def add_patient(reg_id, patient_id, enc_id):
entry = RegistryEntry()
entry.site = RegistryEntry.SITE_AMPATH
entry.child_id = patient_id
entry.apr_id = reg_id
entry.child_initial_enc_id = enc_id
entry.outcome = RegistryEntry.OUTCOME_LIVE
entry.save(using="apr_db")
def handle(self, *args, **options):
"""
python manage.py generate_cohort 2015 1,2,3 100588
"""
year = args[0]
months = args[1].split(',')
if len(args) > 2:
apr_id_start = args[2]
else:
apr_id_start = RegistryEntry.get_max_apr_id()+1
from ampath import livebirths
for month in months:
livebirths.full_monthly_cohort_generation(year=int(year),
month=int(month), apr_starting_id=int(apr_id_start))
apr_id_start = RegistryEntry.get_max_apr_id()+1
def handle(self, *args, **options):
"""
python manage.py faces_cohort 100588
"""
apr_id_start = int(args[0])
months = (
(1, 2014), (2, 2014), (3, 2014), (4, 2014), (5, 2014), (6, 2014),
(7, 2014), (8, 2014), (9, 2014), (10, 2014), (11, 2014), (12, 2014),
)
for batch in months:
cohorts.full_monthly_cohort_generation(batch[0], batch[1],
apr_id_start, True)
apr_id_start = RegistryEntry.get_max_apr_id()+1
def full_monthly_cohort_generation(month=1, year=2014, apr_starting_id=None, save=False):
"""
Standard full method for generating the monthly cohorts that the management
command will call in to.
"""
hei_encs = get_hei_encounters(month=month, year=year)
cur_apr_id = apr_starting_id
for enc in hei_encs:
next_entry = process_hei_encounter(enc, cur_apr_id, save=save)
if next_entry.voided == False and next_entry.apr_id != None:
# logger.info("Incrementing current apr_id, just used %s" % (cur_apr_id,))
cur_apr_id += 1
cur_apr_id = RegistryEntry.get_max_apr_id() + 1
process_nonlive_encounters(month=1, year=2014, apr_starting_id=cur_apr_id, save=save)
def set_non_livebirth_entry(outcome_type, enc):
"""
Encounter is the blue card from when the mother had a marked
stillborn/miscarriage etc.
"""
entry = RegistryEntry()
entry.site = RegistryEntry.SITE_FACES
entry.cohort_date = enc.encounter_datetime.date()
entry.outcome = outcome_type
entry.date_of_outcome = enc.encounter_datetime.date()
entry.save(using=APR_DB)
for mom_enc in enc.patient.encounter_set.all():
encounter_to_encobs(entry, mom_enc, link_field='mother_entry')
entry.check_added_moms_obs = True
try:
set_mother_values(entry)
except Patient.DoesNotExist:
entry.voided = True
entry.voided_reason = RegistryEntry.VOIDED_STILLBIRTH_MOTHER_MISSING
entry.save(using=APR_DB)
def build_stage_1():
"""
In stage 1 of generation we:
1. Get the initial HEI Encounters
2. Create a RegistryEntry for each one
3. Calculate the age of the child at HEI presentation for each one
4. Check if the mother is linked
5. Add the obs for the HEI initial encounter
Essentially, we do anything we can that's on the HEI form (except maybe
format the actual defects in the event that there are some). Also, we see
if we can link the mom.
"""
# 1
hei_enc = get_hei_encounters()
# 2
for enc in hei_enc:
entry = RegistryEntry()
entry.site = RegistryEntry.SITE_FACES
entry.child_id = enc.patient_id
entry.cohort_date = enc.encounter_datetime.date()
# TODO May need to add a check to look at the section titled:
# FINAL HEI OUTCOMES AT EXIT
entry.outcome = RegistryEntry.OUTCOME_LIVE
entry.date_of_outcome = enc.patient.patient.birthdate
entry.gender = enc.patient.patient.gender
entry.check_initial_paeds_lookup = True
# 3
entry.age_first_seen = (entry.cohort_date - entry.date_of_outcome).days
# 4
entry.save(using=APR_DB)
mom = get_mom(entry.child_id)
if mom != None:
entry.mother_id = mom
entry.check_mother_linked = True
mom_patient = Patient.objects.using(FACES_OPENMRS_DB).get(pk=entry.mother_id)
for mom_enc in mom_patient.encounter_set.all():
encounter_to_encobs(entry, mom_enc, link_field='mother_entry')
entry.check_added_moms_obs = True
else:
entry.voided = True
entry.voided_reason = RegistryEntry.VOIDED_MOTHER_NOT_LINKED
entry.save(using=APR_DB)
set_mother_values(entry)
# 5
encounter_to_encobs(entry, enc)
entry.check_added_child_obs = True
set_child_values(entry)
entry.save(using=APR_DB)
def run378form(f378, cur_apr_id, save_entries=False):
logger.info("Starting 378 encounter: %s" % (f378.encounter_id,))
