add more tests

test/unittests/pipelines/t1_linear/test_anat_linear_pipeline.py

@@ -244,3 +244,123 @@ def test_anat_linear_get_processed_visits_cropped_images(
     # pipeline always find an empty list of processed images because we want cropped images
     # and the CAPS folder only contains un-cropped images
     assert pipeline.get_processed_images() == []
+
+
+@pytest.mark.parametrize(
+    "config,remaining_subjects,remaining_sessions",
+    [
+        ({}, ["sub-01", "sub-01", "sub-02"], ["ses-M000", "ses-M006", "ses-M000"]),
+        (
+            {
+                "pipelines": {"t1_linear": {"uncropped_image": False}},
+                "subjects": {"sub-01": ["ses-M006"]},
+            },
+            ["sub-01", "sub-02"],
+            ["ses-M000", "ses-M000"],
+        ),
+        (
+            {
+                "pipelines": {"t1_linear": {"uncropped_image": False}},
+                "subjects": {"sub-01": ["ses-M000", "ses-M006"]},
+            },
+            ["sub-02"],
+            ["ses-M000"],
+        ),
+        (
+            {
+                "pipelines": {"t1_linear": {"uncropped_image": False}},
+                "subjects": {
+                    "sub-01": ["ses-M000", "ses-M006"],
+                    "sub-02": ["ses-M000"],
+                },
+            },
+            [],
+            [],
+        ),
+    ],
+)
+def test_determine_subject_and_session_to_process(
+    tmp_path, mocker, config, remaining_subjects, remaining_sessions
+):
+    from clinica.pipelines.t1_linear.anat_linear_pipeline import AnatLinear
+
+    mocker.patch(
+        "clinica.utils.check_dependency._get_ants_version",
+        return_value=Version("2.2.1"),
+    )
+    bids = build_bids_directory(
+        tmp_path / "bids", {"sub-01": ["ses-M000", "ses-M006"], "sub-02": ["ses-M000"]}
+    )
+    caps = build_caps_directory(tmp_path / "caps", config)
+    pipeline = AnatLinear(
+        bids_directory=str(bids),
+        caps_directory=str(caps),
+        parameters={"uncropped_image": False},
+    )
+    pipeline.determine_subject_and_session_to_process()
+    pipeline2 = AnatLinear(
+        bids_directory=str(bids),
+        caps_directory=str(caps),
+        parameters={"uncropped_image": True},
+    )
+    pipeline2.determine_subject_and_session_to_process()
+
+    assert pipeline.subjects == remaining_subjects
+    assert pipeline.sessions == remaining_sessions
+    assert pipeline2.subjects == ["sub-01", "sub-01", "sub-02"]
+    assert pipeline2.sessions == ["ses-M000", "ses-M006", "ses-M000"]
+
+
+@pytest.mark.parametrize(
+    "configuration,expected_message",
+    [
+        (
+            {
+                "pipelines": {"t1_linear": {"uncropped_image": False}},
+                "subjects": {
+                    "sub-01": ["ses-M000", "ses-M006"],
+                    "sub-02": ["ses-M000"],
+                },
+            },
+            (
+                "Clinica found already processed images for 3 visit(s):"
+                "\n- sub-01 ses-M000\n- sub-01 ses-M006\n- sub-02 ses-M000"
+                "\nThose visits will be ignored by Clinica."
+            ),
+        ),
+        (
+            {
+                "pipelines": {"t1_linear": {"uncropped_image": False}},
+                "subjects": {"sub-01": ["ses-M000", "ses-M006"]},
+            },
+            (
+                "Clinica found already processed images for 2 visit(s):"
+                "\n- sub-01 ses-M000\n- sub-01 ses-M006"
+                "\nThose visits will be ignored by Clinica."
+            ),
+        ),
+    ],
+)
+def test_determine_subject_and_session_to_process_warning(
+    tmp_path, mocker, configuration, expected_message
+):
+    from clinica.pipelines.t1_linear.anat_linear_pipeline import AnatLinear
+
+    mocker.patch(
+        "clinica.utils.check_dependency._get_ants_version",
+        return_value=Version("2.2.1"),
+    )
+    bids = build_bids_directory(
+        tmp_path / "bids", {"sub-01": ["ses-M000", "ses-M006"], "sub-02": ["ses-M000"]}
+    )
+    caps = build_caps_directory(tmp_path / "caps", configuration)
+    pipeline = AnatLinear(
+        bids_directory=str(bids),
+        caps_directory=str(caps),
+        parameters={"uncropped_image": False},
+    )
+    with pytest.warns(
+        UserWarning,
+        match=re.escape(f"In the provided CAPS folder {caps}, {expected_message}"),
+    ):
+        pipeline.determine_subject_and_session_to_process()