def document(self, doc: libsbml.SBMLDocument) -> Dict[str, str]:
"""Info for SBMLDocument.
:param doc: SBMLDocument
:return: information dictionary for SBMLDocument
"""
d = self.sbase_dict(doc)
packages: Dict[str, Any] = {}
packages["document"] = {
"level": doc.getLevel(),
"version": doc.getVersion()
}
plugins: List[Dict[str, Any]] = []
for k in range(doc.getNumPlugins()):
plugin: libsbml.SBMLDocumentPlugin = doc.getPlugin(k)
prefix: str = plugin.getPrefix()
version: int = plugin.getPackageVersion()
plugins.append({"prefix": prefix, "version": version})
packages["plugins"] = plugins
d["packages"] = packages
return d
def info_document(self, doc: libsbml.SBMLDocument) -> Dict[str, str]:
"""Info dictionary for SBaseRef.
:param doc: SBMLDocument
:return: information dictionary for SBMLDocument
"""
info = self.info_sbase(doc)
packages = [
f'<span class="package">L{doc.getLevel()}V{doc.getVersion()}</span>'
]
for k in range(doc.getNumPlugins()):
plugin = doc.getPlugin(k)
prefix = plugin.getPrefix()
version = plugin.getPackageVersion()
packages.append(
f'<span class="package">{prefix}-V{version}</span>')
info["packages"] = " ".join(packages)
return info
def flatten_external_model_definitions(
doc: libsbml.SBMLDocument,
validate: bool = False) -> libsbml.SBMLDocument:
"""Converts all ExternalModelDefinitions to ModelDefinitions.
I.e. the definition of models in external files are read
and directly included in the top model. The resulting
comp model consists than only of a single file.
The model refs in the submodel do not change in the process,
so no need to update the submodels.
:param doc: SBMLDocument
:param validate: validation flag
:return: SBMLDocument with ExternalModelDefinitions replaced
"""
logger.debug("* flattenExternalModelDefinitions")
# FIXME: handle multiple levels of hierarchies. Recursively to handle the ExternalModelDefinitions of submodels
logger.warning(
"flattenExternalModelDefinitions is experimental and does not work recursively!"
)
comp_doc = doc.getPlugin("comp")
if comp_doc is None:
logger.warning(
"Model is not a comp model, no ExternalModelDefinitions")
return doc
emd_list = comp_doc.getListOfExternalModelDefinitions()
if (emd_list is None) or (len(emd_list) == 0):
# no ExternalModelDefinitions
logger.warning("Model does not contain any ExternalModelDefinitions")
return doc
else:
emd_ids = []
for emd in emd_list:
logger.debug(emd)
emd_ids.append(emd.getId())
# get the model definition from the model
ref_model = emd.getReferencedModel()
ref_doc = ref_model.getSBMLDocument()
# print(ref_model)
for k in range(ref_doc.getNumPlugins()):
plugin = ref_doc.getPlugin(k)
# print(k, plugin)
# enable the package on the main SBMLDocument
uri = plugin.getURI()
prefix = plugin.getPrefix()
doc.enablePackage(uri, prefix, True)
# print("\n")
# add model definition for model
md = libsbml.ModelDefinition(ref_model)
comp_doc.addModelDefinition(md)
# remove the emds afterwards
for emd_id in emd_ids:
# remove the emd from the model
comp_doc.removeExternalModelDefinition(emd_id)
# validate
if validate:
validate_doc(doc)
return doc
