| --- |
| title: MediCode |
| sdk: docker |
| pinned: false |
| --- |
| |
| # Medicode |
|
|
| ## Getting started |
|
|
| ### Prerequisites |
|
|
| 1. ffmpeg for audio processing in Bumblebee's speech-to-text serving: `brew install ffmpeg`. |
| 2. Postgres and pgvector for storing data and vector embeddings: `brew install pgvector`. |
|
|
| ### Running the server |
|
|
| To start your Phoenix server: |
|
|
| - Run `mix setup` to install and setup dependencies |
| - Run `mix build_code_vectors` to download the ICD-9 codelist, precompute vectors, and store the results in the database. |
| - PDF generation is managed with [ChromicPDF](https://github.com/bitcrowd/chromic_pdf/tree/2c13cd2690204e6a30d817e72a3d1ef13e8a2441) which assumes an executable is available at [these locations](https://github.com/bitcrowd/chromic_pdf/blob/2c13cd2690204e6a30d817e72a3d1ef13e8a2441/lib/chromic_pdf/pdf/chrome_runner.ex#L64). If you are having trouble getting Chrome to launch, this [StackExchange](https://apple.stackexchange.com/a/467415) was useful. |
| - Start Phoenix endpoint with `mix phx.server` or inside IEx with `iex -S mix phx.server` |
|
|
| Now you can visit [`localhost:4000`](http://localhost:4000) from your browser. |
|
|
| Ready to run in production? Please [check our deployment guides](https://hexdocs.pm/phoenix/deployment.html). |
|
|
| ## Deployment |
|
|
| The app is configured to deploy to Fly.io via a `fly.toml` file. To deploy, run `fly deploy` within the app's directory. |
|
|
| ### Precomputing code vectors |
|
|
| To build the code vectors for the ICD-9 codelist for the deployed environment: |
|
|
| 1. Connect to the server with `fly ssh console`. |
| 2. Run `/app/bin/medicode eval Medicode.Release.precompute_code_vectors`. This will prepare the vectors in the database if they are not present. |
|
|
| ### Livebook |
|
|
| In addition to connecting to the deployed application via `iex`, Livebook supports connecting to the running application. Connecting a Livebook instance to the deployed application involves the following: |
|
|
| 1. Install and setup Wireguard with a peer connection for Fly.io: [Step by Step](https://fly.io/docs/networking/private-networking/#install-your-wireguard-app) |
| 2. Install and start Livebook: [Livebook.dev](https://livebook.dev/) |
| 3. [Connecting Livebook to a Production App](https://fly.io/docs/elixir/advanced-guides/connect-livebook-to-your-app/) requires a node name and cookie value: |
|
|
| - Node name: `medicode@myipfromfly` ("myipfromfly" can be retrieved with `fly ips private --app medical-transcription-cpu`) |
| - Cookie value: `0gfxcPtwryKxI2O1N0eFAg9p4MJGC-oUGShgj_wgvNEGiba5EDEJFA==` (this value is set in `fly.toml`) |
|
|
| ## Run in Docker |
|
|
| 1. Create a local volume: `docker volume create ml-data` |
| 2. Ensure the volume is writeable: `docker run --rm -v ml-data:/data busybox /bin/sh -c 'touch /data/.initialized && chmod 1777 /data'`. More background: |
|
|
| - What the initial `1` for `chmod` means: <https://www.linuxnix.com/sticky-bit-set-linux/> |
| - How to update the permissions of a mounted volume: <https://serverfault.com/a/984599> |
|
|
| 3. Build the image with: `docker build . -t headwayio/medicode` |
| 4. Run a container with: `docker run --env-file ./.env -p 4000:4000 headwayio/medicode` |
|
|
| ### Caveats |
|
|
| You may need to make a few changes to get the app running in Docker at the moment: |
|
|
| - In `lib/medicode/application.ex`, comment out the `DNSCluster` child spec. |
| - In `rel/env.sh.eex`, comment out the `ERL_AFLAGS`, `RELEASE_DISTRIBUTION`, and `RELEASE_NODE` environment variables. |
|
|
| ## Learn more |
|
|
| - Official website: <https://www.phoenixframework.org/> |
| - Guides: <https://hexdocs.pm/phoenix/overview.html> |
| - Docs: <https://hexdocs.pm/phoenix> |
| - Forum: <https://elixirforum.com/c/phoenix-forum> |
| - Source: <https://github.com/phoenixframework/phoenix> |
|
|
