Fix add_all_interventions RTSS error and being dependent on smc_df problem

examples/test.py

@@ -0,0 +1,71 @@
+import emod_api.campaign as campaign
+import numpy as np
+import pandas as pd
+from snt.hbhi.set_up_interventions import InterventionSuite
+from emod_api.interventions.common import BroadcastEvent, DelayedIntervention
+from emodpy_malaria.interventions.common import add_triggered_campaign_delay_event
+from snt.hbhi.set_up_interventions import add_all_interventions
+from emodpy_malaria.interventions.vaccine import add_scheduled_vaccine, add_triggered_vaccine
+import manifest
+
+def non_snt_camp():
+    import emod_api.campaign as campaign
+    campaign.schema_path = manifest.schema_file
+
+    delay_distribution = {"Delay_Period_Distribution": "CONSTANT_DISTRIBUTION",
+                          "Delay_Period_Constant": 274}
+    event_name = "RTSS_1_eligible"
+    broadcast_event = BroadcastEvent(campaign, event_name)
+    delayed_event = DelayedIntervention(campaign, Configs=[broadcast_event],
+                                        Delay_Dict=delay_distribution)
+    add_triggered_campaign_delay_event(campaign, start_day=1,
+                                       trigger_condition_list=['Births'],
+                                       demographic_coverage=0.504,
+                                       individual_intervention=delayed_event)
+    add_triggered_vaccine(campaign,
+                          start_day=1,
+                          trigger_condition_list=["RTSS_1_eligible"],
+                          intervention_name='RTSS',
+                          broadcast_event='Received_Vaccine',
+                          vaccine_type="AcquisitionBlocking",
+                          vaccine_initial_effect=0.8,
+                          vaccine_box_duration=0,
+                          vaccine_decay_time_constant=592.4067,
+                          efficacy_is_multiplicative=False)
+
+    return campaign
+
+
+def snt_camp():
+    import emod_api.campaign as campaign
+    campaign.schema_path = manifest.schema_file
+
+    int_suite =  InterventionSuite()
+    int_suite.rtss_auto_changeips = False
+
+    rtss_df = pd.DataFrame({
+        'DS_Name': ['Yomou'],
+        'coverage_levels': [0.504],
+        'round': [3],
+        'vaccine': ['simple'],
+        'initial_killing': [0.8],
+        'decay_time_constant': [592.4067],
+        'rtss_touchpoints': [274],
+        'decay_class': ['WaningEffectExponential'],
+        'RTSS_day': [1],
+        'deploy_type': ['EPI'],
+        'distribution_name': ['CONSTANT_DISTRIBUTION'],
+        'distribution_std': [1]
+    })
+    print(rtss_df)
+    add_all_interventions(campaign, int_suite, my_ds="Yomou",
+                          rtss_df=rtss_df)
+
+    return campaign
+
+
+camp1 = non_snt_camp()
+camp2 = snt_camp()
+
+camp1.save("camp1.json")
+camp2.save("camp2.json")

snt/hbhi/set_up_general.py

@@ -167,8 +167,8 @@ def set_input_files(config, my_ds, archetype_ds=None, demographic_suffix='',
     else:
         ds = my_ds
 
-    config.parameters['District_Sanitaire'] = 'my_ds'
-    config.parameters['Archetype'] = 'archetype_ds'
+    # config.parameters['District_Sanitaire'] = 'my_ds'
+    # config.parameters['Archetype'] = 'archetype_ds'
 
     if demographic_suffix is not None:
         config.parameters.Demographics_Filenames = [
@@ -196,7 +196,7 @@ def set_input_files(config, my_ds, archetype_ds=None, demographic_suffix='',
     return {'DS_Name': my_ds}
 
 
-def add_input_files(task, iopath, my_ds, archetype_ds=None, demographic_suffix='',
+def add_input_files(task, inputpath, my_ds, archetype_ds=None, demographic_suffix='',
                     climate_suffix='', climate_prefix=True, use_archetype=True):
     """
     Add assets corresponding to the filename parameters set in set_input_files.
@@ -232,58 +232,58 @@ def add_input_files(task, iopath, my_ds, archetype_ds=None, demographic_suffix='
 
     if demographic_suffix is not None:
         demog_path = os.path.join(ds, f'{ds}_demographics{demographic_suffix}.json')
-        task.common_assets.add_asset(os.path.join(iopath, 'simulation_inputs', demog_path),
+        task.common_assets.add_asset(os.path.join(inputpath, demog_path),
                                      relative_path=str(Path(demog_path).parent), fail_on_duplicate=False)
 
