lsst-pipe-base 30.0.1rc1__py3-none-any.whl → 30.2025.5100__py3-none-any.whl

lsst/pipe/base/quantum_graph/ingest_graph.py

@@ -1,413 +0,0 @@
-# This file is part of pipe_base.
-#
-# Developed for the LSST Data Management System.
-# This product includes software developed by the LSST Project
-# (http://www.lsst.org).
-# See the COPYRIGHT file at the top-level directory of this distribution
-# for details of code ownership.
-#
-# This software is dual licensed under the GNU General Public License and also
-# under a 3-clause BSD license. Recipients may choose which of these licenses
-# to use; please see the files gpl-3.0.txt and/or bsd_license.txt,
-# respectively.  If you choose the GPL option then the following text applies
-# (but note that there is still no warranty even if you opt for BSD instead):
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
-
-"""A tool for ingesting provenance quantum graphs (written by the `aggregator`
-module) and [re-]ingesting other datasets (metadata/logs/configs) backed by the
-same file.  This "finalizes" the RUN collection, prohibiting (at least
-conceptually) further processing.
-
-This always proceeds in three steps, so we can resume efficiently:
-
-1. First we ask the butler to "forget" any metadata/log/config datasets that
-   exist in the output RUN collection, removing any record of them from the
-   butler database while preserving their files.
-
-2. Next we ingest the ``run_provenance`` graph dataset itself.
-
-3. Finally, in batches of quanta, we use a
-   `~lsst.daf.butler.QuantumBackedButler` to delete the original
-   metadata/log/config files and ingest new versions of those datasets into the
-   butler.
-
-Thus, at any point, if the ``run_provenance`` dataset has not been ingested,
-we know any metadata/log/config datasets that have been ingested are backed by
-the original files.
-
-Moreover, if the ``run_provenance`` dataset has been ingested, any existing
-metadata/log/config datasets must be backed by the graph file, and the original
-files for those datasets will have been deleted.
-
-We also know that at all times the metadata/log/config *content* is safely
-present in either the original files in the butler storage or in an
-already-ingested ``run_provenance`` dataset.
-"""
-
-from __future__ import annotations
-
-__all__ = ("ingest_graph",)
-
-import dataclasses
-import itertools
-import os
-import uuid
-from collections.abc import Iterator
-from contextlib import contextmanager
-
-from lsst.daf.butler import (
-    Butler,
-    Config,
-    DataCoordinate,
-    DatasetRef,
-    DatasetType,
-    FileDataset,
-    QuantumBackedButler,
-)
-from lsst.daf.butler.registry.sql_registry import SqlRegistry
-from lsst.resources import ResourcePath, ResourcePathExpression
-from lsst.utils.logging import getLogger
-
-from ..automatic_connection_constants import PROVENANCE_DATASET_TYPE_NAME, PROVENANCE_STORAGE_CLASS
-from ._provenance import (
-    ProvenanceDatasetInfo,
-    ProvenanceInitQuantumInfo,
-    ProvenanceQuantumGraph,
-    ProvenanceQuantumGraphReader,
-    ProvenanceQuantumInfo,
-)
-from .formatter import ProvenanceFormatter
-
-_LOG = getLogger(__name__)
-
-
-def ingest_graph(
-    butler_config: str | Config,
-    uri: ResourcePathExpression | None = None,
-    *,
-    transfer: str | None = "move",
-    batch_size: int = 10000,
-    output_run: str | None = None,
-) -> None:
-    """Ingest a provenance graph into a butler repository.
-
-    Parameters
-    ----------
-    butler_config : `str`
-        Path or alias for the butler repository, or a butler repository config
-        object.
-    uri : `lsst.resources.ResourcePathExpression` or `None`, optional
-        Location of the provenance quantum graph to ingest.  `None` indicates
-        that the quantum graph has already been ingested, but other ingests
-        and/or deletions failed and need to be resumed.
-    transfer : `str` or `None`, optional
-        Transfer mode to use when ingesting graph. Matches those supported
-        by `lsst.resources.ResourcePath.transfer_from`.
-    batch_size : `int`, optional
-        Number of datasets to process in each transaction.
-    output_run : `str`, optional
-        Output `~lsst.daf.butler.CollectionType.RUN` collection name.  Only
-        needs to be provided if ``uri`` is `None`.  If it is provided the
-        output run in the graph is checked against it.
