Sign upLogin

ncbo/bioportal_web_ui

View on GitHub
Star

Showing 628 of 628 total issues

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

lunr.Index.prototype.field = function (fieldName, opts) {
  var opts = opts || {},
      field = { name: fieldName, boost: opts.boost || 1 }

  this._fields.push(field)
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 880..886

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 84.

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 jumpTo_formatItem has 61 lines of code (exceeds 25 allowed). Consider refactoring.
Open

function jumpTo_formatItem(row) {
    var specials = new RegExp("[.*+?|()\\[\\]{}\\\\]", "g"), // .*+?|()[]{}\
        keywords = jQuery(jumpTo_searchBoxSelector).val().trim().replace(specials, "\\$&").split(' ').join('|'),
        regex = new RegExp('(' + keywords + ')', 'gi');
    var resultTypeSpan = jQuery("<span>");
Severity: Major
Found in public/javascripts/widgets/quick_jump.js - About 2 hrs to fix

    Method show has 61 lines of code (exceeds 25 allowed). Consider refactoring.
    Open

      def show
    # Hack to make ontologyid and conceptid work in addition to id and ontology params
    params[:id] = params[:id].nil? ? params[:ontologyid] : params[:id]
    params[:ontology] = params[:ontology].nil? ? params[:id] : params[:ontology]
    Severity: Major
    Found in app/controllers/ontologies_controller.rb - About 2 hrs to fix

      Method concept_properties2hash has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring.
      Open

        def concept_properties2hash(properties)
    # NOTE: example properties
    #
    # properties
    #=> #<struct
      Severity: Minor
      Found in app/helpers/concepts_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

      Function $Browser has 60 lines of code (exceeds 25 allowed). Consider refactoring.
      Open

      angular.mock.$Browser = function() {
  var self = this;

  this.isMock = true;
  self.$$url = "http://server/";
      Severity: Major
      Found in public/browse/lib/angular-mocks/angular-mocks.js - About 2 hrs to fix

        Method get_class has 60 lines of code (exceeds 25 allowed). Consider refactoring.
        Open

          def get_class(params)

    if @ontology.flat?

      ignore_concept_param = params[:conceptid].nil? ||
        Severity: Major
        Found in app/controllers/application_controller.rb - About 2 hrs to fix

          Function get_annotations has 59 lines of code (exceeds 25 allowed). Consider refactoring.
          Open

          function get_annotations() {
  jQuery("#results_error").html("");
  jQuery("#annotator_error").html("");

  // Validation
          Severity: Major
          Found in app/assets/javascripts/bp_annotator.js - About 2 hrs to fix

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

            lunr.SortedSet.prototype.clone = function () {
  var clone = new lunr.SortedSet

  clone.elements = this.toArray()
  clone.length = clone.elements.length
            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/sorted_set.js on lines 197..204

            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 82.

            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.clone = function () {
  var clone = new lunr.SortedSet

  clone.elements = this.toArray()
  clone.length = clone.elements.length
            Severity: Major
            Found in public/browse/lib/lunr.js/lib/sorted_set.js and 1 other location - About 2 hrs to fix
            public/browse/lib/lunr.js/lunr.js on lines 739..746

            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 82.

            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 quick_jump.js has 264 lines of code (exceeds 250 allowed). Consider refactoring.
            Open

            // jQuery check, if it's not present then include it
// jQuery check, if it's not present then include it
function bpMinVersion(min, actual) {
  function parseVersionString (str) {
    if (typeof(str) != 'string') { return false; }
            Severity: Minor
            Found in public/javascripts/widgets/quick_jump.js - About 2 hrs to fix

              Class AdminController has 22 methods (exceeds 20 allowed). Consider refactoring.
              Open

              class AdminController < ApplicationController
  layout :determine_layout
  before_action :cache_setup

  DEBUG_BLACKLIST = [:"$,", :$ADDITIONAL_ONTOLOGY_DETAILS, :$rdebug_state, :$PROGRAM_NAME, :$LOADED_FEATURES, :$KCODE, :$-i, :$rails_rake_task, :$$, :$gems_build_rake_task, :$daemons_stop_proc, :$VERBOSE, :$DAEMONS_ARGV, :$daemons_sigterm, :$DEBUG_BEFORE, :$stdout, :$-0, :$-l, :$-I, :$DEBUG, :$', :$gems_rake_task, :$_, :$CODERAY_DEBUG, :$-F, :$", :$0, :$=, :$FILENAME, :$?, :$!, :$rdebug_in_irb, :$-K, :$TESTING, :$fileutils_rb_have_lchmod, :$EMAIL_EXCEPTIONS, :$binding, :$-v, :$>, :$SAFE, :$/, :$fileutils_rb_have_lchown, :$-p, :$-W, :$:, :$__dbg_interface, :$stderr, :$\, :$&, :$<, :$debug, :$;, :$~, :$-a, :$DEBUG_RDOC, :$CGI_ENV, :$LOAD_PATH, :$-d, :$*, :$., :$-w, :$+, :$@, :$`, :$stdin, :$1, :$2, :$3, :$4, :$5, :$6, :$7, :$8, :$9]
              Severity: Minor
              Found in app/controllers/admin_controller.rb - About 2 hrs to fix

