1 | #!/usr/bin/env python |
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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 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 functions from file Flexparttools to this file tools |
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20 | # - added function get_list_as_string |
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21 | # - seperated args and control interpretation |
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22 | # |
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23 | # @License: |
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24 | # (C) Copyright 2014-2018. |
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25 | # |
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26 | # This software is licensed under the terms of the Apache Licence Version 2.0 |
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27 | # which can be obtained at http://www.apache.org/licenses/LICENSE-2.0. |
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28 | # |
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29 | # @Modul Description: |
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30 | # This module contains a couple of helpful functions which are |
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31 | # used in different places in flex_extract. |
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32 | # |
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33 | # @Module Content: |
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34 | # - get_cmdline_arguments |
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35 | # - clean_up |
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36 | # - my_error |
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37 | # - normal_exit |
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38 | # - product |
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39 | # - silent_remove |
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40 | # - init128 |
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41 | # - to_param_id |
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42 | # - get_list_as_string |
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43 | # - make_dir |
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44 | # |
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45 | #******************************************************************************* |
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46 | |
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47 | # ------------------------------------------------------------------------------ |
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48 | # MODULES |
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49 | # ------------------------------------------------------------------------------ |
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50 | import os |
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51 | import errno |
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52 | import sys |
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53 | import glob |
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54 | import subprocess |
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55 | import traceback |
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56 | import exceptions |
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57 | from argparse import ArgumentParser, ArgumentDefaultsHelpFormatter |
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58 | |
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59 | # ------------------------------------------------------------------------------ |
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60 | # FUNCTIONS |
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61 | # ------------------------------------------------------------------------------ |
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62 | |
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63 | def none_or_str(value): |
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64 | '''Converts the input string into pythons None-type if the string |
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65 | contains string "None". |
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66 | |
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67 | Parameters |
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68 | ---------- |
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69 | value : :obj:`string` |
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70 | String to be checked for the "None" word. |
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71 | |
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72 | Return |
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73 | ------ |
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74 | None or value: |
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75 | Return depends on the content of the input value. If it was "None", |
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76 | then the python type None is returned. Otherwise the string itself. |
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77 | ''' |
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78 | if value == 'None': |
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79 | return None |
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80 | return value |
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81 | |
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82 | def none_or_int(value): |
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83 | '''Converts the input string into pythons None-type if the string |
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84 | contains string "None". Otherwise it is converted to an integer value. |
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85 | |
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86 | Parameters |
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87 | ---------- |
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88 | value : :obj:`string` |
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89 | String to be checked for the "None" word. |
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90 | |
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91 | Return |
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92 | ------ |
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93 | None or int(value): |
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94 | Return depends on the content of the input value. If it was "None", |
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95 | then the python type None is returned. Otherwise the string is |
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96 | converted into an integer value. |
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97 | ''' |
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98 | if value == 'None': |
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99 | return None |
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100 | return int(value) |
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101 | |
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102 | def get_cmdline_arguments(): |
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103 | '''Decomposes the command line arguments and assigns them to variables. |
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104 | Apply default values for non mentioned arguments. |
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105 | |
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106 | Parameters |
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107 | ---------- |
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108 | |
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109 | Return |
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110 | ------ |
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111 | args : :obj:`Namespace` |
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112 | Contains the commandline arguments from script/program call. |
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113 | ''' |
