def main(nid, extract_type_id, code_system_id, launch_set_id):
"""Collect source metadata."""
print_log_message("Reading disaggregation data for source metadata phase.")
# in stata, this was pulled using corrections phase output (step 3)
# use data after all garbage codes have been set (step 3 produces ZZZ)
# but before any redistribution (including HIV redistribution)
df = get_phase_output("disaggregation", nid=nid,
extract_type_id=extract_type_id)
data_type_id = get_value_from_nid(nid, "data_type_id", extract_type_id)
source = get_value_from_nid(nid, "source", extract_type_id)
representative_id = get_value_from_nid(nid, "representative_id",
extract_type_id)
df = run_phase(df, nid, extract_type_id, data_type_id, source,
representative_id, code_system_id)
print_log_message(
"Writing {n} rows of output for launch set {ls}, nid {nid}, extract "
"{e}".format(n=len(df), ls=launch_set_id, e=extract_type_id, nid=nid)
)
write_phase_output(df, 'sourcemetadata', nid,
extract_type_id, launch_set_id)
def main(nid, extract_type_id, launch_set_id):
"""Run the noise reduction phase."""
# download data from input database
print_log_message("Beginning noise reduction phase")
data_type_id = get_value_from_nid(nid,
'data_type_id',
extract_type_id=extract_type_id)
source = get_value_from_nid(nid, 'source', extract_type_id=extract_type_id)
model_group = get_value_from_nid(nid,
'model_group',
extract_type_id=extract_type_id)
malaria_model_group = get_malaria_model_group_from_nid(
nid, extract_type_id)
df = run_phase(nid, extract_type_id, launch_set_id, data_type_id, source,
model_group, malaria_model_group)
print_log_message(
"Writing {n} rows of output for launch set {ls}, nid {nid}, extract "
"{e}".format(n=len(df), ls=launch_set_id, nid=nid, e=extract_type_id))
ids = [
'age_group_id', 'cause_id', 'extract_type_id', 'location_id',
'year_id', 'site_id', 'sex_id', 'nid'
]
df[ids] = df[ids].astype(int)
write_phase_output(df, 'noisereduction', nid, extract_type_id,
launch_set_id)
def main(nid, extract_type_id, code_system_id, launch_set_id, remove_decimal):
"""Main method"""
start_time = time.time()
df = get_claude_data(
"disaggregation", nid=nid, extract_type_id=extract_type_id
)
data_type_id = get_value_from_nid(nid, 'data_type_id', extract_type_id=extract_type_id)
iso3 = get_value_from_nid(nid, 'iso3', extract_type_id=extract_type_id)
df = run_pipeline(df, nid, extract_type_id, code_system_id, remove_decimal, data_type_id, iso3)
run_time = time.time() - start_time
print_log_message("Finished in {} seconds".format(run_time))
write_phase_output(
df, "misdiagnosiscorrection", nid, extract_type_id, launch_set_id
)
return df
def main(nid, extract_type_id, code_system_id, launch_set_id):
cause_set_version_id = CONF.get_id('cause_set_version')
location_set_version_id = CONF.get_id('location_set_version')
pop_run_id = CONF.get_id('pop_run')
env_run_id = CONF.get_id('env_run')
# need to use special age/sex distribution for Norway based on National data
if get_value_from_nid(nid, 'iso3',
extract_type_id=extract_type_id) == 'NOR':
distribution_set_version_id = CONF.get_id(
'NOR_distribution_set_version')
else:
distribution_set_version_id = CONF.get_id('distribution_set_version')
# download data from input database
df = get_claude_data('formatted',
nid=nid,
extract_type_id=extract_type_id,
location_set_version_id=location_set_version_id)
assert len(df) != 0, ("Dataframe is empty."
" Are you sure this source is in"
"the input database?")
