def autoupdateftp():
ftp_host, ftp_name, ftp_pwd, ftp_path, keep_update_dirs, exclude_dirs, root_dir = read_conf(
)
from ftputil import FTPHost
from ftputil.error import FTPError
from ftputil.error import TemporaryError
try:
ftp_s = FTPHost(ftp_host, ftp_name, ftp_pwd)
except FTPError as e:
print('cannot connect ftp sever ---- ' + str(e))
exit(0)
if ftp_path != '/':
ftp_s.chdir(ftp_path)
try:
ftp_s.keep_alive()
except TemporaryError as e:
print('Program execute exception ---- ' + str(e))
exit(0)
import os
if keep_update_dirs == '/':
if exclude_dirs != '':
download_file(ftp_s, keep_update_dirs, root_dir, exclude_dirs)
else:
download_file(ftp_s, keep_update_dirs, root_dir)
else:
sdirs = keep_update_dirs.split(',')
for dir in sdirs:
download_file(ftp_s, dir.strip(), root_dir + os.sep + dir.strip())
ftp_s.close()
def upload_to_sra(self):
# Print #
print self.s.short_name
# Connect #
print "Connecting..."
ftp = FTPHost(sra.ftp_server, sra.ftp_login, str(sra.ftp_password))
# Make directory #
print "Making directories..."
ftp.makedirs(self.directory)
# Upload #
dest_path = self.directory + self.name
print "Uploading to '%s' (%s)..." % (dest_path, self.s.p.raw_sff.size)
ftp.upload(self.s.p.raw_sff, dest_path)
# Return #
ftp.close()
def upload_to_ena(self):
# Connect #
print "Connecting..."
ftp = FTPHost(ftp_server, ftp_login, str(ftp_password))
# Gzip if not there yet #
if not self.raw_gz.exists:
self.raw.fwd.gzip_to(self.p.raw_forward_gz)
self.raw.rev.gzip_to(self.p.raw_reverse_gz)
# Make directory #
directory = '/ILLUMITAG/run%03d/pool%02d/sample%02d/'
directory = directory % (self.pool.run_num, self.pool.num, self.num)
print "Making directories..."
ftp.makedirs(directory)
# Upload #
base_path = directory + 'run%03d_pool%02d_sample%02d_{}_reads.fastq.gz'
base_path = base_path % (self.pool.run_num, self.pool.num, self.num)
print "Uploading forward..."
ftp.upload(self.p.raw_forward_gz, base_path.format("forward"))
print "Uploading reverse..."
ftp.upload(self.p.raw_reverse_gz, base_path.format("reverse"))
# Return #
ftp.close()
def upload_to_sra(self, verbose=True):
"""They have an FTP site where you should drop the files first"""
# Print #
if verbose: print self.s.short_name + ' (' + self.s.name + ')'
# Connect #
if verbose: print "Connecting..."
ftp = FTPHost(ftp_server, ftp_login, str(ftp_password))
# Gzip if not there yet #
if not self.s.raw_gz.exists:
self.s.raw.fwd.gzip_to(self.s.p.raw_forward_gz)
self.s.raw.rev.gzip_to(self.s.p.raw_reverse_gz)
# Make directory #
if verbose: print "Making directories..."
ftp.makedirs(self.directory)
# Upload #
base_path = self.directory + self.base_name
if verbose: print "Uploading forward..."
ftp.upload(self.s.p.raw_forward_gz, base_path.format("forward"))
if verbose: print "Uploading reverse..."
ftp.upload(self.s.p.raw_reverse_gz, base_path.format("reverse"))
# Return #
ftp.close()
while True:
server = input("Set server address: ")
if server == "":
server = "192.168.0.81"
user = input("User: "******"":
user = "******"
password = input("Password: "******"":
password = "******"
try:
ftp_host = FTPHost(server, user, password)
break
except error.PermanentError as e:
print(e)
actions(ftp_host)
except KeyboardInterrupt:
print("Force exit...")
if ftp_host:
ftp_host.close()
# names = ftp_host.listdir(ftp_host.curdir)
# for name in names:
# if ftp_host.path.isfile(name):
# ftp_host.download(name, name) # remote, local
# # Make a new directory and copy a remote file into it.
# with ftp_host.open("~/test.txt", "rb") as source:
# with ftp_host.open("index.html", "wb") as target:
# ftp_host.copyfileobj(source, target) # similar to shutil.copyfileobj
