Remove global session object

Fixes #12

alembic/versions/71df5b41ae41_initial_schema.py

@@ -113,6 +113,7 @@ def upgrade():
         ),
         Column("status", Enum(TransferStatus), nullable=False),
         Column("uploader", String(256), nullable=False),
+        Column("upload_name", String(256), nullable=False),
         Column("source", String(256), nullable=False),
         Column("transfer_size", BigInteger, nullable=False),
         Column("transfer_checksum", String(256), nullable=False),

librarian_background/check_integrity.py

@@ -9,8 +9,10 @@
 
 from schedule import CancelJob
 
-from librarian_server.database import session, query
 from librarian_server.orm import StoreMetadata, Instance
+from librarian_server.database import get_session
+
+from sqlalchemy.orm import Session
 
 
 logger = logging.getLogger("schedule")
@@ -26,9 +28,9 @@ class CheckIntegrity(Task):
     age_in_days: int
     "Age in days of the files to check. I.e. only check files younger than this (we assume older files are fine as they've been checked before)"
 
-    def get_store(self) -> StoreMetadata:
+    def get_store(self, session: Session) -> StoreMetadata:
         possible_metadata = (
-            query(StoreMetadata).filter(StoreMetadata.name == self.store_name).first()
+            session.query(StoreMetadata).filter_by(name=self.store_name).first()
         )
 
         if not possible_metadata:
@@ -37,8 +39,15 @@ def get_store(self) -> StoreMetadata:
         return possible_metadata
 
     def on_call(self):
+        with get_session() as session:
+            return self.core(session=session)
+
+    def core(self, session: Session):
+        """
+        Frame this out with the session so that it is automatically closed.
+        """
         try:
-            store = self.get_store()
+            store = self.get_store(session=session)
         except ValueError:
             # Store doesn't exist. Cancel this job.
             logger.error(
@@ -51,9 +60,8 @@ def on_call(self):
 
         # Now we can query the database for all files that were uploaded in the past age_in_days days.
         files = (
-            query(Instance)
-            .filter(Instance.store == store)
-            .filter(Instance.created_time > start_time)
+            session.query(Instance)
+            .filter(Instance.store == store and Instance.created_time > start_time)
             .all()
         )
 

librarian_background/create_clone.py

@@ -12,8 +12,10 @@
 from schedule import CancelJob
 from pathlib import Path
 
-from librarian_server.database import session, query
 from librarian_server.orm import StoreMetadata, Instance, CloneTransfer, TransferStatus
+from librarian_server.database import get_session
+
+from sqlalchemy.orm import Session
 
 
 logger = logging.getLogger("schedule")
@@ -33,19 +35,23 @@ class CreateLocalClone(Task):
 
     # TODO: In the future, we could implement a _rolling_ n day clone here, i.e. only keep the last n days of files on the clone_to store.
 
-    def get_store(self, name: str) -> StoreMetadata:
+    def get_store(self, name: str, session: Session) -> StoreMetadata:
         possible_metadata = (
-            query(StoreMetadata).filter(StoreMetadata.name == name).first()
+            session.query(StoreMetadata).filter_by(name=name).first()
         )
 
         if not possible_metadata:
             raise ValueError(f"Store {name} does not exist.")
 
         return possible_metadata
-
+    
     def on_call(self):
+        with get_session() as session:
+            return self.core(session=session)
+
+    def core(self, session: Session):
         try:
-            store_from = self.get_store(self.clone_from)
+            store_from = self.get_store(self.clone_from, session)
         except ValueError:
             # Store doesn't exist. Cancel this job.
             logger.error(
@@ -54,7 +60,7 @@ def on_call(self):
             return CancelJob
 
         try:
-            store_to = self.get_store(self.clone_to)
+            store_to = self.get_store(self.clone_to, session)
         except ValueError:
             # Store doesn't exist. Cancel this job.
             logger.error(
@@ -67,7 +73,7 @@ def on_call(self):
 
