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Function onSuccessAction has a Cognitive Complexity of 21 (exceeds 5 allowed). Consider refactoring.
Open

UpdateCheck.prototype.onSuccessAction = function(data, ontology, deferredObj) {
  var self = this;
  delete data["success"];
  updateInfo = data["update_info"];
Severity: Minor
Found in app/assets/javascripts/bp_admin.js - About 2 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

Method build_tree has a Cognitive Complexity of 21 (exceeds 5 allowed). Consider refactoring.
Open

  def build_tree(node, string, id)
    if node.children.nil? || node.children.length < 1
      return string # unchanged
    end
    node.children.sort! {|a,b| (a.prefLabel || a.id).downcase <=> (b.prefLabel || b.id).downcase}
Severity: Minor
Found in app/helpers/application_helper.rb - About 2 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 4 locations. Consider refactoring.
Open

    OPTIONS = {
      autoclose:         false,
      beforeExpand:      false,
      afterExpand:       false,
      afterExpandError:  false,
Severity: Major
Found in public/widgets/jquery.ncbo.tree-2.0.0.js and 3 other locations - About 2 hrs to fix
public/widgets/jquery.ncbo.tree-2.0.1.js on lines 44..62
public/widgets/jquery.ncbo.tree-2.0.2.js on lines 44..62
public/widgets/jquery.ncbo.tree.js on lines 38..56

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 93.

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 4 locations. Consider refactoring.
Open

    OPTIONS = {
      autoclose:         false,
      beforeExpand:      false,
      afterExpand:       false,
      afterExpandError:  false,
Severity: Major
Found in public/widgets/jquery.ncbo.tree-2.0.1.js and 3 other locations - About 2 hrs to fix
public/widgets/jquery.ncbo.tree-2.0.0.js on lines 44..62
public/widgets/jquery.ncbo.tree-2.0.2.js on lines 44..62
public/widgets/jquery.ncbo.tree.js on lines 38..56

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 93.

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 4 locations. Consider refactoring.
Open

    OPTIONS = {
      autoclose:         false,
      beforeExpand:      false,
      afterExpand:       false,
      afterExpandError:  false,
Severity: Major
Found in public/widgets/jquery.ncbo.tree.js and 3 other locations - About 2 hrs to fix
public/widgets/jquery.ncbo.tree-2.0.0.js on lines 44..62
public/widgets/jquery.ncbo.tree-2.0.1.js on lines 44..62
public/widgets/jquery.ncbo.tree-2.0.2.js on lines 44..62

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 93.

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 4 locations. Consider refactoring.
Open

    OPTIONS = {
      autoclose:         false,
      beforeExpand:      false,
      afterExpand:       false,
      afterExpandError:  false,
Severity: Major
Found in public/widgets/jquery.ncbo.tree-2.0.2.js and 3 other locations - About 2 hrs to fix
public/widgets/jquery.ncbo.tree-2.0.0.js on lines 44..62
public/widgets/jquery.ncbo.tree-2.0.1.js on lines 44..62
public/widgets/jquery.ncbo.tree.js on lines 38..56

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 93.

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

rec.insertSampleKeywords = function() {
    rec.enableEdition();
    var text = "Backpain, White blood cell, Carcinoma, Cavity of stomach, Ductal Carcinoma in Situ, Adjuvant chemotherapy, Axillary lymph node staging, Mastectomy, tamoxifen, serotonin reuptake inhibitors, Invasive Breast Cancer, hormone receptor positive breast cancer, ovarian ablation, premenopausal women, surgical management, biopsy of breast tumor, Fine needle aspiration, entinel lymph node, breast preservation, adjuvant radiation therapy, prechemotherapy, Inflammatory Breast Cancer, ovarian failure, Bone scan, lumpectomy, brain metastases, pericardial effusion, aromatase inhibitor, postmenopausal, Palliative care, Guidelines, Stage IV breast cancer disease, Trastuzumab, Breast MRI examination";
    jQuery("#inputText").focus();
    jQuery("#inputText").val(text);
Severity: Major
Found in app/assets/javascripts/bp_recommender.js and 1 other location - About 2 hrs to fix
app/assets/javascripts/bp_recommender.js on lines 42..49

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 92.

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

rec.insertSampleText = function() {
    rec.enableEdition();
    var text = 'Primary treatment of DCIS now includes 3 options: lumpectomy without lymph node surgery plus whole breast radiation (category 1); total mastectomy with or without sentinel node biopsy with or without reconstruction (category 2A); lumpectomy without lymph node surgery without radiation (category 2B). Workup for patients with clinical stage l, llA, llB, or T3,N1,M0 disease was reorganized to distinguish optional additional studies from those recommended for all of these patients. Recommendation for locoregional treatment for patients with clinical stage l, llA, llB, or T3,N1,M0 disease with 1-3 positive axillary nodes following total mastectomy was changed from "Consider" to "Strongly consider" postmastectomy radiation therapy. ';
    jQuery("#inputText").focus();
    jQuery("#inputText").val(text);
Severity: Major
Found in app/assets/javascripts/bp_recommender.js and 1 other location - About 2 hrs to fix
app/assets/javascripts/bp_recommender.js on lines 51..58

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 92.

