lakesuperior_legacy/lakesuperior/store/ldp_rs/lmdb_triplestore.pyx

import logging

from functools import wraps

from rdflib import Graph
from rdflib.graph import DATASET_DEFAULT_GRAPH_ID as RDFLIB_DEFAULT_GRAPH_URI
from rdflib.term import Node

from lakesuperior.store.base_lmdb_store import (
        KeyExistsError, KeyNotFoundError, LmdbError)
from lakesuperior.store.base_lmdb_store cimport _check

from cpython.mem cimport PyMem_Malloc, PyMem_Realloc, PyMem_Free
from cython.parallel import prange
from libc.stdlib cimport free
from libc.string cimport memcpy

cimport lakesuperior.cy_include.cylmdb as lmdb
cimport lakesuperior.cy_include.cytpl as tpl

from lakesuperior.store.base_lmdb_store cimport (
        BaseLmdbStore, data_v, dbi, key_v)
from lakesuperior.store.ldp_rs.term cimport (
        HLEN, Hash, deserialize, hash_, serialize)


DEF KLEN = 5
"""
Fixed length for term keys.

4 or 5 is a safe range. 4 allows for ~4 billion (256 ** 4) unique terms
in the store. 5 allows ~1 trillion terms. While these numbers may seem
huge (the total number of Internet pages indexed by Google as of 2018 is 45
billions), it must be reminded that the keys cannot be reused, so a
repository that deletes a lot of triples may burn through a lot of terms.

If a repository runs ot of keys it can no longer store new terms and must
be migrated to a new database, which will regenerate and compact the keys.

For smaller repositories it should be safe to set this value to 4, which
could improve performance since keys make up the vast majority of record
exchange between the store and the application. However it is sensible not
to expose this value as a configuration option.

TODO: Explore the option to use size_t (8 bits, or in some architectures,
4 bits). If the overhead of handling 8
vs. 5 bytes is not huge (and maybe counterbalanced by x86_64 arch optimizations
for 8-byte words) it may be worth using those instead of char[5] to simplify
the code significantly.
"""

DEF DBL_KLEN = KLEN * 2
DEF TRP_KLEN = KLEN * 3
DEF QUAD_KLEN = KLEN * 4

DEF KEY_START = b'\x01'
"""
Lexical sequence start. ``\\x01`` is fine since no special characters are
used, but it's good to leave a spare for potential future use.
"""

DEF FIRST_KEY = KEY_START * KLEN
"""First key of a sequence."""

DEF IDX_OP_ADD = '_idx_add'
DEF IDX_OP_REMOVE = '_idx_remove'


ctypedef unsigned char Key[KLEN]
ctypedef unsigned char DoubleKey[DBL_KLEN]
ctypedef unsigned char TripleKey[TRP_KLEN]
ctypedef unsigned char QuadKey[QUAD_KLEN]

cdef unsigned char first_key[KLEN]
memcpy(first_key, FIRST_KEY, KLEN)

cdef unsigned char lookup_rank[3]
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

If we want to get fancy, this can be rebalanced from time to time by
looking up the number of keys in (s:po, p:so, o:sp).
"""

cdef unsigned char lookup_ordering[3][3]
lookup_ordering = [
    [0, 1, 2], # spo
    [1, 0, 2], # pso
    [2, 0, 1], # osp
]


cdef unsigned char lookup_ordering_2bound[3][3]
lookup_ordering_2bound = [
    [1, 2, 0], # po:s
    [0, 2, 1], # so:p
    [0, 1, 2], # sp:o
]



logger = logging.getLogger(__name__)


cdef class ResultSet:
    """
    Pre-allocated result set.

    Data in the set are stored as a 1D contiguous array of characters.
    Access to elements at an arbitrary index position is achieved by using the
    ``itemsize`` property multiplied by the index number.

    Key properties:

    ``ct``: number of elements in the set.
    ``itemsize``: size of each element, in bytes. All elements have the same
        size.
    ``size``: Total size, in bytes, of the data set. This is the product of
        ``itemsize`` and ``ct``.
    """
    cdef:
        readonly unsigned char *data
        readonly unsigned char itemsize
        readonly size_t ct, size

    def __cinit__(self, size_t ct, unsigned char itemsize):
        """
        Initialize and allocate memory for the data set.

        :param size_t ct: Number of elements to be accounted for.
        :param unsigned char itemsize: Size of an individual item.
            Note that the ``itemsize`` is an unsigned char,
            i.e. an item can be at most 255 bytes. This is for economy reasons,
            since many multiplications are done between ``itemsize`` and other
            char variables.
        """
        self.ct = ct
        self.itemsize = itemsize
        self.size = self.itemsize * self.ct

        #logger.debug('Got malloc sizes: {}, {}'.format(ct, itemsize))
        #logger.debug(
        #    'Allocating {0} ({1}x{2}) bytes of ResultSet data...'.format(
        #        self.size, self.ct, self.itemsize))
        self.data = <unsigned char *>PyMem_Malloc(ct * itemsize)
        if not self.data:
            raise MemoryError()
        #logger.debug('...done allocating @ {0:x}.'.format(
        #        <unsigned long>self.data))


    def __dealloc__(self):
        """
        Free the memory.

        This is called when the Python instance is garbage collected, which
        makes it handy to safely pass a ResultSet instance across functions.
        """
        #logger.debug(
        #    'Releasing {0} ({1}x{2}) bytes of ResultSet @ {3:x}...'.format(
        #        self.size, self.ct, self.itemsize,
        #        <unsigned long>self.data))
        PyMem_Free(self.data)
        #logger.debug('...done releasing.')


    cdef void resize(self, size_t ct) except *:
        """
        Resize the result set. Uses ``PyMem_Realloc``.

        Note that resizing to a smaller size does not copy or reallocate the
        data, resizing to a larger size does.

        Also, note that only the number of items can be changed, the item size
        cannot.

        :param size_t ct: Number of items in the result set.
        """
        cdef unsigned char *tmp
        self.ct = ct
        self.size = self.itemsize * self.ct

        #logger.debug(
        #    'Resizing ResultSet to {0} ({1}x{2}) bytes @ {3:x}...'.format(
        #        self.itemsize * ct, ct, self.itemsize,
        #        <unsigned long>self.data))
        tmp = <unsigned char *>PyMem_Realloc(self.data, ct * self.itemsize)
        if not tmp:
            raise MemoryError()
        #logger.debug('...done resizing.')

        self.data = tmp


    # Access methods.

    def to_tuple(self):
        """
        Return the data set as a Python tuple.

        :rtype: tuple
        """
        return tuple(
                self.data[i: i + self.itemsize]
                for i in range(0, self.size, self.itemsize))


    def get_item_obj(self, i):
        """
        Get an item at a given index position.

        :rtype: bytes
        """
        return self.get_item(i)[: self.itemsize]


    cdef unsigned char *get_item(self, i):
        """
        Get an item at a given index position. Cython-level method.

        The item size is known by the ``itemsize`` property of the object.

