bolognese 2.0.1 → 2.3.9

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 (567) hide show
  1. checksums.yaml +4 -4
  2. data/.github/workflows/ci.yml +1 -1
  3. data/.github/workflows/release.yml +2 -2
  4. data/Gemfile.lock +9 -9
  5. data/README.md +1 -1
  6. data/bolognese.gemspec +4 -5
  7. data/lib/bolognese/author_utils.rb +5 -5
  8. data/lib/bolognese/datacite_utils.rb +12 -5
  9. data/lib/bolognese/metadata_utils.rb +2 -1
  10. data/lib/bolognese/readers/citeproc_reader.rb +6 -0
  11. data/lib/bolognese/readers/crossref_reader.rb +37 -4
  12. data/lib/bolognese/readers/datacite_reader.rb +6 -10
  13. data/lib/bolognese/readers/schema_org_reader.rb +26 -4
  14. data/lib/bolognese/utils.rb +20 -13
  15. data/lib/bolognese/version.rb +1 -1
  16. data/lib/bolognese/writers/datacite_json_writer.rb +1 -4
  17. data/lib/bolognese/writers/jats_writer.rb +4 -1
  18. data/lib/bolognese/writers/schema_org_writer.rb +5 -1
  19. data/resources/kernel-4/include/datacite-contributorType-v4.xsd +3 -1
  20. data/resources/kernel-4/include/datacite-dateType-v4.xsd +3 -1
  21. data/resources/kernel-4/include/datacite-relatedIdentifierType-v4.xsd +5 -2
  22. data/resources/kernel-4/include/datacite-relationType-v4.xsd +7 -3
  23. data/resources/kernel-4/include/datacite-resourceType-v4.xsd +5 -1
  24. data/resources/kernel-4/include/datacite-titleType-v4.xsd +1 -1
  25. data/resources/kernel-4/metadata.xsd +2 -1
  26. data/resources/kernel-4.6/include/datacite-contributorType-v4.xsd +37 -0
  27. data/resources/kernel-4.6/include/datacite-dateType-v4.xsd +27 -0
  28. data/resources/kernel-4.6/include/datacite-descriptionType-v4.xsd +19 -0
  29. data/resources/kernel-4.6/include/datacite-funderIdentifierType-v4.xsd +16 -0
  30. data/resources/kernel-4.6/include/datacite-nameType-v4.xsd +10 -0
  31. data/resources/kernel-4.6/include/datacite-numberType-v4.xsd +12 -0
  32. data/resources/kernel-4.6/include/datacite-relatedIdentifierType-v4.xsd +37 -0
  33. data/resources/kernel-4.6/include/datacite-relationType-v4.xsd +57 -0
  34. data/resources/kernel-4.6/include/datacite-resourceType-v4.xsd +49 -0
  35. data/resources/kernel-4.6/include/datacite-titleType-v4.xsd +14 -0
  36. data/resources/kernel-4.6/include/xml.xsd +286 -0
  37. data/resources/kernel-4.6/metadata.xsd +712 -0
  38. metadata +31 -554
  39. data/spec/array_spec.rb +0 -22
  40. data/spec/author_utils_spec.rb +0 -253
  41. data/spec/cli_spec.rb +0 -226
  42. data/spec/datacite_utils_spec.rb +0 -207
  43. data/spec/doi_utils_spec.rb +0 -314
  44. data/spec/find_from_format_spec.rb +0 -114
  45. data/spec/fixtures/aida.json +0 -82
  46. data/spec/fixtures/cgimp_package.json +0 -18
  47. data/spec/fixtures/cit_package.json +0 -19
  48. data/spec/fixtures/citeproc-no-author.json +0 -26
  49. data/spec/fixtures/citeproc-no-categories.json +0 -21
  50. data/spec/fixtures/citeproc.json +0 -32
  51. data/spec/fixtures/codemeta.json +0 -86
  52. data/spec/fixtures/codemeta_v2.json +0 -86
  53. data/spec/fixtures/crosscite.json +0 -63
  54. data/spec/fixtures/crossref.bib +0 -14
  55. data/spec/fixtures/crossref.ris +0 -15
  56. data/spec/fixtures/crossref.xml +0 -606
  57. data/spec/fixtures/datacite-empty-sizes.xml +0 -57
  58. data/spec/fixtures/datacite-example-ROR-nameIdentifiers.xml +0 -117
  59. data/spec/fixtures/datacite-example-affiliation.xml +0 -114
  60. data/spec/fixtures/datacite-example-ancientdates-v4.3.xml +0 -29
  61. data/spec/fixtures/datacite-example-complicated-tba.xml +0 -56
  62. data/spec/fixtures/datacite-example-complicated-v3.0.xml +0 -48
  63. data/spec/fixtures/datacite-example-complicated-v4.0.xml +0 -54
  64. data/spec/fixtures/datacite-example-complicated-v4.1.xml +0 -57
  65. data/spec/fixtures/datacite-example-dissertation-v4.4.xml +0 -56
  66. data/spec/fixtures/datacite-example-escaped-text.xml +0 -56
  67. data/spec/fixtures/datacite-example-full-v4.4.xml +0 -114
  68. data/spec/fixtures/datacite-example-full-v4.5.xml +0 -255
  69. data/spec/fixtures/datacite-example-geolocation-2.xml +0 -141
  70. data/spec/fixtures/datacite-example-geolocation.xml +0 -66
  71. data/spec/fixtures/datacite-example-nameIdentifier-with-schemeURI.xml +0 -94
  72. data/spec/fixtures/datacite-example-polygon-v4.1.xml +0 -163
  73. data/spec/fixtures/datacite-example-relateditems-with-attributes.xml +0 -61
  74. data/spec/fixtures/datacite-example-relateditems.xml +0 -61
  75. data/spec/fixtures/datacite-example-xs-string.xml +0 -28
  76. data/spec/fixtures/datacite-formats-with-xs.xml +0 -22
  77. data/spec/fixtures/datacite-funderIdentifier.xml +0 -98
