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Fix: De/Serialize SpanGroups including the SpanGroup keys (#10707)
* fix: De/Serialize `SpanGroups` including the SpanGroup keys This prevents the loss of `SpanGroup`s that have the same .name as other `SpanGroup`s within the same `SpanGroups` object (upon de/serialization of the `SpanGroups`). Fixes #10685 * Maintain backwards compatibility for serialized `SpanGroups` (serialized as: a list of `SpanGroup`s, or b'') * Add tests for `SpanGroups` deserialization backwards-compatibility * Move a `SpanGroups` de/serialization test (test_issue10685) to tests/serialize/test_serialize_spangroups.py * Output a warning if deserializing a `SpanGroups` with duplicate .name-d `SpanGroup`s * Minor refactor * `SpanGroups.from_bytes` handles only `list` and `dict` types with `dict` as the expected default * For lists, keep first rather than last value encountered * Update error message * Rename and update tests * Update to preserve list serialization of SpanGroups To avoid breaking compatibility of serialized `Doc` and `DocBin` with earlier versions of spacy v3, revert back to a list-only serialization, but update the names just for serialization so that the SpanGroups keys override the SpanGroup names. * Preserve object identity and current key overwrite * Preserve SpanGroup object identity * Preserve last rather than first span group from SpanGroup list format without SpanGroups keys * Update inline comments * Fix types * Add type info for SpanGroup.copy * Deserialize `SpanGroup`s as copies when a single SpanGroup is the value for more than 1 `SpanGroups` key. This is because we serialize `SpanGroups` as dicts (to maintain backward- and forward-compatibility) and we can't assume `SpanGroup`s with the same bytes/serialization were the same (identical) object, pre-serialization. * Update spacy/tokens/_dict_proxies.py * Add more SpanGroups serialization tests Test that serialized SpanGroups maintain their Span order * small clarification on older spaCy version * Update spacy/tests/serialize/test_serialize_span_groups.py Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com> Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
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@ -204,6 +204,11 @@ class Warnings(metaclass=ErrorsWithCodes):
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"for the corpora used to train the language. Please check "
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"`nlp.meta[\"sources\"]` for any relevant links.")
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W119 = ("Overriding pipe name in `config` is not supported. Ignoring override '{name_in_config}'.")
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W120 = ("Unable to load all spans in Doc.spans: more than one span group "
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"with the name '{group_name}' was found in the saved spans data. "
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"Only the last span group will be loaded under "
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"Doc.spans['{group_name}']. Skipping span group with values: "
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"{group_values}")
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class Errors(metaclass=ErrorsWithCodes):
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161
spacy/tests/serialize/test_serialize_span_groups.py
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161
spacy/tests/serialize/test_serialize_span_groups.py
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@ -0,0 +1,161 @@
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import pytest
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from spacy.tokens import Span, SpanGroup
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from spacy.tokens._dict_proxies import SpanGroups
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@pytest.mark.issue(10685)
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def test_issue10685(en_tokenizer):
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"""Test `SpanGroups` de/serialization"""
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# Start with a Doc with no SpanGroups
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doc = en_tokenizer("Will it blend?")
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# Test empty `SpanGroups` de/serialization:
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assert len(doc.spans) == 0
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doc.spans.from_bytes(doc.spans.to_bytes())
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assert len(doc.spans) == 0
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# Test non-empty `SpanGroups` de/serialization:
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doc.spans["test"] = SpanGroup(doc, name="test", spans=[doc[0:1]])
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doc.spans["test2"] = SpanGroup(doc, name="test", spans=[doc[1:2]])
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def assert_spangroups():
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assert len(doc.spans) == 2
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assert doc.spans["test"].name == "test"
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assert doc.spans["test2"].name == "test"
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assert list(doc.spans["test"]) == [doc[0:1]]
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assert list(doc.spans["test2"]) == [doc[1:2]]
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# Sanity check the currently-expected behavior
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assert_spangroups()
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# Now test serialization/deserialization:
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doc.spans.from_bytes(doc.spans.to_bytes())
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assert_spangroups()
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def test_span_groups_serialization_mismatches(en_tokenizer):
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"""Test the serialization of multiple mismatching `SpanGroups` keys and `SpanGroup.name`s"""
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doc = en_tokenizer("How now, brown cow?")
