public void test_Validation_CVTerm2()
{
CVTerm cv = new CVTerm();
assertTrue( cv != null );
assertEquals( false, (cv.hasRequiredAttributes()) );
cv.setQualifierType(libsbml.BIOLOGICAL_QUALIFIER);
assertEquals( false, (cv.hasRequiredAttributes()) );
cv.setBiologicalQualifierType(libsbml.BQB_IS);
assertEquals( false, (cv.hasRequiredAttributes()) );
cv.addResource("ggg");
assertEquals( true, (cv.hasRequiredAttributes()) );
cv = null;
}
public void test_Validation_CVTerm1()
{
CVTerm cv = new CVTerm();
assertTrue( cv != null );
assertEquals( false, (cv.hasRequiredAttributes()) );
cv.setQualifierType(libsbml.MODEL_QUALIFIER);
assertEquals( false, (cv.hasRequiredAttributes()) );
cv.setModelQualifierType(libsbml.BQM_IS);
assertEquals( false, (cv.hasRequiredAttributes()) );
cv.addResource("ggg");
assertEquals( true, (cv.hasRequiredAttributes()) );
cv = null;
}
public void test_CVTerm_set_get()
{
CVTerm term = new CVTerm(libsbml.MODEL_QUALIFIER);
assertTrue( term != null );
assertTrue( term.getQualifierType() == libsbml.MODEL_QUALIFIER );
term.setModelQualifierType(libsbml.BQM_IS);
assertTrue( term != null );
assertTrue( term.getQualifierType() == libsbml.MODEL_QUALIFIER );
assertTrue( term.getModelQualifierType() == libsbml.BQM_IS );
term.setQualifierType(libsbml.BIOLOGICAL_QUALIFIER);
term.setBiologicalQualifierType(libsbml.BQB_IS);
assertTrue( term.getQualifierType() == libsbml.BIOLOGICAL_QUALIFIER );
assertTrue( term.getBiologicalQualifierType() == libsbml.BQB_IS );
term = null;
}
public static int Main(string[] args)
{
SBMLDocument d;
long errors, n;
Species s;
if (args.Length != 2)
{
Console.WriteLine(" usage: addCVTerms <input-filename> <output-filename>");
Console.WriteLine(" Adds controlled vocabulary term to a species");
return 2;
}
d = libsbml.readSBML(args[0]);
errors = d.getNumErrors();
if (errors > 0)
{
Console.WriteLine("Read Error(s):");
d.printErrors();
Console.WriteLine("Correct the above and re-run.");
}
else
{
n = d.getModel().getNumSpecies();
if (n <= 0)
{
Console.WriteLine("Model has no species.\n Cannot add CV terms\n");
}
else
{
s = d.getModel().getSpecies(0);
CVTerm cv = new CVTerm();
cv.setQualifierType(libsbml.BIOLOGICAL_QUALIFIER);
cv.setBiologicalQualifierType(libsbml.BQB_IS_VERSION_OF);
cv.addResource("http://www.geneontology.org/#GO:0005892");
CVTerm cv2 = new CVTerm();
cv2.setQualifierType(libsbml.BIOLOGICAL_QUALIFIER);
cv2.setBiologicalQualifierType(libsbml.BQB_IS);
cv2.addResource("http://www.geneontology.org/#GO:0005895");
CVTerm cv1 = new CVTerm();
cv1.setQualifierType(libsbml.BIOLOGICAL_QUALIFIER);
cv1.setBiologicalQualifierType(libsbml.BQB_IS_VERSION_OF);
cv1.addResource("http://www.ebi.ac.uk/interpro/#IPR002394");
s.addCVTerm(cv);
s.addCVTerm(cv2);
s.addCVTerm(cv1);
libsbml.writeSBML(d, args[1]);
}
}
return (int)errors;
}
public void test_CVTerm_setBiolQualifierType()
{
CVTerm term = new CVTerm(libsbml.BIOLOGICAL_QUALIFIER);
assertTrue( term != null );
assertTrue( term.getQualifierType() == libsbml.BIOLOGICAL_QUALIFIER );
assertTrue( term.getModelQualifierType() == libsbml.BQM_UNKNOWN );
assertTrue( term.getBiologicalQualifierType() == libsbml.BQB_UNKNOWN );
int i = term.setBiologicalQualifierType(libsbml.BQB_IS);
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
assertTrue( term.getQualifierType() == libsbml.BIOLOGICAL_QUALIFIER );
assertTrue( term.getBiologicalQualifierType() == libsbml.BQB_IS );
assertTrue( term.getModelQualifierType() == libsbml.BQM_UNKNOWN );
i = term.setQualifierType(libsbml.MODEL_QUALIFIER);
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
assertTrue( term.getQualifierType() == libsbml.MODEL_QUALIFIER );
assertTrue( term.getModelQualifierType() == libsbml.BQM_UNKNOWN );
assertTrue( term.getBiologicalQualifierType() == libsbml.BQB_UNKNOWN );
i = term.setBiologicalQualifierType(libsbml.BQB_IS);
assertTrue( i == libsbml.LIBSBML_INVALID_ATTRIBUTE_VALUE );
assertTrue( term.getQualifierType() == libsbml.MODEL_QUALIFIER );
assertTrue( term.getModelQualifierType() == libsbml.BQM_UNKNOWN );
assertTrue( term.getBiologicalQualifierType() == libsbml.BQB_UNKNOWN );
term = null;
}
public void 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(libsbml.BIOLOGICAL_QUALIFIER);
cv.setBiologicalQualifierType(libsbml.BQB_IS_VERSION_OF);
cv.addResource("http://www.geneontology.org/#GO:0005892");
m2.addCVTerm(cv);
XMLNode ann = RDFAnnotationParser.parseModelHistory(m2);
string 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);
{
assertEquals( true, equals(expected,ann.toXMLString()) );
}
{
}
}