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driver.py
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driver.py
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# -*- coding: utf-8 -*-
# Owlready2
# Copyright (C) 2017-2019 Jean-Baptiste LAMY
# LIMICS (Laboratoire d'informatique médicale et d'ingénierie des connaissances en santé), UMR_S 1142
# University Paris 13, Sorbonne paris-Cité, Bobigny, France
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Lesser General Public License for more details.
# You should have received a copy of the GNU Lesser General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
from functools import lru_cache
import owlready2
from owlready2.base import *
from owlready2.base import _universal_datatype_2_abbrev
owlready2_optimized = None
try: import owlready2_optimized
except:
print("* Owlready2 * Warning: optimized Cython parser module 'owlready2_optimized' is not available, defaulting to slower Python implementation", file = sys.stderr)
pass
INT_DATATYPES = { "http://www.w3.org/2001/XMLSchema#integer", "http://www.w3.org/2001/XMLSchema#byte", "http://www.w3.org/2001/XMLSchema#short", "http://www.w3.org/2001/XMLSchema#int", "http://www.w3.org/2001/XMLSchema#long", "http://www.w3.org/2001/XMLSchema#unsignedByte", "http://www.w3.org/2001/XMLSchema#unsignedShort", "http://www.w3.org/2001/XMLSchema#unsignedInt", "http://www.w3.org/2001/XMLSchema#unsignedLong", "http://www.w3.org/2001/XMLSchema#negativeInteger", "http://www.w3.org/2001/XMLSchema#nonNegativeInteger", "http://www.w3.org/2001/XMLSchema#positiveInteger" }
FLOAT_DATATYPES = { "http://www.w3.org/2001/XMLSchema#decimal", "http://www.w3.org/2001/XMLSchema#double", "http://www.w3.org/2001/XMLSchema#float", "http://www.w3.org/2002/07/owl#real" }
class BaseGraph(object):
_SUPPORT_CLONING = False
#READ_METHODS = ["_refactor", "_new_numbered_iri", "_abbreviate", "_unabbreviate",
# "get_triple_sp", "_get_data_triple_triple_sp", "get_triple_po", "_get_obj_triples_transitive_sp", "_get_obj_triples_transitive_po", "_get_obj_triples_transitive_sym", "_get_obj_triples_transitive_sp_indirect", "get_triples", "_get_data_triple_triples", "get_triples_s", "get_triples_sp", "_get_data_triple_triples_sp", "get_triples_po", "get_pred", "get_quads", "_get_triple_data_triples_sp", "_get_triple_data_triple_sp", "_get_triples_sp", "has_triple", "_has_data_triple_triple", "_del_triple", "_del_data_triple"]
#WRITE_METHODS = ["_add_triple", "_set_triple", "_add_data_triple", "_set_data_triple"]
BASE_METHODS = ["_refactor", "_new_numbered_iri", "_abbreviate", "_unabbreviate",
"_get_obj_triples_cspo_cspo", "_get_obj_triples_spo_spo", "_get_obj_triples_sp_co", "_get_obj_triples_s_po",
"_get_obj_triples_po_s", "_get_obj_triples_sp_o", "_get_obj_triple_sp_o", "_get_obj_triple_po_s", "_has_obj_triple_spo", "_del_obj_triple_raw_spo",
"_get_obj_triples_spi_o", "_get_obj_triples_pio_s",
"_get_data_triples_spod_spod", "_get_data_triples_sp_od", "_get_data_triple_sp_od", "_get_data_triples_s_pod", "_has_data_triple_spod", "_del_data_triple_raw_spod",
"_get_triples_spod_spod", "_get_triples_sp_od", "_get_triple_sp_od", "_get_triples_s_pod", "_get_triples_s_p", "_get_obj_triples_o_p",
"_get_obj_triples_transitive_sp", "_get_obj_triples_transitive_po", "_get_obj_triples_transitive_sym", "_get_obj_triples_transitive_sp_indirect"]
WORLD_METHODS = [] # "get_equivs_s_o"
ONTO_METHODS = ["_add_obj_triple_raw_spo", "_set_obj_triple_raw_spo", "_add_data_triple_raw_spod", "_set_data_triple_raw_spod"]
