briard 2.4.2 → 2.6.1

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Files changed (83) hide show
  1. checksums.yaml +4 -4
  2. data/.github/workflows/codeql-analysis.yml +72 -0
  3. data/.github/workflows/rubocop.yml +50 -0
  4. data/.gitignore +1 -0
  5. data/.rubocop.yml +144 -620
  6. data/.rubocop_todo.yml +76 -0
  7. data/CHANGELOG.md +18 -0
  8. data/Gemfile +2 -0
  9. data/Gemfile.lock +43 -9
  10. data/Rakefile +1 -1
  11. data/{bolognese.gemspec → briard.gemspec} +46 -39
  12. data/lib/briard/array.rb +2 -2
  13. data/lib/briard/author_utils.rb +79 -71
  14. data/lib/briard/cli.rb +12 -13
  15. data/lib/briard/crossref_utils.rb +73 -61
  16. data/lib/briard/datacite_utils.rb +132 -106
  17. data/lib/briard/doi_utils.rb +10 -10
  18. data/lib/briard/metadata.rb +96 -106
  19. data/lib/briard/metadata_utils.rb +87 -78
  20. data/lib/briard/readers/bibtex_reader.rb +65 -65
  21. data/lib/briard/readers/cff_reader.rb +88 -70
  22. data/lib/briard/readers/citeproc_reader.rb +90 -84
  23. data/lib/briard/readers/codemeta_reader.rb +68 -50
  24. data/lib/briard/readers/crosscite_reader.rb +2 -2
  25. data/lib/briard/readers/crossref_reader.rb +249 -210
  26. data/lib/briard/readers/datacite_json_reader.rb +3 -3
  27. data/lib/briard/readers/datacite_reader.rb +225 -189
  28. data/lib/briard/readers/npm_reader.rb +49 -42
  29. data/lib/briard/readers/ris_reader.rb +82 -80
  30. data/lib/briard/readers/schema_org_reader.rb +182 -159
  31. data/lib/briard/string.rb +1 -1
  32. data/lib/briard/utils.rb +4 -4
  33. data/lib/briard/version.rb +3 -1
  34. data/lib/briard/whitelist_scrubber.rb +11 -4
  35. data/lib/briard/writers/bibtex_writer.rb +14 -8
  36. data/lib/briard/writers/cff_writer.rb +33 -26
  37. data/lib/briard/writers/codemeta_writer.rb +19 -15
  38. data/lib/briard/writers/csv_writer.rb +6 -4
  39. data/lib/briard/writers/datacite_json_writer.rb +8 -2
  40. data/lib/briard/writers/jats_writer.rb +33 -28
  41. data/lib/briard/writers/rdf_xml_writer.rb +1 -1
  42. data/lib/briard/writers/ris_writer.rb +30 -18
  43. data/lib/briard/writers/turtle_writer.rb +1 -1
  44. data/lib/briard.rb +6 -6
  45. data/rubocop.sarif +0 -0
  46. data/spec/array_spec.rb +5 -5
  47. data/spec/author_utils_spec.rb +151 -132
  48. data/spec/datacite_utils_spec.rb +135 -83
  49. data/spec/doi_utils_spec.rb +168 -164
  50. data/spec/find_from_format_spec.rb +69 -69
  51. data/spec/fixtures/vcr_cassettes/Briard_Metadata/sanitize/onlies_keep_specific_tags.yml +65 -0
  52. data/spec/fixtures/vcr_cassettes/Briard_Metadata/sanitize/removes_a_tags.yml +65 -0
  53. data/spec/metadata_spec.rb +91 -90
  54. data/spec/readers/bibtex_reader_spec.rb +43 -38
  55. data/spec/readers/cff_reader_spec.rb +165 -153
  56. data/spec/readers/citeproc_reader_spec.rb +45 -40
  57. data/spec/readers/codemeta_reader_spec.rb +128 -115
  58. data/spec/readers/crosscite_reader_spec.rb +34 -24
  59. data/spec/readers/crossref_reader_spec.rb +1098 -939
  60. data/spec/readers/datacite_json_reader_spec.rb +53 -40
  61. data/spec/readers/datacite_reader_spec.rb +1541 -1337
  62. data/spec/readers/npm_reader_spec.rb +48 -43
  63. data/spec/readers/ris_reader_spec.rb +53 -47
  64. data/spec/readers/schema_org_reader_spec.rb +329 -267
  65. data/spec/spec_helper.rb +6 -5
  66. data/spec/utils_spec.rb +371 -347
  67. data/spec/writers/bibtex_writer_spec.rb +143 -143
  68. data/spec/writers/cff_writer_spec.rb +96 -90
  69. data/spec/writers/citation_writer_spec.rb +34 -33
  70. data/spec/writers/citeproc_writer_spec.rb +226 -224
  71. data/spec/writers/codemeta_writer_spec.rb +18 -16
  72. data/spec/writers/crosscite_writer_spec.rb +91 -73
  73. data/spec/writers/crossref_writer_spec.rb +99 -91
  74. data/spec/writers/csv_writer_spec.rb +70 -70
  75. data/spec/writers/datacite_json_writer_spec.rb +78 -68
  76. data/spec/writers/datacite_writer_spec.rb +417 -322
  77. data/spec/writers/jats_writer_spec.rb +177 -161
  78. data/spec/writers/rdf_xml_writer_spec.rb +68 -63
  79. data/spec/writers/ris_writer_spec.rb +162 -162
  80. data/spec/writers/schema_org_writer_spec.rb +329 -294
  81. data/spec/writers/turtle_writer_spec.rb +47 -47
  82. metadata +242 -166
  83. data/.github/workflows/release.yml +0 -47
data/spec/writers/turtle_writer_spec.rb CHANGED
@@ -3,83 +3,83 @@
3
3
  require 'spec_helper'
4
4
 
