This repository has been archived by the owner on Mar 13, 2020. It is now read-only.
forked from KNMI/impactwps
-
Notifications
You must be signed in to change notification settings - Fork 0
/
SimpleDRSChecker.py
725 lines (631 loc) · 33.7 KB
/
SimpleDRSChecker.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
## @package SimpleDRSChecker
# Very simple DRS checker made for the CLIPC project.
# Follows document http://www.clipc.eu/media/clipc/org/documents/other/metadata_standards_for_climate_impact_indicators-v1.pdf.
#
# @author Maarten Plieger - [email protected]
# @version 0.02
# DONE: When are we dealing with model DRS and when general DRS? Ruth: Check by sourceDataID attribute
# DONE: output_frequency needs to be validated: Not possible.
# DONE: reference_period needs to be validated
# DONE: Ask Ruth: Check why Activity and activity occurs
# DONE: Ask Ruth: Check why sourceDataID and sourceDataId occurs
# DONE: Ask Ruth: time_coverage_start should be mandatory attribute with format YYYYMMDD, as it is used as StartTime in the drsnames. Or startTime in drsname needs to be optional.
# DONE: Ask Ruth: tile-nnnnn should become tilennnnn or tilenr in the metadata document as it is a delimiter. E.g <StartTime-EndTime>
#<VariableName>_<package>_<institution>_<GCMName>_<ExperimentName>_<EnsembleMember>_<RCMName>_<RCMRealisation>_<domain>_<BcName>_<BcObsName>_<BcRefPeriod>_<frequency>_<StartTime-EndTime>_<Reference_period>_<tilennnnn>
#prcptot_icclim-4-1-0_KNMI_GFDL-ESM2M-none-GFDL-ESM2M_rcp45_r1i1p1_SMHI-RCA4_v1_rcp4.5 or v1?_EUR-44_SMHI-DBS43_EOBSv10_1981-2010_yr_20060101-20991231_2006-2099_none.nc
#prcptot_icclim-4-2-3_KNMI_GFDL-ESM2M_r1i1p1_SMHI-RCA4_v1_EUR-44_SMHI-DBS43_EOBS10-1981-2010_yr_20060101-20991231.nc
import datetime as dt # Python standard library datetime module
import numpy as np
import netCDF4
import fnmatch
import os
import datetime
import sys
import re
fixFiles=False
cfOnly=False
## The SimpleDRSChecker class
#
# Use checkFile method.
class SimpleDRSChecker:
## The constructor.
def __init__(self):
return
nrOfErrors = 0
errorString = ""
stdOutString = ""
DRSDatasetname=""
DRSFilename=""
DRS = {
"CORDEX":{
"requiredGlobalAttributes":{
'institute_id':{},
'contact':{},
'rcm_version_id':{},
'product':{},
'CORDEX_domain':{},
'creation_date':{'validator':['datetimeYYYY-MM-DDTHH_MM_SSZ']},
'frequency':{},
'model_id':{},
'driving_model_id':{},
'driving_experiment':{},
"driving_model_ensemble_member":{},
'experiment_id':{},
'project_id':{}
},
"drsMappings": {
'variable':'@var',
'institute':'institute_id',
'product':'product',
'experiment':'experiment_id',
'ensemble':'driving_model_ensemble_member',
'model':'model_id',
'driving_model':'driving_model_id',
'frequency':'frequency',
'project':'project_id',
'domain':'CORDEX_domain',
'model_version':'rcm_version_id'
},
"drsConstructors":{
"filename":"@<VariableName>@_<domain>_<driving_model>_<experiment>_<ensemble>_<model>_<model_version>_<frequency>_@<version>@.nc",
"dataset": "<project>.<product>.<domain>.<institute>.<driving_model>_<experiment>_<ensemble>_<model>_<model_version>_<frequency>_@<VariableName>@_@<version>@.nc"
}
},
"CLIPCModelDRS":{
"requiredGlobalAttributes":{
'Conventions':{},
'activity':{'validator':['activity_is_clipc']},
'title':{'validator':['checklengthisatleast3']},
'summary':{},
'variable_name':{},
'product':{},
'comment':{},
'references':{},
'package_name':{},
'package_references':{},
'institution_id':{},
'institution_url':{},
'contact':{},
'contributor_name':{},
'contributor_role':{},
