equipment pkgs

src/scripts/data_file_processing/healthsystem/equipment/equipment_availability_estimation.py

@@ -322,6 +322,12 @@
                                                   .drop_duplicates() \
                                                   .pipe(lambda x: x.set_index(x['Item_code'].astype(int)))['Category'] \
                                                   .to_dict()
+# Manually declare the price category for equipment items added manually
+# 402: Endoscope: 'Cost >= $1000'
+equipment_price_category_mapper[402] = 'Cost >= $1000'
+# 403: Electrocardiogram: 'Cost >= $1000'
+equipment_price_category_mapper[403] = 'Cost >= $1000'
+
 equipment_price_category = final_equipment_availability_export_full.index.get_level_values('Item_Code') \
                                                                          .map(equipment_price_category_mapper)
 final_equipment_availability_export_full = final_equipment_availability_export_full.groupby(

src/tlo/methods/bladder_cancer.py

@@ -897,9 +897,7 @@ def apply(self, person_id, squeeze_factor):
 
         if cons_avail:
             # If consumables are available and the treatment will go ahead - update the equipment
-            # TODO: DISCUSSED - replace with package and call here
-            self.add_equipment({'Infusion pump', 'Drip stand', 'Laparotomy Set',
-                                   'Blood pressure machine', 'Pulse oximeter'})
+            self.add_equipment(self.healthcare_system.equipment.from_pkg_names('Major Surgery'))
 
             # Record date and stage of starting treatment
             df.at[person_id, "bc_date_treatment"] = self.sim.date

src/tlo/methods/breast_cancer.py

@@ -796,9 +796,7 @@ def apply(self, person_id, squeeze_factor):
 
         if cons_available:
             # If consumables are available and the treatment will go ahead - add the used equipment
-            # TODO: DISCUSSED - link to new surgical pacakge
-            self.add_equipment({'Infusion pump', 'Drip stand', 'Laparotomy Set',
-                                   'Blood pressure machine', 'Pulse oximeter'})
+            self.add_equipment(self.healthcare_system.equipment.from_pkg_names('Major Surgery'))
 
             # Log the use of adjuvant chemotherapy
             self.get_consumables(

src/tlo/methods/cardio_metabolic_disorders.py

@@ -1799,13 +1799,7 @@ def apply(self, person_id, squeeze_factor):
             data=('This is HSI_CardioMetabolicDisorders_SeeksEmergencyCareAndGetsTreatment: '
                   f'The squeeze-factor is {squeeze_factor}.'),
         )
-        # to do @eva/joe - DISCUSSED, make ICU package and use here
-        self.add_equipment({'Analyser, Combined Chemistry and Electrolytes',
-                               'Analyser, Haematology',
-                               'Patient monitor', 'Drip stand',
-                               'Infusion pump', 'Blood pressure machine',
-                               'Pulse oximeter', 'Trolley, emergency', 'Stethoscope',
-                               'Oxygen cylinder, with regulator'})
+        self.add_equipment(self.healthcare_system.equipment.from_pkg_names('ICU'))
 
         for _ev in self.events_to_investigate:
             self.do_for_each_event_to_be_investigated(_ev)

src/tlo/methods/care_of_women_during_pregnancy.py

@@ -1440,8 +1440,9 @@ def apply(self, person_id, squeeze_factor):
 
             #  =================================== INTERVENTIONS ====================================================
             # Add equipment used during first ANC visit not directly related to interventions
+            self.add_equipment(self.healthcare_system.equipment.from_pkg_names('ANC'))
             self.add_equipment(
-                {'Weighing scale', 'Height Pole (Stadiometer)', 'MUAC tape', 'Measuring tapes',
+                {'Height Pole (Stadiometer)', 'MUAC tape',
                  'Ultrasound, combined 2/4 pole interferential with vacuum and dual frequency 1-3MHZ'})
 
             # First all women, regardless of ANC contact or gestation, undergo urine and blood pressure measurement
@@ -1529,9 +1530,9 @@ def apply(self, person_id, squeeze_factor):
 