        :rtype: unsigned char*
        """
        return self.data + self.itemsize * i



def use_data(fn):
    """
    Decorator to indicate that a set operation between two SimpleGraph
    instances should use the ``data`` property of the second term. The second
    term can also be a simple set.
    """
    @wraps(fn)
    def _wrapper(self, other):
        if isinstance(other, SimpleGraph):
            other = other.data
    return _wrapper


cdef class SimpleGraph:
    """
    Fast and simple implementation of a graph.

    Most functions should mimic RDFLib's graph with less overhead. It uses
        the same funny but functional slicing notation.

    An instance of this class can be converted to a ``rdflib.Graph`` instance.
    """

    cdef:
        readonly set data

    def __init__(
            self, set data=set(), tuple lookup=(), store=None):
        """
        Initialize the graph with pre-existing data or by looking up a store.

        Either ``data``, or both ``lookup`` and ``store``, can be provided.
        ``lookup`` and ``store`` have precedence. If none of them is specified,
        an empty graph is initialized.

        :param rdflib.URIRef uri: The graph URI.
            This will serve as the subject for some queries.
        :param set data: Initial data as a set of 3-tuples of RDFLib terms.
        :param tuple lookup: tuple of a 3-tuple of lookup terms, and a context.
            E.g. ``((URIRef('urn:ns:a'), None, None), URIRef('urn:ns:ctx'))``.
            Any and all elements may be ``None``.
        :param lmdbStore store: the store to look data up.
        """
        if data:
            self.data = set(data)
        else:
            if not lookup:
                self.data = set()
            else:
                if store is None:
                    raise ValueError('Store not specified for triple lookup.')
                self._data_from_lookup(lookup, store)


    cdef void _data_from_lookup(
            self, tuple lookup, LmdbTriplestore store) except *:
        """
        Look up triples in the triplestore and load them into ``data``.

        :param tuple lookup: 3-tuple of RDFlib terms or ``None``.
        :param LmdbTriplestore store: Reference to a LMDB triplestore. This
            is normally set to ``lakesuperior.env.app_globals.rdf_store``.
        """
        cdef:
            size_t i
            unsigned char spok[TRP_KLEN]

        self.data = set()
        with store.txn_ctx():
            keyset = store.triple_keys(*lookup)
            for i in range(keyset.ct):
                spok = keyset.data + i * TRP_KLEN
                self.data.add(store.from_trp_key(spok[: TRP_KLEN]))


    # Basic set operations.

    def add(self, dataset):
        """ Set union. """
        self.data.add(dataset)

    def remove(self, item):
        """
        Remove one item from the graph.

        :param tuple item: A 3-tuple of RDFlib terms. Only exact terms, i.e.
            wildcards are not accepted.
        """
        self.data.remove(item)

    def __len__(self):
        """ Number of triples in the graph. """
        return len(self.data)

    @use_data
    def __eq__(self, other):
        """ Equality operator between ``SimpleGraph`` instances. """
        return self.data == other

    def __repr__(self):
        """
        String representation of the graph.

        It provides the number of triples in the graph and memory address of
            the instance.
        """
        return (f'<{self.__class__.__name__} @{hex(id(self))} '
            f'length={len(self.data)}>')

    def __str__(self):
        """ String dump of the graph triples. """
        return str(self.data)

    @use_data
    def __sub__(self, other):
        """ Set subtraction. """
        return self.data - other

    @use_data
    def __isub__(self, other):
        """ In-place set subtraction. """
        self.data -= other
        return self

    @use_data
    def __and__(self, other):
        """ Set intersection. """
        return self.data & other

    @use_data
    def __iand__(self, other):
        """ In-place set intersection. """
        self.data &= other
        return self

    @use_data
    def __or__(self, other):
        """ Set union. """
        return self.data | other

    @use_data
    def __ior__(self, other):
        """ In-place set union. """
        self.data |= other
        return self

    @use_data
    def __xor__(self, other):
        """ Set exclusive intersection (XOR). """
        return self.data ^ other

    @use_data
    def __ixor__(self, other):
        """ In-place set exclusive intersection (XOR). """
        self.data ^= other
        return self

    def __contains__(self, item):
        """
        Whether the graph contains a triple.

        :rtype: boolean
        """
        return item in self.data

    def __iter__(self):
        """ Graph iterator. It iterates over the set triples. """
        return self.data.__iter__()


    # Slicing.

    def __getitem__(self, item):
        """
        Slicing function.

        It behaves similarly to `RDFLib graph slicing
        <https://rdflib.readthedocs.io/en/stable/utilities.html#slicing-graphs>`__
        """
        if isinstance(item, slice):
            s, p, o = item.start, item.stop, item.step
            return self._slice(s, p, o)
        else:
            raise TypeError(f'Wrong slice format: {item}.')


    cpdef void set(self, tuple trp) except *:
        """
        Set a single value for subject and predicate.

        Remove all triples matching ``s`` and ``p`` before adding ``s p o``.
        """
        self.remove_triples((trp[0], trp[1], None))
        if None in trp:
            raise ValueError(f'Invalid triple: {trp}')
        self.data.add(trp)


    cpdef void remove_triples(self, pattern) except *:
        """
        Remove triples by pattern.

        The pattern used is similar to :py:meth:`LmdbTripleStore.delete`.
        """
        s, p, o = pattern
        for match in self.lookup(s, p, o):
            logger.debug(f'Removing from graph: {match}.')
            self.data.remove(match)


    cpdef object as_rdflib(self):
        """
        Return the data set as an RDFLib Graph.

        :rtype: rdflib.Graph
        """
        gr = Graph()
        for trp in self.data:
            gr.add(trp)

        return gr


    cdef _slice(self, s, p, o):
        """
        Return terms filtered by other terms.

        This behaves like the rdflib.Graph slicing policy.
        """
        if s is None and p is None and o is None:
            return self.data
        elif s is None and p is None:
            return {(r[0], r[1]) for r in self.data if r[2] == o}
        elif s is None and o is None:
            return {(r[0], r[2]) for r in self.data if r[1] == p}
        elif p is None and o is None:
            return {(r[1], r[2]) for r in self.data if r[0] == s}
        elif s is None:
            return {r[0] for r in self.data if r[1] == p and r[2] == o}
        elif p is None:
            return {r[1] for r in self.data if r[0] == s and r[2] == o}
        elif o is None:
            return {r[2] for r in self.data if r[0] == s and r[1] == p}
        else:
            # all given
            return (s,p,o) in self.data


    cpdef lookup(self, s, p, o):
        """
        Look up triples by a pattern.
        """
        logger.debug(f'Looking up in graph: {s}, {p}, {o}.')
        if s is None and p is None and o is None:
            return self.data
        elif s is None and p is None:
            return {r for r in self.data if r[2] == o}
        elif s is None and o is None:
            return {r for r in self.data if r[1] == p}
        elif p is None and o is None:
            return {r for r in self.data if r[0] == s}
        elif s is None:
            return {r for r in self.data if r[1] == p and r[2] == o}
        elif p is None:
            return {r for r in self.data if r[0] == s and r[2] == o}
        elif o is None:
            return {r for r in self.data if r[0] == s and r[1] == p}
        else:
            # all given
            return (s,p,o) if (s, p, o) in self.data else set()


    cpdef set terms(self, str type):
        """
        Get all terms of a type: subject, predicate or object.

