unipept 2.1.1 → 2.2.2
Sign up to get free protection for your applications and to get access to all the features.
- checksums.yaml +4 -4
- data/.github/dependabot.yml +9 -0
- data/.github/workflows/ci.yml +6 -27
- data/.rakeTasks +7 -0
- data/.rubocop.yml +2 -0
- data/.ruby-version +1 -1
- data/CITATION.cff +30 -0
- data/Gemfile +2 -2
- data/Gemfile.lock +60 -41
- data/README.md +2 -2
- data/Rakefile +4 -4
- data/VERSION +1 -1
- data/lib/batch_iterator.rb +16 -0
- data/lib/commands/prot2pept.rb +1 -2
- data/lib/commands/unipept/api_runner.rb +10 -12
- data/lib/commands/unipept/config.rb +1 -1
- data/lib/commands/unipept/pept2taxa.rb +1 -5
- data/lib/commands/unipept/taxa2tree.rb +74 -0
- data/lib/commands/unipept.rb +25 -1
- data/lib/commands/uniprot.rb +4 -5
- data/lib/configuration.rb +6 -7
- data/lib/formatters.rb +108 -36
- data/lib/server_message.rb +2 -4
- data/test/commands/unipept/test_api_runner.rb +8 -7
- data/test/commands/unipept/test_config.rb +1 -1
- data/test/commands/unipept/test_pept2ec.rb +11 -11
- data/test/commands/unipept/test_pept2funct.rb +15 -15
- data/test/commands/unipept/test_pept2go.rb +10 -10
- data/test/commands/unipept/test_pept2interpro.rb +26 -26
- data/test/commands/unipept/test_pept2lca.rb +2 -2
- data/test/commands/unipept/test_pept2prot.rb +2 -2
- data/test/commands/unipept/test_pept2taxa.rb +2 -4
- data/test/commands/unipept/test_peptinfo.rb +16 -16
- data/test/commands/unipept/test_taxa2lca.rb +2 -2
- data/test/commands/unipept/test_taxa2tree.rb +68 -0
- data/test/commands/unipept/test_taxonomy.rb +2 -2
- data/test/helper.rb +10 -0
- data/test/support/api_stub.rb +60 -0
- data/test/support/resources/pept2ec.json +55 -0
- data/test/support/resources/pept2funct.json +73 -0
- data/test/support/resources/pept2go.json +43 -0
- data/test/support/resources/pept2interpro.json +43 -0
- data/test/support/resources/pept2lca.json +14 -0
- data/test/support/resources/pept2prot.json +422 -0
- data/test/support/resources/pept2taxa.json +194 -0
- data/test/support/resources/peptinfo.json +70 -0
- data/test/support/resources/taxa2tree.json +194 -0
- data/test/support/resources/taxonomy.json +22 -0
- data/test/test_configuration.rb +1 -1
- data/test/test_formatters.rb +5 -5
- data/test/test_output_writer.rb +1 -1
- data/test/test_server_message.rb +2 -2
- data/test.taxa +4 -0
- data/unipept.gemspec +32 -21
- metadata +26 -9
data/unipept.gemspec
CHANGED
|
@@ -1,17 +1,17 @@
|
|
|
1
|
-
# Generated by
|
|
1
|
+
# Generated by juwelier
|
|
2
2
|
# DO NOT EDIT THIS FILE DIRECTLY
|
|
3
|
-
# Instead, edit
|
|
3
|
+
# Instead, edit Juwelier::Tasks in Rakefile, and run 'rake gemspec'
|
|
4
4
|
# -*- encoding: utf-8 -*-
|
|
5
|
-
# stub: unipept 2.
|
|
5
|
+
# stub: unipept 2.2.2 ruby lib
|
|
6
6
|
|
|
7
7
|
Gem::Specification.new do |s|
|
|
8
8
|
s.name = "unipept".freeze
|
|
9
|
-
s.version = "2.
