mirror of
https://github.com/explosion/spaCy.git
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e2b70df012
* Use isort with Black profile * isort all the things * Fix import cycles as a result of import sorting * Add DOCBIN_ALL_ATTRS type definition * Add isort to requirements * Remove isort from build dependencies check * Typo
542 lines
21 KiB
Python
542 lines
21 KiB
Python
import warnings
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from collections import defaultdict
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from pathlib import Path
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from typing import Any, Callable, Dict, Iterable, List, Optional, Sequence, Tuple, Union
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import srsly
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from ..errors import Errors, Warnings
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from ..language import Language
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from ..matcher import Matcher, PhraseMatcher
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from ..matcher.levenshtein import levenshtein_compare
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from ..scorer import get_ner_prf
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from ..tokens import Doc, Span
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from ..training import Example
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from ..util import SimpleFrozenList, ensure_path, from_disk, registry, to_disk
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from .pipe import Pipe
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DEFAULT_ENT_ID_SEP = "||"
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PatternType = Dict[str, Union[str, List[Dict[str, Any]]]]
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@Language.factory(
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"entity_ruler",
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assigns=["doc.ents", "token.ent_type", "token.ent_iob"],
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default_config={
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"phrase_matcher_attr": None,
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"matcher_fuzzy_compare": {"@misc": "spacy.levenshtein_compare.v1"},
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"validate": False,
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"overwrite_ents": False,
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"ent_id_sep": DEFAULT_ENT_ID_SEP,
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"scorer": {"@scorers": "spacy.entity_ruler_scorer.v1"},
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},
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default_score_weights={
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"ents_f": 1.0,
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"ents_p": 0.0,
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"ents_r": 0.0,
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"ents_per_type": None,
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},
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)
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def make_entity_ruler(
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nlp: Language,
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name: str,
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phrase_matcher_attr: Optional[Union[int, str]],
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matcher_fuzzy_compare: Callable,
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validate: bool,
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overwrite_ents: bool,
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ent_id_sep: str,
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scorer: Optional[Callable],
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):
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return EntityRuler(
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nlp,
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name,
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phrase_matcher_attr=phrase_matcher_attr,
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matcher_fuzzy_compare=matcher_fuzzy_compare,
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validate=validate,
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overwrite_ents=overwrite_ents,
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ent_id_sep=ent_id_sep,
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scorer=scorer,
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)
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def entity_ruler_score(examples, **kwargs):
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return get_ner_prf(examples)
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@registry.scorers("spacy.entity_ruler_scorer.v1")
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def make_entity_ruler_scorer():
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return entity_ruler_score
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class EntityRuler(Pipe):
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"""The EntityRuler lets you add spans to the `Doc.ents` using token-based
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rules or exact phrase matches. It can be combined with the statistical
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`EntityRecognizer` to boost accuracy, or used on its own to implement a
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purely rule-based entity recognition system. After initialization, the
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component is typically added to the pipeline using `nlp.add_pipe`.
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DOCS: https://spacy.io/api/entityruler
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USAGE: https://spacy.io/usage/rule-based-matching#entityruler
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"""
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def __init__(
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self,
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nlp: Language,
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name: str = "entity_ruler",
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*,
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phrase_matcher_attr: Optional[Union[int, str]] = None,
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matcher_fuzzy_compare: Callable = levenshtein_compare,
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validate: bool = False,
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overwrite_ents: bool = False,
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ent_id_sep: str = DEFAULT_ENT_ID_SEP,
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patterns: Optional[List[PatternType]] = None,
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scorer: Optional[Callable] = entity_ruler_score,
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) -> None:
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"""Initialize the entity ruler. If patterns are supplied here, they
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need to be a list of dictionaries with a `"label"` and `"pattern"`
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key. A pattern can either be a token pattern (list) or a phrase pattern
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(string). For example: `{'label': 'ORG', 'pattern': 'Apple'}`.
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nlp (Language): The shared nlp object to pass the vocab to the matchers
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and process phrase patterns.
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name (str): Instance name of the current pipeline component. Typically
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passed in automatically from the factory when the component is
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added. Used to disable the current entity ruler while creating
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phrase patterns with the nlp object.
