dwc-archive 0.9.11 → 1.1.3
Sign up to get free protection for your applications and to get access to all the features.
- checksums.yaml +5 -5
- data/.gitignore +1 -0
- data/.rspec +2 -1
- data/.rubocop.yml +23 -0
- data/.ruby-version +1 -1
- data/.travis.yml +4 -7
- data/CHANGELOG +4 -0
- data/Gemfile +3 -1
- data/LICENSE +1 -1
- data/README.md +114 -109
- data/Rakefile +13 -36
- data/dwc-archive.gemspec +23 -19
- data/features/step_definitions/dwc-creator_steps.rb +5 -5
- data/features/step_definitions/dwc-reader_steps.rb +47 -28
- data/features/support/env.rb +1 -1
- data/lib/dwc_archive.rb +124 -0
- data/lib/dwc_archive/archive.rb +60 -0
- data/lib/dwc_archive/classification_normalizer.rb +382 -0
- data/lib/dwc_archive/core.rb +25 -0
- data/lib/{dwc-archive → dwc_archive}/errors.rb +10 -0
- data/lib/dwc_archive/expander.rb +88 -0
- data/lib/{dwc-archive → dwc_archive}/extension.rb +5 -3
- data/lib/dwc_archive/generator.rb +91 -0
- data/lib/{dwc-archive → dwc_archive}/generator_eml_xml.rb +40 -33
- data/lib/{dwc-archive → dwc_archive}/generator_meta_xml.rb +21 -20
- data/lib/dwc_archive/gnub_taxon.rb +14 -0
- data/lib/dwc_archive/ingester.rb +106 -0
- data/lib/dwc_archive/metadata.rb +57 -0
- data/lib/dwc_archive/taxon_normalized.rb +23 -0
- data/lib/dwc_archive/version.rb +6 -0
- data/lib/dwc_archive/xml_reader.rb +90 -0
- data/spec/files/file with characters(3).gz b/data/spec/files/file with → characters(3).tar.gz +0 -0
- data/spec/files/generator_eml.xml +1 -1
- data/spec/lib/classification_normalizer_spec.rb +96 -105
- data/spec/lib/core_spec.rb +43 -41
- data/spec/lib/darwin_core_spec.rb +108 -138
- data/spec/lib/generator_eml_xml_spec.rb +12 -11
- data/spec/lib/generator_meta_xml_spec.rb +12 -11
- data/spec/lib/generator_spec.rb +73 -74
- data/spec/lib/gnub_taxon_spec.rb +15 -17
- data/spec/lib/metadata_spec.rb +50 -41
- data/spec/lib/taxon_normalized_spec.rb +62 -65
- data/spec/lib/xml_reader_spec.rb +9 -12
- data/spec/spec_helper.rb +54 -51
- metadata +101 -87
- data/.rvmrc +0 -1
- data/lib/dwc-archive.rb +0 -107
- data/lib/dwc-archive/archive.rb +0 -40
- data/lib/dwc-archive/classification_normalizer.rb +0 -427
- data/lib/dwc-archive/core.rb +0 -19
- data/lib/dwc-archive/expander.rb +0 -85
- data/lib/dwc-archive/generator.rb +0 -86
- data/lib/dwc-archive/ingester.rb +0 -101
- data/lib/dwc-archive/metadata.rb +0 -48
- data/lib/dwc-archive/version.rb +0 -3
- data/lib/dwc-archive/xml_reader.rb +0 -80
data/spec/lib/xml_reader_spec.rb
CHANGED
@@ -1,18 +1,15 @@
|
|
1
|
-
|
1
|
+
# frozen_string_literal: true
|
2
2
|
|
3
|
-
describe DarwinCore::XmlReader do
|
4
|
-
|
5
|
-
|
3
|
+
describe DarwinCore::XmlReader do
|
4
|
+
describe ".from_xml" do
|
5
|
+
let(:file) { File.expand_path("../files/meta.xml", __dir__) }
|
6
|
+
subject { DarwinCore::XmlReader.from_xml(File.read(file)) }
|
6
7
|
|
7
8
|
it "reads xml to hash" do
|
8
|
-
|
9
|
-
|
10
|
-
expect(
|
11
|
-
|
12
|
-
expect(meta[:archive][:core].keys.sort).