     if climate_suffix is not None:
         if climate_prefix:
             file_path = os.path.join(ds, f'{ds}_air_temperature_daily{climate_suffix}.bin')
-            task.common_assets.add_asset(os.path.join(iopath, 'simulation_inputs', file_path),
+            task.common_assets.add_asset(os.path.join(inputpath, file_path),
                                          relative_path=str(Path(file_path).parent), fail_on_duplicate=False)
             file_path = os.path.join(ds, f'{ds}_air_temperature_daily{climate_suffix}.bin.json')
-            task.common_assets.add_asset(os.path.join(iopath, 'simulation_inputs', file_path),
+            task.common_assets.add_asset(os.path.join(inputpath, file_path),
                                          relative_path=str(Path(file_path).parent), fail_on_duplicate=False)
 
             file_path = os.path.join(ds, f'{ds}_rainfall_daily{climate_suffix}.bin')
-            task.common_assets.add_asset(os.path.join(iopath, 'simulation_inputs', file_path),
+            task.common_assets.add_asset(os.path.join(inputpath, file_path),
                                          relative_path=str(Path(file_path).parent), fail_on_duplicate=False)
             file_path = os.path.join(ds, f'{ds}_rainfall_daily{climate_suffix}.bin.json')
-            task.common_assets.add_asset(os.path.join(iopath, 'simulation_inputs', file_path),
+            task.common_assets.add_asset(os.path.join(inputpath, file_path),
                                          relative_path=str(Path(file_path).parent), fail_on_duplicate=False)
 
             file_path = os.path.join(ds, f'{ds}_relative_humidity_daily{climate_suffix}.bin')
-            task.common_assets.add_asset(os.path.join(iopath, 'simulation_inputs', file_path),
+            task.common_assets.add_asset(os.path.join(inputpath, file_path),
                                          relative_path=str(Path(file_path).parent), fail_on_duplicate=False)
             file_path = os.path.join(ds, f'{ds}_relative_humidity_daily{climate_suffix}.bin.json')
-            task.common_assets.add_asset(os.path.join(iopath, 'simulation_inputs', file_path),
+            task.common_assets.add_asset(os.path.join(inputpath, file_path),
                                          relative_path=str(Path(file_path).parent), fail_on_duplicate=False)
         else:
             file_path = os.path.join(ds, f'air_temperature_daily{climate_suffix}.bin')
-            task.common_assets.add_asset(os.path.join(iopath, 'simulation_inputs', file_path),
+            task.common_assets.add_asset(os.path.join(inputpath, file_path),
                                          relative_path=str(Path(file_path).parent), fail_on_duplicate=False)
             file_path = os.path.join(ds, f'air_temperature_daily{climate_suffix}.bin.json')
-            task.common_assets.add_asset(os.path.join(iopath, 'simulation_inputs', file_path),
+            task.common_assets.add_asset(os.path.join(inputpath, file_path),
                                          relative_path=str(Path(file_path).parent), fail_on_duplicate=False)
 
             file_path = os.path.join(ds, f'rainfall_daily{climate_suffix}.bin')
-            task.common_assets.add_asset(os.path.join(iopath, 'simulation_inputs', file_path),
+            task.common_assets.add_asset(os.path.join(inputpath, file_path),
                                          relative_path=str(Path(file_path).parent), fail_on_duplicate=False)
             file_path = os.path.join(ds, f'rainfall_daily{climate_suffix}.bin.json')
-            task.common_assets.add_asset(os.path.join(iopath, 'simulation_inputs', file_path),
+            task.common_assets.add_asset(os.path.join(inputpath, file_path),
                                          relative_path=str(Path(file_path).parent), fail_on_duplicate=False)
 
             file_path = os.path.join(ds, f'relative_humidity_daily{climate_suffix}.bin')
-            task.common_assets.add_asset(os.path.join(iopath, 'simulation_inputs', file_path),
+            task.common_assets.add_asset(os.path.join(inputpath, file_path),
                                          relative_path=str(Path(file_path).parent), fail_on_duplicate=False)
             file_path = os.path.join(ds, f'relative_humidity_daily{climate_suffix}.bin.json')
-            task.common_assets.add_asset(os.path.join(iopath, 'simulation_inputs', file_path),
+            task.common_assets.add_asset(os.path.join(inputpath, file_path),
                                          relative_path=str(Path(file_path).parent), fail_on_duplicate=False)
 
 
 def setup_ds(config, manifest, platform, my_ds, archetype_ds=None,
              pull_from_serialization=False,
              burnin_id='', ser_date=50 * 365,
-             burnin_fname='',
+             burnin_df=None,
              rel_abund_df=None, lhdf=None, use_arch_burnin=True,
              from_arch=None, demographic_suffix='',
              climate_suffix='',
@@ -379,7 +379,7 @@ def setup_ds(config, manifest, platform, my_ds, archetype_ds=None,
         if burnin_id:
             ser_df = platform.create_sim_directory_df(burnin_id)  # TODO: or we can pass ser_df in
         else:
-            ser_df = pd.read_csv(burnin_fname)
+            ser_df = burnin_df
 
         if use_arch_burnin:
             ser_df = ser_df[ser_df[ds_name] == archetype_ds]

snt/hbhi/set_up_interventions.py

@@ -129,7 +129,7 @@ def add_hs_from_file(self, campaign, row, duration):
                 'rate': rates
             })
         add_treatment_seeking(campaign, start_day=start_day, targets=targets, drug=['Artemether', 'Lumefantrine'],
-                              duration=duration)
+                              duration=duration, broadcast_event_name='Received_Treatment')
 
