1 | #!/usr/bin/env python |
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2 | # -*- coding: utf-8 -*- |
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3 | #************************************************************************ |
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4 | # ToDo AP |
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5 | # - check my_error |
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6 | # - check normal_exit |
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7 | # - check get_list_as_string |
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8 | # - seperate args and control interpretation |
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9 | #************************************************************************ |
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10 | #******************************************************************************* |
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11 | # @Author: Anne Philipp (University of Vienna) |
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12 | # |
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13 | # @Date: May 2018 |
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14 | # |
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15 | # @Change History: |
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16 | # October 2014 - Anne Fouilloux (University of Oslo) |
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17 | # - created functions silent_remove and product (taken from ECMWF) |
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18 | # |
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19 | # November 2015 - Leopold Haimberger (University of Vienna) |
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20 | # - created functions: interpret_args_and_control, clean_up |
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21 | # my_error, normal_exit, init128, to_param_id |
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22 | # |
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23 | # April 2018 - Anne Philipp (University of Vienna): |
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24 | # - applied PEP8 style guide |
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25 | # - added documentation |
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26 | # - moved all functions from file Flexparttools to this file tools |
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27 | # - added function get_list_as_string |
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28 | # |
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29 | # @License: |
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30 | # (C) Copyright 2014-2018. |
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31 | # |
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32 | # This software is licensed under the terms of the Apache Licence Version 2.0 |
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33 | # which can be obtained at http://www.apache.org/licenses/LICENSE-2.0. |
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34 | # |
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35 | # @Modul Description: |
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36 | # This module contains a couple of helpful functions which are |
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37 | # used in different places in flex_extract. |
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38 | # |
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39 | # @Module Content: |
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40 | # - interpret_args_and_control |
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41 | # - clean_up |
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42 | # - my_error |
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43 | # - normal_exit |
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44 | # - product |
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45 | # - silent_remove |
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46 | # - init128 |
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47 | # - to_param_id |
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48 | # - get_list_as_string |
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49 | # |
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50 | #******************************************************************************* |
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51 | |
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52 | # ------------------------------------------------------------------------------ |
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53 | # MODULES |
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54 | # ------------------------------------------------------------------------------ |
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55 | import os |
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56 | import errno |
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57 | import sys |
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58 | import glob |
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59 | import inspect |
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60 | import subprocess |
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61 | import traceback |
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62 | from argparse import ArgumentParser, ArgumentDefaultsHelpFormatter |
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63 | import numpy as np |
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64 | |
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65 | # software specific class from flex_extract |
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66 | from ControlFile import ControlFile |
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67 | |
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68 | # ------------------------------------------------------------------------------ |
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69 | # FUNCTIONS |
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70 | # ------------------------------------------------------------------------------ |
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71 | |
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72 | def interpret_args_and_control(): |
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73 | ''' |
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74 | @Description: |
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75 | Assigns the command line arguments and reads CONTROL file |
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76 | content. Apply default values for non mentioned arguments. |
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77 | |
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78 | @Input: |
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79 | <nothing> |
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80 | |
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81 | @Return: |
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82 | args: instance of ArgumentParser |
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83 | Contains the commandline arguments from script/program call. |
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84 | |
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85 | c: instance of class ControlFile |
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86 | Contains all necessary information of a CONTROL file. The parameters |
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87 | are: DAY1, DAY2, DTIME, MAXSTEP, TYPE, TIME, STEP, CLASS, STREAM, |
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88 | NUMBER, EXPVER, GRID, LEFT, LOWER, UPPER, RIGHT, LEVEL, LEVELIST, |
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89 | RESOL, GAUSS, ACCURACY, OMEGA, OMEGADIFF, ETA, ETADIFF, DPDETA, |
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90 | SMOOTH, FORMAT, ADDPAR, WRF, CWC, PREFIX, ECSTORAGE, ECTRANS, |
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91 | ECFSDIR, MAILOPS, MAILFAIL, GRIB2FLEXPART, DEBUG, INPUTDIR, |
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92 | OUTPUTDIR, FLEXPART_ROOT_SCRIPTS |
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93 | For more information about format and content of the parameter see |
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94 | documentation. |
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95 | |
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96 | ''' |
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97 | parser = ArgumentParser(description='Retrieve FLEXPART input from \ |
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98 | ECMWF MARS archive', |
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99 | formatter_class=ArgumentDefaultsHelpFormatter) |
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100 | |
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101 | # the most important arguments |
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102 | parser.add_argument("--start_date", dest="start_date", |
