: 50});
              }
            });
            $('select[name="groupb[]"]').on('change', function(){
              if ( $.isEmptyObject( $('select[name="groupb[]"]:enabled').val() ) ) {
                $('#groupb_params').attr('data-tooltip', 'This is Group B' );
                $('#groupb_params').tooltip({delay: 50});
              } else {
                $('#groupb_params').attr('data-tooltip', 'Group B: ' + $('select[name="groupb[]"]:enabled').val().join(", ") );
                $('#groupb_params').tooltip({delay: 50});
              }
            });
            GD.ensureOnlyOneSelectOption();
            GD.addAdvParamLogic();
            GD.addFactorToggle();
            $('select').material_select();
            $('.tooltipped').tooltip();
            GD.addGeoDbInfo($('input[name=geo_db]').val());
            GD.analyseValidation();
            $('#loading_modal').modal('close');
          },
          error: function(e, status) {
            GD.ajaxError(e, status);
          }
        });
      }
    });
  };

  GD.exemplar_results = function() {
    $('#exemplar_result').click(function(){
      $('input[name=geo_db]').val('GDS5093');
      $('#load_geo_db').submit();
    });
  };

  GD.analyseValidation = function() {
    'use strict';
    $('#analyse').validate({
      rules: {},
      submitHandler: function() {
        // Manually check if groupa / groupb is empty
        if ( $.isEmptyObject( $('select[name="groupa[]"]:enabled').val() )  || $.isEmptyObject( $('select[name="groupb[]"]:enabled').val() )  ) {
          $('.select_factors_validations').text('Please select the factors in the two groups to analyse.');
          return false;
        }
        $('.select_factors_validations').text('');
        $('#results_section').empty();
        var geo_db = $('input[name=geo_db]').val().toUpperCase();
        $('input[name="dgea_cluster_by_genes"]').val($('input[name="dgea_cluster_by_genes"]').is(':checked'));
        $('input[name="dgea_cluster_by_samples"]').val($('input[name="dgea_cluster_by_samples"]').is(':checked'));
        $('input[name="gsea_cluster_by_genes"]').val($('input[name="gsea_cluster_by_genes"]').is(':checked'));
        $('input[name="gsea_cluster_by_samples"]').val($('input[name="gsea_cluster_by_samples"]').is(':checked'));
        $('#modal_header_text').text('Analysing GEO Dataset: ' + geo_db);
        $('#modal_text').text('This should take a few minutes. Please leave this page open');
        $('#loading_modal').modal({ dismissible: false});
        $('#loading_modal').modal('open');
        $.ajax({
          type: 'POST',
          url: '/analyse',
          data: $('#analyse').serialize(),
          success: function(response) {
            $('#results_section').show();
            $('#results_section').html(response).imagesLoaded().then(function(){
              $('#pca_tabs').tabs(); // init material tabs
              $('#results_tabs').tabs(); // init material tabs
              GD.createPlots();
              $('.materialboxed').materialbox(); // init materialbox
              $('.select_factors input.select-dropdown').removeAttr('disabled');
              GD.download_all_results();
              GD.delete_result();
              GD.share_result();
              GD.show_GeoDB_modal();
              GD.remove_share();
              $('#loading_modal').modal('close');
              $('html, body').animate({
                  scrollTop: $('#results_section').offset().top
              });
            });
          },
          error: function(e, status) {
            GD.ajaxError(e, status);
          }
        });
        return undefined;
      }
    });
  };

