@manuscripts/transform 4.3.53 → 4.4.1

package/src/jats/__tests__/__fixtures__/jats-example-front-only.xml

@@ -0,0 +1,26 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!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">
+<article xmlns:xlink="http://www.w3.org/1999/xlink">
+  <front>
+    <article-meta>
+      <title-group>
+        <article-title>A complete manuscript</article-title>
+      </title-group>
+      <contrib-group content-type="authors">
+        <contrib contrib-type="author" id="MPContributor_975F60A6-2080-451B-A8E3-93F587BF3DEC">
+          <name>
+            <surname>User</surname>
+            <given-names>Developer</given-names>
+          </name>
+        </contrib>
+      </contrib-group>
+      <counts>
+        <count count-type="box" count="0" />
+        <fig-count count="0" />
+        <table-count count="0" />
+        <equation-count count="0" />
+        <ref-count count="2" />
+        <word-count count="2910" /></counts>
+    </article-meta>
+  </front>
+</article>

package/src/jats/__tests__/__fixtures__/jats-example-full.xml

@@ -0,0 +1,209 @@
+<?xml version="1.0" encoding="utf-8"?>
+<!DOCTYPE article PUBLIC "-//NLM//DTD JATS (Z39.96) Journal Archiving and Interchange DTD v1.1 20151215//EN" "https://jats.nlm.nih.gov/archiving/1.1/JATS-archivearticle1.dtd">
+<article article-type="research-article" dtd-version="1.1" xml:lang="en" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:mml="http://www.w3.org/1998/Math/MathML">
+  <front>
+    <journal-meta>
+      <journal-id journal-id-type="publisher-id">Journal Publisher ID</journal-id>
+      <journal-id journal-id-type="nlm-ta">Journal NLM ID</journal-id>
+      <journal-title-group>
+        <journal-title>Journal Title</journal-title>
+        <abbrev-journal-title abbrev-type="pubmed">PubMed Abbreviated Journal Title</abbrev-journal-title>
+      </journal-title-group>
+      <issn>1234-5678</issn>
+      <publisher><publisher-name>Publisher Name</publisher-name></publisher>
+    </journal-meta>
+    <article-meta>
+      <article-id pub-id-type="publisher-id">123412341234</article-id>
+      <title-group>
+        <article-title>This is the Article Title</article-title>
+        <subtitle>Which has a Subtitle</subtitle>
+      </title-group>
+      <contrib-group>
+        <contrib contrib-type="author" corresp="yes"><name><surname>Day</surname><given-names>Nathan</given-names></name><role>Member, IEEE</role><xref ref-type="fn" rid="afn1"><sup>1</sup></xref><xref ref-type="corresp" rid="cor1"><sup>*</sup></xref><xref ref-type="aff" rid="aff1"></xref></contrib>
+        <aff id="aff1">School of Hard Knocks, <institution>University of Life</institution>, <addr-line><city>Houston</city>, <state>TX</state></addr-line>, <country>USA</country>.</aff>
+      </contrib-group>
+      <author-notes><corresp id="cor1"><label>*</label>Correspondence: <email xlink:href="nday@inera.com">nday@inera.com</email>.</corresp>
+        <fn id="afn1">
+          <label>1</label><p>Author_Footnote.</p></fn>
+        <fn fn-type="con">
+          <label>Author Contributions</label>
+          <p>Author Contibutions are described here.</p></fn>
+        <fn id="afn2">
+          <p content-type="fn-title">Disclaimer</p>
+          <p>This is an unlabelled author footnote with a separate title.</p></fn>
+      </author-notes>
+      <pub-date pub-type="ppub"><day>05</day><year></year></pub-date>
+      <volume></volume>
+      <history>
+        <date date-type="received"><day>01</day><month>04</month><year>2009</year></date><date date-type="rev-recd"><day>02</day><month>05</month><year>2009</year></date><date date-type="accepted"><day>12</day><month>05</month><year>2009</year></date>
