1 | #!/usr/bin/env python |
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2 | # -*- coding: utf-8 -*- |
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3 | #******************************************************************************* |
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4 | # @Author: Leopold Haimberger (University of Vienna) |
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5 | # |
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6 | # @Date: November 2015 |
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7 | # |
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8 | # @Change History: |
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9 | # |
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10 | # February 2018 - Anne Philipp (University of Vienna): |
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11 | # - applied PEP8 style guide |
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12 | # - added documentation |
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13 | # - applied some minor modifications in programming style/structure |
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14 | # - changed name of class Control to ControlFile for more |
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15 | # self-explanation naming |
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16 | # - outsource of class ControlFile |
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17 | # - initialisation of class attributes ( to avoid high number of |
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18 | # conditional statements and set default values ) |
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19 | # - divided assignment of attributes and the check of conditions |
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20 | # - outsourced the commandline argument assignments to control attributes |
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21 | # |
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22 | # @License: |
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23 | # (C) Copyright 2015-2018. |
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24 | # |
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25 | # This software is licensed under the terms of the Apache Licence Version 2.0 |
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26 | # which can be obtained at http://www.apache.org/licenses/LICENSE-2.0. |
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27 | # |
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28 | # @Class Description: |
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29 | # The CONTROL file is the steering part of the FLEXPART extraction |
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30 | # software. All necessary parameters needed to retrieve the data fields |
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31 | # from the MARS archive for driving FLEXPART are set in a CONTROL file. |
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32 | # Some specific parameters like the start and end dates can be overwritten |
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33 | # by the command line parameters, but in generel all parameters needed |
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34 | # for a complete set of fields for FLEXPART can be set in the CONTROL file. |
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35 | # |
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36 | # @Class Content: |
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37 | # - __init__ |
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38 | # - __read_controlfile__ |
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39 | # - __str__ |
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40 | # - assign_args_to_control |
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41 | # - assign_envs_to_control |
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42 | # - check_conditions |
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43 | # - check_install_conditions |
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44 | # - to_list |
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45 | # |
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46 | # @Class Attributes: |
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47 | # |
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48 | # |
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49 | #******************************************************************************* |
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50 | |
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51 | # ------------------------------------------------------------------------------ |
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52 | # MODULES |
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53 | # ------------------------------------------------------------------------------ |
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54 | import os |
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55 | import re |
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56 | import sys |
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57 | import inspect |
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58 | |
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59 | # software specific classes and modules from flex_extract |
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60 | sys.path.append('../') |
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61 | import _config |
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62 | from mods.tools import my_error |
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63 | |
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64 | # ------------------------------------------------------------------------------ |
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65 | # CLASS |
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66 | # ------------------------------------------------------------------------------ |
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67 | class ControlFile(object): |
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68 | ''' |
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69 | Class containing the information of the flex_extract CONTROL file. |
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70 | |
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71 | Contains all the parameters of CONTROL file, which are e.g.: |
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72 | DAY1(start_date), DAY2(end_date), DTIME, MAXSTEP, TYPE, TIME, |
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73 | STEP, CLASS(marsclass), STREAM, NUMBER, EXPVER, GRID, LEFT, |
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74 | LOWER, UPPER, RIGHT, LEVEL, LEVELIST, RESOL, GAUSS, ACCURACY, |
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75 | OMEGA, OMEGADIFF, ETA, ETADIFF, DPDETA, SMOOTH, FORMAT, |
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76 | ADDPAR, WRF, CWC, PREFIX, ECSTORAGE, ECTRANS, ECFSDIR, |
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77 | MAILOPS, MAILFAIL, GRIB2FLEXPART, FLEXPARTDIR, |
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78 | BASETIME, DATE_CHUNK, DEBUG, INPUTDIR, OUTPUTDIR, FLEXPART_ROOT_SCRIPTS |
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79 | |
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80 | For more information about format and content of the parameter |
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81 | see documentation. |
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82 | |
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83 | ''' |
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84 | |
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85 | def __init__(self, filename): |
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86 | ''' |
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87 | @Description: |
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88 | Initialises the instance of ControlFile class and defines |