'date_created':{'validator':['datetimeYYYYMMDD']},
'date_issued':{'validator':['datetimeYYYYMMDD']},
'date_modified':{'validator':['datetimeYYYYMMDD']},
'realisation_id':{},
'source_data_id':{},
'source_data_id_comment':{},
'invar_platform':{},
'invar_platform_id':{},
'invar_satellite_algorithm':{},
'invar_satellite_sensor':{},
'invar_rcm_model_id':{},
'invar_rcm_model_realization_id':{},
'invar_rcm_model_driver':{},
'invar_reanalysis_id':{},
'invar_gcm_model_id':{},
'invar_experiment_name':{},
'invar_ensemble_member':{},
'invar_bc_method_id':{},
'invar_bc_observation_id':{},
'invar_bc_period':{'validator':['datetimeYYYY-YYYY']},
'invar_variable_name':{},
'invar_tracking_id':{'validator':['validate_uuid']},
'reference_period':{'validator':['datetimeYYYY-YYYY']},
'time_coverage_start':{'validator':['datetimeYYYYMMDD','checklengthisatleast3']},
'time_coverage_end':{},
'output_frequency':{}, # TODO validate
'cdm_datatype':{},
'domain':{},
'geospatial_bounds':{},
'geospatial_lat_min':{'validator':['geospatial_lat_degrees_north']},
'geospatial_lat_max':{'validator':['geospatial_lat_degrees_north']},
'geospatial_lat_resolution':{'validator':['geospatial_resolution']},
'geospatial_lon_min':{'validator':['geospatial_lon_degrees_east']},
'geospatial_lon_max':{'validator':['geospatial_lon_degrees_east']},
'geospatial_lon_resolution':{'validator':['geospatial_resolution']},
'tile':{'validator':['tilennnnn']},
'tracking_id':{'validator':['checklengthisatleast3','validate_uuid']},
'keywords':{'validator':['clipckeywordvalidator']},
'history':{}
},
"drsMappings": {
'activity':'activity',
'VariableName':'variable_name',
'product':'product',
'package':'package_name',
'domain':'domain',
'institution':'institution_id',
'sourceDataID':'source_data_id',
'sourceDataId':'source_data_id',
'frequency':'output_frequency',
'StartTime':'time_coverage_start',
'EndTime':'time_coverage_end',
'Reference_period':'reference_period',
'tilennnnn':'tile',#tile-nnnnn will not work, because in that case it looks like two attributes.
'GCMName':['invar_rcm_model_driver','invar_reanalysis_id','invar_gcm_model_id'],
'ExperimentName':'invar_experiment_name',
'EnsembleMember':'invar_ensemble_member',
'RCMName':'invar_rcm_model_id',
'RCMRealisation':'invar_rcm_model_realization_id',
'BcName':'invar_bc_method_id',
'BcObsName':'invar_bc_observation_id',
'BcRefPeriod':'invar_bc_period',
},
"drsConstructors":{
"filename":"<VariableName>_<package>_<institution>_<GCMName>_<ExperimentName>_<EnsembleMember>_[IndicatorRealisation_][<RCMName>_<RCMRealisation>_<domain>_][<BcName>_<BcObsName>_<BcRefPeriod>_] <frequency>_<StartTime-EndTime>_[<Reference_period>_][<tilennnnn>].nc",
"dataset": "<activity>.<product>.<package>.<institution>.<GCMName>.<ExperimentName>.<EnsembleMember>.[<RCMName>.<RCMRealisation>.<domain>.][<BcName>.<BcObsName>.<BcRefPeriod>.]<frequency>.[<Reference_period>.]<VariableName>"
}
},
"CLIPCGeneralDRS":{
"requiredGlobalAttributes":{
'Conventions':{},
'activity':{'validator':['activity_is_clipc']},
'title':{'validator':['checklengthisatleast3']},
'summary':{},
'variable_name':{},
'product':{},
'comment':{},
'references':{},
'package_name':{},
'package_references':{},
'institution_id':{},
'institution_url':{},
'contact':{},
'contributor_name':{},
'contributor_role':{},
'date_created':{'validator':['datetimeYYYYMMDD']},
'date_issued':{'validator':['datetimeYYYYMMDD']},
'date_modified':{'validator':['datetimeYYYYMMDD']},
'realisation_id':{},
'source_data_id':{},
'source_data_id_comment':{},
'invar_platform':{},