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114 | |
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115 | parser = ArgumentParser(description='Retrieve FLEXPART input from \ |
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116 | ECMWF MARS archive', |
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117 | formatter_class=ArgumentDefaultsHelpFormatter) |
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118 | |
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119 | # the most important arguments |
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120 | parser.add_argument("--start_date", dest="start_date", |
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121 | type=none_or_str, default=None, |
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122 | help="start date YYYYMMDD") |
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123 | parser.add_argument("--end_date", dest="end_date", |
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124 | type=none_or_str, default=None, |
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125 | help="end_date YYYYMMDD") |
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126 | parser.add_argument("--date_chunk", dest="date_chunk", |
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127 | type=none_or_int, default=None, |
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128 | help="# of days to be retrieved at once") |
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129 | parser.add_argument("--controlfile", dest="controlfile", |
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130 | type=none_or_str, default='CONTROL.temp', |
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131 | help="file with CONTROL parameters") |
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132 | |
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133 | # parameter for extra output information |
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134 | parser.add_argument("--debug", dest="debug", |
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135 | type=none_or_int, default=None, |
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136 | help="debug mode - leave temporary files intact") |
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137 | parser.add_argument("--request", dest="request", |
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138 | type=none_or_int, default=None, |
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139 | help="list all mars request in file mars_requests.dat \ |
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140 | and skip submission to mars") |
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141 | parser.add_argument("--public", dest="public", |
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142 | type=none_or_int, default=None, |
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143 | help="public mode - retrieves the public datasets") |
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144 | |
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145 | # some arguments that override the default in the CONTROL file |
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146 | parser.add_argument("--basetime", dest="basetime", |
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147 | type=none_or_int, default=None, |
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148 | help="base such as 00 or 12 (for half day retrievals)") |
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149 | parser.add_argument("--step", dest="step", |
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150 | type=none_or_str, default=None, |
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151 | help="steps such as 00/to/48") |
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152 | parser.add_argument("--levelist", dest="levelist", |
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153 | type=none_or_str, default=None, |
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154 | help="Vertical levels to be retrieved, e.g. 30/to/60") |
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155 | parser.add_argument("--area", dest="area", |
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156 | type=none_or_str, default=None, |
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157 | help="area defined as north/west/south/east") |
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158 | |
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159 | # set the working directories |
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160 | parser.add_argument("--inputdir", dest="inputdir", |
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161 | type=none_or_str, default=None, |
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162 | help="root directory for storing intermediate files") |
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163 | parser.add_argument("--outputdir", dest="outputdir", |
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164 | type=none_or_str, default=None, |
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165 | help="root directory for storing output files") |
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166 | parser.add_argument("--flexpart_root_scripts", dest="flexpart_root_scripts", |
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167 | type=none_or_str, default=None, |
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168 | help="FLEXPART root directory (to find grib2flexpart \ |
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169 | and COMMAND file)\n Normally flex_extract resides in \ |
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170 | the scripts directory of the FLEXPART distribution") |
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171 | |
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172 | # this is only used by prepare_flexpart.py to rerun a postprocessing step |
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173 | parser.add_argument("--ppid", dest="ppid", |
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174 | type=none_or_int, default=None, |
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175 | help="specify parent process id for \ |
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176 | rerun of prepare_flexpart") |
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177 | |
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178 | # arguments for job submission to ECMWF, only needed by submit.py |
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179 | parser.add_argument("--job_template", dest='job_template', |
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180 | type=none_or_str, default="job.temp", |
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181 | help="job template file for submission to ECMWF") |
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182 | parser.add_argument("--queue", dest="queue", |
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183 | type=none_or_str, default=None, |
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184 | help="queue for submission to ECMWF \ |
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185 | (e.g. ecgate or cca )") |
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186 | |
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187 | args = parser.parse_args() |
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188 | |
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189 | return args |
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190 | |
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191 | def read_ecenv(filepath): |
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192 | '''Reads the file into a dictionary where the key values are the parameter |
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193 | names. |
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194 | |
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195 | Parameters |
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196 | ---------- |
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197 | filepath : :obj:`string` |
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198 | Path to file where the ECMWF environment parameters are stored. |
