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harvest_from_thredds.py
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harvest_from_thredds.py
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#!/usr/bin/env python
# This script performs the following actions:
# - subsets of Thredds datasets (see config) are downloaded to local file
# - accumulated precipitation is converted to hourly precipitation
# - downloaded files are finally merged into aggregates:
# <model>_aggrecate.nc
# This script should be run routinely e.g. every 1 hour
# In case of delay/problems, it might help to delete
# everything in download folder
#
# Knut-Frode Dagestad
# MET Norway, Dec 2018
import os
import glob
import json
import sys
import shutil
import requests
from datetime import datetime, timedelta
from netCDF4 import Dataset, num2date
import numpy as np
from nco import Nco
from nco import custom as c
import urllib.request
def get_names_and_urls(name, opt):
fnames = []
urls = []
for days in [-1, 0]: # yesterday and today
for hour in opt['hours']:
time = (datetime.now()+timedelta(days=days))
time = time.replace(hour=hour, minute=0,
second=0, microsecond=0)
if time > datetime.now():
continue
if name == 'norkyst':
# For NorKyst, URLs do not mach beginning of data
time = time + timedelta(hours=24)
fnames.append(time.strftime(name+'_%Y%m%d%H.nc'))
urls.append(time.strftime(opt['url']))
# Remove duplicates
fnames_unique = []
urls_unique = []
for i in range(len(urls)):
if urls[i] not in urls_unique:
urls_unique.append(urls[i])
fnames_unique.append(fnames[i])
return fnames_unique, urls_unique
def download(config):
days_to_keep = config['days_to_keep']
# Download new data
if not os.path.exists(config['download_folder']):
os.mkdir(config['download_folder'])
nco = Nco(debug=True)
for name, opt in config['sources'].items():
if name[0] == '#':
print('Skipping ' + name[1::])
continue
print('='*30)
print(name)
print('-'*30)
sys.stdout.flush()
folder = os.path.join(config['download_folder'], name)
if not os.path.exists(folder):
os.mkdir(folder)
agg_file = os.path.join(folder, name + '_aggregate.nc')
try:
if config['testing'] is True:
opt['opt'].append(opt['subset'])
new_download = False
print(opt['url'])
if opt['url'] == datetime.now().strftime(opt['url']):
###########################
# Download from aggregate
###########################
if 'stride' in opt:
stride = opt['stride']
else:
stride = 1
d = Dataset(opt['url'])
remote_tvar = d.variables['time']
remote_time = num2date(remote_tvar[-2:], remote_tvar.units)
remote_time_step = remote_time[1] - remote_time[0]
local_time_step = remote_time_step*stride
remote_end_time = remote_time[1]
remote_num_times = len(remote_tvar)
if os.path.exists(agg_file):
l = Dataset(agg_file)
local_tvar = l.variables['time']
local_time = num2date(local_tvar[:], local_tvar.units)
if remote_end_time <= local_time[-1] + local_time_step:
print('No new data for %s, last time: %s' % (name, local_time[-1]))
continue
download_from = remote_end_time - timedelta(hours=opt['forecast_hours'])
if download_from > local_time[-1]:
download_from = local_time[-1]
newfile = False
else:
download_from = datetime.now() - timedelta(days=1) # Only 1 day, otherwise too large file
newfile = True
# Find temporal subset to download
last_index = remote_num_times - stride + 1
if stride == 1:
last_index = last_index - 1
