from __future__ import annotations

from gfa_core.mas.tools.stage_identity import merge_manifest_identity_params, resolve_stage_identity


def test_postflight_manifest_identity_overrides_stale_task_identity(tmp_path):
    workspace_root = tmp_path / "workspace"
    (workspace_root / "job_manifest" / "final").mkdir(parents=True)
    stale_params = {
        "prefix": "Si.HDZIP",
        "scopeId": "HDZIP.target-Si.target_only",
        "scopeMode": "target_only",
        "analysisRoute": "single_species",
        "memberSetId": "HDZIP.target-Si.target_only:single_species:all_members",
        "targetSpecies": ["Si"],
        "referenceSpecies": [],
    }
    manifest = {
        "stage": "combo",
        "prefix": "Si.HDZIP",
        "scope_id": "HDZIP.target-Si.ref-At.target_plus_reference",
        "analysis_route": "subfamily_evidence",
        "member_set_id": "HDZIP.target-Si.ref-At.target_plus_reference:subfamily_evidence:domain_refined",
        "stage_context": {
            "scope_mode": "target_plus_reference",
            "family": "HDZIP",
            "target_species": ["Si"],
            "reference_species": ["At"],
            "selected_species": ["Si", "At"],
        },
    }

    merged = merge_manifest_identity_params(stale_params, manifest)
    identity = resolve_stage_identity(
        stage="combo",
        prefix="Si.HDZIP",
        params=merged,
        job_id="job_manifest",
        workspace_root=workspace_root,
    )

    assert identity.scope_id == "HDZIP.target-Si.ref-At.target_plus_reference"
    assert identity.scope_mode == "target_plus_reference"
    assert identity.analysis_route == "subfamily_evidence"
    assert identity.member_set_id == "HDZIP.target-Si.ref-At.target_plus_reference:subfamily_evidence:domain_refined"
    assert identity.reference_species == ["At"]


def test_postflight_manifest_identity_preserves_unscoped_regular_combo():
    merged = merge_manifest_identity_params(
        {
            "prefix": "Ft.SPL",
            "scopeId": "SPL.target-Ft.target_only",
            "analysisRoute": "single_species",
            "memberSetId": "SPL.target-Ft.target_only:single_species:all_members",
        },
        {"stage": "combo", "prefix": "Ft.SPL", "status": "success"},
    )

    assert merged["prefix"] == "Ft.SPL"
    assert "scopeId" not in merged
    assert "scope_id" not in merged
    assert "analysisRoute" not in merged
    assert "analysis_route" not in merged
    assert "memberSetId" not in merged
    assert "member_set_id" not in merged


def test_postflight_manifest_identity_merges_wgs_index_identity():
    manifest = {
        "stage": "wgs_index",
        "prefix": "Os",
        "status": "success",
        "wgs_reference_id": "wgs-reference:" + "b" * 64,
        "wgs_analysis_id": "wgs-analysis:" + "c" * 64,
    }

    merged = merge_manifest_identity_params({"prefix": "Os"}, manifest)

    assert merged["wgsReferenceId"] == manifest["wgs_reference_id"]
    assert merged["wgsAnalysisId"] == manifest["wgs_analysis_id"]