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KB & NEL to/from bytes (#8113)
* unit test for pickling KB * add pickling test for NEL * KB to_bytes and from_bytes * NEL to_bytes and from_bytes * xfail pickle tests for now * fix docs * cleanup
This commit is contained in:
Sofie Van Landeghem
GitHub
parent
f6128c06b0
commit
202943bc8c
115
spacy/kb.pyx
115
spacy/kb.pyx
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@ -93,6 +93,15 @@ cdef class KnowledgeBase:
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self.vocab = vocab
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self._create_empty_vectors(dummy_hash=self.vocab.strings[""])
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def initialize_entities(self, int64_t nr_entities):
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self._entry_index = PreshMap(nr_entities + 1)
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self._entries = entry_vec(nr_entities + 1)
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self._vectors_table = float_matrix(nr_entities + 1)
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def initialize_aliases(self, int64_t nr_aliases):
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self._alias_index = PreshMap(nr_aliases + 1)
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self._aliases_table = alias_vec(nr_aliases + 1)
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@property
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def entity_vector_length(self):
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"""RETURNS (uint64): length of the entity vectors"""
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@ -144,8 +153,7 @@ cdef class KnowledgeBase:
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raise ValueError(Errors.E140)
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nr_entities = len(set(entity_list))
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self._entry_index = PreshMap(nr_entities+1)
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self._entries = entry_vec(nr_entities+1)
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self.initialize_entities(nr_entities)
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i = 0
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cdef KBEntryC entry
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@ -325,6 +333,102 @@ cdef class KnowledgeBase:
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return 0.0
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def to_bytes(self, **kwargs):
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"""Serialize the current state to a binary string.
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"""
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def serialize_header():
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header = (self.get_size_entities(), self.get_size_aliases(), self.entity_vector_length)
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return srsly.json_dumps(header)
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def serialize_entries():
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i = 1
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tuples = []
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for entry_hash, entry_index in sorted(self._entry_index.items(), key=lambda x: x[1]):
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entry = self._entries[entry_index]
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assert entry.entity_hash == entry_hash
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assert entry_index == i
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tuples.append((entry.entity_hash, entry.freq, entry.vector_index))
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i = i + 1
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return srsly.json_dumps(tuples)
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def serialize_aliases():
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i = 1
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headers = []
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indices_lists = []
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probs_lists = []
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for alias_hash, alias_index in sorted(self._alias_index.items(), key=lambda x: x[1]):
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alias = self._aliases_table[alias_index]
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assert alias_index == i
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candidate_length = len(alias.entry_indices)
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headers.append((alias_hash, candidate_length))
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indices_lists.append(alias.entry_indices)
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probs_lists.append(alias.probs)
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i = i + 1
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headers_dump = srsly.json_dumps(headers)
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indices_dump = srsly.json_dumps(indices_lists)
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probs_dump = srsly.json_dumps(probs_lists)
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return srsly.json_dumps((headers_dump, indices_dump, probs_dump))
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serializers = {
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"header": serialize_header,
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"entity_vectors": lambda: srsly.json_dumps(self._vectors_table),
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"entries": serialize_entries,
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"aliases": serialize_aliases,
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}
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return util.to_bytes(serializers, [])
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def from_bytes(self, bytes_data, *, exclude=tuple()):
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"""Load state from a binary string.
