def test_Model_getCompartmentById(self):
c1 = libsbml.Compartment(2, 4)
c2 = libsbml.Compartment(2, 4)
c1.setId("A")
c2.setId("B")
self.M.addCompartment(c1)
self.M.addCompartment(c2)
self.assert_(self.M.getNumCompartments() == 2)
self.assert_(self.M.getCompartment("A") != c1)
self.assert_(self.M.getCompartment("B") != c2)
self.assert_(self.M.getCompartment("C") == None)
pass
def test_Model_getCompartment(self):
c1 = libsbml.Compartment(2, 4)
c2 = libsbml.Compartment(2, 4)
c1.setId("A")
c2.setId("B")
self.M.addCompartment(c1)
self.M.addCompartment(c2)
self.assert_(self.M.getNumCompartments() == 2)
c1 = self.M.getCompartment(0)
c2 = self.M.getCompartment(1)
self.assert_(("A" == c1.getId()))
self.assert_(("B" == c2.getId()))
pass
def test_Compartment_copyConstructor(self):
o1 = libsbml.Compartment(2,4)
o1.setId("c")
o1.setOutside("c2")
self.assert_( o1.getId() == "c" )
self.assert_( o1.getOutside() == "c2" )
o2 = libsbml.Compartment(o1)
self.assert_( o2.getId() == "c" )
self.assert_( o2.getOutside() == "c2" )
self.assert_( o2.getParentSBMLObject() == o1.getParentSBMLObject() )
o2 = None
o1 = None
pass
def test_Compartment_assignmentOperator(self):
o1 = libsbml.Compartment(2,4)
o1.setId("c")
o1.setOutside("c2")
self.assert_( o1.getId() == "c" )
self.assert_( o1.getOutside() == "c2" )
o2 = libsbml.Compartment(2,4)
o2 = o1
self.assert_( o2.getId() == "c" )
self.assert_( o2.getOutside() == "c2" )
self.assert_( o2.getParentSBMLObject() == o1.getParentSBMLObject() )
o2 = None
o1 = None
pass
def test_Compartment(self):
c = libsbml.Compartment(2, 4)
self.assertEqual(False, (c.hasRequiredAttributes()))
c.setId("c")
self.assertEqual(True, c.hasRequiredAttributes())
c = None
pass
def test_L3_Compartment_initDefaults(self):
c = libsbml.Compartment(3, 1)
c.setId("A")
self.assertEqual(True, c.isSetId())
self.assertEqual(False, c.isSetName())
self.assertEqual(False, c.isSetSize())
self.assertEqual(False, c.isSetVolume())
self.assertEqual(False, c.isSetUnits())
self.assertEqual(False, c.isSetConstant())
self.assertEqual(False, c.isSetSpatialDimensions())
c.initDefaults()
self.assert_(("A" == c.getId()))
self.assert_(c.getName() == "")
self.assert_(("litre" == c.getUnits()))
self.assert_(c.getSpatialDimensions() == 3)
self.assert_(c.getSize() == 1)
self.assert_(c.getConstant() == True)
self.assertEqual(True, c.isSetId())
self.assertEqual(False, c.isSetName())
self.assertEqual(False, c.isSetSize())
self.assertEqual(False, c.isSetVolume())
self.assertEqual(True, c.isSetUnits())
self.assertEqual(True, c.isSetConstant())
self.assertEqual(True, c.isSetSpatialDimensions())
_dummyList = [c]
_dummyList[:] = []
del _dummyList
pass
def test_L3_Compartment_createWithNS(self):
xmlns = libsbml.XMLNamespaces()
xmlns.add("http://www.sbml.org", "testsbml")
sbmlns = libsbml.SBMLNamespaces(3, 1)
sbmlns.addNamespaces(xmlns)
c = libsbml.Compartment(sbmlns)
self.assert_(c.getTypeCode() == libsbml.SBML_COMPARTMENT)
self.assert_(c.getMetaId() == "")
self.assert_(c.getNotes() == None)
self.assert_(c.getAnnotation() == None)
self.assert_(c.getLevel() == 3)
self.assert_(c.getVersion() == 1)
self.assert_(c.getNamespaces() != None)
self.assert_(c.getNamespaces().getLength() == 2)
self.assert_(c.getId() == "")
