unipept 1.4.0 → 1.4.1

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data/.rubocop.yml CHANGED
@@ -1,9 +1,8 @@
1
1
  AllCops:
2
- Include:
3
- - ''
4
2
  Exclude:
5
3
  - 'unipept.gemspec'
6
4
  - 'vendor/**/*'
5
+ - 'Rakefile'
7
6
 
8
7
  Style/ClassAndModuleChildren:
9
8
  EnforcedStyle: compact
@@ -30,3 +29,7 @@ Metrics/MethodLength:
30
29
  Enabled: false
31
30
  Metrics/BlockLength:
32
31
  Enabled: false
32
+ Naming/HeredocDelimiterNaming:
33
+ Enabled: false
34
+ Naming/UncommunicativeMethodParamName:
35
+ Enabled: false
data/.travis.yml CHANGED
@@ -1,10 +1,9 @@
1
1
  language: ruby
2
2
  rvm:
3
- - 2.4.0
4
- - 2.3.3
5
- - 2.2.6
6
- - 2.1.9
7
- - 2.0.0
3
+ - 2.6.0
4
+ - 2.5.3
5
+ - 2.4.4
6
+ - 2.3.7
8
7
 
9
8
  install:
10
9
  - gem update --system
data/Gemfile CHANGED
@@ -3,15 +3,14 @@ source 'http://rubygems.org'
3
3
  # Example:
4
4
  # gem "activesupport", ">= 2.3.5"
5
5
 
6
- # for now, stay on version 2.11 because of a bug
7
- gem 'cri', '2.11'
6
+ gem 'cri', '~>2.15.3'
8
7
  gem 'typhoeus', '~> 1.1'
9
8
 
10
9
  group :development do
11
- gem 'rake', '~> 10.4'
10
+ gem 'coveralls', '~> 0', require: false
12
11
  gem 'minitest', '~> 5.7'
12
+ gem 'rake', '~> 10.4'
13
13
  gem 'rubocop', '~>0.32'
14
- gem 'coveralls', '~> 0', require: false
15
14
  end
16
15
 
17
16
  group :release do
data/Gemfile.lock CHANGED
@@ -11,7 +11,7 @@ GEM
11
11
  term-ansicolor (~> 1.3)
12
12
  thor (~> 0.19.4)
13
13
  tins (~> 1.6)
14
- cri (2.11.0)
14
+ cri (2.15.3)
15
15
  colored (~> 1.2)
16
16
  descendants_tracker (0.0.4)
17
17
  thread_safe (~> 0.3, >= 0.3.1)
@@ -97,7 +97,7 @@ PLATFORMS
97
97
 
98
98
  DEPENDENCIES
99
99
  coveralls (~> 0)
100
- cri (= 2.11)
100
+ cri (~> 2.15.3)
101
101
  jeweler
102
102
  minitest (~> 5.7)
103
103
  rake (~> 10.4)
data/Rakefile CHANGED
@@ -1,12 +1,10 @@
1
- # encoding: utf-8
2
-
3
1
  require 'rubygems'
4
2
  require 'bundler'
5
3
  begin
6
4
  Bundler.setup(:default, :development)
7
5
  rescue Bundler::BundlerError => e
8
- $stderr.puts e.message
9
- $stderr.puts 'Run `bundle install` to install missing gems'
6
+ warn e.message
7
+ warn 'Run `bundle install` to install missing gems'
10
8
  exit e.status_code
11
9
  end
12
10
  require 'rake'
@@ -17,7 +15,7 @@ begin
17
15
  Jeweler::Tasks.new do |gem|
18
16
  # gem is a Gem::Specification... see http://guides.rubygems.org/specification-reference/ for more options
19
17
  gem.name = 'unipept'
20
- gem.executables = %w(unipept prot2pept peptfilter uniprot)
18
+ gem.executables = %w[unipept prot2pept peptfilter uniprot]
21
19
  gem.homepage = 'http://unipept.ugent.be'
22
20
  gem.license = 'MIT'
23
21
  gem.summary = 'Command line interface to Unipept web services.'
@@ -32,7 +30,7 @@ begin
32
30
  end
33
31
  Jeweler::RubygemsDotOrgTasks.new
34
32
  rescue LoadError
35
- # do nothing
33
+ # do nothing
36
34
  end
37
35
 
