Sign upLogin

bio-miga/miga

View on GitHub
Star

Showing 839 of 1,651 total issues

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

  def generate_project_page(p)
    # Redirect page
    write_file(p, '../index.html') { build_from_template('redirect.html') }

    # Summaries
Severity: Minor
Found in lib/miga/cli/action/browse.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.

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

  def get_files_and_type
    files = cli.files
    file_type = nil
    if files.empty?
      cli.ensure_par({ dataset: '-D' },
Severity: Minor
Found in lib/miga/cli/action/add.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

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

  def perform
    p = cli.load_project
    ud = p.unregistered_datasets
    ud.each do |dn|
      cli.puts dn
Severity: Minor
Found in lib/miga/cli/action/find.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.

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

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

  def perform
    ds = cli.load_and_filter_datasets(cli[:silent])
    p  = cli.load_project
    exit(ds.empty? ? 1 : 0) if cli[:silent]
Severity: Minor
Found in lib/miga/cli/action/ls.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 perform is too high. [10/7]
Open

  def perform
    unless cli[:value].nil?
      cli.ensure_par(
        { key: '-k' },
        '%<name>s is mandatory when --value is set: provide %<flag>s'
Severity: Minor
Found in lib/miga/cli/action/option.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

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

  def format_table(ds, header, &blk)
    io = cli[:output].nil? ? $stdout : File.open(cli[:output], 'w')
    cli.say 'Collecting metadata'
    k = 0
    cli.table(
Severity: Minor
Found in lib/miga/cli/action/ls.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 perform
    glob = get_sub_cli
    p = cli.load_project
    load_ncbi_taxonomy_dump
    glob.each do |sub_cli|
Severity: Minor
Found in lib/miga/cli/action/get.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 db_requested is too high. [18.36/15]
Open

  def db_requested(manif)
    [:recommended, :test].each do |n|
      if cli[:database] == n
        raise "This host has no #{n} database" if manif[n].nil?
Severity: Minor
Found in lib/miga/cli/action/db.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 find_software is too high. [18.87/15]
Open

  def find_software(exec)
    path = nil
    loop do
      d_path = File.dirname(run_cmd(cli, ['which', exec], raise: false))
      if cli[:ask] || d_path == '.'
Severity: Minor
Found in lib/miga/cli/action/init.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 perform is too high. [18.79/15]
Open

  def perform
    if cli[:result] && r = cli.load_result
      cli[:remove] ? r.remove! : r.unlink
    elsif d = cli.load_dataset
      cli.load_project.unlink_dataset(d.name)
Severity: Minor
Found in lib/miga/cli/action/rm.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 seqs_length has 50 lines of code (exceeds 25 allowed). Consider refactoring.
Open

  def seqs_length(file, format, opts = {})
    opts[:gc] = true if opts[:skew]
    fh = file =~ /\.gz/ ? Zlib::GzipReader.open(file) : File.open(file, 'r')
    l = []
    gc = 0
Severity: Minor
Found in lib/miga/common/format.rb - About 2 hrs to fix

Method test_add_result_other has 50 lines of code (exceeds 25 allowed). Consider refactoring.
Open

  def test_add_result_other
    d2 = project.add_dataset('ds_add_result_other')
    Dir.mkdir(
      File.join(
        project.path, 'data', '07.annotation', '01.function', '01.essential',
Severity: Minor
Found in test/dataset_test.rb - About 2 hrs to fix

Method perform has 49 lines of code (exceeds 25 allowed). Consider refactoring.
Open

  def perform
    # Load environment variables if requested (typically by the daemon)
    if cli[:env]
      cli[:project] ||= ENV['PROJECT']
      cli[:dataset] ||= ENV['DATASET']
Severity: Minor
Found in lib/miga/cli/action/run.rb - About 1 hr to fix

Method parse_cli has 48 lines of code (exceeds 25 allowed). Consider refactoring.
Open

  def parse_cli
    cli.expect_files = true
    cli.defaults = { ref: true, ignore_dups: false }
    cli.parse do |opt|
      opt.separator 'You can create multiple datasets with a single command; ' \
Severity: Minor
Found in lib/miga/cli/action/add.rb - About 1 hr to fix

Method download_file_ftp has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.
Open

  def download_file_ftp(connection, file = nil, target = nil)
    # Open connection unless passed
    close_conn = false
    if connection.is_a?(String) || connection.is_a?(Symbol) ||
          connection.is_a?(URI)
Severity: Minor
Found in lib/miga/common/net.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 save_bidirectional has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.
Open

  def save_bidirectional(a, dist)
    each_database_file(a) do |db_file, metric, result, rank|
      next if rank == :haai # No need for hAAI to be bidirectional
      next if result == :taxonomy # Taxonomy is never bidirectional
Severity: Minor
Found in lib/miga/cli/action/doctor/base.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 get_files_and_type has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.
Open

  def get_files_and_type
    files = cli.files
    file_type = nil
    if files.empty?
      cli.ensure_par({ dataset: '-D' },
Severity: Minor
Found in lib/miga/cli/action/add.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 remote_list has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.
Open

  def remote_list
    cli.say 'Downloading genome list'
    current_page = 1
    total_pages  = 1
    ds = {}
Severity: Minor
Found in lib/miga/cli/action/download/seqcode.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 next_task has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.
Open

  def next_task(tasks = nil, save = false)
    tasks ||= result_dirs.keys
    tasks.find do |t|
      if ignore_task?(t)
        # Do not run if this step is to be ignored
Severity: Minor
Found in lib/miga/common/with_result.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

Severity
Category
Status
Source
Language