briard 2.4.1 → 2.6.0
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- checksums.yaml +4 -4
- data/.github/workflows/codeql-analysis.yml +72 -0
- data/.github/workflows/rubocop.yml +50 -0
- data/.rubocop.yml +144 -620
- data/.rubocop_todo.yml +76 -0
- data/CHANGELOG.md +22 -0
- data/Gemfile +2 -0
- data/Gemfile.lock +43 -6
- data/Rakefile +1 -1
- data/{bolognese.gemspec → briard.gemspec} +46 -38
- 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/turtle_writer_spec.rb +47 -47
- metadata +250 -160
- data/.github/workflows/release.yml +0 -47
@@ -3,130 +3,143 @@
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require 'spec_helper'
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describe Briard::Metadata, vcr: true do
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let(:fixture_path) {
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let(:fixture_path) { 'spec/fixtures/' }
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context
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it
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input = fixture_path
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subject =
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expect(subject.raw).to eq(
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context 'get schema_org raw' do
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it 'BlogPosting' do
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input = "#{fixture_path}schema_org.json"
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subject = described_class.new(input: input)
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expect(subject.raw).to eq(File.read(input).strip)
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end
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end
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context
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it
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input =
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subject =
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context 'get schema_org metadata' do
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it 'BlogPosting' do
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input = 'https://blog.front-matter.io/posts/eating-your-own-dog-food'
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subject = described_class.new(input: input, from: 'schema_org')
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expect(subject.valid?).to be true
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expect(subject.id).to eq(
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expect(subject.url).to eq(
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expect(subject.types).to eq(
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expect(subject.
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expect(subject.
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expect(subject.
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expect(subject.
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expect(subject.id).to eq('https://doi.org/10.53731/r79vxn1-97aq74v-ag58n')
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expect(subject.url).to eq('https://blog.front-matter.io/posts/eating-your-own-dog-food')
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expect(subject.types).to eq('bibtex' => 'article', 'citeproc' => 'article-newspaper',
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'resourceTypeGeneral' => 'Preprint', 'ris' => 'GEN', 'schemaOrg' => 'Article')
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expect(subject.creators).to eq([{ 'affiliation' => [], 'familyName' => 'Fenner',
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'givenName' => 'Martin', 'name' => 'Fenner, Martin', 'nameIdentifiers' => [{ 'nameIdentifier' => 'https://orcid.org/0000-0003-1419-2405', 'nameIdentifierScheme' => 'ORCID', 'schemeUri' => 'https://orcid.org' }], 'nameType' => 'Personal' }])
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expect(subject.titles).to eq([{ 'title' => 'Eating your own Dog Food' }])
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expect(subject.descriptions.first['description']).to start_with('Eating your own dog food')
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expect(subject.subjects).to eq([{ 'subject' => 'feature' }])
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expect(subject.dates).to eq([{ 'date' => '2016-12-20T00:00:00Z', 'dateType' => 'Issued' },
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{ 'date' => '2022-08-15T09:06:22Z', 'dateType' => 'Updated' }])
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expect(subject.publication_year).to eq('2016')
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expect(subject.related_identifiers.length).to eq(0)
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expect(subject.publisher).to eq(
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expect(subject.publisher).to eq('Front Matter')
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end
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it
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input =
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subject =
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it 'BlogPosting with new DOI' do
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input = 'https://blog.front-matter.io/posts/eating-your-own-dog-food'
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subject = described_class.new(input: input, doi: '10.5438/0000-00ss')
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expect(subject.valid?).to be true
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expect(subject.id).to eq(
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expect(subject.doi).to eq(
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expect(subject.url).to eq(
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expect(subject.types).to eq(
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expect(subject.id).to eq('https://doi.org/10.5438/0000-00ss')
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expect(subject.doi).to eq('10.5438/0000-00ss')
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expect(subject.url).to eq('https://blog.front-matter.io/posts/eating-your-own-dog-food')
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expect(subject.types).to eq('bibtex' => 'article', 'citeproc' => 'article-newspaper',
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'resourceTypeGeneral' => 'Preprint', 'ris' => 'GEN', 'schemaOrg' => 'Article')
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end
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it
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input = fixture_path
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subject =
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it 'BlogPosting with type as array' do
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input = "#{fixture_path}schema_org_type_as_array.json"
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subject = described_class.new(input: input)
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expect(subject.valid?).to be true
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expect(subject.id).to eq(
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expect(subject.url).to eq(
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expect(subject.types).to eq(
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expect(subject.
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expect(subject.
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expect(subject.
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expect(subject.