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103 | help="start date YYYYMMDD") |
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104 | parser.add_argument("--end_date", dest="end_date", |
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105 | help="end_date YYYYMMDD") |
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106 | parser.add_argument("--date_chunk", dest="date_chunk", default=None, |
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107 | help="# of days to be retrieved at once") |
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108 | |
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109 | # some arguments that override the default in the CONTROL file |
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110 | parser.add_argument("--basetime", dest="basetime", |
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111 | help="base such as 00/12 (for half day retrievals)") |
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112 | parser.add_argument("--step", dest="step", |
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113 | help="steps such as 00/to/48") |
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114 | parser.add_argument("--levelist", dest="levelist", |
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115 | help="Vertical levels to be retrieved, e.g. 30/to/60") |
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116 | parser.add_argument("--area", dest="area", |
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117 | help="area defined as north/west/south/east") |
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118 | |
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119 | # set the working directories |
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120 | parser.add_argument("--inputdir", dest="inputdir", default=None, |
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121 | help="root directory for storing intermediate files") |
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122 | parser.add_argument("--outputdir", dest="outputdir", default=None, |
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123 | help="root directory for storing output files") |
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124 | parser.add_argument("--flexpart_root_scripts", dest="flexpart_root_scripts", |
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125 | help="FLEXPART root directory (to find grib2flexpart \ |
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126 | and COMMAND file)\n Normally ECMWFDATA resides in \ |
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127 | the scripts directory of the FLEXPART distribution") |
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128 | |
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129 | # this is only used by prepare_flexpart.py to rerun a postprocessing step |
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130 | parser.add_argument("--ppid", dest="ppid", |
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131 | help="Specify parent process id for \ |
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132 | rerun of prepare_flexpart") |
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133 | |
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134 | # arguments for job submission to ECMWF, only needed by submit.py |
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135 | parser.add_argument("--job_template", dest='job_template', |
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136 | default="job.temp", |
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137 | help="job template file for submission to ECMWF") |
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138 | parser.add_argument("--queue", dest="queue", |
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139 | help="queue for submission to ECMWF \ |
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140 | (e.g. ecgate or cca )") |
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141 | parser.add_argument("--controlfile", dest="controlfile", |
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142 | default='CONTROL.temp', |
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143 | help="file with CONTROL parameters") |
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144 | parser.add_argument("--debug", dest="debug", default=0, |
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145 | help="Debug mode - leave temporary files intact") |
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146 | |
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147 | args = parser.parse_args() |
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148 | |
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149 | # create instance of ControlFile for specified controlfile |
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150 | # and assign the parameters (and default values if necessary) |
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151 | try: |
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152 | c = ControlFile(args.controlfile) |
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153 | except IOError: |
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154 | try: |
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155 | LOCAL_PYTHON_PATH = os.path.dirname(os.path.abspath( |
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156 | inspect.getfile(inspect.currentframe()))) |
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157 | c = ControlFile(LOCAL_PYTHON_PATH + args.controlfile) |
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158 | except IOError: |
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159 | print 'Could not read CONTROL file "' + args.controlfile + '"' |
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160 | print 'Either it does not exist or its syntax is wrong.' |
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161 | print 'Try "' + sys.argv[0].split('/')[-1] + \ |
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162 | ' -h" to print usage information' |
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163 | exit(1) |
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164 | |
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165 | # check for having at least a starting date |
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166 | if args.start_date is None and getattr(c, 'start_date') is None: |
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167 | print 'start_date specified neither in command line nor \ |
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168 | in CONTROL file ' + args.controlfile |
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169 | print 'Try "' + sys.argv[0].split('/')[-1] + \ |
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170 | ' -h" to print usage information' |
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171 | exit(1) |
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172 | |
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173 | # save all existing command line parameter to the ControlFile instance |
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174 | # if parameter is not specified through the command line or CONTROL file |
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175 | # set default values |
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176 | if args.start_date is not None: |
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177 | c.start_date = args.start_date |
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178 | if args.end_date is not None: |
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179 | c.end_date = args.end_date |
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180 | if c.end_date is None: |
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181 | c.end_date = c.start_date |
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182 | if args.date_chunk is not None: |
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183 | c.date_chunk = args.date_chunk |
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184 | |
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185 | if not hasattr(c, 'debug'): |
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186 | c.debug = args.debug |
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187 | |
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188 | if args.inputdir is None and args.outputdir is None: |
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189 | c.inputdir = '../work' |
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190 | c.outputdir = '../work' |
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191 | else: |
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192 | if args.inputdir is not None: |
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193 | c.inputdir = args.inputdir |
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194 | if args.outputdir is None: |
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195 | c.outputdir = args.inputdir |
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196 | if args.outputdir is not None: |
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197 | c.outputdir = args.outputdir |
