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- import logging
- import sys
- import rdflib
- #from cython.parallel import prange
- from rdflib.graph import DATASET_DEFAULT_GRAPH_ID as RDFLIB_DEFAULT_GRAPH_URI
- from lakesuperior.store.base_lmdb_store import (
- KeyExistsError, KeyNotFoundError, LmdbError)
- from lakesuperior.util.toolbox import get_tree_size
- from libc.stdlib cimport malloc, free
- cimport lakesuperior.cy_include.collections as cc
- cimport lakesuperior.cy_include.cylmdb as lmdb
- from lakesuperior.model.base cimport (
- FIRST_KEY, KLEN, DBL_KLEN, TRP_KLEN, QUAD_KLEN,
- Key, DoubleKey, TripleKey, QuadKey,
- Buffer, buffer_dump
- )
- from lakesuperior.store.base_lmdb_store cimport (
- _check, BaseLmdbStore, data_v, dbi, key_v)
- from lakesuperior.model.rdf.graph cimport Graph
- from lakesuperior.model.rdf.term cimport (
- Term, deserialize_to_rdflib, serialize_from_rdflib)
- from lakesuperior.model.rdf.triple cimport BufferTriple
- from lakesuperior.model.structures.hash cimport (
- HLEN_128 as HLEN, Hash128, hash128)
- # Integer keys and values are stored in the system's native byte order.
- # Therefore they must be parsed left-to-right if the system is big-endian,
- # and right-to-left if little-endian, in order to maintain the correct
- # sorting order.
- BIG_ENDIAN = sys.byteorder == 'big'
- LSUP_REVERSEKEY = 0 if BIG_ENDIAN else lmdb.MDB_REVERSEKEY
- LSUP_REVERSEDUP = 0 if BIG_ENDIAN else lmdb.MDB_REVERSEDUP
- INT_KEY_MASK = lmdb.MDB_INTEGERKEY | LSUP_REVERSEKEY
- INT_DUP_KEY_MASK = (
- lmdb.MDB_DUPSORT | lmdb.MDB_DUPFIXED | lmdb.MDB_INTEGERKEY
- | LSUP_REVERSEKEY | LSUP_REVERSEDUP
- )
- INT_DUP_MASK = (
- lmdb.MDB_DUPSORT | lmdb.MDB_DUPFIXED | lmdb.MDB_INTEGERDUP
- | LSUP_REVERSEKEY | LSUP_REVERSEDUP
- )
- cdef:
- # Term key to serialized term
- DbLabel DB_T_ST = 't:st___',
- # Joined triple keys to context key
- DbLabel DB_SPO_C = 'spo:c__',
- # This has empty values and is used to keep track of empty contexts.
- DbLabel DB_C_ = 'c:_____',
- # Prefix to namespace
- DbLabel DB_PFX_NS = 'pfx:ns_',
- # Indices
- # Namespace to prefix
- DbLabel DB_NS_PFX = 'ns:pfx_',
- # Term hash to term key
- DbLabel DB_TH_T = 'th:t___',
- # 1-bound lookups
- DbLabel DB_S_PO = 's:po___',
- DbLabel DB_P_SO = 'p:so___',
- DbLabel DB_O_SP = 'o:sp___',
- # 2-bound lookups
- DbLabel DB_PO_S = 'po:s___',
- DbLabel DB_SO_P = 'so:p___',
- DbLabel DB_SP_O = 'sp:o___',
- # Context lookup
- DbLabel DB_C_SPO = 'c:spo__',
- lookup_rank = [0, 2, 1]
- """
- Order in which keys are looked up if two terms are bound.
- The indices with the smallest average number of values per key should be
- looked up first.
- 0 = s:po
- 1 = p:so
- 2 = o:sp
- """
- lookup_ordering = [
- [0, 1, 2], # spo
- [1, 0, 2], # pso
- [2, 0, 1], # osp
- ]
- lookup_ordering_2bound = [
- [1, 2, 0], # po:s
- [0, 2, 1], # so:p
- [0, 1, 2], # sp:o
- ]
- lookup_indices = [
- DB_S_PO,
- DB_P_SO,
- DB_O_SP,
- DB_PO_S,
- DB_SO_P,
- DB_SP_O,
- ]
- logger = logging.getLogger(__name__)
- cdef class LmdbTriplestore(BaseLmdbStore):
- """
- Low-level triplestore layer.
- This class extends the general-purpose :py:class:`BaseLmdbStore` and maps
- triples and contexts to key-value records in LMDB. It can be used in the
- application context (``env.app_globals.rdf_store``), or an independent
- instance can be spun up in an arbitrary disk location.
- This class provides the base for the RDFlib-compatible backend in the
- :py:class:`lakesuperior.store.ldp_rs.lmdb_store.LmdbStore`.
- """
- dbi_labels = [
- DB_T_ST,
- DB_SPO_C,
- DB_C_,
- DB_PFX_NS,
- DB_NS_PFX,
- DB_TH_T,
- DB_S_PO,
- DB_P_SO,
- DB_O_SP,
- DB_PO_S,
- DB_SO_P,
- DB_SP_O,
- DB_C_SPO,
- ]
- dbi_flags = {
- DB_C_: INT_KEY_MASK,
- DB_T_ST: INT_KEY_MASK,
- DB_S_PO: INT_DUP_KEY_MASK,
- DB_P_SO: INT_DUP_KEY_MASK,
- DB_O_SP: INT_DUP_KEY_MASK,
- DB_PO_S: INT_DUP_MASK,
- DB_SO_P: INT_DUP_MASK,
- DB_SP_O: INT_DUP_MASK,
- DB_C_SPO: INT_DUP_KEY_MASK,
- DB_SPO_C: INT_DUP_MASK,
- }
- logger.debug(f'DBI flags: {dbi_flags}')
- flags = 0
- options = {
- 'map_size': 1024 ** 4 # 1Tb.
