Visualizando todo grafo com anzograph

.env.example

@@ -0,0 +1,44 @@
+# TTL path used as a fallback by the owl-imports combiner when COMBINE_ENTRY_LOCATION is not set.
+TTL_PATH=/data/merged_ontologies_pruned_patched.ttl
+
+# Backend behavior
+INCLUDE_BNODES=false
+
+# Graph snapshot limits (used by Go backend defaults/validation)
+DEFAULT_NODE_LIMIT=800000
+DEFAULT_EDGE_LIMIT=2000000
+MAX_NODE_LIMIT=10000000
+MAX_EDGE_LIMIT=20000000
+
+# SPARQL paging: number of triples per batch (LIMIT/OFFSET)
+EDGE_BATCH_SIZE=100000
+
+# Owl imports combiner service (docker-compose `owl_imports_combiner`)
+COMBINE_OWL_IMPORTS_ON_START=true
+COMBINE_ENTRY_LOCATION=/data/vkg.ttl
+COMBINE_OUTPUT_LOCATION=/data/vkg_full.ttl
+# COMBINE_OUTPUT_NAME=combined_ontology.ttl # Only used if COMBINE_OUTPUT_LOCATION is not set.
+COMBINE_FORCE=true
+
+# AnzoGraph / SPARQL endpoint settings
+SPARQL_HOST=http://anzograph:8080
+# SPARQL_ENDPOINT=http://anzograph:8080/sparql
+SPARQL_USER=admin
+SPARQL_PASS=Passw0rd1
+
+# File URI as seen by the AnzoGraph container (used by SPARQL `LOAD`) # Currently not used.
+SPARQL_DATA_FILE=file:///opt/shared-files/o3po.ttl # Currently not used.
+# SPARQL_GRAPH_IRI=http://example.org/graph
+
+# Startup behavior for AnzoGraph mode
+SPARQL_LOAD_ON_START=false
+SPARQL_CLEAR_ON_START=false
+SPARQL_READY_TIMEOUT_S=10
+
+# Dev UX
+CORS_ORIGINS=http://localhost:5173
+VITE_BACKEND_URL=http://backend:8000
+
+# Debugging
+LOG_SNAPSHOT_TIMINGS=false
+FREE_OS_MEMORY_AFTER_SNAPSHOT=false

.gitignore

@@ -1,4 +1,9 @@
 .direnv/
 .envrc
 .env
+backend/.env
+frontend/node_modules/
+frontend/dist/
+.npm/
+.vite/
 data/

README.md

@@ -1,67 +1,108 @@
-# Large Instanced Ontology Visualizer
+# Visualizador Instanciados
 
-An experimental visualizer designed to render and explore massive instanced ontologies (millions of nodes) with interactive performance.
+This repo is a Docker Compose stack for visualizing large RDF/OWL graphs stored in **AnzoGraph**. It includes:
 
-## 🚀 The Core Challenge
-Ontologies with millions of instances present a significant rendering challenge for traditional graph visualization tools. This project solves this by:
-1.  **Selective Rendering:** Only rendering up to a set limit of nodes (e.g., 2 million) at any given time.
-2.  **Adaptive Sampling:** When zoomed out, it provides a representative spatial sample of the nodes. When zoomed in, the number of nodes within the viewport naturally falls below the rendering limit, allowing for 100% detail with zero performance degradation.
-3.  **Spatial Indexing:** Using a custom Quadtree to manage millions of points in memory and efficiently determine visibility.
+- A **Go backend** that queries AnzoGraph via SPARQL and serves a cached graph snapshot + selection queries.
+- A **React/Vite frontend** that renders nodes/edges with WebGL2 and supports “selection query” + “graph query” modes.
+- A **Python one-shot service** to combine `owl:imports` into a single Turtle file.
+- An **AnzoGraph** container (SPARQL endpoint).
 
-## 🛠 Technical Architecture
+## Quick start (Docker Compose)
 
-### 1. Data Pipeline & AnzoGraph Integration
-The project features an automated pipeline to extract and prepare data from an **AnzoGraph** DB:
--   **SPARQL Extraction:** `scripts/fetch_from_db.ts` connects to AnzoGraph via its SPARQL endpoint. It fetches a seed set of subjects and their related triples, identifying "primary" nodes (objects of `rdf:type`).
--   **Graph Classification:** Instances are categorized to distinguish between classes and relationships.
--   **Force-Directed Layout:** `scripts/compute_layout.ts` calculates 2D positions for the nodes using a **Barnes-Hut** optimized force-directed simulation, ensuring scalability for large graphs.
-
-### 2. Quadtree Spatial Index
-To handle millions of nodes without per-frame object allocation:
--   **In-place Sorting:** The Quadtree (`src/quadtree.ts`) spatially sorts the raw `Float32Array` of positions at build-time.
--   **Index-Based Access:** Leaves store only the index ranges into the sorted array, pointing directly to the data sent to the GPU.
--   **Fast Lookups:** Used for both frustum culling and efficient "find node under cursor" calculations.
-
-### 3. WebGL 2 High-Performance Renderer
-The renderer (`src/renderer.ts`) is built for maximum throughput:
--   **`WEBGL_multi_draw` Extension:** Batches multiple leaf nodes into single draw calls, minimizing CPU overhead.
--   **Zero-Allocation Render Loop:** The frame loop uses pre-allocated typed arrays to prevent GC pauses.
--   **Dynamic Level of Detail (LOD):** 
-    -   **Points:** Always visible, with adaptive density based on zoom.
-    -   **Lines:** Automatically rendered when zoomed in deep enough to see individual relationships (< 20k visible nodes).
-    -   **Selection:** Interactive selection of nodes highlights immediate neighbors (incoming/outgoing edges).
-
-## 🚦 Getting Started
-
-### Prerequisites
--   Docker and Docker Compose
--   Node.js (for local development)
-
-### Deployment
-The project includes a `docker-compose.yml` that spins up both the **AnzoGraph** database and the visualizer app.
+1) Put your TTL file(s) in `./data/` (this folder is volume-mounted into AnzoGraph as `/opt/shared-files`).
+2) Optionally configure `.env` (see `.env.example`).
+3) Start the stack:
 
 ```bash
-# Start the services
-docker-compose up -d
-
-# Inside the app container, the following will run automatically:
-# 1. Fetch data from AnzoGraph (fetch_from_db.ts)
-# 2. Compute the 2D layout (compute_layout.ts)
-# 3. Start the Vite development server
+docker compose up --build
 ```
 
-The app will be available at `http://localhost:5173`.
+Then open the frontend:
 
-## 🖱 Interactions
--   **Drag:** Pan the view.
--   **Scroll:** Zoom in/out at the cursor position.
--   **Click:** Select a node to see its URI/Label and highlight its neighbors.
--   **HUD:** Real-time stats on FPS, nodes drawn, and current sampling ratio.
+- `http://localhost:5173`
 
-## TODO
--   **Positioning:** Use better algorithm to position nodes, trying to avoid as much as possible any edges crossing, but at the same time trying to keep the graph compact. 
--   **Positioning:** Decide how to handle classes which are both instances and classes. 
--   **Functionality:** Find every equipment with a specific property or that participate in a specific process.
--   **Functionality:** Find every equipment which is connecte to a well.
--   **Functionality:** Show every connection witin a specified depth.
--   **Functionality:** Show every element of a specific class.
+Stop everything:
+
+```bash
+docker compose down
+```
+
+## Services
+
+Defined in `docker-compose.yml`:
+
+- `anzograph` (image `cambridgesemantics/anzograph:latest`)
+  - Ports: `8080`, `8443`
+  - Shared files: `./data → /opt/shared-files`
+- `backend` (`./backend_go`)
+  - Port: `8000` (API under `/api/*`)
+  - Talks to AnzoGraph at `SPARQL_HOST` / `SPARQL_ENDPOINT`
+- `frontend` (`./frontend`)
+  - Port: `5173`
+  - Proxies `/api/*` to `VITE_BACKEND_URL`
+- `owl_imports_combiner` (`./python_services/owl_imports_combiner`)
+  - One-shot: optionally produces a combined TTL by following `owl:imports`
+
+Service READMEs:
+
+- `backend_go/README.md`
+- `frontend/README.md`
+- `python_services/owl_imports_combiner/README.md`
+- `anzograph/README.md`
+
+## Repo layout
+
+- `backend_go/` – Go API service (SPARQL → snapshot + selection queries)
+- `frontend/` – React/Vite WebGL renderer
+- `python_services/owl_imports_combiner/` – Python one-shot OWL imports combiner
+- `data/` – local shared volume for TTL inputs/outputs (gitignored)
+- `docker-compose.yml` – service wiring
+- `flake.nix` – optional Nix dev shell
+
+## Configuration
+
+This repo expects a local `.env` file (not committed). Start from `.env.example`.
+
+Common knobs:
+
+- Backend snapshot size: `DEFAULT_NODE_LIMIT`, `DEFAULT_EDGE_LIMIT`, `MAX_NODE_LIMIT`, `MAX_EDGE_LIMIT`
+- SPARQL connectivity: `SPARQL_HOST` or `SPARQL_ENDPOINT`, plus `SPARQL_USER` / `SPARQL_PASS`
+- Load data on backend startup: `SPARQL_LOAD_ON_START=true` with `SPARQL_DATA_FILE=file:///opt/shared-files/<file>.ttl`
+- Frontend → backend proxy: `VITE_BACKEND_URL`
+
+## API (backend)
+
+Base URL: `http://localhost:8000`
+
+- `GET /api/health` – liveness
+- `GET /api/stats` – snapshot stats (uses default limits)
+- `GET /api/graph` – graph snapshot
+  - Query params: `node_limit`, `edge_limit`, `graph_query_id`
+- `GET /api/graph_queries` – available graph snapshot modes (`graph_query_id` values)
+- `GET /api/selection_queries` – available selection-highlight modes (`query_id` values)
+- `POST /api/selection_query` – run a selection query for highlighted neighbors
+  - Body: `{"query_id":"neighbors","selected_ids":[...],"node_limit":...,"edge_limit":...,"graph_query_id":"default"}`
+- `POST /api/sparql` – raw SPARQL passthrough (debug/advanced)
+- `POST /api/neighbors` – legacy alias (same behavior as `query_id="neighbors"`)
+
+## Frontend UI
+
+- Mouse:
+  - Drag: pan
+  - Scroll: zoom
+  - Click: select nodes
+- **Top-right buttons:** “selection query” mode (how neighbors/highlights are computed for the current selection)
+- **Bottom-right buttons:** “graph query” mode (which SPARQL edge set is used to build the graph snapshot; switching reloads the graph)
+
+## Notes on performance/limits
+
+- The backend caches snapshots in memory; tune `DEFAULT_*_LIMIT` if memory is too high.
+- The frontend renders a sampled subset when zoomed out, and only draws edges when fewer than ~20k nodes are visible.
+
+## Nix dev shell (optional)
+
+If you use Nix, `flake.nix` provides a minimal `devShell`:
+
+```bash
+nix develop
+```

anzograph/README.md

@@ -0,0 +1,38 @@
+# AnzoGraph (Docker Compose service)
+
+This repo runs AnzoGraph as an external container image:
+
+- Image: `cambridgesemantics/anzograph:latest`
+- Ports: `8080` (HTTP), `8443` (HTTPS)
+- Volume: `./data → /opt/shared-files`
+
+The backend connects to AnzoGraph via:
+
+- `SPARQL_HOST` (default `http://anzograph:8080`) and the `/sparql` path, or
+- an explicit `SPARQL_ENDPOINT`
+
+## Persistence
+
+The `docker-compose.yml` config mounts named volumes into the AnzoGraph container so its state survives
+container recreation (e.g. `docker compose up --force-recreate`):
+
+- `anzograph_app_home → /opt/anzograph/app-home` (machine-id / user home)
+- `anzograph_persistence → /opt/anzograph/persistence` (database persistence dir)
+- `anzograph_config → /opt/anzograph/config` (settings + activation markers)
+- `anzograph_internal → /opt/anzograph/internal` (internal state, including EULA acceptance marker)
+
+To fully reset AnzoGraph state, remove volumes with `docker compose down -v`.
+
+## Loading data
+
+The backend can optionally load a TTL file on startup (after AnzoGraph is ready):
+
+- `SPARQL_LOAD_ON_START=true`
+- `SPARQL_DATA_FILE=file:///opt/shared-files/<file>.ttl`
+
+Because `./data` is mounted at `/opt/shared-files`, anything placed in `./data` is accessible via a `file:///opt/shared-files/...` URI.
+
+## Notes
+
+- Authentication defaults are configured via the backend env (`SPARQL_USER` / `SPARQL_PASS`).
+- The AnzoGraph container in this repo is not customized; consult the upstream image documentation for persistence, licensing, and advanced configuration.

backend_go/Dockerfile

@@ -0,0 +1,24 @@
+ARG GO_VERSION=1.24
+FROM golang:${GO_VERSION}-alpine AS builder
+
+WORKDIR /src
+
+COPY go.mod /src/go.mod
+
+RUN go mod download
+
+COPY . /src
+
+RUN CGO_ENABLED=0 GOOS=linux go build -trimpath -ldflags="-s -w" -o /out/backend ./
+
+FROM alpine:3.20
+
+RUN apk add --no-cache ca-certificates curl
+
+WORKDIR /app
+
+COPY --from=builder /out/backend /app/backend
+
+EXPOSE 8000
+
+CMD ["/app/backend"]

backend_go/README.md

@@ -0,0 +1,98 @@
+# Backend (Go) – Graph + Selection API
+
+This service exposes a small HTTP API for:
+
+- Building and caching a “graph snapshot” from AnzoGraph via SPARQL (`/api/graph`)
+- Returning available “graph query” and “selection query” modes
+- Running selection queries for the currently selected node IDs
+- (Optionally) issuing raw SPARQL passthrough for debugging
+
+## Run
+
+Via Docker Compose (recommended):
+
+```bash
+docker compose up --build backend
+```
+
+The backend listens on `:8000` (configurable via `LISTEN_ADDR`).
+
+## Configuration (env)
+
+See `backend_go/config.go` for the full set.
+
+Important variables:
+
+- Snapshot limits:
+  - `DEFAULT_NODE_LIMIT`, `DEFAULT_EDGE_LIMIT`
+  - `MAX_NODE_LIMIT`, `MAX_EDGE_LIMIT`
+- SPARQL connectivity:
+  - `SPARQL_HOST` (default `http://anzograph:8080`) or `SPARQL_ENDPOINT`
+  - `SPARQL_USER`, `SPARQL_PASS`
+- Startup behavior:
+  - `SPARQL_LOAD_ON_START`, `SPARQL_CLEAR_ON_START`
+  - `SPARQL_DATA_FILE` (typically `file:///opt/shared-files/<file>.ttl`)
+- Other:
+  - `INCLUDE_BNODES` (include blank nodes in snapshots)
+  - `CORS_ORIGINS`
+
+## Endpoints
+
+- `GET /api/health`
+- `GET /api/stats`
+- `GET /api/graph?node_limit=&edge_limit=&graph_query_id=`
+- `GET /api/graph_queries`
+- `GET /api/selection_queries`
+- `POST /api/selection_query`
+  - Body: `{"query_id":"neighbors","selected_ids":[1,2,3],"node_limit":...,"edge_limit":...,"graph_query_id":"default"}`
+- `POST /api/sparql` (raw passthrough)
+- `POST /api/neighbors` (legacy alias of `query_id="neighbors"`)
+
+## Graph snapshots
+
+Snapshots are built by:
+
+1) Running a SPARQL edge query (controlled by `graph_query_id`)
+2) Converting SPARQL bindings into dense integer node IDs + edge list
+3) Computing a layout and fetching optional `rdfs:label`
+
+Snapshots are cached in-memory keyed by:
+
+- `node_limit`, `edge_limit`, `INCLUDE_BNODES`, `graph_query_id`
+
+## Query registries
+
+### Graph query modes (`graph_query_id`)
+
+Stored under `backend_go/graph_queries/` and listed by `GET /api/graph_queries`.
+
+Built-in modes:
+
+- `default` – `rdf:type` (to `owl:Class`) + `rdfs:subClassOf`
+- `hierarchy` – `rdfs:subClassOf` only
+- `types` – `rdf:type` (to `owl:Class`) only
+
+To add a new mode:
+
+1) Add a new file under `backend_go/graph_queries/` that returns a SPARQL query selecting `?s ?p ?o`.
+2) Register it in `backend_go/graph_queries/registry.go`.
+
+### Selection query modes (`query_id`)
+
+Stored under `backend_go/selection_queries/` and listed by `GET /api/selection_queries`.
+
+Built-in modes:
+
+- `neighbors` – type + subclass neighbors (both directions)
+- `superclasses` – `?sel rdfs:subClassOf ?nbr`
+- `subclasses` – `?nbr rdfs:subClassOf ?sel`
+
+To add a new mode:
+
+1) Add a new file under `backend_go/selection_queries/` that returns neighbor node IDs.
+2) Register it in `backend_go/selection_queries/registry.go`.
+
+## Performance notes
+
+- Memory usage is dominated by the cached snapshot (`[]Node`, `[]Edge`) and the temporary SPARQL JSON unmarshalling step.
+- Tune `DEFAULT_NODE_LIMIT`/`DEFAULT_EDGE_LIMIT` first if memory is too high.

backend_go/config.go

@@ -0,0 +1,190 @@
+package main
+
+import (
+	"fmt"
+	"os"
+	"strconv"
+	"strings"
+	"time"
+)
+
+type Config struct {
+	IncludeBNodes bool
+
+	CorsOrigins string
+
+	DefaultNodeLimit int
+	DefaultEdgeLimit int
+	MaxNodeLimit     int
+	MaxEdgeLimit     int
+
+	EdgeBatchSize int
+
+	FreeOSMemoryAfterSnapshot bool
+	LogSnapshotTimings        bool
+
+	SparqlHost         string
+	SparqlEndpoint     string
+	SparqlUser         string
+	SparqlPass         string
+	SparqlInsecureTLS  bool
+	SparqlDataFile     string
+	SparqlGraphIRI     string
+	SparqlLoadOnStart  bool
+	SparqlClearOnStart bool
+
+	SparqlTimeout      time.Duration
+	SparqlReadyRetries int
+	SparqlReadyDelay   time.Duration
+	SparqlReadyTimeout time.Duration
+
+	ListenAddr string
+}
+
+func LoadConfig() (Config, error) {
+	cfg := Config{
+		IncludeBNodes: envBool("INCLUDE_BNODES", false),
+		CorsOrigins:   envString("CORS_ORIGINS", "*"),
+
+		DefaultNodeLimit: envInt("DEFAULT_NODE_LIMIT", 800_000),
+		DefaultEdgeLimit: envInt("DEFAULT_EDGE_LIMIT", 2_000_000),
+		MaxNodeLimit:     envInt("MAX_NODE_LIMIT", 10_000_000),
+		MaxEdgeLimit:     envInt("MAX_EDGE_LIMIT", 20_000_000),
+		EdgeBatchSize:    envInt("EDGE_BATCH_SIZE", 100_000),
+		FreeOSMemoryAfterSnapshot: envBool("FREE_OS_MEMORY_AFTER_SNAPSHOT", false),
+		LogSnapshotTimings:        envBool("LOG_SNAPSHOT_TIMINGS", false),
+
+		SparqlHost:         envString("SPARQL_HOST", "http://anzograph:8080"),
+		SparqlEndpoint:     envString("SPARQL_ENDPOINT", ""),
+		SparqlUser:         envString("SPARQL_USER", ""),
+		SparqlPass:         envString("SPARQL_PASS", ""),
+		SparqlInsecureTLS:  envBool("SPARQL_INSECURE_TLS", false),
+		SparqlDataFile:     envString("SPARQL_DATA_FILE", ""),
+		SparqlGraphIRI:     envString("SPARQL_GRAPH_IRI", ""),
+		SparqlLoadOnStart:  envBool("SPARQL_LOAD_ON_START", false),
+		SparqlClearOnStart: envBool("SPARQL_CLEAR_ON_START", false),
+
+		SparqlReadyRetries: envInt("SPARQL_READY_RETRIES", 30),
+		ListenAddr:         envString("LISTEN_ADDR", ":8000"),
+	}
+
+	var err error
+	cfg.SparqlTimeout, err = envSeconds("SPARQL_TIMEOUT_S", 300)
+	if err != nil {
+		return Config{}, err
+	}
+	cfg.SparqlReadyDelay, err = envSeconds("SPARQL_READY_DELAY_S", 4)
+	if err != nil {
+		return Config{}, err
+	}
+	cfg.SparqlReadyTimeout, err = envSeconds("SPARQL_READY_TIMEOUT_S", 10)
+	if err != nil {
+		return Config{}, err
+	}
+
+	if cfg.SparqlLoadOnStart && strings.TrimSpace(cfg.SparqlDataFile) == "" {
+		return Config{}, fmt.Errorf("SPARQL_LOAD_ON_START=true but SPARQL_DATA_FILE is not set")
+	}
+
+	if cfg.DefaultNodeLimit < 1 {
+		return Config{}, fmt.Errorf("DEFAULT_NODE_LIMIT must be >= 1")
+	}
+	if cfg.DefaultEdgeLimit < 1 {
+		return Config{}, fmt.Errorf("DEFAULT_EDGE_LIMIT must be >= 1")
+	}
+	if cfg.MaxNodeLimit < 1 {
+		return Config{}, fmt.Errorf("MAX_NODE_LIMIT must be >= 1")
+	}
+	if cfg.MaxEdgeLimit < 1 {
+		return Config{}, fmt.Errorf("MAX_EDGE_LIMIT must be >= 1")
+	}
+	if cfg.DefaultNodeLimit > cfg.MaxNodeLimit {
+		return Config{}, fmt.Errorf("DEFAULT_NODE_LIMIT must be <= MAX_NODE_LIMIT")
+	}
+	if cfg.DefaultEdgeLimit > cfg.MaxEdgeLimit {
+		return Config{}, fmt.Errorf("DEFAULT_EDGE_LIMIT must be <= MAX_EDGE_LIMIT")
+	}
+	if cfg.EdgeBatchSize < 1 {
+		return Config{}, fmt.Errorf("EDGE_BATCH_SIZE must be >= 1")
+	}
+	if cfg.EdgeBatchSize > cfg.MaxEdgeLimit {
+		return Config{}, fmt.Errorf("EDGE_BATCH_SIZE must be <= MAX_EDGE_LIMIT")
+	}
+
+	return cfg, nil
+}
+
+func (c Config) EffectiveSparqlEndpoint() string {
+	if strings.TrimSpace(c.SparqlEndpoint) != "" {
+		return strings.TrimSpace(c.SparqlEndpoint)
+	}
+	return strings.TrimRight(c.SparqlHost, "/") + "/sparql"
+}
+
+func (c Config) corsOriginList() []string {
+	raw := strings.TrimSpace(c.CorsOrigins)
+	if raw == "" || raw == "*" {
+		return []string{"*"}
+	}
+	parts := strings.Split(raw, ",")
+	out := make([]string, 0, len(parts))
+	for _, p := range parts {
+		p = strings.TrimSpace(p)
+		if p == "" {
+			continue
+		}
+		out = append(out, p)
+	}
+	if len(out) == 0 {
+		return []string{"*"}
+	}
+	return out
+}
+
+func envString(name, def string) string {
+	v := os.Getenv(name)
+	if strings.TrimSpace(v) == "" {
+		return def
+	}
+	return v
+}
+
+func envBool(name string, def bool) bool {
+	v := strings.TrimSpace(os.Getenv(name))
+	if v == "" {
+		return def
+	}
+	switch strings.ToLower(v) {
+	case "1", "true", "yes", "y", "on":
+		return true
+	case "0", "false", "no", "n", "off":
+		return false
+	default:
+		return def
+	}
+}
+
+func envInt(name string, def int) int {
+	v := strings.TrimSpace(os.Getenv(name))
+	if v == "" {
+		return def
+	}
+	v = strings.ReplaceAll(v, "_", "")
+	n, err := strconv.Atoi(v)
+	if err != nil {
+		return def
+	}
+	return n
+}
+
+func envSeconds(name string, def float64) (time.Duration, error) {
+	v := strings.TrimSpace(os.Getenv(name))
+	if v == "" {
+		return time.Duration(def * float64(time.Second)), nil
+	}
+	f, err := strconv.ParseFloat(v, 64)
+	if err != nil {
+		return 0, fmt.Errorf("%s must be a number (seconds): %w", name, err)
+	}
+	return time.Duration(f * float64(time.Second)), nil
+}

