1 | |
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2 | # Standard library imports |
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3 | import os, string, time, logging, sys, glob, pkgutil |
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4 | |
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5 | ## pkgutil is used in file_utils |
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6 | # Third party imports |
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7 | |
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8 | ## Local imports with 3rd party dependencies |
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9 | #### netcdf --- currently only support for cmds2 -- re-arranged to facilitate support for alternative modules |
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10 | |
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11 | import file_utils |
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12 | |
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13 | from file_utils import fileMetadata, ncLib |
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14 | |
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15 | # Local imports |
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16 | import utils_c4 as utils |
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17 | import config_c4 as config |
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18 | |
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19 | reload( utils ) |
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20 | |
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21 | |
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22 | #driving_model_ensemble_member = <CMIP5Ensemble_member> |
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23 | #rcm_version_id = <RCMVersionID> |
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24 | |
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25 | class dummy: |
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26 | pass |
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27 | |
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28 | pathTmplDict = { 'CORDEX':'%(project)s/%(product)s/%(domain)s/%(institute)s/%(driving_model)s/%(experiment)s/%(ensemble)s/%(model)s/%(model_version)s/%(frequency)s/%(variable)s/files/%%(version)s/', \ |
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29 | 'SPECS':'%(project)s/%(product)s/%(institute)s/%(model)s/%(experiment)s_%(series)s/%(start_date)s/%(frequency)s/%(realm)s/%(variable)s/%(ensemble)s/files/%%(version)s/', \ |
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30 | 'CMIP5':'%(project)s/%(product)s/%(institute)s/%(model)s/%(experiment)s/%(frequency)s/%(realm)s/%(table)s/%(ensemble)s/files/%%(version)s/%(variable)s/', \ |
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31 | '__def__':'%(project)s/%(product)s/%(institute)s/%(model)s/%(experiment)s/%(frequency)s/%(realm)s/%(variable)s/%(ensemble)s/files/%%(version)s/', \ |
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32 | } |
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33 | |
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34 | class recorder: |
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35 | |
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36 | def __init__(self,project,fileName,type='map',dummy=False): |
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37 | self.dummy = dummy |
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38 | self.file = fileName |
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39 | self.type = type |
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40 | self.pathTmpl = '%(project)s/%(product)s/%(domain)s/%(institute)s/%(driving_model)s/%(experiment)s/%(ensemble)s/%(model)s/%(model_version)s/%(frequency)s/%(variable)s/files/%%(version)s/' |
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41 | self.pathTmpl = pathTmplDict.get(project,pathTmplDict['__def__']) |
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42 | self.records = {} |
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43 | |
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44 | def open(self): |
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45 | if self.type == 'map': |
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46 | self.fh = open( self.file, 'a' ) |
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47 | else: |
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48 | self.sh = shelve.open( self.file ) |
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49 | |
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50 | def close(self): |
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51 | if self.type == 'map': |
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52 | self.fh.close() |
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53 | else: |
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54 | self.sh.close() |
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55 | |
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56 | def add(self,fpath,drs,safe=True): |
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57 | assert self.type == 'map','Can only do map files at present' |
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58 | assert type(drs) == type( {} ), '2nd user argument to method add should be a dictionary [%s]' % type(drs) |
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59 | tpath = self.pathTmpl % drs |
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60 | if not self.dummy: |
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61 | assert os.path.isfile( fpath ), 'File %s not found' % fpath |
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62 | fdate = time.ctime(os.path.getmtime(fpath)) |
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63 | sz = os.stat(fpath).st_size |
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64 | else: |
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65 | fdate = "na" |
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66 | sz = 0 |
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67 | record = '%s | OK | %s | modTime = %s | target = %s ' % (fpath,sz,fdate,tpath) |
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68 | for k in ['creation_date','tracking_id']: |
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69 | if k in drs.keys(): |
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70 | record += ' | %s = %s' % (k,drs[k]) |
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71 | |
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72 | fn = string.split( fpath, '/' )[-1] |
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73 | self.records[fn] = record |
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74 | |
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75 | def modify(self,fn,msg): |
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76 | assert fn in self.records.keys(),'Attempt to modify non-existent record %s, %s' % [fn,str(self.records.keys()[0:10])] |
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77 | if string.find( self.records[fn], '| OK |') == -1: |
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78 | ##print 'File %s already flagged with errors' % fn |
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79 | return |
