1 | #!/usr/bin/env python3 |
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2 | # -*- coding: utf-8 -*- |
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3 | #******************************************************************************* |
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4 | # @Author: Anne Philipp (University of Vienna) |
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5 | # |
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6 | # @Date: May 2018 |
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7 | # |
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8 | # @Change History: |
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9 | # October 2014 - Anne Fouilloux (University of Oslo) |
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10 | # - created functions silent_remove and product (taken from ECMWF) |
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11 | # |
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12 | # November 2015 - Leopold Haimberger (University of Vienna) |
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13 | # - created functions: interpret_args_and_control, clean_up |
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14 | # my_error, normal_exit, init128, to_param_id |
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15 | # |
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16 | # April - December 2018 - Anne Philipp (University of Vienna): |
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17 | # - applied PEP8 style guide |
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18 | # - added documentation |
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19 | # - moved all non class methods from former file Flexparttools in here |
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20 | # - separated args and control interpretation |
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21 | # - added functions get_list_as_string, read_ecenv, send_mail, make_dir, |
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22 | # put_file_to_ecserver, submit_job_to_ecserver, get_informations, |
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23 | # get_dimensions, execute_subprocess, none_or_int, none_or_str |
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24 | # |
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25 | # August 2020 - Leopold Haimberger (University of Vienna) |
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26 | # - added function to check if a specific string is in a file |
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27 | # - added function to overwrite lines in a file which contain specific string |
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28 | # |
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29 | # July 2022 - Anne Tipka (formerly Philipp) |
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30 | # - modified function put_file_to_ecserver to put the file automatically |
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31 | # to $HOME directory, to avoid static path creation |
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32 | # |
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33 | # @License: |
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34 | # (C) Copyright 2014-2020. |
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35 | # Anne Philipp, Leopold Haimberger |
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36 | # |
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37 | # SPDX-License-Identifier: CC-BY-4.0 |
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38 | # |
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39 | # This work is licensed under the Creative Commons Attribution 4.0 |
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40 | # International License. To view a copy of this license, visit |
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41 | # http://creativecommons.org/licenses/by/4.0/ or send a letter to |
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42 | # Creative Commons, PO Box 1866, Mountain View, CA 94042, USA. |
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43 | # |
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44 | # @Methods: |
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45 | # none_or_str |
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46 | # none_or_int |
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47 | # get_cmdline_args |
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48 | # read_ecenv |
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49 | # clean_up |
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50 | # my_error |
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51 | # send_mail |
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52 | # normal_exit |
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53 | # product |
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54 | # silent_remove |
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55 | # init128 |
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56 | # to_param_id |
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57 | # get_list_as_string |
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58 | # make_dir |
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59 | # put_file_to_ecserver |
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60 | # submit_job_to_ecserver |
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61 | # get_informations |
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62 | # get_dimensions |
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63 | # execute_subprocess |
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64 | #******************************************************************************* |
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65 | '''This module contains a collection of diverse tasks within flex_extract. |
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66 | ''' |
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67 | |
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68 | # ------------------------------------------------------------------------------ |
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69 | # MODULES |
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70 | # ------------------------------------------------------------------------------ |
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71 | from __future__ import print_function |
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72 | |
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73 | import os |
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74 | import errno |
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75 | import sys |
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76 | import glob |
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77 | import subprocess |
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78 | import traceback |
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79 | # pylint: disable=unused-import |
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80 | try: |
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81 | import exceptions |
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82 | except ImportError: |
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83 | import builtins as exceptions |
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84 | # pylint: enable=unused-import |
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85 | from datetime import datetime, timedelta |
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86 | from argparse import ArgumentParser, ArgumentDefaultsHelpFormatter |
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87 | |
