Fixed issues with expressions for adding state and updated unit test

mira/modeling/askenet/ops.py

@@ -178,30 +178,29 @@ def remove_state(tm, state_id):
 
 
 @amr_to_mira
-def add_state(tm, state_id: str, value: float, name: str = None, units_mathml: str = None, grounding_ido=None):
+def add_state(tm, state_id: str, value: float, name: str = None, units_mathml: str = None, grounding_ido: str = None,
+ context_str: str = None):
  if grounding_ido:
- grounding = {
- 'identifiers': {'ido': grounding_ido}
- }
+ grounding = {'ido': grounding_ido}
  else:
  grounding = {}
+ if context_str:
+ context = {'context_key': context_str}
+ else:
+ context = {}
  if units_mathml:
- units = {
- 'expression': sstr(mathml_to_expression(units_mathml)),
- 'expression_mathml': units_mathml
- }
+ units = Unit(expression=SympyExprStr(mathml_to_expression(units_mathml)))
  else:
- units = {}
- data = {
- 'id': state_id,
- 'name': name if name else state_id,
- 'grounding': grounding,
- 'units': units
- }
- new_concept = state_to_concept(data)
- new_state = Initial(concept=new_concept, value=value)
+ units = None
+
+ new_concept_new = Concept(name=state_id,
+ display_name=name,
+ identifiers=grounding,
+ units=units,
+ context=context)
+ new_state = Initial(concept=new_concept_new, value=value)
  tm.initials[state_id] = new_state
- static_template = StaticConcept(subject=new_concept)
+ static_template = StaticConcept(subject=new_concept_new)
  tm.templates.append(static_template)
  return tm
 
@@ -221,6 +220,10 @@ def add_transition(tm, new_transition_id, src_id=None, tgt_id=None,
  # that aren't already present
  # option 2, reverse engineer rate law and find parameters and states within
  # the rate law and add to model
+
+ # each transition has inputs such as subjects and controllers and those appear in rate laws as states
+ # look at sympy expression and get free symbols, take out ones that represent the inputs and controllers (states)
+ # whatever remains are parameters for models
  if src_id is None and tgt_id is None:
  ValueError("You must pass in at least one of source and target id")
  rate_law_sympy = SympyExprStr(mathml_to_expression(rate_law_mathml)) \

tests/test_modeling/test_askenet_ops.py

@@ -3,7 +3,7 @@
 from copy import deepcopy as _d
 from mira.modeling.askenet.ops import *
 from sympy import *
-from mira.metamodel.io import mathml_to_expression
+from mira.metamodel.io import mathml_to_expression, expression_to_mathml
 from mira.metamodel.templates import Concept
 
 try:
@@ -322,25 +322,23 @@ def test_remove_state(self):
  self.assertNotIn(removed_state_id, new_observable['expression_mathml'])
 
  @SBMLMATH_REQUIRED
- # Some xml strings do not pass the checks
- # (e.g. replacing the state X for 'E' argument xml string will fail that test, output will be
- # 'expression_mathml': '<apply><times/><exponentiale/><ci>delta</ci></apply>')
  def test_add_state(self):
  amr = _d(self.sir_amr)
  new_state_id = 'TEST'
  new_state_display_name = 'TEST_DISPLAY_NAME'
  new_state_grounding_ido = '5555'
- new_state_grounding = {'identifiers': {
- 'ido': new_state_grounding_ido
- },
- 'modifiers': {}}
- new_state_units = "<apply><times/><ci>X</ci><ci>delta</ci></apply>"
+ context_str = 'TEST_CONTEXT'
+ new_state_grounding = {'identifiers': {'ido': new_state_grounding_ido},
+ 'modifiers': {'context_key': context_str}}
+ new_state_units = "<apply><times/><ci>E</ci><ci>delta</ci></apply>"
  value = 5
+ value_ml = '<cn>5.0</cn>'
 
  new_amr = add_state(amr, state_id=new_state_id, name=new_state_display_name,
  units_mathml=new_state_units,
  grounding_ido=new_state_grounding_ido,
- value=value)
+ value=value,
+ context_str=context_str)
  state_dict = {}
  for state in new_amr['model']['states']:
  name = state.pop('id')
@@ -352,6 +350,15 @@ def test_add_state(self):
  self.assertEqual(state_dict[new_state_id]['units']['expression'], sstr(mathml_to_expression(new_state_units)))
  self.assertEqual(state_dict[new_state_id]['units']['expression_mathml'], new_state_units)
 
+ initials_dict = {}
+ for initial in new_amr['semantics']['ode']['initials']:
+ name = initial.pop('target')
+ initials_dict[name] = initial
+
+ self.assertIn(new_state_id, initials_dict)
+ self.assertEqual(float(initials_dict[new_state_id]['expression']), value)
+ self.assertEqual(initials_dict[new_state_id]['expression_mathml'], value_ml)
+
  def test_remove_transition(self):
  removed_transition = 'inf'
  amr = _d(self.sir_amr)