self.assert_(c.getName() == "")
self.assert_(c.getUnits() == "")
self.assert_(c.getOutside() == "")
self.assertEqual(True, isnan(c.getSpatialDimensionsAsDouble()))
self.assertEqual(True, isnan(c.getVolume()))
self.assert_(c.getConstant() == True)
self.assertEqual(False, c.isSetId())
self.assertEqual(False, c.isSetSpatialDimensions())
self.assertEqual(False, c.isSetName())
self.assertEqual(False, c.isSetSize())
self.assertEqual(False, c.isSetVolume())
self.assertEqual(False, c.isSetUnits())
self.assertEqual(False, c.isSetOutside())
self.assertEqual(False, c.isSetConstant())
_dummyList = [c]
_dummyList[:] = []
del _dummyList
pass
def test_L3_Compartment_hasRequiredAttributes(self): c = libsbml.Compartment(3,1) self.assertEqual( False, c.hasRequiredAttributes() ) c.setId( "id") self.assertEqual( False, c.hasRequiredAttributes() ) c.setConstant(False) self.assertEqual( True, c.hasRequiredAttributes() ) _dummyList = [ c ]; _dummyList[:] = []; del _dummyList pass
def test_Compartment_setCompartmentType4(self):
c = libsbml.Compartment(2, 2)
i = c.setCompartmentType("")
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
self.assertEqual(False, c.isSetCompartmentType())
_dummyList = [c]
_dummyList[:] = []
del _dummyList
pass
def test_Compartment_setConstant2(self):
c = libsbml.Compartment(2, 2)
i = c.setConstant(False)
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
self.assert_(c.getConstant() == False)
_dummyList = [c]
_dummyList[:] = []
del _dummyList
pass
def test_Compartment_setSpatialDimensions5(self):
c = libsbml.Compartment(2, 2)
i = c.setSpatialDimensions(2.2)
self.assert_(i == libsbml.LIBSBML_INVALID_ATTRIBUTE_VALUE)
self.assert_(c.getSpatialDimensions() == 3)
_dummyList = [c]
_dummyList[:] = []
del _dummyList
pass
def test_Compartment_setId2(self):
c = libsbml.Compartment(2, 2)
i = c.setId("1cell")
self.assert_(i == libsbml.LIBSBML_INVALID_ATTRIBUTE_VALUE)
self.assertEqual(False, c.isSetId())
_dummyList = [c]
_dummyList[:] = []
del _dummyList
pass
def test_Compartment_setSpatialDimensions4(self):
c = libsbml.Compartment(2, 2)
i = c.setSpatialDimensions(2.0)
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
self.assert_(c.getSpatialDimensions() == 2)
_dummyList = [c]
_dummyList[:] = []
del _dummyList
pass
def test_sbase_has_read(self):
compartment = libsbml.Compartment(3, 1)
assert compartment is not None
stream = libsbml.XMLInputStream(
"""<?xml version="1.0" encoding="utf-8"?>
<compartment id="vol1" name="compartment 1" size="2.0" />""", False)
compartment.read(stream)
assert compartment.id == 'vol1'
assert compartment.name == 'compartment 1'
assert compartment.volume == 2.0
def test_Compartment_parent_add(self):
c = libsbml.Compartment(2, 4)
c.setId("c")
m = libsbml.Model(2, 4)
m.addCompartment(c)
c = None
lo = m.getListOfCompartments()
self.assert_(lo == m.getCompartment(0).getParentSBMLObject())
self.assert_(m == lo.getParentSBMLObject())
pass
def test_Compartment_setId3(self):
c = libsbml.Compartment(2, 2)
i = c.setId("cell")
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
self.assertEqual(True, c.isSetId())
self.assert_(("cell" == c.getId()))
_dummyList = [c]
_dummyList[:] = []
del _dummyList
pass
def test_Compartment_setCompartmentType2(self):
c = libsbml.Compartment(2, 2)
