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_joint_genotyping_vertical_registration_is_exact() -> None:
    assert STAGE_DEPENDENCIES["wgs_joint_genotyping"] == [
        "wgs_gvcf_combine",
        "wgs_index",
    ]
    assert "wgs_joint_genotyping" in EXECUTABLE_STAGES
    capability = CAPABILITIES["wgs_joint_genotyping"]
    assert {item.role for item in capability.consumes} == {
        "combined_gvcf",
        "combined_gvcf_index",
        "reference_fasta",
        "reference_fai",
        "reference_dict",
    }
    assert {item.role for item in capability.provides} == {
        "joint_vcf",
        "joint_vcf_index",
        "joint_summary",
        "joint_log",
    }
    definition = next(
        item
        for item in StageToolRegistry.STAGE_DEFINITIONS
        if item["id"] == "wgs_joint_genotyping"
    )
    assert definition["script"] == "run_wgs_joint_genotyping.py"
    assert definition["conda_env"] == "ASAW"
    assert capability.env == "ASAW"
    assert definition["required_inputs"] == [
        "wgs_combine_manifest",
        "wgs_index_manifest",
    ]
    assert PlanningAgentV2.REQUIRED_INPUTS["wgs_joint_genotyping"] == []


def test_api_contract_carries_stage08_authorities_tool_and_parameters() -> None:
    request = ExecuteRequest(
        stage="wgs_joint_genotyping",
        wgsCombineManifest="final/Cohort.wgs_gvcf_combine.manifest.json",
        wgsIndexManifest="final/Cohort.wgs_index.manifest.json",
        wgsGatk="/opt/gatk",
        wgsMaxAlternateAlleles=6,
        wgsCallingThreshold=10,
        wgsIncludeNonVariantSites=False,
    )
    assert request.wgsCombineManifest.endswith(
        ".wgs_gvcf_combine.manifest.json"
    )
    assert request.wgsIndexManifest.endswith(".wgs_index.manifest.json")
    assert request.wgsGatk == "/opt/gatk"
    assert request.wgsMaxAlternateAlleles == 6
    assert request.wgsCallingThreshold == 10
    assert request.wgsIncludeNonVariantSites is False