             #  =================================== INTERVENTIONS ====================================================
             # Add equipment used during  ANC visit not directly related to interventions
+            self.add_equipment(self.healthcare_system.equipment.from_pkg_names('ANC'))
             self.add_equipment(
-                {'Weighing scale', 'Measuring tapes', 'Stethoscope, foetal, monaural, Pinard, plastic'
-                 'Ultrasound, combined 2/4 pole interferential with vacuum and dual frequency 1-3MHZ'})
+                {'Ultrasound, combined 2/4 pole interferential with vacuum and dual frequency 1-3MHZ'})
 
             # First we administer the interventions all women will receive at this contact regardless of
             # gestational age
@@ -1617,8 +1618,7 @@ def apply(self, person_id, squeeze_factor):
             df.at[person_id, 'ac_total_anc_visits_current_pregnancy'] += 1
 
             #  =================================== INTERVENTIONS ====================================================
-            self.add_equipment({'Weighing scale', 'Measuring tapes',
-                                   'Stethoscope, foetal, monaural, Pinard, plastic'})
+            self.add_equipment(self.healthcare_system.equipment.from_pkg_names('ANC'))
 
             gest_age_next_contact = self.module.determine_gestational_age_for_next_contact(person_id)
             self.module.interventions_delivered_each_visit_from_anc2(hsi_event=self)
@@ -1692,8 +1692,7 @@ def apply(self, person_id, squeeze_factor):
             df.at[person_id, 'ac_total_anc_visits_current_pregnancy'] += 1
 
             #  =================================== INTERVENTIONS ====================================================
-            self.add_equipment({'Weighing scale', 'Measuring tapes',
-                                   'Stethoscope, foetal, monaural, Pinard, plastic'})
+            self.add_equipment(self.healthcare_system.equipment.from_pkg_names('ANC'))
 
             gest_age_next_contact = self.module.determine_gestational_age_for_next_contact(person_id)
             self.module.interventions_delivered_each_visit_from_anc2(hsi_event=self)
@@ -1762,10 +1761,10 @@ def apply(self, person_id, squeeze_factor):
             self.module.anc_counter[5] += 1
             df.at[person_id, 'ac_total_anc_visits_current_pregnancy'] += 1
 
-            #  =================================== INTERVENTIONS ====================================================
+            #  =================================== INTERVENTIONS ===================================================
+            self.add_equipment(self.healthcare_system.equipment.from_pkg_names('ANC'))
             self.add_equipment(
-                {'Weighing scale', 'Measuring tapes', 'Stethoscope, foetal, monaural, Pinard, plastic'
-                 'Ultrasound, combined 2/4 pole interferential with vacuum and dual frequency 1-3MHZ'})
+                {'Ultrasound, combined 2/4 pole interferential with vacuum and dual frequency 1-3MHZ'})
 
             gest_age_next_contact = self.module.determine_gestational_age_for_next_contact(person_id)
             self.module.interventions_delivered_each_visit_from_anc2(hsi_event=self)
@@ -1896,8 +1895,7 @@ def apply(self, person_id, squeeze_factor):
             df.at[person_id, 'ac_total_anc_visits_current_pregnancy'] += 1
 
             #  =================================== INTERVENTIONS ====================================================
-            self.add_equipment({'Weighing scale', 'Measuring tapes',
-                                   'Stethoscope, foetal, monaural, Pinard, plastic'})
+            self.add_equipment(self.healthcare_system.equipment.from_pkg_names('ANC'))
 
             gest_age_next_contact = self.module.determine_gestational_age_for_next_contact(person_id)
             self.module.interventions_delivered_each_visit_from_anc2(hsi_event=self)
@@ -1952,8 +1950,7 @@ def apply(self, person_id, squeeze_factor):
             self.module.anc_counter[8] += 1
             df.at[person_id, 'ac_total_anc_visits_current_pregnancy'] += 1
 
