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