[812283d] | 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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[54a8a01] | 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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[812283d] | 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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[54a8a01] | 38 | # - __read_controlfile__ |
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[812283d] | 39 | # - __str__ |
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[54a8a01] | 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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[ff99eae] | 44 | # - to_list |
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| 45 | # |
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| 46 | # @Class Attributes: |
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[54a8a01] | 47 | # |
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[812283d] | 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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[54a8a01] | 55 | import sys |
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[812283d] | 56 | import inspect |
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[ff99eae] | 57 | |
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[812283d] | 58 | # ------------------------------------------------------------------------------ |
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| 59 | # CLASS |
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| 60 | # ------------------------------------------------------------------------------ |
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[ff99eae] | 61 | class ControlFile(object): |
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[812283d] | 62 | ''' |
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| 63 | Class containing the information of the flex_extract CONTROL file. |
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| 64 | |
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| 65 | Contains all the parameters of CONTROL file, which are e.g.: |
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| 66 | DAY1(start_date), DAY2(end_date), DTIME, MAXSTEP, TYPE, TIME, |
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| 67 | STEP, CLASS(marsclass), STREAM, NUMBER, EXPVER, GRID, LEFT, |
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| 68 | LOWER, UPPER, RIGHT, LEVEL, LEVELIST, RESOL, GAUSS, ACCURACY, |
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| 69 | OMEGA, OMEGADIFF, ETA, ETADIFF, DPDETA, SMOOTH, FORMAT, |
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| 70 | ADDPAR, WRF, CWC, PREFIX, ECSTORAGE, ECTRANS, ECFSDIR, |
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| 71 | MAILOPS, MAILFAIL, GRIB2FLEXPART, FLEXPARTDIR, |
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| 72 | BASETIME, DATE_CHUNK, DEBUG, INPUTDIR, OUTPUTDIR, FLEXPART_ROOT_SCRIPTS |
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| 73 | |
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| 74 | For more information about format and content of the parameter |
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| 75 | see documentation. |
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| 76 | |
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| 77 | ''' |
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| 78 | |
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| 79 | def __init__(self, filename): |
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| 80 | ''' |
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| 81 | @Description: |
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[54a8a01] | 82 | Initialises the instance of ControlFile class and defines |
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| 83 | all class attributes with default values. Afterwards calls |
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| 84 | function __read_controlfile__ to read parameter from |
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| 85 | Control file. |
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[812283d] | 86 | |
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| 87 | @Input: |
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| 88 | self: instance of ControlFile class |
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| 89 | Description see class documentation. |
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| 90 | |
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| 91 | filename: string |
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| 92 | Name of CONTROL file. |
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| 93 | |
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| 94 | @Return: |
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| 95 | <nothing> |
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| 96 | ''' |
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[54a8a01] | 97 | |
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| 98 | # list of all possible class attributes and their default values |
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| 99 | self.controlfile = filename |
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| 100 | self.start_date = None |
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| 101 | self.end_date = None |
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| 102 | self.date_chunk = 3 |
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| 103 | self.dtime = None |
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| 104 | self.basetime = None |
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| 105 | self.maxstep = None |
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| 106 | self.type = None |
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| 107 | self.time = None |
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| 108 | self.step = None |
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| 109 | self.marsclass = None |
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| 110 | self.stream = None |
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| 111 | self.number = 'OFF' |
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| 112 | self.expver = None |
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| 113 | self.grid = None |
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| 114 | self.area = '' |
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| 115 | self.left = None |
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| 116 | self.lower = None |
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| 117 | self.upper = None |
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| 118 | self.right = None |
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| 119 | self.level = None |
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| 120 | self.levelist = None |
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| 121 | self.resol = None |
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| 122 | self.gauss = 0 |
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| 123 | self.accuracy = 24 |
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| 124 | self.omega = 0 |
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| 125 | self.omegadiff = 0 |
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| 126 | self.eta = 0 |
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| 127 | self.etadiff = 0 |
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| 128 | self.etapar = 77 |
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| 129 | self.dpdeta = 1 |
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| 130 | self.smooth = 0 |
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| 131 | self.format = 'GRIB1' |
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| 132 | self.addpar = None |
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| 133 | self.prefix = 'EN' |
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| 134 | self.cwc = 0 |
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| 135 | self.wrf = 0 |
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| 136 | self.ecfsdir = 'ectmp:/${USER}/econdemand/' |
