#!/usr/bin/env python
# -*- coding: utf-8 -*-
#*******************************************************************************
# @Author: Anne Philipp (University of Vienna)
#
# @Date: May 2018
#
# @Change History:
# October 2014 - Anne Fouilloux (University of Oslo)
# - created functions silent_remove and product (taken from ECMWF)
#
# November 2015 - Leopold Haimberger (University of Vienna)
# - created functions: interpret_args_and_control, clean_up
# my_error, normal_exit, init128, to_param_id
#
# April - December 2018 - Anne Philipp (University of Vienna):
# - applied PEP8 style guide
# - added documentation
# - moved all non class methods from former file Flexparttools in here
# - seperated args and control interpretation
# - added functions get_list_as_string, read_ecenv, send_mail, make_dir,
# put_file_to_ecserver, submit_job_to_ecserver, get_informations,
# get_dimensions, execute_subprocess, none_or_int, none_or_str
#
# @License:
# (C) Copyright 2014-2019.
# Anne Philipp, Leopold Haimberger
#
# This work is licensed under the Creative Commons Attribution 4.0
# International License. To view a copy of this license, visit
# http://creativecommons.org/licenses/by/4.0/ or send a letter to
# Creative Commons, PO Box 1866, Mountain View, CA 94042, USA.
#
# @Methods:
# none_or_str
# none_or_int
# get_cmdline_args
# read_ecenv
# clean_up
# my_error
# send_mail
# normal_exit
# product
# silent_remove
# init128
# to_param_id
# get_list_as_string
# make_dir
# put_file_to_ecserver
# submit_job_to_ecserver
# get_informations
# get_dimensions
# execute_subprocess
#*******************************************************************************
'''This module contains a collection of diverse tasks within flex_extract.
'''
# ------------------------------------------------------------------------------
# MODULES
# ------------------------------------------------------------------------------
from __future__ import print_function
import os
import errno
import sys
import glob
import subprocess
import traceback
try:
import exceptions
except ImportError:
import builtins as exceptions
from datetime import datetime, timedelta
from argparse import ArgumentParser, ArgumentDefaultsHelpFormatter
# ------------------------------------------------------------------------------
# METHODS
# ------------------------------------------------------------------------------
def setup_controldata():
'''Collects, stores and checks controlling arguments from command line,
CONTROL file and ECMWF_ENV file.
Parameters
----------
Return
------
c : ControlFile
Contains all the parameters of CONTROL file and
command line.
ppid : str
Parent process id.
queue : str
Name of queue for submission to ECMWF (e.g. ecgate or cca )
job_template : str
Name of the job template file for submission to ECMWF server.
'''
import _config
from Classes.ControlFile import ControlFile
args = get_cmdline_args()
c = ControlFile(args.controlfile)
c.assign_args_to_control(args)
if os.path.isfile(_config.PATH_ECMWF_ENV):
env_parameter = read_ecenv(_config.PATH_ECMWF_ENV)
c.assign_envs_to_control(env_parameter)
c.check_conditions(args.queue)
return c, args.ppid, args.queue, args.job_template
def none_or_str(value):
'''Converts the input string into pythons None-type if the string
contains string "None".
Parameters
----------
value : str
String to be checked for the "None" word.
Return
------
None or value:
Return depends on the content of the input value. If it was "None",
then the python type None is returned. Otherwise the string itself.
'''
if value == 'None':
return None
return value
def none_or_int(value):
'''Converts the input string into pythons None-type if the string
contains string "None". Otherwise it is converted to an integer value.
Parameters
----------
value : str
String to be checked for the "None" word.
Return
------
None or int(value):
Return depends on the content of the input value. If it was "None",
then the python type None is returned. Otherwise the string is
converted into an integer value.
'''
if value == 'None':
return None
return int(value)
def get_cmdline_args():
'''Decomposes the command line arguments and assigns them to variables.
Apply default values for non mentioned arguments.
Parameters
----------
Return
------
args : Namespace
Contains the commandline arguments from script/program call.
