def test_SBMLNamespaces_constructor(self):
s = None
try:
s = libsbml.SBMLNamespaces(3, 1)
s = libsbml.SBMLNamespaces(self.SN31)
except ValueError:
inst = sys.exc_info()[1]
s = None
pass
self.assert_(s != None)
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 create_merged_doc(model_paths, merged_id="merged"):
"""
Create a comp model from the given model paths.
Warning: This only works if all models are in the same directory.
"""
sbmlns = libsbml.SBMLNamespaces(3, 1)
sbmlns.addPackageNamespace("comp", 1)
doc = libsbml.SBMLDocument(sbmlns)
doc.setPackageRequired("comp", True)
# model
model = doc.createModel()
model.setId(merged_id)
# comp plugin
comp_doc = doc.getPlugin("comp") # type: libsbml.CompSBMLDocumentPlugin
comp_model = model.getPlugin("comp") # type: libsbml.CompModelPlugin
for emd_id, path in model_paths.items():
# create ExternalModelDefinitions
emd = comp.create_ExternalModelDefinition(comp_doc,
emd_id,
source=path)
# add submodel which references the external model definitions
print("emd:", emd)
print("emd_id:", emd_id)
print("comp_model:", comp_model)
comp.add_submodel_from_emd(comp_model, submodel_id=emd_id, emd=emd)
return doc
def create_merged_doc(model_paths: Dict[str, Path],
merged_id: str = "merged") -> libsbml.SBMLDocument:
"""Create a comp model from given model paths.
Warning: This only works if all models are in the same directory.
:param model_paths: Dictionary of id:path
:param merged_id:
:return:
"""
sbmlns = libsbml.SBMLNamespaces(3, 1)
sbmlns.addPackageNamespace("comp", 1)
doc = libsbml.SBMLDocument(sbmlns) # type: libsbml.SBMLDocument
doc.setPackageRequired("comp", True)
# model
model = doc.createModel() # type: libsbml.Model
model.setId(merged_id)
# comp plugin
comp_doc = doc.getPlugin("comp") # type: libsbml.CompSBMLDocumentPlugin
comp_model = model.getPlugin("comp") # type: libsbml.CompModelPlugin
for emd_id, path in model_paths.items():
# create ExternalModelDefinitions
emd = comp.create_ExternalModelDefinition(
comp_doc, emd_id,
source=str(path)) # type: libsbml.ExternalModelDefinition
# add submodel which references the external model definitions
comp.add_submodel_from_emd(comp_model, submodel_id=emd_id, emd=emd)
return doc
def _create_merged_doc(
model_paths: Dict[str, Path],
merged_id: str = "merged",
sbml_level: int = 3,
sbml_version: int = 1,
) -> libsbml.SBMLDocument:
"""Create a comp model from given model paths.
Warning: This only works if all models are in the same directory.
"""
sbmlns = libsbml.SBMLNamespaces(sbml_level, sbml_version)
sbmlns.addPackageNamespace("comp", 1)
doc: libsbml.SBMLDocument = libsbml.SBMLDocument(sbmlns)
doc.setPackageRequired("comp", True)
model: libsbml.Model = doc.createModel()
model.setId(merged_id)
comp_doc: libsbml.CompSBMLDocumentPlugin = doc.getPlugin("comp")
comp_model: libsbml.CompModelPlugin = model.getPlugin("comp")
for emd_id, path in model_paths.items():
# create ExternalModelDefinition
emd: libsbml.ExternalModelDefinition = comp.create_ExternalModelDefinition(
comp_doc, emd_id, source=str(path))
# add submodel which references the external model definition
comp.add_submodel_from_emd(comp_model, submodel_id=emd_id, emd=emd)
return doc
