briard 2.4.2 → 2.6.1
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- checksums.yaml +4 -4
- data/.github/workflows/codeql-analysis.yml +72 -0
- data/.github/workflows/rubocop.yml +50 -0
- data/.gitignore +1 -0
- data/.rubocop.yml +144 -620
- data/.rubocop_todo.yml +76 -0
- data/CHANGELOG.md +18 -0
- data/Gemfile +2 -0
- data/Gemfile.lock +43 -9
- data/Rakefile +1 -1
- data/{bolognese.gemspec → briard.gemspec} +46 -39
- data/lib/briard/array.rb +2 -2
- data/lib/briard/author_utils.rb +79 -71
- data/lib/briard/cli.rb +12 -13
- data/lib/briard/crossref_utils.rb +73 -61
- data/lib/briard/datacite_utils.rb +132 -106
- data/lib/briard/doi_utils.rb +10 -10
- data/lib/briard/metadata.rb +96 -106
- data/lib/briard/metadata_utils.rb +87 -78
- data/lib/briard/readers/bibtex_reader.rb +65 -65
- data/lib/briard/readers/cff_reader.rb +88 -70
- data/lib/briard/readers/citeproc_reader.rb +90 -84
- data/lib/briard/readers/codemeta_reader.rb +68 -50
- data/lib/briard/readers/crosscite_reader.rb +2 -2
- data/lib/briard/readers/crossref_reader.rb +249 -210
- data/lib/briard/readers/datacite_json_reader.rb +3 -3
- data/lib/briard/readers/datacite_reader.rb +225 -189
- data/lib/briard/readers/npm_reader.rb +49 -42
- data/lib/briard/readers/ris_reader.rb +82 -80
- data/lib/briard/readers/schema_org_reader.rb +182 -159
- data/lib/briard/string.rb +1 -1
- data/lib/briard/utils.rb +4 -4
- data/lib/briard/version.rb +3 -1
- data/lib/briard/whitelist_scrubber.rb +11 -4
- data/lib/briard/writers/bibtex_writer.rb +14 -8
- data/lib/briard/writers/cff_writer.rb +33 -26
- data/lib/briard/writers/codemeta_writer.rb +19 -15
- data/lib/briard/writers/csv_writer.rb +6 -4
- data/lib/briard/writers/datacite_json_writer.rb +8 -2
- data/lib/briard/writers/jats_writer.rb +33 -28
- data/lib/briard/writers/rdf_xml_writer.rb +1 -1
- data/lib/briard/writers/ris_writer.rb +30 -18
- data/lib/briard/writers/turtle_writer.rb +1 -1
- data/lib/briard.rb +6 -6
- data/rubocop.sarif +0 -0
- data/spec/array_spec.rb +5 -5
- data/spec/author_utils_spec.rb +151 -132
- data/spec/datacite_utils_spec.rb +135 -83
- data/spec/doi_utils_spec.rb +168 -164
- data/spec/find_from_format_spec.rb +69 -69
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/sanitize/onlies_keep_specific_tags.yml +65 -0
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/sanitize/removes_a_tags.yml +65 -0
- data/spec/metadata_spec.rb +91 -90
- data/spec/readers/bibtex_reader_spec.rb +43 -38
- data/spec/readers/cff_reader_spec.rb +165 -153
- data/spec/readers/citeproc_reader_spec.rb +45 -40
- data/spec/readers/codemeta_reader_spec.rb +128 -115
- data/spec/readers/crosscite_reader_spec.rb +34 -24
- data/spec/readers/crossref_reader_spec.rb +1098 -939
- data/spec/readers/datacite_json_reader_spec.rb +53 -40
- data/spec/readers/datacite_reader_spec.rb +1541 -1337
- data/spec/readers/npm_reader_spec.rb +48 -43
- data/spec/readers/ris_reader_spec.rb +53 -47
- data/spec/readers/schema_org_reader_spec.rb +329 -267
- data/spec/spec_helper.rb +6 -5
- data/spec/utils_spec.rb +371 -347
- data/spec/writers/bibtex_writer_spec.rb +143 -143
- data/spec/writers/cff_writer_spec.rb +96 -90
- data/spec/writers/citation_writer_spec.rb +34 -33
- data/spec/writers/citeproc_writer_spec.rb +226 -224
- data/spec/writers/codemeta_writer_spec.rb +18 -16
- data/spec/writers/crosscite_writer_spec.rb +91 -73
- data/spec/writers/crossref_writer_spec.rb +99 -91
- data/spec/writers/csv_writer_spec.rb +70 -70
- data/spec/writers/datacite_json_writer_spec.rb +78 -68
- data/spec/writers/datacite_writer_spec.rb +417 -322
- data/spec/writers/jats_writer_spec.rb +177 -161
- data/spec/writers/rdf_xml_writer_spec.rb +68 -63
- data/spec/writers/ris_writer_spec.rb +162 -162
