briard 2.0

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Files changed (730) hide show
  1. checksums.yaml +7 -0
  2. data/.github/workflows/build.yml +37 -0
  3. data/.github/workflows/changelog.yml +37 -0
  4. data/.github/workflows/release.yml +47 -0
  5. data/.gitignore +59 -0
  6. data/.rubocop.yml +658 -0
  7. data/CHANGELOG.md +1 -0
  8. data/CITATION +16 -0
  9. data/Gemfile +3 -0
  10. data/Gemfile.lock +226 -0
  11. data/LICENSE.md +21 -0
  12. data/README.md +1030 -0
  13. data/Rakefile +13 -0
  14. data/bin/briard +9 -0
  15. data/bolognese.gemspec +59 -0
  16. data/lib/briard/.env.example +3 -0
  17. data/lib/briard/array.rb +13 -0
  18. data/lib/briard/author_utils.rb +166 -0
  19. data/lib/briard/cli.rb +58 -0
  20. data/lib/briard/crossref_utils.rb +336 -0
  21. data/lib/briard/datacite_utils.rb +395 -0
  22. data/lib/briard/doi_utils.rb +65 -0
  23. data/lib/briard/metadata.rb +285 -0
  24. data/lib/briard/metadata_utils.rb +215 -0
  25. data/lib/briard/pubmed.rb +36 -0
  26. data/lib/briard/readers/bibtex_reader.rb +100 -0
  27. data/lib/briard/readers/citeproc_reader.rb +119 -0
  28. data/lib/briard/readers/codemeta_reader.rb +108 -0
  29. data/lib/briard/readers/crosscite_reader.rb +14 -0
  30. data/lib/briard/readers/crossref_reader.rb +368 -0
  31. data/lib/briard/readers/datacite_json_reader.rb +14 -0
  32. data/lib/briard/readers/datacite_reader.rb +341 -0
  33. data/lib/briard/readers/npm_reader.rb +115 -0
  34. data/lib/briard/readers/ris_reader.rb +114 -0
  35. data/lib/briard/readers/schema_org_reader.rb +263 -0
  36. data/lib/briard/string.rb +7 -0
  37. data/lib/briard/utils.rb +1369 -0
  38. data/lib/briard/version.rb +3 -0
  39. data/lib/briard/whitelist_scrubber.rb +47 -0
  40. data/lib/briard/writers/bibtex_writer.rb +32 -0
  41. data/lib/briard/writers/citation_writer.rb +14 -0
  42. data/lib/briard/writers/citeproc_writer.rb +11 -0
  43. data/lib/briard/writers/codemeta_writer.rb +29 -0
  44. data/lib/briard/writers/crosscite_writer.rb +11 -0
  45. data/lib/briard/writers/crossref_writer.rb +11 -0
  46. data/lib/briard/writers/csv_writer.rb +26 -0
  47. data/lib/briard/writers/datacite_json_writer.rb +11 -0
  48. data/lib/briard/writers/datacite_writer.rb +12 -0
  49. data/lib/briard/writers/jats_writer.rb +134 -0
  50. data/lib/briard/writers/rdf_xml_writer.rb +11 -0
  51. data/lib/briard/writers/ris_writer.rb +29 -0
  52. data/lib/briard/writers/schema_org_writer.rb +51 -0
  53. data/lib/briard/writers/turtle_writer.rb +11 -0
  54. data/lib/briard.rb +31 -0
  55. data/resources/2008/09/xsd.xsl +997 -0
  56. data/resources/crossref/AccessIndicators.xsd +47 -0
  57. data/resources/crossref/JATS-journalpublishing1-3d2-mathml3-elements.xsd +10130 -0
  58. data/resources/crossref/JATS-journalpublishing1-3d2-mathml3.xsd +48 -0
  59. data/resources/crossref/JATS-journalpublishing1-elements.xsd +8705 -0
  60. data/resources/crossref/JATS-journalpublishing1-mathml3-elements.xsd +8608 -0
  61. data/resources/crossref/JATS-journalpublishing1-mathml3.xsd +49 -0
  62. data/resources/crossref/JATS-journalpublishing1.xsd +6176 -0
  63. data/resources/crossref/clinicaltrials.xsd +61 -0
  64. data/resources/crossref/common5.3.1.xsd +1530 -0
  65. data/resources/crossref/crossref5.3.1.xsd +1949 -0
  66. data/resources/crossref/crossref_query_output3.0.xsd +1097 -0
  67. data/resources/crossref/fundref.xsd +49 -0
  68. data/resources/crossref/module-ali.xsd +39 -0
  69. data/resources/crossref/relations.xsd +444 -0
  70. data/resources/datacite-contributorType-v4.xsd +35 -0
  71. data/resources/datacite-dateType-v4.xsd +25 -0
  72. data/resources/datacite-descriptionType-v4.xsd +19 -0
  73. data/resources/datacite-funderIdentifierType-v4.xsd +15 -0
  74. data/resources/datacite-nameType-v4.xsd +10 -0
  75. data/resources/datacite-relatedIdentifierType-v4.xsd +34 -0
  76. data/resources/datacite-relationType-v4.xsd +49 -0
  77. data/resources/datacite-resourceType-v4.xsd +28 -0
  78. data/resources/datacite-titleType-v4.xsd +14 -0
  79. data/resources/kernel-2.1/include/datacite-contributorType-v1.1.xsd +22 -0
  80. data/resources/kernel-2.1/include/datacite-contributorType-v2.xsd +3 -0
  81. data/resources/kernel-2.1/include/datacite-dateType-v1.1.xsd +31 -0
  82. data/resources/kernel-2.1/include/datacite-dateType-v2.xsd +3 -0
  83. data/resources/kernel-2.1/include/datacite-descriptionType-v1.1.xsd +14 -0
  84. data/resources/kernel-2.1/include/datacite-descriptionType-v2.xsd +3 -0
  85. data/resources/kernel-2.1/include/datacite-relatedIdentifierType-v1.1.xsd +24 -0
  86. data/resources/kernel-2.1/include/datacite-relatedIdentifierType-v2.xsd +3 -0
  87. data/resources/kernel-2.1/include/datacite-relationType-v1.1.xsd +29 -0
  88. data/resources/kernel-2.1/include/datacite-relationType-v2.xsd +3 -0
  89. data/resources/kernel-2.1/include/datacite-resourceType-v1.1.xsd +22 -0
  90. data/resources/kernel-2.1/include/datacite-resourceType-v2.xsd +3 -0
  91. data/resources/kernel-2.1/include/datacite-titleType-v1.1.xsd +11 -0
  92. data/resources/kernel-2.1/include/datacite-titleType-v2.xsd +3 -0
  93. data/resources/kernel-2.1/metadata.xsd +315 -0
  94. data/resources/kernel-2.2/include/datacite-contributorType-v2.xsd +29 -0
  95. data/resources/kernel-2.2/include/datacite-dateType-v2.xsd +21 -0
  96. data/resources/kernel-2.2/include/datacite-descriptionType-v2.xsd +15 -0
  97. data/resources/kernel-2.2/include/datacite-relatedIdentifierType-v2.xsd +25 -0
  98. data/resources/kernel-2.2/include/datacite-relationType-v2.xsd +29 -0
  99. data/resources/kernel-2.2/include/datacite-resourceType-v2.xsd +23 -0
