spaCy/spacy/tests/parser/test_ner.py
Connor Brinton 657af5f91f
🏷 Add Mypy check to CI and ignore all existing Mypy errors (#9167)
* 🚨 Ignore all existing Mypy errors

* 🏗 Add Mypy check to CI

* Add types-mock and types-requests as dev requirements

* Add additional type ignore directives

* Add types packages to dev-only list in reqs test

* Add types-dataclasses for python 3.6

* Add ignore to pretrain

* 🏷 Improve type annotation on `run_command` helper

The `run_command` helper previously declared that it returned an
`Optional[subprocess.CompletedProcess]`, but it isn't actually possible
for the function to return `None`. These changes modify the type
annotation of the `run_command` helper and remove all now-unnecessary
`# type: ignore` directives.

* 🔧 Allow variable type redefinition in limited contexts

These changes modify how Mypy is configured to allow variables to have
their type automatically redefined under certain conditions. The Mypy
documentation contains the following example:

```python
def process(items: List[str]) -> None:
    # 'items' has type List[str]
    items = [item.split() for item in items]
    # 'items' now has type List[List[str]]
    ...
```

This configuration change is especially helpful in reducing the number
of `# type: ignore` directives needed to handle the common pattern of:
* Accepting a filepath as a string
* Overwriting the variable using `filepath = ensure_path(filepath)`

These changes enable redefinition and remove all `# type: ignore`
directives rendered redundant by this change.

* 🏷 Add type annotation to converters mapping

* 🚨 Fix Mypy error in convert CLI argument verification

* 🏷 Improve type annotation on `resolve_dot_names` helper

* 🏷 Add type annotations for `Vocab` attributes `strings` and `vectors`

* 🏷 Add type annotations for more `Vocab` attributes

* 🏷 Add loose type annotation for gold data compilation

* 🏷 Improve `_format_labels` type annotation

* 🏷 Fix `get_lang_class` type annotation

* 🏷 Loosen return type of `Language.evaluate`

* 🏷 Don't accept `Scorer` in `handle_scores_per_type`

* 🏷 Add `string_to_list` overloads

* 🏷 Fix non-Optional command-line options

* 🙈 Ignore redefinition of `wandb_logger` in `loggers.py`

*  Install `typing_extensions` in Python 3.8+

The `typing_extensions` package states that it should be used when
"writing code that must be compatible with multiple Python versions".
Since SpaCy needs to support multiple Python versions, it should be used
when newer `typing` module members are required. One example of this is
`Literal`, which is available starting with Python 3.8.

Previously SpaCy tried to import `Literal` from `typing`, falling back
to `typing_extensions` if the import failed. However, Mypy doesn't seem
to be able to understand what `Literal` means when the initial import
means. Therefore, these changes modify how `compat` imports `Literal` by
always importing it from `typing_extensions`.

These changes also modify how `typing_extensions` is installed, so that
it is a requirement for all Python versions, including those greater
than or equal to 3.8.

* 🏷 Improve type annotation for `Language.pipe`

These changes add a missing overload variant to the type signature of
`Language.pipe`. Additionally, the type signature is enhanced to allow
type checkers to differentiate between the two overload variants based
on the `as_tuple` parameter.

Fixes #8772

*  Don't install `typing-extensions` in Python 3.8+

After more detailed analysis of how to implement Python version-specific
type annotations using SpaCy, it has been determined that by branching
on a comparison against `sys.version_info` can be statically analyzed by
Mypy well enough to enable us to conditionally use
`typing_extensions.Literal`. This means that we no longer need to
install `typing_extensions` for Python versions greater than or equal to
3.8! 🎉

These changes revert previous changes installing `typing-extensions`
regardless of Python version and modify how we import the `Literal` type
to ensure that Mypy treats it properly.

