lsst-pipe-base 29.2025.4500__tar.gz → 29.2025.4700__tar.gz

{lsst_pipe_base-29.2025.4500/python/lsst_pipe_base.egg-info → lsst_pipe_base-29.2025.4700}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: lsst-pipe-base
-Version: 29.2025.4500
+Version: 29.2025.4700
 Summary: Pipeline infrastructure for the Rubin Science Pipelines.
 Author-email: Rubin Observatory Data Management <dm-admin@lists.lsst.org>
 License-Expression: BSD-3-Clause OR GPL-3.0-or-later

{lsst_pipe_base-29.2025.4500 → lsst_pipe_base-29.2025.4700}/python/lsst/pipe/base/_status.py

@@ -27,28 +27,37 @@
 
 from __future__ import annotations
 
+__all__ = (
+    "AlgorithmError",
+    "AnnotatedPartialOutputsError",
+    "ExceptionInfo",
+    "InvalidQuantumError",
+    "NoWorkFound",
+    "QuantumAttemptStatus",
+    "QuantumSuccessCaveats",
+    "RepeatableQuantumError",
+    "UnprocessableDataError",
+    "UpstreamFailureNoWorkFound",
+)
+
 import abc
 import enum
 import logging
+import sys
 from typing import TYPE_CHECKING, Any, ClassVar, Protocol
 
+import pydantic
+
 from lsst.utils import introspection
+from lsst.utils.logging import LsstLogAdapter, getLogger
 
 from ._task_metadata import GetSetDictMetadata, NestedMetadataDict
 
 if TYPE_CHECKING:
-    from lsst.utils.logging import LsstLogAdapter
+    from ._task_metadata import TaskMetadata
 
-__all__ = (
-    "AlgorithmError",
-    "AnnotatedPartialOutputsError",
-    "InvalidQuantumError",
-    "NoWorkFound",
-    "QuantumSuccessCaveats",
-    "RepeatableQuantumError",
-    "UnprocessableDataError",
-    "UpstreamFailureNoWorkFound",
-)
+
+_LOG = getLogger(__name__)
 
 
 class QuantumSuccessCaveats(enum.Flag):
@@ -175,6 +184,142 @@ class QuantumSuccessCaveats(enum.Flag):
         }
 