# run the pipeline
df = run_pipeline(nid,
extract_type_id,
launch_set_id,
df,
code_system_id,
code_map_version_id,
cause_set_version_id,
location_set_version_id,
pop_run_id,
env_run_id,
distribution_set_version_id,
diagnostic=False)
# upload to database
write_phase_output(df, 'disaggregation', nid, extract_type_id,
launch_set_id)
def run_pipeline(nid,
extract_type_id,
launch_set_id,
df,
code_system_id,
cause_set_version_id,
location_set_version_id,
pop_run_id,
env_run_id,
distribution_set_version_id,
diagnostic=False):
"""Run the full pipeline"""
cache_options = {
'force_rerun': False,
'block_rerun': True,
'cache_results': False,
'cache_dir': CONF.get_directory('FILEPATH'),
'verbose': False
}
location_meta_df = get_current_location_hierarchy(
location_set_version_id=location_set_version_id, **cache_options)
code_map = get_cause_map(code_system_id=code_system_id, **cache_options)
source = get_value_from_nid(nid, "source", extract_type_id)
print("Overriding causes when necessary")
df = overrides(df, location_meta_df)
print("Dropping data out of scope")
df = drop_data_out_of_scope(df, location_meta_df, source)
if len(df) > 0:
# make sure six minor territories are grouped correctly
assert_no_six_minor_territories(df)
# run mapping
print("\nDeaths before MAPPING: {}".format(df.deaths.sum()))
Mapper = GBDCauseMapper(cause_set_version_id, code_map)
df = Mapper.get_computed_dataframe(df, code_system_id)
if diagnostic:
write_phase_output(df,
'mapping',
nid,
extract_type_id,
launch_set_id,
sub_dirs='diagnostic')
print("\nDeaths before AGESEXSPLIT: {}".format(df.deaths.sum()))
# run age sex splitting
MySplitter = AgeSexSplitter(cause_set_version_id,
pop_run_id,
distribution_set_version_id,
verbose=True,
collect_diagnostics=False)
df = MySplitter.get_computed_dataframe(df, location_meta_df)
if diagnostic:
diag_df = MySplitter.get_diagnostic_dataframe()
write_phase_output(diag_df,
'agesexsplit',
nid,
extract_type_id,
launch_set_id,
sub_dirs='diagnostic')
print("\nDeaths before CORRECTIONS: {}".format(df.deaths.sum()))
# run restrictions corrections
Corrector = RestrictionsCorrector(code_system_id,
cause_set_version_id,
collect_diagnostics=False,
verbose=True)
df = Corrector.get_computed_dataframe(df)
# calculate cc_code for some sources
if source in ['Iran_maternal_surveillance', 'Iran_forensic']:
env_meta_df = get_env(env_run_id=env_run_id, **cache_options)
df = calculate_cc_code(df, env_meta_df, code_map)
print("\nDeaths after adding cc_code: {}".format(df.deaths.sum()))
# adjust deaths for New Zealand by maori/non-maori ethnicities
if source in ["NZL_MOH_ICD9", "NZL_MOH_ICD10"]:
df = correct_maori_non_maori_deaths(df)
print("\nDeaths after Maori/non-Maori adjustment: {}".format(
df.deaths.sum()))
print("\nDeaths at END: {}".format(df.deaths.sum()))
return df
def run_phase(df,
csvid,
nid,
extract_type_id,
lsvid,
pop_run_id,
cmvid,
launch_set_id,
remove_decimal,
write_diagnostics=True):
read_file_cache_options = {
'block_rerun': True,
'cache_dir': CACHE_DIR,
'force_rerun': False,
'cache_results': False
}
iso3 = get_value_from_nid(nid,
'iso3',
extract_type_id=extract_type_id,
location_set_version_id=lsvid)
code_system_id = int(
get_value_from_nid(nid,
'code_system_id',
extract_type_id=extract_type_id))
data_type_id = get_value_from_nid(nid,
'data_type_id',
extract_type_id=extract_type_id)
cause_map = get_cause_map(code_map_version_id=cmvid,
**read_file_cache_options)
orig_deaths_sum = int(df['deaths'].sum())
