Merge pull request #265 from sbmlteam/relax_annot

Relax annot
sbmlteam · Aug 12, 2022 · 326a82a · 326a82a
2 parents f5788b4 + bc15bea
commit 326a82a
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Showing 11 changed files with 103 additions and 35 deletions.
diff --git a/src/sbml/Model.cpp b/src/sbml/Model.cpp
@@ -4578,7 +4578,7 @@ Model::readOtherXML (XMLInputStream& stream)
     if (RDFAnnotationParser::hasHistoryRDFAnnotation(mAnnotation))
     {
       mHistory = RDFAnnotationParser::parseRDFAnnotation(mAnnotation, 
-                                            getMetaId().c_str(), &(stream));
+                                            getMetaId().c_str(), &(stream), this);
 
       if (mHistory != NULL && mHistory->hasRequiredAttributes() == false)
       {

diff --git a/src/sbml/SBase.cpp b/src/sbml/SBase.cpp
@@ -4712,7 +4712,7 @@ SBase::readAnnotation (XMLInputStream& stream)
       if (RDFAnnotationParser::hasHistoryRDFAnnotation(mAnnotation))
       {
         mHistory = RDFAnnotationParser::parseRDFAnnotation(mAnnotation,
-                                                getMetaId().c_str(), &(stream));
+                                                getMetaId().c_str(), &(stream), this);
         if (mHistory != NULL && mHistory->hasRequiredAttributes() == false)
         {
           logError(RDFNotCompleteModelHistory, getLevel(), getVersion(),

diff --git a/src/sbml/SpeciesReference.cpp b/src/sbml/SpeciesReference.cpp
@@ -1213,7 +1213,7 @@ SpeciesReference::readOtherXML (XMLInputStream& stream)
     if (RDFAnnotationParser::hasHistoryRDFAnnotation(mAnnotation))
     {
       mHistory = RDFAnnotationParser::parseRDFAnnotation(mAnnotation, 
-                                            getMetaId().c_str(), &(stream));
+                                            getMetaId().c_str(), &(stream), this);
 
       if (mHistory != NULL && mHistory->hasRequiredAttributes() == false)
       {

diff --git a/src/sbml/annotation/ModelHistory.cpp b/src/sbml/annotation/ModelHistory.cpp
@@ -55,7 +55,8 @@ LIBSBML_CPP_NAMESPACE_BEGIN
  * Creates a new ModelHistory.
  */
  ModelHistory::ModelHistory ():
-  mHasBeenModified (false)
+  mHasBeenModified (false),
+  mParentSBMLObject (NULL)
 {
   mCreatedDate = NULL;
 //  mModifiedDate = NULL;
@@ -112,6 +113,7 @@ ModelHistory::ModelHistory(const ModelHistory& orig)
     mCreatedDate = NULL;
   }
   mHasBeenModified = orig.mHasBeenModified;
+  mParentSBMLObject = orig.mParentSBMLObject;
 
 }
 
@@ -164,6 +166,7 @@ ModelHistory::operator=(const ModelHistory& rhs)
       mCreatedDate = NULL;
 
     mHasBeenModified = rhs.mHasBeenModified;
+    mParentSBMLObject = rhs.mParentSBMLObject;
   }
 
   return *this;
@@ -373,12 +376,25 @@ bool
 ModelHistory::hasRequiredAttributes()
 {
   bool valid = true;
+
+  const SBase * parent = getParentSBMLObject();
 
-  if ( getNumCreators() < 1 ||
-      !isSetCreatedDate()  ||
-      !isSetModifiedDate() )
+  if (parent == NULL || parent->getLevel() < 3)
+  {
+    if (getNumCreators() < 1 ||
+      !isSetCreatedDate() ||
+      !isSetModifiedDate())
+    {
+      return false;
+    }
+  }
+  else
   {
-    valid = false;
+    // remove restriction that dates be present in L3
+    if (getNumCreators() < 1)
+    {
+      return false;
+    }
   }
 
   unsigned int i = 0;
@@ -394,15 +410,19 @@ ModelHistory::hasRequiredAttributes()
     return valid;
   }
 
-  valid = getCreatedDate()->representsValidDate();
-
-  if (!valid) 
+  if (isSetCreatedDate())
   {
-    return valid;
+    valid = getCreatedDate()->representsValidDate();
+    if (!valid)
+    {
+      return valid;
+    }
   }
-  for (i = 0; i < getNumModifiedDates(); ++i)
+  i = 0;
+  while (valid && i < getNumModifiedDates())
   {
     valid = getModifiedDate(i)->representsValidDate();
+    i++;
   }
 
   return valid;
@@ -466,6 +486,38 @@ ModelHistory::resetModifiedFlags()
 }
 /** @endcond */
 
