unipept 1.4.0 → 1.4.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
@@ -5,14 +5,14 @@ module Unipept
5
5
  def test_help
6
6
  out, _err = capture_io_while do
7
7
  assert_raises SystemExit do
8
- Commands::Unipept.run(%w(-h))
8
+ Commands::Unipept.run(%w[-h])
9
9
  end
10
10
  end
11
11
  assert(out.include?('show help for this command'))
12
12
 
13
13
  out, _err = capture_io_while do
14
14
  assert_raises SystemExit do
15
- Commands::Unipept.run(%w(--help))
15
+ Commands::Unipept.run(%w[--help])
16
16
  end
17
17
  end
18
18
  assert(out.include?('show help for this command'))
@@ -21,7 +21,7 @@ module Unipept
21
21
  def test_no_valid_subcommand
22
22
  _out, err = capture_io_while do
23
23
  assert_raises SystemExit do
24
- Commands::Unipept.run(%w())
24
+ Commands::Unipept.run(%w[])
25
25
  end
26
26
  end
27
27
  assert(err.include?('show help for this command'))
@@ -29,7 +29,7 @@ module Unipept
29
29
 
30
30
  def test_version
31
31
  out, _err = capture_io_while do
32
- Commands::Unipept.run(%w(-v))
32
+ Commands::Unipept.run(%w[-v])
33
33
  end
34
34
  assert_equal(VERSION, out.chomp)
35
35
  end
@@ -4,56 +4,56 @@ module Unipept
4
4
  class UniprotTestCase < Unipept::TestCase
5
5
  def test_argument_input
6
6
  out, _err = capture_io_while do
7
- Commands::Uniprot.run(%w(Q6GZX3))
7
+ Commands::Uniprot.run(%w[Q6GZX3])
8
8
  end
9
9
  assert_equal(1, out.split(/\n/).length)
10
10
 
11
11
  out, _err = capture_io_while do
12
- Commands::Uniprot.run(%w(Q6GZX3 Q6GZX4))
12
+ Commands::Uniprot.run(%w[Q6GZX3 Q6GZX4])
13
13
  end
14
14
  assert_equal(2, out.split(/\n/).length)
15
15
 
16
16
  out, _err = capture_io_while do
17
- Commands::Uniprot.run(%w(-f fasta Q6GZX3 Q6GZX4))
17
+ Commands::Uniprot.run(%w[-f fasta Q6GZX3 Q6GZX4])
18
18
  end
19
19
  assert_equal(2, out.count('>'))
20
20
 
21
21
  out, _err = capture_io_while do
22
- Commands::Uniprot.run(%w(--format fasta Q6GZX3 Q6GZX4))
22
+ Commands::Uniprot.run(%w[--format fasta Q6GZX3 Q6GZX4])
23
23
  end
24
24
  assert_equal(2, out.count('>'))
25
25
  end
26
26
 
27
27
  def test_stdin_input
28
28
  out, _err = capture_io_with_input('Q6GZX3') do
29
- Commands::Uniprot.run(%w())
29
+ Commands::Uniprot.run(%w[])
30
30
  end
31
31
  assert_equal(1, out.split(/\n/).length)
32
32
 
33
- out, _err = capture_io_with_input(%w(Q6GZX3 Q6GZX4)) do
34
- Commands::Uniprot.run(%w())
33
+ out, _err = capture_io_with_input(%w[Q6GZX3 Q6GZX4]) do
34
+ Commands::Uniprot.run(%w[])
35
35
  end
36
36
  assert_equal(2, out.split(/\n/).length)
37
37
 
38
- out, _err = capture_io_with_input(%w(Q6GZX3 Q6GZX4)) do
39
- Commands::Uniprot.run(%w(-f fasta))
38
+ out, _err = capture_io_with_input(%w[Q6GZX3 Q6GZX4]) do
39
+ Commands::Uniprot.run(%w[-f fasta])
40
40
  end
41
41
  assert_equal(2, out.count('>'))
42
42
 
43
- out, _err = capture_io_with_input(%w(Q6GZX3 Q6GZX4)) do
44
- Commands::Uniprot.run(%w(--format fasta))
43
+ out, _err = capture_io_with_input(%w[Q6GZX3 Q6GZX4]) do
44
+ Commands::Uniprot.run(%w[--format fasta])
45
45
  end
46
46
  assert_equal(2, out.count('>'))
47
47
  end
48
48
 