|
13
|
-
to eq [:attributes, :field, :files, :id]
|
9
|
+
expect(subject).to be_kind_of Hash
|
10
|
+
expect(subject[:archive].keys.sort).to eq %i[core extension]
|
11
|
+
expect(subject[:archive][:core].keys.sort).
|
12
|
+
to eq %i[attributes field files id]
|
14
13
|
end
|
15
|
-
|
16
14
|
end
|
17
|
-
|
18
15
|
end
|
data/spec/spec_helper.rb
CHANGED
@@ -1,60 +1,63 @@
|
|
1
|
-
#
|
2
|
-
# HACK: to suppress warnings
|
3
|
-
$VERBOSE = nil
|
1
|
+
# frozen_string_literal: true
|
4
2
|
|
5
|
-
require
|
6
|
-
|
3
|
+
require "dwc_archive"
|
4
|
+
require "rspec"
|
5
|
+
require "rspec/mocks"
|
6
|
+
require "socket"
|
7
7
|
|
8
|
-
|
9
|
-
require 'rspec'
|
10
|
-
require 'rspec/mocks'
|
11
|
-
require 'socket'
|
12
|
-
|
13
|
-
RSpec.configure do |config|
|
8
|
+
RSpec.configure do
|
14
9
|
end
|
15
10
|
|
16
11
|
unless defined?(SPEC_CONSTANTS)
|
17
|
-
EML_DATA =
|
18
|
-
|
19
|
-
|
20
|
-
|
12
|
+
EML_DATA =
|
13
|
+
{
|
14
|
+
id: "1234",
|
15
|
+
license: "http://creativecommons.org/licenses/by-sa/3.0/",
|
16
|
+
title: "Test Classification",
|
21
17
|
authors: [
|
22
|
-
{ first_name:
|
23
|
-
last_name:
|
24
|
-
email:
|
25
|
-
organization:
|
26
|
-
position:
|
27
|
-
url:
|
28
|
-
|
29
|
-
|
30
|
-
|
31
|
-
|
18
|
+
{ first_name: "John",
|
19
|
+
last_name: "Doe",
|
20
|
+
email: "jdoe@example.com",
|
21
|
+
organization: "Example",
|
22
|
+
position: "Assistant Professor",
|
23
|
+
url: "http://example.org" },
|
24
|
+
{ first_name: "Jane",
|
25
|
+
last_name: "Doe",
|
26
|
+
email: "jane@example.com" }
|
27
|
+
],
|
32
28
|
metadata_providers: [
|
33
|
-
{ first_name:
|
34
|
-
last_name:
|
35
|
-
email:
|
36
|
-
url:
|
37
|
-
|
29
|
+
{ first_name: "Jim",
|
30
|
+
last_name: "Doe",
|
31
|
+
email: "jimdoe@example.com",
|
32
|
+
url: "http://aggregator.example.org" }
|
33
|
+
],
|
34
|
+
abstract: "test classification",
|
38
35
|
citation:
|
39
|
-
|
40
|
-
url:
|
41
|
-
}
|
36
|
+
"Test classification: Doe John, Doe Jane, Taxnonmy, 10, 1, 2010",
|
37
|
+
url: "http://example.com"
|
38
|
+
}.freeze
|
42
39
|
META_DATA = {
|
43
|
-
extensions:
|
44
|
-
|
45
|
-
|
46
|
-
|
47
|
-
|
48
|
-
|
49
|
-
|
50
|
-
|
51
|
-
|
52
|
-
|
53
|
-
|
54
|
-
|
55
|
-
|
56
|
-
|
57
|
-
|
40
|
+
extensions:
|
41
|
+
[
|
42
|
+
{ fields:
|
43
|
+
[
|
44
|
+
"http://rs.tdwg.org/dwc/terms/TaxonID",
|
45
|
+
"http://rs.tdwg.org/dwc/terms/vernacularName"
|
46
|
+
],
|
47
|
+
ignoreHeaderLines: 1,
|
48
|
+
location: "vern.csv",
|
49
|
+
rowType: "http://rs.gbif.org/terms/1.0/VernacularName" }
|
50
|
+
],
|
51
|
+
core: { fields:
|
52
|
+
[
|
53
|
+
"http://rs.tdwg.org/dwc/terms/taxonID",
|
54
|
+
"http://rs.tdwg.org/dwc/terms/parentNameUsageID",
|
55
|
+
"http://rs.tdwg.org/dwc/terms/scientificName",
|
56
|
+
"http://rs.tdwg.org/dwc/terms/taxonRank"
|
57
|
+
],
|
58
|
+
ignoreHeaderLines: 1,
|
59
|
+
location: "core.csv" }