+/** @cond doxygenLibsbmlInternal */
+
+const SBase * 
+ModelHistory::getParentSBMLObject() const
+{
+  return mParentSBMLObject;
+}
+
+
+bool 
+ModelHistory::isSetParentSBMLObject() const
+{
+  return (mParentSBMLObject != NULL);
+}
+
+
+void 
+ModelHistory::setParentSBMLObject(const SBase * sb)
+{
+  mParentSBMLObject = sb;
+}
+
+
+int 
+ModelHistory::unsetParentSBMLObject()
+{
+  mParentSBMLObject = NULL;
+  return LIBSBML_OPERATION_SUCCESS;
+}
+
+/** @endcond */
+
 
 #endif /* __cplusplus */
 

diff --git a/src/sbml/annotation/ModelHistory.h b/src/sbml/annotation/ModelHistory.h
@@ -385,6 +385,16 @@ class LIBSBML_EXTERN ModelHistory
 
 protected:
   /** @cond doxygenLibsbmlInternal */
+
+  // record the SBML Object on which this ModelHistory is set
+
+  const SBase * getParentSBMLObject() const;
+  bool isSetParentSBMLObject() const;
+  void setParentSBMLObject(const SBase * sb);
+  int unsetParentSBMLObject();
+
+  friend class RDFAnnotationParser;
+
   /* Can have more than one creator. */
 
   List * mCreators;
@@ -400,6 +410,8 @@ class LIBSBML_EXTERN ModelHistory
   List * mModifiedDates;
 
   bool mHasBeenModified;
+  const SBase *mParentSBMLObject;
+
 
 
   /** @endcond */

diff --git a/src/sbml/annotation/RDFAnnotationParser.cpp b/src/sbml/annotation/RDFAnnotationParser.cpp
@@ -248,7 +248,8 @@ ModelHistory*
 RDFAnnotationParser::parseRDFAnnotation(
      const XMLNode * annotation, 
      const char* metaId, 
-     XMLInputStream* stream /*= NULL*/)
+     XMLInputStream* stream /*= NULL*/,
+     const SBase* parent)
 {
   ModelHistory * history = NULL;
 
@@ -310,7 +311,11 @@ RDFAnnotationParser::parseRDFAnnotation(
   {
     history = deriveHistoryFromAnnotation(annotation);
   }
-
+  // add a parent SBase object with level and version
+  if (history != NULL && parent != NULL)
+  {
+    history->setParentSBMLObject(parent);
+  }
   return history;
 }
 
@@ -710,6 +715,7 @@ RDFAnnotationParser::parseModelHistory(const SBase *object)
   {
     return NULL;
   }
+  history->setParentSBMLObject(object);
 
   XMLNode *description = createRDFDescriptionWithHistory(object);
 

diff --git a/src/sbml/annotation/RDFAnnotationParser.h b/src/sbml/annotation/RDFAnnotationParser.h
@@ -139,7 +139,7 @@ class LIBSBML_EXTERN RDFAnnotationParser
    * @return a pointer to the ModelHistory created.
    */
   static ModelHistory* parseRDFAnnotation(const XMLNode *annotation, 
-    const char* metaId = NULL, XMLInputStream* stream = NULL);
+    const char* metaId = NULL, XMLInputStream* stream = NULL, const SBase* parent = NULL);
 
 
   /**

diff --git a/src/sbml/annotation/test/TestRDFAnnotation2.cpp b/src/sbml/annotation/test/TestRDFAnnotation2.cpp
@@ -155,6 +155,8 @@ START_TEST (test_RDFAnnotation2_getModelHistory)
   fail_unless(Date_getHoursOffset(date) == 0);
   fail_unless(Date_getMinutesOffset(date) == 0);
   fail_unless(!strcmp(Date_getDateAsString(date), "2007-01-16T15:31:52Z"));
+
+  fail_unless(ModelHistory_hasRequiredAttributes(history) == 1);
 }
 END_TEST
 

diff --git a/src/sbml/annotation/test/TestRDFAnnotationNestedCVTerms.cpp b/src/sbml/annotation/test/TestRDFAnnotationNestedCVTerms.cpp
@@ -584,6 +584,9 @@ END_TEST
 
