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Complex method Transfer::BetweenPlatesBySubmission#well_to_destination (43.9)
Open

  def well_to_destination # rubocop:todo Metrics/AbcSize
    {}.tap do |sources_to_target|
      # Group the wells based on the submission
      groups = source.wells.in_column_major_order.with_pool_id.group_by(&:pool_id).delete_if { |k, _| k.nil? }.values
Severity: Minor
Found in app/models/transfer/between_plates_by_submission.rb by flog

Flog calculates the ABC score for methods. The ABC score is based on assignments, branches (method calls), and conditions.

You can read more about ABC metrics or the flog tool

Complex method SequencescapeExcel::SpecialisedField::SangerPlateId#update (43.9)
Open

      def update(_attributes = {}) # rubocop:todo Metrics/CyclomaticComplexity, Metrics/MethodLength
        return unless valid? && foreign_barcode_format.present?

        # checking if the plate this well belongs to already has this foreign barcode set in its list of barcodes.
        # or if it contains a foreign barcode with the same format, then update that existing one
Severity: Minor
Found in app/sequencescape_excel/sequencescape_excel/specialised_field/sanger_plate_id.rb by flog

Flog calculates the ABC score for methods. The ABC score is based on assignments, branches (method calls), and conditions.

You can read more about ABC metrics or the flog tool

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

const plateRequest = async (plate_barcode) => {
  try {
    return await window.fetch(PLATE_PATH + encodeURIComponent(plate_barcode), {});
  } catch (error) {
    console.error(error);
Severity: Major
Found in app/frontend/plate-picks/store/actions.js and 1 other location - About 2 hrs to fix
app/frontend/plate-picks/store/actions.js on lines 56..63

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

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

  updatePick: (state, new_attributes) => {
    const found_pick = state.picks[new_attributes.id] || {};
    // Merge the new attributes into the old, and update the pick
    let combined_pick = Object.assign({}, found_pick, new_attributes);
    Vue.set(state.picks, new_attributes.id, combined_pick);
Severity: Major
Found in app/frontend/plate-picks/store/mutations.js and 1 other location - About 2 hrs to fix
app/frontend/plate-picks/store/mutations.js on lines 62..67

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

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

  updatePlate: (state, new_attributes) => {
    const found_plate = state.plates[new_attributes.id] || {};
    // Merge the new attributes into the old, and update the plate
    let combined_plate = Object.assign({}, found_plate, new_attributes);
    Vue.set(state.plates, new_attributes.id, combined_plate);
Severity: Major
Found in app/frontend/plate-picks/store/mutations.js and 1 other location - About 2 hrs to fix
app/frontend/plate-picks/store/mutations.js on lines 107..112

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

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

const batchRequest = async (batch_id) => {
  try {
    return await window.fetch(BATCH_PATH + encodeURIComponent(batch_id), {});
  } catch (error) {
    console.error(error);
Severity: Major
Found in app/frontend/plate-picks/store/actions.js and 1 other location - About 2 hrs to fix
app/frontend/plate-picks/store/actions.js on lines 37..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 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

Complex method RequestsController#update (43.6)
Open

  def update # rubocop:todo Metrics/AbcSize
    @request = Request.find(params[:id])
    authorize! :update, @request

    unless params[:request][:request_type_id].nil?
Severity: Minor
Found in app/controllers/requests_controller.rb by flog

Flog calculates the ABC score for methods. The ABC score is based on assignments, branches (method calls), and conditions.

You can read more about ABC metrics or the flog tool

Complex method AccessionService#post_files (43.5)
Open

  def post_files(file_params) # rubocop:todo Metrics/CyclomaticComplexity
    rc = rest_client_resource

    if configatron.disable_web_proxy == true
      RestClient.proxy = nil
Severity: Minor
Found in app/models/accession_service.rb by flog

Flog calculates the ABC score for methods. The ABC score is based on assignments, branches (method calls), and conditions.

You can read more about ABC metrics or the flog tool

Complex method Robot::Verification::Base#valid_submission? (43.4)
Open

  def valid_submission?(params) # rubocop:todo Metrics/CyclomaticComplexity
    destination_plate_barcode = params[:barcodes][:destination_plate_barcode]
    batch = Batch.find_by(id: params[:batch_id])
    robot = Robot.find_by(id: params[:robot_id])
    user = User.find_by(id: params[:user_id])
Severity: Minor
Found in app/models/robot/verification/base.rb by flog

Flog calculates the ABC score for methods. The ABC score is based on assignments, branches (method calls), and conditions.

You can read more about ABC metrics or the flog tool

Complex method ProjectsController#create (43.1)
Open

  def create # rubocop:todo Metrics/AbcSize, Metrics/MethodLength
    # TODO[5002667]: All of this code should be in a before_create/after_create callback in the Project model ...
    @project = Project.new(params[:project])
    @project.save!
Severity: Minor
Found in app/controllers/projects_controller.rb by flog

Flog calculates the ABC score for methods. The ABC score is based on assignments, branches (method calls), and conditions.

