-
Notifications
You must be signed in to change notification settings - Fork 18
/
Copy pathapirdflib.py
executable file
·606 lines (529 loc) · 18.9 KB
/
apirdflib.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
#!/usr/bin/env python
# -*- coding: UTF-8 -*-
from __future__ import with_statement
import logging
logging.basicConfig(level=logging.INFO) # dev_appserver.py --log_level debug .
log = logging.getLogger(__name__)
import sys
sys.path.append('lib')
import rdflib
from rdflib import Literal
from rdflib.term import URIRef
from rdflib.parser import Parser
from rdflib.serializer import Serializer
from rdflib.plugins.sparql import prepareQuery
import threading
from testharness import *
from sdoutil import *
import api
from apimarkdown import Markdown
import StringIO
rdflib.plugin.register("rdfa", Parser, "pyRdfa.rdflibparsers", "RDFaParser")
rdflib.plugin.register("json-ld", Parser, "rdflib_jsonld.parser", "JsonLDParser")
rdflib.plugin.register("json-ld", Serializer, "rdflib_jsonld.serializer", "JsonLDSerializer")
ATTIC = 'attic'
VOCAB = None
VOCABLEN = 0
ALTVOCAB = "https://schema.org"
STORE = rdflib.Dataset()
#Namespace mapping#############
EXTERNALNAMESPACES = {
'xsd': 'http://www.w3.org/2001/XMLSchema#',
'skos': 'http://www.w3.org/2004/02/skos/core#',
'owl': 'http://www.w3.org/2002/07/owl#',
'rdfa': 'http://www.w3.org/ns/rdfa#',
'dct': 'http://purl.org/dc/terms/',
'foaf': 'http://xmlns.com/foaf/0.1/',
'bibo': 'http://purl.org/ontology/bibo/',
'dc': 'http://purl.org/dc/elements/1.1/',
'dcterms': 'http://purl.org/dc/terms/',
'dctype': 'http://purl.org/dc/dcmitype/',
'dcat': 'http://www.w3.org/ns/dcat#',
'void': 'http://rdfs.org/ns/void#',
'snomed': 'http://purl.bioontology.org/ontology/SNOMEDCT/',
'eli': 'http://data.europa.eu/eli/ontology#'
}
nss = {'core': 'http://schema.org/'}
revNss = {}
NSSLoaded = False
allLayersList = []
context_data = "data/internal-context" #Local file containing context to be used loding .jsonld files
RDFLIBLOCK = threading.Lock() #rdflib uses generators which are not threadsafe
from rdflib.namespace import RDFS, RDF, OWL
SCHEMA = rdflib.Namespace('http://schema.org/')
QUERYGRAPH = None
def queryGraph():
global QUERYGRAPH
if not QUERYGRAPH:
with RDFLIBLOCK:
if not QUERYGRAPH:
QUERYGRAPH = rdflib.Graph()
gs = list(STORE.graphs())
for g in gs:
id = str(g.identifier)
if not id.startswith("http://") and not id.startswith("https://"):#skip some internal graphs
continue
QUERYGRAPH += g
QUERYGRAPH.bind('schema', 'http://schema.org/')
for prefix in EXTERNALNAMESPACES:
QUERYGRAPH.bind(prefix, EXTERNALNAMESPACES[prefix])
pre = api.SdoConfig.prefix()
path = api.SdoConfig.vocabUri()
if pre and path:
QUERYGRAPH.bind(pre, path)
return QUERYGRAPH
def altSameAs(graph):
vocab = api.SdoConfig.baseUri()
sameAs = URIRef("%s/sameAs" % vocab)
#for sub in graph.subjects(None,None):
#if sub.startswith(api.SdoConfig.baseUri()):
#log.info("%s >>>> %s " % (sub,"%s%s" % (ALTVOCAB,sub[VOCABLEN:])))
#graph.add( (sub,sameAs,URIRef("%s%s" % (ALTVOCAB,sub[VOCABLEN:]))) )
def loadNss():
global NSSLoaded
global nss
global revNss
if not NSSLoaded:
NSSLoaded = True
#log.info("allLayersList: %s"% allLayersList)
for i in allLayersList:
if i != "core":
#log.info("Setting %s to %s" % (i, "http://%s.schema.org/" % i))
nss.update({i:"http://%s.schema.org/" % i})
revNss = {v: k for k, v in nss.items()}
def getNss(val):
global nss
loadNss()
try:
return nss[val]
except KeyError:
return ""
def getRevNss(val):
global revNss
loadNss()
try:
return revNss[val]
except KeyError:
return ""
##############################
def load_graph(context, files,prefix=None,vocab=None):
"""Read/parse/ingest schemas from data/*.rdfa."""