- }
- # DB management methods.
- cpdef dict stats(self):
- """
- Gather statistics about the database."""
- st = self._stats()
- st['num_triples'] = st['db_stats'][DB_SPO_C]['ms_entries']
- st['store_size'] = get_tree_size(self.env_path)
- return st
- cpdef size_t _len(self, context=None) except -1:
- """
- Return the length of the dataset.
- The RDFLib interface defines `__len__` in a nonstandard way that
- causes a Cython compilation error, so this method is called by the
- `__len__` method of its Python counterpart.
- """
- cdef:
- size_t ct
- Key ck
- if context is not None:
- ck = self.to_key(context)
- key_v.mv_data = &ck
- key_v.mv_size = KLEN
- cur = self._cur_open(DB_C_SPO)
- try:
- _check(lmdb.mdb_cursor_get(
- cur, &key_v, NULL, lmdb.MDB_SET))
- _check(lmdb.mdb_cursor_count(cur, &ct))
- except KeyNotFoundError:
- return 0
- else:
- return ct
- finally:
- #pass
- self._cur_close(cur)
- else:
- return self.stats()['num_triples']
- ## PRIVATE METHODS ##
- # Triple and graph methods.
- cpdef void add(self, triple, context=None, quoted=False) except *:
- """
- Add a triple and start indexing.
- :param tuple(rdflib.Identifier) triple: Tuple of three identifiers.
- :param context: Context identifier. ``None`` inserts in the default
- graph.
- :type context: rdflib.Identifier or None
- :param bool quoted: Not used.
- """
- cdef:
- lmdb.MDB_cursor *icur
- lmdb.MDB_val spo_v, c_v, null_v, key_v, data_v
- unsigned char i
- Hash128 thash
- QuadKey spock
- Buffer pk_t
- c = self._normalize_context(context)
- if c is None:
- c = RDFLIB_DEFAULT_GRAPH_URI
- s, p, o = triple
- icur = self._cur_open(DB_TH_T)
- try:
- for i, term_obj in enumerate((s, p, o, c)):
- serialize_from_rdflib(term_obj, &pk_t)
- hash128(&pk_t, &thash)
- try:
- key_v.mv_data = thash
- key_v.mv_size = HLEN
- _check(lmdb.mdb_get(
- self.txn, self.get_dbi(DB_TH_T), &key_v, &data_v))
- spock[i] = (<Key*>data_v.mv_data)[0]
- except KeyNotFoundError:
- # If term_obj is not found, add it...
- logger.debug('Hash {} not found. Adding to DB.'.format(
- thash[: HLEN]))
- spock[i] = self._append(&pk_t, dblabel=DB_T_ST)
- # ...and index it.
- key_v.mv_data = thash
- key_v.mv_size = HLEN
- data_v.mv_data = spock + i
- data_v.mv_size = KLEN
- _check(
- lmdb.mdb_cursor_put(icur, &key_v, &data_v, 0),
- 'Error setting key {}.'.format(thash))
- finally:
- self._cur_close(icur)
- spo_v.mv_data = spock # address of sk in spock
- spo_v.mv_size = TRP_KLEN # Grab 3 keys
- c_v.mv_data = spock + 3 # address of ck in spock
- c_v.mv_size = KLEN
- null_v.mv_data = b''
- null_v.mv_size = 0
- try:
- _check(lmdb.mdb_put(
- self.txn, self.get_dbi(DB_C_), &c_v, &null_v,
- lmdb.MDB_NOOVERWRITE))
- except KeyExistsError:
- pass
- try:
- # Add triple:context association.
- _check(lmdb.mdb_put(
- self.txn, self.get_dbi(DB_SPO_C), &spo_v, &c_v,
- lmdb.MDB_NODUPDATA))
- except KeyExistsError:
- pass
- try:
- # Index context:triple association.
- _check(lmdb.mdb_put(
- self.txn, self.get_dbi(DB_C_SPO), &c_v, &spo_v,
- lmdb.MDB_NODUPDATA))
- except KeyExistsError:
- pass
- self._index_triple(IDX_OP_ADD, [spock[0], spock[1], spock[2]])
- cpdef void add_graph(self, c) except *:
- """
- Add a graph (context) to the database.
- This creates an empty graph by associating the graph URI with the
- pickled `None` value. This prevents from removing the graph when all
- triples are removed.
- :param rdflib.URIRef graph: URI of the named graph to add.
- """
- cdef:
- lmdb.MDB_txn *_txn
- Buffer _sc
- Key ck
- c = self._normalize_context(c)
- ck = self.to_key(c)
- if not self._key_exists(<unsigned char*>&ck, KLEN, DB_C_):
- # Insert context term if not existing.
- if self.is_txn_rw:
- #logger.debug('Working in existing RW transaction.')
- _txn = self.txn
- else:
- #logger.debug('Opening a temporary RW transaction.')