        :param str type: One of ``s``, ``p`` or ``o``.
        """
        i = 'spo'.index(type)
        return {r[i] for r in self.data}



cdef class Imr(SimpleGraph):
    """
    In-memory resource data container.

    This is an extension of :py:class:`~SimpleGraph` that adds a subject URI to
    the data set and some convenience methods.

    An instance of this class can be converted to a ``rdflib.Resource``
    instance.

    Some set operations that produce a new object (``-``, ``|``, ``&``, ``^``)
    will create a new ``Imr`` instance with the same subject URI.
    """
    cdef:
        readonly object uri

    def __init__(self, uri, *args, **kwargs):
        """
        Initialize the graph with pre-existing data or by looking up a store.

        Either ``data``, or ``lookup`` *and* ``store``, can be provide.
        ``lookup`` and ``store`` have precedence. If none of them is specified,
        an empty graph is initialized.

        :param rdflib.URIRef uri: The graph URI.
            This will serve as the subject for some queries.
        :param set data: Initial data as a set of 3-tuples of RDFLib terms.
        :param tuple lookup: tuple of a 3-tuple of lookup terms, and a context.
            E.g. ``((URIRef('urn:ns:a'), None, None), URIRef('urn:ns:ctx'))``.
            Any and all elements may be ``None``.
        :param lmdbStore store: the store to look data up.
        """
        super().__init__(*args, **kwargs)

        self.uri = uri


    @property
    def identifier(self):
        """
        IMR URI. For compatibility with RDFLib Resource.

        :rtype: string
        """
        return self.uri


    @property
    def graph(self):
        """
        Return a SimpleGraph with the same data.

        :rtype: SimpleGraph
        """
        return SimpleGraph(self.data)


    def __repr__(self):
        """
        String representation of an Imr.

        This includes the subject URI, number of triples contained and the
        memory address of the instance.
        """
        return (f'<{self.__class__.__name__} @{hex(id(self))} uri={self.uri}, '
            f'length={len(self.data)}>')

    @use_data
    def __sub__(self, other):
        """
        Set difference. This creates a new Imr with the same subject URI.
        """
        return self.__class__(uri=self.uri, data=self.data - other)

    @use_data
    def __and__(self, other):
        """
        Set intersection. This creates a new Imr with the same subject URI.
        """
        return self.__class__(uri=self.uri, data=self.data & other)

    @use_data
    def __or__(self, other):
        """
        Set union. This creates a new Imr with the same subject URI.
        """
        return self.__class__(uri=self.uri, data=self.data | other)

    @use_data
    def __xor__(self, other):
        """
        Set exclusive OR (XOR). This creates a new Imr with the same subject
        URI.
        """
        return self.__class__(uri=self.uri, data=self.data ^ other)


    def __getitem__(self, item):
        """
        Supports slicing notation.
        """
        if isinstance(item, slice):
            s, p, o = item.start, item.stop, item.step
            return self._slice(s, p, o)

        elif isinstance(item, Node):
            # If a Node is given, return all values for that predicate.
            return {
                    r[2] for r in self.data
                    if r[0] == self.uri and r[1] == item}
        else:
            raise TypeError(f'Wrong slice format: {item}.')


    def value(self, p, strict=False):
        """
        Get an individual value.

        :param rdflib.termNode p: Predicate to search for.
        :param bool strict: If set to ``True`` the method raises an error if
            more than one value is found. If ``False`` (the default) only
            the first found result is returned.
        :rtype: rdflib.term.Node
        """
        values = self[p]

        if strict and len(values) > 1:
            raise RuntimeError('More than one value found for {}, {}.'.format(
                    self.uri, p))

        for ret in values:
            return ret

        return None


    cpdef as_rdflib(self):
        """
        Return the IMR as a RDFLib Resource.

        :rtype: rdflib.Resource
        """
        gr = Graph()
        for trp in self.data:
            gr.add(trp)

        return gr.resource(identifier=self.uri)



cdef class LmdbTriplestore(BaseLmdbStore):
    """
    Low-level storage layer.

    This class extends the RDFLib-compatible :py:class:`BaseLmdbStore` and maps
    triples and contexts to key-value records in LMDB.

    This class uses the original LMDB C API rather than the Python bindings,
    because several data manipulations happen after retrieval from the store,
    which are more efficiently performed at the C level.
    """

    dbi_labels = [
        # Main data
        # Term key to serialized term content
        't:st',
        # Joined triple keys to context key
        'spo:c',
        # This has empty values and is used to keep track of empty contexts.
        'c:',
        # Prefix to namespace
        'pfx:ns',

        # Indices
        # Namespace to prefix
        'ns:pfx',
        # Term hash to triple key
        'th:t',
        # Lookups
        's:po',
        'p:so',
        'o:sp',
        'po:s',
        'so:p',
        'sp:o',
        'c:spo',
    ]

    lookup_indices = [
        b's:po',
        b'p:so',
        b'o:sp',
        b'po:s',
        b'so:p',
        b'sp:o',
    ]

    dbi_flags = {
        's:po': lmdb.MDB_DUPSORT | lmdb.MDB_DUPFIXED,
        'p:so': lmdb.MDB_DUPSORT | lmdb.MDB_DUPFIXED,
        'o:sp': lmdb.MDB_DUPSORT | lmdb.MDB_DUPFIXED,
        'po:s': lmdb.MDB_DUPSORT | lmdb.MDB_DUPFIXED,
        'so:p': lmdb.MDB_DUPSORT | lmdb.MDB_DUPFIXED,
        'sp:o': lmdb.MDB_DUPSORT | lmdb.MDB_DUPFIXED,
        'c:spo': lmdb.MDB_DUPSORT | lmdb.MDB_DUPFIXED,
        'spo:c': lmdb.MDB_DUPSORT | lmdb.MDB_DUPFIXED,
    }

    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']['spo:c']['ms_entries']

        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

        if context is not None:
            self._to_key(context, <Key *>key_v.mv_data)
            key_v.mv_size = KLEN

            cur = self._cur_open('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 add(self, triple, context=None, quoted=False):
        """
        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
            unsigned char i
            unsigned char *pk_t
            Hash thash
            # Using Key or TripleKey here breaks Cython. This might be a bug.
            # See https://github.com/cython/cython/issues/2517
            unsigned char spock[QUAD_KLEN]
            unsigned char nkey[KLEN]
            size_t term_size

        c = self._normalize_context(context)
        if c is None:
            c = RDFLIB_DEFAULT_GRAPH_URI

        # TODO: figure out how the RDFLib dispatcher is inherited
        # (and if there is a use for it in a first place)
        #Store.add(self, triple, context)

        s, p, o = triple
        #logger.debug('Trying to add a triple.')
        icur = self._cur_open('th:t')
        try:
            for i, term in enumerate((s, p, o, c)):
                serialize(term, &pk_t, &term_size)
                hash_(pk_t, term_size, &thash)
                try:
                    key_v.mv_data = &thash
                    key_v.mv_size = HLEN
                    _check(lmdb.mdb_get(
                            self.txn, self.get_dbi('th:t'), &key_v, &data_v))
                    memcpy(spock + (i * KLEN), data_v.mv_data, KLEN)
                    #logger.debug('Hash {} found. Not adding.'.format(thash[: HLEN]))
                except KeyNotFoundError:
                    # If term is not found, add it...
                    #logger.debug('Hash {} not found. Adding to DB.'.format(
                    #        thash[: HLEN]))
                    self._append(pk_t, term_size, &nkey, dblabel=b't:st')
                    free(pk_t)
                    memcpy(spock + (i * KLEN), nkey, KLEN)

