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()));
}
{
}
}
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_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)
{
if (args.Length != 2)
{
Console.WriteLine(" usage: addingEvidenceCodes_2 <input-filename> <output-filename>");
Console.WriteLine(" Adds controlled vocabulary term to a species");
Console.WriteLine();
return(2);
}
SBMLDocument d = libsbml.readSBML(args[0]);
long errors = d.getNumErrors();
if (errors > 0)
{
Console.WriteLine("Read Error(s):");
d.printErrors();
Console.WriteLine("Correct the above and re-run.");
}
else
{
long n = d.getModel().getNumSpecies();
if (n <= 0)
{
Console.WriteLine("Model has no species.\n Cannot add CV terms\n");
}
else
{
Species s = d.getModel().getSpecies(0);
/* check that the species has a metaid
* no CVTerms will be added if there is no metaid to reference
*/
if (!s.isSetMetaId())
{
s.setMetaId("metaid_0000052");
}
CVTerm cv1 = new CVTerm(libsbml.BIOLOGICAL_QUALIFIER);
cv1.setBiologicalQualifierType(libsbml.BQB_OCCURS_IN);
cv1.addResource("urn:miriam:obo.go:GO%3A0005764");
s.addCVTerm(cv1);
// now create the additional annotation
//<rdf:Statement>
// <rdf:subject rdf:resource="#metaid_0000052"/>
// <rdf:predicate rdf:resource="http://biomodels.net/biology-qualifiers/occursIn"/>
// <rdf:object rdf:resource="urn:miriam:obo.go:GO%3A0005764"/>
// <bqbiol:isDescribedBy>
// <rdf:Bag>
// <rdf:li rdf:resource="urn:miriam:obo.eco:ECO%3A0000004"/>
// <rdf:li rdf:resource="urn:miriam:pubmed:7017716"/>
// </rdf:Bag>
// </bqbiol:isDescribedBy>
//</rdf:Statement>
/* attributes */
XMLAttributes blank_att = new XMLAttributes();
XMLAttributes resource_att = new XMLAttributes();
/* create the outer statement node */
XMLTriple statement_triple = new XMLTriple("Statement",
"http://www.w3.org/1999/02/22-rdf-syntax-ns#",
"rdf");
XMLToken statement_token = new XMLToken(statement_triple, blank_att);
XMLNode statement = new XMLNode(statement_token);
/*create the subject node */
XMLTriple subject_triple = new XMLTriple("subject",
"http://www.w3.org/1999/02/22-rdf-syntax-ns#",
"rdf");
resource_att.clear();
resource_att.add("rdf:resource", "#" + s.getMetaId());
XMLToken subject_token = new XMLToken(subject_triple, resource_att);
XMLNode subject = new XMLNode(subject_token);
/*create the predicate node */
XMLTriple predicate_triple = new XMLTriple("predicate",
"http://www.w3.org/1999/02/22-rdf-syntax-ns#",
"rdf");
resource_att.clear();
resource_att.add("rdf:resource",
"http://biomodels.net/biology-qualifiers/occursIn");
XMLToken predicate_token = new XMLToken(predicate_triple, resource_att);
XMLNode predicate = new XMLNode(predicate_token);
/*create the object node */
XMLTriple object_triple = new XMLTriple("object",
"http://www.w3.org/1999/02/22-rdf-syntax-ns#",
"rdf");
resource_att.clear();
resource_att.add("rdf:resource", "urn:miriam:obo.go:GO%3A0005764");
XMLToken object_token = new XMLToken(object_triple, resource_att);
XMLNode object_ = new XMLNode(object_token);
/* create the bqbiol node */
XMLTriple bqbiol_triple = new XMLTriple("isDescribedBy",
"http://biomodels.net/biology-qualifiers/",
"bqbiol");
XMLToken bqbiol_token = new XMLToken(bqbiol_triple, blank_att);
