Add MapReduceWorkload scaffold and generic workload execution
This commit is contained in:
@@ -19,6 +19,7 @@ from .artifacts import (
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PortSpec,
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Provenance,
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)
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from .batch import MapReduceWorkload
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from .conformance import (
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CancellationFlag,
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LocalArtifactStore,
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@@ -77,6 +78,7 @@ from .registry import (
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WorkloadDefinition,
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WorkloadDescription,
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WorkloadRegistry,
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workload_allowlist_from_json,
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)
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from .resources import (
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AcceleratorDevice,
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@@ -155,6 +157,7 @@ __all__ = [
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"LocalTaskContext",
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"LoopSpec",
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"MANIFEST_SCHEMA_VERSION",
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"MapReduceWorkload",
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"NegotiatedWorkload",
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"NetworkPolicy",
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"NumericTolerance",
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@@ -207,6 +210,7 @@ __all__ = [
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"WorkloadLimits",
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"WorkloadManifest",
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"WorkloadRegistry",
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"workload_allowlist_from_json",
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"assert_manifest_round_trip",
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"installed_distribution_digest",
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"negotiate_manifest",
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@@ -0,0 +1,554 @@
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"""High-level core-batch-v1 authoring scaffold for map/reduce workloads.
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``MapReduceWorkload`` is the SDK's primary authoring surface for the
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``core-batch-v1`` profile: a subclass declares its identity, parameter
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schema, artifact ports, and three scientific hooks (partitioning, per-shard
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computation, partial merging), and the base class assembles the immutable
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manifest, the map/reduce stages, the workflow DAG, the digest-pinned
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planner/runner/reducer handlers, and the exact-artifact verifier.
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The base class deliberately supports only the static byte-exact map/reduce
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shape with a single external input and one output port. Workloads that need
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a different DAG (for example block-pair tasks with two map inputs) override
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the ``map_stage_inputs``, ``plan_tasks``, ``parse_partial_key``, and
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``validate_partial_keys`` hooks; anything outside the model must use the
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lower-level SDK value objects directly.
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"""
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from __future__ import annotations
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import hashlib
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import shutil
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from pathlib import Path
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from typing import Any, Mapping, Sequence
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from .artifacts import (
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ArtifactCollection,
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ArtifactItem,
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ArtifactRef,
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ArtifactSchema,
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Cardinality,
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CollectionKind,
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OutputManifest,
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PortSpec,
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)
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from .execution import (
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CheckpointPolicy,
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ExecutionProfile,
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NetworkPolicy,
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RetryPolicy,
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)
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from .identity import ComponentRef, VersionRange, WorkloadId
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from .manifest import (
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DeterminismProfile,
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EnvironmentSpec,
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PackageSpec,
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TrustMode,
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VerifierSpec,
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WorkloadLimits,
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WorkloadManifest,
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)
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from .plans import JobRequest, TaskSpec, ValidatedJob, WorkflowPlan
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from .protocols import PlanningContext, ReduceContext, TaskContext
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from .registry import WorkloadDefinition
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from .resources import ResourceRequirements
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from .verification import ExactArtifactVerifier
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from .workflow import ArtifactEdge, PortRef, StageKind, StageSpec, WorkflowSpec
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_EXACT_ARTIFACT = ComponentRef("exact-artifact", 1)
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_EXACT_VERIFIER = ExactArtifactVerifier()
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def _sha256_file(path: Path) -> str:
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digest = hashlib.sha256()
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with path.open("rb") as source:
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for block in iter(lambda: source.read(1024 * 1024), b""):
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digest.update(block)
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return digest.hexdigest()
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def _default_entry_point(module: str, kind: str) -> str:
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return f"{module}:{kind}@v1"
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class MapReduceWorkload:
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"""Base class for static byte-exact map/reduce workloads.
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Required class attributes:
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- ``workload_id``: ``WorkloadId`` identity (name + version);
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- ``parameters_schema``: strict JSON object schema (the registry validates
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``additionalProperties: false`` for the top level);
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- ``input_port``, ``partial_port``, ``output_port``: typed ``PortSpec``
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values for the external input, one map partial, and the final result.
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Scientific hooks (override as needed):
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- ``domain_validate(parameters)``: extra job-parameter validation;
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- ``resolved_parameters(request)``: values carried into the plan;
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- ``partition_input(input_path, parameters, workspace)``: deterministic
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shard splitting; returns one TSV/CSV file per map task;
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- ``plan_tasks(shard_paths, resolved, job, negotiated, map_stage, context)``:
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task construction (default: one task per shard, ``map/<index>``);
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- ``compute_shard(inputs, parameters, output_path)``: one map task;
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``inputs`` maps every ``map_stage_inputs`` port to a materialized file;
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- ``parse_partial_key(key)`` and ``validate_partial_keys(parsed)``:
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partial-key policy for the reducer;
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- ``reduce_partials(partial_paths, parameters, output_path)``: the
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deterministic merge.
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Optional class attributes: ``map_stage_inputs`` (default one ``input``
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port), ``map_parameter_names``, ``reduce_parameter_names``, ``capabilities``,
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``trust_modes``, ``workflow_id``, ``limits``, ``resources``, ``execution``,
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``map_entry_point``, ``reduce_entry_point``.
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"""
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workload_id: WorkloadId
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description: str = ""
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parameters_schema: Mapping[str, Any] = {}
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input_port: PortSpec
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partial_port: PortSpec
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output_port: PortSpec
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map_stage_inputs: Mapping[str, PortSpec] | None = None
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map_parameter_names: tuple[str, ...] = ()
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reduce_parameter_names: tuple[str, ...] = ()
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capabilities: tuple[str, ...] | None = None
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trust_modes: tuple[TrustMode, ...] = (TrustMode.TRUSTED, TrustMode.UNTRUSTED_QUORUM)
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workflow_id: str | None = None
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limits: WorkloadLimits | None = None
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resources: ResourceRequirements | None = None
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execution: ExecutionProfile | None = None
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map_entry_point: str | None = None
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reduce_entry_point: str | None = None
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def __init__(
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self,
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*,
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package_digest: str,
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environment_digest: str,
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) -> None:
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workload_id = self.workload_id
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if not isinstance(workload_id, WorkloadId):
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raise ValueError("workload_id must be a WorkloadId")
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if not isinstance(self.input_port, PortSpec):
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raise ValueError("input_port must be a PortSpec")
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if not isinstance(self.partial_port, PortSpec):
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raise ValueError("partial_port must be a PortSpec")
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if not isinstance(self.output_port, PortSpec):
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raise ValueError("output_port must be a PortSpec")
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if not self.parameters_schema:
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raise ValueError("parameters_schema must be provided")
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module = type(self).__module__
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self.map_entry_point = self.map_entry_point or _default_entry_point(
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module, "map"
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)
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self.reduce_entry_point = self.reduce_entry_point or _default_entry_point(
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module, "reduce"
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)
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self.entry_point = self.map_entry_point
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self.map_stage_inputs = dict(
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self.map_stage_inputs or {"input": self.input_port}
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)
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if set(self.map_stage_inputs) != {"input"} and any(
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port.schema != self.input_port.schema
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for port in self.map_stage_inputs.values()
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):
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raise ValueError(
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"additional map inputs must share the external input schema"
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)
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self.map_parameter_names = tuple(self.map_parameter_names)
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self.reduce_parameter_names = tuple(
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self.reduce_parameter_names or self.map_parameter_names
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)
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self.capabilities = tuple(self.capabilities or (workload_id.name,))
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if workload_id.name not in self.capabilities:
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raise ValueError("capabilities must include the workload name")
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name = workload_id.name
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resources = self.resources or ResourceRequirements(
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profile=f"{name}-cpu-v1",
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cpu_cores=1,
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memory_mb=1024,
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scratch_mb=1024,
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max_duration_seconds=3600,
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)
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execution = self.execution or ExecutionProfile(
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profile=f"{name}-python-process-v1",
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network=NetworkPolicy.TRUSTED,
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timeout_seconds=3600,
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checkpoint=CheckpointPolicy(),
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)
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limits = self.limits or WorkloadLimits(
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max_input_bytes=self.input_port.schema.max_bytes,
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max_tasks=10_000,
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max_output_bytes=self.output_port.schema.max_bytes,
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)
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trust_values = tuple(mode.value for mode in self.trust_modes)
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map_stage = StageSpec(
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stage_id="map",
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kind=StageKind.MAP,
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entry_point=self.map_entry_point,
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needs=(),
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inputs=self.map_stage_inputs,
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outputs={"partial": self.partial_port},
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parameter_names=self.map_parameter_names,
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resources=resources,
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execution=execution,
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retry=RetryPolicy(),
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verifier=_EXACT_ARTIFACT,
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trust_modes=trust_values,
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max_fan_out=limits.max_tasks,
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cacheable=True,
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)
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reduce_input = PortSpec(
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schema=self.partial_port.schema,
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cardinality=Cardinality.MANY,
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collection=CollectionKind.KEYED,
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)
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reduce_stage = StageSpec(
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stage_id="reduce",
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kind=StageKind.REDUCE,
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entry_point=self.reduce_entry_point,
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needs=("map",),
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inputs={"partials": reduce_input},
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outputs={"result": self.output_port},
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parameter_names=self.reduce_parameter_names,
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resources=resources,
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execution=execution,
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retry=RetryPolicy(),
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verifier=_EXACT_ARTIFACT,
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trust_modes=trust_values,
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max_fan_out=1,
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cacheable=True,
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)
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edges = [
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ArtifactEdge(PortRef("input"), PortRef(port, "map"))
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for port in self.map_stage_inputs
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] + [
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ArtifactEdge(PortRef("partial", "map"), PortRef("partials", "reduce")),
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]
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workflow = WorkflowSpec(
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workflow_id=self.workflow_id or f"{name}-map-reduce-v1",
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inputs={"input": self.input_port},
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stages=(map_stage, reduce_stage),
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edges=tuple(edges),
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outputs={"result": PortRef("result", "reduce")},
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max_tasks=limits.max_tasks,
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max_output_bytes=limits.max_output_bytes,
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)
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self.manifest = WorkloadManifest(
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sdk_api=VersionRange(">=1.0,<2.0"),
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protocol=VersionRange(">=1,<2"),
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workload=workload_id,
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description=self.description,
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package=PackageSpec("scimesh", package_digest),
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environment=EnvironmentSpec(
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"python-process",
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environment_digest,
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{"adapter": "sdk-native"},
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),
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parameters_schema=self.parameters_schema,
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workflow=workflow,
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inputs={"input": self.input_port},
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outputs={"result": self.output_port},
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determinism=DeterminismProfile.BYTE_EXACT,
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trust_modes=self.trust_modes,
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verifier=VerifierSpec(_EXACT_ARTIFACT, {}),
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limits=limits,
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capabilities=self.capabilities,
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conformance_profiles=("core-batch-v1",),
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)
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self._exact_verifier = _EXACT_VERIFIER
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self._resources = resources
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self._execution = execution
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self._limits = limits
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# ------------------------------------------------------------------
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# Public assembly
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# ------------------------------------------------------------------
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def definition(self) -> WorkloadDefinition:
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map_entry_point = self.map_entry_point
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reduce_entry_point = self.reduce_entry_point
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assert map_entry_point is not None and reduce_entry_point is not None
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return WorkloadDefinition(
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manifest=self.manifest,
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planner=self,
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runners={map_entry_point: self},
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reducers={reduce_entry_point: self},
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verifiers={_EXACT_ARTIFACT.canonical: self._exact_verifier},
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)
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# ------------------------------------------------------------------
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# Scientific hooks
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# ------------------------------------------------------------------
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def domain_validate(self, parameters: Mapping[str, Any]) -> None:
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"""Extra job-parameter validation beyond the JSON schema."""
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def resolved_parameters(self, request: JobRequest) -> dict[str, Any]:
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"""Values persisted as the plan's resolved parameters."""
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return dict(request.parameters)
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def partition_input(
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self,
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input_path: Path,
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parameters: Mapping[str, Any],
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workspace: Path,
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) -> list[Path]:
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"""Split the materialized input into deterministic shard files."""
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raise NotImplementedError("partition_input must be implemented")
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def plan_tasks(
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self,
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shard_paths: Sequence[Path],
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resolved: Mapping[str, Any],
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job: ValidatedJob,
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negotiated: Any,
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map_stage: StageSpec,
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context: PlanningContext,
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) -> list[TaskSpec]:
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"""Build one map TaskSpec per planned shard."""
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task_parameters = self.task_parameters(resolved)
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tasks: list[TaskSpec] = []
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for index, path in enumerate(shard_paths):
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sealed = context.sink.seal(
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path,
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declaration=self.input_port.schema,
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)
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tasks.append(
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self.task_spec(
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map_stage,
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job,
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negotiated,
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f"map/{index:08d}",
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task_parameters,
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{"input": ArtifactCollection.single(sealed)},
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)
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)
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return tasks
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def task_parameters(self, resolved: Mapping[str, Any]) -> dict[str, Any]:
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"""Project resolved parameters onto the map stage projection."""
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return {
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key: value
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for key, value in resolved.items()
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if key in set(self.map_parameter_names)
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}
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def compute_shard(
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self,
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inputs: Mapping[str, Path],
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parameters: Mapping[str, Any],
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output_path: Path,
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) -> Mapping[str, int | float]:
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"""Compute one map task and write its partial CSV."""
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raise NotImplementedError("compute_shard must be implemented")
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def parse_partial_key(self, key: str) -> Any:
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"""Parse one ``map.<key>`` partial key into an orderable identity."""
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prefix = "map."
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if not key.startswith(prefix):
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raise ValueError("partial key must use map.<eight-digit-index>")
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raw = key[len(prefix) :]
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if len(raw) != 8 or not raw.isdigit():
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raise ValueError("partial key must use map.<eight-digit-index>")
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return int(raw)
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def validate_partial_keys(self, parsed: Sequence[Any]) -> None:
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"""Enforce the reducer's partial-set invariant (default: contiguous)."""
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indices = sorted(int(value) for value in parsed)
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if indices != list(range(len(indices))):
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raise ValueError("partial keys must be complete and contiguous")
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def reduce_partials(
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self,
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partial_paths: Sequence[Path],
|
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parameters: Mapping[str, Any],
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output_path: Path,
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) -> Mapping[str, int | float]:
|
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"""Merge materialized partials into one deterministic final CSV."""
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raise NotImplementedError("reduce_partials must be implemented")
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# ------------------------------------------------------------------
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# Framework handlers
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# ------------------------------------------------------------------
|
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|
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def validate(self, request: JobRequest) -> ValidatedJob:
|
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if request.workload != self.manifest.workload:
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raise ValueError("workload received a request for another workload")
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self.domain_validate(request.parameters)
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return ValidatedJob(request, self.resolved_parameters(request))
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def plan(self, job: ValidatedJob, context: PlanningContext) -> WorkflowPlan:
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if not isinstance(job, ValidatedJob):
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raise ValueError("job must be a ValidatedJob")
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collection = job.request.inputs.get("input")
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if collection is None:
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raise ValueError("workload requires the input port")
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self.input_port.validate_collection(collection, "job input")
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input_path = context.catalog.materialize(collection.items[0].artifact)
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workspace = context.workspace
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workspace.mkdir(parents=True, exist_ok=True)
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resolved = dict(job.resolved_parameters)
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resolved = self.resolved_parameters_for_plan(job, input_path, resolved)
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shard_paths = self.partition_input(input_path, resolved, workspace)
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negotiated = context.negotiated
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map_stage = self.manifest.workflow.stages[0]
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tasks = self.plan_tasks(
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shard_paths, resolved, job, negotiated, map_stage, context
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)
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return self.workflow_plan(job, negotiated, resolved, tasks)
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|
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def resolved_parameters_for_plan(
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self,
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job: ValidatedJob,
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||||
input_path: Path,
|
||||
resolved: dict[str, Any],
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) -> dict[str, Any]:
|
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"""Hook to enrich resolved parameters at plan time (query resolution)."""
