CI
78da099d22
Build pipeline: vsh-ci-build-template-k65s9
Source commit: 532e64485a
Source message: update spatialdata versions
53 lines
1.4 KiB
Python
53 lines
1.4 KiB
Python
import pytest
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import sys
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import mudata as mu
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def test_simple_execution(run_component, tmp_path):
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output = tmp_path / "output.h5mu"
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run_component(
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[
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"--input",
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meta["resources_dir"] + "/xenium_tiny.zarr",
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"--output",
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output,
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]
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)
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assert output.is_file(), "output file was not created"
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mdata = mu.read_h5mu(output)
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assert list(mdata.mod.keys()) == ["rna"], "Expected modality rna"
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adata = mdata.mod["rna"]
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# TODO: update what is checked here when spatialdata from other experimental set-ups are tested (e.g. cosmx, visium)
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assert list(adata.obs.keys()) == [
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"cell_id",
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"transcript_counts",
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"control_probe_counts",
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"genomic_control_counts",
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"control_codeword_counts",
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"unassigned_codeword_counts",
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"deprecated_codeword_counts",
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"total_counts",
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"cell_area",
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"nucleus_area",
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"nucleus_count",
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"segmentation_method",
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"region",
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"z_level",
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"cell_labels",
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]
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assert list(adata.uns.keys()) == ["spatialdata_attrs"]
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assert list(adata.obsm.keys()) == ["spatial"]
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assert list(adata.var.keys()) == ["gene_ids", "feature_types", "genome"]
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assert all(adata.var["feature_types"] == "Gene Expression")
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assert adata.obsm["spatial"].dtype == "float"
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if __name__ == "__main__":
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sys.exit(pytest.main([__file__]))
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