#!/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 "globals.env"

if [[ -z "${WORK_DIR:-}" ]]; then
    source "registry.sh"
fi

source "lib/scaffold.sh"
source "lib/git-crypt.sh"
source "providers/${PROVIDER}.sh"

step "Processing Genome Registry"

for entry in "${GENOMES[@]}"; do
    # 4-field format: name|description|linked_repo|cross_source linked_repo optional (may be empty); cross_source defaults to "no".
    IFS='|' read -r GENOME_NAME GENOME_DESC GENOME_LINKED GENOME_CROSS_SOURCE <<< "$entry"
    GENOME_CROSS_SOURCE="${GENOME_CROSS_SOURCE:-no}"
    export GENOME_NAME GENOME_DESC GENOME_LINKED GENOME_CROSS_SOURCE

    info "Processing: ${GENOME_NAME} (cross_source: ${GENOME_CROSS_SOURCE})..."

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

        git submodule add "${SSH_URL}" "${GENOME_NAME}"

        cd "${GENOME_NAME}"

        git switch -C main

        # 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
        gcrypt_export_key "${GENOME_NAME}"
        gcrypt_print_key_instructions "${GENOME_NAME}"

        cd "${WORK_DIR}/${MASTER_REPO}"
        git add .gitmodules "${GENOME_NAME}"
        git diff --cached --quiet || git commit -m "chore: register submodule ${GENOME_NAME}"
        git push

        # Commit the submodule reference in the master repo
        cd "${WORK_DIR}/${MASTER_REPO}"
        git commit -m "feat: add ${GENOME_NAME} as submodule"
        git push origin main
    fi
done

success "Genome provisioning completed."