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"""
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def deserialize_header(b):
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header = srsly.json_loads(b)
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nr_entities = header[0]
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nr_aliases = header[1]
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entity_vector_length = header[2]
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self.initialize_entities(nr_entities)
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self.initialize_aliases(nr_aliases)
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self.entity_vector_length = entity_vector_length
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def deserialize_vectors(b):
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self._vectors_table = srsly.json_loads(b)
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def deserialize_entries(b):
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cdef KBEntryC entry
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tuples = srsly.json_loads(b)
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i = 1
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for (entity_hash, freq, vector_index) in tuples:
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entry.entity_hash = entity_hash
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entry.freq = freq
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entry.vector_index = vector_index
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entry.feats_row = -1 # Features table currently not implemented
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self._entries[i] = entry
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self._entry_index[entity_hash] = i
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i += 1
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def deserialize_aliases(b):
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cdef AliasC alias
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i = 1
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all_data = srsly.json_loads(b)
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headers = srsly.json_loads(all_data[0])
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indices = srsly.json_loads(all_data[1])
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probs = srsly.json_loads(all_data[2])
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for header, indices, probs in zip(headers, indices, probs):
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alias_hash, candidate_length = header
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alias.entry_indices = indices
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alias.probs = probs
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self._aliases_table[i] = alias
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self._alias_index[alias_hash] = i
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i += 1
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setters = {
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"header": deserialize_header,
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"entity_vectors": deserialize_vectors,
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"entries": deserialize_entries,
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"aliases": deserialize_aliases,
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}
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util.from_bytes(bytes_data, setters, exclude)
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return self
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def to_disk(self, path, exclude: Iterable[str] = SimpleFrozenList()):
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path = ensure_path(path)
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if not path.exists():
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@ -404,10 +508,8 @@ cdef class KnowledgeBase:
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cdef int64_t entity_vector_length
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reader.read_header(&nr_entities, &entity_vector_length)
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self.initialize_entities(nr_entities)
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self.entity_vector_length = entity_vector_length
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self._entry_index = PreshMap(nr_entities+1)
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self._entries = entry_vec(nr_entities+1)
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self._vectors_table = float_matrix(nr_entities+1)
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# STEP 1: load entity vectors
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cdef int i = 0
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@ -445,8 +547,7 @@ cdef class KnowledgeBase:
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# STEP 3: load aliases
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cdef int64_t nr_aliases
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reader.read_alias_length(&nr_aliases)
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self._alias_index = PreshMap(nr_aliases+1)
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self._aliases_table = alias_vec(nr_aliases+1)
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self.initialize_aliases(nr_aliases)
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cdef int64_t nr_candidates
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cdef vector[int64_t] entry_indices
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@ -408,6 +408,48 @@ class EntityLinker(TrainablePipe):
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validate_examples(examples, "EntityLinker.score")
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return Scorer.score_links(examples, negative_labels=[self.NIL])
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def to_bytes(self, *, exclude=tuple()):
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"""Serialize the pipe to a bytestring.
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exclude (Iterable[str]): String names of serialization fields to exclude.
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RETURNS (bytes): The serialized object.
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DOCS: https://spacy.io/api/entitylinker#to_bytes
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"""
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self._validate_serialization_attrs()
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serialize = {}
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if hasattr(self, "cfg") and self.cfg is not None:
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serialize["cfg"] = lambda: srsly.json_dumps(self.cfg)
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serialize["vocab"] = self.vocab.to_bytes
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serialize["kb"] = self.kb.to_bytes
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serialize["model"] = self.model.to_bytes
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return util.to_bytes(serialize, exclude)
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def from_bytes(self, bytes_data, *, exclude=tuple()):
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"""Load the pipe from a bytestring.
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exclude (Iterable[str]): String names of serialization fields to exclude.
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RETURNS (TrainablePipe): The loaded object.
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DOCS: https://spacy.io/api/entitylinker#from_bytes
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"""
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self._validate_serialization_attrs()
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def load_model(b):
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try:
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self.model.from_bytes(b)
