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b/tests/data/test_stream.py |
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import pytest |
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import edsnlp |
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from edsnlp.utils.collections import ld_to_dl |
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try: |
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import torch.nn |
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except ImportError: |
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torch = None |
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def test_map_batches(): |
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items = [1, 2, 3, 4, 5] |
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stream = edsnlp.data.from_iterable(items) |
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stream = stream.map(lambda x: x + 1) # 2, 3, 4, 5, 6 |
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stream = stream.map_batches(lambda x: [sum(x)]) |
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stream = stream.set_processing( |
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num_cpu_workers=2, |
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sort_chunks=False, |
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batch_size=2, |
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) |
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res = list(stream) |
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assert res == [6, 8, 6] # 2+4, 3+5, 6 |
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@pytest.mark.parametrize("num_cpu_workers", [1, 2]) |
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def test_flat_iterable(num_cpu_workers): |
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items = [1, 2, 3, 4] |
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stream = edsnlp.data.from_iterable(items) |
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stream = stream.set_processing(num_cpu_workers=num_cpu_workers) |
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stream = stream.map(lambda x: [x] * x) |
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stream = stream.flatten() |
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res = list(stream.to_iterable(converter=lambda x: x)) |
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assert sorted(res) == [1, 2, 2, 3, 3, 3, 4, 4, 4, 4] |
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@pytest.mark.parametrize("num_gpu_workers", [0, 1, 2]) |
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@pytest.mark.skipif(torch is None, reason="torch not installed") |
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def test_map_gpu(num_gpu_workers): |
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import torch |
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def prepare_batch(batch, device): |
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return {"tensor": torch.tensor(batch).to(device)} |
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def forward(batch): |
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return {"outputs": batch["tensor"] * 2} |
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items = range(15) |
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stream = edsnlp.data.from_iterable(items) |
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if num_gpu_workers == 0: |
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# this is just to fuse tests, and test map_gpu |
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# following a map_batches without specifying a batch size |
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stream = stream.map_batches(lambda x: x) |
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stream = stream.map_gpu(prepare_batch, forward) |
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stream = stream.set_processing( |
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num_gpu_workers=num_gpu_workers, |
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gpu_worker_devices=["cpu"] * num_gpu_workers, |
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sort_chunks=False, |
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batch_size=2, |
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) |
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res = ld_to_dl(stream) |
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res = torch.cat(res["outputs"]) |
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assert set(res.tolist()) == {i * 2 for i in range(15)} |
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# fmt: off |
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@pytest.mark.parametrize( |
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"sort,num_cpu_workers,batch_kwargs,expected", |
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[ |
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(False, 1, {"batch_size": 10, "batch_by": "words"}, [3, 1, 3, 1, 3, 1]), # noqa: E501 |
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(False, 1, {"batch_size": 10, "batch_by": "padded_words"}, [2, 1, 1, 2, 1, 1, 2, 1, 1]), # noqa: E501 |
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(False, 1, {"batch_size": 10, "batch_by": "docs"}, [10, 2]), # noqa: E501 |
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(False, 2, {"batch_size": 10, "batch_by": "words"}, [2, 1, 2, 1, 2, 1, 1, 1, 1]), # noqa: E501 |
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(False, 2, {"batch_size": 10, "batch_by": "padded_words"}, [2, 1, 2, 1, 2, 1, 1, 1, 1]), # noqa: E501 |
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(False, 2, {"batch_size": 10, "batch_by": "docs"}, [6, 6]), # noqa: E501 |
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(True, 2, {"batch_size": 10, "batch_by": "padded_words"}, [3, 3, 2, 1, 1, 1, 1]), # noqa: E501 |
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(False, 2, {"batch_size": "10 words"}, [2, 1, 2, 1, 2, 1, 1, 1, 1]), # noqa: E501 |
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], |
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) |
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# fmt: on |
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def test_map_with_batching(sort, num_cpu_workers, batch_kwargs, expected): |
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nlp = edsnlp.blank("eds") |
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nlp.add_pipe( |
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"eds.matcher", |
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config={ |
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"terms": { |
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"foo": ["This", "is", "a", "sentence", ".", "Short", "snippet", "too"], |
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} |
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}, |
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name="matcher", |
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) |
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samples = [ |
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"This is a sentence.", |
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"Short snippet", |
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"Short snippet too", |
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"This is a very very long sentence that will make more than 10 words", |
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] * 3 |
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stream = edsnlp.data.from_iterable(samples) |