* resolve mypy errors for Strict pydantic types

* refactor code to avoid missing return statement

* fix types of convert CLI command

* avoid list-set confustion in debug_data

* fix typo and formatting

* small fixes to avoid type ignores

* fix types in profile CLI command and make it more efficient

* type fixes in projects CLI

* put one ignore back

* type fixes for render

* fix render types - the sequel

* fix BaseDefault in language definitions

* fix type of noun_chunks iterator - yields tuple instead of span

* fix types in language-specific modules

* 🏷 Expand accepted inputs of `get_string_id`

`get_string_id` accepts either a string (in which case it returns its 
ID) or an ID (in which case it immediately returns the ID). These 
changes extend the type annotation of `get_string_id` to indicate that 
it can accept either strings or IDs.

* 🏷 Handle override types in `combine_score_weights`

The `combine_score_weights` function allows users to pass an `overrides` 
mapping to override data extracted from the `weights` argument. Since it 
allows `Optional` dictionary values, the return value may also include 
`Optional` dictionary values.

These changes update the type annotations for `combine_score_weights` to 
reflect this fact.

* 🏷 Fix tokenizer serialization method signatures in `DummyTokenizer`

* 🏷 Fix redefinition of `wandb_logger`

These changes fix the redefinition of `wandb_logger` by giving a 
separate name to each `WandbLogger` version. For 
backwards-compatibility, `spacy.train` still exports `wandb_logger_v3` 
as `wandb_logger` for now.

* more fixes for typing in language

* type fixes in model definitions

* 🏷 Annotate `_RandomWords.probs` as `NDArray`

* 🏷 Annotate `tok2vec` layers to help Mypy

* 🐛 Fix `_RandomWords.probs` type annotations for Python 3.6

Also remove an import that I forgot to move to the top of the module 😅

* more fixes for matchers and other pipeline components

* quick fix for entity linker

* fixing types for spancat, textcat, etc

* bugfix for tok2vec

* type annotations for scorer

* add runtime_checkable for Protocol

* type and import fixes in tests

* mypy fixes for training utilities

* few fixes in util

* fix import

* 🐵 Remove unused `# type: ignore` directives

* 🏷 Annotate `Language._components`

* 🏷 Annotate `spacy.pipeline.Pipe`

* add doc as property to span.pyi

* small fixes and cleanup

* explicit type annotations instead of via comment

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
Co-authored-by: svlandeg <svlandeg@github.com>
2021-10-14 15:21:40 +02:00

