From 7675f1aab3cd06b41792007ecbe463fa1b83ff7c Mon Sep 17 00:00:00 2001
From: Fred Atherden <43879983+fred-atherden@users.noreply.github.com>
Date: Mon, 2 Dec 2024 13:36:09 +0000
Subject: [PATCH] VOR - account for paths in software-heritage-test-3

---
 src/final-JATS-schematron.sch                                   | 2 +-
 src/final-JATS-schematron.xsl                                   | 2 +-
 src/final-package-JATS-schematron.sch                           | 2 +-
 src/pre-JATS-schematron.sch                                     | 2 +-
 src/pre-JATS-schematron.xsl                                     | 2 +-
 src/schematron.sch                                              | 2 +-
 .../software-heritage-test-2/software-heritage-test-2.sch       | 2 +-
 .../software-heritage-test-3/software-heritage-test-3.sch       | 2 +-
 .../software-heritage-test-5/software-heritage-test-5.sch       | 2 +-
 test/xspec/schematron.sch                                       | 2 +-
 10 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/src/final-JATS-schematron.sch b/src/final-JATS-schematron.sch
index eb28368f8e..28a2366e87 100644
--- a/src/final-JATS-schematron.sch
+++ b/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>
       
diff --git a/src/final-JATS-schematron.xsl b/src/final-JATS-schematron.xsl
index e6671f3304..bf3ffd4a57 100644
--- a/src/final-JATS-schematron.xsl
+++ b/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=.*')"/>
diff --git a/src/final-package-JATS-schematron.sch b/src/final-package-JATS-schematron.sch
index 650a744a10..7955264ea7 100644
--- a/src/final-package-JATS-schematron.sch
+++ b/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>
       
diff --git a/src/pre-JATS-schematron.sch b/src/pre-JATS-schematron.sch
index ddd84d17d2..efa84a5017 100644
--- a/src/pre-JATS-schematron.sch
+++ b/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>
       
diff --git a/src/pre-JATS-schematron.xsl b/src/pre-JATS-schematron.xsl
index 33882b282f..e3aa4cf665 100644
--- a/src/pre-JATS-schematron.xsl
+++ b/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=.*')"/>
diff --git a/src/schematron.sch b/src/schematron.sch
index 2b00f279e7..72547a088d 100644
--- a/src/schematron.sch
+++ b/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=.*')" 
diff --git a/test/tests/gen/software-heritage-tests/software-heritage-test-2/software-heritage-test-2.sch b/test/tests/gen/software-heritage-tests/software-heritage-test-2/software-heritage-test-2.sch
index 8fa8b45d81..1d3143543f 100644
--- a/test/tests/gen/software-heritage-tests/software-heritage-test-2/software-heritage-test-2.sch
+++ b/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>
diff --git a/test/tests/gen/software-heritage-tests/software-heritage-test-3/software-heritage-test-3.sch b/test/tests/gen/software-heritage-tests/software-heritage-test-3/software-heritage-test-3.sch
index 992d343f7e..2f00405331 100644
--- a/test/tests/gen/software-heritage-tests/software-heritage-test-3/software-heritage-test-3.sch
+++ b/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>
diff --git a/test/tests/gen/software-heritage-tests/software-heritage-test-5/software-heritage-test-5.sch b/test/tests/gen/software-heritage-tests/software-heritage-test-5/software-heritage-test-5.sch
index bd1a040e7b..fdcb1b5849 100644
--- a/test/tests/gen/software-heritage-tests/software-heritage-test-5/software-heritage-test-5.sch
+++ b/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>
diff --git a/test/xspec/schematron.sch b/test/xspec/schematron.sch
index cb9d4a5862..f2c5a422a6 100644
--- a/test/xspec/schematron.sch
+++ b/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>