END_TEST
START_TEST (test_Validation_CVTerm2)
{
CVTerm * cv = new CVTerm();
fail_unless(cv != NULL);
fail_unless (!(cv->hasRequiredAttributes()));
cv->setQualifierType(BIOLOGICAL_QUALIFIER);
fail_unless (!(cv->hasRequiredAttributes()));
cv->setBiologicalQualifierType(BQB_IS);
fail_unless (!(cv->hasRequiredAttributes()));
cv->addResource("ggg");
fail_unless ((cv->hasRequiredAttributes()));
delete cv;
}
END_TEST
START_TEST (test_Validation_CVTerm1)
{
CVTerm * cv = new CVTerm();
fail_unless(cv != NULL);
fail_unless (!(cv->hasRequiredAttributes()));
cv->setQualifierType(MODEL_QUALIFIER);
fail_unless (!(cv->hasRequiredAttributes()));
cv->setModelQualifierType(BQM_IS);
fail_unless (!(cv->hasRequiredAttributes()));
cv->addResource("ggg");
fail_unless ((cv->hasRequiredAttributes()));
delete cv;
}
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");
}
}
LIBSBML_CPP_NAMESPACE_USE
int
main (int argc, char *argv[])
{
SBMLDocument* d;
unsigned int errors, n;
Species *s;
if (argc != 3)
{
cout << endl
<< " usage: addCVTerms <input-filename> <output-filename>" << endl
<< " Adds controlled vocabulary term to a species" << 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
{
n = d->getModel()->getNumSpecies();
if (n <= 0)
{
cout << "Model has no species.\n Cannot add CV terms\n";
}
else
{
s = d->getModel()->getSpecies(0);
CVTerm *cv = new CVTerm();
cv->setQualifierType(BIOLOGICAL_QUALIFIER);
cv->setBiologicalQualifierType(BQB_IS_VERSION_OF);
cv->addResource("http://www.geneontology.org/#GO:0005892");
CVTerm *cv2 = new CVTerm();
cv2->setQualifierType(BIOLOGICAL_QUALIFIER);
cv2->setBiologicalQualifierType(BQB_IS);
cv2->addResource("http://www.geneontology.org/#GO:0005895");
CVTerm *cv1 = new CVTerm();
cv1->setQualifierType(BIOLOGICAL_QUALIFIER);
cv1->setBiologicalQualifierType(BQB_IS_VERSION_OF);
cv1->addResource("http://www.ebi.ac.uk/interpro/#IPR002394");
s->addCVTerm(cv);
s->addCVTerm(cv2);
s->addCVTerm(cv1);
writeSBML(d, argv[2]);
}
}
delete d;
return errors;
}