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

        def authorized_required_access_for_owner?
          result = true
          if self.class.respond_to?(:associations_requiring_access_for_owner)
            enforced_associations = self.class.associations_requiring_access_for_owner.keys
            unless enforced_associations.empty?
Severity: Minor
Found in lib/seek/permissions/authorization_enforcement.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

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

  def associate_authors
    publication = @publication
    projects = publication.projects
    projects = current_user.person.projects if projects.empty?
    association = {}
Severity: Minor
Found in app/controllers/publications_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

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

  def search_in_sabiork
     unless params[:compound_name].blank?
       compound_annotation = Seek::SabiorkWebservices.new().get_compound_annotation(params[:compound_name])
       unless compound_annotation.blank?
           synonyms = compound_annotation['synonyms'].inject{|result, s| result.concat("; #{s}")}
Severity: Minor
Found in app/controllers/compounds_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

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

function getMousePos(eventObj)
{
  eventObj = eventObj ? eventObj : window.event;
  var pos;
  if(isNaN(eventObj.layerX))
Severity: Major
Found in app/assets/javascripts/jws/Resizeable_Container/javascript.js and 1 other location - About 2 hrs to fix
app/assets/javascripts/jws/Resizeable_Textbox/javascript.js on lines 128..137

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 2 locations. Consider refactoring.
Open

  function moveStart(eventObj, element)
  {
    if(element == _cornerHandle)
      document.body.style.cursor = 'se-resize';
    else if(element == _bottomEdge)
Severity: Major
Found in app/assets/javascripts/jws/Resizeable_Textbox/javascript.js and 1 other location - About 2 hrs to fix
app/assets/javascripts/jws/Resizeable_Container/javascript.js on lines 352..360

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 2 locations. Consider refactoring.
Open

  function moveStart(eventObj, element)
  {
    if(element == _cornerHandle)
      document.body.style.cursor = 'se-resize';
    else if(element == _bottomEdge)
Severity: Major
Found in app/assets/javascripts/jws/Resizeable_Container/javascript.js and 1 other location - About 2 hrs to fix
app/assets/javascripts/jws/Resizeable_Textbox/javascript.js on lines 359..367

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 2 locations. Consider refactoring.
Open

function getMousePos(eventObj)
{
  eventObj = eventObj ? eventObj : window.event;
  var pos;
  if(isNaN(eventObj.layerX))
Severity: Major
Found in app/assets/javascripts/jws/Resizeable_Textbox/javascript.js and 1 other location - About 2 hrs to fix
app/assets/javascripts/jws/Resizeable_Container/javascript.js on lines 128..137

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

Method log_event has 72 lines of code (exceeds 25 allowed). Consider refactoring.
Open

  def log_event
    User.with_current_user current_user do
      c = self.controller_name.downcase
      a = self.action_name.downcase
Severity: Major
Found in app/controllers/application_controller.rb - About 2 hrs to fix

    File assets_helper.rb has 285 lines of code (exceeds 250 allowed). Consider refactoring.
    Open

    module AssetsHelper
  include ApplicationHelper

  #the prefix used on some field id's, e.g. data_files_data_url
  def asset_field_prefix
    Severity: Minor
    Found in app/helpers/assets_helper.rb - About 2 hrs to fix

      Class AdminsController has 25 methods (exceeds 20 allowed). Consider refactoring.
      Open

      class AdminsController < ApplicationController
  include CommonSweepers

  RESTART_MSG = "Your settings have been updated. If you changed some settings e.g. search, you need to restart some processes.
                 Please see the buttons and explanations below."
      Severity: Minor
      Found in app/controllers/admins_controller.rb - About 2 hrs to fix

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

          def create
    @experimental_condition=ExperimentalCondition.new(params[:experimental_condition])
    @experimental_condition.sop=@sop
    @experimental_condition.sop_version = params[:version]
    new_substances = params[:substance_autocompleter_unrecognized_items] || []
        Severity: Major
        Found in app/controllers/experimental_conditions_controller.rb and 1 other location - About 2 hrs to fix
        app/controllers/studied_factors_controller.rb on lines 20..44

        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 102.

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

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

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

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

        Refactorings

        Further Reading

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

          def create
    @studied_factor=StudiedFactor.new(params[:studied_factor])
    @studied_factor.data_file=@data_file
    @studied_factor.data_file_version = params[:version]
    new_substances = params[:substance_autocompleter_unrecognized_items] || []
        Severity: Major
        Found in app/controllers/studied_factors_controller.rb and 1 other location - About 2 hrs to fix
        app/controllers/experimental_conditions_controller.rb on lines 20..43

        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 102.

        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 unhookEvent(element, eventName, callback)
{
  if(typeof(element) == "string")
    element = document.getElementById(element);
  if(element == null)
        Severity: Major
        Found in app/assets/javascripts/jws/Resizeable_Textbox/javascript.js and 1 other location - About 2 hrs to fix
        app/assets/javascripts/jws/Resizeable_Container/javascript.js on lines 103..113

        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 91.

        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 unhookEvent(element, eventName, callback)
{
  if(typeof(element) == "string")
    element = document.getElementById(element);
  if(element == null)
        Severity: Major
        Found in app/assets/javascripts/jws/Resizeable_Container/javascript.js and 1 other location - About 2 hrs to fix
        app/assets/javascripts/jws/Resizeable_Textbox/javascript.js on lines 103..113

        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 91.

        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 duesseldorf_bode_surgical_mapping has 69 lines of code (exceeds 25 allowed). Consider refactoring.
        Open

            def duesseldorf_bode_surgical_mapping

      gene_modification_regex = /([\w\d]+)([\/+-]+)/

      {
        Severity: Major
        Found in lib/seek/parser_mapper.rb - About 2 hrs to fix

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

            def matching_data_files params_only=false
    
    results = {}

    if Seek::Config.solr_enabled && is_jws_supported?
          Severity: Minor
          Found in app/models/model.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

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

            def cytoscape_node_elements nodes
    cytoscape_node_elements = []
    nodes.each do |node|
      item_type, item_id = node.split('_')
      item = item_type.constantize.find_by_id(item_id)
          Severity: Minor
          Found in app/helpers/i_s_a_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

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

            def render_ontology_class_tree clz, type, selected_uri,depth=0
    list = []
    uri = clz.uri.try(:to_s)
    path = send("#{type}_types_path", :uri => uri, :label => clz.label)
    assays = clz.assays
          Severity: Minor
          Found in app/helpers/suggested_assay_types_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

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

            def runs_table(runs, redirect_to=nil)
    runs.map do |run|
      workflow = run.workflow
      version = run.workflow_version
      workflow_version = workflow.find_version(version)
          Severity: Minor
          Found in app/helpers/runs_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

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

            def avatar(object, size=200, return_image_tag_only=false, url=nil, alt=nil, show_tooltip=true)
    alternative = ""
    title = get_object_title(object)
    if show_tooltip
      tooltip_text = (alt.nil? ? h(title) : alt)
          Severity: Minor
          Found in app/helpers/avatars_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

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