bolognese 2.3.2 → 2.7.0

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 (585) 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 +1 -1
  5. data/Gemfile.lock +196 -164
  6. data/README.md +1 -1
  7. data/bolognese.gemspec +30 -37
  8. data/lib/bolognese/author_utils.rb +2 -44
  9. data/lib/bolognese/citeproc_extensions.rb +48 -0
  10. data/lib/bolognese/datacite_utils.rb +17 -7
  11. data/lib/bolognese/doi_utils.rb +4 -3
  12. data/lib/bolognese/metadata.rb +8 -5
  13. data/lib/bolognese/metadata_utils.rb +18 -4
  14. data/lib/bolognese/readers/citeproc_reader.rb +1 -1
  15. data/lib/bolognese/readers/codemeta_reader.rb +1 -1
  16. data/lib/bolognese/readers/crossref_reader.rb +17 -5
  17. data/lib/bolognese/readers/datacite_reader.rb +22 -48
  18. data/lib/bolognese/readers/ris_reader.rb +1 -1
  19. data/lib/bolognese/readers/schema_org_reader.rb +1 -1
  20. data/lib/bolognese/utils.rb +95 -113
  21. data/lib/bolognese/version.rb +1 -1
  22. data/lib/bolognese/writers/csv_writer.rb +3 -5
  23. data/lib/bolognese/writers/jats_writer.rb +3 -2
  24. data/lib/bolognese.rb +1 -4
  25. data/resources/kernel-4/include/datacite-contributorType-v4.xsd +1 -1
  26. data/resources/kernel-4/include/datacite-dateType-v4.xsd +1 -1
  27. data/resources/kernel-4/include/datacite-relatedIdentifierType-v4.xsd +3 -1
  28. data/resources/kernel-4/include/datacite-relationType-v4.xsd +4 -2
  29. data/resources/kernel-4/include/datacite-resourceType-v4.xsd +4 -1
  30. data/resources/kernel-4/metadata.xsd +4 -1
  31. data/resources/kernel-4.7/include/datacite-contributorType-v4.xsd +37 -0
  32. data/resources/kernel-4.7/include/datacite-dateType-v4.xsd +27 -0
  33. data/resources/kernel-4.7/include/datacite-descriptionType-v4.xsd +19 -0
  34. data/resources/kernel-4.7/include/datacite-funderIdentifierType-v4.xsd +16 -0
  35. data/resources/kernel-4.7/include/datacite-nameType-v4.xsd +10 -0
  36. data/resources/kernel-4.7/include/datacite-numberType-v4.xsd +12 -0
  37. data/resources/kernel-4.7/include/datacite-relatedIdentifierType-v4.xsd +39 -0
  38. data/resources/kernel-4.7/include/datacite-relationType-v4.xsd +59 -0
  39. data/resources/kernel-4.7/include/datacite-resourceType-v4.xsd +52 -0
  40. data/resources/kernel-4.7/include/datacite-titleType-v4.xsd +14 -0
  41. data/resources/kernel-4.7/include/xml.xsd +286 -0
  42. data/resources/kernel-4.7/metadata.xsd +715 -0
  43. metadata +129 -734
  44. data/spec/array_spec.rb +0 -22
  45. data/spec/author_utils_spec.rb +0 -259
  46. data/spec/cli_spec.rb +0 -226
  47. data/spec/datacite_utils_spec.rb +0 -315
  48. data/spec/doi_utils_spec.rb +0 -314
  49. data/spec/find_from_format_spec.rb +0 -114
  50. data/spec/fixtures/aida.json +0 -82
  51. data/spec/fixtures/cgimp_package.json +0 -18
  52. data/spec/fixtures/cit_package.json +0 -19
  53. data/spec/fixtures/citeproc-no-author.json +0 -26
  54. data/spec/fixtures/citeproc-no-categories.json +0 -21
  55. data/spec/fixtures/citeproc.json +0 -36
  56. data/spec/fixtures/codemeta.json +0 -86
  57. data/spec/fixtures/codemeta_v2.json +0 -86
  58. data/spec/fixtures/crosscite.json +0 -63
  59. data/spec/fixtures/crossref.bib +0 -14
  60. data/spec/fixtures/crossref.ris +0 -15
  61. data/spec/fixtures/crossref.xml +0 -606
  62. data/spec/fixtures/crossref_schema_4.6_values.xml +0 -183
  63. data/spec/fixtures/datacite-empty-sizes.xml +0 -57
  64. data/spec/fixtures/datacite-example-ROR-nameIdentifiers.xml +0 -125
  65. data/spec/fixtures/datacite-example-affiliation.xml +0 -114
  66. data/spec/fixtures/datacite-example-ancientdates-v4.3.xml +0 -29
  67. data/spec/fixtures/datacite-example-complicated-tba.xml +0 -56
  68. data/spec/fixtures/datacite-example-complicated-v3.0.xml +0 -48
  69. data/spec/fixtures/datacite-example-complicated-v4.0.xml +0 -54
  70. data/spec/fixtures/datacite-example-complicated-v4.1.xml +0 -57
  71. data/spec/fixtures/datacite-example-dissertation-v4.4.xml +0 -56
  72. data/spec/fixtures/datacite-example-escaped-text.xml +0 -56
  73. data/spec/fixtures/datacite-example-full-v4.4.xml +0 -114
  74. data/spec/fixtures/datacite-example-full-v4.5.xml +0 -255
  75. data/spec/fixtures/datacite-example-full-v4.6.xml +0 -114
  76. data/spec/fixtures/datacite-example-geolocation-2.xml +0 -141
  77. data/spec/fixtures/datacite-example-geolocation.xml +0 -66
  78. data/spec/fixtures/datacite-example-nameIdentifier-with-schemeURI.xml +0 -94
  79. data/spec/fixtures/datacite-example-polygon-v4.1.xml +0 -163
  80. data/spec/fixtures/datacite-example-relateditems-with-attributes.xml +0 -61
  81. data/spec/fixtures/datacite-example-relateditems.xml +0 -61
  82. data/spec/fixtures/datacite-example-xs-string.xml +0 -28
  83. data/spec/fixtures/datacite-formats-with-xs.xml +0 -22
  84. data/spec/fixtures/datacite-funderIdentifier.xml +0 -98
