if prefix not in query.prolog.prefixBindings:
query.prolog.prefixBindings[prefix] = nsInst
goals.extend(
[
(s, p, o)
for s, p, o, c in ReduceGraphPattern(query.query.whereClause.parsedGraphPattern, query.prolog).patterns
]
)
dPreds = [] # p for s,p,o in goals ]
magicRuleNo = 0
bottomUpDerivedPreds = []
topDownDerivedPreds = []
defaultBasePreds = []
defaultDerivedPreds = set()
hybridPredicates = []
mapping = dict(newNsMgr.namespaces())
for edb in options.edb:
pref, uri = edb.split(":")
defaultBasePreds.append(URIRef(mapping[pref] + uri))
noMagic = []
for pred in options.noMagic:
pref, uri = pred.split(":")
noMagic.append(URIRef(mapping[pref] + uri))
if options.ddlGraph:
ddlGraph = Graph().parse(options.ddlGraph, format="n3")
# @TODO: should also get hybrid predicates from DDL graph
defaultDerivedPreds = IdentifyDerivedPredicates(ddlGraph, Graph(), ruleSet)
else:
for idb in options.idb:
pref, uri = idb.split(":")
defaultDerivedPreds.add(URIRef(mapping[pref] + uri))
def main():
from optparse import OptionParser
op = OptionParser('usage: %prog [options] factFile1 factFile2 ... factFileN')
op.add_option('--closure',
action='store_true',
default=False,
help = 'Whether or not to serialize the inferred triples'+
' along with the original triples. Otherwise '+
'(the default behavior), serialize only the inferred triples')
op.add_option('--output',
default='n3',
metavar='RDF_FORMAT',
choices = ['xml',
'TriX',
'n3',
'nt',
'rif',
'rif-xml',
'conflict',
'man-owl'],
help = "Serialize the inferred triples and/or original RDF triples to STDOUT "+
"using the specified RDF syntax ('xml','pretty-xml','nt','turtle', "+
"or 'n3') or to print a summary of the conflict set (from the RETE "+
"network) if the value of this option is 'conflict'. If the the "+
" value is 'rif' or 'rif-xml', Then the rules used for inference "+
"will be serialized as RIF. Finally if the value is 'man-owl', then "+
"the RDF facts are assumed to be OWL/RDF and serialized via Manchester OWL "+
"syntax. The default is %default")
op.add_option('--class',
dest='classes',
action='append',
default=[],
metavar='QNAME',
help = 'Used with --output=man-owl to determine which '+
'classes within the entire OWL/RDF are targetted for serialization'+
'. Can be used more than once')
op.add_option('--property',
action='append',
dest='properties',
default=[],
metavar='QNAME',
help = 'Used with --output=man-owl or --extract to determine which '+
'properties are serialized / extracted. Can be used more than once')
op.add_option('--normalize',
action='store_true',
default=False,
help = "Used with --output=man-owl to attempt to determine if the ontology is 'normalized' [Rector, A. 2003]"+
"The default is %default")
op.add_option('--input-format',
default='xml',
dest='inputFormat',
metavar='RDF_FORMAT',
choices = ['xml', 'trix', 'n3', 'nt', 'rdfa'],
help = "The format of the RDF document(s) which serve as the initial facts "+
" for the RETE network. One of 'xml','n3','trix', 'nt', "+
"or 'rdfa'. The default is %default")
op.add_option('--pDSemantics',
action='store_true',
default=False,
help = 'Used with --dlp to add pD semantics ruleset for semantics not covered '+
'by DLP but can be expressed in definite Datalog Logic Programming'+
' The default is %default')
op.add_option('--stdin',
action='store_true',
default=False,
help = 'Parse STDIN as an RDF graph to contribute to the initial facts. The default is %default ')
op.add_option('--ns',
action='append',
default=[],
metavar="PREFIX=URI",
help = 'Register a namespace binding (QName prefix to a base URI). This '+
'can be used more than once')
op.add_option('--rules',
default=[],
action='append',
default=[],
metavar='PATH_OR_URI',
help = 'The Notation 3 documents to use as rulesets for the RETE network'+
'. Can be specified more than once')
op.add_option('--ruleFacts',
action='store_true',
default=False,
help = "Determines whether or not to attempt to parse initial facts from "+
"the rule graph. The default is %default")
op.add_option('--dlp',
action='store_true',
default=False,
help = 'Use Description Logic Programming (DLP) to extract rules from OWL/RDF. The default is %default')
(options, facts) = op.parse_args()
nsBinds = {'iw':'http://inferenceweb.stanford.edu/2004/07/iw.owl#'}