+      </history>
+      <permissions>
+      </permissions>
+      <abstract abstract-type="teaser">
+        <title>Teaser: Heads up!</title>
+        <p>The direct interaction of phenobarbital with the epidermal growth factor receptor reveals a new network interface in nuclear receptor signaling.</p>
+      </abstract>
+      <abstract>
+        <sec><title>Introduction</title><p>This is a sectionalized abstract.</p></sec>
+        <sec><title>Results</title><p>These are the results of the experiment.</p></sec>
+      </abstract>
+      <kwd-group kwd-group-type="author"><title>Keywords: </title><kwd>Paragraphs</kwd><kwd>exporting</kwd><kwd>testing</kwd><kwd>NLM DTD</kwd></kwd-group>
+    </article-meta>
+    <notes>
+      <def-list list-type="simple" list-content="abbreviations"><title>Abbreviations: </title><def-item><term>UK</term><def><p>United Kingdom</p></def></def-item><def-item><term>USA</term><def><p>United States of America</p></def></def-item></def-list>
+    </notes>
+  </front>
+  <body>
+    <sec sec-type="intro">
+      <title>Introduction</title>
+      <sec>
+        <title>A level 2 subhead</title>
+        <sec>
+          <title>A level 3 subhead</title>
+          <sec>
+            <title>A level 4 subhead</title>
+            <sec>
+              <title>A level 5 subhead</title>
+              <sec sec-type="ethics-statement">
+                <title>Ethics statement</title>
+                <p>Paragraph, see<xref ref-type="fn" rid="fn1"><sup>1</sup></xref> <xref ref-type="disp-formula" rid="eq1">Equation 1</xref> and <xref ref-type="fig" rid="fig1">Figure 1</xref>.</p>
+                <fig id="fig1" position="float" fig-type="half-right"><label>Figure 1</label><caption><p>A picture on the kinds of figures.</p><p>The Fig Caption continues.</p></caption><p>test paragraph</p><graphic xlink:href="123412341234.fig1"></graphic>
+                  <attrib>Source: Wikipedia.</attrib></fig>
+                <fig id="fig1" position="float" fig-type="half-right"><label>Figure 1</label><caption><p>A missing picture on the kinds of figures.</p><p>The Fig Caption continues.</p></caption><p>test paragraph</p><graphic xlink:href="123412341234.fig1" specific-use="MISSING"></graphic>
+                  <attrib>Source: Wikipedia.</attrib></fig>
+              </sec>
+            </sec>
+          </sec>
+        </sec>
+      </sec>
+    </sec>
+    <sec sec-type="materials|methods">
+      <title>Materials and Methods</title>
+      <p>Some more text</p>
+    </sec>
+    <sec sec-type="results">
+      <title>Results</title>
+      <p>Some text that introduces a poem:</p>
+      <verse-group>
+        <verse-line>Poetry</verse-line>
+        <attrib>Source: Wikipedia</attrib>
+      </verse-group>
+      <p>You might1 peruse, e.g., <xref ref-type="boxed-text" rid="b1">Box 1</xref>. See also <xref ref-type="app" rid="appA">Appendix A</xref>.</p>
+      <boxed-text id="b1"><label>Box 1</label><caption><title>Boxed boxes.</title></caption>
+        <sec>
+          <title>Box_Head_1</title>
+          <sec>
+            <title>Box_Head_2</title>
+            <p>Box_Text<xref ref-type="fn" rid="fn2"><sup>&#x2020;</sup></xref></p>
+            <fn-group>
+              <fn>
+                <p>Box Note</p></fn>
+            </fn-group>
+          </sec>
+        </sec></boxed-text>
+      <p>See also, <xref ref-type="bibr" rid="bib1">Day (2008)</xref> and <xref ref-type="table" rid="tbl1">Table 1</xref>.<table-wrap id="tbl1" position="float">
