Release v1.8.1

CHANGELOG.rst

@@ -2,6 +2,14 @@
 Changelog
 ==========
 
++++++++++
+v1.8.1 (23/09/2024)
++++++++++
+
+**Changed**
+
+- Semgented/denoised tomogram images are now sourced from the `ProcessedTomogram` table
+
 +++++++++
 v1.8.0 (28/08/2024)
 +++++++++

Dockerfile

@@ -3,7 +3,7 @@
 # The devcontainer should use the build target and run as root with podman
 # or docker with user namespaces.
 #
-FROM docker.io/library/python:3.12.4-slim-bookworm as build
+FROM docker.io/library/python:3.12.5-slim-bookworm as build
 
 # Add any system dependencies for the developer/build environment here
 RUN apt-get update && apt-get upgrade -y && \
@@ -12,6 +12,7 @@ RUN apt-get update && apt-get upgrade -y && \
     busybox \
     git \
     libmariadb-dev \
+    pkg-config \
     net-tools \
     && rm -rf /var/lib/apt/lists/* \
     && busybox --install
@@ -39,7 +40,7 @@ RUN pip install --upgrade pip && \
     # and replace with a comment to avoid a zero length asset upload later
     sed -i '/file:/s/^/# Requirements for /' lockfiles/requirements.txt
 
-FROM docker.io/library/python:3.12.1-slim-bullseye as runtime
+FROM docker.io/library/python:3.12.5-slim-bookworm as runtime
 
 # Add apt-get system dependecies for runtime here if needed
 RUN apt-get update && apt-get install -y libmariadb-dev

pyproject.toml

@@ -16,15 +16,15 @@ description = "PATO's backend"
 dependencies = [
     "python-multipart~=0.0.9",
     "pika~=1.3.2",
-    "SQLAlchemy~=2.0.31",
-    "fastapi~=0.111.0",
+    "SQLAlchemy~=2.0.34",
+    "fastapi~=0.112.2",
     "uvicorn[standard]~=0.30.1",
     "requests~=2.32.3",
-    "mysqlclient~=2.1.1",
+    "mysqlclient~=2.2.4",
     "mysql-connector-python~=8.2.0",
-    "pydantic~=2.5.3",
+    "pydantic~=2.8.2",
     "types-requests",
-    "lims-utils~=0.2.2"
+    "lims-utils~=0.2.3"
 ]
 dynamic = ["version"]
 license.file = "LICENSE"
@@ -61,6 +61,7 @@ name = "Guilherme de Freitas"
 
 [tool.setuptools_scm]
 write_to = "src/pato/_version.py"
+fallback_version = "1.9.0"
 
 [tool.mypy]
 ignore_missing_imports = true # Ignore missing stubs in imported modules

src/pato/crud/groups.py

@@ -28,7 +28,6 @@ def get_collection_groups(
     search: Optional[str],
     user: GenericUser,
 ) -> Paged[DataCollectionGroupSummaryResponse]:
-
     query = (
         select(
             *unravel(DataCollectionGroup),

src/pato/crud/tomograms.py

@@ -6,6 +6,7 @@
     CTF,
     MotionCorrection,
     Movie,
+    ProcessedTomogram,
     TiltImageAlignment,
     Tomogram,
 )
@@ -31,7 +32,6 @@ def _get_generic_tomogram_file(tomogramId: int, column: Column) -> Optional[str]
     )
 
 
-@validate_path
 def _prepend_denoise(
     base_path: str, image_type: Literal["thumbnail", "movie"], movie_type: MovieType
 ):
@@ -50,6 +50,30 @@ def _prepend_denoise(
     return split_file[0] + denoised_prefix + "".join(split_file[1:3])
 
 
+@validate_path
+def _get_movie(
+    tomogramId: int, movie_type: MovieType, image_type: Literal["thumbnail", "movie"]
+):
+    if movie_type:
+        # If movie_Type is defined, this means that this is not the standard noisy tomogram we're looking for
+        base_path = db.session.scalar(
+            select(ProcessedTomogram.filePath).filter(
+                ProcessedTomogram.tomogramId == tomogramId,
+                ProcessedTomogram.processingType == movie_type.capitalize(),
+            )
+        )
+
+        if base_path:
+            suffix = "_movie.png" if image_type == "movie" else "_thumbnail.jpeg"
+            return base_path.replace(".mrc", suffix)
+
+    column = (
+        Tomogram.tomogramMovie if image_type == "movie" else Tomogram.centralSliceImage
+    )
+    base_path = _get_generic_tomogram_file(tomogramId, column)
+    return _prepend_denoise(base_path, image_type, movie_type)
+
+
 @validate_path
 def _get_shift_plot_path(tomogramId: int):
     return _get_generic_tomogram_file(tomogramId, Tomogram.xyShiftPlot)
@@ -127,13 +151,11 @@ def get_ctf(tomogramId: int):
 
 
 def get_slice_path(tomogramId: int, movie_type: MovieType):
-    base_path = _get_generic_tomogram_file(tomogramId, Tomogram.centralSliceImage)
-    return _prepend_denoise(base_path, "thumbnail", movie_type)
+    return _get_movie(tomogramId, movie_type, "thumbnail")
 
 
 def get_movie_path(tomogramId: int, movie_type: MovieType):
-    base_path = _get_generic_tomogram_file(tomogramId, Tomogram.tomogramMovie)
-    return _prepend_denoise(base_path, "movie", movie_type)
+    return _get_movie(tomogramId, movie_type, "movie")
 
 
 def get_projection_path(tomogramId: int, axis: Literal["xy", "xz"]):

tests/tomograms/test_central_slice.py

@@ -1,5 +1,7 @@
 from unittest.mock import patch
 
+import pytest
+
 from ..conftest import mock_send
 
 
@@ -10,20 +12,13 @@ def test_get(mock_permissions, client):
         assert resp.status_code == 200
 