XMLNode bqbiol = new XMLNode(bqbiol_token);
/* create the bag node */
XMLTriple bag_triple = new XMLTriple("Bag",
"http://www.w3.org/1999/02/22-rdf-syntax-ns#",
"rdf");
XMLToken bag_token = new XMLToken(bag_triple, blank_att);
XMLNode bag = new XMLNode(bag_token);
/* create each li node and add to the bag */
XMLTriple li_triple = new XMLTriple("li",
"http://www.w3.org/1999/02/22-rdf-syntax-ns#",
"rdf");
resource_att.clear();
resource_att.add("rdf:resource", "urn:miriam:obo.eco:ECO%3A0000004");
XMLToken li_token = new XMLToken(li_triple, resource_att);
li_token.setEnd();
XMLNode li = new XMLNode(li_token);
bag.addChild(li);
resource_att.clear();
resource_att.add("rdf:resource", "urn:miriam:pubmed:7017716");
li_token = new XMLToken(li_triple, resource_att);
li_token.setEnd();
li = new XMLNode(li_token);
bag.addChild(li);
/* add the bag to bqbiol */
bqbiol.addChild(bag);
/* add subject, predicate, object and bqbiol to statement */
statement.addChild(subject);
statement.addChild(predicate);
statement.addChild(object_);
statement.addChild(bqbiol);
/* create a top-level RDF element
* this will ensure correct merging
*/
XMLNamespaces xmlns = new XMLNamespaces();
xmlns.add("http://www.w3.org/1999/02/22-rdf-syntax-ns#", "rdf");
xmlns.add("http://purl.org/dc/elements/1.1/", "dc");
xmlns.add("http://purl.org/dc/terms/", "dcterms");
xmlns.add("http://www.w3.org/2001/vcard-rdf/3.0#", "vCard");
xmlns.add("http://biomodels.net/biology-qualifiers/", "bqbiol");
xmlns.add("http://biomodels.net/model-qualifiers/", "bqmodel");
XMLTriple RDF_triple = new XMLTriple("RDF",
"http://www.w3.org/1999/02/22-rdf-syntax-ns#",
"rdf");
XMLToken RDF_token = new XMLToken(RDF_triple, blank_att, xmlns);
XMLNode annotation = new XMLNode(RDF_token);
/* add the staement node to the RDF node */
annotation.addChild(statement);
s.appendAnnotation(annotation);
libsbml.writeSBML(d, args[1]);
}
}
return((int)errors);
}
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 static int Main(string[] args)
{
SBMLDocument d;
long errors, n;
Reaction r;
if (args.Length != 2)
{
Console.Write(Environment.NewLine
+ " usage: addingEvidenceCodes_1 <input-filename> <output-filename>" + Environment.NewLine
+ " Adds controlled vocabulary term to a reaction" + Environment.NewLine
+ Environment.NewLine);
return(2);
}
d = libsbml.readSBML(args[1]);
errors = d.getNumErrors();
if (errors > 0)
{
Console.Write("Read Error(s):" + Environment.NewLine);
d.printErrors();
Console.Write("Correct the above and re-run." + Environment.NewLine);
}
else
{
n = d.getModel().getNumReactions();
if (n <= 0)
{
Console.Write("Model has no reactions.\n Cannot add CV terms\n");
}
else
{
r = d.getModel().getReaction(0);
/* check that the reaction has a metaid
* no CVTerms will be added if there is no metaid to reference
*/
if (!r.isSetMetaId())
{
r.setMetaId("metaid_0000052");
}
CVTerm cv1 = new CVTerm(libsbml.BIOLOGICAL_QUALIFIER);
cv1.setBiologicalQualifierType(libsbml.BQB_IS_DESCRIBED_BY);
cv1.addResource("urn:miriam:obo.eco:ECO%3A0000183");
r.addCVTerm(cv1);
CVTerm cv2 = new CVTerm(libsbml.BIOLOGICAL_QUALIFIER);
cv2.setBiologicalQualifierType(libsbml.BQB_IS);
cv2.addResource("urn:miriam:kegg.reaction:R00756");
