444 lines
17 KiB
Python
444 lines
17 KiB
Python
"""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.
|
|
"""
|
|
|
|
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 ..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,
|
|
concatenate_descriptor_shards,
|
|
validate_descriptor_names,
|
|
write_descriptor_shards,
|
|
)
|
|
|
|
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 {
|
|
"type": "object",
|
|
"additionalProperties": False,
|
|
"properties": {
|
|
"skip_invalid": {
|
|
"type": "boolean",
|
|
"default": True,
|
|
"description": "Skip rows with invalid SMILES instead of failing",
|
|
},
|
|
},
|
|
}
|
|
|
|
|
|
def _input_schema() -> ArtifactSchema:
|
|
return ArtifactSchema(
|
|
SchemaRef("molecule-table", 1),
|
|
"text/tab-separated-values",
|
|
"utf-8",
|
|
max_bytes=10 * 1024 * 1024 * 1024,
|
|
validator=ComponentRef("delimited-table", 1),
|
|
validator_configuration={
|
|
"required_columns": ["canonical_smiles", "chembl_id"],
|
|
},
|
|
max_records=100_000_000,
|
|
canonicalizer="scimesh-tsv-v1",
|
|
)
|
|
|
|
|
|
def _descriptor_schema() -> ArtifactSchema:
|
|
return ArtifactSchema(
|
|
SchemaRef("descriptor-table", 1),
|
|
"text/csv",
|
|
"utf-8",
|
|
max_bytes=100 * 1024 * 1024 * 1024,
|
|
validator=ComponentRef("delimited-table", 1),
|
|
validator_configuration={
|
|
"columns": list(DESCRIPTOR_COLUMNS),
|
|
},
|
|
max_records=100_000_000,
|
|
canonicalizer="descriptor-table-v1",
|
|
)
|
|
|
|
|
|
class DescriptorBatchWorkload:
|
|
"""Manifest-backed planner, runner, and reducer for descriptor-batch.
|
|
|
|
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.
|
|
"""
|
|
|
|
def __init__(
|
|
self,
|
|
*,
|
|
shard_rows: int,
|
|
package_digest: str,
|
|
environment_digest: str,
|
|
) -> None:
|
|
if (
|
|
isinstance(shard_rows, bool)
|
|
or not isinstance(shard_rows, int)
|
|
or shard_rows < 1
|
|
):
|
|
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,
|
|
)
|
|
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},
|
|
)
|
|
|
|
@staticmethod
|
|
def _skip_invalid(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 descriptor_batch_sdk_definition(
|
|
*,
|
|
shard_rows: int = 10_000,
|
|
package_digest: str | None = None,
|
|
environment_digest: str | None = None,
|
|
) -> DescriptorBatchWorkload:
|
|
"""Build the default local descriptor-batch definition for tests."""
|
|
return DescriptorBatchWorkload(
|
|
shard_rows=shard_rows,
|
|
package_digest=package_digest or current_scimesh_package_digest(),
|
|
environment_digest=environment_digest or current_environment_digest(),
|
|
)
|
|
|
|
|
|
def workload_definition() -> WorkloadDefinition:
|
|
"""Installed entry-point factory for the default descriptor-batch definition."""
|
|
return descriptor_batch_sdk_definition().definition()
|