Use 'ImagingSite' instead of 'ImageSite'

Author: tieneupin

src/murfey/util/db.py

@@ -53,7 +53,7 @@ class Session(SQLModel, table=True):  # type: ignore
     visit_end_time: Optional[datetime] = Field(default=None)
 
     # Image sites associated with this session
-    image_sites: List["ImageSite"] = Relationship(
+    imaging_sites: List["ImagingSite"] = Relationship(
         back_populates="session",
         sa_relationship_kwargs={"cascade": "delete"},
     )
@@ -86,7 +86,7 @@ class Session(SQLModel, table=True):  # type: ignore
     )
 
 
-class ImageSite(SQLModel, table=True):  # type: ignore
+class ImagingSite(SQLModel, table=True):  # type: ignore
     """
     Table for recording unique imaging sites in the session. These can then be linked
     to DataCollectionGroup or GridSquare entries as needed.
@@ -101,7 +101,7 @@ class ImageSite(SQLModel, table=True):  # type: ignore
 
     # Link to Session table
     session: Optional["Session"] = Relationship(
-        back_populates="image_series"
+        back_populates="imaging_sites"
     )  # Many to one
     session_id: Optional[int] = Field(
         foreign_key="session.id", default=None, unique=False
@@ -112,15 +112,15 @@ class ImageSite(SQLModel, table=True):  # type: ignore
 
     # Link to data collection group
     data_collection_group: Optional["DataCollectionGroup"] = Relationship(
-        back_populates="image_sites"
+        back_populates="imaging_sites"
     )
     dcg_id: Optional[int] = Field(
         foreign_key="datacollectiongroup.dataCollectionGroupId", default=None
     )
     dcg_name: Optional[str] = Field(default=None)
 
     # Link to grid squares
-    grid_square: Optional["GridSquare"] = Relationship(back_populates="image_sites")
+    grid_square: Optional["GridSquare"] = Relationship(back_populates="imaging_sites")
     grid_square_id: Optional[int] = Field(foreign_key="gridsquare.id", default=None)
 
     # Shape and resolution information
@@ -216,7 +216,7 @@ class DataCollectionGroup(SQLModel, table=True):  # type: ignore
         back_populates="data_collection_group",
         sa_relationship_kwargs={"cascade": "delete"},
     )
-    image_sites: List["ImageSite"] = Relationship(
+    imaging_sites: List["ImagingSite"] = Relationship(
         back_populates="data_collection_group",
         sa_relationship_kwargs={"cascade": "delete"},
     )
@@ -484,7 +484,7 @@ class GridSquare(SQLModel, table=True):  # type: ignore
     pixel_size: Optional[float] = None
     image: str = ""
     session: Optional[Session] = Relationship(back_populates="grid_squares")
-    image_sites: List["ImageSite"] = Relationship(
+    imaging_sites: List["ImagingSite"] = Relationship(
         back_populates="grid_square", sa_relationship_kwargs={"cascade": "delete"}
     )
     foil_holes: List["FoilHole"] = Relationship(

src/murfey/workflows/clem/__init__.py

@@ -10,7 +10,7 @@
 
 from murfey.util.config import get_machine_config
 from murfey.util.db import (
-    ImageSite,
+    ImagingSite,
     Session as MurfeySession,
 )
 
@@ -88,11 +88,11 @@ def get_db_entry(
     # With the database search funcion having been moved out of the FastAPI
     # endpoint, the database now has to be explicitly passed within the FastAPI
     # endpoint function in order for it to be loaded in the correct state.
-    table: Type[Union[ImageSite,]],
+    table: Type[Union[ImagingSite,]],
     session_id: int,
     file_path: Optional[Path] = None,
     series_name: Optional[str] = None,
-) -> Union[ImageSite,]:
+) -> Union[ImagingSite,]:
     """
     Searches the CLEM workflow-related tables in the Murfey database for an entry that
     matches the file path or series name within a given session. Returns the entry if

src/murfey/workflows/clem/register_align_and_merge_results.py

@@ -10,7 +10,7 @@
 from pydantic import BaseModel, field_validator
 from sqlmodel import Session, select
 
-from murfey.util.db import ImageSite
+from murfey.util.db import ImagingSite
 
 logger = logging.getLogger("murfey.workflows.clem.register_align_and_merge_results")
 