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89 | all class attributes with default values. Afterwards calls |
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90 | function __read_controlfile__ to read parameter from |
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91 | Control file. |
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92 | |
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93 | @Input: |
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94 | self: instance of ControlFile class |
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95 | Description see class documentation. |
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96 | |
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97 | filename: string |
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98 | Name of CONTROL file. |
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99 | |
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100 | @Return: |
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101 | <nothing> |
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102 | ''' |
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103 | |
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104 | # list of all possible class attributes and their default values |
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105 | self.controlfile = filename |
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106 | self.start_date = None |
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107 | self.end_date = None |
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108 | self.date_chunk = 3 |
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109 | self.dtime = None |
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110 | self.basetime = None |
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111 | self.maxstep = None |
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112 | self.type = None |
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113 | self.time = None |
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114 | self.step = None |
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115 | self.acctype = None |
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116 | self.acctime = None |
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117 | self.accmaxstep = None |
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118 | self.marsclass = None |
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119 | self.dataset = None |
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120 | self.stream = None |
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121 | self.number = 'OFF' |
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122 | self.expver = '1' |
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123 | self.gaussian = '' |
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124 | self.grid = None |
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125 | self.area = '' |
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126 | self.left = None |
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127 | self.lower = None |
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128 | self.upper = None |
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129 | self.right = None |
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130 | self.level = None |
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131 | self.levelist = None |
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132 | self.resol = None |
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133 | self.gauss = 0 |
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134 | self.accuracy = 24 |
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135 | self.omega = 0 |
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136 | self.omegadiff = 0 |
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137 | self.eta = 0 |
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138 | self.etadiff = 0 |
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139 | self.etapar = 77 |
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140 | self.dpdeta = 1 |
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141 | self.smooth = 0 |
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142 | self.format = 'GRIB1' |
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143 | self.addpar = None |
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144 | self.prefix = 'EN' |
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145 | self.cwc = 0 |
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146 | self.wrf = 0 |
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147 | self.ecfsdir = 'ectmp:/${USER}/econdemand/' |
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148 | self.mailfail = ['${USER}'] |
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149 | self.mailops = ['${USER}'] |
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150 | self.grib2flexpart = 0 |
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151 | self.ecstorage = 0 |
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152 | self.ectrans = 0 |
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153 | self.inputdir = _config.PATH_INPUT_DIR |
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154 | self.outputdir = None |
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155 | self.ecmwfdatadir = _config.PATH_FLEXEXTRACT_DIR |
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156 | self.exedir = _config.PATH_FORTRAN_SRC |
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157 | self.flexpart_root_scripts = None |
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158 | self.makefile = 'Makefile.gfortran' |
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159 | self.destination = None |
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160 | self.gateway = None |
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161 | self.ecuid = None |
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162 | self.ecgid = None |
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163 | self.install_target = None |
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164 | self.debug = 0 |
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165 | self.request = 0 |
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166 | self.public = 0 |
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167 | |
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168 | self.logicals = ['gauss', 'omega', 'omegadiff', 'eta', 'etadiff', |
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169 | 'dpdeta', 'cwc', 'wrf', 'grib2flexpart', 'ecstorage', |
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170 | 'ectrans', 'debug', 'request', 'public'] |
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171 | |
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172 | self.__read_controlfile__() |
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173 | |
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174 | return |
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175 | |
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176 | def __read_controlfile__(self): |
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177 | ''' |
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178 | @Description: |
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179 | Read CONTROL file and assign all CONTROL file variables. |
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180 | |
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181 | @Input: |
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182 | self: instance of ControlFile class |
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183 | Description see class documentation. |
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184 | |
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185 | @Return: |
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186 | <nothing> |
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187 | ''' |
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188 | |
