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Class has too many lines. [220/150]
Open

  class Routes < Sinatra::Base
    # See
    # http://www.sinatrarb.com/configuration.html
    configure do
      # We don't need Rack::MethodOverride. Let's avoid the overhead.
Severity: Minor
Found in lib/sequenceserver/routes.rb by rubocop

This cop checks if the length a class 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.

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

class Foo
  ARRAY = [         # +1
    1,
    2
  ]

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

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

NOTE: This cop also applies for Struct definitions.

Class has too many lines. [214/150]
Open

  class MAKEBLASTDB
    extend Forwardable
    GUESS_SAMPLE_SIZE = 1_048_576

    def_delegators SequenceServer, :config, :sys
Severity: Minor
Found in lib/sequenceserver/makeblastdb.rb by rubocop

This cop checks if the length a class 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.

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

class Foo
  ARRAY = [         # +1
    1,
    2
  ]

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

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

NOTE: This cop also applies for Struct definitions.

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

        _.each(
            this.hit_arr,
            _.bind(function (id, index) {
                this.chordsHide = [];
                this.layoutHide = [];
Severity: Major
Found in public/js/circos.js and 1 other location - About 1 day to fix
public/js/circos.js on lines 484..512

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 252.

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

        _.each(
            this.query_arr,
            _.bind(function (id, index) {
                this.chordsHide = [];
                this.layoutHide = [];
Severity: Major
Found in public/js/circos.js and 1 other location - About 1 day to fix
public/js/circos.js on lines 513..541

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 252.

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

Class has too many lines. [191/150]
Open

    class Report < Report
      def initialize(job)
        super do
          @querydb = job.databases
        end
Severity: Minor
Found in lib/sequenceserver/blast/report.rb by rubocop

This cop checks if the length a class 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.

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

class Foo
  ARRAY = [         # +1
    1,
    2
  ]

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

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

NOTE: This cop also applies for Struct definitions.

Function Track has a Cognitive Complexity of 61 (exceeds 5 allowed). Consider refactoring.
Open

circosJS.Track = function() {
    this.build = function(instance, conf, data) {
        this.dispatch = d3.dispatch('mouseover', 'mouseout');
        this.loadData(data, instance);
        this.conf = this.processConf(conf, this.defaultConf, this.meta, instance, this);
Severity: Minor
Found in public/js/circosjs.js - About 1 day 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 Track has 215 lines of code (exceeds 25 allowed). Consider refactoring.
Open

circosJS.Track = function() {
    this.build = function(instance, conf, data) {
        this.dispatch = d3.dispatch('mouseover', 'mouseout');
        this.loadData(data, instance);
        this.conf = this.processConf(conf, this.defaultConf, this.meta, instance, this);
Severity: Major
Found in public/js/circosjs.js - About 1 day to fix

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

        this.y = (function(_this) {
        return function(d, layout, conf) {
            var angle, height, r;
            height = _this.ratio(d.value, conf.cmin, conf.cmax, conf.outerRadius - conf.innerRadius, false, conf.logscale);
            if (conf.direction === 'in') {
    Severity: Major
    Found in public/js/circosjs.js and 1 other location - About 1 day to fix
    public/js/circosjs.js on lines 708..720

    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 199.

    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

        this.x = (function(_this) {
        return function(d, layout, conf) {
            var angle, height, r;
            height = _this.ratio(d.value, conf.cmin, conf.cmax, conf.outerRadius - conf.innerRadius, false, conf.logscale);
            if (conf.direction === 'in') {
    Severity: Major
    Found in public/js/circosjs.js and 1 other location - About 1 day to fix
    public/js/circosjs.js on lines 721..733

    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 199.

    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

        this.ratio = function(value, min, max, scope, reverse, logScale) {
        var fraction, scaleLogBase, x;
        scaleLogBase = logScale ? 2.3 : 1;
        if (min === max || (value === min && !reverse) || (value === max && reverse)) {
            return 0;
    Severity: Major
    Found in public/js/circosjs.js and 1 other location - About 1 day to fix
    public/js/circosjs.js on lines 734..749

    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 199.