         # Now we can query the database for all files that were uploaded in the past age_in_days days.
         instances: list[Instance] = (
-            query(Instance)
+            session.query(Instance)
             .filter(Instance.store == store_from)
             .filter(Instance.created_time > start_time)
             .all()
@@ -81,7 +87,7 @@ def on_call(self):
             # Check if there is a matching instance already on our clone_to store.
             # If there is, we don't need to clone it.
             if (
-                query(Instance)
+                session.query(Instance)
                 .filter(Instance.store == store_to)
                 .filter(Instance.file == instance.file)
                 .first()
@@ -113,7 +119,7 @@ def on_call(self):
                     f"File {instance.file.name} is too large to fit on store {store_to}. Skipping."
                 )
 
-                transfer.fail_transfer()
+                transfer.fail_transfer(session=session)
 
                 all_transfers_successful = False
 
@@ -136,15 +142,15 @@ def on_call(self):
                             f"Failed to transfer file {instance.path} to store {store_to} using transfer manager {transfer_manager}."
                         )
 
-                        transfer.fail_transfer()
+                        transfer.fail_transfer(session=session)
 
                         continue
                 except FileNotFoundError as e:
                     logger.error(
                         f"File {instance.path} does not exist on store {store_from}. Skipping."
                     )
 
-                    transfer.fail_transfer()
+                    transfer.fail_transfer(session=session)
 
                     all_transfers_successful = False
 
@@ -155,7 +161,7 @@ def on_call(self):
                     f"Failed to transfer file {instance.path} to store {store_to}. Skipping."
                 )
 
-                transfer.fail_transfer()
+                transfer.fail_transfer(session=session)
 
                 all_transfers_successful = False
 
@@ -176,7 +182,7 @@ def on_call(self):
                         f"Expected {instance.file.checksum}, got {path_info.md5}."
                     )
 
-                    transfer.fail_transfer()
+                    transfer.fail_transfer(session=session)
 
                     store_to.store_manager.unstage(staged_path)
 
@@ -193,7 +199,7 @@ def on_call(self):
                 )
                 store_to.store_manager.unstage(staging_name)
 
-                transfer.fail_transfer()
+                transfer.fail_transfer(session=session)
 
                 all_transfers_successful = False
 

librarian_background/recieve_clone.py

@@ -12,7 +12,7 @@
 
 from .task import Task
 
-from librarian_server.database import session, query
+from librarian_server.database import get_session
 from librarian_server.orm import (
     File,
     Instance,
@@ -28,6 +28,10 @@
     CloneCompleteResponse,
 )
 
+from typing import TYPE_CHECKING
+
+from sqlalchemy.orm import Session
+
 logger = logging.getLogger("schedule")
 
 
@@ -39,15 +43,21 @@ class RecieveClone(Task):
     deletion_policy: DeletionPolicy = DeletionPolicy.DISALLOWED
 
     def on_call(self):
+        with get_session() as session:
+            return self.core(session=session)
+
+    def core(self, session: Session):
         """
         Checks for incoming transfers and processes them.
         """
 
         # Find incoming transfers that are ONGOING
-        ongoing_transfers: list[IncomingTransfer] = query(
-            IncomingTransfer, status=TransferStatus.ONGOING
-        ).all()
-
+        ongoing_transfers: list[IncomingTransfer] = (
+            session.query(IncomingTransfer)
+            .filter_by(status=TransferStatus.ONGOING)
+            .all()
+        )
+
         all_transfers_succeeded = True
 
         if len(ongoing_transfers) == 0:
@@ -118,7 +128,7 @@ def on_call(self):
                     path=path_info.path,
                     file=file,
                     store=store,
-                    deletion_policy=self.deletion_policy
+                    deletion_policy=self.deletion_policy,
                 )
 
                 session.add(file)
@@ -132,9 +142,9 @@ def on_call(self):
                 session.commit()
 