  85. data/spec/fixtures/datacite-geolocation-empty.xml +0 -159
  86. data/spec/fixtures/datacite-geolocationpolygons-multiple.xml +0 -76
  87. data/spec/fixtures/datacite-metadata-sample-complicated-v2.2.xml +0 -52
  88. data/spec/fixtures/datacite-multiple-language.xml +0 -38
  89. data/spec/fixtures/datacite-multiple-rights.xml +0 -59
  90. data/spec/fixtures/datacite-schema-2.2.xml +0 -80
  91. data/spec/fixtures/datacite-seriesinformation.xml +0 -46
  92. data/spec/fixtures/datacite-space-in-sizes.xml +0 -52
  93. data/spec/fixtures/datacite-xml-lang.xml +0 -51
  94. data/spec/fixtures/datacite.json +0 -89
  95. data/spec/fixtures/datacite.xml +0 -40
  96. data/spec/fixtures/datacite_blank_name_identifier.xml +0 -22
  97. data/spec/fixtures/datacite_blank_publisher.xml +0 -18
  98. data/spec/fixtures/datacite_dataset.xml +0 -58
  99. data/spec/fixtures/datacite_journal_article.xml +0 -64
  100. data/spec/fixtures/datacite_malformed_creator.xml +0 -52
  101. data/spec/fixtures/datacite_missing_creator.xml +0 -33
  102. data/spec/fixtures/datacite_schema_3.xml +0 -58
  103. data/spec/fixtures/datacite_software.json +0 -21
  104. data/spec/fixtures/datacite_software_missing_comma.json +0 -18
  105. data/spec/fixtures/datacite_software_overlapping_keys.json +0 -18
  106. data/spec/fixtures/datacite_software_version.json +0 -74
  107. data/spec/fixtures/edam_package.json +0 -12
  108. data/spec/fixtures/funding_reference.xml +0 -53
  109. data/spec/fixtures/gtex.xml +0 -71
  110. data/spec/fixtures/maremma/codemeta.json +0 -36
  111. data/spec/fixtures/nist.xml +0 -35
  112. data/spec/fixtures/ns0.xml +0 -2
  113. data/spec/fixtures/pure.bib +0 -14
  114. data/spec/fixtures/pure.ris +0 -15
  115. data/spec/fixtures/pure.xml +0 -188
  116. data/spec/fixtures/ris_bug.ris +0 -9
  117. data/spec/fixtures/schema_4.0.xml +0 -140
  118. data/spec/fixtures/schema_org.json +0 -50
  119. data/spec/fixtures/schema_org_4.6_attributes.json +0 -108
  120. data/spec/fixtures/schema_org_geolocation.json +0 -82
  121. data/spec/fixtures/schema_org_geoshape.json +0 -550
  122. data/spec/fixtures/schema_org_gtex.json +0 -75
  123. data/spec/fixtures/schema_org_list.json +0 -12623
  124. data/spec/fixtures/schema_org_tdl_iodp_invalid_authors.json +0 -25
  125. data/spec/fixtures/schema_org_topmed.json +0 -53
  126. data/spec/fixtures/schema_org_type_as_array.json +0 -41
  127. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_from_id/crossref/default.yml +0 -106
  128. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_from_id/crossref/to_bibtex.yml +0 -106
  129. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_from_id/crossref/to_citation.yml +0 -106
  130. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_from_id/crossref/to_crossref.yml +0 -106
  131. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_from_id/crossref/to_datacite.yml +0 -106
  132. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_from_id/crossref/to_jats.yml +0 -106
  133. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_from_id/crossref/to_schema_org.yml +0 -106
  134. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_from_id/datacite/default.yml +0 -106
  135. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_from_id/datacite/to_bibtex.yml +0 -106
  136. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_from_id/datacite/to_citation.yml +0 -106
  137. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_from_id/datacite/to_datacite.yml +0 -106
  138. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_from_id/datacite/to_datacite_json.yml +0 -106
  139. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_from_id/datacite/to_jats.yml +0 -106
  140. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_from_id/datacite/to_schema_org.yml +0 -106
  141. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_from_id/schema_org/default.yml +0 -117
  142. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_from_id/schema_org/to_datacite.yml +0 -117
  143. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_from_id/schema_org/to_schema_org.yml +0 -115
  144. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/find_from_format_by_id/crossref.yml +0 -54
  145. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/find_from_format_by_id/datacite.yml +0 -54
  146. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/find_from_format_by_id/jalc.yml +0 -54
  147. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/find_from_format_by_id/kisti.yml +0 -54
  148. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/find_from_format_by_id/medra.yml +0 -54
  149. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/find_from_format_by_id/op.yml +0 -54
  150. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/authors_as_string/author.yml +0 -48
