public void setUp()
{
string filename = "../../annotation/test/test-data/annotationL3.xml";
d = libsbml.readSBML(filename);
m = d.getModel();
c = m.getCompartment(0);
}
public void test_SBMLConvertStrict_convertNonStrictSBO()
{
SBMLDocument d = new SBMLDocument(2,4);
Model m = d.createModel();
Compartment c = m.createCompartment();
c.setId( "c");
c.setConstant(false);
(c).setSBOTerm(64);
assertTrue( d.setLevelAndVersion(2,3,true) == false );
assertTrue( d.getLevel() == 2 );
assertTrue( d.getVersion() == 4 );
assertTrue( d.setLevelAndVersion(2,2,true) == false );
assertTrue( d.getLevel() == 2 );
assertTrue( d.getVersion() == 4 );
assertTrue( d.setLevelAndVersion(2,1,true) == true );
assertTrue( d.getLevel() == 2 );
assertTrue( d.getVersion() == 1 );
Compartment c1 = d.getModel().getCompartment(0);
assertTrue( (c1).getSBOTerm() == -1 );
assertTrue( d.setLevelAndVersion(1,2,true) == true );
assertTrue( d.getLevel() == 1 );
assertTrue( d.getVersion() == 2 );
Compartment c2 = d.getModel().getCompartment(0);
assertTrue( (c2).getSBOTerm() == -1 );
d = null;
}
public void test_SBMLConvertStrict_convertL1ParamRule()
{
SBMLDocument d = new SBMLDocument(1,2);
Model m = d.createModel();
Compartment c = m.createCompartment();
c.setId( "c");
Parameter p = m.createParameter();
p.setId( "p");
Parameter p1 = m.createParameter();
p1.setId( "p1");
ASTNode math = libsbml.parseFormula("p");
Rule ar = m.createAssignmentRule();
ar.setVariable( "p1");
ar.setMath(math);
ar.setUnits( "mole");
assertTrue( d.setLevelAndVersion(2,1,true) == true );
assertTrue( d.getLevel() == 2 );
assertTrue( d.getVersion() == 1 );
Rule r1 = d.getModel().getRule(0);
assertTrue( r1.getUnits() == "" );
d = null;
}
public void test_ReadSBML_notes()
{
Reaction r;
KineticLaw kl;
string s = wrapSBML_L2v3("<listOfReactions>" +
"<reaction name='J1'>" +
" <kineticLaw formula='k1*X0'>" +
" <notes>This is a test note.</notes>" +
" <listOfParameters>" +
" <parameter name='k1' value='0'/>" +
" </listOfParameters>" +
" </kineticLaw>" +
"</reaction>" +
"</listOfReactions>");
D = libsbml.readSBMLFromString(s);
M = D.getModel();
r = M.getReaction(0);
kl = r.getKineticLaw();
assertTrue( kl.getNotes() != null );
string notes = kl.getNotes().getChild(0).getCharacters();
assertTrue( ( "This is a test note." != notes ) == false );
}
public void test_Model_ancestor_create()
{
SBMLDocument d = new SBMLDocument();
Model m = d.createModel();
assertTrue( m.getAncestorOfType(libsbml.SBML_DOCUMENT) == d );
Model obj = d.getModel();
assertTrue( obj.getAncestorOfType(libsbml.SBML_DOCUMENT) == d );
d = null;
}
public void test_ReadSBML_line_col_numbers()
{
//setXMLParser();
SBase sb;
string s = "<?xml version='1.0' encoding='UTF-8'?>\n" +
"<sbml xmlns='http://www.sbml.org/sbml/level2' level='2' version='1'>\n" +
" <model id='testModel' name='testModel'>\n" +
" <listOfReactions> <reaction/> </listOfReactions>\n" +
" </model>\n" +
"</sbml>\n";
D = libsbml.readSBMLFromString(s);
M = D.getModel();
assertTrue( M != null );
sb = M;
