From ae6275237558cd68895eeb768668193efd81106a Mon Sep 17 00:00:00 2001
From: Daniel McCloy <dan@mccloy.info>
Date: Wed, 2 Oct 2024 15:34:40 -0500
Subject: [PATCH] almost there [ci skip]

---
 mne_bids_pipeline/tests/test_run.py | 64 +++++++++++++++++++++++++++++
 1 file changed, 64 insertions(+)

diff --git a/mne_bids_pipeline/tests/test_run.py b/mne_bids_pipeline/tests/test_run.py
index 952be5f13..069fccf02 100644
--- a/mne_bids_pipeline/tests/test_run.py
+++ b/mne_bids_pipeline/tests/test_run.py
@@ -4,6 +4,7 @@
 import shutil
 import sys
 from collections.abc import Collection
+from contextlib import nullcontext
 from pathlib import Path
 from typing import TypedDict
 
@@ -204,3 +205,66 @@ def test_run(dataset, monkeypatch, dataset_test, capsys, tmp_path):
     with capsys.disabled():
         print()
         main()
+
+
+@pytest.mark.parametrize("allow_missing_sessions", (False, True))
+def test_missing_sessions(tmp_path, monkeypatch, capsys, allow_missing_sessions):
+    """Test the `allow_missing_sessions` config variable."""
+    dataset = "ds001810"
+    # exclude all except 1 session ("ses-anodalpost")
+    exclude = (
+        "ses-anodalpre",
+        "ses-anodaltDCS",
+        "ses-cathodalpost",
+        "ses-cathodalpre",
+        "ses-cathodaltDCS",
+    )
+    # subset the dataset by symlinking in a temp dir
+    src_dir = Path(f"~/mne_data/{dataset}").expanduser()
+    link_dir = tmp_path / dataset
+    link_dir.mkdir()
+    for dirpath, dirnames, filenames in src_dir.walk():
+        if any(excl in dirpath.parts for excl in exclude):
+            continue
+        for dirname in dirnames:
+            if dirname not in exclude:
+                target = (dirpath / dirname).absolute()
+                link = link_dir / target.relative_to(src_dir)
+                link.mkdir()
+        for fname in filenames:
+            target = (dirpath / fname).absolute()
+            link = link_dir / target.relative_to(src_dir)
+            link.symlink_to(target)
+    # fake a config file
+    config = dict(
+        bids_root=f'"{link_dir}"',
+        deriv_root=f'"{tmp_path / "derivatives" / "mne-bids-pipeline" / dataset}"',
+        interactive=False,
+        subjects=["01"],
+        sessions=["ses-anodalpost", "ses-anodalpre"],
+        ch_types=["eeg"],
+        conditions=["61450", "61511"],
+        allow_missing_sessions=allow_missing_sessions,
+    )
+    config_fname = "config_ds001810_missing_session.py"
+    config_path = tmp_path / config_fname
+    with open(config_path, "w") as fid:
+        for key, val in config.items():
+            fid.write(f"{key} = {val}\n")
+    # set up the context handler
+    context = (
+        nullcontext()
+        if allow_missing_sessions
+        else pytest.raises(RuntimeError, match="is missing session ('ses-anodalpre',)")
+    )
+    # run
+    steps = ("init/_01_init_derivatives_dir",)
+    command = ["mne_bids_pipeline", str(config_path), f'--steps={",".join(steps)}']
+    if "--pdb" in sys.argv:
+        command.append("--n_jobs=1")
+    monkeypatch.setenv("_MNE_BIDS_STUDY_TESTING", "true")
+    monkeypatch.setattr(sys, "argv", command)
+    with capsys.disabled():
+        print()
+        with context:
+            main()