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

jQuery.fn.dataTableExt.oApi.fnSortNeutral = function(oSettings) {
  "use strict";
  /* Remove any current sorting */
  oSettings.aaSorting = [];
  /* Sort display arrays so we get them in numerical order */
Severity: Major
Found in app/assets/javascripts/bp_annotator.js and 1 other location - About 4 hrs to fix
app/assets/javascripts/bp_annotatorplus.js on lines 435..448

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 131.

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

function get_text_markup(text, from, to) {
  var
    text_match = text.substring(from - 1, to),
    // remove everything prior to the preceding three words (using space delimiters):
    text_prefix = text.substring(0, from - 1).replace(/.* ((?:[^ ]* ){2}[^ ]*$)/, "... $1"),
Severity: Major
Found in app/assets/javascripts/bp_annotator.js and 1 other location - About 4 hrs to fix
app/assets/javascripts/bp_annotatorplus.js on lines 629..641

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 130.

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

function get_text_markup(text, from, to) {
  var
    text_match = text.substring(from - 1, to),
    // remove everything prior to the preceding three words (using space delimiters):
    text_prefix = text.substring(0, from - 1).replace(/.* ((?:[^ ]* ){2}[^ ]*$)/, "... $1"),
Severity: Major
Found in app/assets/javascripts/bp_annotatorplus.js and 1 other location - About 4 hrs to fix
app/assets/javascripts/bp_annotator.js on lines 546..558

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 130.

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 animateRun has 117 lines of code (exceeds 25 allowed). Consider refactoring.
Open

      function animateRun(animationEvent, element, className, activeAnimationComplete, styles) {
        var node = extractElementNode(element);
        var elementData = element.data(NG_ANIMATE_CSS_DATA_KEY);
        if (node.getAttribute('class').indexOf(className) == -1 || !elementData) {
          activeAnimationComplete();
Severity: Major
Found in public/browse/lib/angular-animate/angular-animate.js - About 4 hrs to fix

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

    lunr.Store.load = function (serialisedData) {
  var store = new this

  store.length = serialisedData.length
  store.store = Object.keys(serialisedData.store).reduce(function (memo, key) {
    Severity: Major
    Found in public/browse/lib/lunr.js/lib/document_store.js and 1 other location - About 4 hrs to fix
    public/browse/lib/lunr.js/lunr.js on lines 1226..1236

    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 127.

    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

    lunr.Store.load = function (serialisedData) {
  var store = new this

  store.length = serialisedData.length
  store.store = Object.keys(serialisedData.store).reduce(function (memo, key) {
    Severity: Major
    Found in public/browse/lib/lunr.js/lunr.js and 1 other location - About 4 hrs to fix
    public/browse/lib/lunr.js/lib/document_store.js on lines 25..35

    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 127.

    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

    File mustache.js has 354 lines of code (exceeds 250 allowed). Consider refactoring.
    Open

    /*!
 * mustache.js - Logic-less {{mustache}} templates with JavaScript
 * http://github.com/janl/mustache.js
 */
    Severity: Minor
    Found in public/browse/lib/lunr.js/example/mustache.js - About 4 hrs to fix

      Method get_class has a Cognitive Complexity of 30 (exceeds 5 allowed). Consider refactoring.
      Open

        def get_class(params)

    if @ontology.flat?

      ignore_concept_param = params[:conceptid].nil? ||
      Severity: Minor
      Found in app/controllers/application_controller.rb - About 4 hrs to fix

      Cognitive Complexity

      Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

      A method's cognitive complexity is based on a few simple rules:

      • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
      • Code is considered more complex for each "break in the linear flow of the code"
      • Code is considered more complex when "flow breaking structures are nested"

      Further reading

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

      lunr.Index.prototype.toJSON = function () {
  return {
    version: lunr.version,
    fields: this._fields,
    ref: this._ref,
      Severity: Major
      Found in public/browse/lib/lunr.js/lib/index.js and 1 other location - About 4 hrs to fix
      public/browse/lib/lunr.js/lunr.js on lines 1159..1169

      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 123.

      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

      lunr.Index.prototype.toJSON = function () {
  return {
    version: lunr.version,
    fields: this._fields,
    ref: this._ref,
      Severity: Major
      Found in public/browse/lib/lunr.js/lunr.js and 1 other location - About 4 hrs to fix
      public/browse/lib/lunr.js/lib/index.js on lines 379..389

      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 123.

