Blame for README.md

---
title: New Graph Visualization
emoji: 🕸️
colorFrom: blue
colorTo: green
sdk: docker
app_port: 7860
startup_duration_timeout: 1h
pinned: false
---

# New Graph Visualization

Interactive clinical graph explorer (Dash + Cytoscape). **FalkorDB** and the Dash app run in one Docker container — same pattern as [UMLS Graph Explorer](https://huggingface.co/spaces/Raapid/umls-graph-explorer-falkordb).

On each cold start the container loads **1.28M nodes** and **7.6M edges** from staging parquet via GRAPH.BULK (~2–5 min), then serves the UI on port **7860**.

**Live Space:** [Raapid/new-graph-visualization](https://huggingface.co/spaces/Raapid/new-graph-visualization)

Default seed: `A27828238` · Default hop depth: **2**

## Features

- Explore by AUI or CUI with hop depth 1–15 (HIER_ISA + MRREL)
- Toggle MRHIER, semantic (MRREL), AUI→CUI, same-CUI edges
- Path finder between two AUIs
- SAB / TUI / TTY / **category** filters (category from `graph_nodes.parquet`)
- Layout controls (cose-bilkent recommended)

## Hugging Face Space (Docker)

| Variable | Default | Description |
|----------|---------|-------------|
| `PORT` | `7860` | Dash listen port |
| `FALKORDB_GRAPH` | `clinical_graph` | Graph name |
| `REBUILD_GRAPH` | `1` | Reload graph on container start |
| `SKIP_GRAPH_BUILD` | `0` | Set `1` to skip load (debug) |
| `STAGING_DIR` | `/home/user/app/falkor_staging` | Staging parquet directory |
| `REDIS_ARGS` | `--maxmemory 9gb …` | Embedded redis-server memory |

Set Space hardware to **CPU basic** (16 GB RAM) or higher.

### One-time data upload (not in git — ~235 MB total)

```bash
SPACE=Raapid/new-graph-visualization
BASE="/media/anurag/Hard Disk/Graph New"

hf upload $SPACE \
  "$BASE/falkor_staging/concepts.parquet" falkor_staging/concepts.parquet \
  "$BASE/falkor_staging/mrrel_edges.parquet" falkor_staging/mrrel_edges.parquet \
  "$BASE/falkor_staging/hier_edges.parquet" falkor_staging/hier_edges.parquet \
  "$BASE/graph_nodes.parquet" graph_nodes.parquet \
  --repo-type space \
  --commit-message "Add graph staging parquets"
```

## Local Docker

```bash
cd "/media/anurag/Hard Disk/Graph New"
docker build -t new-graph-viz .
docker run --rm --memory=16g -p 7860:7860 new-graph-viz
```

Open [http://localhost:7860](http://localhost:7860).

Requires `falkor_staging/*.parquet` and `graph_nodes.parquet` in the build context (included if present; `bulk_csv/` is excluded via `.dockerignore`).

## Local dev (FalkorDB in separate container)

```bash
docker run -d --name clinical-falkordb -p 6380:6379 --memory 10g falkordb/falkordb:latest
export FALKORDB_PORT=6380 FALKORDB_GRAPH=clinical_graph
python3 build_falkor_graph.py --skip-prepare --rebuild --falkor-port 6380
export PORT=8050
python3 app.py
```

## Data

| File | Role |
|------|------|
| `falkor_staging/concepts.parquet` | FalkorDB Concept nodes |
| `falkor_staging/mrrel_edges.parquet` | MRREL semantic edges |
| `falkor_staging/hier_edges.parquet` | HIER_ISA (from MRHIER) |
| `graph_nodes.parquet` | Category metadata for sidebar filter |

FalkorDB node count (**1,278,278**) matches edge-connected nodes in parquet (orphan nodes excluded at load time).

## Project layout

```
Graph New/
├── app.py
├── graph_backend.py
├── Dockerfile
├── scripts/entrypoint.sh
├── falkor_load/           # GRAPH.BULK loader (container startup)
├── falkor_staging/        # staging parquet (upload to HF separately)
├── prepare_falkor_staging.py
├── build_falkor_graph.py  # local load helper
├── graph_nodes.parquet
├── assets/
└── requirements.txt
```

## Commands

```bash
# Setup
uv venv .venv && source .venv/bin/activate
uv pip install -r requirements.txt

# Rebuild staging from raw parquet
python3 prepare_falkor_staging.py --connected-only

# Load FalkorDB locally
FALKORDB_BULK_SOCKET_TIMEOUT_S=0 python3 build_falkor_graph.py --skip-prepare --rebuild --falkor-port 6380

# Run app
FALKORDB_PORT=6380 FALKORDB_GRAPH=clinical_graph python3 app.py
```