Merge pull request #289 from gyorilab/scenario-5-grounding

Improve scenario 5 import

mira/modeling/amr/stockflow.py

@@ -15,6 +15,12 @@
 class AMRStockFlowModel:
  """A class representing a Stock and Flow Model"""
 
+ SCHEMA_VERSION = "0.1"
+ SCHEMA_URL = (
+ f"https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/"
+ f"stockflow_v{SCHEMA_VERSION}/stockflow/stockflow_schema.json"
+ )
+
  def __init__(self, model: Model):
  """Instantiate a stock and flow model from a generic transition model.
 
@@ -189,7 +195,7 @@ def to_json(self):
  return {
  'header': {
  'name': self.model_name,
- 'schema': '',
+ 'schema': self.SCHEMA_URL,
  'description': self.model_description,
  'schema_name': 'stockflow',
  'model_version': '0.1',

mira/sources/system_dynamics/pysd.py

@@ -3,6 +3,7 @@
 """
 __all__ = ["template_model_from_pysd_model"]
 
+import copy
 import re
 
 import pandas as pd
@@ -35,7 +36,7 @@
 SYMPY_FLOW_RATE_PLACEHOLDER = safe_parse_expr("xxplaceholderxx")
 
 
-def template_model_from_pysd_model(pysd_model, expression_map) -> TemplateModel:
+def template_model_from_pysd_model(pysd_model, expression_map, *, grounding_map=None) -> TemplateModel:
  """Given a model and its accompanying expression_map, extract information from the arguments
  to create an equivalent MIRA template model.
 
@@ -45,6 +46,8 @@ def template_model_from_pysd_model(pysd_model, expression_map) -> TemplateModel:
  The pysd model object
  expression_map : dict[str,str]
  Map of variable name to expression
+ grounding_map: dict[str, Concept]
+ A grounding map, a map from label to Concept
 
  Returns
  -------
@@ -91,7 +94,7 @@ def template_model_from_pysd_model(pysd_model, expression_map) -> TemplateModel:
 
  # process states and build mapping of state to input rate laws and output rate laws
  for index, state in model_states.iterrows():
- concept_state = state_to_concept(state)
+ concept_state = state_to_concept(state, grounding_map=grounding_map)
  concepts[concept_state.name] = concept_state
  all_states.add(concept_state.name)
  symbols[concept_state.name] = sympy.Symbol(concept_state.name)
@@ -353,13 +356,15 @@ def template_model_from_pysd_model(pysd_model, expression_map) -> TemplateModel:
  )
 
 
-def state_to_concept(state) -> Concept:
+def state_to_concept(state, grounding_map=None) -> Concept:
  """Create a MIRA Concept from a state
 
  Parameters
  ----------
  state : pd.Series
  The series that contains state data
+ grounding_map: dict[str, Concept]
+ A grounding map, a map from label to Concept
 
  Returns
  -------
@@ -376,6 +381,17 @@ def state_to_concept(state) -> Concept:
  unit_expr = get_sympy(unit_dict, UNIT_SYMBOLS)
  units_obj = Unit(expression=unit_expr) if unit_expr else None
 
+ # If there's something hacked in, use that directly,
+ # keeping the units and description from the model
+ if grounding_map is not None and name in grounding_map:
+ concept = copy.deepcopy(grounding_map[name])
+ concept.name = name
+ concept.description = description
+ concept.units = units_obj
+ return concept
+ else:
+ print("could not ground", name)
+
  return Concept(name=name, units=units_obj, description=description)
 
 

mira/sources/system_dynamics/vensim.py

@@ -34,13 +34,15 @@
 CONTROL_VARIABLES = {"SAVEPER", "FINAL TIME", "INITIAL TIME", "TIME STEP"}
 
 
-def template_model_from_mdl_file(fname) -> TemplateModel:
+def template_model_from_mdl_file(fname, *, grounding_map=None) -> TemplateModel:
  """Return a template model from a local Vensim file
 
  Parameters
  ----------
  fname : str or pathlib.Path
  The path to the local Vensim file
+ grounding_map: dict[str, Concept]
+ A grounding map, a map from label to Concept
 
  Returns
  -------
@@ -51,16 +53,18 @@ def template_model_from_mdl_file(fname) -> TemplateModel:
  vensim_file = VensimFile(fname)
  expression_map = extract_vensim_variable_expressions(vensim_file.model_text)
 
- return template_model_from_pysd_model(pysd_model, expression_map)
+ return template_model_from_pysd_model(pysd_model, expression_map, grounding_map=grounding_map)
 
 
-def template_model_from_mdl_url(url) -> TemplateModel:
+def template_model_from_mdl_url(url, *, grounding_map=None) -> TemplateModel:
  """Return a template model from a Vensim file provided by an url
 
  Parameters
  ----------
  url : str
  The url to the mdl file
+ grounding_map: dict[str, Concept]
+ A grounding map, a map from label to Concept
 
  Returns
  -------
@@ -75,11 +79,7 @@ def template_model_from_mdl_url(url) -> TemplateModel:
  with temp_file as file:
  file.write(data)
 
- pysd_model = pysd.read_vensim(temp_file.name)
- vensim_file = VensimFile(temp_file.name)
- expression_map = extract_vensim_variable_expressions(vensim_file.model_text)
-
- return template_model_from_pysd_model(pysd_model, expression_map)
+ return template_model_from_mdl_file(temp_file.name, grounding_map=grounding_map)
 
 
 # look past control section

notebooks/hackathon_2024.02/scenario5/grounding_map.csv

@@ -12,7 +12,7 @@ recovered_isolated_symptomatic_mild,ido:0000592/immune population,isolation=ncit
 infectious_symptomatic_mild,ido:0000511/infected population,mild=ncit:C70666
 quarantined_symptomatic_mild,ido:0000511/infected population,quarantined=ncit:C71902/Quarantine|mild=ncit:C70666
 recovered_mild,ido:0000592/immune population,mild=ncit:C70666
-incoming_demand_on_hospital,hospitalization=ncit:C25179/Hospitalization,
+incoming_demand_on_hospital,"",hospitalization=ncit:C25179/Hospitalization
 infected_symptomatic_hospital_overflow,ido:0000511/infected population,hospitalization=ncit:C25179/Hospitalization|surge_capacity=ncit:C173775
 infected_symptomatic_serious_hospital,ido:0000511/infected population,hospitalization=ncit:C25179/Hospitalization|serious_injury_illness_impairment=ncit:C172031
 infected_symptomatic_icu_overflow,ido:0000511/infected population,intensive_care_unit=ncit:C53511|surge_capacity=ncit:C173775