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198 | if args.inputdir is None: |
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199 | c.inputdir = args.outputdir |
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200 | |
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201 | if hasattr(c, 'outputdir') is False and args.outputdir is None: |
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202 | c.outputdir = c.inputdir |
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203 | else: |
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204 | if args.outputdir is not None: |
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205 | c.outputdir = args.outputdir |
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206 | |
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207 | if args.area is not None: |
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208 | afloat = '.' in args.area |
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209 | l = args.area.split('/') |
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210 | if afloat: |
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211 | for i, item in enumerate(l): |
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212 | item = str(int(float(item) * 1000)) |
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213 | c.upper, c.left, c.lower, c.right = l |
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214 | |
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215 | # NOTE: basetime activates the ''operational mode'' |
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216 | if args.basetime is not None: |
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217 | c.basetime = args.basetime |
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218 | |
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219 | if args.step is not None: |
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220 | l = args.step.split('/') |
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221 | if 'to' in args.step.lower(): |
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222 | if 'by' in args.step.lower(): |
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223 | ilist = np.arange(int(l[0]), int(l[2]) + 1, int(l[4])) |
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224 | c.step = ['{:0>3}'.format(i) for i in ilist] |
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225 | else: |
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226 | my_error(None, args.step + ':\n' + |
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227 | 'please use "by" as well if "to" is used') |
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228 | else: |
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229 | c.step = l |
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230 | |
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231 | if args.levelist is not None: |
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232 | c.levelist = args.levelist |
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233 | if 'to' in c.levelist: |
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234 | c.level = c.levelist.split('/')[2] |
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235 | else: |
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236 | c.level = c.levelist.split('/')[-1] |
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237 | |
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238 | if args.flexpart_root_scripts is not None: |
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239 | c.flexpart_root_scripts = args.flexpart_root_scripts |
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240 | |
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241 | return args, c |
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242 | |
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243 | |
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244 | def clean_up(c): |
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245 | ''' |
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246 | @Description: |
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247 | Remove all files from intermediate directory |
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248 | (inputdir from CONTROL file). |
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249 | |
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250 | @Input: |
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251 | c: instance of class ControlFile |
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252 | Contains all the parameters of CONTROL file, which are e.g.: |
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253 | DAY1(start_date), DAY2(end_date), DTIME, MAXSTEP, TYPE, TIME, |
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254 | STEP, CLASS(marsclass), STREAM, NUMBER, EXPVER, GRID, LEFT, |
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255 | LOWER, UPPER, RIGHT, LEVEL, LEVELIST, RESOL, GAUSS, ACCURACY, |
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256 | OMEGA, OMEGADIFF, ETA, ETADIFF, DPDETA, SMOOTH, FORMAT, |
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257 | ADDPAR, WRF, CWC, PREFIX, ECSTORAGE, ECTRANS, ECFSDIR, |
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258 | MAILOPS, MAILFAIL, GRIB2FLEXPART, FLEXPARTDIR, BASETIME |
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259 | DATE_CHUNK, DEBUG, INPUTDIR, OUTPUTDIR, FLEXPART_ROOT_SCRIPTS |
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260 | |
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261 | For more information about format and content of the parameter |
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262 | see documentation. |
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263 | |
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264 | @Return: |
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265 | <nothing> |
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266 | ''' |
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267 | |
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268 | print "clean_up" |
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269 | |
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270 | cleanlist = glob.glob(c.inputdir + "/*") |
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271 | for cl in cleanlist: |
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272 | if c.prefix not in cl: |
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273 | silent_remove(cl) |
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274 | if c.ecapi is False and (c.ectrans == '1' or c.ecstorage == '1'): |
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275 | silent_remove(cl) |
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276 | |
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277 | print "Done" |
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278 | |
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279 | return |
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280 | |
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281 | |
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282 | def my_error(c, message='ERROR'): |
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283 | ''' |
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284 | @Description: |
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285 | Prints a specified error message which can be passed to the function |
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286 | before exiting the program. |
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287 | |
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288 | @Input: |
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289 | c: instance of class ControlFile |
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290 | Contains all the parameters of CONTROL file, which are e.g.: |
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291 | DAY1(start_date), DAY2(end_date), DTIME, MAXSTEP, TYPE, TIME, |
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292 | STEP, CLASS(marsclass), STREAM, NUMBER, EXPVER, GRID, LEFT, |
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293 | LOWER, UPPER, RIGHT, LEVEL, LEVELIST, RESOL, GAUSS, ACCURACY, |
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294 | OMEGA, OMEGADIFF, ETA, ETADIFF, DPDETA, SMOOTH, FORMAT, |
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295 | ADDPAR, WRF, CWC, PREFIX, ECSTORAGE, ECTRANS, ECFSDIR, |
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296 | MAILOPS, MAILFAIL, GRIB2FLEXPART, FLEXPARTDIR, BASETIME |
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297 | DATE_CHUNK, DEBUG, INPUTDIR, OUTPUTDIR, FLEXPART_ROOT_SCRIPTS |
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298 | |
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299 | For more information about format and content of the parameter |
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300 | see documentation. |
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301 | |
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302 | message: string, optional |