if remove_decimal:
print_log_message("Removing decimal from code map")
cause_map['value'] = cause_map['value'].apply(
lambda x: x.replace(".", ""))
if needs_garbage_correction(iso3, data_type_id):
print_log_message("Correcting Garbage for {}".format(iso3))
orig_gc_sum = int(df.query('cause_id == 743')['deaths'].sum())
cause_meta_df = get_current_cause_hierarchy(cause_set_version_id=csvid,
**read_file_cache_options)
age_meta_df = get_ages(**read_file_cache_options)
loc_meta_df = get_current_location_hierarchy(
location_set_version_id=lsvid, **read_file_cache_options)
pop_meta_df = get_pop(pop_run_id=pop_run_id, **read_file_cache_options)
hiv_corrector = HIVCorrector(df,
iso3,
code_system_id,
pop_meta_df,
cause_meta_df,
loc_meta_df,
age_meta_df,
correct_garbage=True)
df = hiv_corrector.get_computed_dataframe()
after_gc_sum = int(df.query('cause_id == 743')['deaths'].sum())
after_deaths_sum = int(df['deaths'].sum())
print_log_message("""
Stage [gc deaths / total deaths]
Before GC correction [{gco} / {to}]
After GC correction [{gca} / {ta}]
""".format(gco=orig_gc_sum,
to=orig_deaths_sum,
gca=after_gc_sum,
ta=after_deaths_sum))
df = add_code_metadata(df, ['value', 'code_system_id'],
code_map=cause_map,
**read_file_cache_options)
assert (df['code_system_id'] == code_system_id).all(), "Variable code " \
"system id {} did not agree with all values of df code " \
"system id: \n{}".format(
code_system_id, df.loc[df['code_system_id'] != code_system_id])
print_log_message("Formatting data for redistribution")
df = format_age_groups(df)
# drop observations with 0 deaths
df = drop_zero_deaths(df)
# merge on redistribution location hierarchy
df = add_rd_locations(df, lsvid)
# fill in any missing stuff that may have come from rd hierarchy
df = fill_missing_df(df, verify_all=True)
df = add_split_group_id_column(df)
# final check to make sure we have all the necessary columns
df = format_columns_for_rd(df, code_system_id)
split_groups = list(df.split_group.unique())
parallel = len(split_groups) > 1
print_log_message("Submitting/Running split groups")
for split_group in split_groups:
# remove intermediate files from previous run
delete_split_group_output(nid, extract_type_id, split_group)
# save to file
split_df = df.loc[df['split_group'] == split_group]
write_split_group_input(split_df, nid, extract_type_id, split_group)
if parallel:
submit_split_group(nid, extract_type_id, split_group,
code_system_id, launch_set_id)
else:
worker_main(nid, extract_type_id, split_group, code_system_id)
if parallel:
print_log_message("Waiting for splits to complete...")
wait('claude_redistributionworker_{}'.format(nid), 30)
print_log_message("Done waiting. Appending them together")
df = read_append_split_groups(split_groups, nid, extract_type_id,
cause_map)
print_log_message("Done appending files - {} rows assembled".format(
len(df)))
df = revert_variables(df)
after_deaths_sum = int(df['deaths'].sum())
before_after_text = """
Before GC redistribution: {a}
After GC redistribution: {b}
""".format(a=orig_deaths_sum, b=after_deaths_sum)
diff = abs(orig_deaths_sum - after_deaths_sum)
diff_threshold = max(.02 * orig_deaths_sum, 5)
if not diff < diff_threshold:
raise AssertionError("Deaths not close.\n" + before_after_text)
else:
print_log_message(before_after_text)
return df
def run_phase(df,
csvid,
nid,
extract_type_id,
lsvid,
pop_run_id,
cmvid,
launch_set_id,
remove_decimal,
write_diagnostics=True):
"""String together processes for redistribution."""