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189 | try: |
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190 | with open(os.path.join(_config.PATH_CONTROLFILES, |
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191 | self.controlfile)) as f: |
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192 | fdata = f.read().split('\n') |
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193 | except IOError: |
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194 | print('Could not read CONTROL file "' + args.controlfile + '"') |
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195 | print('Either it does not exist or its syntax is wrong.') |
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196 | print('Try "' + sys.argv[0].split('/')[-1] + \ |
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197 | ' -h" to print usage information') |
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198 | sys.exit(1) |
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199 | |
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200 | # go through every line and store parameter |
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201 | for ldata in fdata: |
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202 | data = ldata.split() |
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203 | if len(data) > 1: |
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204 | if 'm_' in data[0].lower(): |
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205 | data[0] = data[0][2:] |
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206 | if data[0].lower() == 'class': |
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207 | data[0] = 'marsclass' |
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208 | if data[0].lower() == 'day1': |
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209 | data[0] = 'start_date' |
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210 | if data[0].lower() == 'day2': |
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211 | data[0] = 'end_date' |
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212 | if data[0].lower() == 'addpar': |
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213 | if '/' in data[1]: |
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214 | # remove leading '/' sign from addpar content |
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215 | if data[1][0] == '/': |
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216 | data[1] = data[1][1:] |
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217 | dd = data[1].split('/') |
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218 | data = [data[0]] |
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219 | for d in dd: |
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220 | data.append(d) |
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221 | if len(data) == 2: |
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222 | if '$' in data[1]: |
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223 | setattr(self, data[0].lower(), data[1]) |
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224 | while '$' in data[1]: |
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225 | i = data[1].index('$') |
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226 | j = data[1].find('{') |
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227 | k = data[1].find('}') |
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228 | var = os.getenv(data[1][j+1:k]) |
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229 | if var is not None: |
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230 | data[1] = data[1][:i] + var + data[1][k+1:] |
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231 | else: |
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232 | my_error(self.mailfail, |
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233 | 'Could not find variable ' |
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234 | + data[1][j+1:k] + ' while reading ' + |
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235 | self.controlfile) |
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236 | setattr(self, data[0].lower() + '_expanded', data[1]) |
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237 | else: |
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238 | if data[1].lower() != 'none': |
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239 | setattr(self, data[0].lower(), data[1]) |
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240 | else: |
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241 | setattr(self, data[0].lower(), None) |
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242 | elif len(data) > 2: |
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243 | setattr(self, data[0].lower(), (data[1:])) |
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244 | else: |
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245 | pass |
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246 | |
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247 | return |
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248 | |
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249 | def __str__(self): |
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250 | ''' |
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251 | @Description: |
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252 | Prepares a string which have all the ControlFile |
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253 | class attributes with its associated values. |
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254 | Each attribute is printed in one line and in |
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255 | alphabetical order. |
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256 | |
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257 | Example: |
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258 | 'age': 10 |
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259 | 'color': 'Spotted' |
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260 | 'kids': 0 |
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261 | 'legs': 2 |
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262 | 'name': 'Dog' |
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263 | 'smell': 'Alot' |
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264 | |
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265 | @Input: |
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266 | self: instance of ControlFile class |
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267 | Description see class documentation. |
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268 | |
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269 | @Return: |
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270 | string of ControlFile class attributes with their values |
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271 | ''' |
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272 | import collections |
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273 | |
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274 | attrs = vars(self).copy() |
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275 | attrs = collections.OrderedDict(sorted(attrs.items())) |
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276 | |
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277 | return '\n'.join("%s: %s" % item for item in attrs.items()) |
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278 | |
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279 | def assign_args_to_control(self, args): |
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280 | ''' |
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281 | @Description: |
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282 | Overwrites the existing ControlFile instance attributes with |
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283 | the command line arguments. |
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284 | |
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285 | @Input: |