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88 | # ------------------------------------------------------------------------------ |
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89 | # METHODS |
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90 | # ------------------------------------------------------------------------------ |
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91 | |
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92 | def setup_controldata(): |
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93 | '''Collects, stores and checks controlling arguments from command line, |
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94 | CONTROL file and ECMWF_ENV file. |
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95 | |
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96 | Parameters |
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97 | ---------- |
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98 | |
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99 | Return |
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100 | ------ |
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101 | c : ControlFile |
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102 | Contains all the parameters of CONTROL file and |
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103 | command line. |
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104 | |
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105 | ppid : str |
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106 | Parent process id. |
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107 | |
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108 | queue : str |
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109 | Name of queue for submission to ECMWF (e.g. ecgate or cca ) |
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110 | |
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111 | job_template : str |
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112 | Name of the job template file for submission to ECMWF server. |
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113 | ''' |
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114 | import _config |
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115 | from Classes.ControlFile import ControlFile |
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116 | |
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117 | args = get_cmdline_args() |
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118 | c = ControlFile(args.controlfile) |
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119 | c.assign_args_to_control(args) |
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120 | if os.path.isfile(_config.PATH_ECMWF_ENV): |
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121 | env_parameter = read_ecenv(_config.PATH_ECMWF_ENV) |
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122 | c.assign_envs_to_control(env_parameter) |
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123 | c.check_conditions(args.queue) |
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124 | |
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125 | return c, args.ppid, args.queue, args.job_template |
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126 | |
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127 | def none_or_str(value): |
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128 | '''Converts the input string into Pythons None type if it |
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129 | contains the string "None". |
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130 | |
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131 | Parameters |
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132 | ---------- |
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133 | value : str |
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134 | String to be checked for the "None" word. |
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135 | |
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136 | Return |
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137 | ------ |
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138 | None or value: |
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139 | Return depends on the content of the input value. If it was "None", |
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140 | then the Python type None is returned, otherwise the string itself. |
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141 | ''' |
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142 | if value == 'None': |
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143 | return None |
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144 | return value |
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145 | |
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146 | def none_or_int(value): |
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147 | '''Converts the input string into Pythons None-type if it |
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148 | contains string "None"; otherwise it is converted to an integer value. |
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149 | |
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150 | Parameters |
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151 | ---------- |
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152 | value : str |
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153 | String to be checked for the "None" word. |
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154 | |
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155 | Return |
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156 | ------ |
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157 | None or int(value): |
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158 | Return depends on the content of the input value. If it was "None", |
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159 | then the python type None is returned. Otherwise the string is |
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160 | converted into an integer value. |
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161 | ''' |
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162 | if value == 'None': |
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163 | return None |
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164 | return int(value) |
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165 | |
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166 | def get_cmdline_args(): |
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167 | '''Decomposes the command line arguments and assigns them to variables. |
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168 | Apply default values for arguments not present. |
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169 | |
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170 | Parameters |
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171 | ---------- |
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172 | |
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173 | Return |
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174 | ------ |
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175 | args : Namespace |
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176 | Contains the command line arguments from the script / program call. |
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177 | ''' |
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178 | |
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179 | parser = ArgumentParser(description='Retrieve FLEXPART input from \ |
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180 | ECMWF MARS archive', |
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181 | formatter_class=ArgumentDefaultsHelpFormatter) |