i = c.setCompartmentType("1cell")
self.assert_(i == libsbml.LIBSBML_INVALID_ATTRIBUTE_VALUE)
self.assertEqual(False, c.isSetCompartmentType())
i = c.unsetCompartmentType()
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
self.assertEqual(False, c.isSetCompartmentType())
_dummyList = [c]
_dummyList[:] = []
del _dummyList
pass
def test_Compartment_ancestor_add(self):
c = libsbml.Compartment(2,4)
c.setId("C")
m = libsbml.Model(2,4)
m.addCompartment(c)
c = None
lo = m.getListOfCompartments()
obj = m.getCompartment(0)
self.assert_( obj.getAncestorOfType(libsbml.SBML_MODEL) == m )
self.assert_( obj.getAncestorOfType(libsbml.SBML_LIST_OF) == lo )
self.assert_( obj.getAncestorOfType(libsbml.SBML_DOCUMENT) == None )
self.assert_( obj.getAncestorOfType(libsbml.SBML_EVENT) == None )
pass
def test_Compartment_setVolume2(self):
c = libsbml.Compartment(2, 2)
i = c.setVolume(4)
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
self.assert_(c.getVolume() == 4.0)
self.assertEqual(True, c.isSetVolume())
i = c.unsetVolume()
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
self.assertEqual(False, c.isSetVolume())
_dummyList = [c]
_dummyList[:] = []
del _dummyList
pass
def test_Model_addCompartment5(self):
m = libsbml.Model(2, 2)
c = libsbml.Compartment(2, 2)
c.setId("c")
c1 = libsbml.Compartment(2, 2)
c1.setId("c")
i = m.addCompartment(c)
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
self.assert_(m.getNumCompartments() == 1)
i = m.addCompartment(c1)
self.assert_(i == libsbml.LIBSBML_DUPLICATE_OBJECT_ID)
self.assert_(m.getNumCompartments() == 1)
_dummyList = [c]
_dummyList[:] = []
del _dummyList
_dummyList = [c1]
_dummyList[:] = []
del _dummyList
_dummyList = [m]
_dummyList[:] = []
del _dummyList
pass
def test_internal_consistency_check_99905(self):
d = libsbml.SBMLDocument(2,4)
c = libsbml.Compartment(2,4)
d.setLevelAndVersion(1,2,False)
m = d.createModel()
c.setId("c")
c.setSBOTerm(2)
m.addCompartment(c)
errors = d.checkInternalConsistency()
self.assert_( errors == 1 )
self.assert_( d.getError(0).getErrorId() == 10103 )
d = None
pass
def insertRows(self, position, rows=1, index=QModelIndex()):
self.beginInsertRows(QModelIndex(), position,
position + rows - 1) # mandatory Qt call
for row in range(
rows
): # we don't take the actual row into account as the libSBML always appends at the end
newCompartment = libsbml.Compartment()
self.mainModel.SbmlModel.addCompartment(SBMLEntity(newCompartment))
self.endInsertRows() # mandatory Qt call
self.Dirty = True
return True
def test_Model_addCompartment3(self):
m = libsbml.Model(2, 2)
c = libsbml.Compartment(1, 2)
c.setId("c")
i = m.addCompartment(c)
self.assert_(i == libsbml.LIBSBML_LEVEL_MISMATCH)
self.assert_(m.getNumCompartments() == 0)
_dummyList = [c]
_dummyList[:] = []
del _dummyList
_dummyList = [m]
_dummyList[:] = []
del _dummyList
pass
def test_internal_consistency_check_99903(self):
d = libsbml.SBMLDocument(2,4)
c = libsbml.Compartment(2,4)
d.setLevelAndVersion(1,2,False)
m = d.createModel()
c.setConstant(True)
c.setId("c")
m.addCompartment(c)
r = m.createAssignmentRule()
r.setVariable("c")
r.setFormula("2*3")
errors = d.checkInternalConsistency()
self.assert_( errors == 3 )
d = None
pass