'''
parser = ArgumentParser(description='Retrieve FLEXPART input from \
ECMWF MARS archive',
formatter_class=ArgumentDefaultsHelpFormatter)
# control parameters that override control file values
parser.add_argument("--start_date", dest="start_date",
type=none_or_str, default=None,
help="start date YYYYMMDD")
parser.add_argument("--end_date", dest="end_date",
type=none_or_str, default=None,
help="end_date YYYYMMDD")
parser.add_argument("--date_chunk", dest="date_chunk",
type=none_or_int, default=None,
help="# of days to be retrieved at once")
parser.add_argument("--job_chunk", dest="job_chunk",
type=none_or_int, default=None,
help="# of days to be retrieved within a single job")
parser.add_argument("--controlfile", dest="controlfile",
type=none_or_str, default='CONTROL_EA5',
help="The file with all CONTROL parameters.")
parser.add_argument("--basetime", dest="basetime",
type=none_or_int, default=None,
help="base such as 0 or 12 (for half day retrievals)")
parser.add_argument("--step", dest="step",
type=none_or_str, default=None,
help="Forecast steps such as 00/to/48")
parser.add_argument("--levelist", dest="levelist",
type=none_or_str, default=None,
help="Vertical levels to be retrieved, e.g. 30/to/60")
parser.add_argument("--area", dest="area",
type=none_or_str, default=None,
help="area defined as north/west/south/east")
# some switches
parser.add_argument("--debug", dest="debug",
type=none_or_int, default=None,
help="debug mode - leave temporary files intact")
parser.add_argument("--oper", dest="oper",
type=none_or_int, default=None,
help='operational mode - prepares dates with '
'environment variables')
parser.add_argument("--request", dest="request",
type=none_or_int, default=None,
help="list all mars requests in file mars_requests.dat")
parser.add_argument("--public", dest="public",
type=none_or_int, default=None,
help="public mode - retrieves the public datasets")
parser.add_argument("--rrint", dest="rrint",
type=none_or_int, default=None,
help='Selection of old or new precipitation '
'interpolation:\n'
' 0 - old method\n'
' 1 - new method (additional subgrid points)')
# set directories
parser.add_argument("--inputdir", dest="inputdir",
type=none_or_str, default=None,
help='Path to the temporary directory for the '
'retrieval grib files and other processing files.')
parser.add_argument("--outputdir", dest="outputdir",
type=none_or_str, default=None,
help='Path to the final directory where the final '
'FLEXPART ready input files are stored.')
# this is only used by prepare_flexpart.py to rerun a postprocessing step
parser.add_argument("--ppid", dest="ppid",
type=none_or_str, default=None,
help='This is the specify parent process id of a '
'single flex_extract run to identify the files. '
'It is the second number in the GRIB files.')
# arguments for job submission to ECMWF, only needed by submit.py
parser.add_argument("--job_template", dest='job_template',
type=none_or_str, default="job.temp",
help='The job template file which are adapted to be '
'submitted to the batch system on ECMWF server.')
parser.add_argument("--queue", dest="queue",
type=none_or_str, default=None,
help='The ECMWF server name for submission of the '
'job script to the batch system '
'(e.g. ecgate | cca | ccb)')
args = parser.parse_args()
return args
def read_ecenv(filepath):
'''Reads the file into a dictionary where the key values are the parameter
names.
Parameters
----------
filepath : str
Path to file where the ECMWF environment parameters are stored.
Return
------
envs : dict
Contains the environment parameter ecuid, ecgid, gateway
and destination for ECMWF server environments.
'''
envs= {}
try:
with open(filepath, 'r') as f:
for line in f:
data = line.strip().split()
envs[str(data[0])] = str(data[1])
except OSError as e:
print('... ERROR CODE: ' + str(e.errno))
print('... ERROR MESSAGE:\n \t ' + str(e.strerror))
sys.exit('\n... Error occured while trying to read ECMWF_ENV '
'file: ' + str(filepath))
return envs
def clean_up(c):
'''Remove files from the intermediate directory (inputdir).
It keeps the final FLEXPART input files if program runs without
ECMWF Api and keywords "ectrans" or "ecstorage" are set to "1".
Parameters
----------
c : ControlFile
Contains all the parameters of CONTROL file and
command line.
Return
------
'''
print("... clean inputdir!")
cleanlist = [file for file in glob.glob(os.path.join(c.inputdir, "*"))
if not os.path.basename(file).startswith(c.prefix)]
if cleanlist:
for element in cleanlist:
silent_remove(element)
print("... done!")
else:
print("... nothing to clean!")
return
def my_error(message='ERROR'):
'''Prints a specified error message which can be passed to the function
before exiting the program.
Parameters
----------
message : str, optional
Error message. Default value is "ERROR".
Return
------
'''
trace = '\n'.join(traceback.format_stack())
full_message = message + '\n\n' + trace
print(full_message)
sys.exit(1)
return
def send_mail(users, success_mode, message):
'''Prints a specific exit message which can be passed to the function.
Parameters
----------
users : list of str
Contains all email addresses which should be notified.