  151. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/authors_as_string/no_author.yml +0 -48
  152. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/authors_as_string/single_author.yml +0 -48
  153. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/authors_as_string/with_organization.yml +0 -48
  154. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/change_datacite_metadata/change_state.yml +0 -106
  155. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/change_datacite_metadata/change_title.yml +0 -106
  156. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/change_metadata_as_datacite_xml/change_description.yml +0 -55
  157. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/change_metadata_as_datacite_xml/change_identifiers.yml +0 -55
  158. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/change_metadata_as_datacite_xml/change_license.yml +0 -55
  159. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/change_metadata_as_datacite_xml/change_license_name.yml +0 -55
  160. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/change_metadata_as_datacite_xml/change_license_url.yml +0 -55
  161. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/change_metadata_as_datacite_xml/change_state.yml +0 -55
  162. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/change_metadata_as_datacite_xml/validates_against_schema.yml +0 -55
  163. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/change_metadata_as_datacite_xml/with_data_citation.yml +0 -55
  164. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_api_url/doi.yml +0 -48
  165. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_api_url/doi_with_protocol.yml +0 -48
  166. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_api_url/dx_doi_org_url.yml +0 -48
  167. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_api_url/force_test_resolver.yml +0 -48
  168. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_api_url/https_url.yml +0 -48
  169. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_api_url/test_resolver.yml +0 -48
  170. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_api_url/test_resolver_http.yml +0 -48
  171. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_from_url/doi.yml +0 -48
  172. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_from_url/doi_with_special_characters.yml +0 -48
  173. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_from_url/not_a_doi.yml +0 -48
  174. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_from_url/sandbox_url.yml +0 -48
  175. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_from_url/url.yml +0 -48
  176. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_registration_agency/crossref.yml +0 -99
  177. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_registration_agency/datacite.yml +0 -99
  178. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_registration_agency/jalc.yml +0 -99
  179. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_registration_agency/kisti.yml +0 -99
  180. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_registration_agency/medra.yml +0 -99
  181. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_registration_agency/not_a_valid_prefix.yml +0 -48
  182. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_registration_agency/not_found.yml +0 -99
  183. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_registration_agency/op.yml +0 -99
  184. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_resolver/doi.yml +0 -48
  185. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_resolver/doi_with_protocol.yml +0 -48
  186. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_resolver/dx_doi_org_url.yml +0 -48
  187. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_resolver/force_stage_resolver.yml +0 -48
  188. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_resolver/https_url.yml +0 -48
  189. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_resolver/stage_resolver.yml +0 -48
  190. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_resolver/stage_resolver_http.yml +0 -48
  191. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_from_format_by_ID/crossref.yml +0 -157
  192. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_from_format_by_ID/crossref_doi_not_url.yml +0 -157
  193. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_from_format_by_ID/datacite.yml +0 -157
  194. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_from_format_by_ID/datacite_doi_http.yml +0 -157
  195. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_from_format_by_ID/github.yml +0 -106
  196. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_from_format_by_ID/orcid.yml +0 -106
  197. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_from_format_by_ID/schema_org.yml +0 -106
