567 lines
23 KiB
Python
567 lines
23 KiB
Python
from __future__ import annotations
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import hashlib
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import logging
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from pathlib import Path
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import subprocess
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import time
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from datetime import datetime, timedelta, timezone
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from urllib.request import Request
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import pytest
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from scimesh.worker.config import WorkerConfig
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from scimesh.worker import cli as worker_cli
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from scimesh.worker.cli import build_parser
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from scimesh.worker.coordinator import CoordinatorTransientError
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from scimesh.worker.daemon import LeaseHeartbeat, RunOnceOutcome, WorkerDaemon
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from scimesh.worker.models import (
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ClaimedTask,
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InputArtifact,
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ProducedArtifact,
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RegisteredWorker,
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RunResult,
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UploadedArtifact,
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)
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from scimesh.worker.artifacts import HttpArtifactClient, _SameOriginAuthRedirectHandler, _origin
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from scimesh.worker.runners import SciMeshRunner
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from scimesh.worker.transport import NoRedirectHandler
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class FakeCoordinator:
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def __init__(self, task: ClaimedTask | None) -> None:
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self.task, self.submissions, self.failures, self.heartbeats = task, [], [], []
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def claim(self, worker_id: str, capabilities: tuple[str, ...]) -> ClaimedTask | None:
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task, self.task = self.task, None
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return task
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def register(
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self, name: str, capabilities: tuple[str, ...], cpu_count: int, memory_mb: int | None
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) -> RegisteredWorker:
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return RegisteredWorker("11111111-1111-4111-8111-111111111111", 15)
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def submit(self, task: ClaimedTask, payload: dict) -> None:
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self.submissions.append(payload)
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def fail(self, task: ClaimedTask, payload: dict) -> None:
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self.failures.append(payload)
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def heartbeat(self, task: ClaimedTask, worker_id: str) -> str:
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self.heartbeats.append((task.task_id, task.attempt, worker_id))
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return (datetime.now(timezone.utc) + timedelta(seconds=1)).isoformat()
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class FakeArtifacts:
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def __init__(self, content: bytes) -> None:
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self.content, self.uploaded = content, []
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def download(self, uri: str, destination: Path) -> None:
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destination.write_bytes(self.content)
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def upload(
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self, task: ClaimedTask, worker_id: str, artifact: ProducedArtifact
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) -> UploadedArtifact:
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self.uploaded.append((task.task_id, worker_id, artifact.path))
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content = artifact.path.read_bytes()
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return UploadedArtifact(
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"22222222-2222-4222-8222-222222222222",
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f"https://example.test/tasks/{task.task_id}/artifacts/{artifact.path.name}",
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hashlib.sha256(content).hexdigest(),
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len(content),
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)
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class FakeRunner:
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def __init__(self) -> None:
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self.calls = 0
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def run(self, task: ClaimedTask, task_dir: Path) -> RunResult:
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self.calls += 1
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output = task_dir / "result.csv"
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output.write_text("id,score\na,1\n", encoding="utf-8")
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return RunResult((ProducedArtifact(output, "text/csv"),), {"processed_rows": 1})
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def make_task(content: bytes, checksum: str | None = None) -> ClaimedTask:
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lease = (datetime.now(timezone.utc) + timedelta(seconds=60)).isoformat()
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return ClaimedTask("task-1", 1, lease, "similarity-search", InputArtifact("https://example.test/input", checksum or hashlib.sha256(content).hexdigest()), {"query_id": "CHEMBL1"})
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def daemon(tmp_path: Path, task: ClaimedTask | None, content: bytes):
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coordinator, artifacts, runner = FakeCoordinator(task), FakeArtifacts(content), FakeRunner()
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config = WorkerConfig("https://example.test", "worker-1", tmp_path / "work")
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return WorkerDaemon(config, coordinator, artifacts, runner), coordinator, artifacts, runner, config
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def test_claims_runs_uploads_and_submits_csv(tmp_path: Path) -> None:
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content = b"input fixture"
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worker, coordinator, artifacts, runner, _ = daemon(tmp_path, make_task(content), content)