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expect(subject.id).to eq('https://doi.org/10.5438/4k3m-nyvg')
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expect(subject.url).to eq('https://blog.datacite.org/eating-your-own-dog-food')
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expect(subject.types).to eq('bibtex' => 'article', 'citeproc' => 'post-weblog',
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'resourceTypeGeneral' => 'Preprint', 'ris' => 'GEN', 'schemaOrg' => 'BlogPosting')
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expect(subject.creators).to eq([{ 'affiliation' => [{ 'name' => 'DataCite' }],
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'familyName' => 'Fenner', 'givenName' => 'Martin', 'name' => 'Fenner, Martin', 'nameIdentifiers' => [{ 'nameIdentifier' => 'https://orcid.org/0000-0003-1419-2405', 'nameIdentifierScheme' => 'ORCID', 'schemeUri' => 'https://orcid.org' }], 'nameType' => 'Personal' }])
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expect(subject.titles).to eq([{ 'title' => 'Eating your own Dog Food' }])
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expect(subject.descriptions.first['description']).to start_with('Eating your own dog food')
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expect(subject.subjects).to eq([{ 'subject' => 'datacite' }, { 'subject' => 'doi' },
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{ 'subject' => 'metadata' }, { 'subject' => 'featured' }])
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expect(subject.dates).to eq([{ 'date' => '2016-12-20', 'dateType' => 'Issued' },
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{ 'date' => '2016-12-20', 'dateType' => 'Created' },
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{ 'date' => '2016-12-20', 'dateType' => 'Updated' }])
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expect(subject.publication_year).to eq('2016')
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expect(subject.related_identifiers.length).to eq(3)
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expect(subject.related_identifiers.last).to eq(
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expect(subject.related_identifiers.last).to eq('relatedIdentifier' => '10.5438/55e5-t5c0',
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'relatedIdentifierType' => 'DOI', 'relationType' => 'References', 'resourceTypeGeneral' => 'Text')
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expect(subject.publisher).to eq('DataCite')
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end
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context
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it
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input =
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subject =
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context 'get schema_org metadata front matter' do
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it 'BlogPosting' do
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input = 'https://blog.front-matter.io/posts/step-forward-for-software-citation'
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subject = described_class.new(input: input, from: 'schema_org')
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expect(subject.valid?).to be true
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expect(subject.id).to eq(
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expect(subject.url).to eq(
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expect(subject.types).to eq(
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expect(subject.
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expect(subject.
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expect(subject.
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expect(subject.id).to eq('https://doi.org/10.53731/r9531p1-97aq74v-ag78v')
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expect(subject.url).to eq('https://blog.front-matter.io/posts/step-forward-for-software-citation')
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expect(subject.types).to eq('bibtex' => 'article', 'citeproc' => 'article-newspaper',
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'resourceTypeGeneral' => 'Preprint', 'ris' => 'GEN', 'schemaOrg' => 'Article')
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expect(subject.creators).to eq([{ 'affiliation' => [],
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'familyName' => 'Fenner', 'givenName' => 'Martin', 'name' => 'Fenner, Martin', 'nameIdentifiers' => [{ 'nameIdentifier' => 'https://orcid.org/0000-0003-1419-2405', 'nameIdentifierScheme' => 'ORCID', 'schemeUri' => 'https://orcid.org' }], 'nameType' => 'Personal' }])
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expect(subject.titles).to eq([{ 'title' => "A step forward for software citation: GitHub's enhanced software citation support" }])
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expect(subject.descriptions.first['description']).to start_with('On August 19, GitHub announced software citation')
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expect(subject.subjects).to eq([{ 'subject' => 'news' }])
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expect(subject.dates).to eq([{ 'date' => '2021-08-24T16:57:24Z', 'dateType' => 'Issued' },
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{ 'date' => '2022-08-15T19:05:14Z', 'dateType' => 'Updated' }])
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expect(subject.publication_year).to eq('2021')
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expect(subject.related_identifiers.length).to eq(0)
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expect(subject.container).to eq(
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expect(subject.container).to eq('identifier' => '2749-9952', 'identifierType' => 'ISSN',
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'title' => 'Front Matter', 'type' => 'Blog')
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expect(subject.publisher).to eq('Front Matter')
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end
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end
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it
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input =
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subject =
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it 'zenodo' do
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input = 'https://www.zenodo.org/record/1196821'
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subject = described_class.new(input: input, from: 'schema_org')
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expect(subject.valid?).to be false
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expect(subject.language).to eq(
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expect(subject.language).to eq('eng')
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expect(subject.errors).to eq("49:0: ERROR: Element '{http://datacite.org/schema/kernel-4}publisher': [facet 'minLength'] The value has a length of '0'; this underruns the allowed minimum length of '1'.")
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expect(subject.id).to eq(
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expect(subject.doi).to eq(
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expect(subject.url).to eq(
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expect(subject.types).to eq(
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expect(subject.id).to eq('https://doi.org/10.5281/zenodo.1196821')
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expect(subject.doi).to eq('10.5281/zenodo.1196821')
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expect(subject.url).to eq('https://zenodo.org/record/1196821')
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expect(subject.types).to eq('bibtex' => 'misc', 'citeproc' => 'dataset',
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'resourceTypeGeneral' => 'Dataset', 'ris' => 'DATA', 'schemaOrg' => 'Dataset')
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expect(subject.titles).to eq([{ 'title' => 'PsPM-SC4B: SCR, ECG, EMG, PSR and respiration measurements in a delay fear conditioning task with auditory CS and electrical US' }])
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expect(subject.creators.size).to eq(6)
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expect(subject.creators.first).to eq(
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expect(subject.publisher).to
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expect(subject.publication_year).to eq(
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expect(subject.subjects).to eq([{
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expect(subject.creators.first).to eq('name' => 'Staib, Matthias',
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'nameIdentifiers' => [{ 'nameIdentifier' => 'https://orcid.org/0000-0001-9688-838X', 'nameIdentifierScheme' => 'ORCID', 'schemeUri' => 'https://orcid.org' }],
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'nameType' => 'Personal', 'givenName' => 'Matthias', 'familyName' => 'Staib', 'affiliation' => [{ 'name' => 'University of Zurich, Zurich, Switzerland' }])
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expect(subject.publisher.nil?).to be(true)
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expect(subject.publication_year).to eq('2018')
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expect(subject.subjects).to eq([{ 'subject' => 'pupil size response' },
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{ 'subject' => 'skin conductance response' },
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{ 'subject' => 'electrocardiogram' },
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{ 'subject' => 'electromyogram' },
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{ 'subject' => 'electrodermal activity' },
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{ 'subject' => 'galvanic skin response' },
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{ 'subject' => 'psr' },
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{ 'subject' => 'scr' },
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{ 'subject' => 'ecg' },
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{ 'subject' => 'emg' },
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{ 'subject' => 'eda' },
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{ 'subject' => 'gsr' }])
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end
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it
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input =
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subject =
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it 'pangaea' do
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input = 'https://doi.pangaea.de/10.1594/PANGAEA.836178'
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subject = described_class.new(input: input, from: 'schema_org')
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expect(subject.valid?).to be true
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expect(subject.id).to eq(
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expect(subject.doi).to eq(
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expect(subject.url).to eq(
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expect(subject.types).to eq(
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expect(subject.id).to eq('https://doi.org/10.1594/pangaea.836178')
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expect(subject.doi).to eq('10.1594/pangaea.836178')
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expect(subject.url).to eq('https://doi.pangaea.de/10.1594/PANGAEA.836178')
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expect(subject.types).to eq('bibtex' => 'misc', 'citeproc' => 'dataset',
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'resourceTypeGeneral' => 'Dataset', 'ris' => 'DATA', 'schemaOrg' => 'Dataset')
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expect(subject.titles).to eq([{ 'title' => 'Hydrological and meteorological investigations in a lake near Kangerlussuaq, west Greenland' }])
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expect(subject.creators.size).to eq(8)
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expect(subject.creators.first).to eq(
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expect(subject.
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expect(subject.creators.first).to eq('nameType' => 'Personal', 'name' => 'Johansson, Emma',
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'givenName' => 'Emma', 'familyName' => 'Johansson')
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expect(subject.publisher).to eq('PANGAEA')
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expect(subject.publication_year).to eq('2014')
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end
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# TODO: check redirections
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# expect(subject.creators.first).to eq("familyName"=>"MOGHADDAM", "givenName"=>"M.", "name"=>"MOGHADDAM, M.", "nameType"=>"Personal", "nameIdentifiers"=>[], "affiliation" => [])
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# end
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input =
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subject =
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it 'harvard dataverse' do
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input = 'https://dataverse.harvard.edu/dataset.xhtml?persistentId=doi:10.7910/DVN/NJ7XSO'
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subject = described_class.new(input: input, from: 'schema_org')
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expect(subject.valid?).to be true
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expect(subject.id).to eq(
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expect(subject.doi).to eq(
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expect(subject.types).to eq(
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expect(subject.
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expect(subject.
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expect(subject.id).to eq('https://doi.org/10.7910/dvn/nj7xso')
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expect(subject.doi).to eq('10.7910/dvn/nj7xso')
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expect(subject.types).to eq('bibtex' => 'misc', 'citeproc' => 'dataset',
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'resourceTypeGeneral' => 'Dataset', 'ris' => 'DATA', 'schemaOrg' => 'Dataset')
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expect(subject.titles).to eq([{ 'title' => 'Summary data ankylosing spondylitis GWAS' }])
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expect(subject.container).to eq('identifier' => 'https://dataverse.harvard.edu',
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'identifierType' => 'URL', 'title' => 'Harvard Dataverse', 'type' => 'DataRepository')
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expect(subject.creators).to eq([{
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'name' => 'International Genetics Of Ankylosing Spondylitis Consortium (IGAS)', 'nameIdentifiers' => [], 'affiliation' => []
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}])
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expect(subject.subjects).to eq([{ 'subject' => 'medicine, health and life sciences' },
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{ 'subject' => 'genome-wide association studies' },
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{ 'subject' => 'ankylosing spondylitis' }])
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end
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# TODO check 403 status in DOI resolver
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# TODO: check 403 status in DOI resolver
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# it "harvard dataverse via identifiers.org" do
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# input = "https://identifiers.org/doi/10.7910/DVN/NJ7XSO"
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# subject = Briard::Metadata.new(input: input, from: "schema_org")
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# end
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end
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context
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input = fixture_path
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subject =
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context 'get schema_org metadata as string' do
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it 'BlogPosting' do
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input = "#{fixture_path}schema_org.json"
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subject = described_class.new(input: input)
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expect(subject.valid?).to be true
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expect(subject.language).to eq(
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expect(subject.id).to eq(
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expect(subject.url).to eq(
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expect(subject.types).to eq(
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expect(subject.
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expect(subject.
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expect(subject.
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expect(subject.language).to eq('en')
|
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expect(subject.id).to eq('https://doi.org/10.5438/4k3m-nyvg')
|
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expect(subject.url).to eq('https://blog.datacite.org/eating-your-own-dog-food')
|
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expect(subject.types).to eq('bibtex' => 'article', 'citeproc' => 'post-weblog',
|
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|
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'resourceTypeGeneral' => 'Preprint', 'ris' => 'GEN', 'schemaOrg' => 'BlogPosting')
|
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+
expect(subject.creators).to eq([{ 'familyName' => 'Fenner', 'givenName' => 'Martin', 'name' => 'Fenner, Martin', 'nameIdentifiers' => [{ 'nameIdentifier' => 'https://orcid.org/0000-0003-1419-2405', 'nameIdentifierScheme' => 'ORCID',
|
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|
+
+ 'schemeUri' => 'https://orcid.org' }], 'nameType' => 'Personal' }])
|
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expect(subject.titles).to eq([{ 'title' => 'Eating your own Dog Food' }])
|
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expect(subject.descriptions.first['description']).to start_with('Eating your own dog food')
|
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expect(subject.subjects).to eq([{ 'subject' => 'datacite' }, { 'subject' => 'doi' },
|
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+
{ 'subject' => 'metadata' }, { 'subject' => 'featured' }])
|
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expect(subject.dates).to eq([{ 'date' => '2016-12-20', 'dateType' => 'Issued' },
|
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{ 'date' => '2016-12-20', 'dateType' => 'Created' },
|
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{ 'date' => '2016-12-20', 'dateType' => 'Updated' }])
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expect(subject.publication_year).to eq('2016')
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expect(subject.related_identifiers.length).to eq(3)
|
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expect(subject.related_identifiers.last).to eq(
|
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-
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|
+
expect(subject.related_identifiers.last).to eq('relatedIdentifier' => '10.5438/55e5-t5c0',
|
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|
+
'relatedIdentifierType' => 'DOI', 'relationType' => 'References', 'resourceTypeGeneral' => 'Text')
|
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|
+
expect(subject.publisher).to eq('DataCite')
|
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216
|
end
|
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|
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it
|
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|
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input = fixture_path
|
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subject =
|
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+
it 'GTEx dataset' do
|
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+
input = "#{fixture_path}schema_org_gtex.json"
|
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+
subject = described_class.new(input: input)
|
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expect(subject.valid?).to be true
|
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expect(subject.id).to eq(
|
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|
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expect(subject.identifiers).to eq([{
|
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-
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expect(subject.
|
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expect(subject.
|
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expect(subject.
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expect(subject.
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expect(subject.
|
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expect(subject.
|
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expect(subject.
|
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|
-
|
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|
+
expect(subject.id).to eq('https://doi.org/10.25491/d50j-3083')
|
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+
expect(subject.identifiers).to eq([{ 'identifier' => '687610993',
|
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+
'identifierType' => 'md5' }])
|
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+
expect(subject.url).to eq('https://ors.datacite.org/doi:/10.25491/d50j-3083')
|
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+
expect(subject.content_url).to eq(['https://storage.googleapis.com/gtex_analysis_v7/single_tissue_eqtl_data/GTEx_Analysis_v7_eQTL_expression_matrices.tar.gz'])
|
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|
+
expect(subject.types).to eq('bibtex' => 'misc', 'citeproc' => 'dataset',
|
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|
+
'resourceType' => 'Gene expression matrices', 'resourceTypeGeneral' => 'Dataset', 'ris' => 'DATA', 'schemaOrg' => 'Dataset')
|
230
|
+
expect(subject.creators).to eq([{ 'name' => 'The GTEx Consortium', 'nameType' => 'Organizational',
|
231
|
+
'nameIdentifiers' => [], 'affiliation' => [] }])
|
232
|
+
expect(subject.titles).to eq([{ 'title' => 'Fully processed, filtered and normalized gene expression matrices (in BED format) for each tissue, which were used as input into FastQTL for eQTL discovery' }])
|
233
|
+
expect(subject.version_info).to eq('v7')
|
234
|
+
expect(subject.subjects).to eq([{ 'subject' => 'gtex' }, { 'subject' => 'annotation' },
|
235
|
+
{ 'subject' => 'phenotype' }, { 'subject' => 'gene regulation' }, { 'subject' => 'transcriptomics' }])
|
236
|
+
expect(subject.dates).to eq([{ 'date' => '2017', 'dateType' => 'Issued' }])
|
237
|
+
expect(subject.publication_year).to eq('2017')
|
238
|
+
expect(subject.container).to eq('title' => 'GTEx', 'type' => 'DataRepository')
|
239
|
+
expect(subject.publisher).to eq('GTEx')
|
216
240
|
expect(subject.funding_references.length).to eq(7)
|
217
|
-
expect(subject.funding_references.first).to eq(
|
241
|
+
expect(subject.funding_references.first).to eq(
|
242
|
+
'funderIdentifier' => 'https://doi.org/10.13039/100000052', 'funderIdentifierType' => 'Crossref Funder ID', 'funderName' => 'Common Fund of the Office of the Director of the NIH'
|
243
|
+
)
|
218
244
|
end
|
219
245
|
|
220
|
-
it
|
221
|
-
input = fixture_path
|
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|
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subject =
|
246
|
+
it 'TOPMed dataset' do
|
247
|
+
input = "#{fixture_path}schema_org_topmed.json"
|
248
|
+
subject = described_class.new(input: input)
|
223
249
|
expect(subject.valid?).to be true
|
224
|
-
expect(subject.identifiers).to eq([{
|
225
|
-
|
226
|
-
|
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|
-
|
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|
-
|
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|
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expect(subject.