5
5
  describe Briard::Metadata, vcr: true do
6
- context "write metadata as turtle" do
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- it "Crossref DOI" do
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- input = fixture_path + "crossref.bib"
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- subject = Briard::Metadata.new(input: input, from: "bibtex")
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+ context 'write metadata as turtle' do
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+ it 'Crossref DOI' do
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+ input = "#{fixture_path}crossref.bib"
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+ subject = described_class.new(input: input, from: 'bibtex')
10
10
  ttl = subject.turtle.split("\n")
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- expect(ttl[0]).to eq("@prefix schema: <http://schema.org/> .")
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- expect(ttl[2]).to eq("<https://doi.org/10.7554/elife.01567> a schema:ScholarlyArticle;")
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+ expect(ttl[0]).to eq('@prefix schema: <http://schema.org/> .')
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+ expect(ttl[2]).to eq('<https://doi.org/10.7554/elife.01567> a schema:ScholarlyArticle;')
13
13
  end
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14
 
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- it "Dataset" do
16
- input = "https://doi.org/10.5061/DRYAD.8515"
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- subject = Briard::Metadata.new(input: input, from: "datacite")
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+ it 'Dataset' do
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+ input = 'https://doi.org/10.5061/DRYAD.8515'
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+ subject = described_class.new(input: input, from: 'datacite')
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  expect(subject.valid?).to be true
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  ttl = subject.turtle.split("\n")
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- expect(ttl[0]).to eq("@prefix schema: <http://schema.org/> .")
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- expect(ttl[2]).to eq("<https://doi.org/10.5061/dryad.8515> a schema:Dataset;")
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+ expect(ttl[0]).to eq('@prefix schema: <http://schema.org/> .')
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+ expect(ttl[2]).to eq('<https://doi.org/10.5061/dryad.8515> a schema:Dataset;')
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  end
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23
 
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- it "BlogPosting" do
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- input= "https://doi.org/10.5438/4K3M-NYVG"
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- subject = Briard::Metadata.new(input: input, from: "datacite")
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+ it 'BlogPosting' do
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+ input = 'https://doi.org/10.5438/4K3M-NYVG'
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+ subject = described_class.new(input: input, from: 'datacite')
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  expect(subject.valid?).to be true
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  ttl = subject.turtle.split("\n")
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- expect(ttl[0]).to eq("@prefix schema: <http://schema.org/> .")
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- expect(ttl[2]).to eq("<https://doi.org/10.5438/4k3m-nyvg> a schema:ScholarlyArticle;")
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+ expect(ttl[0]).to eq('@prefix schema: <http://schema.org/> .')
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+ expect(ttl[2]).to eq('<https://doi.org/10.5438/4k3m-nyvg> a schema:ScholarlyArticle;')
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  end
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32
 
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- it "BlogPosting Citeproc JSON" do
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- input = fixture_path + "citeproc.json"
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- subject = Briard::Metadata.new(input: input, from: "citeproc")
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+ it 'BlogPosting Citeproc JSON' do
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+ input = "#{fixture_path}citeproc.json"
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+ subject = described_class.new(input: input, from: 'citeproc')
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  ttl = subject.turtle.split("\n")
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- expect(ttl[0]).to eq("@prefix schema: <http://schema.org/> .")
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- expect(ttl[2]).to eq("<https://doi.org/10.5438/4k3m-nyvg> a schema:BlogPosting;")
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+ expect(ttl[0]).to eq('@prefix schema: <http://schema.org/> .')
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+ expect(ttl[2]).to eq('<https://doi.org/10.5438/4k3m-nyvg> a schema:BlogPosting;')
39
39
  end
40
40
 