+        <label>Table 1</label><caption><title>Kinds of tables</title>
+        <p>This is a table title continued paragraph</p>
+      </caption>
+        <table frame="hsides" rules="groups">
+          <col width="100%"/>
+          <thead>
+            <tr>
+              <th valign="top" align="left" scope="col" style="border-left: solid 0.50pt; border-top: solid 0.50pt; border-right: solid 0.50pt; border-bottom: solid 0.50pt">Table_Head</th>
+            </tr>
+          </thead>
+          <tbody>
+            <tr>
+              <td valign="top" align="left" style="border-left: solid 0.50pt; border-top: solid 0.50pt; border-right: solid 0.50pt; border-bottom: solid 0.50pt">Table_Body*</td>
+            </tr>
+          </tbody>
+        </table><table-wrap-foot>
+        <p>* Table_Footnote</p>
+      </table-wrap-foot></table-wrap>
+        <disp-quote>
+          <p>Block_Quote</p>
+          <attrib>Source: Wikipedia</attrib>
+        </disp-quote>Paragraph_Continued with a graphic <inline-graphic xlink:href="image1"/> in the middle<disp-formula id="eq1"><mml:math id="m1">
+          <mml:mrow>
+            <mml:mstyle displaystyle="true">
+              <mml:mrow><mml:mo>&#x222B;</mml:mo>
+                <mml:mrow></mml:mrow>
+              </mml:mrow>
+            </mml:mstyle><mml:mi>&#x03B8;</mml:mi><mml:msup>
+            <mml:mrow>
+              <mml:mi>cos</mml:mi></mml:mrow>
+            <mml:mrow>
+              <mml:mo>&#x2212;</mml:mo><mml:mn>1</mml:mn></mml:mrow>
+          </mml:msup>
+            <mml:mfenced>
+              <mml:mrow>
+                <mml:mfrac>
+                  <mml:mi>&#x03C0;</mml:mi>
+                  <mml:mn>2</mml:mn>
+                </mml:mfrac>
+                <mml:mo>&#x2212;</mml:mo><mml:mi>&#x03B8;</mml:mi></mml:mrow>
+            </mml:mfenced></mml:mrow>
+        </mml:math><label>(1)</label></disp-formula>where the paragraph continues.</p>
+      <statement><label>H<sub>1</sub></label><p>This is a hypothesis.</p></statement>
+      <list id="L1" list-type="bullet"><list-item><p>Num_Bul_List_1</p>
+        <p>List_1_Continued</p>
+        <list id="L2" list-type="bullet"><list-item><p>Num_Bul_List_2</p>
+          <p>List_2_Continued</p></list-item></list>
+      </list-item><list-item><p>level 1, bullet 2</p></list-item></list>
+    </sec>
+    <sec sec-type="discussion">
+      <title>Discussion</title>
+      <p>Paragraph<list id="L3" list-type="simple"><list-item><p>Unnumbered_List_1</p></list-item>
+        <list-item><p>Another unnumbered item</p></list-item></list>with another paragraph that continues after a list.</p>
+    </sec>
+    <sec sec-type="conclusions">
+      <title>Conclusions</title>
+      <p>Paragraph</p>
+    </sec>
+  </body>
+  <back>
+    <app-group>
+      <app id="appA"><label>Appendix A</label><title>This is an appendix</title>
+        <sec>
+          <title>Appendix_Head_1</title>
+          <sec>
+            <title>Appendix_Head_2</title>
+            <p>Appendix_Text</p>
+          </sec>
+        </sec>
+      </app>
+    </app-group>
+    <ack>
+      <title>Acknowledgements</title>
+      <p>Acknowledgement</p>
+    </ack>
+    <fn-group>
+      <fn fn-type="conflict">
+        <label>Competing Interests</label>
+        <p>This is information about Competing Interests.</p></fn>
+      <fn fn-type="financial-disclosure">
+        <label>Financial Disclosure</label>
+        <p>This is a Financial Disclosure.</p></fn>
+    </fn-group>
+    <sec sec-type="data-availability">
+      <title>Data availability</title>