for nsBind in options.ns:
pref,nsUri = nsBind.split('=')
nsBinds[pref]=nsUri
namespace_manager = NamespaceManager(Graph())
factGraph = Graph()
ruleSet = Ruleset()
for fileN in options.rules:
if options.ruleFacts:
factGraph.parse(fileN,format='n3')
print >>sys.stderr,"Parsing RDF facts from ", fileN
rs = HornFromN3(fileN)
nsBinds.update(rs.nsMapping)
ruleSet.formulae.extend(rs)
#ruleGraph.parse(fileN,format='n3')
ruleSet.nsMapping = nsBinds
for prefix,uri in nsBinds.items():
namespace_manager.bind(prefix, uri, override=False)
closureDeltaGraph = Graph()
closureDeltaGraph.namespace_manager = namespace_manager
factGraph.namespace_manager = namespace_manager
for fileN in facts:
factGraph.parse(fileN,format=options.inputFormat)
if options.stdin:
factGraph.parse(sys.stdin,format=options.inputFormat)
workingMemory = generateTokenSet(factGraph)
rule_store, rule_graph, network = SetupRuleStore(makeNetwork=True)
network.inferredFacts = closureDeltaGraph
network.nsMap = nsBinds
if options.dlp:
dlp=setupDescriptionLogicProgramming(factGraph,
addPDSemantics=options.pDSemantics,
constructNetwork=False)
ruleSet.formulae.extend(dlp)
if options.output == 'rif':
for rule in ruleSet:
print rule
elif options.output == 'man-owl':
cGraph = network.closureGraph(factGraph,readOnly=False)
cGraph.namespace_manager = namespace_manager
Individual.factoryGraph = cGraph
if options.classes:
mapping = dict(namespace_manager.namespaces())
for c in options.classes:
pref,uri=c.split(':')
print Class(URIRef(mapping[pref]+uri)).__repr__(True)
elif options.properties:
mapping = dict(namespace_manager.namespaces())
for p in options.properties:
pref,uri=p.split(':')
print Property(URIRef(mapping[pref]+uri))
else:
for p in AllProperties(cGraph):
print p.identifier
print repr(p)
for c in AllClasses(cGraph):
if options.normalize:
if c.isPrimitive():
primAnc = [sc for sc in c.subClassOf if sc.isPrimitive()]
if len(primAnc)>1:
warnings.warn("Branches of primitive skeleton taxonomy"+
" should form trees: %s has %s primitive parents: %s"%(
c.qname,len(primAnc),primAnc),UserWarning,1)
children = [desc for desc in c.subSumpteeIds()]
for child in children:
for otherChild in [o for o in children if o is not child]:
if not otherChild in [c.identifier
for c in Class(child).disjointWith]:# and\
warnings.warn("Primitive children (of %s) "+
"must be mutually disjoint: %s and %s"%(
c.qname,
Class(child).qname,
Class(otherChild).qname),UserWarning,1)
if not isinstance(c.identifier,BNode):
print c.__repr__(True)
for rule in ruleSet:
network.buildNetworkFromClause(rule)
start = time.time()
network.feedFactsToAdd(workingMemory)
sTime = time.time() - start
if sTime > 1:
sTimeStr = "%s seconds"%sTime
else:
sTime = sTime * 1000
sTimeStr = "%s milli seconds"%sTime
print >>sys.stderr,"Time to calculate closure on working memory: ",sTimeStr
print >>sys.stderr, network
if options.output == 'conflict':
network.reportConflictSet()
elif options.output not in ['rif','rif-xml','man-owl']:
if options.closure:
cGraph = network.closureGraph(factGraph)
cGraph.namespace_manager = namespace_manager
print cGraph.serialize(destination=None,
format=options.output,
base=None)
else:
print network.inferredFacts.serialize(destination=None,
format=options.output,
base=None)
query.prolog.prefixBindings.update(nsBinds)
else:
for prefix, nsInst in nsBinds.items():
if prefix not in query.prolog.prefixBindings:
query.prolog.prefixBindings[prefix] = nsInst
goals.extend([(s, p, o) for s, p, o, c in ReduceGraphPattern(
query.query.whereClause.parsedGraphPattern, query.prolog).patterns
])
dPreds = [] # p for s,p,o in goals ]
magicRuleNo = 0
bottomUpDerivedPreds = []
topDownDerivedPreds = []
defaultBasePreds = []
defaultDerivedPreds = set()
hybridPredicates = []
mapping = dict(newNsMgr.namespaces())
for edb in options.edb:
pref, uri = edb.split(':')
defaultBasePreds.append(URIRef(mapping[pref] + uri))
noMagic = []
for pred in options.noMagic:
pref, uri = pred.split(':')
noMagic.append(URIRef(mapping[pref] + uri))
if options.ddlGraph:
ddlGraph = Graph().parse(options.ddlGraph, format='n3')
# @TODO: should also get hybrid predicates from DDL graph
defaultDerivedPreds = IdentifyDerivedPredicates(
ddlGraph, Graph(), ruleSet)
else:
for idb in options.idb:
pref, uri = idb.split(':')
