bio-miga/miga

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lib/miga/result/stats.rb

Summary

Maintainability
D
1 day
Test Coverage
F
48%

Module has too many lines. [206/100]
Open

module MiGA::Result::Stats
  ##
  # (Re-)calculate and save the statistics for the result
  def compute_stats
    method = :"compute_stats_#{key}"
Severity: Minor
Found in lib/miga/result/stats.rb by rubocop

This cop checks if the length a module exceeds some maximum value. Comment lines can optionally be ignored. The maximum allowed length is configurable.

Assignment Branch Condition size for compute_stats_ssu is too high. [55.34/15]
Open

  def compute_stats_ssu
    stats = {
      ssu: 0, complete_ssu: 0, ssu_fragment: [0.0, '%'],
      lsu: 0, complete_lsu: 0, lsu_fragment: [0.0, '%']
    }
Severity: Minor
Found in lib/miga/result/stats.rb by rubocop

This cop checks that the ABC size of methods is not higher than the configured maximum. The ABC size is based on assignments, branches (method calls), and conditions. See http://c2.com/cgi/wiki?AbcMetric

Method has too many lines. [46/10]
Open

  def compute_stats_ssu
    stats = {
      ssu: 0, complete_ssu: 0, ssu_fragment: [0.0, '%'],
      lsu: 0, complete_lsu: 0, lsu_fragment: [0.0, '%']
    }
Severity: Minor
Found in lib/miga/result/stats.rb by rubocop

This cop checks if the length of a method exceeds some maximum value. Comment lines can optionally be ignored. The maximum allowed length is configurable.

Assignment Branch Condition size for compute_stats_essential_genes is too high. [50.65/15]
Open

  def compute_stats_essential_genes
    stats = {}
    if source.multi?
      stats = { median_copies: 0, mean_copies: 0 }
      File.open(file_path(:report), 'r') do |fh|
Severity: Minor
Found in lib/miga/result/stats.rb by rubocop

This cop checks that the ABC size of methods is not higher than the configured maximum. The ABC size is based on assignments, branches (method calls), and conditions. See http://c2.com/cgi/wiki?AbcMetric

Method has too many lines. [38/10]
Open

  def compute_stats_essential_genes
    stats = {}
    if source.multi?
      stats = { median_copies: 0, mean_copies: 0 }
      File.open(file_path(:report), 'r') do |fh|
Severity: Minor
Found in lib/miga/result/stats.rb by rubocop

This cop checks if the length of a method exceeds some maximum value. Comment lines can optionally be ignored. The maximum allowed length is configurable.

Method compute_stats_ssu has a Cognitive Complexity of 33 (exceeds 5 allowed). Consider refactoring.
Open

  def compute_stats_ssu
    stats = {
      ssu: 0, complete_ssu: 0, ssu_fragment: [0.0, '%'],
      lsu: 0, complete_lsu: 0, lsu_fragment: [0.0, '%']
    }
Severity: Minor
Found in lib/miga/result/stats.rb - About 4 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 has too many lines. [21/10]
Open

  def compute_stats_cds
    s = MiGA::MiGA.seqs_length(file_path(:proteins), :fasta)
    stats = {
      predicted_proteins: s[:n],
      average_length: [s[:avg], 'aa']
Severity: Minor
Found in lib/miga/result/stats.rb by rubocop

This cop checks if the length of a method exceeds some maximum value. Comment lines can optionally be ignored. The maximum allowed length is configurable.

Assignment Branch Condition size for compute_stats_cds is too high. [24.06/15]
Open

  def compute_stats_cds
    s = MiGA::MiGA.seqs_length(file_path(:proteins), :fasta)
    stats = {
      predicted_proteins: s[:n],
      average_length: [s[:avg], 'aa']
Severity: Minor
Found in lib/miga/result/stats.rb by rubocop

This cop checks that the ABC size of methods is not higher than the configured maximum. The ABC size is based on assignments, branches (method calls), and conditions. See http://c2.com/cgi/wiki?AbcMetric

Assignment Branch Condition size for fix_essential_genes_by_domain is too high. [22.72/15]
Open

  def fix_essential_genes_by_domain
    return if file_path(:raw_report)

    tax = source.metadata[:tax]
    return unless tax.nil? || %w[Archaea Bacteria].include?(tax[:d])
Severity: Minor
Found in lib/miga/result/stats.rb by rubocop

