hpcflow 0.1.15__py3-none-any.whl → 0.2.0a271__py3-none-any.whl

hpcflow/sdk/persistence/pending.py

@@ -0,0 +1,948 @@
+"""
+Class to hold the state that is waiting to be committed to disk.
+"""
+
+from __future__ import annotations
+
+from collections import defaultdict
+from collections.abc import Callable
+import contextlib
+from dataclasses import dataclass, field, fields
+from functools import wraps
+import copy
+
+from typing import Any, Generic, TYPE_CHECKING, TypeVar
+from typing_extensions import ParamSpec
+
+import numpy as np
+
+from hpcflow.sdk.log import TimeIt
+from hpcflow.sdk.submission.submission import SUBMISSION_SUBMIT_TIME_KEYS
+from hpcflow.sdk.typing import DataIndex
+from hpcflow.sdk.utils.strings import shorten_list_str
+
+
+from hpcflow.sdk.persistence.types import (
+    AnySTask,
+    AnySElement,
+    AnySElementIter,
+    AnySEAR,
+    AnySParameter,
+)
+
+if TYPE_CHECKING:
+    from collections.abc import Mapping, Sequence
+    from datetime import datetime
+    from logging import Logger
+    from .base import PersistentStore, FileDescriptor, LoopDescriptor
+    from ..app import BaseApp
+    from ..typing import ParamSource
+    from ..core.json_like import JSONed
+
+P = ParamSpec("P")
+T = TypeVar("T")
+
+_commit_method_data_map: dict[str, list[str]] = defaultdict(
+    list
+)  # note: this is updated at module-import time.
+
+
+class PendingChanges(
+    Generic[AnySTask, AnySElement, AnySElementIter, AnySEAR, AnySParameter]
+):
+    """
+    Class to store pending changes and merge them into a persistent store.
+
+    Parameters
+    ----------
+    app: App
+        The main application context.
+    store: PersistentStore
+        The persistent store that owns this object
+    resource_map: CommitResourceMap
+        Map of resources, used when processing commits.
+    """
+
+    # These would be in the docstring except they render really wrongly!
+    # Type Parameters
+    # ---------------
+    # AnySTask
+    #     The type of stored tasks.
+    # AnySElement
+    #     The type of stored elements.
+    # AnySElementIter
+    #     The type of stored element iterations.
+    # AnySEAR
+    #     The type of stored EARs.
+    # AnySParameter
+    #     The type of stored parameters.
+
+    def __init__(
+        self,
+        app: BaseApp,
+        store: PersistentStore[
+            AnySTask, AnySElement, AnySElementIter, AnySEAR, AnySParameter
+        ],
+        resource_map: CommitResourceMap,
+    ):
+        self._app = app
+        self.store = store
+        self.resource_map = resource_map
+
+        #: Keys are new task IDs.
+        self.add_tasks: dict[int, AnySTask] = {}
+        #: Keys are loop IDs, values are loop descriptors.
+        self.add_loops: dict[int, LoopDescriptor] = {}
+        #: Keys are submission IDs, values are submission descriptors.
+        self.add_submissions: dict[int, Mapping[str, JSONed]] = {}
+        #: Keys are element IDs.
+        self.add_elements: dict[int, AnySElement] = {}
+        #: Keys are element iteration IDs.
+        self.add_elem_iters: dict[int, AnySElementIter] = {}
+        #: Keys are element action run IDs.
+        self.add_EARs: dict[int, AnySEAR] = {}
+        #: Keys are parameter indices and values are tuples whose first element is data
+        #: to add and whose second element is the source dict for the new data.
+        self.add_parameters: dict[int, AnySParameter] = {}
+        #: Workflow-related files (inputs, outputs) added to the persistent store.
+        self.add_files: list[FileDescriptor] = []
+        #: Template components to add.
+        self.add_template_components: dict[str, dict[str, dict]] = {}
+        #: Keys are element set IDs, values are descriptors.
+        self.add_element_sets: dict[int, list[Mapping]] = {}
+
+        #: Keys are task IDs, and values are element IDs to add to that task.
+        self.add_elem_IDs: dict[int, list[int]] = {}
+        #: Keys are element IDs, and values are iteration IDs to add to that element.
+        self.add_elem_iter_IDs: dict[int, list[int]] = {}
+        #: Keys are element iteration IDs, then EAR action index, and values are EAR IDs.
+        #: This is a list of EAR IDs to add to a given element iteration action.
+        self.add_elem_iter_EAR_IDs: dict[int, dict[int, list[int]]] = {}
+        #: Submission metadata added at submit-time, including submission parts.
+        self.update_at_submit_metadata: dict[int, dict[str, Any]] = {}
+
+        #: IDs of EARs to mark as initialised.
+        self.set_EARs_initialised: list[int] = []
+        #: Submission IDs and commands file IDs to attach to EARs.
+        self.set_EAR_submission_data: dict[int, tuple[int, int | None]] = {}
+        #: IDs of EARs to mark as skipped.