def test_L3_SpeciesReference_createWithNS(self): xmlns = libsbml.XMLNamespaces() xmlns.add( "http://www.sbml.org", "testsbml") sbmlns = libsbml.SBMLNamespaces(3,1) sbmlns.addNamespaces(xmlns) sr = libsbml.SpeciesReference(sbmlns) self.assert_( sr.getTypeCode() == libsbml.SBML_SPECIES_REFERENCE ) self.assert_( sr.getMetaId() == "" ) self.assert_( sr.getNotes() == None ) self.assert_( sr.getAnnotation() == None ) self.assert_( sr.getLevel() == 3 ) self.assert_( sr.getVersion() == 1 ) self.assert_( sr.getNamespaces() != None ) self.assert_( sr.getNamespaces().getLength() == 2 ) self.assert_( sr.getId() == "" ) self.assert_( sr.getName() == "" ) self.assert_( sr.getSpecies() == "" ) self.assertEqual( True, isnan(sr.getStoichiometry()) ) self.assert_( sr.getConstant() == False ) self.assertEqual( False, sr.isSetId() ) self.assertEqual( False, sr.isSetName() ) self.assertEqual( False, sr.isSetSpecies() ) self.assertEqual( False, sr.isSetStoichiometry() ) self.assertEqual( False, sr.isSetConstant() ) _dummyList = [ sr ]; _dummyList[:] = []; del _dummyList pass
def test_L3_Model_createWithNS(self):
xmlns = libsbml.XMLNamespaces()
xmlns.add("http://www.sbml.org", "testsbml")
sbmlns = libsbml.SBMLNamespaces(3, 1)
sbmlns.addNamespaces(xmlns)
m = libsbml.Model(sbmlns)
self.assert_(m.getTypeCode() == libsbml.SBML_MODEL)
self.assert_(m.getMetaId() == "")
self.assert_(m.getNotes() == None)
self.assert_(m.getAnnotation() == None)
self.assert_(m.getLevel() == 3)
self.assert_(m.getVersion() == 1)
self.assert_(m.getNamespaces() != None)
self.assert_(m.getNamespaces().getLength() == 2)
self.assert_(m.getId() == "")
self.assert_(m.getName() == "")
self.assert_(m.getSubstanceUnits() == "")
self.assert_(m.getTimeUnits() == "")
self.assert_(m.getVolumeUnits() == "")
self.assert_(m.getAreaUnits() == "")
self.assert_(m.getLengthUnits() == "")
self.assert_(m.getConversionFactor() == "")
self.assertEqual(False, m.isSetId())
self.assertEqual(False, m.isSetName())
self.assertEqual(False, m.isSetSubstanceUnits())
self.assertEqual(False, m.isSetTimeUnits())
self.assertEqual(False, m.isSetVolumeUnits())
self.assertEqual(False, m.isSetAreaUnits())
self.assertEqual(False, m.isSetLengthUnits())
self.assertEqual(False, m.isSetConversionFactor())
_dummyList = [m]
_dummyList[:] = []
del _dummyList
pass
def test_L3_Reaction_createWithNS(self):
xmlns = libsbml.XMLNamespaces()
xmlns.add("http://www.sbml.org", "testsbml")
sbmlns = libsbml.SBMLNamespaces(3, 1)
sbmlns.addNamespaces(xmlns)
r = libsbml.Reaction(sbmlns)
self.assert_(r.getTypeCode() == libsbml.SBML_REACTION)
self.assert_(r.getMetaId() == "")
self.assert_(r.getNotes() == None)
self.assert_(r.getAnnotation() == None)
self.assert_(r.getLevel() == 3)
self.assert_(r.getVersion() == 1)
self.assert_(r.getNamespaces() != None)
self.assert_(r.getNamespaces().getLength() == 2)
self.assert_(r.getId() == "")
self.assert_(r.getName() == "")
self.assert_(r.getCompartment() == "")
self.assert_(r.getFast() == False)
self.assert_(r.getReversible() == True)
self.assertEqual(False, r.isSetId())
self.assertEqual(False, r.isSetName())
self.assertEqual(False, r.isSetCompartment())
self.assertEqual(False, r.isSetFast())
self.assertEqual(False, r.isSetReversible())
_dummyList = [r]
_dummyList[:] = []
del _dummyList
pass
def test_SBMLNamespaces_add_and_remove_namespaces(self):
sbmlns = libsbml.SBMLNamespaces( 3,1 )
self.assert_( sbmlns.getLevel() == 3 )
self.assert_( sbmlns.getVersion() == 1 )
sbmlns.addNamespace("http://www.sbml.org/sbml/level3/version1/group/version1", "group")