|
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|
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expect(subject.
|
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|
-
|
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|
-
|
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|
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expect(subject.
|
234
|
-
|
235
|
-
expect(subject.
|
236
|
-
|
237
|
-
expect(subject.
|
250
|
+
expect(subject.identifiers).to eq([{ 'identifier' => '3b33f6b9338fccab0901b7d317577ea3', 'identifierType' => 'md5' },
|
251
|
+
{ 'identifier' => 'ark:/99999/fk41CrU4eszeLUDe',
|
252
|
+
'identifierType' => 'minid' },
|
253
|
+
{ 'identifier' => 'dg.4503/c3d66dc9-58da-411c-83c4-dd656aa3c4b7',
|
254
|
+
'identifierType' => 'dataguid' }])
|
255
|
+
expect(subject.url).to eq('https://ors.datacite.org/doi:/10.23725/8na3-9s47')
|
256
|
+
expect(subject.content_url).to eq([
|
257
|
+
's3://cgp-commons-public/topmed_open_access/197bc047-e917-55ed-852d-d563cdbc50e4/NWD165827.recab.cram', 'gs://topmed-irc-share/public/NWD165827.recab.cram'
|
258
|
+
])
|
259
|
+
expect(subject.types).to eq('bibtex' => 'misc', 'citeproc' => 'dataset',
|
260
|
+
'resourceType' => 'CRAM file', 'resourceTypeGeneral' => 'Dataset', 'ris' => 'DATA', 'schemaOrg' => 'Dataset')
|
261
|
+
expect(subject.creators).to eq([{ 'name' => 'TOPMed IRC', 'nameType' => 'Organizational',
|
262
|
+
'nameIdentifiers' => [], 'affiliation' => [] }])
|
263
|
+
expect(subject.titles).to eq([{ 'title' => 'NWD165827.recab.cram' }])
|
264
|
+
expect(subject.subjects).to eq([{ 'subject' => 'topmed' },
|
265
|
+
{ 'subject' => 'whole genome sequencing' }])
|
266
|
+
expect(subject.dates).to eq([{ 'date' => '2017-11-30', 'dateType' => 'Issued' }])
|
267
|
+
expect(subject.publication_year).to eq('2017')
|
268
|
+
expect(subject.publisher).to eq('TOPMed')
|
269
|
+
expect(subject.related_identifiers).to eq([{ 'relatedIdentifier' => '10.23725/2g4s-qv04',
|
270
|
+
'relatedIdentifierType' => 'DOI', 'relationType' => 'References', 'resourceTypeGeneral' => 'Dataset' }])
|
271
|
+
expect(subject.funding_references).to eq([{
|
272
|
+
'funderIdentifier' => 'https://doi.org/10.13039/100000050', 'funderIdentifierType' => 'Crossref Funder ID', 'funderName' => 'National Heart, Lung, and Blood Institute (NHLBI)'
|
273
|
+
}])
|
238
274
|
end
|
239
275
|
|
240
|
-
it
|
241
|
-
input = fixture_path
|
242
|
-
subject =
|
276
|
+
it 'tdl_iodp dataset' do
|
277
|
+
input = "#{fixture_path}schema_org_tdl_iodp_invalid_authors.json"
|
278
|
+
subject = described_class.new(input: input)
|
243
279
|
expect(subject.valid?).to be false
|
244
280
|
end
|
245
281
|
|
246
|
-
it
|
247
|
-
input = fixture_path
|
248
|
-
subject =
|
282
|
+
it 'geolocation' do
|
283
|
+
input = "#{fixture_path}schema_org_geolocation.json"
|
284
|
+
subject = described_class.new(input: input)
|
249
285
|
|
250
286
|
expect(subject.valid?).to be true
|
251
|
-
expect(subject.identifiers).to eq([{
|
252
|
-
|
287
|
+
expect(subject.identifiers).to eq([{ 'identifier' => 'https://doi.org/10.6071/z7wc73',
|
288
|
+
'identifierType' => 'DOI' }])
|
289
|
+
expect(subject.types).to eq('bibtex' => 'misc', 'citeproc' => 'dataset',
|
290
|
+
'resourceType' => 'dataset', 'resourceTypeGeneral' => 'Dataset', 'ris' => 'DATA', 'schemaOrg' => 'Dataset')
|
253
291
|
expect(subject.creators.length).to eq(6)
|
254
|
-
expect(subject.creators.first).to eq(
|
255
|
-
|
256
|
-
expect(subject.