38
36
  task :test_unit do
@@ -45,7 +43,7 @@ end
45
43
 
46
44
  RuboCop::RakeTask.new(:test_style)
47
45
 
48
- task test: [:test_unit, :test_style]
46
+ task test: %i[test_unit test_style]
49
47
 
50
48
  task default: :test
51
49
 
data/VERSION CHANGED
@@ -1 +1 @@
1
- 1.4.0
1
+ 1.4.1
data/lib/batch_order.rb CHANGED
@@ -11,6 +11,7 @@ module Unipept
11
11
  def wait(i, &block)
12
12
  @order[i] = block
13
13
  return unless i == @current
14
+
14
15
  while order[@current]
15
16
  order.delete(@current).call
16
17
  @current += 1
@@ -22,7 +22,7 @@ module Unipept
22
22
  # file, the value of the option is used.
23
23
  def host
24
24
  # find host in opts first
25
- host = options[:host] ? options[:host] : @configuration['host']
25
+ host = options[:host] || @configuration['host']
26
26
  host = 'http://api.unipept.ugent.be' if host.nil? || host.empty?
27
27
 
28
28
  # add http:// if needed
@@ -40,6 +40,7 @@ module Unipept
40
40
  def input_iterator
41
41
  return arguments.each unless arguments.empty?
42
42
  return IO.foreach(options[:input]) if options[:input]
43
+
43
44
  $stdin.each_line
44
45
  end
45
46
 
@@ -86,6 +87,7 @@ module Unipept
86
87
  # Returns an array of regular expressions containing all the selected fields
87
88
  def selected_fields
88
89
  return @selected_fields unless @selected_fields.nil?
90
+
89
91
  fields = [*options[:select]].map { |f| f.split(',') }.flatten
90
92
  fields.concat(required_fields) if @fasta && !fields.empty?
91
93
  @selected_fields = fields.map { |f| glob_to_regex(f) }
@@ -143,7 +145,7 @@ module Unipept
143
145
  path = error_file_path
144
146
  FileUtils.mkdir_p File.dirname(path)
145
147
  File.open(path, 'w') { |f| f.write message }
146
- $stderr.puts "API request failed! log can be found in #{path}"
148
+ warn "API request failed! log can be found in #{path}"
147
149
  end
148
150
 
149
151
  private
@@ -5,7 +5,7 @@ module Unipept::Commands
5
5
  attr_reader :root_command
6
6
  attr_reader :valid_formats
7
7
 
8
- valid_formats = Set.new %w(fasta txt xml rdf gff sequence)
8
+ valid_formats = Set.new %w[fasta txt xml rdf gff sequence]
9
9
  @root_command = Cri::Command.define do
10
10
  name 'uniprot'
11
11
  summary 'Command line interface to UniProt web services.'
@@ -29,7 +29,7 @@ module Unipept::Commands
29
29
  run do |opts, args, _cmd|
30
30
  format = opts.fetch(:format, 'sequence')
31
31
  unless valid_formats.include? format
32
- $stderr.puts format + ' is not a valid output format. Available formats are: ' + valid_formats.to_a.join(', ')
32
+ warn format + ' is not a valid output format. Available formats are: ' + valid_formats.to_a.join(', ')
33
33
  exit 1
34
34
  end
35
35
  iterator = args.empty? ? $stdin.each_line : args
data/lib/configuration.rb CHANGED
@@ -13,7 +13,7 @@ module Unipept
13
13
  # @param [String] file An optional file name of the YAML file to create the
14
14
  # config from
15
15
  def initialize(file = nil)
16
- @file_name = file ? file : File.join(Dir.home, '.unipeptrc')
16
+ @file_name = file || File.join(Dir.home, '.unipeptrc')
17
17
  @config = if !File.exist? file_name
18
18
  {}
19
19
  else
data/lib/formatters.rb CHANGED
@@ -17,7 +17,7 @@ module Unipept
17
17
  # @return [Formatter] The requested formatter
18
18
  def self.new_for_format(format)
19
19
  formatters[format].new
20
- rescue
20
+ rescue StandardError
21
21
  formatters[default].new
22
22
  end
23
23
 
