211 lines
7.0 KiB
Python
211 lines
7.0 KiB
Python
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from __future__ import annotations
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import inspect
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import json
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from pathlib import Path
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import runpy
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from apps.web.vue3.main import ExecuteRequest
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from gfa_core.mas.agents.planning_v2 import PlanningAgentV2
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from gfa_core.mas.stage_capabilities import CAPABILITIES
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from gfa_core.mas.stage_catalog import EXECUTABLE_STAGES, STAGE_DEPENDENCIES
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from gfa_core.mas.tools.stage_tools import StageToolRegistry
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_CLI_FIXTURES = runpy.run_path(
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str(Path(__file__).with_name("test_wgs_variant_select_cli.py"))
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)
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JOINT_ANALYSIS = _CLI_FIXTURES["JOINT_ANALYSIS"]
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REFERENCE = _CLI_FIXTURES["REFERENCE"]
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SAMPLES = _CLI_FIXTURES["SAMPLES"]
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_joint_authority = _CLI_FIXTURES["_joint_authority"]
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_tool = _CLI_FIXTURES["_tool"]
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def test_wgs_variant_select_vertical_registration_is_exact() -> None:
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assert STAGE_DEPENDENCIES["wgs_variant_select"] == [
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"wgs_joint_genotyping"
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]
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assert "wgs_variant_select" in EXECUTABLE_STAGES
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capability = CAPABILITIES["wgs_variant_select"]
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assert {item.role for item in capability.consumes} == {
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"joint_vcf",
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"joint_vcf_index",
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}
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assert {item.role for item in capability.provides} == {
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"selected_snp_vcf",
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"selected_snp_vcf_index",
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"selected_indel_vcf",
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"selected_indel_vcf_index",
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"variant_select_report",
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}
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definition = next(
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item
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for item in StageToolRegistry.STAGE_DEFINITIONS
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if item["id"] == "wgs_variant_select"
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)
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assert definition["script"] == "run_wgs_variant_select.py"
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assert definition["required_inputs"] == ["wgs_joint_manifest"]
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assert PlanningAgentV2.REQUIRED_INPUTS["wgs_variant_select"] == []
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def test_api_and_worker_boundary_carry_method_and_both_tools() -> None:
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request = ExecuteRequest(
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stage="wgs_variant_select",
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wgsJointManifest="final/Cohort.wgs_joint_genotyping.manifest.json",
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wgsMethod="bcftools",
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wgsGatk="/opt/gatk",
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wgsBcftools="/opt/bcftools",
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)
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assert request.wgsJointManifest.endswith(
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".wgs_joint_genotyping.manifest.json"
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)
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assert request.wgsMethod == "bcftools"
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assert request.wgsGatk == "/opt/gatk"
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assert request.wgsBcftools == "/opt/bcftools"
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parameters = inspect.signature(
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__import__("apps.web.pipeline_backend", fromlist=["run_stage"]).run_stage
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).parameters
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assert "wgs_joint_manifest" in parameters
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assert "wgs_method" in parameters
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assert "wgs_bcftools" in parameters
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def _backend_kwargs(
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workspace: Path,
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joint: Path,
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gatk: Path,
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bcftools: Path,
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method: str,
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) -> dict:
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from apps.web import pipeline_backend
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return {
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"stage": "wgs_variant_select",
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"job": pipeline_backend.JobInfo(
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"job-1", "", str(workspace), str(workspace / "logs"), "now"
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),
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"prefix": "Cohort",
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"wgs_joint_manifest": str(joint),
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"wgs_sample_set_id": SAMPLES,
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"wgs_reference_id": REFERENCE,
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"wgs_joint_analysis_id": JOINT_ANALYSIS,
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"wgs_method": method,
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"wgs_gatk": str(gatk),
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"wgs_bcftools": str(bcftools),
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}
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def test_backend_builds_exact_method_command_and_accepts_fresh_manifest(
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tmp_path: Path, monkeypatch
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) -> None:
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from apps.cli.run_wgs_variant_select import main
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from apps.web import pipeline_backend
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workspace = tmp_path / "workspace"
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joint = _joint_authority(workspace)
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gatk = _tool(tmp_path, "gatk")
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bcftools = _tool(tmp_path, "bcftools")
