@manuscripts/transform 4.3.53 → 4.4.0

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Files changed (172) hide show
  1. package/dist/cjs/jats/__tests__/jats-roundtrip.test.js +3 -3
  2. package/dist/cjs/version.js +1 -1
  3. package/dist/es/jats/__tests__/jats-roundtrip.test.js +3 -3
  4. package/dist/es/version.js +1 -1
  5. package/dist/types/jats/__tests__/utils.d.ts +1 -1
  6. package/dist/types/version.d.ts +1 -1
  7. package/package.json +22 -21
  8. package/src/errors.ts +28 -0
  9. package/src/getVersion.ts +21 -0
  10. package/src/index.ts +28 -0
  11. package/src/jats/__tests__/__fixtures__/debug-example.xml +136 -0
  12. package/src/jats/__tests__/__fixtures__/jats-abstract-no-body.xml +163 -0
  13. package/src/jats/__tests__/__fixtures__/jats-citations.xml +472 -0
  14. package/src/jats/__tests__/__fixtures__/jats-comments.xml +46 -0
  15. package/src/jats/__tests__/__fixtures__/jats-document.xml +134 -0
  16. package/src/jats/__tests__/__fixtures__/jats-example-doc.xml +1235 -0
  17. package/src/jats/__tests__/__fixtures__/jats-example-front-only.xml +26 -0
  18. package/src/jats/__tests__/__fixtures__/jats-example-full.xml +209 -0
  19. package/src/jats/__tests__/__fixtures__/jats-example-no-back.xml +156 -0
  20. package/src/jats/__tests__/__fixtures__/jats-example-no-body.xml +91 -0
  21. package/src/jats/__tests__/__fixtures__/jats-example.xml +221 -0
  22. package/src/jats/__tests__/__fixtures__/jats-fn-group.xml +60 -0
  23. package/src/jats/__tests__/__fixtures__/jats-import-no-refs.xml +1077 -0
  24. package/src/jats/__tests__/__fixtures__/jats-import.xml +1561 -0
  25. package/src/jats/__tests__/__fixtures__/jats-roundtrip.xml +133 -0
  26. package/src/jats/__tests__/__fixtures__/jats-tables-example.xml +2043 -0
  27. package/src/jats/__tests__/__fixtures__/math-fragment.xml +12 -0
  28. package/src/jats/__tests__/__snapshots__/citeproc.test.ts.snap +57 -0
  29. package/src/jats/__tests__/__snapshots__/create-article-node.test.ts.snap +65 -0
  30. package/src/jats/__tests__/__snapshots__/jats-exporter.test.ts.snap +7 -0
  31. package/src/jats/__tests__/__snapshots__/jats-importer.test.ts.snap +59605 -0
  32. package/src/jats/__tests__/__snapshots__/jats-roundtrip.test.ts.snap +18 -0
  33. package/src/jats/__tests__/citations.ts +25 -0
  34. package/src/jats/__tests__/citeproc.test.ts +195 -0
  35. package/src/jats/__tests__/create-article-node.test.ts +29 -0
  36. package/src/jats/__tests__/data/section-categories.ts +212 -0
  37. package/src/jats/__tests__/files.ts +24 -0
  38. package/src/jats/__tests__/jats-exporter.test.ts +223 -0
  39. package/src/jats/__tests__/jats-importer.test.ts +567 -0
  40. package/src/jats/__tests__/jats-roundtrip.test.ts +66 -0
  41. package/src/jats/__tests__/utils.ts +90 -0
  42. package/src/jats/exporter/citeproc.ts +265 -0
  43. package/src/jats/exporter/jats-exporter.ts +2090 -0
  44. package/src/jats/exporter/jats-versions.ts +50 -0
  45. package/src/jats/exporter/labels.ts +101 -0
  46. package/src/jats/importer/create-article-node.ts +52 -0
  47. package/src/jats/importer/jats-comments.ts +111 -0
  48. package/src/jats/importer/jats-dom-parser.ts +1260 -0
  49. package/src/jats/importer/jats-parser-utils.ts +234 -0
  50. package/src/jats/importer/jats-transformations.ts +591 -0
  51. package/src/jats/importer/parse-jats-article.ts +106 -0
  52. package/src/jats/index.ts +21 -0
  53. package/src/jats/types.ts +16 -0
  54. package/src/lib/__tests__/footnotes.test.ts +36 -0
  55. package/src/lib/citeproc.ts +30 -0
  56. package/src/lib/credit-roles.ts +91 -0
  57. package/src/lib/deafults.ts +17 -0
  58. package/src/lib/footnotes.ts +85 -0
  59. package/src/lib/html.ts +56 -0
  60. package/src/lib/section-categories.ts +27 -0
  61. package/src/lib/utils.ts +145 -0
  62. package/src/lib/xml.ts +28 -0
  63. package/src/schema/__tests__/docs.ts +1911 -0
  64. package/src/schema/__tests__/groups.test.ts +61 -0
  65. package/src/schema/__tests__/migration.test.ts +23 -0
  66. package/src/schema/groups.ts +36 -0
  67. package/src/schema/index.ts +286 -0
  68. package/src/schema/marks.ts +254 -0
  69. package/src/schema/migration/migrate.ts +77 -0
  70. package/src/schema/migration/migration-script.ts +26 -0
  71. package/src/schema/migration/migration-scripts/1.2.5.ts +44 -0
  72. package/src/schema/migration/migration-scripts/2.3.22.ts +52 -0
  73. package/src/schema/migration/migration-scripts/3.0.12.ts +33 -0