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80 | s = string.replace( self.records[fn], '| OK |', '| %s |' % msg ) |
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81 | ##print '--> ',s |
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82 | self.records[fn] = s |
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83 | |
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84 | def dumpAll(self,safe=True): |
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85 | keys = self.records.keys() |
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86 | keys.sort() |
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87 | for k in keys: |
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88 | self.dump( self.records[k], safe=safe ) |
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89 | |
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90 | def dump( self, record, safe=True ): |
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91 | if safe: |
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92 | self.open() |
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93 | self.fh.write( record + '\n' ) |
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94 | if safe: |
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95 | self.close() |
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96 | |
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97 | def addErr(self,fpath,reason,safe=True): |
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98 | record = '%s | %s' % (fpath, reason) |
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99 | fn = string.split( fpath, '/' )[-1] |
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100 | self.records[fn] = record |
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101 | |
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102 | class checker: |
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103 | def __init__(self, pcfg, cls,reader,abortMessageCount=-1): |
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104 | self.info = dummy() |
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105 | self.info.pcfg = pcfg |
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106 | self.info.abortMessageCount = abortMessageCount |
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107 | self.calendar = 'None' |
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108 | self.ncReader = reader |
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109 | self.cfn = utils.checkFileName( parent=self.info,cls=cls) |
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110 | self.cga = utils.checkGlobalAttributes( parent=self.info,cls=cls) |
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111 | self.cgd = utils.checkStandardDims( parent=self.info,cls=cls) |
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112 | self.cgg = utils.checkGrids( parent=self.info,cls=cls) |
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113 | self.cls = cls |
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114 | |
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115 | # Define vocabs based on project |
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116 | ##self.vocabs = getVocabs(pcgf) |
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117 | self.vocabs = pcfg.vocabs |
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118 | |
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119 | def checkFile(self,fpath,log=None,attributeMappings=[]): |
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120 | self.calendar = 'None' |
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121 | self.info.log = log |
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122 | |
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123 | fn = string.split( fpath, '/' )[-1] |
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124 | |
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125 | if attributeMappings != []: |
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126 | self.ncReader.loadNc( fpath ) |
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127 | self.ncReader.applyMap( attributeMappings, self.cfn.globalAttributesInFn, log=log ) |
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128 | ncRed = True |
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129 | thisFn = self.ncReader.fn |
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130 | else: |
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131 | ncRed = False |
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132 | thisFn = fn |
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133 | |
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134 | self.cfn.check( thisFn ) |
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135 | if not self.cfn.completed: |
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136 | self.completed = False |
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137 | return |
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138 | if not self.info.pcfg.project[:2] == '__': |
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139 | if not os.path.isfile( fpath ): |
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140 | print 'File %s not found [2]' % fpath |
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141 | self.completed = False |
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142 | return |
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143 | |
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144 | if not ncRed: |
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145 | ##print fpath |
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146 | self.ncReader.loadNc( fpath ) |
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147 | self.ga = self.ncReader.ga |
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148 | self.va = self.ncReader.va |
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149 | self.da = self.ncReader.da |
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150 | |
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151 | if self.cfn.freq != None: |
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152 | vGroup = self.cfn.freq |
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153 | else: |
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154 | vGroup = self.info.pcfg.mipVocabVgmap.get(self.cfn.group,self.cfn.group) |
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155 | self.cga.check( self.ga, self.va, self.cfn.var, vGroup, self.vocabs, self.cfn.fnParts ) |
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156 | if not self.cga.completed: |
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157 | self.completed = False |
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158 | return |
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159 | |
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160 | ##self.cgd.plevRequired = config.plevRequired |
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161 | ##self.cgd.plevValues = config.plevValues |
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162 | ##self.cgd.heightRequired = config.heightRequired |
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163 | ##self.cgd.heightValues = config.heightValues |
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164 | ##self.cgd.heightRange = config.heightRange |
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165 | self.cgd.check( self.cfn.var, self.cfn.freq, self.da, self.va, self.cga.isInstantaneous ) |
