siyuan-ai-companion

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siyuan-ai-companion

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A companion application to use SiYuan note as a knowledge base with OpenAI APIs

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<div align="center">
<a href="https://www.github.com/Firefox2100/siyuan-ai-companion">
<img src="docs/assets/logo-with-background.svg" alt="SiYuan AI Companion logo" height="144">
</a>
<h1>SiYuan AI Companion</h1>

[中文简体](README_zh_CN.md)

A companion service to use SiYuan note as a knowledge base with OpenAI APIs.

![Login Page](https://raw.githubusercontent.com/Firefox2100/siyuan-ai-companion/main/docs/assets/login-screen.png)
![Chat Page](https://raw.githubusercontent.com/Firefox2100/siyuan-ai-companion/main/docs/assets/chat-interface.png)

## License and disclaimer

This project is licensed under the GNU General Public License v3.0 (GPL-3.0). See the [licence file](LICENSE) for details.

This project is not affiliated with or endorsed by SiYuan or OpenAI. It uses their API format, but is not guaranteed to be compatible with their services. If the API format is changed, this project may not work as expected. Even if it works, there is still a possibility that it may adversely affect your data, or your OpenAI service account. Use at your own risk, and be sure to understand what you are doing before using this project.

You are welcomed to inspect the code, propose changes, report bugs, or engage or support the project in any way.

## Motivation and design considerations

This project is designed to solve one of my problems: I switched to SiYuan from Obsidian, and I wanted to use my notes as a knowledge vault for my local running LLMs. For Obsidian, this is as simple as embedding the files and using them for RAG; however, SiYuan stores its data in a JSON-based database, and the raw files contain a lot of metadata that is not useful for LLMs. This project is designed as a proxy to OpenAI compatible APIs, by providing a layer to perform the RAG and add the note contents to the prompt before sending it to the LLM service. It needs to:

- Be minimally intrusive on SiYuan: SiYuan imposes a file-renaming based conflict detection feature. It repeatedly rename a file and check for duplications to ensure that it has exclusive access to its workspace. This companion app needs to work around that restriction to prevent SiYuan from exiting.
- Able to self-host: The stack should be simple enough and uses minimal resources to allow self-hosting on a mid to low-end server.
- Handle as much as data format and structure in SiYuan as possible: SiYuan is not a Markdown based note-taking app, and it allows for more complicated data types and relationships between them. This project should be able to handle as much of that as possible, and provide a way to extract the data in a format that is useful for LLMs.

Based on the considerations, it decided to:

- Instead of reading the raw files of SiYuan and risk corrupting the database, it will use the SiYuan API to read the data. SiYuan exposes a series of REST API, including one SQL-like query endpoint. This project uses the SQL endpoint to read the data block-wise, without ever touching the raw files. This however **requires a SiYuan instance to be running when using the companion app**, for this I recommend deploying a docker container with the SiYuan image.
- Use Qdrant as the vector database to store the embeddings. Qdrant is a high-performance vector database that is easy to set up and use. It provides an official docker image, and can be used in-memory or with persistent storage, depending on the scale and development need.
- Use Quart and APScheduler to provide an ASGI server and a background non-blocking scheduler to handle the API requests and the background tasks.

## Features

- [x] Bundling an UI to easily interact with the service
- [x] Support for OpenAI API proxy
- [x] Support for getting notes from SiYuan
- [x] Support for querying note blocks via last updated time
- [x] Support for embedding note blocks and store them in Qdrant
- [x] Support for querying Qdrant for similar blocks, reconstruct the original note by querying SiYuan API, and generate prompt for OpenAI API
- [x] Support for saving the chat session back into a notebook
- [x] Support for listing all asset files in SiYuan server for integration
- [x] Support for audio transcription and diarisation using local models. This is due to lack of good options for audio transcription and diarisation in self-hosted stacks.

## Installation

This project can be used as a docker image, or run from source code. To run it from source code, install dependencies with pip (preferably in a virtual environment):

```bash
pip install .
```

If used in production, it's recommended to use a production-ready ASGI server, and a standalone Qdrant instance. Assuming the Qdrant is running on `localhost:6333`, and the SiYuan instance is running on `localhost:6806`, you can run the server with:

```bash
export SIYUAN_URL="http://localhost:6806"
export SIYUAN_TOKEN="your-siyuan-token"
export QDRANT_LOCATION="http://localhost:6333"
export QDRANT_COLLECTION_NAME="siyuan_ai_companion"
export OPENAI_URL="https://api.openai.com/v1/"

pip install hypercorn
hypercorn siyuan_ai_companion.asgi:application
```

If using docker, the image has been uploaded to Docker Hub, and can be used with:

```yaml
services:
  siyuan-ai-companion:
    image: firefox2100/siyuan-ai-companion:testing
    restart: always
    container_name: siyuan-ai-companion
    environment:
      SIYUAN_URL: "http://siyuan:6806"
      SIYUAN_TOKEN: "your-siyuan-token"
      QDRANT_LOCATION: "http://qdrant:6333"
      QDRANT_COLLECTION_NAME: "siyuan_ai_companion"
      OPENAI_URL: "https://api.openai.com/v1/"
      COMPANION_TOKEN: "your-companion-token"
      HUGGINGFACE_HUB_TOKEN: "your-huggingface-token"
      # CUDA_VISIBLE_DEVICES: "" # Leave empty to use CPU
      # COMPANION_LOGGING_LEVEL: "INFO"
    ports:
      - "8000:8000"

qdrant:
    image: qdrant/qdrant:latest
    restart: always
    container_name: qdrant
    configs:
      - source: qdrant_config
        target: /qdrant/config/production.yaml
    volumes:
      - ./qdrant_data:/qdrant/storage

siyuan:
    image: b3log/siyuan:latest
    command: [ '--workspace=/siyuan/workspace/', '--accessAuthCode=your-auth-code' ]
    ports:
      - 6806:6806
    volumes:
      - /siyuan/workspace:/siyuan/workspace
    restart: unless-stopped
    environment:
      # A list of time zone identifiers can be found at https://en.wikipedia.org/wiki/List_of_tz_database_time_zones
      - TZ=${YOUR_TIME_ZONE}
      - PUID=${YOUR_USER_PUID}  # Customize user ID
      - PGID=${YOUR_USER_PGID}  # Customize group ID

configs:
  qdrant_config:
    content: |
      log_level: INFO
```