sb = M.getListOfReactions();
sb = M.getReaction(0);
}
public void test_SBMLConvert_convertToL3_stoichiometryMath()
{
SBMLDocument d = new SBMLDocument(2,1);
Model m = d.createModel();
Compartment c = m.createCompartment();
c.setId( "c" );
Species s = m.createSpecies();
s.setId( "s");
s.setCompartment( "c");
Reaction r = m.createReaction();
SpeciesReference sr = r.createReactant();
sr.setSpecies( "s");
StoichiometryMath sm = sr.createStoichiometryMath();
ASTNode ast = libsbml.parseFormula("c*2");
sm.setMath(ast);
assertTrue( m.getNumRules() == 0 );
assertTrue( sr.isSetId() == false );
assertTrue( d.setLevelAndVersion(3,1,false) == true );
m = d.getModel();
r = m.getReaction(0);
sr = r.getReactant(0);
assertTrue( m.getNumRules() == 1 );
assertTrue( sr.isSetId() == true );
Rule rule = m.getRule(0);
assertTrue( sr.getId() == rule.getVariable() );
d = null;
}
public void test_SBMLConvert_convertToL2v4_DuplicateAnnotations_model()
{
SBMLDocument d = new SBMLDocument(2,1);
Model m = d.createModel();
string annotation = "<rdf/>\n<rdf/>";
int i = (m).setAnnotation(annotation);
assertTrue( d.getLevel() == 2 );
assertTrue( d.getVersion() == 1 );
assertTrue( (m).getAnnotation().getNumChildren() == 2 );
assertTrue( d.setLevelAndVersion(2,4,true) == true );
assertTrue( d.getLevel() == 2 );
assertTrue( d.getVersion() == 4 );
m = d.getModel();
assertTrue( (m).getAnnotation().getNumChildren() == 1 );
d = null;
}
public void test_SBMLDocument_setModel3()
{
SBMLDocument d = new SBMLDocument(2,2);
Model m1 = new Model(2,2);
int i = d.setModel(m1);
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
assertTrue( d.getModel() != null );
d = null;
}
public void test_SBMLDocument_setModel()
{
SBMLDocument d = new SBMLDocument(2,4);
Model m1 = new Model(2,4);
Model m2 = new Model(2,4);
Model mout;
assertTrue( d.getModel() == null );
int i = d.setModel(m1);
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
mout = d.getModel();
assertTrue( mout != null );
assertTrue( mout != m1 );
i = d.setModel(d.getModel());
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
mout = d.getModel();
assertTrue( mout != null );
assertTrue( mout != m1 );
i = d.setModel(m2);
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
mout = d.getModel();
assertTrue( mout != null );
assertTrue( mout != m2 );
d = null;
}
public void test_Model_parent_add()
{
SBMLDocument d = new SBMLDocument(2,4);
Model m = new Model(2,4);
d.setModel(m);
assertTrue( d == d.getModel().getParentSBMLObject() );
d = null;
}
public void test_ReadSBML_Model()
{
string s = wrapXML("<sbml level='1' version='1'>" +
" <model name='testModel'></model>" +
"</sbml>");
D = libsbml.readSBMLFromString(s);
M = D.getModel();
assertTrue(( "testModel" == M.getId() ));
}
public void test_ReadSBML_Model_L2()
{
string s = wrapXML("<sbml level='2' version='1'>" +
" <model id='testModel'> </model>" +
"</sbml>");
D = libsbml.readSBMLFromString(s);
M = D.getModel();
assertEquals( true, M.isSetId() );
assertEquals( false, M.isSetName() );
