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Method recursively_set_mime_type has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
Open

def recursively_set_mime_type(list, depth, type)
  depth -= 1
  list.map do |el|
    if depth == 0
      el == "application/x-error" ? el : type
Severity: Minor
Found in lib/taverna_player_callbacks.rb - About 45 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_document has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
Open

    def extract_from_document doc
      doc.root.namespaces.default_prefix = "ss"


      template_sheet = nil
Severity: Minor
Found in lib/seek/data/bio_samples.rb - About 45 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 treatments has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
Open

      def treatments
        Seek::Data::Treatments #this is just to load the class, incase it is already in the cache. Otherwise an underfined class/module error may occur
        Rails.cache.fetch("treatments_#{content_blob.cache_key}") do
          begin
            if content_blob.is_extractable_spreadsheet?
Severity: Minor
Found in lib/seek/data/treatment_extraction.rb - About 45 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 request_publish_approval has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
Open

      def request_publish_approval
        User.with_current_user current_user do
          c = self.controller_name.downcase
          a = self.action_name.downcase
Severity: Minor
Found in lib/seek/publishing/publishing_common.rb - About 45 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 copy_file_between_zips has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
Open

def copy_file_between_zips(src, dest, name, ext)
  if name.ends_with?('.error')
    new_name = name
  else
    new_name = ext.nil? ? name : "#{name}#{ext}"
Severity: Minor
Found in lib/taverna_player_callbacks.rb - About 45 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 cache_remote_content_blob has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
Open

      def cache_remote_content_blob
        blobs = []
        blobs << self.content_blob if self.respond_to?(:content_blob)
        blobs = blobs | self.content_blobs if self.respond_to?(:content_blobs)
        blobs.compact!
Severity: Minor
Found in lib/acts_as_asset.rb - About 45 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 hunt_for_field_values_mapped has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
Open

    def hunt_for_field_values_mapped sheet, field_name, mapping, probing_num_rows = false
      field_values = hunt_for_field_values sheet, mapping[field_name][:column], probing_num_rows
      if field_values && !field_values.empty?

        if probing_num_rows
Severity: Minor
Found in lib/seek/data/bio_samples.rb - About 45 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 bio_samples_population has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
Open

        def bio_samples_population institution_id=nil, to_populate=true
          begin
            if content_blob.is_extractable_spreadsheet?

              bio_samples = nil
Severity: Minor
Found in lib/seek/data/bio_samples_extraction.rb - About 45 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 basic_auth has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
Open

    def basic_auth url, username,password, include_data=true
      
      #This block is to ensure that only urls are encoded if they need it.
      #This is to prevent already encoded urls being re-encoded, which can lead to % being replaced with %25.
      begin
Severity: Minor
Found in lib/seek/remote_downloader.rb - About 45 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

            if(slider.settings.nextSelector){
                $(slider.settings.nextSelector).append(slider.controls.next);
            }
Severity: Minor
Found in app/assets/javascripts/jquery.bxslider.js and 1 other location - About 45 mins to fix
app/assets/javascripts/jquery.bxslider.js on lines 636..638

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 asset_sql(asset_class)
    asset_class_underscored = asset_class.underscore
    'SELECT '+ asset_class_underscored +'_versions.* FROM ' + asset_class_underscored + '_versions ' +
    'INNER JOIN assay_assets ' + 
    'ON assay_assets.asset_id = ' + asset_class_underscored + '_id ' +
Severity: Minor
Found in app/models/assay.rb and 1 other location - About 45 mins to fix
app/models/sample.rb on lines 93..100

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 40.

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(slider.settings.prevSelector){
                $(slider.settings.prevSelector).append(slider.controls.prev);
            }
Severity: Minor
Found in app/assets/javascripts/jquery.bxslider.js and 1 other location - About 45 mins to fix
app/assets/javascripts/jquery.bxslider.js on lines 632..634

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

      respond_to do |format|
        if saved
          flash[:notice] = "technology type was successfully created."
          format.html { redirect_to(:action => "manage") }
          format.xml { head :ok }
Severity: Minor
Found in app/controllers/suggested_technology_types_controller.rb and 1 other location - About 45 mins to fix
app/controllers/suggested_technology_types_controller.rb on lines 82..89

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 40.

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

      respond_to do |format|
        if saved
          flash[:notice] = "technology type was successfully updated."
          format.html { redirect_to(:action => "manage") }
          format.xml { head :ok }
Severity: Minor
Found in app/controllers/suggested_technology_types_controller.rb and 1 other location - About 45 mins to fix
app/controllers/suggested_technology_types_controller.rb on lines 53..60

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 40.

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 asset_sql(asset_class)
    asset_class_underscored = asset_class.underscore
    'SELECT ' + asset_class_underscored + '_versions.* FROM ' + asset_class_underscored + '_versions ' +
        'INNER JOIN sample_assets ' +
        'ON sample_assets.asset_id= '+ asset_class_underscored + '_id ' +
Severity: Minor
Found in app/models/sample.rb and 1 other location - About 45 mins to fix
app/models/assay.rb on lines 80..87

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 40.

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 !doi.blank?
      existing = Publication.find_all_by_doi(doi) - [self]
      if !existing.empty?
        matching_projects = existing.collect(&:projects).flatten.uniq & projects
        if !matching_projects.empty?
Severity: Minor
Found in app/models/publication.rb and 1 other location - About 45 mins to fix
app/models/publication.rb on lines 235..241

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 39.

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 !pubmed_id.blank?
      existing = Publication.find_all_by_pubmed_id(pubmed_id) - [self]
      if !existing.empty?
        matching_projects = existing.collect(&:projects).flatten.uniq & projects
        if !matching_projects.empty?
Severity: Minor
Found in app/models/publication.rb and 1 other location - About 45 mins to fix
app/models/publication.rb on lines 225..231

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 39.

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

    for(var i = 0; i < attribution_settings.length; i++)
        if(attribution_settings[i][0] == attributable_type && attribution_settings[i][2] == attributable_id) {
            attribution_settings.splice(i, 1);
            break;
        }
Severity: Minor
Found in app/assets/javascripts/attribution.js and 1 other location - About 40 mins to fix
app/assets/javascripts/people.js on lines 89..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 49.

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

    for(var i = 0; i < roles.length; i++)
        if(roles[i][2] == id && roles[i][0]==group_id) {
            roles.splice(i, 1);
            break;
        }
Severity: Minor
Found in app/assets/javascripts/people.js and 1 other location - About 40 mins to fix
app/assets/javascripts/attribution.js on lines 81..85

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 49.

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 self.uri_for_path(path, *args)
      options = args.extract_options!
      # defaults:
      options.reverse_merge!(:params => nil)
Severity: Minor
Found in lib/seek/api.rb and 1 other location - About 40 mins to fix
lib/seek/api.rb on lines 34..46

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 38.

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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