Expand test to include include_task_shifting=False case

Author: marghe-molaro

tests/test_healthsystem.py

@@ -1993,89 +1993,102 @@ def apply(self, person_id, squeeze_factor):
         "directory": tmpdir,
         "custom_levels": {"tlo.methods.healthsystem": logging.DEBUG},
     }
-    sim = Simulation(start_date=start_date, seed=seed, log_config=log_config)
+    
+    def simulate(task_shifting_option, Ntarget):
+    
+        sim = Simulation(start_date=start_date, seed=seed, log_config=log_config)
 
-    # Register the core modules and simulate for 0 days
-    sim.register(demography.Demography(resourcefilepath=resourcefilepath),
-                 healthsystem.HealthSystem(resourcefilepath=resourcefilepath,
-                                           capabilities_coefficient=1.0,
-                                           mode_appt_constraints=2,
-                                           include_task_shifting=True,
-                                           ignore_priority=False,
-                                           randomise_queue=True,
-                                           policy_name="",
-                                           use_funded_or_actual_staffing='funded_plus'),
-                 DummyModule()
-                 )
+        # Register the core modules and simulate for 0 days
+        sim.register(demography.Demography(resourcefilepath=resourcefilepath),
+                     healthsystem.HealthSystem(resourcefilepath=resourcefilepath,
+                                               capabilities_coefficient=1.0,
+                                               mode_appt_constraints=2,
+                                               include_task_shifting=task_shifting_option,
+                                               ignore_priority=False,
+                                               randomise_queue=True,
+                                               policy_name="",
+                                               use_funded_or_actual_staffing='funded_plus'),
+                     DummyModule()
+                     )
 
-    tot_population = 100
-    sim.make_initial_population(n=tot_population)
-    sim.simulate(end_date=sim.start_date)
+        tot_population = 100
+        sim.make_initial_population(n=tot_population)
+        sim.simulate(end_date=sim.start_date)
 
-    # Get pointer to the HealthSystemScheduler event
-    healthsystemscheduler = sim.modules['HealthSystem'].healthsystemscheduler
+        # Get pointer to the HealthSystemScheduler event
+        healthsystemscheduler = sim.modules['HealthSystem'].healthsystemscheduler
 
-    # Force entire population in one district (keys_district[0]) and get facility ID
-    person_for_district = {d: i for i, d in enumerate(sim.population.props['district_of_residence'].cat.categories)}
-    keys_district = list(person_for_district.keys())
+        # Force entire population in one district (keys_district[0]) and get facility ID
+        person_for_district = {d: i for i, d in enumerate(sim.population.props['district_of_residence'].cat.categories)}
+        keys_district = list(person_for_district.keys())
 
-    for i in range(0, int(tot_population)):
-        sim.population.props.at[i, 'district_of_residence'] = keys_district[0]
+        for i in range(0, int(tot_population)):
+            sim.population.props.at[i, 'district_of_residence'] = keys_district[0]
 
 
-    # Schedule an identical appointment for all individuals
-    for i in range(0, tot_population):
+        # Schedule an identical appointment for all individuals
+        for i in range(0, tot_population):
 
-        hsi = DummyHSIEvent(module=sim.modules['DummyModule'],
-                            person_id=i,
-                            appt_type='MinorSurg',
-                            level='1a')
+            hsi = DummyHSIEvent(module=sim.modules['DummyModule'],
+                                person_id=i,
+                                appt_type='MinorSurg',
+                                level='1a')
 
-        sim.modules['HealthSystem'].schedule_hsi_event(
-            hsi,
-            topen=sim.date,
-            tclose=sim.date + pd.DateOffset(days=1),
-            # Assign equal priority
-            priority=0
-        )
+            sim.modules['HealthSystem'].schedule_hsi_event(
+                hsi,
+                topen=sim.date,
+                tclose=sim.date + pd.DateOffset(days=1),
+                # Assign equal priority
+                priority=0
+            )
 