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199 | |
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200 | Return |
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201 | ------ |
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202 | envs : :obj:`dictionary` |
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203 | Contains the environment parameter ecuid, ecgid, gateway |
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204 | and destination for ECMWF server environments. |
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205 | ''' |
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206 | envs= {} |
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207 | try: |
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208 | with open(filepath, 'r') as f: |
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209 | for line in f: |
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210 | data = line.strip().split() |
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211 | envs[str(data[0])] = str(data[1]) |
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212 | except OSError as e: |
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213 | print('... ERROR CODE: ' + str(e.errno)) |
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214 | print('... ERROR MESSAGE:\n \t ' + str(e.strerror)) |
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215 | |
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216 | sys.exit('\n... Error occured while trying to read ECMWF_ENV ' |
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217 | 'file: ' + str(filepath)) |
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218 | |
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219 | return envs |
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220 | |
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221 | def clean_up(c): |
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222 | '''Remove files from the intermediate directory (inputdir). |
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223 | |
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224 | It keeps the final FLEXPART input files if program runs without |
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225 | ECMWF Api and keywords "ectrans" or "ecstorage" are set to "1". |
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226 | |
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227 | Parameters |
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228 | ---------- |
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229 | c : :obj:`ControlFile` |
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230 | Contains all the parameters of CONTROL file and |
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231 | command line. |
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232 | |
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233 | Return |
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234 | ------ |
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235 | |
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236 | ''' |
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237 | |
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238 | print("... clean inputdir!") |
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239 | |
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240 | cleanlist = glob.glob(os.path.join(c.inputdir, "*")) |
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241 | |
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242 | if cleanlist: |
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243 | for element in cleanlist: |
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244 | if c.prefix not in element: |
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245 | silent_remove(element) |
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246 | if c.ecapi is False and (c.ectrans == 1 or c.ecstorage == 1): |
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247 | silent_remove(element) |
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248 | print("... done!") |
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249 | else: |
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250 | print("... nothing to clean!") |
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251 | |
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252 | return |
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253 | |
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254 | |
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255 | def my_error(users, message='ERROR'): |
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256 | '''Prints a specified error message which can be passed to the function |
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257 | before exiting the program. |
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258 | |
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259 | Parameters |
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260 | ---------- |
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261 | user : :obj:`list` of :obj:`string` |
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262 | Contains all email addresses which should be notified. |
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263 | It might also contain just the ecmwf user name which wil trigger |
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264 | mailing to the associated email address for this user. |
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265 | |
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266 | message : :obj:`string`, optional |
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267 | Error message. Default value is "ERROR". |
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268 | |
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269 | Return |
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270 | ------ |
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271 | |
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272 | ''' |
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273 | |
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274 | trace = '\n'.join(traceback.format_stack()) |
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275 | full_message = message + '\n\n' + trace |
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276 | |
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277 | print(full_message) |
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278 | |
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279 | send_mail(users, 'ERROR', full_message) |
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280 | |
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281 | sys.exit(1) |
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282 | |
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283 | return |
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284 | |
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285 | |
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286 | def send_mail(users, success_mode, message): |
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287 | '''Prints a specific exit message which can be passed to the function. |
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288 | |
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289 | Parameters |
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290 | ---------- |
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291 | users : :obj:`list` of :obj:`string` |
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292 | Contains all email addresses which should be notified. |
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293 | It might also contain just the ecmwf user name which wil trigger |
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294 | mailing to the associated email address for this user. |
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295 | |
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296 | success_mode : :obj:``string` |
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297 | States the exit mode of the program to put into |
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298 | the mail subject line. |