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| 137 | self.mailfail = ['${USER}'] |
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| 138 | self.mailops = ['${USER}'] |
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| 139 | self.grib2flexpart = 0 |
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| 140 | self.ecstorage = 0 |
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| 141 | self.ectrans = 0 |
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| 142 | self.inputdir = '../work' |
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| 143 | self.outputdir = self.inputdir |
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| 144 | self.ecmwfdatadir = None |
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| 145 | self.exedir = None |
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| 146 | self.flexpart_root_scripts = None |
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| 147 | self.makefile = None |
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| 148 | self.destination = None |
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| 149 | self.gateway = None |
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| 150 | self.ecuid = None |
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| 151 | self.ecgid = None |
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| 152 | self.install_target = None |
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| 153 | self.debug = 0 |
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| 154 | |
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| 155 | self.__read_controlfile__() |
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| 156 | |
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| 157 | return |
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| 158 | |
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| 159 | def __read_controlfile__(self): |
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| 160 | ''' |
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| 161 | @Description: |
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| 162 | Read CONTROL file and assign all CONTROL file variables. |
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| 163 | |
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| 164 | @Input: |
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| 165 | self: instance of ControlFile class |
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| 166 | Description see class documentation. |
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| 167 | |
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| 168 | @Return: |
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| 169 | <nothing> |
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| 170 | ''' |
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[e1228f3] | 171 | from tools import my_error |
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[812283d] | 172 | |
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| 173 | # read whole CONTROL file |
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[54a8a01] | 174 | with open(self.controlfile) as f: |
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[812283d] | 175 | fdata = f.read().split('\n') |
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| 176 | |
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| 177 | # go through every line and store parameter |
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| 178 | for ldata in fdata: |
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| 179 | data = ldata.split() |
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| 180 | if len(data) > 1: |
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| 181 | if 'm_' in data[0].lower(): |
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| 182 | data[0] = data[0][2:] |
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| 183 | if data[0].lower() == 'class': |
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| 184 | data[0] = 'marsclass' |
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| 185 | if data[0].lower() == 'day1': |
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| 186 | data[0] = 'start_date' |
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| 187 | if data[0].lower() == 'day2': |
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| 188 | data[0] = 'end_date' |
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| 189 | if data[0].lower() == 'addpar': |
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| 190 | if '/' in data[1]: |
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| 191 | # remove leading '/' sign from addpar content |
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| 192 | if data[1][0] == '/': |
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| 193 | data[1] = data[1][1:] |
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| 194 | dd = data[1].split('/') |
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| 195 | data = [data[0]] |
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| 196 | for d in dd: |
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| 197 | data.append(d) |
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| 198 | if len(data) == 2: |
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| 199 | if '$' in data[1]: |
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| 200 | setattr(self, data[0].lower(), data[1]) |
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| 201 | while '$' in data[1]: |
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| 202 | i = data[1].index('$') |
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| 203 | j = data[1].find('{') |
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| 204 | k = data[1].find('}') |
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| 205 | var = os.getenv(data[1][j+1:k]) |
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| 206 | if var is not None: |
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| 207 | data[1] = data[1][:i] + var + data[1][k+1:] |
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| 208 | else: |
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[54a8a01] | 209 | my_error(self.mailfail, |
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| 210 | 'Could not find variable ' |
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| 211 | + data[1][j+1:k] + ' while reading ' + |
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| 212 | self.controlfile) |
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[812283d] | 213 | setattr(self, data[0].lower() + '_expanded', data[1]) |
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| 214 | else: |
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| 215 | if data[1].lower() != 'none': |
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| 216 | setattr(self, data[0].lower(), data[1]) |
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| 217 | else: |
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| 218 | setattr(self, data[0].lower(), None) |
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| 219 | elif len(data) > 2: |
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| 220 | setattr(self, data[0].lower(), (data[1:])) |
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| 221 | else: |
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| 222 | pass |
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| 223 | |
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[54a8a01] | 224 | # script directory |
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| 225 | self.ecmwfdatadir = os.path.dirname(os.path.abspath(inspect.getfile( |
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| 226 | inspect.currentframe()))) + '/../' |
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| 227 | |
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| 228 | # Fortran source directory |
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| 229 | self.exedir = self.ecmwfdatadir + 'src/' |
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| 230 | |
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| 231 | return |
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| 232 | |
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| 233 | def __str__(self): |
