def update_complications_from_baseline(apps, schema_editor):
"""Splits the complications model into baseline and followup."""
complications_model_cls = apps.get_model(
"inte_subject.complicationsbaseline")
complications_followup_model_cls = apps.get_model(
"inte_subject.complicationsfollowup")
clinical_review_model_cls = apps.get_model("inte_subject.clinicalreview")
names = [
"stroke",
"heart_attack",
"renal_disease",
"vision",
"numbness",
"foot_ulcers",
]
for clinical_review in clinical_review_model_cls.objects.all():
try:
complications = complications_model_cls.objects.get(
subject_visit=clinical_review.subject_visit)
except ObjectDoesNotExist:
clinical_review.complications = NO
else:
clinical_review.complications = YES
complications_followup = complications_followup_model_cls()
complications_followup.subject_visit = clinical_review.subject_visit
complications_followup.created = clinical_review.created
complications_followup.modified = clinical_review.modified
complications_followup.user_created = clinical_review.user_created
complications_followup.user_modified = clinical_review.user_modified
complications_followup.hostname_created = clinical_review.hostname_created
complications_followup.hostname_modified = clinical_review.hostname_modified
complications_followup.device_created = clinical_review.device_created
complications_followup.device_modified = clinical_review.device_modified
complications_followup.consent_model = clinical_review.consent_model
complications_followup.consent_version = clinical_review.consent_version
complications_followup.site_id = clinical_review.site_id
for name in names:
setattr(complications_followup, name,
getattr(complications, name))
setattr(
complications_followup,
f"{name}_date",
getattr(complications, f"{name}_estimated_date"),
)
complications_followup.complications = complications.complications
complications_followup.other_complications = complications.other_complications
with DisableSignals(disabled_signals=[pre_save]):
complications_followup.save()
complications.delete()
with DisableSignals(disabled_signals=[pre_save]):
clinical_review.save()
print(
"\nDone. Remember to run the INTE managment command to update metadata."
)
def update_appointment_schedule(apps=None):
apps = apps or django_apps
registered_subject_model_cls = apps.get_model(
"edc_registration.registeredsubject")
appointment_model_cls = apps.get_model("edc_appointment.appointment")
subject_visit_model_cls = apps.get_model("inte_subject.subjectvisit")
crfmetadata_model_cls = apps.get_model("edc_metadata.crfmetadata")
for registered_subject in tqdm(
registered_subject_model_cls.objects.all().order_by(
"subject_identifier")):
for index, appointment in enumerate(
appointment_model_cls.objects.filter(
subject_identifier=registered_subject.subject_identifier,
).order_by("timepoint")):
if appointment.timepoint in [
Decimal("0.0"),
Decimal("6.0"),
Decimal("12.0"),
]:
continue
elif appointment.timepoint < Decimal("6.0"):
appointment.visit_code = "1000"
appointment.visit_code_sequence = index
appointment.timepoint = Decimal("0.0")
with DisableSignals(disabled_signals=[pre_save]):
appointment.save()
appointment.refresh_from_db()
try:
subject_visit = subject_visit_model_cls.objects.get(
appointment=appointment)
except ObjectDoesNotExist:
appointment.delete()
else:
crfmetadata_model_cls.objects.filter(
subject_identifier=registered_subject.
subject_identifier,
visit_code=subject_visit.visit_code,
visit_code_sequence=subject_visit.visit_code_sequence,
).update(
visit_code=appointment.visit_code,
visit_code_sequence=appointment.visit_code_sequence,
timepoint=appointment.timepoint,
)
with DisableSignals(disabled_signals=[pre_save]):
subject_visit.visit_code = appointment.visit_code
subject_visit.visit_code_sequence = appointment.visit_code_sequence
subject_visit.save()
else:
with DisableSignals(disabled_signals=[pre_delete]):
appointment.delete()
for appointment in appointment_model_cls.objects.filter(
visit_code_sequence__gt=0):
try:
subject_visit_model_cls.objects.get(appointment=appointment)
except ObjectDoesNotExist:
appointment.delete()
def convert_investigations_to_clinical_review(apps, schema_editor):
try:
investigations_model_cls = apps.get_model(
"inte_subject.investigations")
except LookupError:
pass
else:
clinical_review_model_cls = apps.get_model(
"inte_subject.clinicalreview")
for obj in investigations_model_cls.objects.all():
opts = dict(
created=obj.created,
modified=obj.modified,
user_created=obj.user_created,
user_modified=obj.user_modified,
hostname_created=obj.hostname_created,
hostname_modified=obj.hostname_modified,
device_created=obj.device_created,
device_modified=obj.device_modified,
consent_model=obj.consent_model,
consent_version=obj.consent_version,
site_id=obj.site_id,
subject_visit_id=obj.subject_visit_id,
report_datetime=obj.report_datetime,
hiv_tested=obj.hiv_tested,
hypertension_tested=obj.hypertension_tested,
diabetes_tested=obj.diabetes_tested,
crf_status=obj.crf_status,
crf_status_comments=obj.crf_status_comments,
)
clinical_review = clinical_review_model_cls()
for k, v in opts.items():
setattr(clinical_review, k, v)
with DisableSignals(disabled_signals=[pre_save]):
clinical_review.save()
def update_from_reason_for_visit(apps, schema_editor):
subject_visit_model_cls = apps.get_model("inte_subject.subjectvisit")
reason_for_visit_model_cls = apps.get_model("inte_subject.reasonforvisit")
medications_model_cls = apps.get_model("inte_subject.medications")
for reason_for_visit in reason_for_visit_model_cls.objects.all():
subject_visit = subject_visit_model_cls.objects.get(
id=reason_for_visit.subject_visit_id)
for obj in reason_for_visit.clinic_services.all():
subject_visit.clinic_services.add(obj)
for obj in reason_for_visit.health_services.all():
subject_visit.health_services.add(obj)
medications = medications_model_cls()
medications.created = reason_for_visit.created
medications.modified = reason_for_visit.modified
medications.user_created = reason_for_visit.user_created
medications.user_modified = reason_for_visit.user_modified
medications.hostname_created = reason_for_visit.hostname_created
medications.hostname_modified = reason_for_visit.hostname_modified
medications.device_created = reason_for_visit.device_created
medications.device_modified = reason_for_visit.device_modified
medications.consent_model = reason_for_visit.consent_model
medications.consent_version = reason_for_visit.consent_version
medications.site_id = reason_for_visit.site_id
medications.subject_visit_id = reason_for_visit.subject_visit_id
medications.report_datetime = reason_for_visit.report_datetime
medications.refill_hiv = reason_for_visit.refill_hiv
medications.refill_diabetes = reason_for_visit.refill_diabetes
medications.refill_hypertension = reason_for_visit.refill_hypertension
medications.crf_status = reason_for_visit.crf_status
medications.crf_status_comments = reason_for_visit.crf_status_comments
with DisableSignals(disabled_signals=[pre_save]):
medications.save()
subject_visit.save()
def update_subjectvisit(apps, schema_editor):
"""Adds or removes selection on subject visit clinic services
according to study timepoint.
