from __future__ import annotations

import pytest

from gfa_core.wgs_scientific_identity import (
    WgsIdentityError,
    build_wgs_analysis_id,
    build_wgs_reference_id,
    build_wgs_sample_set_id,
    sha256_file,
)


def test_analysis_identity_changes_with_method():
    args = {
        "stage": "wgs_variant_filter",
        "upstream_sha256s": ["a" * 64],
        "parameters": {"qd": 2.0},
        "tool_versions": {"gatk": "4.6", "bcftools": "1.20"},
    }
    assert build_wgs_analysis_id(**args, method="gatk") != build_wgs_analysis_id(
        **args, method="bcftools"
    )


def test_wgs_sample_set_identity_uses_fastq_contents(tmp_path):
    r1 = tmp_path / "S1_R1.fastq.gz"
    r2 = tmp_path / "S1_R2.fastq.gz"
    r1.write_bytes(b"r1-v1")
    r2.write_bytes(b"r2-v1")
    samples = build_wgs_sample_set_id([{"sample_id": "S1", "r1": str(r1), "r2": str(r2)}])
    assert samples.startswith("wgs-samples:")
    assert len(sha256_file(r1)) == 64
    r1.write_bytes(b"r1-v2")
    assert samples != build_wgs_sample_set_id([{"sample_id": "S1", "r1": str(r1), "r2": str(r2)}])


def test_wgs_identity_prefixes_are_canonical_and_validate_sha256s():
    reference = build_wgs_reference_id("a" * 64)
    assert reference.startswith("wgs-reference:")
    with pytest.raises(WgsIdentityError, match="SHA256"):
        build_wgs_analysis_id(
            stage="wgs_qc",
            upstream_sha256s=["not-a-sha"],
            parameters={},
            tool_versions={},
            method="fastqc",
        )


def test_wgs_sample_set_identity_rejects_parser_bypassing_invalid_records(tmp_path):
    r1 = tmp_path / "S1_R1.fastq"
    r2 = tmp_path / "S1_R2.fastq"
    r1.write_bytes(b"r1")
    r2.write_bytes(b"r2")
    valid = {"sample_id": "S1", "r1": str(r1), "r2": str(r2)}
    invalid_records = [
        {**valid, "sample_id": "unsafe/id"},
        {**valid, "r2": str(r1)},
        {**valid, "r2": ""},
        [valid, valid],
    ]
    for invalid in invalid_records:
        with pytest.raises(WgsIdentityError):
            build_wgs_sample_set_id(invalid if isinstance(invalid, list) else [invalid])
    with pytest.raises(WgsIdentityError, match="unique"):
        build_wgs_sample_set_id([valid, valid])


def test_wgs_analysis_identity_canonicalizes_upstream_hash_order_and_requires_tool_evidence():
    args = {
        "stage": "wgs_variant_filter",
        "parameters": {"qd": 2.0},
        "tool_versions": {"gatk": "4.6"},
        "method": "gatk",
    }
    assert build_wgs_analysis_id(**args, upstream_sha256s=["a" * 64, "b" * 64]) == build_wgs_analysis_id(
        **args, upstream_sha256s=["b" * 64, "a" * 64]
    )
    for tool_versions in ({}, {"": "4.6"}, {"gatk": ""}):
        with pytest.raises(WgsIdentityError, match="tool"):
            build_wgs_analysis_id(**{**args, "tool_versions": tool_versions}, upstream_sha256s=["a" * 64])


@pytest.mark.parametrize("invalid_name", ["S1_R1.txt", "S1_R1.empty.fastq", "reads", "missing.fastq"])
def test_wgs_sample_set_identity_rejects_noncanonical_fastq_paths(tmp_path, invalid_name):
    r2 = tmp_path / "S1_R2.fastq"
    r2.write_bytes(b"r2")
    r1 = tmp_path / invalid_name
    if invalid_name.endswith(".txt"):
        r1.write_bytes(b"r1")
    elif invalid_name.endswith(".empty.fastq"):
        r1.write_bytes(b"")
    elif invalid_name == "reads":
        r1.mkdir()
    with pytest.raises(WgsIdentityError):
        build_wgs_sample_set_id([{"sample_id": "S1", "r1": str(r1), "r2": str(r2)}])


def test_wgs_sample_set_identity_rejects_lexical_alias_mates(tmp_path):
    r1 = tmp_path / "S1_R1.fastq"
    r1.write_bytes(b"r1")
    alias_dir = tmp_path / "alias"
    alias_dir.mkdir()
    lexical_alias = alias_dir / ".." / "S1_R1.fastq"
    with pytest.raises(WgsIdentityError, match="different"):
        build_wgs_sample_set_id([{"sample_id": "S1", "r1": str(r1), "r2": str(lexical_alias)}])


def test_wgs_sample_set_identity_rejects_symlink_alias_mates(tmp_path):
    r1 = tmp_path / "S1_R1.fastq"
    r1.write_bytes(b"r1")
    symlink = tmp_path / "S1_R2.fastq"
    symlink.symlink_to(r1)
    with pytest.raises(WgsIdentityError, match="different"):
        build_wgs_sample_set_id([{"sample_id": "S1", "r1": str(r1), "r2": str(symlink)}])