+        self.set_EAR_skips: dict[int, int] = {}
+        #: Keys are EAR IDs and values are tuples of start time, start dir snapshot, run
+        #: hostname, and port number.
+        self.set_EAR_starts: dict[
+            int, tuple[datetime, dict[str, Any] | None, str, int | None]
+        ] = {}
+        #: Keys are EAR IDs and values are tuples of end time, end dir snapshot, exit
+        #: code, and success boolean.
+        self.set_EAR_ends: dict[
+            int, tuple[datetime, dict[str, Any] | None, int, bool]
+        ] = {}
+        #: Each list item is a tuple of two arrays, the first of which is a run directory
+        #: indices array, and the second of which is an integer array indicating with
+        #: which run ID each run directory is associated.
+        self.set_run_dirs: list[tuple[np.ndarray, np.ndarray]] = []
+
+        #: Keys are IDs of jobscripts.
+        self.set_js_metadata: dict[int, dict[int, dict[str, Any]]] = {}
+
+        #: Keys are IDs of parameters to add or modify, and values are tuples of the
+        #: parameter value, and whether the parameter is a file.
+        self.set_parameters: dict[int, tuple[Any, bool]] = {}
+
+        #: Keys are parameter indices and values are dict parameter sources to merge
+        #: with existing source of that parameter.
+        self.update_param_sources: dict[int, ParamSource] = {}
+        #: Keys are indices of loops, values are descriptions of what to update.
+        self.update_loop_indices: dict[int, dict[str, int]] = {}
+        #: Keys are indices of loops, values are number of iterations.
+        self.update_loop_num_iters: dict[int, list[list[list[int] | int]]] = {}
+        #: Keys are indices of loops, values are list of parent names.
+        self.update_loop_parents: dict[int, list[str]] = {}
+
+        self.update_iter_data_idx: dict[int, DataIndex] = {}
+        self.update_run_data_idx: dict[int, DataIndex] = {}
+
+        self.reset(is_init=True)  # set up initial data structures
+
+    def __bool__(self):
+        """Returns True if there are any outstanding pending items."""
+        return (
+            bool(self.add_tasks)
+            or bool(self.add_loops)
+            or bool(self.add_submissions)
+            or bool(self.add_elements)
+            or bool(self.add_elem_iters)
+            or bool(self.add_EARs)
+            or bool(self.add_elem_IDs)
+            or bool(self.add_elem_iter_IDs)
+            or bool(self.add_elem_iter_EAR_IDs)
+            or bool(self.update_at_submit_metadata)
+            or bool(self.add_parameters)
+            or bool(self.add_files)
+            or bool(self.add_template_components)
+            or bool(self.add_element_sets)
+            or bool(self.set_EARs_initialised)
+            or bool(self.set_EAR_submission_data)
+            or bool(self.set_EAR_starts)
+            or bool(self.set_EAR_ends)
+            or bool(self.set_EAR_skips)
+            or bool(self.set_run_dirs)
+            or bool(self.set_js_metadata)
+            or bool(self.set_parameters)
+            or bool(self.update_param_sources)
+            or bool(self.update_loop_indices)
+            or bool(self.update_loop_num_iters)
+            or bool(self.update_loop_parents)
+            or bool(self.update_iter_data_idx)
+            or bool(self.update_run_data_idx)
+        )
+
+    def where_pending(self) -> list[str]:
+        """
+        Get the list of items for which there is some outstanding pending items.
+        """
+        excluded = {"app", "store", "resource_map"}
+        return [k for k, v in self.__dict__.items() if k not in excluded and bool(v)]
+
+    @property
+    def logger(self) -> Logger:
+        """
+        The logger.
+        """
+        return self._app.persistence_logger
+
+    def commits_data(*data_list: str):
+        """Decorator that wraps `PendingChanges.commit_*` methods with arguments listing
+        which `PendingChanges` attributes must have non-trivial data in them for the method's
+        invocation to be required.
+
+        Notes
+        -----
+        This essentially provides a mapping between `PendingChanges` attributes and
+        `commit_*` methods. This allows us to only open the resources that need updating
+        in `PendingChanges.commit_all`.
+
+        We use a decorator rather than an explicitly declaring the map in
+        `_commit_method_data_map` to make the mapping obvious near the commit methods, and
+        hopefully avoid us forgetting to update `_commit_method_data_map` when we modify
+        or add commit methods in future!
+
+        """
+
+        def decorator(func: Callable[P, T]) -> Callable[P, T]:
+
+            _commit_method_data_map[func.__name__].extend(data_list)
+
+            @wraps(func)
+            def inner(*args, **kwargs) -> T:
+                return func(*args, **kwargs)
+
+            return inner
+
+        return decorator
+
+    def get_pending_resource_map_groups(self) -> dict[tuple[str, ...], list[str]]:
+        """Retrive resource map groups, where values are filtered to include only those
+        commit methods that must be invoked, due to pending data associated with those
+        methods.
