#429 : ensure that annotations / notes of kvps are written

Author: fbergmann

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

@@ -432,10 +432,18 @@ START_TEST(test_FbcExtension_create_and_write_L3V1V3)
   // check annotations on several types
   FbcSBasePlugin* sbaseplugin = dynamic_cast<FbcSBasePlugin*>(compartment->getPlugin("fbc"));
 
+  auto* term = new CVTerm();
+  term->setQualifierType(BIOLOGICAL_QUALIFIER);
+  term->setBiologicalQualifierType(BQB_IS);
+  term->addResource("MyResourceThatWillBeWrittenAndRead");
+
   KeyValuePair * kvp = sbaseplugin->createKeyValuePair();
   kvp->setKey("key");
   kvp->setUri("my_annotation");
   kvp->setValue("comp-value");
+  kvp->setMetaId("metaid_kvp");
+
+  kvp->addCVTerm(term);
 
   FbcSBasePlugin* sbaseplugin1 = dynamic_cast<FbcSBasePlugin*>(species->getPlugin("fbc"));
 
@@ -471,14 +479,17 @@ START_TEST(test_FbcExtension_create_and_write_L3V1V3)
   string s1 = writeSBMLToStdString(document);
 
   //cout << s1 << endl;
+  fail_unless(s1.find("MyResourceThatWillBeWrittenAndRead") != string::npos);
 
   char *filename = safe_strcat(TestDataDirectory, "fbc_example2_v3.xml");
   SBMLDocument *document1 = readSBMLFromFile(filename);
   string s2 = writeSBMLToStdString(document1);
+  fail_unless(s2.find("MyResourceThatWillBeWrittenAndRead") != string::npos);
 
   //cout << endl << s2 << endl;
   fail_unless(s1 == s2);
 
+
   delete sbmlns;
   delete document;
   delete document1;

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

@@ -10,7 +10,19 @@
       <compartment id="comp" spatialDimensions="3" size="1" constant="true">
         <annotation>
           <listOfKeyValuePairs xmlns="http://sbml.org/fbc/keyvaluepair">
-            <keyValuePair key="key" value="comp-value" uri="my_annotation"/>
+            <keyValuePair key="key" value="comp-value" uri="my_annotation">
+              <annotation>
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+                  <rdf:Description rdf:about="#metaid_kvp">
+                    <bqbiol:is>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="MyResourceThatWillBeWrittenAndRead"/>
+                      </rdf:Bag>
+                    </bqbiol:is>
+                  </rdf:Description>
+                </rdf:RDF>
+              </annotation>
+            </keyValuePair>
           </listOfKeyValuePairs>
         </annotation>
       </compartment>

src/sbml/packages/fbc/sbml/KeyValuePair.cpp

@@ -1144,6 +1144,11 @@ KeyValuePair::toXML() const
   XMLToken token = XMLToken(triple, att, xmlns);
   XMLNode node(token);
 
+  if(mNotes) node.addChild(*this->mNotes);
+  const_cast <KeyValuePair *> (this)->syncAnnotation();
+  if(mAnnotation) node.addChild(*this->mAnnotation);  
+
+
   return node;
 }