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phrase_matcher_attr (int / str): Token attribute to match on, passed
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to the internal PhraseMatcher as `attr`.
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matcher_fuzzy_compare (Callable): The fuzzy comparison method for the
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internal Matcher. Defaults to
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spacy.matcher.levenshtein.levenshtein_compare.
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validate (bool): Whether patterns should be validated, passed to
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Matcher and PhraseMatcher as `validate`
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patterns (iterable): Optional patterns to load in.
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overwrite_ents (bool): If existing entities are present, e.g. entities
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added by the model, overwrite them by matches if necessary.
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ent_id_sep (str): Separator used internally for entity IDs.
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scorer (Optional[Callable]): The scoring method. Defaults to
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spacy.scorer.get_ner_prf.
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DOCS: https://spacy.io/api/entityruler#init
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"""
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self.nlp = nlp
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self.name = name
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self.overwrite = overwrite_ents
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self.token_patterns = defaultdict(list) # type: ignore
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self.phrase_patterns = defaultdict(list) # type: ignore
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self._validate = validate
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self.matcher_fuzzy_compare = matcher_fuzzy_compare
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self.matcher = Matcher(
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nlp.vocab, validate=validate, fuzzy_compare=self.matcher_fuzzy_compare
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)
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self.phrase_matcher_attr = phrase_matcher_attr
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self.phrase_matcher = PhraseMatcher(
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nlp.vocab, attr=self.phrase_matcher_attr, validate=validate
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)
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self.ent_id_sep = ent_id_sep
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self._ent_ids = defaultdict(tuple) # type: ignore
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if patterns is not None:
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self.add_patterns(patterns)
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self.scorer = scorer
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def __len__(self) -> int:
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"""The number of all patterns added to the entity ruler."""
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n_token_patterns = sum(len(p) for p in self.token_patterns.values())
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n_phrase_patterns = sum(len(p) for p in self.phrase_patterns.values())
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return n_token_patterns + n_phrase_patterns
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def __contains__(self, label: str) -> bool:
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"""Whether a label is present in the patterns."""
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return label in self.token_patterns or label in self.phrase_patterns
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def __call__(self, doc: Doc) -> Doc:
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"""Find matches in document and add them as entities.
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doc (Doc): The Doc object in the pipeline.
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RETURNS (Doc): The Doc with added entities, if available.
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DOCS: https://spacy.io/api/entityruler#call
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"""
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error_handler = self.get_error_handler()
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try:
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matches = self.match(doc)
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self.set_annotations(doc, matches)
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return doc
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except Exception as e:
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return error_handler(self.name, self, [doc], e)
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def match(self, doc: Doc):
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self._require_patterns()
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with warnings.catch_warnings():
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warnings.filterwarnings("ignore", message="\\[W036")
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matches = list(self.matcher(doc)) + list(self.phrase_matcher(doc))
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final_matches = set(
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[(m_id, start, end) for m_id, start, end in matches if start != end]
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)
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get_sort_key = lambda m: (m[2] - m[1], -m[1])
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final_matches = sorted(final_matches, key=get_sort_key, reverse=True)
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return final_matches
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def set_annotations(self, doc, matches):
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"""Modify the document in place"""
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entities = list(doc.ents)
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new_entities = []
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seen_tokens = set()
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for match_id, start, end in matches:
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if any(t.ent_type for t in doc[start:end]) and not self.overwrite:
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continue
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# check for end - 1 here because boundaries are inclusive
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if start not in seen_tokens and end - 1 not in seen_tokens:
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if match_id in self._ent_ids:
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label, ent_id = self._ent_ids[match_id]
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span = Span(doc, start, end, label=label, span_id=ent_id)
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else:
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span = Span(doc, start, end, label=match_id)
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new_entities.append(span)
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entities = [
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e for e in entities if not (e.start < end and e.end > start)
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]
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seen_tokens.update(range(start, end))
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doc.ents = entities + new_entities
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@property
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def labels(self) -> Tuple[str, ...]:
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"""All labels present in the match patterns.
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RETURNS (set): The string labels.