+
+        Notes
+        -----
+        This method allows us to open only those resources that need to be updated, given
+        the state of pending data.
+        """
+
+        where_pending = self.where_pending()
+        pending_groups = {}
+        for res_names, methods in self.resource_map.groups.items():
+            req_methods = [
+                meth_i
+                for meth_i in methods
+                if any(
+                    dat_j in where_pending for dat_j in _commit_method_data_map[meth_i]
+                )
+            ]
+            if req_methods:
+                pending_groups[res_names] = req_methods
+
+        return pending_groups
+
+    @TimeIt.decorator
+    def commit_all(self) -> None:
+        """Commit all pending changes to disk."""
+        self.logger.info(f"committing all pending changes: {self.where_pending()}")
+
+        if not self:
+            self.logger.debug("commit: no pending changes to commit.")
+            return
+
+        for resources, methods in self.get_pending_resource_map_groups().items():
+            # for each resource, enter `using_resource` context manager in "update" mode:
+            with contextlib.ExitStack() as stack:
+                for res in resources:
+                    stack.enter_context(
+                        self.store.using_resource(res, "update")  # type: ignore[call-overload]
+                    )
+                for meth in methods:
+                    getattr(self, meth)()
+
+        assert not (self)
+
+    @TimeIt.decorator
+    @commits_data("add_tasks")
+    def commit_tasks(self) -> None:
+        """Commit pending tasks to disk."""
+        if self.add_tasks:
+            tasks = self.store.get_tasks_by_IDs(self.add_tasks)
+            task_ids = set(self.add_tasks)
+            self.logger.debug(f"commit: adding pending tasks with IDs: {task_ids!r}")
+            self.store._append_tasks(tasks)
+            self.store.num_tasks_cache = None  # invalidate cache
+            # pending element IDs that belong to pending tasks are now committed:
+            self.add_elem_IDs = {
+                k: v for k, v in self.add_elem_IDs.items() if k not in task_ids
+            }
+        self._clear_add_tasks()
+
+    @TimeIt.decorator
+    @commits_data("add_loops")
+    def commit_loops(self) -> None:
+        """Commit pending loops to disk."""
+        if self.add_loops:
+            # retrieve pending loops, including pending changes to num_added_iterations:
+            loops = self.store.get_loops_by_IDs(self.add_loops)
+            loop_ids = set(self.add_loops)
+            self.logger.debug(f"commit: adding pending loops with indices {loop_ids!r}")
+            self.store._append_loops(loops)
+
+            # pending num_added_iters and parents that belong to pending loops are now
+            # committed:
+            self.update_loop_num_iters = {
+                k: v for k, v in self.update_loop_num_iters.items() if k not in loop_ids
+            }
+            self.update_loop_parents = {
+                k: v for k, v in self.update_loop_parents.items() if k not in loop_ids
+            }
+
+        self._clear_add_loops()
+
+    @TimeIt.decorator
+    @commits_data("add_submissions")
+    def commit_submissions(self) -> None:
+        """Commit pending submissions to disk."""
+        if self.add_submissions:
+            # retrieve pending submissions:
+            subs = self.store.get_submissions_by_ID(
+                self.add_submissions
+            )  # TODO: I think this just returns add_submissions?
+            sub_ids = set(self.add_submissions)
+            self.logger.debug(
+                f"commit: adding pending submissions with indices {sub_ids!r}"
+            )
+            self.store._append_submissions(subs)
+        self._clear_add_submissions()
+
+    @TimeIt.decorator
+    @commits_data("update_at_submit_metadata")
+    def commit_at_submit_metadata(self) -> None:
+        """
+        Commit to disk pending at-submit-time metadata, including submission parts.
+        """
+        if self.update_at_submit_metadata:
+            self.logger.debug("commit: adding pending at-submit metadata")
+            self.store._update_at_submit_metadata(self.update_at_submit_metadata)
+        self._clear_at_submit_metadata()
+
+    @TimeIt.decorator
+    @commits_data("add_elem_IDs")
+    def commit_elem_IDs(self) -> None:
+        """
+        Commit pending element ID updates to disk.
+        """
+        # TODO: could be batched up?
+        for task_ID, elem_IDs in self.add_elem_IDs.items():
+            self.logger.debug(
+                f"commit: adding pending element IDs to task {task_ID!r}: {elem_IDs!r}."
+            )
+            self.store._append_task_element_IDs(task_ID, elem_IDs)
+            self.store.task_cache.pop(task_ID, None)  # invalidate cache
+        self._clear_add_elem_IDs()
+
+    @TimeIt.decorator
+    @commits_data("add_elements")
+    def commit_elements(self) -> None:
+        """
+        Commit pending elements to disk.