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286 | self: instance of ControlFile class |
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287 | Description see class documentation. |
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288 | |
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289 | args: instance of ArgumentParser |
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290 | Contains the commandline arguments from script/program call. |
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291 | |
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292 | @Return: |
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293 | <nothing> |
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294 | ''' |
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295 | |
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296 | # get dictionary of command line parameters and eliminate all |
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297 | # parameters which are None (were not specified) |
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298 | args_dict = vars(args) |
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299 | arguments = {k : args_dict[k] for k in args_dict |
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300 | if args_dict[k] != None} |
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301 | |
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302 | # assign all passed command line arguments to ControlFile instance |
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303 | for k, v in arguments.iteritems(): |
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304 | setattr(self, str(k), v) |
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305 | |
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306 | return |
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307 | |
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308 | def assign_envs_to_control(self, envs): |
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309 | ''' |
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310 | @Description: |
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311 | Assigns the ECMWF environment parameter. |
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312 | |
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313 | @Input: |
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314 | envs: dict of strings |
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315 | Contains the ECMWF environment parameternames "ECUID", "ECGID", |
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316 | "DESTINATION" and "GATEWAY" with its corresponding values. |
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317 | They were read from the file "ECMWF_ENV". |
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318 | |
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319 | @Return: |
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320 | <nothing> |
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321 | ''' |
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322 | |
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323 | for k, v in envs.iteritems(): |
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324 | setattr(self, str(k).lower(), str(v)) |
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325 | |
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326 | return |
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327 | |
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328 | def check_conditions(self, queue): |
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329 | ''' |
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330 | @Description: |
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331 | Checks a couple of necessary attributes and conditions, |
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332 | such as if they exist and contain values. |
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333 | Otherwise set default values. |
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334 | |
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335 | @Input: |
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336 | self: instance of ControlFile class |
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337 | Description see class documentation. |
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338 | |
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339 | queue: string |
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340 | Name of the queue if submitted to the ECMWF servers. |
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341 | Used to check if ecuid, ecgid, gateway and destination |
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342 | are set correctly and are not empty. |
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343 | |
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344 | @Return: |
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345 | <nothing> |
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346 | ''' |
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347 | from mods.tools import my_error |
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348 | import numpy as np |
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349 | |
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350 | # check for having at least a starting date |
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351 | # otherwise program is not allowed to run |
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352 | if not self.start_date: |
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353 | print('start_date specified neither in command line nor \ |
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354 | in CONTROL file ' + self.controlfile) |
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355 | print('Try "' + sys.argv[0].split('/')[-1] + |
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356 | ' -h" to print usage information') |
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357 | sys.exit(1) |
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358 | |
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359 | # retrieve just one day if end_date isn't set |
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360 | if not self.end_date: |
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361 | self.end_date = self.start_date |
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362 | |
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363 | # basetime has only two possible values |
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364 | if self.basetime: |
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365 | if int(self.basetime) != 0 and int(self.basetime) != 12: |
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366 | print('Basetime has an invalid value!') |
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367 | print('Basetime = ' + str(self.basetime)) |
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368 | sys.exit(1) |
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369 | |
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370 | # assure consistency of levelist and level |
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371 | # up-to-date available maximum level numbers at ECMWF, 05.10.2018 |
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372 | max_level_list = [16, 19, 31, 40, 50, 60, 62, 91, 137] |
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373 | if not self.levelist and not self.level: |
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374 | print('Warning: neither levelist nor level \ |
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375 | specified in CONTROL file') |
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376 | sys.exit(1) |
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377 | elif not self.levelist and self.level: |
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378 | self.levelist = '1/to/' + self.level |
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379 | elif (self.levelist and not self.level) or \ |