|
60
|
+
}.freeze
|
58
61
|
CORE_DATA = [
|
59
62
|
["http://rs.tdwg.org/dwc/terms/taxonID",
|
60
63
|
"http://rs.tdwg.org/dwc/terms/parentNameUsageID",
|
@@ -63,16 +66,16 @@ unless defined?(SPEC_CONSTANTS)
|
|
63
66
|
[1, 0, "Plantae", "kingdom"],
|
64
67
|
[2, 1, "Betula", "genus"],
|
65
68
|
[3, 2, "Betula verucosa", "species"]
|
66
|
-
]
|
69
|
+
].freeze
|
67
70
|
EXTENSION_DATA = [
|
68
71
|
["http://rs.tdwg.org/dwc/terms/TaxonID",
|
69
|
-
|
72
|
+
"http://rs.tdwg.org/dwc/terms/vernacularName"],
|
70
73
|
[1, "Plants"],
|
71
74
|
[1, "Растения"],
|
72
75
|
[2, "Birch"],
|
73
76
|
[2, "Береза"],
|
74
77
|
[3, "Wheeping Birch"],
|
75
78
|
[3, "Береза плакучая"]
|
76
|
-
]
|
79
|
+
].freeze
|
77
80
|
SPEC_CONSTANTS = true
|
78
81
|
end
|
metadata
CHANGED
@@ -1,171 +1,184 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: dwc-archive
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version:
|
4
|
+
version: 1.1.3
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Dmitry Mozzherin
|
8
|
-
autorequire:
|
8
|
+
autorequire:
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
|
-
date:
|
11
|
+
date: 2021-01-22 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
|
-
name:
|
14
|
+
name: biodiversity
|
15
15
|
requirement: !ruby/object:Gem::Requirement
|
16
16
|
requirements:
|
17
|
-
- - ~>
|
17
|
+
- - "~>"
|
18
18
|
- !ruby/object:Gem::Version
|
19
|
-
version:
|
19
|
+
version: 5.1.2
|
20
20
|
type: :runtime
|
21
21
|
prerelease: false
|
22
22
|
version_requirements: !ruby/object:Gem::Requirement
|
23
23
|
requirements:
|
24
|
-
- - ~>
|
24
|
+
- - "~>"
|
25
25
|
- !ruby/object:Gem::Version
|
26
|
-
version:
|
26
|
+
version: 5.1.2
|
27
27
|
- !ruby/object:Gem::Dependency
|
28
|
-
name:
|
28
|
+
name: nokogiri
|
29
29
|
requirement: !ruby/object:Gem::Requirement
|
30
30
|
requirements:
|
31
|
-
- - ~>
|
31
|
+
- - "~>"
|
32
32
|
- !ruby/object:Gem::Version
|
33
|
-
version: '
|
33
|
+
version: '1.11'
|
34
34
|
type: :runtime
|
35
35
|
prerelease: false
|
36
36
|
version_requirements: !ruby/object:Gem::Requirement
|
37
37
|
requirements:
|
38
|
-
- - ~>
|
38
|
+
- - "~>"
|
39
39
|
- !ruby/object:Gem::Version
|
40
|
-
version: '
|
40
|
+
version: '1.11'
|
41
41
|
- !ruby/object:Gem::Dependency
|
42
|
-
name:
|
42
|
+
name: bundler
|
43
43
|
requirement: !ruby/object:Gem::Requirement
|
44
44
|
requirements:
|
45
|
-
- - ~>
|
45
|
+
- - "~>"
|
46
46
|
- !ruby/object:Gem::Version
|
47
|
-
version: '
|
48
|
-
type: :
|
47
|
+
version: '2.2'
|
48
|
+
type: :development
|
49
49
|
prerelease: false
|
50
50
|
version_requirements: !ruby/object:Gem::Requirement
|
51
51
|
requirements:
|
52
|
-
- - ~>
|
52
|
+
- - "~>"
|
53
53
|
- !ruby/object:Gem::Version
|
54
|
-
version: '
|
54
|
+
version: '2.2'
|
55
55
|
- !ruby/object:Gem::Dependency
|
56
|
-
name:
|
56
|
+
name: byebug
|
57
57
|