- _check(lmdb.mdb_txn_begin(self.dbenv, NULL, 0, &_txn))
- # Open new R/W transactions.
- try:
- # Add to list of contexts.
- key_v.mv_data = &ck
- key_v.mv_size = KLEN
- data_v.mv_data = &ck # Whatever, length is zero anyways
- data_v.mv_size = 0
- _check(lmdb.mdb_put(
- _txn, self.get_dbi(DB_C_), &key_v, &data_v, 0
- ))
- if not self.is_txn_rw:
- _check(lmdb.mdb_txn_commit(_txn))
- # Kick the main transaction to see the new terms.
- lmdb.mdb_txn_reset(self.txn)
- _check(lmdb.mdb_txn_renew(self.txn))
- except:
- if not self.is_txn_rw:
- lmdb.mdb_txn_abort(_txn)
- raise
- cpdef void _remove(self, tuple triple_pattern, context=None) except *:
- cdef:
- lmdb.MDB_val spok_v, ck_v
- TripleKey spok_cur
- Key ck
- if context is not None:
- try:
- ck = self.to_key(context)
- except KeyNotFoundError:
- # If context is specified but not found, return to avoid
- # deleting the wrong triples.
- return
- # Get the matching pattern.
- match_set = self.triple_keys(triple_pattern, context)
- dcur = self._cur_open(DB_SPO_C)
- icur = self._cur_open(DB_C_SPO)
- try:
- spok_v.mv_size = TRP_KLEN
- # If context was specified, remove only associations with that context.
- match_set.keys.seek()
- if context is not None:
- ck_v.mv_data = &ck
- ck_v.mv_size = KLEN
- while match_set.keys.get_next(&spok_cur):
- spok_v.mv_data = spok_cur
- # Delete spo:c entry.
- try:
- _check(lmdb.mdb_cursor_get(
- dcur, &spok_v, &ck_v, lmdb.MDB_GET_BOTH))
- except KeyNotFoundError:
- pass
- else:
- _check(lmdb.mdb_cursor_del(dcur, 0))
- # Restore ck after delete.
- ck_v.mv_data = &ck
- # Delete c:spo entry.
- try:
- _check(lmdb.mdb_cursor_get(
- icur, &ck_v, &spok_v, lmdb.MDB_GET_BOTH))
- except KeyNotFoundError:
- pass
- else:
- _check(lmdb.mdb_cursor_del(icur, 0))
- # Delete lookup indices, only if no other context
- # association is present.
- # spok_v has changed on mdb_cursor_del. Restore.
- spok_v.mv_data = spok_cur
- try:
- _check(lmdb.mdb_cursor_get(
- dcur, &spok_v, NULL, lmdb.MDB_SET))
- except KeyNotFoundError:
- self._index_triple(IDX_OP_REMOVE, spok_cur)
- # If no context is specified, remove all associations.
- else:
- logger.debug('Removing triples in all contexts.')
- # Loop over all SPO matching the triple pattern.
- while match_set.keys.get_next(&spok_cur):
- spok_v.mv_data = spok_cur
- # Loop over all context associations for this SPO.
- try:
- _check(lmdb.mdb_cursor_get(
- dcur, &spok_v, &ck_v, lmdb.MDB_SET_KEY))
- except KeyNotFoundError:
- # Move on to the next SPO.
- continue
- else:
- ck = (<Key*>ck_v.mv_data)[0]
- while True:
- # Delete c:spo association.
- try:
- _check(lmdb.mdb_cursor_get(
- icur, &ck_v, &spok_v, lmdb.MDB_GET_BOTH))
- except KeyNotFoundError:
- pass
- else:
- lmdb.mdb_cursor_del(icur, 0)
- # Restore the pointer to the deleted SPO.
- spok_v.mv_data = spok_cur
- # Move on to next associated context.
- try:
- _check(lmdb.mdb_cursor_get(
- dcur, &spok_v, &ck_v, lmdb.MDB_NEXT_DUP))
- except KeyNotFoundError:
- break
- # Then delete the spo:c association.
- try:
- _check(lmdb.mdb_cursor_get(
- dcur, &spok_v, &ck_v, lmdb.MDB_SET))
- except KeyNotFoundError:
- pass
- else:
- lmdb.mdb_cursor_del(dcur, lmdb.MDB_NODUPDATA)
- self._index_triple(IDX_OP_REMOVE, spok_cur)
- finally:
- self._cur_close(dcur)
- self._cur_close(icur)
- cdef void _index_triple(self, int op, TripleKey spok) except *:
- """
- Update index for a triple and context (add or remove).
- :param str op: one of ``IDX_OP_ADD`` or ``IDX_OP_REMOVE``.
- :param TripleKey spok: Triple key to index.
- """
- cdef:
- DoubleKey dbl_keys[3]
- size_t i = 0
- lmdb.MDB_val key_v, dbl_key_v
- dbl_keys = [
- [spok[1], spok[2]], # pok
- [spok[0], spok[2]], # sok
- [spok[0], spok[1]], # spk
- ]
- #logger.debug(f'''Indices:
- #spok: {[spok[0], spok[1], spok[2]]}
- #sk: {spok[0]}
- #pk: {spok[1]}
- #ok: {spok[2]}
- #pok: {dbl_keys[0]}
- #sok: {dbl_keys[1]}
- #spk: {dbl_keys[2]}
- #''')
- key_v.mv_size = KLEN
- dbl_key_v.mv_size = DBL_KLEN
- #logger.debug('Start indexing: {}.'.format(spok[: TRP_KLEN]))
- #if op == IDX_OP_REMOVE:
- # logger.debug(f'Remove {spok[0]} from indices.')