assertTrue(( "testModel" == M.getId() ));
}
public void test_ReadSBML_metaid_Unit()
{
SBase sb;
UnitDefinition ud;
string s = wrapSBML_L2v1("<listOfUnitDefinitions>" +
" <unitDefinition metaid='ud'>" +
" <listOfUnits metaid='lou'>" +
" <unit metaid='u'/>" +
" </listOfUnits>" +
" </unitDefinition>" +
"</listOfUnitDefinitions>");
D = libsbml.readSBMLFromString(s);
M = D.getModel();
assertTrue( M != null );
ud = M.getUnitDefinition(0);
sb = ud;
assertEquals( true, sb.isSetMetaId() );
assertTrue(( "ud" == sb.getMetaId() ));
sb = ud.getListOfUnits();
assertEquals( true, sb.isSetMetaId() );
assertTrue(( "lou" == sb.getMetaId() ));
sb = ud.getUnit(0);
assertEquals( true, sb.isSetMetaId() );
assertTrue(( "u" == sb.getMetaId() ));
}
public void test_ReadSBML_metaid_Reaction()
{
SBase sb;
Reaction r;
string s = wrapSBML_L2v1("<listOfReactions>" +
" <reaction metaid='r'>" +
" <listOfReactants metaid='lor'>" +
" <speciesReference metaid='sr1'/>" +
" </listOfReactants>" +
" <listOfProducts metaid='lop'>" +
" <speciesReference metaid='sr2'/>" +
" </listOfProducts>" +
" <listOfModifiers metaid='lom'>" +
" <modifierSpeciesReference metaid='msr'/>" +
" </listOfModifiers>" +
" <kineticLaw metaid='kl'/>" +
" </reaction>" +
"</listOfReactions>");
D = libsbml.readSBMLFromString(s);
M = D.getModel();
assertTrue( M != null );
r = M.getReaction(0);
sb = r;
assertEquals( true, sb.isSetMetaId() );
assertTrue(( "r" == sb.getMetaId() ));
sb = r.getListOfReactants();
assertEquals( true, sb.isSetMetaId() );
assertTrue(( "lor" == sb.getMetaId() ));
sb = r.getReactant(0);
assertEquals( true, sb.isSetMetaId() );
assertTrue(( "sr1" == sb.getMetaId() ));
sb = r.getListOfProducts();
assertEquals( true, sb.isSetMetaId() );
assertTrue(( "lop" == sb.getMetaId() ));
sb = r.getProduct(0);
assertEquals( true, sb.isSetMetaId() );
assertTrue(( "sr2" == sb.getMetaId() ));
sb = r.getListOfModifiers();
assertEquals( true, sb.isSetMetaId() );
assertTrue(( "lom" == sb.getMetaId() ));
sb = r.getModifier(0);
assertEquals( true, sb.isSetMetaId() );
assertTrue(( "msr" == sb.getMetaId() ));
sb = r.getKineticLaw();
assertEquals( true, sb.isSetMetaId() );
assertTrue(( "kl" == sb.getMetaId() ));
}
public void test_ReadSBML_metaid_ListOf()
{
SBase sb;
string s = wrapSBML_L2v1("<listOfFunctionDefinitions metaid='lofd'/>" +
"<listOfUnitDefinitions metaid='loud'/>" +
"<listOfCompartments metaid='loc'/>" +
"<listOfSpecies metaid='los'/>" +
"<listOfParameters metaid='lop'/>" +
"<listOfRules metaid='lor'/>" +
"<listOfReactions metaid='lorx'/>" +
"<listOfEvents metaid='loe'/>");
D = libsbml.readSBMLFromString(s);
M = D.getModel();
assertTrue( M != null );
sb = M.getListOfFunctionDefinitions();
assertEquals( true, sb.isSetMetaId() );
assertTrue(( "lofd" == sb.getMetaId() ));
sb = M.getListOfUnitDefinitions();
assertEquals( true, sb.isSetMetaId() );
assertTrue(( "loud" == sb.getMetaId() ));
sb = M.getListOfCompartments();
assertEquals( true, sb.isSetMetaId() );
assertTrue(( "loc" == sb.getMetaId() ));
sb = M.getListOfSpecies();