@@ -32,7 +32,7 @@ module Unipept
32
32
  #
33
33
  # @return [Array<String>] The list of available formatters
34
34
  def self.available
35
- formatters.select { |_key, value| !value.hidden? }.keys
35
+ formatters.reject { |_key, value| value.hidden? }.keys
36
36
  end
37
37
 
38
38
  # @return [String] The type of the default formatter: csv
@@ -19,6 +19,7 @@ module Unipept
19
19
  def print
20
20
  return unless $stdout.tty?
21
21
  return if recently_fetched?
22
+
22
23
  resp = fetch_server_message
23
24
  update_fetched
24
25
  puts resp unless resp.empty?
@@ -39,114 +39,114 @@ module Unipept
39
39
 
40
40
  def test_default_min_length_argument
41
41
  out, _err = capture_io_with_input('A' * 6) do
42
- Commands::Peptfilter.run(%w())
42
+ Commands::Peptfilter.run(%w[])
43
43
  end
44
44
  assert_equal('A' * 6, out.chomp)
45
45
 
46
46
  out, _err = capture_io_with_input('A' * 5) do
47
- Commands::Peptfilter.run(%w())
47
+ Commands::Peptfilter.run(%w[])
48
48
  end
49
49
  assert_equal('A' * 5, out.chomp)
50
50
 
51
51
  out, _err = capture_io_with_input('A' * 4) do
52
- Commands::Peptfilter.run(%w())
52
+ Commands::Peptfilter.run(%w[])
53
53
  end
54
54
  assert_equal('', out.chomp)
55
55
  end
56
56
 
57
57
  def test_default_max_length_argument
58
58
  out, _err = capture_io_with_input('A' * 49) do
59
- Commands::Peptfilter.run(%w())
59
+ Commands::Peptfilter.run(%w[])
60
60
  end
61
61
  assert_equal('A' * 49, out.chomp)
62
62
 
63
63
  out, _err = capture_io_with_input('A' * 50) do
64
- Commands::Peptfilter.run(%w())
64
+ Commands::Peptfilter.run(%w[])
65
65
  end
66
66
  assert_equal('A' * 50, out.chomp)
67
67
 
68
68
  out, _err = capture_io_with_input('A' * 51) do
69
- Commands::Peptfilter.run(%w())
69
+ Commands::Peptfilter.run(%w[])
70
70
  end
71
71
  assert_equal('', out.chomp)
72
72
  end
73
73
 
74
74
  def test_with_min_argument
75
75
  out, _err = capture_io_with_input('A' * 6) do
76
- Commands::Peptfilter.run(%w(--minlen 7))
76
+ Commands::Peptfilter.run(%w[--minlen 7])
77
77
  end
78
78
  assert_equal('', out.chomp)
79
79
 
80
80
  out, _err = capture_io_with_input('A' * 4) do
81
- Commands::Peptfilter.run(%w(--minlen 3))
81
+ Commands::Peptfilter.run(%w[--minlen 3])
82
82
  end
83
83
  assert_equal('A' * 4, out.chomp)
84
84
  end
85
85
 
86
86
  def test_with_max_argument
87
87
  out, _err = capture_io_with_input('A' * 45) do
88
- Commands::Peptfilter.run(%w(--maxlen 40))
88
+ Commands::Peptfilter.run(%w[--maxlen 40])
89
89
  end
90
90
  assert_equal('', out.chomp)
91
91
 
92
92
  out, _err = capture_io_with_input('A' * 55) do
93
- Commands::Peptfilter.run(%w(--maxlen 60))
93
+ Commands::Peptfilter.run(%w[--maxlen 60])
94
94
  end
95
95
  assert_equal('A' * 55, out.chomp)
96
96
  end
97
97
 
