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get_data.py
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import pysftp
import os
import traceback
import logging
import fnmatch
from datetime import datetime
from secret import login_credentials # secret login info in separate file
#from settings import local_settings # local settings info in separate file
from settings import *
# alternatively: enter here
# class login_credentials():
# def __init__(self):
# self.host = "imagen2.cea.fr"
# self.user = "myusername"
# self.pswd = "mypassword"
##### functions
def setup_logger(name, log_file, level):
"""To setup as many loggers as you want"""
handler = logging.FileHandler(log_file)
handler.setFormatter(formatter)
logger = logging.getLogger(name)
logger.setLevel(level)
logger.addHandler(handler)
if level >= logging.INFO:
handler = logging.StreamHandler()
handler.setFormatter(formatter)
logger.addHandler(handler)
return logger
def make_dir(local_path):
if not os.path.exists(local_path):
os.makedirs(local_path)
try:
log_it("directory created: " +local_path, logging.INFO)
except:
pass
def log_it(msg,level):
for lg in logger:
lg.log(level,msg)
lc = login_credentials()
ls = local_settings()
make_dir(ls.local_path)
make_dir(ls.log_path)
now_str = datetime.now().strftime("%Y-%m-%d_%H-%M-%S")
formatter = logging.Formatter('%(asctime)s %(levelname)s %(message)s')
#logging.basicConfig(filename='get_data'+now_str+'.log', level=logging.WARNING)
#logging.basicConfig(filename='get_data'+now_str+'.log', level=logging.WARNING)
# construct to separate loggers for debugging and warning
logger_info = [{"name":'info_logger',"level":logging.INFO},
{"name":'debug_logger',"level":logging.DEBUG}]
logger=[]
for li in logger_info:
logger.append(setup_logger(li["name"], os.path.join(ls.log_path,li["name"]+'_get_data_'+now_str+'.log'), li["level"]))
# info_logger = setup_logger('info_logger', 'info_get_data_'+now_str+'.log', logging.INFO)
# info_logger.info("###logfile for download process (info and warnings)")
# # detailed debug log
# debug_logger = setup_logger('debug_logger', 'debug_get_data_'+now_str+'.log', logging.DEBUG)
# debug_logger.info("###logfile for download process (detailled debugging log)")
try:
with pysftp.Connection(host=lc.host, username=lc.user, password=lc.pswd) as sftp:
log_it("Connection to " + lc.host + " successfully established ... ", logging.INFO)
for dl_i, dl in enumerate(dl_tasks):
try:
log_it("working on: download setting " + str(dl_i+1) +"/" + str(len(dl_tasks))+" : " + dl.description, logging.INFO)
for td in dl.time_dirs:
if dl.mode == "overall":
log_it("downloading complete folders (one folder containing data of many subjects)", logging.INFO)
try:
base_remote_dir = os.path.join(ls.remote_path, td)
if sftp.exists(base_remote_dir):
sftp.chdir(base_remote_dir)
local_dir = os.path.join(ls.local_path, td)
make_dir(local_dir)
for o_dir in dl.overall_dirs:
log_it("downloading folder " + os.path.join(base_remote_dir, o_dir) +
" --> " + os.path.join(local_dir, o_dir), logging.INFO)
try:
if os.path.exists(os.path.join(local_dir,o_dir)):
log_it("local folder " + local_dir +" exists, download is skipped! Check if you already have tha data, delete local folder if you want to re-download ", logging.WARN)
elif not sftp.exists(o_dir):
log_it(os.path.join(base_remote_dir,o_dir) + " does not exist on " + lc.host, logging.WARN)
else:
sftp.get_r(o_dir, local_dir)
log_it("overall folder download successful!",logging.INFO)
except:
log_it("overall folder download not successful!", logging.WARN)
exc_str = traceback.format_exc(limit=3)
log_it(exc_str, logging.DEBUG)
else:
log_it(base_remote_dir + " does not exist on " + lc.host, logging.WARN)
except:
log_it("problem with directory " + base_remote_dir, logging.WARN)
exc_str = traceback.format_exc(limit=3)
log_it(exc_str, logging.DEBUG)
else:
try:
base_remote_dir = os.path.join(ls.remote_path, td, dl.intermed_dir1)
if sftp.exists(base_remote_dir):
sftp.chdir(base_remote_dir)
if len(dl.subjs) == 0:
log_it("getting available subjects from folder " + base_remote_dir, logging.INFO)
subjs = sftp.listdir()
log_it("downloading from " + str(len(subjs)) + " subject directories in " + base_remote_dir, logging.INFO)
else:
subjs = dl.subjs
for subj in subjs:
if dl.mode == "subjects":
local_dir = os.path.join(ls.local_path, td, dl.intermed_dir1)
make_dir(local_dir)
log_it("downloading folder " + os.path.join(base_remote_dir, subj) +
" --> " + os.path.join(local_dir,subj), logging.INFO)
try:
if os.path.exists(os.path.join(local_dir, subj)):
