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 __init__(self, msg, config_file):
log.info(msg)
self.dom = xml.dom.minidom.parseString(msg)
self.galaxy_host = get_value(self.dom, 'galaxy_host')
self.api_key = get_value(self.dom, 'api_key')
self.sequencer_host = get_value(self.dom, 'data_host')
self.sequencer_username = get_value(self.dom, 'data_user')
self.sequencer_password = get_value(self.dom, 'data_password')
self.request_id = get_value(self.dom, 'request_id')
self.sample_id = get_value(self.dom, 'sample_id')
self.library_id = get_value(self.dom, 'library_id')
self.folder_id = get_value(self.dom, 'folder_id')
self.dataset_files = []
count = 0
while True:
dataset_id = get_value_index(self.dom, 'dataset_id', count)
file = get_value_index(self.dom, 'file', count)
name = get_value_index(self.dom, 'name', count)
if file:
self.dataset_files.append(
dict(name=name, dataset_id=int(dataset_id), file=file))
else:
break
count = count + 1
# read config variables
config = ConfigParser.ConfigParser()
retval = config.read(config_file)
if not retval:
error_msg = 'FATAL ERROR: Unable to open config file %s.' % config_file
log.error(error_msg)
sys.exit(1)
try:
self.config_id_secret = config.get("app:main", "id_secret")
except ConfigParser.NoOptionError, e:
self.config_id_secret = "USING THE DEFAULT IS NOT SECURE!"
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 __init__( self, msg, config_file ):
log.info( msg )
self.dom = xml.dom.minidom.parseString( msg )
self.galaxy_host = get_value( self.dom, 'galaxy_host' )
self.api_key = get_value( self.dom, 'api_key' )
self.sequencer_host = get_value( self.dom, 'data_host' )
self.sequencer_username = get_value( self.dom, 'data_user' )
self.sequencer_password = get_value( self.dom, 'data_password' )
self.request_id = get_value( self.dom, 'request_id' )
self.sample_id = get_value( self.dom, 'sample_id' )
self.library_id = get_value( self.dom, 'library_id' )
self.folder_id = get_value( self.dom, 'folder_id' )
self.dataset_files = []
count=0
while True:
dataset_id = get_value_index( self.dom, 'dataset_id', count )
file = get_value_index( self.dom, 'file', count )
name = get_value_index( self.dom, 'name', count )
if file:
self.dataset_files.append( dict( name=name,
dataset_id=int( dataset_id ),
file=file ) )
else:
break
count=count+1
# read config variables
config = ConfigParser.ConfigParser()
retval = config.read( config_file )
if not retval:
error_msg = 'FATAL ERROR: Unable to open config file %s.' % config_file
log.error( error_msg )
sys.exit(1)
try:
self.config_id_secret = config.get( "app:main", "id_secret" )
except ConfigParser.NoOptionError,e:
self.config_id_secret = "USING THE DEFAULT IS NOT SECURE!"
