"""Test bed for FBC version 3.
For latest SBML fbc v3 specification see
https://github.com/bgoli/sbml-fbc-spec/blob/main/sf_svn/spec/main.pdf
"""
from logging import getLogger
from pathlib import Path
import libsbml
# from sbmlutils.console import console
[docs]logger = getLogger(__name__)
[docs]def check(value: int, message: str) -> bool:
"""Check the libsbml return value and prints message if something happened.
If 'value' is None, prints an error message constructed using
'message' and then exits with status code 1. If 'value' is an integer,
it assumes it is a libSBML return status code. If the code value is
LIBSBML_OPERATION_SUCCESS, returns without further action; if it is not,
prints an error message constructed using 'message' along with text from
libSBML explaining the meaning of the code, and exits with status code 1.
"""
valid = True
if value is None:
logger.error(f"Error: LibSBML returned a null value trying to <{message}>.")
valid = False
elif isinstance(value, int):
if value != libsbml.LIBSBML_OPERATION_SUCCESS:
logger.error(f"Error encountered trying to '{message}'.")
logger.error(
f"LibSBML returned error code {str(value)}: "
f"{libsbml.OperationReturnValue_toString(value).strip()}"
)
valid = False
return valid
# create document with new fbc version 3 namespace
[docs]sbmlns: libsbml.SBMLNamespaces = libsbml.SBMLNamespaces(3, 1)
sbmlns.addPkgNamespace("fbc", 3)
[docs]doc: libsbml.SBMLDocument = libsbml.SBMLDocument(sbmlns)
[docs]doc_fbc: libsbml.FbcSBMLDocumentPlugin = doc.getPlugin("fbc")
doc_fbc.setRequired(False)
[docs]model: libsbml.Model = doc.createModel()
[docs]model_fbc: libsbml.FbcModelPlugin = model.getPlugin("fbc")
model_fbc.setStrict(True)
# Support for key value pairs exists
[docs]c: libsbml.Compartment = model.createCompartment()
c.setId("c1")
c.setSize(1.0)
c.setConstant(True)
[docs]s1: libsbml.Species = model.createSpecies()
s1.setId("s1")
s1.setCompartment("c1")
s1.setInitialConcentration(1.0)
s1.setConstant(False)
s1.setHasOnlySubstanceUnits(False)
s1.setBoundaryCondition(False)
# KeyValuePair on Species
[docs]s1_fbc: libsbml.FbcSpeciesPlugin = s1.getPlugin("fbc")
[docs]kvp_list: libsbml.ListOfKeyValuePairs = s1_fbc.getListOfKeyValuePairs()
kvp_list.setXmlns("http://sbml.org/fbc/keyvaluepair")
[docs]kvp: libsbml.KeyValuePair = kvp_list.createKeyValuePair()
check(kvp.setKey("testdata"), "Set Key on KeyValuePair")
check(kvp.setValue("1.0"), "Set Value on KeyValuePair")
[docs]s2: libsbml.Species = model.createSpecies()
s2.setId("s2")
s2.setCompartment("c1")
s2.setInitialConcentration(1.0)
s2.setConstant(False)
s2.setHasOnlySubstanceUnits(False)
s2.setBoundaryCondition(False)
# p1: libsbml.Parameter = model.createParameter()
# p1.setId("lb")
# p1.setValue(-100)
# p1.setConstant(True)
# # KeyValue Pair on parameter
# p1_fbc: libsbml.FbcSpeciesPlugin = p1.getPlugin("fbc")
# kvp_list: libsbml.ListOfKeyValuePairs = p1_fbc.getListOfKeyValuePairs()
# # kvp_list.setXmlns("http://sbml.org/fbc/keyvaluepair")
# kvp: libsbml.KeyValuePair = kvp_list.createKeyValuePair()
# check(kvp.setKey("pdata"), "Set Key on KeyValuePair")
# check(kvp.setValue("10.0"), "Set Value on KeyValuePair")
#
# p2: libsbml.Parameter = model.createParameter()
# p2.setId("ub")
# p2.setValue(100)
# p2.setConstant(True)
# Support exists for user constraints
[docs]reaction: libsbml.Reaction = model.createReaction()
reaction.setId("r1")
reaction.setReversible(True)
reaction.setFast(False)
[docs]fbc_reaction: libsbml.FbcReactionPlugin = reaction.getPlugin("fbc")
fbc_reaction.setUpperFluxBound("ub")
fbc_reaction.setLowerFluxBound("lb")
[docs]reactant: libsbml.SpeciesReference = reaction.createReactant()
reactant.setSpecies("s1")
reactant.setConstant(True)
reactant.setStoichiometry(1.0)
[docs]product: libsbml.SpeciesReference = reaction.createProduct()
product.setSpecies("s2")
product.setConstant(True)
product.setStoichiometry(1.0)
[docs]constraint: libsbml.UserDefinedConstraint = model_fbc.createUserDefinedConstraint()
constraint.setId("constraint1")
constraint.setLowerBound("lb")
constraint.setUpperBound("ub")
[docs]component: libsbml.UserDefinedConstraintComponent = (
constraint.createUserDefinedConstraintComponent()
)
component.setCoefficient(10.0)
component.setVariable("r1")
component.setVariableType(libsbml.FBC_FBCVARIABLETYPE_LINEAR)
[docs]sbml_str: str = libsbml.writeSBMLToString(doc)
print("-" * 80)
# console.log(sbml_str)
print(sbml_str)
print("-" * 80)
# checking that SBML string can be read again
[docs]doc2 = libsbml.readSBMLFromString(sbml_str)
if doc2.getNumErrors() > 0:
if doc2.getError(0).getErrorId() == libsbml.XMLFileUnreadable:
[docs] err_message = "Unreadable SBML file"
elif doc2.getError(0).getErrorId() == libsbml.XMLFileOperationError:
err_message = "Problems reading SBML file: XMLFileOperationError"
else:
err_message = "SBMLDocumentErrors encountered while reading the SBML file."
# log_sbml_errors_for_doc(doc)
logger.error(f"`read_sbml` error `{err_message}`")
for k in range(doc2.getNumErrors()):
error: libsbml.SBMLError = doc2.getError(k)
print(f"Error {k}")
print(error.getMessage())
# from sbmlutils.io import validate_sbml
# from sbmlutils.validation import ValidationOptions
#
#
# validate_sbml(
# source=sbml_str, validation_options=ValidationOptions(units_consistency=False)
# )
# sbml_path = Path("fbc_version3.xml")
# with open("fbc_version3.xml", "w") as f_sbml:
# f_sbml.write(sbml_str)
#
# validate_sbml(
# source=sbml_path, validation_options=ValidationOptions(units_consistency=False)
# )