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

function insertSampleText(event) {
  "use strict";
  event.preventDefault();
  var text = "Melanoma is a malignant tumor of melanocytes which are found predominantly in skin but also in the bowel and the eye.";
  jQuery("#annotation_text").focus();
Severity: Minor
Found in app/assets/javascripts/bp_annotator.js and 1 other location - About 55 mins to fix
app/assets/javascripts/bp_annotatorplus.js on lines 34..40

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 54.

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

lunr.Vector = function () {
  this._magnitude = null
  this.list = undefined
  this.length = 0
}
Severity: Minor
Found in public/browse/lib/lunr.js/lib/vector.js and 1 other location - About 55 mins to fix
public/browse/lib/lunr.js/lunr.js on lines 429..433

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 54.

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

lunr.Vector = function () {
  this._magnitude = null
  this.list = undefined
  this.length = 0
}
Severity: Minor
Found in public/browse/lib/lunr.js/lunr.js and 1 other location - About 55 mins to fix
public/browse/lib/lunr.js/lib/vector.js on lines 12..16

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 54.

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

    begin
      # Try to create an intelligent subscribe button.
      if ontology_id.start_with? 'http'
        ont = LinkedData::Client::Models::Ontology.find(ontology_id)
      else
Severity: Minor
Found in app/helpers/notes_helper.rb and 1 other location - About 55 mins to fix
app/helpers/application_helper.rb on lines 196..206

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 46.

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

    begin
      # Try to create an intelligent subscribe button.
      if ontology_id.start_with? 'http'
        ont = LinkedData::Client::Models::Ontology.find(ontology_id)
      else
Severity: Minor
Found in app/helpers/application_helper.rb and 1 other location - About 55 mins to fix
app/helpers/notes_helper.rb on lines 143..153

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 46.

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 clear_goo_cache
    response = { errors: '', success: '' }

    begin
      LinkedData::Client::HTTP.post("#{ADMIN_URL}clear_goo_cache", params, raw: true)
Severity: Minor
Found in app/controllers/admin_controller.rb and 1 other location - About 55 mins to fix
app/controllers/admin_controller.rb on lines 124..134

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 46.

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 clear_http_cache
    response = { errors: '', success: '' }

    begin
      LinkedData::Client::HTTP.post("#{ADMIN_URL}clear_http_cache", params, raw: true)
Severity: Minor
Found in app/controllers/admin_controller.rb and 1 other location - About 55 mins to fix
app/controllers/admin_controller.rb on lines 112..122

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 46.

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

Function locationFor has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
Open

lunr.SortedSet.prototype.locationFor = function (elem, start, end) {
  var start = start || 0,
      end = end || this.elements.length,
      sectionLength = end - start,
      pivot = start + Math.floor(sectionLength / 2),
Severity: Minor
Found in public/browse/lib/lunr.js/lib/sorted_set.js - About 55 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

Function intersect has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
Open

lunr.SortedSet.prototype.intersect = function (otherSet) {
  var intersectSet = new lunr.SortedSet,
      i = 0, j = 0,
      a_len = this.length, b_len = otherSet.length,
      a = this.elements, b = otherSet.elements
Severity: Minor
Found in public/browse/lib/lunr.js/lib/sorted_set.js - About 55 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 redirect_new_api has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
Open

  def redirect_new_api(class_view = false)
    # Hack to make ontologyid and conceptid work in addition to id and ontology params
    params[:ontology] = params[:ontology].nil? ? params[:ontologyid] : params[:ontology]
    # Error checking
    if params[:ontology].nil? || params[:id] && params[:ontology].nil?
Severity: Minor
Found in app/controllers/application_controller.rb - About 55 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 simplify_ontology_model has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
Open

  def simplify_ontology_model(ont_model)
    id = nil
    if ont_model.instance_of? Hash
      id = ont_model['@id']
    elsif ont_model.instance_of? LinkedData::Client::Models::Ontology
Severity: Minor
Found in app/controllers/application_controller.rb - About 55 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 massage_annotated_classes has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
Open

  def massage_annotated_classes(annotations, options)
    # Get the class details required for display, assume this is necessary
    # for every element of the annotations array because the API returns a set.
    # Use the batch REST API to get all the annotated class prefLabels.
    start = Time.now
Severity: Minor
Found in app/controllers/annotatorplus_controller.rb - About 55 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 create has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
Open

  def create
    @errors = validate(params[:user])
    if @errors.empty?
      logged_in_user = LinkedData::Client::Models::User.authenticate(params[:user][:username], params[:user][:password])
      if logged_in_user && !logged_in_user.errors
Severity: Minor
Found in app/controllers/login_controller.rb - About 55 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 show has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
Open

  def show
    params[:id] = params[:id] || params[:conceptid]

    if params[:id].blank?
      render text: 'Error: You must provide a valid concept id'
Severity: Minor
Found in app/controllers/concepts_controller.rb - About 55 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 massage_annotated_classes has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
Open

  def massage_annotated_classes(annotations, options)
    # Get the class details required for display, assume this is necessary
    # for every element of the annotations array because the API returns a set.
    # Use the batch REST API to get all the annotated class prefLabels.
    start = Time.now
Severity: Minor
Found in app/controllers/annotator_controller.rb - About 55 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 (typeof resultObjects[i].image === 'string') {
            $('>a', item).prepend('<img src="' + resultObjects[i].image + '" />');
          }
Severity: Minor
Found in public/widgets/jquery.ncbo.autocomplete.js and 1 other location - About 55 mins to fix
public/widgets/jquery.ncbo.autocomplete.js on lines 195..197

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 53.

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 (typeof resultObjects[i].extra === 'string') {
            $('>a', item).append('<small>' + resultObjects[i].extra + '</small>');
          }
Severity: Minor
Found in public/widgets/jquery.ncbo.autocomplete.js and 1 other location - About 55 mins to fix
public/widgets/jquery.ncbo.autocomplete.js on lines 191..193

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 53.

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

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

  def get_semantic_types
    semantic_types = {}
    sty_ont = LinkedData::Client::Models::Ontology.find_by_acronym('STY').first
    return semantic_types if sty_ont.nil?
    # The first 500 items should be more than sufficient to get all semantic types.
Severity: Minor
Found in app/controllers/annotatorplus_controller.rb and 1 other location - About 55 mins to fix
app/controllers/annotator_controller.rb on lines 82..92

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 44.

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

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

  def get_semantic_types
    semantic_types = {}
    sty_ont = LinkedData::Client::Models::Ontology.find_by_acronym('STY').first
    return semantic_types if sty_ont.nil?
    # The first 500 items should be more than sufficient to get all semantic types.
Severity: Minor
Found in app/controllers/annotator_controller.rb and 1 other location - About 55 mins to fix
app/controllers/annotatorplus_controller.rb on lines 107..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 44.

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

Function $httpBackend has 7 arguments (exceeds 4 allowed). Consider refactoring.
Open

  function $httpBackend(method, url, data, callback, headers, timeout, withCredentials) {
Severity: Major
Found in public/browse/lib/angular-mocks/angular-mocks.js - About 50 mins to fix
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