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166 | self.calendar = self.cgd.calendar |
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167 | if not self.cgd.completed: |
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168 | self.completed = False |
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169 | return |
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170 | |
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171 | if self.info.pcfg.doCheckGrids: |
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172 | ##self.cgg.rotatedPoleGrids = config.rotatedPoleGrids |
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173 | ##self.cgg.interpolatedGrids = config.interpolatedGrids |
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174 | self.cgg.check( self.cfn.var, self.cfn.domain, self.da, self.va ) |
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175 | |
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176 | if not self.cgg.completed: |
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177 | self.completed = False |
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178 | return |
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179 | self.completed = True |
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180 | self.drs = self.cga.getDrs() |
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181 | self.drs['project'] = self.info.pcfg.project |
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182 | self.errorCount = self.cfn.errorCount + self.cga.errorCount + self.cgd.errorCount + self.cgg.errorCount |
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183 | |
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184 | class c4_init: |
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185 | |
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186 | def __init__(self,args=None): |
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187 | self.logByFile = True |
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188 | self.policyFileLogfileMode = 'w' |
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189 | self.policyBatchLogfileMode = 'np' |
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190 | if args==None: |
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191 | args = sys.argv[1:] |
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192 | nn = 0 |
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193 | |
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194 | self.attributeMappingFile = None |
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195 | self.recordFile = 'Rec.txt' |
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196 | self.logDir = 'logs_02' |
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197 | self.errs = [] |
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198 | |
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199 | # Set default project to "CORDEX" |
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200 | self.project = "CORDEX" |
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201 | self.holdExceptions = False |
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202 | forceLogOrg = None |
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203 | |
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204 | while len(args) > 0: |
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205 | next = args.pop(0) |
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206 | if next == '-f': |
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207 | flist = [args.pop(0),] |
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208 | self.logByFile = False |
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209 | elif next == '--log': |
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210 | x = args.pop(0) |
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211 | assert x in ['single','multi','s','m'], 'unrecognised logging option (--log): %s' % (x) |
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212 | if x in ['multi','m']: |
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213 | forceLogOrg = 'multi' |
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214 | elif x in ['single','s']: |
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215 | forceLogOrg = 'single' |
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216 | elif next == '--flfmode': |
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217 | lfmk = args.pop(0) |
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218 | assert lfmk in ['a','n','np','w','wo'], 'Unrecognised file logfile mode (--flfmode): %s' % lfmk |
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219 | self.policyFileLogfileMode = lfmk |
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220 | elif next == '--blfmode': |
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221 | lfmk = args.pop(0) |
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222 | assert lfmk in ['a','n','np','w','wo'], 'Unrecognised batch logfile mode (--blfmode): %s' % lfmk |
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223 | self.policyBatchLogfileMode = lfmk |
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224 | elif next == '-d': |
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225 | fdir = args.pop(0) |
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226 | flist = glob.glob( '%s/*.nc' % fdir ) |
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227 | elif next == '-D': |
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228 | flist = [] |
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229 | fdir = args.pop(0) |
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230 | for root, dirs, files in os.walk( fdir, followlinks=True ): |
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231 | for f in files: |
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232 | fpath = '%s/%s' % (root,f) |
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233 | if (os.path.isfile( fpath ) or os.path.islink( fpath )) and f[-3:] == '.nc': |
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234 | flist.append( fpath ) |
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235 | elif next == '-R': |
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236 | self.recordFile = args.pop(0) |
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237 | elif next == '--ld': |
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238 | self.logDir = args.pop(0) |
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239 | elif next in ['--catchAllExceptions','--cae']: |
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240 | self.holdExceptions = True |
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241 | elif next == '--aMap': |
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242 | self.attributeMappingFile = args.pop(0) |
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243 | assert os.path.isfile( self.attributeMappingFile ), 'The token "--aMap" should be followed by the path or name of a file' |
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244 | elif next == "-p": |
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245 | self.project = args.pop(0) |
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246 | else: |
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247 | print 'Unused argument: %s' % next |