import os.path
import glob
import re
if not isinstance(files,list):
files = [files]
#log.info("Loading %s graph." % context)
for f in files:
if f.startswith("file://"):
f = f[7:]
if(f[-5:] == ".rdfa"):
format = "rdfa"
elif(f[-7:] == ".jsonld"):
format = "json-ld"
elif(f[-4:] == ".ttl"):
format = "turtle"
else:
log.info("Unrecognised file format: %s" % f)
return
if(format == "rdfa" or format == "turtle"):
uri = getNss(context)
g = STORE.graph(URIRef(uri))
g.parse(f,format=format)
if len(context) and context != "core":
STORE.bind(context,uri)
elif(format == "json-ld"):
STORE.parse(f,format=format, context=context_data)
namespaceAdd(STORE,prefix=prefix,path=vocab)
namespaceAdd(STORE,prefix=api.SdoConfig.prefix(),path=api.SdoConfig.vocabUri())
for prefix in EXTERNALNAMESPACES:
namespaceAdd(STORE,prefix=prefix, path=EXTERNALNAMESPACES[prefix])
nss = STORE.namespaces()
QUERYGRAPH = None #In case we have loaded graphs since the last time QUERYGRAPH was set
def rdfQueryStore(q,graph):
res = []
with RDFLIBLOCK:
retrys = 0
#Under very heavy loads rdflib has been know to throw exceptions - hense the retry loop
while True:
try:
res = list(graph.query(q))
break
except Exception as e:
log.error("Exception from within rdflib: %s" % e.message)
if retrys > 5:
log.error("Giving up after %s" % retrys)
raise
else:
log.error("Retrying again after %s retrys" % retrys)
retrys += 1
return res
def rdfGetTriples(id):
"""All triples with node as subject."""
targets = []
fullId = id
#log.info("rdfgetTriples(%s)" % fullId)
if ':' in id: #Includes full path or namespaces
fullId = id
else:
#fullId = api.SdoConfig.baseUri() + "/" + id
fullId = api.SdoConfig.baseUri() + id
#log.info("rdfgetTriples(%s)" % fullId)
first = True
unit = None
homeSetTo = None
typeOfInLayers = []
q = "SELECT ?g ?p ?o WHERE {GRAPH ?g {<%s> ?p ?o }}" % fullId
log.info("%s" % q)
res = rdfQueryStore(q,STORE)
#log.info("rdfgetTriples RES: %s: %s" % (len(res), res))
for row in res:
# if source == "http://meta.schema.org/":
# log.info("Triple: %s %s %s %s" % (source, row.p, row.o, row.g))
layer = str(getRevNss(str(row.g)))
if first:
first = False
unit = api.Unit.GetUnitNoLoad(id,True)
s = stripID(fullId)
p = stripID(row.p)
if p == "rdf:type":
typeOfInLayers.append(layer)
elif(p == "isPartOf"):
if(unit.home != None and unit.home != layer):
log.info("WARNING Cannot set %s home to %s - already set to: %s" % (s,layer,unit.home))
unit.home = layer
homeSetTo = layer
elif(p == "category"):
unit.category = row.o
prop = api.Unit.GetUnit(p,True)
if isinstance(row.o,rdflib.Literal):
api.Triple.AddTripleText(unit, prop, row.o, layer)
else:
api.Triple.AddTriple(unit, prop, api.Unit.GetUnit(stripID(row.o),True), layer)
""" Default Unit.home to core if not specificly set with an 'isPartOf' triple """
if(unit and homeSetTo == None):
if('core' in typeOfInLayers or len(typeOfInLayers) == 0):
unit.home = 'core'
else:
log.info("WARNING: %s defined in extensions %s but has no 'isPartOf' triple - cannot default home to core!" % (id,typeOfInLayers))
return unit
def rdfGetSourceTriples(target):
"""All source nodes for a specified arc pointing to a specified node (within any of the specified layers)."""
