ehr_records = kb.get_ehr_records()
logging.info('Loaded %d EHR records' % len(ehr_records))
ehr_lookup = {}
for rec in ehr_records:
key = get_ehr_key(rec)
ehr_lookup.setdefault(rec['i_id'], {}).setdefault(key, []).append(rec)
logger.debug('Loaded EHR lookup table, %d individuals involved' %
len(ehr_lookup.keys()))
for ind, records in ehr_lookup.iteritems():
for k, vals in records.iteritems():
if len(vals) > 1:
logger.info(
'##### Individual %s has %d duplicated EHR records #####' %
(ind, len(vals)))
logger.debug(vals)
for v in vals[1:]:
logger.info('Invalidating record %r' % v)
kb.invalidate_ehr_records(v['i_id'],
timestamp=v['timestamp'],
archetype=v['archetype'],
grouper_id=v['g_id'],
field=v['fields'].keys()[0],
field_value=str(
v['fields'].values()[0]))
if __name__ == '__main__':
main(sys.argv[1:])
kb = KB(driver='omero')(host, user, passwd)
logging.info('Loading EHR records')
ehr_records = kb.get_ehr_records()
logging.info('Loaded %d EHR records' % len(ehr_records))
ehr_lookup = {}
for rec in ehr_records:
key = get_ehr_key(rec)
ehr_lookup.setdefault(rec['i_id'], {}).setdefault(key,[]).append(rec)
logger.debug('Loaded EHR lookup table, %d individuals involved' %
len(ehr_lookup.keys()))
for ind, records in ehr_lookup.iteritems():
for k, vals in records.iteritems():
if len(vals) > 1:
logger.info('##### Individual %s has %d duplicated EHR records #####' % (ind,
len(vals)))
logger.debug(vals)
for v in vals[1:]:
logger.info('Invalidating record %r' % v)
kb.invalidate_ehr_records(v['i_id'], timestamp = v['timestamp'],
archetype = v['archetype'],
grouper_id = v['g_id'],
field = v['fields'].keys()[0],
field_value = str(v['fields'].values()[0]))
if __name__ == '__main__':
main(sys.argv[1:])
