| 1 | import string, os, re, stat, sys |
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| 2 | |
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| 3 | ncdumpCmd = 'ncdump' |
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| 4 | ncdumpCmd = '/usr/local/5/bin/ncdump' |
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| 5 | ## |
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| 6 | |
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| 7 | class mipTableScan: |
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| 8 | |
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| 9 | def __init__(self, vats = ['standard_name','long_name','units','cell_methods'] ): |
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| 10 | self.vats = vats |
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| 11 | self.re_cmor_mip2 = re.compile( 'dimensions:(?P<dims>.*?):::' ) |
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| 12 | self.re_vats = { } |
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| 13 | for v in vats: |
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| 14 | self.re_vats[v] = re.compile( '%s:(?P<dims>.*?):::' % v ) |
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| 15 | ## |
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| 16 | def scan_table(self,ll,log,asDict=False,appendTo=None,lax=False,tag=None): |
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| 17 | |
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| 18 | lll0 = map( string.strip, ll ) |
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| 19 | lll = [] |
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| 20 | for l in lll0: |
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| 21 | if len(l) != 0: |
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| 22 | if l[0] != '!': |
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| 23 | lll.append(string.split(l,'!')[0]) |
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| 24 | sll = [] |
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| 25 | sll.append( ['header',[]] ) |
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| 26 | for l in lll: |
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| 27 | k = string.split( l, ':' )[0] |
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| 28 | if k in ['variable_entry','axis_entry']: |
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| 29 | sll.append( [k,[]] ) |
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| 30 | sll[-1][1].append(l) |
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| 31 | |
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| 32 | eee = [] |
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| 33 | for s in sll: |
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| 34 | if s[0] == 'variable_entry': |
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| 35 | bits = string.split(s[1][0],':') |
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| 36 | assert len(bits) == 2, 'Can not unpack: %s' % str(s[1]) |
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| 37 | k,var = map( string.strip, string.split(s[1][0],':') ) |
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| 38 | aa = {'standard_name':None, 'long_name':None,'units':None,'cell_methods':None } |
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| 39 | ds = 'scalar' |
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| 40 | for l in s[1][1:]: |
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| 41 | bits = string.split(l,':') |
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| 42 | k = string.strip(bits[0]) |
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| 43 | v = string.strip( string.join( bits[1:], ':' ) ) |
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| 44 | if k == 'dimensions': |
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| 45 | ds = string.split(v) |
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| 46 | else: |
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| 47 | aa[k] = v |
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| 48 | eee.append( (var,ds,aa,tag) ) |
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| 49 | |
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| 50 | |
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| 51 | checkOldMethod = False |
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| 52 | if checkOldMethod: |
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| 53 | ssss = string.join( lll, ':::' ) |
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| 54 | vitems = string.split( ssss, ':::variable_entry:' )[1:] |
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| 55 | |
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| 56 | ee = [] |
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| 57 | for i in vitems: |
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| 58 | b1 = string.split( i, ':::')[0] |
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| 59 | var = string.strip( b1 ) |
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| 60 | aa = {} |
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| 61 | for v in self.vats: |
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| 62 | mm = self.re_vats[v].findall(i) |
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| 63 | if len(mm) == 1: |
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| 64 | aa[v] = string.strip(mm[0]) |
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| 65 | else: |
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| 66 | aa[v] = 'None' |
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| 67 | |
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| 68 | mm = self.re_cmor_mip2.findall( i ) |
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| 69 | if len(mm) == 1: |
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| 70 | ds = string.split( string.strip(mm[0]) ) |
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| 71 | elif len(mm) == 0: |
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| 72 | ds = 'scalar' |
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| 73 | else: |
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| 74 | if log != None: |
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| 75 | log.warn( 'Mistake?? in scan_table %s' % str(mm) ) |
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| 76 | ds = mm |
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| 77 | raise 'Mistake?? in scan_table %s' % str(mm) |
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| 78 | ee.append( (var,ds,aa,tag) ) |
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| 79 | |
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| 80 | for k in range(len(ee) ): |
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| 81 | if ee[k][0:2] == eee[k][0:2] and ee[k][2]['standard_name'] == eee[k][2]['standard_name'] and ee[k][2]['long_name'] == eee[k][2]['long_name']: |
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| 82 | print 'OK:::', ee[k] |
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| 83 | else: |
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| 84 | print 'DIFF: ',ee[k],eee[k] |
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| 85 | |
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| 86 | if not asDict: |
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| 87 | return tuple( eee ) |
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| 88 | else: |
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| 89 | ff = {} |
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| 90 | for l in eee: |
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| 91 | ff[l[0]] = ( l[1], l[2], l[3] ) |
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| 92 | if appendTo != None: |
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| 93 | for k in ff.keys(): |
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| 94 | assert ff[k][1].has_key( 'standard_name' ), 'No standard name in %s:: %s' % (k,str(ff[k][1].keys())) |
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| 95 | if appendTo.has_key(k): |
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| 96 | if lax and ff[k][1]['standard_name'] != appendTo[k][1]['standard_name']: |
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| 97 | print 'ERROR[X1]: Inconsistent entry definitions %s:: %s [%s] --- %s [%s]' % (k,ff[k][1],ff[k][2], appendTo[k][1], appendTo[k][2]) |
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| 98 | if not lax: |
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| 99 | assert ff[k][1] == appendTo[k][1], 'Inconsistent entry definitions %s:: %s [%s] --- %s [%s]' % (k,ff[k][1],ff[k][2], appendTo[k][1], appendTo[k][2]) |
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| 100 | else: |
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| 101 | appendTo[k] = ff[k] |
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| 102 | return appendTo |
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| 103 | else: |
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| 104 | return ff |
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| 105 | ## |