|
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return resolved
|
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|
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def workflow_plan(
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self,
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job: ValidatedJob,
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||||
negotiated: Any,
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||||
resolved: Mapping[str, Any],
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||||
tasks: Sequence[TaskSpec],
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||||
) -> WorkflowPlan:
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return WorkflowPlan(
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workload=self.manifest.workload,
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package_digest=self.manifest.package.digest,
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||||
manifest_digest=self.manifest.digest,
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trust_mode=job.request.trust_mode,
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sdk_api_version=negotiated.sdk_api_version,
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protocol_version=negotiated.protocol_version,
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manifest_schema_version=self.manifest.manifest_schema_version,
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workflow_schema_version=self.manifest.workflow.schema_version,
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||||
environment_digest=self.manifest.environment.digest,
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||||
verifier=self.manifest.verifier.verifier,
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||||
selected_features=negotiated.selected_features,
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||||
optional_fallbacks=negotiated.optional_fallbacks,
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||||
workflow_id=self.manifest.workflow.workflow_id,
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||||
resolved_parameters=dict(resolved),
|
||||
tasks=tuple(tasks),
|
||||
)
|
||||
|
||||
def task_spec(
|
||||
self,
|
||||
map_stage: StageSpec,
|
||||
job: ValidatedJob,
|
||||
negotiated: Any,
|
||||
task_key: str,
|
||||
parameters: Mapping[str, Any],
|
||||
inputs: Mapping[str, ArtifactCollection],
|
||||
) -> TaskSpec:
|
||||
assert map_stage.verifier is not None
|
||||
return TaskSpec(
|
||||
workload=self.manifest.workload,
|
||||
package_digest=self.manifest.package.digest,
|
||||
manifest_digest=self.manifest.digest,
|
||||
trust_mode=job.request.trust_mode,
|
||||
sdk_api_version=negotiated.sdk_api_version,
|
||||
protocol_version=negotiated.protocol_version,
|
||||
manifest_schema_version=self.manifest.manifest_schema_version,
|
||||
workflow_schema_version=self.manifest.workflow.schema_version,
|
||||
environment_digest=self.manifest.environment.digest,
|
||||
verifier=map_stage.verifier,
|
||||
selected_features=negotiated.selected_features,
|
||||
optional_fallbacks=negotiated.optional_fallbacks,
|
||||
task_key=task_key,
|
||||
stage_id=map_stage.stage_id,
|
||||
parameters=parameters,
|
||||
inputs=inputs,
|
||||
expected_outputs=map_stage.outputs,
|
||||
resources=map_stage.resources,
|
||||
execution=map_stage.execution,
|
||||
).validate_stage(map_stage)
|
||||
|
||||
def run(self, context: TaskContext) -> OutputManifest:
|
||||
context.cancellation.raise_if_cancelled()
|
||||
workspace = context.workspace
|
||||
workspace.mkdir(parents=True, exist_ok=True)
|
||||
inputs: dict[str, Path] = {}
|
||||
for name, port in self.map_stage_inputs.items():
|
||||
collection = context.task.inputs.get(name)
|
||||
if collection is None:
|
||||
raise ValueError(f"map task requires the {name} input")
|
||||
port.validate_collection(collection, f"map input {name}")
|
||||
assert collection.items
|
||||
inputs[name] = context.catalog.materialize(collection.items[0].artifact)
|
||||
output_path = workspace / "result.csv"
|
||||
metrics = self.compute_shard(
|
||||
inputs,
|
||||
context.task.parameters,
|
||||
output_path,
|
||||
)
|
||||
context.cancellation.raise_if_cancelled()
|
||||
sealed = context.sink.seal(
|
||||
output_path,
|
||||
declaration=self.partial_port.schema,
|
||||
)
|
||||
return OutputManifest(
|
||||
context.task.task_key,
|
||||
{"partial": ArtifactCollection.single(sealed)},
|
||||
metrics,
|
||||
context.provenance,
|
||||
).validate_against(
|
||||
context.task.expected_outputs,
|
||||
max_output_bytes=self._limits.max_output_bytes,
|
||||
)
|
||||
|
||||
def reduce(self, context: ReduceContext) -> OutputManifest:
|
||||
context.cancellation.raise_if_cancelled()
|
||||
collection = context.accepted_inputs.get("partials")
|
||||
if collection is None:
|
||||
raise ValueError("reducer requires a non-empty keyed partial collection")
|
||||
if collection.kind is not CollectionKind.KEYED or not collection.items:
|
||||
raise ValueError("reducer requires a non-empty keyed partial collection")
|
||||
self.manifest.workflow.stages[1].inputs["partials"].validate_collection(
|
||||
collection,
|
||||
"reducer partials",
|
||||
)
|
||||
parsed = [self.parse_partial_key(item.key or "") for item in collection.items]
|
||||
self.validate_partial_keys(parsed)
|
||||
expected_keys = context.task.expected_input_keys.get("partials")
|
||||
if expected_keys is None or {item.key for item in collection.items} != set(
|
||||
expected_keys
|
||||
):
|
||||
raise ValueError("partial keys do not match the coordinator expected set")
|
||||
workspace = context.workspace
|
||||
workspace.mkdir(parents=True, exist_ok=True)
|
||||
partial_paths: list[Path] = []
|
||||
for index, item in sorted(
|
||||
enumerate(collection.items),
|
||||
key=lambda entry: entry[1].key or "",
|
||||
):
|
||||
artifact: ArtifactRef = item.artifact
|
||||
source = context.catalog.materialize(artifact)
|
||||
target = workspace / artifact.artifact_id
|
||||
if source.resolve() != target.resolve():
|
||||
shutil.copyfile(source, target)
|
||||
if _sha256_file(target) != artifact.sha256:
|
||||
raise ValueError("materialized partial checksum does not match")
|
||||
partial_paths.append(target)
|
||||
result_path = workspace / "result.csv"
|
||||
metrics = self.reduce_partials(
|
||||
partial_paths,
|
||||
context.task.parameters,
|
||||
result_path,
|
||||
)
|
||||
context.cancellation.raise_if_cancelled()
|
||||
sealed = context.sink.seal(
|
||||
result_path,
|
||||
declaration=self.output_port.schema,
|
||||
)
|
||||
return OutputManifest(
|
||||
context.task.task_key,
|
||||
{"result": ArtifactCollection.single(sealed)},
|
||||
metrics,
|
||||
context.provenance,
|
||||
).validate_against(
|
||||
context.task.expected_outputs,
|
||||
max_output_bytes=self._limits.max_output_bytes,
|
||||
)
|
||||
+216
-56
@@ -24,8 +24,20 @@ from .identity import ComponentRef, WorkloadId
|
||||
from .integrity import installed_distribution_digest
|
||||
from .manifest import WorkloadManifest
|
||||
from .plans import JobRequest, ValidatedJob, WorkflowPlan
|
||||
from .protocols import Planner, PlanningContext, PlanningResources, Reducer, Runner, Verifier
|
||||
from .runtime import CompatibilityError, NegotiatedWorkload, RuntimeCapabilities, negotiate_manifest
|
||||
from .protocols import (
|
||||
Planner,
|
||||
PlanningContext,
|
||||
PlanningResources,
|
||||
Reducer,
|
||||
Runner,
|
||||
Verifier,
|
||||
)
|
||||
from .runtime import (
|
||||
CompatibilityError,
|
||||
NegotiatedWorkload,
|
||||
RuntimeCapabilities,
|
||||
negotiate_manifest,
|
||||
)
|
||||
from .schema import validate_parameter_instance
|
||||
from .workflow import StageKind
|
||||
|
||||
@@ -51,11 +63,11 @@ def _validate_entry_point_ownership(entry_point: metadata.EntryPoint) -> None:
|
||||
raise ValueError("workload entry point has an invalid module path")
|
||||
|
||||
raw_top_level = distribution.read_text("top_level.txt")
|
||||
declared = {
|
||||
line.strip()
|
||||
for line in raw_top_level.splitlines()
|
||||
if line.strip()
|
||||
} if raw_top_level is not None else set()
|
||||
declared = (
|
||||
{line.strip() for line in raw_top_level.splitlines() if line.strip()}
|
||||
if raw_top_level is not None
|
||||
else set()
|
||||
)
|
||||
root_name = parts[0]
|
||||
if root_name not in declared:
|
||||
raise ValueError("workload entry point module is outside its distribution")
|
||||
@@ -81,9 +93,18 @@ def _validate_entry_point_ownership(entry_point: metadata.EntryPoint) -> None:
|
||||
ownership_root = package_root.resolve()
|
||||
candidates = [
|
||||
*(Path(str(module_base) + suffix) for suffix in machinery.SOURCE_SUFFIXES),
|
||||
*(Path(str(module_base) + suffix) for suffix in machinery.EXTENSION_SUFFIXES),
|
||||
*(module_base / ("__init__" + suffix) for suffix in machinery.SOURCE_SUFFIXES),
|
||||
*(module_base / ("__init__" + suffix) for suffix in machinery.EXTENSION_SUFFIXES),
|
||||
*(
|
||||
Path(str(module_base) + suffix)
|
||||
for suffix in machinery.EXTENSION_SUFFIXES
|
||||
),
|
||||
*(
|
||||
module_base / ("__init__" + suffix)
|
||||
for suffix in machinery.SOURCE_SUFFIXES
|
||||
),
|
||||
*(
|
||||
module_base / ("__init__" + suffix)
|
||||
for suffix in machinery.EXTENSION_SUFFIXES
|
||||
),
|
||||
]
|
||||
else:
|
||||
if len(parts) != 1:
|
||||
@@ -92,7 +113,10 @@ def _validate_entry_point_ownership(entry_point: metadata.EntryPoint) -> None:
|
||||
module_base = Path(distribution.locate_file(root_name))
|
||||
candidates = [
|
||||
*(Path(str(module_base) + suffix) for suffix in machinery.SOURCE_SUFFIXES),
|
||||
*(Path(str(module_base) + suffix) for suffix in machinery.EXTENSION_SUFFIXES),
|
||||
*(
|
||||
Path(str(module_base) + suffix)
|
||||
for suffix in machinery.EXTENSION_SUFFIXES
|
||||
),
|
||||
]
|
||||
existing = tuple(candidate for candidate in candidates if candidate.is_file())
|
||||
if len(existing) != 1 or not existing[0].resolve().is_relative_to(ownership_root):
|
||||
@@ -126,7 +150,9 @@ class WorkloadDefinition:
|
||||
for name, handler in values.items():
|
||||
canonical = require_string(name, f"{field} entry point", max_length=256)
|
||||
if not callable(getattr(handler, method, None)):
|
||||
raise ValueError(f"definition {field} handler must implement {method}")
|
||||
raise ValueError(
|
||||
f"definition {field} handler must implement {method}"
|
||||
)
|
||||
copied[canonical] = handler
|
||||
object.__setattr__(self, field, MappingProxyType(copied))
|
||||
for stage in self.manifest.workflow.stages:
|
||||
@@ -149,23 +175,39 @@ class WorkloadDefinition:
|
||||
)
|
||||
verifier_key = self.manifest.verifier.verifier.canonical
|
||||
if verifier_key not in self.verifiers:
|
||||
raise ValueError(f"definition has no installed manifest verifier: {verifier_key}")
|
||||
raise ValueError(
|
||||
f"definition has no installed manifest verifier: {verifier_key}"
|
||||
)
|
||||
for key, verifier in self.verifiers.items():
|
||||
try:
|
||||
declared_identity = ComponentRef.from_dict(key)
|
||||
except ValueError as error:
|
||||
raise ValueError("definition verifier keys must be component identities") from error
|
||||
if declared_identity.canonical != key or getattr(verifier, "identity", None) != declared_identity:
|
||||
raise ValueError("definition verifier handler identity does not match its key")
|
||||
raise ValueError(
|
||||
"definition verifier keys must be component identities"
|
||||
) from error
|
||||
if (
|
||||
declared_identity.canonical != key
|
||||
or getattr(verifier, "identity", None) != declared_identity
|
||||
):
|
||||
raise ValueError(
|
||||
"definition verifier handler identity does not match its key"
|
||||
)
|
||||
manifest_verifier = self.verifiers[verifier_key]
|
||||
handler_configuration = getattr(manifest_verifier, "configuration", None)
|
||||
if handler_configuration is None:
|
||||
if self.manifest.verifier.configuration:
|
||||
raise ValueError("manifest verifier configuration is not bound by its handler")
|
||||
raise ValueError(
|
||||
"manifest verifier configuration is not bound by its handler"
|
||||
)
|
||||
elif dict(handler_configuration) != dict(self.manifest.verifier.configuration):
|
||||
raise ValueError("manifest verifier configuration does not match its handler")
|
||||
raise ValueError(
|
||||
"manifest verifier configuration does not match its handler"
|
||||
)
|
||||
for stage in self.manifest.workflow.stages:
|
||||
if stage.verifier is not None and stage.verifier.canonical not in self.verifiers:
|
||||
if (
|
||||
stage.verifier is not None
|
||||
and stage.verifier.canonical not in self.verifiers
|
||||
):
|
||||
raise ValueError(
|
||||
f"definition has no installed stage verifier: {stage.verifier.canonical}"
|
||||
)
|
||||
@@ -178,13 +220,54 @@ class AllowedPackage:
|
||||
digest: str
|
||||
|
||||
def __post_init__(self) -> None:
|
||||
distribution = require_string(self.distribution, "distribution", max_length=128).lower()
|
||||
distribution = require_string(
|
||||
self.distribution, "distribution", max_length=128
|
||||
).lower()
|
||||
if not re.fullmatch(r"[a-z0-9]+(?:[-_.][a-z0-9]+)*", distribution):
|
||||
raise ValueError("distribution must be a canonical Python distribution name")
|
||||
raise ValueError(
|
||||
"distribution must be a canonical Python distribution name"
|
||||
)
|
||||
object.__setattr__(self, "distribution", distribution.replace("_", "-"))
|
||||
if not isinstance(self.workload, WorkloadId):
|
||||
raise ValueError("allowed workload must be a WorkloadId")
|
||||
object.__setattr__(self, "digest", require_sha256(self.digest, "allowed digest", prefixed=True))
|
||||
object.__setattr__(
|
||||
self, "digest", require_sha256(self.digest, "allowed digest", prefixed=True)
|
||||
)
|
||||
|
||||
|
||||
def workload_allowlist_from_json(value: object) -> tuple[AllowedPackage, ...]:
|
||||
"""Parse a JSON array of ``{distribution, name, version, digest}`` allowlist entries."""
|
||||
import json
|
||||
|
||||
if value is None or value == "":
|
||||
return ()
|
||||
if not isinstance(value, str):
|
||||
raise ValueError("workload allowlist must be a JSON array")
|
||||
try:
|
||||
decoded = json.loads(value)
|
||||
except (TypeError, json.JSONDecodeError, RecursionError) as error:
|
||||
raise ValueError("workload allowlist must be valid JSON") from error
|
||||
if not isinstance(decoded, list):
|
||||
raise ValueError("workload allowlist must be a JSON array")
|
||||
entries: list[AllowedPackage] = []
|
||||
for item in decoded:
|
||||
if not isinstance(item, dict) or not {
|
||||
"distribution",
|
||||
"name",
|
||||
"version",
|
||||
"digest",
|
||||
}.issubset(item):
|
||||
raise ValueError(
|
||||
"workload allowlist entries need distribution, name, version, and digest"
|
||||
)
|
||||
entries.append(
|
||||
AllowedPackage(
|
||||
str(item["distribution"]),
|
||||
WorkloadId(str(item["name"]), str(item["version"])),
|
||||
str(item["digest"]),
|
||||
)
|
||||
)
|
||||
return tuple(entries)
|
||||
|
||||
|
||||
@dataclass(frozen=True, slots=True)
|
||||
@@ -223,14 +306,18 @@ class WorkloadRegistry:
|
||||
self._enabled: set[tuple[str, str, str]] = set()
|
||||
self._lock = RLock()
|
||||
|
||||
def register(self, definition: WorkloadDefinition, *, enabled: bool = False) -> None:
|
||||
def register(
|
||||
self, definition: WorkloadDefinition, *, enabled: bool = False
|
||||
) -> None:
|
||||
if not isinstance(definition, WorkloadDefinition):
|
||||
raise ValueError("definition must be a WorkloadDefinition")
|
||||
workload = definition.manifest.workload
|
||||
key = (workload.name, workload.version)
|
||||
with self._lock:
|
||||
if key in self._definitions:
|
||||
raise ValueError(f"workload version already registered: {workload.name}@{workload.version}")
|
||||
raise ValueError(
|
||||
f"workload version already registered: {workload.name}@{workload.version}"
|
||||
)
|
||||
self._definitions[key] = definition
|
||||
if enabled:
|
||||
self._enabled.add((*key, definition.manifest.package.digest))
|
||||
@@ -240,7 +327,9 @@ class WorkloadRegistry:
|
||||
with self._lock:
|
||||
definition = self._registered(name, version)
|
||||
if digest != definition.manifest.package.digest:
|
||||
raise ValueError("package digest does not match the registered manifest")
|
||||
raise ValueError(
|
||||
"package digest does not match the registered manifest"
|
||||
)
|
||||
self._enabled.add((definition.manifest.workload.name, version, digest))
|
||||
|
||||
def disable(self, name: str, version: str, package_digest: str) -> None:
|
||||
@@ -257,7 +346,9 @@ class WorkloadRegistry:
|
||||
try:
|
||||
return self._definitions[(canonical, version)]
|
||||
except KeyError as error:
|
||||
raise ValueError(f"unknown workload version: {canonical}@{version}") from error
|
||||
raise ValueError(
|
||||
f"unknown workload version: {canonical}@{version}"
|
||||
) from error
|
||||
|
||||
def require(
|
||||
self,
|
||||
@@ -270,10 +361,21 @@ class WorkloadRegistry:
|
||||
digest = require_sha256(package_digest, "package_digest", prefixed=True)
|
||||
with self._lock:
|
||||
definition = self._registered(name, version)
|
||||
identity = (definition.manifest.workload.name, definition.manifest.workload.version, digest)
|
||||
if digest != definition.manifest.package.digest or identity not in self._enabled:
|
||||
identity = (
|
||||
definition.manifest.workload.name,
|
||||
definition.manifest.workload.version,
|
||||
digest,
|
||||
)
|
||||
if (
|
||||
digest != definition.manifest.package.digest
|
||||
or identity not in self._enabled
|
||||
):
|
||||
raise ValueError("workload package digest is not enabled")
|
||||
negotiated = negotiate_manifest(definition.manifest, runtime) if runtime is not None else None
|
||||
negotiated = (
|
||||
negotiate_manifest(definition.manifest, runtime)
|
||||
if runtime is not None
|
||||
else None
|
||||
)
|
||||
return definition, negotiated
|
||||
|
||||
def plan(
|
||||
@@ -293,31 +395,41 @@ class WorkloadRegistry:
|
||||
runtime=runtime,
|
||||
)
|
||||
assert negotiated is not None
|
||||
self._validate_request_compatibility(request, definition.manifest, runtime, negotiated)
|
||||
self._validate_request_compatibility(
|
||||
request, definition.manifest, runtime, negotiated
|
||||
)
|
||||
self._validate_request_shape(request, definition.manifest)
|
||||
validated = definition.planner.validate(request)
|
||||
if not isinstance(validated, ValidatedJob) or validated.request != request:
|
||||
raise ValueError("planner.validate must return a ValidatedJob for the same request")
|
||||
raise ValueError(
|
||||
"planner.validate must return a ValidatedJob for the same request"
|
||||
)
|
||||
plan = definition.planner.plan(
|
||||
validated,
|
||||
_NegotiatedPlanningContext(context, negotiated),
|
||||
)
|
||||
if not isinstance(plan, WorkflowPlan) or plan.workload != request.workload:
|
||||
raise ValueError("planner.plan must return a WorkflowPlan for the requested workload")
|
||||
raise ValueError(
|
||||
"planner.plan must return a WorkflowPlan for the requested workload"
|
||||
)
|
||||
if (
|
||||
plan.package_digest != definition.manifest.package.digest
|
||||
or plan.manifest_digest != definition.manifest.digest
|
||||
or plan.trust_mode is not request.trust_mode
|
||||
or plan.sdk_api_version != runtime.sdk_api_version
|
||||
or plan.protocol_version != runtime.protocol_version
|
||||
or plan.manifest_schema_version != definition.manifest.manifest_schema_version
|
||||
or plan.workflow_schema_version != definition.manifest.workflow.schema_version
|
||||
or plan.manifest_schema_version
|
||||
!= definition.manifest.manifest_schema_version
|
||||
or plan.workflow_schema_version
|
||||
!= definition.manifest.workflow.schema_version
|
||||
or plan.environment_digest != definition.manifest.environment.digest
|
||||
or plan.verifier != definition.manifest.verifier.verifier
|
||||
or plan.selected_features != negotiated.selected_features
|
||||
or plan.optional_fallbacks != negotiated.optional_fallbacks
|
||||
):
|
||||
raise ValueError("planner plan does not carry the selected immutable workload pin")
|
||||
raise ValueError(
|
||||
"planner plan does not carry the selected immutable workload pin"
|
||||
)
|
||||
plan.validate_workflow(definition.manifest.workflow)
|
||||
self._validate_plan_limits(request, plan, definition.manifest)
|
||||
return WorkflowPlan.from_json(plan.to_json())
|
||||
@@ -369,7 +481,9 @@ class WorkloadRegistry:
|
||||
)
|
||||
|
||||
@staticmethod
|
||||
def _validate_request_shape(request: JobRequest, manifest: WorkloadManifest) -> None:
|
||||
def _validate_request_shape(
|
||||
request: JobRequest, manifest: WorkloadManifest
|
||||
) -> None:
|
||||
if set(request.inputs) != set(manifest.inputs):
|
||||
raise ValueError("job input ports do not match the manifest")
|
||||
total_bytes = 0
|
||||
@@ -380,7 +494,9 @@ class WorkloadRegistry:
|
||||
for item in request.inputs[name].items:
|
||||
existing = artifact_references.get(item.artifact.artifact_id)
|
||||
if existing is not None and existing != item.artifact:
|
||||
raise ValueError("job reuses an artifact ID with conflicting metadata")
|
||||
raise ValueError(
|
||||
"job reuses an artifact ID with conflicting metadata"
|
||||
)
|
||||
artifact_references[item.artifact.artifact_id] = item.artifact
|
||||
if total_bytes > manifest.limits.max_input_bytes:
|
||||
raise ValueError("job inputs exceed the manifest byte limit")
|
||||
@@ -388,7 +504,15 @@ class WorkloadRegistry:
|
||||
raise ValueError("job inputs exceed the manifest artifact limit")
|
||||
import json
|
||||
from ._validation import thaw_json
|
||||
if len(json.dumps(thaw_json(request.parameters), allow_nan=False).encode("utf-8")) > manifest.limits.max_parameter_bytes:
|
||||
|
||||
if (
|
||||
len(
|
||||
json.dumps(thaw_json(request.parameters), allow_nan=False).encode(
|
||||
"utf-8"
|
||||
)
|
||||
)
|
||||
> manifest.limits.max_parameter_bytes
|
||||
):
|
||||
raise ValueError("job parameters exceed the manifest byte limit")
|
||||
validate_parameter_instance(request.parameters, manifest.parameters_schema)
|
||||
|
||||
@@ -408,13 +532,23 @@ class WorkloadRegistry:
|
||||
for item in collection.items:
|
||||
existing = references.get(item.artifact.artifact_id)
|
||||
if existing is not None and existing != item.artifact:
|
||||
raise ValueError("workflow plan reuses an artifact ID with conflicting metadata")
|
||||
raise ValueError(
|
||||
"workflow plan reuses an artifact ID with conflicting metadata"
|
||||
)
|
||||
references[item.artifact.artifact_id] = item.artifact
|
||||
if len(canonical_json(task.parameters).encode("utf-8")) > manifest.limits.max_parameter_bytes:
|
||||
raise ValueError("planned task parameters exceed the manifest byte limit")
|
||||
if (
|
||||
len(canonical_json(task.parameters).encode("utf-8"))
|
||||
> manifest.limits.max_parameter_bytes
|
||||
):
|
||||
raise ValueError(
|
||||
"planned task parameters exceed the manifest byte limit"
|
||||
)
|
||||
if len(references) > manifest.limits.max_artifacts:
|
||||
raise ValueError("workflow plan exceeds the manifest artifact limit")
|
||||
if len(canonical_json(plan.resolved_parameters).encode("utf-8")) > manifest.limits.max_parameter_bytes:
|
||||
if (
|
||||
len(canonical_json(plan.resolved_parameters).encode("utf-8"))
|
||||
> manifest.limits.max_parameter_bytes
|
||||
):
|
||||
raise ValueError("resolved parameters exceed the manifest byte limit")
|
||||
|
||||
def descriptions(self) -> tuple[WorkloadDescription, ...]:
|
||||
@@ -455,7 +589,10 @@ class WorkloadRegistry:
|
||||
for key, approval in allowed.items():
|
||||
if _normalized_distribution_name(key[0]) != distribution:
|
||||
continue
|
||||
if entry_point.name != f"{approval.workload.name}@{approval.workload.version}":
|
||||
if (
|
||||
entry_point.name
|
||||
!= f"{approval.workload.name}@{approval.workload.version}"
|
||||
):
|
||||
continue
|
||||
_validate_entry_point_ownership(entry_point)
|
||||
# Import policy is process-global, so installed discovery is
|
||||
@@ -463,9 +600,12 @@ class WorkloadRegistry:
