bolognese 2.3.2 → 2.4.0

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 (555) hide show
  1. checksums.yaml +4 -4
  2. data/Gemfile.lock +1 -1
  3. data/README.md +1 -1
  4. data/bolognese.gemspec +1 -2
  5. data/lib/bolognese/author_utils.rb +1 -1
  6. data/lib/bolognese/datacite_utils.rb +13 -6
  7. data/lib/bolognese/metadata.rb +4 -1
  8. data/lib/bolognese/metadata_utils.rb +6 -0
  9. data/lib/bolognese/readers/crossref_reader.rb +3 -4
  10. data/lib/bolognese/readers/datacite_reader.rb +5 -32
  11. data/lib/bolognese/utils.rb +48 -4
  12. data/lib/bolognese/version.rb +1 -1
  13. metadata +5 -547
  14. data/spec/array_spec.rb +0 -22
  15. data/spec/author_utils_spec.rb +0 -259
  16. data/spec/cli_spec.rb +0 -226
  17. data/spec/datacite_utils_spec.rb +0 -315
  18. data/spec/doi_utils_spec.rb +0 -314
  19. data/spec/find_from_format_spec.rb +0 -114
  20. data/spec/fixtures/aida.json +0 -82
  21. data/spec/fixtures/cgimp_package.json +0 -18
  22. data/spec/fixtures/cit_package.json +0 -19
  23. data/spec/fixtures/citeproc-no-author.json +0 -26
  24. data/spec/fixtures/citeproc-no-categories.json +0 -21
  25. data/spec/fixtures/citeproc.json +0 -36
  26. data/spec/fixtures/codemeta.json +0 -86
  27. data/spec/fixtures/codemeta_v2.json +0 -86
  28. data/spec/fixtures/crosscite.json +0 -63
  29. data/spec/fixtures/crossref.bib +0 -14
  30. data/spec/fixtures/crossref.ris +0 -15
  31. data/spec/fixtures/crossref.xml +0 -606
  32. data/spec/fixtures/crossref_schema_4.6_values.xml +0 -183
  33. data/spec/fixtures/datacite-empty-sizes.xml +0 -57
  34. data/spec/fixtures/datacite-example-ROR-nameIdentifiers.xml +0 -125
  35. data/spec/fixtures/datacite-example-affiliation.xml +0 -114
  36. data/spec/fixtures/datacite-example-ancientdates-v4.3.xml +0 -29
  37. data/spec/fixtures/datacite-example-complicated-tba.xml +0 -56
  38. data/spec/fixtures/datacite-example-complicated-v3.0.xml +0 -48
  39. data/spec/fixtures/datacite-example-complicated-v4.0.xml +0 -54
  40. data/spec/fixtures/datacite-example-complicated-v4.1.xml +0 -57
  41. data/spec/fixtures/datacite-example-dissertation-v4.4.xml +0 -56
  42. data/spec/fixtures/datacite-example-escaped-text.xml +0 -56
  43. data/spec/fixtures/datacite-example-full-v4.4.xml +0 -114
  44. data/spec/fixtures/datacite-example-full-v4.5.xml +0 -255
  45. data/spec/fixtures/datacite-example-full-v4.6.xml +0 -114
  46. data/spec/fixtures/datacite-example-geolocation-2.xml +0 -141
  47. data/spec/fixtures/datacite-example-geolocation.xml +0 -66
  48. data/spec/fixtures/datacite-example-nameIdentifier-with-schemeURI.xml +0 -94
  49. data/spec/fixtures/datacite-example-polygon-v4.1.xml +0 -163
  50. data/spec/fixtures/datacite-example-relateditems-with-attributes.xml +0 -61
  51. data/spec/fixtures/datacite-example-relateditems.xml +0 -61
  52. data/spec/fixtures/datacite-example-xs-string.xml +0 -28
  53. data/spec/fixtures/datacite-formats-with-xs.xml +0 -22
  54. data/spec/fixtures/datacite-funderIdentifier.xml +0 -98
  55. data/spec/fixtures/datacite-geolocation-empty.xml +0 -159
  56. data/spec/fixtures/datacite-geolocationpolygons-multiple.xml +0 -76
  57. data/spec/fixtures/datacite-metadata-sample-complicated-v2.2.xml +0 -52
  58. data/spec/fixtures/datacite-multiple-language.xml +0 -38
  59. data/spec/fixtures/datacite-multiple-rights.xml +0 -59
  60. data/spec/fixtures/datacite-schema-2.2.xml +0 -80
  61. data/spec/fixtures/datacite-seriesinformation.xml +0 -46
  62. data/spec/fixtures/datacite-space-in-sizes.xml +0 -52
  63. data/spec/fixtures/datacite-xml-lang.xml +0 -51
  64. data/spec/fixtures/datacite.json +0 -89
  65. data/spec/fixtures/datacite.xml +0 -40
  66. data/spec/fixtures/datacite_blank_name_identifier.xml +0 -22
  67. data/spec/fixtures/datacite_blank_publisher.xml +0 -18
  68. data/spec/fixtures/datacite_dataset.xml +0 -58
  69. data/spec/fixtures/datacite_journal_article.xml +0 -64
  70. data/spec/fixtures/datacite_malformed_creator.xml +0 -52
  71. data/spec/fixtures/datacite_missing_creator.xml +0 -33
  72. data/spec/fixtures/datacite_schema_3.xml +0 -58
  73. data/spec/fixtures/datacite_software.json +0 -21
  74. data/spec/fixtures/datacite_software_missing_comma.json +0 -18
  75. data/spec/fixtures/datacite_software_overlapping_keys.json +0 -18
  76. data/spec/fixtures/datacite_software_version.json +0 -74
  77. data/spec/fixtures/edam_package.json +0 -12
  78. data/spec/fixtures/funding_reference.xml +0 -53
  79. data/spec/fixtures/gtex.xml +0 -71
  80. data/spec/fixtures/maremma/codemeta.json +0 -36
  81. data/spec/fixtures/nist.xml +0 -35
  82. data/spec/fixtures/ns0.xml +0 -2
  83. data/spec/fixtures/pure.bib +0 -14
  84. data/spec/fixtures/pure.ris +0 -15
  85. data/spec/fixtures/pure.xml +0 -188
  86. data/spec/fixtures/ris_bug.ris +0 -9
  87. data/spec/fixtures/schema_4.0.xml +0 -140
  88. data/spec/fixtures/schema_org.json +0 -50
  89. data/spec/fixtures/schema_org_4.6_attributes.json +0 -108
  90. data/spec/fixtures/schema_org_geolocation.json +0 -82
  91. data/spec/fixtures/schema_org_geoshape.json +0 -550
  92. data/spec/fixtures/schema_org_gtex.json +0 -75
  93. data/spec/fixtures/schema_org_list.json +0 -12623
  94. data/spec/fixtures/schema_org_tdl_iodp_invalid_authors.json +0 -25
  95. data/spec/fixtures/schema_org_topmed.json +0 -53
  96. data/spec/fixtures/schema_org_type_as_array.json +0 -41
  97. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_from_id/crossref/default.yml +0 -106
  98. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_from_id/crossref/to_bibtex.yml +0 -106
  99. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_from_id/crossref/to_citation.yml +0 -106
  100. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_from_id/crossref/to_crossref.yml +0 -106
  101. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_from_id/crossref/to_datacite.yml +0 -106
  102. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_from_id/crossref/to_jats.yml +0 -106
  103. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_from_id/crossref/to_schema_org.yml +0 -106
  104. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_from_id/datacite/default.yml +0 -106
  105. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_from_id/datacite/to_bibtex.yml +0 -106
  106. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_from_id/datacite/to_citation.yml +0 -106
  107. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_from_id/datacite/to_datacite.yml +0 -106
  108. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_from_id/datacite/to_datacite_json.yml +0 -106
  109. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_from_id/datacite/to_jats.yml +0 -106
  110. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_from_id/datacite/to_schema_org.yml +0 -106
  111. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_from_id/schema_org/default.yml +0 -117
  112. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_from_id/schema_org/to_datacite.yml +0 -117
  113. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_from_id/schema_org/to_schema_org.yml +0 -115