  100. data/resources/kernel-2.2/include/datacite-titleType-v2.xsd +10 -0
  101. data/resources/kernel-2.2/metadata.xsd +316 -0
  102. data/resources/kernel-3/include/datacite-contributorType-v3.1.xsd +35 -0
  103. data/resources/kernel-3/include/datacite-dateType-v3.xsd +21 -0
  104. data/resources/kernel-3/include/datacite-descriptionType-v3.xsd +17 -0
  105. data/resources/kernel-3/include/datacite-relatedIdentifierType-v3.1.xsd +30 -0
  106. data/resources/kernel-3/include/datacite-relationType-v3.1.xsd +38 -0
  107. data/resources/kernel-3/include/datacite-resourceType-v3.xsd +26 -0
  108. data/resources/kernel-3/include/datacite-titleType-v3.xsd +12 -0
  109. data/resources/kernel-3/include/xml.xsd +286 -0
  110. data/resources/kernel-3/metadata.xsd +380 -0
  111. data/resources/kernel-3.0/include/datacite-contributorType-v3.xsd +33 -0
  112. data/resources/kernel-3.0/include/datacite-dateType-v3.xsd +21 -0
  113. data/resources/kernel-3.0/include/datacite-descriptionType-v3.xsd +17 -0
  114. data/resources/kernel-3.0/include/datacite-relatedIdentifierType-v3.xsd +27 -0
  115. data/resources/kernel-3.0/include/datacite-relationType-v3.xsd +33 -0
  116. data/resources/kernel-3.0/include/datacite-resourceType-v3.xsd +26 -0
  117. data/resources/kernel-3.0/include/datacite-titleType-v3.xsd +12 -0
  118. data/resources/kernel-3.0/include/xml.xsd +286 -0
  119. data/resources/kernel-3.0/metadata.xsd +377 -0
  120. data/resources/kernel-3.1/include/datacite-contributorType-v3.1.xsd +35 -0
  121. data/resources/kernel-3.1/include/datacite-dateType-v3.xsd +21 -0
  122. data/resources/kernel-3.1/include/datacite-descriptionType-v3.xsd +17 -0
  123. data/resources/kernel-3.1/include/datacite-relatedIdentifierType-v3.1.xsd +30 -0
  124. data/resources/kernel-3.1/include/datacite-relationType-v3.1.xsd +38 -0
  125. data/resources/kernel-3.1/include/datacite-resourceType-v3.xsd +26 -0
  126. data/resources/kernel-3.1/include/datacite-titleType-v3.xsd +12 -0
  127. data/resources/kernel-3.1/include/xml.xsd +286 -0
  128. data/resources/kernel-3.1/metadata.xsd +380 -0
  129. data/resources/kernel-4/include/datacite-contributorType-v4.xsd +35 -0
  130. data/resources/kernel-4/include/datacite-dateType-v4.xsd +25 -0
  131. data/resources/kernel-4/include/datacite-descriptionType-v4.xsd +19 -0
  132. data/resources/kernel-4/include/datacite-funderIdentifierType-v4.xsd +16 -0
  133. data/resources/kernel-4/include/datacite-nameType-v4.xsd +10 -0
  134. data/resources/kernel-4/include/datacite-numberType-v4.xsd +12 -0
  135. data/resources/kernel-4/include/datacite-relatedIdentifierType-v4.xsd +34 -0
  136. data/resources/kernel-4/include/datacite-relationType-v4.xsd +51 -0
  137. data/resources/kernel-4/include/datacite-resourceType-v4.xsd +43 -0
  138. data/resources/kernel-4/include/datacite-titleType-v4.xsd +14 -0
  139. data/resources/kernel-4/include/xml.xsd +286 -0
  140. data/resources/kernel-4/metadata.xsd +707 -0
  141. data/resources/kernel-4.0/include/datacite-contributorType-v4.xsd +35 -0
  142. data/resources/kernel-4.0/include/datacite-dateType-v4.xsd +21 -0
  143. data/resources/kernel-4.0/include/datacite-descriptionType-v4.xsd +19 -0
  144. data/resources/kernel-4.0/include/datacite-funderIdentifierType-v4.xsd +15 -0
  145. data/resources/kernel-4.0/include/datacite-relatedIdentifierType-v4.xsd +32 -0
  146. data/resources/kernel-4.0/include/datacite-relationType-v4.xsd +39 -0
  147. data/resources/kernel-4.0/include/datacite-resourceType-v4.xsd +26 -0
  148. data/resources/kernel-4.0/include/datacite-titleType-v4.xsd +14 -0
  149. data/resources/kernel-4.0/include/xml.xsd +286 -0
  150. data/resources/kernel-4.0/metadata.xsd +470 -0
  151. data/resources/kernel-4.1/include/datacite-contributorType-v4.xsd +35 -0
  152. data/resources/kernel-4.1/include/datacite-dateType-v4.1.xsd +23 -0
  153. data/resources/kernel-4.1/include/datacite-descriptionType-v4.xsd +19 -0
  154. data/resources/kernel-4.1/include/datacite-funderIdentifierType-v4.xsd +15 -0
  155. data/resources/kernel-4.1/include/datacite-nameType-v4.1.xsd +10 -0
  156. data/resources/kernel-4.1/include/datacite-relatedIdentifierType-v4.xsd +32 -0
  157. data/resources/kernel-4.1/include/datacite-relationType-v4.1.xsd +46 -0
  158. data/resources/kernel-4.1/include/datacite-resourceType-v4.1.xsd +28 -0
  159. data/resources/kernel-4.1/include/datacite-titleType-v4.xsd +14 -0
  160. data/resources/kernel-4.1/include/xml.xsd +286 -0
  161. data/resources/kernel-4.1/metadata.xsd +483 -0
  162. data/resources/kernel-4.2/include/datacite-contributorType-v4.xsd +35 -0
  163. data/resources/kernel-4.2/include/datacite-dateType-v4.xsd +25 -0
  164. data/resources/kernel-4.2/include/datacite-descriptionType-v4.xsd +19 -0
  165. data/resources/kernel-4.2/include/datacite-funderIdentifierType-v4.xsd +15 -0
  166. data/resources/kernel-4.2/include/datacite-nameType-v4.xsd +10 -0
  167. data/resources/kernel-4.2/include/datacite-relatedIdentifierType-v4.xsd +34 -0
  168. data/resources/kernel-4.2/include/datacite-relationType-v4.xsd +49 -0
  169. data/resources/kernel-4.2/include/datacite-resourceType-v4.xsd +28 -0
  170. data/resources/kernel-4.2/include/datacite-titleType-v4.xsd +14 -0
  171. data/resources/kernel-4.2/include/xml.xsd +286 -0
  172. data/resources/kernel-4.2/metadata.xsd +479 -0
  173. data/resources/kernel-4.3/include/datacite-contributorType-v4.xsd +35 -0
  174. data/resources/kernel-4.3/include/datacite-dateType-v4.xsd +25 -0
  175. data/resources/kernel-4.3/include/datacite-descriptionType-v4.xsd +19 -0
  176. data/resources/kernel-4.3/include/datacite-funderIdentifierType-v4.xsd +16 -0
