from __future__ import annotations

import re

import pytest

from gfa_core.gwas_scientific_identity import (
    GwasIdentityError,
    build_covariate_scope_id,
    build_identity_recipe,
    build_phenotype_scope_id,
    materialize_stage_identity,
    new_run_id,
)


SHA_A = "a" * 64
SHA_B = "b" * 64
SHA_C = "c" * 64


def test_phenotype_scope_is_canonical_and_sensitive_to_selected_trait() -> None:
    first = build_phenotype_scope_id(
        phenotype_sha256=SHA_A,
        sample_column="ID",
        trait_column="GC_BLUP",
        trait_name="heading_days",
        retained_sample_ids=["S1", "S2"],
    )
    same = build_phenotype_scope_id(
        trait_name="heading_days",
        retained_sample_ids=["S1", "S2"],
        trait_column="GC_BLUP",
        sample_column="ID",
        phenotype_sha256=SHA_A,
    )
    changed = build_phenotype_scope_id(
        phenotype_sha256=SHA_A,
        sample_column="ID",
        trait_column="other_trait",
        trait_name="heading_days",
        retained_sample_ids=["S1", "S2"],
    )
    assert first == same
    assert first.startswith("phenotype:")
    assert changed != first


def test_covariate_scope_requires_verified_source_genotype() -> None:
    with pytest.raises(GwasIdentityError, match="source genotype"):
        build_covariate_scope_id(
            q_sha256=SHA_A,
            fam_sha256=SHA_B,
            source_genotype_scope_id="",
            k=2,
        )
    scope = build_covariate_scope_id(
        q_sha256=SHA_A,
        fam_sha256=SHA_B,
        source_genotype_scope_id=f"genotype:{SHA_C}",
        k=2,
    )
    assert scope.startswith("covariate:")


def test_recipe_does_not_fabricate_downstream_identity() -> None:
    recipe = build_identity_recipe(
        stage="gwas_mlm",
        required_artifact_roles=["tassel_hapmap", "kinship_matrix", "trait_table", "covariate_table"],
        parameters={"p3d": True},
        method_version="tassel_mlm.v1",
        contract_version="v1",
        tool_versions={"tassel": "5.2.96"},
    )
    assert "analysis_scope_id" not in recipe
    assert "model_scope_id" not in recipe
    with pytest.raises(GwasIdentityError, match="missing authoritative artifact"):
        materialize_stage_identity(
            recipe,
            upstream_artifacts={"tassel_hapmap": {"sha256": SHA_A}},
            data_scopes={"genotype_scope_id": f"genotype:{SHA_A}"},
        )


def test_materialized_model_identity_uses_every_authoritative_hash() -> None:
    roles = ["tassel_hapmap", "kinship_matrix", "trait_table", "covariate_table"]
    recipe = build_identity_recipe(
        stage="gwas_mlm",
        required_artifact_roles=roles,
        parameters={"p3d": True},
        method_version="tassel_mlm.v1",
        contract_version="v1",
        tool_versions={"tassel": "5.2.96"},
    )
    artifacts = {role: {"sha256": str(index) * 64} for index, role in enumerate(roles, start=1)}
    scopes = {
        "genotype_scope_id": f"genotype:{SHA_A}",
        "phenotype_scope_id": f"phenotype:{SHA_B}",
        "covariate_scope_id": f"covariate:{SHA_C}",
    }
    identity = materialize_stage_identity(recipe, artifacts, scopes)
    changed = {role: dict(value) for role, value in artifacts.items()}
    changed["kinship_matrix"]["sha256"] = "9" * 64
    changed_identity = materialize_stage_identity(recipe, changed, scopes)

    assert identity["model_scope_id"].startswith("gwas-model:")
    assert identity["analysis_scope_id"].startswith("gwas-analysis:")
    assert identity["model_scope_id"] != changed_identity["model_scope_id"]
    assert identity["analysis_scope_id"] != changed_identity["analysis_scope_id"]


def test_plot_has_own_analysis_scope_and_preserves_source_model_scope() -> None:
    recipe = build_identity_recipe(
        stage="gwas_plot",
        required_artifact_roles=["mlm_association"],
        parameters={"format": "png"},
        method_version="cmplot.v1",
        contract_version="v1",
        tool_versions={"CMplot": "4.5.1"},
    )
    source = f"gwas-model:{SHA_A}"
    identity = materialize_stage_identity(
        recipe,
        {"mlm_association": {"sha256": SHA_B}},
        {"source_model_scope_id": source},
    )
    assert identity["source_model_scope_id"] == source
    assert identity["analysis_scope_id"].startswith("gwas-analysis:")
    assert identity["analysis_scope_id"] != source


def test_run_id_is_stage_scoped_and_unique() -> None:
    first = new_run_id("gwas_mlm")
    second = new_run_id("gwas_mlm")
    assert re.fullmatch(r"gwas_mlm_\d{8}T\d{6}Z_[0-9a-f]{8}", first)
    assert first != second