From 734adfec320b287b2c08b58be3b8bf349892a2ba Mon Sep 17 00:00:00 2001
From: Salih Altun <muhammedsalihaltun@gmail.com>
Date: Mon, 7 Jun 2021 12:05:47 +0300
Subject: [PATCH] Undo node class name changes in validation files

  Addressing https://github.com/iVis-at-Bilkent/newt/issues/658#issuecomment-855708750
---
 app/resources/libsbgn-0.3.xsd |  2 +-
 templatelibsbgn.xslt          | 18 +++++++++---------
 2 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/app/resources/libsbgn-0.3.xsd b/app/resources/libsbgn-0.3.xsd
index 9e6e0e05c..5c803e7d4 100644
--- a/app/resources/libsbgn-0.3.xsd
+++ b/app/resources/libsbgn-0.3.xsd
@@ -663,7 +663,7 @@
                                 <xsd:enumeration value="nucleic acid feature multimer"/>
                                 <xsd:enumeration value="complex"/>
                                 <xsd:enumeration value="complex multimer"/>
-                                <xsd:enumeration value="empty set"/>
+                                <xsd:enumeration value="source and sink"/>
                                 <!-- Activities (AF) -->
                                 <!-- perturbation is deprecated in AF as Activity Node in milestone 3. -->
                                 <xsd:enumeration value="perturbation"/>
diff --git a/templatelibsbgn.xslt b/templatelibsbgn.xslt
index 37cc88df7..e988626ce 100644
--- a/templatelibsbgn.xslt
+++ b/templatelibsbgn.xslt
@@ -75,7 +75,7 @@
 <axsl:template match="sbgn:arc[@class='consumption']" priority="1000" mode="M8"><svrl:fired-rule xmlns:svrl="http://purl.oclc.org/dsdl/svrl" context="sbgn:arc[@class='consumption']"/><axsl:variable name="id" select="@id"/><axsl:variable name="source" select="@source"/><axsl:variable name="class" select="//sbgn:glyph[@id=$source]/@class"/>
 
 		<!--ASSERT error-->
-<axsl:choose><axsl:when test="     $class='macromolecule' or      $class='macromolecule multimer' or     $class='simple chemical' or     $class='unspecified entity' or      $class='complex multimer' or       $class='complex' or      $class='nucleic acid feature' or      $class='simple chemical multimer' or      $class='nucleic acid feature multimer' or      $class='empty set'"/><axsl:otherwise><svrl:failed-assert xmlns:svrl="http://purl.oclc.org/dsdl/svrl" test="$class='macromolecule' or $class='macromolecule multimer' or $class='simple chemical' or $class='unspecified entity' or $class='complex multimer' or $class='complex' or $class='nucleic acid feature' or $class='simple chemical multimer' or $class='nucleic acid feature multimer' or $class='empty set'"><axsl:attribute name="id">pd10101</axsl:attribute><axsl:attribute name="role">error</axsl:attribute><axsl:attribute name="location"><axsl:apply-templates select="." mode="schematron-select-full-path"/></axsl:attribute><svrl:text>Arc with class consumption must have source reference to glyph of EPN classes
+<axsl:choose><axsl:when test="     $class='macromolecule' or      $class='macromolecule multimer' or     $class='simple chemical' or     $class='unspecified entity' or      $class='complex multimer' or       $class='complex' or      $class='nucleic acid feature' or      $class='simple chemical multimer' or      $class='nucleic acid feature multimer' or      $class='source and sink'"/><axsl:otherwise><svrl:failed-assert xmlns:svrl="http://purl.oclc.org/dsdl/svrl" test="$class='macromolecule' or $class='macromolecule multimer' or $class='simple chemical' or $class='unspecified entity' or $class='complex multimer' or $class='complex' or $class='nucleic acid feature' or $class='simple chemical multimer' or $class='nucleic acid feature multimer' or $class='source and sink'"><axsl:attribute name="id">pd10101</axsl:attribute><axsl:attribute name="role">error</axsl:attribute><axsl:attribute name="location"><axsl:apply-templates select="." mode="schematron-select-full-path"/></axsl:attribute><svrl:text>Arc with class consumption must have source reference to glyph of EPN classes
 			</svrl:text> <svrl:diagnostic-reference diagnostic="id">
 <axsl:text/><axsl:value-of select="$id"/><axsl:text/></svrl:diagnostic-reference> <svrl:diagnostic-reference diagnostic="source">
 <axsl:text/><axsl:value-of select="$source"/><axsl:text/></svrl:diagnostic-reference> <svrl:diagnostic-reference diagnostic="class">
@@ -98,10 +98,10 @@
 
