Merge pull request #814 from elifesciences/pr-814

RP - add comment checks
elifesciences · Feb 11, 2025 · ce08941 · ce08941
2 parents 4e4ae85 + fdf2ddc
commit ce08941
Show file tree

Hide file tree

Showing 11 changed files with 1,058 additions and 594 deletions.
diff --git a/src/rp-schematron-base.sch b/src/rp-schematron-base.sch
@@ -895,6 +895,18 @@
           id="mixed-citation-child-1"><name/> in reference (id=<value-of select="ancestor::ref/@id"/>) is empty, which cannot be correct.</report>
       </rule>
     </pattern>
+
+  <pattern id="comment">
+      <rule context="comment" id="comment-checks">
+        <assert test="parent::mixed-citation"
+          role="error" 
+          id="comment-1"><name/> is only supported within mixed-citation, but this one is in <value-of select="parent::*/name()"/>.</assert>
+
+        <assert test="matches(lower-case(.),'^((in|under) (preparation|press|review)|submitted)$')"
+          role="warning" 
+          id="comment-2"><name/> contains the content '<value-of select="."/>'. Is the tagging correct?</assert>
+      </rule>
+  </pattern>
 
     <pattern id="back">
       <rule context="back" id="back-tests">

diff --git a/src/rp-schematron.sch b/src/rp-schematron.sch
@@ -518,6 +518,12 @@
      </rule></pattern><pattern id="mixed-citation-child-checks-pattern"><rule context="mixed-citation/*" id="mixed-citation-child-checks">
         <report test="not(*) and (normalize-space(.)='')" role="error" id="mixed-citation-child-1">[mixed-citation-child-1] <name/> in reference (id=<value-of select="ancestor::ref/@id"/>) is empty, which cannot be correct.</report>
       </rule></pattern>
+
+  <pattern id="comment-checks-pattern"><rule context="comment" id="comment-checks">
+        <assert test="parent::mixed-citation" role="error" id="comment-1">[comment-1] <name/> is only supported within mixed-citation, but this one is in <value-of select="parent::*/name()"/>.</assert>
+
+        <assert test="matches(lower-case(.),'^((in|under) (preparation|press|review)|submitted)$')" role="warning" id="comment-2">[comment-2] <name/> contains the content '<value-of select="."/>'. Is the tagging correct?</assert>
+      </rule></pattern>
 
