[efdb01a] | 1 | #!/usr/bin/env python |
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| 2 | # -*- coding: utf-8 -*- |
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| 3 | #************************************************************************ |
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| 4 | # TODO AP |
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[991df6a] | 5 | # - check myerror |
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| 6 | # - check normalexit |
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| 7 | # - check getListAsString |
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| 8 | # - seperate args and control interpretation |
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[efdb01a] | 9 | #************************************************************************ |
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[991df6a] | 10 | #******************************************************************************* |
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| 11 | # @Author: Anne Philipp (University of Vienna) |
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| 12 | # |
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| 13 | # @Date: May 2018 |
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| 14 | # |
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| 15 | # @Change History: |
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| 16 | # October 2014 - Anne Fouilloux (University of Oslo) |
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| 17 | # - created functions silentremove and product (taken from ECMWF) |
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| 18 | # |
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| 19 | # November 2015 - Leopold Haimberger (University of Vienna) |
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| 20 | # - created functions: interpret_args_and_control, cleanup |
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| 21 | # myerror, normalexit, init128, toparamId |
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| 22 | # |
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| 23 | # April 2018 - Anne Philipp (University of Vienna): |
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| 24 | # - applied PEP8 style guide |
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| 25 | # - added documentation |
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| 26 | # - moved all functions from file FlexpartTools to this file Tools |
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| 27 | # - added function getListAsString |
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| 28 | # |
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| 29 | # @License: |
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| 30 | # (C) Copyright 2014-2018. |
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| 31 | # |
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| 32 | # This software is licensed under the terms of the Apache Licence Version 2.0 |
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| 33 | # which can be obtained at http://www.apache.org/licenses/LICENSE-2.0. |
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| 34 | # |
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| 35 | # @Modul Description: |
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| 36 | # This module contains a couple of helpful functions which are |
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| 37 | # used in different places in flex_extract. |
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| 38 | # |
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| 39 | # @Module Content: |
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| 40 | # - interpret_args_and_control |
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| 41 | # - cleanup |
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| 42 | # - myerror |
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| 43 | # - normalexit |
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| 44 | # - product |
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| 45 | # - silentremove |
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| 46 | # - init128 |
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| 47 | # - toparamId |
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| 48 | # - getListAsString |
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| 49 | # |
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| 50 | #******************************************************************************* |
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[efdb01a] | 51 | |
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| 52 | # ------------------------------------------------------------------------------ |
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| 53 | # MODULES |
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| 54 | # ------------------------------------------------------------------------------ |
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| 55 | import os |
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| 56 | import errno |
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| 57 | import sys |
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| 58 | import glob |
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[991df6a] | 59 | import traceback |
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[efdb01a] | 60 | from numpy import * |
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| 61 | from gribapi import * |
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[991df6a] | 62 | from argparse import ArgumentParser, ArgumentDefaultsHelpFormatter |
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| 63 | |
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| 64 | # software specific class from flex_extract |
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| 65 | from ControlFile import ControlFile |
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[efdb01a] | 66 | |
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| 67 | # ------------------------------------------------------------------------------ |
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| 68 | # FUNCTIONS |
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| 69 | # ------------------------------------------------------------------------------ |
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| 70 | |
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| 71 | def interpret_args_and_control(): |
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| 72 | ''' |
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| 73 | @Description: |
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[991df6a] | 74 | Assigns the command line arguments and reads CONTROL file |
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[efdb01a] | 75 | content. Apply default values for non mentioned arguments. |
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| 76 | |
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| 77 | @Input: |
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| 78 | <nothing> |
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| 79 | |
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| 80 | @Return: |
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| 81 | args: instance of ArgumentParser |
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| 82 | Contains the commandline arguments from script/program call. |
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| 83 | |
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[991df6a] | 84 | c: instance of class ControlFile |
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| 85 | Contains all necessary information of a CONTROL file. The parameters |