backend_go/go.mod

@@ -0,0 +1,3 @@
+module visualizador_instanciados/backend_go
+
+go 1.22

backend_go/graph_export.go

@@ -0,0 +1,96 @@
+package main
+
+type termKey struct {
+	termType string
+	key      string
+}
+
+type graphAccumulator struct {
+	includeBNodes bool
+	nodeLimit     int
+	nodeIDByKey   map[termKey]uint32
+	nodes         []Node
+	edges         []Edge
+	preds         *PredicateDict
+}
+
+func newGraphAccumulator(nodeLimit int, includeBNodes bool, edgeCapHint int, preds *PredicateDict) *graphAccumulator {
+	if preds == nil {
+		preds = NewPredicateDict(nil)
+	}
+	return &graphAccumulator{
+		includeBNodes: includeBNodes,
+		nodeLimit:     nodeLimit,
+		nodeIDByKey:   make(map[termKey]uint32),
+		nodes:         make([]Node, 0, min(nodeLimit, 4096)),
+		edges:         make([]Edge, 0, min(edgeCapHint, 4096)),
+		preds:         preds,
+	}
+}
+
+func (g *graphAccumulator) getOrAddNode(term sparqlTerm) (uint32, bool) {
+	if term.Type == "" || term.Value == "" {
+		return 0, false
+	}
+	if term.Type == "literal" {
+		return 0, false
+	}
+
+	var key termKey
+	var node Node
+
+	if term.Type == "bnode" {
+		if !g.includeBNodes {
+			return 0, false
+		}
+		key = termKey{termType: "bnode", key: term.Value}
+		node = Node{ID: 0, TermType: "bnode", IRI: "_:" + term.Value, Label: nil, X: 0, Y: 0}
+	} else {
+		key = termKey{termType: "uri", key: term.Value}
+		node = Node{ID: 0, TermType: "uri", IRI: term.Value, Label: nil, X: 0, Y: 0}
+	}
+
+	if existing, ok := g.nodeIDByKey[key]; ok {
+		return existing, true
+	}
+	if len(g.nodes) >= g.nodeLimit {
+		return 0, false
+	}
+	nid := uint32(len(g.nodes))
+	g.nodeIDByKey[key] = nid
+	node.ID = nid
+	g.nodes = append(g.nodes, node)
+	return nid, true
+}
+
+func (g *graphAccumulator) addBindings(bindings []map[string]sparqlTerm) {
+	for _, b := range bindings {
+		sTerm := b["s"]
+		oTerm := b["o"]
+		pTerm := b["p"]
+
+		sid, okS := g.getOrAddNode(sTerm)
+		oid, okO := g.getOrAddNode(oTerm)
+		if !okS || !okO {
+			continue
+		}
+
+		predID, ok := g.preds.GetOrAdd(pTerm.Value)
+		if !ok {
+			continue
+		}
+
+		g.edges = append(g.edges, Edge{
+			Source:      sid,
+			Target:      oid,
+			PredicateID: predID,
+		})
+	}
+}
+
+func min(a, b int) int {
+	if a < b {
+		return a
+	}
+	return b
+}

backend_go/graph_queries/default.go

@@ -0,0 +1,65 @@
+package graph_queries
+
+import "fmt"
+
+func defaultEdgeQuery(limit int, offset int, includeBNodes bool) string {
+	bnodeFilter := ""
+	if !includeBNodes {
+		bnodeFilter = "FILTER(!isBlank(?s) && !isBlank(?o))"
+	}
+
+	return fmt.Sprintf(`
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+
+SELECT ?s ?p ?o
+WHERE {
+  {
+    VALUES ?p { rdf:type }
+    ?s ?p ?o .
+    ?o rdf:type owl:Class .
+  }
+  UNION
+  {
+    VALUES ?p { rdfs:subClassOf }
+    ?s ?p ?o .
+  }
+  FILTER(!isLiteral(?o))
+  %s
+}
+ORDER BY ?s ?p ?o
+LIMIT %d
+OFFSET %d
+`, bnodeFilter, limit, offset)
+}
+
+func defaultPredicateQuery(includeBNodes bool) string {
+	bnodeFilter := ""
+	if !includeBNodes {
+		bnodeFilter = "FILTER(!isBlank(?s) && !isBlank(?o))"
+	}
+
+	return fmt.Sprintf(`
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+
+SELECT DISTINCT ?p
+WHERE {
+  {
+    VALUES ?p { rdf:type }
+    ?s ?p ?o .
+    ?o rdf:type owl:Class .
+  }
+  UNION
+  {
+    VALUES ?p { rdfs:subClassOf }
+    ?s ?p ?o .
+  }
+  FILTER(!isLiteral(?o))
+  %s
+}
+ORDER BY ?p
+`, bnodeFilter)
+}

backend_go/graph_queries/hierarchy.go

@@ -0,0 +1,45 @@
+package graph_queries
+
+import "fmt"
+
+func hierarchyEdgeQuery(limit int, offset int, includeBNodes bool) string {
+	bnodeFilter := ""
+	if !includeBNodes {
+		bnodeFilter = "FILTER(!isBlank(?s) && !isBlank(?o))"
+	}
+
+	return fmt.Sprintf(`
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+
+SELECT ?s ?p ?o
+WHERE {
+  VALUES ?p { rdfs:subClassOf }
+  ?s ?p ?o .
+  FILTER(!isLiteral(?o))
+  %s
+}
+ORDER BY ?s ?p ?o
+LIMIT %d
+OFFSET %d
+`, bnodeFilter, limit, offset)
+}
+
+func hierarchyPredicateQuery(includeBNodes bool) string {
+	bnodeFilter := ""
+	if !includeBNodes {
+		bnodeFilter = "FILTER(!isBlank(?s) && !isBlank(?o))"
+	}
+
+	return fmt.Sprintf(`
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+
+SELECT DISTINCT ?p
+WHERE {
+  VALUES ?p { rdfs:subClassOf }
+  ?s ?p ?o .
+  FILTER(!isLiteral(?o))
+  %s
+}
+ORDER BY ?p
+`, bnodeFilter)
+}

backend_go/graph_queries/registry.go

@@ -0,0 +1,26 @@
+package graph_queries
+
+const DefaultID = "default"
+
+var definitions = []Definition{
+	{Meta: Meta{ID: DefaultID, Label: "Default"}, EdgeQuery: defaultEdgeQuery, PredicateQuery: defaultPredicateQuery},
+	{Meta: Meta{ID: "hierarchy", Label: "Hierarchy"}, EdgeQuery: hierarchyEdgeQuery, PredicateQuery: hierarchyPredicateQuery},
+	{Meta: Meta{ID: "types", Label: "Types"}, EdgeQuery: typesOnlyEdgeQuery, PredicateQuery: typesOnlyPredicateQuery},
+}
+
+func List() []Meta {
+	out := make([]Meta, 0, len(definitions))
+	for _, d := range definitions {
+		out = append(out, d.Meta)
+	}
+	return out
+}
+
+func Get(id string) (Definition, bool) {
+	for _, d := range definitions {
+		if d.Meta.ID == id {
+			return d, true
+		}
+	}
+	return Definition{}, false
+}

backend_go/graph_queries/types.go

@@ -0,0 +1,12 @@
+package graph_queries
+
+type Meta struct {
+	ID    string `json:"id"`
+	Label string `json:"label"`
+}
+
+type Definition struct {
+	Meta      Meta
+	EdgeQuery func(limit int, offset int, includeBNodes bool) string
+	PredicateQuery func(includeBNodes bool) string
+}

backend_go/graph_queries/types_only.go

@@ -0,0 +1,49 @@
+package graph_queries
+
+import "fmt"
+
+func typesOnlyEdgeQuery(limit int, offset int, includeBNodes bool) string {
+	bnodeFilter := ""
+	if !includeBNodes {
+		bnodeFilter = "FILTER(!isBlank(?s) && !isBlank(?o))"
+	}
+
+	return fmt.Sprintf(`
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+
+SELECT ?s ?p ?o
+WHERE {
+  VALUES ?p { rdf:type }
+  ?s ?p ?o .
+  ?o rdf:type owl:Class .
+  FILTER(!isLiteral(?o))
+  %s
+}
+ORDER BY ?s ?p ?o
+LIMIT %d
+OFFSET %d
+`, bnodeFilter, limit, offset)
+}
+
+func typesOnlyPredicateQuery(includeBNodes bool) string {
+	bnodeFilter := ""
+	if !includeBNodes {
+		bnodeFilter = "FILTER(!isBlank(?s) && !isBlank(?o))"
+	}
+
+	return fmt.Sprintf(`
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+
+SELECT DISTINCT ?p
+WHERE {
+  VALUES ?p { rdf:type }
+  ?s ?p ?o .
+  ?o rdf:type owl:Class .
+  FILTER(!isLiteral(?o))
+  %s
+}
+ORDER BY ?p
+`, bnodeFilter)
+}

backend_go/graph_snapshot.go

@@ -0,0 +1,341 @@
+package main
+
+import (
+	"context"
+	"encoding/json"
+	"fmt"
+	"log"
+	"runtime"
+	"runtime/debug"
+	"sort"
+	"strings"
+	"time"
+
+	graphqueries "visualizador_instanciados/backend_go/graph_queries"
+)
+
+const (
+	rdfsLabelIRI   = "http://www.w3.org/2000/01/rdf-schema#label"
+)
+
+func fetchGraphSnapshot(
+	ctx context.Context,
+	sparql *AnzoGraphClient,
+	cfg Config,
+	nodeLimit int,
+	edgeLimit int,
+	graphQueryID string,
+) (GraphResponse, error) {
+	start := time.Now()
+	logStats := func(stage string) {
+		if !cfg.LogSnapshotTimings {
+			return
+		}
+		var ms runtime.MemStats
+		runtime.ReadMemStats(&ms)
+		log.Printf(
+			"[snapshot] %s graph_query_id=%s node_limit=%d edge_limit=%d elapsed=%s alloc=%dMB heap_inuse=%dMB sys=%dMB numgc=%d",
+			stage,
+			graphQueryID,
+			nodeLimit,
+			edgeLimit,
+			time.Since(start).Truncate(time.Millisecond),
+			ms.Alloc/1024/1024,
+			ms.HeapInuse/1024/1024,
+			ms.Sys/1024/1024,
+			ms.NumGC,
+		)
+	}
+
+	def, ok := graphqueries.Get(graphQueryID)
+	if !ok {
+		return GraphResponse{}, fmt.Errorf("unknown graph_query_id: %s", graphQueryID)
+	}
+
+	// Build predicate dictionary (predicate IRI -> uint32 ID) before fetching edges.
+	preds, err := func() (*PredicateDict, error) {
+		logStats("predicates_query_start")
+		predQ := def.PredicateQuery(cfg.IncludeBNodes)
+		t0 := time.Now()
+		rawPred, err := sparql.Query(ctx, predQ)
+		if err != nil {
+			return nil, fmt.Errorf("predicates query failed: %w", err)
+		}
+		if cfg.LogSnapshotTimings {
+			log.Printf("[snapshot] predicates_query_returned bytes=%d query_time=%s", len(rawPred), time.Since(t0).Truncate(time.Millisecond))
+		}
+		var predRes sparqlResponse
+		t1 := time.Now()
+		if err := json.Unmarshal(rawPred, &predRes); err != nil {
+			return nil, fmt.Errorf("predicates unmarshal failed: %w", err)
+		}
+		if cfg.LogSnapshotTimings {
+			log.Printf("[snapshot] predicates_unmarshal_done bindings=%d unmarshal_time=%s", len(predRes.Results.Bindings), time.Since(t1).Truncate(time.Millisecond))
+		}
+		predicateIRIs := make([]string, 0, len(predRes.Results.Bindings))
+		for _, b := range predRes.Results.Bindings {
+			pTerm, ok := b["p"]
+			if !ok || pTerm.Type != "uri" || pTerm.Value == "" {
+				continue
+			}
+			predicateIRIs = append(predicateIRIs, pTerm.Value)
+		}
+		logStats("predicates_dict_built")
+		return NewPredicateDict(predicateIRIs), nil
+	}()
+	if err != nil {
+		return GraphResponse{}, err
+	}
+
+	// Fetch edges in batches to avoid decoding a single huge SPARQL JSON response.
+	logStats("edges_batched_start")
+	batchSize := cfg.EdgeBatchSize
+	acc := newGraphAccumulator(nodeLimit, cfg.IncludeBNodes, min(edgeLimit, batchSize), preds)
+
+	totalBindings := 0
+	convAllT0 := time.Now()
+	for batch, offset := 0, 0; offset < edgeLimit; batch, offset = batch+1, offset+batchSize {
+		limit := batchSize
+		remaining := edgeLimit - offset
+		if remaining < limit {
+			limit = remaining
+		}
+
+		logStats(fmt.Sprintf("edges_batch_start batch=%d offset=%d limit=%d", batch, offset, limit))
+		bindings, err := func() ([]map[string]sparqlTerm, error) {
+			edgesQ := def.EdgeQuery(limit, offset, cfg.IncludeBNodes)
+			t0 := time.Now()
+			raw, err := sparql.Query(ctx, edgesQ)
+			if err != nil {
+				return nil, fmt.Errorf("edges query failed: %w", err)
+			}
+			if cfg.LogSnapshotTimings {
+				log.Printf("[snapshot] edges_batch_query_returned batch=%d offset=%d limit=%d bytes=%d query_time=%s", batch, offset, limit, len(raw), time.Since(t0).Truncate(time.Millisecond))
+			}
+
+			var res sparqlResponse
+			t1 := time.Now()
+			if err := json.Unmarshal(raw, &res); err != nil {
+				return nil, fmt.Errorf("edges unmarshal failed: %w", err)
+			}
+			if cfg.LogSnapshotTimings {
+				log.Printf("[snapshot] edges_batch_unmarshal_done batch=%d bindings=%d unmarshal_time=%s", batch, len(res.Results.Bindings), time.Since(t1).Truncate(time.Millisecond))
+			}
+			return res.Results.Bindings, nil
+		}()
+		if err != nil {
+			return GraphResponse{}, fmt.Errorf("edges batch=%d offset=%d limit=%d: %w", batch, offset, limit, err)
+		}
+
+		got := len(bindings)
+		totalBindings += got
+		if got == 0 {
+			bindings = nil
+			logStats(fmt.Sprintf("edges_batch_done_empty batch=%d offset=%d", batch, offset))
+			break
+		}
+
+		convT0 := time.Now()
+		acc.addBindings(bindings)
+		if cfg.LogSnapshotTimings {
+			log.Printf(
+				"[snapshot] edges_batch_convert_done batch=%d got_bindings=%d total_bindings=%d nodes=%d edges=%d convert_time=%s",
+				batch,
+				got,
+				totalBindings,
+				len(acc.nodes),
+				len(acc.edges),
+				time.Since(convT0).Truncate(time.Millisecond),
+			)
+		}
+
+		// Make the batch eligible for GC.
+		bindings = nil
+		logStats(fmt.Sprintf("edges_batch_done batch=%d offset=%d", batch, offset))
+		if cfg.FreeOSMemoryAfterSnapshot {
+			debug.FreeOSMemory()
+			logStats(fmt.Sprintf("edges_batch_free_os_memory_done batch=%d offset=%d", batch, offset))
+		}
+
+		if got < limit {
+			break
+		}
+	}
+	if cfg.LogSnapshotTimings {
+		log.Printf("[snapshot] convert_batches_done total_bindings=%d total_time=%s", totalBindings, time.Since(convAllT0).Truncate(time.Millisecond))
+	}
+	logStats("edges_batched_done")
+
+	nodes := acc.nodes
+	edges := acc.edges
+
+	// Layout: invert edges for hierarchy (target -> source).
+	hierEdges := make([][2]int, 0, len(edges))
+	for _, e := range edges {
+		hierEdges = append(hierEdges, [2]int{int(e.Target), int(e.Source)})
+	}
+
+	layers, cycleErr := levelSynchronousKahnLayers(len(nodes), hierEdges)
+	if cycleErr != nil {
+		sample := make([]string, 0, 20)
+		for _, nid := range cycleErr.RemainingNodeIDs {
+			if len(sample) >= 20 {
+				break
+			}
+			if nid >= 0 && nid < len(nodes) {
+				sample = append(sample, nodes[nid].IRI)
+			}
+		}
+		cycleErr.RemainingIRISample = sample
+		return GraphResponse{}, cycleErr
+	}
+
+	idToIRI := make([]string, len(nodes))
+	for i := range nodes {
+		idToIRI[i] = nodes[i].IRI
+	}
+	for _, layer := range layers {
+		sortLayerByIRI(layer, idToIRI)
+	}
+
+	xs, ys := radialPositionsFromLayers(len(nodes), layers, 5000.0)
+	for i := range nodes {
+		nodes[i].X = xs[i]
+		nodes[i].Y = ys[i]
+	}
+
+	// Attach labels for URI nodes.
+	iris := make([]string, 0)
+	for _, n := range nodes {
+		if n.TermType == "uri" && n.IRI != "" {
+			iris = append(iris, n.IRI)
+		}
+	}
+	if len(iris) > 0 {
+		labelByIRI, err := fetchRDFSLabels(ctx, sparql, iris, 500)
+		if err != nil {
+			return GraphResponse{}, fmt.Errorf("fetch rdfs:label failed: %w", err)
+		}
+		for i := range nodes {
+			if nodes[i].TermType != "uri" {
+				continue
+			}
+			lbl, ok := labelByIRI[nodes[i].IRI]
+			if !ok {
+				continue
+			}
+			val := lbl
+			nodes[i].Label = &val
+		}
+	}
+
+	meta := &GraphMeta{
+		Backend:        "anzograph",
+		TTLPath:        nil,
+		SparqlEndpoint: cfg.EffectiveSparqlEndpoint(),
+		IncludeBNodes:  cfg.IncludeBNodes,
+		GraphQueryID:   graphQueryID,
+		Predicates:     preds.IRIs(),
+		NodeLimit:      nodeLimit,
+		EdgeLimit:      edgeLimit,
+		Nodes:          len(nodes),
+		Edges:          len(edges),
+	}
+
+	return GraphResponse{Nodes: nodes, Edges: edges, Meta: meta}, nil
+}
+
+type bestLabel struct {
+	score int
+	value string
+}
+
+func fetchRDFSLabels(
+	ctx context.Context,
+	sparql *AnzoGraphClient,
+	iris []string,
+	batchSize int,
+) (map[string]string, error) {
+	best := make(map[string]bestLabel)
+
+	for i := 0; i < len(iris); i += batchSize {
+		end := i + batchSize
+		if end > len(iris) {
+			end = len(iris)
+		}
+		batch := iris[i:end]
+
+		values := make([]string, 0, len(batch))
+		for _, u := range batch {
+			values = append(values, "<"+u+">")
+		}
+
+		q := fmt.Sprintf(`
+SELECT ?s ?label
+WHERE {
+  VALUES ?s { %s }
+  ?s <%s> ?label .
+}
+`, strings.Join(values, " "), rdfsLabelIRI)
+
+		raw, err := sparql.Query(ctx, q)
+		if err != nil {
+			return nil, err
+		}
+
+		var res sparqlResponse
+		if err := json.Unmarshal(raw, &res); err != nil {
+			return nil, fmt.Errorf("failed to parse SPARQL JSON: %w", err)
+		}
+
+		for _, b := range res.Results.Bindings {
+			sTerm, ok := b["s"]
+			if !ok || sTerm.Value == "" {
+				continue
+			}
+			lblTerm, ok := b["label"]
+			if !ok || lblTerm.Type != "literal" || lblTerm.Value == "" {
+				continue
+			}
+
+			score := labelScore(lblTerm.Lang)
+			prev, ok := best[sTerm.Value]
+			if !ok || score > prev.score {
+				best[sTerm.Value] = bestLabel{score: score, value: lblTerm.Value}
+			}
+		}
+	}
+
+	out := make(map[string]string, len(best))
+	for iri, v := range best {
+		out[iri] = v.value
+	}
+	return out, nil
+}
+
+func labelScore(lang string) int {
+	lang = strings.ToLower(strings.TrimSpace(lang))
+	if lang == "en" {
+		return 3
+	}
+	if lang == "" {
+		return 2
+	}
+	return 1
+}
+
+func sortIntsUnique(xs []int) []int {
+	if len(xs) == 0 {
+		return xs
+	}
+	sort.Ints(xs)
+	out := xs[:0]
+	var last int
+	for i, v := range xs {
+		if i == 0 || v != last {
+			out = append(out, v)
+		}
+		last = v
+	}
+	return out
+}

backend_go/http_helpers.go

@@ -0,0 +1,23 @@
+package main
+
+import (
+	"encoding/json"
+	"io"
+	"net/http"
+)
+
+func writeJSON(w http.ResponseWriter, status int, v any) {
+	w.Header().Set("Content-Type", "application/json")
+	w.WriteHeader(status)
+	enc := json.NewEncoder(w)
+	_ = enc.Encode(v)
+}
+
+func writeError(w http.ResponseWriter, status int, msg string) {
+	writeJSON(w, status, ErrorResponse{Detail: msg})
+}
+
+func decodeJSON(r io.Reader, dst any) error {
+	dec := json.NewDecoder(r)
+	return dec.Decode(dst)
+}

backend_go/layout.go

@@ -0,0 +1,148 @@
+package main
+
+import (
+	"fmt"
+	"math"
+	"sort"
+)
+
+type CycleError struct {
+	Processed        int
+	Total            int
+	RemainingNodeIDs []int
+	RemainingIRISample []string
+}
+
+func (e *CycleError) Error() string {
+	msg := fmt.Sprintf("Cycle detected in subClassOf graph (processed %d/%d nodes).", e.Processed, e.Total)
+	if len(e.RemainingIRISample) > 0 {
+		msg += " Example nodes: " + stringsJoin(e.RemainingIRISample, ", ")
+	}
+	return msg
+}
+
+func levelSynchronousKahnLayers(nodeCount int, edges [][2]int) ([][]int, *CycleError) {
+	n := nodeCount
+	if n <= 0 {
+		return [][]int{}, nil
+	}
+
+	adj := make([][]int, n)
+	indeg := make([]int, n)
+
+	for _, e := range edges {
+		u, v := e[0], e[1]
+		if u == v {
+			continue
+		}
+		if u < 0 || u >= n || v < 0 || v >= n {
+			continue
+		}
+		adj[u] = append(adj[u], v)
+		indeg[v]++
+	}
+
+	q := make([]int, 0, n)
+	for i, d := range indeg {
+		if d == 0 {
+			q = append(q, i)
+		}
+	}
+
+	layers := make([][]int, 0)
+	processed := 0
+	for len(q) > 0 {
+		layer := append([]int(nil), q...)
+		q = q[:0]
+		layers = append(layers, layer)
+
+		for _, u := range layer {
+			processed++
+			for _, v := range adj[u] {
+				indeg[v]--
+				if indeg[v] == 0 {
+					q = append(q, v)
+				}
+			}
+		}
+	}
+
+	if processed != n {
+		remaining := make([]int, 0)
+		for i, d := range indeg {
+			if d > 0 {
+				remaining = append(remaining, i)
+			}
+		}
+		return nil, &CycleError{Processed: processed, Total: n, RemainingNodeIDs: remaining}
+	}
+
+	return layers, nil
+}
+
+func radialPositionsFromLayers(nodeCount int, layers [][]int, maxR float64) (xs []float64, ys []float64) {
+	n := nodeCount
+	if n <= 0 {
+		return []float64{}, []float64{}
+	}
+
+	xs = make([]float64, n)
+	ys = make([]float64, n)
+	if len(layers) == 0 {
+		return xs, ys
+	}
+
+	twoPi := 2.0 * math.Pi
+	golden := math.Pi * (3.0 - math.Sqrt(5.0))
+
+	layerCount := float64(len(layers))
+	denom := layerCount + 1.0
+
+	for li, layer := range layers {
+		m := len(layer)
+		if m == 0 {
+			continue
+		}
+		r := (float64(li+1) / denom) * maxR
+		offset := math.Mod(float64(li)*golden, twoPi)
+
+		if m == 1 {
+			nid := layer[0]
+			if nid >= 0 && nid < n {
+				xs[nid] = r * math.Cos(offset)
+				ys[nid] = r * math.Sin(offset)
+			}
+			continue
+		}
+
+		step := twoPi / float64(m)
+		for j, nid := range layer {
+			if nid < 0 || nid >= n {
+				continue
+			}
+			t := offset + step*float64(j)
+			xs[nid] = r * math.Cos(t)
+			ys[nid] = r * math.Sin(t)
+		}
+	}
+
+	return xs, ys
+}
+
+func sortLayerByIRI(layer []int, idToIRI []string) {
+	sort.Slice(layer, func(i, j int) bool {
+		return idToIRI[layer[i]] < idToIRI[layer[j]]
+	})
+}
+
+func stringsJoin(parts []string, sep string) string {
+	if len(parts) == 0 {
+		return ""
+	}
+	out := parts[0]
+	for i := 1; i < len(parts); i++ {
+		out += sep
+		out += parts[i]
+	}
+	return out
+}