  177. data/resources/kernel-4.3/include/datacite-nameType-v4.xsd +10 -0
  178. data/resources/kernel-4.3/include/datacite-relatedIdentifierType-v4.xsd +34 -0
  179. data/resources/kernel-4.3/include/datacite-relationType-v4.xsd +49 -0
  180. data/resources/kernel-4.3/include/datacite-resourceType-v4.xsd +28 -0
  181. data/resources/kernel-4.3/include/datacite-titleType-v4.xsd +14 -0
  182. data/resources/kernel-4.3/include/xml.xsd +286 -0
  183. data/resources/kernel-4.3/metadata.xsd +515 -0
  184. data/resources/kernel-4.4/include/datacite-contributorType-v4.xsd +35 -0
  185. data/resources/kernel-4.4/include/datacite-dateType-v4.xsd +25 -0
  186. data/resources/kernel-4.4/include/datacite-descriptionType-v4.xsd +19 -0
  187. data/resources/kernel-4.4/include/datacite-funderIdentifierType-v4.xsd +16 -0
  188. data/resources/kernel-4.4/include/datacite-nameType-v4.xsd +10 -0
  189. data/resources/kernel-4.4/include/datacite-numberType-v4.xsd +12 -0
  190. data/resources/kernel-4.4/include/datacite-relatedIdentifierType-v4.xsd +34 -0
  191. data/resources/kernel-4.4/include/datacite-relationType-v4.xsd +51 -0
  192. data/resources/kernel-4.4/include/datacite-resourceType-v4.xsd +43 -0
  193. data/resources/kernel-4.4/include/datacite-titleType-v4.xsd +14 -0
  194. data/resources/kernel-4.4/include/xml.xsd +286 -0
  195. data/resources/kernel-4.4/metadata.xsd +707 -0
  196. data/resources/oecd/dfg-mappings.json +1866 -0
  197. data/resources/oecd/for-mappings.json +1099 -0
  198. data/resources/oecd/fos-mappings.json +198 -0
  199. data/resources/schema_org/jsonldcontext.json +7477 -0
  200. data/resources/spdx/licenses.json +5297 -0
  201. data/resources/xml.xsd +286 -0
  202. data/spec/array_spec.rb +22 -0
  203. data/spec/author_utils_spec.rb +193 -0
  204. data/spec/cli_spec.rb +226 -0
  205. data/spec/datacite_utils_spec.rb +178 -0
  206. data/spec/doi_utils_spec.rb +314 -0
  207. data/spec/find_from_format_spec.rb +114 -0
  208. data/spec/fixtures/aida.json +82 -0
  209. data/spec/fixtures/cgimp_package.json +18 -0
  210. data/spec/fixtures/cit_package.json +19 -0
  211. data/spec/fixtures/citeproc-no-author.json +26 -0
  212. data/spec/fixtures/citeproc-no-categories.json +21 -0
  213. data/spec/fixtures/citeproc.json +30 -0
  214. data/spec/fixtures/codemeta.json +86 -0
  215. data/spec/fixtures/codemeta_v2.json +86 -0
  216. data/spec/fixtures/crosscite.json +63 -0
  217. data/spec/fixtures/crossref.bib +14 -0
  218. data/spec/fixtures/crossref.ris +15 -0
  219. data/spec/fixtures/crossref.xml +606 -0
  220. data/spec/fixtures/datacite-empty-sizes.xml +57 -0
  221. data/spec/fixtures/datacite-example-affiliation.xml +114 -0
  222. data/spec/fixtures/datacite-example-ancientdates-v4.3.xml +29 -0
  223. data/spec/fixtures/datacite-example-complicated-tba.xml +56 -0
  224. data/spec/fixtures/datacite-example-complicated-v3.0.xml +48 -0
  225. data/spec/fixtures/datacite-example-complicated-v4.0.xml +54 -0
  226. data/spec/fixtures/datacite-example-complicated-v4.1.xml +57 -0
  227. data/spec/fixtures/datacite-example-dissertation-v4.4.xml +56 -0
  228. data/spec/fixtures/datacite-example-escaped-text.xml +56 -0
  229. data/spec/fixtures/datacite-example-full-v4.4.xml +114 -0
  230. data/spec/fixtures/datacite-example-geolocation-2.xml +141 -0
  231. data/spec/fixtures/datacite-example-geolocation.xml +66 -0
  232. data/spec/fixtures/datacite-example-polygon-v4.1.xml +163 -0
  233. data/spec/fixtures/datacite-example-relateditems.xml +61 -0
  234. data/spec/fixtures/datacite-example-xs-string.xml +28 -0
  235. data/spec/fixtures/datacite-formats-with-xs.xml +22 -0
  236. data/spec/fixtures/datacite-funderIdentifier.xml +78 -0
  237. data/spec/fixtures/datacite-geolocation-empty.xml +159 -0
  238. data/spec/fixtures/datacite-geolocationpolygons-multiple.xml +76 -0
  239. data/spec/fixtures/datacite-metadata-sample-complicated-v2.2.xml +52 -0
  240. data/spec/fixtures/datacite-multiple-language.xml +38 -0
  241. data/spec/fixtures/datacite-multiple-rights.xml +59 -0
  242. data/spec/fixtures/datacite-schema-2.2.xml +80 -0
  243. data/spec/fixtures/datacite-seriesinformation.xml +41 -0
  244. data/spec/fixtures/datacite-space-in-sizes.xml +52 -0
  245. data/spec/fixtures/datacite-xml-lang.xml +51 -0
  246. data/spec/fixtures/datacite.json +83 -0
  247. data/spec/fixtures/datacite.xml +40 -0
  248. data/spec/fixtures/datacite_dataset.xml +58 -0
  249. data/spec/fixtures/datacite_malformed_creator.xml +52 -0
  250. data/spec/fixtures/datacite_missing_creator.xml +33 -0
  251. data/spec/fixtures/datacite_schema_3.xml +58 -0
  252. data/spec/fixtures/datacite_software.json +21 -0
  253. data/spec/fixtures/datacite_software_missing_comma.json +18 -0
  254. data/spec/fixtures/datacite_software_overlapping_keys.json +18 -0
  255. data/spec/fixtures/datacite_software_version.json +74 -0
  256. data/spec/fixtures/edam_package.json +12 -0
  257. data/spec/fixtures/funding_reference.xml +53 -0
  258. data/spec/fixtures/gtex.xml +71 -0
  259. data/spec/fixtures/maremma/codemeta.json +36 -0
  260. data/spec/fixtures/nist.xml +35 -0
  261. data/spec/fixtures/ns0.xml +2 -0
  262. data/spec/fixtures/pure.bib +14 -0
  263. data/spec/fixtures/pure.ris +15 -0
  264. data/spec/fixtures/pure.xml +188 -0
  265. data/spec/fixtures/ris_bug.ris +9 -0
  266. data/spec/fixtures/schema_4.0.xml +140 -0
  267. data/spec/fixtures/schema_org.json +49 -0
  268. data/spec/fixtures/schema_org_front-matter.json +32 -0
  269. data/spec/fixtures/schema_org_geolocation.json +82 -0
  270. data/spec/fixtures/schema_org_geoshape.json +550 -0
  271. data/spec/fixtures/schema_org_gtex.json +75 -0
  272. data/spec/fixtures/schema_org_list.json +12623 -0