This cop checks that the ABC size of methods is not higher than the configured maximum. The ABC size is based on assignments, branches (method calls), and conditions. See http://c2.com/cgi/wiki?AbcMetric

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

  def compute_stats_essential_genes
    stats = {}
    if source.multi?
      stats = { median_copies: 0, mean_copies: 0 }
      File.open(file_path(:report), 'r') do |fh|
Severity: Minor
Found in lib/miga/result/stats.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

Perceived complexity for compute_stats_essential_genes is too high. [13/7]
Open

  def compute_stats_essential_genes
    stats = {}
    if source.multi?
      stats = { median_copies: 0, mean_copies: 0 }
      File.open(file_path(:report), 'r') do |fh|
Severity: Minor
Found in lib/miga/result/stats.rb by rubocop

This cop tries to produce a complexity score that's a measure of the complexity the reader experiences when looking at a method. For that reason it considers when nodes as something that doesn't add as much complexity as an if or a &&. Except if it's one of those special case/when constructs where there's no expression after case. Then the cop treats it as an if/elsif/elsif... and lets all the when nodes count. In contrast to the CyclomaticComplexity cop, this cop considers else nodes as adding complexity.

Example:

def my_method                   # 1
  if cond                       # 1
    case var                    # 2 (0.8 + 4 * 0.2, rounded)
    when 1 then func_one
    when 2 then func_two
    when 3 then func_three
    when 4..10 then func_other
    end
  else                          # 1
    do_something until a && b   # 2
  end                           # ===
end                             # 7 complexity points

Perceived complexity for compute_stats_ssu is too high. [13/7]
Open

  def compute_stats_ssu
    stats = {
      ssu: 0, complete_ssu: 0, ssu_fragment: [0.0, '%'],
      lsu: 0, complete_lsu: 0, lsu_fragment: [0.0, '%']
    }
Severity: Minor
Found in lib/miga/result/stats.rb by rubocop

This cop tries to produce a complexity score that's a measure of the complexity the reader experiences when looking at a method. For that reason it considers when nodes as something that doesn't add as much complexity as an if or a &&. Except if it's one of those special case/when constructs where there's no expression after case. Then the cop treats it as an if/elsif/elsif... and lets all the when nodes count. In contrast to the CyclomaticComplexity cop, this cop considers else nodes as adding complexity.

Example:

def my_method                   # 1
  if cond                       # 1
    case var                    # 2 (0.8 + 4 * 0.2, rounded)
    when 1 then func_one
    when 2 then func_two
    when 3 then func_three
    when 4..10 then func_other
    end
  else                          # 1
    do_something until a && b   # 2
  end                           # ===
end                             # 7 complexity points

Cyclomatic complexity for compute_stats_ssu is too high. [12/6]
Open

  def compute_stats_ssu
    stats = {
      ssu: 0, complete_ssu: 0, ssu_fragment: [0.0, '%'],
      lsu: 0, complete_lsu: 0, lsu_fragment: [0.0, '%']
    }
Severity: Minor
Found in lib/miga/result/stats.rb by rubocop

This cop checks that the cyclomatic complexity of methods is not higher than the configured maximum. The cyclomatic complexity is the number of linearly independent paths through a method. The algorithm counts decision points and adds one.

An if statement (or unless or ?:) increases the complexity by one. An else branch does not, since it doesn't add a decision point. The && operator (or keyword and) can be converted to a nested if statement, and ||/or is shorthand for a sequence of ifs, so they also add one. Loops can be said to have an exit condition, so they add one.

Method has too many lines. [15/10]
Open

  def compute_stats_raw_reads
    stats = {}
    seq_opts = { gc: true, x: true, skew: true }
    if self[:files][:pair1].nil?
      s = MiGA::MiGA.seqs_length(file_path(:single), :fastq, seq_opts)
Severity: Minor
Found in lib/miga/result/stats.rb by rubocop

This cop checks if the length of a method exceeds some maximum value. Comment lines can optionally be ignored. The maximum allowed length is configurable.

Method has too many lines. [15/10]
Open

  def compute_stats_assembly
    s = MiGA::MiGA.seqs_length(
      file_path(:largecontigs), :fasta,
      n50: true, gc: true, x: true, skew: true
    )
Severity: Minor
Found in lib/miga/result/stats.rb by rubocop

This cop checks if the length of a method exceeds some maximum value. Comment lines can optionally be ignored. The maximum allowed length is configurable.

