Implemented add_transition (unfinished as currently newly added state…

…s and parameters are not showing in the output amr) and its accompanying unit test

mira/modeling/askenet/ops.py

@@ -6,7 +6,7 @@
 from .petrinet import template_model_to_petrinet_json
 from mira.metamodel.io import mathml_to_expression
 from mira.metamodel.template_model import Parameter, Distribution, Observable
-from mira.metamodel.templates import Concept
+from mira.metamodel.templates import NaturalConversion, NaturalProduction, NaturalDegradation
 
 
 def amr_to_mira(func):
@@ -171,18 +171,21 @@ def remove_transition(tm, transition_id):
  return tm
 
 
-# @amr_to_mira
-# def add_transition(tm, rate_law, src_id=None, tgt_id=None):
-# if not src_id and not tgt_id:
-# print("You must pass in at least one of source and target id")
-# return tm
-# sympy_expression = mathml_to_expression(rate_law)
-# if src_id is None and tgt_id is not None:
-# pass
-# if src_id is not None and tgt_id is None:
-# pass
-# else:
-# pass
+@amr_to_mira
+def add_transition(tm, new_transition_id, rate_law_mathml, src_id=None, tgt_id=None):
+ rate_law_sympy = SympyExprStr(mathml_to_expression(rate_law_mathml))
+ if src_id is None and tgt_id is None:
+ print("You must pass in at least one of source and target id")
+ elif src_id is None and tgt_id:
+ template = NaturalProduction(name=new_transition_id, outcome=tgt_id, rate_law=rate_law_sympy)
+ tm.templates.append(template)
+ elif src_id and tgt_id is None:
+ template = NaturalDegradation(name=new_transition_id, subject=src_id, rate_law=rate_law_sympy)
+ tm.templates.append(template)
+ else:
+ template = NaturalConversion(name=new_transition_id, subject=src_id, outcome=tgt_id, rate_law=rate_law_sympy)
+ tm.templates.append(template)
+ return tm
 
 
 @amr_to_mira

tests/test_modeling/test_askenet_ops.py

@@ -1,11 +1,10 @@
 import unittest
 import requests
-import pandas as pd
 from copy import deepcopy as _d
 from mira.modeling.askenet.ops import *
-# from sympy.parsing.sympy_parser import parse_expr
 from sympy import *
 from mira.metamodel.io import mathml_to_expression
+from mira.metamodel.templates import Concept
 
 
 class TestAskenetOperations(unittest.TestCase):
@@ -269,18 +268,6 @@ def test_add_parameter(self):
  expression_xml="<apply><times/><ci>E</ci><ci>delta</ci></apply>",
  value=.5, distribution_type='Uniform1', min_value=.05, max_value=.8)
 
- # def test_replace_initial_id(self):
- # old_id = 'S'
- # new_id = 'TEST'
- # amr = _d(self.sir_amr)
- # new_amr = replace_initial_id(amr, old_id, new_id)
- # old_semantics_ode_initials = amr['semantics']['ode']['initials']
- # new_semantics_ode_initials = new_amr['semantics']['ode']['initials']
- #
- # for old_initials, new_initials in zip(old_semantics_ode_initials, new_semantics_ode_initials):
- # if old_initials['target'] == old_id:
- # self.assertEqual(new_initials['target'], new_id)
-
  def test_remove_state(self):
  removed_state_id = 'S'
  amr = _d(self.sir_amr)
@@ -335,13 +322,72 @@ def test_remove_transition(self):
  for new_transition in new_model_transition:
  self.assertNotEquals(removed_transition, new_transition['id'])
 
- # def test_add_transition(self):
- # new_transition_src_id = 'test'
- # new_transition_tgt_id = 'MORE'
- # expression_xml = '<apply><plus/><ci>X</ci><cn>8</cn></apply>'
- # amr = _d(self.sir_amr)
- #
- # new_amr = add_transition(amr, expression_xml, src_id=new_transition_src_id)
+ def test_add_transition(self):
+ infected = Concept(name="infected_population", identifiers={"ido": "0000511"})
+ recovered = Concept(name="immune_population", identifiers={"ido": "0000592"})
+ expression_xml = "<apply><times/><ci>E</ci><ci>delta</ci></apply>"
+ new_transition_id = 'test'
+ old_natural_conversion_amr = _d(self.sir_amr)
+ old_natural_production_amr = _d(self.sir_amr)
+ old_natural_degradation_amr = _d(self.sir_amr)
+
+ # NaturalConversion
+ new_natural_conversion_amr = add_transition(old_natural_conversion_amr, new_transition_id, expression_xml,
+ src_id=infected,
+ tgt_id=recovered)
+ natural_conversion_transition_dict = {}
+ natural_conversion_rates_dict = {}
+ for transition in new_natural_conversion_amr['model']['transitions']:
+ name = transition.pop('id')
+ natural_conversion_transition_dict[name] = transition
+
+ for rate in new_natural_conversion_amr['semantics']['ode']['rates']:
+ name = rate.pop('target')
+ natural_conversion_rates_dict[name] = rate
+
+ self.assertIn(new_transition_id, natural_conversion_transition_dict)
+ self.assertIn(new_transition_id, natural_conversion_rates_dict)
+ self.assertEqual(expression_xml, natural_conversion_rates_dict[new_transition_id]['expression_mathml'])
+ self.assertEqual(sstr(mathml_to_expression(expression_xml)),
+ natural_conversion_rates_dict[new_transition_id]['expression'])
+
+ # NaturalProduction
+ new_natural_production_amr = add_transition(old_natural_production_amr, new_transition_id, expression_xml,
+ tgt_id=recovered)
+ natural_production_transition_dict = {}
+ natural_production_rates_dict = {}
+ for transition in new_natural_production_amr['model']['transitions']:
+ name = transition.pop('id')
+ natural_production_transition_dict[name] = transition
+
+ for rate in new_natural_production_amr['semantics']['ode']['rates']:
+ name = rate.pop('target')
+ natural_production_rates_dict[name] = rate
+
+ self.assertIn(new_transition_id, natural_production_transition_dict)
+ self.assertIn(new_transition_id, natural_production_rates_dict)
+ self.assertEqual(expression_xml, natural_production_rates_dict[new_transition_id]['expression_mathml'])
+ self.assertEqual(sstr(mathml_to_expression(expression_xml)),
+ natural_production_rates_dict[new_transition_id]['expression'])
+
+ # NaturalDegradation
+ new_natural_degradation_amr = add_transition(old_natural_degradation_amr, new_transition_id, expression_xml,
+ src_id=infected)
+ natural_degradation_transition_dict = {}
+ natural_degradation_rates_dict = {}
+ for transition in new_natural_degradation_amr['model']['transitions']:
+ name = transition.pop('id')
+ natural_degradation_transition_dict[name] = transition
+
+ for rate in new_natural_degradation_amr['semantics']['ode']['rates']:
+ name = rate.pop('target')
+ natural_degradation_rates_dict[name] = rate
+
+ self.assertIn(new_transition_id, natural_degradation_transition_dict)
+ self.assertIn(new_transition_id, natural_degradation_rates_dict)
+ self.assertEqual(expression_xml, natural_degradation_rates_dict[new_transition_id]['expression_mathml'])
+ self.assertEqual(sstr(mathml_to_expression(expression_xml)),
+ natural_degradation_rates_dict[new_transition_id]['expression'])
 
  def test_replace_rate_law_sympy(self):
  transition_id = 'inf'