def set_mother_arvs(entry, save_entries=False):
"""
Look up and set ARV's for mom. Returns a list of new ARV's.
"""
schemafile = './apr/registry-schema.json'
with open(schemafile) as f:
schema = json.loads(f.read())
arvs = schema['ampath-mapping']['arvs']
arvset = []
begin_date = entry.date_of_outcome - datetime.timedelta(360*2)
log_data(entry, "Beginning date for searching ARVs %s" % (begin_date,), 'arvs', 1088)
encobs = Obs.objects.using(AMRS_DB).filter(voided=0,
obs_datetime__gte=begin_date,
obs_datetime__lte=entry.date_of_outcome,
person_id=entry.mother_id).order_by('obs_datetime')
course = 1
cur_arv = None
for encob in encobs:
if encob.concept_id == 1088:
if encob.value_coded_id != cur_arv:
cur_arv = encob.value_coded_id
arvt = ArvTherapy()
arvt.registry_entry = entry
arvt.course = course
arvt.medcode = arvs[str(cur_arv)]['medcode']
arvt.date_began = encob.obs_datetime.date()
log_data(entry, "Using ARV %s %s" % (encob.concept_id, encob.obs_datetime,), 'arv', 1088)
if save_entries:
arvt.save(using=APR_DB)
arvset.append(arvt)
course += 1
else:
log_data(entry, "Skipping cur ARV %s %s" % (encob.concept_id, encob.obs_datetime,), 'arv', 1088)
pass
# Go through and adjust the end dates as well as the ongoing flag
for idx, arvt in enumerate(arvset):
if len(arvset) == 1:
arvt.ongoing = 1
elif idx == 0:
arvt.ongoing = 0
arvt.date_ended = arvset[idx+1].date_began
elif idx == (len(arvset)-1):
arvt.ongoing = 1
else:
arvt.ongoing = 0
arvt.date_ended = arvset[idx+1].date_began
print("Saving the updated status...")
arvt.save(using=APR_DB)
return arvset
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
