from spacy.errors import AlignmentError from spacy.gold import biluo_tags_from_offsets, offsets_from_biluo_tags from spacy.gold import spans_from_biluo_tags, GoldParse, iob_to_biluo, align from spacy.gold import GoldCorpus, docs_to_json, Example, DocAnnotation from spacy.lang.en import English from spacy.syntax.nonproj import is_nonproj_tree from spacy.tokens import Doc from spacy.util import compounding, minibatch from .util import make_tempdir import pytest import srsly @pytest.fixture def doc(): text = "Sarah's sister flew to Silicon Valley via London." tags = ["NNP", "POS", "NN", "VBD", "IN", "NNP", "NNP", "IN", "NNP", "."] pos = [ "PROPN", "PART", "NOUN", "VERB", "ADP", "PROPN", "PROPN", "ADP", "PROPN", "PUNCT", ] morphs = [ "NounType=prop|Number=sing", "Poss=yes", "Number=sing", "Tense=past|VerbForm=fin", "", "NounType=prop|Number=sing", "NounType=prop|Number=sing", "", "NounType=prop|Number=sing", "PunctType=peri", ] # head of '.' is intentionally nonprojective for testing heads = [2, 0, 3, 3, 3, 6, 4, 3, 7, 5] deps = [ "poss", "case", "nsubj", "ROOT", "prep", "compound", "pobj", "prep", "pobj", "punct", ] lemmas = [ "Sarah", "'s", "sister", "fly", "to", "Silicon", "Valley", "via", "London", ".", ] biluo_tags = ["U-PERSON", "O", "O", "O", "O", "B-LOC", "L-LOC", "O", "U-GPE", "O"] cats = {"TRAVEL": 1.0, "BAKING": 0.0} nlp = English() doc = nlp(text) for i in range(len(tags)): doc[i].tag_ = tags[i] doc[i].pos_ = pos[i] doc[i].morph_ = morphs[i] doc[i].lemma_ = lemmas[i] doc[i].dep_ = deps[i] doc[i].head = doc[heads[i]] doc.ents = spans_from_biluo_tags(doc, biluo_tags) doc.cats = cats doc.is_tagged = True doc.is_parsed = True return doc @pytest.fixture() def merged_dict(): return { "ids": [1, 2, 3, 4, 5, 6, 7], "words": ["Hi", "there", "everyone", "It", "is", "just", "me"], "tags": ["INTJ", "ADV", "PRON", "PRON", "AUX", "ADV", "PRON"], "sent_starts": [1, 0, 0, 1, 0, 0, 0, 0], } def test_gold_biluo_U(en_vocab): words = ["I", "flew", "to", "London", "."] spaces = [True, True, True, False, True] doc = Doc(en_vocab, words=words, spaces=spaces) entities = [(len("I flew to "), len("I flew to London"), "LOC")] tags = biluo_tags_from_offsets(doc, entities) assert tags == ["O", "O", "O", "U-LOC", "O"] def test_gold_biluo_BL(en_vocab): words = ["I", "flew", "to", "San", "Francisco", "."] spaces = [True, True, True, True, False, True] doc = Doc(en_vocab, words=words, spaces=spaces) entities = [(len("I flew to "), len("I flew to San Francisco"), "LOC")] tags = biluo_tags_from_offsets(doc, entities) assert tags == ["O", "O", "O", "B-LOC", "L-LOC", "O"] def test_gold_biluo_BIL(en_vocab): words = ["I", "flew", "to", "San", "Francisco", "Valley", "."] spaces = [True, True, True, True, True, False, True] doc = Doc(en_vocab, words=words, spaces=spaces) entities = [(len("I flew to "), len("I flew to San Francisco Valley"), "LOC")] tags = biluo_tags_from_offsets(doc, entities) assert tags == ["O", "O", "O", "B-LOC", "I-LOC", "L-LOC", "O"] def test_gold_biluo_overlap(en_vocab): words = ["I", "flew", "to", "San", "Francisco", "Valley", "."] spaces = [True, True, True, True, True, False, True] doc = Doc(en_vocab, words=words, spaces=spaces) entities = [ (len("I flew to "), len("I flew to San Francisco Valley"), "LOC"), (len("I flew to "), len("I flew to San Francisco"), "LOC"), ] with pytest.raises(ValueError): biluo_tags_from_offsets(doc, entities) def test_gold_biluo_misalign(en_vocab): words = ["I", "flew", "to", "San", "Francisco", "Valley."] spaces = [True, True, True, True, True, False] doc = Doc(en_vocab, words=words, spaces=spaces) entities = [(len("I flew to "), len("I flew to San Francisco