'invar_platform_id':{},
'invar_satellite_algorithm':{},
'invar_satellite_sensor':{},
'invar_rcm_model_id':{},
'invar_rcm_model_realization_id':{},
'invar_rcm_model_driver':{},
'invar_reanalysis_id':{},
'invar_gcm_model_id':{},
'invar_experiment_name':{},
'invar_ensemble_member':{},
'invar_bc_method_id':{},
'invar_bc_observation_id':{},
'invar_bc_period':{},
'invar_variable_name':{},
'invar_tracking_id':{'validator':['validate_uuid']},
'reference_period':{'validator':['datetimeYYYY-YYYY']},
'time_coverage_start':{'validator':['datetimeYYYYMMDD','checklengthisatleast3']},
'time_coverage_end':{},
'output_frequency':{}, # TODO validate
'cdm_datatype':{},
'domain':{},
'geospatial_bounds':{},
'geospatial_lat_min':{'validator':['geospatial_lat_degrees_north']},
'geospatial_lat_max':{'validator':['geospatial_lat_degrees_north']},
'geospatial_lat_resolution':{'validator':['geospatial_resolution']},
'geospatial_lon_min':{'validator':['geospatial_lon_degrees_east']},
'geospatial_lon_max':{'validator':['geospatial_lon_degrees_east']},
'geospatial_lon_resolution':{'validator':['geospatial_resolution']},
'tile':{'validator':['tilennnnn']},
'tracking_id':{'validator':['checklengthisatleast3','validate_uuid']},
'keywords':{'validator':['clipckeywordvalidator']},
'history':{}
},
"drsMappings": {
'activity':'activity',
'VariableName':'variable_name',
'product':'product',
'package':'package_name',
'domain':'domain',
'institution':'institution_id',
'sourceDataID':'source_data_id',
'sourceDataId':'source_data_id',
'frequency':'output_frequency',
'StartTime':'time_coverage_start',
'EndTime':'time_coverage_end',
'Reference_period':'reference_period',
'tilennnnn':'tile',#tile-nnnnn will not work, because in that case it looks like two attributes.
'version':'version'
},
"drsConstructors":{
"filename":"<VariableName>_<package>_<institution>_<sourceDataID>_<frequency>_<StartTime-EndTime>_[<Reference_period>_][<tilennnnn>].nc",
"dataset": "<activity>.<product>.<package>.<domain>.<institution>.<sourceDataID>.<frequency>.[<Reference_period>].<VariableName>"
}
}
}
def printmessage(self,message):
self.stdOutString = self.stdOutString +message+"\n"
return
def printerror(self,message):
self.printmessage("[ERROR]\t"+message)
self.nrOfErrors = self.nrOfErrors +1
self.errorString = self.errorString+("Error nr %d: "%(self.nrOfErrors))+str(message)+"\n"
return
## Returns nonzero if there are errors, otherwise returns zero ##
# @return Returns non zero if errors occured
def hasErrors(self):
if self.nrOfErrors != 0:
return 1
return 0
## Validates DRS facet values for a given validator
# @param self The object pointer
# @param value The DRS value of the netcdf attribute
# @param validator The validator to use
# @param nc_attr The name of the netcdf attribute
def __validate(self,value,validator,nc_attr):
if validator == "validate_uuid":
if(value == " " or value == ""):
return True
regex = re.compile('^[a-f0-9]{8}-?[a-f0-9]{4}-?4[a-f0-9]{3}-?[89ab][a-f0-9]{3}-?[a-f0-9]{12}\Z', re.I)
match = regex.match(value)
if bool(match) == False:
self.printerror('Unable to validate attribute [%s] with value [%s]: should be in form [00000000-0000-4000-0000-000000000000]' % (nc_attr,value))
return False
return True
if validator == "geospatial_lat_degrees_north":
if type(value)!=type("S"):
return True
if len(value)<2:
self.printerror('Unable to validate attribute [%s] with value [%s]: should be in form [value<space>degrees_north]' % (nc_attr,value))
return False
newvalue = value.split(" ");
if len(newvalue)<2:
self.printerror('Unable to validate attribute [%s] with value [%s]: should be in form [value<space>degrees_north]' % (nc_attr,value))
return False
if(newvalue[1]!="degrees_north"):
self.printerror('Unable to validate attribute [%s] with value [%s]: should be in form [value<space>degrees_north]' % (nc_attr,value))
return False
return True
if validator == "geospatial_lon_degrees_east":
if type(value)!=type("S"):
return True
if len(value)<2:
self.printerror('Unable to validate attribute [%s] with value [%s]: should be in form [value<space>degrees_east]' % (nc_attr,value))
return False
newvalue = value.split(" ");
if len(newvalue)<2:
self.printerror('Unable to validate attribute [%s] with value [%s]: should be in form [value<space>degrees_east]' % (nc_attr,value))
return False
if(newvalue[1]!="degrees_east"):
self.printerror('Unable to validate attribute [%s] with value [%s]: should be in form [value<space>degrees_east]' % (nc_attr,value))
return False
return True
if validator == "geospatial_resolution":
if type(value)!=type("S"):
return True
if len(value)<2:
self.printerror('Unable to validate attribute [%s] with value [%s]: length should be at least 2 characters' % (nc_attr,value))
return False
newvalue = value.split(" ");
if len(newvalue)<2:
self.printerror('Unable to validate attribute [%s] with value [%s]: should be in form [value<space>unit]' % (nc_attr,value))
return False
return True
if validator == "checklengthisatleast3":
if len(value)<3:
self.printerror('Unable to validate attribute [%s] with value [%s]: this attribute needs to be specified' % (nc_attr,value))
return False
else:
return True
if validator == "datetimeYYYY-MM-DDTHH_MM_SSZ":
try:
datetime.datetime.strptime(value,'%Y-%m-%dT%H:%M:%SZ')
except:
self.printerror('Unable to validate datetime attribute [%s] with value [%s] against [YYYY-MM-DDTHH:MM:SSZ]' % (nc_attr,value))
return False
return True
if validator == "datetimeYYYYMMDD":
# Date must be either "YYYYMMDD" or " " or ""
if(value == " " or value == ""):
return True
try:
datetime.datetime.strptime(value,'%Y%m%d')
except:
self.printerror('Unable to validate datetime attribute [%s] with value [%s] against [YYYYMMDD]' % (nc_attr,value))
return False
return True
if validator == "datetimeYYYY-YYYY":
# Date must be either "YYYY-YYYY" or " " or ""
if(value == " " or value == ""):
return True
try:
if len(value) != 4+1+4:
raise ValueError('Length is not 9')
values = value.split("-")
if len(values) != 2:
raise ValueError('Does not consist of two YYYY parts')
datetime.datetime.strptime(values[0],'%Y')
datetime.datetime.strptime(values[1],'%Y')
except:
self.printerror('Unable to validate datetime attribute [%s] with value [%s] against [YYYY-YYYY]' % (nc_attr,value))
return False
return True
if validator == "activity_is_clipc":
if value == "clipc":
return True
else:
self.printerror('Unable to validate activity [%s]. This should be [clipc]' % value)
return False
if validator == "tilennnnn":
if(value == " " or value == ""):
return True
if len(value) == 5:
if value.isdigit():
return True
else:
self.printerror('Unable to validate tilennnnn [%s]. Length is OK, but not all characters are nunbers.' % value)
return False
else:
self.printerror('Unable to validate tilennnnn [%s]. This should either be an empty string or have a length of 5 digits.' % value)
return False
if validator == "clipckeywordvalidator":
if len(value.split(","))>=2:
return True;
else:
self.printerror('Unable to validate clipc keywords [%s]. This should have at least two values comma separated]' % value)