|
257
|
-
|
258
|
-
|
259
|
-
|
260
|
-
|
261
|
-
|
262
|
-
|
263
|
-
|
264
|
-
|
265
|
-
|
266
|
-
|
267
|
-
expect(subject.
|
268
|
-
expect(subject.
|
269
|
-
expect(subject.
|
292
|
+
expect(subject.creators.first).to eq('familyName' => 'Bales', 'givenName' => 'Roger',
|
293
|
+
'name' => 'Bales, Roger', 'nameType' => 'Personal')
|
294
|
+
expect(subject.titles).to eq([{ 'title' => 'Southern Sierra Critical Zone Observatory (SSCZO), Providence Creek meteorological data, soil moisture and temperature, snow depth and air temperature' }])
|
295
|
+
expect(subject.subjects).to eq([{ 'subject' => 'earth sciences' },
|
296
|
+
{ 'subject' => 'soil moisture' },
|
297
|
+
{ 'subject' => 'soil temperature' },
|
298
|
+
{ 'subject' => 'snow depth' },
|
299
|
+
{ 'subject' => 'air temperature' },
|
300
|
+
{ 'subject' => 'water balance' },
|
301
|
+
{ 'subject' => 'nevada' },
|
302
|
+
{ 'subject' => 'sierra (mountain range)' }])
|
303
|
+
expect(subject.dates).to eq([{ 'date' => '2013', 'dateType' => 'Issued' },
|
304
|
+
{ 'date' => '2014-10-17', 'dateType' => 'Updated' }])
|
305
|
+
expect(subject.publication_year).to eq('2013')
|
306
|
+
expect(subject.publisher).to eq('UC Merced')
|
307
|
+
expect(subject.funding_references).to eq([{ 'funderName' => 'National Science Foundation, Division of Earth Sciences, Critical Zone Observatories' }])
|
308
|
+
expect(subject.geo_locations).to eq([{
|
309
|
+
'geoLocationPlace' => 'Providence Creek (Lower, Upper and P301)', 'geoLocationPoint' => {
|
310
|
+
'pointLatitude' => '37.047756', 'pointLongitude' => '-119.221094'
|
311
|
+
}
|
312
|
+
}])
|
270
313
|
end
|
271
314
|
|
272
|
-
it
|
273
|
-
input = fixture_path
|
274
|
-
subject =
|
315
|
+
it 'geolocation geoshape' do
|
316
|
+
input = "#{fixture_path}schema_org_geoshape.json"
|
317
|
+
subject = described_class.new(input: input)
|
275
318
|
|
276
319
|
expect(subject.valid?).to be true
|
277
|
-
expect(subject.language).to eq(
|
278
|
-
expect(subject.id).to eq(
|
279
|
-
expect(subject.types).to eq(
|
320
|
+
expect(subject.language).to eq('en')
|
321
|
+
expect(subject.id).to eq('https://doi.org/10.1594/pangaea.842237')
|
322
|
+
expect(subject.types).to eq('bibtex' => 'misc', 'citeproc' => 'dataset',
|
323
|
+
'resourceTypeGeneral' => 'Dataset', 'ris' => 'DATA', 'schemaOrg' => 'Dataset')
|
280
324
|
expect(subject.creators.length).to eq(2)
|
281
|
-
expect(subject.creators.first).to eq(
|
282
|
-
|
283
|
-
expect(subject.
|
284
|
-
expect(subject.
|
285
|
-
expect(subject.
|
286
|
-
expect(subject.
|
325
|
+
expect(subject.creators.first).to eq('name' => 'Tara Oceans Consortium, Coordinators',
|
326
|
+
'nameType' => 'Organizational', 'nameIdentifiers' => [], 'affiliation' => [])
|
327
|
+
expect(subject.titles).to eq([{ 'title' => 'Registry of all stations from the Tara Oceans Expedition (2009-2013)' }])
|
328
|
+
expect(subject.dates).to eq([{ 'date' => '2015-02-03', 'dateType' => 'Issued' }])
|
329
|
+
expect(subject.publication_year).to eq('2015')
|
330
|
+
expect(subject.publisher).to eq('PANGAEA')
|
331
|
+
expect(subject.geo_locations).to eq([{ 'geoLocationBox' => { 'eastBoundLongitude' => '174.9006',
|
332
|
+
'northBoundLatitude' => '79.6753', 'southBoundLatitude' => '-64.3088', 'westBoundLongitude' => '-168.5182' } }])
|
287
333
|
end
|
288
334
|
|
289
|
-
it
|
290
|
-
data =
|
335
|
+
it 'schema_org list' do
|
336
|
+
data = File.read("#{fixture_path}schema_org_list.json").strip
|
291
337
|
input = JSON.parse(data).first.to_json
|
292
|
-
subject =
|
338
|
+
subject = described_class.new(input: input)
|
293
339
|
expect(subject.valid?).to be true
|
294
|
-
expect(subject.id).to eq(
|
295
|
-
expect(subject.identifiers).to eq([{
|
296
|
-
|
297
|
-
|
298
|
-
|
299
|
-
|
300
|
-
expect(subject.
|
301
|
-
expect(subject.
