Showing 186 of 1,651 total issues
Method parse_cli
has 26 lines of code (exceeds 25 allowed). Consider refactoring. Open
def parse_cli
cli.defaults = { units: false, tabular: false }
cli.parse do |opt|
cli.opt_object(opt, [:project, :dataset_opt])
cli.opt_filter_datasets(opt)
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Method merge_bidir_tmp
has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring. Open
def merge_bidir_tmp(tmp)
tmp_done = File.join(tmp, 'chunks.txt')
chunks = File.readlines(tmp_done)[0].chomp.to_i
lower_tr = []
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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_to
has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring. Open
def save_to(project, name = nil, is_ref = true, metadata_def = {})
name ||= ids.join('_').miga_name
project = MiGA::Project.new(project) if project.is_a? String
MiGA::Dataset.exist?(project, name) and
raise "Dataset #{name} exists in the project, aborting..."
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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_block
has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring. Open
def run_block(&blk)
busy_attempts ||= 0
io_attempts ||= 0
SQLite3::Database.new(path) { |conn| blk[conn] }
rescue SQLite3::BusyException => e
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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_entry
has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring. Open
def save_entry(name, body, p)
cli.say " Locating remote dataset: #{name}"
body[:md][:metadata_only] = true if cli[:only_md]
rd = MiGA::RemoteDataset.new(body[:ids], body[:db], body[:universe])
if cli[:get_md]
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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 closest_relative_tax
has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring. Open
def closest_relative_tax(cr)
cli.puts "Closest relative: #{cr[0]} with AAI: #{cr[1]}."
p = cli.load_project
if cli[:ref_project]
if (ref = p.option(:ref_project)).nil?
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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 format_result_stats
has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring. Open
def format_result_stats(res)
res.stats.map do |k, v|
v = [v, ''] unless v.is_a? Array
v[0] = ('%.3g' % v[0]) if v[0].is_a? Float
"<b>#{format_name(k)}:</b> #{v[0]}#{v[1]}<br/>"
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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]
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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 net_method
has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring. Open
def net_method(method, uri, *opts)
attempts ||= 0
uri = URI.parse(uri) if uri.is_a? String
DEBUG "#{method.to_s.upcase}: #{uri} #{opts}"
case method.to_sym
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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 each_file
has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring. Open
def each_file(&blk)
return to_enum(:each_file) unless block_given?
@data[:files] ||= {}
self[:files].each do |k, files|
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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 add_dataset
has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring. Open
def add_dataset(name)
unless metadata[:datasets].include? name
d = MiGA::Dataset.new(self, name)
@metadata[:datasets] << name
@dataset_names_hash[name] = true if @dataset_names_hash
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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 stop
has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring. Open
def stop(opts = [], wait = true)
if active?
say 'Sending termination message'
FileUtils.touch(terminate_file)
sleep(0.5) while active? if wait
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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 configure_qsub_msub_daemon
has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring. Open
def configure_qsub_msub_daemon(v)
flavor = v[:type] == 'msub' ? 'msub' :
cli.ask_user('Select qsub flavor', 'torque', %w[torque sge])
queue = cli.ask_user('What queue should I use?', nil, nil, true)
v[:latency] = cli.ask_user('How long should I sleep? (in secs)', '150').to_i
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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 perform
has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring. 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)
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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 download_opts
has 7 arguments (exceeds 4 allowed). Consider refactoring. Open
universe, db, ids, format, file = nil, extra = {}, obj = nil)
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Method perform
has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring. Open
def perform
cli.load_project_or_dataset.each_result do |sym, res|
cli.puts "#{"#{sym}\tjson\t" if cli[:details]}#{res.path}" if cli[:json]
res.each_file do |k, f|
cli.puts "#{"#{sym}\t#{k}\t" if cli[:details]}#{res.dir}/#{f}"
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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 normalize_rank
has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring. Open
def normalize_rank(rank)
return unless rank
return rank.to_sym if @@_KNOWN_RANKS_H[rank.to_sym]
rank = rank.to_s.downcase
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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 add_result
has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring. Open
def add_result(task, save = true, opts = {})
task = task.to_sym
return nil if result_dirs[task].nil?
base = File.join(project.path, 'data', result_dirs[task], result_base)
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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|
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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 create_remote_dataset
has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring. Open
def create_remote_dataset(sub_cli, p)
sub_cli.ensure_par(dataset: '-D', ids: '-I')
unless sub_cli[:api_key].nil?
if sub_cli[:universe] == :web && sub_cli[:db] == :assembly_gz
ENV['NCBI_API_KEY'] = sub_cli[:api_key]
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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"