def setup():
shared.setup()
global t_new, t_old, t_new_e, t_old_e, t_client_new, t_client_old, g_skip_shock
g_skip_shock = not shared.services["shock_service_url"].startswith("http")
t_new = AssemblyAPI(shared.services, shared.token, assembly_new)
t_new_e = _Assembly(shared.services, shared.token, assembly_new)
t_old = AssemblyAPI(shared.services, shared.token, assembly_old)
t_old_e = _KBaseGenomes_ContigSet(shared.services, shared.token,
assembly_old)
t_client_new = AssemblyClientAPI(shared.services["assembly_service_url"],
shared.token, assembly_new)
t_client_old = AssemblyClientAPI(shared.services["assembly_service_url"],
shared.token, assembly_old)
done = False
while not done:
results = ws.list_objects({
"workspaces": [fix_workspace],
"type": "KBaseGenomeAnnotations.Assembly",
"skip": skip,
"limit": limit
})
if len(results) == 0:
done = True
for x in results:
count += 1
ac = AssemblyAPI(services,
token,
ref="{}/{}".format(fix_workspace, x[1]))
handle_ref = ac.get_data()["fasta_handle_ref"]
shock_node_id = None
try:
handle = hc.hids_to_handles([handle_ref])[0]
shock_node_id = handle["id"]
except Exception, e:
print "Failed to retrieve handle {} from {}".format(
handle_ref, services["handle_service_url"])
_log.exception(e)
shock_node_id = handle_ref
print "#" * 80
print x[1], shock_node_id