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DOCS: https://spacy.io/api/entityruler#labels
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"""
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keys = set(self.token_patterns.keys())
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keys.update(self.phrase_patterns.keys())
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all_labels = set()
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for l in keys:
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if self.ent_id_sep in l:
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label, _ = self._split_label(l)
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all_labels.add(label)
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else:
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all_labels.add(l)
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return tuple(sorted(all_labels))
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def initialize(
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self,
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get_examples: Callable[[], Iterable[Example]],
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*,
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nlp: Optional[Language] = None,
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patterns: Optional[Sequence[PatternType]] = None,
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):
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"""Initialize the pipe for training.
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get_examples (Callable[[], Iterable[Example]]): Function that
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returns a representative sample of gold-standard Example objects.
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nlp (Language): The current nlp object the component is part of.
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patterns Optional[Iterable[PatternType]]: The list of patterns.
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DOCS: https://spacy.io/api/entityruler#initialize
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"""
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self.clear()
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if patterns:
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self.add_patterns(patterns) # type: ignore[arg-type]
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@property
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def ent_ids(self) -> Tuple[Optional[str], ...]:
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"""All entity ids present in the match patterns `id` properties
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RETURNS (set): The string entity ids.
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DOCS: https://spacy.io/api/entityruler#ent_ids
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"""
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keys = set(self.token_patterns.keys())
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keys.update(self.phrase_patterns.keys())
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all_ent_ids = set()
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for l in keys:
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if self.ent_id_sep in l:
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_, ent_id = self._split_label(l)
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all_ent_ids.add(ent_id)
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return tuple(all_ent_ids)
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@property
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def patterns(self) -> List[PatternType]:
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"""Get all patterns that were added to the entity ruler.
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RETURNS (list): The original patterns, one dictionary per pattern.
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DOCS: https://spacy.io/api/entityruler#patterns
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"""
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all_patterns = []
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for label, patterns in self.token_patterns.items():
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for pattern in patterns:
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ent_label, ent_id = self._split_label(label)
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p = {"label": ent_label, "pattern": pattern}
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if ent_id:
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p["id"] = ent_id
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all_patterns.append(p)
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for label, patterns in self.phrase_patterns.items():
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for pattern in patterns:
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ent_label, ent_id = self._split_label(label)
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p = {"label": ent_label, "pattern": pattern.text}
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if ent_id:
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p["id"] = ent_id
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all_patterns.append(p)
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return all_patterns
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def add_patterns(self, patterns: List[PatternType]) -> None:
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"""Add patterns to the entity ruler. A pattern can either be a token
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pattern (list of dicts) or a phrase pattern (string). For example:
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{'label': 'ORG', 'pattern': 'Apple'}
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{'label': 'GPE', 'pattern': [{'lower': 'san'}, {'lower': 'francisco'}]}
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patterns (list): The patterns to add.
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DOCS: https://spacy.io/api/entityruler#add_patterns
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"""
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# disable the nlp components after this one in case they hadn't been initialized / deserialised yet
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try:
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current_index = -1
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for i, (name, pipe) in enumerate(self.nlp.pipeline):
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if self == pipe:
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current_index = i
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break
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subsequent_pipes = [pipe for pipe in self.nlp.pipe_names[current_index:]]
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except ValueError:
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subsequent_pipes = []
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with self.nlp.select_pipes(disable=subsequent_pipes):
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token_patterns = []
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phrase_pattern_labels = []
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phrase_pattern_texts = []
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phrase_pattern_ids = []
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for entry in patterns:
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if isinstance(entry["pattern"], str):
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phrase_pattern_labels.append(entry["label"])
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phrase_pattern_texts.append(entry["pattern"])
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phrase_pattern_ids.append(entry.get("id"))
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elif isinstance(entry["pattern"], list):
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token_patterns.append(entry)
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phrase_patterns = []
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for label, pattern, ent_id in zip(
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phrase_pattern_labels,
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self.nlp.pipe(phrase_pattern_texts),
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phrase_pattern_ids,
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):
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phrase_pattern = {"label": label, "pattern": pattern}
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if ent_id:
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phrase_pattern["id"] = ent_id
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phrase_patterns.append(phrase_pattern)
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for entry in token_patterns + phrase_patterns: # type: ignore[operator]
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label = entry["label"] # type: ignore
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if "id" in entry:
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ent_label = label
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label = self._create_label(label, entry["id"])
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key = self.matcher._normalize_key(label)
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self._ent_ids[key] = (ent_label, entry["id"])
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pattern = entry["pattern"] # type: ignore
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if isinstance(pattern, Doc):
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self.phrase_patterns[label].append(pattern)
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self.phrase_matcher.add(label, [pattern]) # type: ignore
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elif isinstance(pattern, list):
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self.token_patterns[label].append(pattern)
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self.matcher.add(label, [pattern])
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else:
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raise ValueError(Errors.E097.format(pattern=pattern))
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def clear(self) -> None:
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"""Reset all patterns."""
