def add_item(self, item, form, case_id, question, answer,
audit_log_id_ref):
answer = oc_format_date(answer)
answer = oc_format_time(answer, self._domain.get_default_timezone())
oc_user = self._get_oc_user(form.auth_context['user_id'])
if getattr(form, 'deprecated_form_id',
None) and question in self.question_items[
form.deprecated_form_id]:
# This form has been edited on HQ. Fetch original item
item_dict, study_event = self.question_items[
form.deprecated_form_id][question]
if item_dict['value'] != answer:
self.edit_item(item_dict, form, question, answer,
audit_log_id_ref, oc_user)
else:
item_dict, study_event = self.get_item_dict(
item, form, case_id, question)
if item_dict and item_dict['value'] != answer:
# This form has been submitted more than once for a non-repeating item group. This is an edit.
self.edit_item(item_dict, form, question, answer,
audit_log_id_ref, oc_user)
else:
item_dict['value'] = answer
if AUDIT_LOGS:
audit_log_id_ref['id'] += 1
item_dict['audit_logs'] = [{
'id':
'AL_{}'.format(audit_log_id_ref['id']),
'user_id':
oc_user.user_id,
'username':
oc_user.username,
'full_name':
oc_user.full_name,
'timestamp':
form.received_on,
'audit_type':
'Item data value updated',
'reason':
'initial value',
'new_value':
answer,
'value_type':
question,
}]
mu_oid = get_item_measurement_unit(self._domain_name, item)
if mu_oid:
item_dict['measurement_unit_oid'] = mu_oid
if study_event.start_datetime is None or form.form['meta'][
'timeStart'] < study_event.start_datetime:
study_event.start_datetime = form.form['meta']['timeStart']
if study_event.end_datetime is None or form.form['meta'][
'timeEnd'] > study_event.end_datetime:
study_event.end_datetime = form.form['meta']['timeEnd']
def subject_rows(self):
audit_log_id = 0 # To exclude audit logs, set `custom.openclinica.const.AUDIT_LOGS = False`
for case in self.get_subject_cases():
subject = Subject(getattr(case, CC_SUBJECT_KEY), getattr(case, CC_STUDY_SUBJECT_ID), self.domain)
for form in originals_first(case.get_forms()):
updates = form.form['case'].get('update', {})
if updates:
for question, answer in updates.iteritems():
item = get_question_item(self.domain, form.xmlns, question)
if item is None:
# This is a CommCare-only question or form
continue
audit_log_id += 1
subject.add_item(item, form, question, oc_format_date(answer), audit_log_id)
subject.close_form(form)
yield subject
def add_data(self, data, form, audit_log_id_ref):
def get_next_item(question_list):
for question_ in question_list:
item_ = get_question_item(self._domain, form.xmlns, question_)
if item_:
return item_
return None
# If a CommCare form is an OpenClinica repeating item group, then we would need to add a new item
# group. This isn't relevant for this project.
# if form.xmlns in REPEATING_ITEM_GROUP_FORMS:
# pass
for key, value in data.iteritems():
if key in _reserved_keys:
continue
if isinstance(value, list):
# Repeat group
# NOTE: We need to assume that repeat groups can't be edited in later form submissions
item = get_next_item(value)
if item is None:
# None of the questions in this group are OpenClinica items
continue
self.add_item_group(item, form)
for v in value:
# TODO: More testing
if not isinstance(v, dict):
raise OpenClinicaIntegrationError(
'CommCare question value is an unexpected data type. Form XMLNS: "{}"'.format(
form.xmlns))
self.add_data(v, form, audit_log_id_ref)
elif isinstance(value, dict):
# Group
self.add_data(value, form, audit_log_id_ref)
else:
# key is a question and value is its answer
item = get_question_item(self._domain, form.xmlns, key)
if item is None:
# This is a CommCare-only question or form
continue
self.add_item(item, form, key, oc_format_date(value), audit_log_id_ref)
def add_item(self, item, form, case_id, question, answer, audit_log_id_ref):
answer = oc_format_date(answer)
answer = oc_format_time(answer, self._domain.get_default_timezone())
oc_user = self._get_oc_user(form.auth_context['user_id'])
if getattr(form, 'deprecated_form_id', None) and question in self.question_items[form.deprecated_form_id]:
# This form has been edited on HQ. Fetch original item
item_dict, study_event = self.question_items[form.deprecated_form_id][question]
if item_dict['value'] != answer:
self.edit_item(item_dict, form, question, answer, audit_log_id_ref, oc_user)
else:
item_dict, study_event = self.get_item_dict(item, form, case_id, question)
if item_dict and item_dict['value'] != answer:
# This form has been submitted more than once for a non-repeating item group. This is an edit.
self.edit_item(item_dict, form, question, answer, audit_log_id_ref, oc_user)
else:
item_dict['value'] = answer
if AUDIT_LOGS:
audit_log_id_ref['id'] += 1
item_dict['audit_logs'] = [{
'id': 'AL_{}'.format(audit_log_id_ref['id']),
'user_id': oc_user.user_id,
'username': oc_user.username,
'full_name': oc_user.full_name,
'timestamp': form.received_on,
'audit_type': 'Item data value updated',
'reason': 'initial value',
'new_value': answer,
'value_type': question,
}]
mu_oid = get_item_measurement_unit(self._domain_name, item)
if mu_oid:
item_dict['measurement_unit_oid'] = mu_oid
if study_event.start_datetime is None or form.form['meta']['timeStart'] < study_event.start_datetime:
study_event.start_datetime = form.form['meta']['timeStart']
if study_event.end_datetime is None or form.form['meta']['timeEnd'] > study_event.end_datetime:
study_event.end_datetime = form.form['meta']['timeEnd']