                    # ...and index it.
                    #logger.debug('Indexing on th:t: {}: {}'.format(
                    #        thash[: HLEN], nkey[: KLEN]))
                    key_v.mv_data = thash
                    key_v.mv_size = HLEN
                    data_v.mv_data = nkey
                    data_v.mv_size = KLEN
                    _check(
                        lmdb.mdb_cursor_put(icur, &key_v, &data_v, 0),
                        'Error setting key {}.'.format(thash))
        finally:
            #pass
            self._cur_close(icur)
            #logger.debug('Triple add action completed.')

        spo_v.mv_data = spock
        spo_v.mv_size = TRP_KLEN
        c_v.mv_data = spock + TRP_KLEN
        c_v.mv_size = KLEN
        null_v.mv_data = b''
        null_v.mv_size = 0

        #logger.debug('Adding context.')
        try:
            _check(lmdb.mdb_put(
                self.txn, self.get_dbi('c:'), &c_v, &null_v,
                lmdb.MDB_NOOVERWRITE))
        except KeyExistsError:
            pass
        #logger.debug('Added c:.')
        try:
            # Add triple:context association.
            _check(lmdb.mdb_put(
                self.txn, self.get_dbi('spo:c'), &spo_v, &c_v,
                lmdb.MDB_NODUPDATA))
        except KeyExistsError:
            pass
        #logger.debug('Added spo:c.')
        try:
            # Index context:triple association.
            _check(lmdb.mdb_put(
                self.txn, self.get_dbi('c:spo'), &c_v, &spo_v,
                lmdb.MDB_NODUPDATA))
        except KeyExistsError:
            pass
        #logger.debug('Added c:spo.')

        #logger.debug('All main data entered. Indexing.')
        self._index_triple(IDX_OP_ADD, spock[: TRP_KLEN])


    cpdef add_graph(self, graph):
        """
        Add a graph 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.

        This may be called by read-only operations:
        https://github.com/RDFLib/rdflib/blob/master/rdflib/graph.py#L1623
        In which case it needs to open a write transaction. This is not ideal
        but the only way to handle datasets in RDFLib.

        :param rdflib.URIRef graph: URI of the named graph to add.
        """
        cdef:
            unsigned char *pk_c
            size_t pk_size

        if isinstance(graph, Graph):
            graph = graph.identifier

        serialize(graph, &pk_c, &pk_size)
        self._add_graph(pk_c, pk_size)
        free(pk_c)


    cpdef void _add_graph(
            self, unsigned char *pk_c, size_t pk_size) except *:
        """
        Add a graph.

        :param pk_c: Pickled context URIRef object.
        :type pk_c: unsigned char*
        :param pk_size: Size of pickled string.
        :type pk_size: size_t
        """
        cdef:
            Hash c_hash
            unsigned char ck[KLEN]
            lmdb.MDB_txn *tmp_txn
            lmdb.MDB_cursor *th_cur
            lmdb.MDB_cursor *pk_cur
            lmdb.MDB_cursor *ck_cur

        hash_(pk_c, pk_size, &c_hash)
        #logger.debug('Adding a graph.')
        if not self._key_exists(c_hash, HLEN, b'th:t'):
            # Insert context term if not existing.
            if self.is_txn_rw:
                #logger.debug('Working in existing RW transaction.')
                # Use existing R/W transaction.
                # Main entry.
                self._append(pk_c, pk_size, &ck, b't:st')
                # Index.
                self._put(c_hash, HLEN, ck, KLEN, b'th:t')
                # Add to list of contexts.
                self._put(ck, KLEN, b'', 0, 'c:')
            else:
                # Open new R/W transactions.
                #logger.debug('Opening a temporary RW transaction.')
                _check(lmdb.mdb_txn_begin(self.dbenv, NULL, 0, &tmp_txn))
                try:
                    self._append(
                            pk_c, pk_size, &ck, dblabel=b't:st', txn=tmp_txn)
                    # Index.
                    self._put(c_hash, HLEN, ck, KLEN, b'th:t', txn=tmp_txn)
                    # Add to list of contexts.
                    self._put(ck, KLEN, b'', 0, b'c:', txn=tmp_txn)
                    _check(lmdb.mdb_txn_commit(tmp_txn))
                    #logger.debug('Temp RW transaction closed.')
                except:
                    lmdb.mdb_txn_abort(tmp_txn)
                    raise


    cpdef void _remove(self, tuple triple_pattern, context=None) except *:
        cdef:
            unsigned char spok[TRP_KLEN]
            size_t i = 0
            Key ck
            lmdb.MDB_val spok_v, ck_v

        #logger.debug('Removing triple: {}'.format(triple_pattern))
        if context is not None:
            try:
                self._to_key(context, &ck)
            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('spo:c')
        icur = self._cur_open('c:spo')

        try:
            spok_v.mv_size = TRP_KLEN
            # If context was specified, remove only associations with that context.
            if context is not None:
                #logger.debug('Removing triples in matching context.')
                ck_v.mv_data = ck
                ck_v.mv_size = KLEN
                while i < match_set.ct:
                    memcpy(
                            spok, match_set.data + match_set.itemsize * i,
                            TRP_KLEN)
                    spok_v.mv_data = spok
                    # 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.mv_data = spok
                        try:
                            _check(lmdb.mdb_cursor_get(
                                dcur, &spok_v, NULL, lmdb.MDB_SET))
                        except KeyNotFoundError:
                            self._index_triple(IDX_OP_REMOVE, spok)
                    i += 1

            # 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 i < match_set.ct:
                    spok = match_set.data + match_set.itemsize * i
                    spok_v.mv_data = spok
                    # 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
                        logger.debug(f'Removing {spok[: TRP_KLEN]} from main.')
                        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
                            # 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)
                            #ck_v.mv_data = ck # Unnecessary?
                    finally:
                        i += 1

        finally:
            #pass
            #logger.debug('Closing spo:c in _remove.')
            self._cur_close(dcur)
            #logger.debug('Closing c:spo in _remove.')
            self._cur_close(icur)


    cdef void _index_triple(self, str op, TripleKey spok) except *:
        """
        Update index for a triple and context (add or remove).