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except AttributeError:
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raise ValueError(Errors.E149) from None
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deserialize = {}
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if hasattr(self, "cfg") and self.cfg is not None:
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deserialize["cfg"] = lambda b: self.cfg.update(srsly.json_loads(b))
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deserialize["vocab"] = lambda b: self.vocab.from_bytes(b)
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deserialize["kb"] = lambda b: self.kb.from_bytes(b)
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deserialize["model"] = load_model
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util.from_bytes(bytes_data, deserialize, exclude)
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return self
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def to_disk(
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self, path: Union[str, Path], *, exclude: Iterable[str] = SimpleFrozenList()
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) -> None:
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@ -2,7 +2,7 @@ from typing import Callable, Iterable
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import pytest
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from numpy.testing import assert_equal
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from spacy.attrs import ENT_KB_ID
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from spacy.compat import pickle
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from spacy.kb import KnowledgeBase, get_candidates, Candidate
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from spacy.vocab import Vocab
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@ -11,7 +11,7 @@ from spacy.ml import load_kb
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from spacy.scorer import Scorer
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from spacy.training import Example
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from spacy.lang.en import English
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from spacy.tests.util import make_tempdir
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from spacy.tests.util import make_tempdir, make_tempfile
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from spacy.tokens import Span
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@ -290,6 +290,9 @@ def test_vocab_serialization(nlp):
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assert candidates[0].alias == adam_hash
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assert candidates[0].alias_ == "adam"
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assert kb_new_vocab.get_vector("Q2") == [2]
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assert_almost_equal(kb_new_vocab.get_prior_prob("Q2", "douglas"), 0.4)
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def test_append_alias(nlp):
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"""Test that we can append additional alias-entity pairs"""
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@ -546,6 +549,98 @@ def test_kb_serialization():
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assert "RandomWord" in nlp2.vocab.strings
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@pytest.mark.xfail(reason="Needs fixing")
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def test_kb_pickle():
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# Test that the KB can be pickled
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nlp = English()
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kb_1 = KnowledgeBase(nlp.vocab, entity_vector_length=3)
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kb_1.add_entity(entity="Q2146908", freq=12, entity_vector=[6, -4, 3])
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assert not kb_1.contains_alias("Russ Cochran")
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kb_1.add_alias(alias="Russ Cochran", entities=["Q2146908"], probabilities=[0.8])
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assert kb_1.contains_alias("Russ Cochran")
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data = pickle.dumps(kb_1)
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kb_2 = pickle.loads(data)
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assert kb_2.contains_alias("Russ Cochran")
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@pytest.mark.xfail(reason="Needs fixing")
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def test_nel_pickle():
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# Test that a pipeline with an EL component can be pickled
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def create_kb(vocab):
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kb = KnowledgeBase(vocab, entity_vector_length=3)
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kb.add_entity(entity="Q2146908", freq=12, entity_vector=[6, -4, 3])
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kb.add_alias(alias="Russ Cochran", entities=["Q2146908"], probabilities=[0.8])
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return kb
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nlp_1 = English()
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nlp_1.add_pipe("ner")
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entity_linker_1 = nlp_1.add_pipe("entity_linker", last=True)
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entity_linker_1.set_kb(create_kb)
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assert nlp_1.pipe_names == ["ner", "entity_linker"]
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assert entity_linker_1.kb.contains_alias("Russ Cochran")
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data = pickle.dumps(nlp_1)
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nlp_2 = pickle.loads(data)
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assert nlp_2.pipe_names == ["ner", "entity_linker"]
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entity_linker_2 = nlp_2.get_pipe("entity_linker")
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assert entity_linker_2.kb.contains_alias("Russ Cochran")
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def test_kb_to_bytes():
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# Test that the KB's to_bytes method works correctly
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nlp = English()
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kb_1 = KnowledgeBase(nlp.vocab, entity_vector_length=3)
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kb_1.add_entity(entity="Q2146908", freq=12, entity_vector=[6, -4, 3])
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kb_1.add_entity(entity="Q66", freq=9, entity_vector=[1, 2, 3])
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kb_1.add_alias(alias="Russ Cochran", entities=["Q2146908"], probabilities=[0.8])
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kb_1.add_alias(alias="Boeing", entities=["Q66"], probabilities=[0.5])
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kb_1.add_alias(alias="Randomness", entities=["Q66", "Q2146908"], probabilities=[0.1, 0.2])
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assert kb_1.contains_alias("Russ Cochran")
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kb_bytes = kb_1.to_bytes()
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kb_2 = KnowledgeBase(nlp.vocab, entity_vector_length=3)
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assert not kb_2.contains_alias("Russ Cochran")
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kb_2 = kb_2.from_bytes(kb_bytes)
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# check that both KBs are exactly the same
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assert kb_1.get_size_entities() == kb_2.get_size_entities()
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assert kb_1.entity_vector_length == kb_2.entity_vector_length
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assert kb_1.get_entity_strings() == kb_2.get_entity_strings()