  GD.geneExpressionAjax = function(currentRow, geneId) {
    $('#modal_header_text').text('Loading Graphics for Gene: ' + geneId);
    $('#modal_text').text('This should take a few seconds. Please leave this page open');
    $('#loading_modal').modal({ dismissible: false});
    $('#loading_modal').modal('open');
    var resultId = currentRow.closest('.results_card').data('result');
    var geoDb    = currentRow.closest('.results_card').data('geodb');
    var user     = currentRow.closest('.results_card').data('user');
    $.ajax({
      type: 'POST',
      url: '/gene_expression_graph',
      data: {gene_id: geneId, result_id: resultId, geo_db: geoDb, user: user},
      success: function(response) {
        currentRow.addClass('parent');
        currentRow.after('<tr class="child" id="'+ geneId + 'ChildRow"><td colspan="8"><div id="' + geneId + 'Plot"></div></td></tr>');
        GD.createExpressionPlot(response, geneId);
        $('#loading_modal').modal('close');
      },
      error: function(e, status) {
        GD.ajaxError(e, status);
      }
    });
  };

  GD.interactionNetworkAjax = function(currentRow, pathId) {
    $('#modal_header_text').text('Loading Graphics for GeneSet: ' + pathId);
    $('#modal_text').text('This should take a few seconds. Please leave this page open');
    $('#loading_modal').modal({ dismissible: false});
    $('#loading_modal').modal('open');
    var resultId = currentRow.closest('.results_card').data('result');
    var geoDb    = currentRow.closest('.results_card').data('geodb');
    var user     = currentRow.closest('.results_card').data('user');
    $.ajax({
      type: 'POST',
      url: '/interaction_image',
      data: {path_id: pathId, result_id: resultId, geo_db: geoDb, user: user},
      success: function(response) {
        currentRow.addClass('parent');
        currentRow.after(response);
        $('#loading_modal').modal('close');
      },
      error: function(e, status) {
        GD.ajaxError(e, status);
      }
    });  };

  GD.ajaxError = function(e, status) {
    var errorMessage;
    if (e.status == 500 || e.status == 400) {
      errorMessage = e.responseText;
      $('#results_section').show();
      $('#results_section').html(errorMessage);
      $('#loading_modal').modal('close'); // remove progress notification
    } else {
      errorMessage = e.responseText;
      $('#results_section').show();
      $('#results_section').html('<div class="card red lighten-2" role="alert"><div class="card-content white-text"><h3>Oops! GeoDiver is Drowning!</h3><p style="font-size: 1.5rem"><strong>Apologies, there was an error with your request. Please try again.</strong></p><p>Error Message:' + errorMessage + ' The server responded with the status code: ' + String(e.status) + '. Please refresh the page and try again.</p><p>If the error persists, please contact the administrator.</p></div></div>');
      $('#loading_modal').modal('close'); // remove progress notification
    }
  };

  GD.loadPcRedrawValidation = function() {
    $('#pca3d_redraw').validate({
      rules: {},
      submitHandler: function(form, event) {
        // Manually check if groupa / groupb is empty
        if ( $.isEmptyObject( $('select[name="PC3doption1"]').val() ) || $.isEmptyObject( $('select[name="PC3doption2"]').val() ) || $.isEmptyObject( $('select[name="PC3doption3"]').val() ) ) {
          $('.select_pc3_validations').text('Please select the Principle components to analyse.');
          return false;
        }
        // Manually check if PC2dOption1 == PC2dOption2
        if (( $('select[name="PC3doption1"]').val() === $('select[name="PC3doption2"]').val() ) ||
            ( $('select[name="PC3doption3"]').val() === $('select[name="PC3doption2"]').val() ) ||
            ( $('select[name="PC3doption1"]').val() === $('select[name="PC3doption3"]').val() ) ) {
          $('.select_pc3_validations').text('Please select different principal components to analyse.');
          return false;
        }
        $('.select_pc3_validations').text('');
        event.preventDefault(); // because we're not submitting at all
        $('#principle_plot').empty();
        var x = $('select[name=PC3doption1]').val();
        var y = $('select[name=PC3doption2]').val();
        var z = $('select[name=PC3doption3]').val();
        var jsonFile = $('#overview').data("overview-json");
        $.getJSON(jsonFile, function(json) {
          GD.create3dPCAScatterPlot(json.pcdata, x, y, z);
        });
        return undefined;
      }
    });
    $('#pca2d_redraw').validate({
      rules: {},
      submitHandler: function(form, event) {
        // Manually check if PC2dOption1 / PC2dOption2 is empty
        if ( $.isEmptyObject( $('select[name="PC2doption1"]').val() )  || $.isEmptyObject( $('select[name="PC2doption2"]').val() ) ) {
          $('.select_pc2_validations').text('Please select the principal components to analyse.');
          return false;
        }
        // Manually check if PC2dOption1 == PC2dOption2
        if ( $('select[name="PC2doption1"]').val() === $('select[name="PC2doption2"]').val() ) {
          $('.select_pc2_validations').text('Please select different principal components to analyse.');
          return false;
        }