# what to do about caching throughout the phase
read_file_cache_options = {
'block_rerun': True,
'cache_dir': CACHE_DIR,
'force_rerun': False,
'cache_results': False
}
# the iso3 of this data
iso3 = get_value_from_nid(nid,
'iso3',
extract_type_id=extract_type_id,
location_set_version_id=lsvid)
# the code system id
code_system_id = int(
get_value_from_nid(nid,
'code_system_id',
extract_type_id=extract_type_id))
# the data type
data_type_id = get_value_from_nid(nid,
'data_type_id',
extract_type_id=extract_type_id)
# cause map
cause_map = get_cause_map(code_map_version_id=cmvid,
**read_file_cache_options)
orig_deaths_sum = int(df['deaths'].sum())
if remove_decimal:
print_log_message("Removing decimal from code map")
cause_map['value'] = cause_map['value'].apply(
lambda x: x.replace(".", ""))
if needs_garbage_correction(iso3, data_type_id):
print_log_message("Correcting Garbage for {}".format(iso3))
orig_gc_sum = int(df.query('cause_id == 743')['deaths'].sum())
cause_meta_df = get_current_cause_hierarchy(cause_set_version_id=csvid,
**read_file_cache_options)
# get age group ids
age_meta_df = get_ages(**read_file_cache_options)
loc_meta_df = get_current_location_hierarchy(
location_set_version_id=lsvid, **read_file_cache_options)
pop_meta_df = get_pop(pop_run_id=pop_run_id, **read_file_cache_options)
# Move garbage to hiv first
hiv_corrector = HIVCorrector(df,
iso3,
code_system_id,
pop_meta_df,
cause_meta_df,
loc_meta_df,
age_meta_df,
correct_garbage=True)
df = hiv_corrector.get_computed_dataframe()
after_gc_sum = int(df.query('cause_id == 743')['deaths'].sum())
after_deaths_sum = int(df['deaths'].sum())
print_log_message("""
Stage [gc deaths / total deaths]
Before GC correction [{gco} / {to}]
After GC correction [{gca} / {ta}]
""".format(gco=orig_gc_sum,
to=orig_deaths_sum,
gca=after_gc_sum,
ta=after_deaths_sum))
df = add_code_metadata(df, ['value', 'code_system_id'],
code_map=cause_map,
**read_file_cache_options)
# recognizing that it is weird for code_system_id to come from two places,
# make sure they are consistent
assert (df['code_system_id'] == code_system_id).all(), "Variable code " \
"system id {} did not agree with all values of df code " \
"system id: \n{}".format(
code_system_id, df.loc[df['code_system_id'] != code_system_id])
print_log_message("Formatting data for redistribution")
# do we have all the packages we need?
# verify_packages(df)
# format age groups to match package parameters
df = format_age_groups(df)
# drop observations with 0 deaths
df = drop_zero_deaths(df)
# merge on redistribution location hierarchy
df = add_rd_locations(df, lsvid)
# fill in any missing stuff that may have come from rd hierarchy
df = fill_missing_df(df, verify_all=True)
# create split groups
# NO SPLIT GROUP NEEDED
df = add_split_group_id_column(df)
# final check to make sure we have all the necessary columns
df = format_columns_for_rd(df, code_system_id)
split_groups = list(df.split_group.unique())
parallel = len(split_groups) > 1
print_log_message("Submitting/Running split groups")
for split_group in split_groups:
# remove intermediate files from previous run
delete_split_group_output(nid, extract_type_id, split_group)
# save to file
split_df = df.loc[df['split_group'] == split_group]
write_split_group_input(split_df, nid, extract_type_id, split_group)
# submit jobs or just run them here
if parallel:
submit_split_group(nid, extract_type_id, split_group,
code_system_id, launch_set_id)
else:
worker_main(nid, extract_type_id, split_group, code_system_id)
if parallel:
print_log_message("Waiting for splits to complete...")
# wait until all jobs for a given nid have completed
# eventually need logic for files not being present
wait('claude_redistributionworker_{}'.format(nid), 30)
# This seems to be necessary to wait for files
print_log_message("Done waiting. Appending them together")
# append split groups together
df = read_append_split_groups(split_groups, nid, extract_type_id,
cause_map)
print_log_message("Done appending files - {} rows assembled".format(
len(df)))
df = revert_variables(df)
after_deaths_sum = int(df['deaths'].sum())
before_after_text = """
Before GC redistribution: {a}
After GC redistribution: {b}
""".format(a=orig_deaths_sum, b=after_deaths_sum)
diff = abs(orig_deaths_sum - after_deaths_sum)
# bad if change 2% or 5 deaths, whichever is greater
# (somewhat arbitrary, just trying to avoid annoying/non-issue failures)
diff_threshold = max(.02 * orig_deaths_sum, 5)
if not diff < diff_threshold:
raise AssertionError("Deaths not close.\n" + before_after_text)
else:
print_log_message(before_after_text)
return df
def run_phase(df, nid, extract_type_id, pop_run_id, cause_set_version_id,
location_set_version_id):
"""Run the full phase, chaining together computational elements."""