assertEquals( true, sb.isSetMetaId() );
assertTrue(( "los" == sb.getMetaId() ));
sb = M.getListOfParameters();
assertEquals( true, sb.isSetMetaId() );
assertTrue(( "lop" == sb.getMetaId() ));
sb = M.getListOfRules();
assertEquals( true, sb.isSetMetaId() );
assertTrue(( "lor" == sb.getMetaId() ));
sb = M.getListOfReactions();
assertEquals( true, sb.isSetMetaId() );
assertTrue(( "lorx" == sb.getMetaId() ));
sb = M.getListOfEvents();
assertEquals( true, sb.isSetMetaId() );
assertTrue(( "loe" == sb.getMetaId() ));
}
public void test_ReadSBML_metaid_Event()
{
SBase sb;
Event e;
string s = wrapSBML_L2v1("<listOfEvents>" +
" <event metaid='e'>" +
" <listOfEventAssignments metaid='loea'>" +
" <eventAssignment metaid='ea'/>" +
" </listOfEventAssignments>" +
" </event>" +
"</listOfEvents>");
D = libsbml.readSBMLFromString(s);
M = D.getModel();
assertTrue( M != null );
e = M.getEvent(0);
sb = e;
assertEquals( true, sb.isSetMetaId() );
assertTrue(( "e" == sb.getMetaId() ));
sb = e.getListOfEventAssignments();
assertEquals( true, sb.isSetMetaId() );
assertTrue(( "loea" == sb.getMetaId() ));
sb = e.getEventAssignment(0);
assertEquals( true, sb.isSetMetaId() );
assertTrue(( "ea" == sb.getMetaId() ));
}
public void test_ReadSBML_metaid()
{
SBase sb;
string s = wrapSBML_L2v1("<listOfFunctionDefinitions>" +
" <functionDefinition metaid='fd'/>" +
"</listOfFunctionDefinitions>" +
"<listOfUnitDefinitions>" +
" <unitDefinition metaid='ud'/>" +
"</listOfUnitDefinitions>" +
"<listOfCompartments>" +
" <compartment metaid='c'/>" +
"</listOfCompartments>" +
"<listOfSpecies>" +
" <species metaid='s'/>" +
"</listOfSpecies>" +
"<listOfParameters>" +
" <parameter metaid='p'/>" +
"</listOfParameters>" +
"<listOfRules>" +
" <rateRule metaid='rr'/>" +
"</listOfRules>" +
"<listOfReactions>" +
" <reaction metaid='rx'/>" +
"</listOfReactions>" +
"<listOfEvents>" +
" <event metaid='e'/>" +
"</listOfEvents>");
D = libsbml.readSBMLFromString(s);
M = D.getModel();
assertTrue( M != null );
sb = M.getFunctionDefinition(0);
assertEquals( true, sb.isSetMetaId() );
assertTrue(( "fd" == sb.getMetaId() ));
sb = M.getUnitDefinition(0);
assertEquals( true, sb.isSetMetaId() );
assertTrue(( "ud" == sb.getMetaId() ));
sb = M.getCompartment(0);
assertEquals( true, sb.isSetMetaId() );
assertTrue(( "c" == sb.getMetaId() ));
sb = M.getSpecies(0);
assertEquals( true, sb.isSetMetaId() );
assertTrue(( "s" == sb.getMetaId() ));
sb = M.getParameter(0);
assertEquals( true, sb.isSetMetaId() );
assertTrue(( "p" == sb.getMetaId() ));
sb = M.getRule(0);
assertEquals( true, sb.isSetMetaId() );
assertTrue(( "rr" == sb.getMetaId() ));
sb = M.getReaction(0);
assertEquals( true, sb.isSetMetaId() );
assertTrue(( "rx" == sb.getMetaId() ));
sb = M.getEvent(0);
assertEquals( true, sb.isSetMetaId() );
assertTrue(( "e" == sb.getMetaId() ));
}
public void test_SBMLConvertStrict_convertToL1()
{
SBMLDocument d = new SBMLDocument(2,4);
Model m = d.createModel();
(m).setMetaId( "_m");
Compartment c = m.createCompartment();