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182 | |
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183 | # control parameters that override control file values |
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184 | parser.add_argument("--start_date", dest="start_date", |
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185 | type=none_or_str, default=None, |
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186 | help="start date YYYYMMDD") |
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187 | parser.add_argument("--end_date", dest="end_date", |
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188 | type=none_or_str, default=None, |
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189 | help="end_date YYYYMMDD") |
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190 | parser.add_argument("--date_chunk", dest="date_chunk", |
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191 | type=none_or_int, default=None, |
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192 | help="# of days to be retrieved at once") |
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193 | parser.add_argument("--job_chunk", dest="job_chunk", |
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194 | type=none_or_int, default=None, |
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195 | help="# of days to be retrieved within a single job") |
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196 | parser.add_argument("--controlfile", dest="controlfile", |
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197 | type=none_or_str, default='CONTROL_EA5', |
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198 | help="The file with all CONTROL parameters.") |
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199 | parser.add_argument("--basetime", dest="basetime", |
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200 | type=none_or_int, default=None, |
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201 | help="base time such as 0 or 12 (for half day retrievals)") |
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202 | parser.add_argument("--step", dest="step", |
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203 | type=none_or_str, default=None, |
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204 | help="Forecast steps such as 00/to/48") |
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205 | parser.add_argument("--levelist", dest="levelist", |
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206 | type=none_or_str, default=None, |
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207 | help="Vertical levels to be retrieved, e.g. 30/to/60") |
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208 | parser.add_argument("--area", dest="area", |
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209 | type=none_or_str, default=None, |
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210 | help="area, defined by north/west/south/east") |
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211 | |
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212 | # some switches |
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213 | parser.add_argument("--debug", dest="debug", |
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214 | type=none_or_int, default=None, |
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215 | help="debug mode - temporary files will be conserved") |
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216 | parser.add_argument("--oper", dest="oper", |
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217 | type=none_or_int, default=None, |
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218 | help='operational mode - prepares dates from ' |
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219 | 'environment variables') |
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220 | parser.add_argument("--request", dest="request", |
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221 | type=none_or_int, default=None, |
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222 | help="list all MARS requests in file mars_requests.dat") |
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223 | parser.add_argument("--public", dest="public", |
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224 | type=none_or_int, default=None, |
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225 | help="public mode - retrieves public datasets") |
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226 | parser.add_argument("--rrint", dest="rrint", |
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227 | type=none_or_int, default=None, |
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228 | help='Selection of old or new ' |
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229 | 'interpolation method for precipitation:\n' |
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230 | ' 0 - old method\n' |
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231 | ' 1 - new method (additional subgrid points)') |
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232 | |
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233 | # set directories |
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234 | parser.add_argument("--inputdir", dest="inputdir", |
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235 | type=none_or_str, default=None, |
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236 | help='Path to temporary directory for ' |
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237 | 'retrieved grib files and other processing files.') |
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238 | parser.add_argument("--outputdir", dest="outputdir", |
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239 | type=none_or_str, default=None, |
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240 | help='Path to final directory where ' |
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241 | 'FLEXPART input files will be stored.') |
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242 | |
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243 | # this is only used by prepare_flexpart.py to rerun a postprocessing step |
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244 | parser.add_argument("--ppid", dest="ppid", |
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245 | type=none_or_str, default=None, |
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246 | help='This is the specify the parent process id of a ' |
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247 | 'single flex_extract run to identify the files. ' |
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248 | 'It is the second number in the GRIB files.') |
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249 | |
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250 | # arguments for job submission to ECMWF, only needed by submit.py |
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251 | parser.add_argument("--job_template", dest='job_template', |
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252 | type=none_or_str, default="job.temp", |
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253 | help='Job template file. Will be used for submission ' |
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254 | 'to the batch system on the ECMWF server after ' |
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255 | 'modification.') |
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256 | parser.add_argument("--queue", dest="queue", |
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257 | type=none_or_str, default=None, |
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258 | help='The name of the ECMWF server name where the' |
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259 | 'job script is to be submitted ' |
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260 | '(e.g. ecgate | cca | ccb)') |