def sub_graph(self, user_context): return self.__class__(self, user_context)
def context_2_user_context(self, context): raise NotImplementedError
def parse(self, f): raise NotImplementedError
def save(self, f, format = "pretty-xml", filter = None): raise NotImplementedError
def _abbreviate (self, iri, create_if_missing = True): return iri
def _unabbreviate(self, iri): return iri
def _get_obj_triples_transitive_sp(self, s, p, already = None):
if already is None: already = set()
else:
if s in already: return already
already.add(s)
for o in self._get_obj_triples_sp_o(s, p):
self._get_obj_triples_transitive_sp(o, p, already)
return already
def _get_obj_triples_transitive_po(self, p, o, already = None):
if already is None: already = set()
else:
if o in already: return already
already.add(o)
for s in self._get_obj_triples_po_s(p, o):
self._get_obj_triples_transitive_po(p, s, already)
return already
def _get_obj_triples_transitive_sym(self, s, p, already = None):
if already is None: already = set()
else:
if s in already: return already
already.add(s)
for s2 in self._get_obj_triples_po_s(p, s): self._get_obj_triples_transitive_sym(s2, p, already)
for s2 in self._get_obj_triples_sp_o(s, p): self._get_obj_triples_transitive_sym(s2, p, already)
return already
def _get_obj_triples_transitive_sp_indirect(self, s, predicates_inverses, already = None):
if already is None: already = set()
else:
if s in already: return already
already.add(s)
for (predicate, inverse) in predicates_inverses:
for o in self._get_obj_triples_sp_o(s, predicate): self._get_obj_triples_transitive_sp_indirect(o, predicates_inverses, already)
if inverse:
for o in self._get_obj_triples_po_s(inverse, s): self._get_obj_triples_transitive_sp_indirect(o, predicates_inverses, already)
return already
def dump(self, format = "ntriples", file = None):
import io
s = io.BytesIO()
self.save(s, format)
print(s.getvalue().decode("utf8"), file = file)
def __bool__(self): return True # To avoid that "if graph:" call __len__()
class BaseMainGraph(BaseGraph):
def parse(self, f): raise NotImplementedError
def save(self, f, format = "rdfxml", **kargs): _save(f, format, self, **kargs)
class BaseSubGraph(BaseGraph):
def __init__(self, parent, onto):
self.parent = parent
self.onto = onto
def parse(self, f, format = None, delete_existing_triples = True, default_base = ""):
format = format or _guess_format(f)
if format == "ntriples":
objs, datas, on_prepare_obj, on_prepare_data, insert_objs, insert_datas, new_blank, _abbreviate, on_finish = self.create_parse_func(getattr(f, "name", ""), delete_existing_triples)
try:
current_line = 0
if owlready2_optimized:
owlready2_optimized.parse_ntriples(f, objs, datas, insert_objs, insert_datas, _abbreviate, new_blank, default_base)
else:
splitter = re.compile("\s")
bn_src_2_sql = {}
line = f.readline().decode("utf8")
while line:
current_line += 1
if (not line.startswith("#")) and (not line.startswith("\n")):
if not line.endswith("\n"): line = "%s\n" % line
s,p,o = splitter.split(line[:-3], 2)
if s.startswith("<"): s = s[1:-1]
elif s.startswith("_"):
bn = bn_src_2_sql.get(s)
if bn is None: bn = bn_src_2_sql[s] = new_blank()
s = bn
p = p[1:-1]
if o.startswith("<"): on_prepare_obj(s, p, o[1:-1])
elif o.startswith("_"):
bn = bn_src_2_sql.get(o)
if bn is None: bn = bn_src_2_sql[o] = new_blank()
on_prepare_obj(s, p, bn)
elif o.startswith('"'):
o, d = o.rsplit('"', 1)
if d.startswith("^"):
d = d[3:-1]
if d in INT_DATATYPES: o = int (o[1:])
