def make_plugin_json(primary_key,
report_dir,
plugin,
plugin_out_dir,
net_location,
url_root,
username,
runlevel=RunLevel.DEFAULT,
blockId='',
block_dirs=["."],
instance_config={}):
try:
ion_params, warn = getparameter(
os.path.join(report_dir, 'ion_params_00.json'))
except:
ion_params = getparameter_minimal(
os.path.join(report_dir, 'ion_params_00.json'))
json_obj = {
"runinfo":
get_runinfo(ion_params, primary_key, report_dir, plugin,
plugin_out_dir, net_location, url_root, username, runlevel,
blockId),
"runplugin":
get_runplugin(ion_params, runlevel, blockId, block_dirs),
"expmeta":
get_expmeta(ion_params, report_dir),
"pluginconfig":
get_pluginconfig(plugin, instance_config),
"globalconfig":
get_globalconfig(),
"plan":
get_plan(ion_params),
"sampleinfo":
ion_params.get("sampleInfo", {}),
"datamanagement":
get_datamanagement(primary_key),
}
# IonReporterUploader_V1_0 compatibility shim
if plugin["name"] == "IonReporterUploader_V1_0" and plugin.get(
"userInput", ""):
json_obj["plan"]["irworkflow"] = plugin["userInput"][0].get("Workflow")
return json_obj
def make_plugin_json(
primary_key,
report_dir,
plugin,
plugin_out_dir,
net_location,
url_root,
username,
runlevel=RunLevel.DEFAULT,
blockId="",
block_dirs=["."],
instance_config={},
):
try:
ion_params, warn = getparameter(os.path.join(report_dir, "ion_params_00.json"))
except:
ion_params = getparameter_minimal(os.path.join(report_dir, "ion_params_00.json"))
json_obj = {
"runinfo": get_runinfo(
ion_params,
primary_key,
report_dir,
plugin,
plugin_out_dir,
net_location,
url_root,
username,
runlevel,
blockId,
),
"runplugin": get_runplugin(ion_params, runlevel, blockId, block_dirs),
"expmeta": get_expmeta(ion_params, report_dir),
"pluginconfig": get_pluginconfig(plugin, instance_config),
"globalconfig": get_globalconfig(),
"plan": get_plan(ion_params),
"sampleinfo": ion_params.get("sampleInfo", {}),
}
# IonReporterUploader_V1_0 compatibility shim
if plugin["name"] == "IonReporterUploader_V1_0" and plugin.get("userInput", ""):
json_obj["plan"]["irworkflow"] = plugin["userInput"][0].get("Workflow")
return json_obj
help='alignment')
args = parser.parse_args()
if args.verbose:
print "BlockTLScript:", args
if not args.do_sigproc and not args.do_basecalling and not args.do_alignment:
parser.print_help()
sys.exit(1)
#ensure we permit read/write for owner and group output files.
os.umask(0002)
blockprocessing.printheader()
env, warn = explogparser.getparameter()
print warn
blockprocessing.write_version()
sys.stdout.flush()
sys.stderr.flush()
#-------------------------------------------------------------
# Connect to Job Server
#-------------------------------------------------------------
try:
jobserver = xmlrpclib.ServerProxy(
"http://%s:%d" %
(cluster_settings.JOBSERVER_HOST, cluster_settings.JOBSERVER_PORT),
verbose=False,
allow_none=True)
parser.add_argument('-z', '--do-zipping', dest='do_zipping', action='store_true', help='zipping')
args = parser.parse_args()
if args.verbose:
print "MergeTLScript:",args
if not args.do_sigproc and not args.do_basecalling and not args.do_zipping:
parser.print_help()
sys.exit(1)
#ensure we permit read/write for owner and group output files.
os.umask(0002)
blockprocessing.printheader()
env,warn = explogparser.getparameter()
blockprocessing.write_version()
sys.stdout.flush()
sys.stderr.flush()
#-------------------------------------------------------------
# Connect to Job Server
#-------------------------------------------------------------
try:
jobserver = xmlrpclib.ServerProxy("http://%s:%d" %
(cluster_settings.JOBSERVER_HOST, cluster_settings.JOBSERVER_PORT),
verbose=False, allow_none=True)
primary_key_file = os.path.join(os.getcwd(),'primary.key')
except:
traceback.print_exc()
parser = argparse.ArgumentParser()
parser.add_argument('-v', dest='verbose', action='store_true')
parser.add_argument('-f', '--forward', required=False, dest='forwarddir', default='.', help='forward run report')
parser.add_argument('-r', '--reverse', required=False, dest='reversedir', default='.', help='reverse run report')
parser.add_argument('-o', '--output', required=False, dest='outdir', default='.', help='output directory')
parser.add_argument('param', default='paramfile', help='param file')
args = parser.parse_args()
args.verbose = True
if args.verbose:
print "args:",args
blockprocessing.printheader()
env,warn = explogparser.getparameter()
print warn
#-------------------------------------------------------------
# Update Report Status to 'Started'
#-------------------------------------------------------------
try:
jobserver = xmlrpclib.ServerProxy("http://%s:%d" % (JOBSERVER_HOST, JOBSERVER_PORT), verbose=False, allow_none=True)
debugging_cwd = os.getcwd()
except:
traceback.print_exc()
def set_result_status(status):
try:
primary_key_file = os.path.join(os.getcwd(),'primary.key')
jobserver.updatestatus(primary_key_file, status, True)
