CI
cd0af18851
Build pipeline: vsh-ci-dev-k8tz4
Source commit: 2dbe3b7231
Source message: Fix pointers to test resources
146 lines
5.4 KiB
Python
146 lines
5.4 KiB
Python
import sys
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import os
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import pytest
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import subprocess
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import re
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import mudata as mu
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import anndata as ad
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from openpipelinetestutils.asserters import assert_annotation_objects_equal
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import os
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## VIASH START
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meta = {
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"resources_dir": "resources_test"
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}
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## VIASH END
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input_file = f"{meta['resources_dir']}/pbmc_1k_protein_v3/pbmc_1k_protein_v3_filtered_feature_bc_matrix.h5mu"
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reference_file = f"{meta['resources_dir']}/annotation_test_data/TS_Blood_filtered.h5mu"
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cl_nlp_emb_file = f"{meta['resources_dir']}/annotation_test_data/ontology/cl.ontology.nlp.emb"
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cl_ontology_file = f"{meta['resources_dir']}/annotation_test_data/ontology/cl.ontology"
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cl_obo_file = f"{meta['resources_dir']}/annotation_test_data/ontology/cl.obo"
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model_file = f"{meta['resources_dir']}/annotation_test_data/onclass_model/example_file_model"
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@pytest.fixture
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def swap_gene_symbol(random_h5mu_path):
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def wrapper(input_mudata_file, modality):
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input_mudata = mu.read_h5mu(input_mudata_file)
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input_adata = input_mudata.mod[modality]
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adata = input_adata.copy()
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adata.var["ensemblid"] = list(adata.var.index)
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adata.var.index = [re.sub("\\.[0-9]+$", "", s) for s in adata.var["gene_symbol"]]
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input_mudata.mod[modality] = adata
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swapped_input_mudata_file = random_h5mu_path()
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input_mudata.write_h5mu(swapped_input_mudata_file)
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return swapped_input_mudata_file
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return wrapper
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def test_simple_execution(run_component, random_h5mu_path):
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output_file = random_h5mu_path()
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run_component([
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"--input", input_file,
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"--reference", reference_file,
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"--reference_obs_target", "cell_ontology_class",
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"--cl_nlp_emb_file", cl_nlp_emb_file,
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"--cl_ontology_file", cl_ontology_file,
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"--cl_obo_file", cl_obo_file,
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"--max_iter", "10",
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"--output", output_file
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])
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assert os.path.exists(output_file), "Output file does not exist"
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input_mudata = mu.read_h5mu(input_file)
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output_mudata = mu.read_h5mu(output_file)
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assert_annotation_objects_equal(input_mudata.mod["prot"],
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output_mudata.mod["prot"])
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assert list(output_mudata.mod["rna"].obs.keys()) == ['onclass_pred',
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'onclass_prob']
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obs_values = output_mudata.mod["rna"].obs["onclass_prob"]
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assert all(0 <= value <= 1 for value in obs_values), ".obs at cell_ontology_class_prob has values outside the range [0, 1]"
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def test_custom_obs(run_component, random_h5mu_path):
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output_file = random_h5mu_path()
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run_component([
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"--input", input_file,
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"--reference", reference_file,
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"--reference_obs_target", "cell_ontology_class",
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"--output_obs_predictions", "dummy_pred_1",
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"--output_obs_probability", "dummy_prob_1",
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"--cl_nlp_emb_file", cl_nlp_emb_file,
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"--cl_ontology_file", cl_ontology_file,
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"--cl_obo_file", cl_obo_file,
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"--max_iter", "10",
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"--output", output_file
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])
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assert os.path.exists(output_file), "Output file does not exist"
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input_mudata = mu.read_h5mu(input_file)
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output_mudata = mu.read_h5mu(output_file)
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assert_annotation_objects_equal(input_mudata.mod["prot"],
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output_mudata.mod["prot"])
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assert set(output_mudata.mod["rna"].obs.keys()) == {'dummy_pred_1', 'dummy_prob_1'}
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obs_keys = ['dummy_prob_1']
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for key in obs_keys:
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obs_values = output_mudata.mod["rna"].obs[key]
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assert all(0 <= value <= 1 for value in obs_values), f".obs at {key} has values outside the range [0, 1]"
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def test_no_model_no_reference_error(run_component, random_h5mu_path):
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output_file = random_h5mu_path()
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with pytest.raises(subprocess.CalledProcessError) as err:
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run_component([
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"--input", input_file,
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"--output", output_file,
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"--cl_nlp_emb_file", cl_nlp_emb_file,
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"--cl_ontology_file", cl_ontology_file,
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"--cl_obo_file", cl_obo_file,
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"--reference_obs_target", "cell_ontology_class"
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])
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assert re.search(r"ValueError: Make sure to provide either 'model' or 'reference', but not both.",
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err.value.stdout.decode('utf-8'))
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def test_pretrained_model(run_component, random_h5mu_path, swap_gene_symbol):
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output_file = random_h5mu_path()
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swapped_input_file = swap_gene_symbol(input_file, "rna")
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run_component([
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"--input", swapped_input_file,
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"--cl_nlp_emb_file", cl_nlp_emb_file,
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"--cl_ontology_file", cl_ontology_file,
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"--cl_obo_file", cl_obo_file,
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"--reference_obs_target", "cell_ontology_class",
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"--model", model_file,
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"--output", output_file
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])
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assert os.path.exists(output_file), "Output file does not exist"
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input_mudata = mu.read_h5mu(input_file)
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output_mudata = mu.read_h5mu(output_file)
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assert_annotation_objects_equal(input_mudata.mod["prot"],
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output_mudata.mod["prot"])
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assert list(output_mudata.mod["rna"].obs.keys()) == ['onclass_pred',
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'onclass_prob']
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obs_values = output_mudata.mod["rna"].obs["onclass_prob"]
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assert all(0 <= value <= 1 for value in obs_values), ".obs at cell_ontology_class_prob has values outside the range [0, 1]"
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if __name__ == '__main__':
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sys.exit(pytest.main([__file__])) |