|
||||
# cache prefix prevents pre-existing package pyc files from
|
||||
# being consumed, while dont_write_bytecode keeps the
|
||||
# measured source tree unchanged during both load and factory.
|
||||
with _DISCOVERY_IMPORT_LOCK, TemporaryDirectory(
|
||||
prefix="scimesh-discovery-cache-"
|
||||
) as cache_prefix:
|
||||
with (
|
||||
_DISCOVERY_IMPORT_LOCK,
|
||||
TemporaryDirectory(
|
||||
prefix="scimesh-discovery-cache-"
|
||||
) as cache_prefix,
|
||||
):
|
||||
measured_before = installed_distribution_digest(entry_point.dist)
|
||||
if measured_before != approval.digest:
|
||||
raise ValueError(
|
||||
@@ -479,44 +619,64 @@ class WorkloadRegistry:
|
||||
loaded = entry_point.load()
|
||||
definition = (
|
||||
loaded()
|
||||
if callable(loaded) and not isinstance(loaded, WorkloadDefinition)
|
||||
if callable(loaded)
|
||||
and not isinstance(loaded, WorkloadDefinition)
|
||||
else loaded
|
||||
)
|
||||
finally:
|
||||
sys.pycache_prefix = previous_cache_prefix
|
||||
sys.dont_write_bytecode = previous_bytecode_policy
|
||||
if installed_distribution_digest(entry_point.dist) != measured_before:
|
||||
if (
|
||||
installed_distribution_digest(entry_point.dist)
|
||||
!= measured_before
|
||||
):
|
||||
raise ValueError(
|
||||
"installed package content changed while loading its entry point"
|
||||
)
|
||||
if not isinstance(definition, WorkloadDefinition):
|
||||
raise ValueError("workload entry point must provide a WorkloadDefinition")
|
||||
raise ValueError(
|
||||
"workload entry point must provide a WorkloadDefinition"
|
||||
)
|
||||
if definition.manifest.workload != approval.workload:
|
||||
raise ValueError("discovered workload identity does not match its allowlist entry")
|
||||
raise ValueError(
|
||||
"discovered workload identity does not match its allowlist entry"
|
||||
)
|
||||
if definition.manifest.package.distribution != approval.distribution:
|
||||
raise ValueError("discovered package identity does not match its allowlist entry")
|
||||
raise ValueError(
|
||||
"discovered package identity does not match its allowlist entry"
|
||||
)
|
||||
if definition.manifest.package.digest != approval.digest:
|
||||
raise ValueError("discovered package digest does not match its allowlist entry")
|
||||
raise ValueError(
|
||||
"discovered package digest does not match its allowlist entry"
|
||||
)
|
||||
if key in discovered:
|
||||
raise ValueError("multiple installed entry points match one allowlist entry")
|
||||
raise ValueError(
|
||||
"multiple installed entry points match one allowlist entry"
|
||||
)
|
||||
pending.append(definition)
|
||||
discovered.add(key)
|
||||
break
|
||||
missing = sorted(set(allowed) - discovered)
|
||||
if missing:
|
||||
identities = ", ".join(f"{name}@{version}" for _, name, version in missing)
|
||||
raise ValueError("allowlisted workload entry points were not installed: " + identities)
|
||||
raise ValueError(
|
||||
"allowlisted workload entry points were not installed: " + identities
|
||||
)
|
||||
pending_keys = [
|
||||
(definition.manifest.workload.name, definition.manifest.workload.version)
|
||||
for definition in pending
|
||||
]
|
||||
if len(pending_keys) != len(set(pending_keys)):
|
||||
raise ValueError("multiple allowlisted distributions provide one workload version")
|
||||
raise ValueError(
|
||||
"multiple allowlisted distributions provide one workload version"
|
||||
)
|
||||
with self._lock:
|
||||
conflicts = [key for key in pending_keys if key in self._definitions]
|
||||
if conflicts:
|
||||
name, version = conflicts[0]
|
||||
raise ValueError(f"workload version already registered: {name}@{version}")
|
||||
raise ValueError(
|
||||
f"workload version already registered: {name}@{version}"
|
||||
)
|
||||
definitions = dict(self._definitions)
|
||||
enabled = set(self._enabled)
|
||||
for key, definition in zip(pending_keys, pending):
|
||||
|
||||
@@ -77,7 +77,9 @@ def main(argv: list[str] | None = None) -> int:
|
||||
config = WorkerConfig.from_environment(overrides)
|
||||
except (TypeError, ValueError) as error:
|
||||
parser.error(str(error))
|
||||
logging.basicConfig(level=logging.INFO, format="%(asctime)s %(levelname)s %(message)s")
|
||||
logging.basicConfig(
|
||||
level=logging.INFO, format="%(asctime)s %(levelname)s %(message)s"
|
||||
)
|
||||
# One shared token strategy backs both clients: a worker key (exchanged and
|
||||
# refreshed) or a static bearer token, decided by what the config carries.
|
||||
tokens = provider_from_config(
|
||||
@@ -95,7 +97,7 @@ def main(argv: list[str] | None = None) -> int:
|
||||
HttpArtifactClient(
|
||||
config.coordinator_url, config.request_timeout, token_provider=tokens
|
||||
),
|
||||
SciMeshRunner(),
|
||||
SciMeshRunner.for_worker(config),
|
||||
).run_forever()
|
||||
return 0 if completed_without_interruption else 130
|
||||
|
||||
|
||||
+78
-13
@@ -2,6 +2,7 @@
|
||||
|
||||
from __future__ import annotations
|
||||
|
||||
import json
|
||||
from dataclasses import dataclass
|
||||
from math import isfinite
|
||||
from pathlib import Path
|
||||
@@ -10,6 +11,8 @@ import socket
|
||||
from typing import Mapping
|
||||
from urllib.parse import urlsplit
|
||||
|
||||
from scimesh.sdk.registry import AllowedPackage, workload_allowlist_from_json
|
||||
|
||||
|
||||
def _clean_url(value: object | None) -> str | None:
|
||||
"""Normalise an optional URL: drop a blank one, strip a trailing slash."""
|
||||
@@ -31,6 +34,24 @@ def _positive_number(value: object, name: str, *, allow_zero: bool = False) -> N
|
||||
raise ValueError(f"{name} must be {qualifier}")
|
||||
|
||||
|
||||
def _capabilities(value: object) -> tuple[str, ...]:
|
||||
"""Parse a comma-separated capability list into unique non-empty names."""
|
||||
if value is None:
|
||||
return ("similarity-search", "similarity_search")
|
||||
if not isinstance(value, str) or not value.strip():
|
||||
raise ValueError("capabilities must be a comma-separated list")
|
||||
names = tuple(
|
||||
dict.fromkeys(item.strip() for item in value.split(",") if item.strip())
|
||||
)
|
||||
if not names:
|
||||
raise ValueError("capabilities cannot be empty")
|
||||
return names
|
||||
|
||||
|
||||
def _workload_allowlist(value: object) -> tuple[AllowedPackage, ...]:
|
||||
return workload_allowlist_from_json(value)
|
||||
|
||||
|
||||
@dataclass(frozen=True)
|
||||
class WorkerConfig:
|
||||
coordinator_url: str
|
||||
@@ -60,6 +81,11 @@ class WorkerConfig:
|
||||
"similarity-search",
|
||||
"similarity_search",
|
||||
)
|
||||
# Optional allowlist of installed SDK workload packages to execute. When
|
||||
# empty, the worker runs the built-in similarity-search only. Entries are
|
||||
# ``{distribution, name, version, digest}`` JSON objects matching the
|
||||
# installed ``scimesh.workloads`` entry points.
|
||||
workload_allowlist: tuple[AllowedPackage, ...] = ()
|
||||
|
||||
def __post_init__(self) -> None:
|
||||
parsed = urlsplit(self.coordinator_url)
|
||||
@@ -72,8 +98,14 @@ class WorkerConfig:
|
||||
if us.scheme not in {"http", "https"} or not us.hostname:
|
||||
raise ValueError("userservice_url must be an absolute HTTP(S) URL")
|
||||
if self.worker_key is not None and not self.userservice_url:
|
||||
raise ValueError("worker_key requires userservice_url (SCIMESH_USERSERVICE_URL)")
|
||||
if isinstance(self.cpu_count, bool) or not isinstance(self.cpu_count, int) or self.cpu_count < 1:
|
||||
raise ValueError(
|
||||
"worker_key requires userservice_url (SCIMESH_USERSERVICE_URL)"
|
||||
)
|
||||
if (
|
||||
isinstance(self.cpu_count, bool)
|
||||
or not isinstance(self.cpu_count, int)
|
||||
or self.cpu_count < 1
|
||||
):
|
||||
raise ValueError("cpu_count must be positive")
|
||||
if self.worker_id is not None and not isinstance(self.worker_id, str):
|
||||
raise ValueError("worker_id must be a string when set")
|
||||
@@ -87,7 +119,9 @@ class WorkerConfig:
|
||||
_positive_number(self.request_timeout, "request_timeout")
|
||||
_positive_number(self.heartbeat_interval, "heartbeat_interval")
|
||||
if self.cleanup_after_seconds is not None:
|
||||
_positive_number(self.cleanup_after_seconds, "cleanup_after_seconds", allow_zero=True)
|
||||
_positive_number(
|
||||
self.cleanup_after_seconds, "cleanup_after_seconds", allow_zero=True
|
||||
)
|
||||
if self.max_tasks is not None:
|
||||
if (
|
||||
isinstance(self.max_tasks, bool)
|
||||
@@ -99,6 +133,18 @@ class WorkerConfig:
|
||||
raise ValueError("exit_when_idle must be a boolean")
|
||||
if not self.capabilities:
|
||||
raise ValueError("capabilities cannot be empty")
|
||||
if any(
|
||||
not isinstance(capability, str) or not capability.strip()
|
||||
for capability in self.capabilities
|
||||
):
|
||||
raise ValueError("capabilities must contain non-empty names")
|
||||
if len(self.capabilities) != len(set(self.capabilities)):
|
||||
raise ValueError("capabilities must be unique")
|
||||
if any(
|
||||
not isinstance(package, AllowedPackage)
|
||||
for package in self.workload_allowlist
|
||||
):
|
||||
raise ValueError("workload_allowlist must contain AllowedPackage values")
|
||||
# Runner subprocesses use a task directory as their cwd. Keep the
|
||||
# configured root absolute so input/output paths remain valid there
|
||||
# even when the CLI received a convenient relative --work-dir value.
|
||||
@@ -111,7 +157,9 @@ class WorkerConfig:
|
||||
"""Build config from environment, allowing typed CLI values to override it."""
|
||||
values = overrides or {}
|
||||
|
||||
def value(name: str, environment: str, default: object | None = None) -> object | None:
|
||||
def value(
|
||||
name: str, environment: str, default: object | None = None
|
||||
) -> object | None:
|
||||
override = values.get(name)
|
||||
return override if override is not None else os.getenv(environment, default)
|
||||
|
||||
@@ -122,20 +170,37 @@ class WorkerConfig:
|
||||
cpu_count = value("cpu_count", "SCIMESH_CPU_COUNT", os.cpu_count() or 1)
|
||||
memory_mb = value("memory_mb", "SCIMESH_MEMORY_MB")
|
||||
max_tasks = value("max_tasks", "SCIMESH_MAX_TASKS")
|
||||
capabilities = value("capabilities", "SCIMESH_CAPABILITIES")
|
||||
allowlist = value("workload_allowlist", "SCIMESH_WORKLOAD_ALLOWLIST")
|
||||
worker_id = value("worker_id", "SCIMESH_WORKER_ID")
|
||||
work_dir = value("work_dir", "SCIMESH_WORK_DIR", "./scimesh-worker-data")
|
||||
worker_name = value("worker_name", "SCIMESH_WORKER_NAME", socket.gethostname())
|
||||
poll_interval = value("poll_interval", "SCIMESH_POLL_INTERVAL", "2")
|
||||
request_timeout = value("request_timeout", "SCIMESH_REQUEST_TIMEOUT", "30")
|
||||
heartbeat_interval = value(
|
||||
"heartbeat_interval", "SCIMESH_HEARTBEAT_INTERVAL", "15"
|
||||
)
|
||||
bearer_token = value("bearer_token", "SCIMESH_BEARER_TOKEN")
|
||||
worker_key = value("worker_key", "SCIMESH_WORKER_KEY")
|
||||
userservice_url = _clean_url(
|
||||
value("userservice_url", "SCIMESH_USERSERVICE_URL")
|
||||
)
|
||||
return cls(
|
||||
coordinator_url=url.rstrip("/"),
|
||||
worker_id=value("worker_id", "SCIMESH_WORKER_ID"),
|
||||
work_dir=Path(value("work_dir", "SCIMESH_WORK_DIR", "./scimesh-worker-data")),
|
||||
worker_name=str(value("worker_name", "SCIMESH_WORKER_NAME", socket.gethostname())),
|
||||
worker_id=str(worker_id) if worker_id is not None else None,
|
||||
work_dir=Path(str(work_dir)),
|
||||
worker_name=str(worker_name),
|
||||
cpu_count=int(cpu_count),
|
||||
memory_mb=int(memory_mb) if memory_mb is not None else None,
|
||||
poll_interval=float(value("poll_interval", "SCIMESH_POLL_INTERVAL", "2")),
|
||||
request_timeout=float(value("request_timeout", "SCIMESH_REQUEST_TIMEOUT", "30")),
|
||||
heartbeat_interval=float(value("heartbeat_interval", "SCIMESH_HEARTBEAT_INTERVAL", "15")),
|
||||
bearer_token=value("bearer_token", "SCIMESH_BEARER_TOKEN"),
|
||||
worker_key=value("worker_key", "SCIMESH_WORKER_KEY"),
|
||||
userservice_url=_clean_url(value("userservice_url", "SCIMESH_USERSERVICE_URL")),
|
||||
poll_interval=float(poll_interval),
|
||||
request_timeout=float(request_timeout),
|
||||
heartbeat_interval=float(heartbeat_interval),
|
||||
bearer_token=str(bearer_token) if bearer_token is not None else None,
|
||||
worker_key=str(worker_key) if worker_key is not None else None,
|
||||
userservice_url=userservice_url,
|
||||
cleanup_after_seconds=float(cleanup) if cleanup else None,
|
||||
max_tasks=int(max_tasks) if max_tasks is not None else None,
|
||||
exit_when_idle=bool(values.get("exit_when_idle", False)),
|
||||
capabilities=_capabilities(capabilities),
|
||||
workload_allowlist=_workload_allowlist(allowlist),
|
||||
)
|
||||
|
||||
+91
-47
@@ -3,13 +3,20 @@
|
||||
The runner is a v1-wire bridge: the coordinator still claims flat tasks and
|
||||
the worker still uploads one partial CSV, but execution goes through the
|
||||
SDK-built workload's own Runner handler with a real ``TaskSpec``,
|
||||
provenance, resource reservation, and a content-addressed local store. No
|
||||
legacy distributed-protocol code is involved.
