tests changed

tests/test_commands.py

@@ -1,161 +1,148 @@
 from pathlib import Path
-
+import os
 import pandas as pd
 import pytest
 from click.testing import CliRunner
 from quantmsutils.quantmsutilsc import cli
 
+# Define constants at the top for better maintainability
 TESTS_DIR = Path(__file__).parent
-
-
-# test for the create_diann_cfg command in cli
-def test_create_diann_cfg_help():
-    runner = CliRunner()
-    result = runner.invoke(cli, ["dianncfg", "--help"])
-
-    assert result.exit_code == 0
-
-
-# test for the mzml_statistics command in cli
-def test_mzml_statistics_help():
-    runner = CliRunner()
-    result = runner.invoke(cli, ["mzmlstats", "--help"])
-
-    assert result.exit_code == 0
-
-
-# test for the diann_convert command in cli
-def test_diann_convert_help():
-    runner = CliRunner()
-    result = runner.invoke(cli, ["diann2mztab", "--help"])
-
-    assert result.exit_code == 0
-
-
-# test for the extract_sample_from_expdesign command in cli
-def test_extract_sample_from_expdesign_help():
+TEST_DATA_DIR = TESTS_DIR / "test_data"
+DIANN_TEST_DIR = TEST_DATA_DIR / "diann2mztab"
+BSA_IDXML_FILE = TEST_DATA_DIR / "BSA1_F1_msgf_idx_fdr_idpep_switched_filter.idXML"
+BSA_SPECTRA_FILE = TEST_DATA_DIR / "BSA1_F1_spectrum_df.parquet"
+BSA_MZML_FILE = TEST_DATA_DIR / "BSA1_F1.mzML"
+BSA_MS_INFO_FILE = TEST_DATA_DIR / "BSA1_F1_ms_info.parquet"
+BSA_TEST_MS_INFO_FILE = TEST_DATA_DIR / "BSA1_F1_test_ms_info.parquet"
+TMT_MZML_FILE = TEST_DATA_DIR / "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML"
+TMT_MS_INFO_FILE = TEST_DATA_DIR / "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01_ms_info.parquet"
+
+
+# Helper function to create a CLI runner and run a command
+def run_cli_command(command, args=None):
     runner = CliRunner()
-    result = runner.invoke(cli, ["openms2sample", "--help"])
+    if args:
+        result = runner.invoke(cli, [command] + args)
+    else:
+        result = runner.invoke(cli, [command, "--help"])
+    return result
 
-    assert result.exit_code == 0
 
+class TestCLIHelpMessages:
+    """Test class for CLI help messages"""
 
