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SysMO-DB/seek

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lib/seek/parser_mapper.rb

Summary

Maintainability
F
6 days
Test Coverage

Method dortmund_hengstler_mapping has a Cognitive Complexity of 60 (exceeds 5 allowed). Consider refactoring.
Open

    def dortmund_hengstler_mapping

      age_regex = /(\d+-?\d*)\s*(day|week|month|year)s?/i
      treatment_regex = /(\d*\.?\d*)\s*(\w+\/\w+)\s*([\w\.\s,']*),?\s+([\w\.]*)/
      incubation_time_regex = /(\d+\.?\d*)(\w{1})/
Severity: Minor
Found in lib/seek/parser_mapper.rb - 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

File parser_mapper.rb has 518 lines of code (exceeds 250 allowed). Consider refactoring.
Open

module Seek

  class ParserMapper
Severity: Major
Found in lib/seek/parser_mapper.rb - About 1 day to fix

    Method dortmund_bcat_ko_mapping has a Cognitive Complexity of 54 (exceeds 5 allowed). Consider refactoring.
    Open

        def dortmund_bcat_ko_mapping

      age_regex = /(\d+-?\d*)\s*(day|week|month|year)s?/i
      treatment_substance_regex = /.*\((control|treated)\s?=\s?(.*)\)/i
      treatment_concentration_unit_regex = /(\d*[,\.]?\d*)\s*([\w\s\/]*).*$/
    Severity: Minor
    Found in lib/seek/parser_mapper.rb - 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

    Method dortmund_hengstler_mapping has 123 lines of code (exceeds 25 allowed). Consider refactoring.
    Open

        def dortmund_hengstler_mapping

      age_regex = /(\d+-?\d*)\s*(day|week|month|year)s?/i
      treatment_regex = /(\d*\.?\d*)\s*(\w+\/\w+)\s*([\w\.\s,']*),?\s+([\w\.]*)/
      incubation_time_regex = /(\d+\.?\d*)(\w{1})/
    Severity: Major
    Found in lib/seek/parser_mapper.rb - About 4 hrs to fix

      Method dortmund_bcat_ko_mapping has 102 lines of code (exceeds 25 allowed). Consider refactoring.
      Open

          def dortmund_bcat_ko_mapping

      age_regex = /(\d+-?\d*)\s*(day|week|month|year)s?/i
      treatment_substance_regex = /.*\((control|treated)\s?=\s?(.*)\)/i
      treatment_concentration_unit_regex = /(\d*[,\.]?\d*)\s*([\w\s\/]*).*$/
      Severity: Major
      Found in lib/seek/parser_mapper.rb - About 4 hrs to fix

        Method duesseldorf_bode_mapping has 76 lines of code (exceeds 25 allowed). Consider refactoring.
        Open

            def duesseldorf_bode_mapping

      concentration_regex = /(\d*,?\.?\d*).*/
      gene_modification_regex = /([\w\d]+)([\/+-]+)/
        Severity: Major
        Found in lib/seek/parser_mapper.rb - About 3 hrs to fix

          Method duesseldorf_bode_surgical_mapping has 69 lines of code (exceeds 25 allowed). Consider refactoring.
          Open

              def duesseldorf_bode_surgical_mapping

      gene_modification_regex = /([\w\d]+)([\/+-]+)/

      {
          Severity: Major
          Found in lib/seek/parser_mapper.rb - About 2 hrs to fix

            Method duesseldorf_bode_mapping has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.
            Open

                def duesseldorf_bode_mapping

      concentration_regex = /(\d*,?\.?\d*).*/
      gene_modification_regex = /([\w\d]+)([\/+-]+)/
            Severity: Minor
            Found in lib/seek/parser_mapper.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 empty_mapping has 48 lines of code (exceeds 25 allowed). Consider refactoring.
            Open

                def empty_mapping # defines basic mapping to start with, not that useful for the real parsing business ;-)
      {
          :name => "",
          :data_row_offset => 1, # add this to the row of a header column to get to row with the first data element
            Severity: Minor
            Found in lib/seek/parser_mapper.rb - About 1 hr to fix

              Method jena_mapping has 48 lines of code (exceeds 25 allowed). Consider refactoring.
              Open

                  def jena_mapping
      {
          :name => "jena",
          :data_row_offset => 2,
              Severity: Minor
              Found in lib/seek/parser_mapper.rb - About 1 hr to fix

                Method duesseldorf_bode_surgical_mapping has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.
                Open

                    def duesseldorf_bode_surgical_mapping

      gene_modification_regex = /([\w\d]+)([\/+-]+)/

      {
                Severity: Minor
                Found in lib/seek/parser_mapper.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

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

                              :assay_mapping => {

                  :assay_sheet_name => "Tabelle2",
                  :parsing_direction => "vertical",
                  :probing_column => :"creator.last_name",
                Severity: Major
                Found in lib/seek/parser_mapper.rb and 1 other location - About 1 hr to fix
                lib/seek/parser_mapper.rb on lines 608..626

                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 59.

                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

                          :assay_mapping => {

              :assay_sheet_name => "Tabelle1",
              :parsing_direction => "vertical",
              :probing_column => :"creator.last_name",
                Severity: Major
                Found in lib/seek/parser_mapper.rb and 1 other location - About 1 hr to fix
                lib/seek/parser_mapper.rb on lines 513..531

                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 59.

                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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