feature: Implement saving operations to / reading from the on-disk storage

.github/workflows/tests-e2e.yml

@@ -33,6 +33,7 @@ jobs:
           pip install -r dev_requirements.txt
 
       - name: Run tests
+        timeout-minutes: 30
         env:
           NEPTUNE_API_TOKEN: ${{ secrets.E2E_API_TOKEN }}
           NEPTUNE_E2E_PROJECT: ${{ secrets.E2E_PROJECT }}

src/neptune_scale/api/attribute.py

@@ -15,7 +15,8 @@
 
 from neptune_scale.api.metrics import Metrics
 from neptune_scale.sync.metadata_splitter import MetadataSplitter
-from neptune_scale.sync.operations_queue import OperationsQueue
+from neptune_scale.sync.operations_repository import OperationsRepository
+from neptune_scale.sync.sequence_tracker import SequenceTracker
 
 __all__ = ("Attribute", "AttributeStore")
 
@@ -65,11 +66,14 @@ class AttributeStore:
     end consuming the queue (which would be SyncProcess).
     """
 
-    def __init__(self, project: str, run_id: str, operations_queue: OperationsQueue) -> None:
+    def __init__(
+        self, project: str, run_id: str, operations_repo: OperationsRepository, sequence_tracker: SequenceTracker
+    ) -> None:
         self._project = project
         self._run_id = run_id
-        self._operations_queue = operations_queue
+        self._operations_repo = operations_repo
         self._attributes: dict[str, Attribute] = {}
+        self._sequence_tracker = sequence_tracker
 
     def __getitem__(self, path: str) -> "Attribute":
         path = cleanup_path(path)
@@ -108,9 +112,10 @@ def log(
             remove_tags=tags_remove,
         )
 
-        for operation, metadata_size in splitter:
-            key = metrics.batch_key() if metrics is not None else None
-            self._operations_queue.enqueue(operation=operation, size=metadata_size, key=key)
+        operations = list(splitter)
+        sequence_id = self._operations_repo.save_update_run_snapshots(operations)
+
+        self._sequence_tracker.update_sequence_id(sequence_id)
 
 
 class Attribute:

src/neptune_scale/api/metrics.py

@@ -1,6 +1,5 @@
 from __future__ import annotations
 
-from collections.abc import Hashable
 from dataclasses import dataclass
 from typing import (
     Optional,
@@ -40,6 +39,3 @@ def __post_init__(self) -> None:
             self.preview_completion = None
         if self.preview_completion is not None:
             verify_value_between("preview_completion", self.preview_completion, 0.0, 1.0)
-
-    def batch_key(self) -> Hashable:
-        return (self.step, self.preview, self.preview_completion)

src/neptune_scale/api/run.py

@@ -4,6 +4,14 @@
 
 from __future__ import annotations
 
+from pathlib import Path
+from types import TracebackType
+
+from neptune_scale.sync.operations_repository import (
+    Metadata,
+    OperationsRepository,
+)
+
 __all__ = ["Run"]
 
 import atexit
@@ -22,7 +30,6 @@
 
 from neptune_api.proto.neptune_pb.ingest.v1.common_pb2 import ForkPoint
 from neptune_api.proto.neptune_pb.ingest.v1.common_pb2 import Run as CreateRun
-from neptune_api.proto.neptune_pb.ingest.v1.pub.ingest_pb2 import RunOperation
 