  114. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/find_from_format_by_id/crossref.yml +0 -54
  115. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/find_from_format_by_id/datacite.yml +0 -54
  116. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/find_from_format_by_id/jalc.yml +0 -54
  117. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/find_from_format_by_id/kisti.yml +0 -54
  118. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/find_from_format_by_id/medra.yml +0 -54
  119. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/find_from_format_by_id/op.yml +0 -54
  120. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/authors_as_string/author.yml +0 -48
  121. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/authors_as_string/no_author.yml +0 -48
  122. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/authors_as_string/single_author.yml +0 -48
  123. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/authors_as_string/with_organization.yml +0 -48
  124. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/change_datacite_metadata/change_state.yml +0 -106
  125. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/change_datacite_metadata/change_title.yml +0 -106
  126. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/change_metadata_as_datacite_xml/change_description.yml +0 -55
  127. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/change_metadata_as_datacite_xml/change_identifiers.yml +0 -55
  128. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/change_metadata_as_datacite_xml/change_license.yml +0 -55
  129. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/change_metadata_as_datacite_xml/change_license_name.yml +0 -55
  130. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/change_metadata_as_datacite_xml/change_license_url.yml +0 -55
  131. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/change_metadata_as_datacite_xml/change_state.yml +0 -55
  132. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/change_metadata_as_datacite_xml/validates_against_schema.yml +0 -55
  133. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/change_metadata_as_datacite_xml/with_data_citation.yml +0 -55
  134. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_api_url/doi.yml +0 -48
  135. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_api_url/doi_with_protocol.yml +0 -48
  136. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_api_url/dx_doi_org_url.yml +0 -48
  137. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_api_url/force_test_resolver.yml +0 -48
  138. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_api_url/https_url.yml +0 -48
  139. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_api_url/test_resolver.yml +0 -48
  140. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_api_url/test_resolver_http.yml +0 -48
  141. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_from_url/doi.yml +0 -48
  142. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_from_url/doi_with_special_characters.yml +0 -48
  143. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_from_url/not_a_doi.yml +0 -48
  144. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_from_url/sandbox_url.yml +0 -48
  145. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_from_url/url.yml +0 -48
  146. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_registration_agency/crossref.yml +0 -99
  147. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_registration_agency/datacite.yml +0 -99
  148. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_registration_agency/jalc.yml +0 -99
  149. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_registration_agency/kisti.yml +0 -99
  150. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_registration_agency/medra.yml +0 -99
  151. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_registration_agency/not_a_valid_prefix.yml +0 -48
  152. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_registration_agency/not_found.yml +0 -99
  153. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_registration_agency/op.yml +0 -99
  154. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_resolver/doi.yml +0 -48
  155. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_resolver/doi_with_protocol.yml +0 -48
  156. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_resolver/dx_doi_org_url.yml +0 -48
  157. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_resolver/force_stage_resolver.yml +0 -48
  158. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_resolver/https_url.yml +0 -48
  159. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_resolver/stage_resolver.yml +0 -48
  160. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_resolver/stage_resolver_http.yml +0 -48
  161. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_from_format_by_ID/crossref.yml +0 -157
  162. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_from_format_by_ID/crossref_doi_not_url.yml +0 -157
  163. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_from_format_by_ID/datacite.yml +0 -157
  164. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_from_format_by_ID/datacite_doi_http.yml +0 -157
  165. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_from_format_by_ID/github.yml +0 -106
  166. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_from_format_by_ID/orcid.yml +0 -106
  167. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_from_format_by_ID/schema_org.yml +0 -106
  168. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_from_format_by_ID/unknown_DOI_registration_agency.yml +0 -157
  169. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_from_format_from_file/bibtex.yml +0 -106
  170. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_from_format_from_file/citeproc.yml +0 -106
  171. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_from_format_from_file/codemeta.yml +0 -106
  172. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_from_format_from_file/crosscite.yml +0 -106
  173. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_from_format_from_file/crossref.yml +0 -106
  174. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_from_format_from_file/datacite.yml +0 -106
  175. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_from_format_from_file/datacite_json.yml +0 -106
  176. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_from_format_from_file/ris.yml +0 -106
  177. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_from_format_from_file/schema_org.yml +0 -106
  178. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_from_format_from_string/crosscite.yml +0 -106
  179. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/fos/hsh_to_fos_for_match.yml +0 -48
  180. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/fos/hsh_to_fos_for_with_schemeUri_in_hash.yml +0 -48
  181. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/fos/hsh_to_fos_match.yml +0 -48
  182. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/fos/hsh_to_fos_no_match.yml +0 -48
  183. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/fos/name_to_fos_for_match.yml +0 -48