backend_go/main.go

@@ -0,0 +1,35 @@
+package main
+
+import (
+	"context"
+	"log"
+	"net/http"
+	"time"
+)
+
+func main() {
+	cfg, err := LoadConfig()
+	if err != nil {
+		log.Fatal(err)
+	}
+
+	sparql := NewAnzoGraphClient(cfg)
+	if err := sparql.Startup(context.Background()); err != nil {
+		log.Fatal(err)
+	}
+
+	api := &APIServer{
+		cfg:       cfg,
+		sparql:    sparql,
+		snapshots: NewGraphSnapshotService(sparql, cfg),
+	}
+
+	srv := &http.Server{
+		Addr:              cfg.ListenAddr,
+		Handler:           api.handler(),
+		ReadHeaderTimeout: 5 * time.Second,
+	}
+
+	log.Printf("backend listening on %s", cfg.ListenAddr)
+	log.Fatal(srv.ListenAndServe())
+}

backend_go/models.go

@@ -0,0 +1,82 @@
+package main
+
+type ErrorResponse struct {
+	Detail string `json:"detail"`
+}
+
+type HealthResponse struct {
+	Status string `json:"status"`
+}
+
+type Node struct {
+	ID       uint32  `json:"id"`
+	TermType string  `json:"termType"` // "uri" | "bnode"
+	IRI      string  `json:"iri"`
+	Label    *string `json:"label"`
+	X        float64 `json:"x"`
+	Y        float64 `json:"y"`
+}
+
+type Edge struct {
+	Source    uint32 `json:"source"`
+	Target    uint32 `json:"target"`
+	PredicateID uint32 `json:"predicate_id"`
+}
+
+type GraphMeta struct {
+	Backend        string  `json:"backend"`
+	TTLPath        *string `json:"ttl_path"`
+	SparqlEndpoint string  `json:"sparql_endpoint"`
+	IncludeBNodes  bool    `json:"include_bnodes"`
+	GraphQueryID   string  `json:"graph_query_id"`
+	Predicates     []string `json:"predicates,omitempty"` // index = predicate_id
+	NodeLimit      int     `json:"node_limit"`
+	EdgeLimit      int     `json:"edge_limit"`
+	Nodes          int     `json:"nodes"`
+	Edges          int     `json:"edges"`
+}
+
+type GraphResponse struct {
+	Nodes []Node    `json:"nodes"`
+	Edges []Edge    `json:"edges"`
+	Meta  *GraphMeta `json:"meta"`
+}
+
+type StatsResponse struct {
+	Backend        string  `json:"backend"`
+	TTLPath        *string `json:"ttl_path"`
+	SparqlEndpoint *string `json:"sparql_endpoint"`
+	ParsedTriples  int     `json:"parsed_triples"`
+	Nodes          int     `json:"nodes"`
+	Edges          int     `json:"edges"`
+}
+
+type SparqlQueryRequest struct {
+	Query string `json:"query"`
+}
+
+type NeighborsRequest struct {
+	SelectedIDs  []uint32 `json:"selected_ids"`
+	NodeLimit    *int     `json:"node_limit,omitempty"`
+	EdgeLimit    *int     `json:"edge_limit,omitempty"`
+	GraphQueryID  *string `json:"graph_query_id,omitempty"`
+}
+
+type NeighborsResponse struct {
+	SelectedIDs []uint32 `json:"selected_ids"`
+	NeighborIDs []uint32 `json:"neighbor_ids"`
+}
+
+type SelectionQueryRequest struct {
+	QueryID      string   `json:"query_id"`
+	SelectedIDs  []uint32 `json:"selected_ids"`
+	NodeLimit    *int     `json:"node_limit,omitempty"`
+	EdgeLimit    *int     `json:"edge_limit,omitempty"`
+	GraphQueryID  *string `json:"graph_query_id,omitempty"`
+}
+
+type SelectionQueryResponse struct {
+	QueryID     string   `json:"query_id"`
+	SelectedIDs []uint32 `json:"selected_ids"`
+	NeighborIDs []uint32 `json:"neighbor_ids"`
+}

backend_go/predicate_dict.go

@@ -0,0 +1,40 @@
+package main
+
+type PredicateDict struct {
+	idByIRI map[string]uint32
+	iriByID []string
+}
+
+func NewPredicateDict(predicates []string) *PredicateDict {
+	idByIRI := make(map[string]uint32, len(predicates))
+	iriByID := make([]string, 0, len(predicates))
+	for _, iri := range predicates {
+		if iri == "" {
+			continue
+		}
+		if _, ok := idByIRI[iri]; ok {
+			continue
+		}
+		id := uint32(len(iriByID))
+		idByIRI[iri] = id
+		iriByID = append(iriByID, iri)
+	}
+	return &PredicateDict{idByIRI: idByIRI, iriByID: iriByID}
+}
+
+func (d *PredicateDict) GetOrAdd(iri string) (uint32, bool) {
+	if iri == "" {
+		return 0, false
+	}
+	if id, ok := d.idByIRI[iri]; ok {
+		return id, true
+	}
+	id := uint32(len(d.iriByID))
+	d.idByIRI[iri] = id
+	d.iriByID = append(d.iriByID, iri)
+	return id, true
+}
+
+func (d *PredicateDict) IRIs() []string {
+	return d.iriByID
+}

backend_go/selection_queries/helpers.go

@@ -0,0 +1,101 @@
+package selection_queries
+
+import (
+	"encoding/json"
+	"fmt"
+	"sort"
+	"strings"
+)
+
+func nodeKey(termType, iri string) string {
+	return termType + "\x00" + iri
+}
+
+func valuesTerm(n NodeRef) string {
+	if n.TermType == "uri" {
+		if n.IRI == "" {
+			return ""
+		}
+		return "<" + n.IRI + ">"
+	}
+	if n.TermType == "bnode" {
+		if n.IRI == "" {
+			return ""
+		}
+		if strings.HasPrefix(n.IRI, "_:") {
+			return n.IRI
+		}
+		return "_:" + n.IRI
+	}
+	return ""
+}
+
+func termKeyFromSparqlTerm(term sparqlTerm, includeBNodes bool) (string, bool) {
+	if term.Type == "" || term.Value == "" {
+		return "", false
+	}
+	if term.Type == "literal" {
+		return "", false
+	}
+	if term.Type == "bnode" {
+		if !includeBNodes {
+			return "", false
+		}
+		return nodeKey("bnode", "_:"+term.Value), true
+	}
+	if term.Type == "uri" {
+		return nodeKey("uri", term.Value), true
+	}
+	return "", false
+}
+
+func selectedNodesFromIDs(idx Index, selectedIDs []uint32, includeBNodes bool) ([]NodeRef, map[uint32]struct{}) {
+	out := make([]NodeRef, 0, len(selectedIDs))
+	set := make(map[uint32]struct{}, len(selectedIDs))
+	for _, nid := range selectedIDs {
+		n, ok := idx.IDToNode[nid]
+		if !ok {
+			continue
+		}
+		if n.TermType == "bnode" && !includeBNodes {
+			continue
+		}
+		out = append(out, n)
+		set[nid] = struct{}{}
+	}
+	return out, set
+}
+
+func idsFromBindings(raw []byte, varName string, idx Index, selectedSet map[uint32]struct{}, includeBNodes bool) ([]uint32, error) {
+	var res sparqlResponse
+	if err := json.Unmarshal(raw, &res); err != nil {
+		return nil, fmt.Errorf("failed to parse SPARQL JSON: %w", err)
+	}
+
+	neighborSet := make(map[uint32]struct{})
+	for _, b := range res.Results.Bindings {
+		term, ok := b[varName]
+		if !ok {
+			continue
+		}
+		key, ok := termKeyFromSparqlTerm(term, includeBNodes)
+		if !ok {
+			continue
+		}
+		nid, ok := idx.KeyToID[key]
+		if !ok {
+			continue
+		}
+		if _, sel := selectedSet[nid]; sel {
+			continue
+		}
+		neighborSet[nid] = struct{}{}
+	}
+
+	ids := make([]uint32, 0, len(neighborSet))
+	for nid := range neighborSet {
+		ids = append(ids, nid)
+	}
+	sort.Slice(ids, func(i, j int) bool { return ids[i] < ids[j] })
+	return ids, nil
+}

backend_go/selection_queries/neighbors.go

@@ -0,0 +1,76 @@
+package selection_queries
+
+import (
+	"context"
+	"fmt"
+	"strings"
+)
+
+func neighborsQuery(selectedNodes []NodeRef, includeBNodes bool) string {
+	valuesTerms := make([]string, 0, len(selectedNodes))
+	for _, n := range selectedNodes {
+		t := valuesTerm(n)
+		if t == "" {
+			continue
+		}
+		valuesTerms = append(valuesTerms, t)
+	}
+
+	if len(valuesTerms) == 0 {
+		return "SELECT ?nbr WHERE { FILTER(false) }"
+	}
+
+	bnodeFilter := ""
+	if !includeBNodes {
+		bnodeFilter = "FILTER(!isBlank(?nbr))"
+	}
+
+	values := strings.Join(valuesTerms, " ")
+	return fmt.Sprintf(`
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+
+SELECT DISTINCT ?nbr
+WHERE {
+  VALUES ?sel { %s }
+  {
+    ?sel rdf:type ?o .
+    ?o rdf:type owl:Class .
+    BIND(?o AS ?nbr)
+  }
+  UNION
+  {
+    ?s rdf:type ?sel .
+    ?sel rdf:type owl:Class .
+    BIND(?s AS ?nbr)
+  }
+  UNION
+  {
+    ?sel rdfs:subClassOf ?o .
+    BIND(?o AS ?nbr)
+  }
+  UNION
+  {
+    ?s rdfs:subClassOf ?sel .
+    BIND(?s AS ?nbr)
+  }
+  FILTER(!isLiteral(?nbr))
+  FILTER(?nbr != ?sel)
+  %s
+}
+`, values, bnodeFilter)
+}
+
+func runNeighbors(ctx context.Context, q Querier, idx Index, selectedIDs []uint32, includeBNodes bool) ([]uint32, error) {
+	selectedNodes, selectedSet := selectedNodesFromIDs(idx, selectedIDs, includeBNodes)
+	if len(selectedNodes) == 0 {
+		return []uint32{}, nil
+	}
+
+	raw, err := q.Query(ctx, neighborsQuery(selectedNodes, includeBNodes))
+	if err != nil {
+		return nil, err
+	}
+	return idsFromBindings(raw, "nbr", idx, selectedSet, includeBNodes)
+}

backend_go/selection_queries/registry.go

@@ -0,0 +1,33 @@
+package selection_queries
+
+var definitions = []Definition{
+	{
+		Meta: Meta{ID: "neighbors", Label: "Neighbors"},
+		Run:  runNeighbors,
+	},
+	{
+		Meta: Meta{ID: "superclasses", Label: "Superclasses"},
+		Run:  runSuperclasses,
+	},
+	{
+		Meta: Meta{ID: "subclasses", Label: "Subclasses"},
+		Run:  runSubclasses,
+	},
+}
+
+func List() []Meta {
+	out := make([]Meta, 0, len(definitions))
+	for _, d := range definitions {
+		out = append(out, d.Meta)
+	}
+	return out
+}
+
+func Get(id string) (Definition, bool) {
+	for _, d := range definitions {
+		if d.Meta.ID == id {
+			return d, true
+		}
+	}
+	return Definition{}, false
+}

backend_go/selection_queries/sparql_types.go

@@ -0,0 +1,14 @@
+package selection_queries
+
+type sparqlTerm struct {
+	Type  string `json:"type"`
+	Value string `json:"value"`
+	Lang  string `json:"xml:lang,omitempty"`
+}
+
+type sparqlResponse struct {
+	Results struct {
+		Bindings []map[string]sparqlTerm `json:"bindings"`
+	} `json:"results"`
+}
+

backend_go/selection_queries/subclasses.go

@@ -0,0 +1,54 @@
+package selection_queries
+
+import (
+	"context"
+	"fmt"
+	"strings"
+)
+
+func subclassesQuery(selectedNodes []NodeRef, includeBNodes bool) string {
+	valuesTerms := make([]string, 0, len(selectedNodes))
+	for _, n := range selectedNodes {
+		t := valuesTerm(n)
+		if t == "" {
+			continue
+		}
+		valuesTerms = append(valuesTerms, t)
+	}
+
+	if len(valuesTerms) == 0 {
+		return "SELECT ?nbr WHERE { FILTER(false) }"
+	}
+
+	bnodeFilter := ""
+	if !includeBNodes {
+		bnodeFilter = "FILTER(!isBlank(?nbr))"
+	}
+
+	values := strings.Join(valuesTerms, " ")
+	return fmt.Sprintf(`
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+
+SELECT DISTINCT ?nbr
+WHERE {
+  VALUES ?sel { %s }
+  ?nbr rdfs:subClassOf ?sel .
+  FILTER(!isLiteral(?nbr))
+  FILTER(?nbr != ?sel)
+  %s
+}
+`, values, bnodeFilter)
+}
+
+func runSubclasses(ctx context.Context, q Querier, idx Index, selectedIDs []uint32, includeBNodes bool) ([]uint32, error) {
+	selectedNodes, selectedSet := selectedNodesFromIDs(idx, selectedIDs, includeBNodes)
+	if len(selectedNodes) == 0 {
+		return []uint32{}, nil
+	}
+
+	raw, err := q.Query(ctx, subclassesQuery(selectedNodes, includeBNodes))
+	if err != nil {
+		return nil, err
+	}
+	return idsFromBindings(raw, "nbr", idx, selectedSet, includeBNodes)
+}

backend_go/selection_queries/superclasses.go

@@ -0,0 +1,54 @@
+package selection_queries
+
+import (
+	"context"
+	"fmt"
+	"strings"
+)
+
+func superclassesQuery(selectedNodes []NodeRef, includeBNodes bool) string {
+	valuesTerms := make([]string, 0, len(selectedNodes))
+	for _, n := range selectedNodes {
+		t := valuesTerm(n)
+		if t == "" {
+			continue
+		}
+		valuesTerms = append(valuesTerms, t)
+	}
+
+	if len(valuesTerms) == 0 {
+		return "SELECT ?nbr WHERE { FILTER(false) }"
+	}
+
+	bnodeFilter := ""
+	if !includeBNodes {
+		bnodeFilter = "FILTER(!isBlank(?nbr))"
+	}
+
+	values := strings.Join(valuesTerms, " ")
+	return fmt.Sprintf(`
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+
+SELECT DISTINCT ?nbr
+WHERE {
+  VALUES ?sel { %s }
+  ?sel rdfs:subClassOf ?nbr .
+  FILTER(!isLiteral(?nbr))
+  FILTER(?nbr != ?sel)
+  %s
+}
+`, values, bnodeFilter)
+}
+
+func runSuperclasses(ctx context.Context, q Querier, idx Index, selectedIDs []uint32, includeBNodes bool) ([]uint32, error) {
+	selectedNodes, selectedSet := selectedNodesFromIDs(idx, selectedIDs, includeBNodes)
+	if len(selectedNodes) == 0 {
+		return []uint32{}, nil
+	}
+
+	raw, err := q.Query(ctx, superclassesQuery(selectedNodes, includeBNodes))
+	if err != nil {
+		return nil, err
+	}
+	return idsFromBindings(raw, "nbr", idx, selectedSet, includeBNodes)
+}

backend_go/selection_queries/types.go

@@ -0,0 +1,28 @@
+package selection_queries
+
+import "context"
+
+type Querier interface {
+	Query(ctx context.Context, query string) ([]byte, error)
+}
+
+type NodeRef struct {
+	ID       uint32
+	TermType string // "uri" | "bnode"
+	IRI      string
+}
+
+type Index struct {
+	IDToNode map[uint32]NodeRef
+	KeyToID  map[string]uint32
+}
+
+type Meta struct {
+	ID    string `json:"id"`
+	Label string `json:"label"`
+}
+
+type Definition struct {
+	Meta Meta
+	Run  func(ctx context.Context, q Querier, idx Index, selectedIDs []uint32, includeBNodes bool) ([]uint32, error)
+}

backend_go/selection_query.go

@@ -0,0 +1,32 @@
+package main
+
+import (
+	"context"
+	"fmt"
+
+	selectionqueries "visualizador_instanciados/backend_go/selection_queries"
+)
+
+func runSelectionQuery(
+	ctx context.Context,
+	sparql *AnzoGraphClient,
+	snapshot GraphResponse,
+	queryID string,
+	selectedIDs []uint32,
+	includeBNodes bool,
+) ([]uint32, error) {
+	def, ok := selectionqueries.Get(queryID)
+	if !ok {
+		return nil, fmt.Errorf("unknown query_id: %s", queryID)
+	}
+
+	idToNode := make(map[uint32]selectionqueries.NodeRef, len(snapshot.Nodes))
+	keyToID := make(map[string]uint32, len(snapshot.Nodes))
+	for _, n := range snapshot.Nodes {
+		nr := selectionqueries.NodeRef{ID: n.ID, TermType: n.TermType, IRI: n.IRI}
+		idToNode[n.ID] = nr
+		keyToID[n.TermType+"\x00"+n.IRI] = n.ID
+	}
+
+	return def.Run(ctx, sparql, selectionqueries.Index{IDToNode: idToNode, KeyToID: keyToID}, selectedIDs, includeBNodes)
+}

backend_go/server.go

@@ -0,0 +1,304 @@
+package main
+
+import (
+	"fmt"
+	"log"
+	"net/http"
+	"strconv"
+	"strings"
+
+	graphqueries "visualizador_instanciados/backend_go/graph_queries"
+	selectionqueries "visualizador_instanciados/backend_go/selection_queries"
+)
+
+type APIServer struct {
+	cfg       Config
+	sparql    *AnzoGraphClient
+	snapshots *GraphSnapshotService
+}
+
+func (s *APIServer) handler() http.Handler {
+	mux := http.NewServeMux()
+	mux.HandleFunc("/api/health", s.handleHealth)
+	mux.HandleFunc("/api/stats", s.handleStats)
+	mux.HandleFunc("/api/sparql", s.handleSparql)
+	mux.HandleFunc("/api/graph", s.handleGraph)
+	mux.HandleFunc("/api/graph_queries", s.handleGraphQueries)
+	mux.HandleFunc("/api/selection_queries", s.handleSelectionQueries)
+	mux.HandleFunc("/api/selection_query", s.handleSelectionQuery)
+	mux.HandleFunc("/api/neighbors", s.handleNeighbors)
+
+	return s.corsMiddleware(mux)
+}
+
+func (s *APIServer) corsMiddleware(next http.Handler) http.Handler {
+	origins := s.cfg.corsOriginList()
+	allowAll := len(origins) == 1 && origins[0] == "*"
+	allowed := make(map[string]struct{}, len(origins))
+	for _, o := range origins {
+		allowed[o] = struct{}{}
+	}
+
+	return http.HandlerFunc(func(w http.ResponseWriter, r *http.Request) {
+		origin := r.Header.Get("Origin")
+		if origin != "" {
+			if allowAll {
+				w.Header().Set("Access-Control-Allow-Origin", "*")
+			} else if _, ok := allowed[origin]; ok {
+				w.Header().Set("Access-Control-Allow-Origin", origin)
+				w.Header().Add("Vary", "Origin")
+			}
+			w.Header().Set("Access-Control-Allow-Methods", "GET,POST,OPTIONS")
+			w.Header().Set("Access-Control-Allow-Headers", "*")
+		}
+
+		if r.Method == http.MethodOptions {
+			w.WriteHeader(http.StatusNoContent)
+			return
+		}
+
+		next.ServeHTTP(w, r)
+	})
+}
+
+func (s *APIServer) handleHealth(w http.ResponseWriter, r *http.Request) {
+	if r.Method != http.MethodGet {
+		w.WriteHeader(http.StatusMethodNotAllowed)
+		return
+	}
+	writeJSON(w, http.StatusOK, HealthResponse{Status: "ok"})
+}
+
+func (s *APIServer) handleStats(w http.ResponseWriter, r *http.Request) {
+	if r.Method != http.MethodGet {
+		w.WriteHeader(http.StatusMethodNotAllowed)
+		return
+	}
+
+	ctx := r.Context()
+	snap, err := s.snapshots.Get(ctx, s.cfg.DefaultNodeLimit, s.cfg.DefaultEdgeLimit, graphqueries.DefaultID)
+	if err != nil {
+		log.Printf("handleStats: snapshot error: %v", err)
+		writeError(w, http.StatusInternalServerError, err.Error())
+		return
+	}
+
+	endpoint := snap.Meta.SparqlEndpoint
+	writeJSON(w, http.StatusOK, StatsResponse{
+		Backend:        snap.Meta.Backend,
+		TTLPath:        snap.Meta.TTLPath,
+		SparqlEndpoint: &endpoint,
+		ParsedTriples:  len(snap.Edges),
+		Nodes:          len(snap.Nodes),
+		Edges:          len(snap.Edges),
+	})
+}
+
+func (s *APIServer) handleSparql(w http.ResponseWriter, r *http.Request) {
+	if r.Method != http.MethodPost {
+		w.WriteHeader(http.StatusMethodNotAllowed)
+		return
+	}
+
+	var req SparqlQueryRequest
+	if err := decodeJSON(r.Body, &req); err != nil || strings.TrimSpace(req.Query) == "" {
+		writeError(w, http.StatusUnprocessableEntity, "invalid request body")
+		return
+	}
+
+	raw, err := s.sparql.Query(r.Context(), req.Query)
+	if err != nil {
+		writeError(w, http.StatusBadGateway, err.Error())
+		return
+	}
+
+	w.Header().Set("Content-Type", "application/json")
+	w.WriteHeader(http.StatusOK)
+	_, _ = w.Write(raw)
+}
+
+func (s *APIServer) handleGraph(w http.ResponseWriter, r *http.Request) {
+	if r.Method != http.MethodGet {
+		w.WriteHeader(http.StatusMethodNotAllowed)
+		return
+	}
+
+	nodeLimit, err := intQuery(r, "node_limit", s.cfg.DefaultNodeLimit)
+	if err != nil || nodeLimit < 1 || nodeLimit > s.cfg.MaxNodeLimit {
+		writeError(w, http.StatusUnprocessableEntity, fmt.Sprintf("node_limit must be between 1 and %d", s.cfg.MaxNodeLimit))
+		return
+	}
+	edgeLimit, err := intQuery(r, "edge_limit", s.cfg.DefaultEdgeLimit)
+	if err != nil || edgeLimit < 1 || edgeLimit > s.cfg.MaxEdgeLimit {
+		writeError(w, http.StatusUnprocessableEntity, fmt.Sprintf("edge_limit must be between 1 and %d", s.cfg.MaxEdgeLimit))
+		return
+	}
+
+		graphQueryID := strings.TrimSpace(r.URL.Query().Get("graph_query_id"))
+		if graphQueryID == "" {
+			graphQueryID = graphqueries.DefaultID
+		}
+		if _, ok := graphqueries.Get(graphQueryID); !ok {
+			writeError(w, http.StatusUnprocessableEntity, "unknown graph_query_id")
+			return
+		}
+
+	snap, err := s.snapshots.Get(r.Context(), nodeLimit, edgeLimit, graphQueryID)
+	if err != nil {
+		log.Printf("handleGraph: snapshot error graph_query_id=%s node_limit=%d edge_limit=%d err=%v", graphQueryID, nodeLimit, edgeLimit, err)
+		if _, ok := err.(*CycleError); ok {
+			writeError(w, http.StatusUnprocessableEntity, err.Error())
+			return
+		}
+		writeError(w, http.StatusInternalServerError, err.Error())
+		return
+	}
+
+	writeJSON(w, http.StatusOK, snap)
+}
+
+func (s *APIServer) handleGraphQueries(w http.ResponseWriter, r *http.Request) {
+	if r.Method != http.MethodGet {
+		w.WriteHeader(http.StatusMethodNotAllowed)
+		return
+	}
+	writeJSON(w, http.StatusOK, graphqueries.List())
+}
+
+func (s *APIServer) handleSelectionQueries(w http.ResponseWriter, r *http.Request) {
+	if r.Method != http.MethodGet {
+		w.WriteHeader(http.StatusMethodNotAllowed)
+		return
+	}
+	writeJSON(w, http.StatusOK, selectionqueries.List())
+}
+
+func (s *APIServer) handleSelectionQuery(w http.ResponseWriter, r *http.Request) {
+	if r.Method != http.MethodPost {
+		w.WriteHeader(http.StatusMethodNotAllowed)
+		return
+	}
+
+	var req SelectionQueryRequest
+	if err := decodeJSON(r.Body, &req); err != nil || strings.TrimSpace(req.QueryID) == "" {
+		writeError(w, http.StatusUnprocessableEntity, "invalid request body")
+		return
+	}
+	if _, ok := selectionqueries.Get(req.QueryID); !ok {
+		writeError(w, http.StatusUnprocessableEntity, "unknown query_id")
+		return
+	}
+	if len(req.SelectedIDs) == 0 {
+		writeJSON(w, http.StatusOK, SelectionQueryResponse{
+			QueryID:     req.QueryID,
+			SelectedIDs: req.SelectedIDs,
+			NeighborIDs: []uint32{},
+		})
+		return
+	}
+
+	graphQueryID := graphqueries.DefaultID
+	if req.GraphQueryID != nil && strings.TrimSpace(*req.GraphQueryID) != "" {
+		graphQueryID = strings.TrimSpace(*req.GraphQueryID)
+	}
+	if _, ok := graphqueries.Get(graphQueryID); !ok {
+		writeError(w, http.StatusUnprocessableEntity, "unknown graph_query_id")
+		return
+	}
+
+	nodeLimit := s.cfg.DefaultNodeLimit
+	edgeLimit := s.cfg.DefaultEdgeLimit
+	if req.NodeLimit != nil {
+		nodeLimit = *req.NodeLimit
+	}
+	if req.EdgeLimit != nil {
+		edgeLimit = *req.EdgeLimit
+	}
+	if nodeLimit < 1 || nodeLimit > s.cfg.MaxNodeLimit || edgeLimit < 1 || edgeLimit > s.cfg.MaxEdgeLimit {
+		writeError(w, http.StatusUnprocessableEntity, "invalid node_limit/edge_limit")
+		return
+	}
+
+	snap, err := s.snapshots.Get(r.Context(), nodeLimit, edgeLimit, graphQueryID)
+	if err != nil {
+		writeError(w, http.StatusInternalServerError, err.Error())
+		return
+	}
+
+	ids, err := runSelectionQuery(r.Context(), s.sparql, snap, req.QueryID, req.SelectedIDs, s.cfg.IncludeBNodes)
+	if err != nil {
+		writeError(w, http.StatusBadGateway, err.Error())
+		return
+	}
+
+	writeJSON(w, http.StatusOK, SelectionQueryResponse{
+		QueryID:     req.QueryID,
+		SelectedIDs: req.SelectedIDs,
+		NeighborIDs: ids,
+	})
+}
+
+func (s *APIServer) handleNeighbors(w http.ResponseWriter, r *http.Request) {
+	if r.Method != http.MethodPost {
+		w.WriteHeader(http.StatusMethodNotAllowed)
+		return
+	}
+
+	var req NeighborsRequest
+	if err := decodeJSON(r.Body, &req); err != nil {
+		writeError(w, http.StatusUnprocessableEntity, "invalid request body")
+		return
+	}
+	if len(req.SelectedIDs) == 0 {
+		writeJSON(w, http.StatusOK, NeighborsResponse{SelectedIDs: req.SelectedIDs, NeighborIDs: []uint32{}})
+		return
+	}
+
+	graphQueryID := graphqueries.DefaultID
+	if req.GraphQueryID != nil && strings.TrimSpace(*req.GraphQueryID) != "" {
+		graphQueryID = strings.TrimSpace(*req.GraphQueryID)
+	}
+	if _, ok := graphqueries.Get(graphQueryID); !ok {
+		writeError(w, http.StatusUnprocessableEntity, "unknown graph_query_id")
+		return
+	}
+
+	nodeLimit := s.cfg.DefaultNodeLimit
+	edgeLimit := s.cfg.DefaultEdgeLimit
+	if req.NodeLimit != nil {
+		nodeLimit = *req.NodeLimit
+	}
+	if req.EdgeLimit != nil {
+		edgeLimit = *req.EdgeLimit
+	}
+	if nodeLimit < 1 || nodeLimit > s.cfg.MaxNodeLimit || edgeLimit < 1 || edgeLimit > s.cfg.MaxEdgeLimit {
+		writeError(w, http.StatusUnprocessableEntity, "invalid node_limit/edge_limit")
+		return
+	}
+
+	snap, err := s.snapshots.Get(r.Context(), nodeLimit, edgeLimit, graphQueryID)
+	if err != nil {
+		writeError(w, http.StatusInternalServerError, err.Error())
+		return
+	}
+
+	nbrs, err := runSelectionQuery(r.Context(), s.sparql, snap, "neighbors", req.SelectedIDs, s.cfg.IncludeBNodes)
+	if err != nil {
+		writeError(w, http.StatusBadGateway, err.Error())
+		return
+	}
+
+	writeJSON(w, http.StatusOK, NeighborsResponse{SelectedIDs: req.SelectedIDs, NeighborIDs: nbrs})
+}
+
+func intQuery(r *http.Request, name string, def int) (int, error) {
+	raw := strings.TrimSpace(r.URL.Query().Get(name))
+	if raw == "" {
+		return def, nil
+	}
+	n, err := strconv.Atoi(raw)
+	if err != nil {
+		return 0, err
+	}
+	return n, nil
+}

