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Ensure that doc.ents preserves kb_id annotations (#4294)

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* bugfix: ensure doc.ents preserves kb_id annotations

* fix backward compatibility

* additional test
This commit is contained in:
Sofie Van Landeghem 2019-09-16 15:18:37 +02:00 committed by Ines Montani
parent 57f4c088be
commit 03ac29f437
2 changed files with 40 additions and 5 deletions
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29
spacy/tests/pipeline/test_entity_linker.py
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@ -6,6 +6,7 @@ import pytest
from spacy.kb import KnowledgeBase from spacy.kb import KnowledgeBase
from spacy.lang.en import English from spacy.lang.en import English
from spacy.pipeline import EntityRuler from spacy.pipeline import EntityRuler
from spacy.tokens import Span
@pytest.fixture @pytest.fixture
@ -171,3 +172,31 @@ def test_preserving_links_asdoc(nlp):
for s_ent in sent_doc.ents: for s_ent in sent_doc.ents:
if s_ent.text == orig_text: if s_ent.text == orig_text:
assert s_ent.kb_id_ == orig_kb_id assert s_ent.kb_id_ == orig_kb_id
def test_preserving_links_ents(nlp):
"""Test that doc.ents preserves KB annotations"""
text = "She lives in Boston. He lives in Denver."
doc = nlp(text)
assert len(list(doc.ents)) == 0
boston_ent = Span(doc, 3, 4, label="LOC", kb_id="Q1")
doc.ents = [boston_ent]
assert len(list(doc.ents)) == 1
assert list(doc.ents)[0].label_ == "LOC"
assert list(doc.ents)[0].kb_id_ == "Q1"
def test_preserving_links_ents_2(nlp):
"""Test that doc.ents preserves KB annotations"""
text = "She lives in Boston. He lives in Denver."
doc = nlp(text)
assert len(list(doc.ents)) == 0
loc = doc.vocab.strings.add("LOC")
q1 = doc.vocab.strings.add("Q1")
doc.ents = [(loc, q1, 3, 4)]
assert len(list(doc.ents)) == 1
assert list(doc.ents)[0].label_ == "LOC"
assert list(doc.ents)[0].kb_id_ == "Q1"

16
spacy/tokens/doc.pyx
View File

@ -534,7 +534,7 @@ cdef class Doc:
cdef attr_t entity_type cdef attr_t entity_type
cdef int ent_start, ent_end cdef int ent_start, ent_end
for ent_info in ents: for ent_info in ents:
entity_type, ent_start, ent_end = get_entity_info(ent_info) entity_type, kb_id, ent_start, ent_end = get_entity_info(ent_info)
for token_index in range(ent_start, ent_end): for token_index in range(ent_start, ent_end):
if token_index in tokens_in_ents.keys(): if token_index in tokens_in_ents.keys():
raise ValueError(Errors.E103.format( raise ValueError(Errors.E103.format(
@ -542,7 +542,7 @@ cdef class Doc:
tokens_in_ents[token_index][1], tokens_in_ents[token_index][1],
self.vocab.strings[tokens_in_ents[token_index][2]]), self.vocab.strings[tokens_in_ents[token_index][2]]),
span2=(ent_start, ent_end, self.vocab.strings[entity_type]))) span2=(ent_start, ent_end, self.vocab.strings[entity_type])))
tokens_in_ents[token_index] = (ent_start, ent_end, entity_type) tokens_in_ents[token_index] = (ent_start, ent_end, entity_type, kb_id)
cdef int i cdef int i
for i in range(self.length): for i in range(self.length):
self.c[i].ent_type = 0 self.c[i].ent_type = 0
@ -551,16 +551,18 @@ cdef class Doc:
cdef attr_t ent_type cdef attr_t ent_type
cdef int start, end cdef int start, end
for ent_info in ents: for ent_info in ents:
ent_type, start, end = get_entity_info(ent_info) ent_type, ent_kb_id, start, end = get_entity_info(ent_info)
if ent_type is None or ent_type < 0: if ent_type is None or ent_type < 0:
# Mark as O # Mark as O
for i in range(start, end): for i in range(start, end):
self.c[i].ent_type = 0 self.c[i].ent_type = 0
self.c[i].ent_kb_id = 0
self.c[i].ent_iob = 2 self.c[i].ent_iob = 2
else: else:
# Mark (inside) as I # Mark (inside) as I
for i in range(start, end): for i in range(start, end):
self.c[i].ent_type = ent_type self.c[i].ent_type = ent_type
self.c[i].ent_kb_id = ent_kb_id
self.c[i].ent_iob = 1 self.c[i].ent_iob = 1
# Set start as B # Set start as B
self.c[start].ent_iob = 3 self.c[start].ent_iob = 3
@ -1251,10 +1253,14 @@ def fix_attributes(doc, attributes):
def get_entity_info(ent_info): def get_entity_info(ent_info):
if isinstance(ent_info, Span): if isinstance(ent_info, Span):
ent_type = ent_info.label ent_type = ent_info.label
ent_kb_id = ent_info.kb_id
start = ent_info.start start = ent_info.start
end = ent_info.end end = ent_info.end
elif len(ent_info) == 3: elif len(ent_info) == 3:
ent_type, start, end = ent_info ent_type, start, end = ent_info
ent_kb_id = 0
elif len(ent_info) == 4:
ent_type, ent_kb_id, start, end = ent_info
else: else:
ent_id, ent_type, start, end = ent_info ent_id, ent_kb_id, ent_type, start, end = ent_info
return ent_type, start, end return ent_type, ent_kb_id, start, end