     <pattern id="back-tests-pattern"><rule context="back" id="back-tests">
 

diff --git a/src/rp-schematron.xsl b/src/rp-schematron.xsl
diff --git a/test/tests/rp/comment-checks/comment-1/comment-1.sch b/test/tests/rp/comment-checks/comment-1/comment-1.sch
@@ -0,0 +1,157 @@
+<schema xmlns="http://purl.oclc.org/dsdl/schematron" xmlns:meca="http://manuscriptexchange.org" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:ali="http://www.niso.org/schemas/ali/1.0/" xmlns:file="java.io.File" xmlns:java="http://www.java.com/" xmlns:xsl="http://www.w3.org/1999/XSL/Transform" xmlns:xlink="http://www.w3.org/1999/xlink" queryBinding="xslt2">
+  <title>eLife reviewed preprint schematron</title>
+  <ns uri="http://www.niso.org/schemas/ali/1.0/" prefix="ali"/>
+  <ns uri="http://www.w3.org/XML/1998/namespace" prefix="xml"/>
+  <ns uri="http://www.w3.org/1999/xlink" prefix="xlink"/>
+  <ns uri="http://www.w3.org/2001/XInclude" prefix="xi"/>
+  <ns uri="http://www.w3.org/1998/Math/MathML" prefix="mml"/>
+  <ns uri="http://saxon.sf.net/" prefix="saxon"/>
+  <ns uri="http://purl.org/dc/terms/" prefix="dc"/>
+  <ns uri="http://www.w3.org/2001/XMLSchema" prefix="xs"/>
+  <ns uri="https://elifesciences.org/namespace" prefix="e"/>
+  <ns uri="java.io.File" prefix="file"/>
+  <ns uri="http://www.java.com/" prefix="java"/>
+  <ns uri="http://manuscriptexchange.org" prefix="meca"/>
+  <xsl:function name="e:isbn-sum" as="xs:integer">
+    <xsl:param name="s" as="xs:string"/>
+    <xsl:choose>
+      <xsl:when test="string-length($s) = 10">
+        <xsl:variable name="d1" select="number(substring($s,1,1)) * 10"/>
+        <xsl:variable name="d2" select="number(substring($s,2,1)) * 9"/>
+        <xsl:variable name="d3" select="number(substring($s,3,1)) * 8"/>
+        <xsl:variable name="d4" select="number(substring($s,4,1)) * 7"/>
+        <xsl:variable name="d5" select="number(substring($s,5,1)) * 6"/>
+        <xsl:variable name="d6" select="number(substring($s,6,1)) * 5"/>
+        <xsl:variable name="d7" select="number(substring($s,7,1)) * 4"/>
+        <xsl:variable name="d8" select="number(substring($s,8,1)) * 3"/>
+        <xsl:variable name="d9" select="number(substring($s,9,1)) * 2"/>
+        <xsl:variable name="d10" select="number(substring($s,10,1)) * 1"/>
+        <xsl:value-of select="number($d1 + $d2 + $d3 + $d4 + $d5 + $d6 + $d7 + $d8 + $d9 + $d10) mod 11"/>
+      </xsl:when>
+      <xsl:when test="string-length($s) = 13">
+        <xsl:variable name="d1" select="number(substring($s,1,1))"/>
+        <xsl:variable name="d2" select="number(substring($s,2,1)) * 3"/>
+        <xsl:variable name="d3" select="number(substring($s,3,1))"/>
+        <xsl:variable name="d4" select="number(substring($s,4,1)) * 3"/>
+        <xsl:variable name="d5" select="number(substring($s,5,1))"/>
+        <xsl:variable name="d6" select="number(substring($s,6,1)) * 3"/>
+        <xsl:variable name="d7" select="number(substring($s,7,1))"/>
+        <xsl:variable name="d8" select="number(substring($s,8,1)) * 3"/>
+        <xsl:variable name="d9" select="number(substring($s,9,1))"/>
+        <xsl:variable name="d10" select="number(substring($s,10,1)) * 3"/>
+        <xsl:variable name="d11" select="number(substring($s,11,1))"/>
+        <xsl:variable name="d12" select="number(substring($s,12,1)) * 3"/>
+        <xsl:variable name="d13" select="number(substring($s,13,1))"/>
+        <xsl:value-of select="number($d1 + $d2 + $d3 + $d4 + $d5 + $d6 + $d7 + $d8 + $d9 + $d10 + $d11 + $d12 + $d13) mod 10"/>
+      </xsl:when>
+      <xsl:otherwise>
+        <xsl:value-of select="number('1')"/>
+      </xsl:otherwise>
+    </xsl:choose>
+  </xsl:function>
+  <xsl:function name="e:is-valid-issn" as="xs:boolean">
+      <xsl:param name="s" as="xs:string"/>
+      <xsl:choose>
+        <xsl:when test="not(matches($s,'^\d{4}\-\d{3}[\dX]$'))">
+          <xsl:value-of select="false()"/>
+        </xsl:when>
+        <xsl:otherwise>
+            <xsl:variable name="d1" select="number(substring($s,1,1)) * 8"/>
+            <xsl:variable name="d2" select="number(substring($s,2,1)) * 7"/>
+            <xsl:variable name="d3" select="number(substring($s,3,1)) * 6"/>
+            <xsl:variable name="d4" select="number(substring($s,4,1)) * 5"/>
+            <xsl:variable name="d5" select="number(substring($s,6,1)) * 4"/>
+            <xsl:variable name="d6" select="number(substring($s,7,1)) * 3"/>
+            <xsl:variable name="d7" select="number(substring($s,8,1)) * 2"/>
+            <xsl:variable name="remainder" select="number($d1 + $d2 + $d3 + $d4 + $d5 + $d6 + $d7) mod 11"/>
+            <xsl:variable name="calc" select="if ($remainder=0) then 0 else (11 - $remainder)"/>
+            <xsl:variable name="check" select="if (substring($s,9,1)='X') then 10 else number(substring($s,9,1))"/>
+            <xsl:value-of select="$calc = $check"/>
+        </xsl:otherwise>
+      </xsl:choose>
+    </xsl:function>
+  <xsl:function name="e:get-name" as="xs:string">
+    <xsl:param name="name"/>
+    <xsl:choose>
+      <xsl:when test="$name/given-names[1] and $name/surname[1] and $name/suffix[1]">
+        <xsl:value-of select="concat($name/given-names[1],' ',$name/surname[1],' ',$name/suffix[1])"/>
+      </xsl:when>