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261 | |
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262 | args = parser.parse_args() |
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263 | |
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264 | return args |
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265 | |
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266 | def read_ecenv(filepath): |
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267 | '''Reads the file into a dictionary where the key values are the parameter |
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268 | names. |
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269 | |
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270 | Parameters |
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271 | ---------- |
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272 | filepath : str |
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273 | Path to file where the ECMWF environment parameters are stored. |
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274 | |
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275 | Return |
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276 | ------ |
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277 | envs : dict |
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278 | Contains the environment parameter ecuid, ecgid, gateway |
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279 | and destination for ECMWF server environments. |
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280 | ''' |
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281 | envs = {} |
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282 | try: |
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283 | with open(filepath, 'r') as f: |
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284 | for line in f: |
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285 | data = line.strip().split() |
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286 | envs[str(data[0])] = str(data[1]) |
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287 | except OSError as e: |
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288 | print('... ERROR CODE: ' + str(e.errno)) |
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289 | print('... ERROR MESSAGE:\n \t ' + str(e.strerror)) |
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290 | |
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291 | sys.exit('\n... Error occured while trying to read ECMWF_ENV ' |
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292 | 'file: ' + str(filepath)) |
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293 | |
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294 | return envs |
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295 | |
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296 | def clean_up(c): |
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297 | '''Remove files from the intermediate directory (inputdir). |
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298 | |
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299 | It keeps the final FLEXPART input files if program runs without |
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300 | ECMWF API and keywords "ectrans" or "ecstorage" are set to "1". |
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301 | |
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302 | Parameters |
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303 | ---------- |
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304 | c : ControlFile |
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305 | Contains all the parameters of CONTROL file and |
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306 | command line. |
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307 | |
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308 | Return |
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309 | ------ |
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310 | |
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311 | ''' |
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312 | |
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313 | print("... clean inputdir!") |
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314 | |
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315 | cleanlist = [filename for filename in |
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316 | glob.glob(os.path.join(c.inputdir, "*")) |
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317 | if not os.path.basename(filename).startswith(c.prefix)] |
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318 | |
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319 | if cleanlist: |
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320 | for element in cleanlist: |
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321 | silent_remove(element) |
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322 | print("... done!") |
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323 | else: |
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324 | print("... nothing to clean!") |
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325 | |
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326 | return |
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327 | |
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328 | |
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329 | def my_error(message='ERROR'): |
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330 | '''Prints a specified error message which can be passed to the function |
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331 | before exiting the program. |
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332 | |
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333 | Parameters |
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334 | ---------- |
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335 | message : str, optional |
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336 | Error message. Default value is "ERROR". |
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337 | |
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338 | Return |
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339 | ------ |
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340 | |
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341 | ''' |
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342 | |
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343 | trace = '\n'.join(traceback.format_stack()) |
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344 | full_message = message + '\n\n' + trace |
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345 | |
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346 | print(full_message) |
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347 | |
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348 | sys.exit(1) |
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349 | |
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350 | return |
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351 | |
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352 | |
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353 | def send_mail(users, success_mode, message): |
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354 | '''Prints a specific exit message which can be passed to the function. |
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355 | |
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356 | Parameters |
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357 | ---------- |
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358 | users : list of str |