## Configuration and usage

The application uses environment variables to configure the connection to SiYuan and Qdrant. The following environment variables are used:

- **SIYUAN_URL**: The URL of the SiYuan instance. This is required to read the data from SiYuan. It should be a URL with protocol, e.g. `http://localhost:6806`.
- **SIYUAN_TOKEN**: The token to access the SiYuan API. This is required to read the data from SiYuan. This is NOT the docker auth code, but the one you see within the setting page.
- **QDRANT_LOCATION**: The URL of the Qdrant instance. This is required to store the embeddings. If using in-memory Qdrant, this can be set to `:memory:`.
- **QDRANT_COLLECTION_NAME**: The name of the collection to use in Qdrant. This is required to store the embeddings. If the collection does not exist, it will be created automatically.
- **OPENAI_URL**: The URL of the OpenAI compatible API. This does not need to be reachable from the outside. So if you host your own LLM service, you can set this to a local address, or even a docker network address. As long as it's reachable from the container.
- **OPENAI_TOKEN**: The token to send to OpenAI API, if applicable. If left unset, no `Authorization` header will be sent. Most of the self-hosted LLM services do not require this, but the official OpenAI API does.
- **COMPANION_TOKEN**: The token to access the companion API. Because this companion app has access to, and will respond with, your note content and asset files, it's necessary to secure it if served over the internet. Leave unset to disable authentication.
- **WHISPER_WORKERS**: The number of workers to use for Whisper (via `faster-whisper` library). They will be spawned in a thread pool. When configuring this, take into consideration hyper-threading, how many cores available, and the fact that `pyannote` may use CPU if no GPU is available.
- **HUGGINGFACE_HUB_TOKEN**: The access token to download `pyannote` models from hugging face hub. The models have their own EULA, and you must accept them before downloading, or the download will fail even with a token.
- **SIYUAN_TRANSCRIBE_NOTEBOOK**: The default notebook to store the transcribed audio data into. This can be left empty if you guarantee that each transcription request will have a notebook specified in the request.
- **FORCE_UPDATE_INDEX**: Set this to `true` to force the companion to rebuild the index everytime it restarts. This is useful for development, recovering from a corrupted index, or if the vector index is not persistent in the database.

All requests sent to the API are passed to the OpenAI compatible API, with all original headers. This service does not check whether your request format is correct, have the right headers or anything related to the API, except for the prompt field.

This service uses only `SELECT` queries at the SQL endpoint. It does not modify the existing data, only read, download and create new notes. In theory, it should not affect the note data or damage it in any way. However, it is recommended to back up your data before using this service, just in case. If unforeseen errors occur, it may send more than one request to the OpenAI API, which may incur additional costs; if possible, use a separate API key when using this service, one that is rate limited or have a low spending cost.

## How to use the features

### Authenticate the requests

If the `COMPANION_TOKEN` is set, all requests must carry an `Authorization` header with the token, such as:

```bash
curl -H "Authorization: Bearer your-token-here" https://your.companion.com/assets/
```

The token can be set as any string of any length that HTTP request can support.

If the upstream OpenAI service needs a token as well, this can be set in the environment variables as `OPENAI_TOKEN`. Before proxying the request, the service will remove the companion token (if any), and if this is set, it will add the `Authorization` header with the token to the request. The companion token is never sent anywhere else.

### Retrieval-Augmented Generation (RAG)

The core feature of this service is to enable RAG on SiYuan notes. This does not require any user actions, and will be done automatically when you send a request for inference. Specifically:

This service will query SiYuan every 5 minutes to see if there's an update on the note content. Once found, it will use the updated content to regenerate the index and embeddings. This is done in the background, and will only generate for the updated (or newly created) blocks for minimal resource usage.

Upon receiving a request at `/openai/v1/completions` or `/openai/v1/chat/completions`, it will embed the prompt and query the Qdrant index for similar blocks. It will then retrieve the **whole note** containing the top 5 relevant blocks. It then segments the document based on the Markdown structure, and sends the most relevent segments to the LLM. Semantic segmentation is not yet implemented due to the heavy resource usage when segmenting the documents: processing a long passage may take minutes, if not hours, on a CPU-only setup.

### Transcribe audio files

As another feature I needed for myself, I added the ability to transcribe audio files. By sending a request to specify which asset audio file to transcribe, the service can automatically download it (and delete it once done), use `faster-whisper` and `pyannote` to transcribe and diarise the audio, and store the result in a new note. The note will be created in the notebook specified in the request, or in the default notebook set in the environment variable `SIYUAN_TRANSCRIBE_NOTEBOOK`. The note will contain the transcription and the inferred speakers.

> **Note**: Using CLI or postman to trigger transcription is not ideal. I'm planning to build a UI for this service, or possibly a plugin for SiYuan note, to allow users to select the file or even chat directly with LLM via the endpoints exposed by this service. However I'm not familiar with SiYuan plugin development, typescript or Vue.js. If you're interested in helping out it will be much appreciated.

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