 
-def test_get_denoised(mock_permissions, exists_mock, client):
-    """Get denoised central slice for tomogram"""
-    with patch("pato.routes.tomograms.FileResponse.__call__", new=mock_send):
-        resp = client.get("/tomograms/1/centralSlice?movieType=denoised")
-        assert resp.status_code == 200
-        exists_mock.assert_called_with("/dls/test.denoised_thumbnail.png")
-
-
-def test_get_segmented(mock_permissions, exists_mock, client):
-    """Get segmented central slice for tomogram"""
+@pytest.mark.parametrize("movie_type, expected", [("segmented", "denoised_segmented"), ("denoised", "denoised")])
+def test_get_movie_type(mock_permissions, exists_mock, client, movie_type, expected):
+    """Get central slice for tomogram by processing type"""
     with patch("pato.routes.tomograms.FileResponse.__call__", new=mock_send):
-        resp = client.get("/tomograms/1/centralSlice?movieType=segmented")
+        resp = client.get(f"/tomograms/1/centralSlice?movieType={movie_type}")
         assert resp.status_code == 200
-        exists_mock.assert_called_with("/dls/test.denoised_segmented_thumbnail.png")
+        exists_mock.assert_called_with(f"/dls/test.{expected}_thumbnail.png")
 
 
 def test_get_denoised_invalid_name(mock_permissions, exists_mock, client):
@@ -44,3 +39,11 @@ def test_inexistent_file(mock_permissions, client):
     """Try to get central slice for tomogram not in database"""
     resp = client.get("/tomograms/221/centralSlice")
     assert resp.status_code == 404
+
+@pytest.mark.parametrize("movie_type, expected", [("segmented", "denoised_segmented"), ("denoised", "denoised")])
+def test_get_movie_type_processed(mock_permissions, exists_mock, client, movie_type, expected):
+    """Get central slice for tomogram by processing type from ProcessedTomogram table"""
+    with patch("pato.routes.tomograms.FileResponse.__call__", new=mock_send):
+        resp = client.get(f"/tomograms/3/centralSlice?movieType={movie_type}")
+        assert resp.status_code == 200
+        exists_mock.assert_called_with(f"/dls/test.{expected}_thumbnail.jpeg")

tests/tomograms/test_movie.py

@@ -1,5 +1,7 @@
 from unittest.mock import patch
 
+import pytest
+
 from tests.conftest import mock_send
 
 
@@ -9,23 +11,14 @@ def test_get_movie(mock_permissions, client):
         resp = client.get("/tomograms/1/movie")
     assert resp.status_code == 200
 
-
-def test_get_denoised(mock_permissions, exists_mock, client):
-    """Get denoised movie"""
-    with patch("pato.routes.tomograms.FileResponse.__call__", new=mock_send):
-        resp = client.get("/tomograms/1/movie?movieType=denoised")
-        exists_mock.assert_called_with("/dls/test.denoised_movie.png")
-    assert resp.status_code == 200
-
-
-def test_get_segmented(mock_permissions, exists_mock, client):
-    """Get segmented movie"""
+@pytest.mark.parametrize("movie_type, expected", [("segmented", "denoised_segmented"), ("denoised", "denoised")])
+def test_get_movie_processing_type(mock_permissions, exists_mock, client, movie_type, expected):
+    """Get movie by processing type"""
     with patch("pato.routes.tomograms.FileResponse.__call__", new=mock_send):
-        resp = client.get("/tomograms/1/movie?movieType=segmented")
-        exists_mock.assert_called_with("/dls/test.denoised_segmented_movie.png")
+        resp = client.get(f"/tomograms/1/movie?movieType={movie_type}")
+        exists_mock.assert_called_with(f"/dls/test.{expected}_movie.png")
     assert resp.status_code == 200
 
-
 def test_get_denoised_invalid_name(mock_permissions, exists_mock, client):
     """Get denoised movie (with non-conforming filename)"""
     with patch("pato.routes.tomograms.FileResponse.__call__", new=mock_send):
@@ -44,3 +37,11 @@ def test_inexistent_db(mock_permissions, client):
     """Try to get movie image that does not exist in database"""
     resp = client.get("/tomograms/999/movie")
     assert resp.status_code == 404
+
+@pytest.mark.parametrize("movie_type, expected", [("segmented", "denoised_segmented"), ("denoised", "denoised")])
+def test_get_movie_type_processed(mock_permissions, exists_mock, client, movie_type, expected):
+    """Get denoised movie from ProcessedTomogram table"""
+    with patch("pato.routes.tomograms.FileResponse.__call__", new=mock_send):
+        resp = client.get(f"/tomograms/3/movie?movieType={movie_type}")
+        exists_mock.assert_called_with(f"/dls/test.{expected}_movie.png")
+    assert resp.status_code == 200