- ensure that annotation ns is correct, allow using l3v2

fixes #241 and #244
sbmlteam · Jul 14, 2022 · e087303 · e087303
1 parent 30ae4dc
commit e087303
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Showing 6 changed files with 197 additions and 159 deletions.
diff --git a/src/sbml/packages/fbc/extension/FbcSBasePlugin.cpp b/src/sbml/packages/fbc/extension/FbcSBasePlugin.cpp
@@ -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 */
+
+
 
 
 

diff --git a/src/sbml/packages/fbc/extension/test/TestWriteFbcExtension.cpp b/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

diff --git a/src/sbml/packages/fbc/extension/test/test-data/fbc_example2_v3.xml b/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>
diff --git a/src/sbml/packages/fbc/sbml/KeyValuePair.cpp b/src/sbml/packages/fbc/sbml/KeyValuePair.cpp
@@ -236,10 +236,9 @@ int
 KeyValuePair::setId(const std::string& id)
 {
   unsigned int coreLevel = getLevel();
-  unsigned int coreVersion = getVersion();
   unsigned int pkgVersion = getPackageVersion();
 
-  if (coreLevel == 3 && coreVersion == 1 && pkgVersion == 3)
+  if (coreLevel == 3 && pkgVersion == 3)
   {
     return SyntaxChecker::checkAndSetSId(id, mId);
   }
@@ -257,10 +256,9 @@ int
 KeyValuePair::setName(const std::string& name)
 {
   unsigned int coreLevel = getLevel();
-  unsigned int coreVersion = getVersion();
   unsigned int pkgVersion = getPackageVersion();
 
-  if (coreLevel == 3 && coreVersion == 1 && pkgVersion == 3)
+  if (coreLevel == 3 && pkgVersion == 3)
   {
     mName = name;
     return LIBSBML_OPERATION_SUCCESS;
@@ -279,10 +277,9 @@ int
 KeyValuePair::setKey(const std::string& key)
 {
   unsigned int coreLevel = getLevel();
-  unsigned int coreVersion = getVersion();
   unsigned int pkgVersion = getPackageVersion();
 
-  if (coreLevel == 3 && coreVersion == 1 && pkgVersion == 3)
+  if (coreLevel == 3 && pkgVersion == 3)
   {
     mKey = key;
     return LIBSBML_OPERATION_SUCCESS;
@@ -301,10 +298,9 @@ int
 KeyValuePair::setValue(const std::string& value)
 {
   unsigned int coreLevel = getLevel();
-  unsigned int coreVersion = getVersion();
   unsigned int pkgVersion = getPackageVersion();
 
-  if (coreLevel == 3 && coreVersion == 1 && pkgVersion == 3)
+  if (coreLevel == 3 && pkgVersion == 3)
   {
     mValue = value;
     return LIBSBML_OPERATION_SUCCESS;
@@ -323,10 +319,9 @@ int
 KeyValuePair::setUri(const std::string& uri)
 {
   unsigned int coreLevel = getLevel();
-  unsigned int coreVersion = getVersion();
   unsigned int pkgVersion = getPackageVersion();
 
-  if (coreLevel == 3 && coreVersion == 1 && pkgVersion == 3)
+  if (coreLevel == 3 && pkgVersion == 3)
   {
     mUri = uri;
     return LIBSBML_OPERATION_SUCCESS;
@@ -860,10 +855,9 @@ KeyValuePair::addExpectedAttributes(ExpectedAttributes& attributes)
   SBase::addExpectedAttributes(attributes);
 
   unsigned int level = getLevel();
-  unsigned int coreVersion = getVersion();
   unsigned int pkgVersion = getPackageVersion();
 
-  if (level == 3 && coreVersion == 1 && pkgVersion == 3)
+  if (level == 3 && pkgVersion == 3)
   {
     attributes.add("id");
     attributes.add("name");
@@ -1122,16 +1116,16 @@ KeyValuePair::writeL3V1V3Attributes(XMLOutputStream& stream) const
 /** @endcond */
 
 
-/*
-* Creates an XMLNode object from this.
-*/
-XMLNode 
-KeyValuePair::toXML() const
-{
-  XMLNamespaces xmlns = XMLNamespaces();
-  XMLTriple triple = XMLTriple(getElementName(), "", "");
-  XMLAttributes att = XMLAttributes();
-
+/*
+* Creates an XMLNode object from this.
+*/
+XMLNode 
+KeyValuePair::toXML() const
+{
+  XMLNamespaces xmlns = XMLNamespaces();
+  XMLTriple triple = XMLTriple(getElementName(), "", "");
+  XMLAttributes att = XMLAttributes();
+
   if (isSetId() == true)
   {
     att.add("id", mId);
@@ -1156,14 +1150,14 @@ KeyValuePair::toXML() const
   {
     att.add("uri", mUri);
   }
-
-  XMLToken token = XMLToken(triple, att, xmlns);
-  XMLNode node(token);
-
-  return node;
-}
-
-
+
+  XMLToken token = XMLToken(triple, att, xmlns);
+  XMLNode node(token);
+
+  return node;
+}
+
+
 
 
 #endif /* __cplusplus */