def ions(self):
"""Dictionary of the ions involved in this mechanism"""
if self.__ions is None:
nmodl = _nmodl()
lookup_visitor = nmodl.visitor.AstLookupVisitor()
ions = lookup_visitor.lookup(self.ast,
nmodl.ast.AstNodeType.USEION)
result = {}
for ion in ions:
name = nmodl.to_nmodl(ion.name)
read = [nmodl.to_nmodl(item) for item in ion.readlist]
write = [nmodl.to_nmodl(item) for item in ion.writelist]
if ion.valence:
valence = int(nmodl.to_nmodl(ion.valence.value))
else:
valence = None
ontology_id = None
try:
ontology_id = ion.ontology_id
except:
# older versions of the NMODL library didn't support .ontology_id
pass
result[name] = {
'read': read,
'write': write,
'charge': valence,
'ontology_id': ontology_id
}
self.__ions = result
# return a copy
return dict(self.__ions)
def test_ast_construction(self):
string = ast.String("tau")
name = ast.Name(string)
assert nmodl.to_nmodl(name) == 'tau'
int_macro = nmodl.ast.Integer(1, ast.Name(ast.String("x")))
assert nmodl.to_nmodl(int_macro) == 'x'
statements = []
block = ast.StatementBlock(statements)
neuron_block = ast.NeuronBlock(block)
assert nmodl.to_nmodl(neuron_block) == 'NEURON {\n}'
def test_set_parent(self):
x_name = ast.Name(ast.String("x"))
y_name = ast.Name(ast.String("y"))
int_macro = nmodl.ast.Integer(1, x_name)
y_name.parent = int_macro # setting the parent
int_macro.macro = y_name
assert nmodl.to_nmodl(int_macro) == 'y'
def ontology_ids(self):
nmodl = _nmodl()
lookup_visitor = nmodl.visitor.AstLookupVisitor()
try:
onts = lookup_visitor.lookup(self.ast, nmodl.ast.AstNodeType.ONTOLOGY_STATEMENT)
except AttributeError:
raise Exception("nmodl module out of date; missing support for ontology declarations")
return [nmodl.to_nmodl(ont.ontology_id) for ont in onts]
def test_ast_node_str(self):
string = ast.String("tau")
name = ast.Name(string)
assert str(name) == nmodl.to_nmodl(name)