  198. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_from_format_by_ID/unknown_DOI_registration_agency.yml +0 -157
  199. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_from_format_from_file/bibtex.yml +0 -106
  200. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_from_format_from_file/citeproc.yml +0 -106
  201. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_from_format_from_file/codemeta.yml +0 -106
  202. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_from_format_from_file/crosscite.yml +0 -106
  203. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_from_format_from_file/crossref.yml +0 -106
  204. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_from_format_from_file/datacite.yml +0 -106
  205. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_from_format_from_file/datacite_json.yml +0 -106
  206. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_from_format_from_file/ris.yml +0 -106
  207. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_from_format_from_file/schema_org.yml +0 -106
  208. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_from_format_from_string/crosscite.yml +0 -106
  209. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/fos/hsh_to_fos_for_match.yml +0 -48
  210. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/fos/hsh_to_fos_for_with_schemeUri_in_hash.yml +0 -48
  211. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/fos/hsh_to_fos_match.yml +0 -48
  212. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/fos/hsh_to_fos_no_match.yml +0 -48
  213. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/fos/name_to_fos_for_match.yml +0 -48
  214. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/fos/name_to_fos_match.yml +0 -48
  215. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/fos/name_to_fos_no_match.yml +0 -48
  216. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/from_schema_org/with_id.yml +0 -48
  217. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/from_schema_org_creators/with_affiliation.yml +0 -48
  218. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/from_schema_org_creators/without_affiliation.yml +0 -48
  219. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_codemeta_metadata/maremma.yml +0 -75
  220. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_codemeta_metadata/metadata_reports.yml +0 -75
  221. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/DOI_with_ORCID_ID.yml +0 -103
  222. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/DOI_with_SICI_DOI.yml +0 -102
  223. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/DOI_with_data_citation.yml +0 -106
  224. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/JaLC.yml +0 -137
  225. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/KISTI.yml +0 -158
  226. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/OP.yml +0 -100
  227. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/affiliation_is_space.yml +0 -101
  228. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/another_book.yml +0 -138
  229. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/another_book_chapter.yml +0 -100
  230. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/article_id_as_page_number.yml +0 -101
  231. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/author_literal.yml +0 -108
  232. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/book.yml +0 -99
  233. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/book_chapter.yml +0 -170
  234. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/book_chapter_with_RDF_for_container.yml +0 -99
  235. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/book_oup.yml +0 -98
  236. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/component.yml +0 -120
  237. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/dataset.yml +0 -130
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  562. data/spec/readers/codemeta_reader_spec.rb +0 -138
  563. data/spec/readers/crosscite_reader_spec.rb +0 -43
  564. data/spec/readers/crossref_reader_spec.rb +0 -1133
  565. data/spec/readers/datacite_json_reader_spec.rb +0 -82
  566. data/spec/readers/datacite_reader_spec.rb +0 -1853
  567. data/spec/readers/npm_reader_spec.rb +0 -68
  568. data/spec/readers/ris_reader_spec.rb +0 -78
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  570. data/spec/spec_helper.rb +0 -95
  571. data/spec/utils_spec.rb +0 -666
  572. data/spec/writers/bibtex_writer_spec.rb +0 -195
  573. data/spec/writers/citation_writer_spec.rb +0 -61
  574. data/spec/writers/citeproc_writer_spec.rb +0 -299
  575. data/spec/writers/codemeta_writer_spec.rb +0 -45
  576. data/spec/writers/crosscite_writer_spec.rb +0 -129
  577. data/spec/writers/crossref_writer_spec.rb +0 -21
  578. data/spec/writers/csv_writer_spec.rb +0 -94
