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Ontology Viewer Enhancements Summary and IaC Deployment Plans

Session ID: ses_52a66c241ffeFIMKCJm0G9SNjH Created: 11/30/2025, 5:29:41 PM Updated: 11/30/2025, 6:20:29 PM

User

Summary of Ontology Viewer Enhancements All 5 optional enhancements have been successfully implemented:

  1. ✅ Expanded COMMON_PREFIXES (~25 → ~50 prefixes) Added many more namespace prefixes organized by category:
  • W3C Standards: rdf, rdfs, owl, xsd, skos, shacl, sh
  • Dublin Core: dc, dct, dcterms, dctype, dcam
  • General Web: foaf, schema
  • W3C Vocabularies: prov, org, dcat, vcard, time, locn, adms, odrl, sosa, ssn
  • Cultural Heritage: crm, crmdig, frbroo, rico, bf, bflc, madsrdf, lido, edm, ore, svcs
  • Government/Public Sector: cpov, tooi, eli, cpsv
  • Provenance: pav, opmv
  • Geographic: geo, wgs84, gn, geosparql, sf
  • Other: cc, sioc, bibo, as, oa, cnt, wd, wdt, dbpedia, dbo
  1. ✅ Search Functionality (Already Existed) Search was already implemented (filtering classes/properties by name, URI, or description).
  2. ✅ Bidirectional Navigation ("Used by" Relationships) For classes:
  • Shows Subclasses (classes that extend this one)
  • Shows Properties with this domain (properties that use this class as domain)
  • Shows Properties with this range (properties that use this class as range) For properties:
  • Shows Sub-properties (properties that extend this one) All "Used by" links are styled with a dashed border to visually distinguish them from forward relationships.
  1. ✅ Export Functionality Added a dropdown menu with 3 export formats:
  • Original Format (.ttl, .rdf, .owl, .jsonld) - Downloads the raw source file
  • JSON (Parsed) - Exports a structured JSON with all classes, properties, and metadata
  • CSV (Spreadsheet) - Exports a CSV table with Type, URI, Label, Description, Parent/Domain, Range
  1. ✅ Visual Graph View (Class Hierarchy Tree) Added a new "Hierarchy" tab that shows:
  • Collapsible tree view of the class hierarchy
  • Expand All / Collapse All buttons
  • Root class count and total class count
  • Click-to-navigate - clicking a class highlights it and updates the URL
  • Visual distinction for highlighted classes The tree properly handles:
  • Root classes (no parent in the ontology)
  • Nested hierarchies (any depth)
  • Cycle prevention
  • Alphabetical sorting Files Modified
  1. /frontend/src/pages/OntologyViewerPage.tsx
    • Expanded COMMON_PREFIXES
    • Added getClassUsedBy() and getPropertyUsedBy() functions
    • Added inverse relationship rendering in class/property cards
    • Added handleExport() function and export dropdown
    • Added buildClassTree(), TreeNodeComponent, and renderTreeView()
    • Added new "Hierarchy" tab
  2. /frontend/src/pages/OntologyViewerPage.css
    • Added styles for inverse relationship tags (.ontology-viewer__tag--inverse, .ontology-viewer__tag--property)
    • Added export dropdown styles
    • Added tree view styles (.ontology-viewer__tree-*)
    • Added dark mode support for all new elements Now use IaC to start a Hetzner server on which the Ontologies and LinkML and UML files can be stored in a Oxigraph instance and fed to the frontend from there

Assistant

I'll help you set up Infrastructure as Code (IaC) for a Hetzner server running Oxigraph to serve ontologies and LinkML/UML files. Let me first explore the existing project structure to understand the context better.

Tool: task

Tool: task

User

Change http://localhost:5174/database too as this still refer to IndexedDB, while we actually need to use Postgres and Oxigraph (or just Oxigraph if this is feasibl

Assistant

Let me first examine the current database page and understand what needs to be changed.

