bool
RDFAnnotationParser::hasHistoryRDFAnnotation(const XMLNode *annotation)
{
bool hasHistoryRDF = false;
if (!RDFAnnotationParser::hasRDFAnnotation(annotation))
{
return hasHistoryRDF;
}
// check whether the annotation relates to Model History
ModelHistory *temp = deriveHistoryFromAnnotation(annotation);
/* ok I relaxed the test so that an invalid model could be stored
* but need to check that it resembles an model history in some
* way otherwise any RDF could be a model history
*/
if (temp != NULL) // && temp->getNumCreators() > 0)
{
if (temp->getNumCreators() > 0
|| temp->isSetCreatedDate() == true
|| temp->isSetModifiedDate() == true )
{
hasHistoryRDF = true;
}
}
delete temp;
return hasHistoryRDF;
}
bool
RDFAnnotationParser::hasHistoryRDFAnnotation(const XMLNode *annotation)
{
bool hasHistoryRDF = false;
if (!RDFAnnotationParser::hasRDFAnnotation(annotation))
{
return hasHistoryRDF;
}
// check whether the annotation relates to Model History
ModelHistory *temp = parseRDFAnnotation(annotation);
if (temp && temp->getNumCreators() > 0)
{
hasHistoryRDF = true;
}
delete temp;
return hasHistoryRDF;
}
/*
* takes a Model creator information
* and creates the RDF annotation
*/
XMLNode *
RDFAnnotationParser::parseModelHistory(const SBase *object)
{
if (object->getLevel() < 3 && object->getTypeCode() != SBML_MODEL)
{
return NULL;
}
ModelHistory * history = object->getModelHistory();
if (history == NULL)
{
return NULL;
}
XMLNode *description = createRDFDescription(object);
/* create the basic triples */
XMLTriple li_triple = XMLTriple("li",
"http://www.w3.org/1999/02/22-rdf-syntax-ns#",
"rdf");
XMLTriple bag_triple = XMLTriple("Bag",
"http://www.w3.org/1999/02/22-rdf-syntax-ns#",
"rdf");
XMLTriple creator_triple = XMLTriple("creator",
"http://purl.org/dc/elements/1.1/",
"dc");
XMLTriple N_triple = XMLTriple("N",
"http://www.w3.org/2001/vcard-rdf/3.0#",
"vCard");
XMLTriple Family_triple = XMLTriple("Family",
"http://www.w3.org/2001/vcard-rdf/3.0#",
"vCard");
XMLTriple Given_triple = XMLTriple("Given",
"http://www.w3.org/2001/vcard-rdf/3.0#",
"vCard");
XMLTriple Email_triple = XMLTriple("EMAIL",
"http://www.w3.org/2001/vcard-rdf/3.0#",
"vCard");
XMLTriple Org_triple = XMLTriple("ORG",
"http://www.w3.org/2001/vcard-rdf/3.0#",
"vCard");
XMLTriple Orgname_triple = XMLTriple("Orgname",
"http://www.w3.org/2001/vcard-rdf/3.0#",
"vCard");
XMLTriple created_triple = XMLTriple("created",
"http://purl.org/dc/terms/",
"dcterms");
XMLTriple modified_triple = XMLTriple("modified",
"http://purl.org/dc/terms/",
"dcterms");
XMLTriple W3CDTF_triple = XMLTriple("W3CDTF",
"http://purl.org/dc/terms/",
"dcterms");
XMLTriple empty_triple = XMLTriple( "", "", "");
/* attributes */
XMLAttributes blank_att = XMLAttributes();
XMLAttributes parseType_att = XMLAttributes();
parseType_att.add("rdf:parseType", "Resource");
/* tokens */
XMLToken bag_token = XMLToken(bag_triple, blank_att);
XMLToken li_token = XMLToken(li_triple, parseType_att);
// for L2V4 it was realised that it was invalid for the creator
// to have a parseType attribute
XMLToken creator_token;
if (object->getLevel() > 2 ||
(object->getLevel() == 2 && object->getVersion() > 3))
{
creator_token = XMLToken(creator_triple, blank_att);
}
else
{
creator_token = XMLToken(creator_triple, parseType_att);
}
XMLToken N_token = XMLToken(N_triple, parseType_att);
XMLToken created_token = XMLToken(created_triple, parseType_att);
XMLToken modified_token = XMLToken(modified_triple, parseType_att);
XMLToken Family_token = XMLToken(Family_triple, blank_att);
XMLToken Given_token = XMLToken(Given_triple, blank_att);
XMLToken Email_token = XMLToken(Email_triple, blank_att);
// for L2V4 it was realised that the VCard:ORG
// should have a parseType attribute
XMLToken Org_token;
if (object->getLevel() > 2 ||
(object->getLevel() == 2 && object->getVersion() > 3))
{
Org_token = XMLToken(Org_triple, parseType_att);
}
else
{
Org_token = XMLToken(Org_triple, blank_att);
}
XMLToken Orgname_token = XMLToken(Orgname_triple, blank_att);
XMLToken W3CDTF1_token = XMLToken(W3CDTF_triple, blank_att);
XMLToken W3CDTF2_token = XMLToken(W3CDTF_triple, blank_att);
XMLToken empty_token = XMLToken("");
/* nodes */
XMLNode bag = XMLNode(bag_token);
XMLNode created = XMLNode(created_token);
XMLNode modified= XMLNode(modified_token);
XMLNode W3CDTF1 = XMLNode(W3CDTF1_token);
XMLNode W3CDTF2 = XMLNode(W3CDTF2_token);
//
// The following XMLNode objects are used only
// in the for loop below (for each ModelCreator object
// in ModelHistory object) and reset in each step.