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303 | Error message. Default value is "ERROR". |
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304 | |
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305 | @Return: |
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306 | <nothing> |
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307 | ''' |
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308 | |
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309 | print message |
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310 | |
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311 | # comment if user does not want email notification directly from python |
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312 | try: |
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313 | target = [] |
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314 | target.extend(c.mailfail) |
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315 | except AttributeError: |
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316 | target = [] |
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317 | target.extend(os.getenv('USER')) |
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318 | |
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319 | for t in target: |
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320 | p = subprocess.Popen(['mail', '-s ECMWFDATA v7.0 ERROR', |
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321 | os.path.expandvars(t)], |
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322 | stdin=subprocess.PIPE, |
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323 | stdout=subprocess.PIPE, |
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324 | stderr=subprocess.PIPE, |
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325 | bufsize=1) |
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326 | tr = '\n'.join(traceback.format_stack()) |
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327 | pout = p.communicate(input=message + '\n\n' + tr)[0] |
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328 | print 'Email sent to ' + os.path.expandvars(t) + ' ' + pout.decode() |
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329 | |
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330 | exit(1) |
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331 | |
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332 | return |
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333 | |
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334 | |
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335 | def normal_exit(c, message='Done!'): |
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336 | ''' |
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337 | @Description: |
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338 | Prints a specific exit message which can be passed to the function. |
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339 | |
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340 | @Input: |
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341 | c: instance of class ControlFile |
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342 | Contains all the parameters of CONTROL file, which are e.g.: |
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343 | DAY1(start_date), DAY2(end_date), DTIME, MAXSTEP, TYPE, TIME, |
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344 | STEP, CLASS(marsclass), STREAM, NUMBER, EXPVER, GRID, LEFT, |
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345 | LOWER, UPPER, RIGHT, LEVEL, LEVELIST, RESOL, GAUSS, ACCURACY, |
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346 | OMEGA, OMEGADIFF, ETA, ETADIFF, DPDETA, SMOOTH, FORMAT, |
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347 | ADDPAR, WRF, CWC, PREFIX, ECSTORAGE, ECTRANS, ECFSDIR, |
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348 | MAILOPS, MAILFAIL, GRIB2FLEXPART, FLEXPARTDIR, BASETIME |
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349 | DATE_CHUNK, DEBUG, INPUTDIR, OUTPUTDIR, FLEXPART_ROOT_SCRIPTS |
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350 | |
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351 | For more information about format and content of the parameter |
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352 | see documentation. |
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353 | |
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354 | message: string, optional |
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355 | Message for exiting program. Default value is "Done!". |
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356 | |
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357 | @Return: |
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358 | <nothing> |
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359 | |
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360 | ''' |
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361 | print message |
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362 | |
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363 | # comment if user does not want notification directly from python |
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364 | try: |
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365 | target = [] |
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366 | target.extend(c.mailops) |
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367 | for t in target: |
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368 | p = subprocess.Popen(['mail', '-s ECMWFDATA v7.0 normal exit', |
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369 | os.path.expandvars(t)], |
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370 | stdin=subprocess.PIPE, |
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371 | stdout=subprocess.PIPE, |
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372 | stderr=subprocess.PIPE, |
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373 | bufsize=1) |
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374 | pout = p.communicate(input=message+'\n\n')[0] |
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375 | print 'Email sent to ' + os.path.expandvars(t) + ' ' + pout.decode() |
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376 | finally: |
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377 | pass |
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378 | |
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379 | return |
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380 | |
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381 | |
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382 | def product(*args, **kwds): |
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383 | ''' |
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384 | @Description: |
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385 | This method is taken from an example at the ECMWF wiki website. |
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386 | https://software.ecmwf.int/wiki/display/GRIB/index.py; 2018-03-16 |
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387 | |
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388 | This method combines the single characters of the passed arguments |
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389 | with each other. So that each character of each argument value |
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390 | will be combined with each character of the other arguments as a tuple. |
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391 | |
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392 | Example: |
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393 | product('ABCD', 'xy') --> Ax Ay Bx By Cx Cy Dx Dy |
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394 | product(range(2), repeat = 3) --> 000 001 010 011 100 101 110 111 |
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395 | |
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396 | @Input: |
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397 | *args: tuple |
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398 | Positional arguments (arbitrary number). |
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399 | |
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400 | **kwds: dictionary |
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401 | Contains all the keyword arguments from *args. |
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402 | |
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403 | @Return: |
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404 | prod: tuple |
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405 | Return will be done with "yield". A tuple of combined arguments. |
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406 | See example in description above. |
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407 | ''' |
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408 | pools = map(tuple, args) * kwds.get('repeat', 1) |
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409 | result = [[]] |
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410 | for pool in pools: |
