Merge pull request #243 from sbmlteam/fbc-v3-fix

 #241:issues with fbc v3

Author: fbergmann

VERSION.txt

@@ -1 +1 @@
-5.19.5
+5.19.6

configure

@@ -1,7 +1,7 @@
 #! /bin/sh
 # From configure.ac Revision.
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.69 for libSBML 5.19.5.
+# Generated by GNU Autoconf 2.69 for libSBML 5.19.6.
 #
 # Report bugs to <[email protected]>.
 #
@@ -735,8 +735,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='libSBML'
 PACKAGE_TARNAME='libsbml'
-PACKAGE_VERSION='5.19.5'
-PACKAGE_STRING='libSBML 5.19.5'
+PACKAGE_VERSION='5.19.6'
+PACKAGE_STRING='libSBML 5.19.6'
 PACKAGE_BUGREPORT='[email protected]'
 PACKAGE_URL='http://sbml.org/Software/libSBML'
 
@@ -1629,7 +1629,7 @@ if test "$ac_init_help" = "long"; then
   # Omit some internal or obsolete options to make the list less imposing.
   # This message is too long to be a string in the A/UX 3.1 sh.
   cat <<_ACEOF
-\`configure' configures libSBML 5.19.5 to adapt to many kinds of systems.
+\`configure' configures libSBML 5.19.6 to adapt to many kinds of systems.
 
 Usage: $0 [OPTION]... [VAR=VALUE]...
 
@@ -1695,7 +1695,7 @@ fi
 
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of libSBML 5.19.5:";;
+     short | recursive ) echo "Configuration of libSBML 5.19.6:";;
    esac
   cat <<\_ACEOF
 
@@ -1851,7 +1851,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-libSBML configure 5.19.5
+libSBML configure 5.19.6
 generated by GNU Autoconf 2.69
 
 Copyright (C) 2012 Free Software Foundation, Inc.
@@ -2570,7 +2570,7 @@ cat >config.log <<_ACEOF
 This file contains any messages produced by compilers while
 running configure, to aid debugging if configure makes a mistake.
 
-It was created by libSBML $as_me 5.19.5, which was
+It was created by libSBML $as_me 5.19.6, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
 
   $ $0 $@
@@ -27754,7 +27754,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
 # report actual input values of CONFIG_FILES etc. instead of their
 # values after options handling.
 ac_log="
-This file was extended by libSBML $as_me 5.19.5, which was
+This file was extended by libSBML $as_me 5.19.6, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
 
   CONFIG_FILES    = $CONFIG_FILES
@@ -27817,7 +27817,7 @@ _ACEOF
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
 ac_cs_version="\\
-libSBML config.status 5.19.5
+libSBML config.status 5.19.6
 configured by $0, generated by GNU Autoconf 2.69,
   with options \\"\$ac_cs_config\\"
 

src/sbml/common/libsbml-version.h

@@ -51,7 +51,7 @@
  *
  * A version string of the form "1.2.3".
  */
-#define LIBSBML_DOTTED_VERSION	"5.19.5"
+#define LIBSBML_DOTTED_VERSION	"5.19.6"
 
 
 /**

src/sbml/packages/fbc/extension/FbcSBasePlugin.cpp

@@ -230,7 +230,7 @@ FbcSBasePlugin::createKeyValuePair()
 
   try
   {
-    FBC_CREATE_NS(fbcns, getSBMLNamespaces());
+    FBC_CREATE_NS_WITH_VERSION(fbcns, getSBMLNamespaces(), getPackageVersion());
     kvp = new KeyValuePair(fbcns);
     delete fbcns;
   }
@@ -872,87 +872,94 @@ FbcSBasePlugin::createObject(XMLInputStream& stream)
 
