spaCy/spacy/kb/kb.pyx

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Refactor KB for easier customization (#11268) * Add implementation of batching + backwards compatibility fixes. Tests indicate issue with batch disambiguation for custom singular entity lookups. * Fix tests. Add distinction w.r.t. batch size. * Remove redundant and add new comments. * Adjust comments. Fix variable naming in EL prediction. * Fix mypy errors. * Remove KB entity type config option. Change return types of candidate retrieval functions to Iterable from Iterator. Fix various other issues. * Update spacy/pipeline/entity_linker.py Co-authored-by: Paul O'Leary McCann <polm@dampfkraft.com> * Update spacy/pipeline/entity_linker.py Co-authored-by: Paul O'Leary McCann <polm@dampfkraft.com> * Update spacy/kb_base.pyx Co-authored-by: Paul O'Leary McCann <polm@dampfkraft.com> * Update spacy/kb_base.pyx Co-authored-by: Paul O'Leary McCann <polm@dampfkraft.com> * Update spacy/pipeline/entity_linker.py Co-authored-by: Paul O'Leary McCann <polm@dampfkraft.com> * Add error messages to NotImplementedErrors. Remove redundant comment. * Fix imports. * Remove redundant comments. * Rename KnowledgeBase to InMemoryLookupKB and BaseKnowledgeBase to KnowledgeBase. * Fix tests. * Update spacy/errors.py Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com> * Move KB into subdirectory. * Adjust imports after KB move to dedicated subdirectory. * Fix config imports. * Move Candidate + retrieval functions to separate module. Fix other, small issues. * Fix docstrings and error message w.r.t. class names. Fix typing for candidate retrieval functions. * Update spacy/kb/kb_in_memory.pyx Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com> * Update spacy/ml/models/entity_linker.py Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com> * Fix typing. * Change typing of mentions to be Span instead of Union[Span, str]. * Update docs. * Update EntityLinker and _architecture docs. * Update website/docs/api/entitylinker.md Co-authored-by: Paul O'Leary McCann <polm@dampfkraft.com> * Adjust message for E1046. * Re-add section for Candidate in kb.md, add reference to dedicated page. * Update docs and docstrings. * Re-add section + reference for KnowledgeBase.get_alias_candidates() in docs. * Update spacy/kb/candidate.pyx * Update spacy/kb/kb_in_memory.pyx * Update spacy/pipeline/legacy/entity_linker.py * Remove canididate.md. Remove mistakenly added config snippet in entity_linker.py. Co-authored-by: Paul O'Leary McCann <polm@dampfkraft.com> Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
2022-09-08 08:38:07 +00:00
# cython: infer_types=True, profile=True
from pathlib import Path
from typing import Iterable, Tuple, Union
Refactor KB for easier customization (#11268) * Add implementation of batching + backwards compatibility fixes. Tests indicate issue with batch disambiguation for custom singular entity lookups. * Fix tests. Add distinction w.r.t. batch size. * Remove redundant and add new comments. * Adjust comments. Fix variable naming in EL prediction. * Fix mypy errors. * Remove KB entity type config option. Change return types of candidate retrieval functions to Iterable from Iterator. Fix various other issues. * Update spacy/pipeline/entity_linker.py Co-authored-by: Paul O'Leary McCann <polm@dampfkraft.com> * Update spacy/pipeline/entity_linker.py Co-authored-by: Paul O'Leary McCann <polm@dampfkraft.com> * Update spacy/kb_base.pyx Co-authored-by: Paul O'Leary McCann <polm@dampfkraft.com> * Update spacy/kb_base.pyx Co-authored-by: Paul O'Leary McCann <polm@dampfkraft.com> * Update spacy/pipeline/entity_linker.py Co-authored-by: Paul O'Leary McCann <polm@dampfkraft.com> * Add error messages to NotImplementedErrors. Remove redundant comment. * Fix imports. * Remove redundant comments. * Rename KnowledgeBase to InMemoryLookupKB and BaseKnowledgeBase to KnowledgeBase. * Fix tests. * Update spacy/errors.py Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com> * Move KB into subdirectory. * Adjust imports after KB move to dedicated subdirectory. * Fix config imports. * Move Candidate + retrieval functions to separate module. Fix other, small issues. * Fix docstrings and error message w.r.t. class names. Fix typing for candidate retrieval functions. * Update spacy/kb/kb_in_memory.pyx Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com> * Update spacy/ml/models/entity_linker.py Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com> * Fix typing. * Change typing of mentions to be Span instead of Union[Span, str]. * Update docs. * Update EntityLinker and _architecture docs. * Update website/docs/api/entitylinker.md Co-authored-by: Paul O'Leary McCann <polm@dampfkraft.com> * Adjust message for E1046. * Re-add section for Candidate in kb.md, add reference to dedicated page. * Update docs and docstrings. * Re-add section + reference for KnowledgeBase.get_alias_candidates() in docs. * Update spacy/kb/candidate.pyx * Update spacy/kb/kb_in_memory.pyx * Update spacy/pipeline/legacy/entity_linker.py * Remove canididate.md. Remove mistakenly added config snippet in entity_linker.py. Co-authored-by: Paul O'Leary McCann <polm@dampfkraft.com> Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
2022-09-08 08:38:07 +00:00
from cymem.cymem cimport Pool
from ..errors import Errors
