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.
checksums.yaml CHANGED
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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'))