- data/spec/writers/schema_org_writer_spec.rb +329 -294
- data/spec/writers/turtle_writer_spec.rb +47 -47
- metadata +242 -166
- data/.github/workflows/release.yml +0 -47
data/spec/datacite_utils_spec.rb
CHANGED
@@ -3,41 +3,54 @@
|
|
3
3
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require 'spec_helper'
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4
4
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5
5
|
describe Briard::Metadata, vcr: true do
|
6
|
-
|
6
|
+
subject { described_class.new(input: input, from: 'datacite') }
|
7
7
|
|
8
|
-
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8
|
+
let(:input) { 'https://doi.org/10.5061/DRYAD.8515' }
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9
9
|
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10
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-
context
|
11
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-
it
|
12
|
-
xml = Nokogiri::XML::Builder.new(:
|
10
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+
context 'insert_identifier' do
|
11
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+
it 'doi' do
|
12
|
+
xml = Nokogiri::XML::Builder.new(encoding: 'UTF-8') do |xml|
|
13
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+
subject.insert_identifier(xml)
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14
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+
end.to_xml
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13
15
|
response = Maremma.from_xml(xml)
|
14
|
-
expect(response[
|
16
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+
expect(response['identifier']).to eq('identifierType' => 'DOI',
|
17
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+
'__content__' => '10.5061/dryad.8515')
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15
18
|
end
|
16
19
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end
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17
20
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18
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-
context
|
19
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-
it
|
20
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-
xml = Nokogiri::XML::Builder.new(:
|
21
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+
context 'insert_creators' do
|
22
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+
it 'insert' do
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23
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xml = Nokogiri::XML::Builder.new(encoding: 'UTF-8') do |xml|
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24
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+
subject.insert_creators(xml)
|
25
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+
end.to_xml
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21
26
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response = Maremma.from_xml(xml)
|
22
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-
expect(response.dig(
|
27
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+
expect(response.dig('creators',
|
28
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+
'creator').first).to eq(
|
29
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+
'affiliation' => { '__content__' => 'Centre International de Recherches Médicales de Franceville',
|
30
|
+
'affiliationIdentifier' => 'https://ror.org/01wyqb997', 'affiliationIdentifierScheme' => 'ROR' }, 'creatorName' => { '__content__' => 'Ollomo, Benjamin', 'nameType' => 'Personal' }, 'familyName' => 'Ollomo', 'givenName' => 'Benjamin'
|
31
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+
)
|
23
32
|
end
|
24
33
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end
