#!/usr/bin/env bash
# =============================================================================
# scripts/add-genome.sh
# Helper to add a single new genome to the existing infrastructure.
# =============================================================================

set -euo pipefail
source "lib/output.sh"
source "globals.env"
source "registry.sh"

GENOME_NAME="${1:-}"
GENOME_DESC="${2:-}"
GENOME_LINKED="${3:-}"      # optional: linked project repo reference
GENOME_CROSS_SOURCE="${4:-no}" # optional: cross_source flag (default: no)

# 1. Check mandatory arguments first
if [[ -z "$GENOME_NAME" || -z "$GENOME_DESC" ]]; then
    error "Missing arguments."
    echo "Usage: $0 <genome-name> <description> [linked-repo] [cross_source]"
    echo "  cross_source: yes|no (default: no)"
    exit 1
fi

# 2. Then validate the flag if a non-default value was passed
if [[ "$GENOME_CROSS_SOURCE" != "yes" && "$GENOME_CROSS_SOURCE" != "no" ]]; then
    error "Invalid cross_source value: $GENOME_CROSS_SOURCE"
    echo "cross_source must be 'yes' or 'no'"
    exit 1
fi

step "Adding New Genome: ${GENOME_NAME}"

# Build a 4-field registry entry (linked_repo may be empty, cross_source defaults to no)
GENOMES=("${GENOME_NAME}|${GENOME_DESC}|${GENOME_LINKED}|${GENOME_CROSS_SOURCE}")

# NOTE — Maintenance smell
# We source setup-genomes.sh as a library/orchestrator hybrid. This works because:
#   - registry.sh is guarded against double-source (idempotent guard)
#   - setup-genomes.sh checks WORK_DIR before re-sourcing registry.sh
#   - GENOMES is built locally just before the source, so it is not clobbered
# However, sourcing an orchestration script as a library makes the control flow
# harder to trace. If this grows, refactor into a shared function (e.g. setup_one_genome)
# called by both add-genome.sh and setup-genomes.sh.

source "scripts/setup-genomes.sh"

success "Genome '${GENOME_NAME}' added and linked successfully!"