  273. data/spec/fixtures/schema_org_tdl_iodp_invalid_authors.json +25 -0
  274. data/spec/fixtures/schema_org_topmed.json +53 -0
  275. data/spec/fixtures/schema_org_type_as_array.json +41 -0
  276. data/spec/fixtures/vcr_cassettes/Briard_CLI/convert_from_id/crossref/default.yml +121 -0
  277. data/spec/fixtures/vcr_cassettes/Briard_CLI/convert_from_id/crossref/to_bibtex.yml +121 -0
  278. data/spec/fixtures/vcr_cassettes/Briard_CLI/convert_from_id/crossref/to_citation.yml +121 -0
  279. data/spec/fixtures/vcr_cassettes/Briard_CLI/convert_from_id/crossref/to_crossref.yml +121 -0
  280. data/spec/fixtures/vcr_cassettes/Briard_CLI/convert_from_id/crossref/to_datacite.yml +121 -0
  281. data/spec/fixtures/vcr_cassettes/Briard_CLI/convert_from_id/crossref/to_jats.yml +121 -0
  282. data/spec/fixtures/vcr_cassettes/Briard_CLI/convert_from_id/crossref/to_schema_org.yml +121 -0
  283. data/spec/fixtures/vcr_cassettes/Briard_CLI/convert_from_id/datacite/default.yml +110 -0
  284. data/spec/fixtures/vcr_cassettes/Briard_CLI/convert_from_id/datacite/to_bibtex.yml +110 -0
  285. data/spec/fixtures/vcr_cassettes/Briard_CLI/convert_from_id/datacite/to_citation.yml +110 -0
  286. data/spec/fixtures/vcr_cassettes/Briard_CLI/convert_from_id/datacite/to_datacite.yml +110 -0
  287. data/spec/fixtures/vcr_cassettes/Briard_CLI/convert_from_id/datacite/to_datacite_json.yml +110 -0
  288. data/spec/fixtures/vcr_cassettes/Briard_CLI/convert_from_id/datacite/to_jats.yml +110 -0
  289. data/spec/fixtures/vcr_cassettes/Briard_CLI/convert_from_id/datacite/to_schema_org.yml +110 -0
  290. data/spec/fixtures/vcr_cassettes/Briard_CLI/convert_from_id/schema_org/default.yml +117 -0
  291. data/spec/fixtures/vcr_cassettes/Briard_CLI/convert_from_id/schema_org/to_datacite.yml +117 -0
  292. data/spec/fixtures/vcr_cassettes/Briard_CLI/convert_from_id/schema_org/to_schema_org.yml +117 -0
  293. data/spec/fixtures/vcr_cassettes/Briard_CLI/find_from_format_by_id/crossref.yml +52 -0
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  667. data/spec/fixtures/vcr_cassettes/Briard_Metadata/write_metadata_as_jats_xml/with_data_citation_schema_org.yml +117 -0
  668. data/spec/fixtures/vcr_cassettes/Briard_Metadata/write_metadata_as_jats_xml/with_editor.yml +66 -0
  669. data/spec/fixtures/vcr_cassettes/Briard_Metadata/write_metadata_as_rdf_xml/BlogPosting.yml +61 -0
  670. data/spec/fixtures/vcr_cassettes/Briard_Metadata/write_metadata_as_rdf_xml/BlogPosting_schema_org.yml +117 -0
  671. data/spec/fixtures/vcr_cassettes/Briard_Metadata/write_metadata_as_rdf_xml/journal_article.yml +72 -0
  672. data/spec/fixtures/vcr_cassettes/Briard_Metadata/write_metadata_as_rdf_xml/maremma.yml +75 -0
  673. data/spec/fixtures/vcr_cassettes/Briard_Metadata/write_metadata_as_rdf_xml/with_pages.yml +69 -0
  674. data/spec/fixtures/vcr_cassettes/Briard_Metadata/write_metadata_as_ris/BlogPosting.yml +61 -0
  675. data/spec/fixtures/vcr_cassettes/Briard_Metadata/write_metadata_as_ris/BlogPosting_schema_org.yml +117 -0
  676. data/spec/fixtures/vcr_cassettes/Briard_Metadata/write_metadata_as_ris/Dataset.yml +61 -0
  677. data/spec/fixtures/vcr_cassettes/Briard_Metadata/write_metadata_as_ris/alternate_name.yml +61 -0
  678. data/spec/fixtures/vcr_cassettes/Briard_Metadata/write_metadata_as_ris/journal_article.yml +72 -0
  679. data/spec/fixtures/vcr_cassettes/Briard_Metadata/write_metadata_as_ris/keywords_with_subject_scheme.yml +61 -0
  680. data/spec/fixtures/vcr_cassettes/Briard_Metadata/write_metadata_as_ris/maremma.yml +75 -0
  681. data/spec/fixtures/vcr_cassettes/Briard_Metadata/write_metadata_as_ris/with_pages.yml +69 -0
  682. data/spec/fixtures/vcr_cassettes/Briard_Metadata/write_metadata_as_schema_org/Funding.yml +110 -0
  683. data/spec/fixtures/vcr_cassettes/Briard_Metadata/write_metadata_as_schema_org/Funding_OpenAIRE.yml +110 -0
  684. data/spec/fixtures/vcr_cassettes/Briard_Metadata/write_metadata_as_schema_org/Schema_org_JSON.yml +61 -0
  685. data/spec/fixtures/vcr_cassettes/Briard_Metadata/write_metadata_as_schema_org/Schema_org_JSON_Cyark.yml +110 -0
  686. data/spec/fixtures/vcr_cassettes/Briard_Metadata/write_metadata_as_schema_org/Schema_org_JSON_IsSupplementTo.yml +110 -0
  687. data/spec/fixtures/vcr_cassettes/Briard_Metadata/write_metadata_as_schema_org/Schema_org_JSON_isReferencedBy.yml +61 -0
  688. data/spec/fixtures/vcr_cassettes/Briard_Metadata/write_metadata_as_schema_org/alternate_identifiers.yml +61 -0
  689. data/spec/fixtures/vcr_cassettes/Briard_Metadata/write_metadata_as_schema_org/data_catalog.yml +61 -0
  690. data/spec/fixtures/vcr_cassettes/Briard_Metadata/write_metadata_as_schema_org/geo_location_box.yml +61 -0
  691. data/spec/fixtures/vcr_cassettes/Briard_Metadata/write_metadata_as_schema_org/interactive_resource_without_dates.yml +61 -0
  692. data/spec/fixtures/vcr_cassettes/Briard_Metadata/write_metadata_as_schema_org/journal_article.yml +72 -0
  693. data/spec/fixtures/vcr_cassettes/Briard_Metadata/write_metadata_as_schema_org/maremma_schema_org_JSON.yml +75 -0
  694. data/spec/fixtures/vcr_cassettes/Briard_Metadata/write_metadata_as_schema_org/series_information.yml +61 -0
  695. data/spec/fixtures/vcr_cassettes/Briard_Metadata/write_metadata_as_schema_org/subject_scheme.yml +61 -0
  696. data/spec/fixtures/vcr_cassettes/Briard_Metadata/write_metadata_as_schema_org/subject_scheme_multiple_keywords.yml +61 -0
  697. data/spec/fixtures/vcr_cassettes/Briard_Metadata/write_metadata_as_turtle/BlogPosting.yml +61 -0
  698. data/spec/fixtures/vcr_cassettes/Briard_Metadata/write_metadata_as_turtle/BlogPosting_schema_org.yml +117 -0