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248 | nn+=1 |
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249 | assert nn==0, 'Aborting because of unused arguments' |
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250 | |
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251 | if self.project == 'CMIP5': |
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252 | fl0 = [] |
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253 | for f in flist: |
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254 | if string.find( f, '/latest/' ) != -1: |
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255 | fl0.append(f) |
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256 | flist = fl0 |
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257 | |
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258 | if forceLogOrg != None: |
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259 | if forceLogOrg == 'single': |
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260 | self.logByFile = False |
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261 | else: |
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262 | self.logByFile = True |
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263 | |
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264 | if self.project[:2] == '__': |
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265 | flist = [] |
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266 | ss = 'abcdefgijk' |
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267 | ss = 'abcdefgijklmnopqrstuvwxyz' |
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268 | ss = 'abc' |
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269 | for i in range(10): |
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270 | v = 'v%s' % i |
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271 | for a in ss: |
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272 | for b in ss: |
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273 | flist.append( '%s_day_%s_%s_1900-1909.nc' % (v,a,b) ) |
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274 | flist.sort() |
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275 | fnl = [] |
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276 | for f in flist: |
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277 | fn = string.split(f, '/')[-1] |
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278 | fnl.append(fn) |
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279 | nd = 0 |
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280 | dupl = [] |
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281 | for k in range(len(fnl)-1): |
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282 | if fnl[k] == fnl[k-1]: |
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283 | nd += 1 |
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284 | dupl.append( fnl[k] ) |
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285 | self.dupDict = {} |
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286 | for f in dupl: |
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287 | self.dupDict[f] = 0 |
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288 | if nd != 0: |
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289 | self.errs.append( 'Duplicate file names encountered: %s' % nd ) |
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290 | self.errs.append( dupl ) |
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291 | self.flist = flist |
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292 | self.fnl = fnl |
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293 | if not os.path.isdir( self.logDir ): |
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294 | os.mkdir( self.logDir ) |
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295 | |
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296 | tstring1 = '%4.4i%2.2i%2.2i_%2.2i%2.2i%2.2i' % time.gmtime()[0:6] |
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297 | self.batchLogfile = '%s/qcBatchLog_%s.txt' % ( self.logDir,tstring1) |
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298 | ## default appending to myapp.log; mode='w' forces a new file (deleting old contents). |
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299 | self.logger = logging.getLogger('c4logger') |
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300 | if self.policyBatchLogfileMode in ['n','np']: |
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301 | assert not os.path.isfile( self.batchLogfile ), '%s exists and policy set to new file' % self.batchLogfile |
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302 | m = self.policyBatchLogfileMode[0] |
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303 | if m == 'n': |
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304 | m = 'w' |
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305 | if m == 'a': |
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306 | self.hdlr = logging.FileHandler(self.batchLogfile) |
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307 | else: |
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308 | self.hdlr = logging.FileHandler(self.batchLogfile,mode=m) |
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309 | formatter = logging.Formatter('%(asctime)s %(levelname)s %(message)s') |
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310 | self.hdlr.setFormatter(formatter) |
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311 | self.logger.setLevel(logging.INFO) |
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312 | self.logger.addHandler(self.hdlr) |
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313 | |
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314 | self.attributeMappings = [] |
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315 | self.attributeMappingsLog = None |
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316 | if self.attributeMappingFile != None: |
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317 | for l in open( self.attributeMappingFile ).readlines(): |
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318 | if l[0] != '#': |
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319 | bb = string.split( string.strip(l), '|' ) |
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320 | assert len(bb) ==2, "Error in experimental module attributeMapping -- configuration line not scanned [%s]" % str(l) |
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321 | bits = string.split( bb[0], ';' ) |
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322 | cl = [] |
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323 | for b in bits: |
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324 | cl.append( string.split(b, '=' ) ) |
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325 | self.attributeMappings.append( ('am001',cl, string.split(bb[1],'=') ) ) |
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326 | self.attributeMappingsLog = open( 'attributeMappingsLog.txt', 'w' ) |
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327 | |
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328 | def getFileLog( self, fn, flf=None ): |
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329 | if flf == None: |
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330 | tstring2 = '%4.4i%2.2i%2.2i' % time.gmtime()[0:3] |
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331 | if fn in self.dupDict.keys(): |