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# Some variety:
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# 1 SpanGroup where its name matches its key
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# 2 SpanGroups that have the same name--which is not a key
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# 2 SpanGroups that have the same name--which is a key
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# 1 SpanGroup that is a value for 2 different keys (where its name is a key)
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# 1 SpanGroup that is a value for 2 different keys (where its name is not a key)
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groups = doc.spans
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groups["key1"] = SpanGroup(doc, name="key1", spans=[doc[0:1], doc[1:2]])
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groups["key2"] = SpanGroup(doc, name="too", spans=[doc[3:4], doc[4:5]])
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groups["key3"] = SpanGroup(doc, name="too", spans=[doc[1:2], doc[0:1]])
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groups["key4"] = SpanGroup(doc, name="key4", spans=[doc[0:1]])
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groups["key5"] = SpanGroup(doc, name="key4", spans=[doc[0:1]])
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sg6 = SpanGroup(doc, name="key6", spans=[doc[0:1]])
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groups["key6"] = sg6
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groups["key7"] = sg6
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sg8 = SpanGroup(doc, name="also", spans=[doc[1:2]])
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groups["key8"] = sg8
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groups["key9"] = sg8
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regroups = SpanGroups(doc).from_bytes(groups.to_bytes())
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# Assert regroups == groups
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assert regroups.keys() == groups.keys()
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for key, regroup in regroups.items():
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# Assert regroup == groups[key]
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assert regroup.name == groups[key].name
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assert list(regroup) == list(groups[key])
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@pytest.mark.parametrize(
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"spans_bytes,doc_text,expected_spangroups,expected_warning",
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# The bytestrings below were generated from an earlier version of spaCy
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# that serialized `SpanGroups` as a list of SpanGroup bytes (via SpanGroups.to_bytes).
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# Comments preceding the bytestrings indicate from what Doc they were created.
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[
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# Empty SpanGroups:
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(b"\x90", "", {}, False),
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# doc = nlp("Will it blend?")
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# doc.spans['test'] = SpanGroup(doc, name='test', spans=[doc[0:1]])
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(
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b"\x91\xc4C\x83\xa4name\xa4test\xa5attrs\x80\xa5spans\x91\xc4(\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x01\x00\x00\x00\x00\x00\x00\x00\x04",
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"Will it blend?",
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{"test": {"name": "test", "spans": [(0, 1)]}},
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False,
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),
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# doc = nlp("Will it blend?")
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# doc.spans['test'] = SpanGroup(doc, name='test', spans=[doc[0:1]])
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# doc.spans['test2'] = SpanGroup(doc, name='test', spans=[doc[1:2]])
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(
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b"\x92\xc4C\x83\xa4name\xa4test\xa5attrs\x80\xa5spans\x91\xc4(\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x01\x00\x00\x00\x00\x00\x00\x00\x04\xc4C\x83\xa4name\xa4test\xa5attrs\x80\xa5spans\x91\xc4(\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x01\x00\x00\x00\x02\x00\x00\x00\x05\x00\x00\x00\x07",
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"Will it blend?",
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# We expect only 1 SpanGroup to be in doc.spans in this example
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# because there are 2 `SpanGroup`s that have the same .name. See #10685.
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{"test": {"name": "test", "spans": [(1, 2)]}},
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True,
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),
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# doc = nlp('How now, brown cow?')