return False
## Expands DRS into an array with optional and mandatory attributes. Mode can be optional, mandatory or unknown.
# @param self The object pointer
# @param currentDRSStandard The name of the current DRS standard,e.g. CLIPC or CORDEX
# @return the array with the expanded DRS
def __expandDRSMapping(self,drsMappingFilenameOrder):
parsedFacetDRS = []
facet = ""
mode = ""
mandatory_optional = 0 # means mandatory
for i in range(0,len(drsMappingFilenameOrder)):
c=drsMappingFilenameOrder[i]
if c == "[":
mandatory_optional=1
if c == "]" or c == "@":
mandatory_optional=0
if c == "@":
mandatory_optional=2
if c == "<":
facet=""
mode="recordfacet"
if c == ">":
if mandatory_optional == 0:
parsedFacetDRS.append({facet:"M"});
elif mandatory_optional == 1:
parsedFacetDRS.append({facet:"O"});
elif mandatory_optional == 2:
parsedFacetDRS.append({facet:"U"});
mode=""
if mode=="recording":
facet=facet+c
if mode=="recordfacet":
mode="recording"
return parsedFacetDRS
## Generates the DRS name for a filename or a dataset
# @param self The object pointer
# @param nc_fid The NetCDF4 dataset pointer
# @param baseName The filename without the prefixed path
# @param currentDRSStandard The name of the current DRS standard,e.g. CLIPC or CORDEX
def __generateDRSName(self,nc_fid,currentDRSStandard, filename_or_dataset = "filename",separator=None):
if separator == None:
if filename_or_dataset=="filename":
separator="_"
else:
separator="."
parsedFacetDRS = self.__expandDRSMapping(self.DRS[currentDRSStandard]["drsConstructors"][filename_or_dataset]);
nc_attrs = self.__getGlobalAttributes(nc_fid)
drsMappings = self.DRS[currentDRSStandard]["drsMappings"]
suggestedFileName = "";
usedDRSFileNameMapping = "";
for i in range(0,len(parsedFacetDRS)):
facetName = parsedFacetDRS[i].keys()[0]
mo = parsedFacetDRS[i].values()[0] # mandatory or optional
# Get facetValue, e.g compose time_coverage_start-time_coverage_end from multiple attributes
fs = facetName.split("-")
facetValue = ""
for drsFacet in fs:
netcdfAttrName=[]
try:
netcdfAttrName=drsMappings[drsFacet]
if type(netcdfAttrName) == type("String"):
netcdfAttrName = [netcdfAttrName]
except:
if mo != "U":
self.printerror("DRS facet '%s' is unknown" % drsFacet)
pass
# Loop over the netcdf attributes names and compose the drsfacet.
for f in netcdfAttrName:
#self.printmessage(str(f))
if f in nc_attrs:
v = "Unable to read nc attribute value"
try:
v = nc_fid.getncattr(f)
except:
self.printerror('Unable to read netcdf attribute %s as string. Have you provided a string type in your netcdf attribute?' % (f))
pass
if v == " ":
v=""
if len(v)>0:
#self.printmessage("[INFO]\tFound attribute ["+drsFacet+"]/["+f+"] = "+v)
if len(facetValue) > 0:
facetValue= facetValue+"-"
if drsFacet == "BcRefPeriod":
facetValue=facetValue+"bcref-"
facetValue=facetValue+v
else:
self.printmessage("[INFO]\tAttribute ["+drsFacet+"]/["+f+"] is not filled in")
fnFacetPart=""
if len(facetValue)>0:
fnFacetPart=facetValue
else:
if mo == "M":
fnFacetPart="<%s>"%facetName
if mo == "U":
fnFacetPart="*"
if len(fnFacetPart)>0:
if len(usedDRSFileNameMapping)>0 and usedDRSFileNameMapping[-1]!=separator:
usedDRSFileNameMapping = usedDRSFileNameMapping +separator
usedDRSFileNameMapping = usedDRSFileNameMapping+"<"+facetName+">"
if len(suggestedFileName)>0 and suggestedFileName[-1]!=separator:
suggestedFileName = suggestedFileName +separator
suggestedFileName = suggestedFileName + fnFacetPart
return suggestedFileName,usedDRSFileNameMapping
## Validates the filename against the found DRS.
# @param self The object pointer
# @param nc_fid The NetCDF4 dataset pointer
# @param baseName The filename without the prefixed path
# @param currentDRSStandard The name of the current DRS standard,e.g. CLIPC or CORDEX
def __validateFileName(self,nc_fid,baseName,currentDRSStandard):
suggestedFileName,usedDRSFileNameMapping = self.__generateDRSName(nc_fid,currentDRSStandard);
suggestedFileName = suggestedFileName + ".nc"
self.DRSFilename = suggestedFileName
self.printmessage("[INFO]\tUsed DRS file mapping: "+usedDRSFileNameMapping)
self.printmessage("[INFO]\tDRS Filename: "+suggestedFileName)
# Now test if the composed filename from the drs metadata matches the given filename
if fnmatch.fnmatch(baseName,suggestedFileName):
self.printmessage("[OK]\tFilename matches %s" %(suggestedFileName))
return True
else:
self.printerror("Derived DRS filename\n[%s] does not match NetCDF filename\n[%s]" %(suggestedFileName,baseName))
return False
## Returns the global attributes for a netCDF4 dataset
# @param self The object pointer
# @param nc_fid The NetCDF4 dataset pointer
def __getGlobalAttributes(self,nc_fid):
nc_attrs = nc_fid.ncattrs()
return nc_attrs
## Generate the DRS id
# @param self The object pointer
# @param nc_fid The NetCDF4 dataset pointer
# @param baseName The filename without the prefixed path
# @param currentDRSStandard The name of the current DRS standard,e.g. CLIPC or CORDEX
def generateDRSDatasetIdentifier(self,nc_fid,currentDRSStandard):
suggestedFileName,usedDRSFileNameMapping = self.__generateDRSName(nc_fid,currentDRSStandard,"dataset");
self.DRSDatasetname = suggestedFileName
self.printmessage("[INFO]\tUsed DRS dataset mapping: "+usedDRSFileNameMapping)
self.printmessage("[INFO]\tDRS Dataset: %s"%suggestedFileName)
return
## Check basic CF conventions
# @param nc_fid The netcdf file object
def checkCF(self,nc_fid):
nc_attrs = nc_fid.ncattrs()
hasCalendar = False
if "time" not in nc_fid.variables:
self.printerror("time variable not found");
return
if "calendar" in nc_fid.variables["time"].ncattrs():
hasCalendar = True
if "units" not in nc_fid.variables["time"].ncattrs():
self.printerror("time variable has no units attribute");
if "time_bnds" in nc_fid.variables:
if "units" not in nc_fid.variables["time_bnds"].ncattrs():
if fixFiles == False:
self.printerror("time_bnds variable has no units attribute");
else:
nc_fid.variables["time_bnds"].setncattr("units",nc_fid.variables["time"].getncattr("units"))
if hasCalendar:
if "calendar" not in nc_fid.variables["time_bnds"].ncattrs():
if fixFiles == False:
self.printerror("time_bnds variable has no calendar attribute while time variable has a calendar attribute");
else:
nc_fid.variables["time_bnds"].setncattr("calendar",nc_fid.variables["time"].getncattr("calendar"))
#Check variable units as well
if "variable_name" not in nc_attrs:
self.printerror("global attribute variable_name is not defined");
return
variable_name = nc_fid.getncattr("variable_name")
if variable_name not in nc_fid.variables:
self.printerror("Variable advertised in variable_name not found");
return
if "units" not in nc_fid.variables[variable_name].ncattrs():
if fixFiles == False:
self.printerror("units are missing for variable "+str(variable_name));
else:
nc_fid.variables[variable_name].setncattr("units","-")
if "long_name" not in nc_fid.variables[variable_name].ncattrs():
self.printerror("long_name are missing for variable "+str(variable_name));
self.printerror("standard_name are missing for variable "+str(variable_name));