+        """
+        if self.add_elements:
+            elems = self.store.get_elements(self.add_elements)
+            elem_ids = set(self.add_elements)
+            self.logger.debug(f"commit: adding pending elements with IDs: {elem_ids!r}")
+            self.store._append_elements(elems)
+            # pending iter IDs that belong to pending elements are now committed:
+            self.add_elem_iter_IDs = {
+                k: v for k, v in self.add_elem_iter_IDs.items() if k not in elem_ids
+            }
+        self._clear_add_elements()
+
+    @TimeIt.decorator
+    @commits_data("add_element_sets")
+    def commit_element_sets(self) -> None:
+        """
+        Commit pending element sets to disk.
+        """
+        # TODO: could be batched up?
+        for task_id, es_js in self.add_element_sets.items():
+            self.logger.debug("commit: adding pending element sets.")
+            self.store._append_element_sets(task_id, es_js)
+        self._clear_add_element_sets()
+
+    @TimeIt.decorator
+    @commits_data("add_elem_iter_IDs")
+    def commit_elem_iter_IDs(self) -> None:
+        """
+        Commit pending element iteration ID updates to disk.
+        """
+        # TODO: could be batched up?
+        for elem_ID, iter_IDs in self.add_elem_iter_IDs.items():
+            self.logger.debug(
+                f"commit: adding pending element iteration IDs to element {elem_ID!r}: "
+                f"{iter_IDs!r}."
+            )
+            self.store._append_elem_iter_IDs(elem_ID, iter_IDs)
+            self.store.element_cache.pop(elem_ID, None)  # invalidate cache
+        self._clear_add_elem_iter_IDs()
+
+    @TimeIt.decorator
+    @commits_data("add_elem_iters")
+    def commit_elem_iters(self) -> None:
+        """
+        Commit pending element iterations to disk.
+        """
+        if self.add_elem_iters:
+            iters = self.store.get_element_iterations(self.add_elem_iters)
+            iter_ids = set(self.add_elem_iters)
+            self.logger.debug(
+                f"commit: adding pending element iterations with IDs: {iter_ids!r}"
+            )
+            self.store._append_elem_iters(iters)
+            # pending EAR IDs that belong to pending iters are now committed:
+            add_elem_iter_EAR_IDs_cur = copy.deepcopy(self.add_elem_iter_EAR_IDs)
+            self._clear_add_elem_iter_EAR_IDs()  # reset to empty nested defaultdict
+            for iter_id, all_run_IDs in add_elem_iter_EAR_IDs_cur.items():
+                # only re-assign iter_IDs that have not been comitted above:
+                if iter_id not in iter_ids:
+                    for act_idx, run_IDs in all_run_IDs.items():
+                        self.add_elem_iter_EAR_IDs[iter_id][act_idx].extend(run_IDs)
+
+            # pending EARs_initialised that belong to pending iters are now committed:
+            self.set_EARs_initialised = [
+                i for i in self.set_EARs_initialised if i not in iter_ids
+            ]
+        self._clear_add_elem_iters()
+
+    @TimeIt.decorator
+    @commits_data("add_elem_iter_EAR_IDs")
+    def commit_elem_iter_EAR_IDs(self) -> None:
+        """
+        Commit pending element action run ID updates to disk.
+        """
+        # TODO: could be batched up?
+        for iter_ID, act_EAR_IDs in self.add_elem_iter_EAR_IDs.items():
+            self.logger.debug(
+                f"commit: adding pending EAR IDs to element iteration {iter_ID!r}: "
+                f"{dict(act_EAR_IDs)!r}."
+            )
+            for act_idx, EAR_IDs in act_EAR_IDs.items():
+                self.store._append_elem_iter_EAR_IDs(iter_ID, act_idx, EAR_IDs)
+            self.store.element_iter_cache.pop(iter_ID, None)  # invalidate cache
+        self._clear_add_elem_iter_EAR_IDs()
+
+    @TimeIt.decorator
+    @commits_data("add_EARs")
+    def commit_EARs(self) -> None:
+        """
+        Commit pending element action runs to disk.
+        """
+        if self.add_EARs:
+            EARs = self.store.get_EARs(self.add_EARs)
+            EAR_ids = list(self.add_EARs)
+            self.logger.debug(f"commit: adding pending EARs with IDs: {EAR_ids!r}")
+            self.store._append_EARs(EARs)
+            self.store.num_EARs_cache = None  # invalidate cache
+            # pending start/end times/snapshots, submission indices, and skips that belong
+            # to pending EARs are now committed (accounted for in `get_EARs` above):
+            self.set_EAR_submission_data = {
+                k: v for k, v in self.set_EAR_submission_data.items() if k not in EAR_ids
+            }
+            self.set_EAR_skips = {
+                k: v for k, v in self.set_EAR_skips.items() if k not in EAR_ids
+            }
+            self.set_EAR_starts = {
+                k: v for k, v in self.set_EAR_starts.items() if k not in EAR_ids
+            }
+            self.set_EAR_ends = {
+                k: v for k, v in self.set_EAR_ends.items() if k not in EAR_ids
+            }
+
+        self._clear_add_EARs()
+
+    @TimeIt.decorator
+    @commits_data("set_run_dirs")
+    def commit_set_run_dirs(self) -> None:
+        """
+        Commit pending run directory indices.