  579. data/spec/writers/datacite_json_writer_spec.rb +0 -112
  580. data/spec/writers/datacite_writer_spec.rb +0 -578
  581. data/spec/writers/jats_writer_spec.rb +0 -208
  582. data/spec/writers/rdf_xml_writer_spec.rb +0 -93
  583. data/spec/writers/ris_writer_spec.rb +0 -207
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  585. data/spec/writers/turtle_writer_spec.rb +0 -102
@@ -1,58 +0,0 @@
1
- <?xml version="1.0" encoding="UTF-8"?>
2
- <resource xmlns="http://datacite.org/schema/kernel-3" xmlns:dim="http://www.dspace.org/xmlns/dspace/dim" xmlns:dryad="http://purl.org/dryad/terms/" xmlns:dspace="http://www.dspace.org/xmlns/dspace/dim" xmlns:mets="http://www.loc.gov/METS/" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://datacite.org/schema/kernel-3 http://schema.datacite.org/meta/kernel-3/metadata.xsd">
3
- <identifier identifierType="DOI">10.5061/DRYAD.8515</identifier>
4
- <version>1</version>
5
- <creators>
6
- <creator>
7
- <creatorName>Ollomo, Benjamin</creatorName>
8
- </creator>
9
- <creator>
10
- <creatorName>Durand, Patrick</creatorName>
11
- </creator>
12
- <creator>
13
- <creatorName>Prugnolle, Franck</creatorName>
14
- </creator>
15
- <creator>
16
- <creatorName>Douzery, Emmanuel J. P.</creatorName>
17
- </creator>
18
- <creator>
19
- <creatorName>Arnathau, Céline</creatorName>
20
- </creator>
21
- <creator>
22
- <creatorName>Nkoghe, Dieudonné</creatorName>
23
- </creator>
24
- <creator>
25
- <creatorName>Leroy, Eric</creatorName>
26
- </creator>
27
- <creator>
28
- <creatorName>Renaud, François</creatorName>
29
- </creator>
30
- </creators>
31
- <titles>
32
- <title>Data from: A new malaria agent in African hominids.</title>
33
- </titles>
34
- <publisher>Dryad Digital Repository</publisher>
35
- <publicationYear>2011</publicationYear>
36
- <subjects>
37
- <subject>Phylogeny</subject>
38
- <subject>Malaria</subject>
39
- <subject>Parasites</subject>
40
- <subject>Taxonomy</subject>
41
- <subject>Mitochondrial genome</subject>
42
- <subject>Africa</subject>
43
- <subject>Plasmodium</subject>
44
- </subjects>
45
- <resourceType resourceTypeGeneral="Dataset">DataPackage</resourceType>
46
- <alternateIdentifiers>
47
- <alternateIdentifier alternateIdentifierType="citation">Ollomo B, Durand P, Prugnolle F, Douzery EJP, Arnathau C, Nkoghe D, Leroy E, Renaud F (2009) A new malaria agent in African hominids. PLoS Pathogens 5(5): e1000446.</alternateIdentifier>
48
- </alternateIdentifiers>
49
- <relatedIdentifiers>
50
- <relatedIdentifier relatedIdentifierType="DOI" relationType="HasPart">10.5061/DRYAD.8515/1</relatedIdentifier>
51
- <relatedIdentifier relatedIdentifierType="DOI" relationType="HasPart">10.5061/DRYAD.8515/2</relatedIdentifier>
52
- <relatedIdentifier relatedIdentifierType="DOI" relationType="IsReferencedBy">10.1371/JOURNAL.PPAT.1000446</relatedIdentifier>
53
- <relatedIdentifier relatedIdentifierType="PMID" relationType="IsReferencedBy">19478877</relatedIdentifier>
54
- </relatedIdentifiers>
55
- <rightsList>
56
- <rights rightsURI="http://creativecommons.org/publicdomain/zero/1.0/" />
57
- </rightsList>
58
- </resource>
@@ -1,21 +0,0 @@
1
- {
2
- "id": "https://doi.org/10.5063/f1m61h5x",
3
- "types": {
4
- "resource-type-general": "Software",
5
- "resource-type": "Software"
6
- },
7
- "doi": "10.5063/F1M61H5X",
8
- "creators": [{
9
- "type": "Person",
10
- "name": "Matthew B. Jones",
11
- "givenName": "Matthew B.",
12
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- We also highlight mcmc-simbio, a smaller toolbox within txtlsim for performing concurrent Bayesian parameter inference on Simbiology models. Concurrent inference here means that a common set of parameters can be identified using data from an ensemble of different circuits and experiments, with each experiment informing a subset of the parameters. The combination of the concurrence feature with the fact that Markov chain Monte Carlo based Bayesian inference methods allow for the direct visualization of parameter non-identifiability enables the design of ensembles of experiments that reduce such non-identifiability.
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- Finally, we end with a method for performing model order reduction on transcription and translation elongation models while maintaining the ability of these models to track resource consumption. We show that due to their network topology, our models cannot be brought into the two-timescale form of singular perturbation theory when written in species concentration coordinates. We identify a coordinate system in which singular perturbation theory may be applied to chemical reaction networks more naturally, and use this to achieve the desired model reduction.</description>
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