def annotate_sbase(sbase: libsbml.SBase, annotation: Annotation):
""" Annotate SBase based on given annotation data
:param sbase: libsbml.SBase
:param annotation: Annotation
:return:
"""
qualifier, resource = annotation.qualifier.value, annotation.resource
cv = libsbml.CVTerm() # type: libsbml.CVTerm
# set correct type of qualifier
if qualifier.startswith("BQB"):
cv.setQualifierType(libsbml.BIOLOGICAL_QUALIFIER)
sbml_qualifier = ModelAnnotator.get_SBMLQualifier(qualifier)
cv.setBiologicalQualifierType(sbml_qualifier)
elif qualifier.startswith('BQM'):
cv.setQualifierType(libsbml.MODEL_QUALIFIER)
sbml_qualifier = ModelAnnotator.get_SBMLQualifier(qualifier)
cv.setModelQualifierType(sbml_qualifier)
else:
LOGGER.error('Unsupported qualifier: {}'.format(qualifier))
cv.addResource(resource)
# meta id has to be set
if not sbase.isSetMetaId():
sbase.setMetaId(utils.create_metaid(sbase))
success = sbase.addCVTerm(cv)
if success != 0:
LOGGER.error("RDF not written: ", success)
LOGGER.error(libsbml.OperationReturnValue_toString(success))
LOGGER.error("{}, {}, {}".format(object, qualifier, resource))
def set_fields(self, obj: libsbml.SBase):
if self.sid is not None:
if not libsbml.SyntaxChecker.isValidSBMLSId(self.sid):
logging.error(
"The id `{self.sid}` is not a valid SBML SId on `{obj}`. "
"The SId syntax is defined as:"
"\tletter ::= 'a'..'z','A'..'Z'"
"\tdigit ::= '0'..'9'"
"\tidChar ::= letter | digit | '_'"
"\tSId ::= ( letter | '_' ) idChar*"
)
obj.setId(self.sid)
if self.name is not None:
obj.setName(self.name)
if self.sboTerm is not None:
obj.setSBOTerm(self.sboTerm)
if self.metaId is not None:
obj.setMetaId(self.metaId)
if self.annotations:
for a_tuple in self.annotations:
ModelAnnotator.annotate_sbase(
sbase=obj,
annotation=Annotation.from_tuple(a_tuple)
)
self.create_uncertainties(obj)
def annotate_sbase(sbase: libsbml.SBase, annotation: Annotation) -> None:
"""Annotate SBase based on given annotation data.
:param sbase: libsbml.SBase
:param annotation: Annotation
:return:
"""
qualifier, resource = annotation.qualifier.value, annotation.resource
cv: libsbml.CVTerm = libsbml.CVTerm()
# set correct type of qualifier
if isinstance(qualifier, str):
if qualifier.startswith("BQB"):
cv.setQualifierType(libsbml.BIOLOGICAL_QUALIFIER)
sbml_qualifier = ModelAnnotator.get_SBMLQualifier(qualifier)
success = check(
cv.setBiologicalQualifierType(str(sbml_qualifier)),
f"Set biological qualifier: '{sbml_qualifier}'",
)
if success != 0:
logger.error(
f"Could not set biological qualifier: {qualifier}")
elif qualifier.startswith("BQM"):
cv.setQualifierType(libsbml.MODEL_QUALIFIER)
sbml_qualifier = ModelAnnotator.get_SBMLQualifier(qualifier)
success = check(
cv.setModelQualifierType(str(sbml_qualifier)),
f"Set model qualifier: '{sbml_qualifier}'",
)
if success != 0:
logger.error(f"Could not set model qualifier: {qualifier}")
else:
logger.error(f"Unsupported qualifier: '{qualifier}'")
else:
msg = (f"qualifier is not a string, but: '{qualifier}' of type "
f"'{type(qualifier)}'.")
logger.error(msg)
raise ValueError(msg)
success = check(cv.addResource(resource),
f"Add resource: '{resource}'")
if success != 0:
logger.error(f"Could not add resource: {resource}")
# meta id has to be set
if not sbase.isSetMetaId():
sbase.setMetaId(utils.create_metaid(sbase))
success = sbase.addCVTerm(cv)
if success != 0:
logger.error(
f"Annotation RDF for CVTerm could not be written: {cv}")
logger.error(libsbml.OperationReturnValue_toString(success))
logger.error(f"{sbase}, {qualifier}, {resource}")
def set_fields(self, obj: libsbml.SBase):
if self.sid is not None:
obj.setId(self.sid)
if self.name is not None:
obj.setName(self.name)
if self.sboTerm is not None:
obj.setSBOTerm(self.sboTerm)
if self.metaId is not None:
obj.setMetaId(self.metaId)
self.create_uncertainties(obj)