+      <p>This is some information about data availability.</p>
+    </sec>
+    <ref-list>
+      <title>References</title>
+      <ref id="bib1"><mixed-citation publication-type="journal"><person-group person-group-type="author"><string-name><surname>Day</surname>, <given-names>R.N.</given-names></string-name></person-group> (<year>2008</year>). &#x201C;<article-title>This is the article title.</article-title>&#x201D; <source>EDCC</source>, <volume>3</volume>(<issue>2</issue>): <fpage>123</fpage>-<lpage>134</lpage>.</mixed-citation></ref>
+    </ref-list>
+    <bio>
+      <p>Author Biography in a single paragraph.</p>
+    </bio>
+    <bio>
+      <title>Nathan Day</title>
+      <p><inline-graphic xlink:href="ArcFullTextParaExportTest-Image001"/></p>
+      <p>This is a biography of Nathan Day.</p>
+    </bio>
+    <fn-group><fn id="fn1">
+      <p>This is a footnote.</p></fn><fn id="fn2">
+      <p>Footnote called out in a box</p></fn>
+    </fn-group>
+  </back>
+</article>

package/src/jats/__tests__/__fixtures__/jats-example-no-back.xml

@@ -0,0 +1,156 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!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">
+<article xmlns:xlink="http://www.w3.org/1999/xlink">
+  <front>
+    <article-meta>
+      <title-group>
+        <article-title>A complete manuscript</article-title>
+      </title-group>
+      <contrib-group content-type="authors">
+        <contrib contrib-type="author" id="MPContributor_975F60A6-2080-451B-A8E3-93F587BF3DEC">
+          <name>
+            <surname>User</surname>
+            <given-names>Developer</given-names>
+          </name>
+        </contrib>
+      </contrib-group>
+      <counts>
+        <count count-type="box" count="0" />
+        <fig-count count="0" />
+        <table-count count="0" />
+        <equation-count count="0" />
+        <ref-count count="2" />
+        <word-count count="2910" /></counts>
+    </article-meta>
+  </front>
+  <body>
+    <sec id="MPSection_AB23BC7F-F0A3-46FB-AEDD-54405C032E5E">
+      <title>Paragraphs</title>
+      <p id="MPParagraphElement_5BF50210-0758-40D1-831A-DCD814577FD0">A paragraph.</p>
+    </sec>
+    <sec id="MPSection_A4926F2B-B6DF-4974-B18F-05FEC8CA8003">
+      <title>Lists</title>
+      <list list-type="order">
+        <list-item>
+          <p>An ordered list</p>
+        </list-item>
+        <list-item>
+          <p>With two items</p>
+        </list-item>
+      </list>
+      <list list-type="order">
+        <list-item>
+          <p>An ordered list</p>
+          <list list-type="order">
+            <list-item>
+              <p>With a nested ordered list</p>
+            </list-item>
+            <list-item>
+              <p>With two items</p>
+            </list-item>
+          </list>
+        </list-item>
+      </list>
+      <list list-type="bullet">
+        <list-item>
+          <p>A bullet list</p>
+          <list list-type="bullet">
+            <list-item>
+              <p>With a nested bullet list</p>
+            </list-item>
+            <list-item>
+              <p>With two items</p>
+            </list-item>
+          </list>
+        </list-item>
+      </list>
+      <list list-type="bullet">
+        <list-item>
+          <p>A bullet list</p>
+          <list list-type="order">
+            <list-item>
+              <p>With a nested ordered list</p>
+            </list-item>
+            <list-item>
+              <p>With two items</p>
+            </list-item>
+          </list>
+        </list-item>
+      </list>
+    </sec>
+    <sec id="MPSection_2E0A7E51-F531-47C3-B585-AA86506D3DE4">