|
25
34
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26
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-
context
|
27
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-
it
|
28
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-
xml = Nokogiri::XML::Builder.new(:
|
35
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context 'insert_contributors' do
|
36
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it 'none' do
|
37
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+
xml = Nokogiri::XML::Builder.new(encoding: 'UTF-8') do |xml|
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38
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subject.insert_contributors(xml)
|
39
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+
end.to_xml
|
29
40
|
response = Maremma.from_xml(xml)
|
30
|
-
expect(response).to
|
41
|
+
expect(response.nil?).to be(true)
|
31
42
|
end
|
32
43
|
end
|
33
44
|
|
34
|
-
context
|
35
|
-
it
|
36
|
-
person = {
|
37
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-
type =
|
38
|
-
xml = Nokogiri::XML::Builder.new(:
|
45
|
+
context 'insert_person' do
|
46
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+
it 'creator only name' do
|
47
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+
person = { 'name' => 'Carberry, Josiah' }
|
48
|
+
type = 'creator'
|
49
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+
xml = Nokogiri::XML::Builder.new(encoding: 'UTF-8') do |xml|
|
50
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subject.insert_person(xml, person, type)
|
51
|
+
end.to_xml
|
39
52
|
response = Maremma.from_xml(xml)
|
40
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-
expect(response).to eq(
|
53
|
+
expect(response).to eq('creatorName' => 'Carberry, Josiah')
|
41
54
|
end
|
42
55
|
|
43
56
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# it "creator given and family name" do
|
@@ -49,35 +62,45 @@ describe Briard::Metadata, vcr: true do
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49
62
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# end
|
50
63
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end
|
51
64
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52
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-
context
|
53
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-
it
|
54
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-
xml = Nokogiri::XML::Builder.new(:
|
65
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+
context 'insert_titles' do
|
66
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+
it 'insert' do
|
67
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+
xml = Nokogiri::XML::Builder.new(encoding: 'UTF-8') do |xml|
|
68
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+
subject.insert_titles(xml)
|
69
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+
end.to_xml
|
55
70
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response = Maremma.from_xml(xml)
|
56
|
-
expect(response.dig(
|
71
|
+
expect(response.dig('titles',
|
72
|
+
'title')).to eq('Data from: A new malaria agent in African hominids.')
|
57
73
|
end
|
58
74
|
end
|
59
75
|
|
60
|
-
context
|
61
|
-
it
|
62
|
-
xml = Nokogiri::XML::Builder.new(:
|
76
|
+
context 'insert_publisher' do
|
77
|
+
it 'insert' do
|
78
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+
xml = Nokogiri::XML::Builder.new(encoding: 'UTF-8') do |xml|
|
79
|
+
subject.insert_publisher(xml)
|
80
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+
end.to_xml
|
63
81
|
response = Maremma.from_xml(xml)
|
64
|
-
expect(response[
|
82
|
+
expect(response['publisher']).to eq('Dryad')
|
65
83
|
end
|
66
84
|
end
