Implemented jmzTab mzTab validation unit test

Noble-Lab · Aug 6, 2024 · ead0b9d · ead0b9d
1 parent 8b6d41e
commit ead0b9d
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Showing 7 changed files with 33 additions and 123 deletions.
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -26,6 +26,11 @@ jobs:
       uses: actions/setup-python@v5
       with:
         python-version: "3.10"
+    - name: Set up Java
+      uses: actions/setup-java@v3
+      with:
+        distribution: 'zulu'
+        java-version: '22'
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
@@ -40,17 +45,6 @@ jobs:
     - name: Run unit and system tests
       run: |
         pytest --cov=casanovo tests/
-    - name: Set up Java
-      uses: actions/setup-java@v3
-      with:
-        distribution: 'zulu'
-        java-version: '22'
-    - name: Run mzTab validation (Windows)
-      if: runner.os == 'Windows'
-      run: tests\mzTab_validation\validateMzTab.bat
-    - name: Run mzTab validation (Linux/macOS)
-      if: runner.os != 'Windows'
-      run: tests/mzTab_validation/validateMzTab.sh
     - name: Upload coverage to codecov
       uses: codecov/codecov-action@v4
       with:

diff --git a/tests/mzTab_validation/jmzTabValidator.jar → tests/jmzTabValidator.jar b/tests/mzTab_validation/jmzTabValidator.jar → tests/jmzTabValidator.jar
diff --git a/tests/mzTab_validation/ting_config.yaml b/tests/mzTab_validation/ting_config.yaml
diff --git a/tests/mzTab_validation/tiny_model.ckpt b/tests/mzTab_validation/tiny_model.ckpt
diff --git a/tests/mzTab_validation/validateMzTab.bat b/tests/mzTab_validation/validateMzTab.bat
diff --git a/tests/mzTab_validation/validateMzTab.sh b/tests/mzTab_validation/validateMzTab.sh
diff --git a/tests/test_integration.py b/tests/test_integration.py
@@ -1,11 +1,14 @@
 import functools
+import subprocess
 from pathlib import Path
 
 import pyteomics.mztab
 from click.testing import CliRunner
 
 from casanovo import casanovo
 
+TEST_DIR = Path(__file__).resolve().parent
+
 
 def test_train_and_run(
     mgf_small, mzml_small, tiny_config, tmp_path, monkeypatch
@@ -50,7 +53,7 @@ def test_train_and_run(
     result = run(eval_args)
     assert result.exit_code == 0
 
-    # Finally try predicting:
+    # Try predicting:
     output_filename = tmp_path / "test.mztab"
     predict_args = [
         "sequence",
@@ -86,6 +89,30 @@ def test_train_and_run(
     assert psms.loc[4, "sequence"] == "PEPTLDEK"
     assert psms.loc[4, "spectra_ref"] == "ms_run[2]:scan=111"
 
+    # Validate mztab output
+    validate_args = [
+        "java",
+        "-jar",
+        f"{TEST_DIR}/jmzTabValidator.jar",
+        "--check",
+        f"inFile={output_filename}",
+    ]
+
+    validate_result = subprocess.run(
+        validate_args,
+        stdout=subprocess.PIPE,
+        stderr=subprocess.PIPE,
+        text=True,
+    )
+
+    assert validate_result.returncode == 0
+    assert not any(
+        [
+            line.startswith("[Error-")
+            for line in validate_result.stdout.splitlines()
+        ]
+    )
+
 
 def test_auxilliary_cli(tmp_path, monkeypatch):
     """Test the secondary CLI commands"""