def tearDown(self):
fs = hdfs.hdfs("", 0)
fs.delete(self.local_wd)
fs.close()
fs = hdfs.hdfs("default", 0)
fs.delete(self.hdfs_wd)
fs.close()
def write(writeFlag):
if (writeFlag == True):
# instantiate hadoop
hdfs.hdfs()
targetPath = config.targetPath;
targetDirectory = config.targetDirectory;
sourceFile = config.sourceFile;
print("Target Path: " + targetPath);
print("Target Directory: " + targetDirectory);
print("Source Path: " + sourceFile);
dumpFile = open(sourceFile, "r");
fullText = dumpFile.read();
dumpFile.close();
# write to hadoop
#hdfs.mkdir(targetDirectory)
hdfs.dump(fullText, targetPath)
#hdfs.cp(sourceFile, targetPath)
#print (hdfs.ls("test4"))
#files = hdfs.ls("test4")
# read from hadoop
#hdfs.get("test4/hello.txt", "/tmp/hello.txt")
#with open("/tmp/hello.txt") as f:
# print f.read()
#print(hdfs.ls("test", "hduser1"))
#text = hdfs.load("test/hello.txt")
#print text
def tearDown(self):
fs = hdfs.hdfs("", 0)
fs.delete(self.local_wd)
fs.close()
fs = hdfs.hdfs("default", 0)
fs.delete(self.hdfs_wd)
fs.close()
def capacity(self):
fs = hdfs.hdfs("", 0)
self.assertRaises(RuntimeError, fs.capacity)
fs.close()
if not hdfs.default_is_local():
fs = hdfs.hdfs("default", 0)
cap = fs.capacity()
self.assertGreaterEqual(cap, 0)
def capacity(self):
fs = hdfs.hdfs("", 0)
self.assertRaises(RuntimeError, fs.capacity)
fs.close()
if not hdfs.default_is_local():
fs = hdfs.hdfs("default", 0)
cap = fs.capacity()
self.assertGreaterEqual(cap, 0)
def cache(self):
orig_fs = hdfs.hdfs(*self.hp_cases[0])
for host, port in self.hp_cases[1:]:
fs = hdfs.hdfs(host, port)
self.assertTrue(fs.fs is orig_fs.fs)
fs.close()
self.assertFalse(orig_fs.closed)
orig_fs.close()
self.assertTrue(orig_fs.closed)
def cache(self):
hdfs.hdfs._CACHE.clear()
orig_fs = hdfs.hdfs(*self.hp_cases[0])
for host, port in self.hp_cases[1:]:
fs = hdfs.hdfs(host, port)
self.assertTrue(fs.fs is orig_fs.fs)
fs.close()
self.assertFalse(orig_fs.closed)
orig_fs.close()
self.assertTrue(orig_fs.closed)
def _hdfs_filesystem():
"""Retrieve references to the local and HDFS file system.
Need to be able to specify host/port. For now, works off defaults.
"""
fs = hdfs("default", 0)
lfs = hdfs("", 0)
try:
yield fs, lfs
finally:
fs.close()
lfs.close()
def cache(self):
for (h1, p1), (h2, p2) in product(self.hp_cases, repeat=2):
hdfs.hdfs._CACHE.clear()
hdfs.hdfs._ALIASES = {"host": {}, "port": {}, "user": {}} # FIXME
with hdfs.hdfs(h1, p1) as fs1:
with hdfs.hdfs(h2, p2) as fs2:
print ' * %r vs %r' % ((h1, p1), (h2, p2))
self.assertTrue(fs2.fs is fs1.fs)
for fs in fs1, fs2:
self.assertFalse(fs.closed)
for fs in fs1, fs2:
self.assertTrue(fs.closed)
def cache(self):
for (h1, p1), (h2, p2) in product(self.hp_cases, repeat=2):
hdfs.hdfs._CACHE.clear()
hdfs.hdfs._ALIASES = {"host": {}, "port": {}, "user": {}} # FIXME
with hdfs.hdfs(h1, p1) as fs1:
with hdfs.hdfs(h2, p2) as fs2:
print ' * %r vs %r' % ((h1, p1), (h2, p2))
self.assertTrue(fs2.fs is fs1.fs)
for fs in fs1, fs2:
self.assertFalse(fs.closed)
for fs in fs1, fs2:
self.assertTrue(fs.closed)
def copyFileToHDFSFolder(localpath, hdfspath):
"""
Copies a file from a local or HDFS to an HDFS location
:param localpath: path to local file
:param hdfspath: path to target file on HDFS
:return: None
"""
if localpath.startswith('file:/'):
lf = H.hdfs("", 0)
else:
lf = H.hdfs()
h = H.hdfs()
lf.copy(localpath, h, hdfspath)
def read(readFlag):
print(readFlag);
if (readFlag == True):
targetFile = config.targetFile.strip()
targetDirectory = config.targetDirectory.strip()
targetPath = config.targetPath
print(targetPath)
# instantiate hadoop
hdfs.hdfs()
# read from hadoop
fileToRead = hdfs.open(targetPath)
print(fileToRead.read())
def save_checkpoint(path, session=None):
if session is None:
session = tf.get_default_session()
if session is None:
raise RuntimeError("no session specified and no current session")
saver = tf.train.Saver()
wd = tempfile.mkdtemp(prefix="pydeep_")
sub_d = hdfs.path.splitext(hdfs.path.basename(path))[0]
abs_d = os.path.join(wd, sub_d)
os.makedirs(abs_d)
saver.save(session, os.path.join(abs_d, Model.CHECKPOINT_NAME))
zip_fn = "%s.zip" % abs_d
shutil.make_archive(*zip_fn.rsplit(".", 1), root_dir=abs_d)
with hdfs.hdfs() as fs, hdfs.hdfs("", 0) as local_fs:
local_fs.copy(zip_fn, fs, path)
def stat_on_local(self):
wd_ = tempfile.mkdtemp(prefix='pydoop_', suffix=UNI_CHR)
p_ = os.path.join(wd_, make_random_str())
if hdfs.default_is_local():
wd, p = wd_, p_
host = "default"
else:
wd, p = ('file:%s' % _ for _ in (wd_, p_))
host = ""
fs = hdfs.hdfs(host, 0)
with fs.open_file(p_, 'w') as fo:
fo.write(make_random_str())
info = fs.get_path_info(p_)
fs.close()
s = hdfs.path.stat(p)
os_s = os.stat(p_)
for n in dir(s):
if n.startswith('st_'):
try:
exp_v = getattr(os_s, n)
except AttributeError:
try:
exp_v = info[self.NMAP[n]]
except KeyError:
continue
self.assertEqual(getattr(s, n), exp_v)
self.__check_extra_args(s, info)
self.__check_wrapper_funcs(p)
hdfs.rmr(wd)
def run(self):
if self.options is None:
raise RuntimeError("You must call parse_cmd_line before run")
if self.logger.isEnabledFor(logging.DEBUG):
self.logger.debug("Running Seqal")
self.logger.debug("Properties:\n%s", "\n".join( sorted([ "%s = %s" % (str(k), str(v)) for k,v in self.properties.iteritems() ]) ))
self.logger.info("Input: %s; Output: %s; reference: %s", self.options.input, self.options.output, self.options.reference)
try:
self.hdfs = phdfs.hdfs('default', 0)
self.__validate()
self.remote_bin_name = tempfile.mktemp(prefix='seqal_bin.', suffix=str(random.random()), dir='')
try:
with self.hdfs.open_file(self.remote_bin_name, 'w') as script:
self.__write_pipes_script(script)
full_name = self.hdfs.get_path_info(self.remote_bin_name)['name']
return seal_utilities.run_pipes(full_name, self.options.input, self.options.output,
properties=self.properties, args_list=self.left_over_args)
finally:
try:
self.hdfs.delete(self.remote_bin_name) # delete the temporary pipes script from HDFS
self.logger.debug("pipes script %s deleted", self.remote_bin_name)
except:
self.logger.error("Error deleting the temporary pipes script %s from HDFS", self.remote_bin_name)
## don't re-raise the exception. We're on our way out
finally:
if self.hdfs:
tmp = self.hdfs
self.hdfs = None
tmp.close()
self.logger.debug("HDFS closed")
def connect(self):
for host, port in self.hp_cases:
for user in self.u_cases:
expected_user = user or CURRENT_USER
fs = hdfs.hdfs(host, port, user=user)
self.assertEqual(fs.user, expected_user)
fs.close()
def build_map(self, top_dir):
"""\
For each subdir (corresponding to an image class), build the full
list of (filename, offset) pair where each bottleneck dump can be
retrieved.
{'dandelion': [
('part-m-00000', 0),
('part-m-00000', 8192),
...
('part-m-00003', 163840)
],
'roses': [
('part-m-00000', 0),
...
]}
"""
m = {}
basename = hdfs.path.basename
with hdfs.hdfs() as fs:
for stat in fs.list_directory(top_dir):
if stat['kind'] != 'directory':
continue
subd = stat['name']
positions = []
for s in fs.list_directory(subd):
bname = basename(s["name"])
if bname.startswith("_"):
continue
assert s["size"] % self.record_size == 0
for i in range(0, s["size"], self.record_size):
positions.append((bname, i))
m[basename(subd)] = positions
return m
def __create_data_file(self):
host, port, path = split_hdfs_path(self.data_file_name)
fs = hdfs(host, port)
f = fs.open_file(path, os.O_WRONLY, 0, 0, 0)
f.write(self.f.getvalue())
f.close()
fs.close()
class StorageHandler:
hdfsobj = hdfs.hdfs()
def __init__(self, host, port):
self.hdfsobj = hdfs.hdfs(host,
port,
user="******",
groups=["vagrant"])
def pwd(self):
return self.hdfsobj.working_directory()
def listDirectory(self, path="/"):
return self.hdfsobj.list_directory(path)
def delete(self, path):
self.hdfsobj.delete(path, False)
def put(self, source, destination):
hdfs.put(source, destination)
def copyFile(self, source, destination):
self.hdfsobj.copy(source, self.hdfsobj, destination)
def write(self, path, mod, data):
with hdfs.open(path, mod) as f:
f.write(data)
def __init__(self, tableName, host='192.168.60.64', infoTable='runInfo'):
self.tableName = tableName
self.conn = happybase.Connection(host)
self.table = self.conn.table(infoTable)
self.eventdb = self.conn.table('HEP:' + tableName)
self.escape = escape()
self.fs = hdfs.hdfs(host=host, port=8022, user='******')
def connect(self):
for host, port in self.hp_cases:
for user in self.u_cases:
expected_user = user or CURRENT_USER
fs = hdfs.hdfs(host, port, user=user)
self.assertEqual(fs.user, expected_user)
fs.close()
def setUp(self):
if hdfs.default_is_local():
self.root = "file:"
else:
fs = hdfs.hdfs("default", 0)
self.root = "hdfs://%s:%s" % (fs.host, fs.port)
fs.close()
def __warn_user_if_wd_maybe_unreadable(self, abs_remote_path):
"""
Check directories above the remote module and issue a warning if
they are not traversable by all users.
The reasoning behind this is mainly aimed at set-ups with a centralized
Hadoop cluster, accessed by all users, and where the Hadoop task tracker
user is not a superuser; an example may be if you're running a shared
Hadoop without HDFS (using only a POSIX shared file system). The task
tracker correctly changes user to the job requester's user for most
operations, but not when initializing the distributed cache, so jobs who
want to place files not accessible by the Hadoop user into dist cache fail.
"""
host, port, path = hdfs.path.split(abs_remote_path)
if host == '' and port == 0: # local file system
host_port = "file:///"
else:
# FIXME: this won't work with any scheme other than hdfs:// (e.g., s3)
host_port = "hdfs://%s:%s/" % (host, port)
path_pieces = path.strip('/').split(os.path.sep)
fs = hdfs.hdfs(host, port)
for i in xrange(0, len(path_pieces)):
part = os.path.join(host_port, os.path.sep.join(path_pieces[0:i+1]))
permissions = fs.get_path_info(part)['permissions']
if permissions & 0111 != 0111:
self.logger.warning(
"the remote module %s may not be readable\n" +
"by the task tracker when initializing the distributed cache.\n" +
"Permissions on path %s: %s", abs_remote_path, part, oct(permissions))
break
def setUp(self):
if hdfs.default_is_local():
self.root = "file:"
else:
fs = hdfs.hdfs("default", 0)
self.root = "hdfs://%s:%s" % (fs.host, fs.port)
fs.close()
def get():
""" Get a handle to pydoop hdfs using the default namenode (specified in hadoop config)
Returns:
Pydoop hdfs handle
"""
return hdfs.hdfs('default', 0, user=project_user())
def __warn_user_if_wd_maybe_unreadable(self, abs_remote_path):
"""
Check directories above the remote module and issue a warning if
they are not traversable by all users.
The reasoning behind this is mainly aimed at set-ups with a
centralized Hadoop cluster, accessed by all users, and where
the Hadoop task tracker user is not a superuser; an example
may be if you're running a shared Hadoop without HDFS (using
only a POSIX shared file system). The task tracker correctly
changes user to the job requester's user for most operations,
but not when initializing the distributed cache, so jobs who
want to place files not accessible by the Hadoop user into
dist cache fail.
"""
host, port, path = hdfs.path.split(abs_remote_path)
if host == '' and port == 0: # local file system
host_port = "file:///"
else:
# FIXME: this won't work with any scheme other than
# hdfs:// (e.g., s3)
host_port = "hdfs://%s:%s/" % (host, port)
path_pieces = path.strip('/').split(os.path.sep)
fs = hdfs.hdfs(host, port)
for i in range(0, len(path_pieces)):
part = os.path.join(host_port,
os.path.sep.join(path_pieces[0:i + 1]))
permissions = fs.get_path_info(part)['permissions']
if permissions & 0o111 != 0o111:
self.logger.warning(
("remote module %s may not be readable by the task "
"tracker when initializing the distributed cache. "
"Permissions on %s: %s"), abs_remote_path, part,
oct(permissions))
break
def stat_on_local(self):
wd_ = tempfile.mkdtemp(prefix='pydoop_', suffix=UNI_CHR)
p_ = os.path.join(wd_, make_random_str())
if hdfs.default_is_local():
wd, p = wd_, p_
host = "default"
else:
wd, p = ('file:%s' % _ for _ in (wd_, p_))
host = ""
fs = hdfs.hdfs(host, 0)
with fs.open_file(p_, 'w') as fo:
fo.write(make_random_str())
info = fs.get_path_info(p_)
fs.close()
s = hdfs.path.stat(p)
os_s = os.stat(p_)
for n in dir(s):
if n.startswith('st_'):
try:
exp_v = getattr(os_s, n)
except AttributeError:
try:
exp_v = info[self.NMAP[n]]
except KeyError:
continue
self.assertEqual(getattr(s, n), exp_v)
self.__check_extra_args(s, info)
self.__check_wrapper_funcs(p)
hdfs.rmr(wd)
def load_checkpoint(path, session=None):
if session is None:
session = tf.get_default_session()
if session is None:
raise RuntimeError("no session specified and no current session")
wd = tempfile.mkdtemp(prefix="pydeep_")
zip_fn = os.path.join(wd, hdfs.path.basename(path))
with hdfs.hdfs() as fs, hdfs.hdfs("", 0) as local_fs:
fs.copy(path, local_fs, zip_fn)
unpack_dir = os.path.splitext(zip_fn)[0]
shutil.unpack_archive(zip_fn, unpack_dir)
ckpt_path = os.path.join(unpack_dir, Model.CHECKPOINT_NAME)
metagraph_path = "%s.meta" % ckpt_path
if not os.path.isfile(metagraph_path):
raise RuntimeError("checkpoint files not found in %s" % zip_fn)
saver = tf.train.import_meta_graph(metagraph_path)
saver.restore(session, ckpt_path)
def __init__(self, context):
super(WholeFileReader, self).__init__(context)
self.logger = LOGGER.getChild("WholeFileReader")
raw_split = context.get_input_split(raw=True)
self.isplit = OpaqueInputSplit().read(io.BytesIO(raw_split))
self.paths = self.isplit.payload
self.n_paths = len(self.paths)
self.fs = hdfs.hdfs()
def clearLocatie():
"""
Removes the locatie parquet table, if it exists
:return: None
"""
h = hdfs()
if h.exists(LOCATIE):
h.delete(LOCATIE)
def clearTelling():
"""
Removes the telling parquet table, if it exists
:return: None
"""
h = hdfs()
if h.exists(TELLING):
h.delete(TELLING)
def get_res(output_dir):
fs = hdfs()
data = []
for x in fs.list_directory(output_dir):
if os.path.split(x['path'])[-1].startswith('part-'):
with fs.open_file(x['path']) as f:
data.append(f.read())
all_data = ''.join(data)
return pts.parse_mr_output(all_data, vtype=int)
def get_res(output_dir):
fs = hdfs()
data = []
for x in fs.list_directory(output_dir):
if os.path.split(x['path'])[-1].startswith('part-'):
with fs.open_file(x['path'], 'rt') as f:
data.append(f.read())
all_data = ''.join(data)
return pts.parse_mr_output(all_data, vtype=int)
def __init__(self, context):
super(FastaReader, self).__init__()
self.logger = logging.getLogger(self.__class__.__name__)
self.isplit = InputSplit(context.getInputSplit())
self.host, self.port, self.fpath = split_hdfs_path(self.isplit.filename)
self.fs = hdfs(self.host, self.port)
self.file = self.fs.open_file(self.fpath, os.O_RDONLY)
self._iterator = (SeqIO.parse(self.file, "fasta") if
self.isplit.offset == 0 else None)
def compute_vc(input_dir):
fs = hdfs()
data = []
for x in fs.list_directory(input_dir):
with fs.open_file(x['path']) as f:
data.append(f.read())
all_data = ''.join(data)
vowels = re.findall('[AEIOUY]', all_data.upper())
return Counter(vowels)
def compute_vc(input_dir):
fs = hdfs()
data = []
for x in fs.list_directory(input_dir):
with fs.open_file(x['path']) as f:
data.append(f.read())
all_data = ''.join(data)
vowels = re.findall('[AEIOUY]', all_data.upper())
return Counter(vowels)
def __init__(self, context):
super(FastaReader, self).__init__()
self.logger = logging.getLogger(self.__class__.__name__)
self.isplit = InputSplit(context.getInputSplit())
self.host, self.port, self.fpath = split_hdfs_path(
self.isplit.filename)
self.fs = hdfs(self.host, self.port)
self.file = self.fs.open_file(self.fpath, os.O_RDONLY)
self._iterator = (SeqIO.parse(self.file, "fasta")
if self.isplit.offset == 0 else None)
def runTest(self):
current_user = getpass.getuser()
cwd = os.getcwd()
os.chdir(tempfile.gettempdir())
for user in None, current_user, "nobody":
expected_user = current_user
fs = hdfs.hdfs("", 0, user=user)
self.assertEqual(fs.user, expected_user)
fs.close()
os.chdir(cwd)
def clearResults(name=""):
"""
Clears target result parquet table name, or all result parquet tables if no name is given
:param name: the target result parquet table name
:return: None
"""
p = path.join(RESULT_DIR, name)
h = hdfs()
if h.exists(p):
h.delete(p)
def runTest(self):
current_user = getpass.getuser()
cwd = os.getcwd()
os.chdir(tempfile.gettempdir())
for user in None, current_user, "nobody":
expected_user = current_user
fs = hdfs.hdfs("", 0, user=user)
self.assertEqual(fs.user, expected_user)
fs.close()
os.chdir(cwd)
def main(directory, topic, byline):
#get a hdfs object
myHdfs = hdfs.hdfs()
myPath = myHdfs.walk(directory)
# a global variable
global producer
# Get a producer object
producer = KafkaProducer(bootstrap_servers=["node4:6667"],
compression_type='gzip',
acks=1,
retries=2)
for myfile in myPath:
#Skip directory recursive
if myfile["kind"] == "directory":
logger.debug("ignoring %s" % (myfile))
continue
elif myfile["kind"] == "file":
pass
else:
raise Exception, "Unknown kind %s for %s" % (myfile["kind"],
myfile["name"])
#Skip name in particoular
if "_SUCCESS" in myfile["name"] or "_temporary" in myfile["name"]:
logger.debug("ignoring %s" % (myfile))
continue
#Skip 0 size files
if myfile["size"] == 0:
logger.debug("ignoring %s" % (myfile))
continue
logger.info("Working on %s" % (myfile["name"]))
#call processChunk if I want to submit chunk
if byline is False:
processChunk(myfile, topic)
else:
#Otherwise submit line by line
processLine(myfile, topic)
#with file open
logger.info("Completed %s" % (myfile["name"]))
#sleep some time
time.sleep(1)
# for all files in HDFS
producer.close()
def get_hosts(self):
if hdfs.default_is_local():
# only run on HDFS
return
hdfs.dump(self.data, self.hdfs_paths[0], mode="wb")
fs = hdfs.hdfs("default", 0)
hs = fs.get_hosts(self.hdfs_paths[0], 0, 10)
self.assertTrue(len(hs) > 0)
self.assertRaises(ValueError, fs.get_hosts, self.hdfs_paths[0], -10,
10)
self.assertRaises(ValueError, fs.get_hosts, self.hdfs_paths[0], 0, -10)
def main():
fs = hdfs.hdfs()
try:
root = "%s/%s" % (fs.working_directory(), TEST_ROOT)
if not isdir(fs, root):
sys.exit("%r does not exist" % root)
print "BS(MB)\tBYTES"
for k, v in usage_by_bs(fs, root).iteritems():
print "%.1f\t%d" % (k / float(MB), v)
finally:
fs.close()
def main():
fs = hdfs.hdfs()
try:
root = "%s/%s" % (fs.working_directory(), TEST_ROOT)
if not isdir(fs, root):
sys.exit("%r does not exist" % root)
print "BS(MB)\tBYTES"
for k, v in usage_by_bs(fs, root).iteritems():
print "%.1f\t%d" % (k / float(MB), v)
finally:
fs.close()
def Get_stock_ticks(code, time_to_market):
import tushare as ts
import pandas as pd
import logging
import datetime as dt
import os
import socket
import pydoop.hdfs as hdfs
import shutil
if time_to_market != 0:
logger = logging.getLogger("D_stock")
logger_handler = logging.FileHandler("/tmp/D_stock.log")
logger_handler.setFormatter(
logging.Formatter("%(asctime)s -- %(message)s"))
logger_handler.setLevel(logging.DEBUG)
logger.setLevel(logging.DEBUG)
logger.addHandler(logger_handler)
logger.info(">" * 15 + code + ">" * 15)
all_days = pd.date_range(start=str(time_to_market),
end=dt.date.today(),
freq="B")
all_days = [x.date() for x in all_days]
for day in all_days[::-1]:
logger.info("Saving " + code + "@" + str(day) + "...")
while True:
try:
df = ts.get_tick_data(code, date=day)
except Exception as e:
print e
continue
break
if df.index.size > 3:
dir_name = "/tmp/ticks/" + str(code)
if not os.path.exists(dir_name):
os.makedirs(dir_name)
file_name = dir_name + "/" + str(day) + ".csv"
df.to_csv(file_name)
"""
Write to HDFS
"""
if os.path.exists(dir_name):
s = hdfs.hdfs(host="spark-1", port=9000)
if not s.exists("ticks"):
s.create_directory("ticks")
hdfs.put(dir_name, "./ticks/")
shutil.rmtree(dir_name)
logger.info("<" * 15 + code + "<" * 15)
return (socket.gethostname(), code)
def get_hosts(self):
if hdfs.default_is_local():
# only run on HDFS
return
hdfs.dump(self.data, self.hdfs_paths[0])
fs = hdfs.hdfs("default", 0)
hs = fs.get_hosts(self.hdfs_paths[0], 0, 10)
self.assertTrue(len(hs) > 0)
self.assertRaises(
ValueError, fs.get_hosts, self.hdfs_paths[0], -10, 10
)
self.assertRaises(ValueError, fs.get_hosts, self.hdfs_paths[0], 0, -10)
def run(self):
if self.options is None:
raise RuntimeError("You must call parse_cmd_line before run")
if self.logger.isEnabledFor(logging.DEBUG):
self.logger.debug("Running Seqal")
self.logger.debug(
"Properties:\n%s", "\n".join(
sorted([
"%s = %s" % (str(k), str(v))
for k, v in self.properties.iteritems()
])))
self.logger.info("Input: %s; Output: %s; reference: %s",
self.options.input, self.options.output,
self.options.reference)
try:
self.hdfs = phdfs.hdfs('default', 0)
self.__validate()
self.remote_bin_name = tempfile.mktemp(prefix='seqal_bin.',
suffix=str(random.random()),
dir='')
try:
with self.hdfs.open_file(self.remote_bin_name, 'w') as script:
self.__write_pipes_script(script)
full_name = self.hdfs.get_path_info(
self.remote_bin_name)['name']
return hadut.run_pipes(full_name,
self.options.input,
self.options.output,
properties=self.properties,
args_list=self.left_over_args)
finally:
try:
self.hdfs.delete(
self.remote_bin_name
) # delete the temporary pipes script from HDFS
self.logger.debug("pipes script %s deleted",
self.remote_bin_name)
except:
self.logger.error(
"Error deleting the temporary pipes script %s from HDFS",
self.remote_bin_name)
## don't re-raise the exception. We're on our way out
finally:
if self.hdfs:
tmp = self.hdfs
self.hdfs = None
tmp.close()
self.logger.debug("HDFS closed")
def main(args):
host, port, out_dir = hdfs.path.split(args.out_dir)
fs = hdfs.hdfs(host, port)
fs.create_directory(out_dir)
join = os.path.join
for dt, path in get_images(args.in_dir):
out_path = join(out_dir, f"{dt.strftime(OUT_FMT)}.png")
if not args.overwrite and fs.exists(out_path):
continue
with io.open(path, "rb") as fi:
with fs.open_file(out_path, "wb") as fo:
fo.write(fi.read())
def copy(self):
local_fs = hdfs.hdfs('', 0)
local_wd = make_wd(local_fs)
from_path = os.path.join(local_wd, uuid.uuid4().hex)
content = uuid.uuid4().hex
with open(from_path, "w") as f:
f.write(content)
to_path = self._make_random_file()
local_fs.copy(from_path, self.fs, to_path)
local_fs.close()
with self.fs.open_file(to_path) as f:
self.assertEqual(f.read(), content)
shutil.rmtree(local_wd)
def main(directory, topic, byline):
#get a hdfs object
myHdfs = hdfs.hdfs()
myPath = myHdfs.walk(directory)
# a global variable
global producer
# Get a producer object
producer = KafkaProducer(bootstrap_servers=["node4:6667"], compression_type='gzip', acks=1, retries=2)
for myfile in myPath:
#Skip directory recursive
if myfile["kind"] == "directory":
logger.debug("ignoring %s" %(myfile))
continue
elif myfile["kind"] == "file":
pass
else:
raise Exception, "Unknown kind %s for %s" %(myfile["kind"], myfile["name"])
#Skip name in particoular
if "_SUCCESS" in myfile["name"] or "_temporary" in myfile["name"]:
logger.debug("ignoring %s" %(myfile))
continue
#Skip 0 size files
if myfile["size"] == 0:
logger.debug("ignoring %s" %(myfile))
continue
logger.info("Working on %s" %(myfile["name"]))
#call processChunk if I want to submit chunk
if byline is False:
processChunk(myfile, topic)
else:
#Otherwise submit line by line
processLine(myfile, topic)
#with file open
logger.info("Completed %s" %(myfile["name"]))
#sleep some time
time.sleep(1)
# for all files in HDFS
producer.close()
def Get_stock_ticks(code, time_to_market):
import tushare as ts
import pandas as pd
import logging
import datetime as dt
import os
import socket
import pydoop.hdfs as hdfs
import shutil
if time_to_market !=0:
logger = logging.getLogger("D_stock")
logger_handler=logging.FileHandler("/tmp/D_stock.log")
logger_handler.setFormatter(logging.Formatter("%(asctime)s -- %(message)s"))
logger_handler.setLevel(logging.DEBUG)
logger.setLevel(logging.DEBUG)
logger.addHandler(logger_handler)
logger.info(">"*15+code+">"*15)
all_days=pd.date_range(start=str(time_to_market),end=dt.date.today(),freq="B")
all_days=[x.date() for x in all_days]
for day in all_days[::-1]:
logger.info("Saving "+code+"@"+str(day)+"...")