 
+class ExceptionInfo(pydantic.BaseModel):
+    """Information about an exception that was raised."""
+
+    type_name: str
+    """Fully-qualified Python type name for the exception raised."""
+
+    message: str
+    """String message included in the exception."""
+
+    metadata: dict[str, float | int | str | bool | None]
+    """Additional metadata included in the exception."""
+
+    @classmethod
+    def _from_metadata(cls, md: TaskMetadata) -> ExceptionInfo:
+        """Construct from task metadata.
+
+        Parameters
+        ----------
+        md : `TaskMetadata`
+            Metadata about the error, as written by
+            `AnnotatedPartialOutputsError`.
+
+        Returns
+        -------
+        info : `ExceptionInfo`
+            Information about the exception.
+        """
+        result = cls(type_name=md["type"], message=md["message"], metadata={})
+        if "metadata" in md:
+            raw_err_metadata = md["metadata"].to_dict()
+            for k, v in raw_err_metadata.items():
+                # Guard against error metadata we wouldn't be able to serialize
+                # later via Pydantic; don't want one weird value bringing down
+                # our ability to report on an entire run.
+                if isinstance(v, float | int | str | bool):
+                    result.metadata[k] = v
+                else:
+                    _LOG.debug(
+                        "Not propagating nested or JSON-incompatible exception metadata key %s=%r.", k, v
+                    )
+        return result
+
+    # Work around the fact that Sphinx chokes on Pydantic docstring formatting,
+    # when we inherit those docstrings in our public classes.
+    if "sphinx" in sys.modules and not TYPE_CHECKING:
+
+        def copy(self, *args: Any, **kwargs: Any) -> Any:
+            """See `pydantic.BaseModel.copy`."""
+            return super().copy(*args, **kwargs)
+
+        def model_dump(self, *args: Any, **kwargs: Any) -> Any:
+            """See `pydantic.BaseModel.model_dump`."""
+            return super().model_dump(*args, **kwargs)
+
+        def model_dump_json(self, *args: Any, **kwargs: Any) -> Any:
+            """See `pydantic.BaseModel.model_dump_json`."""
+            return super().model_dump(*args, **kwargs)
+
+        def model_copy(self, *args: Any, **kwargs: Any) -> Any:
+            """See `pydantic.BaseModel.model_copy`."""
+            return super().model_copy(*args, **kwargs)
+
+        @classmethod
+        def model_construct(cls, *args: Any, **kwargs: Any) -> Any:  # type: ignore[misc, override]
+            """See `pydantic.BaseModel.model_construct`."""
+            return super().model_construct(*args, **kwargs)
+
+        @classmethod
+        def model_json_schema(cls, *args: Any, **kwargs: Any) -> Any:
+            """See `pydantic.BaseModel.model_json_schema`."""
+            return super().model_json_schema(*args, **kwargs)
+
+        @classmethod
+        def model_validate(cls, *args: Any, **kwargs: Any) -> Any:
+            """See `pydantic.BaseModel.model_validate`."""
+            return super().model_validate(*args, **kwargs)
+
+        @classmethod
+        def model_validate_json(cls, *args: Any, **kwargs: Any) -> Any:
+            """See `pydantic.BaseModel.model_validate_json`."""
+            return super().model_validate_json(*args, **kwargs)
+
+        @classmethod
+        def model_validate_strings(cls, *args: Any, **kwargs: Any) -> Any:
+            """See `pydantic.BaseModel.model_validate_strings`."""
+            return super().model_validate_strings(*args, **kwargs)
+
+
+class QuantumAttemptStatus(enum.Enum):
+    """Enum summarizing an attempt to run a quantum."""
+
+    UNKNOWN = -3
+    """The status of this attempt is unknown.
+
+    This usually means no logs or metadata were written, and it at least could
+    not be determined whether the quantum was blocked by an upstream failure
+    (if it was definitely blocked, `BLOCKED` is set instead).
+    """
+
+    LOGS_MISSING = -2
+    """Task metadata was written for this attempt but logs were not.
+
+    This is a rare condition that requires a hard failure (i.e. the kind that
+    can prevent a ``finally`` block from running or I/O from being durable) at
+    a very precise time.
+    """
+
+    FAILED = -1
+    """Execution of the quantum failed.
+
+    This is always set if the task metadata dataset was not written but logs
+    were, as is the case when a Python exception is caught and handled by the
+    execution system.  It may also be set in cases where logs were not written
+    either, but other information was available (e.g. from higher-level
+    orchestration tooling) to mark it as a failure.
+    """
+
+    BLOCKED = 0
+    """This quantum was not executed because an upstream quantum failed.
+
+    Upstream quanta with status `UNKNOWN` or `FAILED` are considered blockers;
+    `LOGS_MISSING` is not.
+    """
+
+    SUCCESSFUL = 1
+    """This quantum was successfully executed.
+
+    Quanta may be considered successful even if they do not write any outputs
+    or shortcut early by raising `NoWorkFound` or one of its variants.  They
+    may even be considered successful if they raise
+    `AnnotatedPartialOutputsError` if the executor is configured to treat that
+    exception as a non-failure.  See `QuantumSuccessCaveats` for details on how
+    these "successes with caveats" are reported.
+    """
+
+
 class GetSetDictMetadataHolder(Protocol):
     """Protocol for objects that have a ``metadata`` attribute that satisfies
     `GetSetDictMetadata`.

{lsst_pipe_base-29.2025.4500 → lsst_pipe_base-29.2025.4700}/python/lsst/pipe/base/log_capture.py

@@ -29,28 +29,105 @@ from __future__ import annotations
 
 __all__ = ["LogCapture"]
 
+import dataclasses
 import logging
 import os
 import shutil
 import tempfile
+import uuid
 from collections.abc import Iterator
 from contextlib import contextmanager, suppress
 from logging import FileHandler
 
-from lsst.daf.butler import Butler, FileDataset, LimitedButler, Quantum
-from lsst.daf.butler.logging import ButlerLogRecordHandler, ButlerLogRecords, ButlerMDC, JsonLogFormatter
+import pydantic
 