elif d in FLOAT_DATATYPES: o = float(o[1:])
else: o = o[1:].encode("raw-unicode-escape").decode("unicode-escape")
else:
o = o[1:].encode("raw-unicode-escape").decode("unicode-escape")
on_prepare_data(s, p, o, d)
line = f.readline().decode("utf8")
onto_base_iri = on_finish()
except Exception as e:
if len(self) == 0:
self._add_obj_triple_raw_spo(self.onto.storid, rdf_type, owl_ontology)
if current_line:
raise OwlReadyOntologyParsingError("NTriples parsing error (or unrecognized file format) in %s, line %s." % (getattr(f, "name", getattr(f, "url", "???")), current_line)) from e
else:
raise OwlReadyOntologyParsingError("NTriples parsing error (or unrecognized file format) in %s." % getattr(f, "name", getattr(f, "url", "???"))) from e
elif format == "rdfxml":
objs, datas, on_prepare_obj, on_prepare_data, insert_objs, insert_datas, new_blank, _abbreviate, on_finish = self.create_parse_func(getattr(f, "name", ""), delete_existing_triples)
try:
if owlready2_optimized:
owlready2_optimized.parse_rdfxml(f, objs, datas, insert_objs, insert_datas, _abbreviate, new_blank, default_base)
else:
import owlready2.rdfxml_2_ntriples
owlready2.rdfxml_2_ntriples.parse(f, on_prepare_obj, on_prepare_data, new_blank, default_base)
onto_base_iri = on_finish()
except OwlReadyOntologyParsingError as e:
if len(self) == 0: self._add_obj_triple_raw_spo(self.onto.storid, rdf_type, owl_ontology)
raise e
elif format == "owlxml":
objs, datas, on_prepare_obj, on_prepare_data, insert_objs, insert_datas, new_blank, _abbreviate, on_finish = self.create_parse_func(getattr(f, "name", ""), delete_existing_triples)
try:
if owlready2_optimized:
owlready2_optimized.parse_owlxml(f, objs, datas, insert_objs, insert_datas, _abbreviate, new_blank, default_base)
else:
import owlready2.owlxml_2_ntriples
owlready2.owlxml_2_ntriples.parse(f, on_prepare_obj, on_prepare_data, new_blank, default_base)
onto_base_iri = on_finish()
except OwlReadyOntologyParsingError as e:
if len(self) == 0: self._add_obj_triple_raw_spo(self.onto.storid, rdf_type, owl_ontology)
raise e
else:
raise ValueError("Unsupported format %s." % format)
return onto_base_iri
def save(self, f, format = "rdfxml", commit = False, **kargs):
if commit: self.parent.commit()
_save(f, format, self, **kargs)
def _guess_format(f):
if f.seekable():
s = f.read(1000)
f.seek(0)
else:
s = f.peek(1000).lstrip()
if isinstance(s, str): s = s.encode("utf8")
if s.startswith(b"\xef\xbb\xbf"): s = s[3:] # Ignore byte-order mask
if not s.lstrip().startswith(b"<"): return "ntriples"
if s[s.find(b"\n") -1] == b".": return "ntriples"
if s.split(b"\n", 1)[0].endswith(b"."): return "ntriples"
if (b"<!DOCTYPE Ontology" in s) or (b"<!DOCTYPE owl:Ontology" in s) or (b"<Ontology xmlns=" in s): return "owlxml"
return "rdfxml"
def _save(f, format, graph, filter = None):
if format == "ntriples":
_unabbreviate = lru_cache(None)(graph._unabbreviate)
for s,p,o,d in graph._iter_triples():
if filter and callable(filter) and not filter(graph, s, p, o, d): continue
if s < 0: s = "_:%s" % (-s)
else: s = "<%s>" % _unabbreviate(s)
p = "<%s>" % _unabbreviate(p)
if d is None:
if o < 0: o = "_:%s" % (-o)
else: o = "<%s>" % _unabbreviate(o)
else:
if isinstance(o, str): o = o.replace('\\', '\\\\').replace('"', '\\"').replace('\n', '\\n')
if isinstance(d, str) and d.startswith("@"): o = '"%s"%s' % (o, d)
elif d == 0: o = '"%s"' % o
else: o = '"%s"^^<%s>' % (o, _unabbreviate(d)) # Unabbreviate datatype's iri
f.write(("%s %s %s .\n" % (s, p, o)).encode("utf8"))