-
-    Notes
-    -----
-    After this operation, any further processing done in the
-    `~lsst.daf.butler.CollectionType.RUN` collection will not be included in
-    the provenance.
-
-    If this process is interrupted, it can pick up where it left off if run
-    again (at the cost of some duplicate work to figure out how much progress
-    it had made).
-    """
-    with _GraphIngester.open(butler_config, uri, output_run) as helper:
-        helper.fetch_already_ingested_datasets()
-        if not helper.graph_already_ingested:
-            assert uri is not None
-            helper.forget_ingested_datasets(batch_size=batch_size)
-            helper.ingest_graph_dataset(uri, transfer=transfer)
-        helper.clean_and_reingest_datasets(batch_size=batch_size)
-        if helper.directories_to_delete:
-            _LOG.info(
-                "Deleting %d directories after checking that they are empty.",
-                len(helper.directories_to_delete),
-            )
-            n_deleted: int = 0
-            for top in sorted(helper.directories_to_delete):
-                nonempty: set[str] = set()
-                for root, dirnames, filenames in os.walk(top, topdown=False):
-                    if filenames:
-                        nonempty.add(root)
-                    for dirname in dirnames:
-                        dirpath = os.path.join(root, dirname)
-                        if dirpath in nonempty:
-                            nonempty.add(root)
-                        else:
-                            os.rmdir(dirpath)
-                if nonempty:
-                    _LOG.warning(
-                        "Directory %r was not deleted because it unexpectedly still had files in it.",
-                        top,
-                    )
-                else:
-                    os.rmdir(root)
-                    n_deleted += 1
-            _LOG.info("Deleted %d directories.", n_deleted)
-
-
-@dataclasses.dataclass
-class _GraphIngester:
-    butler_config: str | Config
-    butler: Butler
-    graph: ProvenanceQuantumGraph
-    graph_already_ingested: bool
-    n_datasets: int
-    datasets_already_ingested: set[uuid.UUID] = dataclasses.field(default_factory=set)
-    directories_to_delete: set[str] = dataclasses.field(default_factory=set)
-
-    @property
-    def output_run(self) -> str:
-        return self.graph.header.output_run
-
-    @classmethod
-    @contextmanager
-    def open(
-        cls,
-        butler_config: str | Config,
-        uri: ResourcePathExpression | None,
-        output_run: str | None,
-    ) -> Iterator[_GraphIngester]:
-        with Butler.from_config(butler_config, collections=output_run, writeable=True) as butler:
-            butler.registry.registerDatasetType(
-                DatasetType(PROVENANCE_DATASET_TYPE_NAME, butler.dimensions.empty, PROVENANCE_STORAGE_CLASS)
-            )
-            graph, graph_already_ingested = cls.read_graph(butler, uri)
-            if output_run is not None and graph.header.output_run != output_run:
-                raise ValueError(
-                    f"Given output run {output_run!r} does not match the graph "
-                    f"header {graph.header.output_run!r}."
-                )
-            n_datasets = 2 * len(graph.quantum_only_xgraph) + len(graph.init_quanta)
-            yield cls(
-                butler_config=butler_config,
-                butler=butler,
-                graph=graph,
-                graph_already_ingested=graph_already_ingested,
-                n_datasets=n_datasets,
-            )
-
-    @staticmethod
-    def read_graph(
-        butler: Butler,
-        uri: ResourcePathExpression | None,
-    ) -> tuple[ProvenanceQuantumGraph, bool]:
-        if uri is not None:
-            _LOG.info("Reading the pre-ingest provenance graph.")
-            with ProvenanceQuantumGraphReader.open(uri) as reader:
-                reader.read_quanta()
-                reader.read_init_quanta()
-                graph = reader.graph
-            already_ingested = (
-                butler.find_dataset(PROVENANCE_DATASET_TYPE_NAME, collections=[graph.header.output_run])
-                is not None
-            )
-            return graph, already_ingested
-        else:
-            _LOG.info("Reading the already-ingested provenance graph.")