- #else:
- # logger.debug(f'Add {spok[0]} to indices.')
- while i < 3:
- cur1 = self._cur_open(lookup_indices[i]) # s:po, p:so, o:sp
- cur2 = self._cur_open(lookup_indices[i + 3])# po:s, so:p, sp:o
- try:
- key_v.mv_data = spok + i
- dbl_key_v.mv_data = dbl_keys[i]
- # Removal op indexing.
- if op == IDX_OP_REMOVE:
- try:
- _check(lmdb.mdb_cursor_get(
- cur1, &key_v, &dbl_key_v, lmdb.MDB_GET_BOTH))
- except KeyNotFoundError:
- pass
- else:
- _check(lmdb.mdb_cursor_del(cur1, 0))
- # Restore pointers after delete.
- key_v.mv_data = spok + i
- dbl_key_v.mv_data = dbl_keys[i]
- try:
- _check(lmdb.mdb_cursor_get(
- cur2, &dbl_key_v, &key_v, lmdb.MDB_GET_BOTH))
- except KeyNotFoundError:
- pass
- else:
- _check(lmdb.mdb_cursor_del(cur2, 0))
- # Addition op indexing.
- elif op == IDX_OP_ADD:
- try:
- _check(lmdb.mdb_cursor_put(
- cur1, &key_v, &dbl_key_v, lmdb.MDB_NODUPDATA))
- except KeyExistsError:
- pass
- try:
- _check(lmdb.mdb_cursor_put(
- cur2, &dbl_key_v, &key_v, lmdb.MDB_NODUPDATA))
- except KeyExistsError:
- pass
- else:
- raise ValueError(
- 'Index operation \'{}\' is not supported.'.format(op))
- i += 1
- finally:
- #pass
- self._cur_close(cur1)
- self._cur_close(cur2)
- cpdef void _remove_graph(self, object gr_uri) except *:
- """
- Delete a context.
- """
- cdef:
- Hash128 chash
- Key ck
- lmdb.MDB_val ck_v, chash_v
- Buffer pk_c
- # Gather information on the graph prior to deletion.
- try:
- ck = self.to_key(gr_uri)
- except KeyNotFoundError:
- return
- # Remove all triples and indices associated with the graph.
- self._remove((None, None, None), gr_uri)
- # Remove the graph if it is in triples.
- self._remove((gr_uri, None, None))
- self._remove((None, None, gr_uri))
- # Clean up all terms related to the graph.
- serialize_from_rdflib(gr_uri, &pk_c)
- hash128(&pk_c, &chash)
- ck_v.mv_size = KLEN
- chash_v.mv_size = HLEN
- try:
- ck_v.mv_data = &ck
- _check(lmdb.mdb_del(self.txn, self.get_dbi(DB_C_), &ck_v, NULL))
- ck_v.mv_data = &ck
- _check(lmdb.mdb_del(self.txn, self.get_dbi(DB_T_ST), &ck_v, NULL))
- chash_v.mv_data = chash
- _check(lmdb.mdb_del(self.txn, self.get_dbi(DB_TH_T), &chash_v, NULL))
- except KeyNotFoundError:
- pass
- # Lookup methods.
- def contexts(self, triple=None):
- """
- Get a list of all contexts.
- :rtype: set(URIRef)
- """
- cdef:
- size_t sz, i
- Key* match
- try:
- self.all_contexts(&match, &sz, triple)
- ret = set()
- for i in range(sz):
- ret.add(self.from_key(match[i]))
- finally:
- free(match)
- return ret
- def triples(self, triple_pattern, context=None):
- """
- Generator over matching triples.
- :param tuple triple_pattern: 3 RDFLib terms
- :param context: Context graph, if available.
- :type context: rdflib.Graph or None
- :rtype: Iterator
- :return: Generator over triples and contexts in which each result has
- the following format::
- (s, p, o), generator(contexts)
- Where the contexts generator lists all context that the triple appears
- in.
- """
- cdef:
- size_t i = 0
- TripleKey it_cur
- lmdb.MDB_val key_v, data_v
- # This sounds strange, RDFLib should be passing None at this point,
- # but anyway...
- context = self._normalize_context(context)
- logger.debug(
- 'Getting triples for: {}, {}'.format(triple_pattern, context))
- rset = self.triple_keys(triple_pattern, context)
- #logger.debug('Triple keys found: {}'.format(rset.data[:rset.size]))
- cur = self._cur_open(DB_SPO_C)
- try:
- key_v.mv_size = TRP_KLEN
- rset.keys.seek()
- while rset.keys.get_next(&it_cur):
- key_v.mv_data = it_cur
- # Get contexts associated with each triple.
- contexts = []
- # This shall never be MDB_NOTFOUND.
- _check(lmdb.mdb_cursor_get(cur, &key_v, &data_v, lmdb.MDB_SET))
- while True:
- c_uri = self.from_key((<Key*>data_v.mv_data)[0])
- contexts.append(
- Graph(self, uri=c_uri)
- )
- try:
- _check(lmdb.mdb_cursor_get(
- cur, &key_v, &data_v, lmdb.MDB_NEXT_DUP))
- except KeyNotFoundError:
- break
- yield (
- (
- self.from_key((<Key*>key_v.mv_data)[0]),
- self.from_key((<Key*>key_v.mv_data)[1]),
- self.from_key((<Key*>key_v.mv_data)[2]),
- ),
- tuple(contexts)
- )
- finally:
- self._cur_close(cur)
- cpdef Graph triple_keys(
- self, tuple triple_pattern, context=None, uri=None
- ):
- """
- Top-level lookup method.