elif format == "nquads":
_unabbreviate = lru_cache(None)(graph._unabbreviate)
c_2_iri = { c : iri for c, iri in graph._iter_ontology_iri() }
for c,s,p,o,d in graph._iter_triples(True):
if filter and callable(filter) and not filter(graph, s, p, o, d, c): continue
if s < 0: s = "_:%s" % (-s)
else: s = "<%s>" % _unabbreviate(s)
p = "<%s>" % _unabbreviate(p)
if d is None:
if o < 0: o = "_:%s" % (-o)
else: o = "<%s>" % _unabbreviate(o)
else:
if isinstance(o, str): o = o.replace('\\', '\\\\').replace('"', '\\"').replace('\n', '\\n')
if isinstance(d, str) and d.startswith("@"): o = '"%s"%s' % (o, d)
elif d == 0: o = '"%s"' % o
else: o = '"%s"^^<%s>' % (o, _unabbreviate(d)) # Unabbreviate datatype's iri
f.write(("<%s> %s %s %s .\n" % (c_2_iri[c], s, p, o)).encode("utf8"))
elif format == "rdfxml":
@lru_cache(None)
def _unabbreviate(storid):
r = graph._unabbreviate(storid).replace("&", "&")
if r.startswith(base_iri):
if base_iri.endswith("/"): return r[len(base_iri) :]
else: return r[len(base_iri) - 1 :]
return r
base_iri = graph._iter_ontology_iri(graph.c)
xmlns = {
"http://www.w3.org/1999/02/22-rdf-syntax-ns#" : "rdf:",
"http://www.w3.org/2001/XMLSchema#" : "xsd:",
"http://www.w3.org/2000/01/rdf-schema#" : "rdfs:",
"http://www.w3.org/2002/07/owl#" : "owl:",
}
if isinstance(base_iri, str):
if base_iri.endswith("/"):
xmlns[base_iri] = ""
else:
xmlns[base_iri[:-1]] = ""
xmlns[base_iri ] = "#"
else:
base_iri = " " # Non-null, non-URL
xmlns_abbbrevs = set(xmlns.values())
@lru_cache(None)
def abbrev(x):
splitted = x.rsplit("#", 1)
splitted_s = x.rsplit("/", 1)
if (len(splitted ) == 2) and (len(splitted_s) == 2) and (len(splitted[1]) < len(splitted_s[1])):
left = splitted[0] + "#"
elif (len(splitted_s) == 2):
splitted = splitted_s
left = splitted[0] + "/"
else: return x
xmln = xmlns.get(left)
if not xmln:
xmln0 = splitted[0].rsplit("/", 1)[1][:4]
if not xmln0[0] in "abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ": xmln0 = "x_" + xmln0
xmln = xmln0 + ":"
i = 2
while xmln in xmlns_abbbrevs: xmln = "%s%s:" % (xmln0, i) ; i += 1
xmlns[left] = xmln = xmln
xmlns_abbbrevs.add(xmln)
return xmln + splitted[1]
lines = []
liness = {}
for type in [
"owl:Ontology",
"owl:ObjectProperty",
"owl:DatatypeProperty",
"owl:AnnotationProperty",
"owl:AllDisjointProperties",
"owl:Class",
"owl:AllDisjointClasses",
"owl:NamedIndividual",
"owl:AllDifferent",
"", ]:
liness[type] = l = []
lines.append(l)
bn_2_inner_list = defaultdict(list)
inner_lists_used = set()
tags_with_list = {
"owl:intersectionOf",
"owl:unionOf",
"owl:members",
"owl:distinctMembers",
"owl:oneOf",
}
bad_types = {
"rdf:Description",
"owl:FunctionalProperty",
"owl:InverseFunctionalProperty",
"owl:TransitiveProperty",
"owl:SymmetricProperty",
"owl:ReflexiveProperty",
"owl:IrreflexiveProperty",
"owl:NamedIndividual",
}
def parse_list(bn):
has_literal = False
r = []
while bn and (bn != rdf_nil):
inner_lists_used.add(id(bn_2_inner_list[bn]))
#first = graph._get_obj_triple_sp_o(bn, rdf_first)
first, d = graph._get_triple_sp_od(bn, rdf_first)
if not ((d is None) and (first == rdf_nil)):
if not d is None: has_literal = True
r.append((first, d))
bn = graph._get_obj_triple_sp_o(bn, rdf_rest)
return has_literal, r
def purge():
nonlocal s_lines, current_s, type
if current_s < 0:
l = bn_2_inner_list[current_s]
current_s = 0
else:
#l = liness.get(type) or l = lines[-1]
l = liness.get(type)
if l is None: l = lines[-1]
if s_lines:
if current_s < 0:
l.append("""<%s rdf:nodeID="node%s">""" % (type, -current_s))
