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restore support for species references #1358

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Merged
FFroehlich merged 3 commits into from
Dec 10, 2020
Merged

restore support for species references #1358

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fa0a950
restore support for species references
FFroehlich Dec 9, 2020
332bb5f
fixup and improve error message
FFroehlich Dec 9, 2020
68bc5b6
Merge branch 'develop' into fix_sbml_sref
FFroehlich Dec 10, 2020
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18 changes: 7 additions & 11 deletions python/amici/sbml_import.py
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Original file line number Diff line number Diff line change
Expand Up @@ -459,15 +459,6 @@ def _gather_base_locals(self):

self.add_local_symbol(c.getId(), _get_identifier_symbol(c))

for r in self.sbml.getListOfRules():
if not isinstance(self.sbml.getElementBySId(r.getVariable()),
sbml.SpeciesReference) \
or self._sympy_from_sbml_math(r) is None:
continue

self.add_local_symbol(r.getVariable(),
symbol_with_assumptions(r.getVariable()))

for r in self.sbml.getListOfReactions():
for e in itt.chain(r.getListOfReactants(), r.getListOfProducts()):
if not (e.isSetId() and e.isSetStoichiometry()) or \
Expand Down Expand Up @@ -505,8 +496,13 @@ def add_local_symbol(self, key: str, value: sp.Expr):
if key in itt.chain(self._local_symbols.keys(),
['True', 'False', 'pi']):
raise SBMLException(
'AMICI does not support SBML models containing '
f'variables with SId {key}.'
f'AMICI tried to add a local symbol {key} with value {value}, '
f'but {key} was already instantiated with '
f'{self._local_symbols[key]}. This means either that there '
f'are multiple SBML element with SId {key}, which is '
f'invalid SBML, or that the employed SId {key} is a special '
'reserved symbol in AMICI. This can be fixed by renaming '
f'the element with SId {key}.'
)
self._local_symbols[key] = value

Expand Down