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# MedicalTranscription
## 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.
* 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/medical_transcription eval MedicalTranscription.Release.precompute_code_vectors`. This will prepare the vectors in the database if they are not present.
## 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/medical_transcription`
4. Run a container with: `docker run --env-file ./.env -p 4000:4000 headwayio/medical_transcription`
### Caveats
You may need to make a few changes to get the app running in Docker at the moment:
- In `lib/medical_transcription/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
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