return
## Checks a NetCDF file by a filename.
# @param fileName The filename or opendap url for the netcdf file
# @param projectName The name of the project,e.g. CLIPC or CORDEX
def checkFile(self,fileName,projectName):
self.nrOfErrors = 0
self.errorString = ""
self.stdOutString = ""
self.DRSDatasetname=""
self.DRSFilename=""
baseName= os.path.basename(fileName)
if fixFiles == True:
nc_fid = netCDF4.Dataset(fileName,'a')
else:
nc_fid = netCDF4.Dataset(fileName,'a')
nc_attrs = self.__getGlobalAttributes(nc_fid)
currentDRSStandard= projectName
if cfOnly == False:
#if nc_attrs #TODO determine if this is the model version or the general version
if projectName == "CLIPC":
""" By default the CLIPCGeneralDRS is used """
currentDRSStandard = "CLIPCGeneralDRS"
""" Check if this is the MODELDRS """
""" invar_rcm_model_driver','invar_reanalysis_id','invar_gcm_model_id' """
try:
invar_rcm_model_driver = nc_fid.getncattr("invar_rcm_model_driver")
invar_reanalysis_id = nc_fid.getncattr("invar_reanalysis_id")
invar_gcm_model_id = nc_fid.getncattr("invar_gcm_model_id")
source_data_id = nc_fid.getncattr("source_data_id")
""" sourceDataID must be left empty if the model DRS is used. When sourceDataID is provided general DRS is used. """
if len(source_data_id) < 3:
currentDRSStandard = "CLIPCModelDRS"
self.printmessage("[INFO]\tDetected the CLIPC Model DRS standard because source_data_id is empty.")
else:
self.printmessage("[INFO]\tDetected the CLIPC General DRS standard because source_data_id is set to [%s]."%source_data_id)
if len(invar_gcm_model_id) > 3 :
if len(invar_rcm_model_driver) > 3 :
self.printerror('invar_rcm_model_driver: Too many attributes composing the GCMName are defined. Please fill out either invar_rcm_model_driver, invar_reanalysis_id or invar_gcm_model_id')
if len(invar_reanalysis_id) > 3 :
self.printerror('invar_reanalysis_id: Too many attributes composing the GCMName are defined. Please fill out either invar_rcm_model_driver, invar_reanalysis_id or invar_gcm_model_id')
except:
self.printmessage(str(sys.exc_info()[0]))
pass
self.printmessage('[INFO]\tUsing %s standard'%currentDRSStandard)
requiredGlobalAttributes = self.DRS[currentDRSStandard]["requiredGlobalAttributes"]
for nc_attr in requiredGlobalAttributes:
if nc_attr in nc_attrs:
nc_attr_value = "Unable to read nc attribute value"
try:
nc_attr_value = nc_fid.getncattr(nc_attr)
except:
self.printerror('Unable to read netcdf attribute %s as string. Have you provided a string type in your netcdf attribute?' % (nc_attr))
pass
validator = None
try:
validator = requiredGlobalAttributes[nc_attr]["validator"]
except:
pass
if validator!= None:
valid = True
for v in validator:
if self.__validate(nc_attr_value,v,nc_attr) == False:
#self.printerror('Validator [%s] failed\t"%s" = "%s"' % (v,nc_attr,nc_attr_value))
valid = False
if valid == True:
self.printmessage('[OK]\tValidated\t"%s" = "%s"' % (nc_attr,nc_attr_value))
else:
self.printmessage('[OK]\tFound\t\t"%s" = "%s" ' % (nc_attr,nc_attr_value))
else:
self.printerror('%s is missing' % (nc_attr))
#Validate filename
self.__validateFileName(nc_fid,baseName,currentDRSStandard)
#Generate the DRS id
self.generateDRSDatasetIdentifier(nc_fid,currentDRSStandard)
#Check basic CF stuff
self.checkCF(nc_fid)
self.printmessage("[INFO]\tNr of found errors: %d" % self.nrOfErrors)
if cfOnly == False:
self.printmessage("[DRSFilename] [%s]"%self.DRSFilename)
self.printmessage("[DRSDatasetname][%s]"%self.DRSDatasetname)
if self.nrOfErrors == 0:
self.printmessage("[GOOD]\tFile has been validated with zero errors! Well done!")
if self.nrOfErrors != 0:
self.printmessage("[ERROR]\tFile is not conforming '%s' DRS standard. %d issue(s) found" % (currentDRSStandard,self.nrOfErrors))
self.errorString = self.errorString+str("Please note: using [%s]." %(currentDRSStandard))
return