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| 106 | ## this class carries a logging method, and is used to carry information about datasets being parsed. |
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| 107 | ## |
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| 108 | class qcHandler: |
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| 109 | |
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| 110 | def __init__( self, qcc, log, baseDir, logPasses=True ): |
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| 111 | self.datasets = {} |
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| 112 | self.groups = {} |
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| 113 | self.baseDir = baseDir |
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| 114 | self.logPasses = logPasses |
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| 115 | self.log = log |
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| 116 | self.nofail = True |
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| 117 | self.hasTimeRange = False |
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| 118 | for k in qcc.datasets.keys(): |
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| 119 | self.datasets[k] = {} |
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| 120 | for g in qcc.groups: |
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| 121 | self.groups[g[0]] = { 'pat':g[1]} |
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| 122 | self.msg = {} |
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| 123 | self.msgk = {} |
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| 124 | self.msg['CQC.101.001.001'] = 'File size above 10 bytes' |
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| 125 | self.msg['CQC.101.001.002'] = 'File name matches DRS syntax' |
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| 126 | self.msg['CQC.101.001.003'] = 'File name time component matches DRS syntax' |
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| 127 | self.msg['CQC.101.001.004'] = 'File name component not in vocabulary' |
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| 128 | self.msg['CQC.101.001.005'] = 'File name component does not match regex' |
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| 129 | self.msg['CQC.101.001.006'] = 'File name component does not match regex list' |
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| 130 | self.msg['CQC.101.001.007'] = 'File name component does not match regex list with constraints' |
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| 131 | self.msg['CQC.102.002.001'] = 'File name time components in ADS have same length' |
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| 132 | self.msg['CQC.102.002.002'] = 'File name time components in ADS do not overlap' |
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| 133 | self.msg['CQC.102.002.003'] = 'File name time components in ADS have no gaps' |
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| 134 | self.msg['CQC.102.002.004'] = 'File name time components in ADS have correct gap for monthly data' |
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| 135 | self.msg['CQC.102.002.005'] = 'File name time components present for multi-file dataset' |
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| 136 | self.msg['CQC.102.002.006'] = 'Consistency checks' |
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| 137 | self.msg['CQC.102.002.007'] = 'Required variables' |
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| 138 | self.msg['CQC.102.002.008'] = 'Required data variables' |
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| 139 | self.msg['CQC.102.002.009'] = 'File is a recognised NetCDF format' |
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| 140 | self.msg['CQC.102.002.010'] = 'Variable attributes match tables' |
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| 141 | self.msg['CQC.200.003.001'] = 'NetCDF files occur at one directory level' |
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| 142 | self.msg['CQC.103.003.002'] = 'Conformant version directory' |
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| 143 | self.msg['CQC.103.003.003'] = 'Latest link points to most recent version' |
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| 144 | self.msg['CQC.200.003.004'] = 'ads occurs in a single directory' |
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| 145 | self.msg['CQC.104.004.001'] = 'Consistent global attributes across experiment' |
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| 146 | self.msg['CQC.105.004.002'] = 'Valid calendar attribute' |
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| 147 | self.msg['CQC.101.004.003'] = 'Regular time step in file' |
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| 148 | self.msg['CQC.102.004.004'] = 'Regular time step between files' |
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| 149 | self.msg['CQC.102.004.005'] = 'Exceptions to regular time period' |
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| 150 | self.msg['CQC.102.004.005'] = 'Consistent global attributes across ADS' |
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| 151 | self.msg['CQC.105.004.006'] = 'Consistent global attributes across ensemble' |
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| 152 | self.msg['CQC.101.004.007'] = 'Required global attributes' |
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| 153 | self.msg['CQC.103.900.001'] = 'Identifiedmost recent version' |
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| 154 | self.msg['CQC.103.003.005'] = 'Version directories identified in directory containing "latest"' |
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| 155 | ## error keys: when these occur, further processing of that file is blocked. |
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| 156 | self.errorKeys = ['CQC.101.001.001', 'CQC.101.001.002'] |
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| 157 | ## keys in this list will not be recorded as failed tests. |
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| 158 | self.ignoreKeys = [] |
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| 159 | for k in self.msg.keys(): |
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| 160 | self.msgk[k] = 0 |
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| 161 | |
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| 162 | def _log( self, key, item, msg, ok=False ): |
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| 163 | if ok: |
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| 164 | if self.logPasses: |
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| 165 | thisMsg = '%s OK: %s: %s: %s' % (key,item,self.msg[key], msg) |
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| 166 | self.log.info( thisMsg ) |
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| 167 | return |
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| 168 | |
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| 169 | if key not in self.ignoreKeys: |
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| 170 | self.nofail = False |
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| 171 | item = string.replace( item, self.baseDir, '' ) |
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| 172 | if key in self.errorKeys: |
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| 173 | self.log.error( '%s [ERROR] FAIL !(%s): %s: %s' % (key,self.msg[key], item,msg)) |
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| 174 | self.noerror = False |
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| 175 | else: |
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| 176 | thisMsg = '%s FAIL !(%s): %s: %s' % (key,self.msg[key],item, msg) |
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| 177 | self.log.info( thisMsg ) |
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| 178 | |
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| 179 | self.msgk[key] += 1 |
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| 180 | |
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| 181 | class dirParser: |
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| 182 | |
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| 183 | def __init__(self, qcc, linksOnly=True): |
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| 184 | self.nclevs = [] |
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| 185 | self.qcc = qcc |
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| 186 | self.dirNames = {} |
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| 187 | self.count_nc = 0 |
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| 188 | self.linksOnly=linksOnly |
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| 189 | |
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| 190 | def parse( self, handler,dir, files ): |
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| 191 | handler.log.info( 'Directory: %s [%s]' % (dir, len(files)) ) |
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| 192 | bits = string.split(dir,'/') |
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| 193 | thisLev = len(bits) |
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| 194 | files.sort() |