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332 | tag = '__%2.2i' % self.dupDict[fn] |
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333 | self.dupDict[fn] += 1 |
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334 | else: |
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335 | tag = '' |
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336 | self.fileLogfile = '%s/%s%s__qclog_%s.txt' % (self.logDir,fn[:-3],tag,tstring2) |
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337 | if self.policyFileLogfileMode in ['n','np']: |
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338 | assert not os.path.isfile( self.fileLogfile ), '%s exists and policy set to new file' % self.fileLogfile |
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339 | m = self.policyFileLogfileMode[0] |
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340 | if m == 'n': |
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341 | m = 'w' |
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342 | else: |
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343 | m = 'a' |
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344 | self.fileLogfile = flf |
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345 | |
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346 | self.fLogger = logging.getLogger('fileLog_%s_%s' % (fn,m)) |
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347 | if m == 'a': |
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348 | self.fHdlr = logging.FileHandler(self.fileLogfile) |
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349 | else: |
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350 | self.fHdlr = logging.FileHandler(self.fileLogfile,mode=m) |
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351 | fileFormatter = logging.Formatter('%(message)s') |
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352 | self.fHdlr.setFormatter(fileFormatter) |
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353 | self.fLogger.addHandler(self.fHdlr) |
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354 | self.fLogger.setLevel(logging.INFO) |
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355 | return self.fLogger |
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356 | |
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357 | def closeFileLog(self): |
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358 | self.fLogger.removeHandler(self.fHdlr) |
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359 | self.fHdlr.close() |
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360 | if self.policyFileLogfileMode in ['wo','np']: |
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361 | os.popen( 'chmod %s %s;' % (444, self.fileLogfile) ) |
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362 | |
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363 | def closeBatchLog(self): |
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364 | self.logger.removeHandler(self.hdlr) |
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365 | self.hdlr.close() |
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366 | if self.policyBatchLogfileMode in ['wo','np']: |
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367 | os.popen( 'chmod %s %s;' % (444, self.batchLogfile) ) |
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368 | |
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369 | |
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370 | class main: |
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371 | |
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372 | def __init__(self,args=None,abortMessageCount=-1,printInfo=False,monitorFileHandles = False): |
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373 | logDict = {} |
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374 | ecount = 0 |
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375 | c4i = c4_init(args=args) |
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376 | isDummy = c4i.project[:2] == '__' |
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377 | if (ncLib == dummy) and (not isDummy): |
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378 | print ncLib, c4i.project |
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379 | print 'Cannot proceed with non-dummy project without cdms' |
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380 | raise |
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381 | pcfg = config.projectConfig( c4i.project ) |
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382 | ncReader = fileMetadata(dummy=isDummy, attributeMappingsLog=c4i.attributeMappingsLog) |
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383 | self.cc = checker(pcfg, c4i.project, ncReader,abortMessageCount=abortMessageCount) |
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384 | rec = recorder( c4i.project, c4i.recordFile, dummy=isDummy ) |
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385 | if monitorFileHandles: |
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386 | self.monitor = utils.sysMonitor() |
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387 | else: |
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388 | self.monitor = None |
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389 | |
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390 | cal = None |
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391 | c4i.logger.info( 'Starting batch -- number of file: %s' % (len(c4i.flist)) ) |
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392 | if len( c4i.errs ) > 0: |
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393 | for i in range(0,len( c4i.errs ), 2 ): |
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394 | c4i.logger.info( c4i.errs[i] ) |
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395 | |
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396 | self.cc.info.amapListDraft = [] |
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397 | cbv = utils.checkByVar( parent=self.cc.info,cls=c4i.project,monitor=self.monitor) |
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398 | cbv.impt( c4i.flist ) |
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399 | if printInfo: |
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400 | print cbv.info |
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401 | |
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402 | fileLogOpen = False |
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403 | self.resList = [] |
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404 | for f in c4i.flist: |
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405 | rv = False |
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406 | ec = None |
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407 | if monitorFileHandles: |
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408 | nofhStart = self.monitor.get_open_fds() |
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409 | fn = string.split(f,'/')[-1] |
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410 | c4i.logger.info( 'Starting: %s' % fn ) |
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411 | try: |
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412 | ### need to have a unique name, otherwise get mixing of logs despite close statement below. |