Cyclomatic complexity for compute_stats_essential_genes is too high. [11/6]
Open

  def compute_stats_essential_genes
    stats = {}
    if source.multi?
      stats = { median_copies: 0, mean_copies: 0 }
      File.open(file_path(:report), 'r') do |fh|
Severity: Minor
Found in lib/miga/result/stats.rb by rubocop

This cop checks that the cyclomatic complexity of methods is not higher than the configured maximum. The cyclomatic complexity is the number of linearly independent paths through a method. The algorithm counts decision points and adds one.

An if statement (or unless or ?:) increases the complexity by one. An else branch does not, since it doesn't add a decision point. The && operator (or keyword and) can be converted to a nested if statement, and ||/or is shorthand for a sequence of ifs, so they also add one. Loops can be said to have an exit condition, so they add one.

Method has too many lines. [13/10]
Open

  def compute_stats_taxonomy
    stats = {}
    return stats unless file_path(:intax_test)

    File.open(file_path(:intax_test), 'r') do |fh|
Severity: Minor
Found in lib/miga/result/stats.rb by rubocop

This cop checks if the length of a method exceeds some maximum value. Comment lines can optionally be ignored. The maximum allowed length is configurable.

Method has too many lines. [13/10]
Open

  def fix_essential_genes_by_domain
    return if file_path(:raw_report)

    tax = source.metadata[:tax]
    return unless tax.nil? || %w[Archaea Bacteria].include?(tax[:d])
Severity: Minor
Found in lib/miga/result/stats.rb by rubocop

This cop checks if the length of a method exceeds some maximum value. Comment lines can optionally be ignored. The maximum allowed length is configurable.

Method compute_stats_ssu has 46 lines of code (exceeds 25 allowed). Consider refactoring.
Open

  def compute_stats_ssu
    stats = {
      ssu: 0, complete_ssu: 0, ssu_fragment: [0.0, '%'],
      lsu: 0, complete_lsu: 0, lsu_fragment: [0.0, '%']
    }
Severity: Minor
Found in lib/miga/result/stats.rb - About 1 hr to fix

Method compute_stats_essential_genes has 38 lines of code (exceeds 25 allowed). Consider refactoring.
Open

  def compute_stats_essential_genes
    stats = {}
    if source.multi?
      stats = { median_copies: 0, mean_copies: 0 }
      File.open(file_path(:report), 'r') do |fh|
Severity: Minor
Found in lib/miga/result/stats.rb - About 1 hr to fix

Method compute_stats_taxonomy has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.
Open

  def compute_stats_taxonomy
    stats = {}
    return stats unless file_path(:intax_test)

    File.open(file_path(:intax_test), 'r') do |fh|
Severity: Minor
Found in lib/miga/result/stats.rb - About 1 hr 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_stats_cds has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
Open

  def compute_stats_cds
    s = MiGA::MiGA.seqs_length(file_path(:proteins), :fasta)
    stats = {
      predicted_proteins: s[:n],
      average_length: [s[:avg], 'aa']
Severity: Minor
Found in lib/miga/result/stats.rb - About 1 hr 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 fix_essential_genes_by_domain has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

  def fix_essential_genes_by_domain
    return if file_path(:raw_report)

    tax = source.metadata[:tax]
    return unless tax.nil? || %w[Archaea Bacteria].include?(tax[:d])
Severity: Minor
Found in lib/miga/result/stats.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

Use =~ in places where the MatchData returned by #match will not be used.
Open

          if /^! (Mean|Median) number of copies per model: (.*)\./.match(ln)
Severity: Minor
Found in lib/miga/result/stats.rb by rubocop

This cop identifies the use of Regexp#match or String#match, which returns #<MatchData>/nil. The return value of =~ is an integral index/nil and is more performant.

Example:

# bad
do_something if str.match(/regex/)
while regex.match('str')
  do_something
end

# good
method(str =~ /regex/)
return value unless regex =~ 'str'

Use =~ in places where the MatchData returned by #match will not be used.
Open

          if /^! (Completeness|Contamination): (.*)%/.match(ln)
Severity: Minor
Found in lib/miga/result/stats.rb by rubocop

This cop identifies the use of Regexp#match or String#match, which returns #<MatchData>/nil. The return value of =~ is an integral index/nil and is more performant.

