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test/remote_dataset_test.rb

Summary

Maintainability
A
0 mins
Test Coverage
A
100%

Class has too many lines. [177/100]
Open

class RemoteDatasetTest < Test::Unit::TestCase
  include TestHelper

  def setup
    initialize_miga_home
Severity: Minor
Found in test/remote_dataset_test.rb by rubocop

This cop checks if the length a class exceeds some maximum value. Comment lines can optionally be ignored. The maximum allowed length is configurable.

Assignment Branch Condition size for test_gtdb_alt_taxonomy is too high. [29.15/15]
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
Severity: Minor
Found in test/remote_dataset_test.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. [23/10]
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)
Severity: Minor
Found in test/remote_dataset_test.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 test_ncbi_datasets_request is too high. [23.35/15]
Open

  def test_ncbi_datasets_request
    rd = MiGA::RemoteDataset.new({ taxons: 'Bos' }, :genome, :ncbi_datasets)
    u = rd.download_uri
    h = rd.download_headers
    p = rd.download_payload
Severity: Minor
Found in test/remote_dataset_test.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 test_ncbi_datasets_download_request is too high. [22.56/15]
Open

  def test_ncbi_datasets_download_request
    # No remote access needed
    rd = MiGA::RemoteDataset.new(
      'GCF_004684205.1', :genome, :ncbi_datasets_download
    )
Severity: Minor
Found in test/remote_dataset_test.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. [16/10]
Open

  def test_ncbi_datasets_download_request
    # No remote access needed
    rd = MiGA::RemoteDataset.new(
      'GCF_004684205.1', :genome, :ncbi_datasets_download
    )
Severity: Minor
Found in test/remote_dataset_test.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 test_gtdb_taxonomy is too high. [19.1/15]
Open

  def test_gtdb_taxonomy
    declare_remote_access
    rd = MiGA::RemoteDataset.new('GCA_018200315.1', :assembly, :gtdb)
    md = rd.get_metadata
    assert(!md[:is_type])
Severity: Minor
Found in test/remote_dataset_test.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. [13/10]
Open

  def test_ncbi_datasets_request
    rd = MiGA::RemoteDataset.new({ taxons: 'Bos' }, :genome, :ncbi_datasets)
    u = rd.download_uri
    h = rd.download_headers
    p = rd.download_payload
Severity: Minor
Found in test/remote_dataset_test.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 test_update_metadata is too high. [18.25/15]
Open

  def test_update_metadata
    declare_remote_access
    hiv1 = 'GCF_000856385.1'
    d1 = MiGA::Dataset.new(project, 'd1')
    assert_nil(d1.metadata[:ncbi_assembly])
Severity: Minor
Found in test/remote_dataset_test.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 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)
Severity: Minor
Found in test/remote_dataset_test.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 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
Severity: Minor
Found in test/remote_dataset_test.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. [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
Severity: Minor
Found in test/remote_dataset_test.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 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)
Severity: Minor
Found in test/remote_dataset_test.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 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)
Severity: Minor
Found in test/remote_dataset_test.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

Add parentheses to nested method call u.is_a? URI.
Open

    assert(u.is_a? URI)
Severity: Minor
Found in test/remote_dataset_test.rb by rubocop

This cop checks for unparenthesized method calls in the argument list of a parenthesized method call.

Example:

# good
method1(method2(arg), method3(arg))

# bad
method1(method2 arg, method3, arg)

Add parentheses to nested method call md[:tax].is_a? MiGA::Taxonomy.
Open

    assert(md[:tax].is_a? MiGA::Taxonomy)
Severity: Minor
Found in test/remote_dataset_test.rb by rubocop

This cop checks for unparenthesized method calls in the argument list of a parenthesized method call.

Example:

# good
method1(method2(arg), method3(arg))

# bad
method1(method2 arg, method3, arg)

Add parentheses to nested method call h.is_a? Hash.
Open

    assert(h.is_a? Hash)
Severity: Minor
Found in test/remote_dataset_test.rb by rubocop

This cop checks for unparenthesized method calls in the argument list of a parenthesized method call.

Example:

# good
method1(method2(arg), method3(arg))

# bad
method1(method2 arg, method3, arg)

Add parentheses to nested method call md[:tax].is_a? MiGA::Taxonomy.
Open

    assert(md[:tax].is_a? MiGA::Taxonomy)
Severity: Minor
Found in test/remote_dataset_test.rb by rubocop

This cop checks for unparenthesized method calls in the argument list of a parenthesized method call.