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# doc.spans['key1'] = SpanGroup(doc, name='key1', spans=[doc[0:1], doc[1:2]])
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# doc.spans['key2'] = SpanGroup(doc, name='too', spans=[doc[3:4], doc[4:5]])
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# doc.spans['key3'] = SpanGroup(doc, name='too', spans=[doc[1:2], doc[0:1]])
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# doc.spans['key4'] = SpanGroup(doc, name='key4', spans=[doc[0:1]])
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# doc.spans['key5'] = SpanGroup(doc, name='key4', spans=[doc[0:1]])
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(
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b"\x95\xc4m\x83\xa4name\xa4key1\xa5attrs\x80\xa5spans\x92\xc4(\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x01\x00\x00\x00\x00\x00\x00\x00\x03\xc4(\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x01\x00\x00\x00\x02\x00\x00\x00\x04\x00\x00\x00\x07\xc4l\x83\xa4name\xa3too\xa5attrs\x80\xa5spans\x92\xc4(\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x03\x00\x00\x00\x04\x00\x00\x00\t\x00\x00\x00\x0e\xc4(\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x04\x00\x00\x00\x05\x00\x00\x00\x0f\x00\x00\x00\x12\xc4l\x83\xa4name\xa3too\xa5attrs\x80\xa5spans\x92\xc4(\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x01\x00\x00\x00\x02\x00\x00\x00\x04\x00\x00\x00\x07\xc4(\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x01\x00\x00\x00\x00\x00\x00\x00\x03\xc4C\x83\xa4name\xa4key4\xa5attrs\x80\xa5spans\x91\xc4(\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x01\x00\x00\x00\x00\x00\x00\x00\x03\xc4C\x83\xa4name\xa4key4\xa5attrs\x80\xa5spans\x91\xc4(\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x01\x00\x00\x00\x00\x00\x00\x00\x03",
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"How now, brown cow?",
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{
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"key1": {"name": "key1", "spans": [(0, 1), (1, 2)]},
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"too": {"name": "too", "spans": [(1, 2), (0, 1)]},
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"key4": {"name": "key4", "spans": [(0, 1)]},
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},
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True,
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),
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],
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)
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def test_deserialize_span_groups_compat(
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en_tokenizer, spans_bytes, doc_text, expected_spangroups, expected_warning
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):
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"""Test backwards-compatibility of `SpanGroups` deserialization.
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This uses serializations (bytes) from a prior version of spaCy (before 3.3.1).
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spans_bytes (bytes): Serialized `SpanGroups` object.
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doc_text (str): Doc text.
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expected_spangroups (dict):
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Dict mapping every expected (after deserialization) `SpanGroups` key
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to a SpanGroup's "args", where a SpanGroup's args are given as a dict:
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{"name": span_group.name,
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"spans": [(span0.start, span0.end), ...]}
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expected_warning (bool): Whether a warning is to be expected from .from_bytes()
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--i.e. if more than 1 SpanGroup has the same .name within the `SpanGroups`.
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"""
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doc = en_tokenizer(doc_text)
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if expected_warning:
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with pytest.warns(UserWarning):
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doc.spans.from_bytes(spans_bytes)
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else:
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# TODO: explicitly check for lack of a warning
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doc.spans.from_bytes(spans_bytes)
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assert doc.spans.keys() == expected_spangroups.keys()
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for name, spangroup_args in expected_spangroups.items():
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assert doc.spans[name].name == spangroup_args["name"]
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spans = [Span(doc, start, end) for start, end in spangroup_args["spans"]]
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assert list(doc.spans[name]) == spans
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def test_span_groups_serialization(en_tokenizer):
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doc = en_tokenizer("0 1 2 3 4 5 6")
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span_groups = SpanGroups(doc)
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spans = [doc[0:2], doc[1:3]]
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sg1 = SpanGroup(doc, spans=spans)
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span_groups["key1"] = sg1
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span_groups["key2"] = sg1
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span_groups["key3"] = []
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reloaded_span_groups = SpanGroups(doc).from_bytes(span_groups.to_bytes())
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assert span_groups.keys() == reloaded_span_groups.keys()
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for key, value in span_groups.items():
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assert all(
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span == reloaded_span
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for span, reloaded_span in zip(span_groups[key], reloaded_span_groups[key])
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)
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@ -1,10 +1,11 @@
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from typing import Iterable, Tuple, Union, Optional, TYPE_CHECKING
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from typing import Dict, Iterable, List, Tuple, Union, Optional, TYPE_CHECKING
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import warnings
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import weakref
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from collections import UserDict
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import srsly
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from .span_group import SpanGroup
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from ..errors import Errors
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from ..errors import Errors, Warnings
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if TYPE_CHECKING:
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@ -16,7 +17,7 @@ if TYPE_CHECKING:
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# Why inherit from UserDict instead of dict here?