        :param str op: 'add' or 'remove'.
        :param TripleKey spok: Triple key.
        """
        cdef:
            unsigned char keys[3][KLEN]
            unsigned char dbl_keys[3][DBL_KLEN]
            size_t i = 0
            lmdb.MDB_val key_v, dbl_key_v

        keys[0] = spok # sk
        keys[1] = spok + KLEN # pk
        keys[2] = spok + DBL_KLEN # ok

        dbl_keys[0] = spok + KLEN # pok
        memcpy(&dbl_keys[1], spok, KLEN) # sok, 1st part
        memcpy(&dbl_keys[1][KLEN], spok + DBL_KLEN, KLEN) # sok, 2nd part
        dbl_keys[2] = spok # spk
        #logger.debug('''Indices:
        #spok: {}
        #sk: {}
        #pk: {}
        #ok: {}
        #pok: {}
        #sok: {}
        #spk: {}
        #'''.format(
        #        spok[:TRP_KLEN],
        #        keys[0][:KLEN], keys[1][:KLEN], keys[2][:KLEN],
        #        dbl_keys[0][:DBL_KLEN], dbl_keys[1][:DBL_KLEN], dbl_keys[2][:DBL_KLEN]))
        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[ : TRP_KLEN]} from indices.')
        else:
            logger.debug(f'Add {spok[ : TRP_KLEN]} to indices.')

        while i < 3:
            cur1 = self._cur_open(self.lookup_indices[i]) # s:po, p:so, o:sp
            cur2 = self._cur_open(self.lookup_indices[i + 3])# po:s, so:p, sp:o
            try:
                key_v.mv_data = keys[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))
                        logger.debug(f'Removed: {keys[i][: KLEN]}, '
                                f'{dbl_keys[i][: DBL_KLEN]}')
                    except KeyNotFoundError:
                        logger.debug(f'Not found in index: {keys[i][: KLEN]}, '
                                f'{dbl_keys[i][: DBL_KLEN]}')
                        pass
                    else:
                        _check(lmdb.mdb_cursor_del(cur1, 0))

                    # Restore pointers after delete.
                    key_v.mv_data = keys[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))
                        logger.debug(f'Removed: {dbl_keys[i][: DBL_KLEN]}, '
                                f'{keys[i][: KLEN]}')
                    except KeyNotFoundError:
                        logger.debug(f'Not found in index: '
                                f'{dbl_keys[i][: DBL_KLEN]}, '
                                f'{keys[i][: KLEN]}')
                        pass
                    else:
                        _check(lmdb.mdb_cursor_del(cur2, 0))

                # Addition op indexing.
                elif op == IDX_OP_ADD:
                    logger.debug('Adding to index `{}`: {}, {}'.format(
                        self.lookup_indices[i],
                        (<unsigned char *>key_v.mv_data)[ : key_v.mv_size],
                        (<unsigned char *>dbl_key_v.mv_data)[ : dbl_key_v.mv_size]))

                    try:
                        _check(lmdb.mdb_cursor_put(
                                cur1, &key_v, &dbl_key_v, lmdb.MDB_NODUPDATA))
                    except KeyExistsError:
                        logger.debug(f'Key {keys[i][: KLEN]} exists already.')
                        pass

                    logger.debug('Adding to index `{}`: {}, {}'.format(
                        self.lookup_indices[i + 3],
                        (<unsigned char *>dbl_key_v.mv_data)[ : dbl_key_v.mv_size],
                        (<unsigned char *>key_v.mv_data)[ : key_v.mv_size]))

                    try:
                        _check(lmdb.mdb_cursor_put(
                                cur2, &dbl_key_v, &key_v, lmdb.MDB_NODUPDATA))
                    except KeyExistsError:
                        logger.debug(f'Double key {dbl_keys[i][: DBL_KLEN]} exists already.')
                        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:
            Hash chash
            unsigned char ck[KLEN]
            unsigned char *pk_c
            size_t c_size
            lmdb.MDB_val ck_v, chash_v

        #logger.debug('Deleting context: {}'.format(gr_uri))
        #logger.debug('Pickled context: {}'.format(serialize(gr_uri)))

        # Gather information on the graph prior to deletion.
        try:
            self._to_key(gr_uri, &ck)
        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(gr_uri, &pk_c, &c_size)
        hash_(pk_c, c_size, &chash)
        free(pk_c)

        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(b'c:'), &ck_v, NULL))
            ck_v.mv_data = ck
            _check(lmdb.mdb_del(self.txn, self.get_dbi(b't:st'), &ck_v, NULL))
            chash_v.mv_data = chash
            _check(lmdb.mdb_del(self.txn, self.get_dbi(b'th:t'), &chash_v, NULL))
        except KeyNotFoundError:
            pass


    # Lookup methods.

    # TODO Deprecate RDFLib API?
    def contexts(self, triple=None):
        """
        Get a list of all contexts.

        :rtype: Iterator(rdflib.Graph)
        """
        for ctx_uri in self.all_contexts(triple):
            yield Graph(identifier=self.from_key(ctx_uri), store=self)


    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, j = 0
            unsigned char spok[TRP_KLEN]
            unsigned char ck[KLEN]
            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('spo:c')
        try:
            key_v.mv_size = TRP_KLEN
            for i in range(rset.ct):
                #logger.debug('Checking contexts for triples: {}'.format(
                #    (rset.data + i * TRP_KLEN)[:TRP_KLEN]))
                key_v.mv_data = rset.data + i * TRP_KLEN
                # 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)
                    contexts.append(Graph(identifier=c_uri, store=self))
                    try:
                        _check(lmdb.mdb_cursor_get(
                            cur, &key_v, &data_v, lmdb.MDB_NEXT_DUP))
                    except KeyNotFoundError:
                        break

                #logger.debug('Triple keys before yield: {}: {}.'.format(
                #    (<TripleKey>key_v.mv_data)[:TRP_KLEN], tuple(contexts)))
                yield self.from_trp_key(
                    (<TripleKey>key_v.mv_data)[: TRP_KLEN]), tuple(contexts)
                #logger.debug('After yield.')
        finally:
            self._cur_close(cur)


    cpdef ResultSet triple_keys(self, tuple triple_pattern, context=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
        """
        # TODO: Improve performance by allowing passing contexts as a tuple.
        cdef:
            unsigned char tk[KLEN]
            unsigned char ck[KLEN]
            unsigned char spok[TRP_KLEN]
            #unsigned char *pk_c
            size_t ct = 0, flt_j = 0, i = 0, j = 0, pg_offset = 0, c_size
            lmdb.MDB_cursor *icur
            lmdb.MDB_val key_v, data_v
            ResultSet flt_res, ret

        if context is not None:
            #serialize(context, &pk_c, &c_size)
            try:
                self._to_key(context, &ck)
            except KeyNotFoundError:
                # Context not found.
                return ResultSet(0, TRP_KLEN)

            icur = self._cur_open('c:spo')

            try:
                key_v.mv_data = ck
                key_v.mv_size = KLEN

                # s p o c
                if all(triple_pattern):
                    #logger.debug('Lookup: s p o c')
                    for i, term in enumerate(triple_pattern):
                        try:
                            self._to_key(term, &tk)
                        except KeyNotFoundError:
                            # Context not found.
                            return ResultSet(0, TRP_KLEN)
                        memcpy(spok + (KLEN * i), tk, KLEN)
                        if tk is NULL:
                            # A term in the triple is not found.
                            return ResultSet(0, TRP_KLEN)
                    data_v.mv_data = spok
                    data_v.mv_size = TRP_KLEN
                    #logger.debug(
                    #        'Found spok {}. Matching with context {}'.format(
                    #            (<TripleKey>data_v.mv_data)[: TRP_KLEN],
                    #            (<Key>key_v.mv_data)[: 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 ResultSet(0, TRP_KLEN)
                    ret = ResultSet(1, TRP_KLEN)
                    memcpy(ret.data, spok, TRP_KLEN)

                    return ret

                # ? ? ? c
                elif not any(triple_pattern):
                    # Get all triples from the context
                    #logger.debug('Lookup: ? ? ? c')
                    try:
                        _check(lmdb.mdb_cursor_get(
                            icur, &key_v, &data_v, lmdb.MDB_SET))
                    except KeyNotFoundError:
                        # Triple not found.
                        return ResultSet(0, TRP_KLEN)

