Highcharts.theme = {
  colors: ['#acf19e', '#f9ba85', '#9dc8f1', '#28a745', '#c0c0c0', '#e15a5a', '#24CBE5', '#64E572', '#FF9655', '#FFF263', '#6AF9C4']
};
Highcharts.setOptions(Highcharts.theme);
var colors = Highcharts.getOptions().colors;
var param = {};
var metrics_table, rawdata_table;
//Default qc_measure to draw histogram
var default_qc_measure = "High Quality Exonic Rate";
var default_field = "high_quality_exonic_rate";

$(document).ready(function () {

  //plot three bar charts
  drawStudySummary("RNA-seq", "summary_barchart_rnaseq", colors[3]);
  drawStudySummary("Methylation", "summary_barchart_methylation", colors[8]);
  drawStudySummary("Metabolomics", "summary_barchart_metabolomics", colors[7]);
  drawStudySummary("Proteomics", "summary_barchart_proteomics", colors[5]);

  //plot line/area chart
  drawProgressOverTime();

  //Generate summary table
  updateSummary();

  //generate metrics table tabulator
  metrics_table = new Tabulator("#qc_metrics_table", {
    placeholder: 'No result found.',
    layout: "fitColumns",
    movableRows:true,
    tooltips: true,
    autoColumns:false,
    selectable: 1,
    ajaxURL: '/omics/lib/qc_metrics_table.php',
    ajaxConfig: 'GET',
    pagination: 'remote',
    responsiveLayout: false,
    columns: [
      {rowHandle:true, formatter:"handle", headerSort:false, width:30, minWidth:30},
      {title: 'QC Measures', field: 'full_attribute', headerFilter: "input", headerFilterPlaceholder:"Search", width: "35%", tooltip:
        function (row) { return row.getData().description; }
      },
      {title: 'Mean', field: 'mean' },
      {title: 'SD', field: 'sd'},
      {title: 'Min', field: 'min', download: true},
      {title: '25%', field: 'pct25', visible:false, download: true },
      {title: 'Median', field: 'median'},
      {title: '75%', field: 'pct75', visible:false, download: true },
      {title: 'Max', field: 'max', download: true },
    ],
    rowClick: function(e, row){
      param["field"] = row.getData().field_name;
      param["study"] = $("#sel_study_histogram").val();
      param["compare"] = $("#sel_study_two").val();
      param["label"]= row.getData().full_attribute;
      drawHistogram(param);
    },
    rowFormatter: function(row){
      if(row.getData().full_attribute == default_qc_measure) {
        row.select();
      }
    },
  });


  //hide pagination footer controls
  $("#qc_metrics_table .tabulator-footer").hide();

  //download qc metrics data
  $("#download-table-metrics").click(function(){
    metrics_table.download("csv", "omics-table-metrics.tsv", {delimiter: '\t'});
  });

  $("#sel_study_histogram, #sel_study_two").on('change', function() {
    param['study'] = $("#sel_study_histogram").val();
    param['compare'] = $("#sel_study_two").val();
    drawHistogram(param);
  });

  //Draw default histogram using pre-defined qc measure
  if($("#study_dropdown").hasClass("hidden")) {
    var opts = studyDropdown("RNA-seq","All studies",true);
    $("#sel_study_histogram").append(opts);
    opts = studyDropdown("RNA-seq", "", true);
    $("#sel_study_two").append(opts);
    $("#study_dropdown").removeClass("hidden");
  }
  param["field"] = default_field;
  param["study"] = "All studies";
  param["label"]= default_qc_measure;
  drawHistogram(param);

});