 from neptune_scale.api.attribute import AttributeStore
 from neptune_scale.api.metrics import Metrics
@@ -35,6 +42,7 @@
 )
 from neptune_scale.exceptions import (
     NeptuneApiTokenNotProvided,
+    NeptuneConflictingDataInLocalStorage,
     NeptuneProjectNotProvided,
 )
 from neptune_scale.net.serialization import (
@@ -46,20 +54,15 @@
     ErrorsQueue,
 )
 from neptune_scale.sync.lag_tracking import LagTracker
-from neptune_scale.sync.operations_queue import OperationsQueue
 from neptune_scale.sync.parameters import (
     MAX_EXPERIMENT_NAME_LENGTH,
-    MAX_QUEUE_SIZE,
     MAX_RUN_ID_LENGTH,
     MINIMAL_WAIT_FOR_ACK_SLEEP_TIME,
     MINIMAL_WAIT_FOR_PUT_SLEEP_TIME,
     STOP_MESSAGE_FREQUENCY,
 )
+from neptune_scale.sync.sequence_tracker import SequenceTracker
 from neptune_scale.sync.sync_process import SyncProcess
-from neptune_scale.util.abstract import (
-    Resource,
-    WithResources,
-)
 from neptune_scale.util.envs import (
     API_TOKEN_ENV_NAME,
     PROJECT_ENV_NAME,
@@ -74,7 +77,7 @@
 logger = get_logger()
 
 
-class Run(WithResources, AbstractContextManager):
+class Run(AbstractContextManager):
     """
     Representation of tracked metadata.
     """
@@ -91,7 +94,7 @@ def __init__(
         creation_time: Optional[datetime] = None,
         fork_run_id: Optional[str] = None,
         fork_step: Optional[Union[int, float]] = None,
-        max_queue_size: int = MAX_QUEUE_SIZE,
+        max_queue_size: Optional[int] = None,
         async_lag_threshold: Optional[float] = None,
         on_async_lag_callback: Optional[Callable[[], None]] = None,
         on_queue_full_callback: Optional[Callable[[BaseException, Optional[float]], None]] = None,
@@ -114,7 +117,7 @@ def __init__(
             creation_time: Custom creation time of the run.
             fork_run_id: If forking from an existing run, ID of the run to fork from.
             fork_step: If forking from an existing run, step number to fork from.
-            max_queue_size: Maximum number of operations in a queue.
+            max_queue_size: Deprecated.
             async_lag_threshold: Threshold for the duration between the queueing and synchronization of an operation
                 (in seconds). If the duration exceeds the threshold, the callback function is triggered.
             on_async_lag_callback: Callback function triggered when the duration between the queueing and synchronization
@@ -134,7 +137,6 @@ def __init__(
         verify_type("creation_time", creation_time, (datetime, type(None)))
         verify_type("fork_run_id", fork_run_id, (str, type(None)))
         verify_type("fork_step", fork_step, (int, float, type(None)))
-        verify_type("max_queue_size", max_queue_size, int)
         verify_type("async_lag_threshold", async_lag_threshold, (int, float, type(None)))
         verify_type("on_async_lag_callback", on_async_lag_callback, (Callable, type(None)))
         verify_type("on_queue_full_callback", on_queue_full_callback, (Callable, type(None)))
@@ -161,8 +163,8 @@ def __init__(
         ):
             raise ValueError("`on_async_lag_callback` must be used with `async_lag_threshold`.")
 
-        if max_queue_size < 1:
-            raise ValueError("`max_queue_size` must be greater than 0.")
+        if max_queue_size is not None:
+            logger.warning("`max_queue_size` is deprecated and will be removed in a future version.")
 
         project = project or os.environ.get(PROJECT_ENV_NAME)
         if project:
@@ -198,12 +200,25 @@ def __init__(
         self._run_id: str = run_id
 
         self._lock = threading.RLock()
-        self._operations_queue: OperationsQueue = OperationsQueue(
-            lock=self._lock,
-            max_size=max_queue_size,
-        )
 