- This method is used by `triples` which returns native Python tuples,
- as well as by other methods that need to iterate and filter triple
- keys without incurring in the overhead of converting them to triples.
- :param tuple triple_pattern: 3 RDFLib terms
- :param context: Context graph or URI, or None.
- :type context: rdflib.term.Identifier or None
- """
- cdef:
- size_t ct = 0, i = 0
- lmdb.MDB_cursor *icur
- lmdb.MDB_val key_v, data_v
- Key tk, ck
- TripleKey spok
- Graph flt_res, ret
- if context is not None:
- try:
- ck = self.to_key(context)
- except KeyNotFoundError:
- # Context not found.
- return Graph(self, uri=uri)
- icur = self._cur_open(DB_C_SPO)
- try:
- key_v.mv_data = &ck
- key_v.mv_size = KLEN
- # s p o c
- if all(triple_pattern):
- for i, term in enumerate(triple_pattern):
- try:
- tk = self.to_key(term)
- except KeyNotFoundError:
- # A term key was not found.
- return Graph(self, uri=uri)
- spok[i] = tk
- data_v.mv_data = spok
- data_v.mv_size = TRP_KLEN
- try:
- _check(lmdb.mdb_cursor_get(
- icur, &key_v, &data_v, lmdb.MDB_GET_BOTH))
- except KeyNotFoundError:
- # Triple not found.
- #logger.debug('spok / ck pair not found.')
- return Graph(self, uri=uri)
- ret = Graph(self, 1, uri=uri)
- ret.keys.add(&spok)
- return ret
- # ? ? ? c
- elif not any(triple_pattern):
- # Get all triples from the context
- try:
- _check(lmdb.mdb_cursor_get(
- icur, &key_v, &data_v, lmdb.MDB_SET))
- except KeyNotFoundError:
- # Triple not found.
- return Graph(self, uri=uri)
- _check(lmdb.mdb_cursor_count(icur, &ct))
- ret = Graph(self, ct, uri=uri)
- _check(lmdb.mdb_cursor_get(
- icur, &key_v, &data_v, lmdb.MDB_GET_MULTIPLE))
- while True:
- # Loop over page data.
- spok_page = <TripleKey*>data_v.mv_data
- for i in range(data_v.mv_size // TRP_KLEN):
- ret.keys.add(spok_page + i)
- try:
- # Get next page.
- _check(lmdb.mdb_cursor_get(
- icur, &key_v, &data_v, lmdb.MDB_NEXT_MULTIPLE))
- except KeyNotFoundError:
- return ret
- # Regular lookup. Filter _lookup() results by context.
- else:
- try:
- res = self._lookup(triple_pattern)
- except KeyNotFoundError:
- return Graph(self, uri=uri)
- key_v.mv_data = &ck
- key_v.mv_size = KLEN
- data_v.mv_size = TRP_KLEN
- flt_res = Graph(self, res.capacity, uri=uri)
- res.keys.seek()
- while res.keys.get_next(&spok):
- data_v.mv_data = spok
- try:
- # Verify that the triple is associated with the
- # context being searched.
- _check(lmdb.mdb_cursor_get(
- icur, &key_v, &data_v, lmdb.MDB_GET_BOTH))
- except KeyNotFoundError:
- continue
- else:
- flt_res.keys.add(&spok)
- return flt_res
- finally:
- self._cur_close(icur)
- # Unfiltered lookup. No context checked.
- else:
- try:
- res = self._lookup(triple_pattern)
- except KeyNotFoundError:
- return Graph(self, uri=uri)
- return res
- cdef Graph _lookup(self, tuple triple_pattern):
- """
- Look up triples in the indices based on a triple pattern.
- :rtype: Iterator
- :return: Matching triple keys.
- """
- cdef:
- size_t ct = 0
- lmdb.MDB_stat db_stat
- lmdb.MDB_val spok_v, ck_v
- TripleKey spok
- Key sk, pk, ok, tk1, tk2, tk3
- s, p, o = triple_pattern
- try:
- if s is not None:
- sk = self.to_key(s)
- if p is not None:
- pk = self.to_key(p)
- if o is not None:
- ok = self.to_key(o)
- except KeyNotFoundError:
- return Graph(self)
- if s is not None:
- tk1 = sk
- if p is not None:
- tk2 = pk
- # s p o
- if o is not None:
- tk3 = ok
- spok_v.mv_data = spok
- spok_v.mv_size = TRP_KLEN
- try:
- spok = [tk1, tk2, tk3]
- _check(lmdb.mdb_get(
- self.txn, self.get_dbi(DB_SPO_C), &spok_v, &ck_v))
- except KeyNotFoundError:
- return Graph(self)
- matches = Graph(self, 1)
- matches.keys.add(&spok)
- return matches
- # s p ?
- return self._lookup_2bound(0, 1, [tk1, tk2])
- if o is not None: # s ? o
- tk2 = ok
- return self._lookup_2bound(0, 2, [tk1, tk2])
- # s ? ?
