def set_model_info(model, notes=None, creators=None, units=None, main_units=None): """ Adds the shared information to the models. :param model: SBMLModel instance :return: """ if creators: history.set_model_history(model, creators=creators) if units: set_units(model, units=units) if main_units: set_main_units(model, main_units=main_units) if notes: set_notes(model, notes=notes)
def test_set_model_history(): creators = [factory.Creator(familyName='Koenig', givenName="Matthias", email="*****@*****.**", organization="Test organisation")] sbmlns = libsbml.SBMLNamespaces(3, 1) doc = libsbml.SBMLDocument(sbmlns) model = doc.createModel() history.set_model_history(model, creators) # check if history was written correctly h = model.getModelHistory() assert h is not None assert h.getNumCreators() == 1 c = h.getCreator(0) assert 'Koenig' == c.getFamilyName() assert 'Matthias' == c.getGivenName() assert '*****@*****.**' == c.getEmail() assert 'Test organisation' == c.getOrganization()
def set_model_info(model, notes=None, creators=None, units=None, main_units=None): """ Adds the shared information to the models. :param model: SBMLModel instance :return: """ if creators: history.set_model_history(model, creators=creators) if units: set_units(model, units=units) if main_units: set_main_units(model, main_units=main_units) if notes: set_notes(model, notes=notes)
def test_set_model_history(): creators = [ factory.Creator(familyName='Koenig', givenName="Matthias", email="*****@*****.**", organization="Test organisation") ] sbmlns = libsbml.SBMLNamespaces(3, 1) doc = libsbml.SBMLDocument(sbmlns) model = doc.createModel() history.set_model_history(model, creators) # check if history was written correctly h = model.getModelHistory() assert h is not None assert h.getNumCreators() == 1 c = h.getCreator(0) assert 'Koenig' == c.getFamilyName() assert 'Matthias' == c.getGivenName() assert '*****@*****.**' == c.getEmail() assert 'Test organisation' == c.getOrganization()
def create_sbml(self, sbml_level=SBML_LEVEL, sbml_version=SBML_VERSION): """ Create the SBML model :return: :rtype: """ from sbmlutils.validation import check logging.info('*'*40) logging.info(self.model_id) logging.info('*' * 40) # create core model sbmlns = libsbml.SBMLNamespaces(sbml_level, sbml_version) # add all the packages # FIXME: only add packages which are required for the model sbmlns.addPackageNamespace("fbc", 2) sbmlns.addPackageNamespace("comp", 1) # sbmlns.addPackageNamespace("distrib", 1) self.doc = libsbml.SBMLDocument(sbmlns) self.doc.setPackageRequired("comp", True) self.doc.setPackageRequired("fbc", False) # self.doc.setPackageRequired("distrib", True) self.model = self.doc.createModel() fbc_plugin = self.model.getPlugin("fbc") fbc_plugin.setStrict(False) # name & id check(self.model.setId(self.model_id), 'set id') check(self.model.setName(self.model_id), 'set name') # notes if hasattr(self, 'notes') and self.notes is not None: factory.set_notes(self.model, self.notes) # history if hasattr(self, 'creators'): history.set_model_history(self.model, self.creators) # model units if hasattr(self, 'model_units'): factory.set_model_units(self.model, self.model_units) # lists ofs for attr in [ 'externalModelDefinitions', 'submodels', 'units', 'functions', 'parameters', 'compartments', 'species', 'assignments', 'rules', 'rate_rules', 'reactions', 'events', 'constraints', 'ports', 'replacedElements', 'deletions', 'objectives', 'layouts' ]: # create the respective objects if hasattr(self, attr): objects = getattr(self, attr) if objects: factory.create_objects(self.model, obj_iter=objects, key=attr) else: logging.warning("Not defined: <{}> ".format(attr))
