Showing 1,637 of 1,651 total issues
Method has too many lines. [12/10] Open
def add_result_trimmed_reads(base, _opts)
return nil unless result_files_exist?(base, '.1.clipped.fastq')
add_files_to_ds_result(
MiGA::Result.new("#{base}.json"), name,
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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 compute_stats_ssu
has 46 lines of code (exceeds 25 allowed). Consider refactoring. Open
def compute_stats_ssu
stats = {
ssu: 0, complete_ssu: 0, ssu_fragment: [0.0, '%'],
lsu: 0, complete_lsu: 0, lsu_fragment: [0.0, '%']
}
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Method opt_object
has 46 lines of code (exceeds 25 allowed). Consider refactoring. Open
def opt_object(opt, what = %i[project dataset])
what.each do |w|
case w
when :project
opt.on(
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Assignment Branch Condition size for test_datasets is too high. [16.28/15] Open
def test_datasets
p = project
d = dataset(0, 'd1')
assert_equal(MiGA::Dataset, d.class)
assert_equal([d], p.datasets)
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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. [11/10] Open
def test_download_file_ftp
declare_remote_access
f = tmpfile('t/test.txt')
d = File.dirname(f)
assert(!Dir.exist?(d))
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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 test_net_ftp is too high. [16.49/15] Open
def test_net_ftp
cjac = 'ftp://ftp.ebi.ac.uk/pub/databases/ena/tsa/' \
'public/gap/GAPJ01.fasta.gz'
n = 'Cjac_L14'
rd = MiGA::RemoteDataset.new(cjac, :assembly_gz, :web)
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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. [11/10] Open
def test_single_raw_reads
dir = 'data/01.raw_reads'
fq = file_path(dir, '.1.fastq')
File.open(fq, 'w') { |fh| fh.puts '@1', 'ACTAC', '+', '####' }
touch_done(dir)
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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 test_save is too high. [16.12/15] Open
def test_save
d2 = project.add_dataset('ds_save')
assert_respond_to(d2, :save)
d2.save
assert_not_predicate(d2, :multi?)
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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 test_declare_alive_loop is too high. [16.28/15] Open
def test_declare_alive_loop
d = TestWithDaemon.new(tmpfile('nope'))
assert_equal(:no_home, d.declare_alive_loop)
d = TestWithDaemon.new(tmpdir)
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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 test_gtdb_request is too high. [16.28/15] Open
def test_gtdb_request
# No remote access needed
rd = MiGA::RemoteDataset.new('g__Macondimonas', :taxon, :gtdb)
u = rd.download_uri
h = rd.download_headers
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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. [11/10] Open
def test_save
d2 = project.add_dataset('ds_save')
assert_respond_to(d2, :save)
d2.save
assert_not_predicate(d2, :multi?)
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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. [11/10] Open
def test_add_result
d2 = project.add_dataset('ds_add_result')
assert_nil(d2.add_result(:koop))
assert_nil(d2.add_result(:raw_reads))
FileUtils.touch(
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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 test_get is too high. [16.49/15] Open
def test_get
hiv2 = 'M30502.1'
{ embl: :ebi, nuccore: :ncbi }.each do |db, universe|
rd = MiGA::RemoteDataset.new(hiv2, db, universe)
assert_equal([hiv2], rd.ids)
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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. [11/10] Open
def test_gtdb_alt_taxonomy
declare_remote_access
rd = MiGA::RemoteDataset.new('GCA_018200315.1', :assembly, :gtdb)
rd.metadata[:get_ncbi_taxonomy] = true
md = rd.get_metadata
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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. [11/10] Open
def test_activate
d = dataset
assert_equal(:incomplete, d.status)
assert_predicate(d, :active?)
d.inactivate! 'Too annoying'
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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. [11/10] Confirmed
def test_add_result
p1 = project
assert_nil(p1.add_result(:doom))
%w[.rds .log .txt .done].each do |x|
assert_nil(p1.add_result(:haai_distances))
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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. [11/10] Open
def parse(&fun)
if expect_operation
@operation = @argv.shift unless argv.first =~ /^-/
end
OptionParser.new do |opt|
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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 test_each_project is too high. [16.28/15] Open
def test_each_project
lair = MiGA::Lair.new(tmpdir)
y = []
lair.each_project { |p| y << p }
assert_equal(3, y.size)
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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. [11/10] Open
def setup
initialize_miga_home(
<<~DAEMON
{ "maxjobs": 1, "ppn": 1, "latency": 1, "varsep": " ",
"var": "{{key}}={{value}}", "cmd": "echo {{task_name}} >/dev/null",
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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. [11/10] Open
def test_dataset_clear_run_counts
dataset.metadata[:_try_something] = 1
dataset.metadata[:_step] = 'Boop'
dataset.metadata[:_not_a_counter] = 1
dataset.save
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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.