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.update = function (doc, emitEvent) {
  var emitEvent = emitEvent === undefined ? true : emitEvent

  this.remove(doc, false)
  this.add(doc, false)
Severity: Major
Found in public/browse/lib/lunr.js/lunr.js and 1 other location - About 2 hrs to fix
public/browse/lib/lunr.js/lib/index.js on lines 230..237

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 92.

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.update = function (doc, emitEvent) {
  var emitEvent = emitEvent === undefined ? true : emitEvent

  this.remove(doc, false)
  this.add(doc, false)
Severity: Major
Found in public/browse/lib/lunr.js/lib/index.js and 1 other location - About 2 hrs to fix
public/browse/lib/lunr.js/lunr.js on lines 1010..1017

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 92.

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 formComplete_setup_functions has 70 lines of code (exceeds 25 allowed). Consider refactoring.
Open

function formComplete_setup_functions() {
  jQuery("input[class*='bp_form_complete']").each(function(){
    var classes = this.className.split(" ");
    var values;
    var ontology_id;
Severity: Major
Found in public/javascripts/widgets/form_complete.js - About 2 hrs to fix

    Method _process_ontologies has a Cognitive Complexity of 20 (exceeds 5 allowed). Consider refactoring.
    Open

      def _process_ontologies(success_keyword, error_keyword, process_proc)
    response = { errors: '', success: '' }

    if params['ontologies'].blank?
      response[:errors] = "No ontologies parameter passed. Syntax: ?ontologies=ONT1,ONT2,...,ONTN"
    Severity: Minor
    Found in app/controllers/admin_controller.rb - About 2 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

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

          "rowCallback": function(row, data, index) {
        var acronym = jQuery('td:first', row).text();
        jQuery(row).attr("id", "tr_" + acronym);

        if (data[data.length - 1] === true) {
    Severity: Major
    Found in app/assets/javascripts/bp_admin.js and 1 other location - About 2 hrs to fix
    app/assets/javascripts/bp_admin.js on lines 929..936

    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 90.

    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

                "rowCallback": function(row, data, index) {
                var acronym = jQuery('td:nth-child(3)', row).text();

                jQuery(row).attr("id", "tr_" + acronym);
                if (data[data.length - 1] === true) {
    Severity: Major
    Found in app/assets/javascripts/bp_admin.js and 1 other location - About 2 hrs to fix
    app/assets/javascripts/bp_admin.js on lines 662..669

    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 90.

    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 application_helper.rb has 281 lines of code (exceeds 250 allowed). Consider refactoring.
    Open

    require 'uri'
require 'cgi'
require 'digest/sha1'
require 'pry' # used in a rescue
    Severity: Minor
    Found in app/helpers/application_helper.rb - About 2 hrs to fix

      Function _ajaxCall has 68 lines of code (exceeds 25 allowed). Consider refactoring.
      Open

      AjaxAction.prototype._ajaxCall = function() {
  var self = this;
  var success = [];
  var errors = [];
  var notices = [];
      Severity: Major
      Found in app/assets/javascripts/bp_admin.js - About 2 hrs to fix

        Identical blocks of code found in 3 locations. Consider refactoring.
        Open

            this.changeOntology = function(ont) {
      var newTree = $("<ul>").append($("<li>").addClass("root"));
      $TREE_CONTAINER.html("");
      TREE = newTree;
      OPTIONS.ontology = ont;
        Severity: Major
        Found in public/widgets/jquery.ncbo.tree-2.0.0.js and 2 other locations - About 2 hrs to fix
        public/widgets/jquery.ncbo.tree-2.0.1.js on lines 121..127
        public/widgets/jquery.ncbo.tree-2.0.2.js on lines 121..127

        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 89.

        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 3 locations. Consider refactoring.
        Open

            this.changeOntology = function(ont) {
      var newTree = $("<ul>").append($("<li>").addClass("root"));
      $TREE_CONTAINER.html("");
      TREE = newTree;
      OPTIONS.ontology = ont;
        Severity: Major
        Found in public/widgets/jquery.ncbo.tree-2.0.1.js and 2 other locations - About 2 hrs to fix
        public/widgets/jquery.ncbo.tree-2.0.0.js on lines 121..127
        public/widgets/jquery.ncbo.tree-2.0.2.js on lines 121..127

        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 89.

        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 3 locations. Consider refactoring.
        Open

            this.changeOntology = function(ont) {
      var newTree = $("<ul>").append($("<li>").addClass("root"));
      $TREE_CONTAINER.html("");
      TREE = newTree;
      OPTIONS.ontology = ont;
        Severity: Major
        Found in public/widgets/jquery.ncbo.tree-2.0.2.js and 2 other locations - About 2 hrs to fix
        public/widgets/jquery.ncbo.tree-2.0.0.js on lines 121..127
        public/widgets/jquery.ncbo.tree-2.0.1.js on lines 121..127

        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 89.

        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 $IntervalProvider has 67 lines of code (exceeds 25 allowed). Consider refactoring.
        Open

        angular.mock.$IntervalProvider = function() {
  this.$get = ['$browser', '$rootScope', '$q', '$$q',
       function($browser,   $rootScope,   $q,   $$q) {
    var repeatFns = [],
        nextRepeatId = 0,
        Severity: Major
        Found in public/browse/lib/angular-mocks/angular-mocks.js - About 2 hrs to fix
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