backend_go/snapshot_service.go

@@ -0,0 +1,76 @@
+package main
+
+import (
+	"context"
+	"sync"
+)
+
+type snapshotKey struct {
+	NodeLimit      int
+	EdgeLimit      int
+	IncludeBNodes  bool
+	GraphQueryID   string
+}
+
+type snapshotInflight struct {
+	ready    chan struct{}
+	snapshot GraphResponse
+	err      error
+}
+
+type GraphSnapshotService struct {
+	sparql *AnzoGraphClient
+	cfg    Config
+
+	mu       sync.Mutex
+	cache    map[snapshotKey]GraphResponse
+	inflight map[snapshotKey]*snapshotInflight
+}
+
+func NewGraphSnapshotService(sparql *AnzoGraphClient, cfg Config) *GraphSnapshotService {
+	return &GraphSnapshotService{
+		sparql:    sparql,
+		cfg:      cfg,
+		cache:    make(map[snapshotKey]GraphResponse),
+		inflight: make(map[snapshotKey]*snapshotInflight),
+	}
+}
+
+func (s *GraphSnapshotService) Get(ctx context.Context, nodeLimit int, edgeLimit int, graphQueryID string) (GraphResponse, error) {
+	key := snapshotKey{NodeLimit: nodeLimit, EdgeLimit: edgeLimit, IncludeBNodes: s.cfg.IncludeBNodes, GraphQueryID: graphQueryID}
+
+	s.mu.Lock()
+	if snap, ok := s.cache[key]; ok {
+		s.mu.Unlock()
+		return snap, nil
+	}
+
+	if inf, ok := s.inflight[key]; ok {
+		ready := inf.ready
+		s.mu.Unlock()
+		select {
+		case <-ctx.Done():
+			return GraphResponse{}, ctx.Err()
+		case <-ready:
+			return inf.snapshot, inf.err
+		}
+	}
+
+	inf := &snapshotInflight{ready: make(chan struct{})}
+	s.inflight[key] = inf
+	s.mu.Unlock()
+
+	snap, err := fetchGraphSnapshot(ctx, s.sparql, s.cfg, nodeLimit, edgeLimit, graphQueryID)
+
+	s.mu.Lock()
+	inf.snapshot = snap
+	inf.err = err
+	delete(s.inflight, key)
+	if err == nil {
+		s.cache[key] = snap
+	}
+	close(inf.ready)
+	s.mu.Unlock()
+
+	return snap, err
+}

backend_go/sparql.go

@@ -0,0 +1,169 @@
+package main
+
+import (
+	"context"
+	"encoding/base64"
+	"fmt"
+	"io"
+	"net/http"
+	"net/url"
+	"strings"
+	"time"
+)
+
+type AnzoGraphClient struct {
+	cfg        Config
+	endpoint   string
+	authHeader string
+	client     *http.Client
+}
+
+func NewAnzoGraphClient(cfg Config) *AnzoGraphClient {
+	endpoint := cfg.EffectiveSparqlEndpoint()
+	authHeader := ""
+	user := strings.TrimSpace(cfg.SparqlUser)
+	pass := strings.TrimSpace(cfg.SparqlPass)
+	if user != "" && pass != "" {
+		token := base64.StdEncoding.EncodeToString([]byte(user + ":" + pass))
+		authHeader = "Basic " + token
+	}
+
+	return &AnzoGraphClient{
+		cfg:        cfg,
+		endpoint:   endpoint,
+		authHeader: authHeader,
+		client:     &http.Client{},
+	}
+}
+
+func (c *AnzoGraphClient) Startup(ctx context.Context) error {
+	if err := c.waitReady(ctx); err != nil {
+		return err
+	}
+
+	if c.cfg.SparqlClearOnStart {
+		if err := c.update(ctx, "CLEAR ALL"); err != nil {
+			return err
+		}
+		if err := c.waitReady(ctx); err != nil {
+			return err
+		}
+	}
+
+	if c.cfg.SparqlLoadOnStart {
+		df := strings.TrimSpace(c.cfg.SparqlDataFile)
+		if df == "" {
+			return fmt.Errorf("SPARQL_LOAD_ON_START=true but SPARQL_DATA_FILE is not set")
+		}
+		giri := strings.TrimSpace(c.cfg.SparqlGraphIRI)
+		if giri != "" {
+			if err := c.update(ctx, fmt.Sprintf("LOAD <%s> INTO GRAPH <%s>", df, giri)); err != nil {
+				return err
+			}
+		} else {
+			if err := c.update(ctx, fmt.Sprintf("LOAD <%s>", df)); err != nil {
+				return err
+			}
+		}
+		if err := c.waitReady(ctx); err != nil {
+			return err
+		}
+	}
+
+	return nil
+}
+
+func (c *AnzoGraphClient) Shutdown(ctx context.Context) error {
+	_ = ctx
+	return nil
+}
+
+func (c *AnzoGraphClient) Query(ctx context.Context, query string) ([]byte, error) {
+	return c.queryWithTimeout(ctx, query, c.cfg.SparqlTimeout)
+}
+
+func (c *AnzoGraphClient) queryWithTimeout(ctx context.Context, query string, timeout time.Duration) ([]byte, error) {
+	ctx2, cancel := context.WithTimeout(ctx, timeout)
+	defer cancel()
+
+	form := url.Values{}
+	form.Set("query", query)
+
+	req, err := http.NewRequestWithContext(ctx2, http.MethodPost, c.endpoint, strings.NewReader(form.Encode()))
+	if err != nil {
+		return nil, err
+	}
+	req.Header.Set("Content-Type", "application/x-www-form-urlencoded")
+	req.Header.Set("Accept", "application/sparql-results+json")
+	if c.authHeader != "" {
+		req.Header.Set("Authorization", c.authHeader)
+	}
+
+	resp, err := c.client.Do(req)
+	if err != nil {
+		return nil, err
+	}
+	defer resp.Body.Close()
+
+	body, err := io.ReadAll(resp.Body)
+	if err != nil {
+		return nil, err
+	}
+	if resp.StatusCode < 200 || resp.StatusCode >= 300 {
+		return nil, fmt.Errorf("sparql query failed: %s: %s", resp.Status, strings.TrimSpace(string(body)))
+	}
+	return body, nil
+}
+
+func (c *AnzoGraphClient) update(ctx context.Context, update string) error {
+	ctx2, cancel := context.WithTimeout(ctx, c.cfg.SparqlTimeout)
+	defer cancel()
+
+	req, err := http.NewRequestWithContext(ctx2, http.MethodPost, c.endpoint, strings.NewReader(update))
+	if err != nil {
+		return err
+	}
+	req.Header.Set("Content-Type", "application/sparql-update")
+	req.Header.Set("Accept", "application/json")
+	if c.authHeader != "" {
+		req.Header.Set("Authorization", c.authHeader)
+	}
+
+	resp, err := c.client.Do(req)
+	if err != nil {
+		return err
+	}
+	defer resp.Body.Close()
+
+	if resp.StatusCode < 200 || resp.StatusCode >= 300 {
+		body, _ := io.ReadAll(resp.Body)
+		return fmt.Errorf("sparql update failed: %s: %s", resp.Status, strings.TrimSpace(string(body)))
+	}
+	return nil
+}
+
+func (c *AnzoGraphClient) waitReady(ctx context.Context) error {
+	var lastErr error
+	for i := 0; i < c.cfg.SparqlReadyRetries; i++ {
+		select {
+		case <-ctx.Done():
+			if lastErr != nil {
+				return fmt.Errorf("anzograph not ready at %s: %w", c.endpoint, lastErr)
+			}
+			return ctx.Err()
+		default:
+		}
+
+		body, err := c.queryWithTimeout(ctx, "ASK WHERE { ?s ?p ?o }", c.cfg.SparqlReadyTimeout)
+		if err == nil {
+			// Ensure it's JSON, not HTML/text during boot.
+			if strings.HasPrefix(strings.TrimSpace(string(body)), "{") {
+				return nil
+			}
+			err = fmt.Errorf("unexpected readiness response: %s", strings.TrimSpace(string(body)))
+		}
+		lastErr = err
+		time.Sleep(c.cfg.SparqlReadyDelay)
+	}
+	return fmt.Errorf("anzograph not ready at %s: %w", c.endpoint, lastErr)
+}

backend_go/sparql_types.go

@@ -0,0 +1,13 @@
+package main
+
+type sparqlTerm struct {
+	Type  string `json:"type"`
+	Value string `json:"value"`
+	Lang  string `json:"xml:lang,omitempty"`
+}
+
+type sparqlResponse struct {
+	Results struct {
+		Bindings []map[string]sparqlTerm `json:"bindings"`
+	} `json:"results"`
+}

docker-compose.yml

@@ -1,23 +1,85 @@
 services:
-  app:
-    build: .
+  owl_imports_combiner:
+    build: ./python_services/owl_imports_combiner
+    environment:
+      - COMBINE_OWL_IMPORTS_ON_START=${COMBINE_OWL_IMPORTS_ON_START:-false}
+      - COMBINE_ENTRY_LOCATION
+      - COMBINE_OUTPUT_LOCATION
+      - COMBINE_OUTPUT_NAME
+      - COMBINE_FORCE=${COMBINE_FORCE:-false}
+      - TTL_PATH=${TTL_PATH:-/data/o3po.ttl}
+    volumes:
+      - ./data:/data:Z
+
+  backend:
+    build: ./backend_go
+    ports:
+      - "8000:8000"
+    environment:
+      - DEFAULT_NODE_LIMIT=${DEFAULT_NODE_LIMIT:-800000}
+      - DEFAULT_EDGE_LIMIT=${DEFAULT_EDGE_LIMIT:-2000000}
+      - MAX_NODE_LIMIT=${MAX_NODE_LIMIT:-10000000}
+      - MAX_EDGE_LIMIT=${MAX_EDGE_LIMIT:-20000000}
+      - INCLUDE_BNODES=${INCLUDE_BNODES:-false}
+      - CORS_ORIGINS=${CORS_ORIGINS:-http://localhost:5173}
+      - SPARQL_HOST=${SPARQL_HOST:-http://anzograph:8080}
+      - SPARQL_ENDPOINT
+      - SPARQL_USER=${SPARQL_USER:-admin}
+      - SPARQL_PASS=${SPARQL_PASS:-Passw0rd1}
+      - SPARQL_DATA_FILE=${SPARQL_DATA_FILE:-file:///opt/shared-files/o3po.ttl}
+      - SPARQL_GRAPH_IRI
+      - SPARQL_LOAD_ON_START=${SPARQL_LOAD_ON_START:-false}
+      - SPARQL_CLEAR_ON_START=${SPARQL_CLEAR_ON_START:-false}
+      - SPARQL_TIMEOUT_S=${SPARQL_TIMEOUT_S:-300}
+      - SPARQL_READY_RETRIES=${SPARQL_READY_RETRIES:-30}
+      - SPARQL_READY_DELAY_S=${SPARQL_READY_DELAY_S:-4}
+      - SPARQL_READY_TIMEOUT_S=${SPARQL_READY_TIMEOUT_S:-10}
+      - EDGE_BATCH_SIZE=${EDGE_BATCH_SIZE:-100000}
+      - FREE_OS_MEMORY_AFTER_SNAPSHOT=${FREE_OS_MEMORY_AFTER_SNAPSHOT:-false}
+      - LOG_SNAPSHOT_TIMINGS=${LOG_SNAPSHOT_TIMINGS:-false}
     depends_on:
-      - anzograph
+      owl_imports_combiner:
+        condition: service_completed_successfully
+      anzograph:
+        condition: service_started
+    volumes:
+      - ./data:/data:Z
+    healthcheck:
+      test: ["CMD", "curl", "-fsS", "http://localhost:8000/api/health"]
+      interval: 5s
+      timeout: 3s
+      retries: 60
+
+  frontend:
+    build: ./frontend
     ports:
       - "5173:5173"
-    env_file:
-      - .env
-    command: sh -c "npm run layout && npm run dev -- --host"
+    environment:
+      - VITE_BACKEND_URL=${VITE_BACKEND_URL:-http://backend:8000}
     volumes:
-      - .:/app:Z
+      - ./frontend:/app
       - /app/node_modules
+    depends_on:
+      backend:
+        condition: service_healthy
   
   anzograph:
     image: cambridgesemantics/anzograph:latest
     container_name: anzograph
+    mem_limit: 20g
     ports:
       - "8080:8080"
       - "8443:8443"
     volumes:
       - ./data:/opt/shared-files:Z
+      # Persist AnzoGraph state across container recreation (EULA acceptance, machine-id, settings, persistence).
+      - anzograph_app_home:/opt/anzograph/app-home
+      - anzograph_persistence:/opt/anzograph/persistence
+      - anzograph_config:/opt/anzograph/config
+      - anzograph_internal:/opt/anzograph/internal
 
+volumes:
+  anzograph_app_home:
+  anzograph_persistence:
+  anzograph_config:
+  anzograph_internal:

frontend/Dockerfile

@@ -2,6 +2,8 @@ FROM node:lts-alpine
 
 WORKDIR /app
 
+EXPOSE 5173
+
 # Copy dependency definitions
 COPY package*.json ./
 
@@ -11,8 +13,5 @@ RUN npm install
 # Copy the rest of the source code
 COPY . .
 
-# Expose the standard Vite port
-EXPOSE 5173
-
-# Compute layout, then start the dev server with --host for external access
-CMD ["sh", "-c", "npm run dev -- --host"]
+# Start the dev server with --host for external access
+CMD ["npm", "run", "dev", "--", "--host", "--port", "5173"]

frontend/README.md

@@ -0,0 +1,45 @@
+# Frontend (React + Vite) – WebGL Graph Renderer
+
+The frontend renders the snapshot from `/api/graph` using WebGL2:
+
+- Nodes are drawn as points
+- Edges are drawn as lines only when sufficiently zoomed in
+- Selection + neighbor highlighting is driven by backend “selection queries”
+
+## Run
+
+Via Docker Compose (recommended):
+
+```bash
+docker compose up --build frontend
+```
+
+Open: `http://localhost:5173`
+
+## Configuration
+
+- `VITE_BACKEND_URL` controls where `/api/*` is proxied (see `frontend/vite.config.ts`).
+
+## UI
+
+- Drag: pan
+- Scroll: zoom
+- Click: select/deselect nodes
+
+Buttons:
+
+- **Top-right:** selection query mode (controls how the backend expands “neighbors” for the current selection)
+- **Bottom-right:** graph query mode (controls which SPARQL edge set the backend uses to build the graph snapshot; switching reloads the graph)
+
+The available modes are discovered from the backend at runtime (`/api/selection_queries` and `/api/graph_queries`).
+
+## Rendering / limits
+
+The renderer uses a quadtree spatial index and draws only a subset when zoomed out:
+
+- Points:
+  - Per-frame cap: `MAX_DRAW = 2_000_000` (sampling over visible leaves)
+- Lines:
+  - Drawn only when fewer than ~20k nodes are “visible” (leaf AABB overlap with the camera frustum)
+
+Selected and “neighbor” nodes are drawn on top using index buffers.

frontend/package.json

@@ -7,7 +7,7 @@
     "dev": "vite",
     "build": "vite build",
     "preview": "vite preview",
-    "layout": "npx tsx scripts/fetch_from_db.ts && npx tsx scripts/compute_layout.ts"
+    "layout": "tsx scripts/compute_layout.ts"
   },
   "dependencies": {
     "@webgpu/types": "^0.1.69",

