CI
9a71302308
Build pipeline: openpipelines-bio.openpipeline-spatial.niche-compass-sxfbq
Source commit: 3edcea085b
Source message: merge edits
190 lines
7.4 KiB
Python
190 lines
7.4 KiB
Python
import os
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import sys
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import mudata as mu
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import numpy as np
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import pytest
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import spatialdata as sd
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def test_simple_execution(run_component, tmp_path):
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input = meta["resources_dir"] + "/xenium_tiny.h5mu"
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input_spatialdata = meta["resources_dir"] + "/xenium_tiny.zarr"
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output = tmp_path / "output.zarr"
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run_component(
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[
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"--input",
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input,
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"--input_spatialdata",
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input_spatialdata,
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"--output",
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output,
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]
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)
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assert os.path.exists(output), "output zarr was not created"
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mdata = mu.read_h5mu(input)
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mod = mdata.mod["rna"]
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sdata = sd.read_zarr(output)
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table = sdata["table"]
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# Check that the main table in the SpatialData object matches the selected modality in the MuData object
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assert table.n_obs == mod.n_obs, (
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"The number of observations in the SpatialData table does not match the selected modality in the MuData object."
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)
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assert table.obs_names.equals(mod.obs_names), (
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"The observation names in the SpatialData table do not match the selected modality in the MuData object."
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)
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assert table.n_vars == mod.n_vars, (
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"The number of variables in the SpatialData table does not match the selected modality in the MuData object."
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)
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assert table.var_names.equals(mod.var_names), (
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"The variable names in the SpatialData table do not match the selected modality in the MuData object."
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)
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assert table.obs.keys().equals(mod.obs.keys()), (
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"The observation metadata columns in the SpatialData table do not match those in the selected modality of the MuData object."
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)
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assert table.var.keys().equals(mod.var.keys()), (
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"The variable metadata columns in the SpatialData table do not match those in the selected modality of the MuData object."
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)
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assert set(table.uns.keys()) == set(mod.uns.keys()), (
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"The unstructured metadata keys in the SpatialData table do not match those in the selected modality of the MuData object."
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)
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assert set(table.obsm.keys()) == set(mod.obsm.keys()), (
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"The obsm keys in the SpatialData table do not match those in the selected modality of the MuData object."
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)
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assert set(table.varm.keys()) == set(mod.varm.keys()), (
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"The varm keys in the SpatialData table do not match those in the selected modality of the MuData object."
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)
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sdata_existing = sd.read_zarr(input_spatialdata)
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# Check that remaining slots in the SpatialData object are filled from the existing SpatialData when provided
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assert sdata.images.keys() == sdata_existing.images.keys(), (
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"The image keys in the output SpatialData do not match those in the existing SpatialData."
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)
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assert sdata.labels.keys() == sdata_existing.labels.keys(), (
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"The label keys in the output SpatialData do not match those in the existing SpatialData."
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)
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assert sdata.shapes.keys() == sdata_existing.shapes.keys(), (
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"The shape keys in the output SpatialData do not match those in the existing SpatialData."
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)
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assert sdata.points.keys() == sdata_existing.points.keys(), (
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"The point keys in the output SpatialData do not match those in the existing SpatialData."
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)
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def test_execution_without_input_spatialdata(run_component, tmp_path):
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input = meta["resources_dir"] + "/xenium_tiny.h5mu"
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output = tmp_path / "output_no_spatialdata.zarr"
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run_component(
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[
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"--input",
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input,
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"--output",
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output,
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]
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)
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assert os.path.exists(output), "output zarr was not created"
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mdata = mu.read_h5mu(input)
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mod = mdata.mod["rna"]
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sdata = sd.read_zarr(output)
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table = sdata["table"]
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# Check that the main table in the SpatialData object matches the selected modality in the MuData object
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assert table.n_obs == mod.n_obs, (
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"The number of observations in the SpatialData table does not match the selected modality in the MuData object."
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)
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assert table.obs_names.equals(mod.obs_names), (
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"The observation names in the SpatialData table do not match the selected modality in the MuData object."
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)
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assert table.n_vars == mod.n_vars, (
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"The number of variables in the SpatialData table does not match the selected modality in the MuData object."
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)
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assert table.var_names.equals(mod.var_names), (
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"The variable names in the SpatialData table do not match the selected modality in the MuData object."
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)
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assert table.obs.keys().equals(mod.obs.keys()), (
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"The observation metadata columns in the SpatialData table do not match those in the selected modality of the MuData object."
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)
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assert table.var.keys().equals(mod.var.keys()), (
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"The variable metadata columns in the SpatialData table do not match those in the selected modality of the MuData object."
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)
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assert set(table.uns.keys()) == set(mod.uns.keys()), (
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"The unstructured metadata keys in the SpatialData table do not match those in the selected modality of the MuData object."
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)
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assert set(table.obsm.keys()) == set(mod.obsm.keys()), (
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"The obsm keys in the SpatialData table do not match those in the selected modality of the MuData object."
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)
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assert set(table.varm.keys()) == set(mod.varm.keys()), (
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"The varm keys in the SpatialData table do not match those in the selected modality of the MuData object."
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)
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# When no existing SpatialData is provided, remaining slots should be empty
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assert len(sdata.images) == 0, (
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"Expected no images when input_spatialdata is not provided."
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)
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assert len(sdata.labels) == 0, (
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"Expected no labels when input_spatialdata is not provided."
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)
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assert len(sdata.shapes) == 0, (
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"Expected no shapes when input_spatialdata is not provided."
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)
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assert len(sdata.points) == 0, (
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"Expected no points when input_spatialdata is not provided."
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)
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def test_execution_with_numpy_region(run_component, tmp_path):
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"""Test that a numpy array region in spatialdata_attrs is handled correctly."""
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input_original = meta["resources_dir"] + "/xenium_tiny.h5mu"
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input_spatialdata = meta["resources_dir"] + "/xenium_tiny.zarr"
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output = tmp_path / "output_numpy_region.zarr"
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# Read the original h5mu and force region to a numpy object array
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mdata = mu.read_h5mu(input_original)
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mod = mdata.mod["rna"]
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attrs = mod.uns["spatialdata_attrs"]
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region = attrs["region"]
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region_list = (
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region.tolist()
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if hasattr(region, "tolist")
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else (region if isinstance(region, list) else [region])
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)
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mod.uns["spatialdata_attrs"]["region"] = np.array(region_list, dtype=object)
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input_modified = tmp_path / "modified_numpy_region.h5mu"
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mdata.write_h5mu(str(input_modified))
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run_component(
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[
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"--input",
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str(input_modified),
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"--input_spatialdata",
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input_spatialdata,
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"--output",
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str(output),
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]
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)
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assert os.path.exists(output), "output zarr was not created"
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sdata = sd.read_zarr(output)
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table = sdata["table"]
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assert table.n_obs == mod.n_obs, (
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"The number of observations in the SpatialData table does not match the selected modality."
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)
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assert table.obs_names.equals(mod.obs_names), (
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"The observation names in the SpatialData table do not match the selected modality."
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)
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if __name__ == "__main__":
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sys.exit(pytest.main([__file__]))
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