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 +4 -4
- data/.rubocop.yml +5 -2
- data/.travis.yml +4 -5
- data/Gemfile +3 -4
- data/Gemfile.lock +2 -2
- data/Rakefile +5 -7
- data/VERSION +1 -1
- data/lib/batch_order.rb +1 -0
- data/lib/commands/unipept/api_runner.rb +4 -2
- data/lib/commands/uniprot.rb +2 -2
- data/lib/configuration.rb +1 -1
- data/lib/formatters.rb +2 -2
- data/lib/server_message.rb +1 -0
- data/test/commands/test_peptfilter.rb +23 -23
- data/test/commands/test_prot2pept.rb +11 -11
- data/test/commands/test_unipept.rb +4 -4
- data/test/commands/test_uniprot.rb +25 -25
- data/test/commands/unipept/test_api_runner.rb +26 -26
- data/test/commands/unipept/test_config.rb +5 -5
- data/test/commands/unipept/test_pept2lca.rb +7 -7
- data/test/commands/unipept/test_pept2prot.rb +7 -7
- data/test/commands/unipept/test_pept2taxa.rb +7 -7
- data/test/commands/unipept/test_taxa2lca.rb +5 -5
- data/test/commands/unipept/test_taxonomy.rb +7 -7
- data/test/helper.rb +2 -2
- data/test/test_batch_iterator.rb +4 -4
- data/unipept.gemspec +12 -12
- metadata +15 -15
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
---
|
2
2
|
SHA256:
|
3
|
-
metadata.gz:
|
4
|
-
data.tar.gz:
|
3
|
+
metadata.gz: 773e25ed2369843012700a657100181e84254c905365d534136d0c1a68606ab7
|
4
|
+
data.tar.gz: 78830dfab3cab145cf248b2bc41d65806a3a4274ab1d48b9be1d530c7f2eb865
|
5
5
|
SHA512:
|
6
|
-
metadata.gz:
|
7
|
-
data.tar.gz:
|
6
|
+
metadata.gz: 55648c665eadd51c119e4091a3e8e110189df97ac70eeceee0a9a508e8b7112cd522dbec23ae55c1172e061b95b192cc383190640ec68dbd316273510640b598
|
7
|
+
data.tar.gz: fdcf5b35931caee76a3acfa6a8be7828f902570e9b6669f4d184b55321dcd0177d9bd363214f4d2b4766b13010eebe15e7e1beed549b4b864a95f71684a178ae
|
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
data/Gemfile
CHANGED
@@ -3,15 +3,14 @@ source 'http://rubygems.org'
|
|
3
3
|
# Example:
|
4
4
|
# gem "activesupport", ">= 2.3.5"
|
5
5
|
|
6
|
-
|
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 '
|
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.
|
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 (
|
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
|
-
|
9
|
-
|
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
|
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: [
|
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.
|
1
|
+
1.4.1
|
data/lib/batch_order.rb
CHANGED
@@ -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]
|
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
|
-
|
148
|
+
warn "API request failed! log can be found in #{path}"
|
147
149
|
end
|
148
150
|
|
149
151
|
private
|
data/lib/commands/uniprot.rb
CHANGED
@@ -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
|
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
|
-
|
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
|
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.
|
35
|
+
formatters.reject { |_key, value| value.hidden? }.keys
|
36
36
|
end
|
37
37
|
|
38
38
|
# @return [String] The type of the default formatter: csv
|
data/lib/server_message.rb
CHANGED
@@ -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
|
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
|
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
|
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
|
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
|
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
|
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
|
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
|
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
|
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
|
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
|
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
|
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
|
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
|
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
|
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
|
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
|
81
|
+
Commands::Prot2pept.run(%w[-h])
|
82
82
|
end
|
83
83
|
end
|
84
84
|
assert(out.include?('show help for this command'))
|