Address more issues with from_json

mira/metamodel/template_model.py

@@ -1,3 +1,5 @@
+import copy
+
 from pydantic import ConfigDict
 
 __all__ = [
@@ -473,6 +475,8 @@ def from_json(cls, data) -> "TemplateModel":
  :
  Returns the newly created template model.
  """
+ # Do a copy just to make sure we don't modify the original data
+ data = copy.deepcopy(data)
  local_symbols = {p: sympy.Symbol(p) for p in data.get("parameters", [])}
  for template_dict in data.get("templates", []):
  # We need to figure out the template class based on the type

mira/metamodel/templates.py

@@ -3,6 +3,8 @@
 
 Regenerate the JSON schema by running ``python -m mira.metamodel.schema``.
 """
+import copy
+
 from pydantic import ConfigDict
 from typing import Literal
 
@@ -376,6 +378,8 @@ def from_json(cls, data) -> "Concept":
  if isinstance(data, Concept):
  return data
  elif data.get('units'):
+ # Copy so we don't update the input
+ data = copy.deepcopy(data)
  data['units'] = Unit.from_json(data['units'])
 
  return cls(**data)
@@ -413,6 +417,8 @@ def from_json(cls, data, rate_symbols=None) -> "Template":
  :
  A Template object
  """
+ # Make a copy to make sure we don't update the input
+ data = copy.deepcopy(data)
  # We make sure to use data such that it's not modified in place,
  # e.g., we don't use pop or overwrite items, otherwise this function
  # would have unintended side effects.

mira/metamodel/units.py

@@ -42,8 +42,8 @@ class Unit(BaseModel):
 
  @classmethod
  def from_json(cls, data: Dict[str, Any]) -> "Unit":
- # Use get_sympy from amr.petrinet, but avoid circular import
- from mira.sources.amr.petrinet import get_sympy
+ # Use get_sympy from sources, but avoid circular import
+ from mira.sources.util import get_sympy
  new_data = data.copy()
  new_data["expression"] = get_sympy(data, local_dict=UNIT_SYMBOLS)
  assert (new_data.get('expression') is None or