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lib/miga/cli/action/download/ncbi.rb

Summary

Maintainability
A
1 hr
Test Coverage

Module has too many lines. [127/100]
Open

module MiGA::Cli::Action::Download::Ncbi
  include MiGA::Cli::Action::Download::Base

  def cli_task_flags(opt)
    cli.opt_flag(
Severity: Minor
Found in lib/miga/cli/action/download/ncbi.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 remote_list is too high. [33.78/15]
Open

  def remote_list
    if cli[:ncbi_list_json] && File.size?(cli[:ncbi_list_json])
      return read_ncbi_list_json(cli[:ncbi_list_json])
    end
Severity: Minor
Found in lib/miga/cli/action/download/ncbi.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. [20/10]
Open

  def remote_list
    if cli[:ncbi_list_json] && File.size?(cli[:ncbi_list_json])
      return read_ncbi_list_json(cli[:ncbi_list_json])
    end
Severity: Minor
Found in lib/miga/cli/action/download/ncbi.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. [17/10]
Open

  def parse_reports_as_datasets(reports)
    ds = {}
    reports.each do |r|
      asm = r[:accession]
      next if asm.nil? || asm.empty? || asm == '-'
Severity: Minor
Found in lib/miga/cli/action/download/ncbi.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. [17/10]
Open

  def cli_task_flags(opt)
    cli.opt_flag(
      opt, 'reference',
      'Download all reference genomes (ignore any other status)'
    )
Severity: Minor
Found in lib/miga/cli/action/download/ncbi.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 read_ncbi_list_json(file)
    cli.say "Reusing remote list: #{file}"
    list = {}
    n_tot = nil
    File.open(file, 'r') do |fh|
Severity: Minor
Found in lib/miga/cli/action/download/ncbi.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 cli_task_flags is too high. [17.72/15]
Open

  def cli_task_flags(opt)
    cli.opt_flag(
      opt, 'reference',
      'Download all reference genomes (ignore any other status)'
    )
Severity: Minor
Found in lib/miga/cli/action/download/ncbi.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 read_ncbi_list_json is too high. [17.72/15]
Open

  def read_ncbi_list_json(file)
    cli.say "Reusing remote list: #{file}"
    list = {}
    n_tot = nil
    File.open(file, 'r') do |fh|
Severity: Minor
Found in lib/miga/cli/action/download/ncbi.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 remote_list_query
    q = { taxons: [cli[:taxon]], filters: {} }
    if cli[:reference]
      q[:filters][:reference_only] = true
    else
Severity: Minor
Found in lib/miga/cli/action/download/ncbi.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 parse_reports_as_datasets is too high. [16.16/15]
Open

  def parse_reports_as_datasets(reports)
    ds = {}
    reports.each do |r|
      asm = r[:accession]
      next if asm.nil? || asm.empty? || asm == '-'
Severity: Minor
Found in lib/miga/cli/action/download/ncbi.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 remote_list is too high. [7/6]
Open

  def remote_list
    if cli[:ncbi_list_json] && File.size?(cli[:ncbi_list_json])
      return read_ncbi_list_json(cli[:ncbi_list_json])
    end
Severity: Minor
Found in lib/miga/cli/action/download/ncbi.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.

Assignment Branch Condition size for write_ncbi_list_json is too high. [15.3/15]
Open

  def write_ncbi_list_json(file, list)
    cli.say "Saving remote list: #{file}"
    File.open(file, 'w') do |fh|
      fh.puts('# %i' % list.size)
      kk = 0
Severity: Minor
Found in lib/miga/cli/action/download/ncbi.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 remote_list has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.
Open

  def remote_list
    if cli[:ncbi_list_json] && File.size?(cli[:ncbi_list_json])
      return read_ncbi_list_json(cli[:ncbi_list_json])
    end
Severity: Minor
Found in lib/miga/cli/action/download/ncbi.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 parse_reports_as_datasets has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

  def parse_reports_as_datasets(reports)
    ds = {}
    reports.each do |r|
      asm = r[:accession]
      next if asm.nil? || asm.empty? || asm == '-'
Severity: Minor
Found in lib/miga/cli/action/download/ncbi.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

Redundant return detected.
Open

    return list
Severity: Minor
Found in lib/miga/cli/action/download/ncbi.rb by rubocop

This cop checks for redundant return expressions.

Example:

def test
  return something
end

def test
  one
  two
  three
  return something
end

It should be extended to handle methods whose body is if/else or a case expression with a default branch.

Prefer annotated tokens (like %<foo>s</foo>) over unannotated tokens (like %s).
Open

      fh.puts('# %i' % list.size)
Severity: Minor
Found in lib/miga/cli/action/download/ncbi.rb by rubocop

Use a consistent style for named format string tokens.

Note: unannotated style cop only works for strings which are passed as arguments to those methods: sprintf, format, %. The reason is that unannotated format is very similar to encoded URLs or Date/Time formatting strings.

Example: EnforcedStyle: annotated (default)

# bad
format('%{greeting}', greeting: 'Hello')
format('%s', 'Hello')

# good
format('%<greeting>s', greeting: 'Hello')</greeting>

Example: EnforcedStyle: template

# bad
format('%<greeting>s', greeting: 'Hello')
format('%s', 'Hello')

# good
format('%{greeting}', greeting: 'Hello')</greeting>

Example: EnforcedStyle: unannotated

# bad
format('%<greeting>s', greeting: 'Hello')
format('%{greeting}', 'Hello')

# good
format('%s', 'Hello')</greeting>

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

    cli.say "Obtaining remote list of datasets"
Severity: Minor
Found in lib/miga/cli/action/download/ncbi.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"

Prefer to_s over string interpolation.
Open

    acc = "#{asm}"
Severity: Minor
Found in lib/miga/cli/action/download/ncbi.rb by rubocop

This cop checks for strings that are just an interpolated expression.

Example:

# bad
"#{@var}"

# good
@var.to_s

# good if @var is already a String
@var

There are no issues that match your filters.

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