 /** @endcond */
 
-/** @cond doxygenLibsbmlInternal */
-/**
-* Synchronizes the annotation of this SBML object.
-*
-* Annotation element (XMLNode* mAnnotation) is synchronized with the
-* current CVTerm objects (List* mCVTerm).
-* Currently, this method is called in getAnnotation, isSetAnnotation,
-* and writeElements methods.
-*/
-void 
-FbcSBasePlugin::writeKeyValuePairsAnnotation(SBase* parentObject) const
-{
-  if (parentObject == NULL) return;
-
-
-  XMLNode *parentAnnotation = parentObject->getAnnotation();
-  if (parentAnnotation != NULL && parentAnnotation->getNumChildren() > 0)
-  {
-//    deleteFbcAnnotation(parentAnnotation);
-  }
-
-  XMLToken ann_token = XMLToken(XMLTriple("annotation", "", ""), XMLAttributes());
-  XMLNode* annt = new XMLNode(ann_token);
-
-
-
-  if (mKeyValuePairs.size() > 0)
-  {
-    XMLAttributes loga_attr = XMLAttributes();
-    loga_attr.add("xmlns", FbcExtension::getXmlnsL3V1V3());
-    XMLToken loga_token = XMLToken(XMLTriple("listOfKeyValuePairs", FbcExtension::getXmlnsL3V1V1(), ""), loga_attr);
-    XMLNode loga = XMLNode(loga_token);
-
-    for (unsigned int i = 0; i < mKeyValuePairs.size(); ++i)
-      loga.addChild(mKeyValuePairs.get(i)->toXML());
-
-    // then add the ones toXML()
-    annt->addChild(loga);
-  }
-
-
-  if (annt && annt->getNumChildren() > 0)
-  {
-    parentObject->appendAnnotation(annt);
-  }
-  delete annt;
-}
-/** @endcond */
-
-
-/** @cond doxygenLibsbmlInternal */
-/**
-* Parse L2 annotation if supported
-*
-*/
-void 
-FbcSBasePlugin::parseAnnotation(SBase *parentObject, XMLNode *pAnnotation)
-{
-  mKeyValuePairs.setSBMLDocument(mSBML);
-  // don't read if we have an invalid node or already a gene associations object
-  if (pAnnotation == NULL || mKeyValuePairs.size() > 0)
-    return;
-
-  // annotation element has been parsed by the parent element
-  // (Model) of this plugin object, thus the annotation element 
-  // set to the above pAnnotation variable is parsed in this block.
-
-  XMLNode& listOfKeyValuePairs = pAnnotation->getChild("listOfKeyValuePairs");
-  if (listOfKeyValuePairs.getNumChildren() == 0)
-    return;
-
-  // read the xml node, overriding that all errors are flagged as 
-  // warnings
-  mKeyValuePairs.read(listOfKeyValuePairs, LIBSBML_OVERRIDE_WARNING);
-  // remove listOfLayouts annotation  
-  parentObject->removeTopLevelAnnotationElement("listOfKeyValuePairs", "", false);
-
-}
-/** @endcond */
-
-
+/** @cond doxygenLibsbmlInternal */
+/**
+* Synchronizes the annotation of this SBML object.
+*
+* Annotation element (XMLNode* mAnnotation) is synchronized with the
+* current CVTerm objects (List* mCVTerm).
+* Currently, this method is called in getAnnotation, isSetAnnotation,
+* and writeElements methods.
+*/
+void 
+FbcSBasePlugin::writeKeyValuePairsAnnotation(SBase* parentObject) const
+{
+  if (parentObject == NULL) return;
+
+
+  XMLNode *parentAnnotation = parentObject->getAnnotation();
+  if (parentAnnotation != NULL && parentAnnotation->getNumChildren() > 0)
+  {
+//    deleteFbcAnnotation(parentAnnotation);
+  }
+
+  XMLToken ann_token = XMLToken(XMLTriple("annotation", "", ""), XMLAttributes());
+  XMLNode* annt = new XMLNode(ann_token);
+
+
+
+  if (mKeyValuePairs.size() > 0)
+  {
+    XMLAttributes loga_attr = XMLAttributes();
+    loga_attr.add("xmlns", mKeyValuePairs.getXmlns());
+    XMLToken loga_token = XMLToken(XMLTriple("listOfKeyValuePairs", mKeyValuePairs.getXmlns(), ""), loga_attr);
+    XMLNode loga = XMLNode(loga_token);
+
+    for (unsigned int i = 0; i < mKeyValuePairs.size(); ++i)
+      loga.addChild(mKeyValuePairs.get(i)->toXML());
+
+    // then add the ones toXML()
+    annt->addChild(loga);
+  }
+
+
+  if (annt && annt->getNumChildren() > 0)
+  {
+    parentObject->appendAnnotation(annt);
+  }
+  delete annt;
+}
+/** @endcond */
+
+
+/** @cond doxygenLibsbmlInternal */
+/**
+* Parse L2 annotation if supported
+*
+*/
+void 
+FbcSBasePlugin::parseAnnotation(SBase *parentObject, XMLNode *pAnnotation)
+{
+  mKeyValuePairs.setSBMLDocument(mSBML);
+  // don't read if we have an invalid node or already a gene associations object
+  if (pAnnotation == NULL || mKeyValuePairs.size() > 0)
+    return;
+
+  // annotation element has been parsed by the parent element
+  // (Model) of this plugin object, thus the annotation element 
+  // set to the above pAnnotation variable is parsed in this block.
+
+  XMLNode& listOfKeyValuePairs = pAnnotation->getChild("listOfKeyValuePairs");
+  if (listOfKeyValuePairs.getNumChildren() == 0)
+    return;
+
+  XMLNamespaces oldNs = listOfKeyValuePairs.getNamespaces();
+  
+  // read the xml node, overriding that all errors are flagged as 
+  // warnings  
+  mKeyValuePairs.read(listOfKeyValuePairs, LIBSBML_OVERRIDE_WARNING);
+
+  // unfortunately the namespaces are overwritten at that point with the one from the 
+  // document, so restore it
+  mKeyValuePairs.setXmlns(&oldNs, listOfKeyValuePairs.getPrefix());
+
+  // remove listOfLayouts annotation  
+  parentObject->removeTopLevelAnnotationElement("listOfKeyValuePairs", "", false);
+
+}
+/** @endcond */
+
+
 