Refactor KB for easier customization (#11268) * Add implementation of batching + backwards compatibility fixes. Tests indicate issue with batch disambiguation for custom singular entity lookups. * Fix tests. Add distinction w.r.t. batch size. * Remove redundant and add new comments. * Adjust comments. Fix variable naming in EL prediction. * Fix mypy errors. * Remove KB entity type config option. Change return types of candidate retrieval functions to Iterable from Iterator. Fix various other issues. * Update spacy/pipeline/entity_linker.py Co-authored-by: Paul O'Leary McCann <polm@dampfkraft.com> * Update spacy/pipeline/entity_linker.py Co-authored-by: Paul O'Leary McCann <polm@dampfkraft.com> * Update spacy/kb_base.pyx Co-authored-by: Paul O'Leary McCann <polm@dampfkraft.com> * Update spacy/kb_base.pyx Co-authored-by: Paul O'Leary McCann <polm@dampfkraft.com> * Update spacy/pipeline/entity_linker.py Co-authored-by: Paul O'Leary McCann <polm@dampfkraft.com> * Add error messages to NotImplementedErrors. Remove redundant comment. * Fix imports. * Remove redundant comments. * Rename KnowledgeBase to InMemoryLookupKB and BaseKnowledgeBase to KnowledgeBase. * Fix tests. * Update spacy/errors.py Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com> * Move KB into subdirectory. * Adjust imports after KB move to dedicated subdirectory. * Fix config imports. * Move Candidate + retrieval functions to separate module. Fix other, small issues. * Fix docstrings and error message w.r.t. class names. Fix typing for candidate retrieval functions. * Update spacy/kb/kb_in_memory.pyx Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com> * Update spacy/ml/models/entity_linker.py Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com> * Fix typing. * Change typing of mentions to be Span instead of Union[Span, str]. * Update docs. * Update EntityLinker and _architecture docs. * Update website/docs/api/entitylinker.md Co-authored-by: Paul O'Leary McCann <polm@dampfkraft.com> * Adjust message for E1046. * Re-add section for Candidate in kb.md, add reference to dedicated page. * Update docs and docstrings. * Re-add section + reference for KnowledgeBase.get_alias_candidates() in docs. * Update spacy/kb/candidate.pyx * Update spacy/kb/kb_in_memory.pyx * Update spacy/pipeline/legacy/entity_linker.py * Remove canididate.md. Remove mistakenly added config snippet in entity_linker.py. Co-authored-by: Paul O'Leary McCann <polm@dampfkraft.com> Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
2022-09-08 08:38:07 +00:00
from ..tokens import Span
from ..util import SimpleFrozenList
from .candidate import Candidate
Refactor KB for easier customization (#11268) * Add implementation of batching + backwards compatibility fixes. Tests indicate issue with batch disambiguation for custom singular entity lookups. * Fix tests. Add distinction w.r.t. batch size. * Remove redundant and add new comments. * Adjust comments. Fix variable naming in EL prediction. * Fix mypy errors. * Remove KB entity type config option. Change return types of candidate retrieval functions to Iterable from Iterator. Fix various other issues. * Update spacy/pipeline/entity_linker.py Co-authored-by: Paul O'Leary McCann <polm@dampfkraft.com> * Update spacy/pipeline/entity_linker.py Co-authored-by: Paul O'Leary McCann <polm@dampfkraft.com> * Update spacy/kb_base.pyx Co-authored-by: Paul O'Leary McCann <polm@dampfkraft.com> * Update spacy/kb_base.pyx Co-authored-by: Paul O'Leary McCann <polm@dampfkraft.com> * Update spacy/pipeline/entity_linker.py Co-authored-by: Paul O'Leary McCann <polm@dampfkraft.com> * Add error messages to NotImplementedErrors. Remove redundant comment. * Fix imports. * Remove redundant comments. * Rename KnowledgeBase to InMemoryLookupKB and BaseKnowledgeBase to KnowledgeBase. * Fix tests. * Update spacy/errors.py Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com> * Move KB into subdirectory. * Adjust imports after KB move to dedicated subdirectory. * Fix config imports. * Move Candidate + retrieval functions to separate module. Fix other, small issues. * Fix docstrings and error message w.r.t. class names. Fix typing for candidate retrieval functions. * Update spacy/kb/kb_in_memory.pyx Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com> * Update spacy/ml/models/entity_linker.py Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com> * Fix typing. * Change typing of mentions to be Span instead of Union[Span, str]. * Update docs. * Update EntityLinker and _architecture docs. * Update website/docs/api/entitylinker.md Co-authored-by: Paul O'Leary McCann <polm@dampfkraft.com> * Adjust message for E1046. * Re-add section for Candidate in kb.md, add reference to dedicated page. * Update docs and docstrings. * Re-add section + reference for KnowledgeBase.get_alias_candidates() in docs. * Update spacy/kb/candidate.pyx * Update spacy/kb/kb_in_memory.pyx * Update spacy/pipeline/legacy/entity_linker.py * Remove canididate.md. Remove mistakenly added config snippet in entity_linker.py. Co-authored-by: Paul O'Leary McCann <polm@dampfkraft.com> Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
2022-09-08 08:38:07 +00:00
cdef class KnowledgeBase:
"""A `KnowledgeBase` instance stores unique identifiers for entities and their textual aliases,
to support entity linking of named entities to real-world concepts.