49
49
  def test_argument_input_priority
50
50
  out, _err = capture_io_with_input('Q6GZX3') do
51
- Commands::Uniprot.run(%w(Q6GZX3 Q6GZX4))
51
+ Commands::Uniprot.run(%w[Q6GZX3 Q6GZX4])
52
52
  end
53
53
  assert_equal(2, out.split(/\n/).length)
54
54
 
55
- out, _err = capture_io_with_input(%w(Q6GZX3 Q6GZX4)) do
56
- Commands::Uniprot.run(%w(Q6GZX3))
55
+ out, _err = capture_io_with_input(%w[Q6GZX3 Q6GZX4]) do
56
+ Commands::Uniprot.run(%w[Q6GZX3])
57
57
  end
58
58
  assert_equal(1, out.split(/\n/).length)
59
59
  end
@@ -61,7 +61,7 @@ module Unipept
61
61
  def test_invalid_format
62
62
  out, err = capture_io_while do
63
63
  assert_raises SystemExit do
64
- Commands::Uniprot.run(%w(--format xxx))
64
+ Commands::Uniprot.run(%w[--format xxx])
65
65
  end
66
66
  end
67
67
  assert_equal('', out)
@@ -70,17 +70,17 @@ module Unipept
70
70
 
71
71
  def test_default_format
72
72
  out_default, _err = capture_io_while do
73
- Commands::Uniprot.run(%w(Q6GZX3))
73
+ Commands::Uniprot.run(%w[Q6GZX3])
74
74
  end
75
75
  assert_equal(1, out_default.split(/\n/).length)
76
76
 
77
77
  out_sequence, _err = capture_io_while do
78
- Commands::Uniprot.run(%w(-f sequence Q6GZX3))
78
+ Commands::Uniprot.run(%w[-f sequence Q6GZX3])
79
79
  end
80
80
  assert_equal(out_default, out_sequence)
81
81
 
82
82
  out_sequence, _err = capture_io_while do
83
- Commands::Uniprot.run(%w(--format sequence Q6GZX3))
83
+ Commands::Uniprot.run(%w[--format sequence Q6GZX3])
84
84
  end
85
85
  assert_equal(out_default, out_sequence)
86
86
  end
@@ -88,37 +88,37 @@ module Unipept
88
88
  def test_format_options
89
89
  # fasta txt xml rdf gff sequence
90
90
  out, err = capture_io_while do
91
- Commands::Uniprot.run(%w(-f fasta Q6GZX3))
91
+ Commands::Uniprot.run(%w[-f fasta Q6GZX3])
92
92
  end
93
93
  assert(!out.empty?)
94
94
  assert(err.empty?)
95
95
 
96
96
  out, err = capture_io_while do
97
- Commands::Uniprot.run(%w(-f txt Q6GZX3))
97
+ Commands::Uniprot.run(%w[-f txt Q6GZX3])
98
98
  end
99
99
  assert(!out.empty?)
100
100
  assert(err.empty?)
101
101
 
102
102
  out, err = capture_io_while do
103
- Commands::Uniprot.run(%w(-f xml Q6GZX3))
103
+ Commands::Uniprot.run(%w[-f xml Q6GZX3])
104
104
  end
105
105
  assert(!out.empty?)
106
106
  assert(err.empty?)
107
107
 
108
108
  out, err = capture_io_while do
109
- Commands::Uniprot.run(%w(-f rdf Q6GZX3))
109
+ Commands::Uniprot.run(%w[-f rdf Q6GZX3])
110
110
  end
111
111
  assert(!out.empty?)
112
112
  assert(err.empty?)
113
113
 
114
114
  out, err = capture_io_while do
115
- Commands::Uniprot.run(%w(-f gff Q6GZX3))
115
+ Commands::Uniprot.run(%w[-f gff Q6GZX3])
116
116
  end
117
117
  assert(!out.empty?)
118
118
  assert(err.empty?)
119
119
 
120
120
  out, err = capture_io_while do
121
- Commands::Uniprot.run(%w(-f sequence Q6GZX3))
121
+ Commands::Uniprot.run(%w[-f sequence Q6GZX3])
122
122
  end
123
123
  assert(!out.empty?)
124
124
  assert(err.empty?)
@@ -127,7 +127,7 @@ module Unipept
127
127
  def test_help
128
128
  out, _err = capture_io_while do
129
129
  assert_raises SystemExit do
130
- Commands::Uniprot.run(%w(-h))
130
+ Commands::Uniprot.run(%w[-h])
131
131
  end
132
132
  end
133
133
  assert(out.include?('show help for this command'))
@@ -8,17 +8,17 @@ module Unipept
8
8
 