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- it "BlogPosting DataCite JSON" do
42
- input = fixture_path + "datacite.json"
43
- subject = Briard::Metadata.new(input: input, from: "datacite_json")
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+ it 'BlogPosting DataCite JSON' do
42
+ input = "#{fixture_path}datacite.json"
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+ subject = described_class.new(input: input, from: 'datacite_json')
44
44
  ttl = subject.turtle.split("\n")
45
- expect(ttl[0]).to eq("@prefix schema: <http://schema.org/> .")
46
- expect(ttl[2]).to eq("<https://doi.org/10.5438/4k3m-nyvg> a schema:ScholarlyArticle;")
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+ expect(ttl[0]).to eq('@prefix schema: <http://schema.org/> .')
46
+ expect(ttl[2]).to eq('<https://doi.org/10.5438/4k3m-nyvg> a schema:ScholarlyArticle;')
47
47
  end
48
48
 
49
- it "BlogPosting schema.org" do
50
- input = "https://blog.front-matter.io/posts/eating-your-own-dog-food//"
51
- subject = Briard::Metadata.new(input: input, from: "schema_org")
49
+ it 'BlogPosting schema.org' do
50
+ input = 'https://blog.front-matter.io/posts/eating-your-own-dog-food//'
51
+ subject = described_class.new(input: input, from: 'schema_org')
52
52
  expect(subject.valid?).to be true
53
53
  ttl = subject.turtle.split("\n")
54
- expect(ttl[0]).to eq("@prefix schema: <http://schema.org/> .")
55
- expect(ttl[2]).to eq("<https://doi.org/10.53731/r79vxn1-97aq74v-ag58n> a schema:Article;")
56
- expect(ttl[3]).to eq(" schema:author <https://orcid.org/0000-0003-1419-2405>;")
54
+ expect(ttl[0]).to eq('@prefix schema: <http://schema.org/> .')
55
+ expect(ttl[2]).to eq('<https://doi.org/10.53731/r79vxn1-97aq74v-ag58n> a schema:Article;')
56
+ expect(ttl[3]).to eq(' schema:author <https://orcid.org/0000-0003-1419-2405>;')
57
57
  end
58
58
 
59
- it "DataONE" do
60
- input = fixture_path + 'codemeta.json'
61
- subject = Briard::Metadata.new(input: input, from: "codemeta")
59
+ it 'DataONE' do
60
+ input = "#{fixture_path}codemeta.json"
61
+ subject = described_class.new(input: input, from: 'codemeta')
62
62
  ttl = subject.turtle.split("\n")
63
- expect(ttl[0]).to eq("@prefix schema: <http://schema.org/> .")
64
- expect(ttl[2]).to eq("<https://doi.org/10.5063/f1m61h5x> a schema:SoftwareSourceCode;")
63
+ expect(ttl[0]).to eq('@prefix schema: <http://schema.org/> .')
64
+ expect(ttl[2]).to eq('<https://doi.org/10.5063/f1m61h5x> a schema:SoftwareSourceCode;')
65
65
  end
66
66
 
67
- it "journal article" do
68
- input = "10.7554/eLife.01567"
69
- subject = Briard::Metadata.new(input: input, from: "crossref")
67
+ it 'journal article' do
68
+ input = '10.7554/eLife.01567'
69
+ subject = described_class.new(input: input, from: 'crossref')
70
70
  expect(subject.valid?).to be true
71
71
  ttl = subject.turtle.split("\n")
72
- expect(ttl[0]).to eq("@prefix schema: <http://schema.org/> .")
73
- expect(ttl[2]).to eq("<https://doi.org/10.7554/elife.01567> a schema:ScholarlyArticle;")
72
+ expect(ttl[0]).to eq('@prefix schema: <http://schema.org/> .')
73
+ expect(ttl[2]).to eq('<https://doi.org/10.7554/elife.01567> a schema:ScholarlyArticle;')
74
74
  end
75
75
 
76
- it "with pages" do
77
- input = "https://doi.org/10.1155/2012/291294"
78
- subject = Briard::Metadata.new(input: input, from: "crossref")
76
+ it 'with pages' do
77
+ input = 'https://doi.org/10.1155/2012/291294'
78
+ subject = described_class.new(input: input, from: 'crossref')
79
79
  expect(subject.valid?).to be true
80
80
  ttl = subject.turtle.split("\n")
81
- expect(ttl[0]).to eq("@prefix schema: <http://schema.org/> .")
82
- expect(ttl[2]).to eq("<https://doi.org/10.1155/2012/291294> a schema:ScholarlyArticle;")
81
+ expect(ttl[0]).to eq('@prefix schema: <http://schema.org/> .')
82
+ expect(ttl[2]).to eq('<https://doi.org/10.1155/2012/291294> a schema:ScholarlyArticle;')
83
83
  end
84
84
  end
85
85
  end