659 lines
23 KiB
Python

import pytest
from numpy.testing import assert_equal
from spacy.attrs import ENT_IOB
from spacy import util, registry
from spacy.lang.en import English
from spacy.language import Language
from spacy.lookups import Lookups
from spacy.pipeline._parser_internals.ner import BiluoPushDown
from spacy.training import Example
from spacy.tokens import Doc, Span
from spacy.vocab import Vocab
import logging
from ..util import make_tempdir
from ...pipeline import EntityRecognizer
from ...pipeline.ner import DEFAULT_NER_MODEL
TRAIN_DATA = [
("Who is Shaka Khan?", {"entities": [(7, 17, "PERSON")]}),
("I like London and Berlin.", {"entities": [(7, 13, "LOC"), (18, 24, "LOC")]}),
]
@pytest.fixture
def neg_key():
return "non_entities"
@pytest.fixture
def vocab():
return Vocab()
@pytest.fixture
def doc(vocab):
return Doc(vocab, words=["Casey", "went", "to", "New", "York", "."])
@pytest.fixture
def entity_annots(doc):
casey = doc[0:1]
ny = doc[3:5]
return [
(casey.start_char, casey.end_char, "PERSON"),
(ny.start_char, ny.end_char, "GPE"),
]
@pytest.fixture
def entity_types(entity_annots):
return sorted(set([label for (s, e, label) in entity_annots]))
@pytest.fixture
def tsys(vocab, entity_types):
actions = BiluoPushDown.get_actions(entity_types=entity_types)
return BiluoPushDown(vocab.strings, actions)
def test_get_oracle_moves(tsys, doc, entity_annots):
example = Example.from_dict(doc, {"entities": entity_annots})
act_classes = tsys.get_oracle_sequence(example, _debug=False)
names = [tsys.get_class_name(act) for act in act_classes]
assert names == ["U-PERSON", "O", "O", "B-GPE", "L-GPE", "O"]
def test_negative_samples_two_word_input(tsys, vocab, neg_key):
"""Test that we don't get stuck in a two word input when we have a negative
span. This could happen if we don't have the right check on the B action.
"""
tsys.cfg["neg_key"] = neg_key
doc = Doc(vocab, words=["A", "B"])
entity_annots = [None, None]
example = Example.from_dict(doc, {"entities": entity_annots})
# These mean that the oracle sequence shouldn't have O for the first
# word, and it shouldn't analyse it as B-PERSON, L-PERSON
example.y.spans[neg_key] = [
Span(example.y, 0, 1, label="O"),
Span(example.y, 0, 2, label="PERSON"),
]
act_classes = tsys.get_oracle_sequence(example)
names = [tsys.get_class_name(act) for act in act_classes]
assert names
assert names[0] != "O"
assert names[0] != "B-PERSON"
assert names[1] != "L-PERSON"
def test_negative_samples_three_word_input(tsys, vocab, neg_key):
"""Test that we exclude a 2-word entity correctly using a negative example."""
tsys.cfg["neg_key"] = neg_key
doc = Doc(vocab, words=["A", "B", "C"])
entity_annots = [None, None, None]
example = Example.from_dict(doc, {"entities": entity_annots})
# These mean that the oracle sequence shouldn't have O for the first
# word, and it shouldn't analyse it as B-PERSON, L-PERSON
example.y.spans[neg_key] = [
Span(example.y, 0, 1, label="O"),
Span(example.y, 0, 2, label="PERSON"),
]
act_classes = tsys.get_oracle_sequence(example)
names = [tsys.get_class_name(act) for act in act_classes]
assert names
assert names[0] != "O"
assert names[1] != "B-PERSON"
def test_negative_samples_U_entity(tsys, vocab, neg_key):
"""Test that we exclude a 2-word entity correctly using a negative example."""
tsys.cfg["neg_key"] = neg_key
doc = Doc(vocab, words=["A"])
entity_annots = [None]
example = Example.from_dict(doc, {"entities": entity_annots})