9
9
  class UnipeptAPIRunnerTestCase < Unipept::TestCase
10
10
  def test_init
11
- runner = new_runner('test', { host: 'test_host' }, %w(a b c))
11
+ runner = new_runner('test', { host: 'test_host' }, %w[a b c])
12
12
  assert_equal('test', runner.command.name)
13
13
  assert_equal('test_host', runner.options[:host])
14
- assert_equal(%w(a b c), runner.arguments)
14
+ assert_equal(%w[a b c], runner.arguments)
15
15
  assert(!runner.configuration.nil?)
16
16
  assert_equal('http://test_host/api/v1/test.json', runner.url)
17
17
  assert(/Unipept CLI - unipept [0-9]*\.[0-9]*\.[0-9]*/.match runner.user_agent)
18
18
  end
19
19
 
20
20
  def test_config_host
21
- runner = new_runner('test', { host: 'http://param_host' }, %w(a b c))
21
+ runner = new_runner('test', { host: 'http://param_host' }, %w[a b c])
22
22
  runner.options.delete(:host)
23
23
  runner.configuration['host'] = 'http://config_host'
24
24
  host = runner.host
@@ -26,14 +26,14 @@ module Unipept
26
26
  end
27
27
 
28
28
  def test_param_host
29
- runner = new_runner('test', { host: 'http://param_host' }, %w(a b c))
29
+ runner = new_runner('test', { host: 'http://param_host' }, %w[a b c])
30
30
  runner.configuration.delete('host')
31
31
  host = runner.host
32
32
  assert_equal('http://param_host', host)
33
33
  end
34
34
 
35
35
  def test_no_host
36
- runner = new_runner('test', { host: 'param_host' }, %w(a b c))
36
+ runner = new_runner('test', { host: 'param_host' }, %w[a b c])
37
37
  runner.configuration.delete('host')
38
38
  runner.options.delete(:host)
39
39
  host = runner.host
@@ -41,66 +41,66 @@ module Unipept
41
41
  end
42
42
 
43
43
  def test_host_priority
44
- runner = new_runner('test', { host: 'http://param_host' }, %w(a b c))
44
+ runner = new_runner('test', { host: 'http://param_host' }, %w[a b c])
45
45
  runner.configuration['host'] = 'http://config_host'
46
46
  host = runner.host
47
47
  assert_equal('http://param_host', host)
48
48
  end
49
49
 
50
50
  def test_http_host
51
- runner = new_runner('test', { host: 'param_host' }, %w(a b c))
51
+ runner = new_runner('test', { host: 'param_host' }, %w[a b c])
52
52
  host = runner.host
53
53
  assert_equal('http://param_host', host)
54
54
  end
55
55
 
56
56
  def test_https_host
57
- runner = new_runner('test', { host: 'https://param_host' }, %w(a b c))
57
+ runner = new_runner('test', { host: 'https://param_host' }, %w[a b c])
58
58
  host = runner.host
59
59
  assert_equal('https://param_host', host)
60
60
  end
61
61
 
62
62
  def test_input_iterator_args
63
- runner = new_runner('test', { host: 'https://param_host' }, %w(a b c))
63
+ runner = new_runner('test', { host: 'https://param_host' }, %w[a b c])
64
64
  output = []
65
65
  runner.input_iterator.each { |el| output << el.chomp }
66
- assert_equal(%w(a b c), output)
66
+ assert_equal(%w[a b c], output)
67
67
  end
68
68
 
69
69
  def test_input_iterator_file
70
- File.open('input_file', 'w') { |file| file.write(%w(a b c).join("\n")) }
70
+ File.open('input_file', 'w') { |file| file.write(%w[a b c].join("\n")) }
71
71
  runner = new_runner('test', host: 'https://param_host', input: 'input_file')
72
72
  output = []
73
73
  runner.input_iterator.each { |el| output << el.chomp }
74
- assert_equal(%w(a b c), output)
74
+ assert_equal(%w[a b c], output)
75
75
  end
76
76
 
77
77
  def test_input_iterator_stdin
78
78
  runner = new_runner('test', host: 'https://param_host')
79
79
  output = []
80
- _out, _err = capture_io_with_input(%w(a b c)) do
80
+ _out, _err = capture_io_with_input(%w[a b c]) do
81
81
  runner.input_iterator.each { |el| output << el.chomp }
82
82
  end
83
- assert_equal(%w(a b c), output)
83
+ assert_equal(%w[a b c], output)
84
84
  end
85
85
 