                 # Callback to the source librarian.
-                librarian: Optional[Librarian] = query(
-                    Librarian, name=transfer.source
-                ).first()
+                librarian: Optional[Librarian] = (
+                    session.query(Librarian).filter_by(name=transfer.source).first()
+                )
 
                 if librarian:
                     # Need to call back
@@ -148,10 +158,12 @@ def on_call(self):
                     )
 
                     try:
-                        response: CloneCompleteResponse = librarian.client.do_pydantic_http_post(
-                            endpoint="/api/v2/clone/complete",
-                            request_model=request,
-                            response_model=CloneCompleteResponse,
+                        response: CloneCompleteResponse = (
+                            librarian.client.do_pydantic_http_post(
+                                endpoint="/api/v2/clone/complete",
+                                request_model=request,
+                                response_model=CloneCompleteResponse,
+                            )
                         )
                     except Exception as e:
                         logger.error(
@@ -168,5 +180,4 @@ def on_call(self):
                 logger.info(f"Transfer {transfer.id} has not yet completed. Skipping.")
                 continue
 
-
         return all_transfers_succeeded

librarian_background/send_clone.py

@@ -12,7 +12,7 @@
 from schedule import CancelJob
 from pathlib import Path
 
-from librarian_server.database import session, query
+from librarian_server.database import get_session()
 from librarian_server.orm import (
     StoreMetadata,
     Instance,
@@ -30,6 +30,13 @@
     CloneOngoingResponse
 )
 
+from typing import TYPE_CHECKING
+
+if TYPE_CHECKING:
+    from hera_librarian import LibrarianClient
+
+from sqlalchemy.orm import Session
+
 logger = logging.getLogger("schedule")
 
 
@@ -49,13 +56,17 @@ class SendClone(Task):
     "Name of the store to prefer when sending files. If None, we will use whatever store is available for sending that file."
 
     def on_call(self):
+        with get_session() as session:
+            return self.core(session=session)
+
+    def core(self, session: Session):
         """
         Creates uploads to the remote librarian as specified.
         """
         # Before even attempting to do anything, get the information about the librarian and create
         # a client connection to it.
-        librarian: Optional[Librarian] = query(
-            Librarian, Librarian.name == self.destination_librarian
+        librarian: Optional[Librarian] = session.query(
+            Librarian).filter_by(name=self.destination_librarian
         ).first()
 
         if librarian is None:
@@ -79,19 +90,19 @@ def on_call(self):
         age_in_days = datetime.timedelta(days=self.age_in_days)
         oldest_file_age = current_time - age_in_days
 
-        files_without_remote_instances: list[File] = query(
-            File,
-            File.create_time > oldest_file_age,
-            File.remote_instances.any(librarian_name=self.destination_librarian),
+        files_without_remote_instances: list[File] = session.query(
+            File).filter(
+            File.create_time > oldest_file_age and
+            File.remote_instances.any(librarian_name=self.destination_librarian)
         ).all()
 
         logger.info(
             f"Found {len(files_without_remote_instances)} files without remote instances."
         )
 
         if self.store_preference is not None:
-            use_store: StoreMetadata = query(
-                StoreMetadata, StoreMetadata.name == self.store_preference
+            use_store: StoreMetadata = session.query(
+                StoreMetadata).filter_by(name = self.store_preference
             ).first()
 
             if use_store is None:
@@ -159,7 +170,7 @@ def on_call(self):
                 )
 
                 # Mark the transfer as failed.
-                transfer.fail_transfer()
+                transfer.fail_transfer(session=session)
                 continue
 
 
@@ -192,7 +203,7 @@ def on_call(self):
                     f"Failed to transfer file {instance.path} to remote store. Skipping."
                 )
 
-                transfer.fail_transfer()
+                transfer.fail_transfer(session=session)
                 continue
 
             # Great! We can now mark the transfer as ONGOING in the background.