                    _check(lmdb.mdb_cursor_count(icur, &ct))
                    ret = ResultSet(ct, TRP_KLEN)
                    logger.debug(f'Entries in c:spo: {ct}')
                    logger.debug(f'Allocated {ret.size} bytes.')

                    logger.debug('Looking in key: {}'.format(
                        (<unsigned char *>key_v.mv_data)[:key_v.mv_size]))
                    _check(lmdb.mdb_cursor_get(
                        icur, &key_v, &data_v, lmdb.MDB_GET_MULTIPLE))
                    while True:
                        #logger.debug(f'Data offset: {pg_offset} Page size: {data_v.mv_size} bytes')
                        #logger.debug('Data page: {}'.format(
                        #        (<unsigned char *>data_v.mv_data)[: data_v.mv_size]))
                        memcpy(ret.data + pg_offset, data_v.mv_data, data_v.mv_size)
                        pg_offset += data_v.mv_size

                        try:
                            _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 ResultSet(0, TRP_KLEN)

                    #logger.debug('Allocating for context filtering.')
                    key_v.mv_data = ck
                    key_v.mv_size = KLEN
                    data_v.mv_size = TRP_KLEN

                    flt_res = ResultSet(res.ct, res.itemsize)
                    while j < res.ct:
                        #logger.debug('Checking row #{}'.format(flt_j))
                        data_v.mv_data = res.data + j * res.itemsize
                        #logger.debug('Checking c:spo {}, {}'.format(
                        #    (<unsigned char *>key_v.mv_data)[: key_v.mv_size],
                        #    (<unsigned char *>data_v.mv_data)[: data_v.mv_size]))
                        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:
                            #logger.debug('Discarding source[{}].'.format(j))
                            continue
                        else:
                            #logger.debug('Copying source[{}] to dest[{}].'.format(
                            #    j, flt_j))
                            memcpy(
                                    flt_res.data + res.itemsize * flt_j,
                                    res.data + res.itemsize * j, res.itemsize)

                            flt_j += 1
                        finally:
                            j += 1

                    # Resize result set to the size of context matches.
                    # This crops the memory block without copying it.
                    flt_res.resize(flt_j)
                    return flt_res
            finally:
                self._cur_close(icur)

        # Unfiltered lookup. No context checked.
        else:
            #logger.debug('No context in query.')
            try:
                res = self._lookup(triple_pattern)
            except KeyNotFoundError:
                return ResultSet(0, TRP_KLEN)
            #logger.debug('Res data before triple_keys return: {}'.format(
            #    res.data[: res.size]))
            return res


    cdef ResultSet _lookup(self, tuple triple_pattern):
        """
        Look up triples in the indices based on a triple pattern.

        :rtype: Iterator
        :return: Matching triple keys.
        """
        cdef:
            TripleKey spok
            lmdb.MDB_stat db_stat
            size_t ct = 0, i = 0
            lmdb.MDB_val spok_v, ck_v

        s, p, o = triple_pattern

        if s is not None:
            if p is not None:
                # s p o
                if o is not None:
                    spok_v.mv_data = spok
                    spok_v.mv_size = TRP_KLEN
                    try:
                        self._to_triple_key(triple_pattern, &spok)
                        _check(lmdb.mdb_get(
                            self.txn, self.get_dbi('spo:c'), &spok_v, &ck_v))
                    except KeyNotFoundError:
                        return ResultSet(0, TRP_KLEN)

                    matches = ResultSet(1, TRP_KLEN)
                    memcpy(matches.data, spok, TRP_KLEN)
                    return matches
                # s p ?
                else:
                    return self._lookup_2bound(0, s, 1, p)
            else:
                # s ? o
                if o is not None:
                    return self._lookup_2bound(0, s, 2, o)
                # s ? ?
                else:
                    return self._lookup_1bound(0, s)
        else:
            if p is not None:
                # ? p o
                if o is not None:
                    return self._lookup_2bound(1, p, 2, o)
                # ? p ?
                else:
                    return self._lookup_1bound(1, p)
            else:
                # ? ? o
                if o is not None:
                    return self._lookup_1bound(2, o)
                # ? ? ?
                else:
                    # Get all triples in the database.
                    logger.debug('Getting all DB triples.')
                    dcur = self._cur_open('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 = ResultSet(ct, TRP_KLEN)
                        logger.debug(f'Triples found: {ct}')
                        if ct == 0:
                            return ResultSet(0, TRP_KLEN)

                        _check(lmdb.mdb_cursor_get(
                                dcur, &key_v, &data_v, lmdb.MDB_FIRST))
                        while True:
                            logger.debug(f'i in 0bound: {i}')
                            memcpy(
                                    ret.data + ret.itemsize * i,
                                    key_v.mv_data, TRP_KLEN)

                            try:
                                _check(lmdb.mdb_cursor_get(
                                    dcur, &key_v, &data_v, lmdb.MDB_NEXT_NODUP))
                            except KeyNotFoundError:
                                break

                            i += 1
                        # Size is guessed from all entries. Unique keys will be
                        # much less than that.
                        ret.resize(i + 1)

                        #logger.debug('Assembled data: {}'.format(ret.data[:ret.size]))
                        return ret
                    finally:
                        self._cur_close(dcur)


    cdef ResultSet _lookup_1bound(self, unsigned char idx, term):
        """
        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 char luk[KLEN]
            unsigned int dbflags
            unsigned char asm_rng[3]
            size_t ct, ret_offset = 0, src_pos, ret_pos
            size_t j # Must be signed for older OpenMP versions
            lmdb.MDB_cursor *icur

        logger.debug(f'lookup 1bound: {idx}, {term}')
        try:
            self._to_key(term, &luk)
        except KeyNotFoundError:
            return ResultSet(0, TRP_KLEN)
        logging.debug('luk: {}'.format(luk))

        term_order = lookup_ordering[idx]
        icur = self._cur_open(self.lookup_indices[idx])
        logging.debug(f'DB label: {self.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 = ResultSet(ct, TRP_KLEN)
            logger.debug(f'Entries for {self.lookup_indices[idx]}: {ct}')
            logger.debug(f'Allocated {ret.size} bytes of data.')
            #logger.debug('First row: {}'.format(
            #        (<unsigned char *>data_v.mv_data)[:DBL_KLEN]))

            # Arrange results according to lookup order.
            asm_rng = [
                KLEN * term_order[0],
                KLEN * term_order[1],
                KLEN * term_order[2],
            ]
            logger.debug('asm_rng: {}'.format(asm_rng[:3]))
            logger.debug('luk: {}'.format(luk))