86
86
  def test_input_iterator_arguments_priority
87
- File.open('input_file', 'w') { |file| file.write(%w(1 2 3).join("\n")) }
88
- runner = new_runner('test', { host: 'https://param_host', input: 'input_file' }, %w(a b c))
87
+ File.open('input_file', 'w') { |file| file.write(%w[1 2 3].join("\n")) }
88
+ runner = new_runner('test', { host: 'https://param_host', input: 'input_file' }, %w[a b c])
89
89
  output = []
90
- _out, _err = capture_io_with_input(%w(1 2 3)) do
90
+ _out, _err = capture_io_with_input(%w[1 2 3]) do
91
91
  runner.input_iterator.each { |el| output << el.chomp }
92
92
  end
93
- assert_equal(%w(a b c), output)
93
+ assert_equal(%w[a b c], output)
94
94
  end
95
95
 
96
96
  def test_input_iterator_file_priority
97
- File.open('input_file', 'w') { |file| file.write(%w(a b c).join("\n")) }
97
+ File.open('input_file', 'w') { |file| file.write(%w[a b c].join("\n")) }
98
98
  runner = new_runner('test', host: 'https://param_host', input: 'input_file')
99
99
  output = []
100
- _out, _err = capture_io_with_input(%w(1 2 3)) do
100
+ _out, _err = capture_io_with_input(%w[1 2 3]) do
101
101
  runner.input_iterator.each { |el| output << el.chomp }
102
102
  end
103
- assert_equal(%w(a b c), output)
103
+ assert_equal(%w[a b c], output)
104
104
  end
105
105
 
106
106
  def test_required_fields
@@ -199,7 +199,7 @@ module Unipept
199
199
  end
200
200
 
201
201
  def test_multiple_selected_fields
202
- runner = new_runner('test', host: 'http://param_host', select: %w(field1 field2))
202
+ runner = new_runner('test', host: 'http://param_host', select: %w[field1 field2])
203
203
  assert_equal([/^field1$/, /^field2$/], runner.selected_fields)
204
204
  end
205
205
 
@@ -348,7 +348,7 @@ module Unipept
348
348
  lambda = runner.handle_response(response, 0, nil)
349
349
  assert(lambda.lambda?)
350
350
  def runner.save_error(input)
351
- $stderr.puts(input)
351
+ warn(input)
352
352
  end
353
353
  out, err = capture_io_while(&lambda)
354
354
  assert_equal('', out)
@@ -361,7 +361,7 @@ module Unipept
361
361
  lambda = runner.handle_response(response, 0, nil)
362
362
  assert(lambda.lambda?)
363
363
  def runner.save_error(input)
364
- $stderr.puts(input)
364
+ warn(input)
365
365
  end
366
366
  out, err = capture_io_while(&lambda)
367
367
  assert_equal('', out)
@@ -374,7 +374,7 @@ module Unipept
374
374
  lambda = runner.handle_response(response, 0, nil)
375
375
  assert(lambda.lambda?)
376
376
  def runner.save_error(input)
377
- $stderr.puts(input)
377
+ warn(input)
378
378
  end
379
379
  out, err = capture_io_while(&lambda)
380
380
  assert_equal('', out)
@@ -385,7 +385,7 @@ module Unipept
385
385
  runner = new_runner('taxonomy', host: 'http://api.unipept.ugent.be')
386
386
  out, err = capture_io_while do
387
387
  def runner.input_iterator
388
- %w(0 1 2).each
388
+ %w[0 1 2].each
389
389
  end
390
390
 
391
391
  def runner.batch_size
@@ -5,14 +5,14 @@ module Unipept
5
5
  def test_help
6
6
  out, _err = capture_io_while do
7
7
  assert_raises SystemExit do
8
- Commands::Unipept.run(%w(config -h))
8
+ Commands::Unipept.run(%w[config -h])
9
9
  end
10
10
  end
11
11
  assert(out.include?('show help for this command'))
12
12
 
