#!/usr/bin/env bash
# Migrate existing chr1 results from the old flat layout to the new per-chrom layout.
# Idempotent — safe to run twice; will only move files that exist at the old path.
#
# Old layout:                          New layout:
#   results/h1_representation/        results/h1_representation/chr1/
#     model.pt                          model.pt
#     gm12878_emb.npy                   gm12878_emb.npy
#     imr90_emb.npy                     imr90_emb.npy
#     metrics.json                      metrics.json
#     evaluation.json                   evaluation.json
#     figures/                          figures/
#   compartments/        (unchanged - stays at top level, filenames per-chrom)
#
# Usage: bash scripts/migrate_chr1_layout.sh
set -euo pipefail

REPO="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
cd "$REPO"

move_if_exists() {
    local src="$1" dst="$2"
    if [ -e "$src" ]; then
        mkdir -p "$(dirname "$dst")"
        echo "  $src -> $dst"
        mv "$src" "$dst"
    fi
}

echo "=== Migrating H1 chr1 results ==="
mkdir -p results/h1_representation/chr1
for f in model.pt gm12878_emb.npy imr90_emb.npy metrics.json evaluation.json; do
    move_if_exists "results/h1_representation/$f" "results/h1_representation/chr1/$f"
done
move_if_exists "results/h1_representation/figures" "results/h1_representation/chr1/figures"

echo ""
echo "=== Migrating H2 chr1 results ==="
mkdir -p results/h2_rewiring/chr1
for f in model.pt control_emb.npy treated_emb.npy \
         drift_full.npy drift_short.npy drift_long.npy \
         anchor_mask.npy anchor_mode.npy null_distribution.npy \
         drift_stats.json metrics.json; do
    move_if_exists "results/h2_rewiring/$f" "results/h2_rewiring/chr1/$f"
done
move_if_exists "results/h2_rewiring/figures" "results/h2_rewiring/chr1/figures"

echo ""
echo "=== Migrating H3 chr1 results ==="
mkdir -p results/h3_longrange/chr1
for d in local_only longrange_only full_const local_const longrange_const; do
    move_if_exists "results/h3_longrange/$d" "results/h3_longrange/chr1/$d"
done
for f in ablation_comparison.json cross_ablation.json; do
    move_if_exists "results/h3_longrange/$f" "results/h3_longrange/chr1/$f"
done
move_if_exists "results/h3_longrange/figures" "results/h3_longrange/chr1/figures"

echo ""
echo "=== Migration complete ==="
echo "Compartments stay at results/h1_representation/compartments/ (per-chrom in filename)"