-        self._attr_store: AttributeStore = AttributeStore(self._project, self._run_id, self._operations_queue)
+        operations_repository_path = _create_repository_path(self._project, self._run_id)
+        self._operations_repo: OperationsRepository = OperationsRepository(
+            db_path=operations_repository_path,
+        )
+        self._operations_repo.init_db()
+        existing_metadata = self._operations_repo.get_metadata()
+
+        # Save metadata if it doesn't exist
+        if existing_metadata is None:
+            self._operations_repo.save_metadata(self._project, self._run_id, fork_run_id, fork_step)
+        # Check for conflicts when not resuming
+        elif not resume:
+            self._check_for_run_conflicts(existing_metadata, fork_run_id, fork_step)
+
+        self._sequence_tracker = SequenceTracker()
+        self._attr_store: AttributeStore = AttributeStore(
+            self._project, self._run_id, self._operations_repo, self._sequence_tracker
+        )
 
         self._errors_queue: ErrorsQueue = ErrorsQueue()
         self._errors_monitor = ErrorsMonitor(
@@ -222,21 +237,20 @@ def __init__(
         self._sync_process = SyncProcess(
             project=self._project,
             family=self._run_id,
-            operations_queue=self._operations_queue.queue,
+            operations_repository_path=operations_repository_path,
             errors_queue=self._errors_queue,
             process_link=self._process_link,
             api_token=input_api_token,
             last_queued_seq=self._last_queued_seq,
             last_ack_seq=self._last_ack_seq,
             last_ack_timestamp=self._last_ack_timestamp,
-            max_queue_size=max_queue_size,
             mode=mode,
         )
         self._lag_tracker: Optional[LagTracker] = None
         if async_lag_threshold is not None and on_async_lag_callback is not None:
             self._lag_tracker = LagTracker(
                 errors_queue=self._errors_queue,
-                operations_queue=self._operations_queue,
+                sequence_tracker=self._sequence_tracker,
                 last_ack_timestamp=self._last_ack_timestamp,
                 async_lag_threshold=async_lag_threshold,
                 on_async_lag_callback=on_async_lag_callback,
@@ -251,6 +265,7 @@ def __init__(
         self._exit_func: Optional[Callable[[], None]] = atexit.register(self._close)
 
         if not resume:
+            # Create a new run
             self._create_run(
                 creation_time=datetime.now() if creation_time is None else creation_time,
                 experiment_name=experiment_name,
@@ -259,28 +274,28 @@ def __init__(
             )
             self.wait_for_processing(verbose=False)
 
+    def _check_for_run_conflicts(
+        self, existing_metadata: Metadata, fork_run_id: Optional[str], fork_step: Optional[float]
+    ) -> None:
+        if existing_metadata.project != self._project or existing_metadata.run_id != self._run_id:
+            # should never happen because we use project and run_id to create the repository path
+            raise NeptuneConflictingDataInLocalStorage()
+        if existing_metadata.parent_run_id == fork_run_id and existing_metadata.fork_step == fork_step:
+            logger.warning(
+                "Run already exists in local storage with the same parent run and fork point. Resuming the run."
+            )
+            return
+        else:
+            # Same run_id but different fork points
+            raise NeptuneConflictingDataInLocalStorage()
+
     def _on_child_link_closed(self, _: ProcessLink) -> None:
         with self._lock:
             if not self._is_closing:
                 logger.error("Child process closed unexpectedly.")
                 self._is_closing = True
                 self.terminate()
 
-    @property
-    def resources(self) -> tuple[Resource, ...]:
-        if self._lag_tracker is not None:
-            return (
-                self._errors_queue,
-                self._operations_queue,
-                self._lag_tracker,
-                self._errors_monitor,
-            )
-        return (
-            self._errors_queue,
-            self._operations_queue,
-            self._errors_monitor,
-        )
-
     def _close(self, *, wait: bool = True) -> None:
         with self._lock:
             if self._is_closing:
@@ -310,7 +325,8 @@ def _close(self, *, wait: bool = True) -> None:
         if threading.current_thread() != self._errors_monitor:
             self._errors_monitor.join()
 
-        super().close()
+        self._operations_repo.close()
+        self._errors_queue.close()
 
     def terminate(self) -> None:
         """
@@ -363,6 +379,14 @@ def close(self) -> None:
             self._exit_func = None
         self._close(wait=True)
 