|
|
9
|
+
s.version = "2.2.2"
|
|
10
10
|
|
|
11
11
|
s.required_rubygems_version = Gem::Requirement.new(">= 0".freeze) if s.respond_to? :required_rubygems_version=
|
|
12
12
|
s.require_paths = ["lib".freeze]
|
|
13
13
|
s.authors = ["Bart Mesuere".freeze, "Pieter Verschaffelt".freeze, "Toon Willems".freeze, "Tom Naessens".freeze]
|
|
14
|
-
s.date = "
|
|
14
|
+
s.date = "2022-04-13"
|
|
15
15
|
s.description = " Command line interface to the Unipept (http://unipept.ugent.be) web services\n (pept2lca, taxa2lca, pept2taxa, pept2prot and taxonomy) and some utility\n commands for handling proteins using the command line.\n".freeze
|
|
16
16
|
s.email = "unipept@ugent.be".freeze
|
|
17
17
|
s.executables = ["unipept".freeze, "prot2pept".freeze, "peptfilter".freeze, "uniprot".freeze]
|
|
@@ -21,9 +21,12 @@ Gem::Specification.new do |s|
|
|
|
21
21
|
]
|
|
22
22
|
s.files = [
|
|
23
23
|
".document",
|
|
24
|
+
".github/dependabot.yml",
|
|
24
25
|
".github/workflows/ci.yml",
|
|
26
|
+
".rakeTasks",
|
|
25
27
|
".rubocop.yml",
|
|
26
28
|
".ruby-version",
|
|
29
|
+
"CITATION.cff",
|
|
27
30
|
"Gemfile",
|
|
28
31
|
"Gemfile.lock",
|
|
29
32
|
"LICENSE.txt",
|
|
@@ -51,6 +54,7 @@ Gem::Specification.new do |s|
|
|
|
51
54
|
"lib/commands/unipept/pept2taxa.rb",
|
|
52
55
|
"lib/commands/unipept/peptinfo.rb",
|
|
53
56
|
"lib/commands/unipept/taxa2lca.rb",
|
|
57
|
+
"lib/commands/unipept/taxa2tree.rb",
|
|
54
58
|
"lib/commands/unipept/taxonomy.rb",
|
|
55
59
|
"lib/commands/uniprot.rb",
|
|
56
60
|
"lib/configuration.rb",
|
|
@@ -59,6 +63,7 @@ Gem::Specification.new do |s|
|
|
|
59
63
|
"lib/retryable_typhoeus.rb",
|
|
60
64
|
"lib/server_message.rb",
|
|
61
65
|
"lib/version.rb",
|
|
66
|
+
"test.taxa",
|
|
62
67
|
"test/commands/test_peptfilter.rb",
|
|
63
68
|
"test/commands/test_prot2pept.rb",
|
|
64
69
|
"test/commands/test_unipept.rb",
|
|
@@ -74,8 +79,20 @@ Gem::Specification.new do |s|
|
|
|
74
79
|
"test/commands/unipept/test_pept2taxa.rb",
|
|
75
80
|
"test/commands/unipept/test_peptinfo.rb",
|
|
76
81
|
"test/commands/unipept/test_taxa2lca.rb",
|
|
82
|
+
"test/commands/unipept/test_taxa2tree.rb",
|
|
77
83
|
"test/commands/unipept/test_taxonomy.rb",
|
|
78
84
|
"test/helper.rb",
|
|
85
|
+
"test/support/api_stub.rb",
|
|
86
|
+
"test/support/resources/pept2ec.json",
|
|
87
|
+
"test/support/resources/pept2funct.json",
|
|
88
|
+
"test/support/resources/pept2go.json",
|
|
89
|
+
"test/support/resources/pept2interpro.json",
|
|
90
|
+
"test/support/resources/pept2lca.json",
|
|
91
|
+
"test/support/resources/pept2prot.json",
|
|
92
|
+
"test/support/resources/pept2taxa.json",
|
|
93
|
+
"test/support/resources/peptinfo.json",
|
|
94
|
+
"test/support/resources/taxa2tree.json",
|
|
95
|
+
"test/support/resources/taxonomy.json",
|
|
79
96
|
"test/test_batch_iterator.rb",
|
|
80
97
|
"test/test_batch_order.rb",
|
|
81
98
|
"test/test_configuration.rb",
|
|
@@ -87,32 +104,26 @@ Gem::Specification.new do |s|
|
|
|
87
104
|
]
|
|
88
105
|
s.homepage = "http://unipept.ugent.be".freeze
|
|
89
106
|
s.licenses = ["MIT".freeze]
|
|
90
|
-
s.required_ruby_version = Gem::Requirement.new(">= 2.
|
|
91
|
-
s.rubygems_version = "3.
|
|
107
|
+
s.required_ruby_version = Gem::Requirement.new(">= 2.6.0".freeze)
|
|
108
|
+
s.rubygems_version = "3.1.4".freeze
|
|
92
109
|
s.summary = "Command line interface to Unipept web services.".freeze
|
|
93
110
|
|
|
94
111
|
if s.respond_to? :specification_version then
|
|
95
112
|
s.specification_version = 4
|
|
113
|
+
end
|
|
96
114
|
|
|
97
|
-
|
|
98
|
-
|
|
99
|
-
|
|
100
|
-
|
|
101
|
-
|
|
102
|
-
|
|
103
|
-
else
|
|
104
|
-
s.add_dependency(%q<cri>.freeze, ["~> 2.15.10"])
|
|
105
|
-
s.add_dependency(%q<typhoeus>.freeze, ["~> 1.3.1"])
|
|
106
|
-
s.add_dependency(%q<minitest>.freeze, ["~> 5.14"])
|
|
107
|
-
s.add_dependency(%q<rake>.freeze, ["~> 13.0.1"])
|
|
108
|
-
s.add_dependency(%q<rubocop>.freeze, ["~> 0.79.0"])
|
|
109
|
-
end
|
|
115
|
+
if s.respond_to? :add_runtime_dependency then
|
|
116
|
+
s.add_runtime_dependency(%q<cri>.freeze, ["~> 2.15.10"])
|
|
117
|
+
s.add_runtime_dependency(%q<typhoeus>.freeze, ["~> 1.3.1"])
|
|
118
|
+
s.add_development_dependency(%q<minitest>.freeze, ["~> 5.14"])
|
|
119
|
+
s.add_development_dependency(%q<rake>.freeze, ["~> 13.0.1"])
|
|
120
|
+
s.add_development_dependency(%q<rubocop>.freeze, ["~> 1.11"])
|
|
110
121
|
else
|
|
111
122
|
s.add_dependency(%q<cri>.freeze, ["~> 2.15.10"])
|
|
112
123
|
s.add_dependency(%q<typhoeus>.freeze, ["~> 1.3.1"])
|
|
113
124
|
s.add_dependency(%q<minitest>.freeze, ["~> 5.14"])
|
|
114
125
|
s.add_dependency(%q<rake>.freeze, ["~> 13.0.1"])
|
|
115
|
-
s.add_dependency(%q<rubocop>.freeze, ["~>
|
|
126
|
+
s.add_dependency(%q<rubocop>.freeze, ["~> 1.11"])
|
|
116
127
|
end
|
|
117
128
|
end
|
|
118
129
|
|
metadata
CHANGED
|
@@ -1,17 +1,17 @@
|
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
|
2
2
|
name: unipept
|
|
3
3
|
version: !ruby/object:Gem::Version
|
|
4
|
-
version: 2.
|
|
4
|
+
version: 2.2.2
|
|
5
5
|
platform: ruby
|
|
6
6
|
authors:
|
|
7
7
|
- Bart Mesuere
|
|
8
8
|
- Pieter Verschaffelt
|
|
9
9
|
- Toon Willems
|
|
10
10
|
- Tom Naessens
|
|
11
|
-
autorequire:
|
|
11
|
+
autorequire:
|
|
12
12
|
bindir: bin
|
|
13
13
|
cert_chain: []
|
|
14
|
-
date:
|
|
14
|
+
date: 2022-04-13 00:00:00.000000000 Z
|
|
15
15
|
dependencies:
|
|
16
16
|
- !ruby/object:Gem::Dependency
|
|
17
17
|
name: cri
|
|
@@ -75,14 +75,14 @@ dependencies:
|
|
|
75
75
|
requirements:
|
|
76
76
|
- - "~>"
|
|
77
77
|
- !ruby/object:Gem::Version
|
|
78
|
-
version:
|
|
78
|
+
version: '1.11'
|
|
79
79
|
type: :development
|
|
80
80
|
prerelease: false
|
|
81
81
|
version_requirements: !ruby/object:Gem::Requirement
|
|
82
82
|
requirements:
|
|
83
83
|
- - "~>"
|
|
84
84
|
- !ruby/object:Gem::Version
|
|
85
|
-
version:
|
|
85
|
+
version: '1.11'
|
|
86
86
|
description: |2
|
|
87
87
|
Command line interface to the Unipept (http://unipept.ugent.be) web services
|
|
88
88
|
(pept2lca, taxa2lca, pept2taxa, pept2prot and taxonomy) and some utility
|
|
@@ -99,9 +99,12 @@ extra_rdoc_files:
|
|
|
99
99
|
- README.md
|
|
100
100
|
files:
|
|
101
