#!/usr/bin/env python3 # -*- 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 # ------------------------------------------------------------------------------ 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 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.temp', help="file with 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="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="select old or new precipitation interpolation \ 0 - old method\ 1 - new method (additional subgrid points)") # set directories parser.add_argument("--inputdir", dest="inputdir", type=none_or_str, default=None, help="root directory for storing intermediate files") parser.add_argument("--outputdir", dest="outputdir", type=none_or_str, default=None, help="root directory for storing output files") parser.add_argument("--flexpartdir", dest="flexpartdir", type=none_or_str, default=None, help="FLEXPART root directory (to find grib2flexpart \ and COMMAND file)\n Normally flex_extract resides in \ the scripts directory of the FLEXPART distribution") # 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="specify parent process id for \ rerun of prepare_flexpart") # 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="job template file for submission to ECMWF") parser.add_argument("--queue", dest="queue", type=none_or_str, default=None, help="queue for submission to ECMWF \ (e.g. ecgate or cca )") 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: for k, v in table.items(): 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 == 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