 
 	<!--RULE -->
-<axsl:template match="sbgn:glyph[@class='empty set']" priority="1000" mode="M10"><svrl:fired-rule xmlns:svrl="http://purl.oclc.org/dsdl/svrl" context="sbgn:glyph[@class='empty set']"/><axsl:variable name="id" select="@id"/><axsl:variable name="count" select="count(//sbgn:arc[(./@class = 'consumption') and (./@source = $id)])"/>
+<axsl:template match="sbgn:glyph[@class='source and sink']" priority="1000" mode="M10"><svrl:fired-rule xmlns:svrl="http://purl.oclc.org/dsdl/svrl" context="sbgn:glyph[@class='source and sink']"/><axsl:variable name="id" select="@id"/><axsl:variable name="count" select="count(//sbgn:arc[(./@class = 'consumption') and (./@source = $id)])"/>
 
 		<!--ASSERT error-->
-<axsl:choose><axsl:when test="$count &lt;= 1"/><axsl:otherwise><svrl:failed-assert xmlns:svrl="http://purl.oclc.org/dsdl/svrl" test="$count &lt;= 1"><axsl:attribute name="id">pd10103</axsl:attribute><axsl:attribute name="role">error</axsl:attribute><axsl:attribute name="location"><axsl:apply-templates select="." mode="schematron-select-full-path"/></axsl:attribute><svrl:text>The empty set glyph can be connected to at most one consumption glyph 
+<axsl:choose><axsl:when test="$count &lt;= 1"/><axsl:otherwise><svrl:failed-assert xmlns:svrl="http://purl.oclc.org/dsdl/svrl" test="$count &lt;= 1"><axsl:attribute name="id">pd10103</axsl:attribute><axsl:attribute name="role">error</axsl:attribute><axsl:attribute name="location"><axsl:apply-templates select="." mode="schematron-select-full-path"/></axsl:attribute><svrl:text>The source and sink glyph can be connected to at most one consumption glyph 
 			</svrl:text> <svrl:diagnostic-reference diagnostic="id">
 <axsl:text/><axsl:value-of select="$id"/><axsl:text/></svrl:diagnostic-reference> <svrl:diagnostic-reference diagnostic="count">
 <axsl:text/><axsl:value-of select="$count"/><axsl:text/></svrl:diagnostic-reference></svrl:failed-assert></axsl:otherwise></axsl:choose><axsl:apply-templates select="*" mode="M10"/></axsl:template><axsl:template match="text()" priority="-1" mode="M10"/><axsl:template match="@*|node()" priority="-2" mode="M10"><axsl:apply-templates select="*" mode="M10"/></axsl:template>
@@ -139,7 +139,7 @@
 <axsl:template match="sbgn:arc[@class='production']" priority="1000" mode="M13"><svrl:fired-rule xmlns:svrl="http://purl.oclc.org/dsdl/svrl" context="sbgn:arc[@class='production']"/><axsl:variable name="id" select="@id"/><axsl:variable name="target" select="@target"/><axsl:variable name="class" select="//sbgn:glyph[@id=$target]/@class"/>
 
 		<!--ASSERT error-->
-<axsl:choose><axsl:when test="     $class='macromolecule' or      $class='macromolecule multimer' or      $class='simple chemical' or     $class='unspecified entity' or      $class='complex multimer' or          $class='complex' or      $class='nucleic acid feature' or      $class='simple chemical multimer' or      $class='nucleic acid feature multimer' or      $class='empty set'"/><axsl:otherwise><svrl:failed-assert xmlns:svrl="http://purl.oclc.org/dsdl/svrl" test="$class='macromolecule' or $class='macromolecule multimer' or $class='simple chemical' or $class='unspecified entity' or $class='complex multimer' or $class='complex' or $class='nucleic acid feature' or $class='simple chemical multimer' or $class='nucleic acid feature multimer' or $class='empty set'"><axsl:attribute name="id">pd10106</axsl:attribute><axsl:attribute name="role">error</axsl:attribute><axsl:attribute name="location"><axsl:apply-templates select="." mode="schematron-select-full-path"/></axsl:attribute><svrl:text>Arc with class production must have target reference to glyph of EPN classes
+<axsl:choose><axsl:when test="     $class='macromolecule' or      $class='macromolecule multimer' or      $class='simple chemical' or     $class='unspecified entity' or      $class='complex multimer' or          $class='complex' or      $class='nucleic acid feature' or      $class='simple chemical multimer' or      $class='nucleic acid feature multimer' or      $class='source and sink'"/><axsl:otherwise><svrl:failed-assert xmlns:svrl="http://purl.oclc.org/dsdl/svrl" test="$class='macromolecule' or $class='macromolecule multimer' or $class='simple chemical' or $class='unspecified entity' or $class='complex multimer' or $class='complex' or $class='nucleic acid feature' or $class='simple chemical multimer' or $class='nucleic acid feature multimer' or $class='source and sink'"><axsl:attribute name="id">pd10106</axsl:attribute><axsl:attribute name="role">error</axsl:attribute><axsl:attribute name="location"><axsl:apply-templates select="." mode="schematron-select-full-path"/></axsl:attribute><svrl:text>Arc with class production must have target reference to glyph of EPN classes
 			</svrl:text> <svrl:diagnostic-reference diagnostic="id">
 <axsl:text/><axsl:value-of select="$id"/><axsl:text/></svrl:diagnostic-reference> <svrl:diagnostic-reference diagnostic="target">
 <axsl:text/><axsl:value-of select="$target"/><axsl:text/></svrl:diagnostic-reference> <svrl:diagnostic-reference diagnostic="class">
@@ -149,10 +149,10 @@
 
