def register_session(server, username, password):
"""
Register a new GenePattern server session for the provided
server, username and password. Return the session.
:param server:
:param username:
:param password:
:return:
"""
# Create the session
session = gp.GPServer(server, username, password)
# Validate username if not empty
valid_username = username != "" and username is not None
# Validate that the server is not already registered
index = get_session_index(server)
new_server = index == -1
# Add the new session to the list
if valid_username and new_server:
sessions.append(session)
# Replace old session is one exists
if valid_username and not new_server:
sessions[index] = session
return session
def get_task(self, line):
args = line.split(" ") # GPServer, task name or lsid
if len(args) != 4:
return 'Incorrect number of args. Need 4: Server URL, username, password, task name or LSID'
server = gp.GPServer(args[0], args[1], args[2])
task = gp.GPTask(server, args[3])
return task
def get_job(self, line):
args = line.split(" ") # GPServer, job number
if len(args) != 4:
return 'Incorrect number of args. Need 4: Server URL, username, password, job number'
server = gp.GPServer(args[0], args[1], args[2])
job = gp.GPJob(server, int(args[3]))
return job
def test_odf_load_gpfile():
gpfile = gp.GPFile(gp.GPServer('http://genepattern.broadinstitute.org/gp', '', ''),
'https://software.broadinstitute.org/cancer/software/genepattern/data/protocols/all_aml_test.preprocessed.comp.marker.odf')
odf = gp.data.ODF(gpfile)
odf_asserts(odf)
def test_gct_load_gpfile():
gpfile = gp.GPFile(gp.GPServer('http://genepattern.broadinstitute.org/gp', '', ''),
'https://software.broadinstitute.org/cancer/software/genepattern/data/all_aml/all_aml_test.gct')
gct = gp.data.GCT(gpfile)
gct_asserts(gct)
module_id = "urn:lsid:8080.root.ppm-sanger-dev.ppm-sanger-dev.dipr.partners.org:genepatternmodules:3:2"
try:
file = sys.argv[1]
except:
print "usage: sanger_gp_ws.py zipped_file_of_.ab1"
exit(0)
print "file: " + os.path.basename(file)
#arguments to use
arg_name = "arg0", "arg1"
arg_val = file, "yoyoyo"
#connect
server = gp.GPServer(url, user, None)
#get available tasks
tasks = server.get_task_list()
for task in tasks:
print "gp task: " + str(task.get_name())
module = tasks[1]
print "module: " + str(module.get_name())
#module args
module.param_load()
params = module.get_parameters()
for param in params: