from __future__ import annotations

from apps.web.vue3.main import ExecuteRequest
from gfa_core.mas.agents.planning_v2 import PlanningAgentV2
from gfa_core.mas.stage_capabilities import CAPABILITIES
from gfa_core.mas.stage_catalog import EXECUTABLE_STAGES, STAGE_DEPENDENCIES
from gfa_core.mas.tools.stage_tools import StageToolRegistry


def test_wgs_gvcf_combine_vertical_registration_is_exact() -> None:
    assert STAGE_DEPENDENCIES["wgs_gvcf_combine"] == [
        "wgs_haplotype_calling",
        "wgs_index",
    ]
    assert "wgs_gvcf_combine" in EXECUTABLE_STAGES
    capability = CAPABILITIES["wgs_gvcf_combine"]
    assert {item.role for item in capability.consumes} == {
        "gvcf",
        "gvcf_index",
        "reference_fasta",
        "reference_fai",
        "reference_dict",
    }
    assert {item.role for item in capability.provides} == {
        "combined_gvcf",
        "combined_gvcf_index",
        "combine_log",
    }
    definition = next(
        item
        for item in StageToolRegistry.STAGE_DEFINITIONS
        if item["id"] == "wgs_gvcf_combine"
    )
    assert definition["script"] == "run_wgs_gvcf_combine.py"
    assert definition["conda_env"] == "ASAW"
    assert capability.env == "ASAW"
    assert definition["required_inputs"] == [
        "wgs_haplotype_manifest",
        "wgs_index_manifest",
    ]
    assert PlanningAgentV2.REQUIRED_INPUTS["wgs_gvcf_combine"] == []


def test_api_contract_carries_stage07_authorities_and_gatk() -> None:
    request = ExecuteRequest(
        stage="wgs_gvcf_combine",
        wgsHaplotypeManifest=(
            "final/Cohort.wgs_haplotype_calling.manifest.json"
        ),
        wgsIndexManifest="final/Cohort.wgs_index.manifest.json",
        wgsGatk="/opt/gatk",
    )
    assert request.wgsHaplotypeManifest.endswith(
        ".wgs_haplotype_calling.manifest.json"
    )
    assert request.wgsIndexManifest.endswith(".wgs_index.manifest.json")
    assert request.wgsGatk == "/opt/gatk"