bio-miga/miga

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lib/miga/cli/action/wf.rb

Summary

Maintainability
C
1 day
Test Coverage

Module has too many lines. [260/100]
Open

module MiGA::Cli::Action::Wf
  def default_opts_for_wf
    cli.expect_files = true
    cli.defaults = {
      clean: false, project_type: :genomes, dataset_type: :popgenome,
Severity: Minor
Found in lib/miga/cli/action/wf.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.

Method has too many lines. [98/10]
Open

  def opts_for_wf(opt, files_desc, params = {})
    {
      multi: false, cleanup: true, project_type: false, ncbi: true, qual: true
    }.each { |k, v| params[k] = v if params[k].nil? }
    opt.on(
Severity: Minor
Found in lib/miga/cli/action/wf.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 opts_for_wf is too high. [62.59/15]
Open

  def opts_for_wf(opt, files_desc, params = {})
    {
      multi: false, cleanup: true, project_type: false, ncbi: true, qual: true
    }.each { |k, v| params[k] = v if params[k].nil? }
    opt.on(
Severity: Minor
Found in lib/miga/cli/action/wf.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 download_datasets is too high. [42.2/15]
Open

  def download_datasets
    # Download datasets from NCBI
    unless cli[:ncbi_taxon].nil?
      what = cli[:ncbi_ref] ? '--reference' :
             cli[:ncbi_draft] ? '--all' : '--complete'
Severity: Minor
Found in lib/miga/cli/action/wf.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 opts_for_wf has 98 lines of code (exceeds 25 allowed). Consider refactoring.
Open

  def opts_for_wf(opt, files_desc, params = {})
    {
      multi: false, cleanup: true, project_type: false, ncbi: true, qual: true
    }.each { |k, v| params[k] = v if params[k].nil? }
    opt.on(
Severity: Major
Found in lib/miga/cli/action/wf.rb - About 3 hrs to fix

Assignment Branch Condition size for run_daemon is too high. [28.6/15]
Open

  def run_daemon
    return if cli[:prepare_and_exit]

    cmd  = ['daemon', 'run', '-P', cli[:outdir], '--shutdown-when-done']
    cmd += ['--json', cli[:daemon_json]] if cli[:daemon_json]
Severity: Minor
Found in lib/miga/cli/action/wf.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. [21/10]
Open

  def opts_for_wf_distances(opt)
    opt.on('--sensitive', 'Alias to: --aai-p blast+ --ani-p blast+') do
      cli[:aai_p] = 'blast+'
      cli[:ani_p] = 'blast+'
    end
Severity: Minor
Found in lib/miga/cli/action/wf.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. [19/10]
Open

  def opt_object_type(opt, obj, multi)
    conf =
      case obj
      when :dataset
        ['type', 'datasets', :dataset_type, MiGA::Dataset]
Severity: Minor
Found in lib/miga/cli/action/wf.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. [18/10]
Open

  def download_datasets
    # Download datasets from NCBI
    unless cli[:ncbi_taxon].nil?
      what = cli[:ncbi_ref] ? '--reference' :
             cli[:ncbi_draft] ? '--all' : '--complete'
Severity: Minor
Found in lib/miga/cli/action/wf.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.

File wf.rb has 262 lines of code (exceeds 250 allowed). Consider refactoring.
Open

module MiGA::Cli::Action::Wf
  def default_opts_for_wf
    cli.expect_files = true
    cli.defaults = {
      clean: false, project_type: :genomes, dataset_type: :popgenome,
Severity: Minor
Found in lib/miga/cli/action/wf.rb - About 2 hrs to fix

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

  def download_datasets
    # Download datasets from NCBI
    unless cli[:ncbi_taxon].nil?
      what = cli[:ncbi_ref] ? '--reference' :
             cli[:ncbi_draft] ? '--all' : '--complete'
Severity: Minor
Found in lib/miga/cli/action/wf.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. [14/10]
Open

  def create_project(stage, p_metadata = {}, d_metadata = {})
    cli.ensure_par(
      outdir: '-o',
      project_type: '--project-type',
      dataset_type: '--dataset-type'
Severity: Minor
Found in lib/miga/cli/action/wf.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 download_datasets is too high. [10/6]
Open

  def download_datasets
    # Download datasets from NCBI
    unless cli[:ncbi_taxon].nil?
      what = cli[:ncbi_ref] ? '--reference' :
             cli[:ncbi_draft] ? '--all' : '--complete'
Severity: Minor
Found in lib/miga/cli/action/wf.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.

Perceived complexity for download_datasets is too high. [10/7]
Open

  def download_datasets
    # Download datasets from NCBI
    unless cli[:ncbi_taxon].nil?
      what = cli[:ncbi_ref] ? '--reference' :
             cli[:ncbi_draft] ? '--all' : '--complete'
Severity: Minor
Found in lib/miga/cli/action/wf.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

Assignment Branch Condition size for opt_object_type is too high. [18.68/15]
Open

  def opt_object_type(opt, obj, multi)
    conf =
      case obj
      when :dataset
        ['type', 'datasets', :dataset_type, MiGA::Dataset]
Severity: Minor
Found in lib/miga/cli/action/wf.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. [12/10]
Open

  def summarize(which = %w[cds assembly essential_genes ssu])
    return if cli[:prepare_and_exit]

    which.each do |r|
      cli.say "Summary: #{r}"
Severity: Minor
Found in lib/miga/cli/action/wf.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 create_project is too high. [17.46/15]
Open

  def create_project(stage, p_metadata = {}, d_metadata = {})
    cli.ensure_par(
      outdir: '-o',
      project_type: '--project-type',
      dataset_type: '--dataset-type'
Severity: Minor
Found in lib/miga/cli/action/wf.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 initialize_empty_project is too high. [17.15/15]
Open

  def initialize_empty_project(metadata)
    call_cli(
      ['new', '-P', cli[:outdir], '-t', cli[:project_type]]
    ) unless MiGA::Project.exist? cli[:outdir]

