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

Open

    initTooltip() {
        this.inputGroup().tooltip({
            trigger: 'manual',
            title: _.bind(function () {
                if (!this.state.hasQuery && !this.state.hasDatabases) {

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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()});
        }

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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

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

Open

  hspStats() {
    // An array to hold text or span elements that make up the line.
    let line = [];

    // Bit score and total score.

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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;

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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.
     */

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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; }

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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;

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Avoid too many return statements within this function.

Open

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

Function renderDatabases has a Cognitive Complexity of 6 (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-md-12' :

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Function determineBlastMethods has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.

Open

    determineBlastMethods() {
        var database_type = this.databaseType;
        var sequence_type = this.sequenceType;

        if (this.refs.query.isEmpty()) {

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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)

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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

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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)

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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

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Function initiate has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.

Open

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

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Function selectHit has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.

Open

    selectHit(id) {
        var checkbox = $('#' + id);
        var num_checked = $('.hit-links :checkbox:checked').length;

        if (!checkbox || !checkbox.val()) {

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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])

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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 = []

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