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Function init has 28 lines of code (exceeds 25 allowed). Consider refactoring.
Open

    this.init = function() {
      ROOT.html($("<span>").html("Loading...").css("font-size", "smaller"));
      $.ajax({
        url: obj.determineHTTPS(OPTIONS.ncboUIURL) + "/ajax/properties/tree",
        data: {
Severity: Minor
Found in app/assets/javascripts/bp_property_tree.js - About 1 hr to fix

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

    lunr.Vector.prototype.similarity = function (otherVector) {
  return this.dot(otherVector) / (this.magnitude() * otherVector.magnitude())
}
    Severity: Major
    Found in public/browse/lib/lunr.js/lunr.js and 1 other location - About 1 hr to fix
    public/browse/lib/lunr.js/lib/vector.js on lines 123..125

    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 57.

    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.prototype.similarity = function (otherVector) {
  return this.dot(otherVector) / (this.magnitude() * otherVector.magnitude())
}
    Severity: Major
    Found in public/browse/lib/lunr.js/lib/vector.js and 1 other location - About 1 hr to fix
    public/browse/lib/lunr.js/lunr.js on lines 540..542

    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 57.

    We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

    The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

    If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

    See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

    Refactorings

    Further Reading

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

      def delete_submission
    response = { errors: '', success: '' }

    begin
      ont = params['acronym']
    Severity: Minor
    Found in app/controllers/admin_controller.rb - About 1 hr to fix

    Cognitive Complexity

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

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

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

    Further reading

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

      def index
    ontology_list = LinkedData::Client::Models::Ontology.all.select { |o| !o.summaryOnly }
    ontologies_mapping_count = LinkedData::Client::HTTP.get("#{MAPPINGS_URL}/statistics/ontologies")
    ontologies_hash = {}
    ontology_list.each do |ontology|
    Severity: Minor
    Found in app/controllers/mappings_controller.rb - About 1 hr to fix

    Cognitive Complexity

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

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

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

    Further reading

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

      def index
    if params[:url] # We were provided with a url to redirect to
      params_string = ""
      # Trigger to switch the placeholders
      first_param = true
    Severity: Minor
    Found in app/controllers/redirect_controller.rb - About 1 hr to fix

    Cognitive Complexity

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

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

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

    Further reading

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

      def format_metric_list(metrics, metric, title)
    return 0 if metric.nil?

    markup = ""
    Severity: Minor
    Found in app/helpers/ontology_metrics_helper.rb - About 1 hr to fix

    Cognitive Complexity

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

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

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

    Further reading

    Function init has 27 lines of code (exceeds 25 allowed). Consider refactoring.
    Open

        this.init = function() {
      $TREE_CONTAINER = element;
      TREE = $("<ul>").append($("<li>").addClass("root"));
      ROOT = $('.root', TREE);
      TREE.css("width", OPTIONS.width).addClass(OPTIONS.treeClass);
    Severity: Minor
    Found in public/widgets/jquery.ncbo.tree-2.0.0.js - About 1 hr to fix

      Function init has 27 lines of code (exceeds 25 allowed). Consider refactoring.
      Open

          this.init = function() {
      $TREE_CONTAINER = element;
      TREE = $("<ul>").append($("<li>").addClass("root"));
      ROOT = $('.root', TREE);
      TREE.css("width", OPTIONS.width).addClass(OPTIONS.treeClass);
      Severity: Minor
      Found in public/widgets/jquery.ncbo.tree-2.0.2.js - About 1 hr to fix

        Function parseName has 27 lines of code (exceeds 25 allowed). Consider refactoring.
        Open

                parseName: function (name) {
            var modName, ext, temp,
                strip = false,
                index = name.indexOf("."),
                isRelative = name.indexOf('./') === 0 ||
        Severity: Minor
        Found in public/browse/lib/lunr.js/example/text.js - About 1 hr to fix

          Function $ExceptionHandlerProvider has 27 lines of code (exceeds 25 allowed). Consider refactoring.
          Open

          angular.mock.$ExceptionHandlerProvider = function() {
  var handler;

  /**
   * @ngdoc method
          Severity: Minor
          Found in public/browse/lib/angular-mocks/angular-mocks.js - About 1 hr to fix

            Function jumpTo_setup_functions has 27 lines of code (exceeds 25 allowed). Consider refactoring.
            Open

            function jumpTo_setup_functions() {
    var extra_params = {
        subtreerootconceptid: encodeURIComponent(BP_search_branch)
    };
    var result_width = 350;
            Severity: Minor
            Found in public/javascripts/widgets/quick_jump.js - About 1 hr to fix

              Function init has 27 lines of code (exceeds 25 allowed). Consider refactoring.
              Open

                  this.init = function() {
      $TREE_CONTAINER = element;
      TREE = $("<ul>").append($("<li>").addClass("root"));
      ROOT = $('.root', TREE);
      TREE.css("width", OPTIONS.width).addClass(OPTIONS.treeClass);
              Severity: Minor
              Found in public/widgets/jquery.ncbo.tree-2.0.1.js - About 1 hr to fix

                Method simplify_ontology_model has 27 lines of code (exceeds 25 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 1 hr to fix

                  Method _process_ontologies has 27 lines of code (exceeds 25 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 1 hr to fix

                    Function _showStatusMessages has 27 lines of code (exceeds 25 allowed). Consider refactoring.
                    Open

                    function _showStatusMessages(success, errors, notices, isAppendMode) {
  if (success.length > 0) {
    if (isAppendMode) {
      var appendStr = (jQuery.trim(jQuery('#success_message').html()).length) ? ", " : "";
      jQuery("#success_message").append(appendStr + success.join(", ")).html();
                    Severity: Minor
                    Found in app/assets/javascripts/bp_admin.js - About 1 hr to fix

                      Method request_term has 27 lines of code (exceeds 25 allowed). Consider refactoring.
                      Open

                        def request_term
    response = {}
    endpoint = "/RequestTerm"
    h_params = {}
    response_raw = nil
                      Severity: Minor
                      Found in app/controllers/ontolobridge_controller.rb - About 1 hr to fix

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

                          var questions = raw.questions.map(function (q) {
    return {
      id: q.question_id,
      title: q.title,
      body: q.body,
                        Severity: Major
                        Found in public/browse/lib/lunr.js/example/index_builder.js and 1 other location - About 1 hr to fix
                        public/browse/lib/lunr.js/example/app.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 56.

                        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

                          var questions = JSON.parse(data).questions.map(function (raw) {
    return {
      id: raw.question_id,
      title: raw.title,
      body: raw.body,
                        Severity: Major
                        Found in public/browse/lib/lunr.js/example/app.js and 1 other location - About 1 hr to fix
                        public/browse/lib/lunr.js/example/index_builder.js on lines 17..24

                        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 56.

                        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 bioportal_autocomplete has 26 lines of code (exceeds 25 allowed). Consider refactoring.
                        Open

                            jQuery.fn.bioportal_autocomplete = function(url, options, data) {
      // Make sure options exists
      options = options || {};
      // Set url as option
      options.url = url;
                        Severity: Minor
                        Found in public/javascripts/JqueryPlugins/autocomplete/crossdomain_autocomplete.js - About 1 hr to fix
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