Valley"), "LOC")] tags = biluo_tags_from_offsets(doc, entities) assert tags == ["O", "O", "O", "-", "-", "-"] def test_roundtrip_offsets_biluo_conversion(en_tokenizer): text = "I flew to Silicon Valley via London." biluo_tags = ["O", "O", "O", "B-LOC", "L-LOC", "O", "U-GPE", "O"] offsets = [(10, 24, "LOC"), (29, 35, "GPE")] doc = en_tokenizer(text) biluo_tags_converted = biluo_tags_from_offsets(doc, offsets) assert biluo_tags_converted == biluo_tags offsets_converted = offsets_from_biluo_tags(doc, biluo_tags) assert offsets_converted == offsets def test_biluo_spans(en_tokenizer): doc = en_tokenizer("I flew to Silicon Valley via London.") biluo_tags = ["O", "O", "O", "B-LOC", "L-LOC", "O", "U-GPE", "O"] spans = spans_from_biluo_tags(doc, biluo_tags) assert len(spans) == 2 assert spans[0].text == "Silicon Valley" assert spans[0].label_ == "LOC" assert spans[1].text == "London" assert spans[1].label_ == "GPE" def test_gold_ner_missing_tags(en_tokenizer): doc = en_tokenizer("I flew to Silicon Valley via London.") biluo_tags = [None, "O", "O", "B-LOC", "L-LOC", "O", "U-GPE", "O"] gold = GoldParse(doc, entities=biluo_tags) # noqa: F841 def test_iob_to_biluo(): good_iob = ["O", "O", "B-LOC", "I-LOC", "O", "B-PERSON"] good_biluo = ["O", "O", "B-LOC", "L-LOC", "O", "U-PERSON"] bad_iob = ["O", "O", '"', "B-LOC", "I-LOC"] converted_biluo = iob_to_biluo(good_iob) assert good_biluo == converted_biluo with pytest.raises(ValueError): iob_to_biluo(bad_iob) def test_roundtrip_docs_to_json(doc): nlp = English() text = doc.text tags = [t.tag_ for t in doc] pos = [t.pos_ for t in doc] morphs = [t.morph_ for t in doc] lemmas = [t.lemma_ for t in doc] deps = [t.dep_ for t in doc] heads = [t.head.i for t in doc] biluo_tags = iob_to_biluo( [t.ent_iob_ + "-" + t.ent_type_ if t.ent_type_ else "O" for t in doc] ) cats = doc.cats # roundtrip to JSON with make_tempdir() as tmpdir: json_file = tmpdir / "roundtrip.json" srsly.write_json(json_file, [docs_to_json(doc)]) goldcorpus = GoldCorpus(train=str(json_file), dev=str(json_file)) reloaded_example = next(goldcorpus.dev_dataset(nlp)) goldparse = reloaded_example.gold assert len(doc) == goldcorpus.count_train() assert text == reloaded_example.text assert tags == goldparse.tags assert pos == goldparse.pos assert morphs == goldparse.morphs assert lemmas == goldparse.lemmas assert deps == goldparse.labels assert heads == goldparse.heads assert biluo_tags == goldparse.ner assert "TRAVEL" in goldparse.cats assert "BAKING" in goldparse.cats assert cats["TRAVEL"] == goldparse.cats["TRAVEL"] assert cats["BAKING"] == goldparse.cats["BAKING"] # roundtrip to JSONL train dicts with make_tempdir() as tmpdir: jsonl_file = tmpdir / "roundtrip.jsonl" srsly.write_jsonl(jsonl_file, [docs_to_json(doc)]) goldcorpus = GoldCorpus(str(jsonl_file), str(jsonl_file)) reloaded_example = next(goldcorpus.dev_dataset(nlp)) goldparse = reloaded_example.gold assert len(doc) == goldcorpus.count_train() assert text == reloaded_example.text assert tags == goldparse.tags assert pos == goldparse.pos assert morphs == goldparse.morphs assert lemmas == goldparse.lemmas assert deps == goldparse.labels assert heads == goldparse.heads assert biluo_tags == goldparse.ner assert "TRAVEL" in goldparse.cats assert "BAKING" in goldparse.cats assert cats["TRAVEL"] == goldparse.cats["TRAVEL"] assert cats["BAKING"] == goldparse.cats["BAKING"] # roundtrip to JSONL tuples with make_tempdir() as tmpdir: jsonl_file = tmpdir / "roundtrip.jsonl" # write to JSONL train dicts srsly.write_jsonl(jsonl_file, [docs_to_json(doc)]) goldcorpus = GoldCorpus(str(jsonl_file), str(jsonl_file)) # load and rewrite as JSONL tuples