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--- |
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title: MediCode |
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sdk: docker |
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pinned: false |
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--- |
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# Medicode |
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## Getting started |
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### Prerequisites |
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1. ffmpeg for audio processing in Bumblebee's speech-to-text serving: `brew install ffmpeg`. |
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2. Postgres and pgvector for storing data and vector embeddings: `brew install pgvector`. |
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### Running the server |
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To start your Phoenix server: |
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- Run `mix setup` to install and setup dependencies |
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- Run `mix build_code_vectors` to download the ICD-9 codelist, precompute vectors, and store the results in the database. |
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- 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. |
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- Start Phoenix endpoint with `mix phx.server` or inside IEx with `iex -S mix phx.server` |
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Now you can visit [`localhost:4000`](http://localhost:4000) from your browser. |
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Ready to run in production? Please [check our deployment guides](https://hexdocs.pm/phoenix/deployment.html). |
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## Deployment |
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The app is configured to deploy to Fly.io via a `fly.toml` file. To deploy, run `fly deploy` within the app's directory. |
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### Precomputing code vectors |
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To build the code vectors for the ICD-9 codelist for the deployed environment: |
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1. Connect to the server with `fly ssh console`. |
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2. Run `/app/bin/medicode eval Medicode.Release.precompute_code_vectors`. This will prepare the vectors in the database if they are not present. |
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### Livebook |
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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: |
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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) |
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2. Install and start Livebook: [Livebook.dev](https://livebook.dev/) |
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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: |
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- Node name: `medicode@myipfromfly` ("myipfromfly" can be retrieved with `fly ips private --app medical-transcription-cpu`) |
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- Cookie value: `0gfxcPtwryKxI2O1N0eFAg9p4MJGC-oUGShgj_wgvNEGiba5EDEJFA==` (this value is set in `fly.toml`) |
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## Run in Docker |
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1. Create a local volume: `docker volume create ml-data` |
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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: |
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- What the initial `1` for `chmod` means: <https://www.linuxnix.com/sticky-bit-set-linux/> |
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- How to update the permissions of a mounted volume: <https://serverfault.com/a/984599> |
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3. Build the image with: `docker build . -t headwayio/medicode` |
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4. Run a container with: `docker run --env-file ./.env -p 4000:4000 headwayio/medicode` |
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### Caveats |
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You may need to make a few changes to get the app running in Docker at the moment: |
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- In `lib/medicode/application.ex`, comment out the `DNSCluster` child spec. |
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- In `rel/env.sh.eex`, comment out the `ERL_AFLAGS`, `RELEASE_DISTRIBUTION`, and `RELEASE_NODE` environment variables. |
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## Learn more |
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- Official website: <https://www.phoenixframework.org/> |
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- Guides: <https://hexdocs.pm/phoenix/overview.html> |
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- Docs: <https://hexdocs.pm/phoenix> |
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- Forum: <https://elixirforum.com/c/phoenix-forum> |
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- Source: <https://github.com/phoenixframework/phoenix> |
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