VOR - account for paths in software-heritage-test-3

src/final-JATS-schematron.sch

@@ -2738,7 +2738,7 @@
 
     <report test="not(ancestor::fig/permissions[contains(.,'phylopic')]) and matches(@xlink:href,'phylopic\.org')" role="warning" id="phylopic-link-check">[phylopic-link-check] This link is to phylopic.org, which is a site where silhouettes/images are typically reproduced from. Please check whether any figures contain reproduced images from this site, and if so whether permissions have been obtained and/or copyright statements are correctly included.</report>
     </rule></pattern><pattern id="software-heritage-tests-pattern"><rule context="ref/element-citation[ext-link[1][contains(@xlink:href,'softwareheritage')]]" id="software-heritage-tests">
-      <let name="version" value="replace(substring-after(ext-link[1]/@xlink:href,'anchor='),'/$','')"/>
+      <let name="version" value="replace(substring-after(ext-link[1]/@xlink:href,'anchor='),'(;path=.*)?/$','')"/>
 
       <assert see="https://elifeproduction.slab.com/posts/archiving-code-zrfi30c5#software-heritage-test-2" test="matches(ext-link[1]/@xlink:href,'.*swh:.:dir.*origin=.*visit=.*anchor=.*')" role="error" id="software-heritage-test-2">[software-heritage-test-2] Software heritage links in references must be the directory link with contextual information. '<value-of select="ext-link[1]/@xlink:href"/>' is not a directory link with contextual information.</assert>
 

src/final-JATS-schematron.xsl

@@ -13866,7 +13866,7 @@
    <!--PATTERN software-heritage-tests-pattern-->
    <!--RULE software-heritage-tests-->
    <xsl:template match="ref/element-citation[ext-link[1][contains(@xlink:href,'softwareheritage')]]" priority="1000" mode="M185">
-      <xsl:variable name="version" select="replace(substring-after(ext-link[1]/@xlink:href,'anchor='),'/$','')"/>
+      <xsl:variable name="version" select="replace(substring-after(ext-link[1]/@xlink:href,'anchor='),'(;path=.*)?/$','')"/>
       <!--ASSERT error-->
       <xsl:choose>
          <xsl:when test="matches(ext-link[1]/@xlink:href,'.*swh:.:dir.*origin=.*visit=.*anchor=.*')"/>

src/final-package-JATS-schematron.sch

@@ -2744,7 +2744,7 @@
 
     <report test="not(ancestor::fig/permissions[contains(.,'phylopic')]) and matches(@xlink:href,'phylopic\.org')" role="warning" id="phylopic-link-check">This link is to phylopic.org, which is a site where silhouettes/images are typically reproduced from. Please check whether any figures contain reproduced images from this site, and if so whether permissions have been obtained and/or copyright statements are correctly included.</report>
     </rule></pattern><pattern id="software-heritage-tests-pattern"><rule context="ref/element-citation[ext-link[1][contains(@xlink:href,'softwareheritage')]]" id="software-heritage-tests">
-      <let name="version" value="replace(substring-after(ext-link[1]/@xlink:href,'anchor='),'/$','')"/>
+      <let name="version" value="replace(substring-after(ext-link[1]/@xlink:href,'anchor='),'(;path=.*)?/$','')"/>
 
       <assert see="https://elifeproduction.slab.com/posts/archiving-code-zrfi30c5#software-heritage-test-2" test="matches(ext-link[1]/@xlink:href,'.*swh:.:dir.*origin=.*visit=.*anchor=.*')" role="error" id="software-heritage-test-2">Software heritage links in references must be the directory link with contextual information. '<value-of select="ext-link[1]/@xlink:href"/>' is not a directory link with contextual information.</assert>
 

src/pre-JATS-schematron.sch

@@ -2683,7 +2683,7 @@
 
     <report test="not(ancestor::fig/permissions[contains(.,'phylopic')]) and matches(@xlink:href,'phylopic\.org')" role="warning" id="phylopic-link-check">[phylopic-link-check] This link is to phylopic.org, which is a site where silhouettes/images are typically reproduced from. Please check whether any figures contain reproduced images from this site, and if so whether permissions have been obtained and/or copyright statements are correctly included.</report>
     </rule></pattern><pattern id="software-heritage-tests-pattern"><rule context="ref/element-citation[ext-link[1][contains(@xlink:href,'softwareheritage')]]" id="software-heritage-tests">
-      <let name="version" value="replace(substring-after(ext-link[1]/@xlink:href,'anchor='),'/$','')"/>
+      <let name="version" value="replace(substring-after(ext-link[1]/@xlink:href,'anchor='),'(;path=.*)?/$','')"/>
 
       <assert see="https://elifeproduction.slab.com/posts/archiving-code-zrfi30c5#software-heritage-test-2" test="matches(ext-link[1]/@xlink:href,'.*swh:.:dir.*origin=.*visit=.*anchor=.*')" role="error" id="software-heritage-test-2">[software-heritage-test-2] Software heritage links in references must be the directory link with contextual information. '<value-of select="ext-link[1]/@xlink:href"/>' is not a directory link with contextual information.</assert>
 

src/pre-JATS-schematron.xsl

@@ -13711,7 +13711,7 @@
    <!--PATTERN software-heritage-tests-pattern-->
    <!--RULE software-heritage-tests-->
    <xsl:template match="ref/element-citation[ext-link[1][contains(@xlink:href,'softwareheritage')]]" priority="1000" mode="M183">
-      <xsl:variable name="version" select="replace(substring-after(ext-link[1]/@xlink:href,'anchor='),'/$','')"/>
+      <xsl:variable name="version" select="replace(substring-after(ext-link[1]/@xlink:href,'anchor='),'(;path=.*)?/$','')"/>
       <!--ASSERT error-->
       <xsl:choose>
          <xsl:when test="matches(ext-link[1]/@xlink:href,'.*swh:.:dir.*origin=.*visit=.*anchor=.*')"/>

src/schematron.sch

@@ -4186,7 +4186,7 @@ else self::*/local-name() = $allowed-p-blocks"
 
