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3 changes: 3 additions & 0 deletions resources/healthsystem/consumables/README.md
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37 changes: 29 additions & 8 deletions src/tlo/methods/consumables.py
Original file line number Diff line number Diff line change
Expand Up @@ -56,6 +56,9 @@ def __init__(self,
self._is_unknown_item_available = None # Whether an unknown item is available, by facility_id
self._not_recognised_item_codes = defaultdict(set) # The item codes requested but which are not recognised.

# Save data
self._availability_data = availability_data

# Save designations
self._item_code_designations = item_code_designations

Expand Down Expand Up @@ -96,14 +99,21 @@ def _update_prob_item_codes_available(self, availability: str):
overriding the availability of specific consumables."""

# Load the original read-in data (create copy so that edits do change the original)
self._prob_item_codes_available = self._processed_consumables_data.copy()
_, self._prob_item_codes_available = self._process_consumables_data(
availability_data=self._availability_data,
availability=availability
)

# Load designations of the consumables
item_code_designations = self._item_code_designations

# Over-ride the data according to option for `availability`
if availability == 'default':
pass
if availability in ('default',
'scenario1', 'scenario2', 'scenario3', 'scenario4',
'scenario5', 'scenario6', 'scenario7', 'scenario8',
'scenario9', 'scenario10', 'scenario11', 'scenario12',
'scenario13', 'scenario14', 'scenario15'):
pass # change already picked up in `self._process_consumables_data()`
elif availability == 'all':
self.override_availability(dict(zip(self.item_codes, repeat(1.0))))
elif availability == 'none':
Expand Down Expand Up @@ -134,16 +144,27 @@ def _update_prob_item_codes_available(self, availability: str):
else:
raise ValueError

def _process_consumables_data(self, availability_data: pd.DataFrame) -> Tuple[set, pd.Series]:
def _process_consumables_data(self, availability_data: pd.DataFrame, availability: str) -> Tuple[set, pd.Series]:
"""Helper function for processing the consumables data, passed in here as pd.DataFrame that has been read-in by
the HealthSystem.
Returns: (i) the set of all recognised item_codes; (ii) pd.Series of the availability of
each consumable at each facility_id during each month.
"""
return (
set(availability_data.item_code),
availability_data.set_index(['month', 'Facility_ID', 'item_code'])['available_prop']
)
assert availability is not None, "This argument cannot be None."

if availability in ('scenario1', 'scenario2', 'scenario3', 'scenario4',
'scenario5', 'scenario6', 'scenario7', 'scenario8',
'scenario9', 'scenario10', 'scenario11', 'scenario12',
'scenario13', 'scenario14', 'scenario15',):
return (
set(availability_data.item_code),
availability_data.set_index(['month', 'Facility_ID', 'item_code'])['available_prop_' + availability]
)
else:
return (
set(availability_data['item_code']),
availability_data.set_index(['month', 'Facility_ID', 'item_code'])['available_prop']
)

def _refresh_availability_of_consumables(self, date: datetime.datetime):
"""Update the availability of all items based on the data for the probability of availability, given the current
Expand Down
7 changes: 6 additions & 1 deletion tests/test_consumables.py
Original file line number Diff line number Diff line change
Expand Up @@ -650,7 +650,12 @@ def test_consumables_availability_modes_that_depend_on_designations(seed):
target_items = items_drug_or_vaccine
elif availability == 'none':
target_items = set()
elif availability == 'default':
elif availability in ('default',
'scenario1', 'scenario2', 'scenario3', 'scenario4',
'scenario5', 'scenario6', 'scenario7', 'scenario8',
'scenario9', 'scenario10', 'scenario11', 'scenario12',
'scenario13', 'scenario14', 'scenario15',
):
continue
else:
raise ValueError(f'Unexpected availability: {availability}')
Expand Down
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