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411 | result = [x + [y] for x in result for y in pool] |
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412 | for prod in result: |
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413 | yield tuple(prod) |
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414 | |
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415 | return |
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416 | |
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417 | |
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418 | def silent_remove(filename): |
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419 | ''' |
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420 | @Description: |
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421 | If "filename" exists , it is removed. |
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422 | The function does not fail if the file does not exist. |
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423 | |
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424 | @Input: |
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425 | filename: string |
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426 | The name of the file to be removed without notification. |
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427 | |
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428 | @Return: |
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429 | <nothing> |
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430 | ''' |
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431 | try: |
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432 | os.remove(filename) |
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433 | except OSError as e: |
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434 | # this would be "except OSError, e:" before Python 2.6 |
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435 | if e.errno is not errno.ENOENT: |
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436 | # errno.ENOENT = no such file or directory |
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437 | raise # re-raise exception if a different error occured |
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438 | |
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439 | return |
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440 | |
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441 | |
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442 | def init128(filepath): |
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443 | ''' |
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444 | @Description: |
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445 | Opens and reads the grib file with table 128 information. |
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446 | |
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447 | @Input: |
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448 | filepath: string |
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449 | Path to file of ECMWF grib table number 128. |
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450 | |
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451 | @Return: |
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452 | table128: dictionary |
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453 | Contains the ECMWF grib table 128 information. |
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454 | The key is the parameter number and the value is the |
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455 | short name of the parameter. |
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456 | ''' |
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457 | table128 = dict() |
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458 | with open(filepath) as f: |
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459 | fdata = f.read().split('\n') |
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460 | for data in fdata: |
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461 | if data[0] != '!': |
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462 | table128[data[0:3]] = data[59:64].strip() |
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463 | |
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464 | return table128 |
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465 | |
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466 | |
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467 | def to_param_id(pars, table): |
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468 | ''' |
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469 | @Description: |
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470 | Transform parameter names to parameter ids |
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471 | with ECMWF grib table 128. |
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472 | |
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473 | @Input: |
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474 | pars: string |
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475 | Addpar argument from CONTROL file in the format of |
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476 | parameter names instead of ids. The parameter short |
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477 | names are sepearted with "/" and they are passed as |
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478 | one single string. |
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479 | |
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480 | table: dictionary |
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481 | Contains the ECMWF grib table 128 information. |
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482 | The key is the parameter number and the value is the |
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483 | short name of the parameter. |
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484 | |
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485 | @Return: |
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486 | ipar: list of integer |
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487 | List of addpar parameters from CONTROL file transformed to |
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488 | parameter ids in the format of integer. |
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489 | ''' |
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490 | cpar = pars.upper().split('/') |
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491 | ipar = [] |
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492 | for par in cpar: |
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493 | for k, v in table.iteritems(): |
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494 | if par == k or par == v: |
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495 | ipar.append(int(k)) |
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496 | break |
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497 | else: |
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498 | print 'Warning: par ' + par + ' not found in table 128' |
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499 | |
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500 | return ipar |
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501 | |
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502 | def get_list_as_string(list_obj, concatenate_sign=', '): |
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503 | ''' |
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504 | @Description: |
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505 | Converts a list of arbitrary content into a single string. |
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506 | |
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507 | @Input: |
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508 | list_obj: list |
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509 | A list with arbitrary content. |
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510 | |
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511 | concatenate_sign: string, optional |
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512 | A string which is used to concatenate the single |
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513 | list elements. Default value is ", ". |
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514 | |
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515 | @Return: |
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516 | str_of_list: string |
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517 | The content of the list as a single string. |
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518 | ''' |
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519 | |
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520 | str_of_list = concatenate_sign.join(str(l) for l in list_obj) |
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521 | |
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522 | return str_of_list |
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