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359 | Contains all email addresses which should be notified. |
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360 | It might also contain just the ecmwf user name which wil trigger |
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361 | mailing to the associated email address for this user. |
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362 | |
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363 | success_mode : str |
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364 | States the exit mode of the program to put into |
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365 | the mail subject line. |
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366 | |
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367 | message : str, optional |
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368 | Message for exiting program. Default value is "Done!". |
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369 | |
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370 | Return |
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371 | ------ |
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372 | |
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373 | ''' |
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374 | |
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375 | for user in users: |
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376 | if '${USER}' in user: |
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377 | user = os.getenv('USER') |
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378 | try: |
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379 | p = subprocess.Popen(['mail', '-s flex_extract_v7.1 ' + |
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380 | success_mode, os.path.expandvars(user)], |
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381 | stdin=subprocess.PIPE, |
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382 | stdout=subprocess.PIPE, |
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383 | stderr=subprocess.PIPE, |
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384 | bufsize=1) |
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385 | pout = p.communicate(input=message + '\n\n')[0] |
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386 | except ValueError as e: |
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387 | print('... ERROR: ' + str(e)) |
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388 | sys.exit('... Email could not be sent!') |
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389 | except OSError as e: |
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390 | print('... ERROR CODE: ' + str(e.errno)) |
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391 | print('... ERROR MESSAGE:\n \t ' + str(e.strerror)) |
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392 | sys.exit('... Email could not be sent!') |
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393 | else: |
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394 | print('Email sent to ' + os.path.expandvars(user)) |
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395 | |
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396 | return |
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397 | |
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398 | |
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399 | def normal_exit(message='Done!'): |
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400 | '''Prints a specific exit message which can be passed to the function. |
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401 | |
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402 | Parameters |
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403 | ---------- |
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404 | message : str, optional |
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405 | Message for exiting program. Default value is "Done!". |
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406 | |
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407 | Return |
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408 | ------ |
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409 | |
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410 | ''' |
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411 | |
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412 | print(str(message)) |
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413 | |
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414 | return |
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415 | |
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416 | |
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417 | def product(*args, **kwds): |
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418 | '''Creates combinations of all passed arguments. |
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419 | |
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420 | This method combines the single characters of the passed arguments |
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421 | with each other in a way that each character of each argument value |
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422 | will be combined with each character of the other arguments as a tuple. |
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423 | |
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424 | Note |
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425 | ---- |
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426 | This method is taken from an example at the ECMWF wiki website. |
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427 | https://software.ecmwf.int/wiki/display/GRIB/index.py; 2018-03-16 |
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428 | |
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429 | It was released under the following license: |
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430 | https://confluence.ecmwf.int/display/ECC/License |
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431 | |
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432 | Example |
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433 | ------- |
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434 | product('ABCD', 'xy') --> Ax Ay Bx By Cx Cy Dx Dy |
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435 | |
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436 | product(range(2), repeat = 3) --> 000 001 010 011 100 101 110 111 |
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437 | |
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438 | Parameters |
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439 | ---------- |
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440 | \*args : list or str |
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441 | Positional arguments (arbitrary number). |
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442 | |
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443 | \*\*kwds : dict |
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444 | Contains all the keyword arguments from \*args. |
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445 | |
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446 | Return |
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447 | ------ |
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448 | prod : :obj:`tuple` |
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449 | Return will be done with "yield". A tuple of combined arguments. |
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450 | See example in description above. |
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451 | ''' |
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452 | try: |
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453 | pools = [tuple(arg) for arg in args] * kwds.get('repeat', 1) |