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assert worker.run_once() == RunOnceOutcome(claimed=True, completed=True)
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assert runner.calls == 1
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assert len(artifacts.uploaded) == 1
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assert coordinator.heartbeats == [("task-1", 1, "worker-1")]
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assert "status" not in coordinator.submissions[0]
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assert coordinator.submissions[0]["result"] == {
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"artifact_id": "22222222-2222-4222-8222-222222222222"
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}
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def test_worker_executes_a_resolved_similarity_search_shard(tmp_path: Path) -> None:
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content = b"chembl_id\tcanonical_smiles\nQUERY\tCCO\nMATCH\tCCCO\nINVALID\tnot-a-smiles\n"
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task = make_task(content)
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task = ClaimedTask(
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task.task_id, task.attempt, task.lease_expires_at, task.workload, task.input,
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{"query_smiles": "CCO", "top_k": 5, "progress_every": 0},
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)
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worker, coordinator, artifacts, _, _ = daemon(tmp_path, task, content)
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worker.runner = SciMeshRunner()
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assert worker.run_once() == RunOnceOutcome(claimed=True, completed=True)
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output = artifacts.uploaded[0][2].read_text(encoding="utf-8")
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assert output.startswith("rank,chembl_id,canonical_smiles,similarity\n")
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metrics = coordinator.submissions[0]["metrics"]
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assert metrics["scanned_rows"] == 3
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assert metrics["valid_molecules"] == 2
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assert metrics["invalid_smiles"] == 1
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assert metrics["matches_emitted"] == 1
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assert isinstance(metrics["elapsed_seconds"], float)
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def test_two_workers_complete_resolved_shards_after_one_retry(tmp_path: Path) -> None:
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content = b"chembl_id\tcanonical_smiles\nQUERY\tCCO\nMATCH\tCCCO\n"
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first = make_task(content)
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first = ClaimedTask(
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"retry-task", 1, first.lease_expires_at, "similarity-search", first.input,
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{"query_smiles": "CCO", "top_k": 5},
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)
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second = ClaimedTask(
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"other-task", 1, first.lease_expires_at, "similarity-search", first.input,
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{"query_smiles": "CCO", "top_k": 5},
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)
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class RetryCoordinator(FakeCoordinator):
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def __init__(self) -> None:
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super().__init__(None)
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self.queue = [first, second]
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self.claimants: list[str] = []
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def claim(self, worker_id: str, capabilities: tuple[str, ...]) -> ClaimedTask | None:
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self.claimants.append(worker_id)
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return self.queue.pop(0) if self.queue else None
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def fail(self, task: ClaimedTask, payload: dict) -> None:
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self.failures.append(payload)
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if task.task_id == "retry-task" and task.attempt == 1 and payload["retryable"]:
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self.queue.append(
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ClaimedTask(
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task.task_id, 2, task.lease_expires_at, task.workload, task.input,
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task.parameters,
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)
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)
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class FailFirstAttempt:
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def __init__(self) -> None:
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self.calls = 0
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self.delegate = SciMeshRunner()
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def run(self, task: ClaimedTask, task_dir: Path) -> RunResult:
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self.calls += 1
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if self.calls == 1:
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raise RuntimeError("simulated retryable shard failure")
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return self.delegate.run(task, task_dir)
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coordinator = RetryCoordinator()
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artifacts = FakeArtifacts(content)
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worker_a = WorkerDaemon(
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WorkerConfig("https://example.test", "worker-a", tmp_path / "worker-a"),
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coordinator, artifacts, FailFirstAttempt(),
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)
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worker_b = WorkerDaemon(
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WorkerConfig("https://example.test", "worker-b", tmp_path / "worker-b"),
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coordinator, artifacts, SciMeshRunner(),
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)
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assert worker_a.run_once() == RunOnceOutcome(claimed=True, completed=False)
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assert worker_b.run_once() == RunOnceOutcome(claimed=True, completed=True)
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assert worker_a.run_once() == RunOnceOutcome(claimed=True, completed=True)
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assert coordinator.claimants == ["worker-a", "worker-b", "worker-a"]
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assert len(coordinator.failures) == 1
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assert coordinator.failures[0]["retryable"] is True