  699. data/spec/fixtures/vcr_cassettes/Briard_Metadata/write_metadata_as_turtle/Dataset.yml +61 -0
  700. data/spec/fixtures/vcr_cassettes/Briard_Metadata/write_metadata_as_turtle/journal_article.yml +72 -0
  701. data/spec/fixtures/vcr_cassettes/Briard_Metadata/write_metadata_as_turtle/with_pages.yml +69 -0
  702. data/spec/fixtures/vivli.xml +1 -0
  703. data/spec/metadata_spec.rb +165 -0
  704. data/spec/readers/bibtex_reader_spec.rb +63 -0
  705. data/spec/readers/citeproc_reader_spec.rb +61 -0
  706. data/spec/readers/codemeta_reader_spec.rb +138 -0
  707. data/spec/readers/crosscite_reader_spec.rb +41 -0
  708. data/spec/readers/crossref_reader_spec.rb +1117 -0
  709. data/spec/readers/datacite_json_reader_spec.rb +80 -0
  710. data/spec/readers/datacite_reader_spec.rb +1655 -0
  711. data/spec/readers/npm_reader_spec.rb +66 -0
  712. data/spec/readers/ris_reader_spec.rb +75 -0
  713. data/spec/readers/schema_org_reader_spec.rb +376 -0
  714. data/spec/spec_helper.rb +94 -0
  715. data/spec/utils_spec.rb +617 -0
  716. data/spec/writers/bibtex_writer_spec.rb +195 -0
  717. data/spec/writers/citation_writer_spec.rb +52 -0
  718. data/spec/writers/citeproc_writer_spec.rb +296 -0
  719. data/spec/writers/codemeta_writer_spec.rb +45 -0
  720. data/spec/writers/crosscite_writer_spec.rb +122 -0
  721. data/spec/writers/crossref_writer_spec.rb +88 -0
  722. data/spec/writers/csv_writer_spec.rb +94 -0
  723. data/spec/writers/datacite_json_writer_spec.rb +90 -0
  724. data/spec/writers/datacite_writer_spec.rb +428 -0
  725. data/spec/writers/jats_writer_spec.rb +193 -0
  726. data/spec/writers/rdf_xml_writer_spec.rb +86 -0
  727. data/spec/writers/ris_writer_spec.rb +208 -0
  728. data/spec/writers/schema_org_writer_spec.rb +369 -0
  729. data/spec/writers/turtle_writer_spec.rb +84 -0
  730. metadata +1347 -0
@@ -0,0 +1,314 @@
1
+ # frozen_string_literal: true
2
+
3
+ require 'spec_helper'
4
+
5
+ describe Briard::Metadata, vcr: true do
6
+ let(:input) { "https://doi.org/10.1101/097196" }
7
+
8
+ subject { Briard::Metadata.new(input: input, from: "crossref") }
9
+
10
+ context "doi resolver" do
11
+ it "doi" do
12
+ doi = "10.5061/DRYAD.8515"
13
+ response = subject.doi_resolver(doi)
14
+ expect(response).to eq("https://doi.org/")
15
+ end
16
+
17
+ it "doi with protocol" do
18
+ doi = "doi:10.5061/DRYAD.8515"
19
+ response = subject.doi_resolver(doi)
20
+ expect(response).to eq("https://doi.org/")
21
+ end
22
+
23
+ it "https url" do
24
+ doi = "https://doi.org/10.5061/dryad.8515"
25
+ response = subject.doi_resolver(doi)
26
+ expect(response).to eq("https://doi.org/")
27
+ end
28
+
29
+ it "dx.doi.org url" do
30
+ doi = "http://dx.doi.org/10.5061/dryad.8515"
31
+ response = subject.doi_resolver(doi)
32
+ expect(response).to eq("https://doi.org/")
33
+ end
34
+
35
+ it "stage resolver" do
36
+ doi = "https://handle.stage.datacite.org/10.5061/dryad.8515"
37
+ response = subject.doi_resolver(doi)
38
+ expect(response).to eq("https://handle.stage.datacite.org/")
39
+ end
40
+
41
+ it "stage resolver http" do
42
+ doi = "http://handle.stage.datacite.org/10.5061/dryad.8515"
43
+ response = subject.doi_resolver(doi)
44
+ expect(response).to eq("https://handle.stage.datacite.org/")
45
+ end
46
+
47
+ it "force stage resolver" do
48
+ doi = "https://doi.org/10.5061/dryad.8515"
49
+ response = subject.doi_resolver(doi, sandbox: true)
50
+ expect(response).to eq("https://handle.stage.datacite.org/")
51
+ end
52
+ end
53
+
54
+ context "doi_api_url" do
55
+ it "doi" do
56
+ doi = "10.5061/DRYAD.8515"
57
+ response = subject.doi_api_url(doi)
58
+ expect(response).to eq("https://api.datacite.org/dois/10.5061/dryad.8515?include=media,client")
59
+ end
60
+
61
+ it "doi with protocol" do
62
+ doi = "doi:10.5061/DRYAD.8515"
63
+ response = subject.doi_api_url(doi)
64
+ expect(response).to eq("https://api.datacite.org/dois/10.5061/dryad.8515?include=media,client")
65
+ end
66
+
67
+ it "https url" do
68
+ doi = "https://doi.org/10.5061/dryad.8515"
69
+ response = subject.doi_api_url(doi)
70
+ expect(response).to eq("https://api.datacite.org/dois/10.5061/dryad.8515?include=media,client")
71
+ end
72
+
73
+ it "dx.doi.org url" do
74
+ doi = "http://dx.doi.org/10.5061/dryad.8515"
75
+ response = subject.doi_api_url(doi)
76
+ expect(response).to eq("https://api.datacite.org/dois/10.5061/dryad.8515?include=media,client")
77
+ end
78
+
79
+ it "test resolver" do
80
+ doi = "https://handle.stage.datacite.org/10.5061/dryad.8515"
81
+ response = subject.doi_api_url(doi)
82
+ expect(response).to eq("https://api.stage.datacite.org/dois/10.5061/dryad.8515?include=media,client")
83
+ end
84
+
85
+ it "test resolver http" do
86
+ doi = "http://handle.stage.datacite.org/10.5061/dryad.8515"
87
+ response = subject.doi_api_url(doi)
88
+ expect(response).to eq("https://api.stage.datacite.org/dois/10.5061/dryad.8515?include=media,client")
89
+ end
90
+
91
+ it "force test resolver" do
92
+ doi = "https://doi.org/10.5061/dryad.8515"
93
+ response = subject.doi_api_url(doi, sandbox: true)
94
+ expect(response).to eq("https://api.stage.datacite.org/dois/10.5061/dryad.8515?include=media,client")
95
+ end
96
+ end
97
+
98
+ context "normalize doi" do
99
+ it "doi" do
100
+ doi = "10.5061/DRYAD.8515"
101
+ response = subject.normalize_doi(doi)
102
+ expect(response).to eq("https://doi.org/10.5061/dryad.8515")
103
+ end
104
+
105
+ it "doi with protocol" do
106
+ doi = "doi:10.5061/DRYAD.8515"
107
+ response = subject.normalize_doi(doi)
108
+ expect(response).to eq("https://doi.org/10.5061/dryad.8515")
109
+ end
110
+
111
+ it "SICI doi" do
112
+ doi = "10.1890/0012-9658(2006)87[2832:tiopma]2.0.co;2"
113