# These mean that the oracle sequence shouldn't have O for the first
# word, and it shouldn't analyse it as B-PERSON, L-PERSON
example.y.spans[neg_key] = [
Span(example.y, 0, 1, label="O"),
Span(example.y, 0, 1, label="PERSON"),
]
act_classes = tsys.get_oracle_sequence(example)
names = [tsys.get_class_name(act) for act in act_classes]
assert names
assert names[0] != "O"
assert names[0] != "U-PERSON"
def test_negative_sample_key_is_in_config(vocab, entity_types):
actions = BiluoPushDown.get_actions(entity_types=entity_types)
tsys = BiluoPushDown(vocab.strings, actions, incorrect_spans_key="non_entities")
assert tsys.cfg["neg_key"] == "non_entities"
# We can't easily represent this on a Doc object. Not sure what the best solution
# would be, but I don't think it's an important use case?
@pytest.mark.skip(reason="No longer supported")
def test_oracle_moves_missing_B(en_vocab):
words = ["B", "52", "Bomber"]
biluo_tags = [None, None, "L-PRODUCT"]
doc = Doc(en_vocab, words=words)
example = Example.from_dict(doc, {"words": words, "entities": biluo_tags})
moves = BiluoPushDown(en_vocab.strings)
move_types = ("M", "B", "I", "L", "U", "O")
for tag in biluo_tags:
if tag is None:
continue
elif tag == "O":
moves.add_action(move_types.index("O"), "")
else:
action, label = tag.split("-")
moves.add_action(move_types.index("B"), label)
moves.add_action(move_types.index("I"), label)
moves.add_action(move_types.index("L"), label)
moves.add_action(move_types.index("U"), label)
moves.get_oracle_sequence(example)
# We can't easily represent this on a Doc object. Not sure what the best solution
# would be, but I don't think it's an important use case?
@pytest.mark.skip(reason="No longer supported")
def test_oracle_moves_whitespace(en_vocab):
words = ["production", "\n", "of", "Northrop", "\n", "Corp.", "\n", "'s", "radar"]
biluo_tags = ["O", "O", "O", "B-ORG", None, "I-ORG", "L-ORG", "O", "O"]
doc = Doc(en_vocab, words=words)
example = Example.from_dict(doc, {"entities": biluo_tags})
moves = BiluoPushDown(en_vocab.strings)
move_types = ("M", "B", "I", "L", "U", "O")
for tag in biluo_tags:
if tag is None:
continue
elif tag == "O":
moves.add_action(move_types.index("O"), "")
else:
action, label = tag.split("-")
moves.add_action(move_types.index(action), label)
moves.get_oracle_sequence(example)
def test_accept_blocked_token():
"""Test succesful blocking of tokens to be in an entity."""
# 1. test normal behaviour
nlp1 = English()
doc1 = nlp1("I live in New York")
config = {}
ner1 = nlp1.create_pipe("ner", config=config)
assert [token.ent_iob_ for token in doc1] == ["", "", "", "", ""]
assert [token.ent_type_ for token in doc1] == ["", "", "", "", ""]
# Add the OUT action
ner1.moves.add_action(5, "")
ner1.add_label("GPE")
# Get into the state just before "New"
state1 = ner1.moves.init_batch([doc1])[0]
ner1.moves.apply_transition(state1, "O")
ner1.moves.apply_transition(state1, "O")
ner1.moves.apply_transition(state1, "O")
# Check that B-GPE is valid.
assert ner1.moves.is_valid(state1, "B-GPE")
# 2. test blocking behaviour
nlp2 = English()
doc2 = nlp2("I live in New York")
config = {}
ner2 = nlp2.create_pipe("ner", config=config)
# set "New York" to a blocked entity
doc2.set_ents([], blocked=[doc2[3:5]], default="unmodified")
assert [token.ent_iob_ for token in doc2] == ["", "", "", "B", "B"]
assert [token.ent_type_ for token in doc2] == ["", "", "", "", ""]
# Check that B-GPE is now invalid.
ner2.moves.add_action(4, "")
ner2.moves.add_action(5, "")
ner2.add_label("GPE")
state2 = ner2.moves.init_batch([doc2])[0]
