lakesuperior_legacy/lakesuperior/model/graph/graph.pyx

import logging

from functools import wraps

from rdflib import Graph
from rdflib.term import Node

from lakesuperior import env

from libc.string cimport memcmp, memcpy
from libc.stdlib cimport free

from cymem.cymem cimport Pool

from lakesuperior.cy_include cimport calg
from lakesuperior.cy_include cimport cylmdb as lmdb
from lakesuperior.model.graph cimport term
from lakesuperior.store.ldp_rs.lmdb_triplestore cimport (
        KLEN, DBL_KLEN, TRP_KLEN, TripleKey)
from lakesuperior.model.structures.keyset cimport Keyset
from lakesuperior.model.base cimport Buffer
from lakesuperior.model.graph.triple cimport BufferTriple
from lakesuperior.model.structures.hash cimport Hash32, hash32

#BUF_PTR_SZ = sizeof(Buffer *)

logger = logging.getLogger(__name__)


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 unsigned int term_hash_fn(const calg.SetValue data):
    """
    Hash function for sets of terms.

    https://fragglet.github.io/c-algorithms/doc/set_8h.html#6c7986a2a80d7a3cb7b9d74e1c6fef97

    :param SetValue *data: Pointer to a Buffer structure.
    """
    cdef:
        Hash32 hash

    hash32(<const Buffer *>&data, &hash)

    return hash


cdef unsigned int trp_hash_fn(calg.SetValue btrp):
    """
    Hash function for sets of (serialized) triples.

    https://fragglet.github.io/c-algorithms/doc/set_8h.html#6c7986a2a80d7a3cb7b9d74e1c6fef97

    This function computes the hash of the concatenated pointer values in the
    s, p, o members of the triple. The triple structure is treated as a byte
    string. This is safe in spite of byte-wise struct evaluation being a
    frowned-upon practice (due to padding issues), because it is assumed that
    the input value is always the same type of structure.

    :param SetItem *data: Pointer to a BufferTriple structure.
    """
    cdef:
        Buffer data
        Hash32 hash

    data.addr = &btrp
    data.sz = sizeof(btrp)
    hash32(&data, &hash)

    return hash


cdef bint buffer_cmp_fn(const calg.SetValue v1, const calg.SetValue v2):
    """
    Compare function for two Buffer objects.

    https://fragglet.github.io/c-algorithms/doc/set_8h.html#40fa2c86d5b003c1b0b0e8dd1e4df9f4
    """
    cdef:
        Buffer b1 = (<Buffer *>v1)[0]
        Buffer b2 = (<Buffer *>v2)[0]

    if b1.sz != b2.sz:
        return False

    return memcmp(b1.addr, b2.addr, b1.sz) == 0


cdef bint triple_cmp_fn(const calg.SetValue v1, const calg.SetValue v2):
    """
    Compare function for two triples in a CAlg set.

    Here, pointers to terms are compared for s, p, o. The pointers should be
    guaranteed to point to unique values (i.e. no two pointers have the same
    term value within a graph).

    https://fragglet.github.io/c-algorithms/doc/set_8h.html#40fa2c86d5b003c1b0b0e8dd1e4df9f4
    """
    cdef:
        BufferTriple t1 = (<BufferTriple *>v1)[0]
        BufferTriple t2 = (<BufferTriple *>v2)[0]

    return(
            t1.s == t2.s and
            t1.p == t2.p and
            t1.o == t2.o)


cdef inline bint lookup_none_cmp_fn(
        const BufferTriple *trp, const Buffer *t1, const Buffer *t2):
    return True


cdef inline bint lookup_s_cmp_fn(
        const BufferTriple *trp, const Buffer *t1, const Buffer *t2):
    """
    Lookup callback compare function for a given s in a triple.

    The function returns ``True`` if ``t1`` matches the first term.

    ``t2`` is not used and is declared only for compatibility with the
    other interchangeable functions.
    """
    return buffer_cmp_fn(t1, trp[0].s)


cdef inline bint lookup_p_cmp_fn(
        const BufferTriple *trp, const Buffer *t1, const Buffer *t2):
    return buffer_cmp_fn(t1, trp[0].p)


cdef inline bint lookup_o_cmp_fn(
        const BufferTriple *trp, const Buffer *t1, const Buffer *t2):
    return buffer_cmp_fn(t1, trp[0].o)


cdef inline bint lookup_sp_cmp_fn(
        const BufferTriple *trp, const Buffer *t1, const Buffer *t2):
    return (
            buffer_cmp_fn(t1, trp[0].s)
            and buffer_cmp_fn(t2, trp[0].p))


cdef inline bint lookup_so_cmp_fn(
        const BufferTriple *trp, const Buffer *t1, const Buffer *t2):
    return (
            buffer_cmp_fn(t1, trp[0].s)
            and buffer_cmp_fn(t2, trp[0].o))


cdef inline bint lookup_po_cmp_fn(
        const BufferTriple *trp, const Buffer *t1, const Buffer *t2):
    return (
            buffer_cmp_fn(t1, trp[0].p)
            and buffer_cmp_fn(t2, trp[0].o))



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. No lookup functions within
    the graph are available at this time.