      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

      File bp_notes.js has 346 lines of code (exceeds 250 allowed). Consider refactoring.
      Open

      var ontNotesTable;
var ont_columns = { archived: 3, date: 7, subjectSort: 2 };

jQuery(".ontologies.show").ready(function(){
  setupNotesFaceboxSizing();
      Severity: Minor
      Found in app/assets/javascripts/bp_notes.js - About 4 hrs to fix

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

        lunr.SortedSet.prototype.add = function () {
  Array.prototype.slice.call(arguments).forEach(function (element) {
    if (~this.indexOf(element)) return
    this.elements.splice(this.locationFor(element), 0, element)
  }, this)
        Severity: Major
        Found in public/browse/lib/lunr.js/lunr.js and 1 other location - About 4 hrs to fix
        public/browse/lib/lunr.js/lib/sorted_set.js on lines 40..47

        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 121.

        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

        lunr.Vector.prototype.magnitude = function () {
  if (this._magniture) return this._magnitude
  var node = this.list,
      sumOfSquares = 0,
      val
        Severity: Major
        Found in public/browse/lib/lunr.js/lunr.js and 1 other location - About 4 hrs to fix
        public/browse/lib/lunr.js/lib/vector.js on lines 72..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 121.

        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

        lunr.SortedSet.prototype.add = function () {
  Array.prototype.slice.call(arguments).forEach(function (element) {
    if (~this.indexOf(element)) return
    this.elements.splice(this.locationFor(element), 0, element)
  }, this)
        Severity: Major
        Found in public/browse/lib/lunr.js/lib/sorted_set.js and 1 other location - About 4 hrs to fix
        public/browse/lib/lunr.js/lunr.js on lines 582..589

        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 121.

        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

        lunr.Vector.prototype.magnitude = function () {
  if (this._magniture) return this._magnitude
  var node = this.list,
      sumOfSquares = 0,
      val
        Severity: Major
        Found in public/browse/lib/lunr.js/lib/vector.js and 1 other location - About 4 hrs to fix
        public/browse/lib/lunr.js/lunr.js on lines 489..502

        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 121.

        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

        lunr.EventEmitter.prototype.removeListener = function (name, fn) {
  if (!this.hasHandler(name)) return

  var fnIndex = this.events[name].indexOf(fn)
  this.events[name].splice(fnIndex, 1)
        Severity: Major
        Found in public/browse/lib/lunr.js/lib/event_emitter.js and 1 other location - About 4 hrs to fix
        public/browse/lib/lunr.js/lunr.js on lines 127..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 119.

        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

        lunr.EventEmitter.prototype.removeListener = function (name, fn) {
  if (!this.hasHandler(name)) return

  var fnIndex = this.events[name].indexOf(fn)
  this.events[name].splice(fnIndex, 1)
        Severity: Major
        Found in public/browse/lib/lunr.js/lunr.js and 1 other location - About 4 hrs to fix
        public/browse/lib/lunr.js/lib/event_emitter.js on lines 44..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 119.

        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 success has 104 lines of code (exceeds 25 allowed). Consider refactoring.
        Open

                    success: function(data) {
                $('.recommenderSpinner').hide();
                if (data) {
                    if (data.length > 0) {
                        $("#recommender-results").empty();
        Severity: Major
        Found in app/assets/javascripts/bp_recommender.js - About 4 hrs to fix

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

          lunr.TokenStore.prototype.remove = function (token, ref) {
  if (!token) return
  var node = this.root

  for (var i = 0; i < token.length; i++) {
          Severity: Major
          Found in public/browse/lib/lunr.js/lib/token_store.js and 1 other location - About 4 hrs to fix
          public/browse/lib/lunr.js/lunr.js on lines 1804..1814

          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 118.

          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.TokenStore.prototype.remove = function (token, ref) {
  if (!token) return
  var node = this.root

  for (var i = 0; i < token.length; i++) {
          Severity: Major
          Found in public/browse/lib/lunr.js/lunr.js and 1 other location - About 4 hrs to fix
          public/browse/lib/lunr.js/lib/token_store.js on lines 144..154

          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 118.

          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

          Severity
          Category
          Status
          Source
          Language