From 7bc3eb2c7dfe3dd170fbed7c5de678f1183c8868 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Sol=C3=A8ne=20Tarride?= <starride@teklia.com>
Date: Mon, 16 Dec 2024 11:02:21 +0100
Subject: [PATCH] Fix lint & tests
---
bio_parser/parse/nested_document.py | 31 +++++----
tests/fixtures/parse/valid_nested.bio | 2 +-
tests/parse/test_nested_document.py | 97 +++++++++++++++++----------
3 files changed, 79 insertions(+), 51 deletions(-)
diff --git a/bio_parser/parse/nested_document.py b/bio_parser/parse/nested_document.py
index 3174959..5e497cc 100644
--- a/bio_parser/parse/nested_document.py
+++ b/bio_parser/parse/nested_document.py
@@ -2,12 +2,14 @@
import logging
import re
from dataclasses import dataclass, field
-from itertools import pairwise
from operator import attrgetter
from pathlib import Path
-from bio_parser.parse.document import Token, Tag, Span
-PARSE_BIO_LINE = re.compile(r"(?P<text>[^\s]+)\s+(?P<labels>(?:[^\s]+(?:\-[^\s]+)?\s*)+)")
+from bio_parser.parse.document import Span, Tag, Token
+
+PARSE_BIO_LINE = re.compile(
+ r"(?P<text>[^\s]+)\s+(?P<labels>(?:[^\s]+(?:\-[^\s]+)?\s*)+)"
+)
"""Regex that parses a line of a BIO file"""
@@ -60,7 +62,7 @@ class NestedToken:
["child", "name"]
"""
return [token.label for token in self.tokens]
-
+
@property
def tags(self) -> list[Tag]:
"""IOB tags of named entity tag.
@@ -70,7 +72,7 @@ class NestedToken:
[<Tag.BEGINNING: 'B'>, <Tag.BEGINNING: 'B'>]
"""
return [token.tag for token in self.tokens]
-
+
@property
def iob_labels(self) -> list[str]:
"""IOB label (Tag + Entity).
@@ -118,7 +120,7 @@ class NestedDocument:
def __post_init__(self):
"""Parses the tokens and the entity spans in the document."""
- current_spans : dict[str, Span] = {} # Keep track of current spans by category
+ current_spans: dict[str, Span] = {} # Keep track of current spans by category
for idx, line in enumerate(self.bio_repr.splitlines()):
try:
nested_token = NestedToken(idx=idx, text=line)
@@ -134,12 +136,11 @@ class NestedDocument:
current_spans = {}
case Tag.INSIDE:
- if token.label in current_spans:
- # Continue current span
- current_spans[token.label].add_token(token)
-
- else:
- Exception, f"Found `{Tag.INSIDE}` before `{Tag.BEGINNING}`."
+ assert (
+ token.label in current_spans
+ ), f"Found `{Tag.INSIDE}` before `{Tag.BEGINNING}`."
+ # Continue current span
+ current_spans[token.label].add_token(token)
case Tag.BEGINNING:
# End existing span if necessary
@@ -175,7 +176,10 @@ class NestedDocument:
def word_entities(self) -> list[tuple[str, str]]:
"""List of entities in the words making up the document."""
return list(
- map(attrgetter("labels", "word"), filter(lambda x: x.labels[0] != None, self.nested_tokens)),
+ map(
+ attrgetter("labels", "word"),
+ filter(lambda x: x.labels[0] is not None, self.nested_tokens),
+ ),
)
@property
@@ -183,7 +187,6 @@ class NestedDocument:
"""Join every word of the span by a whitespace."""
return " ".join(map(attrgetter("word"), self.nested_tokens))
-
@property
def chars(self) -> list[str]:
r"""Characters making up the token.
