dwc-archive 0.9.10 → 1.1.2

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.
Files changed (60) hide show
  1. checksums.yaml +5 -5
  2. data/.gitignore +1 -0
  3. data/.rspec +2 -1
  4. data/.rubocop.yml +23 -0
  5. data/.ruby-version +1 -1
  6. data/.travis.yml +4 -7
  7. data/CHANGELOG +14 -8
  8. data/Gemfile +3 -1
  9. data/LICENSE +1 -1
  10. data/README.md +119 -107
  11. data/Rakefile +13 -36
  12. data/dwc-archive.gemspec +23 -19
  13. data/features/step_definitions/dwc-creator_steps.rb +5 -5
  14. data/features/step_definitions/dwc-reader_steps.rb +47 -28
  15. data/features/support/env.rb +1 -1
  16. data/lib/dwc_archive.rb +124 -0
  17. data/lib/dwc_archive/archive.rb +60 -0
  18. data/lib/dwc_archive/classification_normalizer.rb +382 -0
  19. data/lib/dwc_archive/core.rb +25 -0
  20. data/lib/{dwc-archive → dwc_archive}/errors.rb +10 -0
  21. data/lib/dwc_archive/expander.rb +88 -0
  22. data/lib/{dwc-archive → dwc_archive}/extension.rb +5 -3
  23. data/lib/dwc_archive/generator.rb +91 -0
  24. data/lib/dwc_archive/generator_eml_xml.rb +116 -0
  25. data/lib/dwc_archive/generator_meta_xml.rb +72 -0
  26. data/lib/dwc_archive/gnub_taxon.rb +14 -0
  27. data/lib/dwc_archive/ingester.rb +106 -0
  28. data/lib/dwc_archive/metadata.rb +57 -0
  29. data/lib/dwc_archive/taxon_normalized.rb +23 -0
  30. data/lib/dwc_archive/version.rb +6 -0
  31. data/lib/dwc_archive/xml_reader.rb +90 -0
  32. data/spec/files/file with characters(3).gz b/data/spec/files/file with → characters(3).tar.gz +0 -0
  33. data/spec/files/generator_eml.xml +47 -0
  34. data/spec/files/generator_meta.xml +19 -0
  35. data/spec/lib/classification_normalizer_spec.rb +96 -105
  36. data/spec/lib/core_spec.rb +43 -41
  37. data/spec/lib/darwin_core_spec.rb +108 -138
  38. data/spec/lib/generator_eml_xml_spec.rb +12 -11
  39. data/spec/lib/generator_meta_xml_spec.rb +12 -11
  40. data/spec/lib/generator_spec.rb +77 -69
  41. data/spec/lib/gnub_taxon_spec.rb +15 -17
  42. data/spec/lib/metadata_spec.rb +50 -41
  43. data/spec/lib/taxon_normalized_spec.rb +62 -65
  44. data/spec/lib/xml_reader_spec.rb +9 -12
  45. data/spec/spec_helper.rb +54 -51
  46. metadata +105 -88
  47. data/.rvmrc +0 -1
  48. data/] +0 -40
  49. data/lib/dwc-archive.rb +0 -107
  50. data/lib/dwc-archive/archive.rb +0 -40
  51. data/lib/dwc-archive/classification_normalizer.rb +0 -428
  52. data/lib/dwc-archive/core.rb +0 -17
  53. data/lib/dwc-archive/expander.rb +0 -84
  54. data/lib/dwc-archive/generator.rb +0 -85
  55. data/lib/dwc-archive/generator_eml_xml.rb +0 -86
  56. data/lib/dwc-archive/generator_meta_xml.rb +0 -58
  57. data/lib/dwc-archive/ingester.rb +0 -101
  58. data/lib/dwc-archive/metadata.rb +0 -48
  59. data/lib/dwc-archive/version.rb +0 -3
  60. data/lib/dwc-archive/xml_reader.rb +0 -64
data/spec/lib/xml_reader_spec.rb CHANGED
@@ -1,18 +1,15 @@
1
- require_relative '../spec_helper'
1
+ # frozen_string_literal: true
2
2
 
3
- describe DarwinCore::XmlReader do
4
-
5
- describe '.from_xml' do
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
- file = File.expand_path('../../files/meta.xml', __FILE__)
9
- meta = subject.from_xml(File.read(file))
10
- expect(meta.is_a? Hash).to be_true
11
- expect(meta[:archive].keys.sort).to eq [:core, :extension]
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
- # encoding: utf-8
2
- # HACK: to suppress warnings
3
- $VERBOSE = nil
1
+ # frozen_string_literal: true
4
2
 
5
- require 'coveralls'
6
- Coveralls.wear!