+    def __exit__(
+        self,
+        exc_type: Optional[type[BaseException]],
+        exc_value: Optional[BaseException],
+        traceback: Optional[TracebackType],
+    ) -> None:
+        self.close()
+
     def _create_run(
         self,
         creation_time: datetime,
@@ -376,17 +400,15 @@ def _create_run(
                 parent_project=self._project, parent_run_id=fork_run_id, step=make_step(number=fork_step)
             )
 
-        operation = RunOperation(
-            project=self._project,
-            run_id=self._run_id,
-            create=CreateRun(
-                family=self._run_id,
-                fork_point=fork_point,
-                experiment_id=experiment_name,
-                creation_time=None if creation_time is None else datetime_to_proto(creation_time),
-            ),
+        create_run = CreateRun(
+            family=self._run_id,
+            fork_point=fork_point,
+            experiment_id=experiment_name,
+            creation_time=None if creation_time is None else datetime_to_proto(creation_time),
         )
-        self._operations_queue.enqueue(operation=operation)
+
+        sequence = self._operations_repo.save_create_run(create_run)
+        self._sequence_tracker.update_sequence_id(sequence)
 
     def log_metrics(
         self,
@@ -604,20 +626,20 @@ def _wait(
 
                     # Handle the case where we get notified on `wait_seq` before we actually wait.
                     # Otherwise, we would unnecessarily block, waiting on a notify_all() that never happens.
-                    if wait_seq.value >= self._operations_queue.last_sequence_id:
+                    if wait_seq.value >= self._sequence_tracker.last_sequence_id:
                         break
 
                 with wait_seq:
                     wait_seq.wait(timeout=wait_time)
                     value = wait_seq.value
 
-                last_queued_sequence_id = self._operations_queue.last_sequence_id
+                last_queued_sequence_id = self._sequence_tracker.last_sequence_id
 
                 if value == -1:
-                    if self._operations_queue.last_sequence_id != -1:
+                    if self._sequence_tracker.last_sequence_id != -1:
                         last_print_timestamp = print_message(
                             f"Waiting. No operations were {phrase} yet. Operations to sync: %s",
-                            self._operations_queue.last_sequence_id + 1,
+                            self._sequence_tracker.last_sequence_id + 1,
                             last_print=last_print_timestamp,
                             verbose=verbose,
                         )
@@ -692,3 +714,8 @@ def print_message(msg: str, *args: Any, last_print: Optional[float] = None, verb
         return current_time
 
     return last_print
+
+
+def _create_repository_path(project: str, run_id: str) -> Path:
+    sanitized_project = project.replace("/", "_")
+    return Path(os.getcwd()) / ".neptune" / f"{sanitized_project}_{run_id}.sqlite3"

src/neptune_scale/exceptions.py

@@ -40,6 +40,8 @@
     "NeptuneApiTokenNotProvided",
     "NeptuneTooManyRequestsResponseError",
     "NeptunePreviewStepNotAfterLastCommittedStep",
+    "NeptuneConflictingDataInLocalStorage",
+    "NeptuneLocalStorageInUnsupportedVersion",
 )
 
 from typing import Any
@@ -493,3 +495,13 @@ class NeptunePreviewStepNotAfterLastCommittedStep(NeptuneScaleError):
 the last fully committed (complete) update. Once a complete value is recorded, any preview updates
 must only be added for later steps. Please adjust the order of your updates and try again.
 """
+
+
+class NeptuneLocalStorageInUnsupportedVersion(NeptuneScaleError):
+    message = """The local storage database is in an unsupported version.
+    This may happen when you try to use a database created with a newer version of Neptune Scale with an older version of the library.
+    Please either upgrade Neptune Scale to the latest version or create a new local storage database."""
+
+
+class NeptuneConflictingDataInLocalStorage(NeptuneScaleError):
+    message = """NeptuneConflictingDataInLocalStorage: Conflicting data found in local storage."""