#!/usr/bin/env python3
# Copyright 2026 Emile de Bruyn
# SPDX-License-Identifier: Apache-2.0

"""Make an isolated MotifBench-compatible working copy."""
import argparse
import csv
import shutil
import subprocess
import tempfile
from pathlib import Path

from validate_release import ROOT, residues, validate

UPSTREAM_COMMIT = "d5a714c6a376c701e29dfa66d42a1b13c5e339e0"


def adapt_pdb(source, destination, redesign):
    with source.open() as inp, destination.open("w") as out:
        for line in inp:
            if line.startswith("ATOM  "):
                key = (line[21], int(line[22:26]))
                if key in redesign:
                    if line[12:16].strip() not in {"N", "CA", "C", "O"}:
                        continue
                    line = line[:17] + "UNK" + line[20:]
            out.write(line)


def prepare(upstream, dest):
    upstream = upstream.resolve(strict=True)
    dest = dest.resolve()
    if dest.exists() or dest == upstream or upstream in dest.parents:
        raise ValueError("destination must be a new directory outside the upstream checkout")
    if not dest.parent.is_dir():
        raise ValueError("destination parent directory must already exist")
    commit = subprocess.check_output(
        ["git", "-C", str(upstream), "rev-parse", "HEAD"], text=True
    ).strip()
    if commit != UPSTREAM_COMMIT:
        raise ValueError(f"expected MotifBench commit {UPSTREAM_COMMIT}, found {commit}")
    status = subprocess.check_output(
        ["git", "-C", str(upstream), "status", "--porcelain"], text=True
    )
    if status:
        raise ValueError("MotifBench checkout must be clean")
    validate()
    with (ROOT / "test_cases.csv").open(newline="") as handle:
        cases = list(csv.DictReader(handle))
    with (ROOT / "contig_specifications.csv").open(newline="") as handle:
        reader = csv.DictReader(handle)
        specs = list(reader)
    names = {row["pdb_id"]: f"{i:02d}_{row['pdb_id']}" for i, row in enumerate(cases, 1)}
    with tempfile.TemporaryDirectory(prefix=".bilby-motifbench-", dir=dest.parent) as temp:
        work = Path(temp) / "work"
        shutil.copytree(upstream, work, ignore=shutil.ignore_patterns(".git", "motif_pdbs"))
        (work / "motif_pdbs").mkdir()
        shutil.copy2(ROOT / "test_cases.csv", work / "test_cases.csv")
        for row in cases:
            case = row["pdb_id"]
            adapt_pdb(ROOT / "motif_pdbs" / f"{case}.pdb",
                      work / "motif_pdbs" / f"{names[case]}.pdb",
                      residues(row["redesign_idcs"]))
        with (work / "example" / "contig_specifications.csv").open("w", newline="") as handle:
            writer = csv.DictWriter(handle, fieldnames=["problem", "length", "contig"],
                                    extrasaction="ignore")
            writer.writeheader()
            for row in specs:
                row["problem"] = names[row["problem"]]
                writer.writerow(row)
        work.rename(dest)
    print(f"Created {dest} with {len(cases)} adapted cases; original checkout unchanged.")


def main():
    parser = argparse.ArgumentParser(description=__doc__)
    parser.add_argument("upstream", type=Path, help="clean pinned MotifBench checkout")
    parser.add_argument("destination", type=Path, help="new working directory")
    args = parser.parse_args()
    prepare(args.upstream, args.destination)


if __name__ == "__main__":
    main()