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

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 "${GENOMES[@]}"; do
    # Parse name and description from the array
    IFS='|' read -r GENOME_NAME GENOME_DESC <<< "$entry"
    export GENOME_NAME GENOME_DESC

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

    # 1. Remote Provisioning (Idempotent: skips if exists)
    provider_create_repo "${GENOME_NAME}" "${GENOME_DESC}" "true"

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

    if [ ! -d "${GENOME_PATH}" ]; then
        info "Creating local directory and initializing scaffold..."
        mkdir -p "${GENOME_PATH}"
        cd "${GENOME_PATH}"
        git init

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

        # Create directory structure and apply templates
        scaffold_genome "."
        install_precommit_hook "."

        # Initial commit and push to remote
        git add .
        git commit -m "feat: initial scaffold for ${GENOME_NAME}"

        SSH_URL=$(provider_ssh_url "${GENOME_NAME}")
        git remote add origin "${SSH_URL}"
        git push -u origin main

        # Export the AES key for the user to back up
        gcrypt_export_key "${GENOME_NAME}"

        # 2. Link as submodule in the Master repository
        cd "${WORK_DIR}/${MASTER_REPO}"
        info "Linking ${GENOME_NAME} as a submodule..."
        git submodule add "${SSH_URL}" "${GENOME_NAME}"
        git add .gitmodules "${GENOME_NAME}"
        git commit -m "feat: link submodule ${GENOME_NAME}"
    else
        warn "Genome directory '${GENOME_NAME}' already exists. Skipping local setup."
    fi
done