Maint/firebase collection cleanup

cellpack/autopack/DBRecipeHandler.py

@@ -1,7 +1,6 @@
 import copy
 import logging
 import shutil
-from datetime import datetime, timezone
 from enum import Enum
 from pathlib import Path
 
@@ -10,7 +9,6 @@
 
 import hashlib
 import json
-import requests
 
 from cellpack.autopack.utils import deep_merge
 
@@ -321,36 +319,6 @@ def __init__(self, settings):
         self.settings = settings
 
 
-class ResultDoc:
-    def __init__(self, db):
-        self.db = db
-
-    def handle_expired_results(self):
-        """
-        Check if the results in the database are expired and delete them if the linked object expired.
-        """
-        current_utc = datetime.now(timezone.utc)
-        results = self.db.get_all_docs("results")
-        if results:
-            for result in results:
-                result_data = self.db.doc_to_dict(result)
-                result_age = current_utc - result_data["timestamp"]
-                if result_age.days > 180 and not self.validate_existence(
-                    result_data["url"]
-                ):
-                    self.db.delete_doc("results", self.db.doc_id(result))
-            logging.info("Results cleanup complete.")
-        else:
-            logging.info("No results found in the database.")
-
-    def validate_existence(self, url):
-        """
-        Validate the existence of an S3 object by checking if the URL is accessible.
-        Returns True if the URL is accessible.
-        """
-        return requests.head(url).status_code == requests.codes.ok
-
-
 class DBUploader(object):
     """
     Handles the uploading of data to the database.
@@ -529,23 +497,6 @@ def upload_config(self, config_data, source_path):
         self.db.update_doc("configs", id, config_data)
         return id
 
-    def upload_result_metadata(self, file_name, url):
-        """
-        Upload the metadata of the result file to the database.
-        """
-        if self.db:
-            username = self.db.get_username()
-            timestamp = self.db.create_timestamp()
-            self.db.update_or_create(
-                "results",
-                file_name,
-                {
-                    "user": username,
-                    "timestamp": timestamp,
-                    "url": url,
-                },
-            )
-
     def upload_job_status(
         self,
         dedup_hash,
@@ -887,23 +838,4 @@ def compile_db_recipe_data(db_recipe_data, obj_dict, grad_dict, comp_dict):
         return recipe_data
 
 
-class DBMaintenance(object):
-    """
-    Handles the maintenance of the database.
-    """
-
-    def __init__(self, db_handler):
-        self.db = db_handler
-        self.result_doc = ResultDoc(self.db)
-
-    def cleanup_results(self):
-        """
-        Check if the results in the database are expired and delete them if the linked object expired.
-        """
-        self.result_doc.handle_expired_results()
-
-    def readme_url(self):
-        """
-        Return the URL to the README file for the database setup section.
-        """
-        return "https://github.com/mesoscope/cellpack?tab=readme-ov-file#introduction-to-remote-databases"
+DB_SETUP_README_URL = "https://github.com/mesoscope/cellpack?tab=readme-ov-file#introduction-to-remote-databases"

cellpack/autopack/interface_objects/default_values.py

@@ -9,7 +9,6 @@
     "objects",
     "gradients",
     "recipes",
-    "results",
     "configs",
     "recipes_edited",
 ]

cellpack/autopack/upy/simularium/simularium_helper.py

@@ -22,7 +22,7 @@
 from simulariumio.cellpack import HAND_TYPE, CellpackConverter
 from simulariumio.constants import DISPLAY_TYPE, VIZ_TYPE
 
