Added test to check that the '_scan_directory' class function works for the CLEM workflow with an active blacklist

Author: tieneupin

tests/client/test_watchdir.py

@@ -9,18 +9,10 @@
 from tests.conftest import ExampleVisit
 
 
-@pytest.fixture
-def visit_dir(tmp_path: Path):
-    visit_name = f"{ExampleVisit.proposal_code}{ExampleVisit.proposal_number}-{ExampleVisit.visit_number}"
-    visit_dir = tmp_path / "data" / "2025" / visit_name
-    visit_dir.mkdir(parents=True, exist_ok=True)
-    return visit_dir
-
-
-def test_dirwatcher_initialises(visit_dir: Path):
+def test_dirwatcher_initialises(tmp_path: Path):
     # Check that the DirWatcher initialises with the default attributes
-    watcher = DirWatcher(path=str(visit_dir))
-    assert watcher._basepath == os.fspath(visit_dir)
+    watcher = DirWatcher(path=str(tmp_path))
+    assert watcher._basepath == os.fspath(str(tmp_path))
     assert watcher._lastscan == {}
     assert watcher._file_candidates == {}
     assert watcher._statusbar is None
@@ -36,9 +28,152 @@ def test_dirwatcher_initialises(visit_dir: Path):
     assert watcher._halt_thread is False
 
     # Check that the string representation is as expected
-    assert str(watcher) == f"<DirWatcher ({os.fspath(str(visit_dir))})>"
+    assert str(watcher) == f"<DirWatcher ({os.fspath(str(tmp_path))})>"
+
+
+@pytest.fixture
+def clem_visit_dir(tmp_path: Path):
+    visit_name = f"{ExampleVisit.proposal_code}{ExampleVisit.proposal_number}-{ExampleVisit.visit_number}"
+    visit_dir = tmp_path / "clem" / "data" / "2025" / visit_name
+    visit_dir.mkdir(parents=True, exist_ok=True)
+    return visit_dir
+
+
+@pytest.fixture
+def clem_test_files(clem_visit_dir: Path):
+    # Create test files for the DirWatcher to scan
+    file_list: list[Path] = []
+    project_dir = clem_visit_dir / "images" / "test_grid"
+
+    # Example atlas collection
+    for s in range(20):
+        file_list.append(
+            project_dir
+            / "Overview 1"
+            / "Image 1"
+            / f"Image 1--Stage{str(s).zfill(2)}.tif"
+        )
+    file_list.append(
+        project_dir / "Overview 1" / "Image 1" / "Metadata" / "Image 1.xlif"
+    )
+
+    # Example image stack collection
+    for c in range(3):
+        for z in range(10):
+            file_list.append(
+                project_dir
+                / "TileScan 1"
+                / "Position 1"
+                / f"Position 1--C{str(c).zfill(2)}--Z{str(z).zfill(2)}.tif"
+            )
+    file_list.append(
+        project_dir / "TileScan 1" / "Position 1" / "Metadata" / "Position 1.xlif"
+    )
+
+    # Create all files and directories specified
+    for file in file_list:
+        if not file.parent.exists():
+            file.parent.mkdir(parents=True)
+        if not file.exists():
+            file.touch()
+    return sorted(file_list)
+
+
+@pytest.fixture
+def clem_junk_files(clem_visit_dir: Path):
+    # Create junk files that are to be blacklisted from the CLEM workflow
+    file_list: list[Path] = []
+    project_dir = clem_visit_dir / "images" / "test_grid"
+
+    # Create junk atlas data
+    for n in range(5):
+        for s in range(20):
+            file_list.append(
+                project_dir
+                / "Image 1"
+                / f"Image 1_pmd_{n}"
+                / f"Image 1_pmd_{n}--Stage{str(s).zfill(2)}.tif"
+            )
+        file_list.append(
+            project_dir / "Image 1" / f"Image 1_pmd_{n}" / "Metadata" / "Image 1.xlif"
+        )
+
+    # Creat junk image data
+    for n in range(5):
+        for c in range(3):
+            for z in range(10):
+                file_list.append(
+                    project_dir
+                    / "Position 1"
+                    / f"Position 1_pmd_{n}"
+                    / f"Position 1_pmd_{n}--C{str(c).zfill(2)}--Z{str(z).zfill(2)}.tif"
+                )
+        file_list.append(
+            project_dir
+            / "Position 1"
+            / f"Position 1_pmd_{n}"
+            / "Metadata"
+            / "Position 1.xlif"
+        )
+
+    # Create remaining junk files
+    for file_path in (
+        "1.xlef",
+        "Metadata/IOManagerConfiguation.xlif",
+        "Metadata/Overview 1.xlcf",
+        "Metadata/TileScan 1.xlcf",
+        "Overview 1/Image 1/Image 1_histo.lof",
+        "TileScan 1/Position 1/Position 1_histo.lof",
+        "Overview 1/Image 1/Metadata/Image 1_histo.xlif",
+        "TileScan 1/Position 1/Metadata/Position 1_histo.xlif",
+    ):
+        file_list.append(project_dir / file_path)
+
+    # Create files and directoriees
+    for file in file_list:
+        if not file.parent.exists():
+            file.parent.mkdir(parents=True)
+        if not file.exists():
+            file.touch()
+    return sorted(file_list)
+
+
+scan_directory_params_matrix: tuple[tuple[str, dict[str, list[str]]], ...] = (
+    # Workflow type | Substrings blacklist
+    (
+        "clem",
+        {
+            "directories": [
+                "_pmd_",
+            ],
+            "files": [
+                ".xlef",
+                ".xlcf",
+                "_histo.lof",
+                "_histo.xlif",
+                "IOManagerConfiguation.xlif",
+            ],
+        },
+    ),
+)
+
 
+@pytest.mark.parametrize("test_params", scan_directory_params_matrix)
+def test_scan_directory(
+    clem_visit_dir: Path,
+    clem_test_files: list[Path],
+    clem_junk_files: list[Path],
+    test_params: tuple[str, dict[str, list[str]]],
+):
+    # Unpack test params
+    workflow_type, substrings_blacklist = test_params
 
-@pytest.mark.skip
-def test_scan_directory():
-    pass
+    # Initialise different watchers based on the workflow to test and run the scan
+    if workflow_type == "clem":
+        watcher = DirWatcher(
+            path=str(clem_visit_dir),
+            substrings_blacklist=substrings_blacklist,
+        )
+        result = watcher._scan_directory()
+    # Check that the result does not contain the junk files
+    assert [str(file) for file in clem_test_files] == sorted(result.keys())