Merge branch 'sk/small-fixes' into sk/test-rate-rule-converter-rigoro…

…usly

src/sbml/SBMLErrorTable.h

@@ -11047,8 +11047,7 @@ static const sbmlErrorTableEntry errorTable[] =
     "LibSBML expected to read the annotation into a ModelHistory "
     "object. Unfortunately, some attributes were not present or correct "
     "and the resulting ModelHistory object will not correctly "
-    "produce the annotation.  This functionality will be improved in "
-    "later versions of libSBML. ",
+    "produce the annotation.  ",
     {"",
      "",
      "L2V2 Section 6.3",
@@ -11076,8 +11075,7 @@ static const sbmlErrorTableEntry errorTable[] =
     "LibSBML expected to read the annotation into a ModelHistory "
     "object. Unfortunately, some attributes were not present or correct "
     "and the resulting ModelHistory object is NULL. Thus it will fail to "
-    "produce the annotation.  This functionality will be improved in "
-    "later versions of libSBML. ",
+    "produce the annotation. ",
     {"",
      "",
      "L2V2 Section 6.3",

src/sbml/SBase.cpp

@@ -4576,6 +4576,7 @@ SBase::read (XMLInputStream& stream)
     else if ( next.isStart() )
     {
       const std::string nextName = next.getName();
+      const std::string nextURI = next.getURI();
 #if 0
       cout << "[DEBUG] SBase::read " << nextName << " uri "
            << stream.peek().getURI() << endl;
@@ -4620,7 +4621,7 @@ SBase::read (XMLInputStream& stream)
                    || readAnnotation(stream)
                    || readNotes(stream) ))
       {
-        logUnknownElement(nextName, getLevel(), getVersion());
+        logUnknownElement(nextName, getLevel(), getVersion(), nextURI);
         stream.skipPastEnd( stream.next() );
       }
     }
@@ -5343,11 +5344,17 @@ SBase::logUnknownAttribute( const string& attribute,
 void
 SBase::logUnknownElement( const string& element,
         const unsigned int level,
-        const unsigned int version )
+        const unsigned int version,
+    const string& URI)
 {
   bool logged = false;
   ostringstream msg;
 
+  // if we have an unknown element that is not in an SBML name space
+  // this is perfectly allowed XML
+  if (getPackageName() == "core" && SBMLNamespaces::getSBMLNamespaceURI(level, version) != URI)
+      return;
+
   if (level > 2 && getTypeCode() == SBML_LIST_OF)
   {
     int tc = static_cast<ListOf*>(this)->getItemTypeCode();

src/sbml/SBase.h

@@ -3532,7 +3532,8 @@ newModel.addSpecies(s1);
    */
   void logUnknownElement( const std::string& element,
         const unsigned int level,
-        const unsigned int version );
+        const unsigned int version,
+      const std::string& URI = NULL);
 
 
   /**

src/sbml/validator/test/test-data/sbml-xml-constraints/10102-fail-01-27-20517.xml → src/sbml/validator/test/test-data/libsbml-constraints/99107-fail-01-08.xml

@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <sbml xmlns="http://www.sbml.org/sbml/level3/version1/core"  level="3" version="1" 
-xmlns:appear="http://www.sbml.org/sbml/version1">
+xmlns:appear="http://www.sbml.org/sbml/level3/version1/appear" appear:required="true">
   <model>
     <listOfCompartments>
       <compartment id="c" constant="true" appear:shape="circle"/>

src/sbml/validator/test/test-data/sbml-xml-constraints/10102-fail-01-29-20517.xml → src/sbml/validator/test/test-data/libsbml-constraints/99107-fail-01-09.xml

@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <sbml xmlns="http://www.sbml.org/sbml/level3/version1/core"  level="3" version="1" 
-xmlns:appear="http://www.sbml.org/sbml/version1"
+xmlns:appear="http://www.sbml.org/sbml/level3/version1/appear"
       appear:required="true">
   <model>
     <listOfCompartments>

src/sbml/validator/test/test-data/sbml-xml-constraints/10102-fail-01-28-20517.xml → src/sbml/validator/test/test-data/libsbml-constraints/99108-fail-01-06.xml

@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <sbml xmlns="http://www.sbml.org/sbml/level3/version1/core"  level="3" version="1" 
-xmlns:appear="http://www.sbml.org/sbml/version1"
+xmlns:appear="http://www.sbml.org/sbml/level3/version1/appear"
       appear:required="false">
   <model>
     <listOfCompartments>

src/sbml/validator/test/test-data/sbml-xml-constraints/10102-fail-01-30-20517.xml → src/sbml/validator/test/test-data/sbml-general-consistency-constraints/20517-fail-01-07.xml

@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <sbml xmlns="http://www.sbml.org/sbml/level3/version2/core"  level="3" version="2" 
-xmlns:appear="http://www.sbml.org/sbml/version1">
+xmlns:appear="http://www.sbother">
   <model>
     <listOfCompartments>
       <compartment id="c" constant="true" appear:shape="circle"/>

src/sbml/validator/test/test-data/sbml-xml-constraints/10102-fail-01-32-20517.xml → src/sbml/validator/test/test-data/sbml-general-consistency-constraints/20517-fail-01-08.xml

@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <sbml xmlns="http://www.sbml.org/sbml/level3/version2/core"  level="3" version="2" 
-xmlns:appear="http://www.sbml.org/sbml/version1"
+xmlns:appear="http://www.something.else"
       appear:required="true">
   <model>
     <listOfCompartments>

src/sbml/validator/test/test-data/sbml-xml-constraints/10102-fail-01-31-20517.xml → src/sbml/validator/test/test-data/sbml-general-consistency-constraints/20517-fail-01-09.xml

@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <sbml xmlns="http://www.sbml.org/sbml/level3/version2/core"  level="3" version="2" 
-xmlns:appear="http://www.sbml.org/sbml/version1"
+xmlns:appear="http://www.something.else"
       appear:required="false">
   <model>
     <listOfCompartments>