  78. data/spec/fixtures/datacite-geolocation-empty.xml +0 -159
  79. data/spec/fixtures/datacite-geolocationpolygons-multiple.xml +0 -76
  80. data/spec/fixtures/datacite-metadata-sample-complicated-v2.2.xml +0 -52
  81. data/spec/fixtures/datacite-multiple-language.xml +0 -38
  82. data/spec/fixtures/datacite-multiple-rights.xml +0 -59
  83. data/spec/fixtures/datacite-schema-2.2.xml +0 -80
  84. data/spec/fixtures/datacite-seriesinformation.xml +0 -46
  85. data/spec/fixtures/datacite-space-in-sizes.xml +0 -52
  86. data/spec/fixtures/datacite-xml-lang.xml +0 -51
  87. data/spec/fixtures/datacite.json +0 -89
  88. data/spec/fixtures/datacite.xml +0 -40
  89. data/spec/fixtures/datacite_dataset.xml +0 -58
  90. data/spec/fixtures/datacite_malformed_creator.xml +0 -52
  91. data/spec/fixtures/datacite_missing_creator.xml +0 -33
  92. data/spec/fixtures/datacite_schema_3.xml +0 -58
  93. data/spec/fixtures/datacite_software.json +0 -21
  94. data/spec/fixtures/datacite_software_missing_comma.json +0 -18
  95. data/spec/fixtures/datacite_software_overlapping_keys.json +0 -18
  96. data/spec/fixtures/datacite_software_version.json +0 -74
  97. data/spec/fixtures/edam_package.json +0 -12
  98. data/spec/fixtures/funding_reference.xml +0 -53
  99. data/spec/fixtures/gtex.xml +0 -71
  100. data/spec/fixtures/maremma/codemeta.json +0 -36
  101. data/spec/fixtures/nist.xml +0 -35
  102. data/spec/fixtures/ns0.xml +0 -2
  103. data/spec/fixtures/pure.bib +0 -14
  104. data/spec/fixtures/pure.ris +0 -15
  105. data/spec/fixtures/pure.xml +0 -188
  106. data/spec/fixtures/ris_bug.ris +0 -9
  107. data/spec/fixtures/schema_4.0.xml +0 -140
  108. data/spec/fixtures/schema_org.json +0 -49
  109. data/spec/fixtures/schema_org_geolocation.json +0 -82
  110. data/spec/fixtures/schema_org_geoshape.json +0 -550
  111. data/spec/fixtures/schema_org_gtex.json +0 -75
  112. data/spec/fixtures/schema_org_list.json +0 -12623
  113. data/spec/fixtures/schema_org_tdl_iodp_invalid_authors.json +0 -25
  114. data/spec/fixtures/schema_org_topmed.json +0 -53
  115. data/spec/fixtures/schema_org_type_as_array.json +0 -41
  116. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_from_id/crossref/default.yml +0 -106
  117. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_from_id/crossref/to_bibtex.yml +0 -106
  118. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_from_id/crossref/to_citation.yml +0 -106
  119. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_from_id/crossref/to_crossref.yml +0 -106
  120. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_from_id/crossref/to_datacite.yml +0 -106
  121. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_from_id/crossref/to_jats.yml +0 -106
  122. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_from_id/crossref/to_schema_org.yml +0 -106
  123. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_from_id/datacite/default.yml +0 -106
  124. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_from_id/datacite/to_bibtex.yml +0 -106
  125. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_from_id/datacite/to_citation.yml +0 -106
  126. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_from_id/datacite/to_datacite.yml +0 -106
  127. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_from_id/datacite/to_datacite_json.yml +0 -106
  128. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_from_id/datacite/to_jats.yml +0 -106
  129. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_from_id/datacite/to_schema_org.yml +0 -106
  130. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_from_id/schema_org/default.yml +0 -117
  131. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_from_id/schema_org/to_datacite.yml +0 -117
  132. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_from_id/schema_org/to_schema_org.yml +0 -115
  133. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/find_from_format_by_id/crossref.yml +0 -54
  134. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/find_from_format_by_id/datacite.yml +0 -54
  135. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/find_from_format_by_id/jalc.yml +0 -54
  136. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/find_from_format_by_id/kisti.yml +0 -54
  137. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/find_from_format_by_id/medra.yml +0 -54
  138. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/find_from_format_by_id/op.yml +0 -54
  139. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/authors_as_string/author.yml +0 -48