-            self.add_equipment({'Weighing scale', 'Measuring tapes',
-                                   'Stethoscope, foetal, monaural, Pinard, plastic'})
+            self.add_equipment(self.healthcare_system.equipment.from_pkg_names('ANC'))
 
             self.module.interventions_delivered_each_visit_from_anc2(hsi_event=self)
 

src/tlo/methods/contraception.py

@@ -1206,7 +1206,7 @@ def apply(self, person_id, squeeze_factor):
                 self.add_equipment({
                     'Cusco’s/ bivalved Speculum (small, medium, large)', 'Lamp, Anglepoise'
                 })
-                # TO DO: @Eva - DISCUSSED add equip for minor surgery
+                self.add_equipment(self.healthcare_system.equipment.from_pkg_names('Minor Surgery'))
             elif _new_contraceptive == 'IUD':
                 self.add_equipment({
                     'Cusco’s/ bivalved Speculum (small, medium, large)', 'Sponge Holding Forceps'

src/tlo/methods/equipment.py

@@ -1,6 +1,6 @@
 import warnings
 from collections import defaultdict
-from typing import Counter, Iterable, Literal, Set, Union
+from typing import Counter, Dict, Iterable, Literal, Set, Union
 
 import numpy as np
 import pandas as pd
@@ -77,6 +77,7 @@ def __init__(
 
         # - Data structures for quick look-ups for items and descriptors
         self._item_code_lookup = self.catalogue.set_index('Item_Description')['Item_Code'].to_dict()
+        self._pkg_lookup = self._create_pkg_lookup()
         self._all_item_descriptors = set(self._item_code_lookup.keys())
         self._all_item_codes = set(self._item_code_lookup.values())
         self._all_fac_ids = self.master_facilities_list['Facility_ID'].unique()
@@ -134,11 +135,11 @@ def parse_items(self, items: Union[int, str, Iterable[int], Iterable[str]]) -> S
 
         def check_item_codes_recognised(item_codes: set[int]):
             if not item_codes.issubset(self._all_item_codes):
-                warnings.warn(f'Item code(s) "{item_codes}" not recognised.')
+                warnings.warn(f'At least one item code was unrecognised: "{item_codes}".')
 
         def check_item_descriptors_recognised(item_descriptors: set[str]):
             if not item_descriptors.issubset(self._all_item_descriptors):
-                warnings.warn(f'Item descriptor(s) "{item_descriptors}" not recognised.')
+                warnings.warn(f'At least one item descriptor was unrecognised "{item_descriptors}".')
 
         # Make into a set if it is not one already
         if isinstance(items, (str, int)):
@@ -248,13 +249,37 @@ def set_of_keys_or_empty_set(x: Union[set, dict]):
                 data=row.to_dict(),
             )
 
-    def lookup_item_codes_from_pkg_name(self, pkg_name: str) -> Set[int]:
-        """Convenience function to find the set of item_codes that are grouped under a package name in the catalogue.
-        It is expected that this is used by the disease module once and then the resulting equipment item_codes are
-        saved on the module."""
-        df = self.catalogue
+    def from_pkg_names(self, pkg_names: Union[str, Iterable[str]]) -> Set[int]:
+        """Convenience function to find the set of item_codes that are grouped under requested package name(s) in the
+        catalogue."""
+        # Make into a set if it is not one already
+        if isinstance(pkg_names, (str, int)):
+            pkg_names = set([pkg_names])
+        else:
+            pkg_names = set(pkg_names)
 
-        if pkg_name not in df['Pkg_Name'].unique():
-            raise ValueError(f'That Pkg_Name is not in the catalogue: {pkg_name=}')
+        item_codes = set()
+        for pkg_name in pkg_names:
+            if pkg_name in self._pkg_lookup.keys():
+                item_codes.update(self._pkg_lookup[pkg_name])
+            else:
+                raise ValueError(f'That Pkg_Name is not in the catalogue: {pkg_name=}')
+
+        return item_codes
 