requirement: !ruby/object:Gem::Requirement
|
58
58
|
requirements:
|
59
|
-
- - ~>
|
59
|
+
- - "~>"
|
60
60
|
- !ruby/object:Gem::Version
|
61
|
-
version: '
|
61
|
+
version: '11.1'
|
62
62
|
type: :development
|
63
63
|
prerelease: false
|
64
64
|
version_requirements: !ruby/object:Gem::Requirement
|
65
65
|
requirements:
|
66
|
-
- - ~>
|
66
|
+
- - "~>"
|
67
67
|
- !ruby/object:Gem::Version
|
68
|
-
version: '
|
68
|
+
version: '11.1'
|
69
69
|
- !ruby/object:Gem::Dependency
|
70
|
-
name:
|
70
|
+
name: cucumber
|
71
71
|
requirement: !ruby/object:Gem::Requirement
|
72
72
|
requirements:
|
73
|
-
- - ~>
|
73
|
+
- - "~>"
|
74
74
|
- !ruby/object:Gem::Version
|
75
|
-
version: '
|
75
|
+
version: '5'
|
76
76
|
type: :development
|
77
77
|
prerelease: false
|
78
78
|
version_requirements: !ruby/object:Gem::Requirement
|
79
79
|
requirements:
|
80
|
-
- - ~>
|
80
|
+
- - "~>"
|
81
81
|
- !ruby/object:Gem::Version
|
82
|
-
version: '
|
82
|
+
version: '5'
|
83
83
|
- !ruby/object:Gem::Dependency
|
84
|
-
name:
|
84
|
+
name: git
|
85
85
|
requirement: !ruby/object:Gem::Requirement
|
86
86
|
requirements:
|
87
|
-
- - ~>
|
87
|
+
- - "~>"
|
88
88
|
- !ruby/object:Gem::Version
|
89
|
-
version: '
|
89
|
+
version: '1.8'
|
90
90
|
type: :development
|
91
91
|
prerelease: false
|
92
92
|
version_requirements: !ruby/object:Gem::Requirement
|
93
93
|
requirements:
|
94
|
-
- - ~>
|
94
|
+
- - "~>"
|
95
95
|
- !ruby/object:Gem::Version
|
96
|
-
version: '
|
96
|
+
version: '1.8'
|
97
97
|
- !ruby/object:Gem::Dependency
|
98
|
-
name:
|
98
|
+
name: rake
|
99
99
|
requirement: !ruby/object:Gem::Requirement
|
100
100
|
requirements:
|
101
|
-
- - ~>
|
101
|
+
- - "~>"
|
102
102
|
- !ruby/object:Gem::Version
|
103
|
-
version: '
|
103
|
+
version: '13'
|
104
104
|
type: :development
|
105
105
|
prerelease: false
|
106
106
|
version_requirements: !ruby/object:Gem::Requirement
|
107
107
|
requirements:
|
108
|
-
- - ~>
|
108
|
+
- - "~>"
|
109
109
|
- !ruby/object:Gem::Version
|
110
|
-
version: '
|
110
|
+
version: '13'
|
111
111
|
- !ruby/object:Gem::Dependency
|
112
|
-
name:
|
112
|
+
name: rspec
|
113
113
|
requirement: !ruby/object:Gem::Requirement
|
114
114
|
requirements:
|
115
|
-
- - ~>
|
115
|
+
- - "~>"
|
116
116
|
- !ruby/object:Gem::Version
|
117
|
-
version: '
|
117
|
+
version: '3.10'
|
118
118
|
type: :development
|
119
119
|
prerelease: false
|
120
120
|
version_requirements: !ruby/object:Gem::Requirement
|
121
121
|
requirements:
|
122
|
-
- - ~>
|
122
|
+
- - "~>"
|
123
123
|
- !ruby/object:Gem::Version
|
124
|
-
version: '
|
124
|
+
version: '3.10'
|
125
125
|
- !ruby/object:Gem::Dependency
|
126
|
-
name:
|
126
|
+
name: rubocop
|
127
127
|
requirement: !ruby/object:Gem::Requirement
|
128
128
|
requirements:
|
129
|
-
- - ~>
|
129
|
+
- - "~>"
|
130
130
|
- !ruby/object:Gem::Version
|
131
|
-
version: '1.