@@ -84,12 +84,12 @@ def register_align_and_merge_result(
         try:
             if not (
                 clem_img_series := murfey_db.exec(
-                    select(ImageSite)
-                    .where(ImageSite.session_id == session_id)
-                    .where(ImageSite.series_name == result.series_name)
+                    select(ImagingSite)
+                    .where(ImagingSite.session_id == session_id)
+                    .where(ImagingSite.series_name == result.series_name)
                 ).one_or_none()
             ):
-                clem_img_series = ImageSite(
+                clem_img_series = ImagingSite(
                     session_id=session_id, series_name=result.series_name
                 )
             clem_img_series.composite_created = True

src/murfey/workflows/clem/register_preprocessing_results.py

@@ -86,19 +86,19 @@ def _get_color_flags(
     return color_flags
 
 
-def _register_clem_image_site(
+def _register_clem_imaging_site(
     session_id: int,
     result: CLEMPreprocessingResult,
     murfey_db: Session,
 ):
     if not (
         clem_img_site := murfey_db.exec(
-            select(MurfeyDB.ImageSite)
-            .where(MurfeyDB.ImageSite.session_id == session_id)
-            .where(MurfeyDB.ImageSite.site_name == result.series_name)
+            select(MurfeyDB.ImagingSite)
+            .where(MurfeyDB.ImagingSite.session_id == session_id)
+            .where(MurfeyDB.ImagingSite.site_name == result.series_name)
         ).one_or_none()
     ):
-        clem_img_site = MurfeyDB.ImageSite(
+        clem_img_site = MurfeyDB.ImagingSite(
             session_id=session_id, series_name=result.series_name
         )
 
@@ -281,12 +281,12 @@ def _register_dcg_and_atlas(
 
     if not (
         clem_img_site := murfey_db.exec(
-            select(MurfeyDB.ImageSite)
-            .where(MurfeyDB.ImageSite.session_id == session_id)
-            .where(MurfeyDB.ImageSite.site_name == result.series_name)
+            select(MurfeyDB.ImagingSite)
+            .where(MurfeyDB.ImagingSite.session_id == session_id)
+            .where(MurfeyDB.ImagingSite.site_name == result.series_name)
         ).one_or_none()
     ):
-        clem_img_site = MurfeyDB.ImageSite(
+        clem_img_site = MurfeyDB.ImagingSite(
             session_id=session_id, series_name=result.series_name
         )
 
@@ -314,10 +314,10 @@ def _register_grid_square(
     # Check if an atlas has been registered
     if not (
         atlas_entry := murfey_db.exec(
-            select(MurfeyDB.ImageSite)
-            .where(MurfeyDB.ImageSite.session_id == session_id)
-            .where(MurfeyDB.ImageSite.dcg_name == dcg_name)
-            .where(MurfeyDB.ImageSite.data_type == "atlas")
+            select(MurfeyDB.ImagingSite)
+            .where(MurfeyDB.ImagingSite.session_id == session_id)
+            .where(MurfeyDB.ImagingSite.dcg_name == dcg_name)
+            .where(MurfeyDB.ImagingSite.data_type == "atlas")
         ).one_or_none()
     ):
         logger.info(
@@ -327,10 +327,10 @@ def _register_grid_square(
 
     # Check if there are CLEM entries to register
     if clem_img_site_to_register := murfey_db.exec(
-        select(MurfeyDB.ImageSite)
-        .where(MurfeyDB.ImageSite.session_id == session_id)
-        .where(MurfeyDB.ImageSite.dcg_name == dcg_name)
-        .where(MurfeyDB.ImageSite.data_type == "grid_square")
+        select(MurfeyDB.ImagingSite)
+        .where(MurfeyDB.ImagingSite.session_id == session_id)
+        .where(MurfeyDB.ImagingSite.dcg_name == dcg_name)
+        .where(MurfeyDB.ImagingSite.data_type == "grid_square")
     ).all():
         if (
             atlas_entry.x0 is not None
@@ -521,7 +521,7 @@ def run(message: dict, murfey_db: Session) -> dict[str, bool]:
             return {"success": False, "requeue": False}
         try:
             # Register items in Murfey database
-            _register_clem_image_site(
+            _register_clem_imaging_site(
                 session_id=session_id,
                 result=result,
                 murfey_db=murfey_db,

tests/workflows/clem/test_register_preprocessing_results.py

@@ -15,7 +15,7 @@
     COLOR_FLAGS_MURFEY_TO_ISPYB,
     _determine_collection_mode,
     _get_color_flags,
-    _register_clem_image_site,
+    _register_clem_imaging_site,
     _register_dcg_and_atlas,
     _register_grid_square,
     _snake_to_camel_case,
@@ -173,8 +173,8 @@ def test_get_color_flags(test_params: tuple[list[str], dict[str, bool]]):
     assert _get_color_flags(colors) == expected_result
 
 
-def test_register_clem_image_site():
-    _register_clem_image_site
+def test_register_clem_imaging_site():
+    _register_clem_imaging_site
 
 
 @pytest.mark.parametrize(
@@ -243,7 +243,7 @@ def test_run(
 
     # Mock the registration helper functions
     mock_register_clem_series = mocker.patch(
-        "murfey.workflows.clem.register_preprocessing_results._register_clem_image_site"
+        "murfey.workflows.clem.register_preprocessing_results._register_clem_imaging_site"
     )
     mock_register_dcg_and_atlas = mocker.patch(
         "murfey.workflows.clem.register_preprocessing_results._register_dcg_and_atlas"