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299 | |
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300 | message : :obj:`string`, optional |
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301 | Message for exiting program. Default value is "Done!". |
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302 | |
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303 | Return |
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304 | ------ |
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305 | |
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306 | ''' |
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307 | |
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308 | for user in users: |
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309 | if '${USER}' in user: |
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310 | user = os.getenv('USER') |
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311 | try: |
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312 | p = subprocess.Popen(['mail', '-s flex_extract_v7.1 ' + |
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313 | success_mode, os.path.expandvars(user)], |
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314 | stdin=subprocess.PIPE, |
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315 | stdout=subprocess.PIPE, |
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316 | stderr=subprocess.PIPE, |
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317 | bufsize=1) |
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318 | pout = p.communicate(input=message + '\n\n')[0] |
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319 | except ValueError as e: |
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320 | print('... ERROR: ' + str(e)) |
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321 | sys.exit('... Email could not be sent!') |
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322 | except OSError as e: |
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323 | print('... ERROR CODE: ' + str(e.errno)) |
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324 | print('... ERROR MESSAGE:\n \t ' + str(e.strerror)) |
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325 | sys.exit('... Email could not be sent!') |
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326 | else: |
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327 | print('Email sent to ' + os.path.expandvars(user)) |
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328 | |
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329 | return |
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330 | |
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331 | |
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332 | def normal_exit(message='Done!'): |
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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 | Parameters |
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336 | ---------- |
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337 | message : :obj:`string`, optional |
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338 | Message for exiting program. Default value is "Done!". |
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339 | |
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340 | Return |
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341 | ------ |
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342 | |
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343 | ''' |
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344 | |
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345 | print(str(message)) |
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346 | |
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347 | return |
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348 | |
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349 | |
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350 | def product(*args, **kwds): |
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351 | '''Creates combinations of all passed arguments. |
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352 | |
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353 | This method combines the single characters of the passed arguments |
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354 | with each other. So that each character of each argument value |
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355 | will be combined with each character of the other arguments as a tuple. |
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356 | |
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357 | Note |
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358 | ---- |
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359 | This method is taken from an example at the ECMWF wiki website. |
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360 | https://software.ecmwf.int/wiki/display/GRIB/index.py; 2018-03-16 |
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361 | |
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362 | Example |
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363 | ------- |
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364 | product('ABCD', 'xy') --> Ax Ay Bx By Cx Cy Dx Dy |
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365 | |
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366 | product(range(2), repeat = 3) --> 000 001 010 011 100 101 110 111 |
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367 | |
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368 | Parameters |
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369 | ---------- |
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370 | \*args : :obj:`list` or :obj:`string` |
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371 | Positional arguments (arbitrary number). |
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372 | |
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373 | \*\*kwds : :obj:`dictionary` |
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374 | Contains all the keyword arguments from \*args. |
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375 | |
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376 | Return |
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377 | ------ |
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378 | prod : :obj:`tuple` |
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379 | Return will be done with "yield". A tuple of combined arguments. |
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380 | See example in description above. |
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381 | ''' |
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382 | try: |
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383 | pools = map(tuple, args) * kwds.get('repeat', 1) |
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384 | result = [[]] |
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385 | for pool in pools: |
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386 | result = [x + [y] for x in result for y in pool] |
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387 | for prod in result: |
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388 | yield tuple(prod) |
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389 | except TypeError as e: |
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390 | sys.exit('... PRODUCT GENERATION FAILED!') |
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391 | |
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392 | return |
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393 | |
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394 | |
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395 | def silent_remove(filename): |
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396 | '''Remove file if it exists. |
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397 | The function does not fail if the file does not exist. |
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398 | |
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399 | Parameters |
