Avoid deeply nested control flow statements.

Open

            for (trackId in store) {
                svg.select('.' + trackId).remove();
                delete store[trackId];
            }

Consider simplifying this complex logical expression.

Open

    if ('source_id' in sample && 'source_start' in sample && 'source_end' && 'target_id' in sample && 'target_start' in sample && 'target_end' in sample) {
        data = data.map(function(datum) {
            var elts;
            elts = [datum.source_id, datum.source_start, datum.source_end, datum.target_id, datum.target_start, datum.target_end];
            if (datum.value != null) {

Function asMailtoHref has 5 arguments (exceeds 4 allowed). Consider refactoring.

Open

export default function asMailtoHref(querydb, program, numQueries, url, isOpenAccess) {

Function composeEmail has 5 arguments (exceeds 4 allowed). Consider refactoring.

Open

function composeEmail(dbsArr, program, numQueries, url, isOpenAccess) {

Method make_blast_database has 5 arguments (exceeds 4 allowed). Consider refactoring.

Open

    def make_blast_database(action, file, title, type, non_parse_seqids = false)

Function processConf has 5 arguments (exceeds 4 allowed). Consider refactoring.

Open

    this.processConf = function(conf, defaultConf, meta, instance, utils) {

Function graphIt has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.

Open

    graphIt($queryDiv, $graphDiv, index, howMany, opts, inhits) {
    /* barHeight: Height of each hit track.
     * legend: Height reserved for the overview legend.
     * margin: Margin around the svg element.
     */

• Read up
  Read up

Function graphControls has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.

Open

    graphControls($queryDiv, $graphDiv, isInit, opts, hits) {
        var MIN_HITS_TO_SHOW = 20;

        var totalHits, shownHits, lessButton, moreButton;

• Read up
  Read up

Function draw_axes has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.

Open

    draw_axes() {
        var space, len;
        len = this._scale_y.ticks().length;
        if (len >= 5) {
            space = 5;

• Read up
  Read up

Method raise! has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.

Open

      def raise!
        return true if exitstatus.zero? && !File.zero?(stdout)

        case exitstatus
        when 1..2

• Read up
  Read up

Function renderDatabases has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.

Open

    renderDatabases(category) {
        // Panel name and column width.
        var panelTitle = category[0].toUpperCase() +
            category.substring(1).toLowerCase() + ' databases';
        var columnClass = this.categories().length === 1 ? 'col-span-2' : '';

• Read up
  Read up

Function type has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.

Open

    type() {
        let sequence = this.value().trim();
        // FASTQ detected, but we don't know if conversion has succeeded yet
        // will notify separately if it does
        if (sequence.startsWith('@') ) { return undefined; }

• Read up
  Read up

Function componentDidUpdate has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.

Open

    componentDidUpdate(_prevProps, prevState) {
        // If there's only one database, select it.
        if (this.databases() && this.databases().length === 1 && this.state.currentlySelectedDatabases.length === 0) {
            this.setState({currentlySelectedDatabases: this.databases()});
        }

• Read up
  Read up

Avoid too many return statements within this function.

Open

            return v / conf.ticks.labelDenominator + conf.ticks.labelSuffix;

Method validate_options has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.

Open

      def validate_options(options)
        return true if !options || (options.is_a?(String) &&
                                    options.strip.empty?)

        fail InputError, 'Invalid characters detected in options.' unless allowed_chars.match(options)

• Read up
  Read up

Method check_num_threads has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.

Open

    def check_num_threads
      num_threads = Integer(config[:num_threads])
      fail NUM_THREADS_INCORRECT unless num_threads.positive?
      logger.debug "Will use #{num_threads} threads to run BLAST."
      if num_threads > 256

• Read up
  Read up

Method write_entries has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.

Open

  def write_entries(entries, path, zipfile)
    entries.each do |e|
      zipfile_path = path == '' ? e : File.join(path, e)
      disk_file_path = File.join(@input_dir, zipfile_path)

• Read up
  Read up

Method update_searchdata_from_job has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.

Open

    def update_searchdata_from_job(searchdata)
      job = fetch_job(params[:job_id])
      return { error: 'Job not found' }.to_json if job.nil?
      return if job.imported_xml_file

• Read up
  Read up

Method probably_fastas has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.

Open

    def probably_fastas
      return @probably_fastas if defined?(@probably_fastas)

      @probably_fastas = []

• Read up
  Read up

Method init_binaries has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.

Open

    def init_binaries
      if config[:bin]
        config[:bin] = File.expand_path config[:bin]
        unless File.exist?(config[:bin]) && File.directory?(config[:bin])
          fail ENOENT.new('bin dir', config[:bin])

• Read up
  Read up