  184. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/fos/name_to_fos_match.yml +0 -48
  185. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/fos/name_to_fos_no_match.yml +0 -48
  186. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/from_schema_org/with_id.yml +0 -48
  187. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/from_schema_org_creators/with_affiliation.yml +0 -48
  188. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/from_schema_org_creators/without_affiliation.yml +0 -48
  189. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_codemeta_metadata/maremma.yml +0 -75
  190. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_codemeta_metadata/metadata_reports.yml +0 -75
  191. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/DOI_with_ORCID_ID.yml +0 -103
  192. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/DOI_with_SICI_DOI.yml +0 -102
  193. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/DOI_with_data_citation.yml +0 -106
  194. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/JaLC.yml +0 -137
  195. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/KISTI.yml +0 -158
  196. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/OP.yml +0 -100
  197. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/affiliation_is_space.yml +0 -101
  198. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/another_book.yml +0 -138
  199. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/another_book_chapter.yml +0 -100
  200. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/article_id_as_page_number.yml +0 -101
  201. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/author_literal.yml +0 -108
  202. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/book.yml +0 -99
  203. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/book_chapter.yml +0 -170
  204. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/book_chapter_with_RDF_for_container.yml +0 -99
  205. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/book_oup.yml +0 -98
  206. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/component.yml +0 -120
  207. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/dataset.yml +0 -130
  208. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/dataset_usda.yml +0 -143
  209. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/date_in_future.yml +0 -101
  210. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/dissertation.yml +0 -129
  211. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/empty_given_name.yml +0 -101
  212. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/invalid_date.yml +0 -101
  213. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/journal_article.yml +0 -100
  214. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/journal_article_original_language_title.yml +0 -99
  215. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/journal_article_with.yml +0 -104
  216. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/journal_article_with_RDF_for_container.yml +0 -99
  217. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/journal_article_with_funding.yml +0 -100
  218. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/journal_issue.yml +0 -127
  219. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/mEDRA.yml +0 -98
  220. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/markup.yml +0 -105
  221. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/missing_creator.yml +0 -100
  222. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/multiple_issn.yml +0 -99
  223. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/multiple_titles.yml +0 -98
  224. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/multiple_titles_with_missing.yml +0 -450
  225. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/not_found_error.yml +0 -97
  226. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/peer_review.yml +0 -103
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  413. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/validate_orcid/validate_orcid_wrong_id.yml +0 -48
  414. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/validate_orcid/validate_orcid_www.yml +0 -48
  415. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/validate_orcid_scheme/validate_orcid_scheme.yml +0 -48
  416. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/validate_orcid_scheme/validate_orcid_scheme_https.yml +0 -48
  417. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/validate_orcid_scheme/validate_orcid_scheme_trailing_slash.yml +0 -48
  418. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/validate_orcid_scheme/validate_orcid_scheme_www.yml +0 -48
  419. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/validate_prefix/doi.yml +0 -48
  420. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/validate_prefix/doi_as_url.yml +0 -48
  421. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/validate_prefix/doi_with_protocol.yml +0 -48
  422. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/validate_prefix/only_prefix.yml +0 -48
  423. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/validate_url/DOI.yml +0 -48
  424. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/validate_url/ISSN.yml +0 -48
  425. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/validate_url/URL.yml +0 -48
  426. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/validate_url/string.yml +0 -48
  427. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_bibtex/BlogPosting.yml +0 -55
  428. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_bibtex/Dataset.yml +0 -55
  429. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_bibtex/authors_with_affiliations.yml +0 -114
  430. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_bibtex/climate_data.yml +0 -55
  431. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_bibtex/from_schema_org.yml +0 -115
  432. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_bibtex/keywords_subject_scheme.yml +0 -55
  433. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_bibtex/maremma.yml +0 -75
  434. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_bibtex/text.yml +0 -55
  435. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_bibtex/with_data_citation.yml +0 -55
  436. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_bibtex/with_pages.yml +0 -52
  437. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_citation/Dataset.yml +0 -55
  438. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_citation/Journal_article.yml +0 -55
  439. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_citation/Journal_article_vancouver_style.yml +0 -55
  440. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_citation/Missing_author.yml +0 -49
  441. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_citation/interactive_resource_without_dates.yml +0 -55
  442. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_citation/software_w/version.yml +0 -55
  443. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_citeproc/Another_dataset.yml +0 -55