-            parameters = {"datasets": [], "read_init_quanta": True}
-            return butler.get(PROVENANCE_DATASET_TYPE_NAME, parameters=parameters), True
-
-    def fetch_already_ingested_datasets(self) -> None:
-        _LOG.info("Querying for existing datasets in %r.", self.output_run)
-        self.datasets_already_ingested.update(self.butler.registry._fetch_run_dataset_ids(self.output_run))
-
-    def iter_datasets(self) -> Iterator[tuple[uuid.UUID, ProvenanceDatasetInfo]]:
-        xgraph = self.graph.bipartite_xgraph
-        for task_label, quanta_for_task in self.graph.quanta_by_task.items():
-            _LOG.verbose(
-                "Batching up metadata and log datasets from %d %s quanta.", len(quanta_for_task), task_label
-            )
-            for quantum_id in quanta_for_task.values():
-                quantum_info: ProvenanceQuantumInfo = xgraph.nodes[quantum_id]
-                metadata_id = quantum_info["metadata_id"]
-                yield metadata_id, xgraph.nodes[metadata_id]
-                log_id = quantum_info["log_id"]
-                yield log_id, xgraph.nodes[log_id]
-        _LOG.verbose("Batching up config datasets from %d tasks.", len(self.graph.init_quanta))
-        for task_label, quantum_id in self.graph.init_quanta.items():
-            init_quantum_info: ProvenanceInitQuantumInfo = xgraph.nodes[quantum_id]
-            config_id = init_quantum_info["config_id"]
-            yield config_id, xgraph.nodes[config_id]
-
-    def forget_ingested_datasets(self, batch_size: int) -> None:
-        _LOG.info(
-            "Dropping database records for metadata/log/config datasets backed by their original files."
-        )
-        to_forget: list[DatasetRef] = []
-        n_forgotten: int = 0
-        n_skipped: int = 0
-        for dataset_id, dataset_info in self.iter_datasets():
-            if dataset_info["produced"] and dataset_id in self.datasets_already_ingested:
-                to_forget.append(self._make_ref_from_info(dataset_id, dataset_info))
-                self.datasets_already_ingested.remove(dataset_id)
-                if len(to_forget) >= batch_size:
-                    n_forgotten += self._run_forget(to_forget, n_forgotten + n_skipped)
-            else:
-                n_skipped += 1
-        n_forgotten += self._run_forget(to_forget, n_forgotten + n_skipped)
-        _LOG.info(
-            "Removed database records for %d metadata/log/config datasets, while %d were already absent.",
-            n_forgotten,
-            n_skipped,
-        )
-
-    def _run_forget(self, to_forget: list[DatasetRef], n_current: int) -> int:
-        if to_forget:
-            _LOG.verbose(
-                "Forgetting a %d-dataset batch; %d/%d forgotten so far or already absent.",
-                len(to_forget),
-                n_current,
-                self.n_datasets,
-            )
-            with self.butler.registry.transaction():
-                self.butler._datastore.forget(to_forget)
-                self.butler.registry.removeDatasets(to_forget)
-        n = len(to_forget)
-        to_forget.clear()
-        return n
-
-    def ingest_graph_dataset(self, uri: ResourcePathExpression, transfer: str | None) -> None:
-        _LOG.info("Ingesting the provenance quantum graph.")
-        dataset_type = DatasetType(
-            PROVENANCE_DATASET_TYPE_NAME, self.butler.dimensions.empty, PROVENANCE_STORAGE_CLASS
-        )
-        self.butler.registry.registerDatasetType(dataset_type)
-        ref = DatasetRef(dataset_type, DataCoordinate.make_empty(self.butler.dimensions), run=self.output_run)
-        uri = ResourcePath(uri)
-        self.butler.ingest(
-            # We use .abspath() since butler assumes paths are relative to the
-            # repo root, while users expects them to be relative to the CWD in
-            # this context.
-            FileDataset(refs=[ref], path=uri.abspath(), formatter=ProvenanceFormatter),
-            transfer=transfer,
-        )
-
-    def clean_and_reingest_datasets(self, batch_size: int) -> None:
-        _LOG.info(
-            "Deleting original metadata/log/config files and re-ingesting them with provenance graph backing."