            _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:
                logger.debug('ret_offset: {}'.format(ret_offset))
                logger.debug(f'Page size: {data_v.mv_size}')
                #logger.debug(
                #        'Got data in 1bound ({}): {}'.format(
                #            data_v.mv_size,
                #            (<unsigned char *>data_v.mv_data)[: data_v.mv_size]))
                for j in prange(data_v.mv_size // DBL_KLEN, nogil=True):
                    src_pos = DBL_KLEN * j
                    ret_pos = (ret_offset + ret.itemsize * j)
                    memcpy(ret.data + ret_pos + asm_rng[0], luk, KLEN)
                    memcpy(ret.data + ret_pos + asm_rng[1],
                            data_v.mv_data + src_pos, KLEN)
                    memcpy(ret.data + ret_pos + asm_rng[2],
                            data_v.mv_data + src_pos + KLEN, KLEN)

                # Increment MUST be done before MDB_NEXT_MULTIPLE otherwise
                # data_v.mv_size will be overwritten with the *next* page size
                # and cause corruption in the output data.
                ret_offset += data_v.mv_size // DBL_KLEN * ret.itemsize

                try:
                    # Get results by the page.
                    _check(lmdb.mdb_cursor_get(
                            icur, &key_v, &data_v, lmdb.MDB_NEXT_MULTIPLE))
                except KeyNotFoundError:
                    # For testing only. Errors will be caught in triples()
                    # when looking for a context.
                    #if ret_offset + ret.itemsize < ret.size:
                    #    raise RuntimeError(
                    #        'Retrieved less values than expected: {} of {}.'
                    #        .format(src_offset, ret.size))
                    return ret

            #logger.debug('Assembled data in 1bound ({}): {}'.format(ret.size, ret.data[: ret.size]))
        finally:
            self._cur_close(icur)


    cdef ResultSet _lookup_2bound(
            self, unsigned char idx1, term1, unsigned char idx2, term2):
        """
        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 char luk1[KLEN]
            unsigned char luk2[KLEN]
            unsigned char luk[DBL_KLEN]
            unsigned int dbflags
            unsigned char asm_rng[3]
            unsigned char term_order[3] # Lookup ordering
            size_t ct, i = 0, ret_offset = 0, ret_pos, src_pos
            size_t j # Must be signed for older OpenMP versions
            lmdb.MDB_cursor *icur
            ResultSet ret

        logging.debug(
                f'2bound lookup for term {term1} at position {idx1} '
                f'and term {term2} at position {idx2}.')
        try:
            self._to_key(term1, &luk1)
            self._to_key(term2, &luk2)
        except KeyNotFoundError:
            return ResultSet(0, TRP_KLEN)
        logging.debug('luk1: {}'.format(luk1[: KLEN]))
        logging.debug('luk2: {}'.format(luk2[: KLEN]))

        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 = KLEN
                else:
                    luk1_offset = KLEN
                    luk2_offset = 0
                dblabel = self.lookup_indices[i + 3] # skip 1bound index labels
                break

            if i == 2:
                raise ValueError(
                        'Indices {} and {} not found in LU keys.'.format(
                            idx1, idx2))

        logger.debug('Term order: {}'.format(term_order[:3]))
        logger.debug('LUK offsets: {}, {}'.format(luk1_offset, luk2_offset))
        # Compose terms in lookup key.
        memcpy(luk + luk1_offset, luk1, KLEN)
        memcpy(luk + luk2_offset, luk2, KLEN)

        logger.debug('Lookup key: {}'.format(luk))

        icur = self._cur_open(dblabel)
        logger.debug('Database label: {}'.format(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 = ResultSet(ct, TRP_KLEN)
            #logger.debug('Entries for {}: {}'.format(self.lookup_indices[idx], ct))
            #logger.debug('First row: {}'.format(
            #        (<unsigned char *>data_v.mv_data)[:DBL_KLEN]))

            # Arrange results according to lookup order.
            asm_rng = [
                KLEN * term_order[0],
                KLEN * term_order[1],
                KLEN * term_order[2],
            ]
            logger.debug('asm_rng: {}'.format(asm_rng[:3]))
            logger.debug('luk: {}'.format(luk))

            _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:
                logger.debug('Got data in 2bound ({}): {}'.format(
                    data_v.mv_size,
                    (<unsigned char *>data_v.mv_data)[: data_v.mv_size]))
                for j in prange(data_v.mv_size // KLEN, nogil=True):
                    src_pos = KLEN * j
                    ret_pos = (ret_offset + ret.itemsize * j)
                    #logger.debug('Page offset: {}'.format(pg_offset))
                    #logger.debug('Ret offset: {}'.format(ret_offset))
                    memcpy(ret.data + ret_pos + asm_rng[0], luk, KLEN)
                    memcpy(ret.data + ret_pos + asm_rng[1], luk + KLEN, KLEN)
                    memcpy(ret.data + ret_pos + asm_rng[2],
                            data_v.mv_data + src_pos, KLEN)
                    #logger.debug('Assembled triple: {}'.format((ret.data + ret_offset)[: TRP_KLEN]))

                ret_offset += data_v.mv_size // KLEN * ret.itemsize

                try:
                    # Get results by the page.
                    _check(lmdb.mdb_cursor_get(
                            icur, &key_v, &data_v, lmdb.MDB_NEXT_MULTIPLE))
                except KeyNotFoundError:
                    # For testing only. Errors will be caught in triples()
                    # when looking for a context.
                    #if ret_offset + ret.itemsize < ret.size:
                    #    raise RuntimeError(
                    #        'Retrieved less values than expected: {} of {}.'
                    #        .format(pg_offset, ret.size))
                    #logger.debug('Assembled data in 2bound ({}): {}'.format(ret.size, ret.data[: ret.size]))
                    return ret
        finally:
            self._cur_close(icur)


    cpdef ResultSet _all_term_keys(self, term_type):
        """
        Return all keys of a (``s:po``, ``p:so``, ``o:sp``) index.
        """
        cdef:
            size_t i = 0
            lmdb.MDB_stat stat

        idx_label = self.lookup_indices['spo'.index(term_type)]
        #logger.debug('Looking for all terms in index: {}'.format(idx_label))
        icur = self._cur_open(idx_label)
        try:
            _check(lmdb.mdb_stat(self.txn, lmdb.mdb_cursor_dbi(icur), &stat))
            # TODO: This may allocate memory for several times the amount
            # needed. Even though it is resized later, we need to know how
            # performance is affected by this.
            ret = ResultSet(stat.ms_entries, KLEN)

            try:
                _check(lmdb.mdb_cursor_get(
                    icur, &key_v, NULL, lmdb.MDB_FIRST))
            except KeyNotFoundError:
                return ResultSet(0, DBL_KLEN)

            while True:
                memcpy(ret.data + ret.itemsize * i, key_v.mv_data, KLEN)

                rc = lmdb.mdb_cursor_get(
                    icur, &key_v, NULL, lmdb.MDB_NEXT_NODUP)
                try:
                    _check(rc)
                except KeyNotFoundError:
                    ret.resize(i + 1)
                    return ret
                i += 1
        finally:
            #pass
            self._cur_close(icur)


    def all_terms(self, term_type):
        """
        Return all terms of a type (``s``, ``p``, or ``o``) in the store.
        """
        for key in self._all_term_keys(term_type).to_tuple():
            #logger.debug('Yielding: {}'.format(key))
            yield self.from_key(key)


    cpdef tuple all_namespaces(self):
        """
        Return all registered namespaces.
        """
        cdef:
            size_t i = 0
            lmdb.MDB_stat stat

        ret = []
        dcur = self._cur_open('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()))
                #logger.debug('Found namespace: {}:{}'.format(<unsigned char *>key_v.mv_data, <unsigned char *>data_v.mv_data))
                try:
                    _check(lmdb.mdb_cursor_get(
                        dcur, &key_v, &data_v, lmdb.MDB_NEXT))
                except KeyNotFoundError:
                    return tuple(ret)

                i += 1
        finally:
            #pass
            self._cur_close(dcur)


    cpdef tuple all_contexts(self, triple=None):
        """
        Get a list of all contexts.