ner2.moves.apply_transition(state2, "O")
ner2.moves.apply_transition(state2, "O")
ner2.moves.apply_transition(state2, "O")
# we can only use U- for "New"
assert not ner2.moves.is_valid(state2, "B-GPE")
assert ner2.moves.is_valid(state2, "U-")
ner2.moves.apply_transition(state2, "U-")
# we can only use U- for "York"
assert not ner2.moves.is_valid(state2, "B-GPE")
assert ner2.moves.is_valid(state2, "U-")
def test_train_empty():
"""Test that training an empty text does not throw errors."""
train_data = [
("Who is Shaka Khan?", {"entities": [(7, 17, "PERSON")]}),
("", {"entities": []}),
]
nlp = English()
train_examples = []
for t in train_data:
train_examples.append(Example.from_dict(nlp.make_doc(t[0]), t[1]))
ner = nlp.add_pipe("ner", last=True)
ner.add_label("PERSON")
nlp.initialize()
for itn in range(2):
losses = {}
batches = util.minibatch(train_examples, size=8)
for batch in batches:
nlp.update(batch, losses=losses)
def test_train_negative_deprecated():
"""Test that the deprecated negative entity format raises a custom error."""
train_data = [
("Who is Shaka Khan?", {"entities": [(7, 17, "!PERSON")]}),
]
nlp = English()
train_examples = []
for t in train_data:
train_examples.append(Example.from_dict(nlp.make_doc(t[0]), t[1]))
ner = nlp.add_pipe("ner", last=True)
ner.add_label("PERSON")
nlp.initialize()
for itn in range(2):
losses = {}
batches = util.minibatch(train_examples, size=8)
for batch in batches:
with pytest.raises(ValueError):
nlp.update(batch, losses=losses)
def test_overwrite_token():
nlp = English()
nlp.add_pipe("ner")
nlp.initialize()
# The untrained NER will predict O for each token
doc = nlp("I live in New York")
assert [token.ent_iob_ for token in doc] == ["O", "O", "O", "O", "O"]
assert [token.ent_type_ for token in doc] == ["", "", "", "", ""]
# Check that a new ner can overwrite O
config = {}
ner2 = nlp.create_pipe("ner", config=config)
ner2.moves.add_action(5, "")
ner2.add_label("GPE")
state = ner2.moves.init_batch([doc])[0]
assert ner2.moves.is_valid(state, "B-GPE")
assert ner2.moves.is_valid(state, "U-GPE")
ner2.moves.apply_transition(state, "B-GPE")
assert ner2.moves.is_valid(state, "I-GPE")
assert ner2.moves.is_valid(state, "L-GPE")
def test_empty_ner():
nlp = English()
ner = nlp.add_pipe("ner")
ner.add_label("MY_LABEL")
nlp.initialize()
doc = nlp("John is watching the news about Croatia's elections")
# if this goes wrong, the initialization of the parser's upper layer is probably broken
result = ["O", "O", "O", "O", "O", "O", "O", "O", "O"]
assert [token.ent_iob_ for token in doc] == result
def test_ruler_before_ner():
"""Test that an NER works after an entity_ruler: the second can add annotations"""
nlp = English()
# 1 : Entity Ruler - should set "this" to B and everything else to empty
patterns = [{"label": "THING", "pattern": "This"}]
ruler = nlp.add_pipe("entity_ruler")
# 2: untrained NER - should set everything else to O
untrained_ner = nlp.add_pipe("ner")
untrained_ner.add_label("MY_LABEL")
nlp.initialize()
ruler.add_patterns(patterns)
doc = nlp("This is Antti Korhonen speaking in Finland")
expected_iobs = ["B", "O", "O", "O", "O", "O", "O"]
expected_types = ["THING", "", "", "", "", "", ""]
assert [token.ent_iob_ for token in doc] == expected_iobs
assert [token.ent_type_ for token in doc] == expected_types
def test_ner_constructor(en_vocab):
config = {
"update_with_oracle_cut_size": 100,
}
cfg = {"model": DEFAULT_NER_MODEL}
model = registry.resolve(cfg, validate=True)["model"]
EntityRecognizer(en_vocab, model, **config)