- return self._lookup_1bound(0, tk1)
- if p is not None:
- tk1 = pk
- if o is not None: # ? p o
- tk2 = ok
- return self._lookup_2bound(1, 2, [tk1, tk2])
- # ? p ?
- return self._lookup_1bound(1, tk1)
- if o is not None: # ? ? o
- tk1 = ok
- return self._lookup_1bound(2, tk1)
- # ? ? ?
- # Get all triples in the database.
- dcur = self._cur_open(DB_SPO_C)
- try:
- _check(
- lmdb.mdb_stat(
- self.txn, lmdb.mdb_cursor_dbi(dcur), &db_stat
- ), 'Error gathering DB stats.'
- )
- ct = db_stat.ms_entries
- ret = Graph(self, ct)
- #logger.debug(f'Triples found: {ct}')
- if ct == 0:
- return Graph(self)
- _check(lmdb.mdb_cursor_get(
- dcur, &key_v, &data_v, lmdb.MDB_FIRST))
- while True:
- spok = <TripleKey>key_v.mv_data
- ret.keys.add(&spok)
- try:
- _check(lmdb.mdb_cursor_get(
- dcur, &key_v, &data_v, lmdb.MDB_NEXT_NODUP))
- except KeyNotFoundError:
- break
- return ret
- finally:
- self._cur_close(dcur)
- cdef Graph _lookup_1bound(self, unsigned char idx, Key luk):
- """
- Lookup triples for a pattern with one bound term.
- :param str idx_name: The index to look up as one of the keys of
- ``_lookup_ordering``.
- :param rdflib.URIRef term: Bound term to search for.
- :rtype: Iterator(bytes)
- :return: SPO keys matching the pattern.
- """
- cdef:
- unsigned int dbflags
- unsigned char term_order[3]
- size_t ct, i
- lmdb.MDB_cursor *icur
- lmdb.MDB_val key_v, data_v
- TripleKey spok
- #logger.debug(f'lookup 1bound: {idx}, {luk}')
- term_order = lookup_ordering[idx]
- icur = self._cur_open(lookup_indices[idx])
- logging.debug(f'DB label: {lookup_indices[idx]}')
- logging.debug('term order: {}'.format(term_order[: 3]))
- try:
- key_v.mv_data = &luk
- key_v.mv_size = KLEN
- _check(lmdb.mdb_cursor_get(icur, &key_v, &data_v, lmdb.MDB_SET))
- _check(lmdb.mdb_cursor_count(icur, &ct))
- # Allocate memory for results.
- ret = Graph(self, ct)
- _check(lmdb.mdb_cursor_get(icur, &key_v, &data_v, lmdb.MDB_SET))
- _check(lmdb.mdb_cursor_get(
- icur, &key_v, &data_v, lmdb.MDB_GET_MULTIPLE))
- while True:
- lu_dset = <DoubleKey*>data_v.mv_data
- for i in range(data_v.mv_size // DBL_KLEN):
- spok[term_order[0]] = luk
- spok[term_order[1]] = lu_dset[i][0]
- spok[term_order[2]] = lu_dset[i][1]
- ret.keys.add(&spok)
- try:
- # Get results by the page.
- _check(lmdb.mdb_cursor_get(
- icur, &key_v, &data_v, lmdb.MDB_NEXT_MULTIPLE))
- except KeyNotFoundError:
- return ret
- finally:
- self._cur_close(icur)
- cdef Graph _lookup_2bound(
- self, unsigned char idx1, unsigned char idx2, DoubleKey tks
- ):
- """
- Look up triples for a pattern with two bound terms.
- :param str idx1: The index to look up as one of the keys of
- ``lookup_ordering_2bound``.
- :param rdflib.URIRef term1: First bound term to search for.
- :rtype: Iterator(bytes)
- :return: SPO keys matching the pattern.
- """
- cdef:
- unsigned char luk1_offset, luk2_offset
- unsigned int dbflags
- unsigned char term_order[3] # Lookup ordering
- size_t ct, i = 0
- lmdb.MDB_cursor* icur
- Graph ret
- DoubleKey luk
- TripleKey spok
- for i in range(3):
- if (
- idx1 in lookup_ordering_2bound[i][: 2]
- and idx2 in lookup_ordering_2bound[i][: 2]):
- term_order = lookup_ordering_2bound[i]
- if term_order[0] == idx1:
- luk1_offset = 0
- luk2_offset = 1
- else:
- luk1_offset = 1
- luk2_offset = 0
- dblabel = lookup_indices[i + 3] # skip 1bound index labels
- break
- if i == 2:
- raise ValueError(
- 'Indices {} and {} not found in LU keys.'.format(
- idx1, idx2))
- # Compose term keys in lookup key.
- luk[luk1_offset] = tks[0]
- luk[luk2_offset] = tks[1]
- icur = self._cur_open(dblabel)
- try:
- key_v.mv_data = luk
- key_v.mv_size = DBL_KLEN
- # Count duplicates for key and allocate memory for result set.
- _check(lmdb.mdb_cursor_get(icur, &key_v, &data_v, lmdb.MDB_SET))
- _check(lmdb.mdb_cursor_count(icur, &ct))
- ret = Graph(self, ct)
- _check(lmdb.mdb_cursor_get(icur, &key_v, &data_v, lmdb.MDB_SET))
- _check(lmdb.mdb_cursor_get(
- icur, &key_v, &data_v, lmdb.MDB_GET_MULTIPLE))
- while True:
- lu_dset = <Key*>data_v.mv_data
- for i in range(data_v.mv_size // KLEN):
- spok[term_order[0]] = luk[0]
- spok[term_order[1]] = luk[1]
- spok[term_order[2]] = lu_dset[i]
- ret.keys.add(&spok)
- try:
- # Get results by the page.