13
13
  out, _err = capture_io_while do
14
14
  assert_raises SystemExit do
15
- Commands::Unipept.run(%w(config --help))
15
+ Commands::Unipept.run(%w[config --help])
16
16
  end
17
17
  end
18
18
  assert(out.include?('show help for this command'))
@@ -21,7 +21,7 @@ module Unipept
21
21
  def test_no_args
22
22
  _out, err = capture_io_while do
23
23
  assert_raises SystemExit do
24
- Commands::Unipept.run(%w(config))
24
+ Commands::Unipept.run(%w[config])
25
25
  end
26
26
  end
27
27
  assert(err.include?('show help for this command'))
@@ -30,7 +30,7 @@ module Unipept
30
30
  def test_too_many_args
31
31
  _out, err = capture_io_while do
32
32
  assert_raises SystemExit do
33
- Commands::Unipept.run(%w(config a b c))
33
+ Commands::Unipept.run(%w[config a b c])
34
34
  end
35
35
  end
36
36
  assert(err.include?('show help for this command'))
@@ -54,7 +54,7 @@ module Unipept
54
54
  config['test'] = value
55
55
  config.save
56
56
  out, _err = capture_io_while do
57
- Commands::Unipept.run(%w(config test))
57
+ Commands::Unipept.run(%w[config test])
58
58
  end
59
59
  config.delete('test')
60
60
  config.save
@@ -31,14 +31,14 @@ module Unipept
31
31
  def test_help
32
32
  out, _err = capture_io_while do
33
33
  assert_raises SystemExit do
34
- Commands::Unipept.run(%w(pept2lca -h))
34
+ Commands::Unipept.run(%w[pept2lca -h])
35
35
  end
36
36
  end
37
37
  assert(out.include?('show help for this command'))
38
38
 
39
39
  out, _err = capture_io_while do
40
40
  assert_raises SystemExit do
41
- Commands::Unipept.run(%w(pept2lca --help))
41
+ Commands::Unipept.run(%w[pept2lca --help])
42
42
  end
43
43
  end
44
44
  assert(out.include?('show help for this command'))
@@ -46,7 +46,7 @@ module Unipept
46
46
 
47
47
  def test_run
48
48
  out, err = capture_io_while do
49
- Commands::Unipept.run(%w(pept2lca --host http://api.unipept.ugent.be AALTER))
49
+ Commands::Unipept.run(%w[pept2lca --host http://api.unipept.ugent.be AALTER])
50
50
  end
51
51
  lines = out.each_line
52
52
  assert_equal('', err)
@@ -57,7 +57,7 @@ module Unipept
57
57
 
58
58
  def test_run_with_fasta_multiple_batches
59
59
  out, err = capture_io_while do
60
- Commands::Unipept.run(%w(pept2lca --host http://api.unipept.ugent.be --batch 2 >test AALTER AALER >tost AALTER))
60
+ Commands::Unipept.run(%w[pept2lca --host http://api.unipept.ugent.be --batch 2 >test AALTER AALER >tost AALTER])
61
61
  end
62
62
  lines = out.each_line
63
63
  assert_equal('', err)
@@ -70,7 +70,7 @@ module Unipept
70
70
 
71
71
  def test_run_with_fasta_multiple_batches_and_select
72
72
  out, err = capture_io_while do
73
- Commands::Unipept.run(%w(pept2lca --host http://api.unipept.ugent.be --batch 2 --select taxon_id >test AALTER AALER >tost AALTER))
73
+ Commands::Unipept.run(%w[pept2lca --host http://api.unipept.ugent.be --batch 2 --select taxon_id >test AALTER AALER >tost AALTER])
74
74
  end
75
75
  lines = out.each_line
76
76
  assert_equal('', err)
@@ -83,7 +83,7 @@ module Unipept
83
83
 
84
84
  def test_run_with_fasta_multiple_batches_json
85
85
  out, err = capture_io_while do
86
- Commands::Unipept.run(%w(pept2lca --host http://api.unipept.ugent.be --batch 2 --format json >test AALTER AALER >tost AALTER))
86
+ Commands::Unipept.run(%w[pept2lca --host http://api.unipept.ugent.be --batch 2 --format json >test AALTER AALER >tost AALTER])
87
87
  end
88
88
  lines = out.each_line
89
89
  assert_equal('', err)
@@ -96,7 +96,7 @@ module Unipept
96
96
 
97
97
  def test_run_with_fasta_multiple_batches_xml
98
98
  out, err = capture_io_while do
99
- Commands::Unipept.run(%w(pept2lca --host http://api.unipept.ugent.be --batch 2 --format xml >test AALTER AALER >tost AALTER))
99
+ Commands::Unipept.run(%w[pept2lca --host http://api.unipept.ugent.be --batch 2 --format xml >test AALTER AALER >tost AALTER])
100
100
  end
101
101
  lines = out.each_line
102
102
  assert_equal('', err)