# Initial Commit Contents

This file defines the deployed contents of the lightweight ENCODE Space and its
separate private runtime-artifact bucket.

## Application and deployment

- `README.md` — project overview and Hugging Face Space metadata.
- `docs/ai/COMMIT_CONTENTS.md` — this auditable release inventory.
- `Dockerfile` — CPU-only backend container listening on port 7860.
- `netlify.toml` and `deploy/` — Netlify build/Drop package that proxies the
  static frontend's API requests to the Hugging Face Space backend.
- `.dockerignore` — excludes development-only files from container builds.
- `.gitignore` — excludes `data/` and the generated parts of `outputs/`.
- `src/requirements.txt` — pinned Python runtime dependencies.

## Backend

- `src/backend/app.py` — FastAPI application and HTTP endpoints.
- `src/backend/codesearch.py` — medical-code retrieval.
- `src/backend/retriever.py` — phenotype retrieval using Vidul's fine-tuned
  embeddings.
- `src/backend/encode.py` — annotation and response handling.
- `src/backend/graph.py` — phenotype detail graph construction.
- `src/backend/models.py` — registry of the retrieval models the UI may offer.
- `src/backend/rxnav.py` — conservative, cached RxNAV/RxNorm completion for
  medication mappings that are absent from packaged outputs.
- `src/backend/__init__.py` — backend package marker.

## Frontend

- `src/frontend/index.html` — browser application shell.
- `src/frontend/app.js` — search, review, and annotation behavior.
- `src/frontend/styles.css` — application styling.

## Private bucket: runtime model and indexes

- `outputs/models/bge_ft_va/` — Vidul's fine-tuned model weights, tokenizer,
  and configuration.
- `outputs/indexes/bge_ft_va/icd_index/` — diagnosis FAISS index and metadata.
- `outputs/indexes/bge_ft_va/med_index/` — medication FAISS index and metadata.
- `outputs/indexes/bge_ft_va/ndc_index/` — NDC FAISS index and metadata.
- `outputs/indexes/bge_ft_va/labchem_index/` — LOINC/lab FAISS index and metadata.
- `outputs/indexes/bge_ft_va/cpt_index/` — procedure FAISS index and metadata.
- `outputs/embeddings/bge_ft_va/code.npy`
- `outputs/embeddings/bge_ft_va/code_meta.json`
- `outputs/embeddings/bge_ft_va/config.json`
- `outputs/embeddings/bge_ft_va/metadata.npy`
- `outputs/embeddings/bge_ft_va/metadata_ids.json`

## Private bucket: runtime phenotype records

- `outputs/canonical/algorithm_components.jsonl`
- `outputs/canonical/canonical_phenotypes.jsonl`
- `outputs/canonical/cipher_links.jsonl`
- `outputs/canonical/code_descriptions.jsonl`
- `outputs/canonical/lab_loinc_map.jsonl`
- `outputs/canonical/loinc_terms.jsonl`
- `outputs/canonical/med_ingredient_map.jsonl`
- `outputs/canonical/rxcui_ingredient_map.jsonl`

## Verification

- `tests/test_retrieval.py` — focused tests for the retained dense-retrieval
  path.
- `tests/test_rxnav_and_deployment.py` — RxNAV provenance and Netlify Drop
  deployment checks.

## Explicitly excluded

Everything under `data/` (raw VA exports, the original application bundle, and
the LOINC and RxNorm distribution archives) and everything the pipeline writes to
`outputs/` — training, evaluation, reranker, facet, profiling, and cached
results, generated demos, and annotations — is excluded from the Space upload,
along with local environments, credentials, and editor settings.

The release contains one retrieval path: Vidul's fine-tuned model, prebuilt
embeddings, and exact dense search. Large runtime assets are stored in
`hf://buckets/hiasgnpsadgd/encode-artifacts` and mounted read-only at
`/home/user/app/outputs`; they are not committed to the Space repository or
copied into the Docker image.