3
+ require "dwc_archive"
4
+ require "rspec"
5
+ require "rspec/mocks"
6
+ require "socket"
7
7
 
8
- require 'dwc-archive'
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
- id: '1234',
19
- license: 'http://creativecommons.org/licenses/by-sa/3.0/',
20
- title: 'Test Classification',
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: 'John',
23
- last_name: 'Doe',
24
- email: 'jdoe@example.com',
25
- organization: 'Example',
26
- position: 'Assistant Professor',
27
- url: 'http://example.org' },
28
- { first_name: 'Jane',
29
- last_name: 'Doe',
30
- email: 'jane@example.com' }
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: 'Jim',
34
- last_name: 'Doe',
35
- email: 'jimdoe@example.com',
36
- url: 'http://aggregator.example.org' }],
37
- abstract: 'test classification',
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
- 'Test classification: Doe John, Doe Jane, Taxnonmy, 10, 1, 2010',
40
- url: 'http://example.com'
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
- {fields: [
45
- 'http://rs.tdwg.org/dwc/terms/TaxonID',
46
- 'http://rs.tdwg.org/dwc/terms/vernacularName'],
47
- ignoreHeaderLines: 1,
48
- location: 'vern.csv',
49
- rowType: 'http://rs.gbif.org/terms/1.0/VernacularName'}],
50
- core: {
51
- fields: [
52
- 'http://rs.tdwg.org/dwc/terms/taxonID',
53
- 'http://rs.tdwg.org/dwc/terms/parentNameUsageID',
54
- 'http://rs.tdwg.org/dwc/terms/scientificName',
55
- 'http://rs.tdwg.org/dwc/terms/taxonRank'],
56
- ignoreHeaderLines: 1,
57
- location: 'core.csv'}}
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
- "http://rs.tdwg.org/dwc/terms/vernacularName"],
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
@@ -1,205 +1,221 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: dwc-archive
3
3
  version: !ruby/object:Gem::Version
4
- version: 0.9.10
4
+ version: 1.1.2
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: 2013-12-27 00:00:00.000000000 Z
11
+ date: 2021-01-19 00:00:00.000000000 Z
12
12
  dependencies:
13
13
  - !ruby/object:Gem::Dependency
14
- name: nokogiri
14
+ name: biodiversity
15
15
  requirement: !ruby/object:Gem::Requirement
16
16
  requirements:
17
- - - ~>
17
+ - - "~>"
18
18
  - !ruby/object:Gem::Version
19
- version: '1.6'
19
+ version: '5'
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: '1.6'
26
+ version: '5'
27
27
  - !ruby/object:Gem::Dependency
28
- name: parsley-store
28
+ name: nokogiri
29
29
  requirement: !ruby/object:Gem::Requirement
30
30
  requirements:
31
- - - ~>
31
+ - - "~>"
32
32
  - !ruby/object:Gem::Version
33
- version: '0.3'
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: '0.3'
40
+ version: '1.11'
41
41
  - !ruby/object:Gem::Dependency
42
- name: archive-tar-minitar
42
+ name: bundler
43
43
  requirement: !ruby/object:Gem::Requirement
44
44
  requirements:
45
- - - ~>
45
+ - - "~>"
46
46
  - !ruby/object:Gem::Version
47
- version: '0.5'
48
- type: :runtime
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: '0.5'
54
+ version: '2.2'
55
55
  - !ruby/object:Gem::Dependency
56
- name: rake
56
+ name: byebug
57
57
  requirement: !ruby/object:Gem::Requirement
58
58
  requirements:
59
- - - ~>
59
+ - - "~>"
60
60
  - !ruby/object:Gem::Version
61
- version: '10.1'
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: '10.1'
68
+ version: '11.1'
69
69
  - !ruby/object:Gem::Dependency
70
- name: bundler
70
+ name: cucumber
71
71
  requirement: !ruby/object:Gem::Requirement
72
72
  requirements:
73
- - - ~>
73
+ - - "~>"
74
74
  - !ruby/object:Gem::Version
75
- version: '1.3'
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: '1.3'
82
+ version: '5'
83
83
  - !ruby/object:Gem::Dependency
84
- name: rspec
84
+ name: git
85
85
  requirement: !ruby/object:Gem::Requirement
86
86
  requirements:
87
- - - ~>
87
+ - - "~>"
88
88
  - !ruby/object:Gem::Version
89
- version: '2.14'
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: '2.14'
96
+ version: '1.8'
97
97
  - !ruby/object:Gem::Dependency
98
- name: cucumber
98
+ name: rake
99
99
  requirement: !ruby/object:Gem::Requirement
100
100
  requirements:
101
- - - ~>
101
+ - - "~>"
102
102
  - !ruby/object:Gem::Version