cache_dir = CONF.get_directory('FILEPATH')
orig_deaths = df['deaths'].sum()
standard_cache_options = {
'force_rerun': False,
'block_rerun': True,
'cache_dir': cache_dir,
'cache_results': False
}
code_system_id = get_value_from_nid(nid,
'code_system_id',
extract_type_id=extract_type_id)
# this queries the database, maybe should be passed in directly
code_system = get_code_system_from_id(code_system_id)
source = get_value_from_nid(nid, 'source', extract_type_id=extract_type_id)
data_type_id = get_value_from_nid(
nid,
'data_type_id',
extract_type_id=extract_type_id,
location_set_version_id=location_set_version_id)
# get cause hierarchy
cause_meta_df = get_current_cause_hierarchy(
cause_set_version_id=cause_set_version_id, **standard_cache_options)
is_vr = data_type_id in [9, 10]
if not skip_hiv_correction(source) and is_vr:
# get location hierarchy
loc_meta_df = get_current_location_hierarchy(
location_set_version_id=location_set_version_id,
**standard_cache_options)
# get population
pop_meta_df = get_pop(pop_run_id=pop_run_id, **standard_cache_options)
# get age metadata
age_meta_df = get_ages(**standard_cache_options)
# get the country
iso3 = get_value_from_nid(
nid,
'iso3',
extract_type_id=extract_type_id,
location_set_version_id=location_set_version_id)
assert pd.notnull(iso3), "Could not find iso3 for nid {}, " \
"extract_type_id {}".format(nid, extract_type_id)
hiv_corrector = HIVCorrector(df,
iso3,
code_system_id,
pop_meta_df,
cause_meta_df,
loc_meta_df,
age_meta_df,
correct_garbage=False)
print_log_message("Running hiv correction for iso3 {}".format(iso3))
df = hiv_corrector.get_computed_dataframe()
if needs_injury_redistribution(source):
print_log_message("Correcting injuries")
if not 'loc_meta_df' in vars():
# get location hierarchy
loc_meta_df = get_current_location_hierarchy(
location_set_version_id=location_set_version_id,
**standard_cache_options)
injury_redistributor = InjuryRedistributor(df, loc_meta_df,
cause_meta_df)
df = injury_redistributor.get_computed_dataframe()
df = combine_with_rd_raw(df, nid, extract_type_id, location_set_version_id)
val_cols = ['deaths', 'deaths_raw', 'deaths_corr', 'deaths_rd']
# run china VR rescaling
if needs_subnational_rescale(source):
china_rescaler = ChinaHospitalUrbanicityRescaler()
df = china_rescaler.get_computed_dataframe(df)
if needs_strata_collapse(source):
# set site id to blank site id and collapse
df['site_id'] = 2
group_cols = list(set(df.columns) - set(val_cols))
df = df.groupby(group_cols, as_index=False)[val_cols].sum()
if is_vr:
# drop if deaths are 0 across all current deaths columns
df = df.loc[df[val_cols].sum(axis=1) != 0]
# restrict causes based on code system
print_log_message("Running bridge mapper")
bridge_mapper = BridgeMapper(source, cause_meta_df, code_system)
df = bridge_mapper.get_computed_dataframe(df)
# run recodes based on expert opinion
print_log_message("Enforcing some very hard priors (expert opinion)")
expert_opinion_recoder = Recoder(cause_meta_df, source, code_system_id,
data_type_id)
df = expert_opinion_recoder.get_computed_dataframe(df)
end_deaths = df['deaths'].sum()
print_log_message("Checking no large loss or gain of deaths")
if abs(orig_deaths - end_deaths) >= (.1 * end_deaths):
diff = round(abs(orig_deaths - end_deaths), 2)
old = round(abs(orig_deaths))
new = round(abs(end_deaths))
raise AssertionError("Change of {} deaths [{}] to [{}]".format(
diff, old, new))
return df
def run_phase(df, nid, extract_type_id, env_run_id, pop_run_id,
location_set_version_id, cause_set_version_id):
cache_dir = CONF.get_directory('db_cache')
source = get_value_from_nid(
nid,
'source',
extract_type_id=extract_type_id,
location_set_version_id=location_set_version_id)
data_type_id = get_value_from_nid(
nid,
'data_type_id',
extract_type_id=extract_type_id,
location_set_version_id=location_set_version_id)
iso3 = get_value_from_nid(nid,
'iso3',
extract_type_id=extract_type_id,
location_set_version_id=location_set_version_id)
standard_cache_options = {
'force_rerun': False,
'block_rerun': True,
'cache_dir': cache_dir,
'cache_results': False
}