frontend/scripts/compute_layout.ts

@@ -0,0 +1,354 @@
+#!/usr/bin/env npx tsx
+/**
+ * Tree-Aware Force Layout
+ *
+ * Generates a random tree (via generate_tree), computes a radial tree layout,
+ * then applies gentle force refinement and writes node_positions.csv.
+ *
+ * Usage: npm run layout
+ */
+
+import { writeFileSync } from "fs";
+import { join, dirname } from "path";
+import { fileURLToPath } from "url";
+import { generateTree } from "./generate_tree.js";
+
+const __dirname = dirname(fileURLToPath(import.meta.url));
+const PUBLIC_DIR = join(__dirname, "..", "public");
+
+// ══════════════════════════════════════════════════════════
+// Configuration
+// ══════════════════════════════════════════════════════════
+
+const ENABLE_FORCE_SIM = true;  // Set to false to skip force simulation
+const ITERATIONS = 100;        // Force iterations (gentle)
+const REPULSION_K = 80;        // Repulsion strength (1% of original 8000)
+const EDGE_LENGTH = 120;       // Desired edge rest length
+const ATTRACTION_K = 0.0002;   // Spring stiffness for edges (1% of original 0.02)
+const THETA = 0.7;             // Barnes-Hut accuracy
+const INITIAL_MAX_DISP = 15;   // Starting max displacement
+const COOLING = 0.998;         // Very slow cooling per iteration
+const MIN_DIST = 0.5;
+const PRINT_EVERY = 10;        // Print progress every N iterations
+
+// Scale radius so the tree is nicely spread
+const RADIUS_PER_DEPTH = EDGE_LENGTH * 1.2;
+
+// ── Special nodes with longer parent-edges ──
+// Add vertex IDs here to give them longer edges to their parent.
+// These nodes (and all their descendants) will be pushed further out.
+const LONG_EDGE_NODES = new Set<number>([
+    // e.g. 42, 99, 150
+]);
+const LONG_EDGE_MULTIPLIER = 3.0;  // How many times longer than normal
+
+// ══════════════════════════════════════════════════════════
+// Generate tree (in-memory)
+// ══════════════════════════════════════════════════════════
+
+const { root, nodeCount: N, childrenOf, parentOf } = generateTree();
+
+const nodeIds: number[] = [];
+for (let i = 0; i < N; i++) nodeIds.push(i);
+
+// Dense index mapping (identity since IDs are 0..N-1)
+const idToIdx = new Map<number, number>();
+for (let i = 0; i < N; i++) idToIdx.set(i, i);
+
+// Edge list as index pairs (child, parent)
+const edges: Array<[number, number]> = [];
+for (const [child, parent] of parentOf) {
+    edges.push([child, parent]);
+}
+
+// Per-node neighbor list (for edge traversal)
+const neighbors: number[][] = Array.from({ length: N }, () => []);
+for (const [a, b] of edges) {
+    neighbors[a].push(b);
+    neighbors[b].push(a);
+}
+
+console.log(`Tree: ${N} nodes, ${edges.length} edges, root=${root}`);
+
+// ══════════════════════════════════════════════════════════
+// Step 1: Radial tree layout (generous spacing, no crossings)
+// ══════════════════════════════════════════════════════════
+
+const x = new Float64Array(N);
+const y = new Float64Array(N);
+const depth = new Uint32Array(N);
+const nodeRadius = new Float64Array(N); // cumulative radius from root
+
+// Compute subtree sizes
+const subtreeSize = new Uint32Array(N).fill(1);
+{
+    const rootIdx = idToIdx.get(root)!;
+    const stack: Array<{ idx: number; phase: "enter" | "exit" }> = [
+        { idx: rootIdx, phase: "enter" },
+    ];
+    while (stack.length > 0) {
+        const { idx, phase } = stack.pop()!;
+        if (phase === "enter") {
+            stack.push({ idx, phase: "exit" });
+            const kids = childrenOf.get(nodeIds[idx]);
+            if (kids) {
+                for (const kid of kids) {
+                    stack.push({ idx: idToIdx.get(kid)!, phase: "enter" });
+                }
+            }
+        } else {
+            const kids = childrenOf.get(nodeIds[idx]);
+            if (kids) {
+                for (const kid of kids) {
+                    subtreeSize[idx] += subtreeSize[idToIdx.get(kid)!];
+                }
+            }
+        }
+    }
+}
+
+// Compute depths & max depth
+let maxDepth = 0;
+{
+    const rootIdx = idToIdx.get(root)!;
+    const stack: Array<{ idx: number; d: number }> = [{ idx: rootIdx, d: 0 }];
+    while (stack.length > 0) {
+        const { idx, d } = stack.pop()!;
+        depth[idx] = d;
+        if (d > maxDepth) maxDepth = d;
+        const kids = childrenOf.get(nodeIds[idx]);
+        if (kids) {
+            for (const kid of kids) {
+                stack.push({ idx: idToIdx.get(kid)!, d: d + 1 });
+            }
+        }
+    }
+}
+
+// BFS radial assignment (cumulative radii to support per-edge lengths)
+{
+    const rootIdx = idToIdx.get(root)!;
+    x[rootIdx] = 0;
+    y[rootIdx] = 0;
+    nodeRadius[rootIdx] = 0;
+
+    interface Entry {
+        idx: number;
+        d: number;
+        aStart: number;
+        aEnd: number;
+    }
+
+    const queue: Entry[] = [{ idx: rootIdx, d: 0, aStart: 0, aEnd: 2 * Math.PI }];
+    let head = 0;
+
+    while (head < queue.length) {
+        const { idx, d, aStart, aEnd } = queue[head++];
+        const kids = childrenOf.get(nodeIds[idx]);
+        if (!kids || kids.length === 0) continue;
+
+        // Sort children by subtree size (largest sectors together for balance)
+        const sortedKids = [...kids].sort(
+            (a, b) => (subtreeSize[idToIdx.get(b)!]) - (subtreeSize[idToIdx.get(a)!])
+        );
+
+        const totalWeight = sortedKids.reduce(
+            (s, k) => s + subtreeSize[idToIdx.get(k)!], 0
+        );
+
+        let angle = aStart;
+        for (const kid of sortedKids) {
+            const kidIdx = idToIdx.get(kid)!;
+            const w = subtreeSize[kidIdx];
+            const sector = (w / totalWeight) * (aEnd - aStart);
+            const mid = angle + sector / 2;
+
+            // Cumulative radius: parent's radius + edge step (longer for special nodes)
+            const step = LONG_EDGE_NODES.has(kid)
+                ? RADIUS_PER_DEPTH * LONG_EDGE_MULTIPLIER
+                : RADIUS_PER_DEPTH;
+            const r = nodeRadius[idx] + step;
+            nodeRadius[kidIdx] = r;
+
+            x[kidIdx] = r * Math.cos(mid);
+            y[kidIdx] = r * Math.sin(mid);
+
+            queue.push({ idx: kidIdx, d: d + 1, aStart: angle, aEnd: angle + sector });
+            angle += sector;
+        }
+    }
+}
+
+console.log(`Radial layout done (depth=${maxDepth}, radius_step=${RADIUS_PER_DEPTH})`);
+
+// ══════════════════════════════════════════════════════════
+// Step 2: Gentle force refinement (preserves non-crossing)
+// ══════════════════════════════════════════════════════════
+
+// Barnes-Hut quadtree for repulsion
+interface BHNode {
+    cx: number; cy: number;
+    mass: number;
+    size: number;
+    children: (BHNode | null)[];
+    bodyIdx: number;
+}
+
+function buildBHTree(): BHNode {
+    let minX = Infinity, maxX = -Infinity, minY = Infinity, maxY = -Infinity;
+    for (let i = 0; i < N; i++) {
+        if (x[i] < minX) minX = x[i];
+        if (x[i] > maxX) maxX = x[i];
+        if (y[i] < minY) minY = y[i];
+        if (y[i] > maxY) maxY = y[i];
+    }
+    const size = Math.max(maxX - minX, maxY - minY, 1) * 1.01;
+    const cx = (minX + maxX) / 2;
+    const cy = (minY + maxY) / 2;
+
+    const root: BHNode = {
+        cx: 0, cy: 0, mass: 0, size,
+        children: [null, null, null, null], bodyIdx: -1,
+    };
+
+    for (let i = 0; i < N; i++) {
+        insert(root, i, cx, cy, size);
+    }
+    return root;
+}
+
+function insert(node: BHNode, idx: number, ncx: number, ncy: number, ns: number): void {
+    if (node.mass === 0) {
+        node.bodyIdx = idx;
+        node.cx = x[idx]; node.cy = y[idx];
+        node.mass = 1;
+        return;
+    }
+    if (node.bodyIdx >= 0) {
+        const old = node.bodyIdx;
+        node.bodyIdx = -1;
+        putInQuadrant(node, old, ncx, ncy, ns);
+    }
+    putInQuadrant(node, idx, ncx, ncy, ns);
+    const tm = node.mass + 1;
+    node.cx = (node.cx * node.mass + x[idx]) / tm;
+    node.cy = (node.cy * node.mass + y[idx]) / tm;
+    node.mass = tm;
+}
+
+function putInQuadrant(node: BHNode, idx: number, ncx: number, ncy: number, ns: number): void {
+    const hs = ns / 2;
+    const qx = x[idx] >= ncx ? 1 : 0;
+    const qy = y[idx] >= ncy ? 1 : 0;
+    const q = qy * 2 + qx;
+    const ccx = ncx + (qx ? hs / 2 : -hs / 2);
+    const ccy = ncy + (qy ? hs / 2 : -hs / 2);
+    if (!node.children[q]) {
+        node.children[q] = {
+            cx: 0, cy: 0, mass: 0, size: hs,
+            children: [null, null, null, null], bodyIdx: -1,
+        };
+    }
+    insert(node.children[q]!, idx, ccx, ccy, hs);
+}
+
+function repulse(node: BHNode, idx: number, fx: Float64Array, fy: Float64Array): void {
+    if (node.mass === 0 || node.bodyIdx === idx) return;
+    const dx = x[idx] - node.cx;
+    const dy = y[idx] - node.cy;
+    const d2 = dx * dx + dy * dy;
+    const d = Math.sqrt(d2) || MIN_DIST;
+
+    if (node.bodyIdx >= 0 || (node.size / d) < THETA) {
+        const f = REPULSION_K * node.mass / (d2 + MIN_DIST);
+        fx[idx] += (dx / d) * f;
+        fy[idx] += (dy / d) * f;
+        return;
+    }
+    for (const c of node.children) {
+        if (c) repulse(c, idx, fx, fy);
+    }
+}
+
+// ── Force simulation ──
+if (ENABLE_FORCE_SIM) {
+    console.log(`Applying gentle forces (${ITERATIONS} steps, 1% strength)...`);
+    const t0 = performance.now();
+    let maxDisp = INITIAL_MAX_DISP;
+
+    for (let iter = 0; iter < ITERATIONS; iter++) {
+        const fx = new Float64Array(N);
+        const fy = new Float64Array(N);
+
+        // 1. Repulsion
+        const tree = buildBHTree();
+        for (let i = 0; i < N; i++) {
+            repulse(tree, i, fx, fy);
+        }
+
+        // 2. Edge attraction (spring toward per-edge rest length)
+        for (const [a, b] of edges) {
+            const dx = x[b] - x[a];
+            const dy = y[b] - y[a];
+            const d = Math.sqrt(dx * dx + dy * dy) || MIN_DIST;
+            const aId = nodeIds[a], bId = nodeIds[b];
+            const isLong = LONG_EDGE_NODES.has(aId) || LONG_EDGE_NODES.has(bId);
+            const restLen = isLong ? EDGE_LENGTH * LONG_EDGE_MULTIPLIER : EDGE_LENGTH;
+            const displacement = d - restLen;
+            const f = ATTRACTION_K * displacement;
+            const ux = dx / d, uy = dy / d;
+            fx[a] += ux * f;
+            fy[a] += uy * f;
+            fx[b] -= ux * f;
+            fy[b] -= uy * f;
+        }
+
+        // 3. Apply forces with displacement cap (cooling reduces it over time)
+        for (let i = 0; i < N; i++) {
+            const mag = Math.sqrt(fx[i] * fx[i] + fy[i] * fy[i]);
+            if (mag > 0) {
+                const cap = Math.min(maxDisp, mag) / mag;
+                x[i] += fx[i] * cap;
+                y[i] += fy[i] * cap;
+            }
+        }
+
+        // 4. Cool down
+        maxDisp *= COOLING;
+
+        if ((iter + 1) % PRINT_EVERY === 0) {
+            let totalForce = 0;
+            for (let i = 0; i < N; i++) totalForce += Math.sqrt(fx[i] * fx[i] + fy[i] * fy[i]);
+            console.log(`  iter ${iter + 1}/${ITERATIONS}  max_disp=${maxDisp.toFixed(2)}  avg_force=${(totalForce / N).toFixed(2)}`);
+        }
+    }
+
+    const elapsed = performance.now() - t0;
+    console.log(`Force simulation done in ${(elapsed / 1000).toFixed(1)}s`);
+} else {
+    console.log("Force simulation SKIPPED (ENABLE_FORCE_SIM = false)");
+}
+
+// ══════════════════════════════════════════════════════════
+// Write output
+// ══════════════════════════════════════════════════════════
+
+// Write node positions
+const outLines: string[] = ["vertex,x,y"];
+for (let i = 0; i < N; i++) {
+    outLines.push(`${nodeIds[i]},${x[i]},${y[i]}`);
+}
+
+const outPath = join(PUBLIC_DIR, "node_positions.csv");
+writeFileSync(outPath, outLines.join("\n") + "\n");
+console.log(`Wrote ${N} positions to ${outPath}`);
+
+// Write edges (so the renderer can draw them)
+const edgeLines: string[] = ["source,target"];
+for (const [child, parent] of parentOf) {
+    edgeLines.push(`${child},${parent}`);
+}
+
+const edgesPath = join(PUBLIC_DIR, "edges.csv");
+writeFileSync(edgesPath, edgeLines.join("\n") + "\n");
+console.log(`Wrote ${edges.length} edges to ${edgesPath}`);

frontend/scripts/generate_tree.ts

@@ -0,0 +1,61 @@
+/**
+ * Random Tree Generator
+ *
+ * Generates a random tree with 1–MAX_CHILDREN children per node.
+ * Exports a function that returns the tree data in memory.
+ */
+
+// ══════════════════════════════════════════════════════════
+// Configuration
+// ══════════════════════════════════════════════════════════
+
+const TARGET_NODES = 100000;      // Approximate number of nodes to generate
+const MAX_CHILDREN = 3;        // Each node gets 1..MAX_CHILDREN children
+
+// ══════════════════════════════════════════════════════════
+// Tree data types
+// ══════════════════════════════════════════════════════════
+
+export interface TreeData {
+    root: number;
+    nodeCount: number;
+    childrenOf: Map<number, number[]>;
+    parentOf: Map<number, number>;
+}
+
+// ══════════════════════════════════════════════════════════
+// Generator
+// ══════════════════════════════════════════════════════════
+
+export function generateTree(): TreeData {
+    const childrenOf = new Map<number, number[]>();
+    const parentOf = new Map<number, number>();
+
+    const root = 0;
+    let nextId = 1;
+    const queue: number[] = [root];
+    let head = 0;
+
+    while (head < queue.length && nextId < TARGET_NODES) {
+        const parent = queue[head++];
+        const nKids = 1 + Math.floor(Math.random() * MAX_CHILDREN); // 1..MAX_CHILDREN
+
+        const kids: number[] = [];
+        for (let c = 0; c < nKids && nextId < TARGET_NODES; c++) {
+            const child = nextId++;
+            kids.push(child);
+            parentOf.set(child, parent);
+            queue.push(child);
+        }
+        childrenOf.set(parent, kids);
+    }
+
+    console.log(`Generated tree: ${nextId} nodes, ${parentOf.size} edges, root=${root}`);
+
+    return {
+        root,
+        nodeCount: nextId,
+        childrenOf,
+        parentOf,
+    };
+}

frontend/src/App.tsx

@@ -0,0 +1,596 @@
+import { useEffect, useRef, useState } from "react";
+import { Renderer } from "./renderer";
+import { fetchGraphQueries } from "./graph_queries";
+import type { GraphQueryMeta } from "./graph_queries";
+import { fetchSelectionQueries, runSelectionQuery } from "./selection_queries";
+import type { GraphMeta, SelectionQueryMeta } from "./selection_queries";
+
+function sleep(ms: number): Promise<void> {
+  return new Promise((r) => setTimeout(r, ms));
+}
+
+export default function App() {
+  const canvasRef = useRef<HTMLCanvasElement>(null);
+  const rendererRef = useRef<Renderer | null>(null);
+  const [status, setStatus] = useState("Waiting for backend…");
+  const [nodeCount, setNodeCount] = useState(0);
+  const [stats, setStats] = useState({
+    fps: 0,
+    drawn: 0,
+    mode: "",
+    zoom: 0,
+    ptSize: 0,
+  });
+  const [error, setError] = useState("");
+  const [hoveredNode, setHoveredNode] = useState<{ x: number; y: number; screenX: number; screenY: number; label?: string; iri?: string } | null>(null);
+  const [selectedNodes, setSelectedNodes] = useState<Set<number>>(new Set());
+  const [graphQueries, setGraphQueries] = useState<GraphQueryMeta[]>([]);
+  const [activeGraphQueryId, setActiveGraphQueryId] = useState<string>("default");
+  const [selectionQueries, setSelectionQueries] = useState<SelectionQueryMeta[]>([]);
+  const [activeSelectionQueryId, setActiveSelectionQueryId] = useState<string>("neighbors");
+  const [backendStats, setBackendStats] = useState<{ nodes: number; edges: number; backend?: string } | null>(null);
+  const graphMetaRef = useRef<GraphMeta | null>(null);
+  const selectionReqIdRef = useRef(0);
+  const graphInitializedRef = useRef(false);
+
+  // Store mouse position in a ref so it can be accessed in render loop without re-renders
+  const mousePos = useRef({ x: 0, y: 0 });
+  const nodesRef = useRef<any[]>([]);
+
+  async function loadGraph(graphQueryId: string, signal: AbortSignal): Promise<void> {
+    const renderer = rendererRef.current;
+    if (!renderer) return;
+
+    setStatus("Fetching graph…");
+    const graphRes = await fetch(`/api/graph?graph_query_id=${encodeURIComponent(graphQueryId)}`, { signal });
+    if (!graphRes.ok) {
+      let detail = "";
+      try {
+        const err = await graphRes.json();
+        if (err && typeof err === "object" && typeof (err as any).detail === "string") {
+          detail = (err as any).detail;
+        }
+      } catch {
+        // ignore
+      }
+      throw new Error(`Failed to fetch graph: ${graphRes.status}${detail ? ` (${detail})` : ""}`);
+    }
+    const graph = await graphRes.json();
+    if (signal.aborted) return;
+
+    const nodes = Array.isArray(graph.nodes) ? graph.nodes : [];
+    const edges = Array.isArray(graph.edges) ? graph.edges : [];
+    const meta = graph.meta || null;
+    const count = nodes.length;
+
+    nodesRef.current = nodes;
+    graphMetaRef.current = meta && typeof meta === "object" ? (meta as GraphMeta) : null;
+
+    // Build positions from backend-provided node coordinates.
+    setStatus("Preparing buffers…");
+    const xs = new Float32Array(count);
+    const ys = new Float32Array(count);
+    for (let i = 0; i < count; i++) {
+      const nx = nodes[i]?.x;
+      const ny = nodes[i]?.y;
+      xs[i] = typeof nx === "number" ? nx : 0;
+      ys[i] = typeof ny === "number" ? ny : 0;
+    }
+    const vertexIds = new Uint32Array(count);
+    for (let i = 0; i < count; i++) {
+      const id = nodes[i]?.id;
+      vertexIds[i] = typeof id === "number" ? id >>> 0 : i;
+    }
+
+    // Build edges as vertex-id pairs.
+    const edgeData = new Uint32Array(edges.length * 2);
+    for (let i = 0; i < edges.length; i++) {
+      const s = edges[i]?.source;
+      const t = edges[i]?.target;
+      edgeData[i * 2] = typeof s === "number" ? s >>> 0 : 0;
+      edgeData[i * 2 + 1] = typeof t === "number" ? t >>> 0 : 0;
+    }
+
+    // Use /api/graph meta; don't do a second expensive backend call.
+    if (meta && typeof meta.nodes === "number" && typeof meta.edges === "number") {
+      setBackendStats({
+        nodes: meta.nodes,
+        edges: meta.edges,
+        backend: typeof meta.backend === "string" ? meta.backend : undefined,
+      });
+    } else {
+      setBackendStats({ nodes: nodes.length, edges: edges.length });
+    }
+
+    setStatus("Building spatial index…");
+    await new Promise((r) => setTimeout(r, 0));
+    if (signal.aborted) return;
+
+    const buildMs = renderer.init(xs, ys, vertexIds, edgeData);
+    setNodeCount(renderer.getNodeCount());
+    setSelectedNodes(new Set());
+    setStatus("");
+    console.log(`Init complete: ${count.toLocaleString()} nodes, ${edges.length.toLocaleString()} edges in ${buildMs.toFixed(0)}ms`);
+  }
+
+  useEffect(() => {
+    const canvas = canvasRef.current;
+    if (!canvas) return;
+
+    let renderer: Renderer;
+    try {
+      renderer = new Renderer(canvas);
+      rendererRef.current = renderer;
+    } catch (e) {
+      setError(e instanceof Error ? e.message : String(e));
+      return;
+    }
+
+    let cancelled = false;
+    const initCtrl = new AbortController();
+    graphInitializedRef.current = false;
+
+    (async () => {
+      try {
+        // Wait for backend (docker-compose also gates startup via healthcheck, but this
+        // handles running the frontend standalone).
+        const deadline = performance.now() + 180_000;
+        let attempt = 0;
+        while (performance.now() < deadline) {
+          attempt++;
+          setStatus(`Waiting for backend… (attempt ${attempt})`);
+          try {
+            const res = await fetch("/api/health");
+            if (res.ok) break;
+          } catch {
+            // ignore and retry
+          }
+          await sleep(1000);
+          if (cancelled) return;
+        }
+
+        let graphQueryToLoad = activeGraphQueryId;
+        try {
+          setStatus("Fetching graph modes…");
+          const gqs = await fetchGraphQueries(initCtrl.signal);
+          if (cancelled || initCtrl.signal.aborted) return;
+          setGraphQueries(gqs);
+          graphQueryToLoad = gqs.some((q) => q.id === graphQueryToLoad) ? graphQueryToLoad : (gqs[0]?.id ?? "default");
+          setActiveGraphQueryId(graphQueryToLoad);
+        } catch {
+          if (cancelled || initCtrl.signal.aborted) return;
+          setGraphQueries([{ id: "default", label: "Default" }]);
+          graphQueryToLoad = "default";
+          setActiveGraphQueryId("default");
+        }
+
+        await loadGraph(graphQueryToLoad, initCtrl.signal);
+        if (cancelled || initCtrl.signal.aborted) return;
+
+        try {
+          const qs = await fetchSelectionQueries(initCtrl.signal);
+          if (cancelled) return;
+          setSelectionQueries(qs);
+          setActiveSelectionQueryId((prev) => (qs.length > 0 && !qs.some((q) => q.id === prev) ? qs[0].id : prev));
+        } catch {
+          if (cancelled) return;
+          setSelectionQueries([{ id: "neighbors", label: "Neighbors" }]);
+          setActiveSelectionQueryId((prev) => (prev ? prev : "neighbors"));
+        }
+
+        graphInitializedRef.current = true;
+      } catch (e) {
+        if (!cancelled) {
+          setError(e instanceof Error ? e.message : String(e));
+        }
+      }
+    })();
+
+    // ── Input handling ──
+    let dragging = false;
+    let didDrag = false; // true if mouse moved significantly during drag
+    let downX = 0;
+    let downY = 0;
+    let lastX = 0;
+    let lastY = 0;
+    const DRAG_THRESHOLD = 5; // pixels
+
+    const onDown = (e: MouseEvent) => {
+      dragging = true;
+      didDrag = false;
+      downX = e.clientX;
+      downY = e.clientY;
+      lastX = e.clientX;
+      lastY = e.clientY;
+    };
+    const onMove = (e: MouseEvent) => {
+      mousePos.current = { x: e.clientX, y: e.clientY };
+      if (!dragging) return;
+
+      // Check if we've moved enough to consider it a drag
+      const dx = e.clientX - downX;
+      const dy = e.clientY - downY;
+      if (Math.abs(dx) > DRAG_THRESHOLD || Math.abs(dy) > DRAG_THRESHOLD) {
+        didDrag = true;
+      }
+
+      renderer.pan(e.clientX - lastX, e.clientY - lastY);
+      lastX = e.clientX;
+      lastY = e.clientY;
+    };
+    const onUp = (e: MouseEvent) => {
+      if (dragging && !didDrag) {
+        // This was a click, not a drag - handle selection
+        const node = renderer.findNodeIndexAt(e.clientX, e.clientY);
+        if (node) {
+          setSelectedNodes((prev: Set<number>) => {
+            const next = new Set(prev);
+            if (next.has(node.index)) {
+              next.delete(node.index); // Deselect if already selected
+            } else {
+              next.add(node.index); // Select
+            }
+            return next;
+          });
+        }
+      }
+      dragging = false;
+      didDrag = false;
+    };
+    const onWheel = (e: WheelEvent) => {
+      e.preventDefault();
+      const factor = e.deltaY > 0 ? 0.9 : 1 / 0.9;
+      renderer.zoomAt(factor, e.clientX, e.clientY);
+    };
+    const onMouseLeave = () => {
+      setHoveredNode(null);
+    };
+
+    canvas.addEventListener("mousedown", onDown);
+    window.addEventListener("mousemove", onMove);
+    window.addEventListener("mouseup", onUp);
+    canvas.addEventListener("wheel", onWheel, { passive: false });
+    canvas.addEventListener("mouseleave", onMouseLeave);
+
+    // ── Render loop ──
+    let frameCount = 0;
+    let lastTime = performance.now();
+    let raf = 0;
+
+    const frame = () => {
+      const result = renderer.render();
+      frameCount++;
+
+      // Find hovered node using quadtree
+      const hit = renderer.findNodeIndexAt(mousePos.current.x, mousePos.current.y);
+      if (hit) {
+        const origIdx = renderer.sortedIndexToOriginalIndex(hit.index);
+        const meta = origIdx === null ? null : nodesRef.current[origIdx];
+        setHoveredNode({
+          x: hit.x,
+          y: hit.y,
+          screenX: mousePos.current.x,
+          screenY: mousePos.current.y,
+          label: meta && typeof meta.label === "string" ? meta.label : undefined,
+          iri: meta && typeof meta.iri === "string" ? meta.iri : undefined,
+        });
+      } else {
+        setHoveredNode(null);
+      }
+
+      const now = performance.now();
+      if (now - lastTime >= 500) {
+        const fps = (frameCount / (now - lastTime)) * 1000;
+        setStats({
+          fps: Math.round(fps),
+          drawn: result.drawnCount,
+          mode: result.mode,
+          zoom: result.zoom,
+          ptSize: result.ptSize,
+        });
+        frameCount = 0;
+        lastTime = now;
+      }
+
+      raf = requestAnimationFrame(frame);
+    };
+    raf = requestAnimationFrame(frame);
+
+    return () => {
+      cancelled = true;
+      initCtrl.abort();
+      cancelAnimationFrame(raf);
+      canvas.removeEventListener("mousedown", onDown);
+      window.removeEventListener("mousemove", onMove);
+      window.removeEventListener("mouseup", onUp);
+      canvas.removeEventListener("wheel", onWheel);
+      canvas.removeEventListener("mouseleave", onMouseLeave);
+    };
+  }, []);
+
+  // Reload graph when the graph query mode changes (after initial load)
+  useEffect(() => {
+    if (!graphInitializedRef.current) return;
+    const renderer = rendererRef.current;
+    if (!renderer) return;
+    if (!activeGraphQueryId) return;
+
+    const ctrl = new AbortController();
+    (async () => {
+      try {
+        await loadGraph(activeGraphQueryId, ctrl.signal);
+      } catch (e) {
+        if (ctrl.signal.aborted) return;
+        setError(e instanceof Error ? e.message : String(e));
+      }
+    })();
+
+    return () => ctrl.abort();
+  }, [activeGraphQueryId]);
+
+  // Sync selection state to renderer
+  useEffect(() => {
+    const renderer = rendererRef.current;
+    if (!renderer) return;
+
+    // Optimistically reflect selection immediately; highlights will be filled in by backend.
+    renderer.updateSelection(selectedNodes, new Set());
+
+    // Invalidate any in-flight request for the previous selection/mode.
+    const reqId = ++selectionReqIdRef.current;
+
+    // Convert selected sorted indices to backend node IDs (graph-export dense IDs).
+    const selectedIds: number[] = [];
+    for (const sortedIdx of selectedNodes) {
+      const origIdx = renderer.sortedIndexToOriginalIndex(sortedIdx);
+      if (origIdx === null) continue;
+      const n = nodesRef.current?.[origIdx];
+      const nodeId = n?.id;
+      if (typeof nodeId !== "number") continue;
+      selectedIds.push(nodeId);
+    }
+
+    if (selectedIds.length === 0) {
+      return;
+    }
+
+    const queryId = (activeSelectionQueryId || selectionQueries[0]?.id || "neighbors").trim();
+
+    const ctrl = new AbortController();
+
+    (async () => {
+      try {
+        const neighborIds = await runSelectionQuery(queryId, selectedIds, graphMetaRef.current, ctrl.signal);
+        if (ctrl.signal.aborted) return;
+        if (reqId !== selectionReqIdRef.current) return;
+
+        const neighborSorted = new Set<number>();
+        for (const id of neighborIds) {
+          if (typeof id !== "number") continue;
+          const sorted = renderer.vertexIdToSortedIndexOrNull(id);
+          if (sorted === null) continue;
+          if (!selectedNodes.has(sorted)) neighborSorted.add(sorted);
+        }
+
+        renderer.updateSelection(selectedNodes, neighborSorted);
+      } catch (e) {
+        if (ctrl.signal.aborted) return;
+        console.warn(e);
+        // Keep the UI usable even if neighbors fail to load.
+        renderer.updateSelection(selectedNodes, new Set());
+      }
+    })();
+
+    return () => ctrl.abort();
+  }, [selectedNodes, activeSelectionQueryId]);
+
+  return (
+    <div style={{ width: "100vw", height: "100vh", overflow: "hidden", background: "#000" }}>
+      <canvas
+        ref={canvasRef}
+        style={{ display: "block", width: "100%", height: "100%" }}
+      />
+
+      {/* Loading overlay */}
+      {status && (
+        <div
+          style={{
+            position: "absolute",
+            inset: 0,
+            display: "flex",
+            alignItems: "center",
+            justifyContent: "center",
+            background: "rgba(0,0,0,0.9)",
+            color: "#0f0",
+            fontFamily: "monospace",
+            fontSize: "16px",
+          }}
+        >
+          {status}
+        </div>
+      )}
+
+      {/* Error overlay */}
+      {error && (
+        <div
+          style={{
+            position: "absolute",
+            inset: 0,
+            display: "flex",
+            alignItems: "center",
+            justifyContent: "center",
+            background: "rgba(0,0,0,0.9)",
+            color: "#f44",
+            fontFamily: "monospace",
+            fontSize: "16px",
+          }}
+        >
+          Error: {error}
+        </div>
+      )}
+
+      {/* HUD */}
+      {!status && !error && (
+        <>
+          <div
+            style={{
+              position: "absolute",
+              top: 10,
+              left: 10,
+              background: "rgba(0,0,0,0.75)",
+              color: "#0f0",
+              fontFamily: "monospace",
+              padding: "8px 12px",
+              fontSize: "12px",
+              lineHeight: "1.6",
+              borderRadius: "4px",
+              pointerEvents: "none",
+            }}
+          >
+            <div>FPS: {stats.fps}</div>
+            <div>Drawn: {stats.drawn.toLocaleString()} / {nodeCount.toLocaleString()}</div>
+            <div>Mode: {stats.mode}</div>
+            <div>Zoom: {stats.zoom < 0.01 ? stats.zoom.toExponential(2) : stats.zoom.toFixed(2)} px/unit</div>
+            <div>Pt Size: {stats.ptSize.toFixed(1)}px</div>
+            <div style={{ color: "#f80" }}>Selected: {selectedNodes.size}</div>
+            {backendStats && (
+              <div style={{ color: "#8f8" }}>
+                Backend{backendStats.backend ? ` (${backendStats.backend})` : ""}: {backendStats.nodes.toLocaleString()} nodes, {backendStats.edges.toLocaleString()} edges
+              </div>
+            )}
+          </div>
+          <div
+            style={{
+              position: "absolute",
+              bottom: 10,
+              left: 10,
+              background: "rgba(0,0,0,0.75)",
+              color: "#888",
+              fontFamily: "monospace",
+              padding: "6px 10px",
+              fontSize: "11px",
+              borderRadius: "4px",
+              pointerEvents: "none",
+            }}
+          >
+            Drag to pan · Scroll to zoom · Click to select
+          </div>
+
+          {/* Selection query buttons */}
+          {selectionQueries.length > 0 && (
+            <div
+              style={{
+                position: "absolute",
+                top: 10,
+                right: 10,
+                display: "flex",
+                flexDirection: "column",
+                gap: "6px",
+                background: "rgba(0,0,0,0.55)",
+                padding: "8px",
+                borderRadius: "6px",
+                border: "1px solid rgba(255,255,255,0.08)",
+                pointerEvents: "auto",
+              }}
+            >
+              {selectionQueries.map((q) => {
+                const active = q.id === activeSelectionQueryId;
+                return (
+                  <button
+                    key={q.id}
+                    onClick={() => setActiveSelectionQueryId(q.id)}
+                    style={{
+                      cursor: "pointer",
+                      fontFamily: "monospace",
+                      fontSize: "12px",
+                      padding: "6px 10px",
+                      borderRadius: "4px",
+                      border: active ? "1px solid rgba(0,255,255,0.8)" : "1px solid rgba(255,255,255,0.12)",
+                      background: active ? "rgba(0,255,255,0.12)" : "rgba(255,255,255,0.04)",
+                      color: active ? "#0ff" : "#bbb",
+                      textAlign: "left",
+                    }}
+                    aria-pressed={active}
+                  >
+                    {q.label}
+                  </button>
+                );
+              })}
+            </div>
+          )}
+
+          {/* Graph query buttons */}
+          {graphQueries.length > 0 && (
+            <div
+              style={{
+                position: "absolute",
+                bottom: 10,
+                right: 10,
+                display: "flex",
+                flexDirection: "column",
+                gap: "6px",
+                background: "rgba(0,0,0,0.55)",
+                padding: "8px",
+                borderRadius: "6px",
+                border: "1px solid rgba(255,255,255,0.08)",
+                pointerEvents: "auto",
+              }}
+            >
+              {graphQueries.map((q) => {
+                const active = q.id === activeGraphQueryId;
+                return (
+                  <button
+                    key={q.id}
+                    onClick={() => setActiveGraphQueryId(q.id)}
+                    style={{
+                      cursor: "pointer",
+                      fontFamily: "monospace",
+                      fontSize: "12px",
+                      padding: "6px 10px",
+                      borderRadius: "4px",
+                      border: active ? "1px solid rgba(0,255,0,0.8)" : "1px solid rgba(255,255,255,0.12)",
+                      background: active ? "rgba(0,255,0,0.12)" : "rgba(255,255,255,0.04)",
+                      color: active ? "#8f8" : "#bbb",
+                      textAlign: "left",
+                    }}
+                    aria-pressed={active}
+                  >
+                    {q.label}
+                  </button>
+                );
+              })}
+            </div>
+          )}
+
+          {/* Hover tooltip */}
+          {hoveredNode && (
+            <div
+              style={{
+                position: "absolute",
+                left: hoveredNode.screenX + 15,
+                top: hoveredNode.screenY + 15,
+                background: "rgba(0,0,0,0.85)",
+                color: "#0ff",
+                fontFamily: "monospace",
+                padding: "6px 10px",
+                fontSize: "12px",
+                borderRadius: "4px",
+                pointerEvents: "none",
+                whiteSpace: "nowrap",
+                border: "1px solid rgba(0,255,255,0.3)",
+                boxShadow: "0 2px 8px rgba(0,0,0,0.5)",
+              }}
+            >
+              <div style={{ color: "#0ff" }}>
+                {hoveredNode.label || hoveredNode.iri || "(unknown)"}
+              </div>
+              <div style={{ color: "#688" }}>
+                ({hoveredNode.x.toFixed(2)}, {hoveredNode.y.toFixed(2)})
+              </div>
+            </div>
+          )}
+        </>
+      )}
+    </div>
+  );
+}