It might also contain just the ecmwf user name which wil trigger
mailing to the associated email address for this user.
success_mode : str
States the exit mode of the program to put into
the mail subject line.
message : str, optional
Message for exiting program. Default value is "Done!".
Return
------
'''
for user in users:
if '${USER}' in user:
user = os.getenv('USER')
try:
p = subprocess.Popen(['mail', '-s flex_extract_v7.1 ' +
success_mode, os.path.expandvars(user)],
stdin=subprocess.PIPE,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
bufsize=1)
pout = p.communicate(input=message.encode() + '\n\n')[0]
except ValueError as e:
print('... ERROR: ' + str(e))
sys.exit('... Email could not be sent!')
except OSError as e:
print('... ERROR CODE: ' + str(e.errno))
print('... ERROR MESSAGE:\n \t ' + str(e.strerror))
sys.exit('... Email could not be sent!')
else:
print('Email sent to ' + os.path.expandvars(user))
return
def normal_exit(message='Done!'):
'''Prints a specific exit message which can be passed to the function.
Parameters
----------
message : str, optional
Message for exiting program. Default value is "Done!".
Return
------
'''
print(str(message))
return
def product(*args, **kwds):
'''Creates combinations of all passed arguments.
This method combines the single characters of the passed arguments
with each other. So that each character of each argument value
will be combined with each character of the other arguments as a tuple.
Note
----
This method is taken from an example at the ECMWF wiki website.
https://software.ecmwf.int/wiki/display/GRIB/index.py; 2018-03-16
Example
-------
product('ABCD', 'xy') --> Ax Ay Bx By Cx Cy Dx Dy
product(range(2), repeat = 3) --> 000 001 010 011 100 101 110 111
Parameters
----------
\*args : list or str
Positional arguments (arbitrary number).
\*\*kwds : dict
Contains all the keyword arguments from \*args.
Return
------
prod : :obj:`tuple`
Return will be done with "yield". A tuple of combined arguments.
See example in description above.
'''
try:
pools = [tuple(arg) for arg in args] * kwds.get('repeat', 1)
result = [[]]
for pool in pools:
result = [x + [y] for x in result for y in pool]
for prod in result:
yield tuple(prod)
except TypeError as e:
sys.exit('... PRODUCT GENERATION FAILED!')
return
def silent_remove(filename):
'''Remove file if it exists.
The function does not fail if the file does not exist.
Parameters
----------
filename : str
The name of the file to be removed without notification.
Return
------
'''
try:
os.remove(filename)
except OSError as e:
# errno.ENOENT = no such file or directory
if e.errno == errno.ENOENT:
pass
else:
raise # re-raise exception if a different error occured
return
def init128(filepath):
'''Opens and reads the grib file with table 128 information.
Parameters
----------
filepath : str
Path to file of ECMWF grib table number 128.
Return
------
table128 : dict
Contains the ECMWF grib table 128 information.
The key is the parameter number and the value is the
short name of the parameter.
'''
table128 = dict()
try:
with open(filepath) as f:
fdata = f.read().split('\n')
except OSError as e:
print('... ERROR CODE: ' + str(e.errno))
print('... ERROR MESSAGE:\n \t ' + str(e.strerror))
sys.exit('\n... Error occured while trying to read parameter '
'table file: ' + str(filepath))
else:
for data in fdata:
if data != '' and data[0] != '!':
table128[data[0:3]] = data[59:65].strip()
return table128
def to_param_id(pars, table):
'''Transform parameter names to parameter ids with ECMWF grib table 128.
Parameters
----------
pars : str
Addpar argument from CONTROL file in the format of
parameter names instead of ids. The parameter short
names are sepearted with "/" and they are passed as
one single string.
table : dict
Contains the ECMWF grib table 128 information.
The key is the parameter number and the value is the
short name of the parameter.
Return
------
ipar : list of int
List of addpar parameters from CONTROL file transformed to
parameter ids in the format of integer.
'''
if not pars:
return []
if not isinstance(pars, str):
pars=str(pars)
cpar = pars.upper().split('/')
ipar = []
for par in cpar:
par = par.strip()
for k, v in table.items():
if par.isdigit():
par = str(int(par)).zfill(3)
if par == k or par == v:
ipar.append(int(k))
break
else:
print('Warning: par ' + par + ' not found in table 128')
return ipar
def to_param_id_with_tablenumber(pars, table):
'''Transform parameter names to parameter ids and add table id.
Conversion with ECMWF grib table 128.