log_it("local folder " + os.path.join(local_dir, subj) + " exists, download is skipped! Check if you already have tha data, delete the local folder if you want to re-download ",
logging.WARN)
elif not sftp.exists(subj):
log_it(os.path.join(base_remote_dir,subj) + " does not exist on " + lc.host,
logging.WARN)
else:
sftp.get_r(subj, local_dir)
log_it("recursive subject download successful! (subject " +subj + ")", logging.INFO)
except:
log_it("subject download not successful! (subject " +subj + ")", logging.WARNING)
exc_str = traceback.format_exc(limit=3)
log_it(exc_str, logging.DEBUG)
#traceback.print_exc(limit=1)
else:
try:
base_remote_dir = os.path.join(ls.remote_path, td, dl.intermed_dir1, subj)
try:
sftp.chdir(base_remote_dir)
log_it("downloading selected content from subject " + subj + " in " +
os.path.join(ls.remote_path, td, dl.intermed_dir1),
logging.INFO)
local_dir = os.path.join(ls.local_path, td, dl.intermed_dir1, subj)
make_dir(local_dir)
except:
log_it("folder " + base_remote_dir + " does not exist on " + lc.host,
logging.WARN)
for dir2 in dl.dirs:
if dl.mode == "dirs":
#l_path = os.path.join(dl.local_path, td, dl.intermed_dir1, subj, dir2)
#make_dir(l_path)
#
#local_dir = os.path.join(dl.local_path)
log_it("downloading folder " + os.path.join(base_remote_dir,dir2) +
" --> " + os.path.join(local_dir,dir2), logging.INFO)
if os.path.exists(os.path.join(local_dir, dir2)):
log_it(
"local folder " + os.path.join(local_dir, dir2) + " exists, download is skipped! Check if you already have tha data, delete the local folder if you want to re-download ",
logging.WARN)
elif not sftp.exists(dir2):
log_it(os.path.join(base_remote_dir, dir2) + " does not exist on " + lc.host,
logging.WARN)
else:
try:
sftp.get_r(dir2, local_dir)
log_it(
"recursive subject download successful! (directory " + dir2 + ")",
logging.INFO)
except:
log_it("folder download not successful!", logging.WARN)
exc_str = traceback.format_exc(limit=3)
log_it(exc_str, logging.DEBUG)
if dl.mode == "files":
dl_dir = os.path.join(ls.remote_path, td, dl.intermed_dir1, subj, dir2)
l_path = os.path.join(ls.local_path, td, dl.intermed_dir1, subj, dir2)
if not sftp.exists(dl_dir):
log_it(dl_dir + " does not exist on " + lc.host,
logging.WARN)
else:
make_dir(l_path)
#get a list of files that satisfies either of dl.subj_files patterns
dl_file_list = set()
for subj_file in dl.subj_files:
dl_file_list.update(set(fnmatch.filter(sftp.listdir(dl_dir), subj_file)))
dl_file_list = list(dl_file_list)
log_it("attempt to download all files matching " +str(dl.subj_files) + " in folder " + dir2, logging.INFO)
for m_file in dl_file_list:
try:
dl_file = os.path.join(dl_dir,m_file)
local_file = os.path.join(l_path, m_file)
log_it("downloading files " + dl_file +
" --> " + local_file, logging.INFO)
#print("remote file:" + dl_file)
#print("local file:" + local_file)
if os.path.exists(local_file):
log_it(
"local folder " + local_file + " exists, download is skipped! Check if you already have tha data, delete the local folder if you want to re-download ",
logging.WARN)
elif not sftp.exists(dl_file):
log_it(dl_file + " does not exist on " + lc.host,
logging.WARN)
else:
try:
sftp.get(dl_file, local_file)
log_it(
"file download successful!",
logging.INFO)
except:
log_it("file download not successful!",
logging.WARN)
exc_str = traceback.format_exc(limit=3)
log_it(exc_str, logging.DEBUG)
except:
log_it("problem downloading file!",logging.WARN)
exc_str = traceback.format_exc(limit=3)
log_it(exc_str, logging.DEBUG)
############### work in progress
except:
log_it("problem with directory " + os.path.join(ls.remote_path, td, dl.intermed_dir1, subj),logging.WARN)
exc_str = traceback.format_exc(limit=3)
log_it(exc_str, logging.DEBUG)
else:
log_it(base_remote_dir + " does not exist on " + lc.host,
logging.WARN)
except:
log_it("problem with directory " + os.path.join(ls.remote_path, td, dl.intermed_dir1), logging.WARN)
exc_str = traceback.format_exc(limit=3)
log_it(exc_str, logging.DEBUG)
except:
log_it("CAUTION: download setting " + str(dl_i + 1) + "/" + str(len(dl_tasks)) + " : " + dl.description + "did not finish without errors!",
logging.WARN)
exc_str = traceback.format_exc(limit=3)
log_it(exc_str, logging.DEBUG)
# connection closed automatically
if sftp._sftp_live == False:
log_it("connection closed", logging.INFO)
except:
log_it("Connection to " + lc.host + " (user:" + lc.user + ") could not be established", logging.WARN)
exc_str = traceback.format_exc(limit=3)
log_it(exc_str, logging.WARN)
#close logging handlers for files to become immediately available
for lgr in logger:
handler = lgr.handlers[0]
lgr.removeHandler(handler)
handler.close()