CI
c6296af264
Build pipeline: test-vsh-ci-build-template-qlrkg
Source commit: 3b5314b60d
Source message: update changelog
70 lines
2.3 KiB
Python
70 lines
2.3 KiB
Python
import pytest
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import os
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import sys
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import spatialdata as sd
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import subprocess
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def test_simple_execution(run_component, tmp_path):
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output_sd_path = tmp_path / "sd"
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run_component(
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[
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"--input",
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meta["resources_dir"] + "/xenium_tiny",
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"--output",
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output_sd_path,
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]
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)
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assert os.path.exists(output_sd_path), "Output zarr folder was not created"
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sdata = sd.read_zarr(output_sd_path)
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assert isinstance(sdata, sd.SpatialData), (
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"the generated output is not a SpatialData object"
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)
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assert os.path.exists(output_sd_path / "images"), "images folder was not created"
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assert os.path.exists(output_sd_path / "labels"), "labels folder was not created"
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assert os.path.exists(output_sd_path / "points"), "images folder was not created"
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assert os.path.exists(output_sd_path / "shapes"), "shapes folder was not created"
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assert os.path.exists(output_sd_path / "tables"), "tables folder was not created"
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assert (output_sd_path / "zmetadata").is_file(), "zmetadata file was not created"
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def test_compressed_input(run_component, tmp_path):
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output_sd_path = tmp_path / "sd"
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zipped_input = tmp_path / "xenium_tiny.zip"
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subprocess.run(
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["zip", "-r", str(zipped_input), "xenium_tiny"],
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cwd=meta["resources_dir"],
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check=True,
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)
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run_component(
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[
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"--input",
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zipped_input,
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"--output",
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output_sd_path,
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]
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)
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assert os.path.exists(output_sd_path), "Output zarr folder was not created"
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sdata = sd.read_zarr(output_sd_path)
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assert isinstance(sdata, sd.SpatialData), (
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"the generated output is not a SpatialData object"
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)
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assert os.path.exists(output_sd_path / "images"), "images folder was not created"
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assert os.path.exists(output_sd_path / "labels"), "labels folder was not created"
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assert os.path.exists(output_sd_path / "points"), "images folder was not created"
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assert os.path.exists(output_sd_path / "shapes"), "shapes folder was not created"
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assert os.path.exists(output_sd_path / "tables"), "tables folder was not created"
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assert (output_sd_path / "zmetadata").is_file(), "zmetadata file was not created"
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if __name__ == "__main__":
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sys.exit(pytest.main([__file__]))
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