-        return set(df.loc[df['Pkg_Name'] == pkg_name, 'Item_Code'].values)
+    def _create_pkg_lookup(self) -> Dict[str, Set[int]]:
+        df = self.catalogue
+        pkg_lookup = dict()
+
+        pkg_names_raw = set(df['Pkg_Name'].unique()[~pd.isnull(df['Pkg_Name'].unique())])
+        all_multiple_pkg_names = set(name for name in pkg_names_raw if ", " in name)
+        all_pkg_names = pkg_names_raw - all_multiple_pkg_names
+        for pkg_name in all_pkg_names:
+            pkg_lookup[pkg_name] = set(df.loc[df['Pkg_Name'] == pkg_name, 'Item_Code'].values)
+        for multiple_pkg_name in all_multiple_pkg_names:
+            for pkg_name in multiple_pkg_name.split(", "):
+                if pkg_name not in all_pkg_names:
+                    pkg_lookup[pkg_name] = set()
+                    all_pkg_names.update({pkg_name})
+                pkg_lookup[pkg_name].update(set(df.loc[df['Pkg_Name'] == multiple_pkg_name, 'Item_Code'].values))
+        return pkg_lookup

src/tlo/methods/labour.py

@@ -2128,9 +2128,7 @@ def surgical_management_of_pph(self, hsi_event):
         if avail and sf_check:
 
             # Add used equipment
-            # Todo: DISCUSSED - @eva surgical package
-            hsi_event.add_equipment(
-                {'Infusion pump', 'Drip stand', 'Laparotomy Set', 'Blood pressure machine', 'Pulse oximeter'})
+            hsi_event.add_equipment(self.healthcare_system.equipment.from_pkg_names('Major Surgery'))
 
             # determine if uterine preserving surgery will be successful
             treatment_success_pph = params['success_rate_pph_surgery'] > self.rng.random_sample()
@@ -3236,9 +3234,7 @@ def apply(self, person_id, squeeze_factor):
             elif (avail and sf_check) or (mni[person_id]['cs_indication'] == 'other'):
 
                 # If intervention is delivered - add used equipment
-                # todo: DISCUSSED @Eva link to surgical equipment package when that exsists
-                self.add_equipment(
-                    {'Infusion pump', 'Drip stand', 'Laparotomy Set', 'Blood pressure machine', 'Pulse oximeter'})
+                self.add_equipment(self.healthcare_system.equipment.from_pkg_names('Major Surgery'))
 
                 person = df.loc[person_id]
                 logger.info(key='caesarean_delivery', data=person.to_dict())

src/tlo/methods/oesophagealcancer.py

@@ -784,9 +784,7 @@ def apply(self, person_id, squeeze_factor):
 
         if cons_avail:
             # If consumables are available and the treatment will go ahead - update the equipment
-            # TODO: DISCUSSED - add surgery package
-            self.add_equipment({'Infusion pump', 'Drip stand', 'Laparotomy Set',
-                                   'Blood pressure machine', 'Pulse oximeter'})
+            self.add_equipment(self.healthcare_system.equipment.from_pkg_names('Major Surgery'))
 
             # Log chemotherapy consumables
             self.get_consumables(

src/tlo/methods/other_adult_cancers.py

@@ -786,9 +786,7 @@ def apply(self, person_id, squeeze_factor):
 
         if cons_available:
             # If consumables are available and the treatment will go ahead - update the equipment
-            # TODO: DISCUSSED - link to surgical equipment package when that exists
-            self.add_equipment({'Infusion pump', 'Drip stand', 'Laparotomy Set',
-                                   'Blood pressure machine', 'Pulse oximeter'})
+            self.add_equipment(self.healthcare_system.equipment.from_pkg_names('Major Surgery'))
 
             # Record date and stage of starting treatment
             df.at[person_id, "oac_date_treatment"] = self.sim.date

src/tlo/methods/prostate_cancer.py

@@ -918,9 +918,7 @@ def apply(self, person_id, squeeze_factor):
 
         if cons_available:
             # If consumables are available and the treatment will go ahead - update the equipment
-            # TODO: DISCUSSED -link to surgical equipment package when that exists
-            self.add_equipment({'Infusion pump', 'Drip stand', 'Laparotomy Set',
-                                   'Blood pressure machine', 'Pulse oximeter'})
+            self.add_equipment(self.healthcare_system.equipment.from_pkg_names('Major Surgery'))
 