    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

        this.ratio = function(value, min, max, scope, reverse, logScale) {
        var fraction, scaleLogBase, x;
        scaleLogBase = logScale ? 2.3 : 1;
        if (min === max || (value === min && !reverse) || (value === max && reverse)) {
            return 0;
    Severity: Major
    Found in public/js/circosjs.js and 1 other location - About 1 day to fix
    public/js/circosjs.js on lines 601..616

    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 199.

    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

        this.getTarget = (function(_this) {
        return function(d, layout) {
            var block, endAngle, result, startAngle;
            d = d.target;
            block = layout.blocks[d.id];
    Severity: Major
    Found in public/js/circosjs.js and 1 other location - About 1 day to fix
    public/js/circosjs.js on lines 433..447

    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 195.

    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

        this.getSource = (function(_this) {
        return function(d, layout) {
            var block, endAngle, result, startAngle;
            d = d.source;
            block = layout.blocks[d.id];
    Severity: Major
    Found in public/js/circosjs.js and 1 other location - About 1 day to fix
    public/js/circosjs.js on lines 448..462

    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 195.

    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 4 locations. Consider refactoring.
    Open

                        {
                        !this.props.data.imported_xml && <li className="hover:bg-gray-200 mb-1">
                            <a href={'download/' + this.props.data.search_id + '.pairwise'}>
                                <div className="relative flex flex-col items-center group">
                                    <div className="flex items-center w-full">
    Severity: Major
    Found in public/js/sidebar.js and 3 other locations - About 7 hrs to fix
    public/js/sidebar.js on lines 317..336
    public/js/sidebar.js on lines 337..356
    public/js/sidebar.js on lines 357..373

    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 184.

    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 4 locations. Consider refactoring.
    Open

                        {
                        !this.props.data.imported_xml && <li className="hover:bg-gray-200 mb-1">
                            <a href={'download/' + this.props.data.search_id + '.full_tsv'}>
                                <div className="relative flex flex-col items-center group">
                                    <div className="flex items-center w-full">
    Severity: Major
    Found in public/js/sidebar.js and 3 other locations - About 7 hrs to fix
    public/js/sidebar.js on lines 317..336
    public/js/sidebar.js on lines 357..373
    public/js/sidebar.js on lines 374..390

    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 184.

    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 4 locations. Consider refactoring.
    Open

                        {
                        !this.props.data.imported_xml && <li className="hover:bg-gray-200 mb-1">
                            <a href={'download/' + this.props.data.search_id + '.xml'}>
                                <div className="relative flex flex-col items-center group">
                                    <div className="flex items-center w-full">
    Severity: Major
    Found in public/js/sidebar.js and 3 other locations - About 7 hrs to fix
    public/js/sidebar.js on lines 317..336
    public/js/sidebar.js on lines 337..356
    public/js/sidebar.js on lines 374..390

    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 184.

    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 4 locations. Consider refactoring.
    Open

                        {
                        !this.props.data.imported_xml && <li className="hover:bg-gray-200 mb-1">
                            <a href={'download/' + this.props.data.search_id + '.std_tsv'}>
                                <div className="relative flex flex-col items-center group">
                                    <div className="flex items-center w-full">
    Severity: Major
    Found in public/js/sidebar.js and 3 other locations - About 7 hrs to fix
    public/js/sidebar.js on lines 337..356
    public/js/sidebar.js on lines 357..373
    public/js/sidebar.js on lines 374..390

    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 184.

    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

        $(document).tooltip({
        position: {
            my: 'center bottom-20',
            at: 'center top',
            using: function( position, feedback ) {
    Severity: Major
    Found in public/js/jquery_world.js and 1 other location - About 6 hrs to fix
    public/js/circos.js on lines 569..591

    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 164.

    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

            $('.circos').tooltip({
            position: {
                my: 'left+3 bottom-3',
                at: 'right bottom',
                using: function(position, feedback) {
    Severity: Major
    Found in public/js/circos.js and 1 other location - About 6 hrs to fix
    public/js/jquery_world.js on lines 49..71

    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 164.

    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 graphIt has 131 lines of code (exceeds 25 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.
     */
    Severity: Major
    Found in public/js/hits_overview.js - About 5 hrs to fix
      Severity
      Category
      Status
      Source
      Language