first_index = np.int32(last_index - stride*np.ceil((remote_end_time - download_from).total_seconds()/local_time_step.total_seconds()) - 1)
new_times = num2date(remote_tvar[first_index:last_index+1], remote_tvar.units)
if newfile is False:
print('%s ends %s -> downloading %s -> %s' % (name, local_time[-1], new_times[0], new_times[-1]))
else:
print('Downloading new file for %s: %s -> %s' % (name, new_times[0], new_times[-1]))
ts = "-d time,%i,%i" % (first_index, last_index)
if stride > 1:
ts = ts + ',%i' % stride
fname = new_times[0].strftime(name+'_%Y%m%d%H.nc')
fullname = os.path.join(folder, fname)
#if newfile:
# fullname = agg_file
options = opt['opt']
options.append(ts)
options.append("-7") # netCDF4 CLASSIC to avoid file size limitation
options.append("--mk_rec_dmn time") # Make time unlimited for aggregation
nco.ncks(input=opt['url'], output=fullname, options=options)
if os.path.exists(fullname):
new_download = True
d.close()
else:
#################################
# Downloading from single URLS
#################################
fnames, urls = get_names_and_urls(name, opt)
for fname, url in zip(fnames, urls):
fullname = os.path.join(folder, fname)
if os.path.exists(fullname):
print('%s exists, skipping' % fullname)
continue
print('Checking: ' + url)
# Check if URL is available
# Using requests, since .netrc file is needed
resp = requests.get(url + '.das', timeout=3)
if resp.status_code >= 400:
print('Requests: error code %s' % resp.status_code)
continue
# Download from URL
print('Downloading %s from %s...' %
(fullname, url))
try:
nco.ncks(input=url, output=fullname,
options=opt['opt'])
if os.path.exists(fullname):
new_download = True
if name in ['meps', 'aromearctic'] and 'acc' in opt['opt']:
print('Converting accumulated precipitation to hourly')
nco.ncap2(input=fullname, output=fullname,
options=['-O'],
spt='\'precipitation_amount=precipitation_amount_acc(1:$time.size-1,0,:,:)-precipitation_amount_acc(0:$time.size-2,0,:,:)\'')
except Exception as e:
print('DOWNLOAD NOT SUCCESSFUL!')
print(e)
print('STOPPING')
#sys.exit('stop')
##################
# Postprocessing
##################
if new_download is False:
print('No download, hence no postprocessing')
continue
else:
print('Postprocessing downloaded data')
# Remove overlapping times from downloaded files
timestep = opt['timestep']
folder = os.path.join(config['download_folder'], name)
catfolder = os.path.join(folder, 'concatenate')
if not os.path.exists(folder):
os.mkdir(folder)
if not os.path.exists(catfolder):
os.mkdir(catfolder)
print(folder, catfolder)
files = sorted(glob.glob(
os.path.join(folder, name + '_??????????.nc')))
print(files)
if len(files)==0:
continue
times = [datetime.strptime(f[-13:-3], '%Y%m%d%H') for f in files]
print('Making aggregate from: ', name, files)
for i in range(len(times)-1,-1,-1):
print(i, times[i])
filename = files[i]
if times[i] < datetime.now() - timedelta(hours=24*(days_to_keep+1)):
print('Deleting old input file:' + filename)
os.remove(filename)
continue
if i == len(times)-1: # Last file in list
print('Using whole file')
else:
print(times, 'times')
steps = (times[i+1]-times[i]).total_seconds()/(timestep*3600)
print(steps, 'steps')
catfile = os.path.join(catfolder, name +
times[i].strftime('_%Y%m%d%H') +
times[i+1].strftime('_%Y%m%d%H.nc'))
print(catfile, 'catfile')
if not os.path.exists(catfile):
print('Cutting...')
