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Similar blocks of code found in 2 locations. Consider refactoring.
Open

                if (_.indexOf(this.chordsHide, index) == -1) {
                    var slen = obj[1] + obj[2];
                    var tlen = obj[4] + obj[5];
                    $('#' + obj[0] + '_' + slen + '_' + obj[3] + '_' + tlen).hide();
                }
Severity: Major
Found in public/js/circos.js and 1 other location - About 2 hrs to fix
public/js/circos.js on lines 427..431

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 91.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Similar blocks of code found in 2 locations. Consider refactoring.
Open

        svg_legend.append('text')
            .attr('class',' legend-text')
            .attr('transform', 'translate(0, ' + options.legend + ')')
            .attr('x', 6.7 * (width - 2 * options.margin) / 10 - options.margin / 2)
            .text('Stronger hits');
Severity: Major
Found in public/js/hits_overview.js and 1 other location - About 2 hrs to fix
public/js/hits_overview.js on lines 180..184

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 89.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Similar blocks of code found in 3 locations. Consider refactoring.
Open

        bin = parentElement.selectAll('.bin').data(function(d) {
            return d.values;
        }).enter().append('path').attr('class', 'bin').attr('opacity', function(d) {
            return d.opacity || conf.opacity;
        }).attr('d', d3.svg.arc().innerRadius(function(d) {
Severity: Major
Found in public/packages/circosJS@1.7.0.js and 2 other locations - About 2 hrs to fix
public/packages/circosJS@1.7.0.js on lines 675..683
public/packages/circosJS@1.7.0.js on lines 819..823

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 89.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Similar blocks of code found in 2 locations. Consider refactoring.
Open

        svg_legend.append('text')
            .attr('class',' legend-text')
            .attr('transform', 'translate(0, ' +options.legend +')')
            .attr('x', 9.5 * (width - 2 * options.margin) / 10 + options.margin / 2)
            .text('Weaker hits');
Severity: Major
Found in public/js/hits_overview.js and 1 other location - About 2 hrs to fix
public/js/hits_overview.js on lines 189..193

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 89.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Similar blocks of code found in 3 locations. Consider refactoring.
Open

        point = parentElement.selectAll('.point').data(function(d) {
            return d.values;
        }).enter().append('path').attr('class', 'point').attr('opacity', function(d) {
            return d.opacity || conf.opacity;
        }).attr('d', d3.svg.symbol().type(conf.glyph.shape).size(conf.glyph.size)).attr('transform', (function(_this) {
Severity: Major
Found in public/packages/circosJS@1.7.0.js and 2 other locations - About 2 hrs to fix
public/packages/circosJS@1.7.0.js on lines 675..683
public/packages/circosJS@1.7.0.js on lines 731..755

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 89.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Similar blocks of code found in 3 locations. Consider refactoring.
Open

    this.renderDatumContainer = (function(_this) {
        return function(instance, parentElement, name, data, conf) {
            var group, track;
            track = parentElement.append('g').attr('class', name);
            return group = _this.renderBlock(track, data, instance._layout, conf);
Severity: Major
Found in public/packages/circosJS@1.7.0.js and 2 other locations - About 2 hrs to fix
public/packages/circosJS@1.7.0.js on lines 771..777
public/packages/circosJS@1.7.0.js on lines 1010..1016

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 88.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Similar blocks of code found in 2 locations. Consider refactoring.
Open

  nsseq() {
    switch (this.props.algorithm) {
      case "blastp":
      case "blastx":
      case "tblastn":
Severity: Major
Found in public/js/hsp.js and 1 other location - About 2 hrs to fix
public/js/hsp.js on lines 240..253

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 88.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Similar blocks of code found in 3 locations. Consider refactoring.
Open

    this.renderDatumContainer = (function(_this) {
        return function(instance, parentElement, name, data, conf) {
            var group, track;
            track = parentElement.append('g').attr('class', name);
            return group = _this.renderBlock(track, data, instance._layout, conf);
Severity: Major
Found in public/packages/circosJS@1.7.0.js and 2 other locations - About 2 hrs to fix
public/packages/circosJS@1.7.0.js on lines 810..816
public/packages/circosJS@1.7.0.js on lines 1010..1016

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 88.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Similar blocks of code found in 3 locations. Consider refactoring.
Open

    this.renderDatumContainer = (function(_this) {
        return function(instance, parentElement, name, data, conf) {
            var group, track;
            track = parentElement.append('g').attr('class', name);
            return group = _this.renderBlock(track, data, instance._layout, conf);
Severity: Major
Found in public/packages/circosJS@1.7.0.js and 2 other locations - About 2 hrs to fix
public/packages/circosJS@1.7.0.js on lines 771..777
public/packages/circosJS@1.7.0.js on lines 810..816

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 88.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Similar blocks of code found in 2 locations. Consider refactoring.
Open

  nqseq() {
    switch (this.props.algorithm) {
      case "blastp":
      case "blastx":
      case "tblastn":
Severity: Major
Found in public/js/hsp.js and 1 other location - About 2 hrs to fix
public/js/hsp.js on lines 259..272

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 88.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Similar blocks of code found in 3 locations. Consider refactoring.
Open

                    {
                        !this.props.data.imported_xml && <li>
                            <a className="btn-link download" data-toggle="tooltip"
                                title="Results in XML format."
                                href={'download/' + this.props.data.search_id + '.xml'}>
Severity: Major
Found in public/js/sidebar.js and 2 other locations - About 2 hrs to fix
public/js/sidebar.js on lines 320..331
public/js/sidebar.js on lines 332..343

