bio-miga/miga

View on GitHub
lib/miga/cli/action/doctor/operations.rb

Summary

Maintainability
C
7 hrs
Test Coverage

Module has too many lines. [134/100]
Open

module MiGA::Cli::Action::Doctor::Operations
  ##
  # Perform refdb operation with MiGA::Cli +cli+
  def check_refdb(cli)
    cli.say 'Checking index format of reference database'

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

Method has too many lines. [28/10]
Open

  def check_mts(cli)
    cli.say 'Looking for unarchived MyTaxa Scan runs'
    cli.load_project.each_dataset do |d|
      res = d.result(:mytaxa_scan)
      next if res.nil?

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. [20/10]
Open

  def check_cds(cli)
    cli.say 'Looking for unzipped genes or proteins'
    n, k = cli.load_project.dataset_names.size, 0
    cli.load_project.each_dataset do |d|
      cli.advance('Datasets:', k += 1, n, false)

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. [20/10]
Open

  def check_files(cli)
    cli.say 'Looking for outdated files in results'
    n, k = cli.load_project.dataset_names.size, 0
    cli.load_project.each_dataset do |d|
      cli.advance('Datasets:', k += 1, n, false)

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 check_mts has a Cognitive Complexity of 19 (exceeds 5 allowed). Consider refactoring.
Open

  def check_mts(cli)
    cli.say 'Looking for unarchived MyTaxa Scan runs'
    cli.load_project.each_dataset do |d|
      res = d.result(:mytaxa_scan)
      next if res.nil?
Severity: Minor
Found in lib/miga/cli/action/doctor/operations.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 has too many lines. [17/10]
Open

  def check_ess(cli)
    cli.say 'Looking for outdated essential genes'
    cli.load_project.each_dataset do |d|
      res = d.result(:essential_genes)
      next if res.nil?

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 check_mts is too high. [22.65/15]
Open

  def check_mts(cli)
    cli.say 'Looking for unarchived MyTaxa Scan runs'
    cli.load_project.each_dataset do |d|
      res = d.result(:mytaxa_scan)
      next if res.nil?

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 check_cds is too high. [21.19/15]
Open

  def check_cds(cli)
    cli.say 'Looking for unzipped genes or proteins'
    n, k = cli.load_project.dataset_names.size, 0
    cli.load_project.each_dataset do |d|
      cli.advance('Datasets:', k += 1, n, false)

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. [15/10]
Open

  def check_status(cli)
    cli.say 'Updating metadata status'
    p = cli.load_project
    n = p.dataset_names.size
    (0 .. cli[:threads] - 1).map do |i|

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 check_ess is too high. [19.52/15]
Open

  def check_ess(cli)
    cli.say 'Looking for outdated essential genes'
    cli.load_project.each_dataset do |d|
      res = d.result(:essential_genes)
      next if res.nil?

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 check_status is too high. [18.79/15]
Open

  def check_status(cli)
    cli.say 'Updating metadata status'
    p = cli.load_project
    n = p.dataset_names.size
    (0 .. cli[:threads] - 1).map do |i|

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 check_files is too high. [17.58/15]
Open

  def check_files(cli)
    cli.say 'Looking for outdated files in results'
    n, k = cli.load_project.dataset_names.size, 0
    cli.load_project.each_dataset do |d|
      cli.advance('Datasets:', k += 1, n, false)

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

Cyclomatic complexity for check_mts is too high. [7/6]
Open

  def check_mts(cli)
    cli.say 'Looking for unarchived MyTaxa Scan runs'
    cli.load_project.each_dataset do |d|
      res = d.result(:mytaxa_scan)
      next if res.nil?

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 check_mts has 28 lines of code (exceeds 25 allowed). Consider refactoring.
Open

  def check_mts(cli)
    cli.say 'Looking for unarchived MyTaxa Scan runs'
    cli.load_project.each_dataset do |d|
      res = d.result(:mytaxa_scan)
      next if res.nil?
Severity: Minor
Found in lib/miga/cli/action/doctor/operations.rb - About 1 hr to fix

Method check_cds has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
Open

  def check_cds(cli)
    cli.say 'Looking for unzipped genes or proteins'
    n, k = cli.load_project.dataset_names.size, 0
    cli.load_project.each_dataset do |d|
      cli.advance('Datasets:', k += 1, n, false)
Severity: Minor
Found in lib/miga/cli/action/doctor/operations.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 check_files has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
Open

  def check_files(cli)
    cli.say 'Looking for outdated files in results'
    n, k = cli.load_project.dataset_names.size, 0
    cli.load_project.each_dataset do |d|
      cli.advance('Datasets:', k += 1, n, false)
Severity: Minor
Found in lib/miga/cli/action/doctor/operations.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 check_ess has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
Open

  def check_ess(cli)
    cli.say 'Looking for outdated essential genes'
    cli.load_project.each_dataset do |d|
      res = d.result(:essential_genes)
      next if res.nil?
Severity: Minor
Found in lib/miga/cli/action/doctor/operations.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 check_status has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
Open

  def check_status(cli)
    cli.say 'Updating metadata status'
    p = cli.load_project
    n = p.dataset_names.size
    (0 .. cli[:threads] - 1).map do |i|
Severity: Minor
Found in lib/miga/cli/action/doctor/operations.rb - About 45 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

TODO found
Open

    # TODO: Find 95%ANI clusters with entries from different species

TODO found
Open

    # TODO: Find AAI values too high or too low for each LCA rank

TODO found
Open

    # TODO: Find different 95%ANI clusters with genomes from the same species

Use next to skip iteration.
Open

        unless ok

Use next to skip iteration instead of a condition at the end.