  444. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_citeproc/BlogPosting.yml +0 -55
  445. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_citeproc/BlogPosting_schema_org.yml +0 -115
  446. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_citeproc/Dataset.yml +0 -55
  447. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_citeproc/container_title.yml +0 -55
  448. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_citeproc/interactive_resource_without_dates.yml +0 -55
  449. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_citeproc/journal_article.yml +0 -55
  450. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_citeproc/keywords_subject_scheme.yml +0 -55
  451. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_citeproc/maremma.yml +0 -75
  452. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_citeproc/missing_creator.yml +0 -49
  453. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_citeproc/multiple_abstracts.yml +0 -55
  454. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_citeproc/organization_author.yml +0 -52
  455. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_citeproc/software.yml +0 -55
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  457. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_citeproc/with_only_first_page.yml +0 -50
  458. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_citeproc/with_pages.yml +0 -52
  459. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_codemeta/SoftwareSourceCode_DataCite.yml +0 -55
  460. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_codemeta/SoftwareSourceCode_DataCite_check_codemeta_v2.yml +0 -55
  461. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_crosscite/datacite_database_attributes.yml +0 -55
  462. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_crosscite/maremma.yml +0 -75
  463. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_crosscite/with_ORCID_ID.yml +0 -52
  464. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_crosscite/with_data_citation.yml +0 -55
  465. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_crosscite/with_data_citation_schema_org.yml +0 -117
  466. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_crossref/from_DataCite.yml +0 -55
  467. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_csv/climate_data.yml +0 -55
  468. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_csv/maremma.yml +0 -75
  469. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_csv/text.yml +0 -55
  470. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_csv/with_data_citation.yml +0 -55
  471. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_csv/with_pages.yml +0 -52
  472. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_datacite_json/maremma.yml +0 -75
  473. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_datacite_json/with_ORCID_ID.yml +0 -52
  474. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_datacite_json/with_data_citation.yml +0 -55
  475. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_datacite_json/with_data_citation_schema_org.yml +0 -117
  476. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_datacite_xml/DOI_not_found.yml +0 -51
  477. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_datacite_xml/Dataset_in_schema_4_0.yml +0 -55
  478. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_datacite_xml/Text_pass-thru.yml +0 -55
  479. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_datacite_xml/Text_pass-thru_with_doi_in_options.yml +0 -55
  480. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_datacite_xml/maremma.yml +0 -75
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  483. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_datacite_xml/with_data_citation_schema_org.yml +0 -115
  484. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_datacite_xml/with_editor.yml +0 -49
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  486. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_jats_xml/Dataset_in_schema_4_0.yml +0 -55
  487. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_jats_xml/Text_pass-thru.yml +0 -55
  488. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_jats_xml/book_chapter.yml +0 -88
  489. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_jats_xml/interactive_resource_without_dates.yml +0 -55
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  492. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_jats_xml/with_data_citation.yml +0 -55
  493. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_jats_xml/with_data_citation_schema_org.yml +0 -117
  494. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_jats_xml/with_editor.yml +0 -49
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  500. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_ris/BlogPosting.yml +0 -55
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  502. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_ris/Dataset.yml +0 -55
  503. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_ris/alternate_name.yml +0 -55
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  505. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_ris/keywords_with_subject_scheme.yml +0 -55
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  508. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_schema_org/Funding.yml +0 -106
  509. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_schema_org/Funding_OpenAIRE.yml +0 -106
  510. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_schema_org/Schema_org_JSON.yml +0 -55
  511. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_schema_org/Schema_org_JSON_Cyark.yml +0 -106
  512. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_schema_org/Schema_org_JSON_IsSupplementTo.yml +0 -106
  513. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_schema_org/Schema_org_JSON_isReferencedBy.yml +0 -55
  514. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_schema_org/alternate_identifiers.yml +0 -55
  515. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_schema_org/data_catalog.yml +0 -55
  516. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_schema_org/geo_location_box.yml +0 -55
  517. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_schema_org/interactive_resource_without_dates.yml +0 -55
  518. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_schema_org/journal_article.yml +0 -55
  519. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_schema_org/maremma_schema_org_JSON.yml +0 -75
  520. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_schema_org/series_information.yml +0 -55
  521. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_schema_org/subject_scheme.yml +0 -55
  522. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_schema_org/subject_scheme_multiple_keywords.yml +0 -55
  523. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_turtle/BlogPosting.yml +0 -55
  524. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_turtle/BlogPosting_schema_org.yml +0 -117
  525. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_turtle/Dataset.yml +0 -55