+        """
+        for run_dir_arr, run_idx in self.set_run_dirs:
+            self.store._set_run_dirs(run_dir_arr, run_idx)
+        self._clear_set_run_dirs()
+
+    @TimeIt.decorator
+    @commits_data("set_EARs_initialised")
+    def commit_EARs_initialised(self) -> None:
+        """
+        Commit pending element action run init state updates to disk.
+        """
+        if self.set_EARs_initialised:
+            iter_ids = self.set_EARs_initialised
+            self.logger.debug(
+                f"commit: setting pending `EARs_initialised` for iteration IDs: "
+                f"{iter_ids!r}."
+            )
+            # TODO: could be batched up?
+            for i in iter_ids:
+                self.store._update_elem_iter_EARs_initialised(i)
+                self.store.element_iter_cache.pop(i, None)  # invalidate cache
+        self._clear_set_EARs_initialised()
+
+    @TimeIt.decorator
+    @commits_data("set_EAR_submission_data")
+    def commit_EAR_submission_indices(self) -> None:
+        """
+        Commit pending element action run submission index updates to disk.
+        """
+        if self.set_EAR_submission_data:
+            self.logger.debug(
+                f"commit: updating submission data: {self.set_EAR_submission_data!r}."
+            )
+            self.store._update_EAR_submission_data(self.set_EAR_submission_data)
+            for EAR_ID_i in self.set_EAR_submission_data:
+                self.store.EAR_cache.pop(EAR_ID_i, None)  # invalidate cache
+            self._clear_EAR_submission_data()
+
+    @TimeIt.decorator
+    @commits_data("set_EAR_starts")
+    def commit_EAR_starts(self) -> None:
+        """
+        Commit pending element action run start information to disk.
+        """
+        updates = self.set_EAR_starts
+        if updates:
+            self.logger.debug(
+                f"commit: registering {len(updates)} run(s) as started: "
+                f"{shorten_list_str(updates)}."
+            )
+            self.store._update_EAR_start(updates)
+            for run_id in updates:
+                self.store.EAR_cache.pop(run_id, None)  # invalidate cache
+        self._clear_set_EAR_starts()
+
+    @TimeIt.decorator
+    @commits_data("set_EAR_ends")
+    def commit_EAR_ends(self) -> None:
+        """
+        Commit pending element action run finish information to disk.
+        """
+        updates = self.set_EAR_ends
+        if updates:
+            self.logger.debug(
+                f"commit: registering {len(updates)} run(s) as ended: "
+                f"{shorten_list_str(updates)}, with exit codes: "
+                f"{shorten_list_str([i[2] for i in updates.values()])}."
+            )
+            self.store._update_EAR_end(updates)
+            for run_id in updates:
+                self.store.EAR_cache.pop(run_id, None)  # invalidate cache
+        self._clear_set_EAR_ends()
+
+    @TimeIt.decorator
+    @commits_data("set_EAR_skips")
+    def commit_EAR_skips(self) -> None:
+        """
+        Commit pending element action skip flags to disk.
+        """
+        updates = self.set_EAR_skips
+        if updates:
+            self.logger.debug(f"commit: setting {len(updates)} run IDs as skipped.")
+            self.store._update_EAR_skip(updates)
+            for run_ID in updates:
+                self.store.EAR_cache.pop(run_ID, None)  # invalidate cache
+        self._clear_set_EAR_skips()
+
+    @TimeIt.decorator
+    @commits_data("set_js_metadata")
+    def commit_js_metadata(self) -> None:
+        """
+        Commit pending jobscript metadata changes to disk.
+        """
+        if self.set_js_metadata:
+            self.logger.debug(
+                f"commit: setting jobscript metadata: {self.set_js_metadata!r}"
+            )
+            self.store._update_js_metadata(self.set_js_metadata)
+        self._clear_set_js_metadata()
+
+    @TimeIt.decorator
+    @commits_data("add_parameters", "set_parameters")
+    def commit_parameters(self) -> None:
+        """Make pending parameters persistent."""
+        if self.add_parameters:
+            params = self.store.get_parameters(self.add_parameters)
+            param_ids = list(self.add_parameters)
+            self.logger.debug(f"commit: adding pending parameters IDs: {param_ids!r}")
+            self.store._append_parameters(params)
+        self._clear_add_parameters()
+
+        if self.set_parameters:
+            param_ids = list(self.set_parameters)
+            self.logger.debug(f"commit: setting values of parameter IDs {param_ids!r}.")
+            self.store._set_parameter_values(self.set_parameters)
+            for id_i in param_ids:
+                self.store.parameter_cache.pop(id_i, None)
+        self._clear_set_parameters()
+
+    @TimeIt.decorator
+    @commits_data("add_files")
+    def commit_files(self) -> None:
+        """Add pending files to the files directory."""