srsly.write_jsonl(jsonl_file, goldcorpus.train_examples) goldcorpus = GoldCorpus(str(jsonl_file), str(jsonl_file)) reloaded_example = next(goldcorpus.dev_dataset(nlp)) goldparse = reloaded_example.gold assert len(doc) == goldcorpus.count_train() assert text == reloaded_example.text assert tags == goldparse.tags assert deps == goldparse.labels assert heads == goldparse.heads assert lemmas == goldparse.lemmas assert biluo_tags == goldparse.ner assert "TRAVEL" in goldparse.cats assert "BAKING" in goldparse.cats assert cats["TRAVEL"] == goldparse.cats["TRAVEL"] assert cats["BAKING"] == goldparse.cats["BAKING"] def test_projective_train_vs_nonprojective_dev(doc): nlp = English() deps = [t.dep_ for t in doc] heads = [t.head.i for t in doc] with make_tempdir() as tmpdir: jsonl_file = tmpdir / "test.jsonl" # write to JSONL train dicts srsly.write_jsonl(jsonl_file, [docs_to_json(doc)]) goldcorpus = GoldCorpus(str(jsonl_file), str(jsonl_file)) train_reloaded_example = next(goldcorpus.train_dataset(nlp)) train_goldparse = train_reloaded_example.gold dev_reloaded_example = next(goldcorpus.dev_dataset(nlp)) dev_goldparse = dev_reloaded_example.gold assert is_nonproj_tree([t.head.i for t in doc]) is True assert is_nonproj_tree(train_goldparse.heads) is False assert heads[:-1] == train_goldparse.heads[:-1] assert heads[-1] != train_goldparse.heads[-1] assert deps[:-1] == train_goldparse.labels[:-1] assert deps[-1] != train_goldparse.labels[-1] assert heads == dev_goldparse.heads assert deps == dev_goldparse.labels def test_ignore_misaligned(doc): nlp = English() text = doc.text with make_tempdir() as tmpdir: jsonl_file = tmpdir / "test.jsonl" data = [docs_to_json(doc)] data[0]["paragraphs"][0]["raw"] = text.replace("Sarah", "Jane") # write to JSONL train dicts srsly.write_jsonl(jsonl_file, data) goldcorpus = GoldCorpus(str(jsonl_file), str(jsonl_file)) with pytest.raises(AlignmentError): train_reloaded_example = next(goldcorpus.train_dataset(nlp)) with make_tempdir() as tmpdir: jsonl_file = tmpdir / "test.jsonl" data = [docs_to_json(doc)] data[0]["paragraphs"][0]["raw"] = text.replace("Sarah", "Jane") # write to JSONL train dicts srsly.write_jsonl(jsonl_file, data) goldcorpus = GoldCorpus(str(jsonl_file), str(jsonl_file)) # doesn't raise an AlignmentError, but there is nothing to iterate over # because the only example can't be aligned train_reloaded_example = list(goldcorpus.train_dataset(nlp, ignore_misaligned=True)) assert len(train_reloaded_example) == 0 def test_make_orth_variants(doc): nlp = English() with make_tempdir() as tmpdir: jsonl_file = tmpdir / "test.jsonl" # write to JSONL train dicts srsly.write_jsonl(jsonl_file, [docs_to_json(doc)]) goldcorpus = GoldCorpus(str(jsonl_file), str(jsonl_file)) # due to randomness, test only that this runs with no errors for now train_reloaded_example = next(goldcorpus.train_dataset(nlp, orth_variant_level=0.2)) train_goldparse = train_reloaded_example.gold # noqa: F841 @pytest.mark.parametrize( "tokens_a,tokens_b,expected", [ (["a", "b", "c"], ["ab", "c"], (3, [-1, -1, 1], [-1, 2], {0: 0, 1: 0}, {})), ( ["a", "b", '"', "c"], ['ab"', "c"], (4, [-1, -1, -1, 1], [-1, 3], {0: 0, 1: 0, 2: 0}, {}), ), (["a", "bc"], ["ab", "c"], (4, [-1, -1], [-1, -1], {0: 0}, {1: 1})), ( ["ab", "c", "d"], ["a", "b", "cd"], (6, [-1, -1, -1], [-1, -1, -1], {1: 2, 2: 2}, {0: 0, 1: 0}), ), ( ["a", "b", "cd"], ["a", "b", "c", "d"], (3, [0, 1, -1], [0, 1, -1, -1], {}, {2: 2, 3: 2}), ), ([" ", "a"], ["a"], (1, [-1, 0], [1], {}, {})), ], ) def test_align(tokens_a, tokens_b, expected): cost, a2b, b2a, a2b_multi, b2a_multi = align(tokens_a, tokens_b) assert (cost, list(a2b), list(b2a), a2b_multi, b2a_multi) == expected # check symmetry cost, a2b, b2a, a2b_multi, b2a_multi = align(tokens_b, tokens_a) assert (cost, list(b2a), list(a2b), b2a_multi, a2b_multi) == expected def test_goldparse_startswith_space(en_tokenizer): text = " a" doc = en_tokenizer(text) g = GoldParse(doc, words=["a"], entities=["U-DATE"], deps=["ROOT"], heads=[0]) assert g.words == [" ", "a"] assert g.ner == [None, "U-DATE"] assert g.labels == [None, "ROOT"] def test_gold_constructor(): """Test that the GoldParse constructor works fine""" nlp = English() doc = nlp("This is a sentence") gold = GoldParse(doc, cats={"cat1": 1.0, "cat2": 0.0}) assert gold.cats["cat1"] assert not gold.cats["cat2"] assert gold.words == ["This", "is", "a", "sentence"] def test_gold_orig_annot(): nlp = English() doc = nlp("This is a sentence") gold = GoldParse(doc, cats={"cat1": 1.0, "cat2": 0.0}) assert gold.orig.words == ["This", "is", "a", "sentence"] assert gold.cats["cat1"] doc_annotation = DocAnnotation(cats={"cat1": 0.0, "cat2": 1.0}) gold2 = GoldParse.from_annotation(doc, doc_annotation, gold.orig) assert gold2.orig.words == ["This", "is", "a", "sentence"] assert not gold2.cats["cat1"] def test_tuple_format_implicit(): """Test tuple format with implicit GoldParse creation""" train_data = [ ("Uber blew through $1 million a week", {"entities": [(0, 4, "ORG")]}), ( "Spotify steps up Asia expansion", {"entities": [(0, 8, "ORG"), (17, 21, "LOC")]}, ), ("Google rebrands its business apps", {"entities": [(0, 6, "ORG")]}), ] _train(train_data) def test_tuple_format_implicit_invalid(): """Test that an error is thrown for an implicit invalid GoldParse field""" train_data = [ ("Uber blew through $1 million a week", {"frumble": [(0, 4, "ORG")]}), ( "Spotify steps up Asia expansion", {"entities": [(0, 8, "ORG"), (17, 21, "LOC")]}, ), ("Google rebrands its business apps", {"entities": [(0, 6, "ORG")]}), ] with pytest.raises(TypeError): _train(train_data) def _train(train_data): nlp = English() ner = nlp.create_pipe("ner") ner.add_label("ORG") ner.add_label("LOC") nlp.add_pipe(ner) optimizer = nlp.begin_training() for i in range(5): losses = {} batches = minibatch(train_data, size=compounding(4.0, 32.0, 1.001)) for batch in batches: nlp.update(batch, sgd=optimizer, losses=losses) def test_split_sents(merged_dict): nlp = English() example = Example() example.set_token_annotation(**merged_dict) assert len(example.get_gold_parses(merge=False, vocab=nlp.vocab)) == 2 assert len(example.get_gold_parses(merge=True, vocab=nlp.vocab)) == 1 split_examples = example.split_sents() assert len(split_examples) == 2 token_annotation_1 = split_examples[0].token_annotation assert token_annotation_1.ids == [1, 2, 3] assert token_annotation_1.words == ["Hi", "there", "everyone"] assert token_annotation_1.tags == ["INTJ", "ADV", "PRON"] assert token_annotation_1.sent_starts == [1, 0, 0] token_annotation_2 = split_examples[1].token_annotation assert token_annotation_2.ids == [4, 5, 6, 7] assert token_annotation_2.words == ["It", "is", "just", "me"] assert token_annotation_2.tags == ["PRON", "AUX", "ADV", "PRON"] assert token_annotation_2.sent_starts == [1, 0, 0, 0] def test_tuples_to_example(merged_dict): ex = Example() ex.set_token_annotation(**merged_dict) cats = {"TRAVEL": 1.0, "BAKING": 0.0} ex.set_doc_annotation(cats=cats) ex_dict = ex.to_dict() assert ex_dict["token_annotation"]["ids"] == merged_dict["ids"] assert ex_dict["token_annotation"]["words"] == merged_dict["words"] assert ex_dict["token_annotation"]["tags"] == merged_dict["tags"] assert ex_dict["token_annotation"]["sent_starts"] == merged_dict["sent_starts"] assert ex_dict["doc_annotation"]["cats"] == cats