You can read more about ABC metrics or the flog tool

Method render_cherrypick_task has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.
Open

  def render_cherrypick_task(_task, params) # rubocop:todo Metrics/CyclomaticComplexity
    if flash[:error].present?
      redirect_to action: 'stage', batch_id: @batch.id, workflow_id: @workflow.id, id: (@stage - 1).to_s
      return
    end
Severity: Minor
Found in app/models/tasks/cherrypick_handler.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 update has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.
Open

  def update # rubocop:todo Metrics/AbcSize
    @study = Study.find(params[:id])

    ActiveRecord::Base.transaction do
      @study.update!(params[:study])
Severity: Minor
Found in app/controllers/studies_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

Complex method ModelExtensions::Order::included (42.9)
Open

  def self.included(base) # rubocop:todo Metrics/AbcSize
    base.class_eval do
      include Validations

      before_validation :merge_in_structured_request_options
Severity: Minor
Found in app/api/model_extensions/order.rb by flog

Flog calculates the ABC score for methods. The ABC score is based on assignments, branches (method calls), and conditions.

You can read more about ABC metrics or the flog tool

Complex method Robot::PickData#generate_picking_data_hash (42.9)
Open

  def generate_picking_data_hash(target_barcode, requests: requests_for_destination_plate)
    data_objects = {}
    source_barcode_to_pick_number = {}

    current_pick_size = lambda { data_objects[data_objects.size]['source'].size }
Severity: Minor
Found in app/models/robot/pick_data.rb by flog

Flog calculates the ABC score for methods. The ABC score is based on assignments, branches (method calls), and conditions.

You can read more about ABC metrics or the flog tool

Complex method Api::Base::json_attribute_for_attribute (42.7)
Open

    def json_attribute_for_attribute(attribute_or_association, *rest) # rubocop:todo Metrics/AbcSize
      json_attribute = attribute_to_json_attribute_mappings[attribute_or_association.to_sym]
      if json_attribute.blank?
        # If we have reached the end of the line, and the attribute_or_association is for what looks like
        # an association, then we'll look it up without the '_id' and return that value.
Severity: Minor
Found in app/models/api/base.rb by flog

Flog calculates the ABC score for methods. The ABC score is based on assignments, branches (method calls), and conditions.

You can read more about ABC metrics or the flog tool

Complex method GelsController#update (42.7)
Open

  def update # rubocop:todo Metrics/AbcSize
    ActiveRecord::Base.transaction do
      params[:wells].keys.each do |well_id|
        well = Well.find(well_id)
        well.well_attribute.update!(gel_pass: params[:wells][well_id][:qc_state])
Severity: Minor
Found in app/controllers/gels_controller.rb by flog

Flog calculates the ABC score for methods. The ABC score is based on assignments, branches (method calls), and conditions.

You can read more about ABC metrics or the flog tool

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

  def grant_role # rubocop:todo Metrics/AbcSize
    @user = User.find(params[:role][:user])
    @project = Project.find(params[:id])
    @role = Role.find_by(name: params[:role][:authorizable_type])
Severity: Major
Found in app/controllers/projects_controller.rb and 1 other location - About 2 hrs to fix
app/controllers/projects_controller.rb on lines 150..170

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

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

  def remove_role # rubocop:todo Metrics/AbcSize
    @user = User.find(params[:role][:user])
    @project = Project.find(params[:id])
    @role = Role.find_by(name: params[:role][:authorizable_type])
Severity: Major
Found in app/controllers/projects_controller.rb and 1 other location - About 2 hrs to fix
app/controllers/projects_controller.rb on lines 124..144

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

Complex method SequencescapeExcel::SpecialisedField::SangerTubeId#update (42.3)
Open

      def update(_attributes = {}) # rubocop:todo Metrics/CyclomaticComplexity, Metrics/MethodLength
        return unless valid? && foreign_barcode_format.present?

        # if this tube's list of barcodes already contains a foreign barcode with the same format then update the
        # existing one
Severity: Minor
Found in app/sequencescape_excel/sequencescape_excel/specialised_field/sanger_tube_id.rb by flog

Flog calculates the ABC score for methods. The ABC score is based on assignments, branches (method calls), and conditions.

You can read more about ABC metrics or the flog tool

File submissions.js has 258 lines of code (exceeds 250 allowed). Consider refactoring.
Open

// Submission workflow jQuery Plugin...
(function (window, $) {
  "use strict";

  var methods = {
Severity: Minor
Found in app/frontend/entrypoints/submissions.js - About 2 hrs to fix
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