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assert kb_1.get_vector("Q2146908") == kb_2.get_vector("Q2146908")
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assert kb_1.get_vector("Q66") == kb_2.get_vector("Q66")
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assert kb_2.contains_alias("Russ Cochran")
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assert kb_1.get_size_aliases() == kb_2.get_size_aliases()
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assert kb_1.get_alias_strings() == kb_2.get_alias_strings()
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assert len(kb_1.get_alias_candidates("Russ Cochran")) == len(kb_2.get_alias_candidates("Russ Cochran"))
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assert len(kb_1.get_alias_candidates("Randomness")) == len(kb_2.get_alias_candidates("Randomness"))
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def test_nel_to_bytes():
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# Test that a pipeline with an EL component can be converted to bytes
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def create_kb(vocab):
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kb = KnowledgeBase(vocab, entity_vector_length=3)
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kb.add_entity(entity="Q2146908", freq=12, entity_vector=[6, -4, 3])
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kb.add_alias(alias="Russ Cochran", entities=["Q2146908"], probabilities=[0.8])
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return kb
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nlp_1 = English()
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nlp_1.add_pipe("ner")
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entity_linker_1 = nlp_1.add_pipe("entity_linker", last=True)
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entity_linker_1.set_kb(create_kb)
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assert entity_linker_1.kb.contains_alias("Russ Cochran")
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assert nlp_1.pipe_names == ["ner", "entity_linker"]
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nlp_bytes = nlp_1.to_bytes()
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nlp_2 = English()
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nlp_2.add_pipe("ner")
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nlp_2.add_pipe("entity_linker", last=True)
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assert nlp_2.pipe_names == ["ner", "entity_linker"]
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assert not nlp_2.get_pipe("entity_linker").kb.contains_alias("Russ Cochran")
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nlp_2 = nlp_2.from_bytes(nlp_bytes)
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kb_2 = nlp_2.get_pipe("entity_linker").kb
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assert kb_2.contains_alias("Russ Cochran")
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assert kb_2.get_vector("Q2146908") == [6, -4, 3]
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assert_almost_equal(kb_2.get_prior_prob(entity="Q2146908", alias="Russ Cochran"), 0.8)
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def test_scorer_links():
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train_examples = []
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nlp = English()
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@ -213,10 +213,10 @@ if there is no prediction.
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> kb_ids = entity_linker.predict([doc1, doc2])
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> ```
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| Name | Description |
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| ----------- | ------------------------------------------- |
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| `docs` | The documents to predict. ~~Iterable[Doc]~~ |
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| **RETURNS** | `List[str]` | The predicted KB identifiers for the entities in the `docs`. ~~List[str]~~ |
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| Name | Description |
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| ----------- | -------------------------------------------------------------------------- |
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| `docs` | The documents to predict. ~~Iterable[Doc]~~ |
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| **RETURNS** | The predicted KB identifiers for the entities in the `docs`. ~~List[str]~~ |
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## EntityLinker.set_annotations {#set_annotations tag="method"}
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@ -341,6 +341,42 @@ Load the pipe from disk. Modifies the object in place and returns it.
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| `exclude` | String names of [serialization fields](#serialization-fields) to exclude. ~~Iterable[str]~~ |
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| **RETURNS** | The modified `EntityLinker` object. ~~EntityLinker~~ |
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## EntityLinker.to_bytes {#to_bytes tag="method"}
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> #### Example
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>
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> ```python
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> entity_linker = nlp.add_pipe("entity_linker")
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> entity_linker_bytes = entity_linker.to_bytes()
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> ```
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Serialize the pipe to a bytestring, including the `KnowledgeBase`.
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| Name | Description |
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| -------------- | ------------------------------------------------------------------------------------------- |
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| _keyword-only_ | |
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| `exclude` | String names of [serialization fields](#serialization-fields) to exclude. ~~Iterable[str]~~ |
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| **RETURNS** | The serialized form of the `EntityLinker` object. ~~bytes~~ |
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## EntityLinker.from_bytes {#from_bytes tag="method"}
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Load the pipe from a bytestring. Modifies the object in place and returns it.
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> #### Example
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>
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> ```python
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> entity_linker_bytes = entity_linker.to_bytes()
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> entity_linker = nlp.add_pipe("entity_linker")
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> entity_linker.from_bytes(entity_linker_bytes)
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> ```
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| Name | Description |
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| -------------- | ------------------------------------------------------------------------------------------- |
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| `bytes_data` | The data to load from. ~~bytes~~ |
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| _keyword-only_ | |
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| `exclude` | String names of [serialization fields](#serialization-fields) to exclude. ~~Iterable[str]~~ |
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| **RETURNS** | The `EntityLinker` object. ~~EntityLinker~~ |
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## Serialization fields {#serialization-fields}
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During serialization, spaCy will export several data fields used to restore
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