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| 195 | skipf = [] |
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| 196 | |
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| 197 | for f in files: |
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| 198 | if os.path.isdir( '%s/%s' % (dir,f) ) and f in self.qcc.omitDirectories: |
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| 199 | skipf.append(f) |
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| 200 | for f in skipf: |
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| 201 | handler.log.info( 'skipping %s' % f ) |
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| 202 | files.pop( files.index(f) ) |
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| 203 | |
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| 204 | # record diretory names at each level |
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| 205 | if thisLev not in self.dirNames.keys(): |
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| 206 | self.dirNames[thisLev] = [] |
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| 207 | if bits[-1] not in self.dirNames[thisLev]: |
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| 208 | self.dirNames[thisLev].append( bits[-1] ) |
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| 209 | |
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| 210 | ncFiles = [] |
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| 211 | for f in files: |
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| 212 | if f[-3:] == ".nc" and (not self.linksOnly or os.path.islink('%s/%s'%(dir,f))): |
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| 213 | ncFiles.append(f) |
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| 214 | |
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| 215 | # record which directory levels contain netcdf files |
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| 216 | if len(ncFiles) and thisLev not in self.nclevs: |
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| 217 | self.nclevs.append( thisLev ) |
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| 218 | |
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| 219 | tbits = [] |
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| 220 | ncFiles.sort() |
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| 221 | self.count_nc += len( ncFiles ) |
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| 222 | dbits = string.split( string.strip(dir,'/'), '/' ) |
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| 223 | for f in ncFiles: |
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| 224 | fpath = '%s/%s' % (dir,f) |
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| 225 | handler.noerror = True |
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| 226 | handler.nofail = True |
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| 227 | |
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| 228 | if not os.path.islink( fpath ): |
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| 229 | fsb = os.stat( fpath )[stat.ST_SIZE] |
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| 230 | else: |
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| 231 | fsb = os.stat( fpath )[stat.ST_SIZE] |
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| 232 | if fsb < 10: |
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| 233 | handler._log( 'CQC.101.001.001', fpath, '' ) |
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| 234 | |
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| 235 | fbits = string.split( string.split(f,'.')[0], self.qcc.fileNameSegments.sep ) |
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| 236 | if not len( fbits ) in self.qcc.fileNameSegments.nn: |
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| 237 | handler._log( 'CQC.101.001.002', fpath, str(fbits) ) |
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| 238 | ###### |
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| 239 | ###### |
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| 240 | else: |
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| 241 | qfns = self.qcc.fileNameSegments |
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| 242 | ns = {} |
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| 243 | for k in range(len(fbits)): |
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| 244 | ns['fn_%s' % qfns.segments[k][1]] = fbits[k] |
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| 245 | if qfns.segments[k][0] == 'vocabulary': |
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| 246 | assert qfns.segments[k][1] in self.qcc.vocab.keys(), '%s not a valid vocabulary name' % qfns.segments[k][1] |
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| 247 | if not fbits[k] in self.qcc.vocab[qfns.segments[k][1]]: |
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| 248 | handler._log( 'CQC.101.001.004', fpath, 'Not in vocab %s' % qfns.segments[k][1] ) |
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| 249 | elif qfns.segments[k][0] == 'abstractVocab': |
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| 250 | assert qfns.segments[k][1] in self.qcc.vocab.keys(), '%s not a valid abstract vocabulary name' % qfns.segments[k][1] |
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| 251 | this = self.qcc.vocab[qfns.segments[k][1]] |
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| 252 | assert this[0] == 'regex', 'Unexpected start of abstractVocab, %s' % str( this ) |
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| 253 | match = False |
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| 254 | for s,t,tt in this[1]: |
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| 255 | if s.match( fbits[k] ): |
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| 256 | match = True |
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| 257 | ## print 'Match [%s] found for %s {%s}' % (t,fbits[k],tt) |
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| 258 | for k in y.groupdict().keys(): |
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| 259 | ns['fnre_%s' % k] = y.groupdict()[k] |
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| 260 | if tt != None: |
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| 261 | ##print 'trying further test' |
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| 262 | tt1 = string.replace(tt,'$','_arg_') |
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| 263 | y = s.match( fbits[k] ) |
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| 264 | for k in y.groupdict().keys(): |
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| 265 | eval( '_arg_%s = int( %s )' % (k,y.groupdict()[k] ) ) |
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| 266 | eval( 'res = tt1' ) |
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| 267 | ##print res |
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| 268 | else: |
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| 269 | pass |
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| 270 | ## print 'no match [%s] for %s ' % (t,fbits[k]) |
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| 271 | |
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| 272 | if not match: |
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| 273 | handler._log( 'CQC.101.001.006', fpath, 'Failed abstractVocab regex tests %s' % fbits[k] ) |
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| 274 | elif qfns.segments[k][0] == 'condAbstractVocab': |
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| 275 | assert qfns.segments[k][1] in self.qcc.vocab.keys(), '%s not a valid abstract vocabulary name' % qfns.segments[k][1] |
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| 276 | this = self.qcc.vocab[qfns.segments[k][1]] |
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| 277 | assert this[0] == 'regex', 'Unexpected start of abstractVocab, %s' % str( this ) |
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| 278 | match = False |
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| 279 | olc = 0 |
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| 280 | for sss in this[1]: |
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| 281 | ol = False |
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| 282 | if sss[0] == '*': |
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| 283 | ol = True |
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| 284 | else: |
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| 285 | for b in string.split(sss[0],','): |
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| 286 | if b in fbits: |
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| 287 | ol = True |
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| 288 | if ol: |
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| 289 | nunc = 0 |
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| 290 | olc += 1 |
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| 291 | for s,t,tt in sss[1]: |
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| 292 | |
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| 293 | if not match: |
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| 294 | y = s.match( fbits[k] ) |