frontend/src/graph_queries/api.ts

@@ -0,0 +1,9 @@
+import type { GraphQueryMeta } from "./types";
+
+export async function fetchGraphQueries(signal?: AbortSignal): Promise<GraphQueryMeta[]> {
+  const res = await fetch("/api/graph_queries", { signal });
+  if (!res.ok) throw new Error(`GET /api/graph_queries failed: ${res.status}`);
+  const data = await res.json();
+  return Array.isArray(data) ? (data as GraphQueryMeta[]) : [];
+}
+

frontend/src/graph_queries/index.ts

@@ -0,0 +1,3 @@
+export { fetchGraphQueries } from "./api";
+export type { GraphQueryMeta } from "./types";
+

frontend/src/graph_queries/types.ts

@@ -0,0 +1,5 @@
+export type GraphQueryMeta = {
+  id: string;
+  label: string;
+};
+

frontend/src/renderer.ts

@@ -80,10 +80,11 @@ export class Renderer {
   // Data
   private leaves: Leaf[] = [];
   private sorted: Float32Array = new Float32Array(0);
+  // order[sortedIdx] = originalIdx (original ordering matches input arrays)
+  private sortedToOriginal: Uint32Array = new Uint32Array(0);
+  private vertexIdToSortedIndex: Map<number, number> = new Map();
   private nodeCount = 0;
   private edgeCount = 0;
-  private neighborMap: Map<number, number[]> = new Map();
-  private sortedToVertexId: Uint32Array = new Uint32Array(0);
   private leafEdgeStarts: Uint32Array = new Uint32Array(0);
   private leafEdgeCounts: Uint32Array = new Uint32Array(0);
   private maxPtSize = 256;
@@ -203,6 +204,7 @@ export class Renderer {
     const { sorted, leaves, order } = buildSpatialIndex(xs, ys);
     this.leaves = leaves;
     this.sorted = sorted;
+    this.sortedToOriginal = order;
 
     // Pre-allocate arrays for render loop (zero-allocation rendering)
     this.visibleLeafIndices = new Uint32Array(leaves.length);
@@ -214,12 +216,6 @@ export class Renderer {
     gl.bufferData(gl.ARRAY_BUFFER, sorted, gl.STATIC_DRAW);
     gl.bindVertexArray(null);
 
-    // Build sorted index → vertex ID mapping for hover lookups
-    this.sortedToVertexId = new Uint32Array(count);
-    for (let i = 0; i < count; i++) {
-      this.sortedToVertexId[i] = vertexIds[order[i]];
-    }
-
     // Build vertex ID → original input index mapping
     const vertexIdToOriginal = new Map<number, number>();
     for (let i = 0; i < count; i++) {
@@ -233,6 +229,13 @@ export class Renderer {
       originalToSorted[order[i]] = i;
     }
 
+    // Build vertex ID → sorted index mapping (used by backend-driven neighbor highlighting)
+    const vertexIdToSortedIndex = new Map<number, number>();
+    for (let i = 0; i < count; i++) {
+      vertexIdToSortedIndex.set(vertexIds[i], originalToSorted[i]);
+    }
+    this.vertexIdToSortedIndex = vertexIdToSortedIndex;
+
     // Remap edges from vertex IDs to sorted indices
     const lineIndices = new Uint32Array(edgeCount * 2);
     let validEdges = 0;
@@ -248,18 +251,6 @@ export class Renderer {
     }
     this.edgeCount = validEdges;
 
-    // Build per-node neighbor list from edges for selection queries
-    const neighborMap = new Map<number, number[]>();
-    for (let i = 0; i < validEdges; i++) {
-      const src = lineIndices[i * 2];
-      const dst = lineIndices[i * 2 + 1];
-      if (!neighborMap.has(src)) neighborMap.set(src, []);
-      neighborMap.get(src)!.push(dst);
-      if (!neighborMap.has(dst)) neighborMap.set(dst, []);
-      neighborMap.get(dst)!.push(src);
-    }
-    this.neighborMap = neighborMap;
-
     // Build per-leaf edge index for efficient visible-only edge drawing
     // Find which leaf each sorted index belongs to
     const nodeToLeaf = new Uint32Array(count);
@@ -339,12 +330,25 @@ export class Renderer {
   }
 
   /**
-   * Get the original vertex ID for a given sorted index.
-   * Useful for looking up URI labels from the URI map.
+   * Map a sorted buffer index (what findNodeIndexAt returns) back to the original
+   * index in the input arrays used to initialize the renderer.
    */
-  getVertexId(sortedIndex: number): number | undefined {
-    if (sortedIndex < 0 || sortedIndex >= this.sortedToVertexId.length) return undefined;
-    return this.sortedToVertexId[sortedIndex];
+  sortedIndexToOriginalIndex(sortedIndex: number): number | null {
+    if (
+      sortedIndex < 0 ||
+      sortedIndex >= this.sortedToOriginal.length
+    ) {
+      return null;
+    }
+    return this.sortedToOriginal[sortedIndex];
+  }
+
+  /**
+   * Convert a backend node ID (node.id from /api/graph) to a sorted index used by the renderer.
+   */
+  vertexIdToSortedIndexOrNull(vertexId: number): number | null {
+    const idx = this.vertexIdToSortedIndex.get(vertexId);
+    return typeof idx === "number" ? idx : null;
   }
 
   /**
@@ -428,10 +432,10 @@ export class Renderer {
 
   /**
    * Update the selection buffer with the given set of node indices.
-   * Also computes neighbors of selected nodes.
-   * Call this whenever React's selection state changes.
+   * Neighbor indices are provided by the backend (SPARQL query) and uploaded separately.
+   * Call this whenever selection or backend neighbor results change.
    */
-  updateSelection(selectedIndices: Set<number>): void {
+  updateSelection(selectedIndices: Set<number>, neighborIndices: Set<number> = new Set()): void {
     const gl = this.gl;
 
     // Upload selected indices
@@ -441,23 +445,11 @@ export class Renderer {
     gl.bufferData(gl.ELEMENT_ARRAY_BUFFER, indices, gl.DYNAMIC_DRAW);
     gl.bindBuffer(gl.ELEMENT_ARRAY_BUFFER, null);
 
-    // Compute neighbors of selected nodes (excluding already selected)
-    const neighborSet = new Set<number>();
-    for (const nodeIdx of selectedIndices) {
-      const nodeNeighbors = this.neighborMap.get(nodeIdx);
-      if (!nodeNeighbors) continue;
-      for (const n of nodeNeighbors) {
-        if (!selectedIndices.has(n)) {
-          neighborSet.add(n);
-        }
-      }
-    }
-
     // Upload neighbor indices
-    const neighborIndices = new Uint32Array(neighborSet);
-    this.neighborCount = neighborIndices.length;
+    const neighborIndexArray = new Uint32Array(neighborIndices);
+    this.neighborCount = neighborIndexArray.length;
     gl.bindBuffer(gl.ELEMENT_ARRAY_BUFFER, this.neighborIbo);
-    gl.bufferData(gl.ELEMENT_ARRAY_BUFFER, neighborIndices, gl.DYNAMIC_DRAW);
+    gl.bufferData(gl.ELEMENT_ARRAY_BUFFER, neighborIndexArray, gl.DYNAMIC_DRAW);
     gl.bindBuffer(gl.ELEMENT_ARRAY_BUFFER, null);
   }
 

frontend/src/selection_queries/api.ts

@@ -0,0 +1,37 @@
+import type { GraphMeta, SelectionQueryMeta } from "./types";
+
+export async function fetchSelectionQueries(signal?: AbortSignal): Promise<SelectionQueryMeta[]> {
+  const res = await fetch("/api/selection_queries", { signal });
+  if (!res.ok) throw new Error(`GET /api/selection_queries failed: ${res.status}`);
+  const data = await res.json();
+  return Array.isArray(data) ? (data as SelectionQueryMeta[]) : [];
+}
+
+export async function runSelectionQuery(
+  queryId: string,
+  selectedIds: number[],
+  graphMeta: GraphMeta | null,
+  signal: AbortSignal
+): Promise<number[]> {
+  const body = {
+    query_id: queryId,
+    selected_ids: selectedIds,
+    node_limit: typeof graphMeta?.node_limit === "number" ? graphMeta.node_limit : undefined,
+    edge_limit: typeof graphMeta?.edge_limit === "number" ? graphMeta.edge_limit : undefined,
+    graph_query_id: typeof graphMeta?.graph_query_id === "string" ? graphMeta.graph_query_id : undefined,
+  };
+
+  const res = await fetch("/api/selection_query", {
+    method: "POST",
+    headers: { "content-type": "application/json" },
+    body: JSON.stringify(body),
+    signal,
+  });
+  if (!res.ok) throw new Error(`POST /api/selection_query failed: ${res.status}`);
+  const data = await res.json();
+  const ids: unknown = data?.neighbor_ids;
+  if (!Array.isArray(ids)) return [];
+  const out: number[] = [];
+  for (const id of ids) if (typeof id === "number") out.push(id);
+  return out;
+}

frontend/src/selection_queries/index.ts

@@ -0,0 +1,3 @@
+export { fetchSelectionQueries, runSelectionQuery } from "./api";
+export type { GraphMeta, SelectionQueryMeta } from "./types";
+

frontend/src/selection_queries/types.ts

@@ -0,0 +1,16 @@
+export type GraphMeta = {
+  backend?: string;
+  ttl_path?: string | null;
+  sparql_endpoint?: string | null;
+  include_bnodes?: boolean;
+  graph_query_id?: string;
+  node_limit?: number;
+  edge_limit?: number;
+  nodes?: number;
+  edges?: number;
+};
+
+export type SelectionQueryMeta = {
+  id: string;
+  label: string;
+};

frontend/vite.config.ts

@@ -0,0 +1,54 @@
+import path from "path";
+import { fileURLToPath } from "url";
+import tailwindcss from "@tailwindcss/vite";
+import react from "@vitejs/plugin-react";
+import { defineConfig } from "vite";
+import { viteSingleFile } from "vite-plugin-singlefile";
+
+const __filename = fileURLToPath(import.meta.url);
+const __dirname = path.dirname(__filename);
+
+// https://vite.dev/config/
+export default defineConfig({
+  plugins: [
+    react(),
+    tailwindcss(),
+    viteSingleFile(),
+    {
+      name: "long-timeouts",
+      configureServer(server) {
+        // Large graph snapshots can take minutes; keep the dev server from killing the request.
+        const httpServer = server.httpServer;
+        if (!httpServer) return;
+        const ms30m = 30 * 60 * 1000;
+        httpServer.headersTimeout = ms30m;
+        httpServer.requestTimeout = ms30m;
+        httpServer.keepAliveTimeout = ms30m;
+      },
+    },
+  ],
+  resolve: {
+    alias: {
+      "@": path.resolve(__dirname, "src"),
+    },
+  },
+  server: {
+    proxy: {
+      // Backend is reachable as http://backend:8000 inside docker-compose; localhost outside.
+      "/api": {
+        target: process.env.VITE_BACKEND_URL || "http://localhost:8000",
+        changeOrigin: true,
+        configure: (proxy) => {
+          proxy.on("error", (err) => {
+            // Surface upstream timeouts/socket errors in `docker compose logs frontend`.
+            console.error("[vite-proxy] /api error:", err);
+          });
+        },
+        // The initial graph snapshot can take minutes with large limits (SPARQL + layout + labels).
+        // Prevent the dev proxy from timing out and returning a 500 to the browser.
+        timeout: 30 * 60 * 1000,
+        proxyTimeout: 30 * 60 * 1000,
+      },
+    },
+  },
+});

public/node_positions.csv

@@ -1 +0,0 @@
-vertex,x,y

public/primary_edges.csv

@@ -1 +0,0 @@
-source,target

public/secondary_edges.csv

@@ -1 +0,0 @@
-source,target

public/uri_map.csv

@@ -1 +0,0 @@
-id,uri,label,isPrimary

python_services/owl_imports_combiner/Dockerfile

@@ -0,0 +1,14 @@
+FROM python:3.12-slim
+
+WORKDIR /app
+
+ENV PYTHONDONTWRITEBYTECODE=1 \
+    PYTHONUNBUFFERED=1
+
+COPY requirements.txt /app/requirements.txt
+RUN pip install --no-cache-dir -r /app/requirements.txt
+
+COPY owl_imports_combiner.py /app/owl_imports_combiner.py
+COPY main.py /app/main.py
+
+CMD ["python", "/app/main.py"]

python_services/owl_imports_combiner/README.md

@@ -0,0 +1,36 @@
+# owl_imports_combiner (Python service)
+
+One-shot utility container that loads an ontology and recursively follows `owl:imports`, then writes a single combined Turtle file.
+
+This is useful to precompute a single TTL for AnzoGraph loading.
+
+## Run
+
+Via Docker Compose:
+
+```bash
+docker compose run --rm owl_imports_combiner
+```
+
+The service mounts `./data → /data`, so use output paths under `/data/...`.
+
+## Environment variables
+
+- `COMBINE_OWL_IMPORTS_ON_START` (default `false`)
+  - If `false`, the container exits without doing anything.
+- `COMBINE_ENTRY_LOCATION`
+  - Entry ontology: local path, `file://` URI, or `http(s)` URL.
+  - If unset, falls back to `TTL_PATH`.
+- `COMBINE_OUTPUT_LOCATION`
+  - Output location (local file path or `file://` URI). Required if entry is an `http(s)` URL.
+- `COMBINE_OUTPUT_NAME` (default `combined_ontology.ttl`)
+  - Used only when `COMBINE_OUTPUT_LOCATION` is unset and entry is a local file.
+- `COMBINE_FORCE` (default `false`)
+  - Overwrite output if it already exists.
+- `LOG_LEVEL` (default `INFO`)
+
+## Behavior
+
+- If the output exists and `COMBINE_FORCE=false`, it skips the combine step.
+- Output is written atomically via a temporary file + rename.
+

python_services/owl_imports_combiner/main.py

@@ -0,0 +1,54 @@
+from __future__ import annotations
+
+import logging
+import os
+
+from owl_imports_combiner import (
+    build_combined_graph,
+    output_location_to_path,
+    resolve_output_location,
+    serialize_graph_to_ttl,
+)
+
+
+logger = logging.getLogger(__name__)
+
+
+def _env_bool(name: str, *, default: bool = False) -> bool:
+    val = os.getenv(name)
+    if val is None:
+        return default
+    return val.strip().lower() in {"1", "true", "yes", "y", "on"}
+
+
+def main() -> None:
+    logging.basicConfig(level=os.getenv("LOG_LEVEL", "INFO").upper())
+
+    if not _env_bool("COMBINE_OWL_IMPORTS_ON_START", default=False):
+        logger.info("Skipping combine step (COMBINE_OWL_IMPORTS_ON_START=false)")
+        return
+
+    entry_location = os.getenv("COMBINE_ENTRY_LOCATION") or os.getenv("TTL_PATH")
+    if not entry_location:
+        raise SystemExit("Set COMBINE_ENTRY_LOCATION (or TTL_PATH) to the ontology file/URL to load.")
+
+    output_name = os.getenv("COMBINE_OUTPUT_NAME", "combined_ontology.ttl")
+    output_location = resolve_output_location(
+        entry_location,
+        output_location=os.getenv("COMBINE_OUTPUT_LOCATION"),
+        output_name=output_name,
+    )
+    output_path = output_location_to_path(output_location)
+
+    force = _env_bool("COMBINE_FORCE", default=False)
+    if output_path.exists() and not force:
+        logger.info("Skipping combine step (output exists): %s", output_location)
+        return
+
+    graph = build_combined_graph(entry_location)
+    logger.info("Finished combining imports; serializing to: %s", output_location)
+    serialize_graph_to_ttl(graph, output_location)
+
+
+if __name__ == "__main__":
+    main()

python_services/owl_imports_combiner/owl_imports_combiner.py

@@ -0,0 +1,96 @@
+from __future__ import annotations
+
+import logging
+import os
+from pathlib import Path
+from urllib.parse import unquote, urlparse
+
+from rdflib import Graph
+from rdflib.namespace import OWL
+
+
+logger = logging.getLogger(__name__)
+
+
+def _is_http_url(location: str) -> bool:
+    scheme = urlparse(location).scheme.lower()
+    return scheme in {"http", "https"}
+
+
+def _is_file_uri(location: str) -> bool:
+    return urlparse(location).scheme.lower() == "file"
+
+
+def _file_uri_to_path(location: str) -> Path:
+    u = urlparse(location)
+    if u.scheme.lower() != "file":
+        raise ValueError(f"Not a file:// URI: {location!r}")
+    return Path(unquote(u.path))
+
+
+def resolve_output_location(
+    entry_location: str,
+    *,
+    output_location: str | None,
+    output_name: str,
+) -> str:
+    if output_location:
+        return output_location
+
+    if _is_http_url(entry_location):
+        raise ValueError(
+            "COMBINE_ENTRY_LOCATION points to an http(s) URL; set COMBINE_OUTPUT_LOCATION to a writable file path."
+        )
+
+    entry_path = _file_uri_to_path(entry_location) if _is_file_uri(entry_location) else Path(entry_location)
+    return str(entry_path.parent / output_name)
+
+
+def _output_destination_to_path(output_location: str) -> Path:
+    if _is_file_uri(output_location):
+        return _file_uri_to_path(output_location)
+    if _is_http_url(output_location):
+        raise ValueError("Output location must be a local file path (or file:// URI), not http(s).")
+    return Path(output_location)
+
+
+def output_location_to_path(output_location: str) -> Path:
+    return _output_destination_to_path(output_location)
+
+
+def build_combined_graph(entry_location: str) -> Graph:
+    """
+    Recursively loads an RDF document (file path, file:// URI, or http(s) URL) and its
+    owl:imports into a single in-memory graph.
+    """
+    combined_graph = Graph()
+    visited_locations: set[str] = set()
+
+    def resolve_imports(location: str) -> None:
+        if location in visited_locations:
+            return
+        visited_locations.add(location)
+
+        logger.info("Loading ontology: %s", location)
+        try:
+            combined_graph.parse(location=location)
+        except Exception as e:
+            logger.warning("Failed to load %s (%s)", location, e)
+            return
+
+        imports = [str(o) for _, _, o in combined_graph.triples((None, OWL.imports, None))]
+        for imported_location in imports:
+            if imported_location not in visited_locations:
+                resolve_imports(imported_location)
+
+    resolve_imports(entry_location)
+    return combined_graph
+
+
+def serialize_graph_to_ttl(graph: Graph, output_location: str) -> None:
+    output_path = _output_destination_to_path(output_location)
+    output_path.parent.mkdir(parents=True, exist_ok=True)
+
+    tmp_path = output_path.with_suffix(output_path.suffix + ".tmp")
+    graph.serialize(destination=str(tmp_path), format="turtle")
+    os.replace(str(tmp_path), str(output_path))