  74. package/src/schema/migration/migration-scripts/3.0.21.ts +50 -0
  75. package/src/schema/migration/migration-scripts/3.0.30.ts +65 -0
  76. package/src/schema/migration/migration-scripts/3.0.31.ts +40 -0
  77. package/src/schema/migration/migration-scripts/3.0.41.ts +37 -0
  78. package/src/schema/migration/migration-scripts/3.0.55.ts +42 -0
  79. package/src/schema/migration/migration-scripts/3.0.56.ts +114 -0
  80. package/src/schema/migration/migration-scripts/4.2.13.ts +37 -0
  81. package/src/schema/migration/migration-scripts/4.2.15.ts +48 -0
  82. package/src/schema/migration/migration-scripts/4.3.23.ts +55 -0
  83. package/src/schema/migration/migration-scripts/4.3.34.ts +132 -0
  84. package/src/schema/migration/migration-scripts/4.3.35.ts +41 -0
  85. package/src/schema/migration/migration-scripts/index.ts +49 -0
  86. package/src/schema/nodes/abstracts.ts +29 -0
  87. package/src/schema/nodes/affiliation.ts +88 -0
  88. package/src/schema/nodes/affiliations.ts +30 -0
  89. package/src/schema/nodes/alt_text.ts +36 -0
  90. package/src/schema/nodes/alt_title.ts +40 -0
  91. package/src/schema/nodes/alt_titles_section.ts +58 -0
  92. package/src/schema/nodes/attachment.ts +46 -0
  93. package/src/schema/nodes/attachments.ts +45 -0
  94. package/src/schema/nodes/attribution.ts +38 -0
  95. package/src/schema/nodes/author_notes.ts +44 -0
  96. package/src/schema/nodes/award.ts +52 -0
  97. package/src/schema/nodes/awards.ts +45 -0
  98. package/src/schema/nodes/backmatter.ts +31 -0
  99. package/src/schema/nodes/bibliography_element.ts +58 -0
  100. package/src/schema/nodes/bibliography_item.ts +108 -0
  101. package/src/schema/nodes/bibliography_section.ts +60 -0
  102. package/src/schema/nodes/blockquote_element.ts +79 -0
  103. package/src/schema/nodes/body.ts +29 -0
  104. package/src/schema/nodes/box_element.ts +67 -0
  105. package/src/schema/nodes/caption.ts +67 -0
  106. package/src/schema/nodes/caption_title.ts +67 -0
  107. package/src/schema/nodes/citation.ts +70 -0
  108. package/src/schema/nodes/comment.ts +50 -0
  109. package/src/schema/nodes/comments.ts +28 -0
  110. package/src/schema/nodes/contributor.ts +87 -0
  111. package/src/schema/nodes/contributors.ts +40 -0
  112. package/src/schema/nodes/core_section.ts +27 -0
  113. package/src/schema/nodes/corresp.ts +49 -0
  114. package/src/schema/nodes/cross_reference.ts +64 -0
  115. package/src/schema/nodes/doc.ts +21 -0
  116. package/src/schema/nodes/embed.ts +55 -0
  117. package/src/schema/nodes/equation.ts +65 -0
  118. package/src/schema/nodes/equation_element.ts +61 -0
  119. package/src/schema/nodes/figure.ts +65 -0
  120. package/src/schema/nodes/figure_element.ts +73 -0
  121. package/src/schema/nodes/footnote.ts +95 -0
  122. package/src/schema/nodes/footnotes_element.ts +69 -0
  123. package/src/schema/nodes/footnotes_section.ts +61 -0
  124. package/src/schema/nodes/general_table_footnote.ts +42 -0
  125. package/src/schema/nodes/graphical_abstract_section.ts +62 -0
  126. package/src/schema/nodes/hard_break.ts +36 -0
  127. package/src/schema/nodes/hero_image.ts +46 -0
  128. package/src/schema/nodes/highlight_marker.ts +68 -0
  129. package/src/schema/nodes/image_element.ts +49 -0
  130. package/src/schema/nodes/inline_equation.ts +68 -0
  131. package/src/schema/nodes/inline_footnote.ts +66 -0
  132. package/src/schema/nodes/keyword.ts +61 -0
  133. package/src/schema/nodes/keyword_group.ts +63 -0
  134. package/src/schema/nodes/keywords.ts +59 -0
  135. package/src/schema/nodes/keywords_element.ts +64 -0
  136. package/src/schema/nodes/link.ts +79 -0
  137. package/src/schema/nodes/list.ts +134 -0
  138. package/src/schema/nodes/listing.ts +91 -0
  139. package/src/schema/nodes/listing_element.ts +61 -0
  140. package/src/schema/nodes/long_desc.ts +36 -0
  141. package/src/schema/nodes/manuscript.ts +86 -0
  142. package/src/schema/nodes/missing_figure.ts +59 -0
  143. package/src/schema/nodes/paragraph.ts +77 -0
  144. package/src/schema/nodes/placeholder.ts +62 -0
  145. package/src/schema/nodes/placeholder_element.ts +60 -0
  146. package/src/schema/nodes/pullquote_element.ts +81 -0
  147. package/src/schema/nodes/quote_image.ts +64 -0
  148. package/src/schema/nodes/section.ts +69 -0
  149. package/src/schema/nodes/section_label.ts +39 -0
  150. package/src/schema/nodes/section_title.ts +58 -0
  151. package/src/schema/nodes/subtitle.ts +40 -0