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| 295 | if y: |
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| 296 | ## print 'Match [%s] found for %s {%s}' % (t,fbits[k],tt) |
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| 297 | nunc += 1 |
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| 298 | for key in y.groupdict().keys(): |
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| 299 | ns['fnre_%s' % key] = y.groupdict()[key] |
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| 300 | ##print '--- Match [%s] found for %s {%s}' % (t,fbits[k],tt) |
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| 301 | if tt != None: |
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| 302 | ## create string with test condition.` |
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| 303 | tt1 = string.replace(tt,'$','_arg_') |
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| 304 | y = s.match( fbits[k] ) |
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| 305 | for key in y.groupdict().keys(): |
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| 306 | locals()['_arg_%s' % key ] = int( y.groupdict()[key] ) |
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| 307 | ##print '_arg_%s' % key , locals()['_arg_%s' % key ] |
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| 308 | res = eval( tt1 ) |
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| 309 | ## print '#####', res,tt1 |
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| 310 | if res: |
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| 311 | match = True |
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| 312 | else: |
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| 313 | match = True |
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| 314 | else: |
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| 315 | ##print 'no match [%s] for %s ' % (t,fbits[k]) |
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| 316 | pass |
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| 317 | ##else: |
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| 318 | ##print 'No overlap for %s, %s' % (sss[0],str(fbits)) |
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| 319 | if olc == 0: |
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| 320 | ##print 'No matches fround for %s' % str(fbits) |
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| 321 | pass |
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| 322 | |
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| 323 | if not match: |
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| 324 | handler._log( 'CQC.101.001.007', fpath, 'Failed constrained regex tests %s (%s unconditional matches)' % (fbits[k], nunc) ) |
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| 325 | elif qfns.segments[k][0] == 'regex-match': |
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| 326 | res = qfns.segments[k][2].match( fbits[k] ) |
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| 327 | if res == None: |
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| 328 | handler._log( 'CQC.101.001.005', fpath, 'Failed regex-match test: %s [%s]' % (fbits[k],qfns.segments[k][1] ) ) |
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| 329 | elif qfns.segments[k][0] == 'vocabulary*': |
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| 330 | pass |
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| 331 | else: |
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| 332 | print 'segment test id %s not recognised' % qfns.segments[k][0] |
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| 333 | raise 'segment test id %s not recognised' % qfns.segments[k][0] |
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| 334 | ################################## |
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| 335 | versionned = False |
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| 336 | if not versionned: |
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| 337 | for k in self.qcc.datasets.keys(): |
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| 338 | if self.qcc.datasets[k].datasetIdArg == 'fileNameBits': |
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| 339 | dsId = self.qcc.datasets[k].getDatasetId( fbits ) |
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| 340 | elif self.qcc.datasets[k].datasetIdArg == 'filePathBits': |
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| 341 | try: |
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| 342 | dsId = self.qcc.datasets[k].getDatasetId( fbits, dbits ) |
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| 343 | except: |
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| 344 | print 'Failed to get dsID:',fbits,dbits |
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| 345 | raise |
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| 346 | else: |
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| 347 | assert False, 'datasetIdMethod %s not supported yet' % self.qcc.datasets[k].datasetIdMethod |
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| 348 | |
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| 349 | if os.path.islink( fpath ): |
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| 350 | dsId += '_lnk' |
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| 351 | if not handler.datasets[k].has_key( dsId ): |
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| 352 | handler.datasets[k][dsId] = [] |
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| 353 | handler.datasets[k][dsId].append( (dir,f, handler.nofail, ns) ) |
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| 354 | |
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| 355 | class dataSetParser: |
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| 356 | |
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| 357 | def __init__(self,qcc, log, handler): |
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| 358 | self.qcc = qcc |
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| 359 | self.log = log |
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| 360 | self.h = handler |
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| 361 | self.re_istr = re.compile( '^[0-9]*$' ) |
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| 362 | |
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| 363 | def parse(self,dsclass, dsid, files, inFileChecks=False, forceInFileChecks=True): |
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| 364 | self.h.nofail = True |
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| 365 | ## allowEndPeriodEqual should only be permitted for time averaged fields, but in this version it is set true for all fields. |
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| 366 | allowEndPeriodEqual = True |
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| 367 | try: |
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| 368 | fns = map( lambda x: x[1], self.qcc.fileNameSegments.segments ) |
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| 369 | except: |
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| 370 | print self.qcc.fileNameSegments.segments |
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| 371 | raise |
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| 372 | dsok = True |
|---|
| 373 | for dir,f, fok, ns in files: |
|---|
| 374 | dsok &= fok |
|---|
| 375 | |
|---|
| 376 | self.h.nofail = dsok |
|---|
| 377 | ## |
|---|
| 378 | ## this test should have a switch -- only to be applied to one category of file group |
|---|
| 379 | ## need dsclass constraints |
|---|
| 380 | ## |
|---|
| 381 | ## constraint: setOnce: |
|---|
| 382 | ## |
|---|
| 383 | if dsok: |
|---|
| 384 | if self.qcc.hasTimeRange: |
|---|
| 385 | allOk = True |
|---|
| 386 | tbl = [] |
|---|
| 387 | for dir,f, fok, ns in files: |
|---|
| 388 | thisOk = True |
|---|
| 389 | fbits = string.split( string.split(f,'.')[0], self.qcc.fileNameSegments.sep ) |
|---|
| 390 | thisOk, tb = self.qcc.timeRange.get( fbits ) |
|---|
| 391 | |
|---|
| 392 | allOk &= thisOk |
|---|
| 393 | tbl.append( tb ) |
|---|
| 394 | |
|---|
| 395 | if allOk: |
|---|
| 396 | kkl = [] |
|---|
| 397 | for tb in tbl: |
|---|
| 398 | kk = 0 |
|---|
| 399 | for i in range(2): |
|---|
| 400 | if tb[i] != None: |
|---|
| 401 | ## tb[i] = int(tb[i]) |
|---|
| 402 | kk+=1 |
|---|
| 403 | kkl.append(kk) |
|---|
| 404 | |
|---|
| 405 | thisOk = True |
|---|
| 406 | cc = '' |
|---|
| 407 | for k in range( len(tbl)-1 ): |
|---|
| 408 | if kkl[k] != kkl[0]: |
|---|
| 409 | thisOk = False |
|---|
| 410 | cc += str(files[k]) |
|---|
| 411 | self.h._log( 'CQC.102.002.001', cc, '', ok=thisOk ) |
|---|
| 412 | |
|---|
| 413 | self.h._log( 'CQC.102.002.005', '%s@%s' % (dsid,dsclass), '', ok=not(thisOk and kkl[0] == 0 and len(files) > 1) ) |
|---|
| 414 | |
|---|
| 415 | if thisOk and kkl[0] == 2: |
|---|
| 416 | cc = '' |
|---|
| 417 | for k in range( len(tbl) -1 ): |
|---|
| 418 | if tbl[k+1][0] < tbl[k][1] or (tbl[k+1][0] == tbl[k][1] and not allowEndPeriodEqual): |
|---|
| 419 | thisOk = False |
|---|
| 420 | cc += '%s, %s [%s,%s];' % (str(files[k]), str(files[k+1]),tbl[k][1],tbl[k+1][0]) |
|---|
| 421 | self.h._log( 'CQC.102.002.002', cc, '', ok=thisOk ) |