|
302
|
-
|
303
|
-
|
304
|
-
expect(subject.
|
305
|
-
|
306
|
-
expect(subject.
|
307
|
-
|
308
|
-
expect(subject.
|
340
|
+
expect(subject.id).to eq('https://doi.org/10.23725/7jg3-v803')
|
341
|
+
expect(subject.identifiers).to eq([{ 'identifier' => 'ark:/99999/fk4E1n6n1YHKxPk', 'identifierType' => 'minid' },
|
342
|
+
{ 'identifier' => 'dg.4503/01b048d0-e128-4cb0-94e9-b2d2cab7563d',
|
343
|
+
'identifierType' => 'dataguid' },
|
344
|
+
{ 'identifier' => 'f9e72bdf25bf4b4f0e581d9218fec2eb',
|
345
|
+
'identifierType' => 'md5' }])
|
346
|
+
expect(subject.url).to eq('https://ors.datacite.org/doi:/10.23725/7jg3-v803')
|
347
|
+
expect(subject.content_url).to eq([
|
348
|
+
's3://cgp-commons-public/topmed_open_access/44a8837b-4456-5709-b56b-54e23000f13a/NWD100953.recab.cram', 'gs://topmed-irc-share/public/NWD100953.recab.cram', 'dos://dos.commons.ucsc-cgp.org/01b048d0-e128-4cb0-94e9-b2d2cab7563d?version=2018-05-26T133719.491772Z'
|
349
|
+
])
|
350
|
+
expect(subject.types).to eq('bibtex' => 'misc', 'citeproc' => 'dataset',
|
351
|
+
'resourceType' => 'CRAM file', 'resourceTypeGeneral' => 'Dataset', 'ris' => 'DATA', 'schemaOrg' => 'Dataset')
|
352
|
+
expect(subject.creators).to eq([{ 'name' => 'TOPMed', 'nameType' => 'Organizational',
|
353
|
+
'nameIdentifiers' => [], 'affiliation' => [] }])
|
354
|
+
expect(subject.titles).to eq([{ 'title' => 'NWD100953.recab.cram' }])
|
355
|
+
expect(subject.subjects).to eq([{ 'subject' => 'topmed' },
|
356
|
+
{ 'subject' => 'whole genome sequencing' }])
|
357
|
+
expect(subject.dates).to eq([{ 'date' => '2017-11-30', 'dateType' => 'Issued' }])
|
358
|
+
expect(subject.publication_year).to eq('2017')
|
359
|
+
expect(subject.publisher).to eq('TOPMed')
|
360
|
+
expect(subject.funding_references).to eq([{
|
361
|
+
'funderIdentifier' => 'https://doi.org/10.13039/100000050', 'funderIdentifierType' => 'Crossref Funder ID', 'funderName' => 'National Heart, Lung, and Blood Institute (NHLBI)'
|
362
|
+
}])
|
309
363
|
end
|
310
364
|
|
311
|
-
it
|
312
|
-
input = fixture_path
|
313
|
-
subject =
|
365
|
+
it 'aida dataset' do
|
366
|
+
input = "#{fixture_path}aida.json"
|
367
|
+
subject = described_class.new(input: input)
|
314
368
|
|
315
369
|
expect(subject.valid?).to be true
|
316
|
-
expect(subject.id).to eq(
|
317
|
-
expect(subject.url).to eq(
|
318
|
-
expect(subject.types).to eq(
|
370
|
+
expect(subject.id).to eq('https://doi.org/10.23698/aida/drov')
|
371
|
+
expect(subject.url).to eq('https://doi.aida.medtech4health.se/10.23698/aida/drov')
|
372
|
+
expect(subject.types).to eq('bibtex' => 'misc', 'citeproc' => 'dataset',
|
373
|
+
'resourceTypeGeneral' => 'Dataset', 'ris' => 'DATA', 'schemaOrg' => 'Dataset')
|
319
374
|
# expect(subject.creators).to eq([{"familyName"=>"Lindman", "givenName"=>"Karin", "name"=>"Lindman, Karin", "nameIdentifiers"=>[{"nameIdentifier"=> "https://orcid.org/0000-0003-1298-517X", "nameIdentifierScheme"=>"ORCID", "schemeUri"=>"https://orcid.org"}], "nameType"=>"Personal"}])
|
320
|
-
expect(subject.titles).to eq([{
|
321
|
-
expect(subject.version_info).to eq(
|
322
|
-
expect(subject.subjects).to eq([{
|
323
|
-
|
324
|
-
|
325
|
-
|
326
|
-
|
327
|
-
expect(subject.
|
328
|
-
expect(subject.
|
329
|
-
expect(subject.
|
330
|
-
expect(subject.