sbmlns.addNamespace("http://www.sbml.org/sbml/level3/version1/layout/version1", "layout")
sbmlns.addNamespace("http://www.sbml.org/sbml/level3/version1/render/version1", "render")
sbmlns.addNamespace("http://www.sbml.org/sbml/level3/version1/multi/version1", "multi")
ns = sbmlns.getNamespaces()
self.assert_( ns.getLength() == 5 )
self.assert_( ns.getURI(0) == "http://www.sbml.org/sbml/level3/version1/core" )
self.assert_( ns.getPrefix(0) == "" )
self.assert_( ns.getURI(1) == "http://www.sbml.org/sbml/level3/version1/group/version1" )
self.assert_( ns.getPrefix(1) == "group" )
self.assert_( ns.getURI(2) == "http://www.sbml.org/sbml/level3/version1/layout/version1" )
self.assert_( ns.getPrefix(2) == "layout" )
self.assert_( ns.getURI(3) == "http://www.sbml.org/sbml/level3/version1/render/version1" )
self.assert_( ns.getPrefix(3) == "render" )
self.assert_( ns.getURI(4) == "http://www.sbml.org/sbml/level3/version1/multi/version1" )
self.assert_( ns.getPrefix(4) == "multi" )
sbmlns.removeNamespace("http://www.sbml.org/sbml/level3/version1/layout/version1")
sbmlns.removeNamespace("http://www.sbml.org/sbml/level3/version1/group/version1")
sbmlns.removeNamespace("http://www.sbml.org/sbml/level3/version1/render/version1")
sbmlns.removeNamespace("http://www.sbml.org/sbml/level3/version1/multi/version1")
pass
def test_L3_Unit_createWithNS(self):
xmlns = libsbml.XMLNamespaces()
xmlns.add("http://www.sbml.org", "testsbml")
sbmlns = libsbml.SBMLNamespaces(3, 1)
sbmlns.addNamespaces(xmlns)
u = libsbml.Unit(sbmlns)
self.assert_(u.getTypeCode() == libsbml.SBML_UNIT)
self.assert_(u.getMetaId() == "")
self.assert_(u.getNotes() == None)
self.assert_(u.getAnnotation() == None)
self.assert_(u.getLevel() == 3)
self.assert_(u.getVersion() == 1)
self.assert_(u.getNamespaces() != None)
self.assert_(u.getNamespaces().getLength() == 2)
self.assert_(u.getKind() == libsbml.UNIT_KIND_INVALID)
self.assertEqual(True, isnan(u.getExponentAsDouble()))
self.assertEqual(True, isnan(u.getMultiplier()))
self.assertEqual(False, u.isSetKind())
self.assertEqual(False, u.isSetExponent())
self.assertEqual(False, u.isSetMultiplier())
self.assertEqual(False, u.isSetScale())
_dummyList = [u]
_dummyList[:] = []
del _dummyList
pass
def test_L3_Parameter_createWithNS(self): xmlns = libsbml.XMLNamespaces() xmlns.add( "http://www.sbml.org", "testsbml") sbmlns = libsbml.SBMLNamespaces(3,1) sbmlns.addNamespaces(xmlns) p = libsbml.Parameter(sbmlns) self.assert_( p.getTypeCode() == libsbml.SBML_PARAMETER ) self.assert_( p.getMetaId() == "" ) self.assert_( p.getNotes() == None ) self.assert_( p.getAnnotation() == None ) self.assert_( p.getLevel() == 3 ) self.assert_( p.getVersion() == 1 ) self.assert_( p.getNamespaces() != None ) self.assert_( p.getNamespaces().getLength() == 2 ) self.assert_( p.getId() == "" ) self.assert_( p.getName() == "" ) self.assert_( p.getUnits() == "" ) self.assertEqual( True, isnan(p.getValue()) ) self.assert_( p.getConstant() == True ) self.assertEqual( False, p.isSetId() ) self.assertEqual( False, p.isSetName() ) self.assertEqual( False, p.isSetValue() ) self.assertEqual( False, p.isSetUnits() ) self.assertEqual( False, p.isSetConstant() ) _dummyList = [ p ]; _dummyList[:] = []; del _dummyList pass
def template_doc_bounds(model_id, create_min_max=True):
""" Create template bounds model.
Adds min and max functions
:param create_min_max:
:param model_id: model identifier
:return: SBMLDocument
"""
sbmlns = libsbml.SBMLNamespaces(SBML_LEVEL, SBML_VERSION, 'comp',
SBML_COMP_VERSION)
doc = libsbml.SBMLDocument(sbmlns)
doc.setPackageRequired(SBML_COMP_NAME, True)
model = doc.createModel()
model.setId("{}_bounds".format(model_id))
model.setName("{} (BOUNDS)".format(model_id))
model.setSBOTerm(comp.SBO_CONTINOUS_FRAMEWORK)
if create_min_max:
objects = [
# definition of min and max
Function('max', 'lambda(x,y, piecewise(x,gt(x,y),y) )',
name='min'),
Function('min', 'lambda(x,y, piecewise(x,lt(x,y),y) )',
name='max'),
]
factory.create_objects(model, objects)
return doc
def test_SBMLNamespaces_L2V1(self):
sbml = libsbml.SBMLNamespaces(2, 1)
self.assert_(sbml.getLevel() == 2)
self.assert_(sbml.getVersion() == 1)
ns = sbml.getNamespaces()
self.assert_(ns.getLength() == 1)
self.assert_(ns.getURI(0) == "http://www.sbml.org/sbml/level2")
self.assert_(ns.getPrefix(0) == "")
sbml = None
pass
def _distrib_doc() -> libsbml.SBMLDocument:
"""Create distrib document."""
sbml_level = 3
sbml_version = 1
sbmlns = libsbml.SBMLNamespaces(sbml_level, sbml_version)
sbmlns.addPackageNamespace("distrib", 1)
doc: libsbml.SBMLDocument = libsbml.SBMLDocument(sbmlns)
doc.setPackageRequired("distrib", True)
return doc
def test_SyntaxChecker_validXHTML(self):
NS24 = libsbml.SBMLNamespaces(2,4)
NS31 = libsbml.SBMLNamespaces(3,1)
toptriple = libsbml.XMLTriple("notes", "", "")
triple = libsbml.XMLTriple("p", "", "")
att = libsbml.XMLAttributes()
ns = libsbml.XMLNamespaces()
ns.add( "http://www.w3.org/1999/xhtml", "")
tt = libsbml.XMLToken("This is my text")
n1 = libsbml.XMLNode(tt)
toptoken = libsbml.XMLToken(toptriple,att)
topnode = libsbml.XMLNode(toptoken)
token = libsbml.XMLToken(triple,att,ns)
node = libsbml.XMLNode(token)
node.addChild(n1)
topnode.addChild(node)
self.assert_( libsbml.SyntaxChecker.hasExpectedXHTMLSyntax(topnode,None) == True )
self.assert_( libsbml.SyntaxChecker.hasExpectedXHTMLSyntax(topnode,NS24) == True )
self.assert_( libsbml.SyntaxChecker.hasExpectedXHTMLSyntax(topnode,NS31) == True )
triple = libsbml.XMLTriple("html", "", "")
token = libsbml.XMLToken(triple,att,ns)
node = libsbml.XMLNode(token)
node.addChild(n1)
topnode.removeChild(0)
topnode.addChild(node)
self.assert_( libsbml.SyntaxChecker.hasExpectedXHTMLSyntax(topnode,None) == True )
self.assert_( libsbml.SyntaxChecker.hasExpectedXHTMLSyntax(topnode,NS24) == False )
self.assert_( libsbml.SyntaxChecker.hasExpectedXHTMLSyntax(topnode,NS31) == True )
triple = libsbml.XMLTriple("html", "", "")
ns.clear()
token = libsbml.XMLToken(triple,att,ns)
node = libsbml.XMLNode(token)
node.addChild(n1)
topnode.removeChild(0)
topnode.addChild(node)
self.assert_( libsbml.SyntaxChecker.hasExpectedXHTMLSyntax(topnode,None) == False )
self.assert_( libsbml.SyntaxChecker.hasExpectedXHTMLSyntax(topnode,NS24) == False )
self.assert_( libsbml.SyntaxChecker.hasExpectedXHTMLSyntax(topnode,NS31) == False )
pass
def _init_sbml_model(self) -> None:
"""Create and initialize the SBML model."""