  526. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_turtle/journal_article.yml +0 -55
  527. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_turtle/with_pages.yml +0 -52
  528. data/spec/fixtures/vivli.xml +0 -1
  529. data/spec/metadata_spec.rb +0 -165
  530. data/spec/readers/bibtex_reader_spec.rb +0 -65
  531. data/spec/readers/citeproc_reader_spec.rb +0 -65
  532. data/spec/readers/codemeta_reader_spec.rb +0 -138
  533. data/spec/readers/crosscite_reader_spec.rb +0 -43
  534. data/spec/readers/crossref_reader_spec.rb +0 -1133
  535. data/spec/readers/datacite_json_reader_spec.rb +0 -82
  536. data/spec/readers/datacite_reader_spec.rb +0 -1853
  537. data/spec/readers/npm_reader_spec.rb +0 -68
  538. data/spec/readers/ris_reader_spec.rb +0 -78
  539. data/spec/readers/schema_org_reader_spec.rb +0 -371
  540. data/spec/spec_helper.rb +0 -95
  541. data/spec/utils_spec.rb +0 -666
  542. data/spec/writers/bibtex_writer_spec.rb +0 -195
  543. data/spec/writers/citation_writer_spec.rb +0 -61
  544. data/spec/writers/citeproc_writer_spec.rb +0 -299
  545. data/spec/writers/codemeta_writer_spec.rb +0 -45
  546. data/spec/writers/crosscite_writer_spec.rb +0 -129
  547. data/spec/writers/crossref_writer_spec.rb +0 -21
  548. data/spec/writers/csv_writer_spec.rb +0 -94
  549. data/spec/writers/datacite_json_writer_spec.rb +0 -112
  550. data/spec/writers/datacite_writer_spec.rb +0 -578
  551. data/spec/writers/jats_writer_spec.rb +0 -208
  552. data/spec/writers/rdf_xml_writer_spec.rb +0 -93
  553. data/spec/writers/ris_writer_spec.rb +0 -207
  554. data/spec/writers/schema_org_writer_spec.rb +0 -418
  555. data/spec/writers/turtle_writer_spec.rb +0 -102
data/spec/fixtures/datacite-example-complicated-v4.0.xml DELETED
@@ -1,54 +0,0 @@
1
- <?xml version="1.0" encoding="UTF-8"?>
2
- <resource xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://datacite.org/schema/kernel-4.0" xsi:schemaLocation="http://datacite.org/schema/kernel-4.0 http://schema.datacite.org/meta/kernel-4.0/metadata.xsd">
3
- <identifier identifierType="DOI">10.5072/testpub</identifier>
4
- <creators>
5
- <creator>
6
- <creatorName>Smith, John</creatorName>
7
- </creator>
8
- <creator>
9
- <creatorName>つまらないものですが</creatorName>
10
- <nameIdentifier nameIdentifierScheme="ISNI" schemeURI="http://isni.org/isni/">0000000134596520</nameIdentifier>
11
- </creator>
12
- </creators>
13
- <titles>
14
- <title>Właściwości rzutowań podprzestrzeniowych</title>
15
- <title titleType="TranslatedTitle">Translation of Polish titles</title>
16
- </titles>
17
- <publisher>Springer</publisher>
18
- <publicationYear>2010</publicationYear>
19
- <subjects>
20
- <subject subjectScheme="DDC">830 German &amp; related literatures</subject>
21
- <subject>Polish Literature</subject>
22
- </subjects>
23
- <contributors>
24
- <contributor contributorType="DataCollector">
25
- <contributorName>Doe, John</contributorName>
26
- <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0001-5393-1421</nameIdentifier>
27
- </contributor>
28
- </contributors>
29
- <language>GER</language>
30
- <resourceType resourceTypeGeneral="Text">Monograph</resourceType>
31
- <alternateIdentifiers>
32
- <alternateIdentifier alternateIdentifierType="ISBN">937-0-4523-12357-6</alternateIdentifier>
33
- </alternateIdentifiers>
34
- <relatedIdentifiers>
35
- <relatedIdentifier relatedIdentifierType="DOI" relationType="IsPartOf">10.5272/oldertestpub</relatedIdentifier>
36
- </relatedIdentifiers>
37
- <sizes>
38
- <size>256 pages</size>
39
- </sizes>
40
- <formats>
41
- <format>pdf</format>
42
- </formats>
43
- <version>2</version>
44
- <rightsList>
45
- <rights rightsURI="http://creativecommons.org/licenses/by-nd/2.0/">Creative Commons Attribution-NoDerivs 2.0 Generic</rights>
46
- </rightsList>
47
- <descriptions>
48
- <description descriptionType="Abstract">
49
- Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. At vero eos et accusam et justo duo dolores et ea rebum. Stet clita kasd gubergren, no sea
50
- takimata sanctus est Lorem ipsum dolor sit amet. Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. At vero eos et accusam et justo duo dolores
51
- et ea rebum. Stet clita kasd gubergren, no sea takimata sanctus est Lorem ipsum dolor sit amet.
52
- </description>
53
- </descriptions>
54
- </resource>
data/spec/fixtures/datacite-example-complicated-v4.1.xml DELETED
@@ -1,57 +0,0 @@
1
- <?xml version="1.0" encoding="UTF-8"?>
2
- <resource xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://datacite.org/schema/kernel-4" xsi:schemaLocation="http://datacite.org/schema/kernel-4 http://schema.datacite.org/meta/kernel-4/metadata.xsd">
3
- <identifier identifierType="DOI">10.5072/testpub</identifier>
4
- <creators>
5
- <creator>
6
- <creatorName nameType="Personal">Smith, John</creatorName>
7
- </creator>
8
- <creator>
9
- <creatorName>つまらないものですが</creatorName>
10
- <nameIdentifier nameIdentifierScheme="ISNI" schemeURI="http://isni.org/isni/">0000000134596520</nameIdentifier>
11
- </creator>
12
- </creators>
13
- <titles>
14
- <title>Właściwości rzutowań podprzestrzeniowych</title>
15
- <title titleType="TranslatedTitle">Translation of Polish titles</title>
16
- </titles>
17
- <publisher>Springer</publisher>
18
- <publicationYear>2010</publicationYear>
19
- <subjects>
20
- <subject subjectScheme="DDC">830 German &amp; related literatures</subject>
21
- <subject>Polish Literature</subject>
22
- </subjects>
23
- <dates>
24
- <date dateType="Other" dateInformation="Correction">2012-12-13</date>
25
- </dates>
26
- <contributors>
27
- <contributor contributorType="DataCollector">
28
- <contributorName>Doe, John</contributorName>
29
- <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0001-5393-1421</nameIdentifier>
30
- </contributor>
31
- </contributors>
32
- <language>GER</language>
33
- <resourceType resourceTypeGeneral="Text">Monograph</resourceType>
34
- <alternateIdentifiers>
35
- <alternateIdentifier alternateIdentifierType="ISBN">937-0-4523-12357-6</alternateIdentifier>
36
- </alternateIdentifiers>
37
- <relatedIdentifiers>
38
- <relatedIdentifier resourceTypeGeneral="Text" relatedIdentifierType="DOI" relationType="IsPartOf">10.5272/oldertestpub</relatedIdentifier>
39
- </relatedIdentifiers>
40
- <sizes>
41
- <size>256 pages</size>
42
- </sizes>
43
- <formats>
44
- <format>pdf</format>
45
- </formats>
46
- <version>2</version>
47
- <rightsList>
48
- <rights xml:lang="eng" rightsURI="http://creativecommons.org/licenses/by-nd/2.0/">Creative Commons Attribution-NoDerivs 2.0 Generic</rights>
49
- </rightsList>
50
- <descriptions>
51
- <description descriptionType="Abstract">
52
- Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. At vero eos et accusam et justo duo dolores et ea rebum. Stet clita kasd gubergren, no sea
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- takimata sanctus est Lorem ipsum dolor sit amet. Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. At vero eos et accusam et justo duo dolores
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- et ea rebum. Stet clita kasd gubergren, no sea takimata sanctus est Lorem ipsum dolor sit amet.