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380 | (self.levelist[-1] != self.level[-1]): |
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381 | self.level = self.levelist.split('/')[-1] |
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382 | else: |
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383 | pass |
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384 | |
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385 | # check if max level is a valid level |
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386 | if int(self.level) not in max_level_list: |
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387 | print('ERROR: ') |
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388 | print('LEVEL must be the maximum level of a specified ' |
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389 | 'level list from ECMWF, e.g.') |
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390 | print('[16, 19, 31, 40, 50, 60, 62, 91 or 137]') |
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391 | print('Check parameter "LEVEL" or the max level of "LEVELIST"!') |
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392 | sys.exit(1) |
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393 | |
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394 | # if area was provided (only from commandline) |
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395 | # decompose area into its 4 components |
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396 | if self.area: |
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397 | components = self.area.split('/') |
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398 | # convert float to integer coordinates |
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399 | if '.' in self.area: |
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400 | components = [str(int(float(item) * 1000)) |
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401 | for i, item in enumerate(components)] |
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402 | self.upper, self.left, self.lower, self.right = components |
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403 | |
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404 | # prepare step list if "/" signs are found |
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405 | if '/' in self.step: |
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406 | steps = self.step.split('/') |
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407 | if 'to' in self.step.lower() and 'by' in self.step.lower(): |
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408 | ilist = np.arange(int(steps[0]), |
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409 | int(steps[2]) + 1, |
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410 | int(steps[4])) |
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411 | self.step = ['{:0>3}'.format(i) for i in ilist] |
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412 | elif 'to' in self.step.lower() and 'by' not in self.step.lower(): |
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413 | my_error(self.mailfail, self.step + ':\n' + |
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414 | 'if "to" is used in steps parameter, \ |
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415 | please use "by" as well') |
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416 | else: |
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417 | self.step = steps |
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418 | |
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419 | # if maxstep wasn't provided |
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420 | # search for it in the "step" parameter |
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421 | if not self.maxstep: |
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422 | self.maxstep = 0 |
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423 | for s in self.step: |
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424 | if int(s) > self.maxstep: |
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425 | self.maxstep = int(s) |
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426 | else: |
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427 | self.maxstep = int(self.maxstep) |
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428 | |
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429 | # set root scripts since it is needed later on |
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430 | if not self.flexpart_root_scripts: |
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431 | self.flexpart_root_scripts = self.ecmwfdatadir |
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432 | |
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433 | if not self.outputdir: |
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434 | self.outputdir = self.inputdir |
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435 | |
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436 | if not isinstance(self.mailfail, list): |
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437 | if ',' in self.mailfail: |
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438 | self.mailfail = self.mailfail.split(',') |
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439 | elif ' ' in self.mailfail: |
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440 | self.mailfail = self.mailfail.split() |
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441 | else: |
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442 | self.mailfail = [self.mailfail] |
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443 | |
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444 | if not isinstance(self.mailops, list): |
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445 | if ',' in self.mailops: |
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446 | self.mailops = self.mailops.split(',') |
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447 | elif ' ' in self.mailops: |
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448 | self.mailops = self.mailops.split() |
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449 | else: |
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450 | self.mailops = [self.mailops] |
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451 | |
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452 | if queue in ['ecgate', 'cca'] and \ |
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453 | not self.gateway or not self.destination or \ |
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454 | not self.ecuid or not self.ecgid: |
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455 | print('\nEnvironment variables GATEWAY, DESTINATION, ECUID and \ |
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456 | ECGID were not set properly!') |
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457 | print('Please check for existence of file "ECMWF_ENV" in the \ |
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458 | python directory!') |
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459 | sys.exit(1) |
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460 | |
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461 | if self.request != 0: |
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462 | marsfile = os.path.join(self.inputdir, |
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463 | _config.FILE_MARS_REQUESTS) |
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464 | if os.path.isfile(marsfile): |
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465 | os.remove(marsfile) |
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466 | |
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467 | # check all logical variables for data type |
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468 | # if its a string change to integer |
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469 | for var in self.logicals: |
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470 | if not isinstance(getattr(self, var), int): |