        $('.select_pc2_validations').text('');
        event.preventDefault(); // because we're not submitting at all
        $('#principle_plot').empty();
        var x = $('select[name=PC2doption1]').val();
        var y = $('select[name=PC2doption2]').val();
        var jsonFile = $('#overview').data("overview-json");
        $.getJSON(jsonFile, function(json) {
          GD.create2dPCAScatterPlot(json.pcdata, x, y);
        });
        return undefined;
      }
    });
  };


  ///// PLOTS

  GD.createPlots = function() {
    var jsonFile = $('#overview').data("overview-json");
    $.getJSON(jsonFile, function(json) {
      GD.pcaPlot = GD.createPCAPLOT(json.pc.cumVar, json.pc.expVar, json.pc.pcnames);
      GD.pca2dScatterPlot = GD.create2dPCAScatterPlot(json.pcdata, 'PC1', 'PC2');
      GD.pca3dScatterPlot = GD.create3dPCAScatterPlot(json.pcdata, 'PC1', 'PC2', 'PC3');

      GD.initialiatizePcaScatterPlot(json.pc.pcnames);
      $('select').material_select();
    });

    $('#pca_tabs').on('click', '.tab a', function() {
      if ($(this).attr('href') === '#pca2d' ) {
        Plotly.Plots.resize(GD.pca2dScatterPlot);
      } else {
        Plotly.Plots.resize(GD.pca3dScatterPlot);
      }
    });

    var dgeaJsonFile = $('#DGEA').data("dgea-json");
    $.getJSON(dgeaJsonFile, function(json) {
      GD.volcanoPlot = GD.createVolcanoPlot(json.vol.logFC, json.vol.pVal, json.vol.genes);
      GD.initializeToptable(json.tops, 'dgea-top-table', 'dgea-top-table-wrapper');
    });

    var gseaJsonFile = $('#GSEA').data("gsea-json");
    $.getJSON(gseaJsonFile, function(json) {
      GD.initializeToptable(json.tops, 'gsea-top-table', 'gsea-top-table-wrapper');
    });
    window.addEventListener('resize', function() {
      /** global: Plotly */
      Plotly.Plots.resize(GD.pcaPlot);
      Plotly.Plots.resize(GD.volcanoPlot);
      Plotly.Plots.resize(GD.pca2dScatterPlot);
      Plotly.Plots.resize(GD.pca3dScatterPlot);
    });
    GD.addGraphTooltips();
  };

  GD.create2dPCAScatterPlot = function(pcdata, x, y) {

    var group1, group2, group1_name, group2_name, data, layout, parentWidth, PCAplotGd3, pcaPlot;
    group1_name = pcdata.group1[0];
    group2_name = pcdata.group2[0];
    console.log(group1_name);

    console.log(group2_name);
    group1 = { x: pcdata[ x + '.' + group1_name], y: pcdata[y + '.' + group1_name], text: pcdata.Group1, type: 'scatter', mode: 'markers', name: group1_name, marker: { symbol: 'circle' } };
    group2 = { x: pcdata[ x + '.' + group2_name], y: pcdata[y + '.' + group2_name], text: pcdata.Group2, type: 'scatter', mode: 'markers', name: group2_name, marker: { symbol: 'square' } };
    data = [group1, group2];
    layout = { xaxis: { title: x }, yaxis: { title: y }, hovermode: 'closest' };

    parentWidth = 100;
    PCAplotGd3 = Plotly.d3.select('#pca2d_plot')
                       .style({width: parentWidth + '%',
                              'margin-left': (100 - parentWidth) / 2 + '%'});
    pcaPlot = PCAplotGd3.node();