Parameters
----------
pars : str
Addpar argument from CONTROL file in the format of
parameter names instead of ids. The parameter short
names are sepearted with "/" and they are passed as
one single string.
table : dict
Contains the ECMWF grib table 128 information.
The key is the parameter number and the value is the
short name of the parameter.
Return
------
spar : str
List of addpar parameters from CONTROL file transformed to
parameter ids in the format of integer.
'''
if not pars:
return []
if not isinstance(pars, str):
pars=str(pars)
cpar = pars.upper().split('/')
spar = []
for par in cpar:
for k, v in table.items():
if par.isdigit():
par = str(int(par)).zfill(3)
if par == k or par == v:
spar.append(k + '.128')
break
else:
print('\n\n\t\tWarning: par ' + par + ' not found in table 128\n\n')
return '/'.join(spar)
def get_list_as_string(list_obj, concatenate_sign=', '):
'''Converts a list of arbitrary content into a single string.
Parameters
----------
list_obj : list of *
A list with arbitrary content.
concatenate_sign : str, optional
A string which is used to concatenate the single
list elements. Default value is ", ".
Return
------
str_of_list : str
The content of the list as a single string.
'''
if not isinstance(list_obj, list):
list_obj = list(list_obj)
str_of_list = concatenate_sign.join(str(l) for l in list_obj)
return str_of_list
def make_dir(directory):
'''Creates a directory.
It gives a warning if the directory already exists and skips process.
The program stops only if there is another problem.
Parameters
----------
directory : str
The path to directory which should be created.
Return
------
'''
try:
os.makedirs(directory)
except OSError as e:
# errno.EEXIST = directory already exists
if e.errno == errno.EEXIST:
print('WARNING: Directory {0} already exists!'.format(directory))
else:
raise # re-raise exception if a different error occured
return
def put_file_to_ecserver(ecd, filename, target, ecuid, ecgid):
'''Uses the ecaccess-file-put command to send a file to the ECMWF servers.
Note
----
The return value is just for testing reasons. It does not have
to be used from the calling function since the whole error handling
is done in here.
Parameters
----------
ecd : str
The path were the file is stored.
filename : str
The name of the file to send to the ECMWF server.
target : str
The target queue where the file should be sent to.
ecuid : str
The user id on ECMWF server.
ecgid : str
The group id on ECMWF server.
Return
------
'''
try:
subprocess.check_output(['ecaccess-file-put',
ecd + '/' + filename,
target + ':/home/ms/' +
ecgid + '/' + ecuid +
'/' + filename],
stderr=subprocess.STDOUT)
except subprocess.CalledProcessError as e:
print('... ERROR CODE: ' + str(e.returncode))
print('... ERROR MESSAGE:\n \t ' + str(e))
print('\n... Do you have a valid ecaccess certification key?')
sys.exit('... ECACCESS-FILE-PUT FAILED!')
except OSError as e:
print('... ERROR CODE: ' + str(e.errno))
print('... ERROR MESSAGE:\n \t ' + str(e.strerror))
print('\n... Most likely the ECACCESS library is not available!')
sys.exit('... ECACCESS-FILE-PUT FAILED!')
return
def submit_job_to_ecserver(target, jobname):
'''Uses ecaccess-job-submit command to submit a job to the ECMWF server.
Note
----
The return value is just for testing reasons. It does not have
to be used from the calling function since the whole error handling
is done in here.
Parameters
----------
target : str
The target where the file should be sent to, e.g. the queue.
jobname : str
The name of the jobfile to be submitted to the ECMWF server.
Return
------
job_id : int
The id number of the job as a reference at the ecmwf server.
'''
try:
job_id = subprocess.check_output(['ecaccess-job-submit', '-queueName',
target, jobname])
except subprocess.CalledProcessError as e:
print('... ERROR CODE: ' + str(e.returncode))
print('... ERROR MESSAGE:\n \t ' + str(e))
print('\n... Do you have a valid ecaccess certification key?')
sys.exit('... ECACCESS-JOB-SUBMIT FAILED!')
except OSError as e:
print('... ERROR CODE: ' + str(e.errno))
print('... ERROR MESSAGE:\n \t ' + str(e.strerror))
print('\n... Most likely the ECACCESS library is not available!')
sys.exit('... ECACCESS-JOB-SUBMIT FAILED!')
return job_id.decode()
def get_informations(filename):
'''Gets basic information from an example grib file.
These information are important for later use and the
initialization of numpy arrays for data storing.
Parameters
----------
filename : str
Name of the file which will be opened to extract basic information.
Return
------
data : dict
Contains basic informations of the ECMWF grib files, e.g.
