Allow l1v5 namespace.

Author: luciansmith

src/sedml/SedBase.cpp

@@ -2233,7 +2233,7 @@ SedBase::read (LIBSBML_CPP_NAMESPACE_QUALIFIER XMLInputStream& stream)
         if (i > -1)
         {
           std::string uri = xmlns->getURI(i);
-          if (uri == SEDML_XMLNS_L1V1 || uri == SEDML_XMLNS_L1V2 || uri == SEDML_XMLNS_L1V3 || uri == SEDML_XMLNS_L1V4)
+          if (uri == SEDML_XMLNS_L1V1 || uri == SEDML_XMLNS_L1V2 || uri == SEDML_XMLNS_L1V3 || uri == SEDML_XMLNS_L1V4 || uri == SEDML_XMLNS_L1V5)
           {
             error = false;
           }

src/sedml/SedDocument.cpp

@@ -3204,8 +3204,12 @@ SedDocument::writeXMLNS(LIBSBML_CPP_NAMESPACE_QUALIFIER XMLOutputStream&
         xmlns.add(SEDML_XMLNS_L1V2);
       else if (getVersion() == 3)
         xmlns.add(SEDML_XMLNS_L1V3);
-      else
+      else if (getVersion() == 4)
         xmlns.add(SEDML_XMLNS_L1V4);
+      else if (getVersion() == 5)
+        xmlns.add(SEDML_XMLNS_L1V5);
+      else
+        xmlns.add(SEDML_XMLNS_L1V5);
 
       mSedNamespaces->setNamespaces(&xmlns);
       thisNs =  const_cast<LIBSBML_CPP_NAMESPACE_QUALIFIER XMLNamespaces *>(getNamespaces());
@@ -3218,8 +3222,12 @@ SedDocument::writeXMLNS(LIBSBML_CPP_NAMESPACE_QUALIFIER XMLOutputStream&
         thisNs->add(SEDML_XMLNS_L1V2);
       else if (getVersion() == 3)
         thisNs->add(SEDML_XMLNS_L1V3);
-      else
+      else if (getVersion() == 4)
         thisNs->add(SEDML_XMLNS_L1V4);
+      else if (getVersion() == 5)
+        thisNs->add(SEDML_XMLNS_L1V5);
+      else
+        thisNs->add(SEDML_XMLNS_L1V5);
     }
   else
     {

src/sedml/SedNamespaces.cpp

@@ -76,6 +76,9 @@ SedNamespaces::initSedNamespace()
     case 4:
       mNamespaces->add(SEDML_XMLNS_L1V4);
       break;
+    case 5:
+      mNamespaces->add(SEDML_XMLNS_L1V5);
+      break;
     }
     break;
   }
@@ -129,6 +132,7 @@ SedNamespaces::getSupportedNamespaces()
   result->add(new SedNamespaces(1,2));
   result->add(new SedNamespaces(1,3));
   result->add(new SedNamespaces(1,4));
+  result->add(new SedNamespaces(1,5));
   return result;
 }
 
@@ -201,6 +205,9 @@ SedNamespaces::getSedNamespaceURI(unsigned int level,
     case 4:
       uri = SEDML_XMLNS_L1V4;
       break;
+    case 5:
+      uri = SEDML_XMLNS_L1V5;
+      break;
     }
     break;
   }
@@ -358,6 +365,12 @@ SedNamespaces::isValidCombination()
       declaredURI.assign(SEDML_XMLNS_L1V4);
     }
 
+    if (xmlns->hasURI(SEDML_XMLNS_L1V5))
+    {
+      ++numNS;
+      declaredURI.assign(SEDML_XMLNS_L1V5);
+    }
+
     // checks if the SED-ML Namespace is explicitly defined.
     for (int i=0; i < xmlns->getLength(); i++)
     {
@@ -420,6 +433,17 @@ SedNamespaces::isValidCombination()
             }
           }
           break;
+        case 5:
+          // the namespaces contains the sedml namespaces
+          // check it is the correct ns for the level/version
+          if (sedmlDeclared)
+          {
+            if (declaredURI != string(SEDML_XMLNS_L1V5))
+            {
+              valid = false;
+            }
+          }
+          break;
         default:
           valid = false;
           break;

src/sedml/SedNamespaces.h

@@ -49,11 +49,12 @@
 namespace LIBSEDML_CPP_NAMESPACE 
 {
   const unsigned int SEDML_DEFAULT_LEVEL   = 1;
-  const unsigned int SEDML_DEFAULT_VERSION = 3;
+  const unsigned int SEDML_DEFAULT_VERSION = 5;
   const char* const SEDML_XMLNS_L1V1   = "http://sed-ml.org/";
   const char* const SEDML_XMLNS_L1V2   = "http://sed-ml.org/sed-ml/level1/version2";
   const char* const SEDML_XMLNS_L1V3   = "http://sed-ml.org/sed-ml/level1/version3";
   const char* const SEDML_XMLNS_L1V4   = "http://sed-ml.org/sed-ml/level1/version4";
+  const char* const SEDML_XMLNS_L1V5   = "http://sed-ml.org/sed-ml/level1/version5";
 }
 #else
 static const unsigned int SEDML_DEFAULT_LEVEL   = 1;
@@ -62,6 +63,7 @@ static const char* const SEDML_XMLNS_L1V1   = "http://sed-ml.org/";
 static const char* const SEDML_XMLNS_L1V2   = "http://sed-ml.org/sed-ml/level1/version2";
 static const char* const SEDML_XMLNS_L1V3   = "http://sed-ml.org/sed-ml/level1/version3";
 static const char* const SEDML_XMLNS_L1V4   = "http://sed-ml.org/sed-ml/level1/version4";
+static const char* const SEDML_XMLNS_L1V5   = "http://sed-ml.org/sed-ml/level1/version5";
 #endif
 
 #ifdef __cplusplus

tests/TestIssues.cpp

@@ -144,6 +144,31 @@ TEST_CASE("Reading / Writing L1V4", "[sedml]")
   delete doc;
 }
 
+TEST_CASE("Reading / Writing L1V5", "[sedml]")
+{
+  std::string fileName = getTestFile("/test-data/noble_1962_local.sedml");
+  SedDocument* doc = readSedMLFromFile(fileName.c_str());
+  REQUIRE (doc->getNumErrors(LIBSEDML_SEV_ERROR) == 0);
+
+  
+  // convert to l1v5
+  doc->setLevel(1); doc->setVersion(5);
+
+  // write to string
+  SedWriter sw;
+  std::string l1v5 = sw.writeSedMLToStdString(doc);
+  REQUIRE(l1v5.find("version=\"5\"") != std::string::npos);
+
+  // don't need doc anymore
+  delete doc;
+
+  // read back
+  doc = readSedMLFromString(l1v5.c_str());
+  REQUIRE(doc->getNumErrors(LIBSEDML_SEV_ERROR) == 0);
+
+  delete doc;
+}
+
 TEST_CASE("Reading L1V4 curve should not require logY", "[sedml]")
 {
   std::string fileName = getTestFile("/test-data/issue_63.sedml");