                Function update_annotations_table has 58 lines of code (exceeds 25 allowed). Consider refactoring.
                Open

                function update_annotations_table(rowsArray) {
  "use strict";
  var ontologies = {},
    classes = {},
    match_types = {},
                Severity: Major
                Found in app/assets/javascripts/bp_annotator.js - About 2 hrs to fix

                  Function update_annotations_table has 58 lines of code (exceeds 25 allowed). Consider refactoring.
                  Open

                  function update_annotations_table(rowsArray) {
  "use strict";
  var ontologies = {},
    classes = {},
    match_types = {},
                  Severity: Major
                  Found in app/assets/javascripts/bp_annotatorplus.js - About 2 hrs to fix

                    File admin_controller.rb has 263 lines of code (exceeds 250 allowed). Consider refactoring.
                    Open

                    class AdminController < ApplicationController
  layout :determine_layout
  before_action :cache_setup

  DEBUG_BLACKLIST = [:"$,", :$ADDITIONAL_ONTOLOGY_DETAILS, :$rdebug_state, :$PROGRAM_NAME, :$LOADED_FEATURES, :$KCODE, :$-i, :$rails_rake_task, :$$, :$gems_build_rake_task, :$daemons_stop_proc, :$VERBOSE, :$DAEMONS_ARGV, :$daemons_sigterm, :$DEBUG_BEFORE, :$stdout, :$-0, :$-l, :$-I, :$DEBUG, :$', :$gems_rake_task, :$_, :$CODERAY_DEBUG, :$-F, :$", :$0, :$=, :$FILENAME, :$?, :$!, :$rdebug_in_irb, :$-K, :$TESTING, :$fileutils_rb_have_lchmod, :$EMAIL_EXCEPTIONS, :$binding, :$-v, :$>, :$SAFE, :$/, :$fileutils_rb_have_lchown, :$-p, :$-W, :$:, :$__dbg_interface, :$stderr, :$\, :$&, :$<, :$debug, :$;, :$~, :$-a, :$DEBUG_RDOC, :$CGI_ENV, :$LOAD_PATH, :$-d, :$*, :$., :$-w, :$+, :$@, :$`, :$stdin, :$1, :$2, :$3, :$4, :$5, :$6, :$7, :$8, :$9]
                    Severity: Minor
                    Found in app/controllers/admin_controller.rb - About 2 hrs to fix

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

                      lunr.Pipeline.prototype.before = function (existingFn, newFn) {
  lunr.Pipeline.warnIfFunctionNotRegistered(newFn)

  var pos = this._stack.indexOf(existingFn)
  this._stack.splice(pos, 0, newFn)
                      Severity: Major
                      Found in public/browse/lib/lunr.js/lib/pipeline.js and 1 other location - About 2 hrs to fix
                      public/browse/lib/lunr.js/lunr.js on lines 349..354

                      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 81.

                      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.Pipeline.prototype.before = function (existingFn, newFn) {
  lunr.Pipeline.warnIfFunctionNotRegistered(newFn)

  var pos = this._stack.indexOf(existingFn)
  this._stack.splice(pos, 0, newFn)
                      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/pipeline.js on lines 149..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 81.

                      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 57 lines of code (exceeds 25 allowed). Consider refactoring.
                      Open

                        function $httpBackend(method, url, data, callback, headers, timeout, withCredentials) {
    var xhr = new MockXhr(),
        expectation = expectations[0],
        wasExpected = false;
                      Severity: Major
                      Found in public/browse/lib/angular-mocks/angular-mocks.js - About 2 hrs to fix

                        Function onSuccessAction has 57 lines of code (exceeds 25 allowed). Consider refactoring.
                        Open

                        AjaxAction.prototype.onSuccessAction = function(data, ontology, deferredObj) {
  var self = this;
  if (!self.isLongOperation) {
    return;
  }
                        Severity: Major
                        Found in app/assets/javascripts/bp_admin.js - About 2 hrs to fix

                          Function formComplete_formatItem has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.
                          Open

                          function formComplete_formatItem(row) {

    var input = this.extraParams.input;
    var BP_include_definitions = jQuery(input).attr("data-bp_include_definitions");
    if (typeof BP_include_definitions === "undefined") {
                          Severity: Minor
                          Found in public/javascripts/widgets/form_complete.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 feedback has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.
                          Open

                            def feedback
    # Show the header/footer or not
    feedback_layout = params[:pop].eql?('true') ? 'popup' : 'ontology'

    # We're using a hidden form field to trigger for error checking
                          Severity: Minor
                          Found in app/controllers/home_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

                          Severity
                          Category
                          Status
                          Source
                          Language