-        )
-        direct_uri = self.butler.getURI(PROVENANCE_DATASET_TYPE_NAME, collections=[self.output_run])
-        qbb = self.make_qbb()
-        to_process: list[DatasetRef] = []
-        n_processed: int = 0
-        n_skipped: int = 0
-        n_not_produced: int = 0
-        for dataset_id, dataset_info in self.iter_datasets():
-            if not dataset_info["produced"]:
-                n_not_produced += 1
-            elif dataset_id not in self.datasets_already_ingested:
-                to_process.append(self._make_ref_from_info(dataset_id, dataset_info))
-                if len(to_process) >= batch_size:
-                    n_processed += self._run_clean_and_ingest(
-                        qbb, direct_uri, to_process, n_processed + n_skipped
-                    )
-            else:
-                n_skipped += 1
-        n_processed += self._run_clean_and_ingest(qbb, direct_uri, to_process, n_processed + n_skipped)
-        _LOG.info(
-            "Deleted and re-ingested %d metadata/log/config datasets "
-            "(%d had already been processed, %d were not produced).",
-            n_processed,
-            n_skipped,
-            n_not_produced,
-        )
-
-    def _run_clean_and_ingest(
-        self, qbb: QuantumBackedButler, direct_uri: ResourcePath, to_process: list[DatasetRef], n_current: int
-    ) -> int:
-        if not to_process:
-            return 0
-        _LOG.verbose(
-            "Deleting and re-ingesting a %d-dataset batch; %d/%d complete.",
-            len(to_process),
-            n_current,
-            self.n_datasets,
-        )
-        sql_registry: SqlRegistry = self.butler._registry  # type: ignore[attr-defined]
-        expanded_refs = sql_registry.expand_refs(to_process)
-        # We need to pass predict=True to keep QBB/FileDatastore from wasting
-        # time doing existence checks, since ResourcePath.mremove will ignore
-        # nonexistent files anyway.
-        original_uris = list(
-            itertools.chain.from_iterable(
-                ref_uris.iter_all() for ref_uris in qbb.get_many_uris(expanded_refs, predict=True).values()
-            )
-        )
-        removal_status = ResourcePath.mremove(original_uris, do_raise=False)
-        for path, status in removal_status.items():
-            if not status.success and not isinstance(status.exception, FileNotFoundError):
-                assert status.exception is not None, "Exception should be set if success=False."
-                status.exception.add_note(f"Attempting to delete original file at {path}.")
-                raise status.exception
-        file_dataset = FileDataset(refs=expanded_refs, path=direct_uri, formatter=ProvenanceFormatter)
-        self.butler.ingest(file_dataset, transfer=None)
-        if len(original_uris) == len(expanded_refs):
-            for uri, ref in zip(original_uris, expanded_refs):
-                if uri.isLocal:
-                    if (
-                        parent_dir := self.find_dataset_type_directory(uri.ospath, ref.datasetType.name)
-                    ) is not None:
-                        self.directories_to_delete.add(parent_dir)
-        elif any(uri.isLocal for uri in original_uris):
-            _LOG.warning(
-                "Not attempting to delete empty metadata/log/config directories because the number "
-                "of paths (%s) did not match the number of datasets (%s).",
-                len(original_uris),
-                len(expanded_refs),
-            )
-        n = len(to_process)
-        to_process.clear()
-        return n
-
-    @staticmethod
-    def _make_ref_from_info(dataset_id: uuid.UUID, dataset_info: ProvenanceDatasetInfo) -> DatasetRef:
-        return DatasetRef(
-            dataset_info["pipeline_node"].dataset_type,
-            dataset_info["data_id"],
-            run=dataset_info["run"],
-            id=dataset_id,
-        )
-
-    def make_qbb(self) -> QuantumBackedButler:
-        dataset_types = {d.name: d.dataset_type for d in self.graph.pipeline_graph.dataset_types.values()}
-        return QuantumBackedButler.from_predicted(
-            config=self.butler_config,
-            predicted_inputs=(),
-            predicted_outputs=(),
-            dimensions=self.butler.dimensions,
-            datastore_records={},
-            dataset_types=dataset_types,
-        )
-
-    def find_dataset_type_directory(self, ospath: str, dataset_type: str) -> str | None:
-        dir_components: list[str] = []
-        for component in os.path.dirname(ospath).split(os.path.sep):
-            dir_components.append(component)
-            # If the full dataset type name is in a single directory path
-            # component, we guess that directory can only have datasets of
-            # that type.
-            if dataset_type in component:
-                return os.path.sep.join(dir_components)
-        return None

lsst_pipe_base-30.0.1rc1.dist-info/RECORD

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