Example:

# bad
do_something if str.match(/regex/)
while regex.match('str')
  do_something
end

# good
method(str =~ /regex/)
return value unless regex =~ 'str'

Missing magic comment # frozen_string_literal: true.
Open

require 'miga/result/base'
Severity: Minor
Found in lib/miga/result/stats.rb by rubocop

This cop is designed to help upgrade to Ruby 3.0. It will add the comment # frozen_string_literal: true to the top of files to enable frozen string literals. Frozen string literals may be default in Ruby 3.0. The comment will be added below a shebang and encoding comment. The frozen string literal comment is only valid in Ruby 2.3+.

Example: EnforcedStyle: when_needed (default)

# The `when_needed` style will add the frozen string literal comment
# to files only when the `TargetRubyVersion` is set to 2.3+.
# bad
module Foo
  # ...
end

# good
# frozen_string_literal: true

module Foo
  # ...
end

Example: EnforcedStyle: always

# The `always` style will always add the frozen string literal comment
# to a file, regardless of the Ruby version or if `freeze` or `<<` are
# called on a string literal.
# bad
module Bar
  # ...
end

# good
# frozen_string_literal: true

module Bar
  # ...
end

Example: EnforcedStyle: never

# The `never` will enforce that the frozen string literal comment does
# not exist in a file.
# bad
# frozen_string_literal: true

module Baz
  # ...
end

# good
module Baz
  # ...
end

Avoid the use of Perl-style backrefs.
Open

            stats["#{$1.downcase}_copies".to_sym] = $2.to_f
Severity: Minor
Found in lib/miga/result/stats.rb by rubocop

This cop looks for uses of Perl-style regexp match backreferences like $1, $2, etc.

Example:

# bad
puts $1

# good
puts Regexp.last_match(1)

Avoid the use of Perl-style backrefs.
Open

        stats[:"#{$1}_pvalue"] = $3.to_f unless $1 == 'root'
Severity: Minor
Found in lib/miga/result/stats.rb by rubocop

This cop looks for uses of Perl-style regexp match backreferences like $1, $2, etc.

Example:

# bad
puts $1

# good
puts Regexp.last_match(1)

Avoid the use of Perl-style backrefs.
Open

        stats[:"#{$1}_pvalue"] = $3.to_f unless $1 == 'root'
Severity: Minor
Found in lib/miga/result/stats.rb by rubocop

This cop looks for uses of Perl-style regexp match backreferences like $1, $2, etc.

Example:

# bad
puts $1

# good
puts Regexp.last_match(1)

Avoid the use of Perl-style backrefs.
Open

            stats["#{$1.downcase}_copies".to_sym] = $2.to_f
Severity: Minor
Found in lib/miga/result/stats.rb by rubocop

This cop looks for uses of Perl-style regexp match backreferences like $1, $2, etc.

Example:

# bad
puts $1

# good
puts Regexp.last_match(1)

Avoid the use of Perl-style backrefs.
Open

            fragment = $1.to_f
Severity: Minor
Found in lib/miga/result/stats.rb by rubocop

This cop looks for uses of Perl-style regexp match backreferences like $1, $2, etc.

Example:

# bad
puts $1

# good
puts Regexp.last_match(1)

Redundant self detected.
Open

    stats = self.respond_to?(method, true) ? send(method) : nil
Severity: Minor
Found in lib/miga/result/stats.rb by rubocop

This cop checks for redundant uses of self.

The usage of self is only needed when:

  • Sending a message to same object with zero arguments in presence of a method name clash with an argument or a local variable.

  • Calling an attribute writer to prevent an local variable assignment.

Note, with using explicit self you can only send messages with public or protected scope, you cannot send private messages this way.

Note we allow uses of self with operators because it would be awkward otherwise.

Example:

# bad
def foo(bar)
  self.baz
end

# good
def foo(bar)
  self.bar  # Resolves name clash with the argument.
end

def foo
  bar = 1
  self.bar  # Resolves name clash with the local variable.
end

def foo
  %w[x y z].select do |bar|
    self.bar == bar  # Resolves name clash with argument of the block.
  end
end

Incorrect indentation detected (column 8 instead of 6).
Open

        # * Bowers et al 2017, DOI: 10.1038/nbt.3893
Severity: Minor
Found in lib/miga/result/stats.rb by rubocop

This cops checks the indentation of comments.