Severity: Minor
Found in lib/miga/cli/action/wf.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

Cyclomatic complexity for run_daemon is too high. [8/6]
Open

  def run_daemon
    return if cli[:prepare_and_exit]

    cmd  = ['daemon', 'run', '-P', cli[:outdir], '--shutdown-when-done']
    cmd += ['--json', cli[:daemon_json]] if cli[:daemon_json]
Severity: Minor
Found in lib/miga/cli/action/wf.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.

Perceived complexity for run_daemon is too high. [8/7]
Open

  def run_daemon
    return if cli[:prepare_and_exit]

    cmd  = ['daemon', 'run', '-P', cli[:outdir], '--shutdown-when-done']
    cmd += ['--json', cli[:daemon_json]] if cli[:daemon_json]
Severity: Minor
Found in lib/miga/cli/action/wf.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 opts_for_wf is too high. [7/6]
Open

  def opts_for_wf(opt, files_desc, params = {})
    {
      multi: false, cleanup: true, project_type: false, ncbi: true, qual: true
    }.each { |k, v| params[k] = v if params[k].nil? }
    opt.on(
Severity: Minor
Found in lib/miga/cli/action/wf.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 opts_for_wf has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
Open

  def opts_for_wf(opt, files_desc, params = {})
    {
      multi: false, cleanup: true, project_type: false, ncbi: true, qual: true
    }.each { |k, v| params[k] = v if params[k].nil? }
    opt.on(
Severity: Minor
Found in lib/miga/cli/action/wf.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 run_daemon has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
Open

  def run_daemon
    return if cli[:prepare_and_exit]

    cmd  = ['daemon', 'run', '-P', cli[:outdir], '--shutdown-when-done']
    cmd += ['--json', cli[:daemon_json]] if cli[:daemon_json]
Severity: Minor
Found in lib/miga/cli/action/wf.rb - About 55 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 each_key instead of each.
Open

    obj.metadata.each do |k, v|
Severity: Minor
Found in lib/miga/cli/action/wf.rb by rubocop

This cop checks for uses of each_key and each_value Hash methods.

Note: If you have an array of two-element arrays, you can put parentheses around the block arguments to indicate that you're not working with a hash, and suppress RuboCop offenses.

Example:

# bad
hash.keys.each { |k| p k }
hash.values.each { |v| p v }
hash.each { |k, _v| p k }
hash.each { |_k, v| p v }

# good
hash.each_key { |k| p k }
hash.each_value { |v| p v }

Unused block argument - v. If it's necessary, use _ or _v as an argument name to indicate that it won't be used.
Open

    obj.metadata.each do |k, v|
Severity: Minor
Found in lib/miga/cli/action/wf.rb by rubocop

This cop checks for unused block arguments.

Example:

# bad

do_something do |used, unused|
  puts used
end

do_something do |bar|
  puts :foo
end

define_method(:foo) do |bar|
  puts :baz
end

Example:

#good

do_something do |used, _unused|
  puts used
end

do_something do
  puts :foo
end

define_method(:foo) do |_bar|
  puts :baz
end

Ternary operators must not be nested. Prefer if or else constructs instead.
Open

             cli[:ncbi_draft] ? '--all' : '--complete'
Severity: Minor
Found in lib/miga/cli/action/wf.rb by rubocop

Use a guard clause instead of wrapping the code inside a conditional expression.
Open

    if cli[:seqcode_type]
Severity: Minor
Found in lib/miga/cli/action/wf.rb by rubocop

Use a guard clause instead of wrapping the code inside a conditional expression

Example:

# bad
def test
  if something
    work
  end
end

# good
def test
  return unless something
  work
end

# also good
def test
  work if something
end

# bad
if something
  raise 'exception'
else
  ok
end

# good
raise 'exception' if something
ok

Avoid multi-line ternary operators, use if or unless instead.
Open

      what = cli[:ncbi_ref] ? '--reference' :
             cli[:ncbi_draft] ? '--all' : '--complete'
Severity: Minor
Found in lib/miga/cli/action/wf.rb by rubocop

This cop checks for multi-line ternary op expressions.

Example:

# bad
a = cond ?
  b : c
a = cond ? b :
    c
a = cond ?
    b :
    c

# good
a = cond ? b : c
a =
  if cond
    b
  else
    c
  end

Missing magic comment # frozen_string_literal: true.
Open

# @package MiGA
Severity: Minor
Found in lib/miga/cli/action/wf.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

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

    call_cli(
      ['new', '-P', cli[:outdir], '-t', cli[:project_type]]
    ) unless MiGA::Project.exist? cli[:outdir]
Severity: Minor
Found in lib/miga/cli/action/wf.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

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

    call_cli(
      [
        'add',
        '--ignore-dups',
        '-P', cli[:outdir],
Severity: Minor
Found in lib/miga/cli/action/wf.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

There are no issues that match your filters.

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