    Instances of this class hold a set of
    :py:class:`~lakesuperior.store.ldp_rs.term.Term` structures that stores
    unique terms within the graph, and a set of
    :py:class:`~lakesuperior.store.ldp_rs.triple.Triple` structures referencing
    those terms. Therefore, no data duplication occurs and the storage is quite
    sparse.

    A graph can be instantiated from a store lookup.

    A SimpleGraph can also be obtained from a
    :py:class:`lakesuperior.store.keyset.Keyset` which is convenient bacause
    a Keyset can be obtained very efficiently from querying a store, then also
    very efficiently filtered and eventually converted into a set of meaningful
    terms.

    An instance of this class can also be converted to and from a
    ``rdflib.Graph`` instance. TODO verify that this frees Cython pointers.
    """

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

        One of ``keyset``, or ``data`` can be provided. If more than
        one of these is provided, precedence is given in the mentioned order.
        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 Keyset keyset: Keyset to create the graph from. Keys will be
            converted to set elements.
        :param lakesuperior.store.ldp_rs.LmdbTripleStore store: store to
            look up the keyset. Only used if ``keyset`` is specified. If not
            set, the environment store is used.
        :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.
        """
        self.store = store or env.app_globals.rdf_store
        self._terms = calg.set_new(term_hash_fn, buffer_cmp_fn)
        self._triples = calg.set_new(trp_hash_fn, triple_cmp_fn)
        self._pool = Pool()

        cdef:
            size_t i = 0
            TripleKey spok
            term.Buffer pk_t

        # Initialize empty data set.
        if keyset:
            # Populate with triples extracted from provided key set.
            self._data_from_keyset(keyset)
        elif data is not None:
            # Populate with provided Python set.
            for s, p, o in data:
                self._add_from_rdflib(s, p, o)


    def __dealloc__(self):
        """
        Free the triple pointers. TODO use a Cymem pool
        """
        free(self._triples)
        free(self._terms)


    @property
    def data(self):
        """
        Triple data as a Python set.

        :rtype: set
        """
        return self._data_as_set()


    cdef void _data_from_lookup(self, tuple trp_ptn, ctx=None) 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]

        with self.store.txn_ctx():
            keyset = self.store.triple_keys(trp_ptn, ctx)
            self.data_from_keyset(keyset)



    cdef void _data_from_keyset(self, Keyset data) except *:
        """Populate a graph from a Keyset."""
        cdef TripleKey spok

        while data.next(spok):
            self._add_from_spok(spok)


    cdef inline void _add_from_spok(self, const TripleKey spok) except *:
        """
        Add a triple from a TripleKey of term keys.
        """
        cdef:
            SPOBuffer s_spo
            BufferTriple trp

        s_spo = <SPOBuffer>self._pool.alloc(3, sizeof(Buffer))

        self.store.lookup_term(spok, s_spo)
        self.store.lookup_term(spok + KLEN, s_spo + 1)
        self.store.lookup_term(spok + DBL_KLEN, s_spo + 2)

        self._add_triple(s_spo, s_spo + 1, s_spo + 2)


    cdef inline void _add_triple(
        self, const Buffer *ss, const Buffer *sp, const Buffer *so
    ) except *:
        """
        Add a triple from 3 (TPL) serialized terms.

        Each of the terms is added to the term set if not existing. The triple
        also is only added if not existing.
        """
        cdef int r
        trp = <BufferTriple *>self._pool.alloc(1, sizeof(BufferTriple))

        print('Inserting terms.')
        calg.set_insert(self._terms, ss)
        print(f'Insert ss result:')
        r = calg.set_insert(self._terms, sp)
        print(f'Insert sp result: {r}')
        r = calg.set_insert(self._terms, so)
        print(f'Insert so result: {r}')

        cdef calg.SetIterator ti
        cdef Buffer *t
        calg.set_iterate(self._terms, &ti)
        while calg.set_iter_has_more(&ti):
            t = <Buffer *>calg.set_iter_next(&ti)

        trp.s = ss
        trp.p = sp
        trp.o = so

        r = calg.set_insert(self._triples, trp)
        print(f'Insert triple result: {r}')

        cdef BufferTriple *tt
        calg.set_iterate(self._triples, &ti)
        while calg.set_iter_has_more(&ti):
            tt = <BufferTriple *>calg.set_iter_next(&ti)


    cdef set _data_as_set(self):
        """
        Convert triple data to a Python set.