|
||||
provenance, resource reservation, and a content-addressed local store.
|
||||
|
||||
The runner is workload-generic: it loads definitions by name (from an
|
||||
explicit mapping, built-in defaults, or installed-package discovery through
|
||||
an administrator allowlist) and executes any workload whose map stage has a
|
||||
single ``input`` port and a single ``partial`` output. Anything else fails
|
||||
closed with a clear message, so adding a workload never requires touching
|
||||
worker code.
|
||||
"""
|
||||
|
||||
from __future__ import annotations
|
||||
|
||||
import hashlib
|
||||
import platform
|
||||
from datetime import datetime, timezone
|
||||
from pathlib import Path
|
||||
from typing import Mapping, Protocol
|
||||
@@ -28,28 +35,21 @@ from scimesh.sdk.conformance import (
|
||||
ScopedArtifactSink,
|
||||
)
|
||||
from scimesh.sdk._validation import canonical_json
|
||||
from scimesh.sdk.identity import SDK_API_VERSION
|
||||
from scimesh.sdk.manifest import TrustMode
|
||||
from scimesh.sdk.plans import TaskSpec
|
||||
from scimesh.sdk.registry import WorkloadDefinition
|
||||
from scimesh.sdk.resources import ResourceAllocation, ResourcePool
|
||||
from scimesh.sdk.registry import WorkloadDefinition, WorkloadRegistry
|
||||
from scimesh.sdk.resources import ResourceAllocation, ResourceInventory, ResourcePool
|
||||
from scimesh.sdk.runtime import (
|
||||
NegotiatedWorkload,
|
||||
RuntimeCapabilities,
|
||||
negotiate_manifest,
|
||||
)
|
||||
from scimesh.sdk.workflow import StageKind
|
||||
from scimesh.workloads.library import default_sdk_runtime
|
||||
from scimesh.workloads.search import similarity_search_sdk_definition
|
||||
|
||||
from .config import WorkerConfig
|
||||
from .models import ClaimedTask, ProducedArtifact, RunResult
|
||||
|
||||
#: Parameters the worker may hand to a map task. ``max_rows`` is a plan-time
|
||||
#: option applied before sharding and is intentionally rejected here.
|
||||
_RUNNER_PARAMETERS = frozenset(
|
||||
{"query_smiles", "top_k", "threshold", "threshold_direction", "progress_every"}
|
||||
)
|
||||
|
||||
|
||||
def _utc_now() -> str:
|
||||
return datetime.now(timezone.utc).isoformat().replace("+00:00", "Z")
|
||||
|
||||
@@ -58,22 +58,93 @@ class Runner(Protocol):
|
||||
def run(self, task: ClaimedTask, task_dir: Path) -> RunResult: ...
|
||||
|
||||
|
||||
def _inventory_for(
|
||||
definitions: Mapping[str, WorkloadDefinition],
|
||||
*,
|
||||
cpu_cores: int,
|
||||
memory_mb: int,
|
||||
) -> ResourceInventory:
|
||||
return ResourceInventory(
|
||||
cpu_cores=cpu_cores,
|
||||
memory_mb=memory_mb,
|
||||
scratch_mb=memory_mb,
|
||||
architecture=platform.machine().lower() or "unknown",
|
||||
environment_digests=tuple(
|
||||
dict.fromkeys(
|
||||
definition.manifest.environment.digest
|
||||
for definition in definitions.values()
|
||||
)
|
||||
),
|
||||
)
|
||||
|
||||
|
||||
def _runtime_for(
|
||||
definitions: Mapping[str, WorkloadDefinition], inventory: ResourceInventory
|
||||
) -> RuntimeCapabilities:
|
||||
return RuntimeCapabilities(
|
||||
sdk_api_version=SDK_API_VERSION,
|
||||
protocol_version="1.0.0",
|
||||
profiles=("core-batch-v1",),
|
||||
features={"artifact-collections": "1.0.0", "exact-verifier": "1.0.0"},
|
||||
workload_capabilities=tuple(sorted(definitions)),
|
||||
inventory=inventory,
|
||||
)
|
||||
|
||||
|
||||
class SciMeshRunner:
|
||||
"""Execute claimed coordinator tasks through the SDK-built workloads."""
|
||||
"""Execute claimed coordinator tasks through SDK-built workloads."""
|
||||
|
||||
def __init__(
|
||||
self,
|
||||
definitions: Mapping[str, WorkloadDefinition] | None = None,
|
||||
*,
|
||||
inventory: ResourceInventory | None = None,
|
||||
runtime: RuntimeCapabilities | None = None,
|
||||
) -> None:
|
||||
self._definitions = dict(definitions or {})
|
||||
if "similarity-search" not in self._definitions:
|
||||
from scimesh.workloads.search import similarity_search_sdk_definition
|
||||
|
||||
self._definitions["similarity-search"] = (
|
||||
similarity_search_sdk_definition().definition()
|
||||
)
|
||||
self._runtime = runtime or default_sdk_runtime()
|
||||
self._inventory = inventory or _inventory_for(
|
||||
self._definitions,
|
||||
cpu_cores=1,
|
||||
memory_mb=1024,
|
||||
)
|
||||
self._runtime = runtime or _runtime_for(self._definitions, self._inventory)
|
||||
self._pool = ResourcePool(self._runtime.inventory, max_concurrency=1)
|
||||
|
||||
@classmethod
|
||||
def for_worker(cls, config: WorkerConfig) -> "SciMeshRunner":
|
||||
"""Build a runner for one worker: discover allowlisted workloads or use built-ins."""
|
||||
definitions: dict[str, WorkloadDefinition] = {}
|
||||
if config.workload_allowlist:
|
||||
registry = WorkloadRegistry()
|
||||
registry.discover_installed(config.workload_allowlist)
|
||||
for description in registry.descriptions():
|
||||
definition, _ = registry.require(
|
||||
description.workload.name,
|
||||
description.workload.version,
|
||||
description.package_digest,
|
||||
)
|
||||
definitions[description.workload.name] = definition
|
||||
if not definitions:
|
||||
raise ValueError("workload_allowlist discovered no workloads")
|
||||
else:
|
||||
from scimesh.workloads.search import similarity_search_sdk_definition
|
||||
|
||||
definitions["similarity-search"] = (
|
||||
similarity_search_sdk_definition().definition()
|
||||
)
|
||||
inventory = _inventory_for(
|
||||
definitions,
|
||||
cpu_cores=config.cpu_count,
|
||||
memory_mb=config.memory_mb or 1024,
|
||||
)
|
||||
return cls(definitions=definitions, inventory=inventory)
|
||||
|
||||
def run(self, task: ClaimedTask, task_dir: Path) -> RunResult:
|
||||
task_dir = task_dir.resolve()
|
||||
workload = task.workload.replace("_", "-")
|
||||
@@ -85,11 +156,14 @@ class SciMeshRunner:
|
||||
map_stage = next(
|
||||
stage for stage in manifest.workflow.stages if stage.kind is StageKind.MAP
|
||||
)
|
||||
if set(map_stage.inputs) != {"input"} or len(map_stage.outputs) != 1:
|
||||
raise ValueError(
|
||||
f"workload {workload} is not executable through the v1 single-input contract"
|
||||
)
|
||||
assert map_stage.verifier is not None
|
||||
input_path = task_dir / "input"
|
||||
if not input_path.is_file():
|
||||
raise ValueError("claimed task input is missing")
|
||||
parameters = self._resolve_parameters(task, input_path)
|
||||
store = LocalArtifactStore(task_dir / "sdk-store")
|
||||
input_ref = store.import_file(
|
||||
input_path,
|
||||
@@ -110,7 +184,7 @@ class SciMeshRunner:
|
||||
optional_fallbacks=negotiated.optional_fallbacks,
|
||||
task_key="map/00000000",
|
||||
stage_id=map_stage.stage_id,
|
||||
parameters=parameters,
|
||||
parameters=task.parameters,
|
||||
inputs={"input": ArtifactCollection.single(input_ref)},
|
||||
expected_outputs=map_stage.outputs,
|
||||
resources=map_stage.resources,
|
||||
@@ -149,28 +223,6 @@ class SciMeshRunner:
|
||||
finally:
|
||||
self._pool.release(allocation.allocation_id)
|
||||
|
||||
@staticmethod
|
||||
def _resolve_parameters(task: ClaimedTask, input_path: Path) -> dict[str, object]:
|
||||
"""Resolve ``query_id`` once per task and reject plan-time options."""
|
||||
parameters = dict(task.parameters)
|
||||
query_id = parameters.get("query_id")
|
||||
query_smiles = parameters.get("query_smiles")
|
||||
if isinstance(query_id, str) and not isinstance(query_smiles, str):
|
||||
from scimesh.chemistry.dataset import find_molecule_by_id
|
||||
from rdkit import Chem
|
||||
|
||||
record = find_molecule_by_id(input_path, query_id)
|
||||
parameters["query_smiles"] = Chem.MolToSmiles(
|
||||
record.molecule, canonical=True
|
||||
)
|
||||
del parameters["query_id"]
|
||||
unknown = set(parameters) - _RUNNER_PARAMETERS
|
||||
if unknown:
|
||||
raise ValueError(
|
||||
"unsupported runner parameters: " + ", ".join(sorted(unknown))
|
||||
)
|
||||
return parameters
|
||||
|
||||
def _provenance(
|
||||
self,
|
||||
definition: WorkloadDefinition,
|
||||
@@ -241,14 +293,6 @@ class SciMeshRunner:
|
||||
spec.expected_outputs,
|
||||
max_output_bytes=max_output_bytes,
|
||||
)
|
||||
if output.provenance != provenance:
|
||||
raise ValueError(
|
||||
"SDK workload output provenance does not match its context"
|
||||
)
|
||||
output.validate_against(
|
||||
spec.expected_outputs,
|
||||
max_output_bytes=spec.resources.max_duration_seconds, # replaced below
|
||||
)
|
||||
sink = context.sink
|
||||
if not isinstance(sink, ScopedArtifactSink):
|
||||
raise ValueError("SDK execution requires a scoped artifact sink")
|
||||
|
||||
@@ -6,6 +6,7 @@ from scimesh.core.registry import WorkloadRegistry
|
||||
from scimesh.workloads.help import HelpWorkload
|
||||
from scimesh.workloads.similarity_graph import SimilarityGraphWorkload
|
||||
from scimesh.workloads.similarity_search import SimilaritySearchWorkload
|
||||
from scimesh.workloads.workload_cli import WorkloadCLI
|
||||
|
||||
|
||||
def register_workloads(registry: WorkloadRegistry) -> None:
|
||||
@@ -13,3 +14,4 @@ def register_workloads(registry: WorkloadRegistry) -> None:
|
||||
registry.register(HelpWorkload())
|
||||
registry.register(SimilaritySearchWorkload())
|
||||
registry.register(SimilarityGraphWorkload())
|
||||
registry.register(WorkloadCLI())
|
||||
|
||||
@@ -1,53 +1,23 @@
|
||||
"""SDK-built ``descriptor-batch`` workload definition and handlers.
|
||||
|
||||
This module is the first non-adapter reference workload built directly on the
|
||||
``core-batch-v1`` profile: an explicit immutable manifest, a static map/reduce
|
||||
workflow, a row-bounded planner, pinned descriptor computation, deterministic
|
||||
shard concatenation, and the exact-artifact verifier. It is the intended
|
||||
first ``untrusted_quorum`` candidate: ``byte_exact`` determinism with whole
|
||||
file SHA-256 agreement from distinct owners.
|
||||
A thin subclass of ``MapReduceWorkload``: the SDK assembles the manifest, the
|
||||
map/reduce stages, the workflow, and the digest-pinned handlers; this module
|
||||
only declares the scientific contract (pinned descriptors, canonical CSV,
|
||||
row-bounded shards, header-preserving concatenation) and the three hooks that
|
||||
partition, compute, and merge.
|
||||
"""
|
||||
|
||||
from __future__ import annotations
|
||||
|
||||
import hashlib
|
||||
import shutil
|
||||
from pathlib import Path
|
||||
from typing import Any, Mapping, Sequence
|
||||
|
||||
from ...sdk.artifacts import (
|
||||
ArtifactCollection,
|
||||
ArtifactItem,
|
||||
ArtifactRef,
|
||||
ArtifactSchema,
|
||||
Cardinality,
|
||||
CollectionKind,
|
||||
OutputManifest,
|
||||
PortSpec,
|
||||
)
|
||||
from scimesh.sdk.artifacts import ArtifactSchema, ComponentRef, PortSpec
|
||||
from scimesh.sdk.batch import MapReduceWorkload
|
||||
from scimesh.sdk.identity import SchemaRef, WorkloadId
|
||||
from scimesh.sdk.registry import WorkloadDefinition
|
||||
|
||||
from ..environment import current_environment_digest, current_scimesh_package_digest
|
||||
from ...sdk.execution import (
|
||||
CheckpointPolicy,
|
||||
ExecutionProfile,
|
||||
NetworkPolicy,
|
||||
RetryPolicy,
|
||||
)
|
||||
from ...sdk.identity import ComponentRef, SchemaRef, VersionRange, WorkloadId
|
||||
from ...sdk.manifest import (
|
||||
DeterminismProfile,
|
||||
EnvironmentSpec,
|
||||
PackageSpec,
|
||||
TrustMode,
|
||||
VerifierSpec,
|
||||
WorkloadLimits,
|
||||
WorkloadManifest,
|
||||
)
|
||||
from ...sdk.plans import JobRequest, TaskSpec, ValidatedJob, WorkflowPlan
|
||||
from ...sdk.protocols import PlanningContext, ReduceContext, TaskContext
|
||||
from ...sdk.registry import WorkloadDefinition
|
||||
from ...sdk.resources import ResourceRequirements
|
||||
from ...sdk.verification import ExactArtifactVerifier
|
||||
from ...sdk.workflow import ArtifactEdge, PortRef, StageKind, StageSpec, WorkflowSpec
|
||||
from .core import (
|
||||
DESCRIPTOR_COLUMNS,
|
||||
compute_descriptor_batch,
|
||||
@@ -59,16 +29,6 @@ from .core import (
|
||||
MAP_ENTRY_POINT = "scimesh.workloads.descriptors.definition:map_descriptors@v1"
|
||||
REDUCE_ENTRY_POINT = "scimesh.workloads.descriptors.definition:reduce_descriptors@v1"
|
||||
|
||||
_DESCRIPTOR_PARAMETERS = ("skip_invalid",)
|
||||
|
||||
|
||||
def _sha256_file(path: Path) -> str:
|
||||
digest = hashlib.sha256()
|
||||
with path.open("rb") as source:
|
||||
for block in iter(lambda: source.read(1024 * 1024), b""):
|
||||
digest.update(block)
|
||||
return digest.hexdigest()
|
||||
|
||||
|
||||
def _parameters_schema() -> dict[str, Any]:
|
||||
return {
|
||||
@@ -114,14 +74,22 @@ def _descriptor_schema() -> ArtifactSchema:
|
||||
)
|
||||
|
||||
|
||||
class DescriptorBatchWorkload:
|
||||
"""Manifest-backed planner, runner, and reducer for descriptor-batch.
|
||||
class DescriptorBatchWorkload(MapReduceWorkload):
|
||||
"""Pinned RDKit 2D descriptor computation, one canonical row per input."""
|
||||
|
||||
The class follows the legacy adapter's structural pattern (one object
|
||||
registered under each stage entry point) while remaining fully SDK-built:
|
||||
sharding is explicit and deterministic, every artifact is sealed through
|
||||
the bridge-owned sink, and no filesystem path ever enters a plan or task.
|
||||
"""
|
||||
workload_id = WorkloadId("descriptor-batch", "1.0.0")
|
||||
description = (
|
||||
"Compute a pinned set of RDKit 2D descriptors, one canonical "
|
||||
"CSV row per input molecule, in deterministic input order."
|
||||
)
|
||||
parameters_schema = _parameters_schema()
|
||||
input_port = PortSpec(_input_schema())
|
||||
partial_port = PortSpec(_descriptor_schema())
|
||||
output_port = PortSpec(_descriptor_schema())
|
||||
map_parameter_names = ("skip_invalid",)
|
||||
reduce_parameter_names = ("skip_invalid",)
|
||||
map_entry_point = MAP_ENTRY_POINT
|
||||
reduce_entry_point = REDUCE_ENTRY_POINT
|
||||
|
||||
def __init__(
|
||||
self,
|
||||
@@ -137,291 +105,51 @@ class DescriptorBatchWorkload:
|
||||
):
|
||||
raise ValueError("shard_rows must be a positive integer")
|
||||
validate_descriptor_names()
|
||||
self.entry_point = MAP_ENTRY_POINT
|
||||
self.shard_rows = shard_rows
|
||||
self.input_port = PortSpec(_input_schema())
|
||||
self.partial_port = PortSpec(_descriptor_schema())
|
||||
self.output_port = PortSpec(_descriptor_schema())
|
||||
resources = ResourceRequirements(
|
||||
profile="descriptor-cpu-v1",
|
||||
cpu_cores=1,
|
||||
memory_mb=1024,
|
||||
scratch_mb=1024,
|
||||
max_duration_seconds=3600,
|
||||
super().__init__(
|
||||
package_digest=package_digest,
|
||||
environment_digest=environment_digest,
|
||||
)
|
||||
execution = ExecutionProfile(
|
||||
profile="descriptor-python-process-v1",
|
||||
network=NetworkPolicy.TRUSTED,
|
||||
timeout_seconds=3600,
|
||||
checkpoint=CheckpointPolicy(),
|
||||
)
|
||||
limits = WorkloadLimits(
|
||||
max_input_bytes=self.input_port.schema.max_bytes,
|
||||
max_tasks=10_000,
|
||||
max_output_bytes=self.output_port.schema.max_bytes,
|
||||
)
|
||||
trust_modes = ("trusted", "untrusted_quorum")
|
||||
map_stage = StageSpec(
|
||||
stage_id="map",
|
||||
kind=StageKind.MAP,
|
||||
entry_point=MAP_ENTRY_POINT,
|
||||
needs=(),
|
||||
inputs={"input": self.input_port},
|
||||
outputs={"partial": self.partial_port},
|
||||
parameter_names=_DESCRIPTOR_PARAMETERS,
|
||||
resources=resources,
|
||||
execution=execution,
|
||||
retry=RetryPolicy(),
|
||||
verifier=ComponentRef("exact-artifact", 1),
|
||||
trust_modes=trust_modes,
|
||||
max_fan_out=limits.max_tasks,
|
||||
cacheable=True,
|
||||
)
|
||||
reduce_input = PortSpec(
|
||||
schema=self.partial_port.schema,
|
||||
cardinality=Cardinality.MANY,
|
||||
collection=CollectionKind.KEYED,
|
||||
)
|
||||
reduce_stage = StageSpec(
|
||||
stage_id="reduce",
|
||||
kind=StageKind.REDUCE,
|
||||
entry_point=REDUCE_ENTRY_POINT,
|
||||
needs=("map",),
|
||||
inputs={"partials": reduce_input},
|
||||
outputs={"result": self.output_port},
|
||||
parameter_names=_DESCRIPTOR_PARAMETERS,
|
||||
resources=resources,
|
||||
execution=execution,
|
||||
retry=RetryPolicy(),
|
||||
verifier=ComponentRef("exact-artifact", 1),
|
||||
trust_modes=trust_modes,
|
||||
max_fan_out=1,
|
||||
cacheable=True,
|
||||
)
|
||||
workflow = WorkflowSpec(
|
||||
workflow_id="descriptor-map-reduce-v1",
|
||||
inputs={"input": self.input_port},
|
||||
stages=(map_stage, reduce_stage),
|
||||
edges=(
|
||||
ArtifactEdge(PortRef("input"), PortRef("input", "map")),
|
||||
ArtifactEdge(PortRef("partial", "map"), PortRef("partials", "reduce")),
|
||||
),
|
||||
outputs={"result": PortRef("result", "reduce")},
|
||||
max_tasks=limits.max_tasks,
|
||||
max_output_bytes=limits.max_output_bytes,
|
||||
)
|
||||
self.manifest = WorkloadManifest(
|
||||
sdk_api=VersionRange(">=1.0,<2.0"),
|
||||
protocol=VersionRange(">=1,<2"),
|
||||
workload=WorkloadId("descriptor-batch", "1.0.0"),
|
||||
description=(
|
||||
"Compute a pinned set of RDKit 2D descriptors, one canonical "
|
||||
"CSV row per input molecule, in deterministic input order."