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471 | setattr(self, var, int(getattr(self, var))) |
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472 | |
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473 | if self.public and not self.dataset: |
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474 | print('ERROR: ') |
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475 | print('If public mars data wants to be retrieved, ' |
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476 | 'the "dataset"-parameter has to be set in the control file!') |
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477 | sys.exit(1) |
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478 | |
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479 | if not isinstance(self.type, list): |
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480 | self.type = [self.type] |
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481 | |
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482 | for i, val in enumerate(self.type): |
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483 | if self.type[i] == 'AN' and int(self.step[i]) != 0: |
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484 | print('Analysis retrievals must have STEP = 0 (is set to 0)') |
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485 | self.type[i] = 0 |
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486 | |
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487 | if not isinstance(self.time, list): |
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488 | self.time = [self.time] |
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489 | |
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490 | if not isinstance(self.step, list): |
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491 | self.step = [self.step] |
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492 | |
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493 | if not self.acctype: |
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494 | print('... Control paramter ACCTYPE was not defined.') |
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495 | try: |
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496 | if len(self.type) > 1 and self.type[1] != 'AN': |
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497 | print('Use old setting by using TYPE[1] for flux forecast!') |
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498 | self.acctype = self.type[1] |
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499 | except: |
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500 | print('Use default value "FC" for flux forecast!') |
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501 | self.acctype='FC' |
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502 | |
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503 | if not self.acctime: |
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504 | print('... Control paramter ACCTIME was not defined.') |
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505 | print('Use default value "00/12" for flux forecast!') |
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506 | self.acctime='00/12' |
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507 | |
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508 | if not self.accmaxstep: |
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509 | print('... Control paramter ACCMAXSTEP was not defined.') |
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510 | print('Use default value "12" for flux forecast!') |
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511 | self.accmaxstep='12' |
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512 | |
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513 | return |
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514 | |
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515 | def check_install_conditions(self): |
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516 | ''' |
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517 | @Description: |
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518 | Checks a couple of necessary attributes and conditions |
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519 | for the installation such as if they exist and contain values. |
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520 | Otherwise set default values. |
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521 | |
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522 | @Input: |
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523 | self: instance of ControlFile class |
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524 | Description see class documentation. |
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525 | |
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526 | @Return: |
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527 | <nothing> |
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528 | ''' |
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529 | |
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530 | if self.install_target and \ |
---|
531 | self.install_target not in ['local', 'ecgate', 'cca']: |
---|
532 | print('ERROR: unknown or missing installation target ') |
---|
533 | print('target: ', self.install_target) |
---|
534 | print('please specify correct installation target ' + |
---|
535 | '(local | ecgate | cca)') |
---|
536 | print('use -h or --help for help') |
---|
537 | sys.exit(1) |
---|
538 | |
---|
539 | if self.install_target and self.install_target != 'local': |
---|
540 | if not self.ecgid or not self.ecuid or \ |
---|
541 | not self.gateway or not self.destination: |
---|
542 | print('Please enter your ECMWF user id and group id as well ' + |
---|
543 | 'as the \nname of the local gateway and the ectrans ' + |
---|
544 | 'destination ') |
---|
545 | print('with command line options --ecuid --ecgid \ |
---|
546 | --gateway --destination') |
---|
547 | print('Try "' + sys.argv[0].split('/')[-1] + \ |
---|
548 | ' -h" to print usage information') |
---|
549 | print('Please consult ecaccess documentation or ECMWF user \ |
---|
550 | support for further details') |
---|
551 | sys.exit(1) |
---|
552 | |
---|
553 | if not self.flexpart_root_scripts: |
---|
554 | self.flexpart_root_scripts = '${HOME}' |
---|
555 | else: |
---|
556 | self.flexpart_root_scripts = self.flexpart_root_scripts |
---|
557 | else: # local |
---|
558 | if not self.flexpart_root_scripts: |
---|
559 | self.flexpart_root_scripts = _config.PATH_FLEXEXTRACT_DIR |
---|
560 | |
---|
561 | return |
---|
562 | |
---|
563 | def to_list(self): |
---|
564 | ''' |
---|
565 | @Description: |
---|
566 | Just generates a list of strings containing the attributes and |
---|
567 | assigned values except the attributes "_expanded", "exedir", |
---|
568 | "ecmwfdatadir" and "flexpart_root_scripts". |
---|
569 | |
---|
570 | @Input: |
---|
571 | self: instance of ControlFile class |
---|
572 | Description see class documentation. |
---|
573 | |
---|
574 | @Return: |
---|
575 | l: list |
---|
576 | A sorted list of the all ControlFile class attributes with |
---|
577 | their values except the attributes "_expanded", "exedir", |
---|
578 | "ecmwfdatadir" and "flexpart_root_scripts". |
---|
579 | ''' |
---|
580 | |
---|
581 | import collections |
---|
582 | |
---|
583 | attrs = collections.OrderedDict(sorted(vars(self).copy().items())) |
---|
584 | |
---|
585 | l = list() |
---|
586 | |
---|
587 | for item in attrs.items(): |
---|
588 | if '_expanded' in item[0]: |
---|
589 | pass |
---|
590 | elif 'exedir' in item[0]: |
---|
591 | pass |
---|
592 | elif 'flexpart_root_scripts' in item[0]: |
---|
593 | pass |
---|
594 | elif 'ecmwfdatadir' in item[0]: |
---|
595 | pass |
---|
596 | else: |
---|
597 | if isinstance(item[1], list): |
---|
598 | stot = '' |
---|
599 | for s in item[1]: |
---|
600 | stot += s + ' ' |
---|
601 | |
---|
602 | l.append("%s %s" % (item[0], stot)) |
---|
603 | else: |
---|
604 | l.append("%s %s" % item) |
---|
605 | |
---|
606 | return sorted(l) |
---|
607 | |
---|