#!/usr/bin/env bash
# =============================================================================
# scripts/setup-genomes.sh
# Iterates through the GENOMES registry to provision remote and local repos.
# =============================================================================

set -euo pipefail
source "lib/output.sh"
source "config.env"
source "lib/scaffold.sh"
source "lib/git-crypt.sh"
source "providers/${PROVIDER}.sh"

step "Processing Genome Registry"

for entry in "${GENOMES[@]}"; do
    IFS='|' read -r GENOME_NAME GENOME_DESC <<< "$entry"
    export GENOME_NAME GENOME_DESC

    info "Processing: ${GENOME_NAME}..."

    # 1. Remote Creation (Idempotent)
    provider_create_repo "${GENOME_NAME}" "${GENOME_DESC}" "true"
    SSH_URL=$(provider_ssh_url "${GENOME_NAME}")

    GENOME_PATH="${WORK_DIR}/${MASTER_REPO}/${GENOME_NAME}"

    if [ ! -d "${GENOME_PATH}" ]; then
        cd "${WORK_DIR}/${MASTER_REPO}"
        info "Linking ${GENOME_NAME} as a submodule..."

        # FIX BUG 1: Adding the submodule clones the empty remote repository
        git submodule add "${SSH_URL}" "${GENOME_NAME}"

        cd "${GENOME_NAME}"

        # IMPORTANT: Initialize git-crypt BEFORE creating any files
        gcrypt_init

        scaffold_genome "."
        install_precommit_hook "."

        # Initial genome push
        git add .
        git commit -m "feat: initial scaffold and git-crypt init for ${GENOME_NAME}"
        git push -u origin main

        # Key export and instructions (Fix Obs B)
        gcrypt_export_key "${GENOME_NAME}"
        gcrypt_print_key_instructions "${GENOME_NAME}"

        # Return to master to consolidate the submodule addition
        cd "${WORK_DIR}/${MASTER_REPO}"
    fi
done

success "Genome provisioning completed."