-def test_diann2mztab_example():
-    runner = CliRunner()
-    result = runner.invoke(
-        cli,
+    @pytest.mark.parametrize(
+        "command",
         [
+            "dianncfg",
+            "mzmlstats",
             "diann2mztab",
-            "--folder",
-            "tests/test_data/diann2mztab/",
-            "--exp_design",
-            "tests/test_data/diann2mztab/PXD026600.sdrf_openms_design.tsv",
-            "--diann_version",
-            "tests/test_data/diann2mztab/versions.yml",
-            "--dia_params",
-            "20.0;ppm;10.0;ppm;Trypsin;Carbamidomethyl (C);Oxidation (M)",
-            "--charge",
-            "3",
-            "--missed_cleavages",
-            "1",
-            "--qvalue_threshold",
-            "0.01",
-        ],
-    )
-    assert result.exit_code == 0
-
-
-# test for the convert_psm command in cli
-def test_convert_psm_help():
-    runner = CliRunner()
-    result = runner.invoke(cli, ["psmconvert", "--help"])
-
-    assert result.exit_code == 0
-
-
-def test_check_samplesheet_help():
-    runner = CliRunner()
-    result = runner.invoke(cli, ["checksamplesheet", "--help"])
-
-    assert result.exit_code == 0
-
-
-# test the validation of an SDRF file
-def test_check_samplesheet_sdrf():
-    runner = CliRunner()
-    result = runner.invoke(
-        cli,
-        [
-            "checksamplesheet",
-            "--is_sdrf",
-            "--exp_design",
-            "tests/test_data/PXD000001.sdrf.tsv",
-        ],
-    )
-
-    assert result.exit_code == 0
-
-
-# test extract_sample_from_expdesign command in cli
-def test_extract_sample_from_expdesign():
-    runner = CliRunner()
-    result = runner.invoke(
-        cli, ["openms2sample", "--expdesign", "tests/test_data/BSA_design_urls.tsv"]
-    )
-
-    assert result.exit_code == 0
-
-
-# test psm conversion command in cli
-def test_convert_psm():
-    runner = CliRunner()
-    result = runner.invoke(
-        cli,
-        [
+            "openms2sample",
             "psmconvert",
-            "--idxml",
-            "tests/test_data/BSA1_F1_msgf_idx_fdr_idpep_switched_filter.idXML",
-            "--spectra_file",
-            "tests/test_data/BSA1_F1_spectrum_df.parquet",
+            "checksamplesheet",
         ],
     )
-
-    assert result.exit_code == 0
-
-
-# test mzml statistics command in cli
-def test_mzml_statistics():
-    runner = CliRunner()
-
-    mzml_path = TESTS_DIR / "test_data" / "BSA1_F1.mzML"
-
-    # check if the file exist, delete it
-    ms_info_path = TESTS_DIR / "test_data" / "BSA1_F1_ms_info.parquet"
-    if ms_info_path.exists():
-        ms_info_path.unlink()
-
-    result = runner.invoke(cli, ["mzmlstats", "--id_only", "--ms_path", mzml_path])
-    table2 = pd.read_parquet(ms_info_path)
-
-    table1 = pd.read_parquet(TESTS_DIR / "test_data" / "BSA1_F1_test_ms_info.parquet")
-    table2 = table2.set_index("scan")
-    table1 = table1.set_index("scan")
-    assert len(table2) == len(table1)
-
-    assert result.exit_code == 0
-
-def test_mzml_statistics_local():
-    runner = CliRunner()
-
-    mzml_path = TESTS_DIR / "test_data" / "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML"
-
-    # check if the file exist, delete it
-    ms_info_path = TESTS_DIR / "test_data" / "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01_ms_info.parquet"
-    if ms_info_path.exists():
-        ms_info_path.unlink()
-
-    result = runner.invoke(cli, ["mzmlstats", "--id_only", "--ms_path", mzml_path])
-    table = pd.read_parquet(ms_info_path)
-
-    assert len(table) > 0
-    assert result.exit_code == 0
+    def test_help_messages(self, command):
+        """Test all CLI help messages with a parametrized test"""
+        result = run_cli_command(command)
+        assert result.exit_code == 0
+        assert "Usage:" in result.output
+
+
+class TestDiannCommands:
+    """Test class for DIA-NN related commands"""
+
+    def test_diann2mztab_example(self):
+        """Test the DIA-NN to mzTab conversion with example data"""
+        args = [
+            "--folder", str(DIANN_TEST_DIR),
+            "--exp_design", str(DIANN_TEST_DIR / "PXD026600.sdrf_openms_design.tsv"),
+            "--diann_version", str(DIANN_TEST_DIR / "versions.yml"),
+            "--dia_params", "20.0;ppm;10.0;ppm;Trypsin;Carbamidomethyl (C);Oxidation (M)",
+            "--charge", "3",
+            "--missed_cleavages", "1",
+            "--qvalue_threshold", "0.01",
+        ]
+        result = run_cli_command("diann2mztab", args)
+        assert result.exit_code == 0
+        # Additional assertions could check for expected output files
+
+
+class TestSamplesheetCommands:
+    """Test class for samplesheet related commands"""
+
+    def test_check_samplesheet_sdrf(self):
+        """Test the validation of an SDRF file"""
+        args = [
+            "--is_sdrf",
+            "--exp_design", str(TEST_DATA_DIR / "PXD000001.sdrf.tsv"),
+        ]
+        result = run_cli_command("checksamplesheet", args)
+        assert result.exit_code == 0
+
+    def test_extract_sample_from_expdesign(self):
+        """Test extracting sample information from experiment design"""
+        args = ["--expdesign", str(TEST_DATA_DIR / "BSA_design_urls.tsv")]
+        result = run_cli_command("openms2sample", args)
+        assert result.exit_code == 0
+        # Could add assertions to check for expected output files
+
+
+class TestPSMConversion:
+    """Test class for PSM conversion commands"""
+
+    def test_convert_psm(self):
+        """Test converting PSM data"""
+        args = [
+            "--idxml", str(BSA_IDXML_FILE),
+            "--spectra_file", str(BSA_SPECTRA_FILE),
+        ]
+        result = run_cli_command("psmconvert", args)
+        assert result.exit_code == 0
+        # Could add assertions to check for expected output files
+
+
+class TestMzMLStatistics:
+    """Test class for mzML statistics commands"""
+
+    @pytest.fixture(autouse=True)
+    def setup_teardown(self):
+        """Setup and teardown for mzML statistics tests"""
+        # Setup - remove output files if they exist
+        if BSA_MS_INFO_FILE.exists():
+            BSA_MS_INFO_FILE.unlink()
+        if TMT_MS_INFO_FILE.exists():
+            TMT_MS_INFO_FILE.unlink()
+        yield
+        # Teardown - can add cleanup code here if needed
+
+    def test_mzml_statistics_bsa(self):
+        """Test mzML statistics on BSA sample"""
+        args = ["--id_only", "--ms_path", str(BSA_MZML_FILE)]
+        result = run_cli_command("mzmlstats", args)
+
+        assert result.exit_code == 0
+        assert BSA_MS_INFO_FILE.exists(), "Output file was not created"
+
+        # Compare with reference data
+        output_table = pd.read_parquet(BSA_MS_INFO_FILE).set_index("scan")
+        reference_table = pd.read_parquet(BSA_TEST_MS_INFO_FILE).set_index("scan")
+
+        assert len(output_table) == len(reference_table), "Number of scans doesn't match"
+        # Could add more specific comparisons of table contents
+
+    def test_mzml_statistics_tmt(self):
+        """Test mzML statistics on TMT sample"""
+        args = ["--id_only", "--ms_path", str(TMT_MZML_FILE)]
+        result = run_cli_command("mzmlstats", args)
+
+        assert result.exit_code == 0
+        assert TMT_MS_INFO_FILE.exists(), "Output file was not created"
+
+        output_table = pd.read_parquet(TMT_MS_INFO_FILE)
+        assert len(output_table) > 0, "Output table is empty"
+
+        # Could add assertions for expected columns or data validation
+        expected_columns = ["scan", "rt", "ms_level", "precursor_charge"]
+        for col in expected_columns:
+            assert col in output_table.columns, f"Expected column {col} missing from output"