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 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_model_history(model: libsbml.Model, creators) -> None:
"""Sets the model history from given creators.
:param model: SBML model
:param creators: list of creators
:return None
"""
if not model.isSetMetaId():
model.setMetaId(create_metaid(sbase=model))
if (creators is None) or (len(creators) == 0):
# at least on
return
else:
# create and set model history
h = _create_history(creators)
check(model.setModelHistory(h), "set model history")
def set_model_history(model, creators):
""" Sets the model history from given creators.
:param model: SBML model
:type model: libsbml.Model
:param creators: list of creators
:type creators:
"""
if not model.isSetMetaId():
model.setMetaId(create_metaid(sbase=model))
if creators is None or len(creators) is 0:
# at least on
return
else:
# create and set model history
h = _create_history(creators)
check(model.setModelHistory(h), 'set model history')