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454 | result = [[]] |
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455 | for pool in pools: |
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456 | result = [x + [y] for x in result for y in pool] |
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457 | for prod in result: |
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458 | yield tuple(prod) |
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459 | except TypeError as e: |
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460 | sys.exit('... PRODUCT GENERATION FAILED!') |
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461 | |
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462 | return |
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463 | |
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464 | |
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465 | def silent_remove(filename): |
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466 | '''Remove file if it exists. |
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467 | The function does not fail if the file does not exist. |
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468 | |
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469 | Parameters |
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470 | ---------- |
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471 | filename : str |
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472 | The name of the file to be removed without notification. |
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473 | |
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474 | Return |
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475 | ------ |
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476 | |
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477 | ''' |
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478 | try: |
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479 | os.remove(filename) |
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480 | except OSError as e: |
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481 | # errno.ENOENT = no such file or directory |
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482 | if e.errno == errno.ENOENT: |
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483 | pass |
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484 | else: |
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485 | raise # re-raise exception if a different error occured |
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486 | |
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487 | return |
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488 | |
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489 | |
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490 | def init128(filepath): |
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491 | '''Opens and reads the grib file with table 128 information. |
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492 | |
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493 | Parameters |
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494 | ---------- |
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495 | filepath : str |
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496 | Path to file of ECMWF grib table number 128. |
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497 | |
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498 | Return |
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499 | ------ |
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500 | table128 : dict |
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501 | Contains the ECMWF grib table 128 information. |
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502 | The key is the parameter number and the value is the |
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503 | short name of the parameter. |
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504 | ''' |
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505 | table128 = dict() |
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506 | try: |
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507 | with open(filepath) as f: |
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508 | fdata = f.read().split('\n') |
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509 | except OSError as e: |
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510 | print('... ERROR CODE: ' + str(e.errno)) |
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511 | print('... ERROR MESSAGE:\n \t ' + str(e.strerror)) |
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512 | |
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513 | sys.exit('\n... Error occured while trying to read parameter ' |
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514 | 'table file: ' + str(filepath)) |
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515 | else: |
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516 | for data in fdata: |
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517 | if data != '' and data[0] != '!': |
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518 | table128[data[0:3]] = data[59:65].strip() |
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519 | |
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520 | return table128 |
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521 | |
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522 | |
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523 | def to_param_id(pars, table): |
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524 | '''Transform parameter names to parameter ids with ECMWF grib table 128. |
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525 | |
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526 | Parameters |
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527 | ---------- |
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528 | pars : str |
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529 | Addpar argument from CONTROL file in the format of |
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530 | parameter names instead of IDs. The parameter short |
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531 | names are separated by "/" and passed as one single string. |
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532 | |
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533 | table : dict |
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534 | Contains the ECMWF grib table 128 information. |
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535 | The key is the parameter number and the value is the |
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536 | short name of the parameter. |
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537 | |
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538 | Return |
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539 | ------ |
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540 | ipar : list of int |
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541 | List of addpar parameters from CONTROL file transformed to |
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542 | parameter ids in the format of integer. |
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543 | ''' |
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544 | if not pars: |
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545 | return [] |
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546 | if not isinstance(pars, str): |
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547 | pars = str(pars) |
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548 | |
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549 | cpar = pars.upper().split('/') |