     <rule context="ref/element-citation[ext-link[1][contains(@xlink:href,'softwareheritage')]]" 
       id="software-heritage-tests">
-      <let name="version" value="replace(substring-after(ext-link[1]/@xlink:href,'anchor='),'/$','')"/>
+      <let name="version" value="replace(substring-after(ext-link[1]/@xlink:href,'anchor='),'(;path=.*)?/$','')"/>
 
       <assert see="https://elifeproduction.slab.com/posts/archiving-code-zrfi30c5#software-heritage-test-2" 
         test="matches(ext-link[1]/@xlink:href,'.*swh:.:dir.*origin=.*visit=.*anchor=.*')" 

test/tests/gen/software-heritage-tests/software-heritage-test-2/software-heritage-test-2.sch

@@ -1362,7 +1362,7 @@
   </xsl:function>
   <pattern id="content-containers">
     <rule context="ref/element-citation[ext-link[1][contains(@xlink:href,'softwareheritage')]]" id="software-heritage-tests">
-      <let name="version" value="replace(substring-after(ext-link[1]/@xlink:href,'anchor='),'/$','')"/>
+      <let name="version" value="replace(substring-after(ext-link[1]/@xlink:href,'anchor='),'(;path=.*)?/$','')"/>
       <assert see="https://elifeproduction.slab.com/posts/archiving-code-zrfi30c5#software-heritage-test-2" test="matches(ext-link[1]/@xlink:href,'.*swh:.:dir.*origin=.*visit=.*anchor=.*')" role="error" id="software-heritage-test-2">Software heritage links in references must be the directory link with contextual information. '<value-of select="ext-link[1]/@xlink:href"/>' is not a directory link with contextual information.</assert>
     </rule>
   </pattern>

test/tests/gen/software-heritage-tests/software-heritage-test-3/software-heritage-test-3.sch

@@ -1362,7 +1362,7 @@
   </xsl:function>
   <pattern id="content-containers">
     <rule context="ref/element-citation[ext-link[1][contains(@xlink:href,'softwareheritage')]]" id="software-heritage-tests">
-      <let name="version" value="replace(substring-after(ext-link[1]/@xlink:href,'anchor='),'/$','')"/>
+      <let name="version" value="replace(substring-after(ext-link[1]/@xlink:href,'anchor='),'(;path=.*)?/$','')"/>
       <assert see="https://elifeproduction.slab.com/posts/archiving-code-zrfi30c5#software-heritage-test-3" test="version[1]=$version" role="error" id="software-heritage-test-3">The version number for Software heritage references must be the revision SWHID without contextual information. '<value-of select="version[1]"/>' is not. Based on the link, the version should be '<value-of select="$version"/>'.</assert>
     </rule>
   </pattern>

test/tests/gen/software-heritage-tests/software-heritage-test-5/software-heritage-test-5.sch

@@ -1362,7 +1362,7 @@
   </xsl:function>
   <pattern id="content-containers">
     <rule context="ref/element-citation[ext-link[1][contains(@xlink:href,'softwareheritage')]]" id="software-heritage-tests">
-      <let name="version" value="replace(substring-after(ext-link[1]/@xlink:href,'anchor='),'/$','')"/>
+      <let name="version" value="replace(substring-after(ext-link[1]/@xlink:href,'anchor='),'(;path=.*)?/$','')"/>
       <report see="https://elifeproduction.slab.com/posts/archiving-code-zrfi30c5#software-heritage-test-5" test="contains(ext-link[1]/@xlink:href,'[…]')" role="error" id="software-heritage-test-5">A Software heritage link contains '[…]', meaning that the link has been copied incorrectly (it is truncated, and cannot be followed).</report>
     </rule>
   </pattern>

test/xspec/schematron.sch

@@ -3223,7 +3223,7 @@
   </pattern>
   <pattern id="software-heritage-tests-pattern">
     <rule context="ref/element-citation[ext-link[1][contains(@xlink:href,'softwareheritage')]]" id="software-heritage-tests">
-      <let name="version" value="replace(substring-after(ext-link[1]/@xlink:href,'anchor='),'/$','')"/>
+      <let name="version" value="replace(substring-after(ext-link[1]/@xlink:href,'anchor='),'(;path=.*)?/$','')"/>
 
       <assert see="https://elifeproduction.slab.com/posts/archiving-code-zrfi30c5#software-heritage-test-2" test="matches(ext-link[1]/@xlink:href,'.*swh:.:dir.*origin=.*visit=.*anchor=.*')" role="error" id="software-heritage-test-2">Software heritage links in references must be the directory link with contextual information. '<value-of select="ext-link[1]/@xlink:href"/>' is not a directory link with contextual information.</assert>