def run(self, readsetId, sequenceName, sequenceStart, sequenceEnd, output):
file = output[0]
# If you have a setting to copy it over, do so
dir = os.environ['OUTPUT_DIRECTORY']
if dir is not None:
bucket = get_bucket_name()
src = file
dst = str.format("/%s/%s/%s_%s_%s-%s.txt" % (
bucket, dir, str(readsetId), str(sequenceName), sequenceStart,
sequenceEnd))
gcs._copy2(src, dst)
logging.info("Copied output file to: %s" % dst)
file = dst
if os.environ['SERVER_SOFTWARE'].startswith('Development'):
url = "http://localhost:8080/_ah/gcs" + file
else:
url = "https://storage.cloud.google.com" + file
logging.info("Genomics pipeline completed. Results: %s", url)
def run(self, readsetId, sequenceName, sequenceStart, sequenceEnd, files):
# If you have a setting to copy it over, do so
local = os.environ['SERVER_SOFTWARE'].startswith('Development')
bucket = get_bucket_name()
dir = os.getenv('OUTPUT_DIRECTORY', 'genomics_mr_results')
path = str.format("/%s/%s/%s/%s" %
(bucket, dir, str(readsetId), str(sequenceName)))
shard = 0
for file in files:
dst = str.format("%s/%s-%s_shard-%03d.txt" %
(path, sequenceStart, sequenceEnd, shard))
gcs._copy2(file, dst)
if local:
url = "http://localhost:8080/_ah/gcs" + dst
logging.info("Output file available here: %s", url)
shard += 1
if local:
logging.info("Genomics pipeline completed. Output files listed above.")
else:
url = "https://storage.cloud.google.com" + path
logging.info("Genomics pipeline completed. Results: %s", url)