|
131
|
+
version: '1.8'
|
132
132
|
type: :development
|
133
133
|
prerelease: false
|
134
134
|
version_requirements: !ruby/object:Gem::Requirement
|
135
135
|
requirements:
|
136
|
-
- - ~>
|
136
|
+
- - "~>"
|
137
137
|
- !ruby/object:Gem::Version
|
138
|
-
version: '1.
|
138
|
+
version: '1.8'
|
139
139
|
- !ruby/object:Gem::Dependency
|
140
|
-
name:
|
140
|
+
name: solargraph
|
141
|
+
requirement: !ruby/object:Gem::Requirement
|
142
|
+
requirements:
|
143
|
+
- - "~>"
|
144
|
+
- !ruby/object:Gem::Version
|
145
|
+
version: '0.40'
|
146
|
+
type: :development
|
147
|
+
prerelease: false
|
148
|
+
version_requirements: !ruby/object:Gem::Requirement
|
149
|
+
requirements:
|
150
|
+
- - "~>"
|
151
|
+
- !ruby/object:Gem::Version
|
152
|
+
version: '0.40'
|
153
|
+
- !ruby/object:Gem::Dependency
|
154
|
+
name: travis
|
141
155
|
requirement: !ruby/object:Gem::Requirement
|
142
156
|
requirements:
|
143
|
-
- - ~>
|
157
|
+
- - "~>"
|
144
158
|
- !ruby/object:Gem::Version
|
145
|
-
version: '1.
|
159
|
+
version: '1.10'
|
146
160
|
type: :development
|
147
161
|
prerelease: false
|
148
162
|
version_requirements: !ruby/object:Gem::Requirement
|
149
163
|
requirements:
|
150
|
-
- - ~>
|
164
|
+
- - "~>"
|
151
165
|
- !ruby/object:Gem::Version
|
152
|
-
version: '1.
|
153
|
-
description:
|
154
|
-
|
155
|
-
|
156
|
-
format into a ruby project."
|
166
|
+
version: '1.10'
|
167
|
+
description: Darwin Core Archive is the current standard exchange format for GLobal
|
168
|
+
Names Architecture modules. This gem makes it easy to incorporate files in Darwin
|
169
|
+
Core Archive format into a ruby project.
|
157
170
|
email:
|
158
171
|
- dmozzherin at gmail dot com
|
159
172
|
executables: []
|
160
173
|
extensions: []
|
161
174
|
extra_rdoc_files: []
|
162
175
|
files:
|
163
|
-
- .document
|
164
|
-
- .gitignore
|
165
|
-
- .rspec
|
166
|
-
- .
|
167
|
-
- .