  152. package/src/schema/nodes/subtitles.ts +51 -0
  153. package/src/schema/nodes/supplement.ts +77 -0
  154. package/src/schema/nodes/supplements.ts +60 -0
  155. package/src/schema/nodes/table.ts +144 -0
  156. package/src/schema/nodes/table_col.ts +76 -0
  157. package/src/schema/nodes/table_element.ts +67 -0
  158. package/src/schema/nodes/table_element_footer.ts +42 -0
  159. package/src/schema/nodes/text.ts +31 -0
  160. package/src/schema/nodes/title.ts +43 -0
  161. package/src/schema/nodes/trans_abstract.ts +58 -0
  162. package/src/schema/nodes/trans_graphical_abstract.ts +67 -0
  163. package/src/schema/types.ts +240 -0
  164. package/src/tests.ts +33 -0
  165. package/src/transformer/id.ts +23 -0
  166. package/src/transformer/index.ts +21 -0
  167. package/src/transformer/node-names.ts +73 -0
  168. package/src/transformer/node-title.ts +111 -0
  169. package/src/transformer/node-types.ts +39 -0
  170. package/src/transformer/node-validator.ts +82 -0
  171. package/src/types.ts +25 -0
  172. package/src/version.ts +1 -0
package/src/jats/__tests__/__fixtures__/jats-roundtrip.xml ADDED
@@ -0,0 +1,133 @@
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+ <?xml version="1.0" encoding="UTF-8"?>
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+ <!DOCTYPE article PUBLIC "-//NLM//DTD JATS (Z39.96) Journal Archiving and Interchange DTD with OASIS Tables with MathML3 v1.2 20190208//EN" "http://jats.nlm.nih.gov/archiving/1.2/JATS-archive-oasis-article1-mathml3.dtd">
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+ <article xmlns:xlink="http://www.w3.org/1999/xlink" article-type="research-article">
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+ <front>
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+ <journal-meta>
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+ <journal-id journal-id-type="nlm-ta">Human Psychopharmacology: Clinical and Experimental</journal-id>
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+ <journal-title-group>
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+ <journal-title>Human Psychopharmacology: Clinical and Experimental</journal-title>
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+ <abbrev-journal-title abbrev-type="pubmed">Human Psychopharmacology: Clinical and Experimental</abbrev-journal-title>
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+ </journal-title-group>
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+ <issn pub-type="ppub">0885-6222</issn>
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+ <issn pub-type="epub">1540-1235</issn>
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+ <publisher>
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+ <publisher-name>John Wiley and Sons</publisher-name>
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+ </publisher>
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+ </journal-meta>
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+ <article-meta>
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+ <article-id pub-id-type="publisher-id">HUP-19-0076</article-id>
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+ <title-group>
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+ <article-title>A complete manuscript</article-title>
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+ </title-group>
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+ <contrib-group>
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+ <contrib contrib-type="author">
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+ <name>
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+ <surname>Macintosh</surname>
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+ <given-names>Alfred</given-names>
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+ </name>
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+ <email xlink:href="macintosh@hotmail.com">flinserl@hotmail.com</email>
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+ <xref ref-type="aff" rid="EDN3-2020-0111-aff3">
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+ <sup>3</sup>
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+ </xref>
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+ </contrib>
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+ <contrib contrib-type="author" corresp="yes">
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+ <name>
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+ <surname>Adam</surname>