* Adds STUDY_DEFINED_TIMEPOINT if scheduled timepoint (XXXX.0)
* Removes if not a scheduled timepoint (XXXX.1+)
"""
subject_visit_model_cls = apps.get_model("inte_subject.subjectvisit")
clinical_services_model_cls = apps.get_model("inte_lists.clinicservices")
study_defined_timepoint = clinical_services_model_cls.objects.get(
name=STUDY_DEFINED_TIMEPOINT
)
for subject_visit in subject_visit_model_cls.objects.all():
if (
subject_visit.visit_code_sequence == 0
and not subject_visit.clinic_services.filter(name=STUDY_DEFINED_TIMEPOINT).exists()
):
subject_visit.clinic_services.add(study_defined_timepoint)
elif (
subject_visit.visit_code_sequence != 0
and subject_visit.clinic_services.filter(name=STUDY_DEFINED_TIMEPOINT).exists()
):
subject_visit.clinic_services.remove(study_defined_timepoint)
with DisableSignals(disabled_signals=[pre_save]):
subject_visit.save()
def convert_clinical_review_hiv_dx(apps, schema_editor):
clinical_review_baseline_model_cls = apps.get_model(
"inte_subject.clinicalreviewbaseline")
for obj in clinical_review_baseline_model_cls.objects.all():
hiv_status = copy(obj.hiv_test)
if hiv_status == NEVER:
obj.hiv_test = NO
obj.hiv_dx = NOT_APPLICABLE
with DisableSignals(disabled_signals=[pre_save]):
obj.save()
elif hiv_status == POS:
obj.hiv_test = YES
obj.hiv_dx = YES
with DisableSignals(disabled_signals=[pre_save]):
obj.save()
elif hiv_status == NEG:
obj.hiv_test = YES
obj.hiv_dx = NO
with DisableSignals(disabled_signals=[pre_save]):
obj.save()
else:
raise DataMigrationError(
f"Invalid response. Got hiv_test==`{hiv_status}`")
def update_medications(apps, schema_editor):
medications_model_cls = apps.get_model("inte_subject.medications")
refill_hiv_model_cls = apps.get_model("inte_subject.drugrefillhiv")
refill_htn_model_cls = apps.get_model("inte_subject.drugrefillhtn")
refill_dm_model_cls = apps.get_model("inte_subject.drugrefilldm")
subject_visit_model_cls = apps.get_model("inte_subject.subjectvisit")
for subject_visit in subject_visit_model_cls.objects.filter(
visit_code_sequence__gt=0).order_by("subject_identifier",
"visit_code",
"visit_code_sequence"):
try:
diagnoses = Diagnoses(subject_visit=subject_visit)
except ClinicalReviewBaselineRequired:
print(
f" * {subject_visit.subject_identifier}: ClinicalReviewBaselineRequired (skipping) [0060]"
)
else:
medications = get_obj(medications_model_cls, subject_visit)
opts = [
("hiv_dx", "refill_hiv", refill_hiv_model_cls),
("htn_dx", "refill_htn", refill_htn_model_cls),
("dm_dx", "refill_dm", refill_dm_model_cls),
]
if medications:
for dx_attr, refill_attr, refill_model_cls in opts:
if getattr(diagnoses, dx_attr):
obj = get_obj(refill_model_cls, subject_visit)
if obj:
setattr(medications, refill_attr, YES)
else:
setattr(medications, refill_attr, NO)
else:
setattr(medications, refill_attr, NOT_APPLICABLE)
with DisableSignals([pre_save]):
medications.save()
print(
"\nDone. Remember to run the INTE managment command to update metadata."
)
def update_visit_and_metadata(apps, schema_editor):
subject_visit_model_cls = apps.get_model("inte_subject.subjectvisit")
for subject_visit in subject_visit_model_cls.objects.all():
with DisableSignals(disabled_signals=[pre_save]):
subject_visit.save()