 
 	<!--RULE -->
-<axsl:template match="sbgn:glyph[@class='empty set']" priority="1000" mode="M14"><svrl:fired-rule xmlns:svrl="http://purl.oclc.org/dsdl/svrl" context="sbgn:glyph[@class='empty set']"/><axsl:variable name="id" select="@id"/><axsl:variable name="count" select="count(//sbgn:arc[(./@class = 'production') and (./@target = $id)])"/>
+<axsl:template match="sbgn:glyph[@class='source and sink']" priority="1000" mode="M14"><svrl:fired-rule xmlns:svrl="http://purl.oclc.org/dsdl/svrl" context="sbgn:glyph[@class='source and sink']"/><axsl:variable name="id" select="@id"/><axsl:variable name="count" select="count(//sbgn:arc[(./@class = 'production') and (./@target = $id)])"/>
 
 		<!--ASSERT error-->
-<axsl:choose><axsl:when test="$count &lt;= 1"/><axsl:otherwise><svrl:failed-assert xmlns:svrl="http://purl.oclc.org/dsdl/svrl" test="$count &lt;= 1"><axsl:attribute name="id">pd10107</axsl:attribute><axsl:attribute name="role">error</axsl:attribute><axsl:attribute name="location"><axsl:apply-templates select="." mode="schematron-select-full-path"/></axsl:attribute><svrl:text>The empty set glyph can be connected to at most one production glyph 
+<axsl:choose><axsl:when test="$count &lt;= 1"/><axsl:otherwise><svrl:failed-assert xmlns:svrl="http://purl.oclc.org/dsdl/svrl" test="$count &lt;= 1"><axsl:attribute name="id">pd10107</axsl:attribute><axsl:attribute name="role">error</axsl:attribute><axsl:attribute name="location"><axsl:apply-templates select="." mode="schematron-select-full-path"/></axsl:attribute><svrl:text>The source and sink glyph can be connected to at most one production glyph 
 			</svrl:text> <svrl:diagnostic-reference diagnostic="id">
 <axsl:text/><axsl:value-of select="$id"/><axsl:text/></svrl:diagnostic-reference> <svrl:diagnostic-reference diagnostic="count">
 <axsl:text/><axsl:value-of select="$count"/><axsl:text/></svrl:diagnostic-reference></svrl:failed-assert></axsl:otherwise></axsl:choose><axsl:apply-templates select="*" mode="M14"/></axsl:template><axsl:template match="text()" priority="-1" mode="M14"/><axsl:template match="@*|node()" priority="-2" mode="M14"><axsl:apply-templates select="*" mode="M14"/></axsl:template>
@@ -214,7 +214,7 @@
 