98
98
  def test_with_lacks_argument
99
99
  out, _err = capture_io_with_input('A' * 10) do
100
- Commands::Peptfilter.run(%w(--lacks B))
100
+ Commands::Peptfilter.run(%w[--lacks B])
101
101
  end
102
102
  assert_equal('A' * 10, out.chomp)
103
103
 
104
104
  out, _err = capture_io_with_input('A' * 10) do
105
- Commands::Peptfilter.run(%w(-l B))
105
+ Commands::Peptfilter.run(%w[-l B])
106
106
  end
107
107
  assert_equal('A' * 10, out.chomp)
108
108
 
109
109
  out, _err = capture_io_with_input('A' * 10) do
110
- Commands::Peptfilter.run(%w(--lacks A))
110
+ Commands::Peptfilter.run(%w[--lacks A])
111
111
  end
112
112
  assert_equal('', out.chomp)
113
113
 
114
114
  out, _err = capture_io_with_input('A' * 10) do
115
- Commands::Peptfilter.run(%w(-l A))
115
+ Commands::Peptfilter.run(%w[-l A])
116
116
  end
117
117
  assert_equal('', out.chomp)
118
118
  end
119
119
 
120
120
  def test_with_contains_argument
121
121
  out, _err = capture_io_with_input('A' * 10) do
122
- Commands::Peptfilter.run(%w(--contains A))
122
+ Commands::Peptfilter.run(%w[--contains A])
123
123
  end
124
124
  assert_equal('A' * 10, out.chomp)
125
125
 
126
126
  out, _err = capture_io_with_input('A' * 10) do
127
- Commands::Peptfilter.run(%w(-c A))
127
+ Commands::Peptfilter.run(%w[-c A])
128
128
  end
129
129
  assert_equal('A' * 10, out.chomp)
130
130
 
131
131
  out, _err = capture_io_with_input('A' * 10) do
132
- Commands::Peptfilter.run(%w(--contains B))
132
+ Commands::Peptfilter.run(%w[--contains B])
133
133
  end
134
134
  assert_equal('', out.chomp)
135
135
 
136
136
  out, _err = capture_io_with_input('A' * 10) do
137
- Commands::Peptfilter.run(%w(-c B))
137
+ Commands::Peptfilter.run(%w[-c B])
138
138
  end
139
139
  assert_equal('', out.chomp)
140
140
  end
141
141
 
142
142
  def test_fasta_input
143
143
  out, _err = capture_io_with_input('>') do
144
- Commands::Peptfilter.run(%w())
144
+ Commands::Peptfilter.run(%w[])
145
145
  end
146
146
  assert_equal('>', out.chomp)
147
147
 
148
148
  out, _err = capture_io_with_input(['>', 'A', 'AALTER', '>']) do
149
- Commands::Peptfilter.run(%w())
149
+ Commands::Peptfilter.run(%w[])
150
150
  end
151
151
  assert_equal(">\nAALTER\n>", out.chomp)
152
152
  end
@@ -154,7 +154,7 @@ module Unipept
154
154
  def test_no_input
155
155
  out, err = capture_io_while do
156
156
  assert_raises SystemExit do
157
- Commands::Peptfilter.run(%w(some argument))
157
+ Commands::Peptfilter.run(%w[some argument])
158
158
  end
159
159
  end
160
160
  assert_equal('', out.chomp)
@@ -163,7 +163,7 @@ module Unipept
163
163
 