|---|
| 422 | |
|---|
| 423 | ### |
|---|
| 424 | ### run group constraints |
|---|
| 425 | ### |
|---|
| 426 | if self.qcc.groupConstraints.has_key( dsclass ): |
|---|
| 427 | for ct in self.qcc.groupConstraints[dsclass]: |
|---|
| 428 | ct.__reset__() |
|---|
| 429 | for dir,f, fok, ns in files: |
|---|
| 430 | if fok: |
|---|
| 431 | ### |
|---|
| 432 | rv,res = ct.check( ns ) |
|---|
| 433 | if rv != 'PASS': |
|---|
| 434 | self.h._log( ct.code, f, ct.msg, False ) |
|---|
| 435 | |
|---|
| 436 | ## |
|---|
| 437 | ## should only do the in-file checks once |
|---|
| 438 | ## intention is to be able to have multiple definitions of groups with different tests |
|---|
| 439 | ## |
|---|
| 440 | files2 = [] |
|---|
| 441 | if (self.h.nofail and inFileChecks) or forceInFileChecks: |
|---|
| 442 | ##print 'starting in-file checks' |
|---|
| 443 | import ncd_parse |
|---|
| 444 | for dir,f, fok, ns in files: |
|---|
| 445 | if fok or forceInFileChecks: |
|---|
| 446 | tmpDumpFile = '/tmp/qc_ncdump_tmp.txt' |
|---|
| 447 | if os.path.isfile( tmpDumpFile ): |
|---|
| 448 | os.unlink( tmpDumpFile ) |
|---|
| 449 | targf = '%s/%s' % (dir,f) |
|---|
| 450 | fsb = os.stat( targf )[stat.ST_SIZE] |
|---|
| 451 | assert fsb > 10, 'Small file slipped through: %s, %s' % (targ,fok) |
|---|
| 452 | cmd = '%s -k %s/%s 2>&1 > %s' % (ncdumpCmd,dir,f,tmpDumpFile) |
|---|
| 453 | res = os.popen( cmd ).readlines() |
|---|
| 454 | ii = open( tmpDumpFile ).readlines() |
|---|
| 455 | if len(ii) == 0: |
|---|
| 456 | this_ok = False |
|---|
| 457 | else: |
|---|
| 458 | this_ok = 'Unknown' not in ii[0] |
|---|
| 459 | self.h._log( 'CQC.102.002.009', '%s/%s' % (dir,f), '', ok=this_ok ) |
|---|
| 460 | files2.append( (dir,f, this_ok, ns) ) |
|---|
| 461 | if this_ok: |
|---|
| 462 | cmd = '%s -h %s/%s > %s' % (ncdumpCmd,dir,f,tmpDumpFile) |
|---|
| 463 | ii = os.popen( cmd ).readlines() |
|---|
| 464 | fsb = os.stat( tmpDumpFile )[stat.ST_SIZE] |
|---|
| 465 | assert fsb > 100, 'ncdump output too small, %s/%s' % (dir,f) |
|---|
| 466 | |
|---|
| 467 | rd = ncd_parse.read_ncdump( tmpDumpFile ) |
|---|
| 468 | rd.parse() |
|---|
| 469 | |
|---|
| 470 | ## |
|---|
| 471 | ## messy hack -- copying globals attributes into a new dictionary |
|---|
| 472 | ## |
|---|
| 473 | for k in rd.gats.keys(): |
|---|
| 474 | ns['g_%s' % k] = rd.gats[k] |
|---|
| 475 | ## rd.vars[k] is a tuple: (dims,atts), where atts is a dictionary of attributes. |
|---|
| 476 | for k in rd.vars.keys(): |
|---|
| 477 | ns['v_%s' % k] = rd.vars[k] |
|---|
| 478 | for k in rd.dims.keys(): |
|---|
| 479 | ns['d_%s' % k] = rd.dims[k] |
|---|
| 480 | |
|---|
| 481 | if self.qcc.attributeTests: |
|---|
| 482 | for a in self.qcc.requiredGlobalAttributes: |
|---|
| 483 | self.h._log( 'CQC.101.004.007', '%s/%s' % (dir,f), 'Attribute: %s' % a, ok=a in rd.gats.keys() ) |
|---|
| 484 | |
|---|
| 485 | if self.qcc.variableTests: |
|---|
| 486 | for dir,f, fok, ns in files2: |
|---|
| 487 | if fok: |
|---|
| 488 | for rv in self.qcc.requiredVariables: |
|---|
| 489 | if rv[0][0] != '$': |
|---|
| 490 | self.h._log( 'CQC.102.002.007', f, 'Required variable %s'% (rv[0]), 'v_%s' % rv[0] in ns.keys()) |
|---|
| 491 | |
|---|
| 492 | if self.qcc.groups: |
|---|
| 493 | for dir,f, fok, ns in files2: |
|---|
| 494 | if fok: |
|---|
| 495 | for g in self.qcc.groups: |
|---|
| 496 | gid = g[1] % ns |
|---|
| 497 | if not self.qcc.groupDict[g[0]].has_key( gid ): |
|---|
| 498 | self.qcc.groupDict[g[0]][ gid ] = [] |
|---|
| 499 | self.qcc.groupDict[g[0]][ gid ].append( ( dir,f,fok) ) |
|---|
| 500 | ## print '%s:: %s' % (g[0],gid) |
|---|
| 501 | |
|---|
| 502 | |
|---|
| 503 | if self.qcc.constraintTests: |
|---|
| 504 | for dir,f, fok, ns in files2: |
|---|
| 505 | if fok: |
|---|
| 506 | for ct in self.qcc.constraints: |
|---|
| 507 | ### |
|---|
| 508 | rv,res = ct.check( ns ) |
|---|
| 509 | if rv != 'PASS': |
|---|
| 510 | self.h._log( ct.code, f, ct.msg, False ) |
|---|
| 511 | |
|---|
| 512 | if self.qcc.variableTests: |
|---|
| 513 | for dir,f, fok, ns in files2: |
|---|
| 514 | if fok: |
|---|
| 515 | for v in self.qcc.dataVariables: |
|---|
| 516 | var = ns[v[1]] |
|---|
| 517 | if v[0] == 'ns': |
|---|
| 518 | isPresent = 'v_%s' % var in ns.keys() |
|---|
| 519 | if v[3]: |
|---|
| 520 | self.h._log( 'CQC.102.002.008', f, '%s [%s::%s]'% (var,v[1],v[2]), isPresent ) |
|---|
| 521 | |
|---|
| 522 | |
|---|
| 523 | class dataset: |
|---|
| 524 | def __init__(self,name): |
|---|
| 525 | self.name = name |
|---|
| 526 | |
|---|
| 527 | class qcConfigParse: |
|---|
| 528 | |
|---|
| 529 | def __init__( self, file, log=None ): |
|---|
| 530 | assert os.path.isfile( file ), '%s not found' % file |
|---|
| 531 | self.firstFile = True |
|---|
| 532 | self.fh = open( file ) |
|---|
| 533 | self.file = file |
|---|
| 534 | self.sections = {} |
|---|
| 535 | self.omitDirectories = ['.svn'] |
|---|
| 536 | self.log = log |
|---|
| 537 | self.mipTables = None |
|---|
| 538 | self.mipMapping = None |
|---|
| 539 | self.hasTimeRange = False |
|---|
| 540 | |
|---|
| 541 | def close(self): |
|---|
| 542 | self.fh.close() |
|---|
| 543 | self.file = None |
|---|
| 544 | |
|---|
| 545 | def open(self,file): |
|---|
| 546 | assert os.path.isfile( file ), '%s not found' % file |
|---|
| 547 | self.fh = open( file ) |
|---|
| 548 | self.file = file |
|---|
| 549 | |
|---|
| 550 | def parse_l0(self): |
|---|
| 551 | f = False |
|---|
| 552 | sname = None |
|---|
| 553 | for l in self.fh.readlines(): |
|---|
| 554 | if f: |
|---|
| 555 | if l[0:4] == 'END ' and string.index( l,sname) == 4: |
|---|
| 556 | f = False |
|---|
| 557 | self._parse_l0_section.close() |
|---|
| 558 | else: |
|---|
| 559 | self._parse_l0_section.add( l ) |
|---|
| 560 | elif l[0:6] == 'START ': |
|---|
| 561 | sname = string.strip( string.split(l)[1] ) |
|---|
| 562 | self._parse_l0_section = section_parser_l0( self, sname ) |
|---|
| 563 | f = True |
|---|
| 564 | |
|---|
| 565 | def parse_l1(self): |
|---|
| 566 | |
|---|
| 567 | if self.firstFile: |
|---|
| 568 | requiredSections = ['FILENAME', 'VOCABULARIES','PATH'] |
|---|
| 569 | else: |
|---|
| 570 | requiredSections = [] |
|---|
| 571 | self.firstFile = False |
|---|
| 572 | |
|---|
| 573 | for s in requiredSections: |
|---|
| 574 | assert s in self.sections.keys(), 'Required section %s not found in %s [parsing %s]' % (s, self.section.keys(),self.file) |
|---|
| 575 | self._parse_l1 = section_parser_l1( self ) |
|---|
| 576 | self._parse_l1.parse( 'GENERAL' ) |
|---|
| 577 | self._parse_l1.parse( 'VOCABULARIES' ) |
|---|
| 578 | if self.mipTables != None: |
|---|
| 579 | assert self.mipMapping != None, '"mipMapping" must be set if MIP tables are used' |
|---|
| 580 | ee = {} |
|---|
| 581 | for m in self.mipTables: |
|---|
| 582 | ee[m] = self.vocab[m] |
|---|
| 583 | self.mipConstraint = Constraint__VarAtts( ee, self.mipMapping,self.vocab['mipVarAtts'] ) |
|---|
| 584 | |
|---|
| 585 | self._parse_l1.parse( 'FILENAME' ) |
|---|
| 586 | self._parse_l1.parse( 'PATH' ) |
|---|
| 587 | self._parse_l1.parse( 'ATTRIBUTES' ) |
|---|
| 588 | self._parse_l1.parse( 'VARIABLES' ) |
|---|
| 589 | self._parse_l1.parse( 'CONSTRAINTS' ) |
|---|
| 590 | self._parse_l1.parse( 'GROUPS' ) |
|---|
| 591 | |
|---|
| 592 | regv = re.compile( 'version=([0-9.]+)' ) |
|---|
| 593 | refs = re.compile( 'separator=(.+)' ) |
|---|
| 594 | revsc = re.compile( 'validSectionCount,(.+)' ) |
|---|
| 595 | |
|---|
| 596 | class section_parser_l1: |
|---|
| 597 | |
|---|
| 598 | def __init__(self,parent): |
|---|
| 599 | self.parent = parent |
|---|
| 600 | self.currentSection = None |
|---|
| 601 | self.gc = {} |
|---|
| 602 | self.parent.constraintTests = False |
|---|
| 603 | |
|---|
| 604 | def _getVersion( self ): |
|---|
| 605 | assert self.currentSection != None, '_getVersion called with no section set' |
|---|
| 606 | x = regv.findall( self.currentSection[0] ) |
|---|
| 607 | assert len(x) == 1, 'valid version not identified at start of section: %s\n%s' % (self.currentSectionName,self.currentSection[0]) |
|---|
| 608 | self.version = x[0] |
|---|
| 609 | |
|---|
| 610 | def parse( self, sname ): |
|---|
| 611 | if self.parent.sections.has_key( sname ): |
|---|
| 612 | |
|---|
| 613 | self.currentSectionName = sname |
|---|
| 614 | self.currentSection = self.parent.sections[sname] |
|---|
| 615 | self._getVersion() |
|---|
| 616 | else: |
|---|
| 617 | self.currentSection = None |
|---|
| 618 | |
|---|
| 619 | ## print 'Parsing %s' % sname |
|---|
| 620 | if sname == 'VOCABULARIES': |
|---|
| 621 | self.parent.vocab = {} |
|---|
| 622 | self.parse_vocabularies() |
|---|
| 623 | elif sname == 'FILENAME': |
|---|
| 624 | self.parse_filename() |
|---|
| 625 | elif sname == 'PATH': |
|---|
| 626 | self.parse_path() |
|---|
| 627 | elif sname == 'ATTRIBUTES': |
|---|
| 628 | self.parse_attributes() |
|---|
| 629 | elif sname == 'VARIABLES': |
|---|
| 630 | self.parse_variables() |
|---|
| 631 | elif sname == 'CONSTRAINTS': |
|---|
| 632 | self.parse_constraints() |
|---|
| 633 | elif sname == 'GENERAL': |
|---|
| 634 | self.parse_general() |
|---|
| 635 | elif sname == 'GROUPS': |
|---|
| 636 | self.parse_groups() |
|---|
| 637 | |
|---|
| 638 | def __get_match( self, regex, line, id ): |
|---|