|
168
|
-
- .travis.yml
|
176
|
+
- ".document"
|
177
|
+
- ".gitignore"
|
178
|
+
- ".rspec"
|
179
|
+
- ".rubocop.yml"
|
180
|
+
- ".ruby-version"
|
181
|
+
- ".travis.yml"
|
169
182
|
- CHANGELOG
|
170
183
|
- Gemfile
|
171
184
|
- LICENSE
|
@@ -177,27 +190,29 @@ files:
|
|
177
190
|
- features/step_definitions/dwc-creator_steps.rb
|
178
191
|
- features/step_definitions/dwc-reader_steps.rb
|
179
192
|
- features/support/env.rb
|
180
|
-
- lib/
|
181
|
-
- lib/
|
182
|
-
- lib/
|
183
|
-
- lib/
|
184
|
-
- lib/
|
185
|
-
- lib/
|
186
|
-
- lib/
|
187
|
-
- lib/
|
188
|
-
- lib/
|
189
|
-
- lib/
|
190
|
-
- lib/
|
191
|
-
- lib/
|
192
|
-
- lib/
|
193
|
-
- lib/
|
193
|
+
- lib/dwc_archive.rb
|
194
|
+
- lib/dwc_archive/archive.rb
|
195
|
+
- lib/dwc_archive/classification_normalizer.rb
|
196
|
+
- lib/dwc_archive/core.rb
|
197
|
+
- lib/dwc_archive/errors.rb
|
198
|
+
- lib/dwc_archive/expander.rb
|
199
|
+
- lib/dwc_archive/extension.rb
|
200
|
+
- lib/dwc_archive/generator.rb
|
201
|
+
- lib/dwc_archive/generator_eml_xml.rb
|
202
|
+
- lib/dwc_archive/generator_meta_xml.rb
|
203
|
+
- lib/dwc_archive/gnub_taxon.rb
|
204
|
+
- lib/dwc_archive/ingester.rb
|
205
|
+
- lib/dwc_archive/metadata.rb
|
206
|
+
- lib/dwc_archive/taxon_normalized.rb
|
207
|
+
- lib/dwc_archive/version.rb
|
208
|
+
- lib/dwc_archive/xml_reader.rb
|
194
209
|
- spec/files/broken.tar.gz
|
195
210
|
- spec/files/data.tar.gz
|
196
211
|
- spec/files/data.zip
|
197
212
|
- spec/files/data_with_quotes.tar.gz
|
198
213
|
- spec/files/eml.xml
|
199
214
|
- spec/files/empty_coreid.tar.gz
|
200
|
-
- spec/files/file with characters(3).gz
|
215
|
+
- spec/files/file with characters(3).tar.gz
|
201
216
|
- spec/files/flat_list.tar.gz
|
202
217
|
- spec/files/generator_eml.xml
|
203
218
|
- spec/files/generator_meta.xml
|
@@ -230,24 +245,23 @@ homepage: http://github.com/GlobalNamesArchitecture/dwc-archive
|
|
230
245
|
licenses:
|
231
246
|
- MIT
|
232
247
|
metadata: {}
|
233
|
-
post_install_message:
|
248
|
+
post_install_message:
|
234
249
|
rdoc_options: []
|
235
250
|
require_paths:
|
236
251
|
- lib
|
237
252
|
required_ruby_version: !ruby/object:Gem::Requirement
|
238
253
|
requirements:
|
239
|
-
- -
|
254
|
+
- - ">="
|
240
255
|
- !ruby/object:Gem::Version
|
241
|
-
version:
|
256
|
+
version: 2.6.0
|
242
257
|
required_rubygems_version: !ruby/object:Gem::Requirement
|
243
258
|
requirements:
|
244
|
-
- -
|
259
|
+
- - ">="
|
245
260
|
- !ruby/object:Gem::Version
|
246
261
|
version: '0'
|
247
262
|
requirements: []
|
248
|
-
|
249
|
-
|
250
|
-
signing_key:
|
263
|
+
rubygems_version: 3.2.6
|
264
|
+
signing_key:
|
251
265
|
specification_version: 4
|
252
266
|
summary: Handler of Darwin Core Archive files
|
253
267
|
test_files:
|
@@ -262,7 +276,7 @@ test_files:
|
|
262
276
|
- spec/files/data_with_quotes.tar.gz
|
263
277
|
- spec/files/eml.xml
|
264
278
|
- spec/files/empty_coreid.tar.gz
|
265
|
-
- spec/files/file with characters(3).gz
|
279
|
+
- spec/files/file with characters(3).tar.gz
|
266
280
|
- spec/files/flat_list.tar.gz
|
267
281
|
- spec/files/generator_eml.xml
|
268
282
|
- spec/files/generator_meta.xml
|