Method spawn_cleanup has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring.

Open

    def spawn_cleanup
      Thread.new do
        loop do
          now = Time.now
          finished_jobs = Job.all.select(&:done?)

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Function calculate_multipliers has 43 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    calculate_multipliers() {
        var sum_query_length = 0;
        var sum_hit_length = 0;
        _.each(
            this.query_arr,

Function render has 41 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    render() {
        return (
            <div
                className="dnd-overlay absolute left-0 top-0 w-full h-full bg-gray-200 bg-opacity-75 z-40"
                style={{ display: 'none' }}>

Method sys has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.

Open

  def self.sys(command, options = {})
    # Available output channels
    channels = %i[stdout stderr]

    # Make temporary files to store output from stdout and stderr.

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Function Grapher has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.

Open

export default function Grapher(Graph) {
    return class extends React.Component {
        constructor(props) {
            super(props);
            this.name = Graph.name();

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Function initiate has 39 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    initiate() {
    // this.width = 700;
        this.width = this.svgContainer.width();
        this.height = 600;
        this.innerRadius = 200;

Function renderForm has 39 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  renderForm() {
    const { email, agreeToTos } = this.state;
    const isSubmitDisabled = !agreeToTos;

    return(

Function buildLayers has 38 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    this.buildLayers = function(data, margin) {
        var block, datum, i, idx, l, lastDatumInLayer, layer, layers, len, len1, m, placed, ref;
        for (idx in data) {
            block = data[idx];
            block.values = block.values.sort(function(a, b) {

Function applyRules has 37 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    this.applyRules = function(rules, data) {
        var datum, i, k, layer, results, rule, v;
        rules = rules || [];
        results = [];
        for (k in data) {

Function Scatter has 36 lines of code (exceeds 25 allowed). Consider refactoring.

Open

circosJS.Scatter = function() {
    circosJS.Track.call(this);
    this.parseData = circosJS.parsePositionValueData;
    this.renderDatumContainer = (function(_this) {
        return function(instance, parentElement, name, data, conf) {

Function Line has 36 lines of code (exceeds 25 allowed). Consider refactoring.

Open

circosJS.Line = function() {
    circosJS.Track.call(this);
    this.parseData = circosJS.parsePositionValueData;
    this.renderDatumContainer = (function(_this) {
        return function(instance, parentElement, name, data, conf) {

Function construct_layout has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.

Open

    construct_layout() {
        var hsp_count = 0;
        var query_count = 0;
        var num_karyotype = 32;
        var num_queries = this.queries.length;

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Function Chord has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.

Open

circosJS.Chord = function() {
    circosJS.Track.call(this);
    this.parseData = circosJS.parseChordData;
    this.applyRules = function(rules, data) {
        var datum, l, len, results, rule;

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Function parsePositionValueData has 35 lines of code (exceeds 25 allowed). Consider refactoring.

Open

circosJS.parsePositionValueData = function(data, layoutSummary) {
    var groups, sample;
    sample = data[0];
    if ('parent_id' in sample && 'position' in sample) {
        data = data.map(function(datum) {

Function drawLegend has 34 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    drawLegend(svg, options, width, height, hits) {
        var svg_legend = svg.append('g')
            .attr('transform',
                'translate(0,' + (height - 1.75 * options.margin) + ')');

Function parsePositionTextData has 34 lines of code (exceeds 25 allowed). Consider refactoring.

Open

circosJS.parsePositionTextData = function(data, layoutSummary) {
    var groups, sample;
    sample = data[0];
    if ('parent_id' in sample && 'position' in sample) {
        data = data.map(function(datum) {

Function renderDatum has 34 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    this.renderDatum = function(parentElement, conf, layout, utils) {
        var bin;
        bin = parentElement.selectAll('.bin').data(function(d) {
            return d.values;
        }).enter().append('path').attr('class', 'bin').attr('opacity', function(d) {

Function hitLinks has 33 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    hitLinks() {
        var btns = [];
        if (!(this.props.imported_xml || this.props.non_parse_seqids)) {
            btns = btns.concat([
                this.viewSequenceButton(),

Function renderAxes has 33 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    this.renderAxes = function(parentElement, conf, layout, data) {
        var axes, axis, x;
        if (conf.axes.minor.spacingType === 'pixel') {
            axes = (function() {
                var l, ref, ref1, ref2, results;

Function hit_details has 33 lines of code (exceeds 25 allowed). Consider refactoring.

Open

                        _.bind(function (hit) {
                            if (hit.number < num_hits) {
                                var hsp_details = _.map(
                                    hit.hsps,
                                    _.bind(function (hsp) {