# ************************************************************
# Get cached metadata
# ************************************************************
print_log_message("Getting cached db resources")
location_hierarchy = get_current_location_hierarchy(
location_set_version_id=location_set_version_id,
**standard_cache_options)
pop_df = get_pop(pop_run_id=pop_run_id, **standard_cache_options)
env_df = get_env(env_run_id=env_run_id, **standard_cache_options)
age_weight_df = get_age_weights(**standard_cache_options)
cause_meta_df = get_current_cause_hierarchy(
cause_set_version_id=cause_set_version_id, **standard_cache_options)
age_meta_df = get_ages(**standard_cache_options)
# ************************************************************
# RAKING
# ************************************************************
# Rake if appropriate based on this logic
if ((data_type_id in [8, 9, 10] and (source != 'Other_Maternal'))
or source in MATERNAL_NR_SOURCES):
if source not in NOT_RAKED_SOURCES:
print_log_message("Raking sub national estimates")
raker = Raker(df, source)
df = raker.get_computed_dataframe(location_hierarchy)
# for the Other_Maternal source we only rake household surveys
elif source == "Other_Maternal":
model_groups = get_datasets(nid,
extract_type_id,
block_rerun=True,
force_rerun=False).model_group.unique()
assert len(model_groups) == 1
model_group = model_groups[0]
if "HH_SURVEYS" in model_group:
if model_group == 'MATERNAL-HH_SURVEYS-IND':
print_log_message("Raking sub national estimates," \
" applying double raking for India Maternal"
)
raker = Raker(df, source, double=True)
df = raker.get_computed_dataframe(location_hierarchy)
else:
print_log_message("Raking sub national estimates")
raker = Raker(df, source)
df = raker.get_computed_dataframe(location_hierarchy)
# ************************************************************
# DROP ZERO SAMPLE SIZE AND RESTRICTED AGE/SEX DATA
# ************************************************************
# data with zero sample size is almost certaintly some anomolous result
# of a program generating data it shouldn't have, and it shouldn't be
# included in codem models. Was probably already dropped, anyway, before
# running noise reduction.
df = df.query('sample_size != 0')
# uploading data before 1980 is a waste of space because neither codem
# nor codviz use it
df = df.loc[df['year_id'] >= 1980]
print_log_message("Enforcing age sex restrictions")
# this actually drops data from the dataframe if it violates age/sex
# restrictions (e.g. male maternity disorders)
df = enforce_asr(df, cause_meta_df, age_meta_df)
# ************************************************************
# FIT EACH DRAW TO NON-ZERO FLOOR
# ************************************************************
print_log_message("Fitting to non-zero floor...")
nonzero_floorer = NonZeroFloorer(df)
df = nonzero_floorer.get_computed_dataframe(pop_df, env_df, cause_meta_df)
# ************************************************************
# AGE AGGREGATION
# ************************************************************
print_log_message("Creating age standardized and all ages groups")
age_aggregator = AgeAggregator(df, pop_df, env_df, age_weight_df)
df = age_aggregator.get_computed_dataframe()
# ************************************************************
# Make CODEm and CoDViz metrics for uncertainty
# ************************************************************
# columns that should be present in the phase output
final_cols = [
'age_group_id', 'cause_id', 'cf_corr', 'cf_final', 'cf_raw', 'cf_rd',
'extract_type_id', 'location_id', 'nid', 'sample_size', 'sex_id',
'site_id', 'year_id'
]
# Use draws to make metrics for uncertainty to
# be used by CODEm and CoDViz
# also creates cf_final from mean of draws
print_log_message("Making metrics for CODEm and CoDViz")
if dataset_has_redistribution_variance(data_type_id, source):
df = RedistributionVarianceEstimator.make_codem_codviz_metrics(
df, pop_df)
final_cols += [
'cf_final_high_rd', 'cf_final_low_rd', 'variance_rd_log_dr',
'variance_rd_logit_cf'
]
# we did this in the old code-- no cfs over 1 nor below 0
for cf_col in ['cf_final', 'cf_rd', 'cf_raw', 'cf_corr']:
df.loc[df[cf_col] > 1, cf_col] = 1