  140. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/authors_as_string/no_author.yml +0 -48
  141. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/authors_as_string/single_author.yml +0 -48
  142. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/authors_as_string/with_organization.yml +0 -48
  143. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/change_datacite_metadata/change_state.yml +0 -106
  144. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/change_datacite_metadata/change_title.yml +0 -106
  145. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/change_metadata_as_datacite_xml/change_description.yml +0 -55
  146. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/change_metadata_as_datacite_xml/change_identifiers.yml +0 -55
  147. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/change_metadata_as_datacite_xml/change_license.yml +0 -55
  148. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/change_metadata_as_datacite_xml/change_license_name.yml +0 -55
  149. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/change_metadata_as_datacite_xml/change_license_url.yml +0 -55
  150. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/change_metadata_as_datacite_xml/change_state.yml +0 -55
  151. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/change_metadata_as_datacite_xml/validates_against_schema.yml +0 -55
  152. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/change_metadata_as_datacite_xml/with_data_citation.yml +0 -55
  153. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_api_url/doi.yml +0 -48
  154. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_api_url/doi_with_protocol.yml +0 -48
  155. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_api_url/dx_doi_org_url.yml +0 -48
  156. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_api_url/force_test_resolver.yml +0 -48
  157. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_api_url/https_url.yml +0 -48
  158. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_api_url/test_resolver.yml +0 -48
  159. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_api_url/test_resolver_http.yml +0 -48
  160. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_from_url/doi.yml +0 -48
  161. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_from_url/doi_with_special_characters.yml +0 -48
  162. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_from_url/not_a_doi.yml +0 -48
  163. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_from_url/sandbox_url.yml +0 -48
  164. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_from_url/url.yml +0 -48
  165. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_registration_agency/crossref.yml +0 -99
  166. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_registration_agency/datacite.yml +0 -99
  167. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_registration_agency/jalc.yml +0 -99
  168. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_registration_agency/kisti.yml +0 -99
  169. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_registration_agency/medra.yml +0 -99
  170. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_registration_agency/not_a_valid_prefix.yml +0 -48
  171. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_registration_agency/not_found.yml +0 -99
  172. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_registration_agency/op.yml +0 -99
  173. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_resolver/doi.yml +0 -48
  174. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_resolver/doi_with_protocol.yml +0 -48
  175. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_resolver/dx_doi_org_url.yml +0 -48
  176. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_resolver/force_stage_resolver.yml +0 -48
  177. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_resolver/https_url.yml +0 -48
  178. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_resolver/stage_resolver.yml +0 -48
  179. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_resolver/stage_resolver_http.yml +0 -48
  180. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_from_format_by_ID/crossref.yml +0 -157
  181. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_from_format_by_ID/crossref_doi_not_url.yml +0 -157
  182. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_from_format_by_ID/datacite.yml +0 -157
  183. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_from_format_by_ID/datacite_doi_http.yml +0 -157
  184. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_from_format_by_ID/github.yml +0 -106