-from cellpack.autopack.DBRecipeHandler import DBMaintenance, DBUploader
+from cellpack.autopack.DBRecipeHandler import DB_SETUP_README_URL
 from cellpack.autopack.interface_objects.database_ids import DATABASE_IDS
 from cellpack.autopack.upy import hostHelper
 from cellpack.autopack.upy.simularium.plots import PlotData
@@ -1388,51 +1388,26 @@ def raycast_test(self, obj, start, end, length, **kw):
     def post_and_open_file(self, file_name, open_results_in_browser, dedup_hash=None):
         simularium_file = Path(f"{file_name}.simularium")
         if dedup_hash is None:
-            file_name, url = simulariumHelper.store_result_file(
-                simularium_file, storage="aws"
-            )
-            if file_name and url:
-                simulariumHelper.store_metadata(
-                    file_name, url, db="firebase"
-                )
-                if open_results_in_browser:
-                    simulariumHelper.open_in_simularium(url)
+            url = simulariumHelper.store_result_file(simularium_file, storage="aws")
+            if url and open_results_in_browser:
+                simulariumHelper.open_in_simularium(url)
 
     @staticmethod
-    def store_result_file(
-        file_path, storage=None, sub_folder="simularium"
-    ):
+    def store_result_file(file_path, storage=None, sub_folder="simularium"):
         if storage == "aws":
             handler = DATABASE_IDS.handlers().get(storage)
             initialized_handler = handler(
                 bucket_name="cellpack-results",
                 sub_folder_name=sub_folder,
                 region_name="us-west-2",
             )
-            file_name, url = initialized_handler.save_file_and_get_url(file_path)
-            if not file_name or not url:
-                db_maintainer = DBMaintenance(initialized_handler)
-                logging.warning(
-                    f"Skipping browser opening, upload credentials not configured. For setup instructions see: {db_maintainer.readme_url()}"
-                )
-        return file_name, url
-
-    @staticmethod
-    def store_metadata(file_name, url, db=None):
-        if db == "firebase":
-            handler = DATABASE_IDS.handlers().get(db)
-            initialized_db = handler(
-                default_db="staging"
-            )  # default to staging for metadata uploads
-            if initialized_db._initialized:
-                db_uploader = DBUploader(initialized_db)
-                db_uploader.upload_result_metadata(file_name, url)
-            else:
-                db_maintainer = DBMaintenance(initialized_db)
+            _, url = initialized_handler.save_file_and_get_url(file_path)
+            if not url:
                 logging.warning(
-                    f"Firebase credentials not found. For setup instructions see: {db_maintainer.readme_url()}. Or try cellPACK web interface: https://cellpack.allencell.org (no setup required)"
+                    f"Skipping browser opening, upload credentials not configured. For setup instructions see: {DB_SETUP_README_URL}"
                 )
-        return
+            return url
+        return None
 
     @staticmethod
     def open_in_simularium(aws_url):

cellpack/bin/upload.py

@@ -3,7 +3,7 @@
 import json
 
 from cellpack.autopack.FirebaseHandler import FirebaseHandler
-from cellpack.autopack.DBRecipeHandler import DBUploader, DBMaintenance
+from cellpack.autopack.DBRecipeHandler import DBUploader, DB_SETUP_README_URL
 from cellpack.autopack.upy.simularium.simularium_helper import simulariumHelper
 from cellpack.autopack.interface_objects.database_ids import DATABASE_IDS
 from cellpack.autopack.loaders.config_loader import ConfigLoader
@@ -90,7 +90,7 @@ def upload(
                     id, _ = db_handler.upload_data("editable_fields", field)
                     editable_fields_ids.append(id)
             if output_file:
-                _, result_url = simulariumHelper.store_result_file(
+                result_url = simulariumHelper.store_result_file(
                     output_file, storage="aws", sub_folder="client"
                 )
             if studio:
@@ -105,9 +105,8 @@ def upload(
                 db_handler.upload_data("example_packings", recipe_metadata)
 
         else:
-            db_maintainer = DBMaintenance(db_handler)
             sys.exit(
-                f"The selected database is not initialized. Please set up Firebase credentials to upload recipes. Refer to the instructions at {db_maintainer.readme_url()} "
+                f"The selected database is not initialized. Please set up Firebase credentials to upload recipes. Refer to the instructions at {DB_SETUP_README_URL} "
             )