 
 	<!--RULE -->
-<axsl:template match="sbgn:map/sbgn:glyph[(@class = 'unspecified entity' or      @class = 'simple chemical' or      @class = 'macromolecule' or      @class = 'nucleic acid feature' or     @class = 'simple chemical multimer' or      @class = 'macromolecule multimer' or      @class = 'nucleic acid feature multimer' or      @class = 'complex' or      @class = 'complex multimer' or      @class = 'empty set' or     @class = 'perturbing agent')]" priority="1000" mode="M19"><svrl:fired-rule xmlns:svrl="http://purl.oclc.org/dsdl/svrl" context="sbgn:map/sbgn:glyph[(@class = 'unspecified entity' or      @class = 'simple chemical' or      @class = 'macromolecule' or      @class = 'nucleic acid feature' or     @class = 'simple chemical multimer' or      @class = 'macromolecule multimer' or      @class = 'nucleic acid feature multimer' or      @class = 'complex' or      @class = 'complex multimer' or      @class = 'empty set' or     @class = 'perturbing agent')]"/><axsl:variable name="id" select="@id"/><axsl:variable name="compartment-count" select="count(//sbgn:glyph[@class='compartment'])"/>
+<axsl:template match="sbgn:map/sbgn:glyph[(@class = 'unspecified entity' or      @class = 'simple chemical' or      @class = 'macromolecule' or      @class = 'nucleic acid feature' or     @class = 'simple chemical multimer' or      @class = 'macromolecule multimer' or      @class = 'nucleic acid feature multimer' or      @class = 'complex' or      @class = 'complex multimer' or      @class = 'source and sink' or     @class = 'perturbing agent')]" priority="1000" mode="M19"><svrl:fired-rule xmlns:svrl="http://purl.oclc.org/dsdl/svrl" context="sbgn:map/sbgn:glyph[(@class = 'unspecified entity' or      @class = 'simple chemical' or      @class = 'macromolecule' or      @class = 'nucleic acid feature' or     @class = 'simple chemical multimer' or      @class = 'macromolecule multimer' or      @class = 'nucleic acid feature multimer' or      @class = 'complex' or      @class = 'complex multimer' or      @class = 'source and sink' or     @class = 'perturbing agent')]"/><axsl:variable name="id" select="@id"/><axsl:variable name="compartment-count" select="count(//sbgn:glyph[@class='compartment'])"/>
 
 		<!--ASSERT error-->
 <axsl:choose><axsl:when test="     (($compartment-count = 0) and not (@compartmentRef)) or (($compartment-count &gt; 0) and @compartmentRef)"/><axsl:otherwise><svrl:failed-assert xmlns:svrl="http://purl.oclc.org/dsdl/svrl" test="(($compartment-count = 0) and not (@compartmentRef)) or (($compartment-count &gt; 0) and @compartmentRef)"><axsl:attribute name="id">pd10112</axsl:attribute><axsl:attribute name="role">error</axsl:attribute><axsl:attribute name="location"><axsl:apply-templates select="." mode="schematron-select-full-path"/></axsl:attribute><svrl:text>If there are compartments defined, top-level glyphs must have a compartment reference
@@ -267,7 +267,7 @@
 <axsl:template match="sbgn:arc[@class='equivalence arc']" priority="1000" mode="M23"><svrl:fired-rule xmlns:svrl="http://purl.oclc.org/dsdl/svrl" context="sbgn:arc[@class='equivalence arc']"/><axsl:variable name="id" select="@id"/><axsl:variable name="source" select="@source"/><axsl:variable name="class" select="//sbgn:glyph[@id=$source]/@class"/>
 
 		<!--ASSERT error-->
-<axsl:choose><axsl:when test="     $class='unspecified entity' or      $class='simple chemical' or     $class='macromolecule' or      $class='macromolecule multimer' or     $class='nucleic acid feature' or      $class='simple chemical multimer' or      $class='nucleic acid feature multimer' or      $class='complex' or      $class='complex multimer' or          $class='empty set' or      $class='perturbing agent'"/><axsl:otherwise><svrl:failed-assert xmlns:svrl="http://purl.oclc.org/dsdl/svrl" test="$class='unspecified entity' or $class='simple chemical' or $class='macromolecule' or $class='macromolecule multimer' or $class='nucleic acid feature' or $class='simple chemical multimer' or $class='nucleic acid feature multimer' or $class='complex' or $class='complex multimer' or $class='empty set' or $class='perturbing agent'"><axsl:attribute name="id">pd10127</axsl:attribute><axsl:attribute name="role">error</axsl:attribute><axsl:attribute name="location"><axsl:apply-templates select="." mode="schematron-select-full-path"/></axsl:attribute><svrl:text>Arc with class equivalence arc must have source reference to glyph of EPN classes
+<axsl:choose><axsl:when test="     $class='unspecified entity' or      $class='simple chemical' or     $class='macromolecule' or      $class='macromolecule multimer' or     $class='nucleic acid feature' or      $class='simple chemical multimer' or      $class='nucleic acid feature multimer' or      $class='complex' or      $class='complex multimer' or          $class='source and sink' or      $class='perturbing agent'"/><axsl:otherwise><svrl:failed-assert xmlns:svrl="http://purl.oclc.org/dsdl/svrl" test="$class='unspecified entity' or $class='simple chemical' or $class='macromolecule' or $class='macromolecule multimer' or $class='nucleic acid feature' or $class='simple chemical multimer' or $class='nucleic acid feature multimer' or $class='complex' or $class='complex multimer' or $class='source and sink' or $class='perturbing agent'"><axsl:attribute name="id">pd10127</axsl:attribute><axsl:attribute name="role">error</axsl:attribute><axsl:attribute name="location"><axsl:apply-templates select="." mode="schematron-select-full-path"/></axsl:attribute><svrl:text>Arc with class equivalence arc must have source reference to glyph of EPN classes
 			</svrl:text> <svrl:diagnostic-reference diagnostic="id">
 <axsl:text/><axsl:value-of select="$id"/><axsl:text/></svrl:diagnostic-reference> <svrl:diagnostic-reference diagnostic="source">
 <axsl:text/><axsl:value-of select="$source"/><axsl:text/></svrl:diagnostic-reference> <svrl:diagnostic-reference diagnostic="class">
@@ -301,7 +301,7 @@
 
