README.md

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 from your browser.

Ready to run in production? Please check our deployment guides.

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