EntityRecognizer(en_vocab, model)
def test_ner_before_ruler():
"""Test that an entity_ruler works after an NER: the second can overwrite O annotations"""
nlp = English()
# 1: untrained NER - should set everything to O
untrained_ner = nlp.add_pipe("ner", name="uner")
untrained_ner.add_label("MY_LABEL")
nlp.initialize()
# 2 : Entity Ruler - should set "this" to B and keep everything else O
patterns = [{"label": "THING", "pattern": "This"}]
ruler = nlp.add_pipe("entity_ruler")
ruler.add_patterns(patterns)
doc = nlp("This is Antti Korhonen speaking in Finland")
expected_iobs = ["B", "O", "O", "O", "O", "O", "O"]
expected_types = ["THING", "", "", "", "", "", ""]
assert [token.ent_iob_ for token in doc] == expected_iobs
assert [token.ent_type_ for token in doc] == expected_types
def test_block_ner():
"""Test functionality for blocking tokens so they can't be in a named entity"""
# block "Antti L Korhonen" from being a named entity
nlp = English()
nlp.add_pipe("blocker", config={"start": 2, "end": 5})
untrained_ner = nlp.add_pipe("ner")
untrained_ner.add_label("MY_LABEL")
nlp.initialize()
doc = nlp("This is Antti L Korhonen speaking in Finland")
expected_iobs = ["O", "O", "B", "B", "B", "O", "O", "O"]
expected_types = ["", "", "", "", "", "", "", ""]
assert [token.ent_iob_ for token in doc] == expected_iobs
assert [token.ent_type_ for token in doc] == expected_types
@pytest.mark.parametrize("use_upper", [True, False])
def test_overfitting_IO(use_upper):
# Simple test to try and quickly overfit the NER component
nlp = English()
ner = nlp.add_pipe("ner", config={"model": {"use_upper": use_upper}})
train_examples = []
for text, annotations in TRAIN_DATA:
train_examples.append(Example.from_dict(nlp.make_doc(text), annotations))
for ent in annotations.get("entities"):
ner.add_label(ent[2])
optimizer = nlp.initialize()
for i in range(50):
losses = {}
nlp.update(train_examples, sgd=optimizer, losses=losses)
assert losses["ner"] < 0.00001
# test the trained model
test_text = "I like London."
doc = nlp(test_text)
ents = doc.ents
assert len(ents) == 1
assert ents[0].text == "London"
assert ents[0].label_ == "LOC"
# Also test the results are still the same after IO
with make_tempdir() as tmp_dir:
nlp.to_disk(tmp_dir)
nlp2 = util.load_model_from_path(tmp_dir)
doc2 = nlp2(test_text)
ents2 = doc2.ents
assert len(ents2) == 1
assert ents2[0].text == "London"
assert ents2[0].label_ == "LOC"
# Ensure that the predictions are still the same, even after adding a new label
ner2 = nlp2.get_pipe("ner")
assert ner2.model.attrs["has_upper"] == use_upper
ner2.add_label("RANDOM_NEW_LABEL")
doc3 = nlp2(test_text)
ents3 = doc3.ents
assert len(ents3) == 1
assert ents3[0].text == "London"
assert ents3[0].label_ == "LOC"
# Make sure that running pipe twice, or comparing to call, always amounts to the same predictions
texts = [
"Just a sentence.",
"Then one more sentence about London.",
"Here is another one.",
"I like London.",
]
batch_deps_1 = [doc.to_array([ENT_IOB]) for doc in nlp.pipe(texts)]
batch_deps_2 = [doc.to_array([ENT_IOB]) for doc in nlp.pipe(texts)]
no_batch_deps = [doc.to_array([ENT_IOB]) for doc in [nlp(text) for text in texts]]
assert_equal(batch_deps_1, batch_deps_2)
assert_equal(batch_deps_1, no_batch_deps)
# test that kb_id is preserved
test_text = "I like London and London."
doc = nlp.make_doc(test_text)
doc.ents = [Span(doc, 2, 3, label="LOC", kb_id=1234)]
ents = doc.ents
assert len(ents) == 1
assert ents[0].text == "London"