|
||||
),
|
||||
package=PackageSpec("scimesh", package_digest),
|
||||
environment=EnvironmentSpec(
|
||||
"python-process",
|
||||
environment_digest,
|
||||
{"adapter": "sdk-native"},
|
||||
),
|
||||
parameters_schema=_parameters_schema(),
|
||||
workflow=workflow,
|
||||
inputs={"input": self.input_port},
|
||||
outputs={"result": self.output_port},
|
||||
determinism=DeterminismProfile.BYTE_EXACT,
|
||||
trust_modes=(TrustMode.TRUSTED, TrustMode.UNTRUSTED_QUORUM),
|
||||
verifier=VerifierSpec(ComponentRef("exact-artifact", 1), {}),
|
||||
limits=limits,
|
||||
capabilities=("descriptor-batch",),
|
||||
conformance_profiles=("core-batch-v1",),
|
||||
)
|
||||
self._exact_verifier = ExactArtifactVerifier()
|
||||
|
||||
def definition(self) -> WorkloadDefinition:
|
||||
return WorkloadDefinition(
|
||||
manifest=self.manifest,
|
||||
planner=self,
|
||||
runners={MAP_ENTRY_POINT: self},
|
||||
reducers={REDUCE_ENTRY_POINT: self},
|
||||
verifiers={self._exact_verifier.identity.canonical: self._exact_verifier},
|
||||
def domain_validate(self, parameters: Mapping[str, Any]) -> None:
|
||||
value = parameters.get("skip_invalid", True)
|
||||
if not isinstance(value, bool):
|
||||
raise ValueError("skip_invalid must be a boolean")
|
||||
|
||||
def partition_input(
|
||||
self,
|
||||
input_path: Path,
|
||||
parameters: Mapping[str, Any],
|
||||
workspace: Path,
|
||||
) -> list[Path]:
|
||||
return write_descriptor_shards(input_path, workspace, self.shard_rows)
|
||||
|
||||
def compute_shard(
|
||||
self,
|
||||
inputs: Mapping[str, Path],
|
||||
parameters: Mapping[str, Any],
|
||||
output_path: Path,
|
||||
) -> Mapping[str, int | float]:
|
||||
return compute_descriptor_batch(
|
||||
inputs["input"],
|
||||
output_path,
|
||||
skip_invalid=self.domain_validate_check(parameters),
|
||||
)
|
||||
|
||||
@staticmethod
|
||||
def _skip_invalid(parameters: Mapping[str, Any]) -> bool:
|
||||
def domain_validate_check(parameters: Mapping[str, Any]) -> bool:
|
||||
value = parameters.get("skip_invalid", True)
|
||||
if not isinstance(value, bool):
|
||||
raise ValueError("skip_invalid must be a boolean")
|
||||
return value
|
||||
|
||||
def validate(self, request: JobRequest) -> ValidatedJob:
|
||||
if request.workload != self.manifest.workload:
|
||||
raise ValueError("descriptor-batch received a request for another workload")
|
||||
self._skip_invalid(request.parameters)
|
||||
return ValidatedJob(request, request.parameters)
|
||||
|
||||
def plan(self, job: ValidatedJob, context: PlanningContext) -> WorkflowPlan:
|
||||
if not isinstance(job, ValidatedJob):
|
||||
raise ValueError("job must be a ValidatedJob")
|
||||
collection = job.request.inputs.get("input")
|
||||
if collection is None:
|
||||
raise ValueError("descriptor-batch requires the input port")
|
||||
self.input_port.validate_collection(collection, "job input")
|
||||
input_artifact = collection.items[0].artifact
|
||||
input_path = context.catalog.materialize(input_artifact)
|
||||
workspace = context.workspace
|
||||
workspace.mkdir(parents=True, exist_ok=True)
|
||||
shard_paths = write_descriptor_shards(
|
||||
input_path,
|
||||
workspace,
|
||||
self.shard_rows,
|
||||
)
|
||||
negotiated = context.negotiated
|
||||
map_stage = self.manifest.workflow.stages[0]
|
||||
assert map_stage.verifier is not None
|
||||
tasks: list[TaskSpec] = []
|
||||
for index, path in enumerate(shard_paths):
|
||||
sealed = context.sink.seal(
|
||||
path,
|
||||
declaration=self.input_port.schema,
|
||||
)
|
||||
tasks.append(
|
||||
TaskSpec(
|
||||
workload=self.manifest.workload,
|
||||
package_digest=self.manifest.package.digest,
|
||||
manifest_digest=self.manifest.digest,
|
||||
trust_mode=job.request.trust_mode,
|
||||
sdk_api_version=negotiated.sdk_api_version,
|
||||
protocol_version=negotiated.protocol_version,
|
||||
manifest_schema_version=self.manifest.manifest_schema_version,
|
||||
workflow_schema_version=self.manifest.workflow.schema_version,
|
||||
environment_digest=self.manifest.environment.digest,
|
||||
verifier=map_stage.verifier,
|
||||
selected_features=negotiated.selected_features,
|
||||
optional_fallbacks=negotiated.optional_fallbacks,
|
||||
task_key=f"map/{index:08d}",
|
||||
stage_id="map",
|
||||
parameters=job.resolved_parameters,
|
||||
inputs={"input": ArtifactCollection.single(sealed)},
|
||||
expected_outputs={"partial": self.partial_port},
|
||||
resources=map_stage.resources,
|
||||
execution=map_stage.execution,
|
||||
)
|
||||
)
|
||||
return WorkflowPlan(
|
||||
workload=self.manifest.workload,
|
||||
package_digest=self.manifest.package.digest,
|
||||
manifest_digest=self.manifest.digest,
|
||||
trust_mode=job.request.trust_mode,
|
||||
sdk_api_version=negotiated.sdk_api_version,
|
||||
protocol_version=negotiated.protocol_version,
|
||||
manifest_schema_version=self.manifest.manifest_schema_version,
|
||||
workflow_schema_version=self.manifest.workflow.schema_version,
|
||||
environment_digest=self.manifest.environment.digest,
|
||||
verifier=self.manifest.verifier.verifier,
|
||||
selected_features=negotiated.selected_features,
|
||||
optional_fallbacks=negotiated.optional_fallbacks,
|
||||
workflow_id=self.manifest.workflow.workflow_id,
|
||||
resolved_parameters=job.resolved_parameters,
|
||||
tasks=tuple(tasks),
|
||||
)
|
||||
|
||||
def run(self, context: TaskContext) -> OutputManifest:
|
||||
context.cancellation.raise_if_cancelled()
|
||||
collection = context.task.inputs.get("input")
|
||||
if collection is None:
|
||||
raise ValueError("descriptor map task requires one input collection")
|
||||
self.input_port.validate_collection(collection, "descriptor map input")
|
||||
source = context.catalog.materialize(collection.items[0].artifact)
|
||||
workspace = context.workspace
|
||||
workspace.mkdir(parents=True, exist_ok=True)
|
||||
input_path = workspace / "input"
|
||||
output_path = workspace / "result.csv"
|
||||
if source.resolve() != input_path.resolve():
|
||||
shutil.copyfile(source, input_path)
|
||||
metrics = compute_descriptor_batch(
|
||||
input_path,
|
||||
output_path,
|
||||
skip_invalid=self._skip_invalid(context.task.parameters),
|
||||
)
|
||||
context.cancellation.raise_if_cancelled()
|
||||
sealed = context.sink.seal(
|
||||
output_path,
|
||||
declaration=self.partial_port.schema,
|
||||
)
|
||||
return OutputManifest(
|
||||
context.task.task_key,
|
||||
{"partial": ArtifactCollection.single(sealed)},
|
||||
metrics,
|
||||
context.provenance,
|
||||
).validate_against(
|
||||
context.task.expected_outputs,
|
||||
max_output_bytes=self.manifest.limits.max_output_bytes,
|
||||
)
|
||||
|
||||
def reduce(self, context: ReduceContext) -> OutputManifest:
|
||||
context.cancellation.raise_if_cancelled()
|
||||
collection = context.accepted_inputs.get("partials")
|
||||
if (
|
||||
collection is None
|
||||
or collection.kind is not CollectionKind.KEYED
|
||||
or not collection.items
|
||||
):
|
||||
raise ValueError(
|
||||
"descriptor reducer requires a non-empty keyed partial collection"
|
||||
)
|
||||
self.manifest.workflow.stages[1].inputs["partials"].validate_collection(
|
||||
collection,
|
||||
"descriptor reducer partials",
|
||||
)
|
||||
workspace = context.workspace
|
||||
workspace.mkdir(parents=True, exist_ok=True)
|
||||
indexed_items: list[tuple[int, ArtifactItem]] = []
|
||||
for item in collection.items:
|
||||
key = item.key or ""
|
||||
prefix = "map."
|
||||
raw_index = key[len(prefix) :] if key.startswith(prefix) else ""
|
||||
if len(raw_index) != 8 or not raw_index.isdigit():
|
||||
raise ValueError(
|
||||
"descriptor partial key must use map.<eight-digit-index>"
|
||||
)
|
||||
indexed_items.append((int(raw_index), item))
|
||||
expected_keys = context.task.expected_input_keys.get("partials")
|
||||
if expected_keys is None or {item.key for item in collection.items} != set(
|
||||
expected_keys
|
||||
):
|
||||
raise ValueError(
|
||||
"descriptor partial keys do not match the coordinator expected set"
|
||||
)
|
||||
if sorted(index for index, _ in indexed_items) != list(
|
||||
range(len(indexed_items))
|
||||
):
|
||||
raise ValueError("descriptor partial keys must be complete and contiguous")
|
||||
partial_paths: list[Path] = []
|
||||
for index, item in sorted(indexed_items):
|
||||
artifact: ArtifactRef = item.artifact
|
||||
source = context.catalog.materialize(artifact)
|
||||
target = workspace / artifact.artifact_id
|
||||
if source.resolve() != target.resolve():
|
||||
shutil.copyfile(source, target)
|
||||
if _sha256_file(target) != artifact.sha256:
|
||||
raise ValueError("materialized partial checksum does not match")
|
||||
partial_paths.append(target)
|
||||
result_path = workspace / "result.csv"
|
||||
metrics = concatenate_descriptor_shards(partial_paths, result_path)
|
||||
context.cancellation.raise_if_cancelled()
|
||||
sealed = context.sink.seal(
|
||||
result_path,
|
||||
declaration=self.output_port.schema,
|
||||
)
|
||||
return OutputManifest(
|
||||
context.task.task_key,
|
||||
{"result": ArtifactCollection.single(sealed)},
|
||||
metrics,
|
||||
context.provenance,
|
||||
).validate_against(
|
||||
context.task.expected_outputs,
|
||||
max_output_bytes=self.manifest.limits.max_output_bytes,
|
||||
)
|
||||
def reduce_partials(
|
||||
self,
|
||||
partial_paths: Sequence[Path],
|
||||
parameters: Mapping[str, Any],
|
||||
output_path: Path,
|
||||
) -> Mapping[str, int | float]:
|
||||
return concatenate_descriptor_shards(partial_paths, output_path)
|
||||
|
||||
|
||||
def descriptor_batch_sdk_definition(
|
||||
@@ -430,7 +158,7 @@ def descriptor_batch_sdk_definition(
|
||||
package_digest: str | None = None,
|
||||
environment_digest: str | None = None,
|
||||
) -> DescriptorBatchWorkload:
|
||||
"""Build the default local descriptor-batch definition for tests."""
|
||||
"""Build the default descriptor-batch definition for tests."""
|
||||
return DescriptorBatchWorkload(
|
||||
shard_rows=shard_rows,
|
||||
package_digest=package_digest or current_scimesh_package_digest(),
|
||||
@@ -439,5 +167,5 @@ def descriptor_batch_sdk_definition(
|
||||
|
||||
|
||||
def workload_definition() -> WorkloadDefinition:
|
||||
"""Installed entry-point factory for the default descriptor-batch definition."""
|
||||
"""Installed entry-point factory for the descriptor-batch workload."""
|
||||
return descriptor_batch_sdk_definition().definition()
|
||||
|
||||
@@ -1,52 +1,30 @@
|
||||
"""SDK-built ``similarity-graph`` workload definition and handlers.
|
||||
|
||||
Built directly on the ``core-batch-v1`` profile: molecules are parsed once
|
||||
into deterministic row-ordered blocks, every block pair ``(i, j)`` with
|
||||
``i <= j`` becomes one map task, and the reducer enforces the CTX-10
|
||||
pair-coverage invariant (every unordered molecule pair compared exactly once)
|
||||
before emitting a deterministically sorted edge list that is byte-identical
|
||||
to the local brute-force reference.
|
||||
A ``MapReduceWorkload`` subclass with two non-default hooks: ``plan_tasks``
|
||||
builds one task per block pair ``(i, j)`` with ``i <= j`` (each task receives
|
||||
two block inputs), and the partial-key hooks parse ``map.<i>x<j>`` keys and
|
||||
enforce the CTX-10 pair-coverage invariant. The final edge list is
|
||||
byte-identical to the local brute-force reference.
|
||||
"""
|
||||
|
||||
from __future__ import annotations
|
||||
|
||||
import hashlib
|
||||
import shutil
|
||||
from pathlib import Path
|
||||
from typing import Any, Mapping
|
||||
from typing import Any, Mapping, Sequence
|
||||
|
||||
from ...sdk.artifacts import (
|
||||
from scimesh.sdk.artifacts import (
|
||||
ArtifactCollection,
|
||||
ArtifactItem,
|
||||
ArtifactRef,
|
||||
ArtifactSchema,
|
||||
Cardinality,
|
||||
CollectionKind,
|
||||
OutputManifest,
|
||||
ComponentRef,
|
||||
PortSpec,
|
||||
)
|
||||
from ...sdk.execution import (
|
||||
CheckpointPolicy,
|
||||
ExecutionProfile,
|
||||
NetworkPolicy,
|
||||
RetryPolicy,
|
||||
)
|
||||
from ...sdk.identity import ComponentRef, SchemaRef, VersionRange, WorkloadId
|
||||
from ...sdk.manifest import (
|
||||
DeterminismProfile,
|
||||
EnvironmentSpec,
|
||||
PackageSpec,
|
||||
TrustMode,
|
||||
VerifierSpec,
|
||||
WorkloadLimits,
|
||||
WorkloadManifest,
|
||||
)
|
||||
from ...sdk.plans import JobRequest, TaskSpec, ValidatedJob, WorkflowPlan
|
||||
from ...sdk.protocols import PlanningContext, ReduceContext, TaskContext
|
||||
from ...sdk.registry import WorkloadDefinition
|
||||
from ...sdk.resources import ResourceRequirements
|
||||
from ...sdk.verification import ExactArtifactVerifier
|
||||
from ...sdk.workflow import ArtifactEdge, PortRef, StageKind, StageSpec, WorkflowSpec
|
||||
from scimesh.sdk.batch import MapReduceWorkload
|
||||
from scimesh.sdk.identity import SchemaRef, WorkloadId
|
||||
from scimesh.sdk.plans import TaskSpec, ValidatedJob
|
||||
from scimesh.sdk.protocols import PlanningContext
|
||||
from scimesh.sdk.registry import WorkloadDefinition
|
||||
from scimesh.sdk.workflow import StageSpec
|
||||
|
||||
from ..environment import current_environment_digest, current_scimesh_package_digest
|
||||
from .core import (
|
||||
block_pair_from_key,
|
||||
@@ -63,15 +41,6 @@ MAP_ENTRY_POINT = "scimesh.workloads.graph.definition:map_graph@v1"
|
||||
REDUCE_ENTRY_POINT = "scimesh.workloads.graph.definition:reduce_graph@v1"
|
||||
|
||||
_MAP_PARAMETERS = ("left_block", "right_block", "threshold", "threshold_direction")
|
||||
_REDUCE_PARAMETERS = ("threshold", "threshold_direction", "block_size", "max_rows")
|
||||
|
||||
|
||||
def _sha256_file(path: Path) -> str:
|
||||
digest = hashlib.sha256()
|
||||
with path.open("rb") as source:
|
||||
for block in iter(lambda: source.read(1024 * 1024), b""):
|
||||
digest.update(block)
|
||||
return digest.hexdigest()
|
||||
|
||||
|
||||
def _parameters_schema() -> dict[str, Any]:
|
||||
@@ -118,141 +87,32 @@ def _edge_schema() -> ArtifactSchema:
|
||||
)
|
||||
|
||||
|
||||
class SimilarityGraphSDKWorkload:
|
||||
"""Manifest-backed planner, runner, and reducer for similarity-graph."""
|
||||
class SimilarityGraphSDKWorkload(MapReduceWorkload):
|
||||
"""Exact sparse Tanimoto graph over deterministic block pairs."""