cv2.addResource("urn:miriam:reactome:REACT_736");
r.addCVTerm(cv2);
libsbml.writeSBML(d, args[1]);
}
}
return((int)errors);
}
public void test_RDFAnnotation_parseCVTerms()
{
XMLNode node = RDFAnnotationParser.parseCVTerms(m.getCompartment(0));
assertTrue(node.getNumChildren() == 1);
XMLNode rdf = node.getChild(0);
assertTrue(("RDF" == rdf.getName()));
assertTrue(("rdf" == rdf.getPrefix()));
assertTrue(("http://www.w3.org/1999/02/22-rdf-syntax-ns#" == rdf.getURI()));
assertTrue(rdf.getNumChildren() == 1);
XMLNode desc = rdf.getChild(0);
assertTrue(("Description" == desc.getName()));
assertTrue(("rdf" == desc.getPrefix()));
assertTrue(("http://www.w3.org/1999/02/22-rdf-syntax-ns#" == desc.getURI()));
assertTrue(desc.getNumChildren() == 1);
XMLNode is1 = desc.getChild(0);
assertTrue(("is" == is1.getName()));
assertTrue(("bqbiol" == is1.getPrefix()));
assertTrue(is1.getNumChildren() == 1);
XMLNode Bag = is1.getChild(0);
assertTrue(("Bag" == Bag.getName()));
assertTrue(("rdf" == Bag.getPrefix()));
assertTrue(("http://www.w3.org/1999/02/22-rdf-syntax-ns#" == Bag.getURI()));
assertTrue(Bag.getNumChildren() == 4);
XMLNode li = Bag.getChild(0);
assertTrue(("li" == li.getName()));
assertTrue(("rdf" == li.getPrefix()));
assertTrue(("http://www.w3.org/1999/02/22-rdf-syntax-ns#" == li.getURI()));
assertTrue(li.getNumChildren() == 0);
XMLNode li1 = Bag.getChild(1);
assertTrue(("li" == li1.getName()));
assertTrue(("rdf" == li1.getPrefix()));
assertTrue(("http://www.w3.org/1999/02/22-rdf-syntax-ns#" == li1.getURI()));
assertTrue(li1.getNumChildren() == 0);
XMLNode li2 = Bag.getChild(2);
assertTrue(("li" == li2.getName()));
assertTrue(("rdf" == li2.getPrefix()));
assertTrue(("http://www.w3.org/1999/02/22-rdf-syntax-ns#" == li2.getURI()));
assertTrue(li2.getNumChildren() == 0);
XMLNode li3 = Bag.getChild(3);
assertTrue(("li" == li3.getName()));
assertTrue(("rdf" == li3.getPrefix()));
assertTrue(("http://www.w3.org/1999/02/22-rdf-syntax-ns#" == li3.getURI()));
assertTrue(li3.getNumChildren() == 0);
node = null;
XMLNode node1 = RDFAnnotationParser.parseCVTerms(null);
assertTrue(node1 == null);
node1 = RDFAnnotationParser.createCVTerms(null);
assertTrue(node1 == null);
node1 = RDFAnnotationParser.parseCVTerms(m.getCompartment(2));
assertTrue(node1 == null);
node1 = RDFAnnotationParser.createCVTerms(m.getCompartment(2));
assertTrue(node1 == null);
node1 = RDFAnnotationParser.parseCVTerms(m);
assertTrue(node1 == null);
node1 = RDFAnnotationParser.createCVTerms(m);
assertTrue(node1 == null);
Compartment c = new Compartment(3, 1);
c.setMetaId("_002");
node1 = RDFAnnotationParser.parseCVTerms(c);
assertTrue(node1 == null);
node1 = RDFAnnotationParser.createCVTerms(c);
assertTrue(node1 == null);
CVTerm cv = new CVTerm(libsbml.BIOLOGICAL_QUALIFIER);
cv.setBiologicalQualifierType(23);
cv.addResource("http://myres");
c.addCVTerm(cv);
node1 = RDFAnnotationParser.createCVTerms(c);
assertTrue(node1 == null);
c = null;
Model m1 = new Model(3, 1);
m1.setMetaId("_002");
cv = new CVTerm(libsbml.MODEL_QUALIFIER);
cv.setModelQualifierType(23);
cv.addResource("http://myres");
m1.addCVTerm(cv);
node1 = RDFAnnotationParser.createCVTerms(m1);
assertTrue(node1 == null);
}