def update_sample_state(message):
dom = xml.dom.minidom.parseString(message.body)
barcode = get_value(dom, 'barcode')
state = get_value(dom, 'state')
api_key = get_value(dom, 'api_key')
log.debug('Barcode: ' + barcode)
log.debug('State: ' + state)
log.debug('API Key: ' + api_key)
# validate
if not barcode or not state or not api_key:
log.debug(
'Incomplete sample_state_update message received. Sample barcode, desired state and user API key is required.'
)
return
# update the sample state in Galaxy db
dbconnstr = config.get("app:main", "database_connection")
galaxydb = GalaxyDbInterface(dbconnstr)
sample_id = galaxydb.get_sample_id(field_name='bar_code', value=barcode)
if sample_id == -1:
log.debug('Invalid barcode.')
return
galaxydb.change_state(sample_id, state)
# after updating the sample state, update request status
request_id = galaxydb.get_request_id(sample_id)
update_request(api_key, request_id)
def recv_callback(msg):
dom = xml.dom.minidom.parseString(msg.body)
barcode = get_value(dom, 'barcode')
state = get_value(dom, 'state')
log.debug('Barcode: '+barcode)
log.debug('State: '+state)
# update the galaxy db
galaxy = GalaxyDbInterface(dbconnstr)
sample_id = galaxy.get_sample_id(field_name='bar_code', value=barcode)
if sample_id == -1:
log.debug('Invalid barcode.')
return
galaxy.change_state(sample_id, state)