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self.token_patterns = defaultdict(list)
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self.phrase_patterns = defaultdict(list)
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self._ent_ids = defaultdict(tuple)
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self.matcher = Matcher(
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self.nlp.vocab,
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validate=self._validate,
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fuzzy_compare=self.matcher_fuzzy_compare,
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)
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self.phrase_matcher = PhraseMatcher(
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self.nlp.vocab, attr=self.phrase_matcher_attr, validate=self._validate
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)
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def remove(self, ent_id: str) -> None:
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"""Remove a pattern by its ent_id if a pattern with this ent_id was added before
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ent_id (str): id of the pattern to be removed
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RETURNS: None
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DOCS: https://spacy.io/api/entityruler#remove
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"""
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label_id_pairs = [
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(label, eid) for (label, eid) in self._ent_ids.values() if eid == ent_id
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]
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if not label_id_pairs:
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raise ValueError(
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Errors.E1024.format(attr_type="ID", label=ent_id, component=self.name)
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)
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created_labels = [
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self._create_label(label, eid) for (label, eid) in label_id_pairs
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]
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# remove the patterns from self.phrase_patterns
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self.phrase_patterns = defaultdict(
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list,
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{
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label: val
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for (label, val) in self.phrase_patterns.items()
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if label not in created_labels
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},
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)
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# remove the patterns from self.token_pattern
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self.token_patterns = defaultdict(
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list,
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{
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label: val
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for (label, val) in self.token_patterns.items()
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if label not in created_labels
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},
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)
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# remove the patterns from self.token_pattern
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for label in created_labels:
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if label in self.phrase_matcher:
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self.phrase_matcher.remove(label)
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else:
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self.matcher.remove(label)
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def _require_patterns(self) -> None:
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"""Raise a warning if this component has no patterns defined."""
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if len(self) == 0:
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warnings.warn(Warnings.W036.format(name=self.name))
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def _split_label(self, label: str) -> Tuple[str, Optional[str]]:
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"""Split Entity label into ent_label and ent_id if it contains self.ent_id_sep
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label (str): The value of label in a pattern entry
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RETURNS (tuple): ent_label, ent_id
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"""
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if self.ent_id_sep in label:
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ent_label, ent_id = label.rsplit(self.ent_id_sep, 1)
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else:
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ent_label = label
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ent_id = None # type: ignore
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return ent_label, ent_id
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def _create_label(self, label: Any, ent_id: Any) -> str:
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"""Join Entity label with ent_id if the pattern has an `id` attribute
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If ent_id is not a string, the label is returned as is.
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label (str): The label to set for ent.label_
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ent_id (str): The label
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RETURNS (str): The ent_label joined with configured `ent_id_sep`
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"""
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if isinstance(ent_id, str):
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label = f"{label}{self.ent_id_sep}{ent_id}"
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return label
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def from_bytes(
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self, patterns_bytes: bytes, *, exclude: Iterable[str] = SimpleFrozenList()
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) -> "EntityRuler":
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"""Load the entity ruler from a bytestring.
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patterns_bytes (bytes): The bytestring to load.
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RETURNS (EntityRuler): The loaded entity ruler.