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assert len(coordinator.submissions) == 2
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def test_no_task_does_not_create_directory(tmp_path: Path) -> None:
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worker, _, _, runner, config = daemon(tmp_path, None, b"")
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assert worker.run_once() == RunOnceOutcome(claimed=False, completed=False)
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assert runner.calls == 0
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assert not config.work_dir.exists()
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def test_once_worker_exits_after_an_empty_claim(tmp_path: Path, caplog: pytest.LogCaptureFixture) -> None:
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caplog.set_level(logging.INFO, logger="scimesh.worker")
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worker, _, _, runner, _ = daemon(tmp_path, None, b"")
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worker.config = WorkerConfig(**{**worker.config.__dict__, "exit_when_idle": True, "max_tasks": 1})
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assert worker.run_forever() is True
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assert runner.calls == 0
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assert "queue_empty" in caplog.text
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def test_worker_stops_after_the_configured_number_of_claims(tmp_path: Path, caplog: pytest.LogCaptureFixture) -> None:
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caplog.set_level(logging.INFO, logger="scimesh.worker")
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content = b"input fixture"
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worker, _, _, runner, _ = daemon(tmp_path, make_task(content), content)
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worker.config = WorkerConfig(**{**worker.config.__dict__, "max_tasks": 1})
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assert worker.run_forever() is True
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assert runner.calls == 1
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assert "max_tasks_reached" in caplog.text
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def test_keyboard_interrupt_stops_worker_without_propagating(tmp_path: Path, caplog: pytest.LogCaptureFixture) -> None:
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caplog.set_level(logging.INFO, logger="scimesh.worker")
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class InterruptingCoordinator(FakeCoordinator):
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def claim(self, worker_id: str, capabilities: tuple[str, ...]) -> ClaimedTask | None:
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raise KeyboardInterrupt
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worker, _, _, _, _ = daemon(tmp_path, None, b"")
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worker.coordinator = InterruptingCoordinator(None)
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assert worker.run_forever() is False
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assert "interrupted" in caplog.text
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def test_interrupting_an_active_task_reports_a_sanitized_failure(tmp_path: Path) -> None:
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content = b"input fixture"
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worker, coordinator, _, _, _ = daemon(tmp_path, make_task(content), content)
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class InterruptingRunner(FakeRunner):
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def run(self, task: ClaimedTask, task_dir: Path) -> RunResult:
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raise KeyboardInterrupt
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worker.runner = InterruptingRunner()
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with pytest.raises(KeyboardInterrupt):
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worker.run_once()
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assert coordinator.failures == [
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{
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"worker_id": "worker-1",
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"attempt": 1,
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"error_code": "InterruptedError",
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"error_message": "worker interrupted by operator",
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"retryable": True,
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}
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]
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def test_max_tasks_counts_successes_not_failed_claims(tmp_path: Path) -> None:
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successful_content = b"successful input"
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class SequencedCoordinator(FakeCoordinator):
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def __init__(self) -> None:
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super().__init__(None)
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self.tasks = [
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make_task(b"bad input", "wrong-checksum"),
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ClaimedTask(
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"task-2",
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1,
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(datetime.now(timezone.utc) + timedelta(seconds=60)).isoformat(),
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"similarity-search",
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InputArtifact(
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"https://example.test/input",
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hashlib.sha256(successful_content).hexdigest(),
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),
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{"query_id": "CHEMBL1"},
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),
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]
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def claim(self, worker_id: str, capabilities: tuple[str, ...]) -> ClaimedTask | None:
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return self.tasks.pop(0) if self.tasks else None
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coordinator = SequencedCoordinator()
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artifacts, runner = FakeArtifacts(successful_content), FakeRunner()
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config = WorkerConfig("https://example.test", "worker-1", tmp_path / "work", max_tasks=1)
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worker = WorkerDaemon(config, coordinator, artifacts, runner)
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assert worker.run_forever() is True
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assert len(coordinator.failures) == 1
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assert len(coordinator.submissions) == 1
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assert runner.calls == 1
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def test_worker_cli_lifecycle_options_are_explicit_and_exclusive() -> None:
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parser = build_parser()
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assert parser.parse_args(["--once"]).once is True
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assert parser.parse_args(["--max-tasks", "2"]).max_tasks == 2
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with pytest.raises(SystemExit):
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parser.parse_args(["--once", "--max-tasks", "2"])
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def test_worker_cli_uses_a_nonzero_exit_code_for_interruption(
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monkeypatch: pytest.MonkeyPatch, tmp_path: Path
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) -> None:
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class InterruptedDaemon:
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def __init__(self, *_: object) -> None:
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pass
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def run_forever(self) -> bool:
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return False
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monkeypatch.setattr(worker_cli, "WorkerDaemon", InterruptedDaemon)
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assert worker_cli.main(
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["--coordinator-url", "https://example.test", "--work-dir", str(tmp_path)]
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) == 130
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@pytest.mark.parametrize("value", [0, -1, True])
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def test_max_tasks_must_be_positive(value: object, tmp_path: Path) -> None:
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with pytest.raises(ValueError, match="max_tasks"):
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WorkerConfig("https://example.test", None, tmp_path, max_tasks=value) # type: ignore[arg-type]
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def test_bad_checksum_reports_failure_without_running(tmp_path: Path) -> None:
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worker, coordinator, _, runner, _ = daemon(tmp_path, make_task(b"actual", "not-the-hash"), b"actual")
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assert worker.run_once() == RunOnceOutcome(claimed=True, completed=False)
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assert runner.calls == 0
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assert coordinator.failures[0]["error_code"] == "ValueError"
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assert coordinator.failures[0]["retryable"] is False
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assert not coordinator.submissions
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def test_failure_reporting_removes_paths_outside_the_worker_directory(tmp_path: Path) -> None:
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worker, coordinator, _, _, _ = daemon(tmp_path, make_task(b"input"), b"input")
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error = subprocess.CalledProcessError(
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1,
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["/home/alice/.venv/bin/python", "-m", "scimesh.cli", "/private/input.tsv"],
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)
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worker._report_failure(make_task(b"input"), error)
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message = coordinator.failures[0]["error_message"]
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assert "/home/alice" not in message
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assert "/private/input.tsv" not in message
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assert "<path>" in message
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def test_directory_creation_failure_is_reported(tmp_path: Path) -> None:
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content = b"input fixture"
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worker, coordinator, _, _, config = daemon(tmp_path, make_task(content), content)
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(config.work_dir / "task-1" / "1").mkdir(parents=True)
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assert worker.run_once() == RunOnceOutcome(claimed=True, completed=False)
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assert coordinator.failures[0]["error_code"] == "FileExistsError"
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def test_transient_claim_error_is_propagated_for_bounded_backoff(tmp_path: Path) -> None:
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class UnavailableCoordinator(FakeCoordinator):
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def claim(self, worker_id: str, capabilities: tuple[str, ...]) -> ClaimedTask | None:
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raise CoordinatorTransientError("temporary outage")
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worker, _, _, _, _ = daemon(tmp_path, None, b"")
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worker.coordinator = UnavailableCoordinator(None)
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with pytest.raises(CoordinatorTransientError):
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worker.run_once()
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def test_task_directories_are_retained_until_cleanup_is_enabled(tmp_path: Path) -> None:
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content = b"input fixture"
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worker, _, _, _, config = daemon(tmp_path, make_task(content), content)
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worker.run_once()
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task_dir = config.work_dir / "task-1" / "1"
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assert task_dir.is_dir()
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worker.config = WorkerConfig(**{**config.__dict__, "cleanup_after_seconds": 0})
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worker._cleanup_expired_directories()
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assert not task_dir.exists()
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def test_input_token_is_sent_only_to_the_coordinator_origin() -> None:
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client = HttpArtifactClient("https://coordinator.example/api", 10, "secret")
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assert client._auth_headers_for("https://coordinator.example/tasks/1/input") == {"Authorization": "Bearer secret"}
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assert client._auth_headers_for("https://bucket.example/presigned") == {}
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def test_relative_input_uri_is_resolved_against_the_coordinator() -> None:
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client = HttpArtifactClient("https://coordinator.example/api", 10, "secret")
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assert client._auth_headers_for("https://coordinator.example/tasks/1/input") == {
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"Authorization": "Bearer secret"
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}
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# The coordinator's contract returns root-relative artifact paths.
