Merge pull request #276 from gyorilab/regnet_fix

Improvements to regnet export

mira/modeling/amr/regnet.py

@@ -2,7 +2,8 @@
 at https://github.com/DARPA-ASKEM/Model-Representations/tree/main/petrinet.
 """
 
-__all__ = ["AMRRegNetModel", "ModelSpecification"]
+__all__ = ["AMRRegNetModel", "ModelSpecification",
+ "template_model_to_regnet_json"]
 
 
 import json
@@ -15,7 +16,7 @@
 
 from mira.metamodel import *
 
-from .. import Model, is_production
+from .. import Model, is_production, is_conversion
 from .utils import add_metadata_annotations
 
 logger = logging.getLogger(__name__)
@@ -68,7 +69,13 @@ def __init__(self, model: Model):
  self.states.append(state_data)
 
  for idx, transition in enumerate(model.transitions.values()):
- if isinstance(transition.template, NaturalDegradation):
+ # Regnets cannot represent conversions (only
+ # production/degradation) so we skip these
+ if is_conversion(transition.template):
+ continue
+ # Natural degradation corresponds to an inherent negative
+ # sign on the state so we have special handling for it
+ elif isinstance(transition.template, NaturalDegradation):
  var = vmap[transition.consumed[0].key]
  if transition.template.rate_law:
  pnames = transition.template.get_parameter_names()
@@ -83,6 +90,8 @@ def __init__(self, model: Model):
  else:
  state['sign'] = False
  continue
+ # Controlled production corresponds to an inherent positive
+ # sign on the state so we have special handling for it
  elif isinstance(transition.template, ControlledProduction):
  var = vmap[transition.produced[0].key]
  if transition.template.rate_law:
@@ -98,6 +107,9 @@ def __init__(self, model: Model):
  else:
  state['sign'] = True
  continue
+ # Beyond these, we can assume that the transition is a
+ # form of production or degradation corresponding to
+ # a regular transition in the regnet framework
  tid = f"t{idx + 1}"
  transition_dict = {'id': tid}
 
@@ -279,6 +291,21 @@ def to_json_file(
  json.dump(js, fh, **kwargs)
 
 
+def template_model_to_regnet_json(tm: TemplateModel):
+ """Convert a template model to a RegNet JSON dict.
+
+ Parameters
+ ----------
+ tm :
+ The template model to convert.
+
+ Returns
+ -------
+ A JSON dict representing the RegNet model.
+ """
+ return AMRRegNetModel(Model(tm)).to_json()
+
+
 class Initial(BaseModel):
  expression: str
  expression_mathml: str

tests/test_modeling/test_regnet.py

@@ -0,0 +1,28 @@
+from mira.sources import amr
+from mira.modeling import Model
+from mira.metamodel.ops import stratify
+
+from mira.modeling.amr.regnet import AMRRegNetModel, \
+ template_model_to_regnet_json
+
+
+def test_regnet_end_to_end():
+ url = 'https://raw.githubusercontent.com/DARPA-ASKEM/' \
+ 'Model-Representations/main/regnet/examples/lotka_volterra.json'
+
+ model = amr.regnet.model_from_url(url)
+
+ model_2_city = stratify(
+ model,
+ key="city",
+ strata=[
+ "Toronto",
+ "Montreal",
+ ],
+ )
+
+ # Smoke tests to make sure exports work
+ ex1 = AMRRegNetModel(Model(model)).to_json()
+ ex2 = AMRRegNetModel(Model(model_2_city)).to_json()
+ assert ex1 == template_model_to_regnet_json(model)
+ assert ex2 == template_model_to_regnet_json(model_2_city)