//update the summary table with numbers
function updateSummary() {
  var dataset = $.ajax({
    url : "/omics/lib/summary_by_center_type.php",
    dataType : "json",
    async : false,
  }).responseText;
  var jsonData = JSON.parse(dataset);
  var total_broad=0;
  var total_nwgc=0;
  var total_usc=0;
  var total_baylor=0;
  var total_nygc=0;
  var total_rna=0;
  var total_methylation=0;
  var total_metabolomics=0;
  var total_proteomics=0;
  var total = 0;
  for(var i=0; i<jsonData.length; i++) {
    var elem = "#"+jsonData[i]["center"].toLowerCase()+"-"+jsonData[i]["datatype"].toLowerCase();
    switch(jsonData[i]["center"]){
      case "Broad":
        total_broad+=Number(jsonData[i]["num"]);
        break;
      case "NWGC":
        total_nwgc+=Number(jsonData[i]["num"]);
        break;
      case "USC":
        total_usc+=Number(jsonData[i]["num"]);
	break;
      case "Baylor":
        total_baylor+=Number(jsonData[i]["num"]);
	break;
      case "NYGC":
 	total_nygc+=Number(jsonData[i]["num"]);
	break;
      default:
    }
    switch(jsonData[i]["datatype"]){
      case "RNA-seq":
        total_rna+=Number(jsonData[i]["num"]);
        break;
      case "Methylation":
        total_methylation+=Number(jsonData[i]["num"]);
        break;
      case "Metabolomics":
        total_metabolomics+=Number(jsonData[i]["num"]);
	break;
      case "Proteomics":
        total_proteomics+=Number(jsonData[i]["num"]);
        break;
      default:
    }
    total=total_rna+total_methylation+total_metabolomics+total_proteomics;
    $(elem).text(Number(jsonData[i]["num"]).toLocaleString('en'));
    $("#total-rna-seq").text(total_rna.toLocaleString('en'));
    $("#total-methylation").text(total_methylation.toLocaleString('en'));
    $("#total-metabolomics").text(total_metabolomics.toLocaleString('en'));
    $("#total-proteomics").text(total_proteomics.toLocaleString('en'));
    $("#broad-total").text(total_broad.toLocaleString('en'));
    $("#nwgc-total").text(total_nwgc.toLocaleString('en'));
    $("#usc-total").text(total_usc.toLocaleString('en'));
    $("#baylor-total").text(total_baylor.toLocaleString('en'));
    $("#nygc-total").text(total_nygc.toLocaleString('en'));
    $("#total-all").html("<strong>"+ total.toLocaleString('en')+"</strong>");
  }
}

function rawDataTable(study="", pageSize=100) {
  //generate Samples raw table tabulator
  rawdata_table = new Tabulator("#sample_raw_table", {
    placeholder: 'No result found.',
    tooltipsHeader: true,
    layout: "fitColumns",
    //height: "700px",
    ajaxURL: '/omics/lib/sample_raw_qc.php',
    ajaxConfig: 'post',
    pagination: 'remote',
    paginationSize: pageSize,
    ajaxSorting: true,
    ajaxFiltering: true,
    responsiveLayout: true,
    ajaxParams: {"study": study},
    columns: [
      { title: 'Samples', 
        columns: [
          {title: 'TORID', field: 'torid', headerFilter:"input", headerFilterPlaceholder:"Search"},
          {title: 'Study', field: 'study_id'}
        ],
      },
      { title: 'QC measures',
        columns: [
          {title: 'High Quality Rate', field: 'high_quality_rate' },
          {title: 'Mapping Rate', field: 'mapping_rate'},
          {title: 'High Quality Exonic Rate', field: 'high_quality_exonic_rate'},
          {title: 'High Quality Intronic Rate', field: 'high_quality_intronic_rate'},
          {title: 'High Quality Intergenic Rate', field: 'high_quality_intergenic_rate'},
          {title: 'Median 3\' bias', field: 'median_3_bias'},
          {title: 'Duplicate Rate of Mapped', field: 'dupli_rate_mapped'},
          {title: 'rRNA Rate', field: 'rrna_rate' },
        ],
      }
    ],
  });
}

function drawStudySummary(topic="RNA-seq", div, color) {
  //dataset for samples
  var dataset = $.ajax({
    url : "/omics/lib/sample_summary.php?topic="+topic,
    dataType : "json",
    async : false,
  }).responseText;
  var jsonData = JSON.parse(dataset);

  //set bar chart options
  var options_summary = {
    chart: {
      renderTo: div,
      type: 'bar',
    },
    xAxis: {
      categories: jsonData['category'],
      title: {
        text: 'Studies'
      },
    },
    title: {
      text:  topic
    },
    subtitle: {
      text: jsonData["total"] + ' total samples'
    },
    yAxis : {
      title : {
        text: 'Total OMICS samples received',
      },
    },
    legend: {
      enabled: false
    },
    plotOptions: {
      series: {
        dataLabels: {
          enabled: true
        },
	animation: false,
        maxPointWidth: 30
      }
    },
    tooltip: {
      style: {
        fontSize: '15px',
      }
    },
    credits: {
      enabled: false
    },
    exporting: {
      buttons: {
        contextButton: {
          menuItems: ['downloadPNG','downloadJPEG','downloadPDF']
        }
      }
    },
    series: [{
      name: 'OMICS samples',
      data: jsonData['dataset'],
      color: color,
    }]
  };
  var barchart = new Highcharts.Chart(options_summary);  
}

function drawProgressOverTime() {
  var jsonData;
  var dataset = $.ajax({
    url : "/omics/lib/progress_overtime.php",
    dataType : "json",
    async : false,
  }).responseText;