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[efdb01a] | 86 | are: DAY1, DAY2, DTIME, MAXSTEP, TYPE, TIME, STEP, CLASS, STREAM, |
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| 87 | NUMBER, EXPVER, GRID, LEFT, LOWER, UPPER, RIGHT, LEVEL, LEVELIST, |
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| 88 | RESOL, GAUSS, ACCURACY, OMEGA, OMEGADIFF, ETA, ETADIFF, DPDETA, |
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| 89 | SMOOTH, FORMAT, ADDPAR, WRF, CWC, PREFIX, ECSTORAGE, ECTRANS, |
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| 90 | ECFSDIR, MAILOPS, MAILFAIL, GRIB2FLEXPART, DEBUG, INPUTDIR, |
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| 91 | OUTPUTDIR, FLEXPART_ROOT_SCRIPTS |
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| 92 | For more information about format and content of the parameter see |
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| 93 | documentation. |
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| 94 | |
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| 95 | ''' |
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| 96 | parser = ArgumentParser(description='Retrieve FLEXPART input from \ |
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| 97 | ECMWF MARS archive', |
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| 98 | formatter_class=ArgumentDefaultsHelpFormatter) |
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| 99 | |
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| 100 | # the most important arguments |
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| 101 | parser.add_argument("--start_date", dest="start_date", |
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| 102 | help="start date YYYYMMDD") |
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| 103 | parser.add_argument("--end_date", dest="end_date", |
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| 104 | help="end_date YYYYMMDD") |
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| 105 | parser.add_argument("--date_chunk", dest="date_chunk", default=None, |
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| 106 | help="# of days to be retrieved at once") |
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| 107 | |
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[991df6a] | 108 | # some arguments that override the default in the CONTROL file |
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[efdb01a] | 109 | parser.add_argument("--basetime", dest="basetime", |
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| 110 | help="base such as 00/12 (for half day retrievals)") |
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| 111 | parser.add_argument("--step", dest="step", |
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| 112 | help="steps such as 00/to/48") |
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| 113 | parser.add_argument("--levelist", dest="levelist", |
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| 114 | help="Vertical levels to be retrieved, e.g. 30/to/60") |
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| 115 | parser.add_argument("--area", dest="area", |
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| 116 | help="area defined as north/west/south/east") |
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| 117 | |
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| 118 | # set the working directories |
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| 119 | parser.add_argument("--inputdir", dest="inputdir", default=None, |
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| 120 | help="root directory for storing intermediate files") |
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| 121 | parser.add_argument("--outputdir", dest="outputdir", default=None, |
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| 122 | help="root directory for storing output files") |
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| 123 | parser.add_argument("--flexpart_root_scripts", dest="flexpart_root_scripts", |
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| 124 | help="FLEXPART root directory (to find grib2flexpart \ |
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| 125 | and COMMAND file)\n\ Normally ECMWFDATA resides in \ |
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| 126 | the scripts directory of the FLEXPART distribution") |
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| 127 | |
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| 128 | # this is only used by prepareFLEXPART.py to rerun a postprocessing step |
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| 129 | parser.add_argument("--ppid", dest="ppid", |
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| 130 | help="Specify parent process id for \ |
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| 131 | rerun of prepareFLEXPART") |
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| 132 | |
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| 133 | # arguments for job submission to ECMWF, only needed by submit.py |
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| 134 | parser.add_argument("--job_template", dest='job_template', |
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| 135 | default="job.temp", |
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| 136 | help="job template file for submission to ECMWF") |
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| 137 | parser.add_argument("--queue", dest="queue", |
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| 138 | help="queue for submission to ECMWF \ |
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| 139 | (e.g. ecgate or cca )") |
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| 140 | parser.add_argument("--controlfile", dest="controlfile", |
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| 141 | default='CONTROL.temp', |
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[991df6a] | 142 | help="file with CONTROL parameters") |
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[efdb01a] | 143 | parser.add_argument("--debug", dest="debug", default=0, |
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| 144 | help="Debug mode - leave temporary files intact") |
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| 145 | |
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| 146 | args = parser.parse_args() |
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| 147 | |
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[991df6a] | 148 | # create instance of ControlFile for specified controlfile |
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[efdb01a] | 149 | # and assign the parameters (and default values if necessary) |
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| 150 | try: |
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[991df6a] | 151 | c = ControlFile(args.controlfile) |
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[efdb01a] | 152 | except IOError: |
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| 153 | try: |
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[991df6a] | 154 | c = ControlFile(localpythonpath + args.controlfile) |
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[efdb01a] | 155 | except: |
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[991df6a] | 156 | print('Could not read CONTROL file "' + args.controlfile + '"') |
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[efdb01a] | 157 | print('Either it does not exist or its syntax is wrong.') |
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| 158 | print('Try "' + sys.argv[0].split('/')[-1] + |
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| 159 | ' -h" to print usage information') |
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| 160 | exit(1) |