assert ents[0].label_ == "LOC"
assert ents[0].kb_id == 1234
doc = nlp.get_pipe("ner")(doc)
ents = doc.ents
assert len(ents) == 2
assert ents[0].text == "London"
assert ents[0].label_ == "LOC"
assert ents[0].kb_id == 1234
# ent added by ner has kb_id == 0
assert ents[1].text == "London"
assert ents[1].label_ == "LOC"
assert ents[1].kb_id == 0
def test_beam_ner_scores():
# Test that we can get confidence values out of the beam_ner pipe
beam_width = 16
beam_density = 0.0001
nlp = English()
config = {
"beam_width": beam_width,
"beam_density": beam_density,
}
ner = nlp.add_pipe("beam_ner", config=config)
train_examples = []
for text, annotations in TRAIN_DATA:
train_examples.append(Example.from_dict(nlp.make_doc(text), annotations))
for ent in annotations.get("entities"):
ner.add_label(ent[2])
optimizer = nlp.initialize()
# update once
losses = {}
nlp.update(train_examples, sgd=optimizer, losses=losses)
# test the scores from the beam
test_text = "I like London."
doc = nlp.make_doc(test_text)
docs = [doc]
beams = ner.predict(docs)
entity_scores = ner.scored_ents(beams)[0]
for j in range(len(doc)):
for label in ner.labels:
score = entity_scores[(j, j + 1, label)]
eps = 0.00001
assert 0 - eps <= score <= 1 + eps
def test_beam_overfitting_IO(neg_key):
# Simple test to try and quickly overfit the Beam NER component
nlp = English()
beam_width = 16
beam_density = 0.0001
config = {
"beam_width": beam_width,
"beam_density": beam_density,
"incorrect_spans_key": neg_key,
}
ner = nlp.add_pipe("beam_ner", config=config)
train_examples = []
for text, annotations in TRAIN_DATA:
train_examples.append(Example.from_dict(nlp.make_doc(text), annotations))
for ent in annotations.get("entities"):
ner.add_label(ent[2])
optimizer = nlp.initialize()
# run overfitting
for i in range(50):
losses = {}
nlp.update(train_examples, sgd=optimizer, losses=losses)
assert losses["beam_ner"] < 0.0001
# test the scores from the beam
test_text = "I like London"
docs = [nlp.make_doc(test_text)]
beams = ner.predict(docs)
entity_scores = ner.scored_ents(beams)[0]
assert entity_scores[(2, 3, "LOC")] == 1.0
assert entity_scores[(2, 3, "PERSON")] == 0.0
assert len(nlp(test_text).ents) == 1
# Also test the results are still the same after IO
with make_tempdir() as tmp_dir:
nlp.to_disk(tmp_dir)
nlp2 = util.load_model_from_path(tmp_dir)
docs2 = [nlp2.make_doc(test_text)]
ner2 = nlp2.get_pipe("beam_ner")
beams2 = ner2.predict(docs2)
entity_scores2 = ner2.scored_ents(beams2)[0]
assert entity_scores2[(2, 3, "LOC")] == 1.0
assert entity_scores2[(2, 3, "PERSON")] == 0.0
# Try to unlearn the entity by using negative annotations
neg_doc = nlp.make_doc(test_text)
neg_ex = Example(neg_doc, neg_doc)
neg_ex.reference.spans[neg_key] = [Span(neg_doc, 2, 3, "LOC")]
neg_train_examples = [neg_ex]
for i in range(20):
losses = {}
nlp.update(neg_train_examples, sgd=optimizer, losses=losses)
# test the "untrained" model
assert len(nlp(test_text).ents) == 0
def test_neg_annotation(neg_key):
"""Check that the NER update works with a negative annotation that is a different label of the correct one,
or partly overlapping, etc"""
nlp = English()
beam_width = 16
beam_density = 0.0001
config = {
"beam_width": beam_width,
"beam_density": beam_density,
"incorrect_spans_key": neg_key,
}
ner = nlp.add_pipe("beam_ner", config=config)
train_text = "Who is Shaka Khan?"
neg_doc = nlp.make_doc(train_text)
ner.add_label("PERSON")
ner.add_label("ORG")
example = Example.from_dict(neg_doc, {"entities": [(7, 17, "PERSON")]})
