public void test_SBase_addCVTerms()
{
CVTerm cv = new CVTerm(libsbml.BIOLOGICAL_QUALIFIER);
cv.setBiologicalQualifierType(libsbml.BQB_ENCODES);
cv.addResource( "foo");
int i = S.addCVTerm(cv);
assertTrue( i == libsbml.LIBSBML_UNEXPECTED_ATTRIBUTE );
assertTrue( S.getNumCVTerms() == 0 );
S.setMetaId( "_id");
i = S.addCVTerm(cv);
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
assertTrue( S.getNumCVTerms() == 1 );
assertTrue( S.getCVTerms() != null );
i = S.addCVTerm(null);
assertTrue( i == libsbml.LIBSBML_OPERATION_FAILED );
assertTrue( S.getNumCVTerms() == 1 );
assertTrue( S.getCVTerms() != null );
CVTerm cv2 = new CVTerm(libsbml.MODEL_QUALIFIER);
i = S.addCVTerm(cv2);
assertTrue( i == libsbml.LIBSBML_INVALID_OBJECT );
assertTrue( S.getNumCVTerms() == 1 );
assertTrue( S.getCVTerms() != null );
cv = null;
cv2 = null;
}
public void test_CVTerm_addResource()
{
CVTerm term = new CVTerm(libsbml.MODEL_QUALIFIER);
string resource = "GO6666";
XMLAttributes xa;
assertTrue( term != null );
assertTrue( term.getQualifierType() == libsbml.MODEL_QUALIFIER );
int i = term.addResource( "");
assertTrue( i == libsbml.LIBSBML_OPERATION_FAILED );
xa = term.getResources();
assertTrue( xa.getLength() == 0 );
i = term.addResource(resource);
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
xa = term.getResources();
assertTrue( xa.getLength() == 1 );
assertTrue(( "rdf:resource" == xa.getName(0) ));
assertTrue(( "GO6666" == xa.getValue(0) ));
term = null;
}
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_copyConstructor()
{
CVTerm CVTerm1 = new CVTerm(libsbml.BIOLOGICAL_QUALIFIER);
CVTerm1.addResource("http://www.geneontology.org/#GO:0005892");
assertTrue( CVTerm1.getQualifierType() == libsbml.BIOLOGICAL_QUALIFIER );
assertTrue( CVTerm1.getResources().getLength() == 1 );
assertTrue( CVTerm1.getResources().getValue(0) == "http://www.geneontology.org/#GO:0005892" );
CVTerm CVTerm2 = new CVTerm(CVTerm1);
assertTrue( CVTerm2.getQualifierType() == libsbml.BIOLOGICAL_QUALIFIER );
assertTrue( CVTerm2.getResources().getLength() == 1 );
assertTrue( CVTerm2.getResources().getValue(0) == "http://www.geneontology.org/#GO:0005892" );
CVTerm2 = null;
CVTerm1 = null;
}
public void test_SBase_addCVTerms()
{
CVTerm cv = new CVTerm(libsbml.BIOLOGICAL_QUALIFIER);
cv.setBiologicalQualifierType(libsbml.BQB_ENCODES);
cv.addResource( "foo");
S.setMetaId( "sbase1");
S.addCVTerm(cv);
assertTrue( S.getNumCVTerms() == 1 );
assertTrue( S.getCVTerms() != null );
XMLAttributes res = S.getCVTerm(0).getResources();
assertTrue(( "foo" == res.getValue(0) ));
CVTerm cv1 = new CVTerm(libsbml.BIOLOGICAL_QUALIFIER);
cv1.setBiologicalQualifierType(libsbml.BQB_IS);
cv1.addResource( "bar");
S.addCVTerm(cv1);
assertTrue( S.getNumCVTerms() == 2 );
CVTerm cv2 = new CVTerm(libsbml.BIOLOGICAL_QUALIFIER);
cv2.setBiologicalQualifierType(libsbml.BQB_IS);
cv2.addResource( "bar1");
S.addCVTerm(cv2);
assertTrue( S.getNumCVTerms() == 2 );
res = S.getCVTerm(1).getResources();
assertTrue( res.getLength() == 2 );
assertTrue(( "bar" == res.getValue(0) ));
assertTrue(( "bar1" == res.getValue(1) ));
CVTerm cv4 = new CVTerm(libsbml.BIOLOGICAL_QUALIFIER);
cv4.setBiologicalQualifierType(libsbml.BQB_IS);
cv4.addResource( "bar1");
S.addCVTerm(cv4);
assertTrue( S.getNumCVTerms() == 2 );
res = S.getCVTerm(1).getResources();
assertTrue( res.getLength() == 2 );
assertTrue(( "bar" == res.getValue(0) ));
assertTrue(( "bar1" == res.getValue(1) ));
CVTerm cv5 = new CVTerm(libsbml.BIOLOGICAL_QUALIFIER);
cv5.setBiologicalQualifierType(libsbml.BQB_HAS_PART);
cv5.addResource( "bar1");
S.addCVTerm(cv5);
assertTrue( S.getNumCVTerms() == 2 );
res = S.getCVTerm(1).getResources();
assertTrue( res.getLength() == 2 );
assertTrue(( "bar" == res.getValue(0) ));
assertTrue(( "bar1" == res.getValue(1) ));
cv = null;
cv2 = null;
cv1 = null;
cv4 = null;
}
public void test_CVTerm_removeResource()
{
CVTerm term = new CVTerm(libsbml.MODEL_QUALIFIER);
string resource = "GO6666";
XMLAttributes xa;