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| 161 | |
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| 162 | # check for having at least a starting date |
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| 163 | if args.start_date is None and getattr(c, 'start_date') is None: |
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| 164 | print('start_date specified neither in command line nor \ |
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[991df6a] | 165 | in CONTROL file ' + args.controlfile) |
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[efdb01a] | 166 | print('Try "' + sys.argv[0].split('/')[-1] + |
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| 167 | ' -h" to print usage information') |
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| 168 | exit(1) |
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| 169 | |
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[991df6a] | 170 | # save all existing command line parameter to the ControlFile instance |
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[efdb01a] | 171 | # if parameter is not specified through the command line or CONTROL file |
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| 172 | # set default values |
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| 173 | if args.start_date is not None: |
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| 174 | c.start_date = args.start_date |
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| 175 | if args.end_date is not None: |
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| 176 | c.end_date = args.end_date |
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| 177 | if c.end_date is None: |
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| 178 | c.end_date = c.start_date |
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| 179 | if args.date_chunk is not None: |
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| 180 | c.date_chunk = args.date_chunk |
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| 181 | |
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| 182 | if not hasattr(c, 'debug'): |
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| 183 | c.debug = args.debug |
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| 184 | |
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| 185 | if args.inputdir is None and args.outputdir is None: |
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| 186 | c.inputdir = '../work' |
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| 187 | c.outputdir = '../work' |
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| 188 | else: |
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| 189 | if args.inputdir is not None: |
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| 190 | c.inputdir = args.inputdir |
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| 191 | if args.outputdir is None: |
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| 192 | c.outputdir = args.inputdir |
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| 193 | if args.outputdir is not None: |
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| 194 | c.outputdir = args.outputdir |
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| 195 | if args.inputdir is None: |
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| 196 | c.inputdir = args.outputdir |
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| 197 | |
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| 198 | if hasattr(c, 'outputdir') is False and args.outputdir is None: |
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| 199 | c.outputdir = c.inputdir |
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| 200 | else: |
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| 201 | if args.outputdir is not None: |
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| 202 | c.outputdir = args.outputdir |
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| 203 | |
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| 204 | if args.area is not None: |
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| 205 | afloat = '.' in args.area |
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| 206 | l = args.area.split('/') |
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| 207 | if afloat: |
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| 208 | for i in range(len(l)): |
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| 209 | l[i] = str(int(float(l[i]) * 1000)) |
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| 210 | c.upper, c.left, c.lower, c.right = l |
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| 211 | |
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| 212 | # NOTE: basetime activates the ''operational mode'' |
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| 213 | if args.basetime is not None: |
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| 214 | c.basetime = args.basetime |
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| 215 | |
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| 216 | if args.step is not None: |
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| 217 | l = args.step.split('/') |
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| 218 | if 'to' in args.step.lower(): |
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| 219 | if 'by' in args.step.lower(): |
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| 220 | ilist = arange(int(l[0]), int(l[2]) + 1, int(l[4])) |
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| 221 | c.step = ['{:0>3}'.format(i) for i in ilist] |
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| 222 | else: |
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| 223 | myerror(None, args.step + ':\n' + |
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| 224 | 'please use "by" as well if "to" is used') |
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| 225 | else: |
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| 226 | c.step = l |
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| 227 | |
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| 228 | if args.levelist is not None: |
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| 229 | c.levelist = args.levelist |
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| 230 | if 'to' in c.levelist: |
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| 231 | c.level = c.levelist.split('/')[2] |
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| 232 | else: |
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| 233 | c.level = c.levelist.split('/')[-1] |
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| 234 | |
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| 235 | if args.flexpart_root_scripts is not None: |
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| 236 | c.flexpart_root_scripts = args.flexpart_root_scripts |
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| 237 | |
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| 238 | return args, c |
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| 239 | |
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| 240 | |
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| 241 | def cleanup(c): |
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| 242 | ''' |
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| 243 | @Description: |
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| 244 | Remove all files from intermediate directory |
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[991df6a] | 245 | (inputdir from CONTROL file). |
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[efdb01a] | 246 | |
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| 247 | @Input: |
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[991df6a] | 248 | c: instance of class ControlFile |