This is an abstract class and requires its operations to be implemented.
DOCS: https://spacy.io/api/kb
"""
def __init__(self, vocab: Vocab, entity_vector_length: int):
"""Create a KnowledgeBase."""
# Make sure abstract KB is not instantiated.
if self.__class__ == KnowledgeBase:
raise TypeError(
Errors.E1046.format(cls_name=self.__class__.__name__)
)
self.vocab = vocab
self.entity_vector_length = entity_vector_length
self.mem = Pool()
def get_candidates_batch(self, mentions: Iterable[Span]) -> Iterable[Iterable[Candidate]]:
"""
Return candidate entities for specified texts. Each candidate defines the entity, the original alias,
and the prior probability of that alias resolving to that entity.
If no candidate is found for a given text, an empty list is returned.
mentions (Iterable[Span]): Mentions for which to get candidates.
RETURNS (Iterable[Iterable[Candidate]]): Identified candidates.
"""
return [self.get_candidates(span) for span in mentions]
def get_candidates(self, mention: Span) -> Iterable[Candidate]:
"""
Return candidate entities for specified text. Each candidate defines the entity, the original alias,
and the prior probability of that alias resolving to that entity.
If the no candidate is found for a given text, an empty list is returned.
mention (Span): Mention for which to get candidates.
RETURNS (Iterable[Candidate]): Identified candidates.
"""
raise NotImplementedError(
Errors.E1045.format(parent="KnowledgeBase", method="get_candidates", name=self.__name__)
)
def get_vectors(self, entities: Iterable[str]) -> Iterable[Iterable[float]]:
"""
Return vectors for entities.
entity (str): Entity name/ID.
RETURNS (Iterable[Iterable[float]]): Vectors for specified entities.
"""
return [self.get_vector(entity) for entity in entities]
def get_vector(self, str entity) -> Iterable[float]:
"""
Return vector for entity.
entity (str): Entity name/ID.
RETURNS (Iterable[float]): Vector for specified entity.
"""
raise NotImplementedError(
Errors.E1045.format(parent="KnowledgeBase", method="get_vector", name=self.__name__)
)
def to_bytes(self, **kwargs) -> bytes:
"""Serialize the current state to a binary string.
RETURNS (bytes): Current state as binary string.
"""
raise NotImplementedError(
Errors.E1045.format(parent="KnowledgeBase", method="to_bytes", name=self.__name__)
)
def from_bytes(self, bytes_data: bytes, *, exclude: Tuple[str] = tuple()):
"""Load state from a binary string.
bytes_data (bytes): KB state.
exclude (Tuple[str]): Properties to exclude when restoring KB.
"""
raise NotImplementedError(
Errors.E1045.format(parent="KnowledgeBase", method="from_bytes", name=self.__name__)
)
def to_disk(self, path: Union[str, Path], exclude: Iterable[str] = SimpleFrozenList()) -> None:
"""
Write KnowledgeBase content to disk.
path (Union[str, Path]): Target file path.
exclude (Iterable[str]): List of components to exclude.
"""
raise NotImplementedError(
Errors.E1045.format(parent="KnowledgeBase", method="to_disk", name=self.__name__)
)
def from_disk(self, path: Union[str, Path], exclude: Iterable[str] = SimpleFrozenList()) -> None:
"""
Load KnowledgeBase content from disk.
path (Union[str, Path]): Target file path.
exclude (Iterable[str]): List of components to exclude.
"""
raise NotImplementedError(
Errors.E1045.format(parent="KnowledgeBase", method="from_disk", name=self.__name__)
)