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

      data_file = DataFile.find(params[:data_file_id])
      if data_file.can_edit? current_user
        @data_file = data_file
        find_display_asset @data_file
      else
Severity: Minor
Found in app/controllers/studied_factors_controller.rb and 1 other location - About 30 mins to fix
app/controllers/experimental_conditions_controller.rb on lines 134..143

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 32.

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 sampling_date_info
    if sampling_date.nil?
      ''
    else
      if try(:sampling_date).hour == 0 and try(:sampling_date).min == 0 and try(:sampling_date).sec == 0 then
Severity: Minor
Found in app/models/sample.rb and 1 other location - About 30 mins to fix
app/models/specimen.rb on lines 163..171

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 32.

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 born_info
    if born.nil?
      ''
    else
      if try(:born).hour == 0 && try(:born).min == 0 && try(:born).sec == 0
Severity: Minor
Found in app/models/specimen.rb and 1 other location - About 30 mins to fix
app/models/sample.rb on lines 183..191

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 32.

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 parent_assay_types_list_links parents
      unless parents.empty?
        parents.collect do |par|
          link_to par.label,assay_types_path(uri: par.uri,label: par.label),:class=>"parent_term"
        end.join(" | ").html_safe
Severity: Minor
Found in app/helpers/assay_types_helper.rb and 1 other location - About 30 mins to fix
app/helpers/technology_types_helper.rb on lines 13..20

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 32.

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

      sop = Sop.find(params[:sop_id])
      if sop.can_edit? current_user
        @sop = sop
        find_display_asset @sop
      else
Severity: Minor
Found in app/controllers/experimental_conditions_controller.rb and 1 other location - About 30 mins to fix
app/controllers/studied_factors_controller.rb on lines 136..145

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 32.

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 seek_stylesheet_tags main='application'
    css = (Seek::Config.css_prepended || "").split(",")
    css << main
    css = css | (Seek::Config.css_appended || "").split(",")
    css.empty? ? "" : stylesheet_link_tag(*css)
Severity: Minor
Found in app/helpers/application_helper.rb and 1 other location - About 30 mins to fix
app/helpers/application_helper.rb on lines 24..29

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 32.

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 parent_technology_types_list_links parents
    unless parents.empty?
      parents.collect do |par|
        link_to par.label,technology_types_path(uri: par.uri,label: par.label),:class=>"parent_term"
      end.join(" | ").html_safe
Severity: Minor
Found in app/helpers/technology_types_helper.rb and 1 other location - About 30 mins to fix
app/helpers/assay_types_helper.rb on lines 14..21

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 32.

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 find_samples_sheet doc
      #sheet = doc.find_first("//ss:sheet[@name='SDRF']")
      #sheet = doc.find_first("//ss:sheet[@name='sdrf']") if sheet.nil?
      #sheet = doc.find_first("//ss:sheet[@name='Sdrf']") if sheet.nil?
      #sheet = hunt_for_sheet(doc, "SDRF") if sheet.nil?
Severity: Minor
Found in lib/seek/data/bio_samples.rb and 1 other location - About 30 mins to fix
lib/seek/data/bio_samples.rb on lines 140..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 32.

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

      def contains_downloadable_items?
        blobs = []
        blobs << self.content_blob if self.respond_to?(:content_blob)
        blobs = blobs | self.content_blobs if self.respond_to?(:content_blobs)
        !blobs.compact.select{|blob| !blob.is_webpage?}.empty?
Severity: Minor
Found in lib/acts_as_versioned_resource.rb and 1 other location - About 25 mins to fix
lib/acts_as_asset.rb on lines 130..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 31.

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 get_people_in_institution institution_id, access_type
      institution = Institution.find(institution_id)
    if institution
      people_in_institution = [] #id, name, access_type
      institution.people.each do |person|
Severity: Minor
Found in app/models/policy.rb and 1 other location - About 25 mins to fix
app/models/policy.rb on lines 438..445

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 31.

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 get_people_in_project project_id, access_type
      project = Project.find(project_id)
    if project
      people_in_project = [] #id, name, access_type
      project.people.each do |person|
Severity: Minor
Found in app/models/policy.rb and 1 other location - About 25 mins to fix
app/models/policy.rb on lines 450..457

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 31.

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

      def contains_downloadable_items?
        blobs = []
        blobs << self.content_blob if self.respond_to?(:content_blob)
        blobs = blobs | self.content_blobs if self.respond_to?(:content_blobs)
        !blobs.compact.select{|blob| !blob.is_webpage?}.empty?
Severity: Minor
Found in lib/acts_as_asset.rb and 1 other location - About 25 mins to fix
lib/acts_as_versioned_resource.rb on lines 70..74

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 31.

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 addSelectedPublication has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

function addSelectedPublication() {
    selected_option_index=$("possible_publications").selectedIndex;
    selected_option=$("possible_publications").options[selected_option_index];
    title=selected_option.text;
    id=selected_option.value;
Severity: Minor
Found in app/assets/javascripts/publication.js - About 25 mins 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 updateSops has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

function updateSops() {
    sop_text='<ul class="related_asset_list">';

    sop_ids=new Array();
Severity: Minor
Found in app/assets/javascripts/assays.js - About 25 mins 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 updateEvents has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

function updateEvents() {
    event_text = '<ul class="related_asset_list">'
    for (var i = 0; i < events_array.length; i++) {
        var event = events_array[i];
        var title = event[0];
Severity: Minor
Found in app/assets/javascripts/associate_events.js - About 25 mins 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 addSelectedDataFile has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

function addSelectedDataFile() {
    selected_option_index=$("possible_data_files").selectedIndex;
    selected_option=$("possible_data_files").options[selected_option_index];
    title=selected_option.text;
    id=selected_option.value;
Severity: Minor
Found in app/assets/javascripts/assays.js - About 25 mins 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 bio_reference has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

  def bio_reference
    if pubmed_id
      Bio::MEDLINE.new(Bio::PubMed.efetch(pubmed_id).first).reference
    else
      #TODO: Bio::Reference supports a 'url' option. Should this be the URL on seek, or the URL of the 'View Publication' button, or neither?
Severity: Minor
Found in app/models/publication.rb - About 25 mins 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 updateModels has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

function updateModels() {
    model_text='<ul class="related_asset_list">';
    type="Model";
    model_ids=new Array();
Severity: Minor
Found in app/assets/javascripts/assays.js - About 25 mins 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 setTheDivStyle has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

function setTheDivStyle() {
if(!readCookie('name_panel')) {
// if cookie not found display the div and create the cookie
//document.getElementById("name_panel").style.display="block";
//createCookie('name_panel', 1);  // 1 day = 24 hours persistence
Severity: Minor
Found in app/assets/javascripts/jws/JWSconstructor_panels.js - About 25 mins 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 hookSearch has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

function hookSearch() {
  var input  = $('#search-field').eq(0);
  var result = $('#search-results').eq(0);
  $(result).show();
Severity: Minor
Found in doc/seek/js/darkfish.js - About 25 mins 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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