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400 | ---------- |
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401 | filename : :obj:`string` |
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402 | The name of the file to be removed without notification. |
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403 | |
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404 | Return |
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405 | ------ |
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406 | |
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407 | ''' |
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408 | try: |
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409 | os.remove(filename) |
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410 | except OSError as e: |
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411 | # errno.ENOENT = no such file or directory |
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412 | if e.errno == errno.ENOENT: |
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413 | pass |
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414 | else: |
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415 | raise # re-raise exception if a different error occured |
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416 | |
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417 | return |
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418 | |
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419 | |
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420 | def init128(filepath): |
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421 | '''Opens and reads the grib file with table 128 information. |
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422 | |
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423 | Parameters |
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424 | ---------- |
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425 | filepath : :obj:`string` |
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426 | Path to file of ECMWF grib table number 128. |
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427 | |
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428 | Return |
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429 | ------ |
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430 | table128 : :obj:`dictionary` |
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431 | Contains the ECMWF grib table 128 information. |
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432 | The key is the parameter number and the value is the |
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433 | short name of the parameter. |
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434 | ''' |
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435 | table128 = dict() |
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436 | try: |
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437 | with open(filepath) as f: |
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438 | fdata = f.read().split('\n') |
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439 | except OSError as e: |
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440 | print('... ERROR CODE: ' + str(e.errno)) |
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441 | print('... ERROR MESSAGE:\n \t ' + str(e.strerror)) |
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442 | |
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443 | sys.exit('\n... Error occured while trying to read parameter ' |
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444 | 'table file: ' + str(filepath)) |
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445 | else: |
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446 | for data in fdata: |
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447 | if data[0] != '!': |
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448 | table128[data[0:3]] = data[59:64].strip() |
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449 | |
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450 | return table128 |
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451 | |
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452 | |
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453 | def to_param_id(pars, table): |
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454 | '''Transform parameter names to parameter ids with ECMWF grib table 128. |
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455 | |
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456 | Parameters |
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457 | ---------- |
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458 | pars : :obj:`string` |
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459 | Addpar argument from CONTROL file in the format of |
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460 | parameter names instead of ids. The parameter short |
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461 | names are sepearted with "/" and they are passed as |
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462 | one single string. |
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463 | |
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464 | table : :obj:`dictionary` |
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465 | Contains the ECMWF grib table 128 information. |
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466 | The key is the parameter number and the value is the |
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467 | short name of the parameter. |
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468 | |
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469 | Return |
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470 | ------ |
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471 | ipar : :obj:`list` of :obj:`integer` |
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472 | List of addpar parameters from CONTROL file transformed to |
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473 | parameter ids in the format of integer. |
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474 | ''' |
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475 | if not pars: |
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476 | return [] |
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477 | if not isinstance(pars, str): |
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478 | pars=str(pars) |
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479 | |
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480 | cpar = pars.upper().split('/') |
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481 | ipar = [] |
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482 | for par in cpar: |
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483 | for k, v in table.iteritems(): |
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484 | if par == k or par == v: |
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485 | ipar.append(int(k)) |
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486 | break |
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487 | else: |
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488 | print('Warning: par ' + par + ' not found in table 128') |
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489 | |
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490 | return ipar |
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491 | |
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492 | def get_list_as_string(list_obj, concatenate_sign=', '): |
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493 | '''Converts a list of arbitrary content into a single string. |
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494 | |
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495 | Parameters |
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496 | ---------- |
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497 | list_obj : :obj:`list` |
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498 | A list with arbitrary content. |
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499 | |
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500 | concatenate_sign : :obj:`string`, optional |