example.reference.spans[neg_key] = [
Span(neg_doc, 2, 4, "ORG"),
Span(neg_doc, 2, 3, "PERSON"),
Span(neg_doc, 1, 4, "PERSON"),
]
optimizer = nlp.initialize()
for i in range(2):
losses = {}
nlp.update([example], sgd=optimizer, losses=losses)
def test_neg_annotation_conflict(neg_key):
# Check that NER raises for a negative annotation that is THE SAME as a correct one
nlp = English()
beam_width = 16
beam_density = 0.0001
config = {
"beam_width": beam_width,
"beam_density": beam_density,
"incorrect_spans_key": neg_key,
}
ner = nlp.add_pipe("beam_ner", config=config)
train_text = "Who is Shaka Khan?"
neg_doc = nlp.make_doc(train_text)
ner.add_label("PERSON")
ner.add_label("LOC")
example = Example.from_dict(neg_doc, {"entities": [(7, 17, "PERSON")]})
example.reference.spans[neg_key] = [Span(neg_doc, 2, 4, "PERSON")]
assert len(example.reference.ents) == 1
assert example.reference.ents[0].text == "Shaka Khan"
assert example.reference.ents[0].label_ == "PERSON"
assert len(example.reference.spans[neg_key]) == 1
assert example.reference.spans[neg_key][0].text == "Shaka Khan"
assert example.reference.spans[neg_key][0].label_ == "PERSON"
optimizer = nlp.initialize()
for i in range(2):
losses = {}
with pytest.raises(ValueError):
nlp.update([example], sgd=optimizer, losses=losses)
def test_beam_valid_parse(neg_key):
"""Regression test for previously flakey behaviour"""
nlp = English()
beam_width = 16
beam_density = 0.0001
config = {
"beam_width": beam_width,
"beam_density": beam_density,
"incorrect_spans_key": neg_key,
}
nlp.add_pipe("beam_ner", config=config)
# fmt: off
tokens = ['FEDERAL', 'NATIONAL', 'MORTGAGE', 'ASSOCIATION', '(', 'Fannie', 'Mae', '):', 'Posted', 'yields', 'on', '30', 'year', 'mortgage', 'commitments', 'for', 'delivery', 'within', '30', 'days', '(', 'priced', 'at', 'par', ')', '9.75', '%', ',', 'standard', 'conventional', 'fixed', '-', 'rate', 'mortgages', ';', '8.70', '%', ',', '6/2', 'rate', 'capped', 'one', '-', 'year', 'adjustable', 'rate', 'mortgages', '.', 'Source', ':', 'Telerate', 'Systems', 'Inc.']
iob = ['B-ORG', 'I-ORG', 'I-ORG', 'L-ORG', 'O', 'B-ORG', 'L-ORG', 'O', 'O', 'O', 'O', 'B-DATE', 'L-DATE', 'O', 'O', 'O', 'O', 'O', 'B-DATE', 'L-DATE', 'O', 'O', 'O', 'O', 'O', 'B-PERCENT', 'L-PERCENT', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'B-PERCENT', 'L-PERCENT', 'O', 'U-CARDINAL', 'O', 'O', 'B-DATE', 'I-DATE', 'L-DATE', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O', 'O']
# fmt: on
doc = Doc(nlp.vocab, words=tokens)
example = Example.from_dict(doc, {"ner": iob})
neg_span = Span(doc, 50, 53, "ORG")
example.reference.spans[neg_key] = [neg_span]
optimizer = nlp.initialize()
for i in range(5):
losses = {}
nlp.update([example], sgd=optimizer, losses=losses)
assert "beam_ner" in losses
def test_ner_warns_no_lookups(caplog):
nlp = English()
assert nlp.lang in util.LEXEME_NORM_LANGS
nlp.vocab.lookups = Lookups()
assert not len(nlp.vocab.lookups)
nlp.add_pipe("ner")
with caplog.at_level(logging.DEBUG):
nlp.initialize()
assert "W033" in caplog.text
caplog.clear()
nlp.vocab.lookups.add_table("lexeme_norm")
nlp.vocab.lookups.get_table("lexeme_norm")["a"] = "A"
with caplog.at_level(logging.DEBUG):
nlp.initialize()
assert "W033" not in caplog.text
@Language.factory("blocker")
class BlockerComponent1:
def __init__(self, nlp, start, end, name="my_blocker"):
self.start = start
self.end = end
self.name = name
def __call__(self, doc):
doc.set_ents([], blocked=[doc[self.start : self.end]], default="unmodified")
return doc