c.setId( "c");
(c).setSBOTerm(240);
Species s = m.createSpecies();
s.setId( "s");
s.setCompartment( "c");
s.setHasOnlySubstanceUnits(true);
assertTrue( d.setLevelAndVersion(1,2,true) == true );
assertTrue( d.getLevel() == 1 );
assertTrue( d.getVersion() == 2 );
Model m1 = d.getModel();
assertTrue( (m1).getMetaId() == "" );
Compartment c1 = m1.getCompartment(0);
assertTrue( (c1).getSBOTerm() == -1 );
Species s1 = m1.getSpecies(0);
assertTrue( s1.getHasOnlySubstanceUnits() == false );
d = null;
}
public void test_ReadSBML_notes_ListOf()
{
SBase sb;
string s = wrapSBML_L2v1("<listOfFunctionDefinitions>" +
" <notes>My Functions</notes>" +
" <functionDefinition/>" +
"</listOfFunctionDefinitions>" +
"<listOfUnitDefinitions>" +
" <notes>My Units</notes>" +
" <unitDefinition/>" +
"</listOfUnitDefinitions>" +
"<listOfCompartments>" +
" <notes>My Compartments</notes>" +
" <compartment/>" +
"</listOfCompartments>");
D = libsbml.readSBMLFromString(s);
M = D.getModel();
assertTrue( M != null );
sb = M.getListOfFunctionDefinitions();
assertEquals( true, sb.isSetNotes() );
string notes = sb.getNotes().getChild(0).getCharacters();
assertTrue( ( "My Functions" != notes ) == false );
sb = M.getListOfUnitDefinitions();
assertEquals( true, sb.isSetNotes() );
notes = sb.getNotes().getChild(0).getCharacters();
assertTrue( ( "My Units" != notes ) == false );
sb = M.getListOfCompartments();
assertEquals( true, sb.isSetNotes() );
notes = sb.getNotes().getChild(0).getCharacters();
assertTrue( ( "My Compartments" != notes ) == false );
}
public void test_ReadSBML_AlgebraicRule()
{
Rule ar;
string s = wrapSBML_L1v2("<listOfRules>" +
" <algebraicRule formula='x + 1'/>" +
"</listOfRules>");
D = libsbml.readSBMLFromString(s);
M = D.getModel();
assertTrue( M.getNumRules() == 1 );
ar = M.getRule(0);
assertTrue(( "x + 1" == ar.getFormula() ));
}
public void test_ReadSBML_notes_xmlns()
{
string s = wrapSBML_L2v3("<notes>" +
" <body xmlns=\"http://www.w3.org/1999/xhtml\">Some text.</body>" +
"</notes>");
D = libsbml.readSBMLFromString(s);
M = D.getModel();
assertTrue( M.getNotes() != null );
XMLNamespaces ns = M.getNotes().getChild(0).getNamespaces();
assertTrue( ns.getLength() == 1 );
assertTrue(( "http://www.w3.org/1999/xhtml" == ns.getURI(0) ));
string notes = M.getNotes().getChild(0).getChild(0).getCharacters();
assertTrue( ( "Some text." != notes ) == false );
}
public void test_SBMLDocument_setModel2()
{
SBMLDocument d = new SBMLDocument(2,2);
Model m1 = new Model(1,2);
int i = d.setModel(m1);
assertTrue( i == libsbml.LIBSBML_LEVEL_MISMATCH );
assertTrue( d.getModel() == null );
d = null;
}
public void test_ReadSBML_Parameter()
{
Parameter p;
string s = wrapSBML_L1v2("<listOfParameters>" +
" <parameter name='Km1' value='2.3' units='second'/>" +
"</listOfParameters>");
D = libsbml.readSBMLFromString(s);
M = D.getModel();
assertTrue( M.getNumParameters() == 1 );
p = M.getParameter(0);
assertTrue(( "Km1" == p.getId() ));
assertTrue(( "second" == p.getUnits() ));