Example: EnforcedStyle: skipmodifierifs (default)

# bad
[1, 2].each do |a|
  if a == 1
    puts a
  end
end

# good
[1, 2].each do |a|
  next unless a == 1
  puts a
end

# good
[1, 2].each do |o|
  puts o unless o == 1
end

Example: EnforcedStyle: always

# With `always` all conditions at the end of an iteration needs to be
# replaced by next - with `skip_modifier_ifs` the modifier if like
# this one are ignored: `[1, 2].each { |a| return 'yes' if a == 1 }`

# bad
[1, 2].each do |o|
  puts o unless o == 1
end

# bad
[1, 2].each do |a|
  if a == 1
    puts a
  end
end

# good
[1, 2].each do |a|
  next unless a == 1
  puts a
end

Missing magic comment # frozen_string_literal: true.
Open


module MiGA::Cli::Action::Doctor::Operations

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

Do not use parallel assignment.
Open

    n, k = cli.load_project.dataset_names.size, 0

Checks for simple usages of parallel assignment. This will only complain when the number of variables being assigned matched the number of assigning variables.

Example:

# bad
a, b, c = 1, 2, 3
a, b, c = [1, 2, 3]

# good
one, two = *foo
a, b = foo()
a, b = b, a

a = 1
b = 2
c = 3

Missing top-level module documentation comment.
Open

module MiGA::Cli::Action::Doctor::Operations

This cop checks for missing top-level documentation of classes and modules. Classes with no body are exempt from the check and so are namespace modules - modules that have nothing in their bodies except classes, other modules, or constant definitions.

The documentation requirement is annulled if the class or module has a "#:nodoc:" comment next to it. Likewise, "#:nodoc: all" does the same for all its children.

Example:

# bad
class Person
  # ...
end

# good
# Description/Explanation of Person class
class Person
  # ...
end

Use i.zero? instead of i == 0.
Open

          cli.advance('Datasets:', k, n, false) if i == 0

This cop checks for usage of comparison operators (==, >, <) to test numbers as zero, positive, or negative. These can be replaced by their respective predicate methods. The cop can also be configured to do the reverse.

The cop disregards #nonzero? as it its value is truthy or falsey, but not true and false, and thus not always interchangeable with != 0.

The cop ignores comparisons to global variables, since they are often populated with objects which can be compared with integers, but are not themselves Interger polymorphic.

Example: EnforcedStyle: predicate (default)

# bad

foo == 0
0 > foo
bar.baz > 0

# good

foo.zero?
foo.negative?
bar.baz.positive?

Example: EnforcedStyle: comparison

# bad

foo.zero?
foo.negative?
bar.baz.positive?

# good

foo == 0
0 > foo
bar.baz > 0

Use next to skip iteration.
Open

        if file !~ /\.gz/

Use next to skip iteration instead of a condition at the end.

Example: EnforcedStyle: skipmodifierifs (default)

# bad
[1, 2].each do |a|
  if a == 1
    puts a
  end
end

# good
[1, 2].each do |a|
  next unless a == 1
  puts a
end

# good
[1, 2].each do |o|
  puts o unless o == 1
end

Example: EnforcedStyle: always

# With `always` all conditions at the end of an iteration needs to be
# replaced by next - with `skip_modifier_ifs` the modifier if like
# this one are ignored: `[1, 2].each { |a| return 'yes' if a == 1 }`

# bad
[1, 2].each do |o|
  puts o unless o == 1
end

# bad
[1, 2].each do |a|
  if a == 1
    puts a
  end
end

# good
[1, 2].each do |a|
  next unless a == 1
  puts a
end

Space inside range literal.
Open

    (0 .. cli[:threads] - 1).map do |i|

Checks for spaces inside range literals.

Example:

# bad
1 .. 3

# good
1..3

# bad
'a' .. 'z'

# good
'a'..'z'

Useless assignment to variable - md.
Open

      md = p&.metadata

This cop checks for every useless assignment to local variable in every scope. The basic idea for this cop was from the warning of ruby -cw:

assigned but unused variable - foo

Currently this cop has advanced logic that detects unreferenced reassignments and properly handles varied cases such as branch, loop, rescue, ensure, etc.

Example:

# bad

def some_method
  some_var = 1
  do_something
end

Example:

# good

def some_method
  some_var = 1
  do_something(some_var)
end

Do not use parallel assignment.
Open

    n, k = cli.load_project.dataset_names.size, 0

Checks for simple usages of parallel assignment. This will only complain when the number of variables being assigned matched the number of assigning variables.

Example:

# bad
a, b, c = 1, 2, 3
a, b, c = [1, 2, 3]

# good
one, two = *foo
a, b = foo()
a, b = b, a

a = 1
b = 2
c = 3

There are no issues that match your filters.

Category
Status