| 639 | x = regex.findall( line ) |
|---|
| 640 | assert len(x) == 1, 'No match found, id=%s, line=%s' % 'id,line' |
|---|
| 641 | return x[0] |
|---|
| 642 | |
|---|
| 643 | def parse_vocabularies(self): |
|---|
| 644 | ## print len( self.currentSection ) |
|---|
| 645 | base = '' |
|---|
| 646 | for l in self.currentSection[1:]: |
|---|
| 647 | bits = map( string.strip, string.split( l, ', ' ) ) |
|---|
| 648 | id = bits[0] |
|---|
| 649 | if id[0:2] == '__': |
|---|
| 650 | assert id[2:] in ['base','mipMapping'], 'vocabulary record not recognised: %s' % l |
|---|
| 651 | if id[2:] == 'base': |
|---|
| 652 | assert os.path.isdir( bits[1] ), '!!!parse_vocabularies: directory %s not found' % bits[1] |
|---|
| 653 | base = bits[1] |
|---|
| 654 | if base[-1] != '/': |
|---|
| 655 | base += '/' |
|---|
| 656 | elif id[2:] == 'mipMapping': |
|---|
| 657 | self.parent.mipMapping = bits[1] |
|---|
| 658 | else: |
|---|
| 659 | isAbstract = False |
|---|
| 660 | if id[0] == '*': |
|---|
| 661 | id = id[1:] |
|---|
| 662 | isAbstract = True |
|---|
| 663 | |
|---|
| 664 | sl = string.split( bits[1], '|' ) |
|---|
| 665 | fromFile = 'file' in sl |
|---|
| 666 | isRegex = 'regex' in sl |
|---|
| 667 | withSub = 'sub' in sl |
|---|
| 668 | isCond = 'cond' in sl |
|---|
| 669 | |
|---|
| 670 | if not fromFile: |
|---|
| 671 | vlist = string.split( bits[2] ) |
|---|
| 672 | else: |
|---|
| 673 | fn = '%s%s' % (base,bits[2]) |
|---|
| 674 | assert os.path.isfile( fn), 'File %s (specified as vocabulary %s) not found' % (fn,bits[0] ) |
|---|
| 675 | ii = open( fn ).readlines() |
|---|
| 676 | bb = string.split( bits[1], '|' ) |
|---|
| 677 | if '1stonline' in sl: |
|---|
| 678 | vlist = [] |
|---|
| 679 | for i in ii: |
|---|
| 680 | if i[0] != '#' and len( string.strip(i) ) > 0: |
|---|
| 681 | vlist.append( string.split( string.strip(i) )[0] ) |
|---|
| 682 | elif '1perline' in sl: |
|---|
| 683 | vlist = map( string.strip, ii ) |
|---|
| 684 | elif 'mip' in sl: |
|---|
| 685 | vlist = self.mipsc.scan_table( ii, self.parent.log ) |
|---|
| 686 | if self.parent.mipTables == None: |
|---|
| 687 | self.parent.mipTables = [] |
|---|
| 688 | self.parent.mipTables.append( id ) |
|---|
| 689 | else: |
|---|
| 690 | assert False, 'file syntax option (%s) not recognised' % bits[1] |
|---|
| 691 | |
|---|
| 692 | if isRegex: |
|---|
| 693 | cr = [] |
|---|
| 694 | if withSub: |
|---|
| 695 | if isCond: |
|---|
| 696 | for ccc in vlist: |
|---|
| 697 | i0 = ccc.index(':') |
|---|
| 698 | cc = ccc[:i0] |
|---|
| 699 | cr0 = [] |
|---|
| 700 | for v in string.split( ccc[i0+1:] ): |
|---|
| 701 | v = string.strip(v) |
|---|
| 702 | if v[0] == '{': |
|---|
| 703 | i1 = v.index('}') |
|---|
| 704 | tt = v[1:i1] |
|---|
| 705 | v = v[i1+1:] |
|---|
| 706 | else: |
|---|
| 707 | tt = None |
|---|
| 708 | v = string.strip( v, "'" ) |
|---|
| 709 | try: |
|---|
| 710 | cr0.append( (re.compile( v % self.gc ),v % self.gc,tt) ) |
|---|
| 711 | except: |
|---|
| 712 | print 'Error trying to compile: ', v % self.gc |
|---|
| 713 | print 'Pattern: ',v |
|---|
| 714 | raise |
|---|
| 715 | ## print 'compiled ' + v % self.gc, tt |
|---|
| 716 | cr.append( (cc,cr0) ) |
|---|
| 717 | else: |
|---|
| 718 | for v in vlist: |
|---|
| 719 | v = string.strip( v, "'" ) |
|---|
| 720 | cr.append( (re.compile( v % self.gc ),v % self.gc) ) |
|---|
| 721 | else: |
|---|
| 722 | for v in vlist: |
|---|
| 723 | v = string.strip( v, "'" ) |
|---|
| 724 | cr.append( (re.compile( v ),v) ) |
|---|
| 725 | self.parent.vocab[id] = ('regex', cr ) |
|---|
| 726 | else: |
|---|
| 727 | self.parent.vocab[id] = vlist[:] |
|---|
| 728 | if id == 'mipVarAtts': |
|---|
| 729 | self.mipsc = mipTableScan( vlist ) |
|---|
| 730 | |
|---|
| 731 | def parse_filename(self): |
|---|
| 732 | sep = self.__get_match( refs, self.currentSection[1], 'File separator' ) |
|---|
| 733 | nn = map( int, string.split( self.__get_match( revsc, self.currentSection[2], 'File separator' ),',') ) |
|---|
| 734 | self.parent.fileNameSegments = fileNameSegments( self.parent, sep, nn ) |
|---|
| 735 | for l in self.currentSection[3:]: |
|---|
| 736 | self.parent.fileNameSegments.add(l) |
|---|
| 737 | self.parent.fileNameSegments.finish() |
|---|
| 738 | |
|---|
| 739 | def parse_attributes(self): |
|---|
| 740 | if self.currentSection == None: |
|---|
| 741 | self.parent.attributeTests = False |
|---|
| 742 | return |
|---|
| 743 | self.parent.requiredGlobalAttributes = [] |
|---|
| 744 | self.parent.attributeTests = True |
|---|
| 745 | for l in self.currentSection[1:]: |
|---|
| 746 | bits = map( string.strip, string.split(l,',')) |
|---|
| 747 | if bits[0] == 'global': |
|---|
| 748 | if bits[2] == 'required': |
|---|
| 749 | self.parent.requiredGlobalAttributes.append( bits[1] ) |
|---|
| 750 | |
|---|
| 751 | def parse_general(self): |
|---|
| 752 | if self.currentSection == None: |
|---|
| 753 | return |
|---|
| 754 | self.parent.requiredGlobalAttributes = [] |
|---|
| 755 | self.parent.dataVariables = [] |
|---|
| 756 | for l in self.currentSection[1:]: |
|---|
| 757 | if l[0] == '$': |
|---|
| 758 | bits = map( string.strip, string.split(l[1:],'=')) |
|---|
| 759 | self.gc[bits[0]] = bits[1] |
|---|
| 760 | else: |
|---|
| 761 | bits = map( string.strip, string.split(l,',')) |
|---|
| 762 | if bits[0] == 'DataVariable': |
|---|
| 763 | if bits[1] == 'byName': |
|---|
| 764 | isRequired = bits[3] == 'required' |
|---|
| 765 | key, msg = ref_to_key( bits[2] ) |
|---|
| 766 | self.parent.dataVariables.append( ('ns',key,msg,isRequired) ) |
|---|
| 767 | |
|---|
| 768 | def parse_groups(self): |
|---|
| 769 | self.parent.groups = [] |
|---|
| 770 | self.parent.groupDict = {} |
|---|
| 771 | if self.currentSection == None: |
|---|
| 772 | return |
|---|
| 773 | for l in self.currentSection[1:]: |
|---|
| 774 | bits = map( string.strip, string.split(l,',')) |
|---|
| 775 | if bits[1] not in self.parent.groupDict.keys(): |
|---|
| 776 | self.parent.groupDict[bits[1]] = {} |
|---|
| 777 | if bits[0] == 'group': |
|---|
| 778 | cc = [] |
|---|
| 779 | for r in string.split( bits[2], '.' ): |
|---|
| 780 | cc.append( '%' + ('(%s)s' % ref_to_key( r )[0] ) ) |
|---|
| 781 | self.parent.groups.append( (bits[1], string.join( cc, '.' ) ) ) |
|---|
| 782 | |
|---|
| 783 | def parse_constraints(self): |
|---|
| 784 | if self.currentSection == None: |
|---|
| 785 | self.parent.constraintTests = False |
|---|
| 786 | return |
|---|
| 787 | self.parent.constraintTests = True |
|---|
| 788 | self.parent.constraints = [] |
|---|
| 789 | self.parent.groupConstraints = {} |
|---|
| 790 | for l in self.currentSection[1:]: |
|---|
| 791 | bits = map( string.strip, string.split(l,',')) |
|---|
| 792 | bb = string.split( bits[0], ':' ) |
|---|
| 793 | if len(bb) == 2: |
|---|
| 794 | gid = bb[0] |
|---|
| 795 | cid = bb[1] |
|---|
| 796 | if gid not in self.parent.groupConstraints.keys(): |
|---|
| 797 | self.parent.groupConstraints[gid] = [] |
|---|
| 798 | else: |
|---|
| 799 | gid = None |
|---|
| 800 | cid = bits[0] |
|---|
| 801 | assert cid in ['identity','onlyOnce','constant','special'], 'constraint id %s not recognised' % cid |
|---|
| 802 | |
|---|
| 803 | if cid == 'identity': |
|---|
| 804 | cstr = Constraint__IdentityChecker( bits[1], bits[2] ) |
|---|
| 805 | elif cid == 'onlyOnce': |
|---|
| 806 | ## print 'Set Constraint only once, %s ' % bits[1] |
|---|
| 807 | cstr = Constraint__OnlyOnce( bits[1] ) |
|---|
| 808 | elif cid == 'constant': |
|---|
| 809 | ## print 'Set Constraint only once, %s ' % bits[1] |
|---|
| 810 | cstr = Constraint__Constant( bits[1] ) |
|---|
| 811 | elif cid == 'special': |
|---|
| 812 | assert bits[1] in ['mip','CordexInterpolatedGrid'], 'Special constraint [%s] not recognised' % bits[1] |
|---|
| 813 | if bits[1] == 'mip': |
|---|
| 814 | cstr = self.parent.mipConstraint |
|---|
| 815 | elif bits[1] == 'CordexInterpolatedGrid': |
|---|
| 816 | cstr = Constraint__CordexInterpolatedGrid() |
|---|
| 817 | |
|---|
| 818 | if gid == None: |
|---|
| 819 | self.parent.constraints.append( cstr ) |
|---|
| 820 | else: |
|---|
| 821 | self.parent.groupConstraints[gid].append( cstr ) |
|---|
| 822 | |
|---|
| 823 | def parse_variables(self): |
|---|
| 824 | if self.currentSection == None: |
|---|
| 825 | self.parent.variableTests = False |
|---|
| 826 | return |
|---|
| 827 | self.parent.variableTests = True |
|---|
| 828 | self.parent.requiredVariables = [] |
|---|
| 829 | for l in self.currentSection[1:]: |
|---|
| 830 | bits = map( string.strip, string.split(l,',')) |
|---|
| 831 | isDimension = bits[0] == 'dimension' |
|---|
| 832 | if bits[2] == 'required': |
|---|
| 833 | if bits[1][0] != '$': |
|---|
| 834 | self.parent.requiredVariables.append( (bits[1],isDimension) ) |
|---|
| 835 | else: |
|---|
| 836 | key,info = ref_to_key( bits[1][1:] ) |
|---|
| 837 | if key == 'VALUE': |
|---|
| 838 | self.parent.requiredVariables.append( (info,isDimension) ) |
|---|
| 839 | else: |
|---|
| 840 | self.parent.requiredVariables.append( ('$%s' % key, isDimension) ) |
|---|
| 841 | |
|---|
| 842 | |
|---|
| 843 | |
|---|
| 844 | def parse_path(self): |
|---|
| 845 | if self.currentSection == None: |
|---|
| 846 | self.pathTests = False |
|---|
| 847 | return |
|---|
| 848 | self.pathTests = True |
|---|