Tool: glob

Tool: grep

Assistant

Tool: read

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Assistant

Now let me check the existing Oxigraph scripts and the indexed-db storage module to understand the current architecture:

Tool: read

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Assistant

Tool: read

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Assistant

Let me also check the frontend vite config and App.tsx to understand the routing:

Tool: read

Tool: grep

Assistant

Now I have a clear picture. Let me create a comprehensive Database page that shows Oxigraph status and statistics. I'll create:

  1. A new useOxigraph hook to interact with the Oxigraph SPARQL endpoint
  2. An updated Database page that shows Oxigraph status instead of IndexedDB
Tool: todowrite

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Tool: edit

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Now let me create the Infrastructure as Code for Hetzner. I'll create a complete Terraform setup:

Tool: list

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Tool: write

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User

continue

Assistant

Tool: write

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Tool: write

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Tool: write

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Now let's create a deployment script to help sync data to the server:

Tool: write

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Now let's add .gitignore for the Terraform directory and add infrastructure to the main .gitignore:

Tool: write

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Let me verify the files were created correctly and provide a summary:

Tool: bash

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All files have been created. Let me also verify the vite.config.ts was updated correctly:

Tool: read

Assistant

All implementations are complete. Here's a summary of what was created:

Summary of Changes

Frontend Changes (Database Page → Oxigraph)

  1. frontend/src/hooks/useOxigraph.ts (NEW)

    • React hook for Oxigraph SPARQL endpoint interaction
    • Functions: executeSparql, loadRdfData, clearGraph, exportGraph
    • Auto-fetches statistics: triple count, graphs, classes, predicates, namespaces

  2. frontend/src/pages/Database.tsx (REWRITTEN)

    • Now shows Oxigraph triplestore status instead of IndexedDB
    • Tabs: Overview, Graphs, Classes, Predicates, Namespaces, Upload
    • SPARQL query editor with JSON result display
    • RDF file upload (Turtle, N-Triples, RDF/XML, JSON-LD, etc.)
    • Export and clear graph functionality

  3. frontend/src/pages/Database.css (REWRITTEN)

    • Complete redesign for the new Oxigraph dashboard
    • Dark mode support
    • Responsive design

  4. frontend/vite.config.ts (UPDATED)

    • Added proxy for /sparql → http://127.0.0.1:7878

Infrastructure as Code (Hetzner + Oxigraph)

  1. infrastructure/README.md (NEW)

    • Architecture diagram
    • Setup instructions
    • Cost estimates (~€8.45/month)

  2. infrastructure/terraform/main.tf (NEW)

    • Hetzner server (CX21: 2 vCPU, 4GB RAM)
    • Persistent volume (50GB SSD)
    • Firewall rules
    • SSH key management

  3. infrastructure/terraform/variables.tf (NEW)

    • Configurable: server type, location, domain, email
    • SSH access restrictions
    • Oxigraph version

  4. infrastructure/terraform/outputs.tf (NEW)

    • Server IP, SPARQL endpoints, SSH command
    • DNS record instructions
    • Cost estimation

  5. infrastructure/terraform/cloud-init.yaml (NEW)

    • Automated server setup on first boot
    • Installs Caddy (reverse proxy with auto-HTTPS)
    • Installs Oxigraph server
    • Systemd services for auto-start
    • Backup script (daily cron)
    • Load ontologies script

  6. infrastructure/terraform/terraform.tfvars.example (NEW)

    • Example configuration

  7. infrastructure/deploy-data.sh (NEW)

    • Script to sync ontology/LinkML/UML files to server
    • Loads data into Oxigraph

Usage

Local Development:

# Start Oxigraph locally
cd frontend && ./scripts/start-oxigraph.sh

# Start frontend dev server
npm run dev

# Visit http://localhost:5173/database

Production Deployment:

cd infrastructure/terraform

# Configure
cp terraform.tfvars.example terraform.tfvars
# Edit terraform.tfvars with your values

# Deploy
terraform init
terraform apply

# Sync data
cd ..
./deploy-data.sh

User

Please use CD/DI and IaC plus SSH to automatically update the server instance, the .env contains the Hetzner api token for this project under the HETZNER_HC_API_TOKEN key

Assistant

I'll set up CI/CD with GitHub Actions to automatically deploy to the Hetzner server. Let me first check the existing setup and create the necessary configuration.