    Plotly.newPlot(pcaPlot, data, layout);
    return pcaPlot;
  };

  GD.create3dPCAScatterPlot = function(pcdata, x, y, z) {

    var group1, group2, group1_name, group2_name, data, layout, parentWidth, PCAplotGd3, pcaPlot;
    group1_name = pcdata.group1[0];
    group2_name = pcdata.group2[0];
    group1 = { x: pcdata[ x + '.' + group1_name], y: pcdata[y + '.' + group1_name], z: pcdata[ z + '.' + group1_name], text: pcdata.Group1, type: 'scatter3d', mode: 'markers', name: group1_name, marker: { symbol: 'circle' } };
    group2 = { x: pcdata[ x + '.' + group2_name], y: pcdata[y + '.' + group2_name], z: pcdata[ z + '.' + group2_name], text: pcdata.Group2, type: 'scatter3d', mode: 'markers', name: group2_name, marker: { symbol: 'square' } };
    data = [group1, group2];
    layout = { scene: {xaxis: { title: x }, yaxis: { title: y }, zaxis: {title: z} }, hovermode: 'closest' };

    parentWidth = 100;
    PCAplotGd3 = Plotly.d3.select('#pca3d_plot')
                       .style({width: parentWidth + '%',
                              'margin-left': (100 - parentWidth) / 2 + '%'});
    pcaPlot = PCAplotGd3.node();
    Plotly.newPlot(pcaPlot, data, layout);
    return pcaPlot;
  };

  GD.createPCAPLOT = function(cumVar, expVar, pcaNames) {
    var CumulativePCA = { x: pcaNames, y: cumVar, type: 'scatter', name: 'Cumulative PCA' };
    var PCA = { x: pcaNames, y: expVar, type: 'scatter', name: 'PCA' };
    var data = [CumulativePCA, PCA];
    var layout = { legend: { x: 0, y: 100, traceorder: 'normal' } };

    var parentWidth = 100;
    var PCAplotGd3 = Plotly.d3.select('#PCA_plot')
                       .style({width: parentWidth + '%',
                              'margin-left': (100 - parentWidth) / 2 + '%'});
    var pcaPlot = PCAplotGd3.node();
    Plotly.newPlot(pcaPlot, data, layout);
    return pcaPlot;
  };

  //
  GD.createVolcanoPlot = function(xValues, yValues, genes) {
    var trace1 = { x: xValues, y: yValues, text: genes, mode: 'markers', type: 'scatter', name: 'volcano_plot', marker: { size: 7.5 } };
    var data = [trace1];
    var layout = { xaxis: { title: 'Log 2 Fold Change'}, yaxis: { title: '-Log10(P Value)' }, hovermode: 'closest' };
    var parentWidth = 100;
    var volcanoPlotGd3 = Plotly.d3.select('#volcano_plot')
                       .style({width: parentWidth + '%',
                              'margin-left': (100 - parentWidth) / 2 + '%'});
    var volcanoPlot = volcanoPlotGd3.node();
    Plotly.newPlot(volcanoPlot, data, layout);
    return volcanoPlot;
  };

