def upload_tfs(organism):
with open('%s.txt' % organism) as infile:
tfs = [line.strip() for line in infile]
data_ws = kbase.workspace(config.get('KBase', 'ws_service_url'),
ws_name=config.get('KBase', 'data_workspace'),
user=config.get('KBase', 'user'),
password=config.get('KBase', 'password'))
print "saving tfs..."
kbase.save_gene_list(data_ws, '%s.tfs' % organism,
'nwportal:nwportal_data/%s.genome' % organism,
tfs)
print "saved"
def get_object(objref):
ws_name, inst_name = objref.split('/')
result_ws = kbase.workspace(config.get('KBase', 'ws_service_url'),
ws_name=ws_name,
user=config.get('KBase', 'user'),
password=config.get('KBase', 'password'))
result = result_ws.get_object(inst_name)
# DEBUG: list workspace objects
#objs = result_ws.ws_service.list_workspace_objects({'workspace': ws_name})
#for obj in objs:
# print obj
# DEBUG END
return result
def get_result_object(jobid):
"""retrieve result data from the job service"""
jobstate = kbase.user_job_state(config.get('KBase', 'ujs_service_url'),
config.get('KBase', 'user'),
config.get('KBase', 'password'),
jobid)
jobstatus = jobstate.get_job_status()
status = jobstatus[1]
if status == 'error':
print "Problem: ", jobstatus[2]
return None
elif status == 'complete':
result_ref = jobstate.get_results()['workspaceids'][0]
print "result at: ", result_ref
ws_name, inst_name = result_ref.split('/')
result_ws = kbase.workspace(config.get('KBase', 'ws_service_url'),
ws_name=ws_name,
user=config.get('KBase', 'user'),
password=config.get('KBase', 'password'))
return result_ws.get_object(inst_name)
def msg_consumer(channel, method, header, body):
params = json.loads(body)
print params
try:
print "logging in to KBase"
ws_service = wsc.Workspace(config.get('KBase', 'ws_service_url'),
user_id=config.get('KBase', 'user'),
password=config.get('KBase', 'password'))
data_ws = kbase.workspace(config.get('KBase', 'ws_service_url'),
config.get('KBase', 'data_workspace'),
ws_service_obj=ws_service)
print "logged in to KBASE data workspace"
# KBase is picky with identifier names, no colons, e.g.
username = params['username']
timestamp = str(time.time())
if params['use_ensemble']:
input_ws_name = 'cm_ensemble-%s-%s' % (username, timestamp)
else:
input_ws_name = 'cm_single-%s-%s' % (username, timestamp)
input_ws_info = kbase.create_workspace(ws_service, input_ws_name)
print "created input workspace under: ", input_ws_info
input_ws = kbase.workspace(config.get('KBase', 'ws_service_url'),
input_ws_name,
ws_service_obj=ws_service)
print "logged in to KBASE input workspace"
organism = params['organism']
genome_name = '%s.genome' % organism
ratios_name = 'ratios-%s-%s' % (organism, timestamp)
string_obj_name = None
operon_obj_name = None
kbase.import_ratios_matrix(input_ws, data_ws, ratios_name, genome_name,
params['ratio_file_path'], sep='\t')
if 'string_file_path' in params:
string_obj_name = 'string-%s-%s' % (organism, timestamp)
kbase.import_string_network(input_ws, string_obj_name,
params['string_file_path'])
print "uploaded STRING network"
if 'operon_file_path' in params:
print "uploading operome..."
operon_obj_name = 'operon-%s-%s' % (organism, timestamp)
kbase.import_mo_operome_file(input_ws, operon_obj_name,
params['operon_file_path'])
print "uploaded operome"
start_cm_single(params['nwp_jobid'], data_ws, input_ws, organism, timestamp,
ratios_name, string_obj_name, operon_obj_name)
channel.basic_ack(delivery_tag=method.delivery_tag)
except:
print "Error occurred"
#channel.basic_cancel()
channel.basic_ack(delivery_tag=method.delivery_tag)
traceback.print_exc()
