def clean_up(self):
logging.info("Cleaning up Google Cloud Platform.")
# Remove dummy files from output directory
try:
logging.debug("Looking for dummy files...")
dummy_search_string = os.path.join(self.final_output_dir,
"**dummy.txt")
dummy_outputs = GoogleCloudHelper.ls(dummy_search_string)
if len(dummy_outputs) > 0:
cmd = "gsutil rm {0}".format(" ".join(dummy_outputs))
proc = sp.Popen(cmd,
stderr=sp.PIPE,
stdout=sp.PIPE,
shell=True)
proc.communicate()
logging.debug("Done killing dummy files!")
except:
logging.warning(
"(%s) Could not remove dummy input files on google cloud!")
# Initiate destroy process on all the instances that haven't been destroyed
for instance_name, instance_obj in self.processors.items():
try:
if instance_name not in self.dealloc_procs:
instance_obj.destroy(wait=False)
except RuntimeError:
logging.warning("(%s) Could not destroy instance!" %
instance_name)
# Now wait for all destroy processes to finish
for instance_name, instance_obj in self.processors.items():
try:
#if instance_obj.get_status() != Processor.OFF:
if instance_name not in self.dealloc_procs:
instance_obj.wait_process("destroy")
except RuntimeError:
logging.warning("(%s) Unable to destroy instance!" %
instance_name)
logging.info("Clean up complete!")
import importlib
configure_import_paths()
configure_logging(3)
ss_file = "/home/alex/Desktop/projects/gap/test/test_runs/qc_report_merge/ss.json"
ss = SampleSet(ss_file)
print ss.get_paths()
print ss.get_data(data_type="qc_report", samples="Jijoye_early2")
print ss.get_data(data_type="qc_report", samples="Jijoye_early1")
exit(0)
######################### Test GCH ls command
print GoogleCloudHelper.ls("gs://derp_test/new_gap_test_1/**dummy.txt")
print GoogleCloudHelper.ls("gs://derp_test/*gasdf")
exit(0)
######################### Test GAPfile updating with modules
from System.Platform.Google import GooglePlatform
from System.Datastore import Datastore
# Test cycle checking algorithm
graph_file = "/home/alex/Desktop/projects/gap/test/test_runs/simple_success/graph.config"
graph = Graph(graph_file)
#print graph
rk_file = "/home/alex/Desktop/projects/gap/test/test_runs/simple_success/rk.config"
rk = ResourceKit(rk_file)