# FIXME: support arbitrary levels and versions
sbmlns = libsbml.SBMLNamespaces(3, 1)
sbmlns.addPackageNamespace("comp", 1)
doc: libsbml.SBMLDocument = libsbml.SBMLDocument(sbmlns)
doc.setPackageRequired("comp", True)
self.doc = doc
model: libsbml.Model = doc.createModel()
model.setNotes(notes)
model.setId(f"Interpolation_{self.method}")
model.setName(f"Interpolation_{self.method}")
self.model = model
def test_FunctionDefinition_createWithNS(self): xmlns = libsbml.XMLNamespaces() xmlns.add( "http://www.sbml.org", "testsbml") sbmlns = libsbml.SBMLNamespaces(2,1) sbmlns.addNamespaces(xmlns) object = libsbml.FunctionDefinition(sbmlns) self.assert_( object.getTypeCode() == libsbml.SBML_FUNCTION_DEFINITION ) self.assert_( object.getMetaId() == "" ) self.assert_( object.getNotes() == None ) self.assert_( object.getAnnotation() == None ) self.assert_( object.getLevel() == 2 ) self.assert_( object.getVersion() == 1 ) self.assert_( object.getNamespaces() != None ) self.assert_( object.getNamespaces().getLength() == 2 ) _dummyList = [ object ]; _dummyList[:] = []; del _dummyList pass
def test_Constraint_createWithNS(self): xmlns = libsbml.XMLNamespaces() xmlns.add( "http://www.sbml.org", "testsbml") sbmlns = libsbml.SBMLNamespaces(2,2) sbmlns.addNamespaces(xmlns) object = libsbml.Constraint(sbmlns) self.assert_( object.getTypeCode() == libsbml.SBML_CONSTRAINT ) self.assert_( object.getMetaId() == "" ) self.assert_( object.getNotes() == None ) self.assert_( object.getAnnotation() == None ) self.assert_( object.getLevel() == 2 ) self.assert_( object.getVersion() == 2 ) self.assert_( object.getNamespaces() != None ) self.assert_( object.getNamespaces().getLength() == 2 ) _dummyList = [ object ]; _dummyList[:] = []; del _dummyList pass
def test_EventAssignment_createWithNS(self): xmlns = libsbml.XMLNamespaces() xmlns.add( "http://www.sbml.org", "testsbml") sbmlns = libsbml.SBMLNamespaces(2,1) sbmlns.addNamespaces(xmlns) object = libsbml.EventAssignment(sbmlns) self.assert_( object.getTypeCode() == libsbml.SBML_EVENT_ASSIGNMENT ) self.assert_( object.getMetaId() == "" ) self.assert_( object.getNotes() == None ) self.assert_( object.getAnnotation() == None ) self.assert_( object.getLevel() == 2 ) self.assert_( object.getVersion() == 1 ) self.assert_( object.getNamespaces() != None ) self.assert_( object.getNamespaces().getLength() == 2 ) _dummyList = [ object ]; _dummyList[:] = []; del _dummyList pass
def test_StoichiometryMath_createWithNS(self): xmlns = libsbml.XMLNamespaces() xmlns.add( "http://www.sbml.org", "testsbml") sbmlns = libsbml.SBMLNamespaces(2,1) sbmlns.addNamespaces(xmlns) object = libsbml.StoichiometryMath(sbmlns) self.assert_( object.getTypeCode() == libsbml.SBML_STOICHIOMETRY_MATH ) self.assert_( object.getMetaId() == "" ) self.assert_( object.getNotes() == None ) self.assert_( object.getAnnotation() == None ) self.assert_( object.getLevel() == 2 ) self.assert_( object.getVersion() == 1 ) self.assert_( object.getNamespaces() != None ) self.assert_( object.getNamespaces().getLength() == 2 ) _dummyList = [ object ]; _dummyList[:] = []; del _dummyList pass
def template_doc_update(model_id):
""" Create template update model.
