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;
}
term1.setValue(DataValue(0.4));
TEST_EQUAL(term1 != term2, true)
term2.setValue(DataValue(0.4));
TEST_EQUAL(term1 != term2, false)
term1.setUnit(CVTerm::Unit("u_acc", "u_name", "u_cv_ref"));
TEST_EQUAL(term1 != term2, true)
term2.setUnit(CVTerm::Unit("u_acc", "u_name", "u_cv_ref"));
TEST_EQUAL(term1 != term2, false)
}
END_SECTION
START_SECTION((bool hasValue() const ))
{
CVTerm term;
TEST_EQUAL(term.hasValue(), false)
term.setValue(DataValue(0.5));
TEST_EQUAL(term.hasValue(), true)
}
END_SECTION
START_SECTION((bool hasUnit() const ))
{
CVTerm term;
TEST_EQUAL(term.hasUnit(), false)
term.setUnit(CVTerm::Unit("u_acc", "u_name", "u_cv_ref"));
TEST_EQUAL(term.hasUnit(), true)
}
END_SECTION
XMLNode *
RDFAnnotationParser::createCVTerms(const SBase * object)
{
if (object == NULL) return NULL;
/* 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");
/* attributes */
XMLAttributes blank_att = XMLAttributes();
/* tokens */
XMLToken bag_token = XMLToken(bag_triple, blank_att);
std::string prefix;
std::string name;
std::string uri;
XMLAttributes *resources;
XMLNode *description = createRDFDescription(object);
/* loop through the cv terms and add */
/* want to add these in blocks of same qualifier */
if (object->getCVTerms())
{
for (unsigned int n = 0; n < object->getCVTerms()->getSize(); n++)
{
CVTerm* current = static_cast <CVTerm *> (object->getCVTerms()->get(n));
if (current == NULL) continue;
if (current->getQualifierType() == MODEL_QUALIFIER)
{
prefix = "bqmodel";
uri = "http://biomodels.net/model-qualifiers/";
const char* term = ModelQualifierType_toString(
current->getModelQualifierType());
if (term == NULL) return NULL;
name = term;
}
else if (current
->getQualifierType() == BIOLOGICAL_QUALIFIER)
{
prefix = "bqbiol";
uri = "http://biomodels.net/biological-qualifiers/";
const char* term = BiolQualifierType_toString(
current->getBiologicalQualifierType());
if (term == NULL) return NULL;
name = term;
}
else
{
continue;
}
resources = current->getResources();
XMLNode bag(bag_token);
for (int r = 0; r < resources->getLength(); r++)
{
XMLAttributes att;
att.add(resources->getName(r), resources->getValue(r));
XMLToken li_token(li_triple, att);
li_token.setEnd();
XMLNode li(li_token);
bag.addChild(li);
}
XMLTriple type_triple(name, uri, prefix);
XMLToken type_token(type_triple, blank_att);
XMLNode type(type_token);
type.addChild(bag);
description->addChild(type);
}
}
return description;
}