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| 249 | Contains all the parameters of CONTROL file, which are e.g.: |
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[efdb01a] | 250 | DAY1(start_date), DAY2(end_date), DTIME, MAXSTEP, TYPE, TIME, |
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| 251 | STEP, CLASS(marsclass), STREAM, NUMBER, EXPVER, GRID, LEFT, |
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| 252 | LOWER, UPPER, RIGHT, LEVEL, LEVELIST, RESOL, GAUSS, ACCURACY, |
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| 253 | OMEGA, OMEGADIFF, ETA, ETADIFF, DPDETA, SMOOTH, FORMAT, |
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| 254 | ADDPAR, WRF, CWC, PREFIX, ECSTORAGE, ECTRANS, ECFSDIR, |
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| 255 | MAILOPS, MAILFAIL, GRIB2FLEXPART, FLEXPARTDIR, BASETIME |
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| 256 | DATE_CHUNK, DEBUG, INPUTDIR, OUTPUTDIR, FLEXPART_ROOT_SCRIPTS |
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| 257 | |
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| 258 | For more information about format and content of the parameter |
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| 259 | see documentation. |
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| 260 | |
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| 261 | @Return: |
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| 262 | <nothing> |
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| 263 | ''' |
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| 264 | |
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| 265 | print("cleanup") |
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| 266 | |
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| 267 | cleanlist = glob.glob(c.inputdir + "/*") |
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| 268 | for cl in cleanlist: |
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| 269 | if c.prefix not in cl: |
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| 270 | silentremove(cl) |
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| 271 | if c.ecapi is False and (c.ectrans == '1' or c.ecstorage == '1'): |
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| 272 | silentremove(cl) |
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| 273 | |
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| 274 | print("Done") |
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| 275 | |
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| 276 | return |
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| 277 | |
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| 278 | |
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| 279 | def myerror(c, message='ERROR'): |
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| 280 | ''' |
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| 281 | @Description: |
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| 282 | Prints a specified error message which can be passed to the function |
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| 283 | before exiting the program. |
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| 284 | |
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| 285 | @Input: |
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[991df6a] | 286 | c: instance of class ControlFile |
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| 287 | Contains all the parameters of CONTROL file, which are e.g.: |
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[efdb01a] | 288 | DAY1(start_date), DAY2(end_date), DTIME, MAXSTEP, TYPE, TIME, |
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| 289 | STEP, CLASS(marsclass), STREAM, NUMBER, EXPVER, GRID, LEFT, |
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| 290 | LOWER, UPPER, RIGHT, LEVEL, LEVELIST, RESOL, GAUSS, ACCURACY, |
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| 291 | OMEGA, OMEGADIFF, ETA, ETADIFF, DPDETA, SMOOTH, FORMAT, |
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| 292 | ADDPAR, WRF, CWC, PREFIX, ECSTORAGE, ECTRANS, ECFSDIR, |
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| 293 | MAILOPS, MAILFAIL, GRIB2FLEXPART, FLEXPARTDIR, BASETIME |
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| 294 | DATE_CHUNK, DEBUG, INPUTDIR, OUTPUTDIR, FLEXPART_ROOT_SCRIPTS |
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| 295 | |
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| 296 | For more information about format and content of the parameter |
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| 297 | see documentation. |
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| 298 | |
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| 299 | message: string, optional |
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| 300 | Error message. Default value is "ERROR". |
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| 301 | |
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| 302 | @Return: |
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| 303 | <nothing> |
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| 304 | ''' |
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| 305 | # uncomment if user wants email notification directly from python |
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| 306 | #try: |
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| 307 | #target = c.mailfail |
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| 308 | #except AttributeError: |
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| 309 | #target = os.getenv('USER') |
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| 310 | |
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| 311 | #if(type(target) is not list): |
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| 312 | #target = [target] |
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| 313 | |
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| 314 | print(message) |
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| 315 | |
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| 316 | # uncomment if user wants email notification directly from python |
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| 317 | #for t in target: |
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| 318 | #p = subprocess.Popen(['mail','-s ECMWFDATA v7.0 ERROR', os.path.expandvars(t)], |
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| 319 | # stdin = subprocess.PIPE, stdout = subprocess.PIPE, |
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| 320 | # stderr = subprocess.PIPE, bufsize = 1) |
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| 321 | #tr = '\n'.join(traceback.format_stack()) |
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| 322 | #pout = p.communicate(input = message+'\n\n'+tr)[0] |
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| 323 | #print 'Email sent to '+os.path.expandvars(t) # +' '+pout.decode() |
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| 324 | |
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| 325 | exit(1) |
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| 326 | |
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| 327 | return |
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| 328 | |
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| 329 | |
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| 330 | def normalexit(c, message='Done!'): |
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| 331 | ''' |
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| 332 | @Description: |
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| 333 | Prints a specific exit message which can be passed to the function. |
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| 334 | |
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| 335 | @Input: |
