mosaic

#!/bin/bash

# Mosaic CLI wrapper script for Docker
# This script enables seamless usage of the Mosaic CLI through Docker
#
# Usage: ./mosaic [mosaic-arguments]
#
# Examples:
#   ./mosaic --help
#   ./mosaic --slide-path /path/to/slide.svs --output-dir /path/to/output
#   ./mosaic --slide-csv /path/to/slides.csv --output-dir /path/to/output
#
# Requirements:
#   - Docker installed and running
#   - NVIDIA Docker runtime (for GPU support)
#   - HF_TOKEN environment variable set
#   - Docker image pulled: docker pull tomp/mosaic-gradio
#
# Note: When using --slide-csv, the CSV file and all referenced slides should be
#       in the same directory tree. Slides can be in subdirectories relative to
#       the CSV file location.

DOCKER_IMAGE="tomp/mosaic-gradio"
USE_GPU=true

die () { echo "FATAL: $*" >&2; exit 1; }

# Check if Docker is available
command -v docker >/dev/null 2>&1 || die "Docker is not installed or not in PATH"

# Check if HF_TOKEN is set
[[ -n $HF_TOKEN ]] || die "HF_TOKEN environment variable is not set. Please set it to your HuggingFace access token."

# Check if nvidia runtime is available
if docker info 2>/dev/null | grep -q nvidia; then
    USE_GPU=true
else
    echo "Warning: NVIDIA Docker runtime not detected. Running without GPU support." >&2
    echo "         To enable GPU support, install the NVIDIA Container Toolkit." >&2
    USE_GPU=false
fi

# Parse arguments to identify paths that need to be mounted
VOLUME_MOUNTS=()
ARGS=()

while [[ $# -gt 0 ]]; do
    ARG="$1"
    case "$ARG" in
        --slide-path)
            shift
            SLIDE_PATH="$1"
            if [[ -n "$SLIDE_PATH" ]]; then
                # Convert to absolute path
                SLIDE_PATH=$(readlink -f "$SLIDE_PATH")
                SLIDE_DIR=$(dirname "$SLIDE_PATH")
                SLIDE_FILE=$(basename "$SLIDE_PATH")
                # Mount the directory containing the slide
                VOLUME_MOUNTS+=("-v" "$SLIDE_DIR:/mnt/slides:ro")
                # Pass the container path to mosaic
                ARGS+=("--slide-path" "/mnt/slides/$SLIDE_FILE")
            fi
            shift
            ;;
        --slide-csv)
            shift
            CSV_PATH="$1"
            if [[ -n "$CSV_PATH" ]]; then
                # Convert to absolute path
                CSV_PATH=$(readlink -f "$CSV_PATH")
                CSV_DIR=$(dirname "$CSV_PATH")
                CSV_FILE=$(basename "$CSV_PATH")
                # Mount the parent directory of CSV (to allow slides in subdirs)
                # This allows the CSV to reference slides with relative paths
                VOLUME_MOUNTS+=("-v" "$CSV_DIR:/mnt/data:ro")
                # Pass the container path to mosaic
                ARGS+=("--slide-csv" "/mnt/data/$CSV_FILE")
            fi
            shift
            ;;
        --output-dir)
            shift
            OUTPUT_DIR="$1"
            if [[ -n "$OUTPUT_DIR" ]]; then
                # Convert to absolute path and create if it doesn't exist
                mkdir -p "$OUTPUT_DIR"
                OUTPUT_DIR=$(readlink -f "$OUTPUT_DIR")
                # Mount the output directory
                VOLUME_MOUNTS+=("-v" "$OUTPUT_DIR:/mnt/output")
                # Pass the container path to mosaic
                ARGS+=("--output-dir" "/mnt/output")
            fi
            shift
            ;;
        *)
            # Pass through all other arguments
            ARGS+=("$ARG")
            shift
            ;;
    esac
done

# Remove duplicate volume mounts
UNIQUE_MOUNTS=$(printf '%s\n' "${VOLUME_MOUNTS[@]}" | awk '!seen[$0]++')
VOLUME_ARGS=()
while IFS= read -r mount; do
    [[ -n "$mount" ]] && VOLUME_ARGS+=("$mount")
done <<< "$UNIQUE_MOUNTS"

# Run the Docker container with the mosaic CLI
# Override the entrypoint to run mosaic command instead of gradio_app
GPU_ARGS=()
if [ "$USE_GPU" = true ]; then
    GPU_ARGS+=("--gpus=all" "--runtime=nvidia")
fi

# Get current user ID and group ID to ensure output files have correct ownership
USER_ID=$(id -u)
GROUP_ID=$(id -g)

docker run --rm \
    "${GPU_ARGS[@]}" \
    --user "${USER_ID}:${GROUP_ID}" \
    --env HF_TOKEN="${HF_TOKEN}" \
    --shm-size=500m \
    "${VOLUME_ARGS[@]}" \
    --entrypoint mosaic \
    "$DOCKER_IMAGE" \
    "${ARGS[@]}"