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DOCS: https://spacy.io/api/entityruler#from_bytes
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"""
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cfg = srsly.msgpack_loads(patterns_bytes)
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self.clear()
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if isinstance(cfg, dict):
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self.add_patterns(cfg.get("patterns", cfg))
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self.overwrite = cfg.get("overwrite", False)
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self.phrase_matcher_attr = cfg.get("phrase_matcher_attr", None)
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self.phrase_matcher = PhraseMatcher(
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self.nlp.vocab,
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attr=self.phrase_matcher_attr,
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)
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self.ent_id_sep = cfg.get("ent_id_sep", DEFAULT_ENT_ID_SEP)
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else:
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self.add_patterns(cfg)
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return self
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def to_bytes(self, *, exclude: Iterable[str] = SimpleFrozenList()) -> bytes:
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"""Serialize the entity ruler patterns to a bytestring.
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RETURNS (bytes): The serialized patterns.
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DOCS: https://spacy.io/api/entityruler#to_bytes
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"""
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serial = {
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"overwrite": self.overwrite,
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"ent_id_sep": self.ent_id_sep,
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"phrase_matcher_attr": self.phrase_matcher_attr,
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"patterns": self.patterns,
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}
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return srsly.msgpack_dumps(serial)
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def from_disk(
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self, path: Union[str, Path], *, exclude: Iterable[str] = SimpleFrozenList()
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) -> "EntityRuler":
|
|
"""Load the entity ruler from a file. Expects a file containing
|
|
newline-delimited JSON (JSONL) with one entry per line.
|
|
|
|
path (str / Path): The JSONL file to load.
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|
RETURNS (EntityRuler): The loaded entity ruler.
|
|
|
|
DOCS: https://spacy.io/api/entityruler#from_disk
|
|
"""
|
|
path = ensure_path(path)
|
|
self.clear()
|
|
depr_patterns_path = path.with_suffix(".jsonl")
|
|
if path.suffix == ".jsonl": # user provides a jsonl
|
|
if path.is_file:
|
|
patterns = srsly.read_jsonl(path)
|
|
self.add_patterns(patterns)
|
|
else:
|
|
raise ValueError(Errors.E1023.format(path=path))
|
|
elif depr_patterns_path.is_file():
|
|
patterns = srsly.read_jsonl(depr_patterns_path)
|
|
self.add_patterns(patterns)
|
|
elif path.is_dir(): # path is a valid directory
|
|
cfg = {}
|
|
deserializers_patterns = {
|
|
"patterns": lambda p: self.add_patterns(
|
|
srsly.read_jsonl(p.with_suffix(".jsonl"))
|
|
)
|
|
}
|
|
deserializers_cfg = {"cfg": lambda p: cfg.update(srsly.read_json(p))}
|
|
from_disk(path, deserializers_cfg, {})
|
|
self.overwrite = cfg.get("overwrite", False)
|
|
self.phrase_matcher_attr = cfg.get("phrase_matcher_attr")
|
|
self.ent_id_sep = cfg.get("ent_id_sep", DEFAULT_ENT_ID_SEP)
|
|
|
|
self.phrase_matcher = PhraseMatcher(
|
|
self.nlp.vocab, attr=self.phrase_matcher_attr
|
|
)
|
|
from_disk(path, deserializers_patterns, {})
|
|
else: # path is not a valid directory or file
|
|
raise ValueError(Errors.E146.format(path=path))
|
|
return self
|
|
|
|
def to_disk(
|
|
self, path: Union[str, Path], *, exclude: Iterable[str] = SimpleFrozenList()
|
|
) -> None:
|
|
"""Save the entity ruler patterns to a directory. The patterns will be
|
|
saved as newline-delimited JSON (JSONL).
|
|
|
|
path (str / Path): The JSONL file to save.
|
|
|
|
DOCS: https://spacy.io/api/entityruler#to_disk
|
|
"""
|
|
path = ensure_path(path)
|
|
cfg = {
|
|
"overwrite": self.overwrite,
|
|
"phrase_matcher_attr": self.phrase_matcher_attr,
|
|
"ent_id_sep": self.ent_id_sep,
|
|
}
|
|
serializers = {
|
|
"patterns": lambda p: srsly.write_jsonl(
|
|
p.with_suffix(".jsonl"), self.patterns
|
|
),
|
|
"cfg": lambda p: srsly.write_json(p, cfg),
|
|
}
|
|
if path.suffix == ".jsonl": # user wants to save only JSONL
|
|
srsly.write_jsonl(path, self.patterns)
|
|
else:
|
|
to_disk(path, serializers, {})
|