def update_status( self, status, dataset_id='All', msg='' ):
'''
Update the data transfer status for this dataset in the database
'''
try:
log.debug( 'Setting status "%s" for dataset "%s" of sample "%s"' % ( status, str( dataset_id ), str( self.sample_id) ) )
sample_dataset_ids = []
if dataset_id == 'All':
for dataset in self.dataset_files:
sample_dataset_ids.append( api.encode_id( self.config_id_secret, dataset[ 'dataset_id' ] ) )
else:
sample_dataset_ids.append( api.encode_id( self.config_id_secret, dataset_id ) )
# update the transfer status
data = {}
data[ 'update_type' ] = SamplesAPIController.update_types.SAMPLE_DATASET[0]
data[ 'sample_dataset_ids' ] = sample_dataset_ids
data[ 'new_status' ] = status
data[ 'error_msg' ] = msg
url = "http://%s/api/samples/%s" % ( self.galaxy_host,
api.encode_id( self.config_id_secret, self.sample_id ) )
log.debug( str( ( self.api_key, url, data)))
retval = api.update( self.api_key, url, data, return_formatted=False )
log.debug( str( retval ) )
except urllib2.URLError, e:
log.debug( 'ERROR( sample_dataset_transfer_status ( %s ) ): %s' % ( url, str( e ) ) )
log.error( traceback.format_exc() )
def add_to_library(self):
'''
This method adds the dataset file to the target data library & folder
by opening the corresponding url in Galaxy server running.
'''
self.update_status(SampleDataset.transfer_status.ADD_TO_LIBRARY)
try:
data = {}
data['folder_id'] = 'F%s' % api.encode_id(self.config_id_secret,
self.folder_id)
data['file_type'] = 'auto'
data['server_dir'] = self.server_dir
data['dbkey'] = ''
data['upload_option'] = 'upload_directory'
data['create_type'] = 'file'
url = "http://%s/api/libraries/%s/contents" % (
self.galaxy_host,
api.encode_id(self.config_id_secret, self.library_id))
log.debug(str((self.api_key, url, data)))
retval = api.submit(self.api_key,
url,
data,
return_formatted=False)
log.debug(str(retval))
except Exception, e:
self.error_and_exit(str(e))
def add_to_library( self ):
'''
This method adds the dataset file to the target data library & folder
by opening the corresponding url in Galaxy server running.
'''
self.update_status( SampleDataset.transfer_status.ADD_TO_LIBRARY )
try:
data = {}
data[ 'folder_id' ] = 'F%s' % api.encode_id( self.config_id_secret, self.folder_id )
data[ 'file_type' ] = 'auto'
data[ 'server_dir' ] = self.server_dir
data[ 'dbkey' ] = ''
data[ 'upload_option' ] = 'upload_directory'
data[ 'create_type' ] = 'file'
url = "http://%s/api/libraries/%s/contents" % ( self.galaxy_host,
api.encode_id( self.config_id_secret, self.library_id ) )
log.debug( str( ( self.api_key, url, data ) ) )
retval = api.submit( self.api_key, url, data, return_formatted=False )
log.debug( str( retval ) )
except Exception, e:
self.error_and_exit( str( e ) )
def update_request( api_key, request_id ):
encoded_request_id = api.encode_id( config.get( "app:main", "id_secret" ), request_id )
data = dict( update_type=RequestsAPIController.update_types.REQUEST )
url = "http://%s:%s/api/requests/%s" % ( config.get(http_server_section, "host"),
config.get(http_server_section, "port"),
encoded_request_id )
log.debug( 'Updating request %i' % request_id )
try:
retval = api.update( api_key, url, data, return_formatted=False )
log.debug( str( retval ) )
except Exception, e:
log.debug( 'ERROR(update_request (%s)): %s' % ( str((self.api_key, url, data)), str(e) ) )
def update_status(self, status, dataset_id='All', msg=''):
'''
Update the data transfer status for this dataset in the database
'''
try:
log.debug('Setting status "%s" for dataset "%s" of sample "%s"' %
(status, str(dataset_id), str(self.sample_id)))
sample_dataset_ids = []
if dataset_id == 'All':
for dataset in self.dataset_files:
sample_dataset_ids.append(
api.encode_id(self.config_id_secret,
dataset['dataset_id']))
else:
sample_dataset_ids.append(
api.encode_id(self.config_id_secret, dataset_id))
# update the transfer status
data = {}
data[
'update_type'] = SamplesAPIController.update_types.SAMPLE_DATASET[
0]
data['sample_dataset_ids'] = sample_dataset_ids
data['new_status'] = status
data['error_msg'] = msg
url = "http://%s/api/samples/%s" % (
self.galaxy_host,
api.encode_id(self.config_id_secret, self.sample_id))
log.debug(str((self.api_key, url, data)))
retval = api.update(self.api_key,
url,
data,
return_formatted=False)
log.debug(str(retval))
except urllib2.URLError, e:
log.debug('ERROR( sample_dataset_transfer_status ( %s ) ): %s' %
(url, str(e)))
log.error(traceback.format_exc())