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- </description>
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- </descriptions>
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- </resource>
data/spec/fixtures/datacite-example-dissertation-v4.4.xml DELETED
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- <?xml version="1.0" encoding="UTF-8"?>
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- <resource xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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- xmlns="http://datacite.org/schema/kernel-4" xsi:schemaLocation="http://datacite.org/schema/kernel-4 http://schema.datacite.org/meta/kernel-4.4/metadata.xsd">
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- <identifier identifierType="DOI">10.5072/100044</identifier>
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- <creators>
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- <creator>
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- <creatorName nameType="Personal">Luo, R</creatorName>
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- </creator>
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- <creator>
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- <creatorName nameType="Personal">Liu, B</creatorName>
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- </creator>
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- <creator>
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- <creatorName nameType="Personal">Xie, Y</creatorName>
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- </creator>
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- <creator>
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- <creatorName nameType="Personal">Li, Z</creatorName>
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- </creator>
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- </creators>
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- <titles>
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- <title xml:lang="en">
21
- Software and supporting material for "SOAPdenovo2: An empirically improved memory-efficient short read de novo assembly"
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- </title>
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- </titles>
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- <publisher xml:lang="en">GigaScience Database</publisher>
25
- <publicationYear>2012</publicationYear>
26
- <subjects>
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- <subject xml:lang="en">DNA (Genetics)</subject>
28
- <subject xml:lang="en">Computer Program</subject>
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- </subjects>
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- <dates>
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- <date dateType="Available">2012-12-13</date>
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- </dates>
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- <language>en</language>
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- <resourceType resourceTypeGeneral="Dissertation"></resourceType>
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- <relatedIdentifiers>
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- <relatedIdentifier relatedIdentifierType="DOI" relationType="IsReferencedBy">10.5072/2047-217X-1-1</relatedIdentifier>
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- <relatedIdentifier relatedIdentifierType="DOI" relationType="Compiles">10.5072/100038</relatedIdentifier>
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- <sizes>
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- <size>31 MB</size>
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- <rights xml:lang="en-US" schemeURI="https://spdx.org/licenses/" rightsIdentifierScheme="SPDX" rightsIdentifier="CC0 1.0" rightsURI="http://creativecommons.org/publicdomain/zero/1.0/"/>
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- </rightsList>
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- <descriptions>
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- <description xml:lang="en" descriptionType="Abstract">
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- SOAPdenovo2 is the latest de novo genome assembly package from BGI's SOAP (short oligonucleotide analysis package) suite of tools (homepage here: http://soap.genomics.org.cn/). Compared to SOAPdenovo1, this new version has the advantage of a new
48
- algorithm design that reduces memory consumption in graph construction, resolves more repeat regions in contig assembly, increases coverage and length in scaffold construction, improves gap closure, and is optimized for large genomes. Using new
49
- sequencing data from the YH (Homo sapiens) diploid genome - the first sequenced Han Chinese individual, an updated assembly was produced (see dataset here: doi:10.5524/100038), with the N50 scores for the contig and scaffold being 3-fold and 50-fold
50
- longer, respectively, than the first published version. The genome coverage increased from 81.16% to 93.91%, and memory consumption was ~2/3 times lower during the point of largest memory consumption. Benchmarking with Assemblathon1 and GAGE datasets
51
- shows that SOAPdenovo2 greatly surpasses its predecessor SOAPdenovo1 and is competitive to other assemblers on both assembly length and accuracy. In order to facilitate readers to repeat and recreate these findings, configured packages with the
52
- compressed pipelines containing all of the necessary shell scripts and tools are available from the BGI FTP server (ftp://public.genomics.org.cn/BGI/SOAPdenovo2). The latest version of SOAPdenovo2 is available from Sourceforge:
53
- http://soapdenovo2.sourceforge.net/ These pipelines will also soon be made available from our data platform as Galaxy workflows: http://galaxy.cbiit.cuhk.edu.hk/
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- </description>
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- </descriptions>
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- </resource>
data/spec/fixtures/datacite-example-escaped-text.xml DELETED
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- <?xml version="1.0" encoding="UTF-8"?>
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- <identifier identifierType="DOI">10.5072/testpub</identifier>
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- <creator>
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- <creatorName nameType="Personal">Smith, John</creatorName>
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- <creator>
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- <titles>
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- <title>Some initial text&lt;the rest of the text won't display.</title>
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- <publisher>Springer</publisher>
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- <publicationYear>2010</publicationYear>
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- <subjects>
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- <subject subjectScheme="DDC">830 German &amp; related literatures</subject>
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- <subject>Polish Literature</subject>
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- </subjects>
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- <dates>
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- <date dateType="Other" dateInformation="Correction">2012-12-13</date>
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- <contributors>
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- <contributor contributorType="DataCollector">
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- <contributorName>Doe, John</contributorName>
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- <language>GER</language>
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- <resourceType resourceTypeGeneral="Text">Monograph</resourceType>
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- <relatedIdentifiers>
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- <relatedIdentifier resourceTypeGeneral="Text" relatedIdentifierType="DOI" relationType="IsPartOf">10.5272/oldertestpub</relatedIdentifier>
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- </relatedIdentifiers>
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- <sizes>
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- <size>256 pages</size>
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- </sizes>
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- <formats>
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- <format>pdf</format>
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- </formats>
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- <version>2</version>
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- <rightsList>
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- <rights xml:lang="eng" rightsURI="http://creativecommons.org/licenses/by-nd/2.0/">Creative Commons Attribution-NoDerivs 2.0 Generic</rights>
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- <descriptions>
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- <description descriptionType="Abstract">
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- Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. At vero eos et accusam et justo duo dolores et ea rebum. Stet clita kasd gubergren, no sea
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- takimata sanctus est Lorem ipsum dolor sit amet. Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. At vero eos et accusam et justo duo dolores
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- et ea rebum. Stet clita kasd gubergren, no sea takimata sanctus est Lorem ipsum dolor sit amet.