id = target.id
target.sourced = True
sources = []
#log.info("rdfGetSourceTriples(%s)" % id)
if ':' in id: #Includes full path or namespaces
fullId = id
else:
#fullId = api.SdoConfig.baseUri() + "/" + id
fullId = api.SdoConfig.baseUri() + id
targ = fullId
if fullId.startswith('http://') or fullId.startswith('https://'):
targ = "<%s>" % fullId
#log.info("rdfGetSourceTriples(%s)" % targ)
q = "SELECT ?g ?s ?p WHERE {GRAPH ?g {?s ?p %s }}" % targ
#log.info("%s" % q)
res = rdfQueryStore(q,STORE)
#log.info("rdfGetSourceTriples: res: %s %s" % (len(res),res))
for row in res:
#log.info("SUB: %s PRED: %s OBJ: %s" % (stripID(row.s),stripID(row.p),stripID(fullId)))
layer = str(getRevNss(str(row.g)))
unit = api.Unit.GetUnit(stripID(row.s),True)
p = stripID(row.p)
prop = api.Unit.GetUnit(p,True)
obj = api.Unit.GetUnit(stripID(fullId),True)
api.Triple.AddTriple(unit, prop, obj, layer)
def countFilter(extension="ALL",includeAttic=False):
excludeAttic = "FILTER NOT EXISTS {?term schema:isPartOf <http://attic.schema.org>}."
if includeAttic or extension == ATTIC:
excludeAttic = ""
extensionSel = ""
if extension == "ALL":
extensionSel = ""
elif extension == "core":
extensionSel = "FILTER NOT EXISTS {?term schema:isPartOf ?ex}."
excludeAttic = ""
else:
extensionSel = "FILTER EXISTS {?term schema:isPartOf <http://%s.schema.org>}." % extension
return extensionSel + "\n" + excludeAttic
TOPSTERMS = None
def rdfgettops():
global TOPSTERMS
#Terms that are Classes AND have no superclass OR have a superclass from another vocab
#plus Terms that of another type (not rdfs:Class or rdf:Property) and that type is from another vocab
#Note: In schema.org this will also return DataTypes
if TOPSTERMS:
return TOPSTERMS
TOPSTERMS = []
query= '''select ?term where {
{
?term a rdfs:Class;
rdfs:subClassOf ?super.
FILTER (!strstarts(str(?super),"%s"))
} UNION {
?term a rdfs:Class.
FILTER NOT EXISTS { ?term rdfs:subClassOf ?p }
} UNION {
?term a ?type.
FILTER NOT EXISTS { ?term a rdfs:Class }
FILTER NOT EXISTS { ?term a rdf:Property }
FILTER (!strstarts(str(?type),"%s"))
}
FILTER (strstarts(str(?term),"%s"))
}
ORDER BY ?term
''' % (api.SdoConfig.vocabUri(),api.SdoConfig.vocabUri(),api.SdoConfig.vocabUri())
#log.info("%s"%query)
res = rdfQueryStore(query,queryGraph())
#log.info("[%s]"%len(res))
for row in res:
TOPSTERMS.append(str(row.term))
return TOPSTERMS
def countTypes(extension="ALL",includeAttic=False):
#log.info("countTypes()")
filter = countFilter(extension=extension, includeAttic=includeAttic)
query= ('''select (count (?term) as ?cnt) where {
?term a rdfs:Class.
?term rdfs:subClassOf* schema:Thing.
%s
}''') % filter
graph = queryGraph()
count = 0
res = rdfQueryStore(query,graph)
for row in res:
count = row.cnt
return count
def countProperties(extension="ALL",includeAttic=False):
filter = countFilter(extension=extension, includeAttic=includeAttic)
query= ('''select (count (?term) as ?cnt) where {
?term a rdf:Property.
