RP - split bioRender flag into v1 and revised

src/rp-schematron-base.sch

@@ -181,9 +181,13 @@
       <let name="is-revised-rp" value="if (descendant::article-meta/pub-history/event/self-uri[@content-type='reviewed-preprint']) then true() else false()"/>
         <let name="rp-version" value="replace(descendant::article-meta[1]/article-id[@specific-use='version'][1],'^.*\.','')"/>
 
-       <report test="matches(lower-case($article-text),'biorend[eo]r')" 
+       <report test="not($is-revised-rp) and matches(lower-case($article-text),'biorend[eo]r')" 
         role="warning" 
-        id="biorender-check">Article text contains a reference to bioRender. Any figures created with bioRender should include a sentence in the caption in the format: "Created with BioRender.com/{figure-code}".</report>
+        id="biorender-check-v1">Article text contains a reference to bioRender. Any figures created with bioRender should include a sentence in the caption in the format: "Created with BioRender.com/{figure-code}".</report>
+
+        <report test="$is-revised-rp and matches(lower-case($article-text),'biorend[eo]r')" 
+        role="warning" 
+        id="biorender-check-revised">Article text contains a reference to bioRender. Any figures created with bioRender should include a sentence in the caption in the format: "Created with BioRender.com/{figure-code}". Since this is a revised RP, check to see if the first (or a previous) version had bioRender links.</report>
 
         <assert test="sub-article[@article-type='editor-report']" 
           role="error" 

src/rp-schematron.sch

@@ -161,7 +161,9 @@
       <let name="is-revised-rp" value="if (descendant::article-meta/pub-history/event/self-uri[@content-type='reviewed-preprint']) then true() else false()"/>
         <let name="rp-version" value="replace(descendant::article-meta[1]/article-id[@specific-use='version'][1],'^.*\.','')"/>
 
-       <report test="matches(lower-case($article-text),'biorend[eo]r')" role="warning" id="biorender-check">[biorender-check] Article text contains a reference to bioRender. Any figures created with bioRender should include a sentence in the caption in the format: "Created with BioRender.com/{figure-code}".</report>
+       <report test="not($is-revised-rp) and matches(lower-case($article-text),'biorend[eo]r')" role="warning" id="biorender-check-v1">[biorender-check-v1] Article text contains a reference to bioRender. Any figures created with bioRender should include a sentence in the caption in the format: "Created with BioRender.com/{figure-code}".</report>
+
+        <report test="$is-revised-rp and matches(lower-case($article-text),'biorend[eo]r')" role="warning" id="biorender-check-revised">[biorender-check-revised] Article text contains a reference to bioRender. Any figures created with bioRender should include a sentence in the caption in the format: "Created with BioRender.com/{figure-code}". Since this is a revised RP, check to see if the first (or a previous) version had bioRender links.</report>
 
         <assert test="sub-article[@article-type='editor-report']" role="error" id="no-assessment">[no-assessment] A Reviewed Preprint must have an eLife Assessment, but this one does not.</assert>
 

src/rp-schematron.xsl

@@ -1528,14 +1528,25 @@
       <xsl:variable name="is-revised-rp" select="if (descendant::article-meta/pub-history/event/self-uri[@content-type='reviewed-preprint']) then true() else false()"/>
       <xsl:variable name="rp-version" select="replace(descendant::article-meta[1]/article-id[@specific-use='version'][1],'^.*\.','')"/>
       <!--REPORT warning-->
-      <xsl:if test="matches(lower-case($article-text),'biorend[eo]r')">
-         <svrl:successful-report xmlns:svrl="http://purl.oclc.org/dsdl/svrl" test="matches(lower-case($article-text),'biorend[eo]r')">
-            <xsl:attribute name="id">biorender-check</xsl:attribute>
+      <xsl:if test="not($is-revised-rp) and matches(lower-case($article-text),'biorend[eo]r')">
+         <svrl:successful-report xmlns:svrl="http://purl.oclc.org/dsdl/svrl" test="not($is-revised-rp) and matches(lower-case($article-text),'biorend[eo]r')">
+            <xsl:attribute name="id">biorender-check-v1</xsl:attribute>
             <xsl:attribute name="role">warning</xsl:attribute>
             <xsl:attribute name="location">
                <xsl:apply-templates select="." mode="schematron-select-full-path"/>
             </xsl:attribute>
-            <svrl:text>[biorender-check] Article text contains a reference to bioRender. Any figures created with bioRender should include a sentence in the caption in the format: "Created with BioRender.com/{figure-code}".</svrl:text>
+            <svrl:text>[biorender-check-v1] Article text contains a reference to bioRender. Any figures created with bioRender should include a sentence in the caption in the format: "Created with BioRender.com/{figure-code}".</svrl:text>
+         </svrl:successful-report>
+      </xsl:if>
+      <!--REPORT warning-->
+      <xsl:if test="$is-revised-rp and matches(lower-case($article-text),'biorend[eo]r')">
+         <svrl:successful-report xmlns:svrl="http://purl.oclc.org/dsdl/svrl" test="$is-revised-rp and matches(lower-case($article-text),'biorend[eo]r')">
+            <xsl:attribute name="id">biorender-check-revised</xsl:attribute>
+            <xsl:attribute name="role">warning</xsl:attribute>
+            <xsl:attribute name="location">
+               <xsl:apply-templates select="." mode="schematron-select-full-path"/>
+            </xsl:attribute>
+            <svrl:text>[biorender-check-revised] Article text contains a reference to bioRender. Any figures created with bioRender should include a sentence in the caption in the format: "Created with BioRender.com/{figure-code}". Since this is a revised RP, check to see if the first (or a previous) version had bioRender links.</svrl:text>
          </svrl:successful-report>
       </xsl:if>
       <!--ASSERT error-->

