110 lines
4.1 KiB
Python
110 lines
4.1 KiB
Python
"""Tests for pipeline.io module."""
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import os
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import tempfile
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import pytest
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import torch
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import h5py
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from pathlib import Path
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from pipeline.io import IOHandler
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class TestIOHandler:
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def test_fetch_files_in_directory(self):
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with tempfile.TemporaryDirectory() as tmpdir:
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Path(tmpdir, "file1.txt").touch()
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Path(tmpdir, "file2.txt").touch()
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subdir = os.path.join(tmpdir, "subdir")
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os.makedirs(subdir)
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Path(subdir, "file3.txt").touch()
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files = IOHandler.fetch_files(tmpdir)
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assert len(files) == 3
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def test_fetch_files_empty_directory(self):
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with tempfile.TemporaryDirectory() as tmpdir:
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assert IOHandler.fetch_files(tmpdir) == []
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def test_fetch_folders_in_directory(self):
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with tempfile.TemporaryDirectory() as tmpdir:
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os.makedirs(os.path.join(tmpdir, "folder1"))
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os.makedirs(os.path.join(tmpdir, "folder2"))
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os.makedirs(os.path.join(tmpdir, "folder1", "nested"))
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folders = IOHandler.fetch_folders(tmpdir)
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assert len(folders) == 3
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def test_fetch_folders_with_filter(self):
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with tempfile.TemporaryDirectory() as tmpdir:
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os.makedirs(os.path.join(tmpdir, "folder1"))
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os.makedirs(os.path.join(tmpdir, "folder2"))
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folders = IOHandler.fetch_folders(
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tmpdir, filter_func=lambda x: "folder1" in x
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)
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assert len(folders) == 1
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def test_save_and_load_h5(self):
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with tempfile.TemporaryDirectory() as tmpdir:
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tensor_group = {
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"sequence": [torch.tensor([1, 2, 3], dtype=torch.int32)],
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"labels": [torch.tensor([4, 5], dtype=torch.int32)],
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}
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IOHandler.save_h5(tmpdir, "test", tensor_group)
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assert os.path.exists(os.path.join(tmpdir, "test.h5"))
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loaded = IOHandler.load_h5(tmpdir, share_memory=False)
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assert "sequence" in loaded
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assert "labels" in loaded
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assert torch.equal(
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loaded["sequence"][0], torch.tensor([1, 2, 3], dtype=torch.int32)
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)
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assert torch.equal(
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loaded["labels"][0], torch.tensor([4, 5], dtype=torch.int32)
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)
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def test_save_h5_creates_directory(self):
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with tempfile.TemporaryDirectory() as tmpdir:
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output_dir = os.path.join(tmpdir, "nested", "output")
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IOHandler.save_h5(output_dir, "test", {"data": [torch.tensor([1, 2, 3])]})
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assert os.path.exists(output_dir)
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assert os.path.exists(os.path.join(output_dir, "test.h5"))
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def test_load_h5_multiple_files(self):
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with tempfile.TemporaryDirectory() as tmpdir:
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for i, data in enumerate([[1, 2, 3], [4, 5, 6]]):
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h5_path = os.path.join(tmpdir, f"file{i}.h5")
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with h5py.File(h5_path, "w") as f:
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grp = f.create_group("data")
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grp.create_dataset("data_0", data=data)
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loaded = IOHandler.load_h5(tmpdir, share_memory=False)
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assert len(loaded["data"]) == 2
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def test_load_h5_with_rglob(self):
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with tempfile.TemporaryDirectory() as tmpdir:
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subdir = os.path.join(tmpdir, "subdir")
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os.makedirs(subdir)
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h5_path = os.path.join(subdir, "nested.h5")
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with h5py.File(h5_path, "w") as f:
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grp = f.create_group("test")
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grp.create_dataset("data_0", data=[1, 2])
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loaded = IOHandler.load_h5(tmpdir, share_memory=False)
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assert "test" in loaded
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assert len(loaded["test"]) == 1
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def test_save_h5_multiple_tensors_per_key(self):
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with tempfile.TemporaryDirectory() as tmpdir:
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tensor_group = {
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"batch": [
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torch.tensor([1, 2]),
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torch.tensor([3, 4, 5]),
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torch.tensor([6]),
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],
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}
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IOHandler.save_h5(tmpdir, "multi", tensor_group)
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loaded = IOHandler.load_h5(tmpdir, share_memory=False)
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assert len(loaded["batch"]) == 3
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