+        if self.add_files:
+            self.logger.debug("commit: adding pending files to the files directory.")
+            self.store._append_files(self.add_files)
+        self._clear_add_files()
+
+    @TimeIt.decorator
+    @commits_data("add_template_components")
+    def commit_template_components(self) -> None:
+        """
+        Commit pending template components to disk.
+        """
+        if self.add_template_components:
+            self.logger.debug("commit: adding template components.")
+            self.store._update_template_components(self.store.get_template_components())
+        self._clear_add_template_components()
+
+    @TimeIt.decorator
+    @commits_data("update_param_sources")
+    def commit_param_sources(self) -> None:
+        """Make pending changes to parameter sources persistent."""
+        if self.update_param_sources:
+            param_ids = list(self.update_param_sources)
+            self.logger.debug(f"commit: updating sources of parameter IDs {param_ids!r}.")
+            self.store._update_parameter_sources(self.update_param_sources)
+            for id_i in param_ids:
+                self.store.param_sources_cache.pop(id_i, None)  # invalidate cache
+            self._clear_update_param_sources()
+
+    @TimeIt.decorator
+    @commits_data("update_loop_indices")
+    def commit_loop_indices(self) -> None:
+        """Make pending update to element iteration loop indices persistent."""
+        updates = self.update_loop_indices
+        if updates:
+            self.logger.debug(
+                f"commit: updating loop indices of {len(updates)} iteration(s)."
+            )
+            self.store._update_loop_index(updates)
+            for iter_ID in updates:
+                self.store.element_iter_cache.pop(iter_ID, None)  # invalidate cache
+        self._clear_update_loop_indices()
+
+    @TimeIt.decorator
+    @commits_data("update_loop_num_iters")
+    def commit_loop_num_iters(self) -> None:
+        """Make pending update to the number of loop iterations."""
+        for index, num_iters in self.update_loop_num_iters.items():
+            self.logger.debug(
+                f"commit: updating loop {index!r} number of iterations to {num_iters!r}."
+            )
+            self.store._update_loop_num_iters(index, num_iters)
+        self._clear_update_loop_num_iters()
+
+    @TimeIt.decorator
+    @commits_data("update_loop_parents")
+    def commit_loop_parents(self) -> None:
+        """Make pending update to additional loop parents."""
+        for index, parents in self.update_loop_parents.items():
+            self.logger.debug(f"commit: updating loop {index!r} parents to {parents!r}.")
+            self.store._update_loop_parents(index, parents)
+        self._clear_update_loop_parents()
+
+    @TimeIt.decorator
+    @commits_data("update_iter_data_idx")
+    def commit_iter_data_idx(self) -> None:
+        if self.update_iter_data_idx:
+            self.store._update_iter_data_indices(self.update_iter_data_idx)
+            self._clear_update_iter_data_idx()
+
+    @TimeIt.decorator
+    @commits_data("update_run_data_idx")
+    def commit_run_data_idx(self) -> None:
+        if self.update_run_data_idx:
+            self.store._update_run_data_indices(self.update_run_data_idx)
+            self._clear_update_run_data_idx()
+
+    def _clear_add_tasks(self) -> None:
+        self.add_tasks = {}
+
+    def _clear_add_loops(self) -> None:
+        self.add_loops = {}
+
+    def _clear_add_submissions(self) -> None:
+        self.add_submissions = {}
+
+    def _clear_at_submit_metadata(self) -> None:
+        self.update_at_submit_metadata = defaultdict(
+            lambda: {i: None for i in SUBMISSION_SUBMIT_TIME_KEYS}
+        )
+
+    def _clear_add_elements(self) -> None:
+        self.add_elements = {}
+
+    def _clear_add_element_sets(self) -> None:
+        self.add_element_sets = defaultdict(list)
+
+    def _clear_add_elem_iters(self) -> None:
+        self.add_elem_iters = {}
+
+    def _clear_add_EARs(self) -> None:
+        self.add_EARs = {}
+
+    def _clear_set_run_dirs(self):
+        self.set_run_dirs = []
+
+    def _clear_add_elem_IDs(self) -> None:
+        self.add_elem_IDs = defaultdict(list)
+
+    def _clear_add_elem_iter_IDs(self) -> None:
+        self.add_elem_iter_IDs = defaultdict(list)
+
+    def _clear_add_elem_iter_EAR_IDs(self) -> None:
+        self.add_elem_iter_EAR_IDs = defaultdict(lambda: defaultdict(list))
+
+    def _clear_set_EARs_initialised(self) -> None:
+        self.set_EARs_initialised = []
+
+    def _clear_EAR_submission_data(self) -> None:
+        self.set_EAR_submission_data = {}
+
+    def _clear_set_EAR_starts(self) -> None:
+        self.set_EAR_starts = {}
+
+    def _clear_set_EAR_ends(self) -> None:
+        self.set_EAR_ends = {}
+
+    def _clear_set_EAR_skips(self) -> None:
+        self.set_EAR_skips = {}
+
+    def _clear_set_js_metadata(self) -> None:
+        self.set_js_metadata = defaultdict(lambda: defaultdict(dict))
+
+    def _clear_add_parameters(self) -> None:
+        self.add_parameters = {}
+
+    def _clear_add_files(self) -> None:
+        self.add_files = []
+
+    def _clear_add_template_components(self) -> None:
+        self.add_template_components = defaultdict(dict)
+
+    def _clear_set_parameters(self) -> None:
+        self.set_parameters = {}
+
+    def _clear_update_param_sources(self) -> None:
+        self.update_param_sources = {}
+
+    def _clear_update_loop_indices(self) -> None:
+        self.update_loop_indices = defaultdict(dict)
+
+    def _clear_update_loop_num_iters(self) -> None:
+        self.update_loop_num_iters = {}
+
+    def _clear_update_loop_parents(self) -> None:
+        self.update_loop_parents = {}
+
+    def _clear_update_iter_data_idx(self):
+        self.update_iter_data_idx = defaultdict(dict)
+
+    def _clear_update_run_data_idx(self):
+        self.update_run_data_idx = defaultdict(dict)
+
+    def reset(self, is_init: bool = False) -> None:
+        """Clear all pending data and prepare to accept new pending data."""