# If we've already done this specific encounter we should skip it and
# move on.
entry = RegistryEntry()
if RegistryEntry.objects.filter(child_initial_enc_id=f378.encounter_id).count() > 0:
logger.info("This encounter id was already processed, skipping and moving on.")
return entry
# 1. Encounter ID
entry.child_initial_enc_id = f378.encounter_id
# 2. Age in days since encounter
entry.age_first_seen = age_in_days_at_encounter(f378)
# 3. Child Patient ID
entry.child_id = f378.patient_id
# Has this child been used previously, if so void the encounter.
duplicate_entries = RegistryEntry.objects.filter(
site=RegistryEntry.SITE_AMPATH, child_id=entry.child_id)
if duplicate_entries.count() > 0:
entry.voided = True
entry.voided_reason = entry.VOIDED_DUPLICATE_CHILD_ENTRY
entry.voided_duplicate = True
child_patient = f378.patient
# 4. Mom Patient ID
entry.mother_id = get_linked_mother(f378)
# 5. Length of Mom's ARV History
entry.length_of_moms_arv_history = previous_encounters_in_days(
entry.mother_id, f378.encounter_datetime.date())
entry.site = RegistryEntry.SITE_AMPATH
entry.cohort_date = f378.encounter_datetime.date()
entry.outcome = entry.OUTCOME_LIVE
entry.date_of_outcome = child_patient.patient.birthdate
entry.age_first_seen = (entry.cohort_date - entry.date_of_outcome).days
entry.gender = child_patient.patient.gender
init_obs = f378.obs_set
# Birth Defect Noted
"""
Field: Birth Defect
If concept 6246 or 6245 is used, we use that checkbox value.
If the birth defect checkbox is left blank, then we look to see if any
of the following concepts are recorded, and if they are we record those
birth defects:
8320, 8321, 8322, 8323, 8324, 8325, 8326, 8327, 8328
aprfield"""
if init_obs.filter(concept_id=6246, value_coded=6242).count() > 0:
entry.birth_defect = RegistryEntry.DEFECT_NO
elif init_obs.filter(concept_id=6245, value_coded=6242).count() > 0:
entry.birth_defect = RegistryEntry.DEFECT_YES
else:
congab_concepts = [8320, 8321, 8322, 8323, 8324, 8325, 8326, 8327, 8328]
congab_obs = init_obs.filter(concept_id__in = congab_concepts, voided=0)
if congab_obs.count() > 0:
entry.birth_defect = RegistryEntry.DEFECT_YES
else:
entry.birth_defect = RegistryEntry.DEFECT_UNKNOWN
# Birth Weight
weight_obs = init_obs.filter(concept_id=5916)
if weight_obs.count() > 0:
entry.birth_weight = weight_obs[0].value_numeric * 1000
if save_entries:
entry.save(using=APR_DB)
if entry.mother_id:
entry.check_mother_linked = True
mother = Patient.objects.using(AMRS_DB).get(
patient_id=entry.mother_id)