-from ._status import InvalidQuantumError
+from lsst.daf.butler import Butler, FileDataset, LimitedButler, Quantum
+from lsst.daf.butler.logging import (
+    ButlerLogRecord,
+    ButlerLogRecordHandler,
+    ButlerLogRecords,
+    ButlerMDC,
+    JsonLogFormatter,
+)
+
+from ._status import ExceptionInfo, InvalidQuantumError
+from ._task_metadata import TaskMetadata
 from .automatic_connection_constants import METADATA_OUTPUT_TEMPLATE
 from .pipeline_graph import TaskNode
 
 _LOG = logging.getLogger(__name__)
 
 
-class _LogCaptureFlag:
-    """Simple flag to enable/disable log-to-butler saving."""
+class _ExecutionLogRecordsExtra(pydantic.BaseModel):
+    """Extra information about a quantum's execution stored with logs.
+
+    This middleware-private model includes information that is not directly
+    available via any public interface, as it is used exclusively for
+    provenance extraction and then made available through the provenance
+    quantum graph.
+    """
+
+    exception: ExceptionInfo | None = None
+    """Exception information for this quantum, if it failed.
+    """
+
+    metadata: TaskMetadata | None = None
+    """Metadata for this quantum, if it failed.
+
+    Metadata datasets are written if and only if a quantum succeeds, but we
+    still want to capture metadata from failed attempts, so we store it in the
+    log dataset.  This field is always `None` when the quantum succeeds,
+    because in that case the metadata is already stored separately.
+    """
+
+    previous_process_quanta: list[uuid.UUID] = pydantic.Field(default_factory=list)
+    """The IDs of other quanta previously executed in the same process as this
+    one.
+    """
+
+    logs: list[ButlerLogRecord] = pydantic.Field(default_factory=list)
+    """Logs for this attempt.
+
+    This is always empty for the most recent attempt, because that stores logs
+    in the main section of the butler log records.
+    """
+
+    previous_attempts: list[_ExecutionLogRecordsExtra] = pydantic.Field(default_factory=list)
+    """Information about previous attempts to run this task within the same
+    `~lsst.daf.butler.CollectionType.RUN` collection.
+
+    This is always empty for any attempt other than the most recent one,
+    as all previous attempts are flattened into one list.
+    """
+
+    def attach_previous_attempt(self, log_records: ButlerLogRecords) -> None:
+        """Attach logs from a previous attempt to this struct.
+
+        Parameters
+        ----------
+        log_records : `ButlerLogRecords`
+            Logs from a past attempt to run a quantum.
+        """
+        previous = self.model_validate(log_records.extra)
+        previous.logs.extend(log_records)
+        self.previous_attempts.extend(previous.previous_attempts)
+        self.previous_attempts.append(previous)
+        previous.previous_attempts.clear()
+
+
+@dataclasses.dataclass
+class _LogCaptureContext:
+    """Controls for log capture returned by the `LogCapture.capture_logging`
+    context manager.
+    """
 
     store: bool = True
+    """Whether to store logs at all."""
+
+    extra: _ExecutionLogRecordsExtra = dataclasses.field(default_factory=_ExecutionLogRecordsExtra)
+    """Extra information about the quantum's execution to store for provenance
+    extraction.
+    """
 
 
 class LogCapture:
@@ -88,7 +165,7 @@ class LogCapture:
         return cls(butler, butler)
 
     @contextmanager
-    def capture_logging(self, task_node: TaskNode, /, quantum: Quantum) -> Iterator[_LogCaptureFlag]:
+    def capture_logging(self, task_node: TaskNode, /, quantum: Quantum) -> Iterator[_LogCaptureContext]:
         """Configure logging system to capture logs for execution of this task.
 