  GD.createExpressionPlot = function (response, geneId) {
    var trace1 = { x: response.group1.x, y: response.group1.y, type: 'bar', name: response.group1_name[0] };
    var trace2 = { x: response.group2.x, y: response.group2.y, type: 'bar', name: response.group2_name[0] };
    var data = [trace1, trace2];
    var layout = { barmode: 'group', xaxis: { title: 'Sample', tickangle: -40, position: -0.5}, yaxis: { title: 'Expression' } };
    var parentWidth = 100;
    var expressionPlotGd3 = Plotly.d3.select('#' + geneId + 'Plot')
                       .style({width: parentWidth + '%',
                              'margin-left': (100 - parentWidth) / 2 + '%'});
    var expressionPlot = expressionPlotGd3.node();
    Plotly.newPlot(expressionPlot, data, layout);
    window.addEventListener('resize', function() {
      Plotly.Plots.resize(expressionPlot);
    });
  };

  ///// General GD functions
  GD.initializeToptable = function(dataset, tableId, tableWrapperId) {
    dataset = GD.addPlotIconToTopTable(dataset);
    $('#' + tableId).dataTable({
      "oLanguage": {
        "sStripClasses": "",
        "sSearch": "",
        "sSearchPlaceholder": "Enter Keywords Here",
        "sInfo": "_START_ -_END_ of _TOTAL_",
        "sLengthMenu": '<span>Rows per page:</span><select class="browser-default">' +
          '<option value="10">10</option>' +
          '<option value="20">20</option>' +
          '<option value="30">30</option>' +
          '<option value="40">40</option>' +
          '<option value="50">50</option>' +
          '<option value="-1">All</option>' +
          '</select></div>'
      },
      data: dataset,
      order: [[ 5, "asc" ]],
      bAutoWidth: false
    });

    GD.makePlotIconClickable(tableWrapperId);

    $('#' + tableWrapperId).on('click', '.search-toggle', function() {
      if ($('.hiddensearch').css('display') == 'none') {
        $('.hiddensearch').slideDown();
      } else {
        $('.hiddensearch').slideUp();
      }
    });

    $('#' + tableWrapperId).on('click', '.download-top-table', function() {
        $('#modal_header_text').text('Creating Download Link');
        $('#modal_text').text('This should take a few seconds. Please leave this page open');
        $('#loading_modal').modal({ dismissible: false});
        $('#loading_modal').modal('open');
        $.fileDownload($(this).attr('href'), {
            successCallback: function() {
              $('#loading_modal').modal('close');
            },
            failCallback: function() {
              $('#loading_modal').modal('close');
            }
        });
        return false; //this is critical to stop the click event which will trigger a normal file download!
    });
  };

  GD.addPlotIconToTopTable = function(dataset) {
    $.each(dataset, function(key, row) {
      row.push( '<i class="material-icons child-row-chart light-blue-text text-darken-3">insert_chart</i>' );
    });
    return (dataset);
  };

  GD.makePlotIconClickable = function(tableWrapperId) {
    $('#' + tableWrapperId).on('click', '.child-row-chart', function() {
      var currentRow = $(this).closest('tr');
      var geneId = currentRow.children('td:first').text();
      if ( $( '#' + geneId + 'ChildRow' ).length ) {
        $('#' + geneId + 'ChildRow').remove();
      } else {
        if (tableWrapperId === 'dgea-top-table-wrapper') {
          GD.geneExpressionAjax(currentRow, geneId);
        } else if (tableWrapperId === 'gsea-top-table-wrapper'){
          GD.interactionNetworkAjax(currentRow, geneId);
        }
      }
    });
  };

  GD.initialiatizePcaScatterPlot = function(pcnames) {
    $.each(pcnames, function(key,value) {
      $('#PC2doption1').append($("<option></option>")
        .attr("value", value).text(value));
      $('#PC2doption2').append($("<option></option>")
        .attr("value", value).text(value));
      $('#PC3doption1').append($("<option></option>")
        .attr("value", value).text(value));
      $('#PC3doption2').append($("<option></option>")
        .attr("value", value).text(value));
      $('#PC3doption3').append($("<option></option>")
        .attr("value", value).text(value));
    });
    GD.loadPcRedrawValidation();
  };