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| 234 | ''' |
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| 235 | @Description: |
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| 236 | Prepares a string which have all the ControlFile |
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| 237 | class attributes with its associated values. |
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| 238 | Each attribute is printed in one line and in |
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| 239 | alphabetical order. |
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| 240 | |
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| 241 | Example: |
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| 242 | 'age': 10 |
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| 243 | 'color': 'Spotted' |
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| 244 | 'kids': 0 |
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| 245 | 'legs': 2 |
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| 246 | 'name': 'Dog' |
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| 247 | 'smell': 'Alot' |
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| 248 | |
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| 249 | @Input: |
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| 250 | self: instance of ControlFile class |
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| 251 | Description see class documentation. |
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| 252 | |
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| 253 | @Return: |
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| 254 | string of ControlFile class attributes with their values |
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| 255 | ''' |
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| 256 | import collections |
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| 257 | |
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| 258 | attrs = vars(self) |
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| 259 | attrs = collections.OrderedDict(sorted(attrs.items())) |
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| 260 | |
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| 261 | return '\n'.join("%s: %s" % item for item in attrs.items()) |
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| 262 | |
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| 263 | def assign_args_to_control(self, args): |
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| 264 | ''' |
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| 265 | @Description: |
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| 266 | Overwrites the existing ControlFile instance attributes with |
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| 267 | the command line arguments. |
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| 268 | |
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| 269 | @Input: |
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| 270 | self: instance of ControlFile class |
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| 271 | Description see class documentation. |
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| 272 | |
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| 273 | args: instance of ArgumentParser |
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| 274 | Contains the commandline arguments from script/program call. |
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| 275 | |
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| 276 | @Return: |
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| 277 | <nothing> |
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| 278 | ''' |
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| 279 | |
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| 280 | # get dictionary of command line parameters and eliminate all |
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| 281 | # parameters which are None (were not specified) |
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| 282 | args_dict = vars(args) |
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| 283 | arguments = {k : args_dict[k] for k in args_dict |
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| 284 | if args_dict[k] != None} |
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| 285 | |
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| 286 | # assign all passed command line arguments to ControlFile instance |
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| 287 | for k, v in arguments.iteritems(): |
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| 288 | setattr(self, str(k), v) |
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| 289 | |
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| 290 | return |
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| 291 | |
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| 292 | def assign_envs_to_control(self, envs): |
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| 293 | ''' |
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| 294 | @Description: |
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| 295 | Assigns the ECMWF environment parameter. |
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| 296 | |
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| 297 | @Input: |
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| 298 | envs: dict of strings |
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| 299 | Contains the ECMWF environment parameternames "ECUID", "ECGID", |
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| 300 | "DESTINATION" and "GATEWAY" with its corresponding values. |
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| 301 | They were read from the file "ECMWF_ENV". |
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| 302 | |
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| 303 | @Return: |
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| 304 | <nothing> |
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| 305 | ''' |
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| 306 | |
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| 307 | for k, v in envs.iteritems(): |
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| 308 | setattr(self, str(k).lower(), str(v)) |
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| 309 | |
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| 310 | return |
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| 311 | |
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| 312 | def check_conditions(self): |
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| 313 | ''' |
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| 314 | @Description: |
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| 315 | Checks a couple of necessary attributes and conditions, |
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| 316 | such as if they exist and contain values. |
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| 317 | Otherwise set default values. |
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| 318 | |
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| 319 | @Input: |
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| 320 | self: instance of ControlFile class |
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| 321 | Description see class documentation. |
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| 322 | |
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| 323 | @Return: |
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| 324 | <nothing> |
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| 325 | ''' |
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| 326 | from tools import my_error |
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| 327 | import numpy as np |
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| 328 | |
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| 329 | # check for having at least a starting date |
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| 330 | # otherwise program is not allowed to run |
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| 331 | if self.start_date is None: |
