Removed database refresh instances from CLEM workflows, as they seem unneeded

Author: tieneupin

src/murfey/server/api/clem.py

@@ -1,7 +1,6 @@
 from __future__ import annotations
 
 import re
-import time
 import traceback
 from ast import literal_eval
 from importlib.metadata import EntryPoint  # type hinting only
@@ -95,16 +94,16 @@ def validate_and_sanitise(
     if not str(full_path).startswith(str(base_path)):
         raise ValueError(f"{file} points to a directory that is not permitted")
 
-    # Check that it's a file, not a directory
-    # Make a couple of attempts to rule out race condition
-    attempts = 0
-    while attempts < 50:
-        if full_path.is_file() is True:
-            break
-        attempts += 1
-        time.sleep(0.1)
-    else:
-        raise ValueError(f"{file} is not a file")
+    # # Check that it's a file, not a directory
+    # # Make a couple of attempts to rule out race condition
+    # attempts = 0
+    # while attempts < 50:
+    #     if full_path.is_file() is True:
+    #         break
+    #     attempts += 1
+    #     time.sleep(0.1)
+    # else:
+    #     raise ValueError(f"{file} is not a file")
 
     # Check that it is of a permitted file type
     if f"{full_path.suffix}" not in valid_file_types:
@@ -194,26 +193,6 @@ def get_db_entry(
         db.add(db_entry)
         db.commit()
 
-        # Make multiple attempts to refresh data in case of race condition
-        attempts = 0
-        while attempts < 50:
-            try:
-                db.refresh(db_entry)
-                break
-            except Exception:
-                logger.warning(
-                    f"Attempt {attempts + 1} at refreshing database entry for "
-                    f"{sanitise(str(file_path if file_path else series_name))!r} failed: \n"
-                    f"{traceback.format_exc()}"
-                )
-                attempts += 1
-                time.sleep(0.1)
-        else:
-            raise RuntimeError(
-                "Maximum number of attempts reached while trying to refresh database "
-                f"entry for {sanitise(str(file_path if file_path else series_name))!r}"
-            )
-
     except Exception:
         raise Exception
 

src/murfey/workflows/clem/__init__.py

@@ -3,7 +3,6 @@
 import logging
 import re
 import time
-import traceback
 from pathlib import Path
 from typing import Optional, Type, Union
 
@@ -190,25 +189,6 @@ def get_db_entry(
         db.add(db_entry)
         db.commit()
 
-        # Make multiple attempts data retrieval attempts in case of race condition
-        attempts = 0
-        while attempts < 50:
-            try:
-                db.refresh(db_entry)
-                break
-            except Exception:
-                logger.warning(
-                    f"Attempt {attempts + 1} at refreshing database entry for "
-                    f"{str(file_path if file_path else series_name)!r} failed: \n"
-                    f"{traceback.format_exc()}"
-                )
-                attempts += 1
-                time.sleep(0.1)
-        else:
-            raise RuntimeError(
-                "Maximum number of attempts reached while trying to refresh database "
-                f"entry for {str(file_path if file_path else series_name)!r}"
-            )
     except Exception:
         raise Exception
 

src/murfey/workflows/clem/register_align_and_merge_results.py

@@ -2,7 +2,6 @@
 
 import json
 import logging
-import time
 import traceback
 from ast import literal_eval
 from pathlib import Path
@@ -95,26 +94,6 @@ def register_align_and_merge_result(
             murfey_db.add(clem_img_series)
             murfey_db.commit()
 
-            # Make multiple attempts to refresh data in case of race condition
-            attempts = 0
-            while attempts < 50:
-                try:
-                    murfey_db.refresh(clem_img_series)
-                    break
-                except Exception:
-                    logger.warning(
-                        f"Attempt {attempts + 1} at refreshing database entry for "
-                        f"{str(result.series_name)!r} failed: \n"
-                        f"{traceback.format_exc()}"
-                    )
-                    attempts += 1
-                    time.sleep(0.1)
-            else:
-                raise RuntimeError(
-                    "Maximum number of attempts reached while trying to refresh database "
-                    f"entry for {result.series_name!r}"
-                )
-
             logger.info(
                 "Align-and-merge processing result registered for "
                 f"{result.series_name!r} series"

src/murfey/workflows/clem/register_preprocessing_results.py

@@ -9,7 +9,6 @@
 
 import json
 import logging
-import time
 import traceback
 from ast import literal_eval
 from pathlib import Path
@@ -121,75 +120,16 @@ def register_lif_preprocessing_result(
             murfey_db.add(clem_img_stk)
             murfey_db.commit()
 