+
+        if not is_init and not self:
+            # no pending changes
+            return
+
+        if not is_init:
+            self.logger.info("resetting pending changes.")
+
+        self._clear_add_tasks()
+        self._clear_add_loops()
+        self._clear_add_submissions()
+        self._clear_at_submit_metadata()
+        self._clear_add_elements()
+        self._clear_add_element_sets()
+        self._clear_add_elem_iters()
+        self._clear_add_EARs()
+        self._clear_set_run_dirs()
+
+        self._clear_set_EARs_initialised()
+        self._clear_add_elem_IDs()
+        self._clear_add_elem_iter_IDs()
+        self._clear_add_elem_iter_EAR_IDs()
+
+        self._clear_add_parameters()
+        self._clear_add_files()
+        self._clear_add_template_components()
+
+        self._clear_EAR_submission_data()
+        self._clear_set_EAR_starts()
+        self._clear_set_EAR_ends()
+        self._clear_set_EAR_skips()
+
+        self._clear_set_js_metadata()
+        self._clear_set_parameters()
+
+        self._clear_update_param_sources()
+        self._clear_update_loop_indices()
+        self._clear_update_loop_num_iters()
+        self._clear_update_loop_parents()
+        self._clear_update_iter_data_idx()
+        self._clear_update_run_data_idx()
+
+
+@dataclass
+class CommitResourceMap:
+    """
+    Map of :py:class:`PendingChanges` commit method names to store resource labels,
+    representing the store resources required by each ``commit_*`` method, for a given
+    :py:class:`~.PersistentStore`.
+
+    When :py:meth:`PendingChanges.commit_all` is called, the resources specified will be
+    opened in "update" mode, for each ``commit_*`` method.
+
+    Notes
+    -----
+    Normally only of interest to implementations of persistent stores.
+    """
+
+    #: Resources for :py:meth:`~.PendingChanges.commit_tasks`.
+    commit_tasks: tuple[str, ...] | None = tuple()
+    #: Resources for :py:meth:`~.PendingChanges.commit_loops`.
+    commit_loops: tuple[str, ...] | None = tuple()
+    #: Resources for :py:meth:`~.PendingChanges.commit_submissions`.
+    commit_submissions: tuple[str, ...] | None = tuple()
+    #: Resources for :py:meth:`~.PendingChanges.commit_at_submit_metadata`.
+    commit_at_submit_metadata: tuple[str, ...] | None = tuple()
+    #: Resources for :py:meth:`~.PendingChanges.commit_elem_IDs`.
+    commit_elem_IDs: tuple[str, ...] | None = tuple()
+    #: Resources for :py:meth:`~.PendingChanges.commit_elements`.
+    commit_elements: tuple[str, ...] | None = tuple()
+    #: Resources for :py:meth:`~.PendingChanges.commit_element_sets`.
+    commit_element_sets: tuple[str, ...] | None = tuple()
+    #: Resources for :py:meth:`~.PendingChanges.commit_elem_iter_IDs`.
+    commit_elem_iter_IDs: tuple[str, ...] | None = tuple()
+    #: Resources for :py:meth:`~.PendingChanges.commit_elem_iters`.
+    commit_elem_iters: tuple[str, ...] | None = tuple()
+    #: Resources for :py:meth:`~.PendingChanges.commit_elem_iter_EAR_IDs`.
+    commit_elem_iter_EAR_IDs: tuple[str, ...] | None = tuple()
+    #: Resources for :py:meth:`~.PendingChanges.commit_EARs_initialised`.