python_services/owl_imports_combiner/requirements.txt

@@ -0,0 +1 @@
+rdflib

scripts/compute_layout.ts

@@ -1,376 +0,0 @@
-#!/usr/bin/env npx tsx
-/**
- * Graph Layout
- *
- * Computes a 2D layout for a general graph (not necessarily a tree).
- * 
- * - Primary nodes (from primary_edges.csv) are placed first in a radial layout
- * - Remaining nodes are placed near their connected primary neighbors
- * - Barnes-Hut force simulation relaxes the layout
- *
- * Reads: primary_edges.csv, secondary_edges.csv
- * Writes: node_positions.csv
- *
- * Usage: npx tsx scripts/compute_layout.ts
- */
-
-import { writeFileSync, readFileSync, existsSync } from "fs";
-import { join, dirname } from "path";
-import { fileURLToPath } from "url";
-
-const __dirname = dirname(fileURLToPath(import.meta.url));
-const PUBLIC_DIR = join(__dirname, "..", "public");
-
-// ══════════════════════════════════════════════════════════
-// Configuration
-// ══════════════════════════════════════════════════════════
-
-const ITERATIONS = 200;         // Force iterations
-const REPULSION_K = 200;        // Repulsion strength
-const EDGE_LENGTH = 80;         // Desired edge rest length
-const ATTRACTION_K = 0.005;     // Spring stiffness for edges
-const INITIAL_MAX_DISP = 20;    // Starting max displacement
-const COOLING = 0.995;          // Cooling per iteration
-const MIN_DIST = 0.5;
-const PRINT_EVERY = 20;         // Print progress every N iterations
-const BH_THETA = 0.8;          // Barnes-Hut opening angle
-
-// Primary node radial placement
-const PRIMARY_RADIUS = 300;     // Radius for primary node ring
-
-// ══════════════════════════════════════════════════════════
-// Read edge data from CSVs
-// ══════════════════════════════════════════════════════════
-
-const primaryPath = join(PUBLIC_DIR, "primary_edges.csv");
-const secondaryPath = join(PUBLIC_DIR, "secondary_edges.csv");
-
-if (!existsSync(primaryPath) || !existsSync(secondaryPath)) {
-    console.error(`Error: Missing input files!`);
-    console.error(`  Expected: ${primaryPath}`);
-    console.error(`  Expected: ${secondaryPath}`);
-    console.error(`  Run 'npx tsx scripts/fetch_from_db.ts' first.`);
-    process.exit(1);
-}
-
-function parseEdges(path: string): Array<[number, number]> {
-    const content = readFileSync(path, "utf-8");
-    const lines = content.trim().split("\n");
-    const edges: Array<[number, number]> = [];
-    for (let i = 1; i < lines.length; i++) {
-        const line = lines[i].trim();
-        if (!line) continue;
-        const [src, tgt] = line.split(",").map(Number);
-        if (!isNaN(src) && !isNaN(tgt)) {
-            edges.push([src, tgt]);
-        }
-    }
-    return edges;
-}
-
-const primaryEdges = parseEdges(primaryPath);
-const secondaryEdges = parseEdges(secondaryPath);
-const allEdges = [...primaryEdges, ...secondaryEdges];
-
-// ══════════════════════════════════════════════════════════
-// Build adjacency
-// ══════════════════════════════════════════════════════════
-
-const allNodes = new Set<number>();
-const primaryNodes = new Set<number>();
-const neighbors = new Map<number, Set<number>>();
-
-function addNeighbor(a: number, b: number) {
-    if (!neighbors.has(a)) neighbors.set(a, new Set());
-    neighbors.get(a)!.add(b);
-    if (!neighbors.has(b)) neighbors.set(b, new Set());
-    neighbors.get(b)!.add(a);
-}
-
-for (const [src, dst] of primaryEdges) {
-    allNodes.add(src);
-    allNodes.add(dst);
-    primaryNodes.add(src);
-    primaryNodes.add(dst);
-    addNeighbor(src, dst);
-}
-
-for (const [src, dst] of secondaryEdges) {
-    allNodes.add(src);
-    allNodes.add(dst);
-    addNeighbor(src, dst);
-}
-
-const N = allNodes.size;
-const nodeIds = Array.from(allNodes).sort((a, b) => a - b);
-const idToIdx = new Map<number, number>();
-nodeIds.forEach((id, idx) => idToIdx.set(id, idx));
-
-console.log(
-    `Read graph: ${N} nodes, ${allEdges.length} edges (P=${primaryEdges.length}, S=${secondaryEdges.length})`
-);
-console.log(`Primary nodes: ${primaryNodes.size}`);
-
-// ══════════════════════════════════════════════════════════
-// Initial placement
-// ══════════════════════════════════════════════════════════
-
-const x = new Float64Array(N);
-const y = new Float64Array(N);
-
-// Step 1: Place primary nodes in a radial layout
-const primaryArr = Array.from(primaryNodes).sort((a, b) => a - b);
-const angleStep = (2 * Math.PI) / Math.max(1, primaryArr.length);
-const radius = PRIMARY_RADIUS * Math.max(1, Math.sqrt(primaryArr.length / 10));
-
-for (let i = 0; i < primaryArr.length; i++) {
-    const idx = idToIdx.get(primaryArr[i])!;
-    const angle = i * angleStep;
-    x[idx] = radius * Math.cos(angle);
-    y[idx] = radius * Math.sin(angle);
-}
-
-console.log(`Placed ${primaryArr.length} primary nodes in radial layout (r=${radius.toFixed(0)})`);
-
-// Step 2: Place remaining nodes near their connected neighbors
-// BFS from already-placed nodes
-const placed = new Set<number>(primaryNodes);
-const queue: number[] = [...primaryArr];
-let head = 0;
-
-while (head < queue.length) {
-    const nodeId = queue[head++];
-    const nodeNeighbors = neighbors.get(nodeId);
-    if (!nodeNeighbors) continue;
-
-    for (const nbId of nodeNeighbors) {
-        if (placed.has(nbId)) continue;
-        placed.add(nbId);
-
-        // Place near this neighbor with some jitter
-        const parentIdx = idToIdx.get(nodeId)!;
-        const childIdx = idToIdx.get(nbId)!;
-        const jitterAngle = Math.random() * 2 * Math.PI;
-        const jitterDist = EDGE_LENGTH * (0.5 + Math.random() * 0.5);
-        x[childIdx] = x[parentIdx] + jitterDist * Math.cos(jitterAngle);
-        y[childIdx] = y[parentIdx] + jitterDist * Math.sin(jitterAngle);
-
-        queue.push(nbId);
-    }
-}
-
-// Handle disconnected nodes (place randomly)
-for (const id of nodeIds) {
-    if (!placed.has(id)) {
-        const idx = idToIdx.get(id)!;
-        const angle = Math.random() * 2 * Math.PI;
-        const r = radius * (1 + Math.random());
-        x[idx] = r * Math.cos(angle);
-        y[idx] = r * Math.sin(angle);
-        placed.add(id);
-    }
-}
-
-console.log(`Initial placement complete: ${placed.size} nodes`);
-
-// ══════════════════════════════════════════════════════════
-// Force-directed layout with Barnes-Hut
-// ══════════════════════════════════════════════════════════
-
-console.log(`Running force simulation (${ITERATIONS} iterations, ${N} nodes, ${allEdges.length} edges)...`);
-
-const t0 = performance.now();
-let maxDisp = INITIAL_MAX_DISP;
-
-for (let iter = 0; iter < ITERATIONS; iter++) {
-    const bhRoot = buildBHTree(x, y, N);
-    const fx = new Float64Array(N);
-    const fy = new Float64Array(N);
-
-    // 1. Repulsion via Barnes-Hut
-    for (let i = 0; i < N; i++) {
-        calcBHForce(bhRoot, x[i], y[i], fx, fy, i, BH_THETA, x, y);
-    }
-
-    // 2. Edge attraction (spring force)
-    for (const [aId, bId] of allEdges) {
-        const a = idToIdx.get(aId)!;
-        const b = idToIdx.get(bId)!;
-        const dx = x[b] - x[a];
-        const dy = y[b] - y[a];
-        const d = Math.sqrt(dx * dx + dy * dy) || MIN_DIST;
-        const displacement = d - EDGE_LENGTH;
-        const f = ATTRACTION_K * displacement;
-        const ux = dx / d;
-        const uy = dy / d;
-        fx[a] += ux * f;
-        fy[a] += uy * f;
-        fx[b] -= ux * f;
-        fy[b] -= uy * f;
-    }
-
-    // 3. Apply forces with displacement capping
-    let totalForce = 0;
-    for (let i = 0; i < N; i++) {
-        const mag = Math.sqrt(fx[i] * fx[i] + fy[i] * fy[i]);
-        totalForce += mag;
-        if (mag > 0) {
-            const cap = Math.min(maxDisp, mag) / mag;
-            x[i] += fx[i] * cap;
-            y[i] += fy[i] * cap;
-        }
-    }
-
-    maxDisp *= COOLING;
-
-    if ((iter + 1) % PRINT_EVERY === 0 || iter === 0) {
-        console.log(
-            `  iter ${iter + 1}/${ITERATIONS}  max_disp=${maxDisp.toFixed(2)}  avg_force=${(totalForce / N).toFixed(2)}`
-        );
-    }
-}
-
-const elapsed = performance.now() - t0;
-console.log(`Force simulation done in ${(elapsed / 1000).toFixed(1)}s`);
-
-// ══════════════════════════════════════════════════════════
-// Write output
-// ══════════════════════════════════════════════════════════
-
-const outLines: string[] = ["vertex,x,y"];
-for (let i = 0; i < N; i++) {
-    outLines.push(`${nodeIds[i]},${x[i]},${y[i]}`);
-}
-
-const outPath = join(PUBLIC_DIR, "node_positions.csv");
-writeFileSync(outPath, outLines.join("\n") + "\n");
-console.log(`Wrote ${N} positions to ${outPath}`);
-console.log(`Layout complete.`);
-
-// ══════════════════════════════════════════════════════════
-// Barnes-Hut Helpers
-// ══════════════════════════════════════════════════════════
-
-interface BHNode {
-    mass: number;
-    cx: number;
-    cy: number;
-    minX: number;
-    maxX: number;
-    minY: number;
-    maxY: number;
-    children?: BHNode[];
-    pointIdx?: number;
-}
-
-function buildBHTree(x: Float64Array, y: Float64Array, n: number): BHNode {
-    let minX = Infinity, maxX = -Infinity, minY = Infinity, maxY = -Infinity;
-    for (let i = 0; i < n; i++) {
-        if (x[i] < minX) minX = x[i];
-        if (x[i] > maxX) maxX = x[i];
-        if (y[i] < minY) minY = y[i];
-        if (y[i] > maxY) maxY = y[i];
-    }
-    const cx = (minX + maxX) / 2;
-    const cy = (minY + maxY) / 2;
-    const halfDim = Math.max(maxX - minX, maxY - minY) / 2 + 0.01;
-
-    const root: BHNode = {
-        mass: 0, cx: 0, cy: 0,
-        minX: cx - halfDim, maxX: cx + halfDim,
-        minY: cy - halfDim, maxY: cy + halfDim,
-    };
-
-    for (let i = 0; i < n; i++) {
-        insertBH(root, i, x[i], y[i], x, y);
-    }
-    calcBHMass(root, x, y);
-    return root;
-}
-
-function insertBH(node: BHNode, idx: number, px: number, py: number, x: Float64Array, y: Float64Array) {
-    if (!node.children && node.pointIdx === undefined) {
-        node.pointIdx = idx;
-        return;
-    }
-
-    if (!node.children && node.pointIdx !== undefined) {
-        const oldIdx = node.pointIdx;
-        node.pointIdx = undefined;
-        subdivideBH(node);
-        insertBH(node, oldIdx, x[oldIdx], y[oldIdx], x, y);
-    }
-
-    if (node.children) {
-        const mx = (node.minX + node.maxX) / 2;
-        const my = (node.minY + node.maxY) / 2;
-        let q = 0;
-        if (px > mx) q += 1;
-        if (py > my) q += 2;
-        insertBH(node.children[q], idx, px, py, x, y);
-    }
-}
-
-function subdivideBH(node: BHNode) {
-    const mx = (node.minX + node.maxX) / 2;
-    const my = (node.minY + node.maxY) / 2;
-    node.children = [
-        { mass: 0, cx: 0, cy: 0, minX: node.minX, maxX: mx, minY: node.minY, maxY: my },
-        { mass: 0, cx: 0, cy: 0, minX: mx, maxX: node.maxX, minY: node.minY, maxY: my },
-        { mass: 0, cx: 0, cy: 0, minX: node.minX, maxX: mx, minY: my, maxY: node.maxY },
-        { mass: 0, cx: 0, cy: 0, minX: mx, maxX: node.maxX, minY: my, maxY: node.maxY },
-    ];
-}
-
-function calcBHMass(node: BHNode, x: Float64Array, y: Float64Array) {
-    if (node.pointIdx !== undefined) {
-        node.mass = 1;
-        node.cx = x[node.pointIdx];
-        node.cy = y[node.pointIdx];
-        return;
-    }
-    if (node.children) {
-        let m = 0, sx = 0, sy = 0;
-        for (const c of node.children) {
-            calcBHMass(c, x, y);
-            m += c.mass;
-            sx += c.cx * c.mass;
-            sy += c.cy * c.mass;
-        }
-        node.mass = m;
-        if (m > 0) {
-            node.cx = sx / m;
-            node.cy = sy / m;
-        } else {
-            node.cx = (node.minX + node.maxX) / 2;
-            node.cy = (node.minY + node.maxY) / 2;
-        }
-    }
-}
-
-function calcBHForce(
-    node: BHNode,
-    px: number, py: number,
-    fx: Float64Array, fy: Float64Array,
-    idx: number, theta: number,
-    x: Float64Array, y: Float64Array,
-) {
-    const dx = px - node.cx;
-    const dy = py - node.cy;
-    const d2 = dx * dx + dy * dy;
-    const dist = Math.sqrt(d2);
-    const width = node.maxX - node.minX;
-
-    if (width / dist < theta || !node.children) {
-        if (node.mass > 0 && node.pointIdx !== idx) {
-            const dEff = Math.max(dist, MIN_DIST);
-            const f = (REPULSION_K * node.mass) / (dEff * dEff);
-            fx[idx] += (dx / dEff) * f;
-            fy[idx] += (dy / dEff) * f;
-        }
-    } else {
-        for (const c of node.children) {
-            calcBHForce(c, px, py, fx, fy, idx, theta, x, y);
-        }
-    }
-}

scripts/fetch_from_db.ts

@@ -1,390 +0,0 @@
-#!/usr/bin/env npx tsx
-/**
- * Fetch RDF Data from AnzoGraph DB
- *
- * 1. Query the first 1000 distinct subject URIs
- * 2. Fetch all triples where those URIs appear as subject or object
- * 3. Identify primary nodes (objects of rdf:type)
- * 4. Write primary_edges.csv, secondary_edges.csv, and uri_map.csv
- *
- * Usage: npx tsx scripts/fetch_from_db.ts [--host http://localhost:8080]
- */
-
-import { writeFileSync } from "fs";
-import { join, dirname } from "path";
-import { fileURLToPath } from "url";
-
-const __dirname = dirname(fileURLToPath(import.meta.url));
-const PUBLIC_DIR = join(__dirname, "..", "public");
-
-// ══════════════════════════════════════════════════════════
-// Configuration
-// ══════════════════════════════════════════════════════════
-
-const RDF_TYPE = "http://www.w3.org/1999/02/22-rdf-syntax-ns#type";
-const BATCH_SIZE = 100; // URIs per VALUES batch query
-const MAX_RETRIES = 30; // Wait up to ~120s for AnzoGraph to start
-const RETRY_DELAY_MS = 4000;
-
-// Path to TTL file inside the AnzoGraph container (mapped via docker-compose volume)
-const DATA_FILE = process.env.SPARQL_DATA_FILE || "file:///opt/shared-files/vkg-materialized.ttl";
-
-// Parse --host flag, default to http://localhost:8080
-function getEndpoint(): string {
-    const hostIdx = process.argv.indexOf("--host");
-    if (hostIdx !== -1 && process.argv[hostIdx + 1]) {
-        return process.argv[hostIdx + 1];
-    }
-    // Inside Docker, use service name; otherwise localhost
-    return process.env.SPARQL_HOST || "http://localhost:8080";
-}
-
-const SPARQL_ENDPOINT = `${getEndpoint()}/sparql`;
-
-// Auth credentials (AnzoGraph defaults)
-const SPARQL_USER = process.env.SPARQL_USER || "admin";
-const SPARQL_PASS = process.env.SPARQL_PASS || "Passw0rd1";
-const AUTH_HEADER = "Basic " + Buffer.from(`${SPARQL_USER}:${SPARQL_PASS}`).toString("base64");
-
-// ══════════════════════════════════════════════════════════
-// SPARQL helpers
-// ══════════════════════════════════════════════════════════
-
-interface SparqlBinding {
-    [key: string]: { type: string; value: string };
-}
-
-function sleep(ms: number): Promise<void> {
-    return new Promise((resolve) => setTimeout(resolve, ms));
-}
-
-async function sparqlQuery(query: string, retries = 5): Promise<SparqlBinding[]> {
-    for (let attempt = 1; attempt <= retries; attempt++) {
-        const controller = new AbortController();
-        const timeout = setTimeout(() => controller.abort(), 300_000); // 5 min timeout
-
-        try {
-            const t0 = performance.now();
-            const response = await fetch(SPARQL_ENDPOINT, {
-                method: "POST",
-                headers: {
-                    "Content-Type": "application/x-www-form-urlencoded",
-                    "Accept": "application/sparql-results+json",
-                    "Authorization": AUTH_HEADER,
-                },
-                body: "query=" + encodeURIComponent(query),
-                signal: controller.signal,
-            });
-            const t1 = performance.now();
-            console.log(`    [sparql] response status=${response.status} in ${((t1 - t0) / 1000).toFixed(1)}s`);
-
-            if (!response.ok) {
-                const text = await response.text();
-                throw new Error(`SPARQL query failed (${response.status}): ${text}`);
-            }
-
-            const text = await response.text();
-            const t2 = performance.now();
-            console.log(`    [sparql] body read (${(text.length / 1024).toFixed(0)} KB) in ${((t2 - t1) / 1000).toFixed(1)}s`);
-
-            const json = JSON.parse(text);
-            return json.results.bindings;
-        } catch (err: any) {
-            clearTimeout(timeout);
-            const msg = err instanceof Error ? err.message : String(err);
-            const isTransient = msg.includes("fetch failed") || msg.includes("Timeout") || msg.includes("ABORT") || msg.includes("abort");
-            if (isTransient && attempt < retries) {
-                console.log(`    [sparql] transient error (attempt ${attempt}/${retries}): ${msg.substring(0, 100)}`);
-                console.log(`    [sparql] retrying in 10s (AnzoGraph may still be indexing after LOAD)...`);
-                await sleep(10_000);
-                continue;
-            }
-            throw err;
-        } finally {
-            clearTimeout(timeout);
-        }
-    }
-    throw new Error("sparqlQuery: should not reach here");
-}
-
-async function waitForAnzoGraph(): Promise<void> {
-    console.log(`Waiting for AnzoGraph at ${SPARQL_ENDPOINT}...`);
-    for (let attempt = 1; attempt <= MAX_RETRIES; attempt++) {
-        try {
-            const response = await fetch(SPARQL_ENDPOINT, {
-                method: "POST",
-                headers: {
-                    "Content-Type": "application/x-www-form-urlencoded",
-                    "Accept": "application/sparql-results+json",
-                    "Authorization": AUTH_HEADER,
-                },
-                body: "query=" + encodeURIComponent("ASK WHERE { ?s ?p ?o }"),
-            });
-            const text = await response.text();
-            // Verify it's actual JSON (not a plain-text error from a half-started engine)
-            JSON.parse(text);
-            console.log(`  AnzoGraph is ready (attempt ${attempt})`);
-            return;
-        } catch (err: any) {
-            const msg = err instanceof Error ? err.message : String(err);
-            console.log(`  Attempt ${attempt}/${MAX_RETRIES}: ${msg.substring(0, 100)}`);
-            if (attempt < MAX_RETRIES) {
-                await sleep(RETRY_DELAY_MS);
-            }
-        }
-    }
-    throw new Error(`AnzoGraph not available after ${MAX_RETRIES} attempts`);
-}
-
-async function sparqlUpdate(update: string): Promise<string> {
-    const response = await fetch(SPARQL_ENDPOINT, {
-        method: "POST",
-        headers: {
-            "Content-Type": "application/sparql-update",
-            "Accept": "application/json",
-            "Authorization": AUTH_HEADER,
-        },
-        body: update,
-    });
-    const text = await response.text();
-    if (!response.ok) {
-        throw new Error(`SPARQL update failed (${response.status}): ${text}`);
-    }
-    return text;
-}
-
-async function loadData(): Promise<void> {
-    console.log(`Loading data from ${DATA_FILE}...`);
-    const t0 = performance.now();
-    const result = await sparqlUpdate(`LOAD <${DATA_FILE}>`);
-    const elapsed = ((performance.now() - t0) / 1000).toFixed(1);
-    console.log(`  Load complete in ${elapsed}s: ${result.substring(0, 200)}`);
-}
-
-// ══════════════════════════════════════════════════════════
-// Step 1: Fetch seed URIs
-// ══════════════════════════════════════════════════════════
-
-async function fetchSeedURIs(): Promise<string[]> {
-    console.log("Querying first 1000 distinct subject URIs...");
-    const t0 = performance.now();
-    const query = `
-SELECT DISTINCT ?s
-WHERE { ?s ?p ?o }
-LIMIT 1000
-`;
-    const bindings = await sparqlQuery(query);
-    const elapsed = ((performance.now() - t0) / 1000).toFixed(1);
-    const uris = bindings.map((b) => b.s.value);
-    console.log(`  Got ${uris.length} seed URIs in ${elapsed}s`);
-    return uris;
-}
-
-// ══════════════════════════════════════════════════════════
-// Step 2: Fetch all triples involving seed URIs
-// ══════════════════════════════════════════════════════════
-
-interface Triple {
-    s: string;
-    p: string;
-    o: string;
-    oType: string; // "uri" or "literal"
-}
-
-async function fetchTriples(seedURIs: string[]): Promise<Triple[]> {
-    console.log(`Fetching triples for ${seedURIs.length} seed URIs (batch size: ${BATCH_SIZE})...`);
-    const allTriples: Triple[] = [];
-
-    for (let i = 0; i < seedURIs.length; i += BATCH_SIZE) {
-        const batch = seedURIs.slice(i, i + BATCH_SIZE);
-        const valuesClause = batch.map((u) => `<${u}>`).join(" ");
-
-        const query = `
-SELECT ?s ?p ?o
-WHERE {
-  VALUES ?uri { ${valuesClause} }
-  {
-    ?uri ?p ?o .
-    BIND(?uri AS ?s)
-  }
-  UNION
-  {
-    ?s ?p ?uri .
-    BIND(?uri AS ?o)
-  }
-}
-`;
-        const bindings = await sparqlQuery(query);
-        for (const b of bindings) {
-            allTriples.push({
-                s: b.s.value,
-                p: b.p.value,
-                o: b.o.value,
-                oType: b.o.type,
-            });
-        }
-
-        const progress = Math.min(i + BATCH_SIZE, seedURIs.length);
-        process.stdout.write(`\r  Fetched triples: batch ${Math.ceil(progress / BATCH_SIZE)}/${Math.ceil(seedURIs.length / BATCH_SIZE)} (${allTriples.length} triples so far)`);
-    }
-    console.log(`\n  Total triples: ${allTriples.length}`);
-    return allTriples;
-}
-
-// ══════════════════════════════════════════════════════════
-// Step 3: Build graph data
-// ══════════════════════════════════════════════════════════
-
-interface GraphData {
-    nodeURIs: string[];        // All unique URIs (subjects & objects that are URIs)
-    uriToId: Map<string, number>;
-    primaryNodeIds: Set<number>; // Nodes that are objects of rdf:type
-    edges: Array<[number, number]>; // [source, target] as numeric IDs
-    primaryEdges: Array<[number, number]>;
-    secondaryEdges: Array<[number, number]>;
-}
-
-function buildGraphData(triples: Triple[]): GraphData {
-    console.log("Building graph data...");
-
-    // Collect all unique URI nodes (skip literal objects)
-    const uriSet = new Set<string>();
-    for (const t of triples) {
-        uriSet.add(t.s);
-        if (t.oType === "uri") {
-            uriSet.add(t.o);
-        }
-    }
-
-    // Assign numeric IDs
-    const nodeURIs = Array.from(uriSet).sort();
-    const uriToId = new Map<string, number>();
-    nodeURIs.forEach((uri, idx) => uriToId.set(uri, idx));
-
-    // Identify primary nodes: objects of rdf:type triples
-    const primaryNodeIds = new Set<number>();
-    for (const t of triples) {
-        if (t.p === RDF_TYPE && t.oType === "uri") {
-            const objId = uriToId.get(t.o);
-            if (objId !== undefined) {
-                primaryNodeIds.add(objId);
-            }
-        }
-    }
-
-    // Build edges (only between URI nodes, skip literal objects)
-    const edgeSet = new Set<string>();
-    const edges: Array<[number, number]> = [];
-    for (const t of triples) {
-        if (t.oType !== "uri") continue;
-        const srcId = uriToId.get(t.s);
-        const dstId = uriToId.get(t.o);
-        if (srcId === undefined || dstId === undefined) continue;
-        if (srcId === dstId) continue; // Skip self-loops
-
-        const key = `${srcId},${dstId}`;
-        if (edgeSet.has(key)) continue; // Deduplicate
-        edgeSet.add(key);
-        edges.push([srcId, dstId]);
-    }
-
-    // Classify edges into primary (touches a primary node) and secondary
-    const primaryEdges: Array<[number, number]> = [];
-    const secondaryEdges: Array<[number, number]> = [];
-    for (const [src, dst] of edges) {
-        if (primaryNodeIds.has(src) || primaryNodeIds.has(dst)) {
-            primaryEdges.push([src, dst]);
-        } else {
-            secondaryEdges.push([src, dst]);
-        }
-    }
-
-    console.log(`  Nodes: ${nodeURIs.length}`);
-    console.log(`  Primary nodes (rdf:type objects): ${primaryNodeIds.size}`);
-    console.log(`  Edges: ${edges.length} (primary: ${primaryEdges.length}, secondary: ${secondaryEdges.length})`);
-
-    return { nodeURIs, uriToId, primaryNodeIds, edges, primaryEdges, secondaryEdges };
-}
-
-// ══════════════════════════════════════════════════════════
-// Step 4: Write CSV files
-// ══════════════════════════════════════════════════════════
-
-function extractLabel(uri: string): string {
-    // Extract local name: after # or last /
-    const hashIdx = uri.lastIndexOf("#");
-    if (hashIdx !== -1) return uri.substring(hashIdx + 1);
-    const slashIdx = uri.lastIndexOf("/");
-    if (slashIdx !== -1) return uri.substring(slashIdx + 1);
-    return uri;
-}
-
-function writeCSVs(data: GraphData): void {
-    // Write primary_edges.csv
-    const pLines = ["source,target"];
-    for (const [src, dst] of data.primaryEdges) {
-        pLines.push(`${src},${dst}`);
-    }
-    const pPath = join(PUBLIC_DIR, "primary_edges.csv");
-    writeFileSync(pPath, pLines.join("\n") + "\n");
-    console.log(`Wrote ${data.primaryEdges.length} primary edges to ${pPath}`);
-
-    // Write secondary_edges.csv
-    const sLines = ["source,target"];
-    for (const [src, dst] of data.secondaryEdges) {
-        sLines.push(`${src},${dst}`);
-    }
-    const sPath = join(PUBLIC_DIR, "secondary_edges.csv");
-    writeFileSync(sPath, sLines.join("\n") + "\n");
-    console.log(`Wrote ${data.secondaryEdges.length} secondary edges to ${sPath}`);
-
-    // Write uri_map.csv (id,uri,label,isPrimary)
-    const uLines = ["id,uri,label,isPrimary"];
-    for (let i = 0; i < data.nodeURIs.length; i++) {
-        const uri = data.nodeURIs[i];
-        const label = extractLabel(uri);
-        const isPrimary = data.primaryNodeIds.has(i) ? "1" : "0";
-        // Escape commas in URIs by quoting
-        const safeUri = uri.includes(",") ? `"${uri}"` : uri;
-        const safeLabel = label.includes(",") ? `"${label}"` : label;
-        uLines.push(`${i},${safeUri},${safeLabel},${isPrimary}`);
-    }
-    const uPath = join(PUBLIC_DIR, "uri_map.csv");
-    writeFileSync(uPath, uLines.join("\n") + "\n");
-    console.log(`Wrote ${data.nodeURIs.length} URI mappings to ${uPath}`);
-}
-
-// ══════════════════════════════════════════════════════════
-// Main
-// ══════════════════════════════════════════════════════════
-
-async function main() {
-    console.log(`SPARQL endpoint: ${SPARQL_ENDPOINT}`);
-    const t0 = performance.now();
-
-    await waitForAnzoGraph();
-    await loadData();
-
-    // Smoke test: simplest possible query to verify connectivity
-    console.log("Smoke test: SELECT ?s ?p ?o LIMIT 3...");
-    const smokeT0 = performance.now();
-    const smokeResult = await sparqlQuery("SELECT ?s ?p ?o WHERE { ?s ?p ?o } LIMIT 3");
-    const smokeElapsed = ((performance.now() - smokeT0) / 1000).toFixed(1);
-    console.log(`  Smoke test OK: ${smokeResult.length} results in ${smokeElapsed}s`);
-    if (smokeResult.length > 0) {
-        console.log(`  First triple: ${smokeResult[0].s.value} ${smokeResult[0].p.value} ${smokeResult[0].o.value}`);
-    }
-
-    const seedURIs = await fetchSeedURIs();
-    const triples = await fetchTriples(seedURIs);
-    const graphData = buildGraphData(triples);
-    writeCSVs(graphData);
-
-    const elapsed = ((performance.now() - t0) / 1000).toFixed(1);
-    console.log(`\nDone in ${elapsed}s`);
-}
-
-main().catch((err) => {
-    console.error("Fatal error:", err);
-    process.exit(1);
-});