def create_sbml(self, sbml_level: int = SBML_LEVEL, sbml_version: int = SBML_VERSION) -> libsbml.SBMLDocument: """Create the SBML model. :return: :rtype: """ logger.info(f"create_sbml: '{self.model_id}'") # create core model sbmlns = libsbml.SBMLNamespaces(sbml_level, sbml_version) # add all the packages # FIXME: only add packages which are required for the model supported_packages = {"fbc", "comp", "distrib"} sbmlns.addPackageNamespace("comp", 1) for package in self.packages: if package not in supported_packages: raise ValueError( f"Supported packages are: '{supported_packages}', " f"but package '{package}' found.") if package == "fbc": sbmlns.addPackageNamespace("fbc", 2) if package == "distrib": sbmlns.addPackageNamespace("distrib", 1) self.doc = libsbml.SBMLDocument(sbmlns) self.model = self.doc.createModel() self.doc.setPackageRequired("comp", True) if "fbc" in self.packages: self.doc.setPackageRequired("fbc", False) fbc_plugin = self.model.getPlugin("fbc") fbc_plugin.setStrict(False) if "distrib" in self.packages: self.doc.setPackageRequired("distrib", True) # name & id if self.model_id: check(self.model.setId(self.model_id), "set id") check(self.model.setName(self.model_id), "set name") else: logger.warning("Model id 'mid' should be set on model") # notes if hasattr(self, "notes") and self.notes is not None: factory.set_notes(self.model, self.notes) # history if hasattr(self, "creators"): history.set_model_history(self.model, self.creators) # model units if hasattr(self, "model_units"): factory.ModelUnits.set_model_units( self.model, self.model_units) # type: ignore # lists ofs for attr in [ "externalModelDefinitions", "submodels", "units", "functions", "parameters", "compartments", "species", "assignments", "rules", "rate_rules", "reactions", "events", "constraints", "ports", "replacedElements", "deletions", "objectives", "layouts", ]: # create the respective objects if hasattr(self, attr): objects = getattr(self, attr) if objects: factory.create_objects(self.model, obj_iter=objects, key=attr) else: logger.debug(f"Not defined: <{attr}>") return self.doc
def create_sbml(self, sbml_level=SBML_LEVEL, sbml_version=SBML_VERSION): """ Create the SBML model :return: :rtype: """ from sbmlutils.validation import check logging.info('*' * 40) logging.info(self.model_id) logging.info('*' * 40) # create core model sbmlns = libsbml.SBMLNamespaces(sbml_level, sbml_version) # add all the packages # FIXME: only add packages which are required for the model sbmlns.addPackageNamespace("fbc", 2) sbmlns.addPackageNamespace("comp", 1) # sbmlns.addPackageNamespace("distrib", 1) self.doc = libsbml.SBMLDocument(sbmlns) self.doc.setPackageRequired("comp", True) self.doc.setPackageRequired("fbc", False) # self.doc.setPackageRequired("distrib", True) self.model = self.doc.createModel() fbc_plugin = self.model.getPlugin("fbc") fbc_plugin.setStrict(False) # name & id check(self.model.setId(self.model_id), 'set id') check(self.model.setName(self.model_id), 'set name') # notes if hasattr(self, 'notes') and self.notes is not None: factory.set_notes(self.model, self.notes) # history if hasattr(self, 'creators'): history.set_model_history(self.model, self.creators) # model units if hasattr(self, 'model_units'): factory.set_model_units(self.model, self.model_units) # lists ofs for attr in [ 'externalModelDefinitions', 'submodels', 'units', 'functions', 'parameters', 'compartments', 'species', 'assignments', 'rules', 'rate_rules', 'reactions', 'events', 'constraints', 'ports', 'replacedElements', 'deletions', 'objectives', 'layouts' ]: # create the respective objects if hasattr(self, attr): objects = getattr(self, attr) if objects: factory.create_objects(self.model, obj_iter=objects, key=attr) else: logging.info("Not defined: <{}> ".format(attr))