|
||||
|
||||
def __init__(
|
||||
self,
|
||||
*,
|
||||
package_digest: str,
|
||||
environment_digest: str,
|
||||
) -> None:
|
||||
self.entry_point = MAP_ENTRY_POINT
|
||||
self.input_port = PortSpec(_molecule_schema())
|
||||
self.block_port = PortSpec(_molecule_schema())
|
||||
self.partial_port = PortSpec(_edge_schema())
|
||||
self.output_port = PortSpec(_edge_schema())
|
||||
resources = ResourceRequirements(
|
||||
profile="graph-cpu-v1",
|
||||
cpu_cores=1,
|
||||
memory_mb=1024,
|
||||
scratch_mb=1024,
|
||||
max_duration_seconds=3600,
|
||||
)
|
||||
execution = ExecutionProfile(
|
||||
profile="graph-python-process-v1",
|
||||
network=NetworkPolicy.TRUSTED,
|
||||
timeout_seconds=3600,
|
||||
checkpoint=CheckpointPolicy(),
|
||||
)
|
||||
limits = WorkloadLimits(
|
||||
max_input_bytes=self.input_port.schema.max_bytes,
|
||||
max_tasks=10_000,
|
||||
max_output_bytes=self.output_port.schema.max_bytes,
|
||||
)
|
||||
trust_modes = ("trusted", "untrusted_quorum")
|
||||
map_stage = StageSpec(
|
||||
stage_id="map",
|
||||
kind=StageKind.MAP,
|
||||
entry_point=MAP_ENTRY_POINT,
|
||||
needs=(),
|
||||
inputs={"left": self.block_port, "right": self.block_port},
|
||||
outputs={"partial": self.partial_port},
|
||||
parameter_names=_MAP_PARAMETERS,
|
||||
resources=resources,
|
||||
execution=execution,
|
||||
retry=RetryPolicy(),
|
||||
verifier=ComponentRef("exact-artifact", 1),
|
||||
trust_modes=trust_modes,
|
||||
max_fan_out=limits.max_tasks,
|
||||
cacheable=True,
|
||||
)
|
||||
reduce_input = PortSpec(
|
||||
schema=self.partial_port.schema,
|
||||
cardinality=Cardinality.MANY,
|
||||
collection=CollectionKind.KEYED,
|
||||
)
|
||||
reduce_stage = StageSpec(
|
||||
stage_id="reduce",
|
||||
kind=StageKind.REDUCE,
|
||||
entry_point=REDUCE_ENTRY_POINT,
|
||||
needs=("map",),
|
||||
inputs={"partials": reduce_input},
|
||||
outputs={"result": self.output_port},
|
||||
parameter_names=_REDUCE_PARAMETERS,
|
||||
resources=resources,
|
||||
execution=execution,
|
||||
retry=RetryPolicy(),
|
||||
verifier=ComponentRef("exact-artifact", 1),
|
||||
trust_modes=trust_modes,
|
||||
max_fan_out=1,
|
||||
cacheable=True,
|
||||
)
|
||||
workflow = WorkflowSpec(
|
||||
workflow_id="graph-block-pairs-v1",
|
||||
inputs={"input": self.input_port},
|
||||
stages=(map_stage, reduce_stage),
|
||||
edges=(
|
||||
ArtifactEdge(PortRef("input"), PortRef("left", "map")),
|
||||
ArtifactEdge(PortRef("input"), PortRef("right", "map")),
|
||||
ArtifactEdge(PortRef("partial", "map"), PortRef("partials", "reduce")),
|
||||
),
|
||||
outputs={"result": PortRef("result", "reduce")},
|
||||
max_tasks=limits.max_tasks,
|
||||
max_output_bytes=limits.max_output_bytes,
|
||||
)
|
||||
self.manifest = WorkloadManifest(
|
||||
sdk_api=VersionRange(">=1.0,<2.0"),
|
||||
protocol=VersionRange(">=1,<2"),
|
||||
workload=WorkloadId("similarity-graph", "1.0.0"),
|
||||
description=(
|
||||
"Exact sparse Tanimoto similarity graph over deterministic "
|
||||
"block pairs with a duplicate-safe, coverage-checked merge."
|
||||
),
|
||||
package=PackageSpec("scimesh", package_digest),
|
||||
environment=EnvironmentSpec(
|
||||
"python-process",
|
||||
environment_digest,
|
||||
{"adapter": "sdk-native"},
|
||||
),
|
||||
parameters_schema=_parameters_schema(),
|
||||
workflow=workflow,
|
||||
inputs={"input": self.input_port},
|
||||
outputs={"result": self.output_port},
|
||||
determinism=DeterminismProfile.BYTE_EXACT,
|
||||
trust_modes=(TrustMode.TRUSTED, TrustMode.UNTRUSTED_QUORUM),
|
||||
verifier=VerifierSpec(ComponentRef("exact-artifact", 1), {}),
|
||||
limits=limits,
|
||||
capabilities=("similarity-graph",),
|
||||
conformance_profiles=("core-batch-v1",),
|
||||
)
|
||||
self._exact_verifier = ExactArtifactVerifier()
|
||||
workload_id = WorkloadId("similarity-graph", "1.0.0")
|
||||
description = (
|
||||
"Exact sparse Tanimoto similarity graph over deterministic "
|
||||
"block pairs with a duplicate-safe, coverage-checked merge."
|
||||
)
|
||||
parameters_schema = _parameters_schema()
|
||||
input_port = PortSpec(_molecule_schema())
|
||||
block_port = PortSpec(_molecule_schema())
|
||||
partial_port = PortSpec(_edge_schema())
|
||||
output_port = PortSpec(_edge_schema())
|
||||
map_stage_inputs = {"left": block_port, "right": block_port}
|
||||
map_parameter_names = _MAP_PARAMETERS
|
||||
reduce_parameter_names = (
|
||||
"threshold",
|
||||
"threshold_direction",
|
||||
"block_size",
|
||||
"max_rows",
|
||||
)
|
||||
workflow_id = "graph-block-pairs-v1"
|
||||
map_entry_point = MAP_ENTRY_POINT
|
||||
reduce_entry_point = REDUCE_ENTRY_POINT
|
||||
|
||||
def definition(self) -> WorkloadDefinition:
|
||||
return WorkloadDefinition(
|
||||
manifest=self.manifest,
|
||||
planner=self,
|
||||
runners={MAP_ENTRY_POINT: self},
|
||||
reducers={REDUCE_ENTRY_POINT: self},
|
||||
verifiers={self._exact_verifier.identity.canonical: self._exact_verifier},
|
||||
)
|
||||
|
||||
@staticmethod
|
||||
def _unit_interval(value: object, name: str) -> float:
|
||||
if isinstance(value, bool) or not isinstance(value, (int, float)):
|
||||
raise ValueError(f"{name} must be a number between 0 and 1")
|
||||
return float(value)
|
||||
|
||||
@staticmethod
|
||||
def _positive_int(value: object, name: str) -> int:
|
||||
if isinstance(value, bool) or not isinstance(value, int) or value < 1:
|
||||
raise ValueError(f"{name} must be a positive integer")
|
||||
return value
|
||||
|
||||
def validate(self, request: JobRequest) -> ValidatedJob:
|
||||
if request.workload != self.manifest.workload:
|
||||
raise ValueError("similarity-graph received a request for another workload")
|
||||
parameters = request.parameters
|
||||
def domain_validate(self, parameters: Mapping[str, Any]) -> None:
|
||||
unknown = set(parameters) - {
|
||||
"threshold",
|
||||
"threshold_direction",
|
||||
@@ -275,102 +135,87 @@ class SimilarityGraphSDKWorkload:
|
||||
self._positive_int(parameters["block_size"], "block_size")
|
||||
if "max_rows" in parameters:
|
||||
self._positive_int(parameters["max_rows"], "max_rows")
|
||||
return ValidatedJob(request, request.parameters)
|
||||
|
||||
def plan(self, job: ValidatedJob, context: PlanningContext) -> WorkflowPlan:
|
||||
if not isinstance(job, ValidatedJob):
|
||||
raise ValueError("job must be a ValidatedJob")
|
||||
collection = job.request.inputs.get("input")
|
||||
if collection is None:
|
||||
raise ValueError("similarity-graph requires the input port")
|
||||
self.input_port.validate_collection(collection, "job input")
|
||||
input_artifact = collection.items[0].artifact
|
||||
input_path = context.catalog.materialize(input_artifact)
|
||||
workspace = context.workspace
|
||||
workspace.mkdir(parents=True, exist_ok=True)
|
||||
parameters = job.resolved_parameters
|
||||
threshold = self._unit_interval(parameters.get("threshold"), "threshold")
|
||||
direction = parameters.get("threshold_direction", "greater")
|
||||
if direction not in {"greater", "less"}:
|
||||
raise ValueError("threshold_direction must be 'greater' or 'less'")
|
||||
@staticmethod
|
||||
def _unit_interval(value: object, name: str) -> float:
|
||||
if isinstance(value, bool) or not isinstance(value, (int, float)):
|
||||
raise ValueError(f"{name} must be a number between 0 and 1")
|
||||
return float(value)
|
||||
|
||||
@staticmethod
|
||||
def _positive_int(value: object, name: str) -> int:
|
||||
if isinstance(value, bool) or not isinstance(value, int) or value < 1:
|
||||
raise ValueError(f"{name} must be a positive integer")
|
||||
return value
|
||||
|
||||
def partition_input(
|
||||
self,
|
||||
input_path: Path,
|
||||
parameters: Mapping[str, Any],
|
||||
workspace: Path,
|
||||
) -> list[Path]:
|
||||
block_size = int(parameters.get("block_size", 1_000))
|
||||
max_rows = parameters.get("max_rows")
|
||||
blocks, stats = parse_molecule_blocks(
|
||||
blocks, _stats = parse_molecule_blocks(
|
||||
input_path,
|
||||
block_size,
|
||||
int(max_rows) if isinstance(max_rows, int) else None,
|
||||
)
|
||||
task_parameters = {
|
||||
"threshold": threshold,
|
||||
"threshold_direction": direction,
|
||||
}
|
||||
negotiated = context.negotiated
|
||||
map_stage = self.manifest.workflow.stages[0]
|
||||
assert map_stage.verifier is not None
|
||||
block_refs: list[ArtifactRef] = []
|
||||
paths: list[Path] = []
|
||||
for index, block in enumerate(blocks):
|
||||
path = workspace / f"block-{index:04d}.tsv"
|
||||
write_block_tsv(block, path)
|
||||
block_refs.append(
|
||||
context.sink.seal(
|
||||
path,
|
||||
declaration=self.block_port.schema,
|
||||
)
|
||||
paths.append(path)
|
||||
return paths
|
||||
|
||||
def plan_tasks(
|
||||
self,
|
||||
shard_paths: Sequence[Path],
|
||||
resolved: Mapping[str, Any],
|
||||
job: ValidatedJob,
|
||||
negotiated: Any,
|
||||
map_stage: StageSpec,
|
||||
context: PlanningContext,
|
||||
) -> list[TaskSpec]:
|
||||
task_parameters = {
|
||||
"threshold": self._unit_interval(resolved.get("threshold"), "threshold"),
|
||||
"threshold_direction": resolved.get("threshold_direction", "greater"),
|
||||
}
|
||||
block_refs = [
|
||||
context.sink.seal(
|
||||
path,
|
||||
declaration=self.input_port.schema,
|
||||
)
|
||||
for path in shard_paths
|
||||
]
|
||||
tasks: list[TaskSpec] = []
|
||||
for left in range(len(blocks)):
|
||||
for right in range(left, len(blocks)):
|
||||
for left in range(len(block_refs)):
|
||||
for right in range(left, len(block_refs)):
|
||||
tasks.append(
|
||||
TaskSpec(
|
||||
workload=self.manifest.workload,
|
||||
package_digest=self.manifest.package.digest,
|
||||
manifest_digest=self.manifest.digest,
|
||||
trust_mode=job.request.trust_mode,
|
||||
sdk_api_version=negotiated.sdk_api_version,
|
||||
protocol_version=negotiated.protocol_version,
|
||||
manifest_schema_version=self.manifest.manifest_schema_version,
|
||||
workflow_schema_version=self.manifest.workflow.schema_version,
|
||||
environment_digest=self.manifest.environment.digest,
|
||||
verifier=map_stage.verifier,
|
||||
selected_features=negotiated.selected_features,
|
||||
optional_fallbacks=negotiated.optional_fallbacks,
|
||||
task_key=f"map/{left:04d}x{right:04d}",
|
||||
stage_id="map",
|
||||
parameters={
|
||||
self.task_spec(
|
||||
map_stage,
|
||||
job,
|
||||
negotiated,
|
||||
f"map/{left:04d}x{right:04d}",
|
||||
{
|
||||
**task_parameters,
|
||||
"left_block": left,
|
||||
"right_block": right,
|
||||
},
|
||||
inputs={
|
||||
{
|
||||
"left": ArtifactCollection.single(block_refs[left]),
|
||||
"right": ArtifactCollection.single(block_refs[right]),
|
||||
},
|
||||
expected_outputs={"partial": self.partial_port},
|
||||
resources=map_stage.resources,
|
||||
execution=map_stage.execution,
|
||||
)
|
||||
)
|
||||
return WorkflowPlan(
|
||||
workload=self.manifest.workload,
|
||||
package_digest=self.manifest.package.digest,
|
||||
manifest_digest=self.manifest.digest,
|
||||
trust_mode=job.request.trust_mode,
|
||||
sdk_api_version=negotiated.sdk_api_version,
|
||||
protocol_version=negotiated.protocol_version,
|
||||
manifest_schema_version=self.manifest.manifest_schema_version,
|
||||
workflow_schema_version=self.manifest.workflow.schema_version,
|
||||
environment_digest=self.manifest.environment.digest,
|
||||
verifier=self.manifest.verifier.verifier,
|
||||
selected_features=negotiated.selected_features,
|
||||
optional_fallbacks=negotiated.optional_fallbacks,
|
||||
workflow_id=self.manifest.workflow.workflow_id,
|
||||
resolved_parameters=dict(parameters),
|
||||
tasks=tuple(tasks),
|
||||
)
|
||||
return tasks
|
||||
|
||||
def run(self, context: TaskContext) -> OutputManifest:
|
||||
context.cancellation.raise_if_cancelled()
|
||||
parameters = context.task.parameters
|
||||
def compute_shard(
|
||||
self,
|
||||
inputs: Mapping[str, Path],
|
||||
parameters: Mapping[str, Any],
|
||||
output_path: Path,
|
||||
) -> Mapping[str, int | float]:
|
||||
left_block = parameters.get("left_block")
|
||||
right_block = parameters.get("right_block")
|
||||
if (
|
||||
@@ -381,106 +226,32 @@ class SimilarityGraphSDKWorkload:
|
||||
):
|
||||
raise ValueError("graph map task requires block indices")
|
||||
diagonal = left_block == right_block
|
||||
left_collection = context.task.inputs.get("left")
|
||||
right_collection = context.task.inputs.get("right")
|
||||
if left_collection is None or right_collection is None:
|
||||
raise ValueError("graph map task requires left and right block inputs")
|
||||
self.block_port.validate_collection(left_collection, "graph map left input")
|
||||
self.block_port.validate_collection(right_collection, "graph map right input")
|
||||
workspace = context.workspace
|
||||
workspace.mkdir(parents=True, exist_ok=True)
|
||||
left_path = context.catalog.materialize(left_collection.items[0].artifact)
|
||||
right_path = context.catalog.materialize(right_collection.items[0].artifact)
|
||||
left_rows = read_block_rows(left_path)
|
||||
right_rows = (
|
||||
left_rows
|
||||
if diagonal and left_path.resolve() == right_path.resolve()
|
||||
else read_block_rows(right_path)
|
||||
)
|
||||
threshold = self._unit_interval(parameters.get("threshold"), "threshold")
|
||||
direction = parameters.get("threshold_direction", "greater")
|
||||
if direction not in {"greater", "less"}:
|
||||
raise ValueError("threshold_direction must be 'greater' or 'less'")
|
||||
left = read_block_rows(inputs["left"])
|
||||
right = left if diagonal else read_block_rows(inputs["right"])
|
||||
checked_pairs = (
|
||||
len(left_rows) * (len(left_rows) - 1) // 2
|
||||
if diagonal
|
||||
else len(left_rows) * len(right_rows)
|
||||
len(left) * (len(left) - 1) // 2 if diagonal else len(left) * len(right)
|
||||
)
|
||||
edges = compute_block_edges(
|
||||
left_rows,
|
||||
right_rows,
|
||||
threshold,
|
||||
direction,
|
||||
)
|
||||
output_path = workspace / "result.csv"
|
||||
edges = compute_block_edges(left, right, threshold, direction)
|
||||
write_edge_csv(output_path, edges)
|
||||
context.cancellation.raise_if_cancelled()
|
||||
sealed = context.sink.seal(
|
||||
output_path,
|
||||
declaration=self.partial_port.schema,
|
||||
)
|
||||
return OutputManifest(
|
||||
context.task.task_key,
|
||||
{"partial": ArtifactCollection.single(sealed)},
|
||||
{"checked_pairs": checked_pairs, "edges_emitted": len(edges)},
|
||||
context.provenance,
|
||||
).validate_against(
|
||||
context.task.expected_outputs,
|
||||
max_output_bytes=self.manifest.limits.max_output_bytes,
|
||||
)
|
||||
return {"checked_pairs": checked_pairs, "edges_emitted": len(edges)}
|
||||
|
||||
def reduce(self, context: ReduceContext) -> OutputManifest:
|
||||
context.cancellation.raise_if_cancelled()
|
||||
collection = context.accepted_inputs.get("partials")
|
||||
if (
|
||||
collection is None
|
||||
or collection.kind is not CollectionKind.KEYED
|
||||
or not collection.items
|
||||
):
|
||||
raise ValueError(
|
||||
"graph reducer requires a non-empty keyed partial collection"
|
||||
)
|
||||
self.manifest.workflow.stages[1].inputs["partials"].validate_collection(
|
||||
collection,
|
||||
"graph reducer partials",
|
||||
)
|
||||
pairs = [block_pair_from_key(item.key or "") for item in collection.items]
|
||||
check_pair_coverage(pairs)
|
||||
expected_keys = context.task.expected_input_keys.get("partials")
|
||||
if expected_keys is None or {item.key for item in collection.items} != set(
|
||||
expected_keys
|
||||
):
|
||||
raise ValueError(
|
||||
"graph partial keys do not match the coordinator expected set"
|
||||
)
|
||||
workspace = context.workspace
|
||||
workspace.mkdir(parents=True, exist_ok=True)
|
||||
partial_paths: list[Path] = []
|
||||
for item in sorted(collection.items, key=lambda value: value.key or ""):
|
||||
artifact: ArtifactRef = item.artifact
|
||||
source = context.catalog.materialize(artifact)
|
||||
target = workspace / artifact.artifact_id
|
||||
if source.resolve() != target.resolve():
|
||||
shutil.copyfile(source, target)
|
||||
if _sha256_file(target) != artifact.sha256:
|
||||
raise ValueError("materialized partial checksum does not match")
|
||||
partial_paths.append(target)
|
||||
result_path = workspace / "result.csv"
|
||||
metrics = merge_edge_partials(partial_paths, result_path)
|
||||
context.cancellation.raise_if_cancelled()
|
||||
sealed = context.sink.seal(
|
||||
result_path,
|
||||
declaration=self.output_port.schema,
|
||||
)
|
||||
return OutputManifest(
|
||||
context.task.task_key,
|
||||
{"result": ArtifactCollection.single(sealed)},
|
||||
metrics,
|
||||
context.provenance,
|
||||
).validate_against(
|
||||
context.task.expected_outputs,
|
||||
max_output_bytes=self.manifest.limits.max_output_bytes,
|
||||
)
|
||||
def parse_partial_key(self, key: str) -> Any:
|
||||
return block_pair_from_key(key)
|
||||
|
||||
def validate_partial_keys(self, parsed: Sequence[Any]) -> None:
|
||||
check_pair_coverage(tuple(parsed))
|
||||
|
||||
def reduce_partials(
|
||||
self,
|
||||
partial_paths: Sequence[Path],
|
||||
parameters: Mapping[str, Any],
|
||||
output_path: Path,
|
||||
) -> Mapping[str, int | float]:
|
||||
return merge_edge_partials(partial_paths, output_path)
|
||||
|
||||
|
||||
def similarity_graph_sdk_definition(
|
||||
|
||||
@@ -27,9 +27,20 @@ __all__ = [
|
||||
]
|
||||
|
||||
|
||||
def default_sdk_registry(*, shard_rows: int = 10_000) -> WorkloadRegistry:
|
||||
"""Registry of every built-in SDK-built workload, all enabled."""