FILTER EXISTS {?term rdfs:label ?l}.
BIND(STR(?term) AS ?strVal).
FILTER(STRLEN(?strVal) >= 18 && SUBSTR(?strVal, 1, 18) = "http://schema.org/").
%s
}''') % filter
graph = queryGraph()
count = 0
res = rdfQueryStore(query,graph)
for row in res:
count = row.cnt
return count
def countEnums(extension="ALL",includeAttic=False):
filter = countFilter(extension=extension, includeAttic=includeAttic)
query= ('''select (count (?term) as ?cnt) where {
?term a ?type.
?type rdfs:subClassOf* <http://schema.org/Enumeration>.
%s
}''') % filter
graph = queryGraph()
count = 0
res = rdfQueryStore(query,graph)
for row in res:
count = row.cnt
return count
def getPathForPrefix(pre):
ns = STORE.namespaces()
for n in ns:
pref, path = n
if str(pre) == str(pref):
return path
return None
def getPrefixForPath(pth):
ns = STORE.namespaces()
for n in ns:
pref, path = n
if str(path) == str(pth):
return pref
return None
def serializeSingleTermGrapth(node,format="json-ld",excludeAttic=True,markdown=True):
graph = buildSingleTermGraph(node=node,excludeAttic=excludeAttic,markdown=markdown)
file = StringIO.StringIO()
kwargs = {'sort_keys': True}
file.write(graph.serialize(format=format,**kwargs))
data = file.getvalue()
file.close()
return data
def buildSingleTermGraph(node,excludeAttic=True,markdown=True):
q = queryGraph()
g = rdflib.Graph()
ns = q.namespaces()
for n in ns:
prefix, path = n
namespaceAdd(g,prefix=prefix,path=path)
namespaceAdd(g,api.SdoConfig.prefix(),api.SdoConfig.vocabUri())
full = "%s%s" % (api.SdoConfig.vocabUri(), node)
n = URIRef(full)
full = str(n)
ret = None
#log.info("NAME %s %s"% (n,full))
atts = None
attic = api.SdoConfig.atticUri()
if attic:
with RDFLIBLOCK:
atts = list(q.triples((n,SCHEMA.isPartOf,URIRef(attic))))
if len(atts):
#log.info("ATTIC TERM %s" % n)
excludeAttic = False
#Outgoing triples
with RDFLIBLOCK:
ret = list(q.triples((n,None,None)))
for (s,p,o) in ret:
#log.info("adding %s %s %s" % (s,p,o))
g.add((s,p,o))
#Incoming triples
with RDFLIBLOCK:
ret = list(q.triples((None,None,n)))
for (s,p,o) in ret:
#log.info("adding %s %s %s" % (s,p,o))
g.add((s,p,o))
#super classes
query='''select * where {
?term (^rdfs:subClassOf*) <%s>.
?term rdfs:subClassOf ?super.
OPTIONAL {
?super ?pred ?obj.
FILTER (strstarts(str(?super),'%s'))
}
}
''' % (n,api.SdoConfig.vocabUri())
#log.info("Query: %s" % query)
ret = rdfQueryStore(query,q)
for row in ret:
#log.info("adding %s %s %s" % (row.term,RDFS.subClassOf,row.super))
g.add((row.term,RDFS.subClassOf,row.super))
pred = row.pred
obj = row.obj
if pred and obj:
g.add((row.super,row.pred,row.obj))
#poperties with superclasses in domain
query='''select * where{
?term (^rdfs:subClassOf*) <%s>.
?prop <http://schema.org/domainIncludes> ?term.
OPTIONAL {
?prop ?pred ?obj.
FILTER (strstarts(str(?prop),'%s'))
}
}
''' % (n,api.SdoConfig.vocabUri())
#log.info("Query: %s" % query)
ret = rdfQueryStore(query,q)
for row in ret:
g.add((row.prop,SCHEMA.domainIncludes,row.term))
pred = row.pred
obj = row.obj
if pred and obj:
g.add((row.prop,row.pred,row.obj))
#super properties
query='''select * where {
?term (^rdfs:subPropertyOf*) <%s>.