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550 | ipar = [] |
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551 | for par in cpar: |
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552 | par = par.strip() |
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553 | for k, v in table.items(): |
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554 | if par.isdigit(): |
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555 | par = str(int(par)).zfill(3) |
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556 | if par == k or par == v: |
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557 | ipar.append(int(k)) |
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558 | break |
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559 | else: |
---|
560 | print('Warning: par ' + par + ' not found in table 128') |
---|
561 | |
---|
562 | return ipar |
---|
563 | |
---|
564 | def to_param_id_with_tablenumber(pars, table): |
---|
565 | '''Transform parameter names to parameter IDs and add table ID. |
---|
566 | |
---|
567 | Conversion with ECMWF grib table 128. |
---|
568 | |
---|
569 | Parameters |
---|
570 | ---------- |
---|
571 | pars : str |
---|
572 | Addpar argument from CONTROL file in the format of |
---|
573 | parameter names instead of ID. The parameter short |
---|
574 | names are separated by "/" and passed as one single string. |
---|
575 | |
---|
576 | table : dict |
---|
577 | Contains the ECMWF grib table 128 information. |
---|
578 | The key is the parameter number and the value is the |
---|
579 | short name of the parameter. |
---|
580 | |
---|
581 | Return |
---|
582 | ------ |
---|
583 | spar : str |
---|
584 | List of addpar parameters from CONTROL file transformed to |
---|
585 | parameter IDs in the format of integer. |
---|
586 | ''' |
---|
587 | if not pars: |
---|
588 | return [] |
---|
589 | if not isinstance(pars, str): |
---|
590 | pars = str(pars) |
---|
591 | |
---|
592 | cpar = pars.upper().split('/') |
---|
593 | spar = [] |
---|
594 | for par in cpar: |
---|
595 | for k, v in table.items(): |
---|
596 | if par.isdigit(): |
---|
597 | par = str(int(par)).zfill(3) |
---|
598 | if par == k or par == v: |
---|
599 | spar.append(k + '.128') |
---|
600 | break |
---|
601 | else: |
---|
602 | print('\n\n\t\tWarning: par ' + par + ' not found in table 128\n\n') |
---|
603 | |
---|
604 | return '/'.join(spar) |
---|
605 | |
---|
606 | def get_list_as_string(list_obj, concatenate_sign=', '): |
---|
607 | '''Converts a list of arbitrary content into a single string using a given |
---|
608 | concatenation character. |
---|
609 | |
---|
610 | Parameters |
---|
611 | ---------- |
---|
612 | list_obj : list of * |
---|
613 | A list with arbitrary content. |
---|
614 | |
---|
615 | concatenate_sign : str, optional |
---|
616 | A string which is used to concatenate the single |
---|
617 | list elements. Default value is ", ". |
---|
618 | |
---|
619 | Return |
---|
620 | ------ |
---|
621 | str_of_list : str |
---|
622 | The content of the list as a single string. |
---|
623 | ''' |
---|
624 | |
---|
625 | if not isinstance(list_obj, list): |
---|
626 | list_obj = list(list_obj) |
---|
627 | str_of_list = concatenate_sign.join(str(l) for l in list_obj) |
---|
628 | |
---|
629 | return str_of_list |
---|
630 | |
---|
631 | def make_dir(directory): |
---|
632 | '''Creates a directory. |
---|
633 | |
---|
634 | If the directory already exists, an information is printed and the creation |
---|
635 | skipped. The program stops only if there is another problem. |
---|
636 | |
---|
637 | Parameters |
---|
638 | ---------- |
---|
639 | directory : str |
---|
640 | The path to directory which should be created. |
---|
641 | |
---|
642 | Return |
---|
643 | ------ |
---|
644 | |
---|
645 | ''' |
---|
646 | try: |
---|
647 | os.makedirs(directory) |
---|
648 | except OSError as e: |
---|
649 | # errno.EEXIST = directory already exists |
---|
650 | if e.errno == errno.EEXIST: |
---|
651 | print('INFORMATION: Directory {0} already exists!'.format(directory)) |
---|
652 | else: |
---|
653 | raise # re-raise exception if a different error occured |
---|
654 | |
---|
655 | return |
---|
656 | |
---|
657 | def put_file_to_ecserver(ecd, filename): |
---|
658 | '''Uses the ecaccess-file-put command to send a file to the ECMWF servers. |
---|
659 | |
---|
660 | Note |
---|
661 | ---- |
---|
662 | The return value is just for testing reasons. It does not have |
---|
663 | to be used from the calling function since the whole error handling |
---|
664 | is done in here. |
---|
665 | |
---|
666 | Parameters |
---|
667 | ---------- |
---|
668 | ecd : str |
---|
669 | The path were the file is stored. |
---|
670 | |
---|
671 | filename : str |
---|
672 | The name of the file to send to the ECMWF server. |
---|
673 | |
---|
674 | Return |
---|
675 | ------ |
---|
676 | |
---|
677 | ''' |
---|
678 | |
---|
679 | try: |
---|
680 | subprocess.check_output(['ecaccess-file-put', |
---|
681 | ecd + '/' + filename], |
---|
682 | stderr=subprocess.STDOUT) |
---|
683 | except subprocess.CalledProcessError as e: |
---|
684 | print('... ERROR CODE: ' + str(e.returncode)) |
---|
685 | print('... ERROR MESSAGE:\n \t ' + str(e)) |
---|
686 | |
---|
687 | print('\n... Do you have a valid ecaccess certification key?') |
---|
688 | sys.exit('... ECACCESS-FILE-PUT FAILED!') |
---|
689 | except OSError as e: |
---|
690 | print('... ERROR CODE: ' + str(e.errno)) |
---|
691 | print('... ERROR MESSAGE:\n \t ' + str(e.strerror)) |
---|
692 | |
---|
693 | print('\n... Most likely the ECACCESS library is not available!') |
---|
694 | sys.exit('... ECACCESS-FILE-PUT FAILED!') |
---|
695 | |
---|
696 | return |
---|
697 | |
---|
698 | def submit_job_to_ecserver(target, jobname): |
---|
699 | '''Uses ecaccess-job-submit command to submit a job to the ECMWF server. |
---|
700 | |
---|
701 | Note |
---|
702 | ---- |
---|
703 | The return value is just for testing reasons. It does not have |
---|
704 | to be used from the calling function since the whole error handling |
---|
705 | is done in here. |
---|
706 | |
---|
707 | Parameters |
---|
708 | ---------- |
---|
709 | target : str |
---|
710 | The target where the file should be sent to, e.g. the queue. |
---|
711 | |
---|
712 | jobname : str |
---|
713 | The name of the jobfile to be submitted to the ECMWF server. |
---|
714 | |
---|
715 | Return |
---|
716 | ------ |
---|
717 | job_id : int |
---|
718 | The id number of the job as a reference at the ECMWF server. |
---|
719 | ''' |
---|
720 | |
---|
721 | try: |
---|
722 | job_id = subprocess.check_output(['ecaccess-job-submit', '-queueName', |
---|
723 | target, jobname]) |
---|
724 | |
---|
725 | except subprocess.CalledProcessError as e: |
---|
726 | print('... ERROR CODE: ' + str(e.returncode)) |
---|
727 | print('... ERROR MESSAGE:\n \t ' + str(e)) |
---|
728 | |
---|
729 | print('\n... Do you have a valid ecaccess certification key?') |
---|
730 | sys.exit('... ecaccess-job-submit FAILED!') |
---|
731 | except OSError as e: |
---|
732 | print('... ERROR CODE: ' + str(e.errno)) |
---|
733 | print('... ERROR MESSAGE:\n \t ' + str(e.strerror)) |
---|
734 | |
---|
735 | print('\n... Most likely the ECACCESS library is not available!') |
---|
736 | sys.exit('... ecaccess-job-submit FAILED!') |
---|
737 | |
---|
738 | return job_id.decode() |
---|
739 | |
---|
740 | |
---|
741 | def get_informations(filename): |
---|
742 | '''Extracts basic information from a sample grib file. |
---|
743 | |
---|
744 | This information is needed for later use and the |
---|
745 | initialization of numpy arrays where data are stored. |
---|
746 | |
---|
747 | Parameters |
---|
748 | ---------- |
---|
749 | filename : str |
---|
750 | Name of the file which will be opened to extract basic information. |
---|
751 | |
---|
752 | Return |
---|
753 | ------ |
---|