+      <title>Figures</title>
+      <fig id="MPFigure_035B52CA-C486-4AC1-B44E-40F36F422686">
+        <caption>
+          <p>Test</p>
+        </caption>
+        <graphic xlink:href="graphic/MPFigure_035B52CA-C486-4AC1-B44E-40F36F422686.jpeg" content-type="half-right" />
+      </fig>
+    </sec>
+    <sec id="MPSection_66B42418-3457-4116-96F1-667D17CBA813">
+      <title>Tables</title>
+      <table-wrap id="MPTableElement_ED394766-2934-4B28-AEFE-EAF97D90D854">
+        <caption>
+          <p>Test</p>
+        </caption>
+        <table id="MPTable_2E556F94-DB53-413B-8592-58358A8DD8DD">
+          <thead>
+            <tr>
+              <td>Test</td>
+              <td>Test</td>
+            </tr>
+          </thead>
+          <tfoot>
+            <tr>
+              <td>Test</td>
+              <td />
+            </tr>
+          </tfoot>
+          <tbody>
+            <tr>
+              <td>Test</td>
+              <td />
+            </tr>
+            <tr>
+              <td />
+              <td>Test</td>
+            </tr>
+          </tbody>
+        </table>
+      </table-wrap>
+    </sec>
+    <sec id="MPSection_61643B99-F34D-46E2-8772-563BC4A7DDB6">
+      <title>Equations</title>
+      <p id="MPParagraphElement_A868D3F9-3F1A-4DA3-BE74-AEF9998A952F">This paragraph contains an inline equation:<inline-formula><tex-math>2+3=5</tex-math></inline-formula></p>
+      <fig id="MPEquationElement_0F637C49-DE6C-4702-974D-5016EC132A1A" fig-type="equation">
+        <disp-formula id="MPEquation_ED92F6D4-52EF-4C70-8C11-4F233B96D126">
+          <tex-math>E=mc^2</tex-math>
+        </disp-formula>
+      </fig>
+    </sec>
+    <sec id="MPSection_27394269-1EB9-47B0-B3F2-11657319C5E1">
+      <title>Listings</title>
+      <fig id="MPListingElement_6FC7712B-85CE-45D9-A6E7-EB2C48CD0F37" fig-type="listing">
+        <code id="MPListing_80FBEC35-C062-4351-A7E6-0515E9D3837D" language="javascript">2+3=5</code>
+      </fig>
+    </sec>
+    <sec id="MPSection_DBCB444D-2469-4EE4-AD80-49AA2E59FC0E">
+      <title>Inline</title>
+      <p id="MPParagraphElement_94310CD9-4A4B-4F98-9D92-DA957E862DA3">This paragraph contains <bold>bold</bold>, <italic>italic</italic>, <underline>underlined</underline>, <sup>superscript</sup> and <sub>subscript</sub> text.</p>
+      <p id="MPParagraphElement_8783E7FC-D562-479A-9BA2-61C6DCD31F35">This paragraph contains <ext-link ext-link-type="uri" xlink:href="https://example.com">a link</ext-link>.</p>
+    </sec>
+    <sec id="MPSection_15F7949D-0FC4-4EE9-BF35-F9BCB62ED54B">
+      <title>Quotes</title>
+      <disp-quote content-type="quote">
+        <p>This is a block quote.</p>
+        <attrib>It came from here.</attrib>
+      </disp-quote>
+    </sec>
+    <sec id="MPSection_A8F4E48A-32A4-4702-814C-F18D2A434EBB">
+      <title>Citations</title>
+      <p id="MPParagraphElement_3EF4BE66-BFE5-4BB4-A9B8-17130F9B3CA1">This paragraph ends with a citation.<xref ref-type="bibr" rid="MPBibliographyItem_787BD4C1-3074-4076-9707-0227D29C1F10">1</xref></p>
+      <p id="MPParagraphElement_51B71DB6-30CC-4273-9975-EA03E3244C8B">This paragraph ends with two citations.<xref ref-type="bibr" rid="MPBibliographyItem_E9EFF971-4380-4DEB-83CF-B0CAA6C32BDF MPBibliographyItem_36EDAD5A-EBA0-47AE-88E6-EBAD385166AE">2,3</xref></p>
+      <p id="MPParagraphElement_6887297E-F834-4F1E-9BC2-0C47F551541B">This paragraph ends with all three citations.<xref ref-type="bibr" rid="MPBibliographyItem_787BD4C1-3074-4076-9707-0227D29C1F10 MPBibliographyItem_36EDAD5A-EBA0-47AE-88E6-EBAD385166AE MPBibliographyItem_E9EFF971-4380-4DEB-83CF-B0CAA6C32BDF">1–3</xref></p>