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calls: list[list[str]] = []
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def fake_run(command, *_args, **_kwargs):
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calls.append(command)
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return main(command[3:])
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monkeypatch.setattr(pipeline_backend, "run_cmd_logged", fake_run)
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for method in ("gatk", "bcftools"):
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message, output = pipeline_backend.run_stage(
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**_backend_kwargs(
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workspace, joint, gatk, bcftools, method
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)
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)
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assert "completed" in message.lower()
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assert output == (
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workspace
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/ "final"
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/ f"Cohort.wgs_variant_select.{method}.manifest.json"
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)
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manifest = json.loads(output.read_text())
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assert manifest["method"] == method
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assert manifest["parameters"]["method"] == method
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assert set(manifest["software"]) == {method}
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command = calls[-1]
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assert command[:3] == [
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pipeline_backend.sys.executable,
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"-m",
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"apps.cli.run_wgs_variant_select",
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]
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assert command[command.index("--joint-manifest") + 1] == str(joint)
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assert command[command.index("--method") + 1] == method
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def test_only_runtime_gatk_failure_returns_real_reason_and_fallback_metadata(
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tmp_path: Path, monkeypatch
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) -> None:
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from apps.cli.run_wgs_variant_select import main
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from apps.web import pipeline_backend
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workspace = tmp_path / "workspace"
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joint = _joint_authority(workspace)
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gatk = _tool(tmp_path, "gatk")
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bcftools = _tool(tmp_path, "bcftools")
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monkeypatch.setenv("FAIL_POINT", "gatk:select:SNP")
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monkeypatch.setattr(
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pipeline_backend,
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"run_cmd_logged",
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lambda command, *_args, **_kwargs: main(command[3:]),
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)
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message, failure_path = pipeline_backend.run_stage(
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**_backend_kwargs(
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workspace, joint, gatk, bcftools, "gatk"
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)
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)
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failure = json.loads(failure_path.read_text())
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assert "SelectVariants SNP failed with exit code 23" in message
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assert "SelectVariants SNP failed with exit code 23" in failure["errors"][0]
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assert failure["fallback_method"] == "bcftools"
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assert failure["method"] == "gatk"
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def test_bcftools_failure_and_upstream_preflight_are_not_fallback_eligible(
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tmp_path: Path, monkeypatch
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) -> None:
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from apps.cli.run_wgs_variant_select import main
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from apps.web import pipeline_backend
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workspace = tmp_path / "workspace"
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joint = _joint_authority(workspace)
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gatk = _tool(tmp_path, "gatk")
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bcftools = _tool(tmp_path, "bcftools")
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monkeypatch.setenv("FAIL_POINT", "bcftools:select:SNP")
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monkeypatch.setattr(
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pipeline_backend,
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"run_cmd_logged",
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lambda command, *_args, **_kwargs: main(command[3:]),
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)
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_, failure_path = pipeline_backend.run_stage(
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**_backend_kwargs(
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workspace, joint, gatk, bcftools, "bcftools"
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)
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)
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failure = json.loads(failure_path.read_text())
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assert "fallback_method" not in failure
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payload = json.loads(joint.read_text())
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payload.pop("wgs_analysis_id")
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joint.write_text(json.dumps(payload))
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message, output = pipeline_backend.run_stage(
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**_backend_kwargs(
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workspace, joint, gatk, bcftools, "gatk"
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)
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)
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assert output is None
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assert "fallback" not in message.lower()
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def test_worker_failure_payload_surfaces_only_manifest_approved_fallback() -> None:
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source = inspect.getsource(
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__import__(
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"gfa_core.mas.tools.stage_tools",
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fromlist=["StageToolExecutor"],
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).StageToolExecutor.execute
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)
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assert 'payload["fallback_method"] = manifest["fallback_method"]' in source
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