         # Severe
         targets = []
@@ -677,7 +677,7 @@ def add_ds_vaccpmc(self, campaign, pmc_df, my_ds):
             num_iiv_groups = 1
 
         pmc_touchpoints_dict = {}
-        for i, tp in enumerate(df['pmc_touchpoints']):
+        for i, tp in enumerate(df[self.pmc_touchpoint_col]):
             pmc_touchpoints_dict[f'{i}'] = tp
 
         add_vaccdrug_campaign(campaign, campaign_type='PMC', start_days=list(df[self.pmc_start_col]),
@@ -838,13 +838,14 @@ def add_all_interventions(campaign, int_suite, my_ds, hs_df=pd.DataFrame(),
         if has_irs > 0:
             event_list.append('Received_IRS')
 
-    if not smc_df[smc_df[int_suite.smc_ds_col] == my_ds].empty:
-        if addtl_smc_func:
-            addtl_smc = addtl_smc_func(campaign, smc_df, my_ds)
-        # has_smc = int_suite.add_ds_smc(cb, smc_df, my_ds)  #  'Received_Campaign_Drugs'
-        has_smc = int_suite.add_ds_vaccsmc(campaign, smc_df, my_ds)  # per default use vaccsmc
-        if has_smc > 0:
-            event_list = event_list + ['Received_SMC_VaccDrug']  # 'Received_Vehicle'
+    if not smc_df.empty:
+        if not smc_df[smc_df[int_suite.smc_ds_col] == my_ds].empty:
+            if addtl_smc_func:
+                addtl_smc = addtl_smc_func(campaign, smc_df, my_ds)
+            # has_smc = int_suite.add_ds_smc(cb, smc_df, my_ds)  #  'Received_Campaign_Drugs'
+            has_smc = int_suite.add_ds_vaccsmc(campaign, smc_df, my_ds)  # per default use vaccsmc
+            if has_smc > 0:
+                event_list = event_list + ['Received_SMC_VaccDrug']  # 'Received_Vehicle'
 
     if not itn_df.empty:
         has_itn = int_suite.add_ds_itns(campaign, itn_df, my_ds)

snt/support_files/malaria_vaccdrug_campaigns.py

@@ -384,7 +384,7 @@ def add_vacc_smc(campaign, start_days, coverages, target_group: dict = None,
                               vaccine_initial_effect=vacc_initial_effect,
                               vaccine_box_duration=vacc_box_duration,
                               vaccine_decay_time_constant=vacc_decay_duration / math.log(2),
-                              efficacy_is_multiplicative=False,
+                              efficacy_is_multiplicative=True,
                               broadcast_event=receiving_vaccine_event)
 
     return {'smc_cov': sum(coverages) / len(coverages),
@@ -521,7 +521,7 @@ def add_vaccdrug_pmc(campaign, start_days: list, coverages: list,
                                       vaccine_initial_effect=vaccine_initial_effect,
                                       vaccine_box_duration=vaccine_box_duration,
                                       vaccine_decay_time_constant=vaccine_decay_duration / math.log(2),
-                                      efficacy_is_multiplicative=False
+                                      efficacy_is_multiplicative=True
                                       )
         else:
             add_triggered_vaccine(campaign,
@@ -535,7 +535,7 @@ def add_vaccdrug_pmc(campaign, start_days: list, coverages: list,
                                   vaccine_initial_effect=vaccine_initial_effect,
                                   vaccine_box_duration=vaccine_box_duration,
                                   vaccine_decay_time_constant=vaccine_decay_duration / math.log(2),
-                                  efficacy_is_multiplicative=False
+                                  efficacy_is_multiplicative=True
                                   )
 
     return {'pmc_cov': sum(coverages) / len(coverages),
@@ -628,7 +628,7 @@ def add_vacc_pmc(campaign, start_days: list, coverages: list, target_group: dict
                                       vaccine_initial_effect=vaccine_initial_effect,
                                       vaccine_box_duration=vaccine_box_duration,
                                       vaccine_decay_time_constant=vaccine_decay_duration / math.log(2),
-                                      efficacy_is_multiplicative=False
+                                      efficacy_is_multiplicative=True
                                       )
 
         else:
@@ -645,7 +645,7 @@ def add_vacc_pmc(campaign, start_days: list, coverages: list, target_group: dict
                                   vaccine_initial_effect=vaccine_initial_effect,
                                   vaccine_box_duration=vaccine_box_duration,
                                   vaccine_decay_time_constant=vaccine_decay_duration / math.log(2),
-                                  efficacy_is_multiplicative=False
+                                  efficacy_is_multiplicative=True
                                   )
 
     return {'pmc_cov': sum(coverages) / len(coverages),