checkDDBase.py
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import os
import sys
import logging
from lxml import etree
import netCDF4 as nc
import numpy as np
import gzip
import pickle
from datetime import datetime
vi_to_exclude = [
'juno_ephem_orb1',
'juno_fgm_orbfull',
'juno_fgm_orb1',
'juno_fgm_orb60',
'juno_jedi_i090',
'juno_jedi_i180',
'juno_jedi_i270',
'juno_jedi_e270',
'juno_jedi_e180',
'juno_jedi_e090',
'juno_fgm_cruise60',
'ros_magob_1s',
]
def datetime_to_ddtime(date_time):
return "%04d%03d%02d%02d%02d%03d" % (date_time.year, int(date_time.timetuple().tm_yday)-1, date_time.hour, date_time.minute, date_time.second, date_time.microsecond/1000.)
def is_sorted(l):
return all(a <= b for a, b in zip(l, l[1:]))
def check_vi(e, cachedir):
name = e.find("NAME").text
logging.info('========== {} =========='.format(name))
base = e.find("NAME").attrib['base']
if base != 'LOCAL':
return True
location = e.find("LOCATION").text
times = e.find("TIMES").text
info = e.find("INFO").text
cache = e.find("CACHE").text
if name == 'iball_acc_all':
# specific VI used to manage users
return True
cachefile = os.path.join(cachedir, name)
if os.path.isfile(cachefile):
with open(cachefile, 'rb') as handle:
cache_check = pickle.load(handle)
else:
cache_check = {}
if not os.path.isdir(location):
logging.error('{} not exists'.format(location))
return False
times_path = os.path.join(location, times)
info_path = os.path.join(location, info)
cache_path = os.path.join(location, cache)
for f in [times_path, info_path, cache_path]:
if not os.path.isfile(f):
logging.error('{} not exists'.format(f))
return False
ds = nc.Dataset(times_path)
for v in ['StartTime', 'StopTime', 'FileName']:
if v not in ds.variables:
logging.error('Missing {} variable in times file'.format(v))
return False
start_times = []
for st in np.array(ds.variables["StartTime"]):
try:
st_str = "".join([k.decode("UTF-8") for k in st])
start_times.append(int(st_str))
except:
logging.error('Cannot parse StartTime in times file')
return False
stop_times = []
for et in np.array(ds.variables["StopTime"]):
try:
et_str = "".join([k.decode("UTF-8") for k in et])
stop_times.append(int(et_str))
except:
logging.error('Cannot parse StopTime in times file')
return False
files_names = []
for fn in np.array(ds.variables["FileName"]):
try:
fn_str = "".join([k.decode("UTF-8") for k in fn])
files_names.append(fn_str)
except:
logging.error('Cannot parse FileName in times file')
return False
if len(start_times) != len(stop_times) or len(start_times) != len(files_names):
logging.error('Incoherence between variables size in times file')
return False
if len(start_times) == 0:
logging.warning('Dataset is empty')
return True
prev = None
for d in start_times:
if prev:
if d < prev:
logging.warning("Previous start time is higher {}".format(d))
prev = d
prev = None
for d in stop_times:
if prev:
if d < prev:
logging.warning("Previous stop time is higher {}".format(d))
prev = d
for i in range(len(start_times)):
if int(start_times[i]) > int(stop_times[i]):
logging.warning("Start time is higher than Stop time {} - {}".format(start_times[i], stop_times[i]))
if os.path.isfile(os.path.join(location,'LOCK')):
logging.warning("LOCK file detected")
for i in range(len(files_names)):
f = files_names[i]
start = start_times[i]
stop = stop_times[i]
gzipped_f = os.path.join(location, f) + ".gz"
if f in cache_check:
if cache_check[f]['status'] and os.path.getmtime(gzipped_f) == cache_check[f]['mtime']:
continue
logging.info(f)
if not os.path.isfile(gzipped_f):
logging.error("Missing data file {}".format(gzipped_f))
continue
try:
cache_check[f] = {
'status': True,
'mtime': os.path.getmtime(gzipped_f)
}
gf = gzip.open(gzipped_f, 'rb')
ncdata = gf.read()
dds = nc.Dataset("in-mem-file", mode='r', memory=ncdata)
except:
logging.error("Cannot load or extract data file {}".format(gzipped_f))
cache_check[f]['status'] = False
continue
for v in ['Time', 'StartTime', 'StopTime']:
if v not in dds.variables:
logging.error("Missing {} variable in data file {}".format(v, gzipped_f))
cache_check[f]['status'] = False
continue
times = []
for t in np.array(dds.variables["Time"]):
if dds['Time'].dtype == np.float64:
# TimeStamp
t_str = datetime_to_ddtime(datetime.utcfromtimestamp(t))
else:
# DDTime
t_str = "".join([k.decode("UTF-8") for k in t])
times.append(int(t_str))
if len(times) != len(set(times)):
logging.warning("Duplicate times in {}".format(gzipped_f))
cache_check[f]['status'] = False
if not is_sorted(times):
logging.warning("Time not sorted in {}".format(gzipped_f))
cache_check[f]['status'] = False
for t in times:
if t < start or t > stop:
logging.warning("Time outside [StartTime, StopTime] detected in {}".format(gzipped_f))
cache_check[f]['status'] = False
break
with open(cachefile, 'wb') as handle:
pickle.dump(cache_check, handle, protocol=pickle.HIGHEST_PROTOCOL)
return True
def check_ddbase(ddsys, vi=None, cachedir=None):
tree=etree.parse(ddsys)
for e in tree.iter(tag="VI"):
if vi and e.find("NAME").text != vi:
continue
if not vi and e.find("NAME").text in vi_to_exclude:
continue
check_vi(e, cachedir)
if __name__ == '__main__':
logging.basicConfig(format='[%(levelname)s] %(message)s', level=logging.INFO)
ddbase = '/data1/DDBASE'
ddsys = os.path.join(ddbase, 'DATA', 'DDsys.xml')
cachedir = os.path.join(os.path.dirname(__file__), '.cache')
if not os.path.exists(cachedir):
os.makedirs(cachedir)
vi = None
if len(sys.argv) > 1:
vi = sys.argv[1]
check_ddbase(ddsys, vi=vi, cachedir=cachedir)