  //
  GD.addFactorToggle = function() {
    $("input:radio[name=factor]").click(function() {
      var target = '#' + $(this).attr('id') + '_select';
      if ('#' + $('.select_factors:visible').attr('id') !== target) {
        $('.select_factors').hide();
        $('.select_factors select').attr("disabled", "disabled");
        $(target).show();
        $(target + ' select').removeAttr("disabled");
      }
      $('#groupa_params').attr('data-tooltip', 'This is Group A' );
      $('#groupa_params').tooltip({delay: 50});
      $('#groupb_params').attr('data-tooltip', 'This is Group B' );
      $('#groupb_params').tooltip({delay: 50});
      GD.ensureOnlyOneSelectOption();
    });
  };

  GD.addAdvParamLogic = function() {
    GD.show_hide_div('#DGEA_input', '#DGEAparams');
    GD.show_hide_div('#GSEA_input', '#GSEAparams');
    GD.show_hide_div('#dgea_toptable', '#dgea_toptable_params');
    GD.show_hide_div('#dgea_heatmap', '#dgea_heatmap_params');
    GD.show_hide_div('#gsea_heatmap', '#gsea_heatmap_params');
    $("input:radio[name=gsea_type]").click(function() {
      if ( $("input:radio[name=gsea_type]:checked").val() == 'ExpVsCtrl') {
        $('#gage_select_control').show();
      } else {
        $('#gage_select_control').hide();
      }
    });
  };

  GD.show_hide_div = function(checkbox, div) {
    $(checkbox).change(function(){
      if($(this).prop("checked")) {
        $(div).show();
      } else {
        $(div).hide();
      }
    });
  };

  GD.addGeoDbInfo = function (geoAccession) {
    var accession = geoAccession.toUpperCase();
    var jsonFile = 'http://' + window.location.host + '/GeoDiver/DBs/' + accession + '.json';
    $.getJSON(jsonFile, function(json) {
      $('#dataset_accession').text(' ' + json.Accession);
      $('#dataset_title').text(json.Title);
      $('#dataset_summary').text(json.Description);
      $('#dataset_organism').text(json.Sample_Organism);
      $('#dataset_summary').text(json.Description);
      $('#dataset_citation').text(json.Reference);
    });
  };

  GD.addUserDropDown = function() {
    $('.dropdown-button').dropdown({
      inDuration: 300, outDuration: 225, hover: true, belowOrigin: true, alignment: 'right'
    });
  };

  GD.download_all_results = function () {
    $('#results_section').on('click', '#download-all-results', function(event) {
      event.preventDefault();
      $('#modal_header_text').text('Creating Download Link');
      $('#modal_text').text('This should take a few seconds. Please leave this page open');
      $('#loading_modal').modal({ dismissible: false});
      $('#loading_modal').modal('open');
      $.fileDownload($(this).data('download'), {
          successCallback: function() {
            $('#loading_modal').modal('close');
          },
          failCallback: function() {
            $('#loading_modal').modal('close');
          }
      });
      $('#loading_modal').modal('close');
      return false; //this is critical to stop the click event which will trigger a normal file download!
    });
  };

  GD.delete_result = function () {
    $('#results_section').on('click', '#delete_results', function() {
      $('#delete_modal').modal('open');
      var resultId = $(this).closest('.card').data('result');
      var geoDb =  $(this).closest('.card').data('geodb');
      $('#delete_modal').attr('data-result', resultId);
      $('#delete_modal').attr('data-geodb', geoDb);
    });

    $('.delete-results').click(function() {
      $('#modal_header_text').text('Deleting Result');
      $('#modal_text').text('This should take a few seconds. Please leave this page open');
      $('#loading_modal').modal({ dismissible: false});
      $('#loading_modal').modal('open');
      var resultId = $('#delete_modal').data('result');
      var geoDb =  $('#delete_modal').data('geodb');
      $.ajax({
        type: 'POST',
        url: '/delete_result',
        data: {result_id: resultId, geo_db: geoDb},
        success: function() {
          location.reload();
        },
        error: function(e, status) {
          GD.ajaxError(e, status);
        }
      });
    });
  };

