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wurmlab/GeneValidator

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

    } else {
      xAxis = d3.svg.axis()
                    .scale(x)
                    .orient("bottom")
                    .ticks(5);
Severity: Minor
Found in aux/source_assets/js/plots.js and 1 other location - About 30 mins to fix
aux/source_assets/js/plots.js on lines 572..577

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 45.

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

    if (title === 'Open Reading Frames in all 6 Frames') {
      xAxis = d3.svg.axis()
                    .scale(x)
                    .orient("bottom")
                    .ticks(0);
Severity: Minor
Found in aux/source_assets/js/plots.js and 1 other location - About 30 mins to fix
aux/source_assets/js/plots.js on lines 577..582

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 45.

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 run has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def run
      raise unless prediction.is_a?(Query)

      start  = Time.now
Severity: Minor
Found in lib/genevalidator/validation_maker_qi.rb - About 25 mins 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

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

    def length_validation_scores(validations, scores)
      lcv = validations.select { |v| v.class == LengthClusterValidationOutput }
      lrv = validations.select { |v| v.class == LengthRankValidationOutput }
      if lcv.length == 1 && lrv.length == 1
        score_lcv = (lcv[0].result == lcv[0].expected)
Severity: Minor
Found in lib/genevalidator/validation.rb - About 25 mins 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

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

    def write_csv
      return unless @opt[:output_formats].include? 'csv'
      File.open(@dirs[:csv_file], 'a') do |file|
        file.puts csv_header.join(',')
        @json_data.each do |data|
Severity: Minor
Found in lib/genevalidator/output_files.rb - About 25 mins 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

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

    def remove_isolated_residues(seq, len = 2)
      gap_starts = seq.to_enum(:scan, /(-\w{1,#{len}}-)/i).map { |_m| $`.size + 1 }
      # remove isolated residues
      gap_starts.each do |i|
        (i..i + len - 1).each { |j| seq[j] = '-' if isalpha(seq[j]) }
Severity: Minor
Found in lib/genevalidator/validation_alignment.rb - About 25 mins 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

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

      def iterate_tabular(file, db_type)
        table_headers = opt[:blast_tabular_options].split(/[ ,]/)
        tab_file      = File.read(opt[:blast_tabular_file])
        rows = CSV.parse(tab_file, col_sep: "\t",
                                   skip_lines: /^#/,
Severity: Minor
Found in lib/genevalidator/get_raw_sequences.rb - About 25 mins 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

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

      def extract_from_local_db(batch, accno = nil, idx_file = nil)
        efile = Tempfile.new('blast_out')
        cmd = batch ? batch_raw_seq_cmd(idx_file) : single_raw_seq_cmd(accno, efile.path)
        `#{cmd}`
        raw_seqs = batch ? File.read(opt[:raw_sequences]) : efile.read
Severity: Minor
Found in lib/genevalidator/get_raw_sequences.rb - About 25 mins 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

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

    def run
      if type.to_s != 'nucleotide'
        @validation_report = ValidationReport.new('', :unapplicable)
        return @validation_report
      end
Severity: Minor
Found in lib/genevalidator/validation_open_reading_frame.rb - About 25 mins 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

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

      def run_blast_on_input_file
        remote = opt[:db].match?(/remote/) ? true : false
        print_blast_info_text(remote)

        log_file = File.join(dirs[:tmp_dir], 'blast_cmd_output.txt')
Severity: Minor
Found in lib/genevalidator/blast.rb - About 25 mins 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

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

      match  = @prediction.definition.match(/QI:#{number}\|(#{number})\|
                                             (#{number})\|#{number}\|
                                             #{number}\|#{number}\|#{number}\|
                                             #{number}\|#{number}/x)
Severity: Minor
Found in lib/genevalidator/validation_maker_qi.rb and 1 other location - About 20 mins to fix
lib/genevalidator/validation.rb on lines 91..93

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 27.

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

      qi_match     = definition.match(/QI:#{number}\|#{number}\|#{number}\|
                                      #{number}\|#{number}\|#{number}\|
                                      #{number}\|#{number}\|#{number}/x)
Severity: Minor
Found in lib/genevalidator/validation.rb and 1 other location - About 20 mins to fix
lib/genevalidator/validation_maker_qi.rb on lines 87..90

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 27.

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

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