+    commit_EARs_initialised: tuple[str, ...] | None = tuple()
+    #: Resources for :py:meth:`~.PendingChanges.commit_EARs`.
+    commit_EARs: tuple[str, ...] | None = tuple()
+    #: Resources for :py:meth:`~.PendingChanges.commit_EAR_submission_indices`.
+    commit_EAR_submission_indices: tuple[str, ...] | None = tuple()
+    #: Resources for :py:meth:`~.PendingChanges.commit_EAR_skips`.
+    commit_EAR_skips: tuple[str, ...] | None = tuple()
+    #: Resources for :py:meth:`~.PendingChanges.commit_EAR_starts`.
+    commit_EAR_starts: tuple[str, ...] | None = tuple()
+    #: Resources for :py:meth:`~.PendingChanges.commit_EAR_ends`.
+    commit_EAR_ends: tuple[str, ...] | None = tuple()
+    #: Resources for :py:meth:`~.PendingChanges.commit_js_metadata`.
+    commit_js_metadata: tuple[str, ...] | None = tuple()
+    #: Resources for :py:meth:`~.PendingChanges.commit_parameters`.
+    commit_parameters: tuple[str, ...] | None = tuple()
+    #: Resources for :py:meth:`~.PendingChanges.commit_files`.
+    commit_files: tuple[str, ...] | None = tuple()
+    #: Resources for :py:meth:`~.PendingChanges.commit_template_components`.
+    commit_template_components: tuple[str, ...] | None = tuple()
+    #: Resources for :py:meth:`~.PendingChanges.commit_param_sources`.
+    commit_param_sources: tuple[str, ...] | None = tuple()
+    #: Resources for :py:meth:`~.PendingChanges.commit_loop_indices`.
+    commit_loop_indices: tuple[str, ...] | None = tuple()
+    #: Resources for :py:meth:`~.PendingChanges.commit_loop_num_iters`.
+    commit_loop_num_iters: tuple[str, ...] | None = tuple()
+    #: Resources for :py:meth:`~.PendingChanges.commit_loop_parents`.
+    commit_loop_parents: tuple[str, ...] | None = tuple()
+    #: Resources for :py:meth:`~.PendingChanges.commit_set_run_dirs`.
+    commit_set_run_dirs: tuple[str, ...] | None = tuple()
+    #: Resources for :py:meth:`~.PendingChanges.commit_iter_data_idx`.
+    commit_iter_data_idx: tuple[str, ...] | None = tuple()
+    #: Resources for :py:meth:`~.PendingChanges.commit_run_data_idx`.
+    commit_run_data_idx: tuple[str, ...] | None = tuple()
+
+    #: A dict whose keys are tuples of resource labels and whose values are lists
+    #: of :py:class:`PendingChanges` commit method names that require those resources.
+    #:
+    #: This grouping allows us to batch up commit methods by resource requirements,
+    #: which in turn means we can potentially minimise, e.g., the number of network
+    #: requests.
+    groups: Mapping[tuple[str, ...], Sequence[str]] = field(
+        init=False, repr=False, compare=False
+    )
+
+    def __post_init__(self):
+        self.groups = self._group_by_resource()
+
+    def _group_by_resource(self) -> Mapping[tuple[str, ...], Sequence[str]]:
+        """
+        Get a dict whose keys are tuples of resource labels and whose values are
+        lists of :py:class:`PendingChanges` commit method names that require those
+        resource.
+
+        This grouping allows us to batch up commit methods by resource requirements,
+        which in turn means we can potentially minimise e.g. the number of network
+        requests.
+        """
+        groups: dict[tuple[str, ...], list[str]] = {}
+        # The dicts are pretending to be insertion-ordered sets
+        cur_res_group: tuple[dict[str, None], list[str]] | None = None
+        for fld in fields(self):
+            if not fld.name.startswith("commit_"):
+                continue
+            res_labels = getattr(self, fld.name)
+
+            if not cur_res_group:
+                # start a new resource group: a mapping between resource labels and the
+                # commit methods that require those resources:
+                cur_res_group = (dict.fromkeys(res_labels), [fld.name])
+
+            elif not res_labels or set(res_labels).intersection(cur_res_group[0]):
+                # there is some overlap between resource labels required in the current
+                # group and this commit method, so we merge resource labels and add the
+                # new commit method:
+                cur_res_group[0].update(dict.fromkeys(res_labels))
+                cur_res_group[1].append(fld.name)
+
+            else:
+                # no overlap between resource labels required in the current group and
+                # those required by this commit method, so append the current group, and
+                # start a new group for this commit method:
+                groups.setdefault(tuple(cur_res_group[0]), []).extend(cur_res_group[1])
+                cur_res_group = (dict.fromkeys(res_labels), [fld.name])
+
+        if cur_res_group:
+            groups.setdefault(tuple(cur_res_group[0]), []).extend(cur_res_group[1])
+
+        return groups