 START_TEST (test_RDFAnnotationNestedCVTerm_dcterms_31)
 {
+  ModelHistory * mh = m31->getModelHistory();
+  fail_unless(mh->hasRequiredAttributes() == true);
+
   XMLNode* node = RDFAnnotationParser::parseModelHistory(m31);
 
   fail_unless(node->getNumChildren() == 1);
@@ -600,7 +603,7 @@ START_TEST (test_RDFAnnotationNestedCVTerm_dcterms_31)
   fail_unless(!strcmp(XMLNode_getName(desc), "Description"));
   fail_unless(!strcmp(XMLNode_getPrefix(desc), "rdf"));
   fail_unless(!strcmp(XMLNode_getURI(desc), "http://www.w3.org/1999/02/22-rdf-syntax-ns#"));
-  fail_unless(XMLNode_getNumChildren(desc) == 3);
+  fail_unless(XMLNode_getNumChildren(desc) == 2);
 
   const XMLNode_t * creator = XMLNode_getChild(desc, 0);
   fail_unless(!strcmp(XMLNode_getName(creator), "creator"));
@@ -671,17 +674,17 @@ START_TEST (test_RDFAnnotationNestedCVTerm_dcterms_31)
   fail_unless(!strcmp(XMLNode_getURI(cr_date), "http://purl.org/dc/terms/"));
   fail_unless(XMLNode_getNumChildren(cr_date) == 1);
 
-  const XMLNode_t * modified = XMLNode_getChild(desc, 2);
-  fail_unless(!strcmp(XMLNode_getName(modified), "modified"));
-  fail_unless(!strcmp(XMLNode_getPrefix(modified), "dcterms"));
-  fail_unless(!strcmp(XMLNode_getURI(modified), "http://purl.org/dc/terms/"));
-  fail_unless(XMLNode_getNumChildren(modified) == 1);
+  //const XMLNode_t * modified = XMLNode_getChild(desc, 2);
+  //fail_unless(!strcmp(XMLNode_getName(modified), "modified"));
+  //fail_unless(!strcmp(XMLNode_getPrefix(modified), "dcterms"));
+  //fail_unless(!strcmp(XMLNode_getURI(modified), "http://purl.org/dc/terms/"));
+  //fail_unless(XMLNode_getNumChildren(modified) == 1);
 
-  const XMLNode_t * mo_date = XMLNode_getChild(created, 0);
-  fail_unless(!strcmp(XMLNode_getName(mo_date), "W3CDTF"));
-  fail_unless(!strcmp(XMLNode_getPrefix(mo_date), "dcterms"));
-  fail_unless(!strcmp(XMLNode_getURI(mo_date), "http://purl.org/dc/terms/"));
-  fail_unless(XMLNode_getNumChildren(mo_date) == 1);
+  //const XMLNode_t * mo_date = XMLNode_getChild(created, 0);
+  //fail_unless(!strcmp(XMLNode_getName(mo_date), "W3CDTF"));
+  //fail_unless(!strcmp(XMLNode_getPrefix(mo_date), "dcterms"));
+  //fail_unless(!strcmp(XMLNode_getURI(mo_date), "http://purl.org/dc/terms/"));
+  //fail_unless(XMLNode_getNumChildren(mo_date) == 1);
 
 
   delete node;
@@ -714,9 +717,6 @@ START_TEST(test_RDFAnnotationNestedCVTerm_writeDC_creator_31)
 		"        <dcterms:created rdf:parseType=\"Resource\">\n"
 		"          <dcterms:W3CDTF>2005-02-02T14:56:11</dcterms:W3CDTF>\n"
 		"        </dcterms:created>\n"
-		"        <dcterms:modified rdf:parseType=\"Resource\">\n"
-		"          <dcterms:W3CDTF>2006-05-30T10:46:02</dcterms:W3CDTF>\n"
-		"        </dcterms:modified>\n"
 		"      </rdf:Description>\n"
 		"    </rdf:RDF>\n"
     "  </annotation>\n"

diff --git a/src/sbml/annotation/test/TestValidation.cpp b/src/sbml/annotation/test/TestValidation.cpp
@@ -133,6 +133,7 @@ END_TEST
 
 START_TEST (test_Validation_ModelHistory1)
 {
+
   ModelHistory * mh = new ModelHistory();
   fail_unless(mh != NULL);
 
@@ -157,7 +158,6 @@ START_TEST (test_Validation_ModelHistory1)
 
   delete mh;
   delete mc;
-  delete date;
 }
 END_TEST
 
@@ -222,7 +222,6 @@ START_TEST (test_Validation_ModelHistory3)
 }
 END_TEST
 
-
 START_TEST (test_Validation_CVTerm1)
 {
   CVTerm * cv = new CVTerm();

diff --git a/src/sbml/annotation/test/test-data/annotationNested-l3v1.xml b/src/sbml/annotation/test/test-data/annotationNested-l3v1.xml
@@ -21,9 +21,6 @@
 					<dcterms:created rdf:parseType="Resource">
 						<dcterms:W3CDTF>2005-02-02T14:56:11</dcterms:W3CDTF>
 					</dcterms:created>
-					<dcterms:modified rdf:parseType="Resource">
-						<dcterms:W3CDTF>2006-05-30T10:46:02</dcterms:W3CDTF>
-					</dcterms:modified>
 				</rdf:Description>
 			</rdf:RDF>
 		</annotation>