def test_SBMLConvert_convertToL1_Species_Amount(self): d = libsbml.SBMLDocument(2,1) m = d.createModel() sid = "C"; c = libsbml.Compartment(2,4) s = libsbml.Species(2,4) c.setId(sid) m.addCompartment(c) s.setCompartment(sid) s.setInitialAmount(2.34) m.addSpecies(s) self.assert_( d.setLevelAndVersion(1,2,True) == True ) self.assert_( s.getInitialAmount() == 2.34 ) _dummyList = [ d ]; _dummyList[:] = []; del _dummyList pass
def test_Model_addCompartment1(self):
m = libsbml.Model(2, 2)
c = libsbml.Compartment(2, 2)
i = m.addCompartment(c)
self.assert_(i == libsbml.LIBSBML_INVALID_OBJECT)
c.setId("c")
i = m.addCompartment(c)
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
self.assert_(m.getNumCompartments() == 1)
_dummyList = [c]
_dummyList[:] = []
del _dummyList
_dummyList = [m]
_dummyList[:] = []
del _dummyList
pass
def test_ListOf_append(self): m = libsbml.Model(2,4) m.createCompartment() loc = m.getListOfCompartments() self.assert_( loc.size() == 1 ) c = libsbml.Compartment(2,4) i = loc.append(c) self.assert_( i == libsbml.LIBSBML_OPERATION_SUCCESS ) self.assert_( loc.size() == 2 ) sp = libsbml.Species(2,4) i = loc.append(sp) self.assert_( i == libsbml.LIBSBML_INVALID_OBJECT ) self.assert_( loc.size() == 2 ) _dummyList = [ m ]; _dummyList[:] = []; del _dummyList _dummyList = [ sp ]; _dummyList[:] = []; del _dummyList pass
def test_Compartment_createWith(self):
c = libsbml.Compartment(2, 4)
c.setId("A")
self.assert_(c.getTypeCode() == libsbml.SBML_COMPARTMENT)
self.assert_(c.getMetaId() == "")
self.assert_(c.getNotes() == None)
self.assert_(c.getAnnotation() == None)
self.assert_(c.getName() == "")
self.assert_(c.getSpatialDimensions() == 3)
self.assert_(("A" == c.getId()))
self.assert_(c.getConstant() == True)
self.assertEqual(True, c.isSetId())
self.assertEqual(False, c.isSetName())
_dummyList = [c]
_dummyList[:] = []
del _dummyList
pass
def test_Compartment_createWithNS(self):
xmlns = libsbml.XMLNamespaces()
xmlns.add("http://www.sbml.org", "testsbml")
sbmlns = libsbml.SBMLNamespaces(2, 1)
sbmlns.addNamespaces(xmlns)
c = libsbml.Compartment(sbmlns)
self.assert_(c.getTypeCode() == libsbml.SBML_COMPARTMENT)
self.assert_(c.getMetaId() == "")
self.assert_(c.getNotes() == None)
self.assert_(c.getAnnotation() == None)
self.assert_(c.getLevel() == 2)
self.assert_(c.getVersion() == 1)
self.assert_(c.getNamespaces() != None)
self.assert_(c.getNamespaces().getLength() == 2)
self.assert_(c.getName() == "")
self.assert_(c.getSpatialDimensions() == 3)
self.assert_(c.getConstant() == True)
_dummyList = [c]
_dummyList[:] = []
del _dummyList
pass
def test_SBMLConvert_convertToL1_Species_Concentration(self): d = libsbml.SBMLDocument(2,1) m = d.createModel() sid = "C"; c = libsbml.Compartment(2,1) s = libsbml.Species(2,1) c.setId(sid) c.setSize(1.2) m.addCompartment(c) s.setId( "s" ) s.setCompartment(sid) s.setInitialConcentration(2.34) m.addSpecies(s) self.assert_( d.setLevelAndVersion(1,2,True) == True ) s1 = m.getSpecies(0) self.assert_( s1 != None ) self.assert_(( "C" == s1.getCompartment() )) self.assert_( m.getCompartment( "C").getSize() == 1.2 ) self.assert_( s1.getInitialConcentration() == 2.34 ) self.assert_( s1.isSetInitialConcentration() == True ) _dummyList = [ d ]; _dummyList[:] = []; del _dummyList pass