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;
}
int
main (int argc, char *argv[])
{
SBMLDocument* d;
unsigned int errors;
if (argc != 3)
{
cout << endl
<< " usage: addModelHistory <input-filename> <output-filename>" << endl
<< endl;
return 2;
}
d = readSBML(argv[1]);
errors = d->getNumErrors();
if (errors > 0)
{
cout << "Read Error(s):" << endl;
d->printErrors(cout);
cout << "Correct the above and re-run." << endl;
}
else
{
ModelHistory * h = new ModelHistory();
ModelCreator *c = new ModelCreator();
c->setFamilyName("Keating");
c->setGivenName("Sarah");
c->setEmail("*****@*****.**");
c->setOrganization("University of Hertfordshire");
int status = h->addCreator(c);
printStatus("Status for addCreator: ", status);
Date * date = new Date("1999-11-13T06:54:32");
Date * date2 = new Date("2007-11-30T06:54:00-02:00");
status = h->setCreatedDate(date);
printStatus("Set created date: ", status);
status = h->setModifiedDate(date2);
printStatus("Set modified date: ", status);
status = d->getModel()->setModelHistory(h);
printStatus("Set model history: ", status);
writeSBML(d, argv[2]);
}
delete d;
return errors;
}
END_TEST
START_TEST (test_RDFAnnotation2_modelWithHistoryAndMultipleModifiedDates)
{
ModelHistory * h = new ModelHistory();
ModelCreator *c = new ModelCreator();
c->setFamilyName("Keating");
c->setGivenName("Sarah");
h->addCreator(c);
Date * d = new Date(2005, 2, 2, 14, 56, 11);
h->setCreatedDate(d);
h->addModifiedDate(d);
h->addModifiedDate(d);
m2->unsetModelHistory();
m2->setModelHistory(h);
XMLNode *ann = RDFAnnotationParser::parseModelHistory(m2);
const char * expected =
"<annotation>\n"
" <rdf:RDF xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" xmlns:dc=\"http://purl.org/dc/elements/1.1/\" xmlns:dcterms=\"http://purl.org/dc/terms/\" xmlns:vCard=\"http://www.w3.org/2001/vcard-rdf/3.0#\" xmlns:bqbiol=\"http://biomodels.net/biology-qualifiers/\" xmlns:bqmodel=\"http://biomodels.net/model-qualifiers/\">\n"
" <rdf:Description rdf:about=\"#_000001\">\n"
" <dc:creator rdf:parseType=\"Resource\">\n"
" <rdf:Bag>\n"
" <rdf:li rdf:parseType=\"Resource\">\n"
" <vCard:N rdf:parseType=\"Resource\">\n"
" <vCard:Family>Keating</vCard:Family>\n"
" <vCard:Given>Sarah</vCard:Given>\n"
" </vCard:N>\n"
" </rdf:li>\n"
" </rdf:Bag>\n"
" </dc:creator>\n"
" <dcterms:created rdf:parseType=\"Resource\">\n"
" <dcterms:W3CDTF>2005-02-02T14:56:11Z</dcterms:W3CDTF>\n"
" </dcterms:created>\n"
" <dcterms:modified rdf:parseType=\"Resource\">\n"
" <dcterms:W3CDTF>2005-02-02T14:56:11Z</dcterms:W3CDTF>\n"
" </dcterms:modified>\n"
" <dcterms:modified rdf:parseType=\"Resource\">\n"
" <dcterms:W3CDTF>2005-02-02T14:56:11Z</dcterms:W3CDTF>\n"
" </dcterms:modified>\n"
" </rdf:Description>\n"
" </rdf:RDF>\n"
"</annotation>";
fail_unless( equals(expected, ann->toXMLString().c_str()) );
delete c;
delete d;
delete h;
delete ann;
}
END_TEST
START_TEST (test_Validation_ModelHistory3)
{
ModelHistory * mh = new ModelHistory();
fail_unless(mh != NULL);
fail_unless (!(mh->hasRequiredAttributes()));