?term rdfs:subPropertyOf ?super.
OPTIONAL {
?super ?pred ?obj.
FILTER (strstarts(str(?super),'%s'))
}
}
''' % (n,api.SdoConfig.vocabUri())
#log.info("Query: %s" % query)
ret = rdfQueryStore(query,q)
for row in ret:
#log.info("adding %s %s %s" % (row.term,RDFS.subPropertyOf,row.super))
g.add((row.term,RDFS.subPropertyOf,row.super))
pred = row.pred
obj = row.obj
if pred and obj:
g.add((row.super,row.pred,row.obj))
#Enumeration for an enumeration value
query='''select * where {
<%s> a ?type.
?type ?pred ?obj.
FILTER NOT EXISTS{?type a rdfs:class}.
}''' % n
ret = rdfQueryStore(query,q)
for row in ret:
#log.info("adding %s %s %s" % (row.type,row.pred,row.obj))
g.add((row.type,row.pred,row.obj))
if excludeAttic: #Remove triples referencing terms part of http://attic.schema.org
trips = list(g.triples((None,None,None)))
with RDFLIBLOCK:
for (s,p,o) in trips:
atts = list(q.triples((s,SCHEMA.isPartOf,URIRef(attic))))
if isinstance(o, URIRef):
atts.extend(q.triples((o,SCHEMA.isPartOf,URIRef(attic))))
for (rs,rp,ro) in atts:
#log.info("Removing %s" % rs)
g.remove((rs,None,None))
g.remove((None,None,rs))
if markdown:
with RDFLIBLOCK:
trips = list(g.triples((None,RDFS.comment,None)))
Markdown.setPre(api.SdoConfig.vocabUri())
for (s,p,com) in trips:
mcom = Markdown.parse(com)
g.remove((s,p,com))
g.add((s,p,Literal(mcom)))
Markdown.setPre()
return g
def stripID (str):
l = len(str)
vocab = api.SdoConfig.vocabUri()
if vocab != 'http://schema.org/' and vocab != 'https://schema.org/':
if l > len(vocab) and str.startswith(vocab):
return str[len(vocab):]
else:
if (l > 17 and (str[:18] == 'http://schema.org/')):
return "schema:" + str[18:]
if (l > 17 and (str[:18] == 'http://schema.org/')):
return str[18:]
elif (l > 24 and (str[:25] == 'http://purl.org/dc/terms/')):
return "dc:" + str[25:]
elif (l > 36 and (str[:37] == 'http://www.w3.org/2000/01/rdf-schema#')):
return "rdfs:" + str[37:]
elif (l > 42 and (str[:43] == 'http://www.w3.org/1999/02/22-rdf-syntax-ns#')):
return "rdf:" + str[43:]
elif (l > 29 and (str[:30] == 'http://www.w3.org/2002/07/owl#')):
return "owl:" + str[30:]
else:
return str
def graphFromFiles(files,prefix=None,path=None):
if not isinstance(files,list):
files = [files]
g = rdflib.Graph()
ns = namespaceAdd(g,prefix=prefix,path=path)
for f in files:
if f.startswith("file://"):
f = f[7:]
if not "://" in f:
f = full_path(f)
#log.info("Trying %s" % f)
try:
g.parse(f,format='json-ld')
msg = ""
if ns:
msg = "with added namespace(%s: \"%s\")" % ns
log.info("graphFromFiles loaded : %s %s" % (f,msg))
except Exception as e:
log.error("graphFromFiles exception %s: %s" % (e,e.message))
pass
return g
NSLIST = {}
def getNamespaces(g=None):
if g == None:
g = queryGraph()
ns = NSLIST.get(g,None)
if not ns:
ns = list(g.namespaces())
NSLIST[g] = ns
return ns
def namespaceAdd(g,prefix=None,path=None):
if prefix and path:
with RDFLIBLOCK:
ns = getNamespaces(g)
for n in ns:
pref, pth = n
if str(prefix) == str(pref): #Already bound
return n
ns1 = rdflib.Namespace(path)
g.bind(prefix,ns1)
return prefix, path
return None