+    </sec>
+  </body>
+</article>

package/src/jats/__tests__/__fixtures__/jats-example-no-body.xml

@@ -0,0 +1,91 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!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">
+<article xmlns:xlink="http://www.w3.org/1999/xlink">
+  <front>
+    <article-meta>
+      <title-group>
+        <article-title>A complete manuscript</article-title>
+      </title-group>
+      <contrib-group content-type="authors">
+        <contrib contrib-type="author" id="MPContributor_975F60A6-2080-451B-A8E3-93F587BF3DEC">
+          <name>
+            <surname>User</surname>
+            <given-names>Developer</given-names>
+          </name>
+        </contrib>
+      </contrib-group>
+      <counts>
+        <count count-type="box" count="0" />
+        <fig-count count="0" />
+        <table-count count="0" />
+        <equation-count count="0" />
+        <ref-count count="2" />
+        <word-count count="2910" /></counts>
+    </article-meta>
+  </front>
+  <back>
+    <ref-list id="MPSection_A83F9050-B6E5-4587-863B-2BD9F6D788FE">
+      <title>Bibliography</title>
+      <ref id="MPBibliographyItem_787BD4C1-3074-4076-9707-0227D29C1F10">
+        <element-citation publication-type="journal">
+          <name>
+            <surname>Case</surname>
+            <given-names>Nat</given-names>
+          </name>
+          <article-title>Creating Graphically Complex Indexes With InDesign</article-title>
+          <source>Cartographic Perspectives</source>
+          <issue>62</issue>
+          <fpage>52</fpage>
+          <lpage>54</lpage>
+          <year>2009</year>
+          <month>3</month>
+          <day>1</day>
+        </element-citation>
+      </ref>
+      <ref id="MPBibliographyItem_E9EFF971-4380-4DEB-83CF-B0CAA6C32BDF">
+        <element-citation publication-type="journal">
+          <article-title>Technique for extracting reusable XML Schema from schema-less XML Documents</article-title>
+          <source>The KIPS Transactions:PartD</source>
+          <volume>10D</volume>
+          <issue>4</issue>
+          <fpage>603</fpage>
+          <lpage>612</lpage>
+          <year>2003</year>
+          <month>8</month>
+          <day>1</day>
+        </element-citation>
+      </ref>
+      <ref id="MPBibliographyItem_36EDAD5A-EBA0-47AE-88E6-EBAD385166AE">
+        <element-citation publication-type="journal">
+          <name>
+            <surname>Kim</surname>
+            <given-names>Jin</given-names>
+          </name>
+          <name>
+            <surname>Kang</surname>
+            <given-names>Hyun-Chul</given-names>
+          </name>
+          <article-title>XML Fragmentation for Resource-Efficient Query Processing over XML Fragment Stream</article-title>
+          <source>The KIPS Transactions:PartD</source>
+          <volume>16D</volume>
+          <issue>1</issue>
+          <fpage>27</fpage>
+          <lpage>42</lpage>
+          <year>2009</year>
+          <month>2</month>
+          <day>28</day>
+        </element-citation>
+      </ref>
+    </ref-list>
+    <fn-group>
+      <fn fn-type="conflict">
+        <p content-type="fn-title">CONFLICT OF INTEREST</p>
+        <p>No conflicts of interest have been declared.</p>
+      </fn>
+      <fn fn-type="financial-disclosure">
+        <p content-type="fn-title">FUNDING INFORMATION</p>
+        <p>This work was supported by the National Natural Science Foundation of China (81771439), Jiangsu Provincial Key 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).</p>
+      </fn>
+    </fn-group>
+  </back>
+</article>