|
||||
def default_sdk_registry(
|
||||
*,
|
||||
shard_rows: int = 10_000,
|
||||
allowlist: tuple[AllowedPackage, ...] | None = None,
|
||||
) -> WorkloadRegistry:
|
||||
"""Registry of every built-in SDK-built workload, all enabled.
|
||||
|
||||
When ``allowlist`` is provided, installed workloads are discovered through
|
||||
the ``scimesh.workloads`` entry points instead of the built-ins.
|
||||
"""
|
||||
registry = WorkloadRegistry()
|
||||
if allowlist:
|
||||
registry.discover_installed(allowlist)
|
||||
return registry
|
||||
registry.register(
|
||||
similarity_search_sdk_definition(shard_rows=shard_rows).definition(),
|
||||
enabled=True,
|
||||
@@ -45,8 +56,17 @@ def default_sdk_registry(*, shard_rows: int = 10_000) -> WorkloadRegistry:
|
||||
return registry
|
||||
|
||||
|
||||
def default_sdk_runtime() -> RuntimeCapabilities:
|
||||
"""Runtime advertising the built-in workloads' capabilities and inventory."""
|
||||
def default_sdk_runtime(
|
||||
*,
|
||||
workload_capabilities: tuple[str, ...] | None = None,
|
||||
environment_digests: tuple[str, ...] | None = None,
|
||||
) -> RuntimeCapabilities:
|
||||
"""Runtime advertising the built-in workloads' capabilities and inventory.
|
||||
|
||||
``workload_capabilities`` and ``environment_digests`` override the built-in
|
||||
defaults, for example when a registry was populated from an allowlist of
|
||||
installed user workloads instead of the built-ins.
|
||||
"""
|
||||
architecture = platform.machine().lower() or "unknown"
|
||||
return RuntimeCapabilities(
|
||||
sdk_api_version=SDK_API_VERSION,
|
||||
@@ -54,15 +74,14 @@ def default_sdk_runtime() -> RuntimeCapabilities:
|
||||
profiles=("core-batch-v1",),
|
||||
features={"artifact-collections": "1.0.0", "exact-verifier": "1.0.0"},
|
||||
workload_capabilities=(
|
||||
"similarity-search",
|
||||
"similarity-graph",
|
||||
"descriptor-batch",
|
||||
workload_capabilities
|
||||
or ("similarity-search", "similarity-graph", "descriptor-batch")
|
||||
),
|
||||
inventory=ResourceInventory(
|
||||
cpu_cores=max(os.cpu_count() or 1, 1),
|
||||
memory_mb=4096,
|
||||
scratch_mb=4096,
|
||||
architecture=architecture,
|
||||
environment_digests=(current_environment_digest(),),
|
||||
environment_digests=environment_digests or (current_environment_digest(),),
|
||||
),
|
||||
)
|
||||
|
||||
@@ -57,14 +57,12 @@ def run_search_shard(
|
||||
) -> dict[str, int]:
|
||||
"""Run one planned shard with the local reference implementation.
|
||||
|
||||
This is the worker entry used by the SDK-built runner. It deliberately
|
||||
accepts only resolved ``query_smiles``: resolving an identifier
|
||||
independently in each shard would make the distributed search
|
||||
scientifically invalid, so identifier resolution happens once in the
|
||||
planner (or at the worker bridge for v1-wire tasks that still carry
|
||||
``query_id``).
|
||||
Accepts either a resolved ``query_smiles`` or a raw ``query_id`` that is
|
||||
resolved against the shard (worker tasks on the v1 wire may still carry
|
||||
the identifier; the SDK planner always resolves it once at plan time).
|
||||
"""
|
||||
allowed = {
|
||||
"query_id",
|
||||
"query_smiles",
|
||||
"top_k",
|
||||
"threshold",
|
||||
@@ -77,6 +75,14 @@ def run_search_shard(
|
||||
f"unsupported similarity-search parameters: {', '.join(sorted(unknown))}"
|
||||
)
|
||||
query_smiles = parameters.get("query_smiles")
|
||||
query_id = parameters.get("query_id")
|
||||
if isinstance(query_id, str) and not isinstance(query_smiles, str):
|
||||
from rdkit import Chem
|
||||
|
||||
from scimesh.chemistry.dataset import find_molecule_by_id
|
||||
|
||||
record = find_molecule_by_id(input_path, query_id)
|
||||
query_smiles = Chem.MolToSmiles(record.molecule, canonical=True)
|
||||
if not isinstance(query_smiles, str) or not query_smiles.strip():
|
||||
raise ValueError("query_smiles is required for a distributed shard")
|
||||
molecule = parse_smiles(query_smiles)
|
||||
|
||||
@@ -1,79 +1,41 @@
|
||||
"""SDK-built ``similarity-search`` workload definition and handlers.
|
||||
|
||||
A direct ``core-batch-v1`` definition (not the legacy adapter): the planner
|
||||
resolves the query once, shards deterministically, each map task computes the
|
||||
local top-k with the reference implementation, and the reducer merges the
|
||||
sorted partials with the same bounded heap and tie-breakers as the local CLI.
|
||||
The manifest declares ``byte_exact`` with the exact-artifact verifier and both
|
||||
``trusted`` and ``untrusted_quorum`` trust modes.
|
||||
A thin subclass of ``MapReduceWorkload``: the SDK assembles the manifest,
|
||||
stages, workflow, and digest-pinned handlers. This module declares the search
|
||||
scientific contract (plan-time query resolution, deterministic sharding, local
|
||||
top-k per shard, bounded heap merge) and the hooks that partition, compute,
|
||||
and merge.
|
||||
"""
|
||||
|
||||
from __future__ import annotations
|
||||
|
||||
import hashlib
|
||||
import shutil
|
||||
from pathlib import Path
|
||||
from typing import Any, Mapping
|
||||
from typing import Any, Mapping, Sequence
|
||||
|
||||
from rdkit import Chem
|
||||
|
||||
from scimesh.chemistry.dataset import find_molecule_by_id, parse_smiles
|
||||
from scimesh.chemistry.fingerprints import FP_RADIUS, FP_SIZE
|
||||
from scimesh.sdk.artifacts import ArtifactSchema, ComponentRef, PortSpec
|
||||
from scimesh.sdk.batch import MapReduceWorkload
|
||||
from scimesh.sdk.identity import SchemaRef, WorkloadId
|
||||
from scimesh.sdk.plans import JobRequest, ValidatedJob
|
||||
from scimesh.sdk.registry import WorkloadDefinition
|
||||
|
||||
from ...sdk.artifacts import (
|
||||
ArtifactCollection,
|
||||
ArtifactItem,
|
||||
ArtifactRef,
|
||||
ArtifactSchema,
|
||||
Cardinality,
|
||||
CollectionKind,
|
||||
OutputManifest,
|
||||
PortSpec,
|
||||
)
|
||||
from ..environment import current_environment_digest, current_scimesh_package_digest
|
||||
from ...sdk.execution import (
|
||||
CheckpointPolicy,
|
||||
ExecutionProfile,
|
||||
NetworkPolicy,
|
||||
RetryPolicy,
|
||||
)
|
||||
from ...sdk.identity import ComponentRef, SchemaRef, VersionRange, WorkloadId
|
||||
from ...sdk.manifest import (
|
||||
DeterminismProfile,
|
||||
EnvironmentSpec,
|
||||
PackageSpec,
|
||||
TrustMode,
|
||||
VerifierSpec,
|
||||
WorkloadLimits,
|
||||
WorkloadManifest,
|
||||
)
|
||||
from ...sdk.plans import JobRequest, TaskSpec, ValidatedJob, WorkflowPlan
|
||||
from ...sdk.protocols import PlanningContext, ReduceContext, TaskContext
|
||||
from ...sdk.registry import WorkloadDefinition
|
||||
from ...sdk.resources import ResourceRequirements
|
||||
from ...sdk.verification import ExactArtifactVerifier
|
||||
from ...sdk.workflow import ArtifactEdge, PortRef, StageKind, StageSpec, WorkflowSpec
|
||||
from .core import merge_search_partials, run_search_shard, write_search_shards
|
||||
|
||||
MAP_ENTRY_POINT = "scimesh.workloads.search.definition:map_search@v1"
|
||||
REDUCE_ENTRY_POINT = "scimesh.workloads.search.definition:reduce_search@v1"
|
||||
|
||||
_MAP_PARAMETERS = (
|
||||
"query_id",
|
||||
"query_smiles",
|
||||
"top_k",
|
||||
"threshold",
|
||||
"threshold_direction",
|
||||
"progress_every",
|
||||
)
|
||||
_REDUCE_PARAMETERS = _MAP_PARAMETERS + ("query_source", "fingerprint")
|
||||
|
||||
|
||||
def _sha256_file(path: Path) -> str:
|
||||
digest = hashlib.sha256()
|
||||
with path.open("rb") as source:
|
||||
for block in iter(lambda: source.read(1024 * 1024), b""):
|
||||
digest.update(block)
|
||||
return digest.hexdigest()
|
||||
|
||||
|
||||
def _parameters_schema() -> dict[str, Any]:
|
||||
@@ -126,8 +88,30 @@ def _search_table_schema(ref: SchemaRef, canonicalizer: str) -> ArtifactSchema:
|
||||
)
|
||||
|
||||
|
||||
class SimilaritySearchSDKWorkload:
|
||||
"""Manifest-backed planner, runner, and reducer for similarity-search."""
|
||||
class SimilaritySearchSDKWorkload(MapReduceWorkload):
|
||||
"""Exact top-k Tanimoto search over deterministic shards with a bounded merge."""
|
||||
|
||||
workload_id = WorkloadId("similarity-search", "1.0.0")
|
||||
description = (
|
||||
"Exact top-k Tanimoto molecular similarity search over "
|
||||
"deterministic TSV shards with a bounded merge."
|
||||
)
|
||||
parameters_schema = _parameters_schema()
|
||||
input_port = PortSpec(_dataset_schema())
|
||||
partial_port = PortSpec(
|
||||
_search_table_schema(
|
||||
SchemaRef("similarity-search-partial", 1), "scimesh-search-partial-v1"
|
||||
)
|
||||
)
|
||||
output_port = PortSpec(
|
||||
_search_table_schema(
|
||||
SchemaRef("similarity-search-result", 1), "scimesh-search-result-v1"
|
||||
)
|
||||
)
|
||||
map_parameter_names = _MAP_PARAMETERS
|
||||
reduce_parameter_names = _MAP_PARAMETERS + ("query_source", "fingerprint")
|
||||
map_entry_point = MAP_ENTRY_POINT
|
||||
reduce_entry_point = REDUCE_ENTRY_POINT
|
||||
|
||||
def __init__(
|
||||
self,
|
||||
@@ -142,122 +126,15 @@ class SimilaritySearchSDKWorkload:
|
||||
or shard_rows < 1
|
||||
):
|
||||
raise ValueError("shard_rows must be a positive integer")
|
||||
self.entry_point = MAP_ENTRY_POINT
|
||||
self.shard_rows = shard_rows
|
||||
self.input_port = PortSpec(_dataset_schema())
|
||||
self.partial_port = PortSpec(
|
||||
_search_table_schema(
|
||||
SchemaRef("similarity-search-partial", 1), "scimesh-search-partial-v1"
|
||||
)
|
||||
super().__init__(
|
||||
package_digest=package_digest,
|
||||
environment_digest=environment_digest,
|
||||
)
|
||||
self.output_port = PortSpec(
|
||||
_search_table_schema(
|
||||
SchemaRef("similarity-search-result", 1), "scimesh-search-result-v1"
|
||||
)
|
||||
)
|
||||
resources = ResourceRequirements(
|
||||
profile="search-cpu-v1",
|
||||
cpu_cores=1,
|
||||
memory_mb=1024,
|
||||
scratch_mb=1024,
|
||||
max_duration_seconds=3600,
|
||||
)
|
||||
execution = ExecutionProfile(
|
||||
profile="search-python-process-v1",
|
||||
network=NetworkPolicy.TRUSTED,
|
||||
timeout_seconds=3600,
|
||||
checkpoint=CheckpointPolicy(),
|
||||
)
|
||||
limits = WorkloadLimits(
|
||||
max_input_bytes=self.input_port.schema.max_bytes,
|
||||
max_tasks=10_000,
|
||||
max_output_bytes=self.output_port.schema.max_bytes,
|
||||
)
|
||||
trust_modes = ("trusted", "untrusted_quorum")
|
||||
map_stage = StageSpec(
|
||||
stage_id="map",
|
||||
kind=StageKind.MAP,
|
||||
entry_point=MAP_ENTRY_POINT,
|
||||
needs=(),
|
||||
inputs={"input": self.input_port},
|
||||
outputs={"partial": self.partial_port},
|
||||
parameter_names=_MAP_PARAMETERS,
|
||||
resources=resources,
|
||||
execution=execution,
|
||||
retry=RetryPolicy(),
|
||||
verifier=ComponentRef("exact-artifact", 1),
|
||||
trust_modes=trust_modes,
|
||||
max_fan_out=limits.max_tasks,
|
||||
cacheable=True,
|
||||
)
|
||||
reduce_input = PortSpec(
|
||||
schema=self.partial_port.schema,
|
||||
cardinality=Cardinality.MANY,
|
||||
collection=CollectionKind.KEYED,
|
||||
)
|
||||
reduce_stage = StageSpec(
|
||||
stage_id="reduce",
|
||||
kind=StageKind.REDUCE,
|
||||
entry_point=REDUCE_ENTRY_POINT,
|
||||
needs=("map",),
|
||||
inputs={"partials": reduce_input},
|
||||
outputs={"result": self.output_port},
|
||||
parameter_names=_REDUCE_PARAMETERS,
|
||||
resources=resources,
|
||||
execution=execution,
|
||||
retry=RetryPolicy(),
|
||||
verifier=ComponentRef("exact-artifact", 1),
|
||||
trust_modes=trust_modes,
|
||||
max_fan_out=1,
|
||||
cacheable=True,
|
||||
)
|
||||
workflow = WorkflowSpec(
|
||||
workflow_id="search-map-reduce-v1",
|
||||
inputs={"input": self.input_port},
|
||||
stages=(map_stage, reduce_stage),
|
||||
edges=(
|
||||
ArtifactEdge(PortRef("input"), PortRef("input", "map")),
|
||||
ArtifactEdge(PortRef("partial", "map"), PortRef("partials", "reduce")),
|
||||
),
|
||||
outputs={"result": PortRef("result", "reduce")},
|
||||
max_tasks=limits.max_tasks,
|
||||
max_output_bytes=limits.max_output_bytes,
|
||||
)
|
||||
self.manifest = WorkloadManifest(
|
||||
sdk_api=VersionRange(">=1.0,<2.0"),
|
||||
protocol=VersionRange(">=1,<2"),
|
||||
workload=WorkloadId("similarity-search", "1.0.0"),
|
||||
description=(
|
||||
"Exact top-k Tanimoto molecular similarity search over "
|
||||
"deterministic TSV shards with a bounded merge."