754 | data : dict |
---|
755 | Contains basic informations of the ECMWF grib files, e.g. |
---|
756 | 'Ni', 'Nj', 'latitudeOfFirstGridPointInDegrees', |
---|
757 | 'longitudeOfFirstGridPointInDegrees', 'latitudeOfLastGridPointInDegrees', |
---|
758 | 'longitudeOfLastGridPointInDegrees', 'jDirectionIncrementInDegrees', |
---|
759 | 'iDirectionIncrementInDegrees', 'missingValue' |
---|
760 | ''' |
---|
761 | from eccodes import codes_grib_new_from_file, codes_get, codes_release |
---|
762 | |
---|
763 | data = {} |
---|
764 | |
---|
765 | # --- open file --- |
---|
766 | print("Opening grib file for extraction of information --- %s" % filename) |
---|
767 | with open(filename, 'rb') as f: |
---|
768 | # load first message from file |
---|
769 | gid = codes_grib_new_from_file(f) |
---|
770 | |
---|
771 | # information needed from grib message |
---|
772 | keys = ['Ni', |
---|
773 | 'Nj', |
---|
774 | 'latitudeOfFirstGridPointInDegrees', |
---|
775 | 'longitudeOfFirstGridPointInDegrees', |
---|
776 | 'latitudeOfLastGridPointInDegrees', |
---|
777 | 'longitudeOfLastGridPointInDegrees', |
---|
778 | 'jDirectionIncrementInDegrees', |
---|
779 | 'iDirectionIncrementInDegrees', |
---|
780 | 'missingValue', |
---|
781 | ] |
---|
782 | |
---|
783 | print('\nInformation extracted: ') |
---|
784 | for key in keys: |
---|
785 | # Get the value of the key in a grib message. |
---|
786 | data[key] = codes_get(gid, key) |
---|
787 | print("%s = %s" % (key, data[key])) |
---|
788 | |
---|
789 | # Free the memory for the message referred as gribid. |
---|
790 | codes_release(gid) |
---|
791 | |
---|
792 | return data |
---|
793 | |
---|
794 | |
---|
795 | def get_dimensions(info, purefc, dtime, index_vals, start_date, end_date): |
---|
796 | '''This function specifies the correct dimensions for x, y, and t. |
---|
797 | |
---|
798 | Parameters |
---|
799 | ---------- |
---|
800 | info : dict |
---|
801 | Contains basic informations of the ECMWF grib files, e.g. |
---|
802 | 'Ni', 'Nj', 'latitudeOfFirstGridPointInDegrees', |
---|
803 | 'longitudeOfFirstGridPointInDegrees', 'latitudeOfLastGridPointInDegrees', |
---|
804 | 'longitudeOfLastGridPointInDegrees', 'jDirectionIncrementInDegrees', |
---|
805 | 'iDirectionIncrementInDegrees', 'missingValue' |
---|
806 | |
---|
807 | purefc : int |
---|
808 | Switch for definition of pure forecast mode or not. |
---|
809 | |
---|
810 | dtime : str |
---|
811 | Time step in hours. |
---|
812 | |
---|
813 | index_vals : list of list of str |
---|
814 | Contains the values from the keys used for a distinct selection |
---|
815 | of GRIB messages in processing the grib files. |
---|
816 | Content looks like e.g.: |
---|
817 | index_vals[0]: ('20171106', '20171107', '20171108') ; date |
---|
818 | index_vals[1]: ('0', '1200', '1800', '600') ; time |
---|
819 | index_vals[2]: ('0', '12', '3', '6', '9') ; stepRange |
---|
820 | |
---|
821 | start_date : str |
---|
822 | The start date of the retrieval job. |
---|
823 | |
---|
824 | end_date : str |
---|
825 | The end date of the retrieval job. |
---|
826 | |
---|
827 | Return |
---|
828 | ------ |
---|
829 | (ix, jy, it) : tuple of int |
---|
830 | Dimension in x-direction, y-direction and in time. |
---|
831 | ''' |
---|
832 | |
---|
833 | ix = info['Ni'] |
---|
834 | |
---|
835 | jy = info['Nj'] |
---|
836 | |
---|
837 | if not purefc: |
---|
838 | it = ((end_date - start_date).days + 1) * 24 // int(dtime) |
---|
839 | else: |
---|
840 | # #no of step * #no of times * #no of days |
---|
841 | it = len(index_vals[2]) * len(index_vals[1]) * len(index_vals[0]) |
---|
842 | |
---|
843 | return (ix, jy, it) |
---|
844 | |
---|
845 | |
---|
846 | def execute_subprocess(cmd_list, error_msg='SUBPROCESS FAILED!'): |
---|
847 | '''Executes a command via a subprocess. |
---|
848 | |
---|
849 | Error handling is done if an error occures. |
---|
850 | |
---|
851 | Parameters |
---|
852 | ---------- |
---|
853 | cmd_list : list of str |
---|
854 | A list of the components for the command line execution. |
---|
855 | They will be concatenated with blank space for the command |
---|
856 | to be submitted, like ['mv', file1, file2] for mv file1 file2. |
---|
857 | |
---|
858 | Return |
---|
859 | ------ |
---|
860 | error_msg : str, optional |
---|
861 | Error message if the subprocess fails. |
---|
862 | By default it will just say "SUBPROCESS FAILED!". |
---|
863 | ''' |
---|
864 | |
---|
865 | try: |
---|
866 | subprocess.check_call(cmd_list) |
---|
867 | except subprocess.CalledProcessError as e: |
---|
868 | print('... ERROR CODE: ' + str(e.returncode)) |
---|
869 | print('... ERROR MESSAGE:\n \t ' + str(e)) |
---|
870 | |
---|
871 | sys.exit('... ' + error_msg) |
---|
872 | except OSError as e: |
---|
873 | print('... ERROR CODE: ' + str(e.errno)) |
---|
874 | print('... ERROR MESSAGE:\n \t ' + str(e.strerror)) |
---|
875 | |
---|
876 | sys.exit('... ' + error_msg) |
---|
877 | |
---|
878 | return |
---|
879 | |
---|
880 | |
---|
881 | def generate_retrieval_period_boundary(c): |
---|
882 | '''Generates retrieval period boundary datetimes from CONTROL information. |
---|
883 | |
---|
884 | Parameters |
---|
885 | ---------- |
---|
886 | c : ControlFile |
---|
887 | Contains all the parameters of CONTROL file and |
---|
888 | command line. |
---|
889 | |
---|
890 | Return |
---|
891 | ------ |
---|
892 | start_period : datetime |
---|
893 | The first timestamp of the actual retrieval period disregarding |
---|
894 | the temporary times which were used for processing reasons. |
---|
895 | |
---|
896 | end_period : datetime |
---|
897 | The last timestamp of the actual retrieval period disregarding |
---|
898 | the temporary times which were used for processing reasons. |
---|
899 | ''' |
---|
900 | # generate start and end timestamp of the retrieval period |
---|
901 | start_period = datetime.strptime(c.start_date + c.time[0], '%Y%m%d%H') |
---|
902 | start_period = start_period + timedelta(hours=int(c.step[0])) |
---|
903 | end_period = datetime.strptime(c.end_date + c.time[-1], '%Y%m%d%H') |
---|
904 | end_period = end_period + timedelta(hours=int(c.step[-1])) |
---|
905 | |
---|
906 | |
---|
907 | return start_period, end_period |
---|
908 | |
---|
909 | |
---|
910 | def check_for_string_in_file(filepath, search_string): |
---|
911 | """ |
---|
912 | Search for a specific string in a file and return True if |
---|
913 | the string was found. |
---|
914 | |
---|
915 | Parameters |
---|
916 | ---------- |
---|
917 | filepath : str |
---|
918 | The full file path which is to be examined. |
---|
919 | |
---|
920 | search_string : str |
---|
921 | The string which is looked up for in the file. |
---|
922 | |
---|
923 | Return |
---|
924 | ------ |
---|
925 | Boolean : |
---|
926 | True : String was found |
---|
927 | False : String was not found |
---|
928 | """ |
---|
929 | with open(filepath, 'r') as fio: |
---|
930 | for line in fio: |
---|
931 | if search_string in line: |
---|
932 | return True |
---|
933 | return False |
---|
934 | |
---|
935 | |
---|
936 | def overwrite_lines_in_file(filepath, search_string, sub_string): |
---|
937 | """ |
---|
938 | Overwrites lines which contain the given search string with the |
---|
939 | substitution string. |
---|
940 | |
---|
941 | Parameters |
---|
942 | ---------- |
---|
943 | search_string : str |
---|
944 | The string which is looked up for in the file. |
---|
945 | |
---|
946 | sub_string : str |
---|
947 | The string which overwrites the search string. |
---|
948 | |
---|
949 | Return |
---|
950 | ------ |
---|
951 | """ |
---|
952 | with open(filepath, 'r') as fio: |
---|
953 | data = fio.readlines() |
---|
954 | |
---|
955 | with open(filepath, 'w') as fio: |
---|
956 | for line in data: |
---|
957 | if search_string in line: |
---|
958 | fio.write(sub_string) |
---|
959 | else: |
---|
960 | fio.write(line) |
---|
961 | |
---|
962 | return |
---|
963 | |
---|