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assert client.coordinator_url == "https://coordinator.example/api"
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def test_redirect_to_external_storage_strips_authorization() -> None:
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handler = _SameOriginAuthRedirectHandler(_origin("https://coordinator.example"))
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source = Request(
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"https://coordinator.example/tasks/1/input", headers={"Authorization": "Bearer secret"}
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)
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redirected = handler.redirect_request(source, None, 302, "Found", {}, "https://bucket.example/presigned")
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assert redirected is not None
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assert redirected.get_header("Authorization") is None
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def test_api_requests_never_follow_redirects() -> None:
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handler = NoRedirectHandler()
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request = Request("https://coordinator.example/tasks/claim", headers={"Authorization": "Bearer secret"})
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assert handler.redirect_request(request, None, 302, "Found", {}, "https://other.example") is None
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def test_lease_is_renewed_while_a_runner_is_still_working(tmp_path: Path) -> None:
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content = b"input fixture"
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worker, coordinator, _, _, config = daemon(tmp_path, make_task(content), content)
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class SlowRunner(FakeRunner):
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def run(self, task: ClaimedTask, task_dir: Path) -> RunResult:
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time.sleep(0.05)
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return super().run(task, task_dir)
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worker.runner = SlowRunner()
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worker.config = WorkerConfig(**{**config.__dict__, "heartbeat_interval": 0.01})
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worker.run_once()
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assert len(coordinator.heartbeats) >= 2
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def test_heartbeat_reschedules_from_the_renewed_lease(tmp_path: Path) -> None:
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class ShortLeaseCoordinator(FakeCoordinator):
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def heartbeat(self, task: ClaimedTask, worker_id: str) -> str:
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self.heartbeats.append((task.task_id, task.attempt, worker_id))
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return (datetime.now(timezone.utc) + timedelta(seconds=0.02)).isoformat()
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config = WorkerConfig(
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"https://example.test", "worker-1", tmp_path / "work", heartbeat_interval=1
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)
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coordinator = ShortLeaseCoordinator(None)
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heartbeat = LeaseHeartbeat(make_task(b"fixture"), coordinator, config)
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heartbeat.start()
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time.sleep(0.06)
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heartbeat.stop()
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assert len(coordinator.heartbeats) >= 3
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def test_runner_maps_graph_and_smiles_search_parameters(tmp_path: Path, monkeypatch: pytest.MonkeyPatch) -> None:
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commands: list[list[str]] = []
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def fake_run(command: list[str], **_: object) -> None:
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commands.append(command)
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output = Path(command[command.index("--output") + 1])
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output.parent.mkdir(parents=True, exist_ok=True)
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output.write_text("a,b\n", encoding="utf-8")
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monkeypatch.setattr("scimesh.worker.runners.subprocess.run", fake_run)
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runner = SciMeshRunner()
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graph = ClaimedTask("graph", 1, "2026-07-30T00:00:00Z", "similarity-graph", InputArtifact("https://example/input", "x"), {"threshold": 0.2, "threshold_direction": "less", "block_size": 42, "max_rows": 7, "progress_every": 0})
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search = ClaimedTask("search", 1, "2026-07-30T00:00:00Z", "similarity-search", InputArtifact("https://example/input", "x"), {"query_smiles": "CCO", "top_k": 3})
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search_dir = tmp_path / "search"
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search_dir.mkdir()
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(search_dir / "input").write_text(
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"chembl_id\tcanonical_smiles\nA\tCCO\nB\tCCCO\n", encoding="utf-8"
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)
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runner.run(graph, tmp_path / "graph")
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result = runner.run(search, search_dir)
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assert "--threshold-direction" in commands[0] and "less" in commands[0]
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assert "--block-size" in commands[0] and "42" in commands[0]
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assert "--max-rows" in commands[0] and "7" in commands[0]
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assert len(commands) == 1
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assert result.metrics == {
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"scanned_rows": 2, "valid_molecules": 2, "invalid_smiles": 0, "matches_emitted": 1,
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}
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def test_runner_accepts_coordinator_workload_names(tmp_path: Path, monkeypatch: pytest.MonkeyPatch) -> None:
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task_dir = tmp_path / "search"
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task_dir.mkdir()
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(task_dir / "input").write_text(
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"chembl_id\tcanonical_smiles\nA\tCCO\nB\tCCCO\n", encoding="utf-8"
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)
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task = ClaimedTask(
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"search", 1, "2026-07-30T00:00:00Z", "similarity_search",
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InputArtifact("https://example/input", "a" * 64), {"query_smiles": "CCO"},
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)
