def add_mother_values_except_arvs(entry):
"""
This will take care of all of moms values except for her ARV regimens.
- date_first_seen
- lmp and/or edd
- age_at_conception
"""
begin_date = entry.date_of_outcome - datetime.timedelta(360)
preg_encobs = (
Obs.objects.using(FACES_OPENMRS_DB)
.filter(
person_id=entry.mother_id, voided=0, obs_datetime__gte=begin_date, obs_datetime__lte=entry.date_of_outcome
)
.order_by("obs_datetime")
)
# Date First Seen
dates_first_seen = preg_encobs.filter(concept_id=1836, value_coded=1065)
# print "How Many Date First Seens: ", len(dates_first_seen)
for seen in dates_first_seen:
# print " ", seen.value, " ", seen.obs_datetime
entry.date_first_seen = seen.obs_datetime
break
# 1450 LAST MONTHLY PERIOD DATE
lmps = preg_encobs.filter(concept_id=1450)
# print "Number LMPS: ", len(lmps)
for lmp in lmps:
entry.lmp = lmp.value
break
# 1451 EXPECTED DELIVERY DATE
edds = preg_encobs.filter(concept_id=1451)
# print "Number EDDS: ", len(edds)
for edd in edds:
entry.edd = edd.value
break
# age at conception
mother_patient = Patient.objects.using(FACES_OPENMRS_DB).get(pk=entry.mother_id)
print "EntryID: ", entry.id, "Motherbirthdate: ", mother_patient.patient.birthdate, " Date first seen: ", entry.date_first_seen
if entry.date_first_seen:
print type(mother_patient.patient.birthdate)
print type(entry.date_first_seen)
entry.age_at_conception = calculate_age(mother_patient.patient.birthdate, entry.date_first_seen.date())
elif entry.lmp:
entry.age_at_conception = calculate_age(mother_patient.patient.birthdate, entry.lmp)
else:
# Use the outcome if we absolutely have to
entry.age_at_conception = calculate_age(mother_patient.patient.birthdate, entry.date_of_outcome)
print "Age: ", entry.age_at_conception
def set_mother_values(entry):
"""
This will take care of all of moms values except for her ARV regimens.
- date_first_seen
- lmp and/or edd
- age_at_conception
"""
begin_date = entry.date_of_outcome - datetime.timedelta(360)
preg_encobs = entry.motherobs.filter(voided=0,
encounter_datetime__gte=begin_date,
encounter_datetime__lte=entry.date_of_outcome).order_by('encounter_datetime')
for encob in preg_encobs:
if encob.concept_id == 1836 and encob.value_coded == 1065:
entry.date_first_seen = encob.encounter_datetime.date()
# Skip the rest if date_first_seen wasn't available.
if entry.date_first_seen == None:
return
preg_encobs = entry.motherobs.filter(voided=0,
encounter_datetime__gte=entry.date_first_seen,
encounter_datetime__lte=entry.date_of_outcome).order_by('encounter_datetime')
for encob in preg_encobs:
if entry.lmp == None and encob.concept_id == 1450:
#entry.lmp = encob.value_datetime
# TODO I believe faces really only uses LMP For this.
pass
elif entry.edd == None and encob.concept_id == 1451:
entry.edd = encob.value_datetime
# age_at_conception
mother_patient = Patient.objects.using(FACES_OPENMRS_DB).get(pk=entry.mother_id)
print "EntryID: ", entry.id, "Motherbirthdate: ", mother_patient.patient.birthdate, " Date first seen: ", entry.date_first_seen
entry.age_at_conception = emrutils.calculate_age(mother_patient.patient.birthdate,
entry.date_first_seen)
print "Age: ", entry.age_at_conception
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