- _check(lmdb.mdb_cursor_get(
- icur, &key_v, &data_v, lmdb.MDB_NEXT_MULTIPLE))
- except KeyNotFoundError:
- return ret
- finally:
- self._cur_close(icur)
- cdef void _all_term_keys(self, term_type, cc.HashSet** tkeys) except *:
- """
- Return all keys of a (``s:po``, ``p:so``, ``o:sp``) index.
- """
- cdef:
- size_t i = 0
- lmdb.MDB_stat stat
- cc.HashSetConf tkeys_conf
- idx_label = lookup_indices['spo'.index(term_type)]
- icur = self._cur_open(idx_label)
- try:
- _check(lmdb.mdb_stat(self.txn, lmdb.mdb_cursor_dbi(icur), &stat))
- cc.hashset_conf_init(&tkeys_conf)
- tkeys_conf.initial_capacity = 1024
- tkeys_conf.load_factor = .75
- tkeys_conf.key_length = KLEN
- tkeys_conf.key_compare = cc.CC_CMP_POINTER
- tkeys_conf.hash = cc.POINTER_HASH
- cc.hashset_new_conf(&tkeys_conf, tkeys)
- try:
- _check(lmdb.mdb_cursor_get(
- icur, &key_v, NULL, lmdb.MDB_FIRST))
- except KeyNotFoundError:
- return
- while True:
- cc.hashset_add(tkeys[0], key_v.mv_data)
- rc = lmdb.mdb_cursor_get(
- icur, &key_v, NULL, lmdb.MDB_NEXT_NODUP)
- try:
- _check(rc)
- except KeyNotFoundError:
- return
- i += 1
- finally:
- self._cur_close(icur)
- def all_terms(self, term_type):
- """
- Return all terms of a type (``s``, ``p``, or ``o``) in the store.
- """
- cdef:
- void* cur
- cc.HashSet* tkeys
- cc.HashSetIter it
- ret = set()
- try:
- self._all_term_keys(term_type, &tkeys)
- cc.hashset_iter_init(&it, tkeys)
- while cc.hashset_iter_next(&it, &cur) != cc.CC_ITER_END:
- ret.add(self.from_key((<Key*>cur)[0]))
- finally:
- if tkeys:
- free(tkeys)
- return ret
- cpdef tuple all_namespaces(self):
- """
- Return all registered namespaces.
- """
- cdef:
- size_t i = 0
- lmdb.MDB_stat stat
- ret = []
- dcur = self._cur_open(DB_PFX_NS)
- try:
- try:
- _check(lmdb.mdb_cursor_get(
- dcur, &key_v, &data_v, lmdb.MDB_FIRST))
- except KeyNotFoundError:
- return tuple()
- while True:
- ret.append((
- (<unsigned char *>key_v.mv_data)[: key_v.mv_size].decode(),
- (<unsigned char *>data_v.mv_data)[: data_v.mv_size].decode()))
- try:
- _check(lmdb.mdb_cursor_get(
- dcur, &key_v, &data_v, lmdb.MDB_NEXT))
- except KeyNotFoundError:
- return tuple(ret)
- i += 1
- finally:
- self._cur_close(dcur)
- cdef void all_contexts(
- self, Key** ctx, size_t* sz, triple=None
- ) except *:
- """
- Get a list of all contexts.
- """
- cdef:
- size_t ct
- lmdb.MDB_stat stat
- lmdb.MDB_val key_v, data_v
- TripleKey spok
- cur = (
- self._cur_open(DB_SPO_C) if triple and all(triple)
- else self._cur_open(DB_C_))
- try:
- if triple and all(triple):
- _check(lmdb.mdb_stat(
- self.txn, lmdb.mdb_cursor_dbi(cur), &stat))
- spok = [
- self.to_key(triple[0]),
- self.to_key(triple[1]),
- self.to_key(triple[2]),
- ]
- key_v.mv_data = spok
- key_v.mv_size = TRP_KLEN
- try:
- _check(lmdb.mdb_cursor_get(
- cur, &key_v, &data_v, lmdb.MDB_SET_KEY))
- except KeyNotFoundError:
- ctx[0] = NULL
- return
- ctx[0] = <Key*>malloc(stat.ms_entries * KLEN)
- sz[0] = 0
- while True:
- ctx[0][sz[0]] = (<Key*>data_v.mv_data)[0]
- sz[0] += 1
- try:
- _check(lmdb.mdb_cursor_get(
- cur, &key_v, &data_v, lmdb.MDB_NEXT_DUP))
- except KeyNotFoundError:
- break
- else:
- _check(lmdb.mdb_stat(
- self.txn, lmdb.mdb_cursor_dbi(cur), &stat))
- try:
- _check(lmdb.mdb_cursor_get(
- cur, &key_v, &data_v, lmdb.MDB_FIRST))
- except KeyNotFoundError:
- ctx[0] = NULL
- return
- ctx[0] = <Key*>malloc(stat.ms_entries * KLEN)
- sz[0] = 0
- while True:
- ctx[0][sz[0]] = (<Key*>key_v.mv_data)[0]
- sz[0] += 1
- try:
- _check(lmdb.mdb_cursor_get(
- cur, &key_v, NULL, lmdb.MDB_NEXT))
- except KeyNotFoundError:
- break
- finally:
- self._cur_close(cur)
- # Key conversion methods.
