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    "# BioDT School & Hackathon 2025\n",
    "\n",
    "This is the central repository of training material that will be used during the BioDT School and Hackathon 2025.\n",
    "\n",
    "\n",
    "## NaaVRE Documentation\n",
    "\n",
    "The documentation of the NaaVRE project can be found [here](https://naavre.net/).\n",
    "\n",
    "\n",
    "## Saving files in NaaVRE workflows with MinIO\n",
    "\n",
    "## MinIO Setup\n",
    "\n",
    "1. Open [MinIO login](https://scruffy.lab.uvalight.net:9001/login)\n",
    "2. Click on **\"Login with SSO (vre)\"**\n",
    "\n",
    "![img.png](static/img.png)\n",
    "\n",
    "**⚠ Warning:**  \n",
    "This service is intended for testing and development purposes.  \n",
    "It is maintained by the LifeWatch VLIC team as “best effort.”  \n",
    "- There is **no guarantee** that your data is safe or that the service will be available.  \n",
    "- **Use at your own risk** and keep backups of important data.\n",
    "\n",
    "---\n",
    "\n",
    "\n",
    "### MinIO Access\n",
    "Choose an identity provider and login:\n",
    "\n",
    "![img.png](static/img2.png)\n",
    "\n",
    "- **Buckets available:**\n",
    "  - `naa-vre-public` (read-only)\n",
    "  - `naa-vre-user-data` (read/write access to a folder with your username, e.g., `[email protected]`)\n",
    "\n",
    "---\n",
    "\n",
    "![img.png](static/img3.png)\n",
    "\n",
    "### Create an Access Key\n",
    "\n",
    "1. Select **\"Access Keys\"**\n",
    "2. Click **\"Create access key\"**\n",
    "3. Click **\"Create\"**\n",
    "4. **Save the keys for later!**\n",
    "\n",
    "---\n",
    "\n",
    "![img.png](static/img4.png)\n",
    "\n",
    "![img.png](static/img5.png)\n",
    "\n",
    "![img.png](static/img6.png)\n",
    "\n",
    "## Use MinIO in NaaVRE\n",
    "\n",
    "1. Open your favorite VRE (see **NaaVRE Getting Started tutorial**)\n",
    "2. Create a new notebook\n",
    "\n",
    "---\n",
    "\n",
    "![img.png](static/img7.png)\n",
    "\n",
    "## R Example\n",
    "\n",
    "```r\n",
    "# Configuration (do not containerize this cell)\n",
    "param_minio_endpoint  = \"scruffy.lab.uvalight.net:9000\"\n",
    "param_minio_region  = \"nl-uvalight\"\n",
    "param_minio_user_prefix  = \"[email protected]\"  # Your personal folder in the naa-vre-user-data bucket\n",
    "secret_minio_access_key   = \"2ny7v9bdV6kVwh7n93SZ\"\n",
    "secret_minio_secret_key   = \"an1SP4eYLx4Awzn42lgVUmeHouPrgNp7cRcBLvrB\"\n",
    "```\n",
    "```r\n",
    "# Access MinIO files\n",
    "install.packages(\"aws.s3\")\n",
    "library(\"aws.s3\")\n",
    "\n",
    "Sys.setenv(\n",
    "  \"AWS_S3_ENDPOINT\"  = param_minio_endpoint,\n",
    "  \"AWS_DEFAULT_REGION\" = param_minio_region,\n",
    "  \"AWS_ACCESS_KEY_ID\" = secret_minio_access_key,\n",
    "  \"AWS_SECRET_ACCESS_KEY\" = secret_minio_secret_key\n",
    ")\n",
    "\n",
    "# List existing buckets\n",
    "bucketlist()\n",
    "\n",
    "# List files in your personal folder in MinIO\n",
    "get_bucket_df(bucket = \"naa-vre-user-data\", prefix = paste0(param_minio_user_prefix, \"/\"))\n",
    "\n",
    "# Upload file to MinIO\n",
    "put_object(\n",
    "  bucket = \"naa-vre-user-data\",\n",
    "  file = \"myfile_local.csv\",\n",
    "  object = paste0(param_minio_user_prefix, \"/myfile.csv\")\n",
    ")\n",
    "\n",
    "# Download file from MinIO\n",
    "save_object(\n",
    "  bucket = \"naa-vre-user-data\",\n",
    "  object = paste0(param_minio_user_prefix, \"/myfile.csv\"),\n",
    "  file = \"myfile_downloaded.csv\"\n",
    ")\n",
    "\n",
    "```\n",
    "\n",
    "## Python example\n",
    "\n",
    "```python\n",
    "# Configuration (do not containerize this cell)\n",
    "param_minio_endpoint = \"scruffy.lab.uvalight.net:9000\"\n",
    "param_minio_user_prefix = \"[email protected]\"  # Your personal folder in the naa-vre-user-data bucket in MinIO\n",
    "secret_minio_access_key = \"2ny7v9bdV6kVwh7n93SZ\"\n",
    "secret_minio_secret_key = \"an1SP4eYLx4Awzn42lgVUmeHouPrgNp7cRcBLvrB\"\n",
    "```\n",
    "\n",
    "```python\n",
    "# Access MinIO files\n",
    "from minio import Minio\n",
    "mc = Minio(endpoint=param_minio_endpoint,\n",
    "           access_key=secret_minio_access_key,\n",
    "           secret_key=secret_minio_secret_key)\n",
    "\n",
    "# List existing buckets: get a list of all available buckets\n",
    "mc.list_buckets()\n",
    "\n",
    "# List files in bucket: get a list of files in a given bucket. For bucket `naa-vre-user-data`, only list files in your personal folder\n",
    "objects = mc.list_objects(\"naa-vre-user-data\", prefix=f\"{param_minio_user_prefix}/\")\n",
    "for obj in objects:\n",
    "    print(obj.object_name)\n",
    "\n",
    "# Upload file to bucket: uploads `myfile_local.csv` to your personal folder on MinIO as `myfile.csv`\n",
    "mc.fput_object(bucket_name=\"naa-vre-user-data\", file_path=\"myfile_local.csv\", object_name=f\"{param_minio_user_prefix}/myfile.csv\")\n",
    "\n",
    "# Download file from bucket: download `myfile.csv` from your personal folder on MinIO and save it locally as `myfile_downloaded.csv`\n",
    "mc.fget_object(bucket_name=\"naa-vre-user-data\", object_name=f\"{param_minio_user_prefix}/myfile.csv\", file_path=\"myfile_downloaded.csv\")\n",
    "```\n",
    "\n",
    "## License\n",
    "\n",
    "This project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details.\n"
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