| 849 | self.datasetIdMethod = None |
|---|
| 850 | self.datasetVersionMode = [None,] |
|---|
| 851 | self.parent.datasets = {} |
|---|
| 852 | datasetHierarchy = None |
|---|
| 853 | for l in self.currentSection[1:]: |
|---|
| 854 | bits = map( string.strip, string.split(l,',')) |
|---|
| 855 | if bits[0] == 'datasetVersion': |
|---|
| 856 | vdsName = bits[1] |
|---|
| 857 | if bits[2] == 'pathElement': |
|---|
| 858 | self.datasetVersionMode = ['pathElement',] |
|---|
| 859 | self.versionPathElement = int( bits[3] ) |
|---|
| 860 | if bits[4] == 'regex': |
|---|
| 861 | self.datasetVersionMode.append( 'regex' ) |
|---|
| 862 | self.datasetVersionRe = re.compile( string.strip( bits[5], '"' ) ) |
|---|
| 863 | else: |
|---|
| 864 | self.datasetVersionMode.append( None ) |
|---|
| 865 | elif bits[0] == 'datasetId': |
|---|
| 866 | thisDs = dataset(bits[1]) |
|---|
| 867 | thisDs.datasetIdMethod = bits[2] |
|---|
| 868 | if bits[2] == 'prints': |
|---|
| 869 | thisDs.getDatasetId = lambda x: bits[3] % x |
|---|
| 870 | thisDs.datasetIdTuple = tuple( bits[4:] ) |
|---|
| 871 | elif bits[2] == 'joinFileNameSegSlice': |
|---|
| 872 | thisSlice = slice( int(bits[4]), int(bits[5]) ) |
|---|
| 873 | thisDs.getDatasetId = dsid1( thisSlice, bits[3] ).get |
|---|
| 874 | thisDs.datasetIdArg = 'fileNameBits' |
|---|
| 875 | elif bits[2] == 'cmip5': |
|---|
| 876 | thisSlice = slice( int(bits[4]), int(bits[5]) ) |
|---|
| 877 | thisDs.getDatasetId = cmip5_dsid( thisSlice, bits[3] ).get |
|---|
| 878 | thisDs.datasetIdArg = 'filePathBits' |
|---|
| 879 | self.parent.datasets[bits[1]] = thisDs |
|---|
| 880 | elif bits[0] == 'datasetHierarchy': |
|---|
| 881 | datasetHierarchy = bits[1:] |
|---|
| 882 | elif bits[0] == 'omitDirectories': |
|---|
| 883 | self.parent.omitDirectories = string.split( string.strip( bits[1] ) ) |
|---|
| 884 | |
|---|
| 885 | if self.datasetVersionMode[0] != None: |
|---|
| 886 | assert vdsName in self.parent.datasets.keys(), 'Invalid dataset specified for version: %s [%s]' % (vdsName, str( self.parent.datasets.keys() ) ) |
|---|
| 887 | self.versionnedDataset = self.parent.datasets[ vdsName ] |
|---|
| 888 | |
|---|
| 889 | if datasetHierarchy == None: |
|---|
| 890 | self.datasetHierarchy = False |
|---|
| 891 | else: |
|---|
| 892 | self.datasetHierarchy = True |
|---|
| 893 | bb = string.split( string.strip( datasetHierarchy[0]), '/' ) |
|---|
| 894 | for b in bb: |
|---|
| 895 | assert b in self.parent.datasets.keys(), 'Invalid dataset hierarchy, %s not among defined datasets' % b |
|---|
| 896 | for k in self.parent.datasets.keys(): |
|---|
| 897 | self.parent.datasets[k].inHierarchy = k in bb |
|---|
| 898 | |
|---|
| 899 | for k in range( len(bb) ): |
|---|
| 900 | if k == 0: |
|---|
| 901 | self.parent.datasets[bb[k]].parent = None |
|---|
| 902 | else: |
|---|
| 903 | self.parent.datasets[bb[k]].parent = self.parent.datasets[bb[k-1]] |
|---|
| 904 | if k == len(bb)-1: |
|---|
| 905 | self.parent.datasets[bb[k]].child = None |
|---|
| 906 | else: |
|---|
| 907 | self.parent.datasets[bb[k]].child = self.parent.datasets[bb[k+1]] |
|---|
| 908 | |
|---|
| 909 | class dsid1: |
|---|
| 910 | |
|---|
| 911 | def __init__(self,slice,sep): |
|---|
| 912 | self.slice = slice |
|---|
| 913 | self.sep = sep |
|---|
| 914 | |
|---|
| 915 | def get(self,x): |
|---|
| 916 | return string.join( x[self.slice], self.sep ) |
|---|
| 917 | |
|---|
| 918 | class cmip5_dsid: |
|---|
| 919 | |
|---|
| 920 | def __init__(self,slice,sep): |
|---|
| 921 | self.slice = slice |
|---|
| 922 | self.sep = sep |
|---|
| 923 | |
|---|
| 924 | def get(self,x,y): |
|---|
| 925 | return '%s_%s.%s' % (string.join( x[self.slice], self.sep ) , y[-2], y[-1] ) |
|---|
| 926 | |
|---|
| 927 | |
|---|
| 928 | class get_trange: |
|---|
| 929 | |
|---|
| 930 | def __init__(self,pat,kseg): |
|---|
| 931 | self.kseg = kseg |
|---|
| 932 | self.re_istr = re.compile( '^[0-9]*$' ) |
|---|
| 933 | if type( pat ) == type( 'x' ): |
|---|
| 934 | self.pat = pat |
|---|
| 935 | self.re = re.compile( pat ) |
|---|
| 936 | else: |
|---|
| 937 | self.re = pat |
|---|
| 938 | |
|---|
| 939 | def _test( self, s): |
|---|
| 940 | return self.re.match( s ) != None |
|---|
| 941 | |
|---|
| 942 | def _get( self, s, handler=None ): |
|---|
| 943 | x = self.re.match( s ) |
|---|
| 944 | tb = [None,None] |
|---|
| 945 | if x == None: |
|---|
| 946 | return False, tuple(tb) |
|---|
| 947 | |
|---|
| 948 | thisOk = True |
|---|
| 949 | tb[0] = x.groupdict().get( 'start', None ) |
|---|
| 950 | tb[1] = x.groupdict().get( 'end', None ) |
|---|
| 951 | if x.groupdict().has_key( 'isClim' ): |
|---|
| 952 | tb.append( x.groupdict()['isClim'] ) |
|---|
| 953 | for i in range(2): |
|---|
| 954 | b = tb[i] |
|---|
| 955 | if b != None: |
|---|
| 956 | if self.re_istr.match( b ) == None: |
|---|
| 957 | if handler != None: |
|---|
| 958 | handler._log( 'CQC.101.001.003', dir + f, 'part of string not an integer' ) |
|---|
| 959 | thisOk = False |
|---|
| 960 | else: |
|---|
| 961 | tb[i] = int(tb[i]) |
|---|
| 962 | |
|---|
| 963 | return thisOk, tb |
|---|
| 964 | |
|---|
| 965 | |
|---|
| 966 | def test(self, l ): |
|---|
| 967 | if len(l) < self.kseg + 1: |
|---|
| 968 | return True |
|---|
| 969 | return self._test( l[self.kseg] ) |
|---|
| 970 | |
|---|
| 971 | def get(self,l): |
|---|
| 972 | if len(l) < self.kseg + 1: |
|---|
| 973 | return True, (None,None) |
|---|
| 974 | return self._get( l[self.kseg] ) |
|---|
| 975 | |
|---|
| 976 | class fileNameSegments: |
|---|
| 977 | def __init__(self, parent, sep, nn ): |
|---|
| 978 | self.sep = sep |
|---|
| 979 | self.nn = nn |
|---|
| 980 | self.nn.sort() |
|---|
| 981 | self.__segments = {} |
|---|
| 982 | self.parent = parent |
|---|
| 983 | |
|---|
| 984 | def add( self, line ): |
|---|
| 985 | bits = map( string.strip, string.split( line, ', ' ) ) |
|---|
| 986 | k = int(bits[0]) |
|---|
| 987 | if bits[1] == 'vocabulary': |
|---|
| 988 | assert bits[2] in self.parent.vocab.keys(), 'Vocabulary specified in file name section not defined in vocab sections, %s' % bits[2] |
|---|
| 989 | |
|---|
| 990 | self.__segments[k] = ('vocabulary',bits[2]) |
|---|
| 991 | elif bits[1][0:5] == 'regex' or bits[2] == 'TimeRange': |
|---|
| 992 | try: |
|---|
| 993 | regex = re.compile( string.strip( bits[3], "'") ) |
|---|
| 994 | except: |
|---|
| 995 | print 'Failed to compile (in re): %s' % bits[3] |
|---|
| 996 | raise |
|---|
| 997 | self.__segments[k] = (bits[1],bits[2], regex) |
|---|
| 998 | else: |
|---|
| 999 | self.__segments[k] = tuple( bits[1:] ) |
|---|
| 1000 | |
|---|
| 1001 | if bits[2] == 'TimeRange': |
|---|
| 1002 | self.parent.hasTimeRange = True |
|---|
| 1003 | self.parent.timeRange = get_trange(regex,k) |
|---|
| 1004 | |
|---|
| 1005 | def finish(self): |
|---|
| 1006 | sl = [] |
|---|
| 1007 | for k in range(self.nn[-1]): |
|---|
| 1008 | sl.append( self.__segments.get( k, None ) ) |
|---|
| 1009 | self.segments = tuple( sl ) |
|---|
| 1010 | |
|---|
| 1011 | class Constraint__CordexInterpolatedGrid: |
|---|
| 1012 | |
|---|
| 1013 | def __init__(self): |
|---|
| 1014 | self.code = 'CQC.999.999.999' |
|---|
| 1015 | self.name = 'CordexInterpolatedGrid' |
|---|
| 1016 | self.mode = 'd' |
|---|
| 1017 | |
|---|
| 1018 | def __reset__(self): |
|---|
| 1019 | pass |
|---|
| 1020 | |
|---|
| 1021 | def check(self,fns): |
|---|
| 1022 | region = fns.get( 'g_CORDEX_domain', 'unset' ) |
|---|
| 1023 | assert region != 'unset', 'CORDEX domain not found in %s' % str(fns.keys()) |
|---|
| 1024 | if region[-3:] != '44i': |
|---|
| 1025 | self.msg = 'Interpolated grid constraint not applicable to region %s' % region |
|---|
| 1026 | return ('PASS',self.msg) |
|---|
| 1027 | print 'WARNING -- check not implemented' |
|---|
| 1028 | self.msg = 'WARNING -- check not implemented' |
|---|
| 1029 | return ('PASS',self.msg) |
|---|
| 1030 | |
|---|
| 1031 | class Constraint__IdentityChecker: |
|---|
| 1032 | |
|---|
| 1033 | def __init__(self, ref1, ref2 ): |
|---|
| 1034 | self.code = 'CQC.102.002.006' |
|---|
| 1035 | self.name = 'IdentityChecker' |
|---|
| 1036 | self.mode = 'd' |
|---|
| 1037 | self.Ref1 = self.__parse_ref(ref1) |
|---|
| 1038 | self.Ref2 = self.__parse_ref(ref2) |
|---|
| 1039 | if self.Ref1 == 'VALUE': |
|---|
| 1040 | self.Ref1 = self.Ref2 |
|---|
| 1041 | self.Ref2 = 'VALUE' |
|---|
| 1042 | if self.Ref2 == 'VALUE': |
|---|
| 1043 | self.mode = 's' |
|---|
| 1044 | |
|---|
| 1045 | if self.mode == 's': |
|---|
| 1046 | self.PassMsg = '%s (%s) equals %s' % (self.Ref1[1], ref1, self.value) |
|---|
| 1047 | self.FailMsg = '%s (%s) not equal %s' % (self.Ref1[1], ref1, self.value) |
|---|
| 1048 | else: |
|---|
| 1049 | self.PassMsg = '%s (%s) not equal %s (%s)' % (self.Ref1[1],ref1, self.Ref2[1],ref2) |
|---|
| 1050 | self.FailMsg = '%s (%s) not equal %s (%s)' % (self.Ref1[1],ref1, self.Ref2[1],ref2) |
|---|
| 1051 | |
|---|
| 1052 | def __parse_ref(self,ref): |
|---|
| 1053 | bits = string.split(ref,'/') |
|---|
| 1054 | assert bits[0] in ['VALUE','PATH','FILENAME','ATTRIBUTES','CONFIG','ARGS'], 'Bad line in CONSTRAINT section of config file' |
|---|
| 1055 | if bits[0] == 'ATTRIBUTES': |
|---|
| 1056 | if bits[1] == 'Global': |
|---|
| 1057 | return ('g_%s' % bits[2],'Global attribute %s' % bits[2] ) |
|---|