:param model_id: model identifier
:return: SBMLDocument
"""
sbmlns = libsbml.SBMLNamespaces(SBML_LEVEL, SBML_VERSION, 'comp',
SBML_COMP_VERSION)
doc = libsbml.SBMLDocument(sbmlns)
doc.setPackageRequired(SBML_COMP_NAME, True)
# model
model = doc.createModel()
model.setId("{}_update".format(model_id))
model.setName("{} (UPDATE)".format(model_id))
model.setSBOTerm(comp.SBO_CONTINOUS_FRAMEWORK)
return doc
def _init_sbml_model(self):
""" Initializes the SBML model.
:return:
:rtype:
"""
sbmlns = libsbml.SBMLNamespaces(3, 1)
sbmlns.addPackageNamespace("comp", 1)
doc = libsbml.SBMLDocument(sbmlns)
doc.setPackageRequired("comp", True)
self.doc = doc
model = doc.createModel()
model.setNotes(notes)
model.setId("Interpolation_{}".format(self.method))
model.setName("Interpolation_{}".format(self.method))
self.model = model
def test_CompartmentType_createWithNS(self):
xmlns = libsbml.XMLNamespaces()
xmlns.add("http://www.sbml.org", "testsbml")
sbmlns = libsbml.SBMLNamespaces(2, 2)
sbmlns.addNamespaces(xmlns)
object = libsbml.CompartmentType(sbmlns)
self.assert_(object.getTypeCode() == libsbml.SBML_COMPARTMENT_TYPE)
self.assert_(object.getMetaId() == "")
self.assert_(object.getNotes() == None)
self.assert_(object.getAnnotation() == None)
self.assert_(object.getLevel() == 2)
self.assert_(object.getVersion() == 2)
self.assert_(object.getNamespaces() != None)
self.assert_(object.getNamespaces().getLength() == 2)
_dummyList = [object]
_dummyList[:] = []
del _dummyList
pass
def test_Delay_createWithNS(self):
xmlns = libsbml.XMLNamespaces()
xmlns.add("http://www.sbml.org", "testsbml")
sbmlns = libsbml.SBMLNamespaces(2, 1)
sbmlns.addNamespaces(xmlns)
object = libsbml.Delay(sbmlns)
self.assert_(object.getTypeCode() == libsbml.SBML_DELAY)
self.assert_(object.getMetaId() == "")
self.assert_(object.getNotes() == None)
self.assert_(object.getAnnotation() == None)
self.assert_(object.getLevel() == 2)
self.assert_(object.getVersion() == 1)
self.assert_(object.getNamespaces() != None)
self.assert_(object.getNamespaces().getLength() == 2)
_dummyList = [object]
_dummyList[:] = []
del _dummyList
pass
def test_AlgebraicRule_createWithNS(self):
xmlns = libsbml.XMLNamespaces()
xmlns.add("http://www.sbml.org", "testsbml")
sbmlns = libsbml.SBMLNamespaces(2, 3)
sbmlns.addNamespaces(xmlns)
r = libsbml.AlgebraicRule(sbmlns)
self.assert_(r.getTypeCode() == libsbml.SBML_ALGEBRAIC_RULE)
self.assert_(r.getMetaId() == "")
self.assert_(r.getNotes() == None)
self.assert_(r.getAnnotation() == None)
self.assert_(r.getLevel() == 2)
self.assert_(r.getVersion() == 3)
self.assert_(r.getNamespaces() != None)
self.assert_(r.getNamespaces().getLength() == 2)
_dummyList = [r]
_dummyList[:] = []
del _dummyList
pass
def template_doc_top(model_id, emds):
""" Create template top model.
Adds the ExternalModelDefinitions and submodels for FBA, BOUNDS & UPDATE model.