164
164
  def test_normal_input
165
165
  out, _err = capture_io_with_input(['A', 'A' * 11, 'AAAAB', 'BBBBB', 'CCCCC', 'CCCCCA']) do
166
- Commands::Peptfilter.run(%w(--minlen 4 --maxlen 10 --lacks B --contains A))
166
+ Commands::Peptfilter.run(%w[--minlen 4 --maxlen 10 --lacks B --contains A])
167
167
  end
168
168
  assert_equal('CCCCCA', out.chomp)
169
169
  end
@@ -171,7 +171,7 @@ module Unipept
171
171
  def test_help
172
172
  out, _err = capture_io_while do
173
173
  assert_raises SystemExit do
174
- Commands::Peptfilter.run(%w(-h))
174
+ Commands::Peptfilter.run(%w[-h])
175
175
  end
176
176
  end
177
177
  assert(out.include?('show help for this command'))
@@ -4,46 +4,46 @@ module Unipept
4
4
  class Prot2peptTestCase < Unipept::TestCase
5
5
  def test_normal_input
6
6
  out, _err = capture_io_with_input('AALTERAALTERPAALTER') do
7
- Commands::Prot2pept.run(%w())
7
+ Commands::Prot2pept.run(%w[])
8
8
  end
9
9
  assert_equal("AALTER\nAALTERPAALTER", out.chomp)
10
10
 
11
11
  out, _err = capture_io_with_input('AALTERAAL*TERPAALTER') do
12
- Commands::Prot2pept.run(%w())
12
+ Commands::Prot2pept.run(%w[])
13
13
  end
14
14
  assert_equal("AALTER\nAAL\nTERPAALTER", out.chomp)
15
15
 
16
16
  out, _err = capture_io_with_input('KRKPR') do
17
- Commands::Prot2pept.run(%w())
17
+ Commands::Prot2pept.run(%w[])
18
18
  end
19
19
  assert_equal("K\nR\nKPR", out.chomp)
20
20
 
21
- out, _err = capture_io_with_input(%w(AALTERAALTERPAALTER AALTERAA)) do
22
- Commands::Prot2pept.run(%w())
21
+ out, _err = capture_io_with_input(%w[AALTERAALTERPAALTER AALTERAA]) do
22
+ Commands::Prot2pept.run(%w[])
23
23
  end
24
24
  assert_equal("AALTER\nAALTERPAALTER\nAALTER\nAA", out.chomp)
25
25
  end
26
26
 
27
27
  def test_fasta_input
28
28
  out, _err = capture_io_with_input(">AKA\nAALTERAALTERPAALTER") do
29
- Commands::Prot2pept.run(%w())
29
+ Commands::Prot2pept.run(%w[])
30
30
  end
31
31
  assert_equal(">AKA\nAALTER\nAALTERPAALTER", out.chomp)
32
32
 
33
33
  out, _err = capture_io_with_input(">AKA\nAAL\nT\nERAALTER\nP\nAALTER") do
34
- Commands::Prot2pept.run(%w())
34
+ Commands::Prot2pept.run(%w[])
35
35
  end
36
36
  assert_equal(">AKA\nAALTER\nAALTERPAALTER", out.chomp)
37
37
 
38
38
  out, _err = capture_io_with_input(">AKA\nAAL\nT\n>\nERAALTER\nP\nAALTER") do
39
- Commands::Prot2pept.run(%w())
39
+ Commands::Prot2pept.run(%w[])
40
40
  end
41
41
  assert_equal(">AKA\nAALT\n>\nER\nAALTERPAALTER", out.chomp)
42
42
  end
43
43
 
44
44
  def test_default_pattern
45
45
  default_out, _err = capture_io_with_input('AALTERAALTERPAALTER') do
46
- Commands::Prot2pept.run(%w())
46
+ Commands::Prot2pept.run(%w[])
47
47
  end
48
48
  assert_equal("AALTER\nAALTERPAALTER", default_out.chomp)
49
49
 
@@ -60,7 +60,7 @@ module Unipept
60
60
 
61
61
  def test_pattern
62
62
  out, _err = capture_io_with_input('AALTERAALTERPAALTER') do
63
- Commands::Prot2pept.run(%w())
63
+ Commands::Prot2pept.run(%w[])
64
64
  end
65
65
  assert_equal("AALTER\nAALTERPAALTER", out.chomp)
66
66
 
@@ -78,7 +78,7 @@ module Unipept
78
78
  def test_help
79
79
  out, _err = capture_io_while do
80
80
  assert_raises SystemExit do
81
- Commands::Prot2pept.run(%w(-h))
81
+ Commands::Prot2pept.run(%w[-h])
82
82
  end
83
83
  end
84
84
  assert(out.include?('show help for this command'))