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| 332 | print 'start_date specified neither in command line nor ' + \ |
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| 333 | 'in CONTROL file ' + self.controlfile |
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| 334 | print 'Try "' + sys.argv[0].split('/')[-1] + \ |
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| 335 | ' -h" to print usage information' |
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| 336 | sys.exit(1) |
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| 337 | |
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| 338 | # retrieve just one day if end_date isn't set |
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| 339 | if self.end_date is None: |
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[812283d] | 340 | self.end_date = self.start_date |
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[54a8a01] | 341 | |
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| 342 | # assure consistency of levelist and level |
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| 343 | if self.levelist is None: |
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| 344 | if self.level is None: |
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| 345 | print 'Warning: neither levelist nor level ' + \ |
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| 346 | 'specified in CONTROL file' |
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| 347 | sys.exit(1) |
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[812283d] | 348 | else: |
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| 349 | self.levelist = '1/to/' + self.level |
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| 350 | else: |
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[54a8a01] | 351 | if 'to' in self.levelist.lower(): |
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[812283d] | 352 | self.level = self.levelist.split('/')[2] |
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| 353 | else: |
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| 354 | self.level = self.levelist.split('/')[-1] |
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| 355 | |
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[54a8a01] | 356 | # if area was provided at command line |
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| 357 | # decompse area into its 4 components |
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| 358 | if self.area: |
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| 359 | afloat = '.' in self.area |
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| 360 | l = self.area.split('/') |
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| 361 | if afloat: |
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| 362 | for i, item in enumerate(l): |
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| 363 | item = str(int(float(item) * 1000)) |
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| 364 | self.upper, self.left, self.lower, self.right = l |
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| 365 | |
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| 366 | # prepare step for correct usage |
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| 367 | if '/' in self.step: |
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| 368 | l = self.step.split('/') |
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| 369 | if 'to' in self.step.lower(): |
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| 370 | if 'by' in self.step.lower(): |
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| 371 | ilist = np.arange(int(l[0]), int(l[2]) + 1, int(l[4])) |
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| 372 | self.step = ['{:0>3}'.format(i) for i in ilist] |
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| 373 | else: |
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| 374 | my_error(self.mailfail, self.step + ':\n' + |
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| 375 | 'if "to" is used, please use "by" as well') |
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| 376 | else: |
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| 377 | self.step = l |
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| 378 | |
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| 379 | # if maxstep wasn't provided |
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| 380 | # search for it in the "step" parameter |
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| 381 | if self.maxstep is None: |
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[812283d] | 382 | self.maxstep = 0 |
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| 383 | for s in self.step: |
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| 384 | if int(s) > self.maxstep: |
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| 385 | self.maxstep = int(s) |
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| 386 | else: |
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| 387 | self.maxstep = int(self.maxstep) |
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| 388 | |
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[54a8a01] | 389 | # set root scripts since it is needed later on |
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| 390 | if not self.flexpart_root_scripts: |
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| 391 | self.flexpart_root_scripts = self.ecmwfdatadir |
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[812283d] | 392 | |
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[54a8a01] | 393 | if not isinstance(self.mailfail, list): |
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| 394 | if ',' in self.mailfail: |
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| 395 | self.mailfail = self.mailfail.split(',') |
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| 396 | elif ' ' in self.mailfail: |
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| 397 | self.mailfail = self.mailfail.split() |
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| 398 | else: |
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| 399 | self.mailfail = [self.mailfail] |
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[812283d] | 400 | |
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[54a8a01] | 401 | if not isinstance(self.mailops, list): |
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| 402 | if ',' in self.mailops: |
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| 403 | self.mailops = self.mailops.split(',') |
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| 404 | elif ' ' in self.mailops: |
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| 405 | self.mailops = self.mailops.split() |
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| 406 | else: |
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| 407 | self.mailops = [self.mailops] |
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| 408 | |
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| 409 | if not self.gateway or not self.destination or \ |
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| 410 | not self.ecuid or not self.ecgid: |
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| 411 | print '\nEnvironment variables GATWAY, DESTINATION, ECUID and ' + \ |
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| 412 | 'ECGID were not set properly!' |
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| 413 | print 'Please check for excistence of file "ECMWF_ENV" in the ' + \ |
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| 414 | 'python directory!' |
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| 415 | sys.exit(1) |
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[812283d] | 416 | |
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| 417 | return |
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| 418 | |
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[54a8a01] | 419 | def check_install_conditions(self): |
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[812283d] | 420 | ''' |
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| 421 | @Description: |
