SCMCP

import pytest import numpy as np import anndata import os from pathlib import Path from scmcp.tool.io import run_io_func, read_func, write_func, io_func, io_tools from unittest.mock import patch, MagicMock, mock_open class MockAnnDataStore: def __init__(self): self.adata_dic = {} self.active = None def test_read_func(): # Test case 1: Reading a directory (10x mtx format) with patch('pathlib.Path.is_dir', return_value=True), \ patch('pathlib.Path.is_file', return_value=False), \ patch('scanpy.read_10x_mtx') as mock_read_10x: mock_adata = anndata.AnnData(X=np.array([[1, 2], [3, 4]])) mock_read_10x.return_value = mock_adata result = read_func(filename="test_dir") mock_read_10x.assert_called_once() assert result is mock_adata # Test case 2: Reading a file with patch('pathlib.Path.is_dir', return_value=False), \ patch('pathlib.Path.is_file', return_value=True), \ patch('scanpy.read') as mock_read: mock_adata = anndata.AnnData(X=np.array([[5, 6], [7, 8]])) mock_read.return_value = mock_adata result = read_func(filename="test.h5ad") mock_read.assert_called_once() assert result is mock_adata # Test case 3: File not found with patch('pathlib.Path.is_dir', return_value=False), \ patch('pathlib.Path.is_file', return_value=False): result = read_func(filename="nonexistent_file") assert result == "there are no file" def test_write_func(): # Create a test AnnData object adata = anndata.AnnData(X=np.array([[1, 2], [3, 4]])) with patch('scanpy.write') as mock_write, \ patch.dict(io_tools, {"write_tool": MagicMock()}): # Mock the inputSchema io_tools["write_tool"].inputSchema = {"properties": {"filename": {}}} result = write_func(adata, "write_tool", {"filename": "test.h5ad"}) mock_write.assert_called_once_with("test.h5ad", adata) assert result["msg"] == "success to save file" def test_run_io_func(): # Create a mock AnnDataStore ads = MockAnnDataStore() # Test case 1: Reading a file with patch('scmcp.tool.io.read_func') as mock_read_func: mock_adata = anndata.AnnData(X=np.array([[1, 2], [3, 4]])) mock_read_func.return_value = mock_adata result = run_io_func(ads, "read_tool", {"filename": "test.h5ad"}) mock_read_func.assert_called_once_with(filename="test.h5ad") assert result is mock_adata assert ads.active == "adata0" assert ads.adata_dic["adata0"] is mock_adata # Test case 2: Reading a file with sampleid ads = MockAnnDataStore() with patch('scmcp.tool.io.read_func') as mock_read_func: mock_adata = anndata.AnnData(X=np.array([[5, 6], [7, 8]])) mock_read_func.return_value = mock_adata result = run_io_func(ads, "read_tool", {"filename": "test.h5ad", "sampleid": "sample1"}) mock_read_func.assert_called_once_with(filename="test.h5ad", sampleid="sample1") assert result is mock_adata assert ads.active == "sample1" assert ads.adata_dic["sample1"] is mock_adata # Test case 3: Writing a file ads = MockAnnDataStore() mock_adata = anndata.AnnData(X=np.array([[9, 10], [11, 12]])) ads.adata_dic["active_sample"] = mock_adata ads.active = "active_sample" with patch('scmcp.tool.io.write_func') as mock_write_func: mock_write_func.return_value = {"filename": "test.h5ad", "msg": "success"} result = run_io_func(ads, "write_tool", {"filename": "test.h5ad"}) mock_write_func.assert_called_once_with(mock_adata, "write_tool", {"filename": "test.h5ad"}) assert result == {"filename": "test.h5ad", "msg": "success"}