Added replace_rate_law_mathml and unit tests and modified unit_test f…

…or test_replace_rate_law_sympy to test both output amr expression and expression_mathml

mira/modeling/askenet/ops.py

@@ -4,6 +4,7 @@
 import mira.metamodel.ops as tmops
 from mira.sources.askenet.petrinet import template_model_from_askenet_json
 from .petrinet import template_model_to_petrinet_json
+from mira.metamodel.io import mathml_to_expression
 
 
 def amr_to_mira(func):
@@ -113,20 +114,17 @@ def remove_transition(tm, transition_id):
 
 
 @amr_to_mira
+# rate law is of type Sympy Expression
 def replace_rate_law_sympy(tm, transition_id, new_rate_law):
  for template in tm.templates:
  if template.name == transition_id:
  template.rate_law = SympyExprStr(new_rate_law)
  return tm
 
 
-# Replace expression with new Content MathML
-# TODO: we need MathML->sympy conversion for this
-# def replace_rate_law_mathml(tm, transition_id, new_rate_law):
-# for template in tm.templates:
-# if template.name == transition_id:
-# template.rate_law = SympyExprStr(new_rate_law)
-# return tm
+def replace_rate_law_mathml(tm, transition_id, new_rate_law):
+ new_rate_law_sympy = mathml_to_expression(new_rate_law)
+ return replace_rate_law_sympy(tm, transition_id, new_rate_law_sympy)
 
 
 @amr_to_mira

tests/test_modeling/test_askenet_ops.py

@@ -2,7 +2,9 @@
 import requests
 from copy import deepcopy as _d
 from mira.modeling.askenet.ops import *
-from sympy.parsing.sympy_parser import parse_expr
+# from sympy.parsing.sympy_parser import parse_expr
+from sympy import *
+from mira.metamodel.io import mathml_to_expression
 
 
 class TestAskenetOperations(unittest.TestCase):
@@ -273,18 +275,35 @@ def test_remove_transition(self):
  def test_replace_rate_law_sympy(self):
 
  transition_id = 'inf'
- new_expression_str = 'TEST'
- new_expression_sympy = parse_expr(new_expression_str)
- amr = _d(self.sir_amr)
+ target_expression_str = '8+X'
+ target_expression_mathml_str = '<apply><plus/><ci>X</ci><cn>8</cn></apply>'
+
+ # Convert new_expression string into Sympy expression
+ new_expression_sympy = parse_expr(target_expression_str)
 
- # what type does new_rate_law need to be?
+ amr = _d(self.sir_amr)
  new_amr = replace_rate_law_sympy(amr, transition_id, new_expression_sympy)
+ new_semantics_ode_rates = new_amr['semantics']['ode']['rates']
+
+ for new_rate in new_semantics_ode_rates:
+ if new_rate['target'] == transition_id:
+ self.assertEqual(sstr(new_expression_sympy), new_rate['expression'])
+ self.assertEqual(sstr(target_expression_mathml_str), new_rate['expression_mathml'])
+
+ def test_replace_rate_law_mathml(self):
+ amr = _d(self.sir_amr)
+ transition_id = 'inf'
+ xml_str = "<apply><times/><ci>E</ci><ci>delta</ci></apply>"
+ sympy_expression = mathml_to_expression(xml_str)
+
+ new_amr = replace_rate_law_mathml(amr, transition_id, xml_str)
 
  new_semantics_ode_rates = new_amr['semantics']['ode']['rates']
 
- for new_rates in new_semantics_ode_rates:
- if new_rates['target'] == transition_id:
- self.assertEqual(new_rates['expression'], new_expression_str)
+ for new_rate in new_semantics_ode_rates:
+ if new_rate['target'] == transition_id:
+ self.assertEqual(new_rate['expression_mathml'], xml_str)
+ self.assertEqual(new_rate['expression'], sstr(sympy_expression))
 
  def test_stratify(self):
  amr = _d(self.sir_amr)