|
375
|
+
expect(subject.titles).to eq([{ 'title' => 'Ovary data from the Visual Sweden project DROID' }])
|
376
|
+
expect(subject.version_info).to eq('1.0')
|
377
|
+
expect(subject.subjects).to eq([{ 'subject' => 'pathology' }, { 'subject' => 'whole slide imaging' },
|
378
|
+
{ 'subject' => 'annotated' }])
|
379
|
+
expect(subject.dates).to eq([{ 'date' => '2019-01-09', 'dateType' => 'Issued' },
|
380
|
+
{ 'date' => '2019-01-09', 'dateType' => 'Created' },
|
381
|
+
{ 'date' => '2019-01-09', 'dateType' => 'Updated' }])
|
382
|
+
expect(subject.publication_year).to eq('2019')
|
383
|
+
expect(subject.id).to eq('https://doi.org/10.23698/aida/drov')
|
384
|
+
expect(subject.publisher).to eq('AIDA')
|
385
|
+
expect(subject.rights_list).to eq([{ 'rights' => 'Restricted access',
|
386
|
+
'rightsUri' => 'https://datasets.aida.medtech4health.se/10.23698/aida/drov#license' }])
|
387
|
+
expect(subject.id).to eq('https://doi.org/10.23698/aida/drov')
|
331
388
|
end
|
332
389
|
|
333
|
-
it
|
334
|
-
subject =
|
335
|
-
|
336
|
-
|
337
|
-
|
338
|
-
|
339
|
-
|
340
|
-
|
341
|
-
|
342
|
-
|
343
|
-
|
344
|
-
|
345
|
-
|
346
|
-
|
347
|
-
|
348
|
-
|
349
|
-
|
390
|
+
it 'from attributes' do
|
391
|
+
subject = described_class.new(input: nil,
|
392
|
+
from: 'schema_org',
|
393
|
+
doi: '10.5281/zenodo.1239',
|
394
|
+
creators: [{ 'type' => 'Person', 'name' => 'Jahn, Najko', 'givenName' => 'Najko',
|
395
|
+
'familyName' => 'Jahn' }],
|
396
|
+
titles: [{ 'title' => 'Publication Fp7 Funding Acknowledgment - Plos Openaire' }],
|
397
|
+
descriptions: [{ 'description' => 'The dataset contains a sample of metadata describing papers' }],
|
398
|
+
publisher: 'Zenodo',
|
399
|
+
publication_year: '2013',
|
400
|
+
dates: [{ 'date' => '2013-04-03',
|
401
|
+
'dateType' => 'Issued' }],
|
402
|
+
funding_references: [{ 'awardNumber' => '246686',
|
403
|
+
'awardTitle' => 'Open Access Infrastructure for Research in Europe',
|
404
|
+
'awardUri' => 'info:eu-repo/grantAgreement/EC/FP7/246686/',
|
405
|
+
'funderIdentifier' => 'https://doi.org/10.13039/501100000780',
|
406
|
+
'funderIdentifierType' => 'Crossref Funder ID',
|
407
|
+
'funderName' => 'European Commission' }],
|
408
|
+
types: {
|
409
|
+
'resourceTypeGeneral' => 'Dataset', 'schemaOrg' => 'Dataset'
|
410
|
+
})
|
350
411
|
|
351
412
|
expect(subject.valid?).to be true
|
352
|
-
expect(subject.doi).to eq(
|
353
|
-
expect(subject.id).to eq(
|
354
|
-
expect(subject.types[
|
355
|
-
expect(subject.types[
|
356
|
-
expect(subject.creators).to eq([{
|
357
|
-
|
358
|
-
expect(subject.
|
359
|
-
expect(subject.
|
360
|
-
expect(subject.
|
361
|
-
expect(subject.
|
362
|
-
expect(subject.
|
363
|
-
|
364
|
-
|
365
|
-
|
366
|
-
|
367
|
-
|
413
|
+
expect(subject.doi).to eq('10.5281/zenodo.1239')
|
414
|
+
expect(subject.id).to eq('https://doi.org/10.5281/zenodo.1239')
|
415
|
+
expect(subject.types['schemaOrg']).to eq('Dataset')
|
416
|
+
expect(subject.types['resourceTypeGeneral']).to eq('Dataset')
|
417
|
+
expect(subject.creators).to eq([{ 'familyName' => 'Jahn', 'givenName' => 'Najko',
|
418
|
+
'name' => 'Jahn, Najko', 'type' => 'Person' }])
|
419
|
+
expect(subject.titles).to eq([{ 'title' => 'Publication Fp7 Funding Acknowledgment - Plos Openaire' }])
|
420
|
+
expect(subject.descriptions.first['description']).to start_with('The dataset contains a sample of metadata describing papers')
|
421
|
+
expect(subject.dates).to eq([{ 'date' => '2013-04-03', 'dateType' => 'Issued' }])
|
422
|
+
expect(subject.publication_year).to eq('2013')
|
423
|
+
expect(subject.publisher).to eq('Zenodo')
|
424
|
+
expect(subject.funding_references).to eq([{ 'awardNumber' => '246686',
|
425
|
+
'awardTitle' => 'Open Access Infrastructure for Research in Europe',
|
426
|
+
'awardUri' => 'info:eu-repo/grantAgreement/EC/FP7/246686/',
|
427
|
+
'funderIdentifier' => 'https://doi.org/10.13039/501100000780',
|
428
|
+
'funderIdentifierType' => 'Crossref Funder ID',
|
429
|
+
'funderName' => 'European Commission' }])
|
368
430
|
end
|
369
431
|
end
|
370
432
|
end
|