Added minimal unit tests for 4 interface methods and unit test for re…

…move_state

mira/modeling/askenet/ops.py

@@ -52,9 +52,6 @@ def replace_transition_id(tm, old_id, new_id):
  return tm
 
 
-# As of now, replace_observable_id replaces both 'id' and 'name' field of an observable in output amr
-# can possibly add a new argument for display name and set observable.display_name to new argument and then change
-# tm to json method to set 'name' field in new_amr['semantics']['ode']['observables'] to observable.display_name
 @amr_to_mira
 def replace_observable_id(tm, old_id, new_id):
  """Replace the ID of an observable."""
@@ -67,8 +64,6 @@ def replace_observable_id(tm, old_id, new_id):
 
 
 @amr_to_mira
-# current bug is that it doesn't return the changed parameter in new_amr['semantics']['ode']['parameters']
-# expected 2 returned parameters in list of parameters, only got 1 (the 1 that wasn't changed)
 def replace_parameter_id(tm, old_id, new_id):
  """Replace the ID of a parameter."""
  for template in tm.templates:
@@ -138,20 +133,20 @@ def replace_rate_law_sympy(tm, transition_id, new_rate_law):
 
 
 @amr_to_mira
-def stratify(**kwargs):
- return tmops.stratify(**kwargs)
+def stratify(*args, **kwargs):
+ return tmops.stratify(*args, **kwargs)
 
 
 @amr_to_mira
-def simplify_rate_laws(**kwargs):
- return tmops.simplify_rate_laws(**kwargs)
+def simplify_rate_laws(*args, **kwargs):
+ return tmops.simplify_rate_laws(*args, **kwargs)
 
 
 @amr_to_mira
-def aggregate_parameters(**kwargs):
- return tmops.aggregate_parameters(**kwargs)
+def aggregate_parameters(*args, **kwargs):
+ return tmops.aggregate_parameters(*args, **kwargs)
 
 
 @amr_to_mira
-def counts_to_dimensionless(**kwargs):
- return tmops.counts_to_dimensionless(**kwargs)
+def counts_to_dimensionless(*args, **kwargs):
+ return tmops.counts_to_dimensionless(*args, **kwargs)

tests/test_modeling/test_askenet_ops.py

@@ -132,8 +132,8 @@ def test_replace_transition_id(self):
  if old_transitions['id'] == old_id:
  self.assertEqual(new_transition['id'], new_id)
 
- # checks for updated id and name field of an observable - suggested change in method definition
- # such that we can use a different value for name rather than reusing new_id
+ # checks for updated id and name field of an observable - suggested change
+ # such that we can use a different value for name field rather than reusing new_id
  def test_replace_observable_id(self):
  old_id = 'noninf'
  new_id = 'testinf'
@@ -149,6 +149,8 @@ def test_replace_observable_id(self):
  if old_observable['id'] == old_id:
  self.assertEqual(new_observable['id'], new_id) and self.assertEqual(new_observable['name'], new_id)
 
+ # current bug is that it doesn't return the changed parameter in new_amr['semantics']['ode']['parameters']
+ # expected 2 returned parameters in list of parameters, only got 1 (the 1 that wasn't changed)
  def test_replace_parameter_id(self):
  old_id = 'beta'
  new_id = 'zeta'
@@ -192,3 +194,72 @@ def test_replace_parameter_id(self):
  mathml_flag = (new_value_in_observable_mathml and old_value_out_observable_mathml)
 
  self.assertTrue(expression_flag and mathml_flag)
+
+ def test_remove_state(self):
+ removed_state = 'S'
+ amr = _d(self.sir_amr)
+
+ new_amr = remove_state(amr, removed_state)
+
+ new_model = new_amr['model']
+ new_model_states = new_model['states']
+ new_model_transitions = new_model['transitions']
+
+ new_semantics_ode = new_amr['semantics']['ode']
+ new_semantics_ode_rates = new_semantics_ode['rates']
+ new_semantics_ode_initials = new_semantics_ode['initials']
+ new_semantics_ode_parameters = new_semantics_ode['parameters']
+ new_semantics_ode_observables = new_semantics_ode['observables']
+
+ for new_state in new_model_states:
+ self.assertTrue(removed_state != new_state['id'])
+
+ for new_transition in new_model_transitions:
+ self.assertNotIn(removed_state, new_transition['input'])
+ self.assertNotIn(removed_state, new_transition['output'])
+
+ # output rates that originally contained targeted state are removed
+ for new_rate in new_semantics_ode_rates:
+ self.assertNotIn(removed_state, new_rate['expression'])
+ self.assertNotIn(removed_state, new_rate['expression_mathml'])
+
+ # initials are bugged, all states removed rather than just targeted removed state in output amr
+ for new_initial in new_semantics_ode_initials:
+ self.assertNotIn(removed_state, new_initial['target'])
+
+ # parameters that are associated in an expression with a removed state are not present in output amr
+ for new_parameter in new_semantics_ode_parameters:
+ self.assertNotIn(removed_state + '0', new_parameter['id'])
+
+ # output observables that originally contained targeted state still exist with targeted state removed
+ # (e.g. 'S+R' -> 'R') if 'S' is the removed state
+ for new_observable in new_semantics_ode_observables:
+ self.assertNotIn(removed_state, new_observable['expression'])
+ self.assertNotIn(removed_state, new_observable['expression_mathml'])
+
+ def test_stratify(self):
+ amr = _d(self.sir_amr)
+ new_amr = stratify(amr, key='city', strata=['boston', 'nyc'])
+
+ self.assertIsInstance(amr, dict)
+ self.assertIsInstance(new_amr, dict)
+
+ def test_simplify_rate_laws(self):
+ amr = _d(self.sir_amr)
+ new_amr = simplify_rate_laws(amr)
+
+ self.assertIsInstance(amr, dict)
+ self.assertIsInstance(new_amr, dict)
+
+ def test_aggregate_parameters(self):
+ amr = _d(self.sir_amr)
+ new_amr = aggregate_parameters(amr)
+
+ self.assertIsInstance(amr, dict)
+ self.assertIsInstance(new_amr, dict)
+
+ def test_counts_to_dimensionless(self):
+ amr = _d(self.sir_amr)
+ new_amr = counts_to_dimensionless(amr, 'ml', .8)
+ self.assertIsInstance(amr, dict)
+ self.assertIsInstance(new_amr, dict)