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if sort: |
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stream = stream.map_batches(lambda x: sorted(x, key=len), batch_size=1000) |
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stream = stream.map_pipeline(nlp) |
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stream = stream.map_batches(len) |
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stream = stream.set_processing( |
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num_cpu_workers=num_cpu_workers, |
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**batch_kwargs, |
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chunk_size=1000, # deprecated |
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split_into_batches_after="matcher", |
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show_progress=True, |
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) |
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assert list(stream) == expected |
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def test_repr(frozen_ml_nlp, tmp_path): |
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items = ["ceci est un test", "ceci est un autre test"] |
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stream = ( |
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edsnlp.data.from_iterable(items, converter=frozen_ml_nlp.make_doc) |
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.map(lambda x: x) |
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.map_pipeline(frozen_ml_nlp, batch_size=2) |
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.map_batches(lambda b: sorted(b, key=len)) |
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.set_processing(num_cpu_workers=2) |
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.write_json(tmp_path / "out_test.jsonl", lines=True, execute=False) |
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) |
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assert "Stream" in repr(stream) |
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@pytest.mark.parametrize("shuffle_reader", [True, False]) |
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def test_shuffle_before_generator(shuffle_reader): |
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def gen_fn(x): |
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yield x |
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yield x |
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items = [1, 2, 3, 4, 5] |
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stream = edsnlp.data.from_iterable(items) |
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stream = stream.map(lambda x: x) |
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stream = stream.shuffle(seed=42, shuffle_reader=shuffle_reader) |
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stream = stream.map(gen_fn) |
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assert stream.reader.shuffle == ("dataset" if shuffle_reader else False) |
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assert len(stream.ops) == (2 if shuffle_reader else 5) |
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res = list(stream) |
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assert res == [4, 4, 2, 2, 3, 3, 5, 5, 1, 1] |
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def test_shuffle_after_generator(): |
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def gen_fn(x): |
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yield x |
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yield x |
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items = [1, 2, 3, 4, 5] |
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stream = edsnlp.data.from_iterable(items) |
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stream = stream.map(lambda x: x) |
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stream = stream.map(gen_fn) |
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stream = stream.shuffle(seed=43) |
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assert stream.reader.shuffle == "dataset" |
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assert len(stream.ops) == 5 |
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res = list(stream) |
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assert res == [1, 2, 4, 3, 1, 3, 5, 5, 4, 2] |
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def test_shuffle_frozen_ml_pipeline(run_in_test_dir, frozen_ml_nlp): |
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stream = edsnlp.data.read_parquet("../resources/docs.parquet", converter="omop") |
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stream = stream.map_pipeline(frozen_ml_nlp, batch_size=2) |
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assert len(stream.ops) == 7 |
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stream = stream.shuffle(batch_by="fragment") |
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assert len(stream.ops) == 7 |
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assert stream.reader.shuffle == "fragment" |
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def test_unknown_shuffle(): |
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items = [1, 2, 3, 4, 5] |
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stream = edsnlp.data.from_iterable(items) |
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stream = stream.map(lambda x: x) |
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with pytest.raises(ValueError): |
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stream.shuffle("unknown") |
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def test_int_shuffle(): |
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items = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10] |
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stream = edsnlp.data.from_iterable(items) |
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stream = stream.map(lambda x: x) |
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stream = stream.shuffle("2 docs", seed=42) |
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assert list(stream) == [2, 1, 4, 3, 5, 6, 8, 7, 10, 9] |
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def test_parallel_preprocess_stop(run_in_test_dir, frozen_ml_nlp): |
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nlp = frozen_ml_nlp |
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stream = edsnlp.data.read_parquet( |
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"../resources/docs.parquet", |
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"omop", |
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loop=True, |
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) |
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stream = stream.map(edsnlp.pipes.split(regex="\n+")) |
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stream = stream.map(nlp.preprocess, kwargs=dict(supervision=True)) |
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stream = stream.batchify("128 words") |
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stream = stream.map(nlp.collate) |
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stream = stream.set_processing(num_cpu_workers=1, process_start_method="spawn") |
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it = iter(stream) |
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total = 0 |
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for _ in zip(it, range(10)): |
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total += 1 |
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assert total == 10 |
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del it |