Sign upLogin

sanger/limber

View on GitHub
Star

Showing 177 of 177 total issues

Function hasExpectedProperties has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

const hasExpectedProperties = (expectedProperties) => {
  return (results) => {
    if (results.length === 0) {
      return { valid: false, message: 'No results retrieved' }
    }
Severity: Minor
Found in app/frontend/javascript/shared/devourApiValidators.js - About 35 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 child_labware_of_plate has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

    def child_labware_of_plate
      labware
        .wells
        .sort_by(&well_order)
        .each_with_object([]) do |well, plates|
Severity: Minor
Found in app/models/robots/bed/pooling_and_splitting.rb - About 35 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 findResults has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

const findResults = (cy, filter) => {
  if (notResults !== undefined) {
    notResults.restore()
  }
Severity: Minor
Found in app/frontend/javascript/pipeline-graph/filterFunctions.js - About 35 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 valid_robot has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

    def valid_robot
      return false unless robot_present_if_required

      return true unless verify_robot? && beds.values.first.labware.present?
Severity: Minor
Found in app/models/robots/robot.rb - About 35 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 validateParameters has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

const validateParameters = function (data) {
  let result

  if (!data) {
    result = {
Severity: Minor
Found in app/frontend/javascript/custom-tagged-plate/tagLayoutFunctions.js - About 35 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

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

const buildPlateObjs = function (number) {
  return buildArray(number, (iteration) => {
    return { state: 'empty', plate: null, index: iteration }
  })
}
Severity: Minor
Found in app/frontend/javascript/shared/plateHelpers.js and 1 other location - About 35 mins to fix
app/frontend/javascript/shared/tubeHelpers.js on lines 3..7

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 46.

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 buildTubeObjs = function (number) {
  return buildArray(number, (iteration) => {
    return { state: 'empty', labware: null, index: iteration }
  })
}
Severity: Minor
Found in app/frontend/javascript/shared/tubeHelpers.js and 1 other location - About 35 mins to fix
app/frontend/javascript/shared/plateHelpers.js on lines 3..7

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 46.

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

Avoid too many return statements within this method.
Open

        return includes.include?(current_state) if includes.present?
Severity: Major
Found in app/models/concerns/presenters/statemachine/feature_in_states.rb - About 30 mins to fix

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

      {
    "resource": "tag",
    "attributes": {
      "oligo": "",
      "map_id": "",
    Severity: Minor
    Found in app/frontend/javascript/shared/resources.js and 1 other location - About 30 mins to fix
    app/frontend/javascript/shared/resources.js on lines 826..838

    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 45.

    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

      {
    "resource": "study",
    "attributes": {
      "name": "",
      "uuid": "",
    Severity: Minor
    Found in app/frontend/javascript/shared/resources.js and 1 other location - About 30 mins to fix
    app/frontend/javascript/shared/resources.js on lines 907..919

    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 45.

    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 request_hash(source_well, child_plate, additional_parameters)
      {
        'source_asset' => source_well.uuid,
        'target_asset' =>
          child_plate
    Severity: Minor
    Found in app/models/labware_creators/pcr_cycles_binned_plate_base.rb and 1 other location - About 30 mins to fix
    app/models/labware_creators/concentration_normalised_plate.rb on lines 25..34

    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 request_hash(source_well, child_plate, additional_parameters)
      {
        'source_asset' => source_well.uuid,
        'target_asset' =>
          child_plate
    Severity: Minor
    Found in app/models/labware_creators/concentration_normalised_plate.rb and 1 other location - About 30 mins to fix
    app/models/labware_creators/pcr_cycles_binned_plate_base.rb on lines 120..129

    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

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

        def compute_well_amounts(wells, multiplication_factor)
      # sort on well coordinate to ensure wells are in plate column order
      wells
        .sort_by(&:coordinate)
        .each_with_object({}) do |well, well_amounts|
    Severity: Minor
    Found in app/models/utility/concentration_binning_calculator.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

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

        def tubes_must_be_of_expected_purpose_type
      return unless file_valid?

      parent_tubes.each do |foreign_barcode, tube_in_db|
        # NB. should be catching missing tubes in previous validation
    Severity: Minor
    Found in app/models/labware_creators/multi_stamp_tubes_using_tube_rack_scan.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

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

        def compute_well_amounts(wells)
      # sort on well coordinate to ensure wells are in plate column order
      wells
        .sort_by(&:coordinate)
        .each_with_object({}) do |well, well_amounts|
    Severity: Minor
    Found in app/models/utility/fixed_normalisation_calculator.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

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

        def concentration_bins(well_amounts) # rubocop:todo Metrics/AbcSize
      # Returns eg. { 1 => [], 2 => [], 3 => [] }
      conc_bins = (1..number_of_bins).index_with { |_bin_number| [] }
      well_amounts.each do |well_locn, amount|
        bins_template.each_with_index do |bin_template, bin_index|
    Severity: Minor
    Found in app/models/utility/concentration_binning_calculator.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 checkForUnacceptablePlatePurpose has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
    Open

    const checkForUnacceptablePlatePurpose = (acceptable_purposes) => {
  return (plate) => {
    if (!acceptable_purposes || acceptable_purposes.length == 0) {
      // return valid if no acceptable purposes are provided
      return validScanMessage()
    Severity: Minor
    Found in app/frontend/javascript/shared/components/plateScanValidators.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 compute_bin_details_by_well has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
    Open

        def compute_bin_details_by_well(well_amounts)
      well_amounts.each_with_object({}) do |(well_locn, amount), well_colours|
        bins_template.each do |bin_template|
          next unless (bin_template['min']...bin_template['max']).cover?(amount)
    Severity: Minor
    Found in app/models/utility/common_dilution_calculations.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

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

        def concentration_bins(norm_details)
      # Returns eg. { 1 => [], 2 => [], 3 => [] }
      conc_bins = (1..number_of_bins).index_with { |_bin_number| [] }
      norm_details.each do |well_locn, details|
        amount = details['amount_in_target']
    Severity: Minor
    Found in app/models/utility/normalised_binning_calculator.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

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

        def child_labware_of_plate
      labware
        .wells
        .sort_by(&well_order)
        .each_with_object([]) do |well, plates|
    Severity: Minor
    Found in app/models/robots/bed/splitting.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

    Severity
    Category
    Status
    Source
    Language