|
67
85
|
|
68
|
-
context
|
69
|
-
it
|
70
|
-
xml = Nokogiri::XML::Builder.new(:
|
86
|
+
context 'insert_publication_year' do
|
87
|
+
it 'insert' do
|
88
|
+
xml = Nokogiri::XML::Builder.new(encoding: 'UTF-8') do |xml|
|
89
|
+
subject.insert_publication_year(xml)
|
90
|
+
end.to_xml
|
71
91
|
response = Maremma.from_xml(xml)
|
72
|
-
expect(response[
|
92
|
+
expect(response['publicationYear']).to eq('2011')
|
73
93
|
end
|
74
94
|
end
|
75
95
|
|
76
|
-
context
|
77
|
-
it
|
78
|
-
xml = Nokogiri::XML::Builder.new(:
|
96
|
+
context 'insert_resource_type' do
|
97
|
+
it 'insert' do
|
98
|
+
xml = Nokogiri::XML::Builder.new(encoding: 'UTF-8') do |xml|
|
99
|
+
subject.insert_resource_type(xml)
|
100
|
+
end.to_xml
|
79
101
|
response = Maremma.from_xml(xml)
|
80
|
-
expect(response[
|
102
|
+
expect(response['resourceType']).to eq('resourceTypeGeneral' => 'Dataset',
|
103
|
+
'__content__' => 'dataset')
|
81
104
|
end
|
82
105
|
end
|
83
106
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|
@@ -89,90 +112,119 @@ describe Briard::Metadata, vcr: true do
|
|
89
112
|
# end
|
90
113
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# end
|
91
114
|
|
92
|
-
context
|
93
|
-
it
|
94
|
-
xml = Nokogiri::XML::Builder.new(:
|
115
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+
context 'insert_dates' do
|
116
|
+
it 'insert' do
|
117
|
+
xml = Nokogiri::XML::Builder.new(encoding: 'UTF-8') do |xml|
|
118
|
+
subject.insert_dates(xml)
|
119
|
+
end.to_xml
|
95
120
|
response = Maremma.from_xml(xml)
|
96
|
-
expect(response.dig(
|
121
|
+
expect(response.dig('dates',
|
122
|
+
'date')).to eq([{ '__content__' => '2011-02-01T17:22:41Z', 'dateType' => 'Available' },
|
123
|
+
{ '__content__' => '2011', 'dateType' => 'Issued' }])
|
97
124
|
end
|
98
125
|
end
|
99
126
|
|
100
|
-
context
|
101
|
-
it
|
102
|
-
xml = Nokogiri::XML::Builder.new(:
|
127
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+
context 'insert_subjects' do
|
128
|
+
it 'insert' do
|
129
|
+
xml = Nokogiri::XML::Builder.new(encoding: 'UTF-8') do |xml|
|
130
|
+
subject.insert_subjects(xml)
|
131
|
+
end.to_xml
|
103
132
|
response = Maremma.from_xml(xml)
|
104
|
-
expect(response.dig(
|
133
|
+
expect(response.dig('subjects',
|
134
|
+
'subject')).to eq(['plasmodium', 'malaria', 'mitochondrial genome',
|
135
|
+
'parasites'])
|
105
136
|
end
|
106
137
|
end
|
107
138
|
|
108
|
-
context
|
109
|
-
it
|
110
|
-
xml = Nokogiri::XML::Builder.new(:
|
139
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+
context 'insert_version' do
|
140
|
+
it 'insert' do
|
141
|
+
xml = Nokogiri::XML::Builder.new(encoding: 'UTF-8') do |xml|
|
142
|
+
subject.insert_version(xml)
|
143
|
+
end.to_xml
|
111
144
|
response = Maremma.from_xml(xml)
|
112
|
-
expect(response.fetch(
|
145
|
+
expect(response.fetch('version', nil)).to eq('1')
|
113
146
|
end
|
114
147
|
end
|
115
148
|
|
116
|
-
context
|
117
|
-
it
|
118
|
-
xml = Nokogiri::XML::Builder.new(:
|
149
|
+
context 'insert_sizes' do
|
150
|
+
it 'insert' do
|
151
|
+
xml = Nokogiri::XML::Builder.new(encoding: 'UTF-8') do |xml|
|
152
|
+
subject.insert_sizes(xml)
|
153
|
+
end.to_xml
|
119
154
|
response = Maremma.from_xml(xml)
|
120
|
-
expect(response.fetch(
|
155
|
+
expect(response.fetch('sizes', nil)).to eq('size' => '107328 bytes')
|
121
156
|
end
|
122
157
|
end
|
123
158
|
|
124
|
-
context
|
125
|
-
|
126
|
-
|
127
|
-
subject { Briard::Metadata.new(input: input, from: "datacite") }
|
159
|
+
context 'insert_formats' do
|
160
|
+
subject { described_class.new(input: input, from: 'datacite') }
|
128
161
|
|
129
|
-
|
130
|
-
|
162
|
+
let(:input) { File.read("#{fixture_path}datacite-empty-sizes.xml") }
|
163
