def configure_env(args):
must_reset = False
for n in "HADOOP_HOME", "HADOOP_CONF_DIR":
v = getattr(args, n.lower())
if v:
os.environ[n] = v
must_reset = True
if must_reset:
hdfs.reset()
def main(argv=sys.argv[1:]):
parser = argparse.ArgumentParser(description=__doc__)
parser.add_argument("--conf-dir", metavar="HADOOP_CONF_DIR")
args = parser.parse_args(argv)
if args.conf_dir:
os.environ["HADOOP_CONF_DIR"] = os.path.abspath(args.conf_dir)
hdfs.reset()
fs = hdfs.hdfs()
print "--- OPEN ---"
dump_status(fs)
print "cwd:", fs.working_directory()
print
fs.close()
print "--- CLOSED ---"
dump_status(fs)
def main(argv=sys.argv[1:]):
parser = argparse.ArgumentParser(description=__doc__)
parser.add_argument("--conf-dir", metavar="HADOOP_CONF_DIR")
args = parser.parse_args(argv)
if args.conf_dir:
os.environ["HADOOP_CONF_DIR"] = os.path.abspath(args.conf_dir)
hdfs.reset()
fs = hdfs.hdfs()
print "--- OPEN ---"
dump_status(fs)
print "cwd:", fs.working_directory()
print
fs.close()
print "--- CLOSED ---"
dump_status(fs)
def main(argv):
parser = make_parser()
opt, args = parser.parse_args()
try:
input_fasta = args[0]
db_archive = args[1]
except IndexError:
parser.print_help()
sys.exit(2)
STR_GENERATOR.prefix = os.path.basename(input_fasta)
logger = logging.getLogger()
for h in logger.handlers:
logger.removeHandler(h)
opt.log_level_str = opt.log_level
opt.log_level = getattr(logging, opt.log_level)
kwargs = {'format': LOG_FORMAT,
'datefmt': LOG_DATEFMT,
'level': opt.log_level}
if opt.log_file:
kwargs['filename'] = opt.log_file
logging.basicConfig(**kwargs)
logger.debug("cli args: %r" % (args,))
logger.debug("cli opts: %s" % opt)
if opt.mr_dump_file:
opt.mr_dump_file = open(opt.mr_dump_file, "w")
else:
opt.mr_dump_file = sys.stderr
if not opt.blast_db:
opt.blast_db = os.path.basename(db_archive).split(".", 1)[0]
logger.info("--blast-db not provided: setting to %r" % opt.blast_db)
os.environ["HADOOP_HOME"] = opt.hadoop_home
if not opt.hadoop:
opt.hadoop = os.path.join(opt.hadoop_home, "bin/hadoop")
if not opt.hadoop_conf_dir:
opt.hadoop_conf_dir = os.path.join(opt.hadoop_home, "conf")
os.environ["HADOOP_CONF_DIR"] = opt.hadoop_conf_dir
hdfs.reset()
fs = hdfs.hdfs()
logger.debug("hdfs params: host=%s, port=%d" % (fs.host, fs.port))
lfs = hdfs.hdfs("", 0)
runner = Runner(fs, lfs, logger)
try:
db_archive_hdfs = runner.upload_archive(db_archive)
blast_input_hdfs = runner.run_f2t(input_fasta, opt)
blast_output_hdfs = runner.run_blast(blast_input_hdfs, db_archive_hdfs,
opt)
runner.collect_output(blast_output_hdfs, opt)
logger.info("all done")
finally:
lfs.close()
fs.close()
if opt.mr_dump_file is not sys.stderr:
opt.mr_dump_file.close()
