def get_all_rows(self):
"""
Rows to appear in the "Subjects" sheet of export_table().
CdiscOdmExportWriter will render this using the odm_export.xml template to combine subjects into a single
ODM XML document.
The values are also used to register new subjects if the web service is enabled.
"""
audit_log_id_ref = {'id': 0} # To exclude audit logs, set `custom.openclinica.const.AUDIT_LOGS = False`
query = self._build_query().case_type(CC_SUBJECT_CASE_TYPE).start(0).size(SIZE_LIMIT)
rows = []
for result in query.scroll():
case = CommCareCase.wrap(result)
if not self.is_subject_selected(case):
continue
subject = Subject.wrap(case, audit_log_id_ref)
row = [
'SS_' + subject.subject_key, # OpenClinica prefixes subject key with "SS_" to make the OID
subject.study_subject_id,
subject.enrollment_date,
subject.sex,
subject.dob,
subject.get_export_data(),
]
rows.append(row)
return rows
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 rows(self):
audit_log_id_ref = {'id': 0} # To exclude audit logs, set `custom.openclinica.const.AUDIT_LOGS = False`
for res in self.es_results['hits'].get('hits', []):
case = CommCareCase.wrap(res['_source'])
if not self.is_subject_selected(case):
continue
subject = Subject.wrap(case, audit_log_id_ref)
row = [
subject.subject_key, # What OpenClinica refers to as Person ID; i.e. OID with the "SS_" prefix
subject.study_subject_id,
subject.enrollment_date,
subject.sex,
subject.dob,
subject.get_report_events(),
]
yield row
def subject_rows(self):
audit_log_id_ref = {'id': 0} # To exclude audit logs, set `custom.openclinica.const.AUDIT_LOGS = False`
for case in self.get_study_subject_cases():
subject = Subject(getattr(case, CC_SUBJECT_KEY), getattr(case, CC_STUDY_SUBJECT_ID), self.domain)
subject.enrollment_date = getattr(case, CC_ENROLLMENT_DATE, None)
subject.sex = getattr(case, CC_SEX, None)
subject.dob = getattr(case, CC_DOB, None)
for form in originals_first(case.get_forms()):
# Pass audit log ID by reference to increment it for each audit log
subject.add_data(form.form, form, audit_log_id_ref)
yield subject
def rows(self):
audit_log_id_ref = {'id': 0} # To exclude audit logs, set `custom.openclinica.const.AUDIT_LOGS = False`
query = self._build_query().case_type(CC_SUBJECT_CASE_TYPE)
for result in query.scroll():
case = CommCareCase.wrap(result)
if not self.is_subject_selected(case):
continue
subject = Subject.wrap(case, audit_log_id_ref)
row = [
subject.subject_key, # What OpenClinica refers to as Person ID; i.e. OID with the "SS_" prefix
subject.study_subject_id,
subject.enrollment_date,
subject.sex,
subject.dob,
subject.get_report_events(),
]
yield row
def get_all_rows(self):
"""
Rows to appear in the "Subjects" sheet of export_table().
CdiscOdmExportWriter will render this using the odm_export.xml template to combine subjects into a single
ODM XML document.
"""
audit_log_id_ref = {'id': 0} # To exclude audit logs, set `custom.openclinica.const.AUDIT_LOGS = False`
query = self._build_query().start(0).size(SIZE_LIMIT)
for result in query.scroll():
case = CommCareCase.wrap(result)
if not self.is_subject_selected(case):
continue
subject = Subject.wrap(case, audit_log_id_ref)
row = [
'SS_' + subject.subject_key, # OpenClinica prefixes subject key with "SS_" to make the OID
subject.study_subject_id,
subject.get_export_data(),
]
yield row