diff --git a/tests/fixtures/parse/valid_nested.bio b/tests/fixtures/parse/valid_nested.bio
index 0064313..3d44c55 100644
--- a/tests/fixtures/parse/valid_nested.bio
+++ b/tests/fixtures/parse/valid_nested.bio
@@ -1,6 +1,6 @@
Charles B-child B-name
né I-child
-Ã I-child
+Ã I-child
Beaune I-child B-location
en I-child
1836 I-child B-date
diff --git a/tests/parse/test_nested_document.py b/tests/parse/test_nested_document.py
index d2474e4..658b775 100644
--- a/tests/parse/test_nested_document.py
+++ b/tests/parse/test_nested_document.py
@@ -1,5 +1,5 @@
import pytest
-from bio_parser.parse.document import Document, Span, Tag, Token
+from bio_parser.parse.document import Tag
from bio_parser.parse.nested_document import NestedDocument, NestedToken
from tests.parse import DATA_DIR
@@ -14,41 +14,61 @@ def nested_document() -> NestedDocument:
def test_parse_document(nested_document: NestedDocument):
# Check words
- assert nested_document.words == ["Charles", "né", "à ", "Beaune", "en", "1836", "père", "Jean", "Bigre", "charpentier", "de", "cette", "paroisse", "mère", "Marie"]
+ assert nested_document.words == [
+ "Charles",
+ "né",
+ "Ã ",
+ "Beaune",
+ "en",
+ "1836",
+ "père",
+ "Jean",
+ "Bigre",
+ "charpentier",
+ "de",
+ "cette",
+ "paroisse",
+ "mère",
+ "Marie",
+ ]
# Check entities
assert nested_document.entities == [
- ("child", "Charles né à Beaune en 1836"),
- ("name", "Charles"),
- ("location", "Beaune"),
- ("date", "1836"),
- ("father", "Jean Bigre charpentier de cette paroisse"),
+ ("child", "Charles né à Beaune en 1836"),
+ ("name", "Charles"),
+ ("location", "Beaune"),
+ ("date", "1836"),
+ ("father", "Jean Bigre charpentier de cette paroisse"),
("name", "Jean"),
- ("surname", "Bigre"),
- ("occupation", "charpentier"),
- ("location", "cette paroisse"),
- ("mother", "Marie"),
- ("name", "Marie")]
+ ("surname", "Bigre"),
+ ("occupation", "charpentier"),
+ ("location", "cette paroisse"),
+ ("mother", "Marie"),
+ ("name", "Marie"),
+ ]
# Check word entities
assert nested_document.word_entities == [
- (["child", "name"], "Charles"),
- (["child"], "né"),
- (["child"], "Ã "),
- (["child", "location"], "Beaune"),
- (["child"], "en"),
- (["child", "date"], "1836"),
- (["father", "name"], "Jean"),
- (["father", "surname"], "Bigre"),
- (["father", "occupation"], "charpentier"),
- (["father"], "de"),
- (["father", "location"], "cette"),
- (["father", "location"], "paroisse"),
- (["mother", "name"], "Marie")
- ]
+ (["child", "name"], "Charles"),
+ (["child"], "né"),
+ (["child"], "Ã "),
+ (["child", "location"], "Beaune"),
+ (["child"], "en"),
+ (["child", "date"], "1836"),
+ (["father", "name"], "Jean"),
+ (["father", "surname"], "Bigre"),
+ (["father", "occupation"], "charpentier"),
+ (["father"], "de"),
+ (["father", "location"], "cette"),
+ (["father", "location"], "paroisse"),
+ (["mother", "name"], "Marie"),
+ ]
# Check text
- assert nested_document.text == "Charles né à Beaune en 1836 père Jean Bigre charpentier de cette paroisse mère Marie"
+ assert (
+ nested_document.text
+ == "Charles né à Beaune en 1836 père Jean Bigre charpentier de cette paroisse mère Marie"
+ )
# Check chars
assert nested_document.chars == list(
@@ -56,7 +76,6 @@ def test_parse_document(nested_document: NestedDocument):
)
-
def test_parse_nested_token(nested_document: NestedDocument):
nested_token: NestedToken = nested_document.nested_tokens[0]
@@ -74,9 +93,9 @@ def test_parse_nested_token(nested_document: NestedDocument):
# Check labels
assert nested_token.char_labels == [
- ['B-child', 'I-child', 'I-child', 'I-child', 'I-child', 'I-child', 'I-child'],
- ['B-name', 'I-name', 'I-name', 'I-name', 'I-name', 'I-name', 'I-name']
- ]
+ ["B-child", "I-child", "I-child", "I-child", "I-child", "I-child", "I-child"],
+ ["B-name", "I-name", "I-name", "I-name", "I-name", "I-name", "I-name"],
+ ]
# Check chars
assert nested_token.chars == ["C", "h", "a", "r", "l", "e", "s"]
@@ -98,9 +117,16 @@ def test_parse_nested_token(nested_document: NestedDocument):
# Check labels
assert nested_token.char_labels == [
- ['I-child', 'I-child', 'I-child', 'I-child', 'I-child', 'I-child'],
- ['B-location', 'I-location', 'I-location', 'I-location', 'I-location', 'I-location']
- ]
+ ["I-child", "I-child", "I-child", "I-child", "I-child", "I-child"],
+ [
+ "B-location",
+ "I-location",
+ "I-location",
+ "I-location",
+ "I-location",
+ "I-location",
+ ],
+ ]
# Check chars
assert nested_token.chars == ["B", "e", "a", "u", "n", "e"]
@@ -121,8 +147,7 @@ def test_parse_nested_token(nested_document: NestedDocument):
assert nested_token.iob_labels == ["O"]
# Check labels
- assert nested_token.char_labels == [['O', 'O', 'O', 'O']]
+ assert nested_token.char_labels == [["O", "O", "O", "O"]]
# Check chars
assert nested_token.chars == ["m", "è", "r", "e"]
-
--
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