101
|
- ".document"
|
|
102
|
+
- ".github/dependabot.yml"
|
|
102
103
|
- ".github/workflows/ci.yml"
|
|
104
|
+
- ".rakeTasks"
|
|
103
105
|
- ".rubocop.yml"
|
|
104
106
|
- ".ruby-version"
|
|
107
|
+
- CITATION.cff
|
|
105
108
|
- Gemfile
|
|
106
109
|
- Gemfile.lock
|
|
107
110
|
- LICENSE.txt
|
|
@@ -129,6 +132,7 @@ files:
|
|
|
129
132
|
- lib/commands/unipept/pept2taxa.rb
|
|
130
133
|
- lib/commands/unipept/peptinfo.rb
|
|
131
134
|
- lib/commands/unipept/taxa2lca.rb
|
|
135
|
+
- lib/commands/unipept/taxa2tree.rb
|
|
132
136
|
- lib/commands/unipept/taxonomy.rb
|
|
133
137
|
- lib/commands/uniprot.rb
|
|
134
138
|
- lib/configuration.rb
|
|
@@ -137,6 +141,7 @@ files:
|
|
|
137
141
|
- lib/retryable_typhoeus.rb
|
|
138
142
|
- lib/server_message.rb
|
|
139
143
|
- lib/version.rb
|
|
144
|
+
- test.taxa
|
|
140
145
|
- test/commands/test_peptfilter.rb
|
|
141
146
|
- test/commands/test_prot2pept.rb
|
|
142
147
|
- test/commands/test_unipept.rb
|
|
@@ -152,8 +157,20 @@ files:
|
|
|
152
157
|
- test/commands/unipept/test_pept2taxa.rb
|
|
153
158
|
- test/commands/unipept/test_peptinfo.rb
|
|
154
159
|
- test/commands/unipept/test_taxa2lca.rb
|
|
160
|
+
- test/commands/unipept/test_taxa2tree.rb
|
|
155
161
|
- test/commands/unipept/test_taxonomy.rb
|
|
156
162
|
- test/helper.rb
|
|
163
|
+
- test/support/api_stub.rb
|
|
164
|
+
- test/support/resources/pept2ec.json
|
|
165
|
+
- test/support/resources/pept2funct.json
|
|
166
|
+
- test/support/resources/pept2go.json
|
|
167
|
+
- test/support/resources/pept2interpro.json
|
|
168
|
+
- test/support/resources/pept2lca.json
|
|
169
|
+
- test/support/resources/pept2prot.json
|
|
170
|
+
- test/support/resources/pept2taxa.json
|
|
171
|
+
- test/support/resources/peptinfo.json
|
|
172
|
+
- test/support/resources/taxa2tree.json
|
|
173
|
+
- test/support/resources/taxonomy.json
|
|
157
174
|
- test/test_batch_iterator.rb
|
|
158
175
|
- test/test_batch_order.rb
|
|
159
176
|
- test/test_configuration.rb
|
|
@@ -166,7 +183,7 @@ homepage: http://unipept.ugent.be
|
|
|
166
183
|
licenses:
|
|
167
184
|
- MIT
|
|
168
185
|
metadata: {}
|
|
169
|
-
post_install_message:
|
|
186
|
+
post_install_message:
|
|
170
187
|
rdoc_options: []
|
|
171
188
|
require_paths:
|
|
172
189
|
- lib
|
|
@@ -174,15 +191,15 @@ required_ruby_version: !ruby/object:Gem::Requirement
|
|
|
174
191
|
requirements:
|
|
175
192
|
- - ">="
|
|
176
193
|
- !ruby/object:Gem::Version
|
|
177
|
-
version: 2.
|
|
194
|
+
version: 2.6.0
|
|
178
195
|
required_rubygems_version: !ruby/object:Gem::Requirement
|
|
179
196
|
requirements:
|
|
180
197
|
- - ">="
|
|
181
198
|
- !ruby/object:Gem::Version
|
|
182
199
|
version: '0'
|
|
183
200
|
requirements: []
|
|
184
|
-
rubygems_version: 3.
|
|
185
|
-
signing_key:
|
|
201
|
+
rubygems_version: 3.1.4
|
|
202
|
+
signing_key:
|
|
186
203
|
specification_version: 4
|
|
187
204
|
summary: Command line interface to Unipept web services.
|
|
188
205
|
test_files: []
|