SCMCP

import pytest import numpy as np import anndata from scmcp.tool.pl import run_pl_func, pl_func from scmcp.util import set_fig_path, add_op_log from unittest.mock import patch, MagicMock, mock_open from pathlib import Path import os import matplotlib.pyplot as plt class MockAnnDataStore: def __init__(self, adata=None): self.adata_dic = {} self.active = "test_adata" if adata is not None: self.adata_dic[self.active] = adata def test_run_pl_func(): os.environ['SCMCP_TRANSPORT'] = "stdio" # Create a simple AnnData object for testing adata = anndata.AnnData(X=np.array([[1, 2, 3], [4, 5, 6], [7, 8, 9]])) # Create a mock AnnDataStore with the test AnnData ads = MockAnnDataStore(adata) # Test case 1: Successfully running pl_pca function mock_fig = MagicMock() mock_fig_path = Path("./figures/pca.png") with patch.dict(pl_func, {"pl_pca": MagicMock(return_value=mock_fig)}): pl_func["pl_pca"].__name__ = "pl_pca" # Create a mock signature with specific parameters mock_signature = MagicMock() mock_parameters = { "adata": MagicMock(), "color": MagicMock(), "use_raw": MagicMock(), "show": MagicMock(), "save": MagicMock() } mock_signature.parameters = mock_parameters with patch("inspect.signature", return_value=mock_signature): with patch("scmcp.util.set_fig_path", return_value=mock_fig_path): with patch("scmcp.util.add_op_log"): result = run_pl_func(ads, "pl_pca", {"color": "leiden", "use_raw": True}) # Verify function was called with correct parameters pl_func["pl_pca"].assert_called_once() args, kwargs = pl_func["pl_pca"].call_args assert args[0] is adata assert kwargs.get("color") == "leiden" assert kwargs.get("use_raw") is True assert kwargs.get("show") is False assert kwargs.get("save") == ".png" # Test case 2: Successfully running pl_embedding function mock_fig = MagicMock() # Use a mock path mock_fig_path = Path("/mock/path/to/figures/embedding.png") with patch.dict(pl_func, {"pl_embedding": MagicMock(return_value=mock_fig)}): pl_func["pl_embedding"].__name__ = "pl_embedding" # Create a mock signature mock_signature = MagicMock() mock_parameters = { "adata": MagicMock(), "basis": MagicMock(), "color": MagicMock(), "title": MagicMock(), # Include title parameter "show": MagicMock(), "save": MagicMock() } mock_signature.parameters = mock_parameters with patch("inspect.signature", return_value=mock_signature): # Ensure set_fig_path returns our mock path with patch("scmcp.util.set_fig_path", return_value=mock_fig_path): with patch("scmcp.util.add_op_log"): result = run_pl_func(ads, "pl_embedding", { "basis": "umap", "color": "leiden", "title": "UMAP Plot" }) # Verify function was called with correct parameters pl_func["pl_embedding"].assert_called_once() args, kwargs = pl_func["pl_embedding"].call_args assert args[0] is adata assert kwargs.get("basis") == "umap" assert kwargs.get("color") == "leiden" assert kwargs.get("title") == "UMAP Plot" # Title should be preserved assert kwargs.get("show") is False assert kwargs.get("save") == ".png" # Test case 3: Error handling for unsupported function with pytest.raises(ValueError, match="Unsupported function: unsupported_func"): run_pl_func(ads, "unsupported_func", {}) # Test case 4: Error handling for exceptions during plotting with patch.dict(pl_func, {"pl_violin": MagicMock(side_effect=Exception("Plotting error"))}): pl_func["pl_violin"].__name__ = "pl_violin" mock_signature = MagicMock() mock_parameters = {"adata": MagicMock(), "show": MagicMock(), "save": MagicMock()} mock_signature.parameters = mock_parameters with patch("inspect.signature", return_value=mock_signature): with pytest.raises(Exception, match="Plotting error"): run_pl_func(ads, "pl_violin", {}) def test_run_pl_func_with_multiple_adatas(): # Test with multiple AnnData objects in the store adata1 = anndata.AnnData(X=np.array([[1, 2], [3, 4]])) adata2 = anndata.AnnData(X=np.array([[5, 6], [7, 8]])) # Create a mock AnnDataStore with multiple AnnData objects ads = MockAnnDataStore() ads.adata_dic["adata1"] = adata1 ads.adata_dic["adata2"] = adata2 ads.active = "adata2" # Set active to adata2 mock_fig = MagicMock() mock_fig_path = Path("./figures/scatter.png") with patch.dict(pl_func, {"pl_scatter": MagicMock(return_value=mock_fig)}): pl_func["pl_scatter"].__name__ = "pl_scatter" mock_signature = MagicMock() mock_parameters = { "adata": MagicMock(), "x": MagicMock(), "y": MagicMock(), "show": MagicMock(), "save": MagicMock() } mock_signature.parameters = mock_parameters with patch("inspect.signature", return_value=mock_signature): # Use patch.object to mock the set_fig_path function directly with patch("scmcp.tool.pl.set_fig_path", return_value=mock_fig_path): with patch("scmcp.tool.pl.add_op_log"): result = run_pl_func(ads, "pl_scatter", {"x": "gene1", "y": "gene2"}) # Verify function was called with the active AnnData (adata2) pl_func["pl_scatter"].assert_called_once() args, kwargs = pl_func["pl_scatter"].call_args assert args[0] is adata2 # Should use the active AnnData assert kwargs.get("x") == "gene1" assert kwargs.get("y") == "gene2" def test_fig_to_bytes(): from scmcp.tool.pl import fig_to_bytes # Create a simple matplotlib figure fig, ax = plt.subplots() ax.plot([1, 2, 3], [4, 5, 6]) # Test with a Figure object with patch("matplotlib.figure.Figure.savefig") as mock_savefig: fig_to_bytes(fig) mock_savefig.assert_called_once() # Test with an Axes object with patch("matplotlib.figure.Figure.savefig") as mock_savefig: fig_to_bytes(ax) mock_savefig.assert_called_once() # Test error handling with patch("matplotlib.figure.Figure.savefig", side_effect=Exception("Error saving figure")): with pytest.raises(Exception, match="Error saving figure"): fig_to_bytes(fig) plt.close(fig) # Clean up