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 87.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Similar blocks of code found in 3 locations. Consider refactoring.
Open

                    {
                        !this.props.data.imported_xml && <li>
                            <a className="btn-link download" data-toggle="tooltip"
                                title="15 columns: query and subject ID; scientific
                                name, alignment length, mismatches, gaps, identity,
Severity: Major
Found in public/js/sidebar.js and 2 other locations - About 2 hrs to fix
public/js/sidebar.js on lines 332..343
public/js/sidebar.js on lines 344..352

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 87.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Similar blocks of code found in 3 locations. Consider refactoring.
Open

                    {
                        !this.props.data.imported_xml && <li>
                            <a className="btn-link download" data-toggle="tooltip"
                                title="44 columns: query and subject ID, GI,
                                accessions, and length; alignment details;
Severity: Major
Found in public/js/sidebar.js and 2 other locations - About 2 hrs to fix
public/js/sidebar.js on lines 320..331
public/js/sidebar.js on lines 344..352

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 87.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Function construct_layout has 64 lines of code (exceeds 25 allowed). Consider refactoring.
Open

    construct_layout() {
        var hsp_count = 0;
        var query_count = 0;
        var num_karyotype = 32;
        var num_queries = this.queries.length;
Severity: Major
Found in public/js/circos.js - About 2 hrs to fix

    Similar blocks of code found in 2 locations. Consider refactoring.
    Open

        data = data.filter(function(datum, index) {
        return circosJS.checkParent(datum[0], index, layoutSummary, 'parent');
    }).filter(function(datum, index) {
        return circosJS.checkNumber({
            position: datum[1],
    Severity: Major
    Found in public/packages/circosJS@1.7.0.js and 1 other location - About 2 hrs to fix
    public/packages/circosJS@1.7.0.js on lines 263..285

    Duplicated Code

    Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

    Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

    When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

    Tuning

    This issue has a mass of 85.

    We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

    The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

    If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

    See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

    Refactorings

    Further Reading

    Similar blocks of code found in 2 locations. Consider refactoring.
    Open

        data = data.filter(function(datum, index) {
        return circosJS.checkParent(datum[0], index, layoutSummary, 'parent');
    }).filter(function(datum, index) {
        return circosJS.checkNumber({
            start: datum[1],
    Severity: Major
    Found in public/packages/circosJS@1.7.0.js and 1 other location - About 2 hrs to fix
    public/packages/circosJS@1.7.0.js on lines 310..323

    Duplicated Code

    Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

    Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

    When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

    Tuning

    This issue has a mass of 85.

    We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

    The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

    If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

    See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

    Refactorings

    Further Reading

    Method has too many lines. [22/15]
    Open

          def initialize(params)
        if params.key?(:xml)
          super do
            @imported_xml_file = File.basename params[:xml]
            # Copy over the XML file to job directory so that a job dir in
    Severity: Minor
    Found in lib/sequenceserver/blast/job.rb by rubocop

    This cop checks if the length of a method exceeds some maximum value. Comment lines can optionally be ignored. The maximum allowed length is configurable.

    You can set literals you want to fold with CountAsOne. Available are: 'array', 'hash', and 'heredoc'. Each literal will be counted as one line regardless of its actual size.

    NOTE: The ExcludedMethods configuration is deprecated and only kept for backwards compatibility. Please use IgnoredMethods instead.

    Example: CountAsOne: ['array', 'heredoc']

    def m
  array = [       # +1
    1,
    2
  ]

  hash = {        # +3
    key: 'value'
  }

  <<~HEREDOC      # +1
    Heredoc
    content.
  HEREDOC
end               # 5 points

    Method has too many lines. [22/15]
    Open

        def spawn_cleanup
      Thread.new do
        loop do
          now = Time.now
          finished_jobs = Job.all.select(&:done?)
    Severity: Minor
    Found in lib/sequenceserver/job_remover.rb by rubocop

    This cop checks if the length of a method exceeds some maximum value. Comment lines can optionally be ignored. The maximum allowed length is configurable.

    You can set literals you want to fold with CountAsOne. Available are: 'array', 'hash', and 'heredoc'. Each literal will be counted as one line regardless of its actual size.

    NOTE: The ExcludedMethods configuration is deprecated and only kept for backwards compatibility. Please use IgnoredMethods instead.

    Example: CountAsOne: ['array', 'heredoc']

    def m
  array = [       # +1
    1,
    2
  ]

  hash = {        # +3
    key: 'value'
  }

  <<~HEREDOC      # +1
    Heredoc
    content.
  HEREDOC
end               # 5 points

    Function removeTracks has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring.
    Open

    circosJS.Core.prototype.removeTracks = function(trackIds) {
    var id, l, len, ref, store, svg, trackId, type;
    svg = d3.select(this.conf.container);
    ref = this.tracks;
    for (type in ref) {
    Severity: Minor
    Found in public/packages/circosJS@1.7.0.js - About 2 hrs to fix

    Cognitive Complexity

    Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

    A method's cognitive complexity is based on a few simple rules:

    • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
    • Code is considered more complex for each "break in the linear flow of the code"
    • Code is considered more complex when "flow breaking structures are nested"

    Further reading

    Function drawLegend has 60 lines of code (exceeds 25 allowed). Consider refactoring.
    Open

        drawLegend() {
        this.ratioHSP = [];
        _.each(
            this.chords_arr,
            _.bind(function (obj) {
    Severity: Major
    Found in public/js/circos.js - About 2 hrs to fix
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