Merge pull request #294 from gyorilab/scenario-5-update

Improve Vensim parser for scenario 5

mira/modeling/amr/stockflow.py

@@ -116,6 +116,8 @@ def __init__(self, model: Model):
  # test to see if parameter is present in any of the rate laws
  used_parameter_flag = False
  for flow in model.transitions.values():
+ if flow.template.rate_law is None:
+ continue
  if sympy.Symbol(key) in flow.template.rate_law.free_symbols:
  used_parameter_flag = True
  break
@@ -181,14 +183,15 @@ def __init__(self, model: Model):
 
  self.flows.append(flow_dict)
 
- for symbol in flow.template.rate_law.free_symbols:
- link_dict = {'id': f'link{link_id}'}
- str_symbol = str(symbol)
+ if flow.template.rate_law is not None:
+ for symbol in flow.template.rate_law.free_symbols:
+ link_dict = {'id': f'link{link_id}'}
+ str_symbol = str(symbol)
 
- link_dict['source'] = str_symbol
- link_dict['target'] = "flow" + fid
- link_id += 1
- self.links.append(link_dict)
+  link_dict['source'] = str_symbol
+  link_dict['target'] = "flow" + fid
+  link_id += 1
+  self.links.append(link_dict)
 
  def to_json(self):
  """Return a JSON dict structure of the Stock and Flow model."""

mira/sources/system_dynamics/vensim.py

@@ -125,20 +125,22 @@ def extract_vensim_variable_expressions(model_text):
  # variable name and accompanying expression
  var_declaration = text.split("~")[0].split("=")
  old_var_name = var_declaration[0].strip()
- text_expression = var_declaration[1]
+ text_expression = var_declaration[1].strip()
 
  # account for variables with expressions that have "=" in them besides the
  # initial "=" character for var declaration, stitch together the expression
  if len(var_declaration) > 2:
  for part_expression_text in var_declaration[2:]:
  text_expression += "=" + part_expression_text
 
- # current way of identifying built-in vensim functions.
+ # vensim has several builtin functions, like MIN(), MAX(), XIDZ(), INTEG()
+ # we pass these along for sympy to just consider like function calls.
  # Hackathon file does not use any built-in functions that don't take a single argument
  # Can account for single argument Vensim functions as well
  # List of Vensim functions: https://www.vensim.com/documentation/22300.html
  # "INTEG" is the keyword used to define a state/stock
- if "," in text_expression and "INTEG" not in text_expression:
+ # however, we can't yet handle if/then/else constructs, so we skip them
+ if "if then else" in text_expression.lower():
  expression_map[old_var_name] = "0"
  continue
 

notebooks/hackathon_2024.02/scenario5/grounding_map.csv

@@ -17,4 +17,4 @@ infected_sym_hospital_overflow,ido:0000511/infected population,hospitalization=n
 infected_sym_serious_hospital,ido:0000511/infected population,hospitalization=ncit:C25179/Hospitalization|serious_injury_illness_impairment=ncit:C172031
 infected_sym_icu_overflow,ido:0000511/infected population,intensive_care_unit=ncit:C53511|surge_capacity=ncit:C173775
 infected_sym_extreme_icu,ido:0000511/infected population,intensive_care_unit=ncit:C53511|immediately_life_threatening_disorder=ncit:C171511
-recovered_from_hospital,ido:0000592/immune population,hospitalization=ncit:C25179/Hospitalization|patient_discharge=ncit:c25166
+recovered_from_hospital,ido:0000592/immune population,hospitalization=ncit:C25179/Hospitalization|patient_discharge=ncit:c25166