Example:

# good
method1(method2(arg), method3(arg))

# bad
method1(method2 arg, method3, arg)

Add parentheses to nested method call u.is_a? URI.
Open

    assert(u.is_a? URI)
Severity: Minor
Found in test/remote_dataset_test.rb by rubocop

This cop checks for unparenthesized method calls in the argument list of a parenthesized method call.

Example:

# good
method1(method2(arg), method3(arg))

# bad
method1(method2 arg, method3, arg)

Add parentheses to nested method call md[:tax].alternative(1).is_a? MiGA::Taxonomy.
Open

    assert(md[:tax].alternative(1).is_a? MiGA::Taxonomy)
Severity: Minor
Found in test/remote_dataset_test.rb by rubocop

This cop checks for unparenthesized method calls in the argument list of a parenthesized method call.

Example:

# good
method1(method2(arg), method3(arg))

# bad
method1(method2 arg, method3, arg)

Add parentheses to nested method call h.is_a? Hash.
Open

    assert(h.is_a? Hash)
Severity: Minor
Found in test/remote_dataset_test.rb by rubocop

This cop checks for unparenthesized method calls in the argument list of a parenthesized method call.

Example:

# good
method1(method2(arg), method3(arg))

# bad
method1(method2 arg, method3, arg)

Add parentheses to nested method call u.is_a? URI.
Open

    assert(u.is_a? URI)
Severity: Minor
Found in test/remote_dataset_test.rb by rubocop

This cop checks for unparenthesized method calls in the argument list of a parenthesized method call.

Example:

# good
method1(method2(arg), method3(arg))

# bad
method1(method2 arg, method3, arg)

Missing magic comment # frozen_string_literal: true.
Open

require 'test_helper'
Severity: Minor
Found in test/remote_dataset_test.rb by rubocop

This cop is designed to help upgrade to Ruby 3.0. It will add the comment # frozen_string_literal: true to the top of files to enable frozen string literals. Frozen string literals may be default in Ruby 3.0. The comment will be added below a shebang and encoding comment. The frozen string literal comment is only valid in Ruby 2.3+.

Example: EnforcedStyle: when_needed (default)

# The `when_needed` style will add the frozen string literal comment
# to files only when the `TargetRubyVersion` is set to 2.3+.
# bad
module Foo
  # ...
end

# good
# frozen_string_literal: true

module Foo
  # ...
end

Example: EnforcedStyle: always

# The `always` style will always add the frozen string literal comment
# to a file, regardless of the Ruby version or if `freeze` or `<<` are
# called on a string literal.
# bad
module Bar
  # ...
end

# good
# frozen_string_literal: true

module Bar
  # ...
end

Example: EnforcedStyle: never

# The `never` will enforce that the frozen string literal comment does
# not exist in a file.
# bad
# frozen_string_literal: true

module Baz
  # ...
end

# good
module Baz
  # ...
end

Add parentheses to nested method call u.is_a? URI.
Open

    assert(u.is_a? URI)
Severity: Minor
Found in test/remote_dataset_test.rb by rubocop

This cop checks for unparenthesized method calls in the argument list of a parenthesized method call.

Example:

# good
method1(method2(arg), method3(arg))

# bad
method1(method2 arg, method3, arg)

Add parentheses to nested method call h.is_a? Hash.
Open

    assert(h.is_a? Hash)
Severity: Minor
Found in test/remote_dataset_test.rb by rubocop

This cop checks for unparenthesized method calls in the argument list of a parenthesized method call.

Example:

# good
method1(method2(arg), method3(arg))

# bad
method1(method2 arg, method3, arg)

Add parentheses to nested method call p.is_a? String.
Open

    assert(p.is_a? String)
Severity: Minor
Found in test/remote_dataset_test.rb by rubocop

This cop checks for unparenthesized method calls in the argument list of a parenthesized method call.

Example:

# good
method1(method2(arg), method3(arg))

# bad
method1(method2 arg, method3, arg)

Add parentheses to nested method call md[:tax].alternative(:gtdb).is_a? MiGA::Taxonomy.
Open

    assert(md[:tax].alternative(:gtdb).is_a? MiGA::Taxonomy)
Severity: Minor
Found in test/remote_dataset_test.rb by rubocop

This cop checks for unparenthesized method calls in the argument list of a parenthesized method call.

Example:

# good
method1(method2(arg), method3(arg))

# bad
method1(method2 arg, method3, arg)

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