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Method depiction has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

    def depiction
      if @depiction
        @depiction
      else
        begin
Severity: Minor
Found in lib/vendor/sqed_to_taxonworks.rb - About 35 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 soft_validators has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

    def soft_validators(only_sets: [], except_sets: [], only_methods: [], except_methods: [], include_flagged: false, fixable: nil, include_superclass: true)
      only_methods = Utilities::Params.arrayify(only_methods)
      return only_methods if !only_methods.empty?

      except_methods = Utilities::Params.arrayify(except_methods)
Severity: Minor
Found in lib/soft_validation.rb - About 35 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 build has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

    def build
      v = object.valid_taxon_name
      base_names = v.historical_taxon_names

      base_names.each do |t|
Severity: Minor
Found in lib/catalog/nomenclature/entry.rb - About 35 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 all_sources has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

    def all_sources
      s  = items.collect{|i| i.source}
      if !object.nil?
        relationship_items.each do |i|
          s << i.object.object_taxon_name.origin_citation.try(:source) if i.object.subject_taxon_name != object  # base_object?
Severity: Minor
Found in lib/catalog/nomenclature/entry.rb - About 35 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 nomenclature_date has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

  def self.nomenclature_date(day = nil, month = nil, year = nil)
    if year.nil?
      nil
    elsif month.nil?
      Time.utc(year.to_i, 12, 31)
Severity: Minor
Found in lib/utilities/dates.rb - About 35 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 load_selenium_config has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

  def self.load_selenium_config(settings)
    invalid = settings.keys - [:browser, :marionette, :firefox_binary_path, :chromedriver_path, :headless]

    raise Error, "#{invalid} are not valid settings for test:selenium." unless invalid.empty?
    raise Error, "Can not find Firefox browser binary #{settings[:firefox_binary_path]}." if settings[:browser] == :firefox && !settings[:firefox_binary_path].blank? && !File.exist?(settings[:firefox_binary_path])
Severity: Minor
Found in lib/settings.rb - About 35 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 replace has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

  def self.replace(original_file, new_file)
    return false unless File.exist?(original_file) && File.exist?(new_file)
    fo = original_file
    ft = fo + '.tmp'
Severity: Minor
Found in lib/utilities/files.rb - About 35 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 all_citations has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

    def all_citations
      c  = items.collect{|i| i.citation}

      if !object.nil?
        relationship_items.each do |i|
Severity: Minor
Found in lib/catalog/nomenclature/entry.rb - About 35 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 fix_2_digit_year has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

  def self.fix_2_digit_year(year)
    if year.length < 4
      year = year.gsub("'", '')
      if year.length < 3
        tny = Time.now.year
Severity: Minor
Found in lib/utilities/dates.rb - About 35 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 any_global_id_facet has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

      def any_global_id_facet
        return nil if any_global_id.empty?
        a = matching_global_id(:subject, any_global_id)
        b = matching_global_id(:object, any_global_id)
        if a && b
Severity: Minor
Found in lib/queries/biological_association/filter.rb - About 35 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 initialize has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

  def initialize(object: nil, type: nil, start_date: nil, end_date: nil)
    raise TaxonWorks::Error, ':object is nil' if object.nil?
    raise TaxonWorks::Error, ':type is nil' if type.nil?
    raise TaxonWorks::Error, 'type is not in the list' if !Catalog::CollectionObject::EVENT_TYPES.include?(type)
    raise TaxonWorks::Error, 'start_date is not a Time' if start_date && !start_date.kind_of?(Time)
Severity: Minor
Found in lib/catalog/collection_object/entry_item.rb - About 35 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 load_action_mailer_smtp_settings has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

  def self.load_action_mailer_smtp_settings(config, settings)
    if settings
      auth = {}
      user = ENV['TW_ACTION_MAILER_SMTP_SETTINGS_USER_NAME']
      pass = ENV['TW_ACTION_MAILER_SMTP_SETTINGS_PASSWORD']
Severity: Minor
Found in lib/settings.rb - About 35 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 symbolize_keys has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

  def self.symbolize_keys(hash)
    hash.inject({}) do |h, (k, v)|
      h[k.is_a?(String) ? k.to_sym : k] = (v.is_a?(Hash) ? symbolize_keys(v) : v)
      h
    end
Severity: Minor
Found in lib/utilities/hashes.rb - About 35 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 bibliography has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

    def self.bibliography(sources)
      b = BibTeX::Bibliography.new
      sources.each do |s|
        next unless s.is_bibtex?
        e = s.to_bibtex
Severity: Minor
Found in lib/vendor/bibtex_ruby.rb - About 35 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 normalize_and_order_dates has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

  def self.normalize_and_order_dates(start_date, end_date)
    if start_date.blank? && end_date.blank? # set entire range
      [ EARLIEST_DATE, today] # 1700-01-01 - Today
    else
      end_date = start_date if end_date.blank?
Severity: Minor
Found in lib/utilities/dates.rb - About 35 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

  def collecting_event_id_param
    retval = nil
    begin
      retval = params.require(:collecting_event_id)
    rescue ActionController::ParameterMissing
Severity: Minor
Found in app/controllers/tasks/collecting_events/parse/stepwise/lat_long_controller.rb and 1 other location - About 35 mins to fix
app/controllers/tasks/collecting_events/parse/stepwise/dates_controller.rb on lines 169..185

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 35.

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

  def collecting_event_id_param
    retval = nil
    begin
      retval = params.require(:collecting_event_id)
    rescue ActionController::ParameterMissing
Severity: Minor
Found in app/controllers/tasks/collecting_events/parse/stepwise/dates_controller.rb and 1 other location - About 35 mins to fix
app/controllers/tasks/collecting_events/parse/stepwise/lat_long_controller.rb on lines 117..132

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 35.

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

  def preview_genbank_batch_file_load 
    if params[:files] 
      @result = BatchFileLoad::Import::Sequences::GenbankInterpreter.new(**batch_params)
      digest_cookie(params[:files][0].tempfile, :batch_file_load_genbank_sequences_md5)
      render 'sequences/batch_file_load/genbank/preview'
Severity: Minor
Found in app/controllers/sequences_controller.rb and 1 other location - About 35 mins to fix
app/controllers/otus_controller.rb on lines 181..189

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 35.

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

  def preview_simple_batch_file_load
    if params[:files]
      @result = BatchFileLoad::Import::Otus::SimpleInterpreter.new(**batch_params)
      digest_cookie(params[:files][0].tempfile, :batch_file_load_simple_md5)
      render 'otus/batch_file_load/simple/preview'
Severity: Minor
Found in app/controllers/otus_controller.rb and 1 other location - About 35 mins to fix
app/controllers/sequences_controller.rb on lines 104..112

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 35.

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 5 locations. Consider refactoring.
Open

  def batch_update
    if r = Otu.batch_update(
        preview: params[:preview],
        otu: otu_params.merge(by: sessions_current_user_id),
        otu_query: params[:otu_query],
Severity: Major
Found in app/controllers/otus_controller.rb and 4 other locations - About 35 mins to fix
app/controllers/asserted_distributions_controller.rb on lines 117..126
app/controllers/biological_associations_controller.rb on lines 171..179
app/controllers/collecting_events_controller.rb on lines 132..140
app/controllers/collection_objects_controller.rb on lines 415..423

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 34.

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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