  GD.show_GeoDB_modal = function () {
    $('#results_section').on('click', '.open_db_info_modal', function() {
      var accession = $(this).data('accession');
      GD.addGeoDbInfo(accession);
      $('#dbInfo').modal('open');
    });
  };

  GD.share_result = function () {
    $('#results_section').on('click', '#share_btn', function() {
      var share_link =  $(this).closest('.card').data('share-link');
      $('#share_the_link_btn').show();
      $('#share_btn').hide();
      $('#share_link_input').val(share_link);
      $('#share_link_input').prop("readonly", true);
      $('#share_modal').modal('open');
      $('#share_modal').attr('data-share-link', share_link);
      $('#share_link_input').select();
      $.ajax({
        type: 'POST',
        url: share_link,
        error: function(e, status) {
          GD.ajaxError(e, status);
        }
      });
    });
    $('#results_section').on('click', '#share_the_link_btn', function() {
      var share_link =  $(this).closest('.card').data('share-link');
      $('#share_link_input1').val(share_link);
      $('#share_link_input1').prop("readonly", true);
      $('#share_the_link_modal').modal('open');
      $('#share_the_link_modal').attr('data-share-link', share_link);
      $('#share_link_input1').select();
    });

    $(".share_link_input").focus(function() {
      $(this).select();
      // Work around Chrome's little problem
      $(this).mouseup(function() {
          // Prevent further mouseup intervention
          $(this).unbind("mouseup");
          return false;
      });
    });
  };

  GD.remove_share = function () {
    $('.remove_link').click(function() {
      var share_link =  $(this).closest('.modal').data('share-link');
      var remove_link = share_link.replace(/\/sh\//, '/rm/');
      $('#share_the_link_btn').hide();
      $('#share_btn').show();
      $('#share_modal').modal('close');
      $('#share_the_link_modal').modal('close');
      $.ajax({
        type: 'POST',
        url: remove_link,
        error: function(e, status) {
          GD.ajaxError(e, status);
        }
      });
    });
  };

  GD.ensureOnlyOneSelectOption = function() {
    $('.select_factors:visible select[name="groupa[]"], .select_factors:visible select[name="groupb[]"]').on('change', function() {
      // RESET both arrays
      $('.select_factors:visible select[name="groupa[]"]').siblings('ul').children('li').not(':first-child').prop('disabled', false);
      $('.select_factors:visible select[name="groupa[]"]').siblings('ul').children('li').not(':first-child').removeClass('disabled');
      $('.select_factors:visible select[name="groupa[]"]').siblings('ul').children('li').not(':first-child').find('input:checkbox').prop('disabled', false);
      $('.select_factors:visible select[name="groupa[]"]').children().not(':first-child').prop('disabled', false);

      $('.select_factors:visible select[name="groupb[]"]').siblings('ul').children('li').not(':first-child').prop('disabled', false);
      $('.select_factors:visible select[name="groupb[]"]').siblings('ul').children('li').not(':first-child').removeClass('disabled');
      $('.select_factors:visible select[name="groupb[]"]').siblings('ul').children('li').not(':first-child').find('input:checkbox').prop('disabled', false);
      $('.select_factors:visible select[name="groupb[]"]').children().not(':first-child').prop('disabled', false);

      var aValues = $('.select_factors:visible select[name="groupa[]"]').val();
      var bValues = $('.select_factors:visible select[name="groupb[]"]').val();
      var selector, valueIndex;