  185. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_from_format_by_ID/orcid.yml +0 -106
  186. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_from_format_by_ID/schema_org.yml +0 -106
  187. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_from_format_by_ID/unknown_DOI_registration_agency.yml +0 -157
  188. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_from_format_from_file/bibtex.yml +0 -106
  189. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_from_format_from_file/citeproc.yml +0 -106
  190. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_from_format_from_file/codemeta.yml +0 -106
  191. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_from_format_from_file/crosscite.yml +0 -106
  192. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_from_format_from_file/crossref.yml +0 -106
  193. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_from_format_from_file/datacite.yml +0 -106
  194. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_from_format_from_file/datacite_json.yml +0 -106
  195. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_from_format_from_file/ris.yml +0 -106
  196. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_from_format_from_file/schema_org.yml +0 -106
  197. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_from_format_from_string/crosscite.yml +0 -106
  198. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/fos/hsh_to_fos_for_match.yml +0 -48
  199. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/fos/hsh_to_fos_for_with_schemeUri_in_hash.yml +0 -48
  200. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/fos/hsh_to_fos_match.yml +0 -48
  201. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/fos/hsh_to_fos_no_match.yml +0 -48
  202. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/fos/name_to_fos_for_match.yml +0 -48
  203. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/fos/name_to_fos_match.yml +0 -48
  204. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/fos/name_to_fos_no_match.yml +0 -48
  205. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/from_schema_org/with_id.yml +0 -48
  206. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/from_schema_org_creators/with_affiliation.yml +0 -48
  207. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/from_schema_org_creators/without_affiliation.yml +0 -48
  208. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_codemeta_metadata/maremma.yml +0 -75
  209. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_codemeta_metadata/metadata_reports.yml +0 -75
  210. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/DOI_with_ORCID_ID.yml +0 -103
  211. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/DOI_with_SICI_DOI.yml +0 -102
  212. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/DOI_with_data_citation.yml +0 -106
  213. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/JaLC.yml +0 -137
  214. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/KISTI.yml +0 -158
  215. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/OP.yml +0 -100
  216. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/affiliation_is_space.yml +0 -101
  217. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/another_book.yml +0 -138
  218. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/another_book_chapter.yml +0 -100
  219. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/article_id_as_page_number.yml +0 -101
  220. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/author_literal.yml +0 -108
  221. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/book.yml +0 -99
  222. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/book_chapter.yml +0 -170
  223. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/book_chapter_with_RDF_for_container.yml +0 -99
  224. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/book_oup.yml +0 -98
  225. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/component.yml +0 -120
  226. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/dataset.yml +0 -130
  227. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/dataset_usda.yml +0 -143
  228. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/date_in_future.yml +0 -101
  229. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/dissertation.yml +0 -129
  230. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/empty_given_name.yml +0 -101
  231. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/invalid_date.yml +0 -101
  232. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/journal_article.yml +0 -100
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