def cvterms(cls, sbase: libsbml.SBase) -> Optional[List]:
"""Parse CVTerms information.
:param sbase: SBase instance
"""
if not sbase.isSetAnnotation():
return None
cvterms = []
for kcv in range(sbase.getNumCVTerms()):
cv: libsbml.CVTerm = sbase.getCVTerm(kcv)
# qualifier
q_type = cv.getQualifierType()
if q_type == libsbml.MODEL_QUALIFIER:
qualifier = ModelQualifierType[cv.getModelQualifierType()]
elif q_type == libsbml.BIOLOGICAL_QUALIFIER:
qualifier = BiologicalQualifierType[
cv.getBiologicalQualifierType()]
else:
raise ValueError(f"Unsupported qualifier type: '{q_type}'")
resources = [
cv.getResourceURI(k) for k in range(cv.getNumResources())
]
cvterms.append({
"qualifier": qualifier,
"resources": resources,
})
# add SBO term as CVTerm
if sbase.isSetSBOTerm():
sbo = sbase.getSBOTermID()
sbo_in_cvs: bool = False
for cv in cvterms:
for resource in cv["resources"]:
if sbo in resource:
sbo_in_cvs = True
break
if not sbo_in_cvs:
cvterms = [{
"qualifier": "BQB_IS",
"resources": [f"https://identifiers.org/{sbo}"],
}] + cvterms
return cvterms
def sbase_dict(cls, sbase: libsbml.SBase) -> Dict[str, Any]:
"""Info dictionary for SBase.
:param sbase: SBase instance for which info dictionary is to be created
:return info dictionary for item
"""
pk = cls._get_pk(sbase)
d = {
"pk": pk,
"sbmlType": cls._sbml_type(sbase),
"id": sbase.getId() if sbase.isSetId() else None,
"metaId": sbase.getMetaId() if sbase.isSetMetaId() else None,
"name": sbase.getName() if sbase.isSetName() else None,
"sbo": sbase.getSBOTermID() if sbase.isSetSBOTerm() else None,
"cvterms": cls.cvterms(sbase),
"history": cls.model_history(sbase),
"notes": sbase.getNotesString() if sbase.isSetNotes() else None,
}
# TODO: add the ports information
if sbase.getTypeCode() in {libsbml.SBML_DOCUMENT, libsbml.SBML_MODEL}:
d["xml"] = None
else:
d["xml"] = sbase.toSBML()
# comp
item_comp = sbase.getPlugin("comp")
if item_comp and type(item_comp) == libsbml.CompSBasePlugin:
# ReplacedBy
if item_comp.isSetReplacedBy():
replaced_by = item_comp.getReplacedBy()
submodel_ref = replaced_by.getSubmodelRef()
d["replacedBy"] = {
"submodelRef": submodel_ref,
"replacedBySbaseref": cls._sbaseref(replaced_by),
}
else:
d["replacedBy"] = None
# ListOfReplacedElements
if item_comp.getNumReplacedElements() > 0:
replaced_elements = []
for rep_el in item_comp.getListOfReplacedElements():
submodel_ref = rep_el.getSubmodelRef()
replaced_elements.append({
"submodelRef":
submodel_ref,
"replacedElementSbaseref":
cls._sbaseref(rep_el),
})
d["replacedElements"] = replaced_elements
else:
d["replacedElements"] = None
# distrib
sbml_distrib: libsbml.DistribSBasePlugin = sbase.getPlugin("distrib")
if sbml_distrib and isinstance(sbml_distrib,
libsbml.DistribSBasePlugin):
d["uncertainties"] = []
for uncertainty in sbml_distrib.getListOfUncertainties():
u_dict = SBMLDocumentInfo.sbase_dict(uncertainty)
u_dict["uncertaintyParameters"] = []
upar: libsbml.UncertParameter
for upar in uncertainty.getListOfUncertParameters():
param_dict = {
"var":
upar.getVar() if upar.isSetVar() else None,
"value":
upar.getValue() if upar.isSetValue() else None,
"units":
upar.getUnits() if upar.isSetUnits() else None,
"type":
upar.getTypeAsString() if upar.isSetType() else None,
"definitionURL":
upar.getDefinitionURL()
if upar.isSetDefinitionURL() else None,
"math":
astnode_to_latex(upar.getMath())
if upar.isSetMath() else None,
}
u_dict["uncertaintyParameters"].append(param_dict)
d["uncertainties"].append(u_dict)
return d