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[991df6a] | 336 | c: instance of class ControlFile |
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| 337 | Contains all the parameters of CONTROL file, which are e.g.: |
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[efdb01a] | 338 | DAY1(start_date), DAY2(end_date), DTIME, MAXSTEP, TYPE, TIME, |
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| 339 | STEP, CLASS(marsclass), STREAM, NUMBER, EXPVER, GRID, LEFT, |
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| 340 | LOWER, UPPER, RIGHT, LEVEL, LEVELIST, RESOL, GAUSS, ACCURACY, |
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| 341 | OMEGA, OMEGADIFF, ETA, ETADIFF, DPDETA, SMOOTH, FORMAT, |
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| 342 | ADDPAR, WRF, CWC, PREFIX, ECSTORAGE, ECTRANS, ECFSDIR, |
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| 343 | MAILOPS, MAILFAIL, GRIB2FLEXPART, FLEXPARTDIR, BASETIME |
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| 344 | DATE_CHUNK, DEBUG, INPUTDIR, OUTPUTDIR, FLEXPART_ROOT_SCRIPTS |
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| 345 | |
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| 346 | For more information about format and content of the parameter |
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| 347 | see documentation. |
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| 348 | |
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| 349 | message: string, optional |
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| 350 | Message for exiting program. Default value is "Done!". |
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| 351 | |
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| 352 | @Return: |
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| 353 | <nothing> |
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| 354 | |
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| 355 | ''' |
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| 356 | # Uncomment if user wants notification directly from python |
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| 357 | #try: |
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| 358 | #target = c.mailops |
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| 359 | #if(type(target) is not list): |
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| 360 | #target = [target] |
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| 361 | #for t in target: |
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| 362 | #p = subprocess.Popen(['mail','-s ECMWFDATA v7.0 normal exit', |
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| 363 | # os.path.expandvars(t)], |
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| 364 | # stdin = subprocess.PIPE, |
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| 365 | # stdout = subprocess.PIPE, |
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| 366 | # stderr = subprocess.PIPE, bufsize = 1) |
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| 367 | #pout = p.communicate(input = message+'\n\n')[0] |
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| 368 | #print pout.decode() |
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| 369 | #except: |
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| 370 | #pass |
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| 371 | |
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| 372 | print(message) |
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| 373 | |
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| 374 | return |
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| 375 | |
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| 376 | |
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| 377 | def product(*args, **kwds): |
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| 378 | ''' |
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| 379 | @Description: |
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| 380 | This method is taken from an example at the ECMWF wiki website. |
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| 381 | https://software.ecmwf.int/wiki/display/GRIB/index.py; 2018-03-16 |
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| 382 | |
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| 383 | This method combines the single characters of the passed arguments |
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| 384 | with each other. So that each character of each argument value |
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| 385 | will be combined with each character of the other arguments as a tuple. |
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| 386 | |
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| 387 | Example: |
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| 388 | product('ABCD', 'xy') --> Ax Ay Bx By Cx Cy Dx Dy |
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| 389 | product(range(2), repeat = 3) --> 000 001 010 011 100 101 110 111 |
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| 390 | |
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| 391 | @Input: |
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| 392 | *args: tuple |
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| 393 | Positional arguments (arbitrary number). |
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| 394 | |
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| 395 | **kwds: dictionary |
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| 396 | Contains all the keyword arguments from *args. |
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| 397 | |
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| 398 | @Return: |
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| 399 | prod: tuple |
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| 400 | Return will be done with "yield". A tuple of combined arguments. |
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| 401 | See example in description above. |
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| 402 | ''' |
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| 403 | pools = map(tuple, args) * kwds.get('repeat', 1) |
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| 404 | result = [[]] |
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| 405 | for pool in pools: |
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| 406 | result = [x + [y] for x in result for y in pool] |
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| 407 | for prod in result: |
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| 408 | yield tuple(prod) |
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| 409 | |
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| 410 | return |
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| 411 | |
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| 412 | |
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| 413 | def silentremove(filename): |
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| 414 | ''' |
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| 415 | @Description: |
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[991df6a] | 416 | If "filename" exists , it is removed. |
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| 417 | The function does not fail if the file does not exist. |
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[efdb01a] | 418 | |
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| 419 | @Input: |
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| 420 | filename: string |
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| 421 | The name of the file to be removed without notification. |
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| 422 | |
