diff --git a/src/murfey/server/__init__.py b/src/murfey/server/__init__.py index 11c4b3b35..3ee46cc80 100644 --- a/src/murfey/server/__init__.py +++ b/src/murfey/server/__init__.py @@ -2940,7 +2940,7 @@ def feedback_callback(header: dict, message: dict) -> None: )[0] result = workflow.load()( message=message, - db=murfey_db, + murfey_db=murfey_db, ) if _transport_object: if result: diff --git a/src/murfey/workflows/clem/register_align_and_merge_results.py b/src/murfey/workflows/clem/register_align_and_merge_results.py index 40d5b3946..b02c56a30 100644 --- a/src/murfey/workflows/clem/register_align_and_merge_results.py +++ b/src/murfey/workflows/clem/register_align_and_merge_results.py @@ -42,7 +42,7 @@ def parse_stringified_list(cls, value): def register_align_and_merge_result( - message: dict, db: Session, demo: bool = False + message: dict, murfey_db: Session, demo: bool = False ) -> bool: """ session_id (recipe) @@ -91,16 +91,16 @@ def register_align_and_merge_result( # Register items in database if not already present try: clem_img_series: CLEMImageSeries = get_db_entry( - db=db, + db=murfey_db, table=CLEMImageSeries, session_id=session_id, series_name=result.series_name, ) clem_img_series.composite_image = str(result.composite_image) clem_img_series.composite_created = True - db.add(clem_img_series) - db.commit() - db.refresh(clem_img_series) + murfey_db.add(clem_img_series) + murfey_db.commit() + murfey_db.refresh(clem_img_series) logger.info( "Align-and-merge processing result registered for " @@ -117,4 +117,4 @@ def register_align_and_merge_result( return True finally: - db.close() + murfey_db.close() diff --git a/src/murfey/workflows/clem/register_preprocessing_results.py b/src/murfey/workflows/clem/register_preprocessing_results.py index bd553d560..396f1109e 100644 --- a/src/murfey/workflows/clem/register_preprocessing_results.py +++ b/src/murfey/workflows/clem/register_preprocessing_results.py @@ -44,7 +44,7 @@ class LIFPreprocessingResult(BaseModel): def register_lif_preprocessing_result( - message: dict, db: Session, demo: bool = False + message: dict, murfey_db: Session, demo: bool = False ) -> bool: """ session_id (recipe) @@ -88,28 +88,28 @@ def register_lif_preprocessing_result( # Register items in database if not already present try: clem_img_stk: CLEMImageStack = get_db_entry( - db=db, + db=murfey_db, table=CLEMImageStack, session_id=session_id, file_path=result.image_stack, ) clem_img_series: CLEMImageSeries = get_db_entry( - db=db, + db=murfey_db, table=CLEMImageSeries, session_id=session_id, series_name=result.series_name, ) clem_metadata: CLEMImageMetadata = get_db_entry( - db=db, + db=murfey_db, table=CLEMImageMetadata, session_id=session_id, file_path=result.metadata, ) clem_lif_file: CLEMLIFFile = get_db_entry( - db=db, + db=murfey_db, table=CLEMLIFFile, session_id=session_id, file_path=result.parent_lif, @@ -120,21 +120,21 @@ def register_lif_preprocessing_result( clem_img_stk.parent_lif = clem_lif_file clem_img_stk.parent_series = clem_img_series clem_img_stk.channel_name = result.channel - db.add(clem_img_stk) - db.commit() - db.refresh(clem_img_stk) + murfey_db.add(clem_img_stk) + murfey_db.commit() + murfey_db.refresh(clem_img_stk) clem_img_series.associated_metadata = clem_metadata clem_img_series.parent_lif = clem_lif_file clem_img_series.number_of_members = result.number_of_members - db.add(clem_img_series) - db.commit() - db.refresh(clem_img_series) + murfey_db.add(clem_img_series) + murfey_db.commit() + murfey_db.refresh(clem_img_series) clem_metadata.parent_lif = clem_lif_file - db.add(clem_metadata) - db.commit() - db.refresh(clem_metadata) + murfey_db.add(clem_metadata) + murfey_db.commit() + murfey_db.refresh(clem_metadata) logger.info( f"LIF preprocessing results registered for {result.series_name!r} " @@ -153,7 +153,7 @@ def register_lif_preprocessing_result( try: image_stacks = [ Path(row) - for row in db.exec( + for row in murfey_db.exec( select(CLEMImageStack.file_path).where( CLEMImageStack.series_id == clem_img_series.id ) @@ -163,7 +163,9 @@ def register_lif_preprocessing_result( f"Found the following images: {[str(file) for file in image_stacks]}" ) instrument_name = ( - db.exec(select(MurfeySession).where(MurfeySession.id == session_id)) + murfey_db.exec( + select(MurfeySession).where(MurfeySession.id == session_id) + ) .one() .instrument_name ) @@ -208,7 +210,7 @@ def register_lif_preprocessing_result( return True finally: - db.close() + murfey_db.close() class TIFFPreprocessingResult(BaseModel): @@ -237,7 +239,7 @@ def parse_stringified_list(cls, value): def register_tiff_preprocessing_result( - message: dict, db: Session, demo: bool = False + message: dict, murfey_db: Session, demo: bool = False ) -> bool: session_id: int = ( @@ -271,19 +273,19 @@ def register_tiff_preprocessing_result( # Register items in database if not already present try: clem_img_stk: CLEMImageStack = get_db_entry( - db=db, + db=murfey_db, table=CLEMImageStack, session_id=session_id, file_path=result.image_stack, ) clem_img_series: CLEMImageSeries = get_db_entry( - db=db, + db=murfey_db, table=CLEMImageSeries, session_id=session_id, series_name=result.series_name, ) clem_metadata: CLEMImageMetadata = get_db_entry( - db=db, + db=murfey_db, table=CLEMImageMetadata, session_id=session_id, file_path=result.metadata, @@ -293,7 +295,7 @@ def register_tiff_preprocessing_result( # Register TIFF files and populate them iteratively first for file in result.parent_tiffs: clem_tiff_file: CLEMTIFFFile = get_db_entry( - db=db, + db=murfey_db, table=CLEMTIFFFile, session_id=session_id, file_path=file, @@ -301,22 +303,22 @@ def register_tiff_preprocessing_result( clem_tiff_file.associated_metadata = clem_metadata clem_tiff_file.child_series = clem_img_series clem_tiff_file.child_stack = clem_img_stk - db.add(clem_tiff_file) - db.commit() - db.refresh(clem_tiff_file) + murfey_db.add(clem_tiff_file) + murfey_db.commit() + murfey_db.refresh(clem_tiff_file) clem_img_stk.associated_metadata = clem_metadata clem_img_stk.parent_series = clem_img_series clem_img_stk.channel_name = result.channel - db.add(clem_img_stk) - db.commit() - db.refresh(clem_img_stk) + murfey_db.add(clem_img_stk) + murfey_db.commit() + murfey_db.refresh(clem_img_stk) clem_img_series.associated_metadata = clem_metadata clem_img_series.number_of_members = result.number_of_members - db.add(clem_img_series) - db.commit() - db.refresh(clem_img_series) + murfey_db.add(clem_img_series) + murfey_db.commit() + murfey_db.refresh(clem_img_series) logger.info( f"TIFF preprocessing results registered for {result.series_name!r} " @@ -335,7 +337,7 @@ def register_tiff_preprocessing_result( try: image_stacks = [ Path(row) - for row in db.exec( + for row in murfey_db.exec( select(CLEMImageStack.file_path).where( CLEMImageStack.series_id == clem_img_series.id ) @@ -345,7 +347,9 @@ def register_tiff_preprocessing_result( f"Found the following images: {[str(file) for file in image_stacks]}" ) instrument_name = ( - db.exec(select(MurfeySession).where(MurfeySession.id == session_id)) + murfey_db.exec( + select(MurfeySession).where(MurfeySession.id == session_id) + ) .one() .instrument_name ) @@ -390,4 +394,4 @@ def register_tiff_preprocessing_result( return True finally: - db.close() + murfey_db.close()