scripts/generate_tree.ts

@@ -1,132 +0,0 @@
-/**
- * Random Tree Generator
- *
- * Generates a random tree with 1–MAX_CHILDREN children per node.
- * Splits edges into primary (depth ≤ PRIMARY_DEPTH) and secondary.
- *
- * Usage: npx tsx scripts/generate_tree.ts
- */
-
-import { writeFileSync } from "fs";
-import { join, dirname } from "path";
-import { fileURLToPath } from "url";
-
-const __dirname = dirname(fileURLToPath(import.meta.url));
-const PUBLIC_DIR = join(__dirname, "..", "public");
-
-// ══════════════════════════════════════════════════════════
-// Configuration
-// ══════════════════════════════════════════════════════════
-
-const TARGET_NODES = 10000;     // Approximate number of nodes to generate
-const MAX_CHILDREN = 4;        // Each node gets 1..MAX_CHILDREN children
-const PRIMARY_DEPTH = 4;       // Nodes at depth ≤ this form the primary skeleton
-
-// ══════════════════════════════════════════════════════════
-// Tree data types
-// ══════════════════════════════════════════════════════════
-
-export interface TreeData {
-    root: number;
-    nodeCount: number;
-    childrenOf: Map<number, number[]>;
-    parentOf: Map<number, number>;
-    depthOf: Map<number, number>;
-    primaryNodes: Set<number>;              // all nodes at depth ≤ PRIMARY_DEPTH
-    primaryEdges: Array<[number, number]>;  // [child, parent] edges within primary
-    secondaryEdges: Array<[number, number]>;// remaining edges
-}
-
-// ══════════════════════════════════════════════════════════
-// Generator
-// ══════════════════════════════════════════════════════════
-
-export function generateTree(): TreeData {
-    const childrenOf = new Map<number, number[]>();
-    const parentOf = new Map<number, number>();
-    const depthOf = new Map<number, number>();
-
-    const root = 0;
-    depthOf.set(root, 0);
-    let nextId = 1;
-    const queue: number[] = [root];
-    let head = 0;
-
-    while (head < queue.length && nextId < TARGET_NODES) {
-        const parent = queue[head++];
-        const parentDepth = depthOf.get(parent)!;
-        const nKids = 1 + Math.floor(Math.random() * MAX_CHILDREN); // 1..MAX_CHILDREN
-
-        const kids: number[] = [];
-        for (let c = 0; c < nKids && nextId < TARGET_NODES; c++) {
-            const child = nextId++;
-            kids.push(child);
-            parentOf.set(child, parent);
-            depthOf.set(child, parentDepth + 1);
-            queue.push(child);
-        }
-        childrenOf.set(parent, kids);
-    }
-
-    // Classify edges and nodes by depth
-    const primaryNodes = new Set<number>();
-    const primaryEdges: Array<[number, number]> = [];
-    const secondaryEdges: Array<[number, number]> = [];
-
-    // Root is always primary
-    primaryNodes.add(root);
-
-    for (const [child, parent] of parentOf) {
-        const childDepth = depthOf.get(child)!;
-        if (childDepth <= PRIMARY_DEPTH) {
-            primaryNodes.add(child);
-            primaryNodes.add(parent);
-            primaryEdges.push([child, parent]);
-        } else {
-            secondaryEdges.push([child, parent]);
-        }
-    }
-
-    console.log(
-        `Generated tree: ${nextId} nodes, ` +
-        `${primaryEdges.length} primary edges (depth ≤ ${PRIMARY_DEPTH}), ` +
-        `${secondaryEdges.length} secondary edges`
-    );
-
-    return {
-        root,
-        nodeCount: nextId,
-        childrenOf,
-        parentOf,
-        depthOf,
-        primaryNodes,
-        primaryEdges,
-        secondaryEdges,
-    };
-}
-
-// ══════════════════════════════════════════════════════════
-// Run if executed directly
-// ══════════════════════════════════════════════════════════
-
-if (import.meta.url === `file://${process.argv[1]}`) {
-    const data = generateTree();
-
-    // Write primary_edges.csv
-    const pLines: string[] = ["source,target"];
-    for (const [child, parent] of data.primaryEdges) {
-        pLines.push(`${child},${parent}`);
-    }
-    const pPath = join(PUBLIC_DIR, "primary_edges.csv");
-    writeFileSync(pPath, pLines.join("\n") + "\n");
-    console.log(`Wrote ${data.primaryEdges.length} edges to ${pPath}`);
-
-    // Write secondary_edges.csv
-    const sLines: string[] = ["source,target"];
-    for (const [child, parent] of data.secondaryEdges) {
-        sLines.push(`${child},${parent}`);
-    }
-    const sPath = join(PUBLIC_DIR, "secondary_edges.csv");
-    writeFileSync(sPath, sLines.join("\n") + "\n");
-    console.log(`Wrote ${data.secondaryEdges.length} edges to ${sPath}`);
-}

src/App.tsx

@@ -1,374 +0,0 @@
-import { useEffect, useRef, useState } from "react";
-import { Renderer } from "./renderer";
-
-export default function App() {
-  const canvasRef = useRef<HTMLCanvasElement>(null);
-  const rendererRef = useRef<Renderer | null>(null);
-  const [status, setStatus] = useState("Loading node positions…");
-  const [nodeCount, setNodeCount] = useState(0);
-  const uriMapRef = useRef<Map<number, { uri: string; label: string; isPrimary: boolean }>>(new Map());
-  const [stats, setStats] = useState({
-    fps: 0,
-    drawn: 0,
-    mode: "",
-    zoom: 0,
-    ptSize: 0,
-  });
-  const [error, setError] = useState("");
-  const [hoveredNode, setHoveredNode] = useState<{ x: number; y: number; screenX: number; screenY: number; index?: number } | null>(null);
-  const [selectedNodes, setSelectedNodes] = useState<Set<number>>(new Set());
-
-  // Store mouse position in a ref so it can be accessed in render loop without re-renders
-  const mousePos = useRef({ x: 0, y: 0 });
-
-  useEffect(() => {
-    const canvas = canvasRef.current;
-    if (!canvas) return;
-
-    let renderer: Renderer;
-    try {
-      renderer = new Renderer(canvas);
-      rendererRef.current = renderer;
-    } catch (e) {
-      setError(e instanceof Error ? e.message : String(e));
-      return;
-    }
-
-    let cancelled = false;
-
-    // Fetch CSVs, parse, and init renderer
-    (async () => {
-      try {
-        setStatus("Fetching data files…");
-        const [nodesResponse, primaryEdgesResponse, secondaryEdgesResponse, uriMapResponse] = await Promise.all([
-          fetch("/node_positions.csv"),
-          fetch("/primary_edges.csv"),
-          fetch("/secondary_edges.csv"),
-          fetch("/uri_map.csv"),
-        ]);
-        if (!nodesResponse.ok) throw new Error(`Failed to fetch nodes: ${nodesResponse.status}`);
-        if (!primaryEdgesResponse.ok) throw new Error(`Failed to fetch primary edges: ${primaryEdgesResponse.status}`);
-        if (!secondaryEdgesResponse.ok) throw new Error(`Failed to fetch secondary edges: ${secondaryEdgesResponse.status}`);
-
-        const [nodesText, primaryEdgesText, secondaryEdgesText, uriMapText] = await Promise.all([
-          nodesResponse.text(),
-          primaryEdgesResponse.text(),
-          secondaryEdgesResponse.text(),
-          uriMapResponse.ok ? uriMapResponse.text() : Promise.resolve(""),
-        ]);
-        if (cancelled) return;
-
-        setStatus("Parsing positions…");
-        const nodeLines = nodesText.split("\n").slice(1).filter(l => l.trim().length > 0);
-        const count = nodeLines.length;
-
-        const xs = new Float32Array(count);
-        const ys = new Float32Array(count);
-        const vertexIds = new Uint32Array(count);
-        for (let i = 0; i < count; i++) {
-          const parts = nodeLines[i].split(",");
-          vertexIds[i] = parseInt(parts[0], 10);
-          xs[i] = parseFloat(parts[1]);
-          ys[i] = parseFloat(parts[2]);
-        }
-
-        setStatus("Parsing edges…");
-        const pLines = primaryEdgesText.split("\n").slice(1).filter(l => l.trim().length > 0);
-        const sLines = secondaryEdgesText.split("\n").slice(1).filter(l => l.trim().length > 0);
-
-        const totalEdges = pLines.length + sLines.length;
-        const edgeData = new Uint32Array(totalEdges * 2);
-
-        let idx = 0;
-        // Parse primary
-        for (let i = 0; i < pLines.length; i++) {
-          const parts = pLines[i].split(",");
-          edgeData[idx++] = parseInt(parts[0], 10);
-          edgeData[idx++] = parseInt(parts[1], 10);
-        }
-        // Parse secondary
-        for (let i = 0; i < sLines.length; i++) {
-          const parts = sLines[i].split(",");
-          edgeData[idx++] = parseInt(parts[0], 10);
-          edgeData[idx++] = parseInt(parts[1], 10);
-        }
-
-        // Parse URI map if available
-        if (uriMapText) {
-          const uriLines = uriMapText.split("\n").slice(1).filter(l => l.trim().length > 0);
-          for (const line of uriLines) {
-            const parts = line.split(",");
-            if (parts.length >= 4) {
-              const id = parseInt(parts[0], 10);
-              const uri = parts[1];
-              const label = parts[2];
-              const isPrimary = parts[3].trim() === "1";
-              uriMapRef.current.set(id, { uri, label, isPrimary });
-            }
-          }
-        }
-
-        if (cancelled) return;
-
-        setStatus("Building spatial index…");
-        await new Promise(r => setTimeout(r, 0));
-
-        const buildMs = renderer.init(xs, ys, vertexIds, edgeData);
-        setNodeCount(renderer.getNodeCount());
-        setStatus("");
-        console.log(`Init complete: ${count.toLocaleString()} nodes, ${totalEdges.toLocaleString()} edges in ${buildMs.toFixed(0)}ms`);
-      } catch (e) {
-        if (!cancelled) {
-          setError(e instanceof Error ? e.message : String(e));
-        }
-      }
-    })();
-
-    // ── Input handling ──
-    let dragging = false;
-    let didDrag = false; // true if mouse moved significantly during drag
-    let downX = 0;
-    let downY = 0;
-    let lastX = 0;
-    let lastY = 0;
-    const DRAG_THRESHOLD = 5; // pixels
-
-    const onDown = (e: MouseEvent) => {
-      dragging = true;
-      didDrag = false;
-      downX = e.clientX;
-      downY = e.clientY;
-      lastX = e.clientX;
-      lastY = e.clientY;
-    };
-    const onMove = (e: MouseEvent) => {
-      mousePos.current = { x: e.clientX, y: e.clientY };
-      if (!dragging) return;
-
-      // Check if we've moved enough to consider it a drag
-      const dx = e.clientX - downX;
-      const dy = e.clientY - downY;
-      if (Math.abs(dx) > DRAG_THRESHOLD || Math.abs(dy) > DRAG_THRESHOLD) {
-        didDrag = true;
-      }
-
-      renderer.pan(e.clientX - lastX, e.clientY - lastY);
-      lastX = e.clientX;
-      lastY = e.clientY;
-    };
-    const onUp = (e: MouseEvent) => {
-      if (dragging && !didDrag) {
-        // This was a click, not a drag - handle selection
-        const node = renderer.findNodeIndexAt(e.clientX, e.clientY);
-        if (node) {
-          setSelectedNodes((prev: Set<number>) => {
-            const next = new Set(prev);
-            if (next.has(node.index)) {
-              next.delete(node.index); // Deselect if already selected
-            } else {
-              next.add(node.index); // Select
-            }
-            return next;
-          });
-        }
-      }
-      dragging = false;
-      didDrag = false;
-    };
-    const onWheel = (e: WheelEvent) => {
-      e.preventDefault();
-      const factor = e.deltaY > 0 ? 0.9 : 1 / 0.9;
-      renderer.zoomAt(factor, e.clientX, e.clientY);
-    };
-    const onMouseLeave = () => {
-      setHoveredNode(null);
-    };
-
-    canvas.addEventListener("mousedown", onDown);
-    window.addEventListener("mousemove", onMove);
-    window.addEventListener("mouseup", onUp);
-    canvas.addEventListener("wheel", onWheel, { passive: false });
-    canvas.addEventListener("mouseleave", onMouseLeave);
-
-    // ── Render loop ──
-    let frameCount = 0;
-    let lastTime = performance.now();
-    let raf = 0;
-
-    const frame = () => {
-      const result = renderer.render();
-      frameCount++;
-
-      // Find hovered node using quadtree
-      const nodeResult = renderer.findNodeIndexAt(mousePos.current.x, mousePos.current.y);
-      if (nodeResult) {
-        setHoveredNode({ x: nodeResult.x, y: nodeResult.y, screenX: mousePos.current.x, screenY: mousePos.current.y, index: nodeResult.index });
-      } else {
-        setHoveredNode(null);
-      }
-
-      const now = performance.now();
-      if (now - lastTime >= 500) {
-        const fps = (frameCount / (now - lastTime)) * 1000;
-        setStats({
-          fps: Math.round(fps),
-          drawn: result.drawnCount,
-          mode: result.mode,
-          zoom: result.zoom,
-          ptSize: result.ptSize,
-        });
-        frameCount = 0;
-        lastTime = now;
-      }
-
-      raf = requestAnimationFrame(frame);
-    };
-    raf = requestAnimationFrame(frame);
-
-    return () => {
-      cancelled = true;
-      cancelAnimationFrame(raf);
-      canvas.removeEventListener("mousedown", onDown);
-      window.removeEventListener("mousemove", onMove);
-      window.removeEventListener("mouseup", onUp);
-      canvas.removeEventListener("wheel", onWheel);
-      canvas.removeEventListener("mouseleave", onMouseLeave);
-    };
-  }, []);
-
-  // Sync selection state to renderer
-  useEffect(() => {
-    if (rendererRef.current) {
-      rendererRef.current.updateSelection(selectedNodes);
-    }
-  }, [selectedNodes]);
-
-  return (
-    <div style={{ width: "100vw", height: "100vh", overflow: "hidden", background: "#000" }}>
-      <canvas
-        ref={canvasRef}
-        style={{ display: "block", width: "100%", height: "100%" }}
-      />
-
-      {/* Loading overlay */}
-      {status && (
-        <div
-          style={{
-            position: "absolute",
-            inset: 0,
-            display: "flex",
-            alignItems: "center",
-            justifyContent: "center",
-            background: "rgba(0,0,0,0.9)",
-            color: "#0f0",
-            fontFamily: "monospace",
-            fontSize: "16px",
-          }}
-        >
-          {status}
-        </div>
-      )}
-
-      {/* Error overlay */}
-      {error && (
-        <div
-          style={{
-            position: "absolute",
-            inset: 0,
-            display: "flex",
-            alignItems: "center",
-            justifyContent: "center",
-            background: "rgba(0,0,0,0.9)",
-            color: "#f44",
-            fontFamily: "monospace",
-            fontSize: "16px",
-          }}
-        >
-          Error: {error}
-        </div>
-      )}
-
-      {/* HUD */}
-      {!status && !error && (
-        <>
-          <div
-            style={{
-              position: "absolute",
-              top: 10,
-              left: 10,
-              background: "rgba(0,0,0,0.75)",
-              color: "#0f0",
-              fontFamily: "monospace",
-              padding: "8px 12px",
-              fontSize: "12px",
-              lineHeight: "1.6",
-              borderRadius: "4px",
-              pointerEvents: "none",
-            }}
-          >
-            <div>FPS: {stats.fps}</div>
-            <div>Drawn: {stats.drawn.toLocaleString()} / {nodeCount.toLocaleString()}</div>
-            <div>Mode: {stats.mode}</div>
-            <div>Zoom: {stats.zoom < 0.01 ? stats.zoom.toExponential(2) : stats.zoom.toFixed(2)} px/unit</div>
-            <div>Pt Size: {stats.ptSize.toFixed(1)}px</div>
-            <div style={{ color: "#f80" }}>Selected: {selectedNodes.size}</div>
-          </div>
-          <div
-            style={{
-              position: "absolute",
-              bottom: 10,
-              left: 10,
-              background: "rgba(0,0,0,0.75)",
-              color: "#888",
-              fontFamily: "monospace",
-              padding: "6px 10px",
-              fontSize: "11px",
-              borderRadius: "4px",
-              pointerEvents: "none",
-            }}
-          >
-            Drag to pan · Scroll to zoom · Click to select
-          </div>
-
-          {/* Hover tooltip */}
-          {hoveredNode && (
-            <div
-              style={{
-                position: "absolute",
-                left: hoveredNode.screenX + 15,
-                top: hoveredNode.screenY + 15,
-                background: "rgba(0,0,0,0.85)",
-                color: "#0ff",
-                fontFamily: "monospace",
-                padding: "6px 10px",
-                fontSize: "12px",
-                borderRadius: "4px",
-                pointerEvents: "none",
-                whiteSpace: "nowrap",
-                border: "1px solid rgba(0,255,255,0.3)",
-                boxShadow: "0 2px 8px rgba(0,0,0,0.5)",
-              }}
-            >
-              {(() => {
-                if (hoveredNode.index !== undefined && rendererRef.current) {
-                  const vertexId = rendererRef.current.getVertexId(hoveredNode.index);
-                  const info = vertexId !== undefined ? uriMapRef.current.get(vertexId) : undefined;
-                  if (info) {
-                    return (
-                      <>
-                        <div style={{ fontWeight: "bold", marginBottom: 2 }}>{info.label}</div>
-                        <div style={{ fontSize: "10px", color: "#8cf", wordBreak: "break-all", maxWidth: 400 }}>{info.uri}</div>
-                        {info.isPrimary && <div style={{ color: "#ff0", fontSize: "10px", marginTop: 2 }}>⭐ Primary (rdf:type)</div>}
-                      </>
-                    );
-                  }
-                }
-                return <>({hoveredNode.x.toFixed(2)}, {hoveredNode.y.toFixed(2)})</>;
-              })()}
-            </div>
-          )}
-        </>
-      )}
-    </div>
-  );
-}

vite.config.ts

@@ -1,19 +0,0 @@
-import path from "path";
-import { fileURLToPath } from "url";
-import tailwindcss from "@tailwindcss/vite";
-import react from "@vitejs/plugin-react";
-import { defineConfig } from "vite";
-import { viteSingleFile } from "vite-plugin-singlefile";
-
-const __filename = fileURLToPath(import.meta.url);
-const __dirname = path.dirname(__filename);
-
-// https://vite.dev/config/
-export default defineConfig({
-  plugins: [react(), tailwindcss(), viteSingleFile()],
-  resolve: {
-    alias: {
-      "@": path.resolve(__dirname, "src"),
-    },
-  },
-});