+ response = subject.normalize_doi(doi)
114
+ expect(response).to eq("https://doi.org/10.1890/0012-9658(2006)87%5B2832:tiopma%5D2.0.co;2")
115
+ end
116
+
117
+ it "https url" do
118
+ doi = "https://doi.org/10.5061/dryad.8515"
119
+ response = subject.normalize_doi(doi)
120
+ expect(response).to eq("https://doi.org/10.5061/dryad.8515")
121
+ end
122
+
123
+ it "dx.doi.org url" do
124
+ doi = "http://dx.doi.org/10.5061/dryad.8515"
125
+ response = subject.normalize_doi(doi)
126
+ expect(response).to eq("https://doi.org/10.5061/dryad.8515")
127
+ end
128
+
129
+ it "not valid doi prefix" do
130
+ doi = "https://doi.org/20.5061/dryad.8515"
131
+ response = subject.normalize_doi(doi)
132
+ expect(response).to be_nil
133
+ end
134
+
135
+ it "doi prefix with string" do
136
+ doi = "https://doi.org/10.506X/dryad.8515"
137
+ response = subject.normalize_doi(doi)
138
+ expect(response).to be_nil
139
+ end
140
+
141
+ it "doi prefix too long" do
142
+ doi = "https://doi.org/10.506123/dryad.8515"
143
+ response = subject.normalize_doi(doi)
144
+ expect(response).to be_nil
145
+ end
146
+
147
+ it "doi from url without doi proxy" do
148
+ doi = "https://handle.net/10.5061/dryad.8515"
149
+ response = subject.normalize_doi(doi)
150
+ expect(response).to be_nil
151
+ end
152
+
153
+ it "url with one slash" do
154
+ doi = "https:/doi.org/10.5061/dryad.8515"
155
+ response = subject.normalize_doi(doi)
156
+ expect(response).to eq("https://doi.org/10.5061/dryad.8515")
157
+ end
158
+
159
+ it "doi from datacite sandbox" do
160
+ doi = "https://handle.stage.datacite.org/10.5438/55e5-t5c0"
161
+ response = subject.normalize_doi(doi)
162
+ expect(response).to eq("https://handle.stage.datacite.org/10.5438/55e5-t5c0")
163
+ end
164
+
165
+ it "doi force datacite sandbox" do
166
+ doi = "10.5438/55e5-t5c0"
167
+ response = subject.normalize_doi(doi, sandbox: true)
168
+ expect(response).to eq("https://handle.stage.datacite.org/10.5438/55e5-t5c0")
169
+ end
170
+ end
171
+
172
+ context "doi_from_url" do
173
+ it "url" do
174
+ doi = subject.doi_from_url("https://doi.org/10.5061/dryad.8515")
175
+ expect(doi).to eq("10.5061/dryad.8515")
176
+ end
177
+
178
+ it "doi" do
179
+ doi = subject.doi_from_url("10.5061/dryad.8515")
180
+ expect(doi).to eq("10.5061/dryad.8515")
181
+ end
182
+
183
+ it "doi with special characters" do
184
+ doi = subject.doi_from_url("10.5067/terra+aqua/ceres/cldtyphist_l3.004")
185
+ expect(doi).to eq("10.5067/terra+aqua/ceres/cldtyphist_l3.004")
186
+ end
187
+
188
+ it "not a doi" do
189
+ doi = subject.doi_from_url("https://doi.org/10.5061")
190
+ expect(doi).to be nil
191
+ end
192
+
193
+ it "sandbox url" do
194
+ doi = subject.doi_from_url("https://handle.stage.datacite.org/10.5438/55e5-t5c0")
195
+ expect(doi).to eq("10.5438/55e5-t5c0")
196
+ end
197
+ end
198
+
199
+ context "doi registration agency" do
200
+ it "datacite" do
201
+ doi = "https://doi.org/10.5061/dryad.8515"
202
+ response = subject.get_doi_ra(doi)
203
+ expect(response).to eq("DataCite")
204
+ end
205
+
206
+ it "crossref" do
207
+ doi = "10.1371/journal.pone.0000030"
208
+ response = subject.get_doi_ra(doi)
209
+ expect(response).to eq("Crossref")
210
+ end
211
+
212
+ it "medra" do
213
+ doi = "https://doi.org/10.1392/roma081203"
214
+ response = subject.get_doi_ra(doi)
215
+ expect(response).to eq("mEDRA")
216
+ end
217
+
218
+ it "kisti" do
219
+ doi = "https://doi.org/10.5012/bkcs.2013.34.10.2889"
220
+ response = subject.get_doi_ra(doi)
221
+ expect(response).to eq("KISTI")
222
+ end
223
+
224
+ it "jalc" do
225
+ doi = "https://doi.org/10.11367/grsj1979.12.283"
226
+ response = subject.get_doi_ra(doi)
227
+ expect(response).to eq("JaLC")
228
+ end
229
+
230
+ it "op" do
231
+ doi = "https://doi.org/10.2791/81962"
232
+ response = subject.get_doi_ra(doi)
233
+ expect(response).to eq("OP")
234
+ end
235
+
236
+ it "not a valid prefix" do
237
+ doi = "https://doi.org/10.a/dryad.8515x"
238
+ response = subject.get_doi_ra(doi)
239
+ expect(response).to be_nil
240
+ end
241
+
242
+ it "not found" do
243
+ doi = "https://doi.org/10.99999/dryad.8515x"
244
+ response = subject.get_doi_ra(doi)
245
+ expect(response).to be_nil
246
+ end
247
+ end
248
+
249
+ context "validate doi" do
250
+ it "doi" do
251
+ doi = "10.5061/dryad.8515"
252
+ response = subject.validate_doi(doi)
253
+ expect(response).to eq("10.5061/dryad.8515")
254
+ end
255
+ end
256
+
257
+ context "validate funder doi" do
258
+ it "funder doi" do
259
+ doi = "10.13039/501100001711"
260
+ response = subject.validate_funder_doi(doi)
261
+ expect(response).to eq("https://doi.org/10.13039/501100001711")
262
+ end
263
+
264
+ it "funder doi without prefix" do
265
+ doi = "501100001711"
266
+ response = subject.validate_funder_doi(doi)
267
+ expect(response).to eq("https://doi.org/10.13039/501100001711")
268
+ end
269
+
270
+ it "non-funder doi" do
271
+ doi = "10.5061/dryad.8515"
272
+ response = subject.validate_funder_doi(doi)
273
+ expect(response).to be_nil
274
+ end
275
+
276
+ it { expect(subject.validate_funder_doi("10.13039/100000050")).to eq "https://doi.org/10.13039/100000050" }
277
+ it { expect(subject.validate_funder_doi("10.13039/100006492")).to eq "https://doi.org/10.13039/100006492" }
278
+ it { expect(subject.validate_funder_doi('http://handle.test.datacite.org/10.13039/100000080')).to eq "https://doi.org/10.13039/100000080" }
279
+ it { expect(subject.validate_funder_doi('https://doi.org/10.13039/100000001')).to eq "https://doi.org/10.13039/100000001" }
280
+ it { expect(subject.validate_funder_doi('http://doi.org/10.13039/501100001711')).to eq "https://doi.org/10.13039/501100001711" }
281