Example:

# bad
  # comment here
def method_name
end

  # comment here
a = 'hello'

# yet another comment
  if true
    true
  end

# good
# comment here
def method_name
end

# comment here
a = 'hello'

# yet another comment
if true
  true
end

Avoid the use of Perl-style backrefs.
Open

      stats[:aai] = [$2.to_f, '%']
Severity: Minor
Found in lib/miga/result/stats.rb by rubocop

This cop looks for uses of Perl-style regexp match backreferences like $1, $2, etc.

Example:

# bad
puts $1

# good
puts Regexp.last_match(1)

Avoid the use of Perl-style backrefs.
Open

            stats[$1.downcase.to_sym][0] = $2.to_f
Severity: Minor
Found in lib/miga/result/stats.rb by rubocop

This cop looks for uses of Perl-style regexp match backreferences like $1, $2, etc.

Example:

# bad
puts $1

# good
puts Regexp.last_match(1)

Avoid the use of Perl-style backrefs.
Open

            stats[$1.downcase.to_sym][0] = $2.to_f
Severity: Minor
Found in lib/miga/result/stats.rb by rubocop

This cop looks for uses of Perl-style regexp match backreferences like $1, $2, etc.

Example:

# bad
puts $1

# good
puts Regexp.last_match(1)

Avoid the use of Perl-style backrefs.
Open

      stats[:closest_relative] = $1
Severity: Minor
Found in lib/miga/result/stats.rb by rubocop

This cop looks for uses of Perl-style regexp match backreferences like $1, $2, etc.

Example:

# bad
puts $1

# good
puts Regexp.last_match(1)

Avoid the use of Perl-style backrefs.
Open

        stats[:"#{$1}_pvalue"] = $3.to_f unless $1 == 'root'
Severity: Minor
Found in lib/miga/result/stats.rb by rubocop

This cop looks for uses of Perl-style regexp match backreferences like $1, $2, etc.

Example:

# bad
puts $1

# good
puts Regexp.last_match(1)

Avoid the use of Perl-style backrefs.
Open

            stats[:codon_table] = $1
Severity: Minor
Found in lib/miga/result/stats.rb by rubocop

This cop looks for uses of Perl-style regexp match backreferences like $1, $2, etc.

Example:

# bad
puts $1

# good
puts Regexp.last_match(1)

Use || instead of or.
Open

    unless asm.nil? or asm[:stats][:total_length].nil?
Severity: Minor
Found in lib/miga/result/stats.rb by rubocop

This cop checks for uses of and and or, and suggests using && and || instead. It can be configured to check only in conditions, or in all contexts.

Example: EnforcedStyle: always (default)

# bad
foo.save and return

# bad
if foo and bar
end

# good
foo.save && return

# good
if foo && bar
end

Example: EnforcedStyle: conditionals

# bad
if foo and bar
end

# good
foo.save && return

# good
foo.save and return

# good
if foo && bar
end

Favor a normal if-statement over a modifier clause in a multiline statement.
Open

    Zlib::GzipReader.open(file_path(:trna_list)) do |fh|
      no = 0
      stats[:trna_count] = 0
      aa = {}
      fh.each_line do |ln|
Severity: Minor
Found in lib/miga/result/stats.rb by rubocop

Checks for uses of if/unless modifiers with multiple-lines bodies.

Example:

# bad
{
  result: 'this should not happen'
} unless cond

# good
{ result: 'ok' } if cond

Prefer single-quoted strings when you don't need string interpolation or special symbols.
Open

    MiGA::MiGA.DEBUG "Fixing essential genes by domain"
Severity: Minor
Found in lib/miga/result/stats.rb by rubocop

Checks if uses of quotes match the configured preference.

Example: EnforcedStyle: single_quotes (default)

# bad
"No special symbols"
"No string interpolation"
"Just text"

# good
'No special symbols'
'No string interpolation'
'Just text'
"Wait! What's #{this}!"

Example: EnforcedStyle: double_quotes

# bad
'Just some text'
'No special chars or interpolation'

# good
"Just some text"
"No special chars or interpolation"
"Every string in #{project} uses double_quotes"

There are no issues that match your filters.

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