assertTrue( term != null );
assertTrue( term.getQualifierType() == libsbml.MODEL_QUALIFIER );
term.addResource(resource);
xa = term.getResources();
assertTrue( xa.getLength() == 1 );
int i = term.removeResource( "CCC");
assertTrue( i == libsbml.LIBSBML_INVALID_ATTRIBUTE_VALUE );
xa = term.getResources();
assertTrue( xa.getLength() == 1 );
i = term.removeResource(resource);
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
xa = term.getResources();
assertTrue( xa.getLength() == 0 );
term = null;
}
public void test_SBase_unsetCVTerms()
{
CVTerm cv = new CVTerm(libsbml.BIOLOGICAL_QUALIFIER);
cv.setBiologicalQualifierType(libsbml.BQB_ENCODES);
cv.addResource( "foo");
S.setMetaId( "sbase1");
S.addCVTerm(cv);
CVTerm cv1 = new CVTerm(libsbml.BIOLOGICAL_QUALIFIER);
cv1.setBiologicalQualifierType(libsbml.BQB_IS);
cv1.addResource( "bar");
S.addCVTerm(cv1);
CVTerm cv2 = new CVTerm(libsbml.BIOLOGICAL_QUALIFIER);
cv2.setBiologicalQualifierType(libsbml.BQB_IS);
cv2.addResource( "bar1");
S.addCVTerm(cv2);
CVTerm cv4 = new CVTerm(libsbml.BIOLOGICAL_QUALIFIER);
cv4.setBiologicalQualifierType(libsbml.BQB_IS);
cv4.addResource( "bar1");
S.addCVTerm(cv4);
assertTrue( S.getNumCVTerms() == 2 );
S.unsetCVTerms();
assertTrue( S.getNumCVTerms() == 0 );
assertTrue( S.getCVTerms() == null );
cv = null;
cv2 = null;
cv1 = null;
cv4 = null;
}
public void test_SBase_unsetAnnotationWithCVTerms()
{
CVTerm cv;
string annt = "<annotation>\n" +
" <test:test xmlns:test=\"http://test.org/test\">this is a test node</test:test>\n" +
"</annotation>";
string annt_with_cvterm = "<annotation>\n" +
" <test:test xmlns:test=\"http://test.org/test\">this is a test node</test:test>\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" +
" <bqbiol:is>\n" +
" <rdf:Bag>\n" +
" <rdf:li rdf:resource=\"http://www.geneontology.org/#GO:0005895\"/>\n" +
" </rdf:Bag>\n" +
" </bqbiol:is>\n" +
" </rdf:Description>\n" +
" </rdf:RDF>\n" +
"</annotation>";
S.setAnnotation(annt);
assertTrue( S.isSetAnnotation() == true );
assertTrue(( annt == S.getAnnotationString() ));
S.unsetAnnotation();
assertTrue( S.isSetAnnotation() == false );
assertTrue( S.getAnnotation() == null );
S.setAnnotation(annt);
S.setMetaId( "_000001");
cv = new CVTerm(libsbml.BIOLOGICAL_QUALIFIER);
cv.setBiologicalQualifierType(libsbml.BQB_IS);
cv.addResource( "http://www.geneontology.org/#GO:0005895");
S.addCVTerm(cv);
assertTrue( S.isSetAnnotation() == true );
assertTrue(( annt_with_cvterm == S.getAnnotationString() ));
S.unsetAnnotation();
assertTrue( S.isSetAnnotation() == false );
assertTrue( S.getAnnotation() == null );
cv = null;
}
public void test_SBase_getQualifiersFromResources()
{
CVTerm cv = new CVTerm(libsbml.BIOLOGICAL_QUALIFIER);
cv.setBiologicalQualifierType(libsbml.BQB_ENCODES);
cv.addResource( "foo");
S.setMetaId( "sbase1");
S.addCVTerm(cv);
assertTrue( S.getResourceBiologicalQualifier( "foo") == libsbml.BQB_ENCODES );
CVTerm cv1 = new CVTerm(libsbml.MODEL_QUALIFIER);
cv1.setModelQualifierType(libsbml.BQM_IS);
cv1.addResource( "bar");
S.addCVTerm(cv1);
assertTrue( S.getResourceModelQualifier( "bar") == libsbml.BQM_IS );
cv = null;
cv1 = null;
}
public void test_SBase_CVTerms()
{
CVTerm cv = new CVTerm(libsbml.BIOLOGICAL_QUALIFIER);
cv.setBiologicalQualifierType(libsbml.BQB_IS);
cv.addResource( "foo");
assertTrue( S.getNumCVTerms() == 0 );
assertTrue( S.getCVTerms() == null );
S.setMetaId( "_id");
S.addCVTerm(cv);
assertTrue( S.getNumCVTerms() == 1 );
assertTrue( S.getCVTerms() != null );
assertTrue( S.getCVTerm(0) != cv );
cv = 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()) );
}
{
}
}
public void test_CVTerm_getResources()
{
CVTerm term = new CVTerm(libsbml.MODEL_QUALIFIER);
string resource = "GO6666";
string resource1 = "OtherURI";
long number;
term.addResource(resource);
term.addResource(resource1);
number = term.getNumResources();
assertTrue( number == 2 );
assertTrue(( "GO6666" == term.getResourceURI(0) ));
assertTrue(( "OtherURI" == term.getResourceURI(1) ));
term = null;
}