// Thus, they are defined only in the block in which
// they are used to avoid a memory leak.
//
// XMLNode * N
// XMLNode * Email
// XMLNode * Org
// XMLNode Family;
// XMLNode Given
// XMLNode Orgname
// XMLNode li
//
/* now add the data from the ModelHistory */
for (unsigned int n = 0; n < history->getNumCreators(); n++)
{
XMLNode * N = 0;
XMLNode * Email = 0;
XMLNode * Org = 0;
ModelCreator* c = history->getCreator(n);
if (c->isSetFamilyName())
{
XMLNode empty(empty_token);
empty.append(c->getFamilyName());
XMLNode Family(Family_token);
Family.addChild(empty);
N = new XMLNode(N_token);
N->addChild(Family);
}
if (c->isSetGivenName())
{
XMLNode empty(empty_token);
empty.append(c->getGivenName());
XMLNode Given(Given_token);
Given.addChild(empty);
if (!N)
{
N = new XMLNode(N_token);
}
N->addChild(Given);
}
if (c->isSetEmail())
{
XMLNode empty(empty_token);
empty.append(c->getEmail());
Email = new XMLNode(Email_token);
Email->addChild(empty);
}
if (c->isSetOrganisation())
{
XMLNode empty(empty_token);
empty.append(c->getOrganisation());
XMLNode Orgname(Orgname_token);
Orgname.addChild(empty);
Org = new XMLNode(Org_token);
Org->addChild(Orgname);
}
XMLNode li(li_token);
if (N)
{
li.addChild(*N);
delete N;
}
if (Email)
{
li.addChild(*Email);
delete Email;
}
if (Org)
{
li.addChild(*Org);
delete Org;
}
if (c->getAdditionalRDF())
{
li.addChild(*(c->getAdditionalRDF()));
}
bag.addChild(li);
}
XMLNode creator(creator_token);
creator.addChild(bag);
description->addChild(creator);
/* created date */
if (history->isSetCreatedDate())
{
XMLNode empty(empty_token);
empty.append(history->getCreatedDate()->getDateAsString());
W3CDTF1.addChild(empty);
created.addChild(W3CDTF1);
description->addChild(created);
}
/* modified date */
if (history->isSetModifiedDate())
{
XMLNode empty(empty_token);
empty.append(history->getModifiedDate(0)->getDateAsString());
W3CDTF2.addChild(empty);
modified.addChild(W3CDTF2);
description->addChild(modified);
for (unsigned int n = 1; n < history->getNumModifiedDates(); n++)
{
XMLNode empty(empty_token);
W3CDTF2.removeChildren();
modified.removeChildren();
empty.append(history->getModifiedDate(n)->getDateAsString());
W3CDTF2.addChild(empty);
modified.addChild(W3CDTF2);
description->addChild(modified);
}
}
// add CVTerms here
XMLNode *CVTerms = createCVTerms(object);
if (CVTerms)
{
for (unsigned int i = 0; i < CVTerms->getNumChildren(); i++)
{
description->addChild(CVTerms->getChild(i));
}
delete CVTerms;
}
XMLNode * RDF = createRDFAnnotation();
RDF->addChild(*description);
delete description;
XMLNode *ann = createAnnotation();
ann->addChild(*RDF);
delete RDF;
return ann;
}