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;
}
Esempio n. 2
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/*
 * 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;
}