Date * date = new Date(2007, 12, 30, 12, 15, 45, 1, 2, 0);
mh->setCreatedDate(date);
fail_unless (!(mh->hasRequiredAttributes()));
mh->setModifiedDate(date);
fail_unless (!(mh->hasRequiredAttributes()));
ModelCreator * mc = new ModelCreator();
mc->setFamilyName("Keating");
mh->addCreator(mc);
fail_unless (!(mh->hasRequiredAttributes()));
delete mh;
}
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;
}
END_TEST
START_TEST ( test_ModelHistory_copyConstructor )
{
ModelHistory * mh = new ModelHistory();
ModelCreator *mc = new ModelCreator();
mc->setFamilyName("Keating");
mc->setGivenName("Sarah");
mc->setEmail("*****@*****.**");
mh->addCreator(mc);
delete mc;
Date * date = new Date(2005, 12, 30, 12, 15, 45, 1, 2, 0);
mh->setCreatedDate(date);
delete date;
fail_unless(mh->getCreatedDate()->getMonth() == 12);
fail_unless(mh->getCreatedDate()->getSecond() == 45);
fail_unless(static_cast <ModelCreator*>
(mh->getListCreators()->get(0))->getFamilyName() == "Keating");
ModelHistory* mh2=new ModelHistory(*mh);
fail_unless(mh2->getCreatedDate()->getMonth() == 12);
fail_unless(mh2->getCreatedDate()->getSecond() == 45);
fail_unless(static_cast <ModelCreator*>(mh2->getListCreators()->get(0))->getFamilyName() == "Keating");
delete mh2;
delete mh;
}
/*
* 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;
}
ModelHistory*
RDFAnnotationParser::parseRDFAnnotation(const XMLNode * annotation)
{
const string& name = annotation->getName();
const XMLNode* RDFTop = NULL;
ModelHistory * history = NULL;
ModelCreator* creator = NULL;
Date * modified = NULL;
Date * created = NULL;
unsigned int n = 0;
// need to find the RDF description opening annotation
if (!name.empty())
{
if (name == "annotation" && annotation->getNumChildren() > 0)
{
while (n < annotation->getNumChildren())
{
const string &name1 = annotation->getChild(n).getName();
if (!name1.empty())
{
if (name1 == "RDF")
{
if (annotation->getChild(n).getNumChildren() > 0)
{
RDFTop = &(annotation->getChild(n).getChild(0));
break;
}
}
}
n++;
}
}
}
// find creation nodes and create history
n = 0;
if (RDFTop)
{
history = new ModelHistory();
while (n < RDFTop->getNumChildren())
{
const string &prefix = RDFTop->getChild(n).getPrefix();
if (!prefix.empty())
{
if (prefix == "dc")
{
// this should be the Bag node containing the list of creators
const XMLNode *creatorNode = &(RDFTop->getChild(n).getChild(0));
for (unsigned int c = 0; c < creatorNode->getNumChildren(); c++)
{
creator = new ModelCreator(creatorNode->getChild(c));
history->addCreator(creator);
delete creator;
}
}
else if (prefix == "dcterms")
{
const string &name2 = RDFTop->getChild(n).getName();
if (!name2.empty())
{
if (RDFTop->getChild(n).getNumChildren() > 0
&& RDFTop->getChild(n).getChild(0).getNumChildren() > 0)
{
if (name2 == "created")
{
created = new Date(RDFTop->getChild(n).getChild(0).
getChild(0).getCharacters());
history->setCreatedDate(created);
delete created;
}
else if (name2 == "modified")
{
modified = new Date(RDFTop->getChild(n).getChild(0).