+ it { expect(subject.validate_funder_doi('https://dx.doi.org/10.13039/501100001711')).to eq "https://doi.org/10.13039/501100001711" }
282
+ it { expect(subject.validate_funder_doi('doi:10.13039/501100001711')).to eq "https://doi.org/10.13039/501100001711" }
283
+ it { expect(subject.validate_funder_doi('10.13039/501100001711')).to eq "https://doi.org/10.13039/501100001711" }
284
+ it { expect(subject.validate_funder_doi('501100001711')).to eq "https://doi.org/10.13039/501100001711" }
285
+ it { expect(subject.validate_funder_doi("https://doi.org/10.13039/5monkeymonkey")).to be_nil }
286
+ it { expect(subject.validate_funder_doi('10.13039/5monkeymonkey')).to be_nil }
287
+ end
288
+
289
+ context "validate prefix" do
290
+ it "doi" do
291
+ doi = "10.5061/dryad.8515"
292
+ response = subject.validate_prefix(doi)
293
+ expect(response).to eq("10.5061")
294
+ end
295
+
296
+ it "doi with protocol" do
297
+ doi = "doi:10.5061/dryad.8515"
298
+ response = subject.validate_prefix(doi)
299
+ expect(response).to eq("10.5061")
300
+ end
301
+
302
+ it "doi as url" do
303
+ doi = "https://doi.org/10.5061/dryad.8515"
304
+ response = subject.validate_prefix(doi)
305
+ expect(response).to eq("10.5061")
306
+ end
307
+
308
+ it "only prefix" do
309
+ doi = "10.5061"
310
+ response = subject.validate_prefix(doi)
311
+ expect(response).to eq("10.5061")
312
+ end
313
+ end
314
+ end
@@ -0,0 +1,114 @@
1
+ # frozen_string_literal: true
2
+
3
+ require 'spec_helper'
4
+ require 'briard/cli'
5
+
6
+ describe Briard::CLI do
7
+ context "find_from_format_by_id", vcr: true do
8
+ let(:subject) do
9
+ described_class.new
10
+ end
11
+
12
+ it "crossref" do
13
+ id = "https://doi.org/10.7554/eLife.01567"
14
+ expect(subject.find_from_format_by_id(id)).to eq("crossref")
15
+ end
16
+
17
+ it "datacite" do
18
+ id = "https://doi.org/10.5061/DRYAD.8515"
19
+ expect(subject.find_from_format_by_id(id)).to eq("datacite")
20
+ end
21
+
22
+ it "medra" do
23
+ id = "https://doi.org/10.1392/roma081203"
24
+ expect(subject.find_from_format_by_id(id)).to eq("medra")
25
+ end
26
+
27
+ it "kisti" do
28
+ id = "https://doi.org/10.5012/bkcs.2013.34.10.2889"
29
+ expect(subject.find_from_format_by_id(id)).to eq("kisti")
30
+ end
31
+
32
+ it "jalc" do
33
+ id = "https://doi.org/10.11367/grsj1979.12.283"
34
+ expect(subject.find_from_format_by_id(id)).to eq("jalc")
35
+ end
36
+
37
+ it "op" do
38
+ id = "https://doi.org/10.2791/81962"
39
+ expect(subject.find_from_format_by_id(id)).to eq("op")
40
+ end
41
+
42
+ it "codemeta" do
43
+ id = "https://github.com/datacite/maremma"
44
+ expect(subject.find_from_format_by_id(id)).to eq("codemeta")
45
+ end
46
+
47
+ it "npm" do
48
+ id = "https://github.com/datacite/bracco/blob/master/package.json"
49
+ expect(subject.find_from_format_by_id(id)).to eq("npm")
50
+ end
51
+
52
+ it "schema_org" do
53
+ id = "https://dataverse.harvard.edu/dataset.xhtml?persistentId=doi:10.7910/DVN/GAOC03"
54
+ expect(subject.find_from_format_by_id(id)).to eq("schema_org")
55
+ end
56
+ end
57
+
58
+ context "find_from_format_by_filename" do
59
+ let(:subject) do
60
+ described_class.new
61
+ end
62
+
63
+ it "npm" do
64
+ filename = "package.json"
65
+ expect(subject.find_from_format_by_filename(filename)).to eq("npm")
66
+ end
67
+ end
68
+
69
+ context "find_from_format_by_string" do
70
+ let(:subject) do
71
+ described_class.new
72
+ end
73
+
74
+ it "crossref" do
75
+ string = IO.read(fixture_path + 'crossref.xml').strip
76
+ expect(subject.find_from_format_by_string(string)).to eq("crossref")
77
+ end
78
+
79
+ it "datacite" do
80
+ string = IO.read(fixture_path + 'datacite.xml').strip
81
+ expect(subject.find_from_format_by_string(string)).to eq("datacite")
82
+ end
83
+
84
+ it "datacite namespaced" do
85
+ string = IO.read(fixture_path + 'ns0.xml').strip
86
+ expect(subject.find_from_format_by_string(string)).to eq("datacite")
87
+ end
88
+
89
+ it "codemeta" do
90
+ string = IO.read(fixture_path + 'codemeta.json').strip
91
+ expect(subject.find_from_format_by_string(string)).to eq("codemeta")
92
+ end
93
+
94
+ it "schema_org" do
95
+ string = IO.read(fixture_path + 'schema_org_topmed.json').strip
96
+ expect(subject.find_from_format_by_string(string)).to eq("schema_org")
97
+ end
98
+
99
+ it "ris" do
100
+ string = IO.read(fixture_path + 'crossref.ris').strip
101
+ expect(subject.find_from_format_by_string(string)).to eq("ris")
102
+ end
103
+
104
+ it "ris from pure" do
105
+ string = IO.read(fixture_path + 'pure.ris').strip
106
+ expect(subject.find_from_format_by_string(string)).to eq("ris")
107
+ end
108
+
109
+ it "bibtex" do
110
+ string = IO.read(fixture_path + 'crossref.bib').strip
111
+ expect(subject.find_from_format_by_string(string)).to eq("bibtex")
112
+ end
113
+ end
114
+ end
@@ -0,0 +1,82 @@
1
+ {
2
+ "@context": "http://schema.org",
3
+ "@type": "Dataset",
4
+ "@id": "https://doi.org/10.23698/aida/drov",
5
+ "name": "Ovary data from the Visual Sweden project DROID",
6
+ "about": "Pathology",
7
+ "url": "https://doi.aida.medtech4health.se/10.23698/aida/drov",
8
+ "author": [{
9
+ "@type": "Person",
10
+ "@id": "https://orcid.org/0000-0003-1298-517X",
11
+ "givenName": "Karin",
12
+ "familyName": "Lindman",
13
+ "name": "Karin Lindman"
14
+ }, {
15
+ "@type": "Person",
16
+ "@id": "https://orcid.org/",
17
+ "givenName": "Jerónimo",
18
+ "familyName": "Rose",
19
+ "name": "Jerónimo F. Rose"
20
+ }, {
21
+ "@type": "Person",
22
+ "@id": "https://orcid.org/",
23
+ "givenName": "Martin",
24
+ "familyName": "Lindvall",
25
+ "name": "Martin Lindvall"
26
+ }, {
27
+ "@type": "Person",
28
+ "@id": "https://orcid.org/0000-0001-7250-234X",
29
+ "givenName": "Caroline",
30