        :rtype: Iterator(rdflib.Graph)
        """
        cdef:
            lmdb.MDB_stat stat
            size_t i = 0
            unsigned char spok[TRP_KLEN]
            unsigned char ck[KLEN]
            lmdb.MDB_cursor_op op

        cur = (
                self._cur_open('spo:c') if triple and all(triple)
                else self._cur_open('c:'))
        try:
            if triple and all(triple):
                _check(lmdb.mdb_stat(
                    self.txn, lmdb.mdb_cursor_dbi(cur), &stat))
                ret = ResultSet(stat.ms_entries, KLEN)

                self._to_triple_key(triple, &spok)
                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:
                    return tuple()

                while True:
                    memcpy(ret.data + ret.itemsize * i, data_v.mv_data, KLEN)
                    try:
                        _check(lmdb.mdb_cursor_get(
                            cur, &key_v, &data_v, lmdb.MDB_NEXT_DUP))
                    except KeyNotFoundError:
                        break

                    i += 1
            else:
                _check(lmdb.mdb_stat(
                    self.txn, lmdb.mdb_cursor_dbi(cur), &stat))
                ret = ResultSet(stat.ms_entries, KLEN)

                try:
                    _check(lmdb.mdb_cursor_get(
                            cur, &key_v, &data_v, lmdb.MDB_FIRST))
                except KeyNotFoundError:
                    return tuple()

                while True:
                    memcpy(
                        ret.data + ret.itemsize * i, key_v.mv_data, KLEN)
                    try:
                        _check(lmdb.mdb_cursor_get(
                            cur, &key_v, NULL, lmdb.MDB_NEXT))
                    except KeyNotFoundError:
                        break

                    i += 1

            return ret.to_tuple()

        finally:
            #pass
            self._cur_close(cur)


    # Key conversion methods.

    cdef object from_key(self, Key key):
        """
        Convert a single or multiple key into one or more terms.

        :param Key key: The key to be converted.
        """
        cdef:
            unsigned char *pk

        key_v.mv_data = key
        key_v.mv_size = KLEN

        _check(
                lmdb.mdb_get(self.txn, self.get_dbi('t:st'), &key_v, &data_v),
                'Error getting data for key \'{}\'.'.format(key))

        return deserialize(
                <unsigned char *>data_v.mv_data, data_v.mv_size)


    cdef tuple from_trp_key(self, TripleKey key):
        """
        Convert a single or multiple key into one or more terms.

        :param Key key: The key to be converted.
        """
        #logger.debug(f'From triple key: {key[: TRP_KLEN]}')
        return (
                self.from_key(key),
                self.from_key(key + KLEN),
                self.from_key(key + DBL_KLEN))


    cdef inline void _to_key(self, term, Key *key) except *:
        """
        Convert a triple, quad or term into a key.

        The key is the checksum of the serialized object, therefore unique for
        that object.

        :param rdflib.Term term: An RDFLib term (URIRef, BNode, Literal).
        :param Key key: Pointer to the key that will be produced.

        :rtype: void
        """
        cdef:
            unsigned char *pk_t
            size_t term_size
            Hash thash

        serialize(term, &pk_t, &term_size)
        #logger.debug('Hashing pickle: {} with lentgh: {}'.format(pk_t, term_size))
        hash_(pk_t, term_size, &thash)
        free(pk_t)
        #logger.debug('Hash to search for: {}'.format(thash[: HLEN]))
        key_v.mv_data = &thash
        key_v.mv_size = HLEN

        dbi = self.get_dbi('th:t')
        logger.debug(f'DBI: {dbi}')
        _check(lmdb.mdb_get(self.txn, dbi, &key_v, &data_v))
        #logger.debug('Found key: {}'.format((<Key>data_v.mv_data)[: KLEN]))

        key[0] = <Key>data_v.mv_data


    cdef inline void _to_triple_key(self, tuple terms, TripleKey *tkey) except *:
        """
        Convert a tuple of 3 terms into a triple key.
        """
        cdef:
            char i = 0
            Key key

        while  i < 3:
            self._to_key(terms[i], &key)
            memcpy(tkey[0] + (KLEN * i), key, KLEN)
            if key is NULL:
                # A term in the triple is not found.
                tkey = NULL
                return
            i += 1


    cdef void _append(
            self, unsigned char *value, size_t vlen, Key *nkey,
            unsigned char *dblabel=b'', lmdb.MDB_txn *txn=NULL,
            unsigned int flags=0) except *:
        """
        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: list(memoryview)
        :return: Last key(s) inserted.
        """
        cdef:
            unsigned char key[KLEN]
            lmdb.MDB_cursor *cur

        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:
            memcpy(nkey[0], first_key, KLEN)
        else:
            memcpy(key, key_v.mv_data, KLEN)
            self._next_key(key, nkey)
        finally:
            #pass
            self._cur_close(cur)

        key_v.mv_data = nkey
        key_v.mv_size = KLEN
        data_v.mv_data = value
        data_v.mv_size = vlen
        #logger.debug('Appending value {} to db {} with key: {}'.format(
        #    value[: vlen], dblabel.decode(), nkey[0][:KLEN]))
        #logger.debug('data size: {}'.format(data_v.mv_size))
        lmdb.mdb_put(
                txn, self.get_dbi(dblabel), &key_v, &data_v,
                flags | lmdb.MDB_APPEND)


    cdef void _next_key(self, const Key key, Key *nkey) except *:
        """
        Calculate the next closest byte sequence in lexicographical order.

        This is used to fill the next available slot after the last one in
        LMDB. Keys are byte strings, which is a convenient way to keep key
        lengths as small as possible since they are referenced in several
        indices.

        This function assumes that all the keys are padded with the `start`
        value up to the `max_len` length.

        :param bytes n: Current byte sequence to add to.
        """
        cdef:
            size_t i = KLEN

        memcpy(nkey[0], key, KLEN)

        #logger.debug('Last key in _next_key: {}'.format(key[0]))
        while i > 0:
            i -= 1
            if nkey[0][i] < 255:
                nkey[0][i] += 1
                break
            # If the value exceeds 255, i.e. the current value is the last one
            else:
                # If we are already at the leftmost byte, and this is already
                # at 255, the sequence is exhausted.
                if i == 0:
                    raise RuntimeError(
                            'BAD DAY: Sequence exhausted. No more '
                            'combinations are possible.')
                # Move one position up and try to increment that.
                else:
                    nkey[0][i] = KEY_START
        #logger.debug('New key: {}'.format(nkey[0][:KLEN]))