|
+
|
164
|
+
it 'insert' do
|
165
|
+
xml = Nokogiri::XML::Builder.new(encoding: 'UTF-8') do |xml|
|
166
|
+
subject.insert_formats(xml)
|
167
|
+
end.to_xml
|
131
168
|
response = Maremma.from_xml(xml)
|
132
|
-
expect(response.fetch(
|
169
|
+
expect(response.fetch('formats', nil)).to eq('format' => 'text')
|
133
170
|
end
|
134
171
|
end
|
135
172
|
|
136
|
-
context
|
137
|
-
it
|
138
|
-
xml = Nokogiri::XML::Builder.new(:
|
173
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+
context 'insert_language' do
|
174
|
+
it 'insert' do
|
175
|
+
xml = Nokogiri::XML::Builder.new(encoding: 'UTF-8') do |xml|
|
176
|
+
subject.insert_language(xml)
|
177
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+
end.to_xml
|
139
178
|
response = Maremma.from_xml(xml)
|
140
|
-
expect(response.fetch(
|
179
|
+
expect(response.fetch('language', nil)).to eq('en')
|
141
180
|
end
|
142
181
|
end
|
143
182
|
|
144
|
-
context
|
145
|
-
it
|
183
|
+
context 'insert_related_identifiers' do
|
184
|
+
it 'related_identifier' do
|
146
185
|
expect(subject.related_identifiers.length).to eq(1)
|
147
|
-
expect(subject.related_identifiers.first).to eq(
|
186
|
+
expect(subject.related_identifiers.first).to eq(
|
187
|
+
'relatedIdentifier' => '10.1371/journal.ppat.1000446', 'relatedIdentifierType' => 'DOI', 'relationType' => 'IsCitedBy'
|
188
|
+
)
|
148
189
|
end
|
149
190
|
|
150
|
-
it
|
151
|
-
xml = Nokogiri::XML::Builder.new(:
|
191
|
+
it 'insert' do
|
192
|
+
xml = Nokogiri::XML::Builder.new(encoding: 'UTF-8') do |xml|
|
193
|
+
subject.insert_related_identifiers(xml)
|
194
|
+
end.to_xml
|
152
195
|
response = Maremma.from_xml(xml)
|
153
|
-
expect(response.dig(
|
196
|
+
expect(response.dig('relatedIdentifiers',
|
197
|
+
'relatedIdentifier')).to eq('__content__' => '10.1371/journal.ppat.1000446',
|
198
|
+
'relatedIdentifierType' => 'DOI', 'relationType' => 'IsCitedBy')
|
154
199
|
end
|
155
200
|
end
|
156
201
|
|
157
|
-
context
|
158
|
-
it
|
159
|
-
xml = Nokogiri::XML::Builder.new(:
|
202
|
+
context 'insert_rights_list' do
|
203
|
+
it 'insert' do
|
204
|
+
xml = Nokogiri::XML::Builder.new(encoding: 'UTF-8') do |xml|
|
205
|
+
subject.insert_rights_list(xml)
|
206
|
+
end.to_xml
|
160
207
|
response = Maremma.from_xml(xml)
|
161
|
-
expect(response.dig(
|
162
|
-
|
163
|
-
|
164
|
-
|
165
|
-
|
208
|
+
expect(response.dig('rightsList',
|
209
|
+
'rights')).to eq('__content__' => 'Creative Commons Zero v1.0 Universal',
|
210
|
+
'rightsIdentifier' => 'cc0-1.0',
|
211
|
+
'rightsIdentifierScheme' => 'SPDX',
|
212
|
+
'rightsURI' => 'https://creativecommons.org/publicdomain/zero/1.0/legalcode',
|
213
|
+
'schemeURI' => 'https://spdx.org/licenses/')
|
166
214
|
end
|
167
215
|
end
|
168
216
|
|
169
|
-
context
|
170
|
-
it
|
171
|
-
input =
|
172
|
-
subject =
|
173
|
-
xml = Nokogiri::XML::Builder.new(:
|
217
|
+
context 'insert_descriptions' do
|
218
|
+
it 'insert' do
|
219
|
+
input = 'https://doi.org/10.5438/4K3M-NYVG'
|
220
|
+
subject = described_class.new(input: input, from: 'datacite')
|
221
|
+
xml = Nokogiri::XML::Builder.new(encoding: 'UTF-8') do |xml|
|
222
|
+
subject.insert_descriptions(xml)
|
223
|
+
end.to_xml
|
174
224
|
response = Maremma.from_xml(xml)
|
175
|
-
expect(response.dig(
|
225
|
+
expect(response.dig('descriptions',
|
226
|
+
'description')).to eq('descriptionType' => 'Abstract',
|
227
|
+
'__content__' => 'Eating your own dog food is a slang term to describe that an organization should itself use the products and services it provides. For DataCite this means that we should use DOIs with appropriate metadata and strategies for long-term preservation for...')
|
176
228
|
end
|
177
229
|
end
|
178
230
|
end
|