-            # Make multiple attempts to refresh data in case of race condition
-            attempts = 0
-            while attempts < 50:
-                try:
-                    murfey_db.refresh(clem_img_stk)
-                    break
-                except Exception:
-                    logger.warning(
-                        f"Attempt {attempts + 1} at refreshing database entry for "
-                        f"{str(result.image_stack)!r} failed: \n"
-                        f"{traceback.format_exc()}"
-                    )
-                    attempts += 1
-                    time.sleep(0.1)
-            else:
-                raise RuntimeError(
-                    "Maximum number of attempts reached while trying to refresh database "
-                    f"entry for {str(result.image_stack)!r}"
-                )
-
             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
             murfey_db.add(clem_img_series)
             murfey_db.commit()
 
-            # Make multiple attempts to refresh data in case of race condition
-            attempts = 0
-            while attempts < 50:
-                try:
-                    murfey_db.refresh(clem_img_series)
-                    break
-                except Exception:
-                    logger.warning(
-                        f"Attempt {attempts + 1} at refreshing database entry for "
-                        f"{str(result.series_name)!r} failed: \n"
-                        f"{traceback.format_exc()}"
-                    )
-                    attempts += 1
-                    time.sleep(0.1)
-            else:
-                raise RuntimeError(
-                    "Maximum number of attempts reached while trying to refresh database "
-                    f"entry for {str(result.series_name)!r}"
-                )
-
             clem_metadata.parent_lif = clem_lif_file
             murfey_db.add(clem_metadata)
             murfey_db.commit()
 
-            # Make multiple attempts to refresh data in case of race condition
-            while attempts < 50:
-                try:
-                    murfey_db.refresh(clem_metadata)
-                    break
-                except Exception:
-                    logger.warning(
-                        f"Attempt {attempts + 1} at refreshing database entry for "
-                        f"{str(result.metadata)!r} failed: \n"
-                        f"{traceback.format_exc()}"
-                    )
-                    attempts += 1
-                    time.sleep(0.1)
-            else:
-                raise RuntimeError(
-                    "Maximum number of attempts reached while trying to refresh database "
-                    f"entry for {str(result.metadata)!r}"
-                )
-
             logger.info(
                 f"LIF preprocessing results registered for {result.series_name!r} "
                 f"{result.channel!r} image stack"
@@ -357,77 +297,17 @@ def register_tiff_preprocessing_result(
                 murfey_db.add(clem_tiff_file)
                 murfey_db.commit()
 
-                # Make multiple attempts to refresh data in case of race condition
-                attempts = 0
-                while attempts < 50:
-                    try:
-                        murfey_db.refresh(clem_tiff_file)
-                        break
-                    except Exception:
-                        logger.warning(
-                            f"Attempt {attempts + 1} at refreshing database entry for "
-                            f"{str(file)!r} failed: \n"
-                            f"{traceback.format_exc()}"
-                        )
-                        attempts += 1
-                        time.sleep(0.1)
-                else:
-                    raise RuntimeError(
-                        "Maximum number of attempts reached while trying to refresh database "
-                        f"entry for {str(file)!r}"
-                    )
-
             clem_img_stk.associated_metadata = clem_metadata
             clem_img_stk.parent_series = clem_img_series
             clem_img_stk.channel_name = result.channel
             murfey_db.add(clem_img_stk)
             murfey_db.commit()
 
-            # Make multiple attempts to refresh data in case of race condition
-            attempts = 0
-            while attempts < 50:
-                try:
-                    murfey_db.refresh(clem_img_stk)
-                    break
-                except Exception:
-                    logger.warning(
-                        f"Attempt {attempts + 1} at refreshing database entry for "
-                        f"{str(result.image_stack)!r} failed: \n"
-                        f"{traceback.format_exc()}"
-                    )
-                    attempts += 1
-                    time.sleep(0.1)
-            else:
-                raise RuntimeError(
-                    "Maximum number of attempts reached while trying to refresh database "
-                    f"entry for {str(result.image_stack)!r}"
-                )
-
             clem_img_series.associated_metadata = clem_metadata
             clem_img_series.number_of_members = result.number_of_members
             murfey_db.add(clem_img_series)
             murfey_db.commit()
 
-            # Make multiple attempts to refresh data in case of race condition
-            attempts = 0
-            while attempts < 50:
-                try:
-                    murfey_db.refresh(clem_img_series)
-                    break
-                except Exception:
-                    logger.warning(
-                        f"Attempt {attempts + 1} at refreshing database entry for "
-                        f"{str(result.series_name)!r} failed: \n"
-                        f"{traceback.format_exc()}"
-                    )
-                    attempts += 1
-                    time.sleep(0.1)
-            else:
-                raise RuntimeError(
-                    "Maximum number of attempts reached while trying to refresh database "
-                    f"entry for {str(result.series_name)!r}"
-                )
-
             logger.info(
                 f"TIFF preprocessing results registered for {result.series_name!r} "
                 f"{result.channel!r} image stack"