         Parameters
@@ -121,7 +198,7 @@ class LogCapture:
         metadata_ref = quantum.outputs[METADATA_OUTPUT_TEMPLATE.format(label=task_node.label)][0]
         mdc["RUN"] = metadata_ref.run
 
-        ctx = _LogCaptureFlag()
+        ctx = _LogCaptureContext()
         log_dataset_name = (
             task_node.log_output.dataset_type_name if task_node.log_output is not None else None
         )
@@ -154,6 +231,12 @@ class LogCapture:
                     # Ensure that the logs are stored in butler.
                     logging.getLogger().removeHandler(log_handler_file)
                     log_handler_file.close()
+                    if ctx.extra:
+                        with open(log_file, "a") as log_stream:
+                            ButlerLogRecords.write_streaming_extra(
+                                log_stream,
+                                ctx.extra.model_dump_json(exclude_unset=True, exclude_defaults=True),
+                            )
                     if ctx.store:
                         self._ingest_log_records(quantum, log_dataset_name, log_file)
                     shutil.rmtree(tmpdir, ignore_errors=True)
@@ -165,7 +248,15 @@ class LogCapture:
                 try:
                     with ButlerMDC.set_mdc(mdc):
                         yield ctx
+                except:
+                    raise
+                else:
+                    # If the quantum succeeded, we don't need to save the
+                    # metadata in the logs, because we'll have saved them in
+                    # the metadata.
+                    ctx.extra.metadata = None
                 finally:
+                    log_handler_memory.records.extra = ctx.extra.model_dump()
                     # Ensure that the logs are stored in butler.
                     logging.getLogger().removeHandler(log_handler_memory)
                     if ctx.store:

{lsst_pipe_base-29.2025.4500 → lsst_pipe_base-29.2025.4700}/python/lsst/pipe/base/pipeline_graph/expressions.py

@@ -45,13 +45,13 @@ import dataclasses
 import functools
 from typing import TYPE_CHECKING, Any, Literal, TypeAlias
 
-from lsst.daf.butler.registry.queries.expressions.parser.ply import lex, yacc
+from lsst.daf.butler.queries.expressions.parser.ply import lex, yacc
 
 from ._exceptions import InvalidExpressionError
 
 if TYPE_CHECKING:
-    from lsst.daf.butler.registry.queries.expressions.parser.parserLex import LexToken
-    from lsst.daf.butler.registry.queries.expressions.parser.parserYacc import YaccProduction
+    from lsst.daf.butler.queries.expressions.parser.parserLex import LexToken
+    from lsst.daf.butler.queries.expressions.parser.parserYacc import YaccProduction
 
 
 class _ParserLex:

{lsst_pipe_base-29.2025.4500 → lsst_pipe_base-29.2025.4700}/python/lsst/pipe/base/quantum_graph/_common.py

@@ -28,6 +28,7 @@
 from __future__ import annotations
 
 __all__ = (
+    "FORMAT_VERSION",
     "BaseQuantumGraph",
     "BaseQuantumGraphReader",
     "BipartiteEdgeInfo",
@@ -60,6 +61,7 @@ import pydantic
 import zstandard
 
 from lsst.daf.butler import DataCoordinate, DataIdValue
+from lsst.daf.butler._rubin import generate_uuidv7
 from lsst.resources import ResourcePath, ResourcePathExpression
 
 from ..pipeline_graph import DatasetTypeNode, Edge, PipelineGraph, TaskImportMode, TaskNode
@@ -91,6 +93,19 @@ DataCoordinateValues: TypeAlias = list[DataIdValue]
 
 _T = TypeVar("_T", bound=pydantic.BaseModel)
 
+FORMAT_VERSION: int = 1
+"""
+File format version number for new files.
+
+This applies to both predicted and provenance QGs, since they usually change
+in concert.
+
+CHANGELOG:
+
+- 0: Initial version.
+- 1: Switched from internal integer IDs to UUIDs in all models.
+"""
+
 
 class IncompleteQuantumGraphError(RuntimeError):
     pass
@@ -99,7 +114,7 @@ class IncompleteQuantumGraphError(RuntimeError):
 class HeaderModel(pydantic.BaseModel):
     """Data model for the header of a quantum graph file."""
 
-    version: int = 0
+    version: int = FORMAT_VERSION
     """File format / data model version number."""
 
     graph_type: str = ""
@@ -157,6 +172,11 @@ class HeaderModel(pydantic.BaseModel):
     quantum graph file).
     """
 
+    provenance_dataset_id: uuid.UUID = pydantic.Field(default_factory=generate_uuidv7)
+    """The dataset ID for provenance quantum graph when it is ingested into
+    a butler repository.
+    """
+
     @classmethod
     def from_old_quantum_graph(cls, old_quantum_graph: QuantumGraph) -> HeaderModel:
         """Extract a header from an old `QuantumGraph` instance.