getChild(0).getCharacters());
history->addModifiedDate(modified);
delete modified;
}
}
}
}
}
n++;
}
}
return history;
}
END_TEST
START_TEST (test_RDFAnnotation2_modelWithHistoryAndCVTerms)
{
ModelHistory * h = new ModelHistory();
ModelCreator *c = new ModelCreator();
c->setFamilyName("Keating");
c->setGivenName("Sarah");
h->addCreator(c);
Date *d = new Date(2008, 11, 17, 18, 37, 0, 0, 0, 0);
h->setCreatedDate(d);
h->setModifiedDate(d);
m2->unsetModelHistory();
m2->setModelHistory(h);
CVTerm *cv = new CVTerm();
cv->setQualifierType(BIOLOGICAL_QUALIFIER);
cv->setBiologicalQualifierType(BQB_IS_VERSION_OF);
cv->addResource("http://www.geneontology.org/#GO:0005892");
m2->addCVTerm(cv);
XMLNode *ann = RDFAnnotationParser::parseModelHistory(m2);
const char * expected =
"<annotation>\n"
" <rdf:RDF xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" xmlns:dc=\"http://purl.org/dc/elements/1.1/\" xmlns:dcterms=\"http://purl.org/dc/terms/\" xmlns:vCard=\"http://www.w3.org/2001/vcard-rdf/3.0#\" xmlns:bqbiol=\"http://biomodels.net/biology-qualifiers/\" xmlns:bqmodel=\"http://biomodels.net/model-qualifiers/\">\n"
" <rdf:Description rdf:about=\"#_000001\">\n"
" <dc:creator rdf:parseType=\"Resource\">\n"
" <rdf:Bag>\n"
" <rdf:li rdf:parseType=\"Resource\">\n"
" <vCard:N rdf:parseType=\"Resource\">\n"
" <vCard:Family>Keating</vCard:Family>\n"
" <vCard:Given>Sarah</vCard:Given>\n"
" </vCard:N>\n"
" </rdf:li>\n"
" </rdf:Bag>\n"
" </dc:creator>\n"
" <dcterms:created rdf:parseType=\"Resource\">\n"
" <dcterms:W3CDTF>2008-11-17T18:37:00Z</dcterms:W3CDTF>\n"
" </dcterms:created>\n"
" <dcterms:modified rdf:parseType=\"Resource\">\n"
" <dcterms:W3CDTF>2008-11-17T18:37:00Z</dcterms:W3CDTF>\n"
" </dcterms:modified>\n"
" <bqbiol:isVersionOf>\n"
" <rdf:Bag>\n"
" <rdf:li rdf:resource=\"http://www.geneontology.org/#GO:0005892\"/>\n"
" </rdf:Bag>\n"
" </bqbiol:isVersionOf>\n"
" </rdf:Description>\n"
" </rdf:RDF>\n"
"</annotation>";
if (ann != NULL)
{
fail_unless( equals(expected, ann->toXMLString().c_str()) );
}
else
{
fail("parseModelHistory failed");
}
}
ModelHistory*
RDFAnnotationParser::deriveHistoryFromAnnotation(
const XMLNode * annotation)
{
ModelHistory * history = NULL;
if (annotation == NULL)
return history;
// the annotation passed in may have a toplevel annotation tag BUT
// it may not be- so need to check
// if it isnt then it must be RDF or we do not have an rdf annotation
bool topLevelIsAnnotation = false;
if (annotation->getName() == "annotation")
{
topLevelIsAnnotation = true;
}
const XMLNode* RDFDesc = NULL;
if (topLevelIsAnnotation == true)
{
RDFDesc = &(annotation->getChild("RDF").getChild("Description"));
}
else
{
if (annotation->getName() == "RDF")
{
RDFDesc = &(annotation->getChild("Description"));
}
}
ModelCreator* creator = NULL;
Date * modified = NULL;
Date * created = NULL;
static const XMLNode outOfRange;
// find creation nodes and create history
if (RDFDesc != NULL)
{
history = new ModelHistory();
const XMLNode *creatorNode = &(RDFDesc->getChild("creator").getChild("Bag"));
if (creatorNode->equals(outOfRange) == false)
{
for (unsigned int c = 0; c < creatorNode->getNumChildren(); c++)
{
creator = new ModelCreator(creatorNode->getChild(c));
history->addCreator(creator);
delete creator;
}
}
const XMLNode *createdNode = &(RDFDesc->getChild("created").getChild("W3CDTF"));
if (createdNode->equals(outOfRange) == false)
{
if (createdNode->getChild(0).isText() == true)
{
created = new Date(createdNode->getChild(0).getCharacters());
history->setCreatedDate(created);
delete created;
}
}
/* there are possibly more than one modified elements */
for (unsigned int n = 0; n < RDFDesc->getNumChildren(); n++)
{
if (RDFDesc->getChild(n).getName() == "modified")
{
const XMLNode *modifiedNode = &(RDFDesc->getChild(n).getChild("W3CDTF"));
if (modifiedNode->equals(outOfRange) == false)
{
if (modifiedNode->getChild(0).isText() == true)
{
modified = new Date(modifiedNode->getChild(0).getCharacters());
history->addModifiedDate(modified);
delete modified;
}
}
}
}
history->resetModifiedFlags();
}
return history;
}