from pathlib import Path

from genomic_consultant.orchestration.phase1_pipeline import run_phase1_pipeline


def test_phase1_pipeline_with_existing_tsv():
    root = Path(__file__).resolve().parents[1]
    tsv = root / "sample_data/example_annotated.tsv"
    panel = root / "configs/panel.example.json"
    acmg = root / "configs/acmg_config.example.yaml"
    result = run_phase1_pipeline(
        samples=None,
        reference_fasta=None,
        workdir=root / "runtime",
        output_prefix="demo",
        acmg_config_path=acmg,
        max_af=0.05,
        panel_path=panel,
        phenotype_id=None,
        phenotype_mapping=None,
        report_format="markdown",
        existing_tsv=tsv,
        skip_call=True,
        skip_annotate=True,
    )
    assert "Panel Report" in result.panel_report
    assert result.tsv_path == tsv