{lsst_pipe_base-29.2025.4500 → lsst_pipe_base-29.2025.4700}/python/lsst/pipe/base/quantum_graph/_multiblock.py

@@ -323,10 +323,11 @@ class AddressReader:
     rows: dict[uuid.UUID, AddressRow] = dataclasses.field(default_factory=dict)
     """Rows that have already been read."""
 
-    rows_by_index: dict[int, AddressRow] = dataclasses.field(default_factory=dict)
-    """Rows that have already been read, keyed by integer index."""
-
     pages: list[AddressPage] = dataclasses.field(default_factory=list)
+    """Descriptions of the file offsets and integer row indexes of pages and
+    flags for whether they have been read already.
+    """
+
     page_bounds: dict[int, PageBounds] = dataclasses.field(default_factory=dict)
     """Mapping from page index to page boundary information."""
 
@@ -502,32 +503,23 @@ class AddressReader:
         self.pages.clear()
         return self.rows
 
-    def find(self, key: uuid.UUID | int) -> AddressRow:
+    def find(self, key: uuid.UUID) -> AddressRow:
         """Read the row for the given UUID or integer index.
 
         Parameters
         ----------
-        key : `uuid.UUID` or `int`
-            UUID or integer index to find.
+        key : `uuid.UUID`
+            UUID to find.
 
         Returns
         -------
         row : `AddressRow`
             Addresses for the given UUID.
         """
-        match key:
-            case uuid.UUID():
-                return self._find_uuid(key)
-            case int():
-                return self._find_index(key)
-            case _:
-                raise TypeError(f"Invalid argument: {key}.")
-
-    def _find_uuid(self, target: uuid.UUID) -> AddressRow:
-        if (row := self.rows.get(target)) is not None:
+        if (row := self.rows.get(key)) is not None:
             return row
         if self.n_rows == 0 or not self.pages:
-            raise LookupError(f"Address for {target} not found.")
+            raise LookupError(f"Address for {key} not found.")
 
         # Use a binary search to find the page containing the target UUID.
         left = 0
@@ -535,35 +527,19 @@ class AddressReader:
         while left <= right:
             mid = left + ((right - left) // 2)
             self._read_page(mid)
-            if (row := self.rows.get(target)) is not None:
+            if (row := self.rows.get(key)) is not None:
                 return row
             bounds = self.page_bounds[mid]
-            if target.int < bounds.uuid_int_begin:
+            if key.int < bounds.uuid_int_begin:
                 right = mid - 1
-            elif target.int > bounds.uuid_int_end:
+            elif key.int > bounds.uuid_int_end:
                 left = mid + 1
             else:
                 # Should have been on this page, but it wasn't.
-                raise LookupError(f"Address for {target} not found.")
+                raise LookupError(f"Address for {key} not found.")
 
         # Ran out of pages to search.
-        raise LookupError(f"Address for {target} not found.")
-
-    def _find_index(self, target: int) -> AddressRow:
-        # First shortcut if we've already loaded this row.
-        if (row := self.rows_by_index.get(target)) is not None:
-            return row
-        if target < 0 or target >= self.n_rows:
-            raise LookupError(f"Address for index {target} not found.")
-        # Since all indexes should be present, we can predict the right page
-        # exactly.
-        page_index = target // self.rows_per_page
-        self._read_page(page_index)
-        try:
-            return self.rows_by_index[target]
-        except KeyError:
-            _LOG.debug("Index find failed: %s should have been in page %s.", target, page_index)
-            raise LookupError(f"Address for {target} not found.") from None
+        raise LookupError(f"Address for {key} not found.")
 
     def _read_page(self, page_index: int, page_stream: BytesIO | None = None) -> bool:
         page = self.pages[page_index]
@@ -586,7 +562,6 @@ class AddressReader:
     def _read_row(self, page_stream: BytesIO) -> AddressRow:
         row = AddressRow.read(page_stream, self.n_addresses, self.int_size)
         self.rows[row.key] = row
-        self.rows_by_index[row.index] = row
         _LOG.debug("Read address row %s.", row)
         return row