# Date First Seen...
# LMP and/or EDD
begin_date = entry.date_of_outcome - datetime.timedelta(360)
log_data(entry, "Beginning date of LMP Search: %s" % (begin_date,), 'lmp')
lmp_obs = Obs.objects.using(AMRS_DB).filter(
concept_id=1836,
obs_datetime__gte=begin_date,
obs_datetime__lte=entry.date_of_outcome,
person_id=entry.mother_id,
voided=0,
).order_by('-obs_datetime')
if lmp_obs.count() > 0:
entry.lmp = lmp_obs[0].value_datetime
for lmp in lmp_obs:
log_data(entry, "Potential LMP Obs/Date: %s , %s" % (lmp.obs_id, lmp.value_datetime), 'lmp', 1836)
# Age at Conception
entry.age_at_conception = calculate_age(mother.patient.birthdate,
entry.date_of_outcome - datetime.timedelta(days=270))
# Mother ARVS
arvset = set_mother_arvs(entry)
if len(arvset) == 0:
entry.voided = True
entry.voided_reason = entry.VOIDED_NO_ARV_HISTORY
entry.voided_no_arv_history = True
else:
entry.check_mother_linked = False
entry.voided = True
entry.voided_reason = RegistryEntry.VOIDED_MOTHER_NOT_LINKED
entry.voided_mother_not_linked = True
# If we're not voided assign an APR ID
if entry.voided == False:
entry.apr_id = cur_apr_id
if save_entries:
entry.save(using=APR_DB)
return entry
def handle(self, *args, **options):
print RegistryEntry.get_max_apr_id()
def process_nonlive_encounter(outcome_type, enc, cur_apr_id, save=False):
"""
Encounter is the blue card from when the mother had a marked
stillborn/miscarriage etc.
"""
entry = RegistryEntry()
entry.site = RegistryEntry.SITE_FACES
entry.mother_id = enc.patient_id
entry.cohort_date = enc.encounter_datetime.date()
entry.outcome = outcome_type
entry.date_of_outcome = enc.encounter_datetime.date()
# If an entry with this mother already exists we will consider it a duplicate,
# considering that our entire timeline is just under 2 years.
duplicate_entries = RegistryEntry.objects.filter(site=RegistryEntry.SITE_FACES, mother_id=entry.mother_id)
if duplicate_entries.count() > 0:
entry.voided = True
entry.voided_reason = entry.VOIDED_DUPLICATE_CHILD_ENTRY
if save:
entry.save(using=APR_DB)
return entry
if save:
entry.save(using=APR_DB)
try:
add_mother_values_except_arvs(entry)
add_mother_arvs(entry, save=save)
except Patient.DoesNotExist:
entry.voided = True
entry.voided_reason = RegistryEntry.VOIDED_STILLBIRTH_MOTHER_MISSING
# If we're not voided assign an APR ID
if entry.voided == False:
entry.apr_id = cur_apr_id
if save:
entry.save(using=APR_DB)
return entry
def process_hei_encounter(enc, apr_id, save=False):
entry = RegistryEntry()
entry.site = RegistryEntry.SITE_FACES
entry.child_id = enc.patient_id
entry.cohort_date = enc.encounter_datetime.date()
entry.child_initial_enc_id = enc.encounter_id
duplicate_entries = RegistryEntry.objects.filter(site=RegistryEntry.SITE_FACES, child_id=entry.child_id)
if duplicate_entries.count() > 0:
entry.voided = True
entry.voided_reason = entry.VOIDED_DUPLICATE_CHILD_ENTRY
# TODO May need to add a check to look at the section titled:
# FINAL HEI OUTCOMES AT EXIT
entry.outcome = RegistryEntry.OUTCOME_LIVE
entry.date_of_outcome = enc.patient.patient.birthdate
entry.gender = enc.patient.patient.gender
entry.age_first_seen = (entry.cohort_date - entry.date_of_outcome).days
# Void entry if they were not seen in the first 3 months
if entry.age_first_seen > 90:
entry.voided = True
entry.voided_reason = RegistryEntry.VOIDED_TOO_OLD_AT_PAEDS_ENC
if save:
entry.save(using=APR_DB)
mom = get_mom(entry.child_id)
if mom != None:
entry.mother_id = mom
else:
entry.voided = True
entry.voided_reason = RegistryEntry.VOIDED_MOTHER_NOT_LINKED
if save:
entry.save(using=APR_DB)
return entry
if save:
entry.save(using=APR_DB)
add_mother_values_except_arvs(entry)
if save:
entry.save(using=APR_DB)
add_mother_arvs(entry, save=save)
add_child_values(entry)
# If we're not voided assign an APR ID
if entry.voided == False:
entry.apr_id = apr_id
if save:
entry.save(using=APR_DB)
return entry