        :rtype: set
        """
        cdef:
            calg.SetIterator ti
            BufferTriple *trp
            term.Term s, p, o

        graph_set = set()

        calg.set_iterate(self._triples, &ti)
        while calg.set_iter_has_more(&ti):
            trp = <BufferTriple *>calg.set_iter_next(&ti)
            if trp == NULL:
                print('Triple is NULL!')
                return graph_set

            graph_set.add((
                term.deserialize_to_rdflib(trp.s),
                term.deserialize_to_rdflib(trp.p),
                term.deserialize_to_rdflib(trp.o),
            ))

        return graph_set


    # Basic set operations.

    def add(self, triple):
        """ Add one triple to the graph. """
        cdef:
            Buffer *ss = <Buffer *>self._pool.alloc(1, sizeof(Buffer))
            Buffer *sp = <Buffer *>self._pool.alloc(1, sizeof(Buffer))
            Buffer *so = <Buffer *>self._pool.alloc(1, sizeof(Buffer))

        s, p, o = triple

        term.serialize_from_rdflib(s, ss, self._pool)
        term.serialize_from_rdflib(p, sp, self._pool)
        term.serialize_from_rdflib(o, so, self._pool)

        self._add_triple(ss, sp, so)


    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 calg.set_num_entries(self._triples)


    @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``.
        """
        if None in trp:
            raise ValueError(f'Invalid triple: {trp}')
        self.remove_triples((trp[0], trp[1], None))
        self.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


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

        This behaves like the rdflib.Graph slicing policy.
        """
        _data = self.data

        logger.debug(f'Slicing graph by: {s}, {p}, {o}.')
        if s is None and p is None and o is None:
            return _data
        elif s is None and p is None:
            return {(r[0], r[1]) for r in _data if r[2] == o}
        elif s is None and o is None:
            return {(r[0], r[2]) for r in _data if r[1] == p}
        elif p is None and o is None:
            return {(r[1], r[2]) for r in _data if r[0] == s}
        elif s is None:
            return {r[0] for r in _data if r[1] == p and r[2] == o}
        elif p is None:
            return {r[1] for r in _data if r[0] == s and r[2] == o}
        elif o is None:
            return {r[2] for r in _data if r[0] == s and r[1] == p}
        else:
            # all given
            return (s,p,o) in _data


    def lookup(self, s, p, o):
        """
        Look up triples by a pattern.

        This function converts RDFLib terms into the serialized format stored
        in the graph's internal structure and compares them bytewise.

        Any and all of the lookup terms can be ``None``.
        """
        cdef:
            BufferTriple trp
            BufferTriple *trp_p
            calg.SetIterator ti
            const Buffer t1
            const Buffer t2
            lookup_fn_t fn

        res = set()

        # Decide comparison logic outside the loop.
        if s is not None and p is not None and o is not None:
            # Return immediately if 3-term match is requested.
            term.serialize_from_rdflib(s, trp.s)
            term.serialize_from_rdflib(p, trp.p)
            term.serialize_from_rdflib(o, trp.o)

            if calg.set_query(self._triples, &trp):
                res.add((s, p, o))

            return res

        elif s is not None:
            term.serialize_from_rdflib(s, &t1)
            if p is not None:
                fn = lookup_sp_cmp_fn
                term.serialize_from_rdflib(p, &t2)
            elif o is not None:
                fn = lookup_so_cmp_fn
                term.serialize_from_rdflib(o, &t2)
            else:
                fn = lookup_s_cmp_fn
        elif p is not None:
            term.serialize_from_rdflib(p, &t1)
            if o is not None:
                fn = lookup_po_cmp_fn
                term.serialize_from_rdflib(o, &t2)
            else:
                fn = lookup_p_cmp_fn
        elif o is not None:
            fn = lookup_o_cmp_fn
            term.serialize_from_rdflib(o, &t1)
        else:
            fn = lookup_none_cmp_fn

        # Iterate over serialized triples.
        calg.set_iterate(self._triples, &ti)
        while calg.set_iter_has_more(&ti):
            trp_p = <BufferTriple *>calg.set_iter_next(&ti)
            if fn(trp_p, &t1, &t2):
                res.add((
                    term.deserialize_to_rdflib(trp_p[0].s),
                    term.deserialize_to_rdflib(trp_p[0].p),
                    term.deserialize_to_rdflib(trp_p[0].o),
                ))

        return res


    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.
    """
    def __init__(self, str 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)