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Method sv_extant_children has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
Open

    def sv_extant_children
      unless self.parent_id.blank?
        if self.is_fossil?
          taxa = Protonym.where(parent_id: self.id)
          z = 0
Severity: Minor
Found in app/models/protonym/soft_validation_extensions.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 person_used_tag has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
Open

  def person_used_tag(person)
    # use_count is SQL based attribute
    if person.respond_to?(:use_count)
      a = ''
      if person.use_count == 0
Severity: Minor
Found in app/helpers/people_helper.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 sample_observation_cell_tag has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
Open

  def sample_observation_cell_tag(observation)
    o = observation
    r = []

    r.push [o.sample_min, o.sample_max].compact.join('-')
Severity: Minor
Found in app/helpers/observations_helper.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 sqed_depiction_buffered_determination_images has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
Open

  def sqed_depiction_buffered_determination_images(collection_object)
    return nil if collection_object.sqed_depictions.empty?
    d = []
    collection_object.sqed_depictions.each do |s|
      begin
Severity: Minor
Found in app/helpers/sqed_depictions_helper.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 project_token_authenticate has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
Open

  def project_token_authenticate
    t = params[:project_token]
    h = request.headers['Project token']

    unless t
Severity: Minor
Found in app/controllers/concerns/token_authentication.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 size has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
Open

  def size
    return nil if size_x.blank? && size_y.blank? && size_z.blank?
    if size_x
      if size_y
        if size_z
Severity: Minor
Found in app/models/container.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_object_navigation_headers has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
Open

    def set_object_navigation_headers(name)
      o = instance_variable_get("@#{name}")

      n = o.next&.id&.to_s
      p = o.previous&.id&.to_s
Severity: Minor
Found in app/controllers/concerns/pagination_headers.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 generate has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
Open

  def self.generate(otus, project_members, reference_csv = nil )
    ::CSV.generate(col_sep: "\t") do |csv|

      csv << %w{
        nameID
Severity: Minor
Found in lib/export/coldp/files/name_relation.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 build_collection_objects has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
Open

    def build_collection_objects
      @total_data_lines = 0
      i = 0

      # loop through rows
Severity: Minor
Found in lib/batch_load/import/collection_objects/buffered_interpreter.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 subject_object_scope has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
Open

      def subject_object_scope(subject_query, object_query, target = 'Otu')
        a = subject_query
        b = object_query

        a_sql, b_sql = nil, nil
Severity: Minor
Found in lib/queries/biological_association/filter.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 topic_year_metadata has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
Open

  def self.topic_year_metadata(entry_item_list)
    h = {}
    entry_item_list.each do |i|
      y = i.nomenclature_date&.year
      y ||= 'unknown'
Severity: Minor
Found in lib/catalog.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 5 locations. Consider refactoring.
Open

  def create
    @repository = Repository.new(repository_params)

    respond_to do |format|
      if @repository.save
Severity: Major
Found in app/controllers/repositories_controller.rb and 4 other locations - About 1 hr to fix
app/controllers/collecting_events_controller.rb on lines 39..47
app/controllers/documents_controller.rb on lines 42..51
app/controllers/geographic_areas_geographic_items_controller.rb on lines 18..27
app/controllers/taxon_determinations_controller.rb on lines 42..51

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 50.

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 to_s has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
Open

  def to_s
    d = data
    str = ''

    d.keys.sort{|a,b| (a || 'zzz') <=> (b || 'zzz')}.each do |c|
Severity: Minor
Found in lib/catalog/distribution/entry.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

  def self.csv(biological_associations)

    data = ApplicationController.helpers.simple_hash(biological_associations)

    tbl = []
Severity: Major
Found in lib/export/csv/biological_associations/simple.rb and 1 other location - About 1 hr to fix
lib/export/csv/biological_associations/extended.rb on lines 25..41

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 50.

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 create
    @geographic_areas_geographic_item = GeographicAreasGeographicItem.new(geographic_areas_geographic_item_params)

    respond_to do |format|
      if @geographic_areas_geographic_item.save
Severity: Major
Found in app/controllers/geographic_areas_geographic_items_controller.rb and 4 other locations - About 1 hr to fix
app/controllers/collecting_events_controller.rb on lines 39..47
app/controllers/documents_controller.rb on lines 42..51
app/controllers/repositories_controller.rb on lines 30..39
app/controllers/taxon_determinations_controller.rb on lines 42..51

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 50.

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 create_modify_gene_descriptor_batch_load
    if params[:file] && digested_cookie_exists?(
        params[:file].tempfile,
        :modify_gene_descriptor_batch_load_descriptors_md5)
      @result = BatchLoad::Import::Descriptors::ModifyGeneDescriptorInterpreter.new(**batch_params)
Severity: Major
Found in app/controllers/descriptors_controller.rb and 1 other location - About 1 hr to fix
app/controllers/sequence_relationships_controller.rb on lines 103..117

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 50.

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 set_identifier_params(params)
    @global_identifiers = boolean_param(params, :global_identifiers)
    @identifier = params[:identifier]
    @identifier_end = integer_param(params, :identifier_end)
    @identifier_exact = boolean_param(params, :identifier_exact)
Severity: Major
Found in lib/queries/concerns/identifiers.rb and 1 other location - About 1 hr to fix
lib/queries/concerns/data_attributes.rb on lines 171..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 50.

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 set_data_attributes_params(params)
    @data_attribute_import_exact_pair = params[:data_attribute_import_exact_pair]
    @data_attribute_import_exact_value = params[:data_attribute_import_exact_value]
    @data_attribute_import_predicate = params[:data_attribute_import_predicate]
    @data_attribute_import_wildcard_value = params[:data_attribute_import_wildcard_value]
Severity: Major
Found in lib/queries/concerns/data_attributes.rb and 1 other location - About 1 hr to fix
lib/queries/concerns/identifiers.rb on lines 135..147

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 50.

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 autocomplete
    confidence_levels = Queries::ControlledVocabularyTerm::Autocomplete.new(params[:term], project_id: sessions_current_project_id, of_type: ['ConfidenceLevel']).autocomplete

    data = confidence_levels.collect do |t|
      str = t.name + ': ' + t.definition
Severity: Major
Found in app/controllers/confidence_levels_controller.rb and 1 other location - About 1 hr to fix
app/controllers/predicates_controller.rb on lines 4..18

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 50.

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 autocomplete
    predicates = Queries::ControlledVocabularyTerm::Autocomplete.new(params[:term], project_id: sessions_current_project_id, type: ['Predicate']).autocomplete

    data = predicates.collect do |t|
      str = t.name + ': ' + t.definition
Severity: Major
Found in app/controllers/predicates_controller.rb and 1 other location - About 1 hr to fix
app/controllers/confidence_levels_controller.rb on lines 19..33

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 50.

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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