Sign upLogin

biotcm/biotcm

View on GitHub
Star

Showing 39 of 39 total issues

Method rescue_symbol has a Cognitive Complexity of 33 (exceeds 5 allowed). Consider refactoring.
Open

    def rescue_symbol(symbol, method = @rescue_method, rehearsal = false)
      return @rescue_history[symbol] if @rescue_history[symbol]

      case method
      when :auto
Severity: Minor
Found in lib/biotcm/databases/hgnc/rescuer.rb - About 4 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

Method parse has a Cognitive Complexity of 25 (exceeds 5 allowed). Consider refactoring.
Open

    def parse(fin)
      # Headline
      names = fin.gets.chomp.split("\t")
      index2identifier = {}
      index_hgncid = nil
Severity: Minor
Found in lib/biotcm/databases/hgnc/parser.rb - About 3 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

Method load has a Cognitive Complexity of 25 (exceeds 5 allowed). Consider refactoring.
Open

    def self.load(
      path = nil,
      prefix: '',
      colname: {
        source: 'Source',
Severity: Minor
Found in lib/biotcm/layer.rb - About 3 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

Class Table has 29 methods (exceeds 20 allowed). Consider refactoring.
Open

  class Table
    # Version
    VERSION = '0.6.1'.freeze

    # Primary key
Severity: Minor
Found in lib/biotcm/table.rb - About 3 hrs to fix

    File table.rb has 311 lines of code (exceeds 250 allowed). Consider refactoring.
    Open

    module BioTCM
  # One of the basic data models used in BioTCM to process
  # {https://github.com/biotcm/biotcm/wiki/Formats#tab .tab files},
  # developed under <b>"strict entry and tolerant exit"</b> philosophy.
  #
    Severity: Minor
    Found in lib/biotcm/table.rb - About 3 hrs to fix

      Method get_pathway has a Cognitive Complexity of 21 (exceeds 5 allowed). Consider refactoring.
      Open

        def self.get_pathway(pathway_id)
    raise ArgumentError, 'Invalid pathway_id' unless (pathway_id = validate_pathway_id(pathway_id))

    file_path = BioTCM.path_to("kegg/#{pathway_id}.xml")
    unless File.exist?(file_path)
      Severity: Minor
      Found in lib/biotcm/databases/kegg.rb - 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

      Method get_pathway has 72 lines of code (exceeds 25 allowed). Consider refactoring.
      Open

        def self.get_pathway(pathway_id)
    raise ArgumentError, 'Invalid pathway_id' unless (pathway_id = validate_pathway_id(pathway_id))

    file_path = BioTCM.path_to("kegg/#{pathway_id}.xml")
    unless File.exist?(file_path)
      Severity: Major
      Found in lib/biotcm/databases/kegg.rb - About 2 hrs to fix

        Method parse has 54 lines of code (exceeds 25 allowed). Consider refactoring.
        Open

            def parse(fin)
      # Headline
      names = fin.gets.chomp.split("\t")
      index2identifier = {}
      index_hgncid = nil
        Severity: Major
        Found in lib/biotcm/databases/hgnc/parser.rb - About 2 hrs to fix

          Method set_row has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.
          Open

              def set_row(row, val)
      # Setter
      if !row.is_a?(String) || (!val.is_a?(Hash) && !val.is_a?(Array))
        raise ArgumentError, 'Illegal argument type'
      elsif val.is_a?(Array) && val.size != col_keys.size
          Severity: Minor
          Found in lib/biotcm/table.rb - About 1 hr 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 set_col has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.
          Open

              def set_col(col, val)
      if !col.is_a?(String) || (!val.is_a?(Hash) && !val.is_a?(Array))
        raise ArgumentError, 'Illegal argument type'
      elsif val.is_a?(Array) && val.size != row_keys.size
        raise ArgumentError, 'Row size not match'
          Severity: Minor
          Found in lib/biotcm/table.rb - About 1 hr 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 load has 45 lines of code (exceeds 25 allowed). Consider refactoring.
          Open

              def self.load(
      path = nil,
      prefix: '',
      colname: {
        source: 'Source',
          Severity: Minor
          Found in lib/biotcm/layer.rb - About 1 hr to fix

            Method extended has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring.
            Open

                def self.extended(mod)
      mod.instance_eval do
        # Initialize instance variables
        @rescue_symbol = true
        @rescue_method = :auto
            Severity: Minor
            Found in lib/biotcm/databases/hgnc/rescuer.rb - About 1 hr 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 rescue_symbol has 41 lines of code (exceeds 25 allowed). Consider refactoring.
            Open

                def rescue_symbol(symbol, method = @rescue_method, rehearsal = false)
      return @rescue_history[symbol] if @rescue_history[symbol]

      case method
      when :auto
            Severity: Minor
            Found in lib/biotcm/databases/hgnc/rescuer.rb - About 1 hr to fix

              Method merge has 38 lines of code (exceeds 25 allowed). Consider refactoring.
              Open

                  def merge(tab)
      raise ArgumentError, 'Only tables could be merged' unless tab.is_a?(self.class)
      raise ArgumentError, 'Primary keys not the same' unless tab.primary_key == primary_key

      # Empty content
              Severity: Minor
              Found in lib/biotcm/table.rb - About 1 hr to fix

                Method to_table has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.
                Open

                        def to_table(seperator: "\t")
          stuff = split(/\r\n|\n/)

          # Comments
          comments = []
                Severity: Minor
                Found in lib/biotcm/table.rb - About 1 hr 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 extended has 34 lines of code (exceeds 25 allowed). Consider refactoring.
                Open

                    def self.extended(mod)
      mod.instance_eval do
        # Initialize instance variables
        @rescue_symbol = true
        @rescue_method = :auto
                Severity: Minor
                Found in lib/biotcm/databases/hgnc/rescuer.rb - About 1 hr to fix

                  Method extract_by_species has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.
                  Open

                    def extract_by_species(filepath, species = 'Homo sapiens')
    fout = File.new(filepath, 'w')
    raise ArgumentError, 'Illegal filepath given' unless fout

    species = find_species_id(species).to_i
                  Severity: Minor
                  Found in lib/biotcm/apps/string_processor.rb - About 1 hr 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 mine_offline has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.
                  Open

                    def mine_offline(query)
    @gene_detector = BioTCM::Apps::GeneDetector.new

    datapath = BioTCM.path_to("tmp/PubmedGeneMiner.#{BioTCM.stamp}.txt")
    as_medline(query).download_abstracts(datapath)
                  Severity: Minor
                  Found in lib/biotcm/apps/pubmed_gene_miner.rb - About 1 hr 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 to_table has 29 lines of code (exceeds 25 allowed). Consider refactoring.
                  Open

                          def to_table(seperator: "\t")
          stuff = split(/\r\n|\n/)

          # Comments
          comments = []
                  Severity: Minor
                  Found in lib/biotcm/table.rb - About 1 hr to fix

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

                    File.open('ppi.v10.homo.sapiens.700.txt', 'w') do |fout|
  File.open('protein.links.detailed.v10.homo.sapiens.txt').each do |line|
    col = line.chomp.split("\t")
    next unless (col[0] = protein2symbol[col[0]]) && (col[1] = protein2symbol[col[1]])
    next unless col.last.to_i >= 700
                    Severity: Major
                    Found in demo/yield_string_ppi.rb and 1 other location - About 1 hr to fix
                    demo/yield_string_ppi.rb on lines 85..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 51.

                    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

                    Severity
                    Category
                    Status
                    Source
                    Language