Showing 1,637 of 1,651 total issues
Perceived complexity for flush! is too high. [9/7] Open
def flush!
# Check for finished jobs
l_say(2, 'Checking for finished jobs')
@jobs_running.select! do |job|
ongoing =
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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 get_type_status_ncbi_asm is too high. [9/7] Open
def get_type_status_ncbi_asm(metadata)
from_type = nil
# Try first from previously pulled NCBI metadata
if metadata[:ncbi_dataset]
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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. [12/10] Confirmed
def get_ncbi_taxid_from_ncbi
# Try first from Assembly data
return get_ncbi_taxid_from_web if db == :assembly
# Try from previously pulled NCBI data
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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. [12/10] Open
def unlink_dataset(name)
d = dataset(name)
return nil if d.nil?
@dataset_names_hash = nil
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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 next_task is too high. [9/7] 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
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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 clean_fasta_file is too high. [8/6] Open
def clean_fasta_file(file, min_len = 1)
tmp_fh = nil
tmp_path = nil
begin
if file =~ /\.gz/
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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.
Cyclomatic complexity for assert_valid_option_value is too high. [8/6] Open
def assert_valid_option_value(key, value, from_string = false)
opt = assert_has_option(key)
value = option_from_string(key, value) if from_string
# nil is always valid, and so are supported tokens
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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.
Cyclomatic complexity for traverse_taxonomy is too high. [8/6] Open
def traverse_taxonomy(tab, dist)
cli.say 'Traversing taxonomy'
rank_i = 0
Taxonomy.KNOWN_RANKS.each do |rank|
next if rank == :ns
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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 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
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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 traverse_taxonomy is too high. [9/7] Open
def traverse_taxonomy(tab, dist)
cli.say 'Traversing taxonomy'
rank_i = 0
Taxonomy.KNOWN_RANKS.each do |rank|
next if rank == :ns
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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 pull_hook is too high. [17.03/15] Open
def pull_hook(event, *event_args)
event = event.to_sym
event_queue = (hooks[event] || [])
event_queue += (metadata[event] || []) if respond_to? :metadata
event_queue.each do |i|
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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 normalize_encoding(body)
# Test encodings
body.force_encoding('utf-8')
%w[iso8859-1 windows-1252 us-ascii ascii-8bit].each do |enc|
break if body.valid_encoding?
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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. [12/10] 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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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 tabulate is too high. [8/6] Open
def tabulate(header, values, tabular = false)
fields = []
fields << header.map(&:to_s) unless tabular && header.all?(&:nil?)
fields << fields.first.map { |h| h.gsub(/\S/, '-') } unless tabular
fields += values.map { |r| r.map { |cell| cell.nil? ? '?' : cell.to_s } }
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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 has too many lines. [12/10] Open
def get_tab_index(dir)
if cli[:index].nil?
ds = cli.load_and_filter_datasets
ds.keep_if { |d| !d.metadata[:tax].nil? }
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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)'
)
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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|
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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 parse_cli
cli.defaults = { test: 'both', ref_project: false }
cli.parse do |opt|
cli.opt_object(opt, [:project, :dataset])
opt.on(
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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. [12/10] Open
def parse_cli
cli.defaults = { force: false, stdin_versions: false }
cli.parse do |opt|
cli.opt_object(opt, [:project, :dataset_opt, :result])
opt.on(
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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. [12/10] Open
def load_result
return @objects[:result] unless @objects[:result].nil?
ensure_par(result: '-r')
obj = load_project_or_dataset
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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.