elif current_s > 0:
current_s = _unabbreviate(current_s)
l.append("""<%s rdf:about="%s">""" % (type, current_s))
else:
l.append("""<%s>""" % type)
l.extend(s_lines)
s_lines = []
l.append("""</%s>""" % type)
else:
if current_s < 0:
l.append("""<%s rdf:nodeID="node%s"/>""" % (type, -current_s))
elif current_s > 0:
current_s = _unabbreviate(current_s)
l.append("""<%s rdf:about="%s"/>""" % (type, current_s))
else:
l.append("""<%s/>""" % type)
if current_s: l.append("")
type = "rdf:Description"
s_lines = []
current_s = ""
for s,p,o,d in graph._iter_triples(False, True):
if filter and callable(filter) and not filter(graph, s, p, o, d): continue
if s != current_s:
if current_s: purge()
current_s = s
type = "rdf:Description"
if (p == rdf_type) and (type == "rdf:Description") and (not o < 0):
t = abbrev(_unabbreviate(o))
if not t in bad_types:
type = t
if type.startswith("#"): type = type[1:]
continue
p = abbrev(_unabbreviate(p))
if p.startswith("#"): p = p[1:]
if not d is None:
if isinstance(o, str): o = o.replace('&', '&').replace('<', '<').replace('>', '>')
if isinstance(d, str) and d.startswith("@"): s_lines.append(""" <%s xml:lang="%s">%s</%s>""" % (p, d[1:], o, p))
elif d: s_lines.append(""" <%s rdf:datatype="%s">%s</%s>""" % (p, _unabbreviate(d), o, p))
else: s_lines.append(""" <%s>%s</%s>""" % (p, o, p))
elif o < 0:
if p in tags_with_list:
list_has_literal, list_elements = parse_list(o)
if list_has_literal:
s_lines.append(""" <%s>""" % p)
def do_i(l, i):
s_lines.append(""" <rdf:Description>""")
o, d = l[i]
if d is None:
s_lines.append(""" <rdf:first><rdf:Description rdf:about="%s"/></rdf:first>""" % o)
else:
if isinstance(d, str) and d.startswith("@"): s_lines.append(""" <rdf:first xml:lang="%s">%s</rdf:first>""" % (d[1:], o))
elif d: s_lines.append(""" <rdf:first rdf:datatype="%s">%s</rdf:first>""" % (_unabbreviate(d), o))
else: s_lines.append(""" <rdf:first>%s</rdf:first>""" % o)
if i < len(l) - 1:
s_lines.append(""" <rdf:rest>""")
do_i(l, i + 1)
s_lines.append(""" </rdf:rest>""")
else:
s_lines.append(""" <rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>""")
s_lines.append(""" </rdf:Description>""")
if list_elements: do_i(list_elements, 0)
else:
s_lines.append(""" <%s rdf:parseType="Collection">""" % p)
for i, d in list_elements:
if i < 0:
l = bn_2_inner_list[i]
inner_lists_used.add(id(l))
s_lines.append(l)
elif isinstance(i, int):
i = _unabbreviate(i)
s_lines.append(""" <rdf:Description rdf:about="%s"/>""" % i)
else:
l = bn_2_inner_list[o]
inner_lists_used.add(id(l))
s_lines.append(""" <%s>""" % p)
s_lines.append(l)
s_lines.append(""" </%s>""" % p)
else:
o = _unabbreviate(o)
s_lines.append(""" <%s rdf:resource="%s"/>""" % (p, o))
purge()
if len(bn_2_inner_list) != len(inner_lists_used):
lines.append([])
for l in bn_2_inner_list.values():
if not id(l) in inner_lists_used:
lines[-1].extend(l)
lines[-1].append("")
def flatten(l, deep = ""):
for i in l:
if isinstance(i, list): yield from flatten(i, "%s " % deep)
else: yield "%s%s" % (deep, i)
decls = []
for iri, abbrev in xmlns.items():
if abbrev == "": decls.append('xml:base="%s"' % iri)
elif abbrev == "#": decls.append('xmlns="%s"' % iri)
else: decls.append('xmlns:%s="%s"' % (abbrev[:-1], iri))
if base_iri.endswith("/"):
decls.append('xmlns="%s"' % base_iri)
f.write(b"""<?xml version="1.0"?>\n""")
f.write(("""<rdf:RDF %s>\n\n""" % "\n ".join(decls)).encode("utf8"))
f.write( """\n""".join(flatten(sum(lines, []))).encode("utf8"))
f.write(b"""\n\n</rdf:RDF>\n""")