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+ <given-names>Rein</given-names>
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+ </name>
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+ <email xlink:href="adam.brys@some.be">rein.brys@inbo.be</email>
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+ </contrib>
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+ </contrib-group>
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+ <author-notes>
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+ <corresp id="EDN3-2020-0111-cor1">Corresponding authors, John Macintosh:
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+ <email xlink:href="macintosh@hotmail.com">macintosh@hotmail.com</email>, ORCID 0000-0003-1215-2987, Adam Brys:
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+ <email xlink:href="adam.brys@some.be">adam.brys@some.be</email>, ORCID 0000-0002-0688-3268
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+ </corresp>
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+ <fn fn-type="con">
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+ <p content-type="fn-title">Author contributions</p>
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+ <p>JM and AB wrote the manuscript. All co-authors provided comments and helped revising the manuscript.</p>
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+ </fn>
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+ <fn fn-type="abbr">
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+ <p content-type="fn-title">Abbreviations</p>
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+ <p>In this story, the Galactic Exploration Unit (GEU) plays a crucial role in interstellar diplomacy and scientific discovery.</p>
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+ </fn>
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+ <p>rana nofal testing</p>
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+ </author-notes>
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+ </article-meta>
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+ </front>
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+ <body>
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+ <sec id="MPSection_2E0A7E51-F531-47C3-B585-AA86506D3DE4">
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+ <title>Figures</title>
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+ <fig id="MPFigure_035B52CA-C486-4AC1-B44E-40F36F422686" fig-type="half-left">
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+ <label>label</label>
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+ <caption>
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+ <title>Caption title</title>
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+ <p>Test1</p>
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+ <p>Test2</p>
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+ </caption>
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+ <p>A paragraph</p>
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+ <graphic xlink:href="graphic/111111.jpeg"/>
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+ <graphic xlink:href="graphic/222222.jpeg" specific-use="MISSING" />
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+ <graphic xlink:href="graphic/333333.jpeg"/>
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+ <attrib>Source: Wikipedia.</attrib>
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+ </fig>
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+ </sec>
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+ </body>
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+ <back>
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+ <fn-group>
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+ <fn fn-type="financial-disclosure">
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+ <p content-type="fn-title">FUNDING INFORMATION</p>
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+ <p>This work was supported by the National Natural Science Foundation of China (81771439), Jiangsu Provincial Key
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+ <xref ref-type="bibr" rid="HUP-19-0076-bib-0001">1</xref>Research and Development Program (BE2020661 and BE2018662), Jiangsu Provincial Health Commission Science Research Program (QNRC2016228, H2019056 and LGY2018010), Jiangsu Provincial Six Talent Peaks Project (WSN-165), Suzhou Municipal Health Commission Science Research Program (SZYJTD201715, LCZX201820, Kjxw2018048 and Gwzx201801), Suzhou Municipal Sci-Tech Bureau Program (SZS201722, SS201706, SYS2019113 and SS2019009), and CAS Key Laboratory of Mental Health, Institute of Psychology (KLMH2019K03).