while True:
try:
df=ts.get_tick_data(code,date=day)
except Exception as e:
print e
continue
break
if df.index.size >3:
dir_name="/tmp/ticks/"+str(code)
if not os.path.exists(dir_name):
os.makedirs(dir_name)
file_name=dir_name+"/"+str(day)+".csv"
df.to_csv(file_name)
"""
Write to HDFS
"""
if os.path.exists(dir_name):
s=hdfs.hdfs(host="spark-1",port=9000)
if not s.exists("ticks"):
s.create_directory("ticks")
hdfs.put(dir_name,"./ticks/")
shutil.rmtree(dir_name)
logger.info("<"*15+code+"<"*15)
return (socket.gethostname(),code)
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 setUp(self):
wd = tempfile.mkdtemp()
wd_bn = os.path.basename(wd)
self.local_wd = "file:%s" % wd
fs = hdfs.hdfs("default", 0)
fs.create_directory(wd_bn)
self.hdfs_wd = fs.get_path_info(wd_bn)["name"]
fs.close()
basenames = ["test_path_%d" % i for i in xrange(2)]
self.local_paths = ["%s/%s" % (self.local_wd, bn) for bn in basenames]
self.hdfs_paths = ["%s/%s" % (self.hdfs_wd, bn) for bn in basenames]
self.data = make_random_data(4*BUFSIZE + BUFSIZE/2)
for path in self.local_paths:
self.assertTrue(path.startswith("file:"))
for path in self.hdfs_paths:
if not hdfs.default_is_local():
self.assertTrue(path.startswith("hdfs:"))
def stat(self):
if hdfs.default_is_local():
return
bn = '%s%s' % (make_random_str(), UNI_CHR)
fn = '/user/%s/%s' % (DEFAULT_USER, bn)
fs = hdfs.hdfs("default", 0)
p = "hdfs://%s:%s%s" % (fs.host, fs.port, fn)
with fs.open_file(fn, 'w') as fo:
fo.write(make_random_str())
info = fs.get_path_info(fn)
fs.close()
s = hdfs.path.stat(p)
for n1, n2 in self.NMAP.iteritems():
attr = getattr(s, n1, None)
self.assertFalse(attr is None)
self.assertEqual(attr, info[n2])
self.__check_extra_args(s, info)
self.__check_wrapper_funcs(p)
hdfs.rmr(p)
def _clean_up_bcl_output(output_dir):
"""
Delete prq files with no data
"""
host, port, _ = phdfs.path.split(output_dir)
fs = phdfs.hdfs(host, port)
count = 0
for item in fs.walk(output_dir):
if item['kind'] == 'file' and item['name'].endswith('.gz') and item['size'] < 30:
if not item['name'].startswith('hdfs://'):
raise RuntimeError("Insanity! Tring to delete %s!", item['name'])
fs.delete(item['name'], recursive=False)
count += 1
logger.info("Removed %d empty files from bcl output", count)
undet_path = os.path.join(output_dir, 'Undetermined')
if phdfs.path.exists(undet_path):
logger.info("Removing reads from Undetermined dataset %s", undet_path)
fs.delete(undet_path)
def main(argv):
try:
depth = int(argv[1])
span = int(argv[2])
except IndexError:
print "Usage: python %s DEPTH SPAN" % argv[0]
sys.exit(2)
fs = hdfs.hdfs()
try:
root = "%s/%s" % (fs.working_directory(), TEST_ROOT)
try:
fs.delete(root)
except IOError:
pass
fs.create_directory(root)
treegen(fs, root, depth, span)
finally:
fs.close()
def rename_compressed_files(self, file_table):
# find the extension
output_files = hdfs.ls(self.output_path)
if len(output_files) == 0:
return
compressor_extension = self.get_compressor_extension(output_files)
self.log.debug("compressor extension is %s", compressor_extension)
hdfs_host, hdfs_port, _ = hdfs.path.split(output_files[0])
if hdfs_host == '':
is_local_fs = True
else:
is_local_fs = False
output_hdfs = hdfs.hdfs(hdfs_host, hdfs_port)
file_table.seek(0)
for mapid, line in enumerate(file_table.xreadlines()):
_, _, relative_output_name = line.rstrip('\n').split('\t')
# we expect the map task ids to be assigned in the same order as the input
# file list, so we can match the input file to an output file by its position
# in the input file list.
hadoop_output = os.path.join(self.output_path, "part-%05d" % mapid) + compressor_extension
desired_file_name = os.path.join(self.output_path, relative_output_name) + compressor_extension
if hadoop_output != desired_file_name:
self.log.debug("renaming %s to %s", hadoop_output, desired_file_name)
if is_local_fs:
# Though we could transparently use hdfs.move for both local fs and hdfs,
# using native methods for the local fs should be faster.
# os.renames automatically creates necessary parent directories for destination.
os.renames(urlparse(hadoop_output).path, urlparse(desired_file_name).path)
else:
# create the output subdirectory, if necessary
dirname = os.path.dirname(relative_output_name)
if dirname:
output_hdfs.create_directory( os.path.join(self.output_path, dirname) )
if output_hdfs.exists(desired_file_name):
raise RuntimeError("Can't overwrite file in output directory: %s" % desired_file_name)
output_hdfs.move(hadoop_output, output_hdfs, desired_file_name)
def setUp(self):
self.fs = hdfs()
self.wd = utils.make_wd(self.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()
def setUp(self):
self.fs = hdfs.hdfs(self.hdfs_host, self.hdfs_port)
self.wd = utils.make_wd(self.fs)