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[54a8a01] | 422 | Checks a couple of necessary attributes and conditions |
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| 423 | for the installation such as if they exist and contain values. |
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| 424 | Otherwise set default values. |
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[812283d] | 425 | |
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| 426 | @Input: |
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| 427 | self: instance of ControlFile class |
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| 428 | Description see class documentation. |
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| 429 | |
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| 430 | @Return: |
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[54a8a01] | 431 | <nothing> |
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[812283d] | 432 | ''' |
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| 433 | |
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[54a8a01] | 434 | if self.install_target and \ |
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| 435 | self.install_target not in ['local', 'ecgate', 'cca']: |
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| 436 | print 'ERROR: unknown or missing installation target ' |
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| 437 | print 'target: ', self.install_target |
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| 438 | print 'please specify correct installation target \ |
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| 439 | (local | ecgate | cca)' |
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| 440 | print 'use -h or --help for help' |
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| 441 | sys.exit(1) |
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| 442 | |
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| 443 | if self.install_target and self.install_target != 'local': |
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| 444 | if not self.ecgid or not self.ecuid or \ |
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| 445 | not self.gateway or not self.destination: |
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| 446 | print 'Please enter your ECMWF user id and group id as well as \ |
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| 447 | the \nname of the local gateway and the ectrans \ |
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| 448 | destination ' |
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| 449 | print 'with command line options --ecuid --ecgid \ |
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| 450 | --gateway --destination' |
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| 451 | print 'Try "' + sys.argv[0].split('/')[-1] + \ |
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| 452 | ' -h" to print usage information' |
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| 453 | print 'Please consult ecaccess documentation or ECMWF user \ |
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| 454 | support for further details' |
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| 455 | sys.exit(1) |
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| 456 | |
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| 457 | if not self.flexpart_root_scripts: |
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| 458 | self.flexpart_root_scripts = '${HOME}' |
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| 459 | else: |
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| 460 | self.flexpart_root_scripts = self.flexpart_root_scripts |
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| 461 | else: |
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| 462 | if not self.flexpart_root_scripts: |
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| 463 | self.flexpart_root_scripts = '../' |
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[812283d] | 464 | |
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[54a8a01] | 465 | if not self.makefile: |
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| 466 | self.makefile = 'Makefile.gfortran' |
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| 467 | |
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| 468 | return |
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[812283d] | 469 | |
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[ff99eae] | 470 | def to_list(self): |
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[812283d] | 471 | ''' |
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| 472 | @Description: |
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| 473 | Just generates a list of strings containing the attributes and |
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| 474 | assigned values except the attributes "_expanded", "exedir", |
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| 475 | "ecmwfdatadir" and "flexpart_root_scripts". |
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| 476 | |
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| 477 | @Input: |
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| 478 | self: instance of ControlFile class |
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| 479 | Description see class documentation. |
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| 480 | |
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| 481 | @Return: |
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| 482 | l: list |
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| 483 | A sorted list of the all ControlFile class attributes with |
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| 484 | their values except the attributes "_expanded", "exedir", |
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| 485 | "ecmwfdatadir" and "flexpart_root_scripts". |
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| 486 | ''' |
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| 487 | |
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[54a8a01] | 488 | import collections |
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| 489 | |
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| 490 | attrs = collections.OrderedDict(sorted(vars(self).items())) |
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| 491 | |
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[812283d] | 492 | l = list() |
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| 493 | |
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| 494 | for item in attrs.items(): |
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| 495 | if '_expanded' in item[0]: |
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| 496 | pass |
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| 497 | elif 'exedir' in item[0]: |
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| 498 | pass |
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| 499 | elif 'flexpart_root_scripts' in item[0]: |
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| 500 | pass |
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| 501 | elif 'ecmwfdatadir' in item[0]: |
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| 502 | pass |
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| 503 | else: |
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[ff99eae] | 504 | if isinstance(item[1], list): |
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[812283d] | 505 | stot = '' |
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| 506 | for s in item[1]: |
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| 507 | stot += s + ' ' |
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| 508 | |
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| 509 | l.append("%s %s" % (item[0], stot)) |
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| 510 | else: |
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| 511 | l.append("%s %s" % item) |
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| 512 | |
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| 513 | return sorted(l) |
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[ff99eae] | 514 | |
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