df.loc[df[cf_col] < 0, cf_col] = 0
df = df[final_cols]
return df
def run_phase(df, nid, extract_type_id, env_run_id, pop_run_id,
location_set_version_id, cause_set_version_id):
cache_dir = CONF.get_directory('db_cache')
source = get_value_from_nid(
nid,
'source',
extract_type_id=extract_type_id,
location_set_version_id=location_set_version_id)
data_type_id = get_value_from_nid(
nid,
'data_type_id',
extract_type_id=extract_type_id,
location_set_version_id=location_set_version_id)
standard_cache_options = {
'force_rerun': False,
'block_rerun': True,
'cache_dir': cache_dir,
'cache_results': False
}
# ************************************************************
# Get cached metadata
# ************************************************************
print_log_message("Getting cached db resources")
location_hierarchy = get_current_location_hierarchy(
location_set_version_id=location_set_version_id,
**standard_cache_options)
pop_df = get_pop(pop_run_id=pop_run_id, **standard_cache_options)
env_df = get_env(env_run_id=env_run_id, **standard_cache_options)
age_weight_df = get_age_weights(**standard_cache_options)
cause_meta_df = get_current_cause_hierarchy(
cause_set_version_id=cause_set_version_id, **standard_cache_options)
age_meta_df = get_ages(**standard_cache_options)
# ************************************************************
# RAKING
# ************************************************************
if ((data_type_id in [8, 9, 10] and (source != "Other_Maternal"))
or source in MATERNAL_NR_SOURCES):
if source not in NOT_RAKED_SOURCES:
print_log_message("Raking sub national estimates")
raker = Raker(df, source)
df = raker.get_computed_dataframe(location_hierarchy)
# for the Other_Maternal source we only rake household surveys
elif source == "Other_Maternal":
model_groups = get_datasets(nid,
extract_type_id,
block_rerun=True,
force_rerun=False).model_group.unique()
assert len(model_groups) == 1
model_group = model_groups[0]
if "HH_SURVEYS" in model_group:
print_log_message("Raking sub national estimates")
raker = Raker(df, source)
df = raker.get_computed_dataframe(location_hierarchy)
# ************************************************************
# DROP ZERO SAMPLE SIZE AND RESTRICTED AGE/SEX DATA
# ************************************************************
df = df.query('sample_size != 0')
df = df.loc[df['year_id'] >= 1980]
print_log_message("Enforcing age sex restrictions")
df = enforce_asr(df, cause_meta_df, age_meta_df)
# ************************************************************
# FIT EACH DRAW TO NON-ZERO FLOOR
# ************************************************************
print_log_message("Fitting to non-zero floor...")
nonzero_floorer = NonZeroFloorer(df)
df = nonzero_floorer.get_computed_dataframe(pop_df, env_df, cause_meta_df)
# ************************************************************
# AGE AGGREGATION
# ************************************************************
print_log_message("Creating age standardized and all ages groups")
age_aggregator = AgeAggregator(df, pop_df, env_df, age_weight_df)
df = age_aggregator.get_computed_dataframe()
# ************************************************************
# Make CODEm and CoDViz metrics for uncertainty
# ************************************************************
# columns that should be present in the phase output
final_cols = [
'age_group_id', 'cause_id', 'cf_corr', 'cf_final', 'cf_raw', 'cf_rd',
'extract_type_id', 'location_id', 'nid', 'sample_size', 'sex_id',
'site_id', 'year_id'
]
print_log_message("Making metrics for CODEm and CoDViz")
if dataset_has_redistribution_variance(data_type_id, source):
df = RedistributionVarianceEstimator.make_codem_codviz_metrics(
df, pop_df)
final_cols += [
'cf_final_high_rd', 'cf_final_low_rd', 'variance_rd_log_dr',
'variance_rd_logit_cf'
]
for cf_col in ['cf_final', 'cf_rd', 'cf_raw', 'cf_corr']:
df.loc[df[cf_col] > 1, cf_col] = 1
df.loc[df[cf_col] < 0, cf_col] = 0
df = df[final_cols]
return df
def run_phase(df, nid, extract_type_id, pop_run_id, cause_set_version_id,
location_set_version_id):
"""Run the full phase, chaining together computational elements."""