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result = SciMeshRunner().run(task, task_dir)
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assert result.metrics["matches_emitted"] == 1
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assert (task_dir / "result.csv").is_file()
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def test_claimed_task_rejects_path_traversal_and_invalid_metadata() -> None:
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payload = {
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"task_id": "../outside",
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"attempt": 1,
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"lease_expires_at": "2026-07-30T00:00:00Z",
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"workload": "similarity-search",
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"input": {"uri": "https://example.test/input", "sha256": "a" * 64},
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"parameters": {},
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}
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with pytest.raises(ValueError, match="invalid claimed-task response"):
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ClaimedTask.from_json(payload)
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payload["task_id"] = "11111111-1111-4111-8111-111111111111"
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payload["input"] = {"uri": "//outside.example/input", "sha256": "a" * 64}
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with pytest.raises(ValueError, match="invalid claimed-task response"):
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ClaimedTask.from_json(payload)
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payload["input"] = {"uri": "/tasks/../outside/input", "sha256": "a" * 64}
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with pytest.raises(ValueError, match="invalid claimed-task response"):
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ClaimedTask.from_json(payload)
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def test_claimed_task_accepts_a_coordinator_relative_input_path() -> None:
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task = ClaimedTask.from_json(
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{
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"task_id": "11111111-1111-4111-8111-111111111111",
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"attempt": 1,
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"lease_expires_at": "2026-07-30T00:00:00Z",
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"workload": "similarity_search",
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"input": {"uri": "/tasks/11111111-1111-4111-8111-111111111111/input", "sha256": "a" * 64},
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"parameters": {},
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}
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)
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assert task.input.uri.startswith("/tasks/")
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def test_uploaded_artifact_requires_complete_durable_metadata() -> None:
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artifact = UploadedArtifact.from_json(
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{
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"artifact_id": "22222222-2222-4222-8222-222222222222",
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"uri": "https://coordinator.example/artifacts/222/download",
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"sha256": "a" * 64,
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"size_bytes": 12,
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}
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)
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assert artifact.size_bytes == 12
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with pytest.raises(ValueError, match="artifact size_bytes"):
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UploadedArtifact.from_json({"artifact_id": "missing"})
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def test_environment_overrides_allow_cli_only_configuration(monkeypatch: pytest.MonkeyPatch, tmp_path: Path) -> None:
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monkeypatch.delenv("SCIMESH_COORDINATOR_URL", raising=False)
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config = WorkerConfig.from_environment(
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{
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"coordinator_url": "https://coordinator.example",
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"work_dir": tmp_path,
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"worker_name": "test-worker",
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}
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)
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assert config.coordinator_url == "https://coordinator.example"
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assert config.worker_id is None
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assert "similarity-search" in config.capabilities
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assert "similarity_search" in config.capabilities
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assert "similarity-graph" not in config.capabilities
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def test_relative_work_dir_is_normalized_for_runner_subprocesses(
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monkeypatch: pytest.MonkeyPatch, tmp_path: Path
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) -> None:
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monkeypatch.chdir(tmp_path)
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config = WorkerConfig("https://coordinator.example", None, Path("./worker-data"))
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assert config.work_dir == tmp_path / "worker-data"
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task_dir = config.work_dir / "task" / "1"
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task_dir.mkdir(parents=True)
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(task_dir / "input").write_text(
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"chembl_id\tcanonical_smiles\nA\tCCO\nB\tCCCO\n", encoding="utf-8"
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|
)
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|
task = ClaimedTask(
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|
"task", 1, "2026-07-30T00:00:00Z", "similarity-search",
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InputArtifact("https://example.test/input", "a" * 64), {"query_smiles": "CCO"},
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)
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SciMeshRunner().run(task, task_dir)
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assert (task_dir / "result.csv").is_file()
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def test_worker_registration_sets_returned_identity(tmp_path: Path) -> None:
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worker, _, _, _, _ = daemon(tmp_path, None, b"")
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worker._register_worker()
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assert worker.worker_id == "11111111-1111-4111-8111-111111111111"
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assert worker.config.heartbeat_interval == 15
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