test/tests/rp/article-tests/biorender-check-revised/biorender-check-revised.sch

@@ -0,0 +1,160 @@
+<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="article-tests-pattern">
+    <rule context="article" id="article-tests">
+      <let name="article-text" value="string-join(for $x in self::*/*[local-name() = 'body' or local-name() = 'back']//*           return           if ($x/ancestor::ref-list) then ()           else if ($x/ancestor::caption[parent::fig] or $x/ancestor::permissions[parent::fig]) then ()           else $x/text(),'')"/>
+      <let name="is-revised-rp" value="if (descendant::article-meta/pub-history/event/self-uri[@content-type='reviewed-preprint']) then true() else false()"/>
+      <let name="rp-version" value="replace(descendant::article-meta[1]/article-id[@specific-use='version'][1],'^.*\.','')"/>
+      <report test="$is-revised-rp and matches(lower-case($article-text),'biorend[eo]r')" role="warning" id="biorender-check-revised">[biorender-check-revised] Article text contains a reference to bioRender. Any figures created with bioRender should include a sentence in the caption in the format: "Created with BioRender.com/{figure-code}". Since this is a revised RP, check to see if the first (or a previous) version had bioRender links.</report>
+    </rule>
+  </pattern>
+  <pattern id="root-pattern">
+    <rule context="root" id="root-rule">
+      <assert test="descendant::article" role="error" id="article-tests-xspec-assert">article must be present.</assert>
+    </rule>
+  </pattern>
+</schema>

test/tests/rp/article-tests/biorender-check-revised/fail.xml

@@ -0,0 +1,11 @@
+<?oxygen SCHSchema="biorender-check-revised.sch"?>
+<!--Context: article
+Test: report    $is-revised-rp and matches(lower-case($article-text),'biorend[eo]r')
+Message: Article text contains a reference to bioRender. Any figures created with bioRender should include a sentence in the caption in the format: "Created with BioRender.com/{figure-code}". Since this is a revised RP, check to see if the first (or a previous) version had bioRender links. -->
+<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>
+        <body>
+            <p>Figure 1 made with BioRender.com</p>
+        </body>
+    </article>
+</root>

test/tests/rp/article-tests/biorender-check-revised/pass.xml

@@ -0,0 +1,16 @@
+<?oxygen SCHSchema="biorender-check-revised.sch"?>
+<!--Context: article
+Test: report    $is-revised-rp and matches(lower-case($article-text),'biorend[eo]r')
+Message: Article text contains a reference to bioRender. Any figures created with bioRender should include a sentence in the caption in the format: "Created with BioRender.com/{figure-code}". Since this is a revised RP, check to see if the first (or a previous) version had bioRender links. -->
+<article>
+    <body>
+        <fig>
+            <caption>
+                <p>Figure 1 made with BioRender.com</p>
+            </caption>
+            <permissions>
+                <license><license-p>© 2024, BioRender Inc. Any parts of this image created with BioRender are not made available under the same license as the Reviewed Preprint, and are © 2024, BioRender Inc.</license-p></license>
+            </permissions>
+        </fig>
+    </body>
+</article>

test/tests/rp/article-tests/biorender-check/biorender-check.sch → test/tests/rp/article-tests/biorender-check-v1/biorender-check-v1.sch

@@ -149,7 +149,7 @@
       <let name="article-text" value="string-join(for $x in self::*/*[local-name() = 'body' or local-name() = 'back']//*           return           if ($x/ancestor::ref-list) then ()           else if ($x/ancestor::caption[parent::fig] or $x/ancestor::permissions[parent::fig]) then ()           else $x/text(),'')"/>
       <let name="is-revised-rp" value="if (descendant::article-meta/pub-history/event/self-uri[@content-type='reviewed-preprint']) then true() else false()"/>
       <let name="rp-version" value="replace(descendant::article-meta[1]/article-id[@specific-use='version'][1],'^.*\.','')"/>
-      <report test="matches(lower-case($article-text),'biorend[eo]r')" role="warning" id="biorender-check">[biorender-check] Article text contains a reference to bioRender. Any figures created with bioRender should include a sentence in the caption in the format: "Created with BioRender.com/{figure-code}".</report>
+      <report test="not($is-revised-rp) and matches(lower-case($article-text),'biorend[eo]r')" role="warning" id="biorender-check-v1">[biorender-check-v1] Article text contains a reference to bioRender. Any figures created with bioRender should include a sentence in the caption in the format: "Created with BioRender.com/{figure-code}".</report>
     </rule>
   </pattern>
   <pattern id="root-pattern">

test/tests/rp/article-tests/biorender-check/fail.xml → test/tests/rp/article-tests/biorender-check-v1/fail.xml

@@ -1,6 +1,6 @@
-<?oxygen SCHSchema="biorender-check.sch"?>
+<?oxygen SCHSchema="biorender-check-v1.sch"?>
 <!--Context: article
-Test: report    matches(lower-case($article-text),'biorend[eo]r')
+Test: report    not($is-revised-rp) and matches(lower-case($article-text),'biorend[eo]r')
 Message: Article text contains a reference to bioRender. Any figures created with bioRender should include a sentence in the caption in the format: "Created with BioRender.com/{figure-code}". -->
 <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>