  jsonData = JSON.parse(dataset);
  //set chart options
  var options_timeline = {
    chart: {
      //renderTo: 'timeline_chart',
      type: 'spline',
      zoomType: 'x',
    },
    xAxis: {
      type: 'datetime',
      dateTimeLabelFormats: {
        month: '%b %Y'
      },
      title: {
        text: 'Arrival Date'
      },
    },
    title: {
      text:  'RNA-seq progress over time',
      style: {
        color: '#1b809e',
        fontWeight: 'normal',
        fontSize: '1.75rem'
      }
    },
    yAxis : {
      title : {
        text: 'Total OMICS samples received',
      },
    },
    tooltip: {
      style: {
        fontSize: '15px',
      },
      formatter: function() {
        return  'By : ' + Highcharts.dateFormat('%b %e, %Y', new Date(this.x))
                + '<br/>Total samples received: ' + this.y;
      }
    },
    legend: {
      enabled: false
    },
    plotOptions: {
      spline: {
        lineWidth: 2,
        dataLabels: {
          enabled: true,
        },
        marker: {
          enabled: true,
          symbol: 'circle',
          states: {
            hover: {
              enabled: true
            }
          }
        }
      },
    },
    credits: {
      enabled: false
    },
    exporting: {
      buttons: {
        contextButton: {
          menuItems: ['downloadPNG','downloadJPEG','downloadPDF']
        }
      }
    },
    series: [{
      name: 'completed samples',
      data: jsonData,
      color: colors[6],
    }]
  };
  var linechart = Highcharts.chart('timeline_chart', options_timeline);
}

function studyDropdown(topic="RNA-seq", firstSel="All studies", addCenter=false) {
  var dataset = $.ajax({
    url : "/omics/lib/sample_summary.php?topic="+topic,
    dataType : "json",
    async : false,
  }).responseText;
  var jsonData = JSON.parse(dataset);
  var studies = jsonData["studies"];
  var selection;
  if(firstSel == "All studies") {
    selection += '<OPTION value="All studies">All studies</OPTION>';
  } else {
    selection += '<OPTION value="">Choose one</OPTION>';
  }
  jQuery.each(studies, function(){
    selection += '<OPTION value="'+this+'">'+this+'</OPTION>';
  });
  if(addCenter) {
    selection += '<OPTION value="Broad">Broad(center)</OPTION>';
    selection += '<OPTION value="NWGC">NWGC(center)</OPTION>';
    selection += '<OPTION value="NYGC">NYGC(center)</OPTION>';
  }
  return selection;
}

function drawHistogram(param) {
  if(param) {
    var json = $.ajax({
      url : "/omics/lib/datasets_by_measure.php",
      data: param,
      dataType : "json",
      async : false,
    }).responseText;

  var jsonColData = JSON.parse(json);
  var subtitle = param['study'] +" ("+jsonColData['data'].length+" samples)";
  subtitle+=(param["compare"])?" vs. "+param["compare"]+" ("+jsonColData["compare"].length+" samples)":"";

  Highcharts.chart('qc_histogram', {
    title: {
      text: jsonColData['label'] 
    },
    subtitle: {
      text: subtitle,		
    },
    xAxis: [{
      title: { text: '' },
      alignTicks: false,
      opposite: true
    }, {
      title: { text: 'QC Value' },
      alignTicks: false,
    }],
    yAxis: [{
      title: { text: '' },
      opposite: true      
    }, {
      title: { text: 'Histogram' },
    }],
    legend:{ enabled:true },
    credits:{ enabled:false },
    tooltip: {
      style: { fontSize: '15px' }
    },
    plotOptions: {
      histogram: {
        accessibility: {
          pointDescriptionFormatter: function (point) {
            var ix = point.index + 1,
              x1 = point.x.toFixed(3),
              x2 = point.x2.toFixed(3),
              val = point.y;
            return ix + '. ' + x1 + ' to ' + x2 + ', ' + val + '.';
          }
        },
       //animation: false
      }
    },
    exporting: {
      buttons: {
        contextButton: {
          menuItems: ['downloadPNG','downloadJPEG','downloadPDF']
        }
      }
    }, 
    series: [{
      name: param["study"],
      type: 'histogram',
      xAxis: 1,
      yAxis: 1,
      baseSeries: 's1',
      zIndex: -1,
      color: colors[7],
    }, {
      name: 'Scatter',
      type: 'scatter',
      data: jsonColData['data'],
      id: 's1',
      marker: {
        radius: 1.5
      },
      visible: false,
      showInLegend: false
    }, {
      name: param["compare"],
      type: 'histogram',
      //pointWidth: 1,
      xAxis: 1,
      yAxis: 1,
      baseSeries: 's2',
      zIndex: -1,
      color: 'rgba(162,20,47,0.60)'
    }, {
      type: 'scatter',
      data: jsonColData['compare'],
      id: 's2',
      visible: false,
      showInLegend: false
    }]
   });
  };	
}