103
- version: '1.3'
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: '1.3'
110
+ version: '13'
111
111
  - !ruby/object:Gem::Dependency
112
- name: coveralls
112
+ name: rspec
113
113
  requirement: !ruby/object:Gem::Requirement
114
114
  requirements:
115
- - - ~>
115
+ - - "~>"
116
116
  - !ruby/object:Gem::Version
117
- version: '0.7'
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: '0.7'
124
+ version: '3.10'
125
125
  - !ruby/object:Gem::Dependency
126
- name: debugger
126
+ name: rubocop
127
127
  requirement: !ruby/object:Gem::Requirement
128
128
  requirements:
129
- - - ~>
129
+ - - "~>"
130
130
  - !ruby/object:Gem::Version
131
- version: '1.6'
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: '1.6'
138
+ version: '1.8'
139
139
  - !ruby/object:Gem::Dependency
140
- name: git
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: '1.2'
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: '1.2'
153
- description: "Darwin Core Archive is the current standard exchange \n format
154
- for GLobal Names Architecture modules. \n This gem makes
155
- it easy to incorporate files in \n Darwin Core Archive
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
- - .ruby-version
167
- - .rvmrc
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
172
185
  - README.md
173
186
  - Rakefile
174
- - ']'
175
187
  - dwc-archive.gemspec
176
188
  - features/dwca-creator.feature
177
189
  - features/dwca-reader.feature
178
190
  - features/step_definitions/dwc-creator_steps.rb
179
191
  - features/step_definitions/dwc-reader_steps.rb
180
192
  - features/support/env.rb
181
- - lib/dwc-archive.rb
182
- - lib/dwc-archive/archive.rb
183
- - lib/dwc-archive/classification_normalizer.rb
184
- - lib/dwc-archive/core.rb
185
- - lib/dwc-archive/errors.rb
186
- - lib/dwc-archive/expander.rb
187
- - lib/dwc-archive/extension.rb
188
- - lib/dwc-archive/generator.rb
189
- - lib/dwc-archive/generator_eml_xml.rb
190
- - lib/dwc-archive/generator_meta_xml.rb
191
- - lib/dwc-archive/ingester.rb
192
- - lib/dwc-archive/metadata.rb
193
- - lib/dwc-archive/version.rb
194
- - lib/dwc-archive/xml_reader.rb
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
195
209
  - spec/files/broken.tar.gz
196
210
  - spec/files/data.tar.gz
197
211
  - spec/files/data.zip
198
212
  - spec/files/data_with_quotes.tar.gz
199
213
  - spec/files/eml.xml
200
214
  - spec/files/empty_coreid.tar.gz
201
- - spec/files/file with characters(3).gz
215
+ - spec/files/file with characters(3).tar.gz
202
216
  - spec/files/flat_list.tar.gz
217
+ - spec/files/generator_eml.xml
218
+ - spec/files/generator_meta.xml
203
219
  - spec/files/gnub.tar.gz
204
220
  - spec/files/invalid.tar.gz
205
221
  - spec/files/junk_dir_inside.zip
@@ -229,24 +245,23 @@ homepage: http://github.com/GlobalNamesArchitecture/dwc-archive
229
245
  licenses:
230
246
  - MIT
231
247
  metadata: {}
232
- post_install_message:
248
+ post_install_message:
233
249
  rdoc_options: []
234
250
  require_paths:
235
251
  - lib
236
252
  required_ruby_version: !ruby/object:Gem::Requirement
237
253
  requirements:
238
- - - '>='
254
+ - - ">="
239
255
  - !ruby/object:Gem::Version
240
- version: '0'
256
+ version: 2.6.0
241
257
  required_rubygems_version: !ruby/object:Gem::Requirement
242
258
  requirements:
243
- - - '>='
259
+ - - ">="
244
260
  - !ruby/object:Gem::Version
245
261
  version: '0'
246
262
  requirements: []
247
- rubyforge_project:
248
- rubygems_version: 2.0.14
249
- signing_key:
263
+ rubygems_version: 3.2.6
264
+ signing_key:
250
265
  specification_version: 4
251
266
  summary: Handler of Darwin Core Archive files
252
267
  test_files:
@@ -261,8 +276,10 @@ test_files:
261
276
  - spec/files/data_with_quotes.tar.gz
262
277
  - spec/files/eml.xml
263
278
  - spec/files/empty_coreid.tar.gz
264
- - spec/files/file with characters(3).gz
279
+ - spec/files/file with characters(3).tar.gz
265
280
  - spec/files/flat_list.tar.gz
281
+ - spec/files/generator_eml.xml
282
+ - spec/files/generator_meta.xml
266
283
  - spec/files/gnub.tar.gz
267
284
  - spec/files/invalid.tar.gz
268
285
  - spec/files/junk_dir_inside.zip