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501 | A string which is used to concatenate the single |
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502 | list elements. Default value is ", ". |
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503 | |
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504 | Return |
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505 | ------ |
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506 | str_of_list : :obj:`string` |
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507 | The content of the list as a single string. |
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508 | ''' |
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509 | |
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510 | if not isinstance(list_obj, list): |
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511 | list_obj = list(list_obj) |
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512 | str_of_list = concatenate_sign.join(str(l) for l in list_obj) |
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513 | |
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514 | return str_of_list |
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515 | |
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516 | def make_dir(directory): |
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517 | '''Creates a directory. |
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518 | |
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519 | It gives a warning if the directory already exists and skips process. |
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520 | The program stops only if there is another problem. |
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521 | |
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522 | Parameters |
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523 | ---------- |
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524 | directory : :obj:`string` |
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525 | The path to directory which should be created. |
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526 | |
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527 | Return |
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528 | ------ |
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529 | |
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530 | ''' |
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531 | try: |
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532 | os.makedirs(directory) |
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533 | except OSError as e: |
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534 | # errno.EEXIST = directory already exists |
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535 | if e.errno == errno.EEXIST: |
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536 | print('WARNING: Directory {0} already exists!'.format(directory)) |
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537 | else: |
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538 | raise # re-raise exception if a different error occured |
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539 | |
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540 | return |
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541 | |
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542 | def put_file_to_ecserver(ecd, filename, target, ecuid, ecgid): |
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543 | '''Uses the ecaccess-file-put command to send a file to the ECMWF servers. |
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544 | |
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545 | Note |
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546 | ---- |
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547 | The return value is just for testing reasons. It does not have |
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548 | to be used from the calling function since the whole error handling |
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549 | is done in here. |
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550 | |
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551 | Parameters |
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552 | ---------- |
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553 | ecd : :obj:`string` |
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554 | The path were the file is stored. |
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555 | |
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556 | filename : :obj:`string` |
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557 | The name of the file to send to the ECMWF server. |
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558 | |
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559 | target : :obj:`string` |
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560 | The target queue where the file should be sent to. |
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561 | |
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562 | ecuid : :obj:`string` |
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563 | The user id on ECMWF server. |
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564 | |
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565 | ecgid : :obj:`string` |
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566 | The group id on ECMWF server. |
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567 | |
---|
568 | Return |
---|
569 | ------ |
---|
570 | |
---|
571 | ''' |
---|
572 | |
---|
573 | try: |
---|
574 | subprocess.check_output(['ecaccess-file-put', |
---|
575 | ecd + '/' + filename, |
---|
576 | target + ':/home/ms/' + |
---|
577 | ecgid + '/' + ecuid + |
---|
578 | '/' + filename], |
---|
579 | stderr=subprocess.STDOUT) |
---|
580 | except subprocess.CalledProcessError as e: |
---|
581 | print('... ERROR CODE: ' + str(e.returncode)) |
---|
582 | print('... ERROR MESSAGE:\n \t ' + str(e)) |
---|
583 | |
---|
584 | print('\n... Do you have a valid ecaccess certification key?') |
---|
585 | sys.exit('... ECACCESS-FILE-PUT FAILED!') |
---|
586 | except OSError as e: |
---|
587 | print('... ERROR CODE: ' + str(e.errno)) |
---|
588 | print('... ERROR MESSAGE:\n \t ' + str(e.strerror)) |
---|
589 | |
---|
590 | print('\n... Most likely the ECACCESS library is not available!') |
---|
591 | sys.exit('... ECACCESS-FILE-PUT FAILED!') |
---|
592 | |
---|
593 | return |
---|
594 | |
---|
595 | def submit_job_to_ecserver(target, jobname): |
---|
596 | '''Uses ecaccess-job-submit command to submit a job to the ECMWF server. |
---|
597 | |
---|
598 | Note |
---|
599 | ---- |
---|
600 | The return value is just for testing reasons. It does not have |
---|
601 | to be used from the calling function since the whole error handling |
---|
602 | is done in here. |
---|
603 | |
---|
604 | Parameters |
---|
605 | ---------- |
---|
606 | target : :obj:`string` |
---|
607 | The target where the file should be sent to, e.g. the queue. |
---|
608 | |
---|
609 | jobname : :obj:`string` |
---|
610 | The name of the jobfile to be submitted to the ECMWF server. |
---|
611 | |
---|
612 | Return |
---|
613 | ------ |
---|
614 | job_id : :obj:`int` |
---|
615 | The id number of the job as a reference at the ecmwf server. |
---|
616 | ''' |
---|
617 | |
---|
618 | try: |
---|
619 | job_id = subprocess.check_output(['ecaccess-job-submit', '-queueName', |
---|
620 | target, jobname]) |
---|
621 | |
---|
622 | except subprocess.CalledProcessError as e: |
---|
623 | print('... ERROR CODE: ' + str(e.returncode)) |
---|
624 | print('... ERROR MESSAGE:\n \t ' + str(e)) |
---|
625 | |
---|
626 | print('\n... Do you have a valid ecaccess certification key?') |
---|
627 | sys.exit('... ECACCESS-JOB-SUBMIT FAILED!') |
---|
628 | except OSError as e: |
---|
629 | print('... ERROR CODE: ' + str(e.errno)) |
---|
630 | print('... ERROR MESSAGE:\n \t ' + str(e.strerror)) |
---|
631 | |
---|
632 | print('\n... Most likely the ECACCESS library is not available!') |
---|
633 | sys.exit('... ECACCESS-JOB-SUBMIT FAILED!') |
---|
634 | |
---|
635 | return job_id |
---|