:param emds:
:param model_id: model identifier
:return: SBMLDocument
"""
sbmlns = libsbml.SBMLNamespaces(SBML_LEVEL, SBML_VERSION, 'comp',
SBML_COMP_VERSION)
doc = libsbml.SBMLDocument(sbmlns)
doc.setPackageRequired(SBML_COMP_NAME, True)
doc.setPackageRequired(SBML_FBC_NAME, False)
# create models and submodels
model = doc.createModel()
model.setId("{}_top".format(model_id))
model.setName("{} (TOP)".format(model_id))
model.setSBOTerm(comp.SBO_CONTINOUS_FRAMEWORK)
# create listOfExternalModelDefinitions
doc_comp = doc.getPlugin(SBML_COMP_NAME)
emd_fba = comp.create_ExternalModelDefinition(
doc_comp,
"{}_fba".format(model_id),
source=emds["{}_fba".format(model_id)])
emd_bounds = comp.create_ExternalModelDefinition(
doc_comp,
"{}_bounds".format(model_id),
source=emds["{}_bounds".format(model_id)])
emd_update = comp.create_ExternalModelDefinition(
doc_comp,
"{}_update".format(model_id),
source=emds["{}_update".format(model_id)])
# add submodel which references the external model definition
doc_model = model.getPlugin(SBML_COMP_NAME)
comp.add_submodel_from_emd(doc_model, submodel_id="fba", emd=emd_fba)
comp.add_submodel_from_emd(doc_model, submodel_id="bounds", emd=emd_bounds)
comp.add_submodel_from_emd(doc_model, submodel_id="update", emd=emd_update)
return doc
def create_port_doc():
sbmlns = libsbml.SBMLNamespaces(3, 1, "comp", 1)
doc = libsbml.SBMLDocument(sbmlns)
doc.setPackageRequired("comp", True)
model = doc.createModel()
model.setId("toy_update")
model.setName("toy (UPDATE submodel)")
model.setSBOTerm(SBO_CONTINOUS_FRAMEWORK)
objects = [
fac.Compartment(
sid="extern",
value=1.0,
unit="m3",
constant=True,
name="external compartment",
),
fac.Species(
sid="A",
name="A",
initialConcentration=10.0,
hasOnlySubstanceUnits=True,
compartment="extern",
),
fac.Species(
sid="C",
name="C",
initialConcentration=0,
hasOnlySubstanceUnits=True,
compartment="extern",
),
fac.Parameter(sid="EX_A",
value=1.0,
constant=False,
sboTerm="SBO:0000613"),
fac.Parameter(sid="EX_C",
value=1.0,
constant=False,
sboTerm="SBO:0000613"),
]
fac.create_objects(model, obj_iter=objects)
return doc
def test_ModifierSpeciesReference_createWithNS(self):
xmlns = libsbml.XMLNamespaces()
xmlns.add("http://www.sbml.org", "testsbml")
sbmlns = libsbml.SBMLNamespaces(2, 1)
sbmlns.addNamespaces(xmlns)
object = libsbml.ModifierSpeciesReference(sbmlns)
self.assert_(
object.getTypeCode() == libsbml.SBML_MODIFIER_SPECIES_REFERENCE)
self.assert_(object.getMetaId() == "")
self.assert_(object.getNotes() == None)
self.assert_(object.getAnnotation() == None)
self.assert_(object.getLevel() == 2)
self.assert_(object.getVersion() == 1)
self.assert_(object.getNamespaces() != None)
n = object.getNamespaces()
self.assert_(n.getLength() == 2)
_dummyList = [object]
_dummyList[:] = []
del _dummyList
pass
def create_fba_doc():
sbmlns = libsbml.SBMLNamespaces(3, 1)
sbmlns.addPackageNamespace("fbc", 2)
sbmlns.addPackageNamespace("comp", 1)
doc = libsbml.SBMLDocument(sbmlns)
doc.setPackageRequired("comp", True)
doc.setPackageRequired("fbc", False)
model = doc.createModel()
mplugin = model.getPlugin("fbc")
mplugin.setStrict(True)
objects = [
fac.Compartment(sid='cell', value=1.0),
fac.Species(sid='A', initialConcentration=0, compartment="cell"),
fac.Species(sid='B', initialConcentration=0, compartment="cell"),
]
fac.create_objects(model, objects)
return doc
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