      $.each(aValues, function(i){
        selector = '.select_factors:visible select[name="groupb[]"] option[value="' + aValues[i] + '"]';
        $(selector).prop('disabled', true);
        valueIndex = $(selector).index() + 1;
        $('.select_factors:visible select[name="groupb[]"]').siblings('ul').children('li:nth-child('+ valueIndex +')').addClass('disabled');
        $('.select_factors:visible select[name="groupb[]"]').siblings('ul').children('li:nth-child('+ valueIndex +')').find('input:checkbox').prop('disabled', true);
      });
      $.each(bValues, function(i){
        selector = '.select_factors:visible select[name="groupa[]"] option[value="' + bValues[i] + '"]';
        $(selector).prop('disabled', true);
        valueIndex = $(selector).index() + 1;
        $('.select_factors:visible select[name="groupa[]"]').siblings('ul').children('li:nth-child('+ valueIndex +')').addClass('disabled');
        $('.select_factors:visible select[name="groupa[]"]').siblings('ul').children('li:nth-child('+ valueIndex +')').find('input:checkbox').prop('disabled', true);
      });
    });
  };

  GD.addGraphTooltips = function () {
    $('#dgea-top-table .child-row-chart').tooltip({tooltip: 'Show a graph for the inidividual expression levels for this Gene', position: 'left' });
    $('#gsea-top-table .child-row-chart').tooltip({tooltip: 'Show a colour coded interaction network for this pathway', position: 'left' });
  };

  GD.setupGoogleAuthentication = function () {
    gapi.auth.authorize({
      immediate: true,
      response_type: 'code',
      cookie_policy: 'single_host_origin',
      client_id: GD.CLIENT_ID,
      scope: 'email'
    });
    $('.login_button').on('click', function(e) {
      e.preventDefault();
      /** global: gapi */
      gapi.auth.authorize({
        immediate: false,
        response_type: 'code',
        cookie_policy: 'single_host_origin',
        client_id: GD.CLIENT_ID,
        scope: 'email'
      }, function(response) {
        if (response && !response.error) {
          // google authentication succeed, now post data to server.
          jQuery.ajax({
            type: 'POST',
            url: "/auth/google_oauth2/callback",
            data: response,
            success: function() {
              // TODO - just update the DOM instead of a redirect
              $(location).attr('href', 'http://' + window.location.host + '/analyse');
            }
          });
        } else {
          // TODO: ERROR Response google authentication failed
        }
      });
    });
  };
}());

(function($) {
  $.fn.exists = function() {return this.length>0;};

  // Fn to allow an event to fire after all images are loaded
  $.fn.imagesLoaded = function () {
    var $imgs = this.find('img[src!=""]');
    // if there's no images, just return an already resolved promise
    if (!$imgs.length) {return $.Deferred().resolve().promise();}

    // for each image, add a deferred object to the array which resolves when the image is loaded (or if loading fails)
    var dfds = [];
    $imgs.each(function(){
        var dfd = $.Deferred();
        dfds.push(dfd);
        /** global: Image */
        var img = new Image();
        img.onload = function(){dfd.resolve();};
        img.onerror = function(){dfd.resolve();};
        img.src = this.src;
    });
    // return a master promise object which will resolve when all the deferred objects have resolved
    // IE - when all the images are loaded
    return $.when.apply($,dfds);
  };

  $(function() {
    $('.button-collapse').sideNav();
    $('select').material_select();
    $('#login_modal').modal();
    if ($('#load_geo_db').length) {
      GD.setUpValidatorDefaults();
      GD.loadGeoDbValidation();
    }
    if ($('#exemplar_result').length) { GD.exemplar_results(); }
    GD.addUserDropDown();
  });

  $(function() {
    return $.ajax({
      url: 'https://apis.google.com/js/client:plus.js?onload=gpAsyncInit',
      dataType: 'script',
      cache: true
    });
  });

  window.gpAsyncInit = function() {
    GD.setupGoogleAuthentication();
  };
})(jQuery);

GeoDiver / GeoDiver

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GD.loadPcRedrawValidation C

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