Artifact Run Updates (#127)

* Attempt 1 at getting the artifact to run

* Updating years throughout, changing to GBD 2023

* forgot isort and black

* V&V'ed the artifact, updated one year call

* Changing hemoglobin to 2021 values following conversation with Ali

* Forgot isort and black again

---------

Co-authored-by: Sylvia Lutze <lutzes@long-slurm-sarchive-p0039.cluster.ihme.washington.edu>
Co-authored-by: Sylvia Lutze <lutzes@long-slurm-sarchive-p0014.cluster.ihme.washington.edu>

Author: 3 people

src/vivarium_gates_nutrition_optimization/constants/data_keys.py

@@ -31,7 +31,7 @@ def log_name(self):
 
 class __Pregnancy(NamedTuple):
     ASFR: str = "covariate.age_specific_fertility_rate.estimate"
-    SBR: str = "covariate.stillbirth_to_live_birth_ratio.estimate"
+    SBR: str = "covariate.stillbirth_20_weeks_to_live_birth_ratio.estimate"
     RAW_INCIDENCE_RATE_MISCARRIAGE: str = (
         "cause.maternal_abortion_and_miscarriage.raw_incidence_rate"
     )

src/vivarium_gates_nutrition_optimization/data/extra_gbd.py

@@ -1,65 +1,65 @@
 from gbd_mapping import sequelae
 from vivarium_gbd_access import constants as gbd_constants
-from vivarium_gbd_access import gbd
 from vivarium_gbd_access import utilities as vi_utils
+from vivarium_gbd_access.gbd import base_data as gbd
 from vivarium_inputs import globals as vi_globals
 from vivarium_inputs import utility_data
 
 from vivarium_gates_nutrition_optimization.constants import data_keys
 from vivarium_gates_nutrition_optimization.data import utilities
 
 
-@gbd.memory.cache
-def load_lbwsg_exposure(location: str):
+@vi_utils.cache
+def load_2021_lbwsg_birth_exposure(location: str):
     entity = utilities.get_entity(data_keys.LBWSG.EXPOSURE)
     location_id = utility_data.get_location_id(location)
-    data = vi_utils.get_draws(
+    data = gbd.get_draws(
         gbd_id_type="rei_id",
         gbd_id=entity.gbd_id,
         source=gbd_constants.SOURCES.EXPOSURE,
         location_id=location_id,
-        year_id=2021,
+        year_id=2022,
         sex_id=gbd_constants.SEX.MALE + gbd_constants.SEX.FEMALE,
         age_group_id=164,  # Birth prevalence
         release_id=gbd_constants.RELEASE_IDS.GBD_2021,
     )
     return data
 
 
-@gbd.memory.cache
+@vi_utils.cache
 def get_all_cause_yld_rate(location: str):
     entity = utilities.get_entity("cause.all_causes.ylds")
     location_id = utility_data.get_location_id(location)
-    data = vi_utils.get_draws(
+    data = gbd.get_draws(
         "cause_id",
         entity.gbd_id,
         source=gbd_constants.SOURCES.COMO,
         location_id=location_id,
-        release_id=gbd_constants.RELEASE_IDS.GBD_2021,
+        release_id=gbd_constants.RELEASE_IDS.GBD_2023,
         measure_id=vi_globals.MEASURES["YLDs"],
         metric_id=3,  # rate
     )
     return data
 
 
-@gbd.memory.cache
+@vi_utils.cache
 def get_maternal_disorder_ylds(location: str, metric_id=None):
     entity = utilities.get_entity(data_keys.MATERNAL_DISORDERS.YLDS)
     location_id = utility_data.get_location_id(location)
-    data = vi_utils.get_draws(
+    data = gbd.get_draws(
         "cause_id",
         entity.gbd_id,
         source=gbd_constants.SOURCES.COMO,
         location_id=location_id,
-        year_id=2021,
-        release_id=gbd_constants.RELEASE_IDS.GBD_2021,
+        year_id=2023,
+        release_id=gbd_constants.RELEASE_IDS.GBD_2023,
         measure_id=vi_globals.MEASURES["YLDs"],
         metric_id=metric_id,
     )
     return data
 
 
-@gbd.memory.cache
+@vi_utils.cache
 def get_anemia_ylds(location: str, metric_id=None):
     anemia_sequelae = [
         sequelae.mild_anemia_due_to_maternal_hemorrhage,
@@ -68,38 +68,39 @@ def get_anemia_ylds(location: str, metric_id=None):
     ]
     anemia_ids = [s.gbd_id for s in anemia_sequelae]
     location_id = utility_data.get_location_id(location)
-    data = vi_utils.get_draws(
+    data = gbd.get_draws(
         "sequela_id",
         anemia_ids,
         source=gbd_constants.SOURCES.COMO,
         location_id=location_id,
-        year_id=2021,
-        release_id=gbd_constants.RELEASE_IDS.GBD_2021,
+        year_id=2023,
+        release_id=gbd_constants.RELEASE_IDS.GBD_2023,
         measure_id=vi_globals.MEASURES["YLDs"],
         metric_id=metric_id,
     )
     return data
 
 
-@gbd.memory.cache
+@vi_utils.cache
 def get_anemia_yld_rate(location: str):
     location_id = utility_data.get_location_id(location)
-    data = vi_utils.get_draws(
+    data = gbd.get_draws(
         "rei_id",
         192,
         source=gbd_constants.SOURCES.COMO,
         location_id=location_id,
-        release_id=gbd_constants.RELEASE_IDS.GBD_2021,
+        release_id=gbd_constants.RELEASE_IDS.GBD_2023,
         measure_id=vi_globals.MEASURES["YLDs"],
         metric_id=3,
     )
     return data
 
 
-@gbd.memory.cache
+## This is left as 2021 because the changes to hemoglobin RRs are very significant and would require other model updates we don't plan to make.
+@vi_utils.cache
 def get_hemoglobin_maternal_disorders_rr():
     """Relative risk associated with one g/dL decrease in hemoglobin concentration below 12 g/dL"""
-    data = vi_utils.get_draws(
+    data = gbd.get_draws(
         gbd_id_type="rei_id",
         gbd_id=95,
         release_id=gbd_constants.RELEASE_IDS.GBD_2021,