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| 423 | @Return: |
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| 424 | <nothing> |
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| 425 | ''' |
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| 426 | try: |
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| 427 | os.remove(filename) |
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| 428 | except OSError as e: |
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| 429 | # this would be "except OSError, e:" before Python 2.6 |
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| 430 | if e.errno is not errno.ENOENT: |
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| 431 | # errno.ENOENT = no such file or directory |
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| 432 | raise # re-raise exception if a different error occured |
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| 433 | |
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| 434 | return |
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| 435 | |
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| 436 | |
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| 437 | def init128(fn): |
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| 438 | ''' |
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| 439 | @Description: |
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| 440 | Opens and reads the grib file with table 128 information. |
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| 441 | |
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| 442 | @Input: |
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| 443 | fn: string |
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| 444 | Path to file of ECMWF grib table number 128. |
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| 445 | |
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| 446 | @Return: |
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| 447 | table128: dictionary |
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| 448 | Contains the ECMWF grib table 128 information. |
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| 449 | The key is the parameter number and the value is the |
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| 450 | short name of the parameter. |
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| 451 | ''' |
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| 452 | table128 = dict() |
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| 453 | with open(fn) as f: |
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| 454 | fdata = f.read().split('\n') |
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| 455 | for data in fdata: |
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| 456 | if data[0] != '!': |
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| 457 | table128[data[0:3]] = data[59:64].strip() |
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| 458 | |
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| 459 | return table128 |
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| 460 | |
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| 461 | |
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| 462 | def toparamId(pars, table): |
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| 463 | ''' |
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| 464 | @Description: |
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| 465 | Transform parameter names to parameter ids |
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| 466 | with ECMWF grib table 128. |
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| 467 | |
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| 468 | @Input: |
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| 469 | pars: string |
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[991df6a] | 470 | Addpar argument from CONTROL file in the format of |
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[efdb01a] | 471 | parameter names instead of ids. The parameter short |
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| 472 | names are sepearted with "/" and they are passed as |
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| 473 | one single string. |
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| 474 | |
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| 475 | table: dictionary |
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| 476 | Contains the ECMWF grib table 128 information. |
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| 477 | The key is the parameter number and the value is the |
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| 478 | short name of the parameter. |
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| 479 | |
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| 480 | @Return: |
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| 481 | ipar: list of integer |
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[991df6a] | 482 | List of addpar parameters from CONTROL file transformed to |
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[efdb01a] | 483 | parameter ids in the format of integer. |
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| 484 | ''' |
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| 485 | cpar = pars.upper().split('/') |
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| 486 | ipar = [] |
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| 487 | for par in cpar: |
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| 488 | found = False |
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| 489 | for k, v in table.iteritems(): |
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| 490 | if par == k or par == v: |
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| 491 | ipar.append(int(k)) |
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| 492 | found = True |
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| 493 | break |
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| 494 | if found is False: |
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| 495 | print('Warning: par ' + par + ' not found in table 128') |
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| 496 | |
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| 497 | return ipar |
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| 498 | |
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[991df6a] | 499 | def getListAsString(listObj): |
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[efdb01a] | 500 | ''' |
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| 501 | @Description: |
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[991df6a] | 502 | Converts a list of arbitrary content into a single string. |
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| 503 | |
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| 504 | @Input: |
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| 505 | listObj: list |
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| 506 | A list with arbitrary content. |
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| 507 | |
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| 508 | @Return: |
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| 509 | strOfList: string |
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| 510 | The content of the list as a single string. |
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[efdb01a] | 511 | ''' |
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[991df6a] | 512 | |
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| 513 | strOfList = ", ".join( str(l) for l in listObj) |
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| 514 | |
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| 515 | return strOfList |
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