 
 	<!--RULE -->
-<axsl:template match="/sbgn:sbgn/sbgn:map/sbgn:glyph[     @class = 'unspecified entity' or      @class = 'simple chemical' or      @class = 'macromolecule' or      @class = 'nucleic acid feature' or     @class = 'simple chemical multimer' or      @class = 'macromolecule multimer' or      @class = 'nucleic acid feature multimer' or      @class = 'complex' or      @class = 'complex multimer' or      @class = 'empty set' or     @class = 'perturbing agent']    " priority="1000" mode="M27"><svrl:fired-rule xmlns:svrl="http://purl.oclc.org/dsdl/svrl" context="/sbgn:sbgn/sbgn:map/sbgn:glyph[     @class = 'unspecified entity' or      @class = 'simple chemical' or      @class = 'macromolecule' or      @class = 'nucleic acid feature' or     @class = 'simple chemical multimer' or      @class = 'macromolecule multimer' or      @class = 'nucleic acid feature multimer' or      @class = 'complex' or      @class = 'complex multimer' or      @class = 'empty set' or     @class = 'perturbing agent']    "/><axsl:variable name="id" select="@id"/><axsl:variable name="class" select="//sbgn:arc[@source = $id or @target = $id]/@class"/>
+<axsl:template match="/sbgn:sbgn/sbgn:map/sbgn:glyph[     @class = 'unspecified entity' or      @class = 'simple chemical' or      @class = 'macromolecule' or      @class = 'nucleic acid feature' or     @class = 'simple chemical multimer' or      @class = 'macromolecule multimer' or      @class = 'nucleic acid feature multimer' or      @class = 'complex' or      @class = 'complex multimer' or      @class = 'source and sink' or     @class = 'perturbing agent']    " priority="1000" mode="M27"><svrl:fired-rule xmlns:svrl="http://purl.oclc.org/dsdl/svrl" context="/sbgn:sbgn/sbgn:map/sbgn:glyph[     @class = 'unspecified entity' or      @class = 'simple chemical' or      @class = 'macromolecule' or      @class = 'nucleic acid feature' or     @class = 'simple chemical multimer' or      @class = 'macromolecule multimer' or      @class = 'nucleic acid feature multimer' or      @class = 'complex' or      @class = 'complex multimer' or      @class = 'source and sink' or     @class = 'perturbing agent']    "/><axsl:variable name="id" select="@id"/><axsl:variable name="class" select="//sbgn:arc[@source = $id or @target = $id]/@class"/>
 
 		<!--ASSERT error-->
 <axsl:choose><axsl:when test="//sbgn:arc[(      @class = 'production' or      @class = 'consumption' or            @class = 'modulation' or       @class = 'stimulation' or       @class = 'catalysis' or       @class = 'inhibition' or       @class = 'necessary stimulation' or       @class = 'logic arc' or       @class = 'equivalence arc' or       @class = 'production') and (@source = $id or @target = $id)]"/><axsl:otherwise><svrl:failed-assert xmlns:svrl="http://purl.oclc.org/dsdl/svrl" test="//sbgn:arc[( @class = 'production' or @class = 'consumption' or @class = 'modulation' or @class = 'stimulation' or @class = 'catalysis' or @class = 'inhibition' or @class = 'necessary stimulation' or @class = 'logic arc' or @class = 'equivalence arc' or @class = 'production') and (@source = $id or @target = $id)]"><axsl:attribute name="id">pd10131</axsl:attribute><axsl:attribute name="role">error</axsl:attribute><axsl:attribute name="location"><axsl:apply-templates select="." mode="schematron-select-full-path"/></axsl:attribute><svrl:text>EPNs should not be orphaned (i.e. they must be associated with at least one arc)