'Ni', 'Nj', 'latitudeOfFirstGridPointInDegrees',
'longitudeOfFirstGridPointInDegrees', 'latitudeOfLastGridPointInDegrees',
'longitudeOfLastGridPointInDegrees', 'jDirectionIncrementInDegrees',
'iDirectionIncrementInDegrees', 'missingValue'
'''
from eccodes import codes_grib_new_from_file, codes_get, codes_release
data = {}
# --- open file ---
print("Opening file for getting information data --- %s" % filename)
with open(filename) as f:
# load first message from file
gid = codes_grib_new_from_file(f)
# information needed from grib message
keys = [
'Ni',
'Nj',
'latitudeOfFirstGridPointInDegrees',
'longitudeOfFirstGridPointInDegrees',
'latitudeOfLastGridPointInDegrees',
'longitudeOfLastGridPointInDegrees',
'jDirectionIncrementInDegrees',
'iDirectionIncrementInDegrees',
'missingValue',
]
print('\nInformations are: ')
for key in keys:
# Get the value of the key in a grib message.
data[key] = codes_get(gid,key)
print("%s = %s" % (key,data[key]))
# Free the memory for the message referred as gribid.
codes_release(gid)
return data
def get_dimensions(info, purefc, dtime, index_vals, start_date, end_date):
'''This function specifies the correct dimensions for x, y and t.
Parameters
----------
info : dict
Contains basic informations of the ECMWF grib files, e.g.
'Ni', 'Nj', 'latitudeOfFirstGridPointInDegrees',
'longitudeOfFirstGridPointInDegrees', 'latitudeOfLastGridPointInDegrees',
'longitudeOfLastGridPointInDegrees', 'jDirectionIncrementInDegrees',
'iDirectionIncrementInDegrees', 'missingValue'
purefc : int
Switch for definition of pure forecast mode or not.
dtime : str
Time step in hours.
index_vals : list of list of str
Contains the values from the keys used for a distinct selection
of grib messages in processing the grib files.
Content looks like e.g.:
index_vals[0]: ('20171106', '20171107', '20171108') ; date
index_vals[1]: ('0', '1200', '1800', '600') ; time
index_vals[2]: ('0', '12', '3', '6', '9') ; stepRange
start_date : str
The start date of the retrieval job.
end_date : str
The end date of the retrieval job.
Return
------
(ix, jy, it) : tuple of int
Dimension in x-direction, y-direction and in time.
'''
ix = info['Ni']
jy = info['Nj']
if not purefc:
it = ((end_date - start_date).days + 1) * 24 // int(dtime)
else:
# #no of step * #no of times * #no of days
it = len(index_vals[2]) * len(index_vals[1]) * len(index_vals[0])
return (ix, jy, it)
def execute_subprocess(cmd_list, error_msg='SUBPROCESS FAILED!'):
'''Executes a command line instruction via a subprocess.
Error handling is done if an error occures.
Parameters
----------
cmd_list : list of str
A list of the components for the command line execution. Each
list entry is a single part of the command which is seperated from
the rest by a blank space.
E.g. ['mv', file1, file2]
Return
------
error_msg : str, optional
The possible error message if the subprocess failed.
By default it will just tell "SUBPROCESS FAILED!".
'''
try:
subprocess.check_call(cmd_list)
except subprocess.CalledProcessError as e:
print('... ERROR CODE: ' + str(e.returncode))
print('... ERROR MESSAGE:\n \t ' + str(e))
sys.exit('... ' + error_msg)
except OSError as e:
print('... ERROR CODE: ' + str(e.errno))
print('... ERROR MESSAGE:\n \t ' + str(e.strerror))
sys.exit('... ' + error_msg)
return
def generate_retrieval_period_boundary(c):
'''Generates retrieval period boundary datetimes from CONTROL information.
Parameters
----------
c : ControlFile
Contains all the parameters of CONTROL file and
command line.
Return
------
start_period : datetime
The first timestamp of the actual retrieval period disregarding
the temporary times which were used for processing reasons.
end_period : datetime
The last timestamp of the actual retrieval period disregarding
the temporary times which were used for processing reasons.
'''
# generate start and end timestamp of the retrieval period
start_period = datetime.strptime(c.start_date + c.time[0], '%Y%m%d%H')
start_period = start_period + timedelta(hours=int(c.step[0]))
end_period = datetime.strptime(c.end_date + c.time[-1], '%Y%m%d%H')
end_period = end_period + timedelta(hours=int(c.step[-1]))
return start_period, end_period