- cdef inline void lookup_term(self, const Key tk, Buffer* data) except *:
- """
- look up a term by key.
- :param Key key: The key to be looked up.
- :param Buffer *data: Buffer structure containing the serialized term.
- """
- cdef:
- lmdb.MDB_val key_v, data_v
- key_v.mv_data = &tk
- key_v.mv_size = KLEN
- _check(
- lmdb.mdb_get(
- self.txn, self.get_dbi(DB_T_ST), &key_v, &data_v
- ),
- f'Error getting data for key \'{tk}\'.'
- )
- data.addr = data_v.mv_data
- data.sz = data_v.mv_size
- cdef object from_key(self, const Key tk):
- """
- Convert a single key into one term.
- :param Key key: The key to be converted.
- """
- cdef Buffer pk_t
- #logger.info(f'From key:{tk}')
- self.lookup_term(tk, &pk_t)
- #logger.info(f'from_key buffer: {buffer_dump(&pk_t)}')
- # TODO Make Term a class and return that.
- return deserialize_to_rdflib(&pk_t)
- cdef Key to_key(self, term) except? 0:
- """
- Convert a term into a key and insert it in the term key store.
- :param rdflib.Term term: An RDFLib term (URIRef, BNode, Literal).
- :param Key key: Key that will be produced.
- :rtype: void
- """
- cdef:
- lmdb.MDB_txn *_txn
- Hash128 thash
- Buffer pk_t
- Key tk
- #logger.info(f'Serializing term: {term}')
- serialize_from_rdflib(term, &pk_t)
- hash128(&pk_t, &thash)
- key_v.mv_data = thash
- key_v.mv_size = HLEN
- try:
- #logger.debug(
- # f'Check {buffer_dump(&pk_t)} with hash '
- # f'{(<unsigned char*>thash)[:HLEN]} in store before adding.'
- #)
- _check(lmdb.mdb_get(
- self.txn, self.get_dbi(DB_TH_T), &key_v, &data_v)
- )
- return (<Key*>data_v.mv_data)[0]
- except KeyNotFoundError:
- #logger.info(f'Adding term {term} to store.')
- # If key is not in the store, add it.
- if self.is_txn_rw:
- # Use existing R/W transaction.
- #logger.info('Working in existing RW transaction.')
- _txn = self.txn
- else:
- # Open new R/W transaction.
- #logger.info('Opening a temporary RW transaction.')
- _check(lmdb.mdb_txn_begin(self.dbenv, NULL, 0, &_txn))
- try:
- # Main entry.
- tk = self._append(&pk_t, DB_T_ST, txn=_txn)
- # Index.
- data_v.mv_data = &tk
- data_v.mv_size = KLEN
- _check(lmdb.mdb_put(
- _txn, self.get_dbi(DB_TH_T), &key_v, &data_v, 0
- ))
- if not self.is_txn_rw:
- _check(lmdb.mdb_txn_commit(_txn))
- # Kick the main transaction to see the new terms.
- lmdb.mdb_txn_reset(self.txn)
- _check(lmdb.mdb_txn_renew(self.txn))
- return tk
- except:
- if not self.is_txn_rw:
- lmdb.mdb_txn_abort(_txn)
- raise
- cdef Key _append(
- self, Buffer *value,
- DbLabel dblabel=b'', lmdb.MDB_txn *txn=NULL,
- unsigned int flags=0
- ) except? 0:
- """
- Append one or more keys and values to the end of a database.
- :param lmdb.Cursor cur: The write cursor to act on.
- :param list(bytes) values: Value(s) to append.
- :rtype: Key
- :return: Key inserted.
- """
- cdef:
- lmdb.MDB_cursor *cur
- Key new_idx
- lmdb.MDB_val key_v, data_v
- if txn is NULL:
- txn = self.txn
- cur = self._cur_open(dblabel, txn=txn)
- try:
- _check(lmdb.mdb_cursor_get(cur, &key_v, NULL, lmdb.MDB_LAST))
- except KeyNotFoundError:
- new_idx = FIRST_KEY
- else:
- new_idx = (<Key*>key_v.mv_data)[0] + 1
- finally:
- self._cur_close(cur)
- key_v.mv_data = &new_idx
- logger.debug(f'New index: {new_idx}')
- #logger.debug('Key data inserted: {}'.format((<unsigned char*>key_v.mv_data)[:KLEN]))
- key_v.mv_size = KLEN
- data_v.mv_data = value.addr
- data_v.mv_size = value.sz
- lmdb.mdb_put(
- txn, self.get_dbi(dblabel), &key_v, &data_v,
- flags | lmdb.MDB_APPEND)
- return new_idx
- def _normalize_context(self, context):
- """
- Normalize a context parameter to conform to the model expectations.
- :param context: Context URI or graph.
- :type context: URIRef or Graph or None
- """
- if isinstance(context, rdflib.Graph):
- if context == self or isinstance(
- context.identifier, rdflib.Variable
- ):
- context = None
- else:
- context = context.identifier
- elif isinstance(context, str):
- context = rdflib.URIRef(context)
- return context
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