try:
# Cut part of file for later concatenation
nco.ncks(input=filename, output=catfile,
options=['-d time,0,%i' % (steps-1)])
# Delete the contents of original file to save space
os.remove(filename)
# Create empty file, to prevent new download
open(filename, 'a').close()
except:
print('Cutting failed, hence removing input file: ' + filename)
os.remove(filename)
try:
os.remove(catfile)
except:
pass
########################
print('Maintainance')
########################
catfiles = sorted(glob.glob(os.path.join(catfolder, name + '*.nc')))
print(catfiles, 'CATFILES')
for i, f in enumerate(catfiles):
starttime = datetime.strptime(f[len(os.path.join(catfolder+name))+2:-14],
'%Y%m%d%H')
endtime = datetime.strptime(f[-13:-3], '%Y%m%d%H')
if endtime < datetime.now() - timedelta(hours=24*days_to_keep):
print('Deleting old catfile:' + f)
os.remove(f)
previous_endtime = endtime
previous_starttime = starttime
continue
if i>0 and starttime < previous_endtime:
print('Overlapping catfiles, cutting the first: (%s, %s)' %
(catfiles[i-1], catfiles[i]))
steps = (previous_endtime-starttime).total_seconds()/(timestep*3600)
totalsteps = (previous_endtime-previous_starttime).total_seconds()/(timestep*3600)
stepstocut = totalsteps - steps
newname = catfiles[i-1][0:-14] + starttime.strftime('_%Y%m%d%H.nc')
nco.ncks(input=catfiles[i-1], output=newname,
options=['-d time,0,%i' % (stepstocut-1)])
os.remove(catfiles[i-1])
previous_endtime = endtime
previous_starttime = starttime
# Finally, concatenate all files in catfolder + latest-file
print(files, 'FILES')
infiles = sorted(glob.glob(os.path.join(
catfolder, name + '*.nc'))) + [files[-1]]
if len(infiles) > 1:
print('Concatinating: ' + str(infiles))
nco.ncra(output=os.path.join(folder, name + '_aggregate.nc'),
input=infiles,
options=['-Y ncrcat', '-O']) # Since Windows lack link ncrcat -> ncra
# https://sourceforge.net/p/nco/discussion/9830/thread/e8b45a9cdb/
elif len(infiles) == 1:
shutil.copyfile(infiles[0], agg_file)
except Exception as e:
print('Downloading failed:')
print(e)
import traceback
print(traceback.format_exc())
for name, opt in config['sources'].items():
tmpfiles = sorted(glob.glob(os.path.join(config['download_folder'], name, '*.nc*tmp')))
for tmpfile in tmpfiles:
print('Deleting tmp-file: ' + tmpfile)
os.remove(tmpfile)
# Sum up the coverage of aggregates
print()
print('=========================================================')
print('Aggregate files:')
for name, opt in config['sources'].items():
if name[0] != '#':
print(os.path.join(config['download_folder'],
name, name + '_aggregate.nc'))
print('=========================================================')
print('Coverage of aggregate files:')
notify = ''
for name, opt in config['sources'].items():
if name[0] == '#':
continue
timestep = opt['timestep']
folder = os.path.join(config['download_folder'], name)
aggfile = os.path.join(folder, name + '_aggregate.nc')
try:
d = Dataset(aggfile)
except:
print('Missing: ' + aggfile)
continue
times = d.variables['time']
times = num2date(times[:], times.units)
d.close()
minushours = np.round((times[0]-datetime.now()).total_seconds()/3600)
plushours = np.round((times[-1]-datetime.now()).total_seconds()/3600)
expected_steps = (plushours-minushours+1)/timestep
if expected_steps != len(times) and name != 'ecmwf' and False: # NB: temporarily disabled for missing times
warn = 'Expected %d steps, files has %d steps' % (
expected_steps, len(times))
else:
warn = ''
if plushours < 24:
warn += ', short forecast'
else:
warn += ''
if minushours > -24:
warn += ', short history'
else:
warn += ''
summary = ('%12s%11sUTC - %9sUTC (%+d, %+d) %s' %
(name, times[0].strftime('%d %b %H'),
times[-1].strftime('%d %b %H'),
minushours, plushours, warn))
print(summary)
if warn != '':
notify = notify + '\n' + summary
print('=========================================================')
if notify != '' and config['email_notification'] is not None:
try:
import smtplib
FROM = '[email protected]'
TO = [config['email_notification']]
message = """From: %s\nTo: %s\nSubject: %s\n\n%s""" % (
FROM, ', '.join(TO),
'Thredds Harvest - short timeseries', notify)
server = smtplib.SMTP('smtp.met.no', port=25)
server.sendmail(FROM, TO, message)
server.quit()
print('Email sent to ' + TO[0])
print(message)
except Exception as ex:
print('Could not send mail report on missing data')
print(ex)
if __name__ == '__main__':
# Import user specific settings
config_file = sys.argv[1]
with open(config_file) as f:
config = json.load(f)
sys.stdout.flush()
download(config)