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# Well, the 'dict' class doesn't necessarily delegate everything nicely,
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# for performance reasons. The UserDict is slower but better behaved.
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# See https://treyhunner.com/2019/04/why-you-shouldnt-inherit-from-list-and-dict-in-python/0ww
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# See https://treyhunner.com/2019/04/why-you-shouldnt-inherit-from-list-and-dict-in-python/
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class SpanGroups(UserDict):
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"""A dict-like proxy held by the Doc, to control access to span groups."""
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@ -53,20 +54,52 @@ class SpanGroups(UserDict):
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return super().setdefault(key, default=default)
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def to_bytes(self) -> bytes:
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# We don't need to serialize this as a dict, because the groups
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# know their names.
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# We serialize this as a dict in order to track the key(s) a SpanGroup
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# is a value of (in a backward- and forward-compatible way), since
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# a SpanGroup can have a key that doesn't match its `.name` (See #10685)
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if len(self) == 0:
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return self._EMPTY_BYTES
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msg = [value.to_bytes() for value in self.values()]
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msg: Dict[bytes, List[str]] = {}
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for key, value in self.items():
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msg.setdefault(value.to_bytes(), []).append(key)
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return srsly.msgpack_dumps(msg)
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def from_bytes(self, bytes_data: bytes) -> "SpanGroups":
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msg = [] if bytes_data == self._EMPTY_BYTES else srsly.msgpack_loads(bytes_data)
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# backwards-compatibility: bytes_data may be one of:
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# b'', a serialized empty list, a serialized list of SpanGroup bytes
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# or a serialized dict of SpanGroup bytes -> keys
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msg = (
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[]
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if not bytes_data or bytes_data == self._EMPTY_BYTES
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else srsly.msgpack_loads(bytes_data)
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)
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self.clear()
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doc = self._ensure_doc()
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for value_bytes in msg:
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group = SpanGroup(doc).from_bytes(value_bytes)
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self[group.name] = group
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if isinstance(msg, list):
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# This is either the 1st version of `SpanGroups` serialization
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# or there were no SpanGroups serialized
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for value_bytes in msg:
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group = SpanGroup(doc).from_bytes(value_bytes)
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if group.name in self:
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# Display a warning if `msg` contains `SpanGroup`s
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# that have the same .name (attribute).
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# Because, for `SpanGroups` serialized as lists,
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# only 1 SpanGroup per .name is loaded. (See #10685)
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warnings.warn(
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Warnings.W120.format(
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group_name=group.name, group_values=self[group.name]
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)
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)
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self[group.name] = group
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else:
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for value_bytes, keys in msg.items():
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group = SpanGroup(doc).from_bytes(value_bytes)
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# Deserialize `SpanGroup`s as copies because it's possible for two
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# different `SpanGroup`s (pre-serialization) to have the same bytes
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# (since they can have the same `.name`).
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self[keys[0]] = group
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for key in keys[1:]:
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self[key] = group.copy()
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return self
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def _ensure_doc(self) -> "Doc":
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@ -24,3 +24,4 @@ class SpanGroup:
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def __getitem__(self, i: int) -> Span: ...
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def to_bytes(self) -> bytes: ...
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def from_bytes(self, bytes_data: bytes) -> SpanGroup: ...
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def copy(self) -> SpanGroup: ...
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