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413 | ### if duplicate file names are present, this will be recorded in the main log, tag appended to file level log name (not yet tested). |
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414 | if c4i.logByFile: |
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415 | fLogger = c4i.getFileLog( fn ) |
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416 | logDict[fn] = c4i.fileLogfile |
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417 | c4i.logger.info( 'Log file: %s' % c4i.fileLogfile ) |
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418 | fileLogOpen = True |
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419 | else: |
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420 | fLogger = c4i.logger |
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421 | |
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422 | fLogger.info( 'Starting file %s' % fn ) |
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423 | ## default appending to myapp.log; mode='w' forces a new file (deleting old contents). |
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424 | self.cc.checkFile( f, log=fLogger,attributeMappings=c4i.attributeMappings ) |
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425 | |
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426 | if self.cc.completed: |
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427 | if cal not in (None, 'None') and self.cc.cgd.varGroup != "fx": |
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428 | if cal != self.cc.calendar: |
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429 | cal_change_err_msg = 'Error: change in calendar attribute %s --> %s' % (cal, self.cc.calendar) |
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430 | c4i.logger.info(cal_change_err_msg) |
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431 | fLogger.info(cal_change_err_msg) |
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432 | self.cc.errorCount += 1 |
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433 | |
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434 | cal = self.cc.calendar |
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435 | ec = self.cc.errorCount |
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436 | rv = ec == 0 |
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437 | self.resList.append( (rv,ec) ) |
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438 | |
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439 | if c4i.logByFile: |
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440 | if self.cc.completed: |
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441 | fLogger.info( 'Done -- error count %s' % self.cc.errorCount ) |
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442 | else: |
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443 | fLogger.info( 'Done -- checks not completed' ) |
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444 | c4i.closeFileLog( ) |
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445 | fileLogOpen = False |
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446 | |
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447 | if self.cc.completed: |
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448 | c4i.logger.info( 'Done -- error count %s' % self.cc.errorCount ) |
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449 | ecount += self.cc.errorCount |
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450 | if self.cc.errorCount == 0: |
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451 | rec.add( f, self.cc.drs ) |
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452 | else: |
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453 | rec.addErr( f, 'ERRORS FOUND | errorCount = %s' % self.cc.errorCount ) |
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454 | else: |
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455 | ecount += 20 |
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456 | c4i.logger.info( 'Done -- testing aborted because of severity of errors' ) |
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457 | rec.addErr( f, 'ERRORS FOUND AND CHECKS ABORTED' ) |
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458 | except: |
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459 | c4i.logger.error("Exception has occured" ,exc_info=1) |
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460 | if fileLogOpen: |
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461 | fLogger.error("xxxxxx: FAILED:: Exception has occured" ,exc_info=1) |
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462 | c4i.closeFileLog( ) |
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463 | fileLogOpen = False |
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464 | rec.addErr( f, 'ERROR: Exception' ) |
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465 | if not c4i.holdExceptions: |
---|
466 | raise |
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467 | if monitorFileHandles: |
---|
468 | nofhEnd = self.monitor.get_open_fds() |
---|
469 | if nofhEnd > nofhStart: |
---|
470 | print 'Open file handles: %s --- %s' % (nofhStart, nofhEnd) |
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471 | |
---|
472 | self.cc.info.log = c4i.logger |
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473 | |
---|
474 | if c4i.project not in ['SPECS','CCMI','CMIP5']: |
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475 | cbv.c4i = c4i |
---|
476 | cbv.setLogDict( logDict ) |
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477 | cbv.check( recorder=rec, calendar=self.cc.calendar) |
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478 | try: |
---|
479 | ecount += cbv.errorCount |
---|
480 | except: |
---|
481 | ecount = None |
---|
482 | ncReader.close() |
---|
483 | if type( self.cc.info.amapListDraft ) == type( [] ) and len( self.cc.info.amapListDraft ) > 0: |
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484 | ll = self.cc.info.amapListDraft |
---|
485 | ll.sort() |
---|
486 | oo = open( 'amapDraft.txt', 'w' ) |
---|
487 | oo.write( ll[0] + '\n' ) |
---|
488 | for i in range( 1,len(ll) ): |
---|
489 | if ll[i] != ll[i-1]: |
---|
490 | oo.write( ll[i] + '\n' ) |
---|
491 | oo.close() |
---|
492 | rec.dumpAll() |
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493 | if printInfo: |
---|
494 | print 'Error count %s' % ecount |
---|
495 | ##c4i.hdlr.close() |
---|
496 | c4i.closeBatchLog() |
---|
497 | self.ok = all( map( lambda x: x[0], self.resList ) ) |
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498 | if __name__ == '__main__': |
---|
499 | main(printInfo=True) |
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500 | |
---|
501 | |
---|
502 | ##else: |
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503 | ##f1 = '/data/u10/cordex/AFR-44/SMHI/ECMWF-ERAINT/evaluation/SMHI-RCA4/v1/day/clh/clh_AFR-44_ECMWF-ERAINT_evaluation_r1i1p1_SMHI-RCA4_v1_day_19810101-19851231.nc' |
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504 | ##f2 = '/data/u10/cordex/AFR-44/SMHI/ECMWF-ERAINT/evaluation/SMHI-RCA4/v1/sem/tas/tas_AFR-44_ECMWF-ERAINT_evaluation_r1i1p1_SMHI-RCA4_v1_sem_200012-201011.nc' |
---|
505 | ##f3 = '/data/u10/cordex/AFR-44i/SMHI/ECMWF-ERAINT/evaluation/SMHI-RCA4/v1/mon/tas/tas_AFR-44i_ECMWF-ERAINT_evaluation_r1i1p1_SMHI-RCA4_v1_mon_199101-200012.nc' |
---|
506 | ##cc.checkFile( f3 ) |
---|