"""API-level smoke tests using FastAPI's TestClient."""
import os
import sys

sys.path.insert(0, os.path.dirname(os.path.dirname(os.path.abspath(__file__))))

from fastapi.testclient import TestClient  # noqa: E402
from api.main import app  # noqa: E402

client = TestClient(app)


def test_health():
    r = client.get("/api/health")
    assert r.status_code == 200
    assert r.json()["status"] == "ok"


def test_index_page_renders():
    r = client.get("/")
    assert r.status_code == 200
    assert "Plant DNA Designer" in r.text


def test_traits_partial():
    r = client.get("/traits/rice")
    assert r.status_code == 200
    assert "Bacterial blight resistance" in r.text


def test_traits_unknown_species_404():
    assert client.get("/traits/nope").status_code == 404


def test_design_endpoint():
    r = client.post("/api/design", json={
        "species": "rice", "gc_target": 45, "traits": ["Drought tolerance"],
        "codon_table": "rice", "protein": "MKAILV", "cas_type": "Cas9 (NGG)",
        "grna_num": 3, "population_size": 20, "generations": 10, "num_sequences": 1,
    })
    assert r.status_code == 200, r.text
    body = r.json()
    assert body["sequence"].startswith("ACGTGG")  # required motif prefix
    assert {"gc_content", "melting_temp", "molecular_weight", "cai", "mrna_stability"}.issubset(set(body["metrics"]))


def test_design_rejects_bad_protein():
    r = client.post("/api/design", json={
        "species": "rice", "traits": ["Drought tolerance"], "protein": "MKZZZ",
        "population_size": 20, "generations": 5,
    })
    assert r.status_code == 422  # pydantic validation


def test_design_requires_trait():
    r = client.post("/api/design", json={
        "species": "rice", "traits": [], "protein": "MKAILV",
        "population_size": 20, "generations": 10,
    })
    assert r.status_code == 400


def test_analyze_endpoint():
    r = client.post("/api/analyze", json={"dna": "TATAATCAATGATAGGCC", "codon_table": "rice"})
    assert r.status_code == 200
    assert "metrics" in r.json() and "motifs" in r.json()


def test_export_fasta():
    r = client.get("/api/export/fasta", params={"dna": "ATGAAAGCT", "name": "rice"})
    assert r.status_code == 200
    assert r.text.startswith(">")


def test_mechanism_endpoint():
    r = client.get("/api/mechanism/Drought tolerance")
    assert r.status_code == 200
    body = r.json()
    assert body["primary_effector"]["gene"] == "DREB2A"
    assert "effectors" in body


def test_mechanism_endpoint_unknown_404():
    assert client.get("/api/mechanism/not a trait").status_code == 404


def test_design_without_protein_uses_trait_effector():
    # No protein supplied → resolved from the trait's validated effector.
    r = client.post("/api/design", json={
        "species": "rice", "gc_target": 45, "traits": ["Drought tolerance"],
        "codon_table": "rice", "cas_type": "Cas9 (NGG)",
        "grna_num": 3, "population_size": 20, "generations": 10, "num_sequences": 1,
    })
    assert r.status_code == 200, r.text
    bt = r.json()["biological_target"]
    assert bt["primary"]["gene"] == "DREB2A"
    assert bt["encoded_protein_source"] == "trait-derived effector"


def test_design_pareto_mode_returns_front():
    r = client.post("/api/design", json={
        "species": "rice", "gc_target": 50, "traits": ["Drought tolerance"],
        "codon_table": "rice", "cas_type": "Cas9 (NGG)", "grna_num": 3,
        "population_size": 30, "generations": 15, "pareto": True,
    })
    assert r.status_code == 200, r.text
    body = r.json()
    assert body["pareto_front"] and len(body["pareto_front"]) >= 1
    assert "axes" in body["pareto_front"][0]
    assert "pareto" in body["ga_report"]["mode"]


def test_design_includes_report_card():
    r = client.post("/api/design", json={
        "species": "rice", "gc_target": 45, "traits": ["Drought tolerance"],
        "codon_table": "rice", "cas_type": "Cas9 (NGG)", "grna_num": 3,
        "population_size": 20, "generations": 10, "num_sequences": 1,
    })
    assert r.status_code == 200, r.text
    card = r.json()["report_card"]
    assert card["grade"] in ("Strong", "Good", "Needs work")
    assert 0 <= card["score"] <= 100
    labels = {it["label"] for it in card["items"]}
    assert {"Expression strength", "Plant safety", "Silencing risk", "Synthesis-ready"}.issubset(labels)
    for it in card["items"]:
        assert it["status"] in ("good", "watch", "fix")