 
 

src/sbml/packages/fbc/extension/test/TestWriteFbcExtension.cpp

@@ -451,10 +451,14 @@ START_TEST(test_FbcExtension_create_and_write_L3V1V3)
 
   FbcSBasePlugin* sbaseplugin3 = dynamic_cast<FbcSBasePlugin*>(objective->getPlugin("fbc"));
 
+  ListOfKeyValuePairs *kvp_list = sbaseplugin3->getListOfKeyValuePairs();
+  fail_unless(kvp_list->isSetXmlns());
+  fail_unless(kvp_list->getXmlns() == "http://sbml.org/fbc/keyvaluepair");
+
   KeyValuePair * kvp3 = sbaseplugin3->createKeyValuePair();
-  kvp3->setKey("key3");
-  kvp3->setUri("my_annotation");
-  kvp3->setValue("objective-value");
+  fail_unless(kvp3->setKey("key3") == LIBSBML_OPERATION_SUCCESS);
+  fail_unless(kvp3->setUri("my_annotation") == LIBSBML_OPERATION_SUCCESS);
+  fail_unless(kvp3->setValue("objective-value") == LIBSBML_OPERATION_SUCCESS);
 
   //FbcSBasePlugin* sbaseplugin4 = dynamic_cast<FbcSBasePlugin*>(document->getPlugin("fbc"));
   //// this dynamic cast is null

src/sbml/packages/fbc/extension/test/test-data/fbc_example2_v3.xml

@@ -1,21 +1,15 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version3" level="3" version="1" fbc:required="false">
-<!--  <annotation>
-    <listOfKeyValuePairs xlns="http://www.sbml.org/sbml/level3/version1/fbc/version3">
-      <keyValuePair key="key4" value="doc-value" uri="my_annotation"/>
-    </listOfKeyValuePairs>
-  </annotation>
-  -->
   <model id="m" fbc:strict="true">
     <annotation>
-      <listOfKeyValuePairs xlns="http://www.sbml.org/sbml/level3/version1/fbc/version3">
+      <listOfKeyValuePairs xmlns="http://sbml.org/fbc/keyvaluepair">
         <keyValuePair key="key2" value="model-value" uri="my_annotation"/>
       </listOfKeyValuePairs>
     </annotation>
     <listOfCompartments>
       <compartment id="comp" spatialDimensions="3" size="1" constant="true">
         <annotation>
-          <listOfKeyValuePairs xlns="http://www.sbml.org/sbml/level3/version1/fbc/version3">
+          <listOfKeyValuePairs xmlns="http://sbml.org/fbc/keyvaluepair">
             <keyValuePair key="key" value="comp-value" uri="my_annotation"/>
           </listOfKeyValuePairs>
         </annotation>
@@ -24,7 +18,7 @@
     <listOfSpecies>
       <species id="S" compartment="comp" boundaryCondition="false" fbc:charge="2.5">
         <annotation>
-          <listOfKeyValuePairs xlns="http://www.sbml.org/sbml/level3/version1/fbc/version3">
+          <listOfKeyValuePairs xmlns="http://sbml.org/fbc/keyvaluepair">
             <keyValuePair key="key1" value="species-value" uri="my_annotation"/>
           </listOfKeyValuePairs>
         </annotation>
@@ -33,7 +27,7 @@
     <fbc:listOfObjectives fbc:activeObjective="obj1">
       <fbc:objective fbc:id="obj1" fbc:type="maximize">
         <annotation>
-          <listOfKeyValuePairs xlns="http://www.sbml.org/sbml/level3/version1/fbc/version3">
+          <listOfKeyValuePairs xmlns="http://sbml.org/fbc/keyvaluepair">
             <keyValuePair key="key3" value="objective-value" uri="my_annotation"/>
           </listOfKeyValuePairs>
         </annotation>
@@ -44,13 +38,10 @@
     </fbc:listOfObjectives>
     <fbc:listOfUserDefinedConstraints>
       <fbc:userDefinedConstraint fbc:id="uc2" fbc:lowerBound="uc2lb" fbc:upperBound="uc2ub">
-
         <fbc:listOfUserDefinedConstraintComponents>
-
           <fbc:userDefinedConstraintComponent fbc:coefficient="2" fbc:variable="Avar" fbc:variableType="linear"/>
         </fbc:listOfUserDefinedConstraintComponents>
       </fbc:userDefinedConstraint>
     </fbc:listOfUserDefinedConstraints>
-
   </model>
 </sbml>