|
||||
),
|
||||
package=PackageSpec("scimesh", package_digest),
|
||||
environment=EnvironmentSpec(
|
||||
"python-process",
|
||||
environment_digest,
|
||||
{"adapter": "sdk-native"},
|
||||
),
|
||||
parameters_schema=_parameters_schema(),
|
||||
workflow=workflow,
|
||||
inputs={"input": self.input_port},
|
||||
outputs={"result": self.output_port},
|
||||
determinism=DeterminismProfile.BYTE_EXACT,
|
||||
trust_modes=(TrustMode.TRUSTED, TrustMode.UNTRUSTED_QUORUM),
|
||||
verifier=VerifierSpec(ComponentRef("exact-artifact", 1), {}),
|
||||
limits=limits,
|
||||
capabilities=("similarity-search",),
|
||||
conformance_profiles=("core-batch-v1",),
|
||||
)
|
||||
self._exact_verifier = ExactArtifactVerifier()
|
||||
|
||||
def definition(self) -> WorkloadDefinition:
|
||||
return WorkloadDefinition(
|
||||
manifest=self.manifest,
|
||||
planner=self,
|
||||
runners={MAP_ENTRY_POINT: self},
|
||||
reducers={REDUCE_ENTRY_POINT: self},
|
||||
verifiers={self._exact_verifier.identity.canonical: self._exact_verifier},
|
||||
)
|
||||
# ------------------------------------------------------------------
|
||||
# Scientific hooks
|
||||
# ------------------------------------------------------------------
|
||||
|
||||
@staticmethod
|
||||
def _string(value: object, name: str) -> str:
|
||||
@@ -283,12 +160,7 @@ class SimilaritySearchSDKWorkload:
|
||||
raise ValueError(f"{name} must be a number between 0 and 1")
|
||||
return float(value)
|
||||
|
||||
def validate(self, request: JobRequest) -> ValidatedJob:
|
||||
if request.workload != self.manifest.workload:
|
||||
raise ValueError(
|
||||
"similarity-search received a request for another workload"
|
||||
)
|
||||
parameters = request.parameters
|
||||
def domain_validate(self, parameters: Mapping[str, Any]) -> None:
|
||||
unknown = set(parameters) - {
|
||||
"query_id",
|
||||
"query_smiles",
|
||||
@@ -322,9 +194,8 @@ class SimilaritySearchSDKWorkload:
|
||||
"threshold_direction"
|
||||
] not in {"greater", "less"}:
|
||||
raise ValueError("threshold_direction must be 'greater' or 'less'")
|
||||
return ValidatedJob(request, self._resolved_parameters(request))
|
||||
|
||||
def _resolved_parameters(self, request: JobRequest) -> dict[str, object]:
|
||||
def resolved_parameters(self, request: JobRequest) -> dict[str, Any]:
|
||||
parameters = request.parameters
|
||||
query_id = parameters.get("query_id")
|
||||
if isinstance(query_id, str):
|
||||
@@ -334,7 +205,7 @@ class SimilaritySearchSDKWorkload:
|
||||
"kind": "smiles",
|
||||
"value": self._string(parameters.get("query_smiles"), "query_smiles"),
|
||||
}
|
||||
resolved: dict[str, object] = {
|
||||
resolved: dict[str, Any] = {
|
||||
"query_source": query_source,
|
||||
"top_k": self._positive_int(parameters.get("top_k", 20), "top_k"),
|
||||
"threshold_direction": parameters.get("threshold_direction", "greater"),
|
||||
@@ -358,192 +229,54 @@ class SimilaritySearchSDKWorkload:
|
||||
)
|
||||
return resolved
|
||||
|
||||
def plan(self, job: ValidatedJob, context: PlanningContext) -> WorkflowPlan:
|
||||
if not isinstance(job, ValidatedJob):
|
||||
raise ValueError("job must be a ValidatedJob")
|
||||
collection = job.request.inputs.get("input")
|
||||
if collection is None:
|
||||
raise ValueError("similarity-search requires the input port")
|
||||
self.input_port.validate_collection(collection, "job input")
|
||||
input_artifact = collection.items[0].artifact
|
||||
input_path = context.catalog.materialize(input_artifact)
|
||||
workspace = context.workspace
|
||||
workspace.mkdir(parents=True, exist_ok=True)
|
||||
resolved = dict(job.resolved_parameters)
|
||||
query_smiles = self._resolve_query(input_path, job.request.parameters)
|
||||
resolved["query_smiles"] = query_smiles
|
||||
max_rows = resolved.get("max_rows")
|
||||
shard_paths = write_search_shards(
|
||||
def resolved_parameters_for_plan(
|
||||
self,
|
||||
job: ValidatedJob,
|
||||
input_path: Path,
|
||||
resolved: dict[str, Any],
|
||||
) -> dict[str, Any]:
|
||||
query_id = job.request.parameters.get("query_id")
|
||||
if isinstance(query_id, str):
|
||||
record = find_molecule_by_id(input_path, query_id)
|
||||
resolved["query_smiles"] = Chem.MolToSmiles(record.molecule, canonical=True)
|
||||
else:
|
||||
supplied = job.request.parameters["query_smiles"]
|
||||
assert isinstance(supplied, str)
|
||||
molecule = parse_smiles(supplied)
|
||||
if molecule is None:
|
||||
raise ValueError("query_smiles is invalid")
|
||||
resolved["query_smiles"] = Chem.MolToSmiles(molecule, canonical=True)
|
||||
return resolved
|
||||
|
||||
def partition_input(
|
||||
self,
|
||||
input_path: Path,
|
||||
parameters: Mapping[str, Any],
|
||||
workspace: Path,
|
||||
) -> list[Path]:
|
||||
max_rows = parameters.get("max_rows")
|
||||
return write_search_shards(
|
||||
input_path,
|
||||
workspace,
|
||||
self.shard_rows,
|
||||
int(max_rows) if isinstance(max_rows, int) else None,
|
||||
)
|
||||
task_parameters = {
|
||||
key: value for key, value in resolved.items() if key in set(_MAP_PARAMETERS)
|
||||
}
|
||||
negotiated = context.negotiated
|
||||
map_stage = self.manifest.workflow.stages[0]
|
||||
assert map_stage.verifier is not None
|
||||
tasks: list[TaskSpec] = []
|
||||
for index, path in enumerate(shard_paths):
|
||||
sealed = context.sink.seal(
|
||||
path,
|
||||
declaration=self.input_port.schema,
|
||||
)
|
||||
tasks.append(
|
||||
TaskSpec(
|
||||
workload=self.manifest.workload,
|
||||
package_digest=self.manifest.package.digest,
|
||||
manifest_digest=self.manifest.digest,
|
||||
trust_mode=job.request.trust_mode,
|
||||
sdk_api_version=negotiated.sdk_api_version,
|
||||
protocol_version=negotiated.protocol_version,
|
||||
manifest_schema_version=self.manifest.manifest_schema_version,
|
||||
workflow_schema_version=self.manifest.workflow.schema_version,
|
||||
environment_digest=self.manifest.environment.digest,
|
||||
verifier=map_stage.verifier,
|
||||
selected_features=negotiated.selected_features,
|
||||
optional_fallbacks=negotiated.optional_fallbacks,
|
||||
task_key=f"map/{index:08d}",
|
||||
stage_id="map",
|
||||
parameters=task_parameters,
|
||||
inputs={"input": ArtifactCollection.single(sealed)},
|
||||
expected_outputs={"partial": self.partial_port},
|
||||
resources=map_stage.resources,
|
||||
execution=map_stage.execution,
|
||||
)
|
||||
)
|
||||
return WorkflowPlan(
|
||||
workload=self.manifest.workload,
|
||||
package_digest=self.manifest.package.digest,
|
||||
manifest_digest=self.manifest.digest,
|
||||
trust_mode=job.request.trust_mode,
|
||||
sdk_api_version=negotiated.sdk_api_version,
|
||||
protocol_version=negotiated.protocol_version,
|
||||
manifest_schema_version=self.manifest.manifest_schema_version,
|
||||
workflow_schema_version=self.manifest.workflow.schema_version,
|
||||
environment_digest=self.manifest.environment.digest,
|
||||
verifier=self.manifest.verifier.verifier,
|
||||
selected_features=negotiated.selected_features,
|
||||
optional_fallbacks=negotiated.optional_fallbacks,
|
||||
workflow_id=self.manifest.workflow.workflow_id,
|
||||
resolved_parameters=resolved,
|
||||
tasks=tuple(tasks),
|
||||
)
|
||||
|
||||
@staticmethod
|
||||
def _resolve_query(input_path: Path, parameters: Mapping[str, object]) -> str:
|
||||
query_id = parameters.get("query_id")
|
||||
if isinstance(query_id, str):
|
||||
record = find_molecule_by_id(input_path, query_id)
|
||||
return Chem.MolToSmiles(record.molecule, canonical=True)
|
||||
supplied = parameters["query_smiles"]
|
||||
assert isinstance(supplied, str)
|
||||
molecule = parse_smiles(supplied)
|
||||
if molecule is None:
|
||||
raise ValueError("query_smiles is invalid")
|
||||
return Chem.MolToSmiles(molecule, canonical=True)
|
||||
def compute_shard(
|
||||
self,
|
||||
inputs: Mapping[str, Path],
|
||||
parameters: Mapping[str, Any],
|
||||
output_path: Path,
|
||||
) -> Mapping[str, int | float]:
|
||||
return run_search_shard(inputs["input"], parameters, output_path)
|
||||
|
||||
def run(self, context: TaskContext) -> OutputManifest:
|
||||
context.cancellation.raise_if_cancelled()
|
||||
collection = context.task.inputs.get("input")
|
||||
if collection is None:
|
||||
raise ValueError("search map task requires one input collection")
|
||||
self.input_port.validate_collection(collection, "search map input")
|
||||
source = context.catalog.materialize(collection.items[0].artifact)
|
||||
workspace = context.workspace
|
||||
workspace.mkdir(parents=True, exist_ok=True)
|
||||
input_path = workspace / "input"
|
||||
output_path = workspace / "result.csv"
|
||||
if source.resolve() != input_path.resolve():
|
||||
shutil.copyfile(source, input_path)
|
||||
metrics = run_search_shard(
|
||||
input_path,
|
||||
context.task.parameters,
|
||||
output_path,
|
||||
)
|
||||
context.cancellation.raise_if_cancelled()
|
||||
sealed = context.sink.seal(
|
||||
output_path,
|
||||
declaration=self.partial_port.schema,
|
||||
)
|
||||
return OutputManifest(
|
||||
context.task.task_key,
|
||||
{"partial": ArtifactCollection.single(sealed)},
|
||||
metrics,
|
||||
context.provenance,
|
||||
).validate_against(
|
||||
context.task.expected_outputs,
|
||||
max_output_bytes=self.manifest.limits.max_output_bytes,
|
||||
)
|
||||
|
||||
def reduce(self, context: ReduceContext) -> OutputManifest:
|
||||
context.cancellation.raise_if_cancelled()
|
||||
collection = context.accepted_inputs.get("partials")
|
||||
if (
|
||||
collection is None
|
||||
or collection.kind is not CollectionKind.KEYED
|
||||
or not collection.items
|
||||
):
|
||||
raise ValueError(
|
||||
"search reducer requires a non-empty keyed partial collection"
|
||||
)
|
||||
self.manifest.workflow.stages[1].inputs["partials"].validate_collection(
|
||||
collection,
|
||||
"search reducer partials",
|
||||
)
|
||||
workspace = context.workspace
|
||||
workspace.mkdir(parents=True, exist_ok=True)
|
||||
indexed_items: list[tuple[int, ArtifactItem]] = []
|
||||
for item in collection.items:
|
||||
key = item.key or ""
|
||||
prefix = "map."
|
||||
raw_index = key[len(prefix) :] if key.startswith(prefix) else ""
|
||||
if len(raw_index) != 8 or not raw_index.isdigit():
|
||||
raise ValueError("search partial key must use map.<eight-digit-index>")
|
||||
indexed_items.append((int(raw_index), item))
|
||||
expected_keys = context.task.expected_input_keys.get("partials")
|
||||
if expected_keys is None or {item.key for item in collection.items} != set(
|
||||
expected_keys
|
||||
):
|
||||
raise ValueError(
|
||||
"search partial keys do not match the coordinator expected set"
|
||||
)
|
||||
if sorted(index for index, _ in indexed_items) != list(
|
||||
range(len(indexed_items))
|
||||
):
|
||||
raise ValueError("search partial keys must be complete and contiguous")
|
||||
partial_paths: list[Path] = []
|
||||
for index, item in sorted(indexed_items):
|
||||
artifact: ArtifactRef = item.artifact
|
||||
source = context.catalog.materialize(artifact)
|
||||
target = workspace / artifact.artifact_id
|
||||
if source.resolve() != target.resolve():
|
||||
shutil.copyfile(source, target)
|
||||
if _sha256_file(target) != artifact.sha256:
|
||||
raise ValueError("materialized partial checksum does not match")
|
||||
partial_paths.append(target)
|
||||
result_path = workspace / "result.csv"
|
||||
metrics = merge_search_partials(
|
||||
partial_paths,
|
||||
context.task.parameters,
|
||||
result_path,
|
||||
)
|
||||
context.cancellation.raise_if_cancelled()
|
||||
sealed = context.sink.seal(
|
||||
result_path,
|
||||
declaration=self.output_port.schema,
|
||||
)
|
||||
return OutputManifest(
|
||||
context.task.task_key,
|
||||
{"result": ArtifactCollection.single(sealed)},
|
||||
metrics,
|
||||
context.provenance,
|
||||
).validate_against(
|
||||
context.task.expected_outputs,
|
||||
max_output_bytes=self.manifest.limits.max_output_bytes,
|
||||
)
|
||||
def reduce_partials(
|
||||
self,
|
||||
partial_paths: Sequence[Path],
|
||||
parameters: Mapping[str, Any],
|
||||
output_path: Path,
|
||||
) -> Mapping[str, int | float]:
|
||||
return merge_search_partials(partial_paths, parameters, output_path)
|
||||
|
||||
|
||||
def similarity_search_sdk_definition(
|
||||
|
||||
@@ -0,0 +1,167 @@
|
||||
"""Generic SDK workload runner CLI: ``scimesh workload list|run``.
|
||||
|
||||
This is a generic SDK tool, not a workload. It lists the enabled SDK-built
|
||||
workloads and executes any of them locally through ``LocalCoreBatchExecutor``,
|
||||
so a user-written workload package can be inspected and verified without
|
||||
touching any other part of the program.
|
||||
"""
|
||||
|
||||
from __future__ import annotations
|
||||
|
||||
import argparse
|
||||
import json
|
||||
import shutil
|
||||
import tempfile
|
||||
from pathlib import Path
|
||||
|
||||
from scimesh.sdk import (
|
||||
ArtifactCollection,
|
||||
JobRequest,
|
||||
LocalArtifactStore,
|
||||
LocalCoreBatchExecutor,
|
||||
)
|
||||
from scimesh.sdk.registry import workload_allowlist_from_json
|
||||
from scimesh.workloads.library import default_sdk_registry, default_sdk_runtime
|
||||
|
||||
|
||||
class WorkloadCLI:
|
||||
"""Inspect and run SDK-built workloads from the command line."""
|
||||
|
||||
name = "workload"
|
||||
help = "List and run SDK-built workloads locally."
|
||||
|
||||
def configure_parser(self, parser: argparse.ArgumentParser) -> None:
|
||||
subparsers = parser.add_subparsers(dest="workload_command", required=True)
|
||||
|
||||
list_parser = subparsers.add_parser(
|
||||
"list", help="List installed and enabled SDK workloads."
|
||||
)
|
||||
list_parser.set_defaults(workload_handler=self.list_workloads)
|
||||
|
||||
run_parser = subparsers.add_parser(
|
||||
"run", help="Run one SDK workload locally against an input file."
|
||||
)
|
||||
run_parser.add_argument(
|
||||
"name", help="Workload name, for example descriptor-batch"
|
||||
)
|
||||
run_parser.add_argument(
|
||||
"--version", help="Exact workload version (default: the enabled one)"
|
||||
)
|
||||
run_parser.add_argument(
|
||||
"--input", required=True, type=Path, help="Input dataset file"
|
||||
)
|
||||
run_parser.add_argument(
|
||||
"--params", default="{}", help="Job parameters as a JSON object"
|
||||
)
|
||||
run_parser.add_argument(
|
||||
"--shard-rows",
|
||||
type=int,
|
||||
default=10_000,
|
||||
help="Rows per planned shard for workloads that shard by rows",
|
||||
)
|
||||
run_parser.add_argument(
|
||||
"-o",
|
||||
"--output",
|
||||
type=Path,
|
||||
default=Path("workload_result.csv"),
|
||||
help="Output path for the final artifact",
|
||||
)
|
||||
run_parser.add_argument(
|
||||
"--work-dir",
|
||||
type=Path,
|
||||
help="Temporary working directory (default: a fresh temporary directory)",
|
||||
)
|
||||
run_parser.set_defaults(workload_handler=self.run_workload)
|
||||
|
||||
def run(self, args: argparse.Namespace) -> int:
|
||||
handler = getattr(args, "workload_handler", None)
|
||||
if handler is None:
|
||||
raise ValueError("select a workload subcommand: list or run")
|
||||
return handler(args)
|
||||
|
||||
@staticmethod
|
||||
def _registry(args: argparse.Namespace):
|
||||
import os
|
||||
|
||||
allowlist = workload_allowlist_from_json(
|
||||
os.getenv("SCIMESH_WORKLOAD_ALLOWLIST")
|
||||
)
|
||||
return default_sdk_registry(
|
||||
shard_rows=getattr(args, "shard_rows", 10_000),
|
||||
allowlist=allowlist,
|
||||
)
|
||||
|
||||
def list_workloads(self, args: argparse.Namespace) -> int:
|
||||
registry = self._registry(args)
|
||||
descriptions = registry.descriptions()
|
||||
if not descriptions:
|
||||
print("No SDK workloads are installed or enabled.")
|
||||
return 0
|
||||
width = max(len(item.workload.name) for item in descriptions)
|
||||
for item in sorted(descriptions, key=lambda value: value.workload.name):
|
||||
digest = item.package_digest.removeprefix("sha256:")[:12]
|
||||
state = "enabled" if item.enabled else "disabled"
|
||||
print(
|
||||
f"{item.workload.name:<{width}} {item.workload.version} "
|
||||
f"{item.description} [{state} {digest}]"
|
||||
)
|
||||
return 0
|
||||
|
||||
def run_workload(self, args: argparse.Namespace) -> int:
|
||||
registry = self._registry(args)
|
||||
descriptions = registry.descriptions()
|
||||
try:
|
||||
parameters = json.loads(args.params)
|
||||
except (TypeError, json.JSONDecodeError, RecursionError) as error:
|
||||
raise ValueError("--params must be a valid JSON object") from error
|
||||
if not isinstance(parameters, dict):
|
||||
raise ValueError("--params must be a JSON object")
|
||||
description = next(
|
||||
(
|
||||
item
|
||||
for item in descriptions
|
||||
if item.workload.name == args.name
|
||||
and (args.version is None or item.workload.version == args.version)
|
||||
),
|
||||
None,
|
||||
)
|
||||
if description is None:
|
||||
raise ValueError(f"unknown or disabled SDK workload: {args.name}")
|
||||
definition, _ = registry.require(
|
||||
description.workload.name,
|
||||
description.workload.version,
|
||||
description.package_digest,
|
||||
)
|
||||
runtime = default_sdk_runtime(
|
||||
workload_capabilities=tuple(item.workload.name for item in descriptions),
|
||||
environment_digests=(definition.manifest.environment.digest,),
|
||||
)
|
||||
if not args.input.is_file():
|
||||
raise ValueError(f"input file does not exist: {args.input}")
|
||||
with tempfile.TemporaryDirectory(prefix="scimesh-workload-") as temporary:
|
||||
root = Path(temporary)
|
||||
store = LocalArtifactStore(root / "artifacts")
|
||||
artifact = store.import_file(
|
||||
args.input,
|
||||
declaration=definition.manifest.inputs["input"].schema,
|
||||
)
|
||||
request = JobRequest(
|
||||
workload=definition.manifest.workload,
|
||||
parameters=parameters,
|
||||
inputs={"input": ArtifactCollection.single(artifact)},
|
||||
)
|
||||
result = LocalCoreBatchExecutor(
|
||||
registry,
|
||||
runtime,
|
||||
store,
|
||||
args.work_dir or root / "attempts",
|
||||
).execute(request, description.package_digest)
|
||||
result_artifact = result.outputs["result"].items[0].artifact
|
||||
source = store.materialize(result_artifact)
|
||||
args.output.parent.mkdir(parents=True, exist_ok=True)
|
||||
shutil.copyfile(source, args.output)
|
||||
print(
|
||||
f"Saved {description.workload.name} result to {args.output} "
|
||||
f"(metrics: {dict(result.metrics)})"
|
||||
)
|
||||
return 0
|
||||
Reference in New Issue
Block a user