# get filepaths
cache_dir = CONF.get_directory('db_cache')
orig_deaths = df['deaths'].sum()
standard_cache_options = {
'force_rerun': False,
'block_rerun': True,
'cache_dir': cache_dir,
'cache_results': False
}
code_system_id = get_value_from_nid(nid,
'code_system_id',
extract_type_id=extract_type_id)
code_system = get_code_system_from_id(code_system_id,
**standard_cache_options)
source = get_value_from_nid(nid, 'source', extract_type_id=extract_type_id)
data_type_id = get_value_from_nid(
nid,
'data_type_id',
extract_type_id=extract_type_id,
location_set_version_id=location_set_version_id)
# get cause hierarchy
cause_meta_df = get_current_cause_hierarchy(
cause_set_version_id=cause_set_version_id, **standard_cache_options)
is_vr = data_type_id in [9, 10]
# run hiv correction on VR, but not Other_Maternal
# countries to correct will be further pruned by the master cause
# selections csv in the hiv corrector class
if not skip_hiv_correction(source) and is_vr:
# get location hierarchy
loc_meta_df = get_current_location_hierarchy(
location_set_version_id=location_set_version_id,
**standard_cache_options)
# get population
pop_meta_df = get_pop(pop_run_id=pop_run_id, **standard_cache_options)
# get age metadata
age_meta_df = get_ages(**standard_cache_options)
# get the country
iso3 = get_value_from_nid(
nid,
'iso3',
extract_type_id=extract_type_id,
location_set_version_id=location_set_version_id)
assert pd.notnull(iso3), "Could not find iso3 for nid {}, " \
"extract_type_id {}".format(nid, extract_type_id)
hiv_corrector = HIVCorrector(df,
iso3,
code_system_id,
pop_meta_df,
cause_meta_df,
loc_meta_df,
age_meta_df,
correct_garbage=False)
print_log_message("Running hiv correction for iso3 {}".format(iso3))
df = hiv_corrector.get_computed_dataframe()
if needs_injury_redistribution(source):
print_log_message("Correcting injuries")
if not 'loc_meta_df' in vars():
# get location hierarchy
loc_meta_df = get_current_location_hierarchy(
location_set_version_id=location_set_version_id,
**standard_cache_options)
injury_redistributor = InjuryRedistributor(df, loc_meta_df,
cause_meta_df)
df = injury_redistributor.get_computed_dataframe()
# apply redistribution of LRI to tb in under 15, non-neonatal ages based
# on location/year specific proportions
print_log_message(
"Applying special redistribution of LRI to TB in under 15")
lri_tb_redistributor = LRIRedistributor(df, cause_meta_df)
df = lri_tb_redistributor.get_computed_dataframe()
# merge in raw and rd here because recodes and bridge mapping should
# also apply to the causes that are in previous phases (raw deaths for
# secret codes need to be moved up to their parent cause, for example)
df = combine_with_rd_raw(df, nid, extract_type_id, location_set_version_id)
val_cols = ['deaths', 'deaths_raw', 'deaths_corr', 'deaths_rd']
# run china VR rescaling
if needs_subnational_rescale(source):
china_rescaler = ChinaHospitalUrbanicityRescaler()
df = china_rescaler.get_computed_dataframe(df)
if needs_strata_collapse(source):
# set site id to blank site id and collapse
df['site_id'] = 2
group_cols = list(set(df.columns) - set(val_cols))
df = df.groupby(group_cols, as_index=False)[val_cols].sum()
if is_vr:
# drop if deaths are 0 across all current deaths columns
df = df.loc[df[val_cols].sum(axis=1) != 0]
# restrict causes based on code system
print_log_message("Running bridge mapper")
bridge_mapper = BridgeMapper(source, cause_meta_df, code_system)
df = bridge_mapper.get_computed_dataframe(df)
# run recodes based on expert opinion
print_log_message("Enforcing some very hard priors (expert opinion)")
expert_opinion_recoder = Recoder(cause_meta_df, source, code_system_id,
data_type_id)
df = expert_opinion_recoder.get_computed_dataframe(df)
end_deaths = df['deaths'].sum()
print_log_message("Checking no large loss or gain of deaths")
if abs(orig_deaths - end_deaths) >= (.1 * end_deaths):
diff = round(abs(orig_deaths - end_deaths), 2)
old = round(abs(orig_deaths))
new = round(abs(end_deaths))
raise AssertionError("Change of {} deaths [{}] to [{}]".format(
diff, old, new))
return df