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- </description>
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- </resource>
data/spec/fixtures/datacite-example-full-v4.4.xml DELETED
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- <?xml version="1.0" encoding="UTF-8"?>
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- <resource xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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- xmlns="http://datacite.org/schema/kernel-4" xsi:schemaLocation="http://datacite.org/schema/kernel-4 http://schema.datacite.org/meta/kernel-4.4/metadata.xsd">
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- <identifier identifierType="DOI">10.5072/example-full</identifier>
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- <creators>
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- <creator>
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- <creatorName nameType="Personal">Miller, Elizabeth</creatorName>
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- <givenName>Elizabeth</givenName>
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- <familyName>Miller</familyName>
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- <nameIdentifier schemeURI="https://orcid.org/" nameIdentifierScheme="ORCID">0000-0001-5000-0007</nameIdentifier>
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- <affiliation>DataCite</affiliation>
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- </creator>
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- </creators>
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- <titles>
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- <title xml:lang="en-US">Full DataCite XML Example</title>
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- <title xml:lang="en-US" titleType="Subtitle">Demonstration of DataCite Properties.</title>
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- </titles>
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- <publisher xml:lang="en">DataCite</publisher>
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- <publicationYear>2014</publicationYear>
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- <subjects>
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- <subject xml:lang="en-US" schemeURI="http://dewey.info/" subjectScheme="dewey" classificationCode="000">computer science</subject>
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- </subjects>
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- <contributor contributorType="ProjectLeader">
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- <contributorName>Starr, Joan</contributorName>
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- <givenName>Joan</givenName>
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- <nameIdentifier schemeURI="https://orcid.org/" nameIdentifierScheme="ORCID">0000-0002-7285-027X</nameIdentifier>
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- <affiliation>California Digital Library</affiliation>
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- <dates>
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- <date dateType="Updated" dateInformation="Updated with 4.4 properties">2021-01-26</date>
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- <language>en-US</language>
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- <resourceType resourceTypeGeneral="Software">XML</resourceType>
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- <alternateIdentifiers>
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- <alternateIdentifier alternateIdentifierType="URL">https://schema.datacite.org/meta/kernel-4.4/example/datacite-example-full-v4.4.xml</alternateIdentifier>
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- </alternateIdentifiers>
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- <relatedIdentifiers>
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- <relatedIdentifier relatedIdentifierType="URL" relationType="HasMetadata" relatedMetadataScheme="citeproc+json" schemeURI="https://github.com/citation-style-language/schema/raw/master/csl-data.json">https://data.datacite.org/application/citeproc+json/10.5072/example-full</relatedIdentifier>
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- <relatedIdentifier relatedIdentifierType="arXiv" relationType="IsReviewedBy" resourceTypeGeneral="Text">arXiv:0706.0001</relatedIdentifier>
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- <size>4 kB</size>
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- </sizes>
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- <formats>
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- <format>application/xml</format>
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- </formats>
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- <version>4.2</version>
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- <rightsList>
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- <rights xml:lang="en-US" schemeURI="https://spdx.org/licenses/" rightsIdentifierScheme="SPDX" rightsIdentifier="CC0 1.0" rightsURI="https://creativecommons.org/publicdomain/zero/1.0/"/>
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- </rightsList>
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- <descriptions>
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- <description xml:lang="en-US" descriptionType="Abstract">XML example of all DataCite Metadata Schema v4.4 properties.</description>
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- <geoLocations>
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- <geoLocation>
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- <geoLocationPlace>Atlantic Ocean</geoLocationPlace>
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- <geoLocationPoint>
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- <pointLongitude>-67.302</pointLongitude>
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- <eastBoundLongitude>-68.211</eastBoundLongitude>
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- </geoLocationBox>
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- <geoLocationPolygon>
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- <polygonPoint>
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- <pointLatitude>41.991</pointLatitude>
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- <pointLongitude>-71.032</pointLongitude>
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- <polygonPoint>
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- <pointLatitude>42.893</pointLatitude>
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- <pointLongitude>-69.622</pointLongitude>
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- <polygonPoint>
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- <pointLatitude>41.991</pointLatitude>
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- <pointLongitude>-68.211</pointLongitude>
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- <polygonPoint>
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- <pointLatitude>41.090</pointLatitude>
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- <pointLongitude>-69.622</pointLongitude>
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- <pointLatitude>41.991</pointLatitude>
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- <pointLongitude>-71.032</pointLongitude>
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- <fundingReferences>
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- <fundingReference>
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- <funderName>National Science Foundation</funderName>
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- <funderIdentifier funderIdentifierType="Crossref Funder ID">https://doi.org/10.13039/100000001</funderIdentifier>
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- <awardNumber>CBET-106</awardNumber>
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- <awardTitle>Full DataCite XML Example</awardTitle>