+ "familyName": "Bivik Stadler",
31
+ "name": "Caroline Bivik Stadler"
32
+ }],
33
+ "publisher": {
34
+ "@type": "Organization",
35
+ "name": "AIDA"
36
+ },
37
+ "copyrightYear": 2019,
38
+ "copyrightHolder": [{
39
+ "@type": "Organization",
40
+ "name": "Linköping University",
41
+ "url": "https://liu.se/"
42
+ }, {
43
+ "@type": "Person",
44
+ "@id": "https://orcid.org/0000-0002-9368-0177",
45
+ "givenName": "Claes",
46
+ "familyName": "Lundström",
47
+ "name": "Claes Lundström"
48
+ }],
49
+ "provider": [{
50
+ "@type": "Person",
51
+ "@id": "https://orcid.org/0000-0002-0128-870X",
52
+ "name": "Karin Lindman",
53
+ "email": "Karin.Lindman@regionostergotland.se"
54
+ }, {
55
+ "@type": "Person",
56
+ "@id": "https://orcid.org/0000-0002-9368-0177",
57
+ "name": "Claes Lundstrom",
58
+ "email": "claes.lundstrom@liu.se"
59
+ }, {
60
+ "@type": "Person",
61
+ "@id": "https://orcid.org/0000-0001-7250-234X",
62
+ "givenName": "Caroline",
63
+ "familyName": "Bivik Stadler",
64
+ "name": "Caroline Bivik Stadler"
65
+ }, {
66
+ "@type": "Person",
67
+ "@id": "https://orcid.org/0000-0001-6443-3604",
68
+ "name": "Joel Hedlund",
69
+ "email": "joel.hedlund@liu.se"
70
+ }],
71
+ "dateCreated": "2019-01-09",
72
+ "datePublished": "2019-01-09",
73
+ "dateModified": "2019-01-09",
74
+ "keywords": "pathology, whole slide imaging, annotated",
75
+ "version": "1.0",
76
+ "description": "This dataset consists of 174 WSI ovary whole slide images (WSI): 158\nmalignant and 16 benign. Eight of the most common, histological definable\ntumour types were annotated: high grade serous carcinoma (HGSC), low grade\nserous carcinoma (LGSC), clear cell carcinoma (CC), endometrioid\nadenocarcinoma (EN), metastastic serous carcinoma (MS), metastatic other\n(MO), serous borderline tumor (SB) and mucinous borderline tumor (MB). Also\nnormal ovarian tissue were annotated. 11258 separate annotations were made.\nFor the benign structures only the epithelial structures, stroma and support\ntissue were annotated.\n",
77
+ "license": {
78
+ "name": "Restricted access",
79
+ "id": "https://datasets.aida.medtech4health.se/10.23698/aida/drov#license"
80
+ },
81
+ "citation": null
82
+ }
@@ -0,0 +1,18 @@
1
+ {
2
+ "name": "fullstack_app",
3
+ "version": "1.0.0",
4
+ "main": "index.js",
5
+ "scripts": {
6
+ "start": "concurrently \"sudo -i service elasticsearch start\" \"cd backend && node --max_old_space_size=8000 server.js\" \"cd client && npm start\""
7
+ },
8
+ "keywords": [],
9
+ "author": "",
10
+ "license": "ISC",
11
+ "dependencies": {
12
+ "concurrently": "^4.1.0",
13
+ "d3": "^5.9.2",
14
+ "monk": "^6.0.6"
15
+ },
16
+ "devDependencies": {},
17
+ "description": ""
18
+ }
@@ -0,0 +1,19 @@
1
+ {
2
+ "name": "CITapp",
3
+ "description": "Concealed Information Test app",
4
+ "version": "1.1.0",
5
+ "scripts": {
6
+ "test": "karma start test/karma.conf.js --single-run"
7
+ },
8
+ "devDependencies": {
9
+ "jasmine-core": "*",
10
+ "karma": "*",
11
+ "karma-chrome-launcher": "^2.2.0",
12
+ "karma-cli": "*",
13
+ "karma-fixture": "^0.2.6",
14
+ "karma-html2js-preprocessor": "*",
15
+ "karma-jasmine": "*",
16
+ "karma-phantomjs-launcher": "*",
17
+ "phantomjs-prebuilt": "*"
18
+ }
19
+ }
@@ -0,0 +1,26 @@
1
+ {
2
+ "type": "post-weblog",
3
+ "id": "https://doi.org/10.5438/4k3m-nyvg",
4
+ "DOI": "10.5438/4k3m-nyvg",
5
+ "URL": "https://blog.datacite.org/eating-your-own-dog-food",
6
+ "title": "Eating your own Dog Food",
7
+ "container-title": "DataCite Blog",
8
+ "publisher": "DataCite",
9
+ "abstract": "Eating your own dog food is a slang term to describe that an organization should itself use the products and services it provides. For DataCite this means that we should use DOIs with appropriate metadata and strategies for long-term preservation for...",
10
+ "categories": [
11
+ "Phylogeny",
12
+ "Malaria",
13
+ "Parasites",
14
+ "Taxonomy",
15
+ "Mitochondrial genome",
16
+ "Africa",
17
+ "Plasmodium"
18
+ ],
19
+ "issued": {
20
+ "date-parts": [
21
+ [
22
+ 2016, 12, 20
23
+ ]
24
+ ]
25
+ }
26
+ }
@@ -0,0 +1,21 @@
1
+ {
2
+ "type": "post-weblog",
3
+ "id": "https://doi.org/10.5072/4k3m-nyvg",
4
+ "DOI": "10.5072/4k3m-nyvg",
5
+ "URL": "https://blog.datacite.org/eating-your-own-dog-food",
6
+ "title": "Eating your own Dog Food",
7
+ "container-title": "DataCite Blog",
8
+ "publisher": "DataCite",
9
+ "abstract": "Eating your own dog food is a slang term to describe that an organization should itself use the products and services it provides. For DataCite this means that we should use DOIs with appropriate metadata and strategies for long-term preservation for...",
10
+ "issued": {
11
+ "date-parts": [
12
+ [
13
+ 2016, 12, 20
14
+ ]
15
+ ]
16
+ },
17
+ "author": [{
18
+ "family": "Fenner",
19
+ "given": "Martin"
20
+ }]
21
+ }
@@ -0,0 +1,30 @@
1
+ {
2
+ "type": "post-weblog",
3
+ "id": "https://doi.org/10.5438/4k3m-nyvg",
4
+ "DOI": "10.5438/4k3m-nyvg",
5
+ "URL": "https://blog.datacite.org/eating-your-own-dog-food",
6
+ "title": "Eating your own Dog Food",
7
+ "container-title": "DataCite Blog",
8
+ "publisher": "DataCite",
9
+ "abstract": "Eating your own dog food is a slang term to describe that an organization should itself use the products and services it provides. For DataCite this means that we should use DOIs with appropriate metadata and strategies for long-term preservation for...",
10
+ "categories": [
11
+ "Phylogeny",
12
+ "Malaria",
13
+ "Parasites",
14
+ "Taxonomy",
15
+ "Mitochondrial genome",
16
+ "Africa",
17
+ "Plasmodium"
18
+ ],
19
+ "issued": {
20
+ "date-parts": [
21
+ [
22
+ 2016, 12, 20
23
+ ]
24
+ ]
25
+ },
26
+ "author": [{
27
+ "family": "Fenner",
28
+ "given": "Martin"
29
+ }]
30
+ }