Added test module for the 'register_atlas' FIB workflow

Author: tieneupin

tests/workflows/fib/test_register_atlas.py

@@ -0,0 +1,83 @@
+from pathlib import Path
+
+import pytest
+from pytest_mock import MockerFixture
+from sqlmodel import Session, select
+
+import murfey.util.db as MurfeyDB
+from murfey.workflows.fib.register_atlas import FIBAtlasMetadata, run
+
+session_id = 10
+visit_name = "cm12345-6"
+instrument_name = "test_instrument"
+
+
+@pytest.fixture
+def visit_dir(tmp_path: Path):
+    visit_dir = tmp_path / "data/2020" / visit_name
+    visit_dir.mkdir(parents=True, exist_ok=True)
+    return visit_dir
+
+
+def test_parse_metadata():
+    pass
+
+
+def test_register_fib_imaging_site():
+    pass
+
+
+def test_run_with_db(
+    mocker: MockerFixture,
+    visit_dir: Path,
+    murfey_db_session: Session,
+):
+    test_file = (
+        visit_dir / "maps/LayersData/Layer/Electron Snapshot/Electron Snapshot.tiff"
+    )
+
+    # Add a test visit to the database
+    if not (
+        session_entry := murfey_db_session.exec(
+            select(MurfeyDB.Session).where(MurfeyDB.Session.id == session_id)
+        ).one_or_none()
+    ):
+        session_entry = MurfeyDB.Session(id=session_id)
+    session_entry.name = visit_name
+    session_entry.visit = visit_name
+    session_entry.instrument_name = instrument_name
+
+    murfey_db_session.add(session_entry)
+    murfey_db_session.commit()
+
+    # Mock the metadata returned from the image file
+    mock_metadata = FIBAtlasMetadata(
+        visit_name=visit_name,
+        file=test_file,
+        voltage=2000,
+        shift_x=0,
+        shift_y=0,
+        len_x=0.003072,
+        len_y=0.002048,
+        pos_x=0.003,
+        pos_y=0.0003,
+        pos_z=0.01,
+        rotation=-1.309,
+        tilt_alpha=0.8,
+        tilt_beta=0,
+        pixels_x=3072,
+        pixels_y=2048,
+        pixel_size_x=1e-6,
+        pixel_size_y=1e-6,
+    )
+    mocker.patch(
+        "murfey.workflows.fib.register_atlas._parse_metadata",
+        return_value=mock_metadata,
+    )
+
+    # Run the function and check that it's run through to completion
+    assert run(
+        session_id=session_id,
+        file=test_file,
+        murfey_db=murfey_db_session,
+    )