-    hsi1 = DummyHSIEvent(module=sim.modules['DummyModule'],
-                         person_id=0,  # Ensures call is on officers in first district
-                         appt_type='MinorSurg',
-                         level='1a')
-    hsi1.initialise()
-    
-    # Get facility ID
-    facID = int((re.search(r'\d+', next(iter(hsi1.expected_time_requests)))).group())
-
-    pharmacy_task_time = hsi1.expected_time_requests['FacilityID_' + str(facID) + '_Officer_Pharmacy']
-    nursing_task_time = hsi1.expected_time_requests['FacilityID_' + str(facID) + '_Officer_Nursing_and_Midwifery']
-    clinical_task_time = hsi1.expected_time_requests['FacilityID_' + str(facID) + '_Officer_Clinical']
- 
-     # Check that first choice of task-shifting officer for Pharmacy is Nursing_and_Midwifery, and get their factor
-    assert 'Nursing_and_Midwifery' == sim.modules['HealthSystem'].global_task_shifting.get('Pharmacy')[0][0]
-    nursing_task_shift_factor = sim.modules['HealthSystem'].global_task_shifting.get('Pharmacy')[1][0]
- 
-    # Number of appts that want to see delivered if pharmacy time is set to zero,
-    # clinical time is set to perform 50 appts, and nursing time is set to perform 50 appts including
-    # both nursing and pharmacy tasks.
+        hsi1 = DummyHSIEvent(module=sim.modules['DummyModule'],
+                             person_id=0,  # Ensures call is on officers in first district
+                             appt_type='MinorSurg',
+                             level='1a')
+        hsi1.initialise()
+        
+        # Get facility ID
+        facID = int((re.search(r'\d+', next(iter(hsi1.expected_time_requests)))).group())
+
+        pharmacy_task_time = hsi1.expected_time_requests['FacilityID_' + str(facID) + '_Officer_Pharmacy']
+        nursing_task_time = hsi1.expected_time_requests['FacilityID_' + str(facID) + '_Officer_Nursing_and_Midwifery']
+        clinical_task_time = hsi1.expected_time_requests['FacilityID_' + str(facID) + '_Officer_Clinical']
+     
+         # Check that first choice of task-shifting officer for Pharmacy is Nursing_and_Midwifery, and get their factor
+        assert 'Nursing_and_Midwifery' == sim.modules['HealthSystem'].global_task_shifting.get('Pharmacy')[0][0]
+        nursing_task_shift_factor = sim.modules['HealthSystem'].global_task_shifting.get('Pharmacy')[1][0]
+     
+        # Always set Pharmacy capabilities to zero. Set Clinical and Nursing capabilities such that Ntarget appointments
+        # can be delivered by relying on task-shifting from Nursing only. Setting Clinical time to Ntarget x clinical_task_time
+        # checks that when task-shifting first option (nurses) where always preferentially chosen over second.
+    # one (clinicians)
+        sim.modules['HealthSystem']._daily_capabilities['FacilityID_' + str(facID) + '_Officer_Pharmacy'] = 0.0
+        sim.modules['HealthSystem']._daily_capabilities['FacilityID_' + str(facID) + '_Officer_Clinical'] = Ntarget*(clinical_task_time)
+        sim.modules['HealthSystem']._daily_capabilities['FacilityID_' + str(facID) + '_Officer_Nursing_and_Midwifery'] = Ntarget*(nursing_task_time + nursing_task_shift_factor*pharmacy_task_time)
+
+        # Run healthsystemscheduler
+        healthsystemscheduler.apply(sim.population)
+        
+        # read the results
+        output = parse_log_file(sim.log_filepath, level=logging.DEBUG)
+        hs_output = output['tlo.methods.healthsystem']['HSI_Event']
+        
+        return hs_output
+        
+    # Pharmacy capabilities set to zero. Clinical and Nursing capabilities initialised such that Ntarget
+    # appointments can be performed iff using task-shifting
     Ntarget = 50
 
-    sim.modules['HealthSystem']._daily_capabilities['FacilityID_' + str(facID) + '_Officer_Pharmacy'] = 0.0
-    sim.modules['HealthSystem']._daily_capabilities['FacilityID_' + str(facID) + '_Officer_Clinical'] = Ntarget*(clinical_task_time)
-    sim.modules['HealthSystem']._daily_capabilities['FacilityID_' + str(facID) + '_Officer_Nursing_and_Midwifery'] = Ntarget*(nursing_task_time + nursing_task_shift_factor*pharmacy_task_time)
-
-    # Run healthsystemscheduler
-    healthsystemscheduler.apply(sim.population)
-
-    # read the results
-    output = parse_log_file(sim.log_filepath, level=logging.DEBUG)
-    hs_output = output['tlo.methods.healthsystem']['HSI_Event']
-
-    # Check that all events could run, even if Pharmacy capabilities were set to zero,
-    # and that when task-shifting first option (nurses) where always preferentially chosen over second
-    # one (clinicians)
+    # Allow for task-shifting to take place, and check that all Ntarget events could run, even if Pharmacy
+    # capabilities were set to zero,
+    hs_output = simulate(task_shifting_option=True, Ntarget=Ntarget)
     assert hs_output['did_run'].sum() == Ntarget
+    
+    # Do not allow for task-shifting to take place, and check that as a result no events could run, since
+    # Pharmacy capabilities were set to zero.
+    hs_output = simulate(task_shifting_option=False, Ntarget=Ntarget)
+    assert hs_output['did_run'].sum() == 0
 
 
 @pytest.mark.slow