assertTrue( p.getValue() == 2.3 );
assertTrue( p.isSetValue() == true );
}
public void test_SBMLDocument_clone()
{
SBMLDocument o1 = new SBMLDocument();
o1.setLevelAndVersion(1,1,false);
Model m = new Model(1,1);
m.setId("foo");
o1.setModel(m);
assertTrue( o1.getLevel() == 1 );
assertTrue( o1.getVersion() == 1 );
assertTrue( o1.getModel().getId() == "foo" );
assertTrue( o1.getModel().getLevel() == 1 );
assertTrue( o1.getModel().getVersion() == 1 );
assertTrue( o1.getModel().getSBMLDocument() == o1 );
SBMLDocument o2 = o1.clone();
assertTrue( o2.getLevel() == 1 );
assertTrue( o2.getVersion() == 1 );
assertTrue( o2.getModel().getId() == "foo" );
assertTrue( o2.getModel().getLevel() == 1 );
assertTrue( o2.getModel().getVersion() == 1 );
assertTrue( o2.getModel().getSBMLDocument() == o2 );
o2 = null;
o1 = null;
}
public void test_ReadSBML_ParameterRule()
{
Rule pr;
string s = wrapSBML_L1v2("<listOfRules>" +
" <parameterRule name='k' formula='k3/k2'/>" +
"</listOfRules>");
D = libsbml.readSBMLFromString(s);
M = D.getModel();
assertTrue( M.getNumRules() == 1 );
pr = M.getRule(0);
assertEquals( true, pr.isParameter() );
assertTrue(( "k" == pr.getVariable() ));
assertTrue(( "k3/k2" == pr.getFormula() ));
assertTrue( pr.getType() == libsbml.RULE_TYPE_SCALAR );
}
public void test_SBMLConvert_convertToL3_localParameters()
{
SBMLDocument d = new SBMLDocument(1,2);
Model m = d.createModel();
Compartment c = m.createCompartment();
c.setId( "c" );
Species s = m.createSpecies();
s.setId( "s");
s.setCompartment( "c");
Reaction r = m.createReaction();
SpeciesReference sr = r.createReactant();
sr.setSpecies( "s");
KineticLaw kl = r.createKineticLaw();
kl.setFormula( "s*k");
Parameter p = kl.createParameter();
p.setId( "k");
assertTrue( kl.getNumLocalParameters() == 0 );
assertTrue( d.setLevelAndVersion(3,1,false) == true );
m = d.getModel();
r = m.getReaction(0);
kl = r.getKineticLaw();
assertTrue( kl.getNumLocalParameters() == 1 );
LocalParameter lp = kl.getLocalParameter(0);
d = null;
}
public void test_Model_ancestor_add()
{
SBMLDocument d = new SBMLDocument(2,4);
Model m = new Model(2,4);
d.setModel(m);
assertTrue( d == d.getModel().getAncestorOfType(libsbml.SBML_DOCUMENT) );
d = null;
}
public void setUp()
{
string filename = "../../annotation/test/test-data/annotation2.xml";
d2 = libsbml.readSBML(filename);
m2 = d2.getModel();
}
public void test_ReadSBML_KineticLaw_Parameter()
{
Reaction r;
KineticLaw kl;
Parameter p;
string s = wrapSBML_L1v2("<listOfReactions>" +
" <reaction name='J1'>" +
" <kineticLaw formula='k1*X0'>" +
" <listOfParameters>" +
" <parameter name='k1' value='0'/>" +
" </listOfParameters>" +
" </kineticLaw>" +
" </reaction>" +
"</listOfReactions>");
D = libsbml.readSBMLFromString(s);
M = D.getModel();
assertTrue( M.getNumReactions() == 1 );
r = M.getReaction(0);
kl = r.getKineticLaw();
assertTrue(( "k1*X0" == kl.getFormula() ));
assertTrue( kl.getNumParameters() == 1 );
p = kl.getParameter(0);
assertTrue(( "k1" == p.getId() ));
assertTrue( p.getValue() == 0 );
}