| 1058 | elif bits[0] == 'FILENAME': |
|---|
| 1059 | return ('fn_%s' % bits[1],'File name component %s' % bits[1] ) |
|---|
| 1060 | elif bits[0] == 'VALUE': |
|---|
| 1061 | self.value = bits[1] |
|---|
| 1062 | return 'VALUE' |
|---|
| 1063 | |
|---|
| 1064 | def __reset__(self): |
|---|
| 1065 | pass |
|---|
| 1066 | |
|---|
| 1067 | def check(self,fns): |
|---|
| 1068 | if self.mode == 's': |
|---|
| 1069 | if fns.has_key( self.Ref1[0] ): |
|---|
| 1070 | if fns[self.Ref1[0]] == self.value: |
|---|
| 1071 | self.msg = self.PassMsg |
|---|
| 1072 | return ('PASS',self.msg) |
|---|
| 1073 | else: |
|---|
| 1074 | self.msg = self.FailMsg + ' [%s]' % fns[self.Ref1[0]] |
|---|
| 1075 | return ('FAIL',self.msg) |
|---|
| 1076 | else: |
|---|
| 1077 | return ('DEFER', 'No entry in fns for %s' % self.Ref1[0]) |
|---|
| 1078 | else: |
|---|
| 1079 | if fns.has_key( self.Ref1[0] ) and fns.has_key( self.Ref2[0] ): |
|---|
| 1080 | if fns[self.Ref1[0]] == fns[self.Ref2[0]]: |
|---|
| 1081 | self.msg = self.PassMsg |
|---|
| 1082 | return ('PASS',self.msg) |
|---|
| 1083 | else: |
|---|
| 1084 | self.msg = self.FailMsg + ' [%s,%s]' % (fns[self.Ref1[0]] , fns[self.Ref2[0]]) |
|---|
| 1085 | return ('FAIL',self.msg) |
|---|
| 1086 | else: |
|---|
| 1087 | return ('DEFER', 'No entry in fns for %s,%s' % (self.Ref1[0],self.Ref2[0])) |
|---|
| 1088 | |
|---|
| 1089 | def parse_ref(ref): |
|---|
| 1090 | bits = string.split(ref,'/') |
|---|
| 1091 | assert bits[0] in ['VALUE','PATH','FILENAME','FILENAMEregex','ATTRIBUTES','CONFIG','ARGS'], 'Bad line in CONSTRAINT section of config file' |
|---|
| 1092 | if bits[0] == 'ATTRIBUTES': |
|---|
| 1093 | if bits[1] == 'Global': |
|---|
| 1094 | return ('g_%s' % bits[2],'Global attribute %s' % bits[2] ) |
|---|
| 1095 | elif bits[0] == 'FILENAME': |
|---|
| 1096 | return ('fn_%s' % bits[1],'File name component %s' % bits[1] ) |
|---|
| 1097 | elif bits[0] == 'FILENAMEregex': |
|---|
| 1098 | return ('fnre_%s' % bits[1],'File name component %s' % bits[1] ) |
|---|
| 1099 | elif bits[0] == 'VALUE': |
|---|
| 1100 | return ('VALUE', bits[1]) |
|---|
| 1101 | |
|---|
| 1102 | class Constraint__OnlyOnce: |
|---|
| 1103 | |
|---|
| 1104 | def __init__(self, ref1): |
|---|
| 1105 | self.code = 'CQC.102.004.005' |
|---|
| 1106 | self.name = 'OnlyOnce' |
|---|
| 1107 | self.nn = 0 |
|---|
| 1108 | self.Ref1 = parse_ref(ref1) |
|---|
| 1109 | self.msg = '%s occurs only once' % self.Ref1[1] |
|---|
| 1110 | |
|---|
| 1111 | def __reset__(self): |
|---|
| 1112 | self.nn = 0 |
|---|
| 1113 | |
|---|
| 1114 | def check(self,fns): |
|---|
| 1115 | if fns.has_key( self.Ref1[0] ): |
|---|
| 1116 | self.nn+=1 |
|---|
| 1117 | if self.nn <= 1: |
|---|
| 1118 | return ('PASS' ,'Occurence rate OK') |
|---|
| 1119 | else: |
|---|
| 1120 | return ('FAIL', '%s occurs too often' % self.Ref1[0] ) |
|---|
| 1121 | else: |
|---|
| 1122 | keys = fns.keys() |
|---|
| 1123 | keys.sort() |
|---|
| 1124 | return ('PASS',None) |
|---|
| 1125 | |
|---|
| 1126 | #### Mip table variable attribute check |
|---|
| 1127 | |
|---|
| 1128 | class Constraint__VarDimsCordexHardWired: |
|---|
| 1129 | def __init__(self, attribVocabs, kpat, keys, logger=None): |
|---|
| 1130 | self.code = 'CQC.102.002.010' |
|---|
| 1131 | self.name = 'VarAtts' |
|---|
| 1132 | self.tables = {} |
|---|
| 1133 | self.keys = keys |
|---|
| 1134 | self.kpat = kpat |
|---|
| 1135 | self.logger = logger |
|---|
| 1136 | self.plev_vars = ['clh','clm','cll','ua850','va850'] |
|---|
| 1137 | |
|---|
| 1138 | class Constraint__VarAtts: |
|---|
| 1139 | |
|---|
| 1140 | def __init__(self, attribVocabs, kpat, keys, logger=None): |
|---|
| 1141 | self.code = 'CQC.102.002.010' |
|---|
| 1142 | self.name = 'VarAtts' |
|---|
| 1143 | self.tables = {} |
|---|
| 1144 | self.keys = keys |
|---|
| 1145 | self.kpat = kpat |
|---|
| 1146 | self.logger = logger |
|---|
| 1147 | for t in attribVocabs.keys(): |
|---|
| 1148 | self.tables[t] = {} |
|---|
| 1149 | for i in attribVocabs[t]: |
|---|
| 1150 | self.tables[t][i[0]] = (i[1],i[2]) |
|---|
| 1151 | self.log( 'i', 'Initialising Constraint__VarAtts, table %s' % t ) |
|---|
| 1152 | |
|---|
| 1153 | def log( self, lev, msg ): |
|---|
| 1154 | if self.logger != None: |
|---|
| 1155 | if lev == 'i': |
|---|
| 1156 | self.logger.info( msg ) |
|---|
| 1157 | elif lev == 'w': |
|---|
| 1158 | self.logger.warn( msg ) |
|---|
| 1159 | |
|---|
| 1160 | def check(self, fns): |
|---|
| 1161 | self.msg = 'starting' |
|---|
| 1162 | mip = self.kpat % fns |
|---|
| 1163 | var = fns['fn_variable'] |
|---|
| 1164 | if not self.tables.has_key( mip ): |
|---|
| 1165 | self.msg = 'VarAtts: no table found -- kpat = %s' % self.kpat |
|---|
| 1166 | return ('FAIL', self.msg ) |
|---|
| 1167 | res = self.__check( mip, var, fns ) |
|---|
| 1168 | return res |
|---|
| 1169 | |
|---|
| 1170 | def __check( self, mip, var, fns ): |
|---|
| 1171 | ms = '' |
|---|
| 1172 | self.log( 'i', 'CHECKING %s' % var ) |
|---|
| 1173 | nf = 0 |
|---|
| 1174 | if not self.tables[mip].has_key(var): |
|---|
| 1175 | self.msg = 'Variable %s not present in table %s' % (var,mip) |
|---|
| 1176 | ##print ('FAIL',self.msg) |
|---|
| 1177 | return ('FAIL', self.msg) |
|---|
| 1178 | assert fns.has_key( 'v_%s' % var ), 'Internal error: attempt to check variable %s which is not in fns' % var |
|---|
| 1179 | mip_dims, mip_ats = self.tables[mip][var] |
|---|
| 1180 | var_dims = fns['v_%s' % var ][0] |
|---|
| 1181 | for k in self.keys: |
|---|
| 1182 | if mip_ats[k] != fns['v_%s' % var ][1][k]: |
|---|
| 1183 | self.log( 'w', 'Variable attribute mismatch: %s -- %s' % (mip_ats[k], str(fns['v_%s' % var ]) ) ) |
|---|
| 1184 | nf += 1 |
|---|
| 1185 | ms += '%s; ' % k |
|---|
| 1186 | else: |
|---|
| 1187 | self.log( 'i', 'Attribute OK: %s' % (self.tables[mip][var][1][k]) ) |
|---|
| 1188 | |
|---|
| 1189 | # unclear how to proceed here -- want to check, e.g., time dimension. -- possibly easiest to have a CORDEX_SPECIAL flag for some ad hoc code.. |
|---|
| 1190 | # ideally get axis information from "axis_entry" in mip tables -- need to improve the scanner for this. |
|---|
| 1191 | ##print 'DIMS: %s -- %s -- %s' % (var, str(mip_dims), str(var_dims)) |
|---|
| 1192 | if nf > 0: |
|---|
| 1193 | if nf == 1: |
|---|
| 1194 | self.msg = 'Failed 1 attribute test: %s' % ms |
|---|
| 1195 | else: |
|---|
| 1196 | self.msg = 'Failed %s attribute tests: %s' % (nf,ms) |
|---|
| 1197 | ##print ('FAIL',self.msg) |
|---|
| 1198 | return ('FAIL',self.msg) |
|---|
| 1199 | else: |
|---|
| 1200 | ##print ('PASS','%s attributes checked' % len(self.keys) ) |
|---|
| 1201 | return ('PASS','%s attributes checked' % len(self.keys) ) |
|---|
| 1202 | |
|---|
| 1203 | #### check whether a NS element is constant |
|---|
| 1204 | class Constraint__Constant: |
|---|
| 1205 | |
|---|
| 1206 | def __init__(self, ref1, required=False): |
|---|
| 1207 | self.code = 'CQC.102.002.006' |
|---|
| 1208 | self.name = 'Constant' |
|---|
| 1209 | self.nn = 0 |
|---|
| 1210 | self.Ref1 = parse_ref(ref1) |
|---|
| 1211 | self.msg = '%s occurs only once' % self.Ref1[1] |
|---|
| 1212 | self.value = None |
|---|
| 1213 | self.required = required |
|---|
| 1214 | |
|---|
| 1215 | def __reset__(self): |
|---|
| 1216 | self.nn = 0 |
|---|
| 1217 | self.value = None |
|---|
| 1218 | |
|---|
| 1219 | def check(self,fns): |
|---|
| 1220 | if fns.has_key( self.Ref1[0] ): |
|---|
| 1221 | if self.value == None: |
|---|
| 1222 | self.value = fns[self.Ref1[0]] |
|---|
| 1223 | return ('DEFER', 'first element') |
|---|
| 1224 | else: |
|---|
| 1225 | if self.value == fns[self.Ref1[0]]: |
|---|
| 1226 | return ('PASS','%s checked' % self.Ref1[0] ) |
|---|
| 1227 | else: |
|---|
| 1228 | return ('FAIL', '%s not constant across file group' % self.Ref1[0] ) |
|---|
| 1229 | else: |
|---|
| 1230 | if self.required: |
|---|
| 1231 | return ('FAIL', 'missing NS element %s' % self.Ref1[0] ) |
|---|
| 1232 | else: |
|---|
| 1233 | return ('PASS',None) |
|---|
| 1234 | |
|---|
| 1235 | def ref_to_key(ref): |
|---|
| 1236 | bits = string.split(ref,'/') |
|---|
| 1237 | assert bits[0] in ['VALUE','PATH','FILENAME','ATTRIBUTES','CONFIG','ARGS'], 'Bad line in CONSTRAINT section of config file' |
|---|
| 1238 | if bits[0] == 'ATTRIBUTES': |
|---|
| 1239 | if bits[1] == 'Global': |
|---|
| 1240 | return ('g_%s' % bits[2],'Global attribute %s' % bits[2] ) |
|---|
| 1241 | elif bits[0] == 'FILENAME': |
|---|
| 1242 | return ('fn_%s' % bits[1],'File name component %s' % bits[1] ) |
|---|
| 1243 | elif bits[0] == 'VALUE': |
|---|
| 1244 | return ('VALUE',bits[1]) |
|---|
| 1245 | |
|---|
| 1246 | class section_parser_l0: |
|---|
| 1247 | |
|---|
| 1248 | def __init__(self,parent,sectionName): |
|---|
| 1249 | self.sname = sectionName |
|---|
| 1250 | self.parent = parent |
|---|
| 1251 | self.lines = [] |
|---|
| 1252 | |
|---|
| 1253 | def add( self, l ): |
|---|
| 1254 | self.lines.append( string.strip( l ) ) |
|---|
| 1255 | |
|---|
| 1256 | def close(self): |
|---|
| 1257 | assert type(self.parent.sections) == type( {} ), 'parent.sections has wrong type (%s), should be a dictionary' % ( str( type( self.parent.sections ) ) ) |
|---|
| 1258 | |
|---|
| 1259 | self.parent.sections[self.sname] = self.lines[:] |
|---|
| 1260 | self.lines = [] |
|---|
