Xmlns in math

src/sbml/math/ASTNode.cpp

@@ -261,6 +261,7 @@ ASTNode::ASTNode (ASTNodeType_t type)
   mStyle		 = "";
   mIsBvar = false;
   mUserData      = NULL;
+  mNamespaces = NULL;
 
   // move to after we have loaded plugins
   //setType(type);
@@ -307,6 +308,7 @@ ASTNode::ASTNode (Token_t* token)
   mStyle		 = "";
   mIsBvar = false;
   mUserData      = NULL;
+  mNamespaces = NULL;
 
   mChildren             = new List;
   mSemanticsAnnotations = new List;
@@ -378,6 +380,7 @@ ASTNode::ASTNode (const ASTNode& orig) :
  ,mStyle                ( orig.mStyle)
  ,mIsBvar               ( orig.mIsBvar)
  ,mUserData             ( orig.mUserData )
+  , mNamespaces         (orig.mNamespaces)
 {
   if (orig.mName)
   {
@@ -426,6 +429,8 @@ ASTNode& ASTNode::operator=(const ASTNode& rhs)
     mStyle                = rhs.mStyle;
     mIsBvar               = rhs.mIsBvar;
     mUserData             = rhs.mUserData;
+    mNamespaces = rhs.mNamespaces;
+
     freeName();
     if (rhs.mName)
     {
@@ -4571,6 +4576,20 @@ ASTNode::derivativeExp(const std::string& variable)
   return derivative;
 }
 
+XMLNamespaces* 
+ASTNode::getDeclaredNamespaces() const
+{
+  return mNamespaces;
+}
+
+
+void 
+ASTNode::setDeclaredNamespaces(const XMLNamespaces* xmlns)
+{
+  mNamespaces = xmlns->clone();
+}
+
+
 #endif /* __cplusplus */
 
 

src/sbml/math/ASTNode.h

@@ -2315,6 +2315,16 @@ setValue(value, 0);
 
   LIBSBML_EXTERN
   void printMath(unsigned int level = 0);
+
+  /** @cond doxygenLibsbmlInternal */
+  LIBSBML_EXTERN
+  XMLNamespaces* getDeclaredNamespaces() const;
+
+  LIBSBML_EXTERN
+  void setDeclaredNamespaces(const XMLNamespaces* xmlns);
+  /** @endcond */
+
+
 protected:
 
   friend class SBMLRateRuleConverter;
@@ -2471,6 +2481,9 @@ setValue(value, 0);
   bool mIsBvar;
   void *mUserData;
   std::string mPackageName;
+
+
+  XMLNamespaces* mNamespaces;
 
   friend class MathMLFormatter;
   friend class MathMLHandler;

src/sbml/math/MathML.cpp

@@ -2129,6 +2129,9 @@ readMathML (XMLInputStream& stream, std::string reqd_prefix, bool inRead)
 
     if (elem.isStart() && elem.isEnd()) return node;
 
+    /* record and explicitly decared namespaces*/
+    node->setDeclaredNamespaces(&(elem.getNamespaces()));
+
     /* check that math tag is followed by an appropriate
      * tag
      */
@@ -2207,28 +2210,42 @@ writeMathML (const ASTNode* node, XMLOutputStream& stream, SBMLNamespaces *sbmln
 {
 
   static const string uri = "http://www.w3.org/1998/Math/MathML";
+  unsigned int level = SBML_DEFAULT_LEVEL;
+  unsigned int version = SBML_DEFAULT_VERSION;
+  if (sbmlns != NULL)
+  {
+    level = sbmlns->getLevel();
+    version = sbmlns->getVersion();
+  }
 
   stream.startElement("math");
   stream.writeAttribute("xmlns", uri);
 
   if (node) 
   {
-  // FIX-ME need to know what level and version
-  if (node->hasUnits())
-  {
-    unsigned int level = SBML_DEFAULT_LEVEL;
-    unsigned int version = SBML_DEFAULT_VERSION;
-    if (sbmlns != NULL)
+    if (node->hasUnits())
     {
-      level = sbmlns->getLevel();
-      version = sbmlns->getVersion();
+      stream.writeAttribute(XMLTriple("sbml", "", "xmlns"),
+        SBMLNamespaces::getSBMLNamespaceURI(level, version));
+    }
+
+    // write any namespaces that have been specifically declared on math element
+    //
+    XMLNamespaces* xmlns = node->getDeclaredNamespaces();
+    if (xmlns != NULL)
+    {
+      for (int i = 0; i < xmlns->getNumNamespaces(); i++)
+      {
+        if (xmlns->getURI(i) == uri || xmlns->getURI(i) == SBMLNamespaces::getSBMLNamespaceURI(level, version))
+        {
+          continue;
+        }
+        stream.writeAttribute(xmlns->getPrefix(i), "xmlns", xmlns->getURI(i));
+
+      }
     }
-
-    stream.writeAttribute(XMLTriple("sbml", "", "xmlns"), 
-      SBMLNamespaces::getSBMLNamespaceURI(level, version));
-  }
 
-  writeNode(*node, stream,sbmlns);
+    writeNode(*node, stream,sbmlns);
   }
 
   stream.endElement("math");

src/sbml/packages/multi/extension/test/TestMultiAST.cpp

@@ -28,6 +28,19 @@ LIBSBML_CPP_NAMESPACE_USE
 
 BEGIN_C_DECLS
 
+static bool
+equals(const char* expected, const char* actual)
+{
+  if (!strcmp(expected, actual)) return true;
+
+  printf("\nStrings are not equal:\n");
+  printf("Expected:\n[%s]\n", expected);
+  printf("Actual:\n[%s]\n", actual);
+
+  return false;
+}
+
+
 
 extern char *TestDataDirectory;
 
@@ -204,6 +217,10 @@ START_TEST (test_multi_create_ci)
   math->addChild(ci);
   math->addChild(ci1);
 
+  // need to add multi ns
+  XMLNamespaces* xmlns = document->getSBMLNamespaces()->getNamespaces();
+  math->setDeclaredNamespaces(xmlns);
+
   kl->setMath(math);
   delete math;
 
@@ -334,6 +351,27 @@ START_TEST(test_multi_ast_plugin)
 END_TEST
 
 
+START_TEST(test_multi_math_ns)
+{
+  const char * expected = "<kineticLaw>\n"
+    "  <math xmlns=\"http://www.w3.org/1998/Math/MathML\" xmlns:multi=\"http://www.sbml.org/sbml/level3/version1/multi/version1\">\n"
+    "    <apply>\n"
+    "      <times/>\n"
+    "      <ci multi:speciesReference=\"r1\"> s1 </ci>\n"
+    "      <ci multi:representationType=\"sum\"> s1 </ci>\n"
+    "    </apply>\n"
+    "  </math>\n"
+    "</kineticLaw>";
+
+    string filename(TestDataDirectory);
+  string cfile = filename + "multi_ci_extension.xml";
+  SBMLDocument* doc = readSBMLFromFile(cfile.c_str());
+  KineticLaw* kl = doc->getModel()->getReaction(0)->getKineticLaw();
+  fail_unless(equals(expected, kl->toSBML()));
+}
+END_TEST
+
+
 Suite *
 create_suite_MultiAST(void)
 {
@@ -344,6 +382,7 @@ create_suite_MultiAST(void)
   tcase_add_test(tcase, test_multi_write_ci);
   tcase_add_test(tcase, test_multi_create_ci);
   tcase_add_test(tcase, test_multi_ast_plugin);
+  tcase_add_test(tcase, test_multi_math_ns);
 
   suite_add_tcase(suite, tcase);