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+ </p>
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+ </fn>
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+ </fn-group>
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+ <ref-list>
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+ <title>References</title>
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+ <ref id="HUP-19-0076-bib-0001">
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+ <element-citation publication-type="journal">
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+ <person-group person-group-type="author">
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+ <string-name>
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+ <surname>Caldwell</surname>
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+ <given-names>C.B.</given-names>
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+ </string-name>
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+ <string-name>
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+ <surname>Gottesman</surname>
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+ <given-names>I.I.</given-names>
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+ </string-name>
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+ </person-group>
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+ <year>1992</year>
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+ <article-title>Schizophrenia-a high-risk factor for suicide: clues to risk reduction.</article-title>
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+ <source>Suicide Life Threat Behav.</source>
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+ <volume>22</volume>
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+ <issue>4</issue>
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+ <fpage>479</fpage>
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+ <lpage>493</lpage>
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+ </element-citation>
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+ </ref>
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+ <ref id="HUP-19-0076-bib-0002">
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+ <element-citation publication-type="journal">
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+ <person-group person-group-type="author">
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+ <string-name>
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+ <surname>Hor</surname>
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+ <given-names>K.</given-names>
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+ </string-name>
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+ <string-name>
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+ <surname>Taylor</surname>
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+ <given-names>M.</given-names>
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+ </string-name>
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+ </person-group>
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+ <year>2010</year>
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+ <article-title>Suicide and schizophrenia: a systematic review of rates and risk factors.</article-title>
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+ <source>J Psychopharmacol.</source>
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+ <volume>24</volume>
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+ <issue>4</issue>
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+ <supplement>Suppl</supplement>
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+ <fpage>81</fpage>
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+ <lpage>90</lpage>
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+ <pub-id pub-id-type="doi">https://doi.org/10.1177/1359786810385490</pub-id>
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+ </element-citation>
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+ </ref>
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+ </ref-list>
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+ </back>
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+ </article>