             # Record date and stage of starting treatment
             df.at[person_id, "pc_date_treatment"] = self.sim.date

src/tlo/methods/rti.py

@@ -3205,8 +3205,7 @@ def apply(self, person_id, squeeze_factor):
         road_traffic_injuries.rti_injury_diagnosis(person_id, self.EXPECTED_APPT_FOOTPRINT)
 
         if 'DiagRadio' in list(self.EXPECTED_APPT_FOOTPRINT.keys()):
-            # TODO: @Eva - DISCUSSED use xray package when available
-            self.add_equipment({'X-ray machine', 'X-ray viewer'})
+            self.add_equipment(self.healthcare_system.equipment.from_pkg_names('X-ray'))
 
         elif 'Tomography' in list(self.EXPECTED_APPT_FOOTPRINT.keys()):
             self.ACCEPTED_FACILITY_LEVEL = '3'
@@ -3513,13 +3512,7 @@ def apply(self, person_id, squeeze_factor):
 
         if df.loc[person_id, 'rt_ISS_score'] > self.hdu_cut_off_iss_score:
 
-            # to do @eva/joe - DISCUSSED, make ICU package and use here
-            self.add_equipment({'Analyser, Combined Chemistry and Electrolytes',
-                                   'Analyser, Haematology',
-                                   'Patient monitor', 'Drip stand',
-                                   'Infusion pump', 'Blood pressure machine',
-                                   'Pulse oximeter', 'Trolley, emergency', 'Stethoscope',
-                                   'Oxygen cylinder, with regulator'})
+            self.add_equipment(self.healthcare_system.equipment.from_pkg_names('ICU'))
 
             mean_icu_days = p['mean_icu_days']
             sd_icu_days = p['sd_icu_days']
@@ -4099,9 +4092,7 @@ def apply(self, person_id, squeeze_factor):
                          data=f"Fracture casts available for person {person_id} {open_fracture_counts} open fractures"
                          )
 
-            # Todo: DISCUSSED @Eva link to surgical equipment package when that exsists
-            self.add_equipment(
-                {'Infusion pump', 'Drip stand', 'Laparotomy Set', 'Blood pressure machine', 'Pulse oximeter'})
+            self.add_equipment(self.healthcare_system.equipment.from_pkg_names('Major Surgery'))
 
             person = df.loc[person_id]
             # update the dataframe to show this person is recieving treatment
@@ -4823,8 +4814,9 @@ def apply(self, person_id, squeeze_factor):
             assert df.loc[person_id, 'rt_diagnosed'], 'This person has not been through a and e'
             assert df.loc[person_id, 'rt_med_int'], 'This person has not been through rti med int'
 
-            # TODO: @eva - DISCUSSED @eva add surgical package
-            self.add_equipment({'Laparotomy Set', 'Infusion pump', 'Drip stand'})
+            # TODO: @Joe to confirm major surgery pkg should be used here (as the original set of equipment here was not
+            #  the full pkg)
+            self.add_equipment(self.healthcare_system.equipment.from_pkg_names('Major Surgery'))
 
             # ------------------------ Track permanent disabilities with treatment -------------------------------------
             # --------------------------------- Perm disability from TBI -----------------------------------------------
@@ -5141,8 +5133,9 @@ def apply(self, person_id, squeeze_factor):
         # todo: think about consequences of certain consumables not being available for minor surgery and model health
         #  outcomes
         if request_outcome:
-            # TODO: DISCUSSED @Eva link to surgical equipment package when that exists
-            self.add_equipment({'Laparotomy Set', 'Infusion pump', 'Drip stand'})
+            # TODO: @Joe to confirm major surgery pkg should be used here (as the original set of equipment here was not
+            #  the full pkg)
+            self.add_equipment(self.healthcare_system.equipment.from_pkg_names('Major Surgery'))
 
             # create a dictionary to store the recovery times for each injury in days
             minor_surg_recov_time_days = {