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- <relatedItems>
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- <relatedItem relationType="IsPublishedIn" relatedItemType="Journal">
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- <relatedItemIdentifier relatedItemIdentifierType="DOI">10.1016/j.physletb.2017.11.044</relatedItemIdentifier>
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- <titles>
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- <title>Physics letters / B</title>
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- <publicationYear>2018</publicationYear>
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- <volume>776</volume>
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- <firstPage>249</firstPage>
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- <lastPage>264</lastPage>
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data/spec/fixtures/datacite-example-full-v4.5.xml DELETED
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- <?xml version="1.0" encoding="UTF-8"?>
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- <!-- Example with all properties -->
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- <resource
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- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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- xmlns="http://datacite.org/schema/kernel-4" xsi:schemaLocation="http://datacite.org/schema/kernel-4 ../metadata.xsd">
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- <identifier identifierType="DOI">10.82433/B09Z-4K37</identifier>
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- <creators>
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- <creator>
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- <creatorName nameType="Personal">ExampleFamilyName, ExampleGivenName</creatorName>
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- <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="https://orcid.org">https://orcid.org/0000-0001-5727-2427</nameIdentifier>
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- <affiliation affiliationIdentifier="https://ror.org/04wxnsj81" affiliationIdentifierScheme="ROR" schemeURI="https://ror.org">ExampleAffiliation</affiliation>
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- <creator>
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- <creatorName xml:lang="en" nameType="Organizational">ExampleOrganization</creatorName>
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- <nameIdentifier nameIdentifierScheme="ROR" schemeURI="https://ror.org">https://ror.org/04wxnsj81</nameIdentifier>
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- </creator>
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- </creators>
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- <titles>
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- <title xml:lang="en">Example Title</title>
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- <title titleType="Subtitle" xml:lang="en">Example Subtitle</title>
23
- <title titleType="TranslatedTitle" xml:lang="fr">Example TranslatedTitle</title>
24
- <title titleType="AlternativeTitle" xml:lang="en">Example AlternativeTitle</title>
25
- </titles>
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- <publisher xml:lang="en" publisherIdentifier="https://ror.org/04z8jg394" publisherIdentifierScheme="ROR" schemeURI="https://ror.org/">Example Publisher</publisher>
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- <publicationYear>2023</publicationYear>
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- <resourceType resourceTypeGeneral="Dataset">Example ResourceType</resourceType>
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- <subjects>
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- <subject subjectScheme="Fields of Science and Technology (FOS)" schemeURI="http://www.oecd.org/science/inno" valueURI="http://www.oecd.org/science/inno/38235147.pdf">FOS: Computer and information sciences</subject>
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- <subject subjectScheme="Australian and New Zealand Standard Research Classification (ANZSRC), 2020" schemeURI="https://www.abs.gov.au/statistics/classifications/australian-and-new-zealand-standard-research-classification-anzsrc" classificationCode="461001">Digital curation and preservation</subject>
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- <subject>Example Subject</subject>
33
- </subjects>
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- <contributors>
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- <contributor contributorType="ContactPerson">
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- <contributorName nameType="Personal">ExampleFamilyName, ExampleGivenName</contributorName>
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- <givenName>ExampleGivenName</givenName>
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- <familyName>ExampleFamilyName</familyName>
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- <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="https://orcid.org">https://orcid.org/0000-0001-5727-2427/</nameIdentifier>
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- <affiliation affiliationIdentifier="https://ror.org/04wxnsj81" affiliationIdentifierScheme="ROR" schemeURI="https://ror.org">ExampleAffiliation</affiliation>
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- </contributor>
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- <contributor contributorType="DataCollector">
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- <contributorName nameType="Personal">ExampleFamilyName, ExampleGivenName</contributorName>
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- </contributor>
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- <contributor contributorType="DataCurator">
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- <contributorName nameType="Personal">ExampleFamilyName, ExampleGivenName</contributorName>
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- </contributor>
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- <contributor contributorType="DataManager">
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- <contributorName nameType="Personal">ExampleFamilyName, ExampleGivenName</contributorName>
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- </contributor>
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- <contributor contributorType="Distributor">
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- <contributorName nameType="Organizational">ExampleOrganization</contributorName>
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- <contributor contributorType="Editor">
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- <contributorName nameType="Personal">ExampleFamilyName, ExampleGivenName</contributorName>
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- <contributor contributorType="HostingInstitution">
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- <contributor contributorType="RegistrationAgency">
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- <contributorName nameType="Organizational">DataCite</contributorName>
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- <contributorName nameType="Organizational">International DOI Foundation</contributorName>
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- <date dateType="Valid">2023-01-01</date>
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- <date dateType="Withdrawn">2023-01-01</date>
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- <date dateType="Other" dateInformation="ExampleDateInformation">2023-01-01</date>
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- <language>en</language>
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- <alternateIdentifier alternateIdentifierType="Local accession number">12345</alternateIdentifier>
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