+      <xsl:when test="not($name/given-names[1]) and $name/surname[1] and $name/suffix[1]">
+        <xsl:value-of select="concat($name/surname[1],' ',$name/suffix[1])"/>
+      </xsl:when>
+      <xsl:when test="$name/given-names[1] and $name/surname[1] and not($name/suffix[1])">
+        <xsl:value-of select="concat($name/given-names[1],' ',$name/surname[1])"/>
+      </xsl:when>
+      <xsl:when test="not($name/given-names[1]) and $name/surname[1] and not($name/suffix[1])">
+        <xsl:value-of select="$name/surname[1]"/>
+      </xsl:when>
+      <xsl:otherwise>
+        <xsl:value-of select="'No elements present'"/>
+      </xsl:otherwise>
+    </xsl:choose>
+  </xsl:function>
+  <xsl:function name="e:get-copyright-holder">
+    <xsl:param name="contrib-group"/>
+    <xsl:variable name="author-count" select="count($contrib-group/contrib[@contrib-type='author'])"/>
+    <xsl:choose>
+      <xsl:when test="$author-count lt 1"/>
+      <xsl:when test="$author-count = 1">
+        <xsl:choose>
+          <xsl:when test="$contrib-group/contrib[@contrib-type='author']/collab">
+            <xsl:value-of select="$contrib-group/contrib[@contrib-type='author']/collab[1]/text()[1]"/>
+          </xsl:when>
+          <xsl:otherwise>
+            <xsl:value-of select="$contrib-group/contrib[@contrib-type='author']/name[1]/surname[1]"/>
+          </xsl:otherwise>
+        </xsl:choose>
+      </xsl:when>
+      <xsl:when test="$author-count = 2">
+        <xsl:choose>
+          <xsl:when test="$contrib-group/contrib[@contrib-type='author']/collab">
+            <xsl:choose>
+              <xsl:when test="$contrib-group/contrib[@contrib-type='author'][1]/collab and $contrib-group/contrib[@contrib-type='author'][2]/collab">
+                <xsl:value-of select="concat($contrib-group/contrib[@contrib-type='author']/collab[1]/text()[1],' &amp; ',$contrib-group/contrib[@contrib-type='author']/collab[2]/text()[1])"/>
+              </xsl:when>
+              <xsl:when test="$contrib-group/contrib[@contrib-type='author'][1]/collab">
+                <xsl:value-of select="concat($contrib-group/contrib[@contrib-type='author'][1]/collab[1]/text()[1],' &amp; ',$contrib-group/contrib[@contrib-type='author'][2]/name[1]/surname[1])"/>
+              </xsl:when>
+              <xsl:otherwise>
+                <xsl:value-of select="concat($contrib-group/contrib[@contrib-type='author'][1]/name[1]/surname[1],' &amp; ',$contrib-group/contrib[@contrib-type='author'][2]/collab[1]/text()[1])"/>
+              </xsl:otherwise>
+            </xsl:choose>
+          </xsl:when>
+          <xsl:otherwise>
+            <xsl:value-of select="concat($contrib-group/contrib[@contrib-type='author'][1]/name[1]/surname[1],' &amp; ',$contrib-group/contrib[@contrib-type='author'][2]/name[1]/surname[1])"/>
+          </xsl:otherwise>
+        </xsl:choose>
+      </xsl:when>
+
+      <xsl:otherwise>
+        <xsl:variable name="is-equal-contrib" select="if ($contrib-group/contrib[@contrib-type='author'][1]/@equal-contrib='yes') then true() else false()"/>
+
+        <xsl:value-of select="concat(e:get-surname($contrib-group/contrib[@contrib-type='author'][1]),' et al')"/>
+      </xsl:otherwise>
+    </xsl:choose>
+  </xsl:function>
+  <xsl:function name="e:get-surname" as="text()">
+    <xsl:param name="contrib"/>
+    <xsl:choose>
+      <xsl:when test="$contrib/collab">
+        <xsl:value-of select="$contrib/collab[1]/text()[1]"/>
+      </xsl:when>
+      <xsl:otherwise>
+        <xsl:value-of select="$contrib//name[1]/surname[1]"/>
+      </xsl:otherwise>
+    </xsl:choose>
+  </xsl:function>
+  <pattern id="comment-checks-pattern">
+    <rule context="comment" id="comment-checks">
+      <assert test="parent::mixed-citation" role="error" id="comment-1">[comment-1] <name/> is only supported within mixed-citation, but this one is in <value-of select="parent::*/name()"/>.</assert>
+    </rule>
+  </pattern>
+  <pattern id="root-pattern">
+    <rule context="root" id="root-rule">
+      <assert test="descendant::comment" role="error" id="comment-checks-xspec-assert">comment must be present.</assert>
+    </rule>
+  </pattern>
+</schema>
diff --git a/test/tests/rp/comment-checks/comment-1/fail.xml b/test/tests/rp/comment-checks/comment-1/fail.xml
@@ -0,0 +1,11 @@
+<?oxygen SCHSchema="comment-1.sch"?>
+<!--Context: comment
+Test: assert    parent::mixed-citation
+Message:  is only supported within mixed-citation, but this one is in . -->
+<root xmlns:ali="http://www.niso.org/schemas/ali/1.0/" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">
+    <article>
+        <p>
+            <comment>In press</comment>
+        </p>
+    </article>
+</root>
diff --git a/test/tests/rp/comment-checks/comment-1/pass.xml b/test/tests/rp/comment-checks/comment-1/pass.xml
@@ -0,0 +1,11 @@
+<?oxygen SCHSchema="comment-1.sch"?>
+<!--Context: comment
+Test: assert    parent::mixed-citation
+Message:  is only supported within mixed-citation, but this one is in . -->
+<root xmlns:ali="http://www.niso.org/schemas/ali/1.0/" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">
+    <article>
+        <mixed-citation>
+            <comment>In press</comment>
+        </mixed-citation>
+    </article>
+</root>