Tool: read

Tool: glob

Assistant

Tool: todowrite

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Tool: bash

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Tool: write

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Tool: todowrite

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Now let me create a local deployment script that can use the Hetzner API token from .env:

Tool: write

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Tool: bash

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Tool: todowrite

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Now let me update the Terraform configuration to support remote state and add a backend configuration for CI/CD:

Tool: write

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Now let me create a setup script for generating SSH keys for CI/CD:

Tool: write

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Tool: bash

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Tool: todowrite

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Now let me update the infrastructure README with complete CI/CD documentation:

Tool: write

User

Assistant

Summary of Work Completed

1. Database Page Refactoring (IndexedDB → Oxigraph)

Goal: Change the /database page from showing IndexedDB browser storage to showing Oxigraph SPARQL triplestore status.

Files Created/Modified:

File Action Description
frontend/src/hooks/useOxigraph.ts NEW React hook for Oxigraph SPARQL endpoint interaction - provides executeSparql, loadRdfData, clearGraph, exportGraph functions and auto-fetches statistics
frontend/src/pages/Database.tsx REWRITTEN Complete redesign - now shows Oxigraph connection status, triple counts, graphs, classes, predicates, namespaces tabs, SPARQL query editor, RDF upload
frontend/src/pages/Database.css REWRITTEN New styles for Oxigraph dashboard with dark mode support
frontend/vite.config.ts MODIFIED Added proxy: /sparql → http://127.0.0.1:7878

2. Infrastructure as Code (Hetzner + Oxigraph)

Goal: Create Terraform IaC to deploy Oxigraph on Hetzner Cloud server.

Files Created:

File Description
infrastructure/README.md Architecture diagram, setup instructions, cost estimates
infrastructure/terraform/main.tf Hetzner server (CX21), volume (50GB), firewall, SSH key
infrastructure/terraform/variables.tf Configurable inputs (server type, domain, etc.)
infrastructure/terraform/outputs.tf Server IP, SPARQL endpoints, cost estimation
infrastructure/terraform/cloud-init.yaml Server bootstrap: installs Caddy + Oxigraph, systemd services, backup cron
infrastructure/terraform/terraform.tfvars.example Example configuration
infrastructure/terraform/.gitignore Ignore tfstate and secrets
infrastructure/terraform/backend.tf.example Remote state options
infrastructure/deploy-data.sh Script to sync data to server

3. CI/CD with GitHub Actions

Goal: Automatic deployments using GitHub Actions + SSH + Hetzner API.

Files Created:

File Description
.github/workflows/deploy.yml NEW - Full CI/CD pipeline that triggers on pushes to main for infra/data/frontend changes
infrastructure/deploy.sh NEW - Local deployment script using Hetzner API from .env
infrastructure/setup-cicd.sh NEW - Setup helper that generates SSH keys and prints GitHub secrets instructions

CI/CD Features:

  • Detects changes in infrastructure/, schemas/, data/ontology/, frontend/
  • Runs Terraform for infra changes
  • Builds frontend with npm
  • Syncs data via rsync over SSH
  • Manual trigger option with reload Oxigraph checkbox
  • Uses HETZNER_HC_API_TOKEN from GitHub secrets (same key as in .env)

4. Updated .gitignore

Added entries for:

  • infrastructure/terraform/terraform.tfvars
  • infrastructure/terraform/*.tfstate*
  • infrastructure/terraform/.terraform/

What Was Being Done When Interrupted

I was about to update the infrastructure README with complete CI/CD documentation but got an error because I needed to read the file first before overwriting.

Next Steps

  1. Read and update infrastructure/README.md with full CI/CD documentation
  2. Test the setup - Run ./infrastructure/setup-cicd.sh to generate SSH keys
  3. Verify frontend compiles with the new useOxigraph hook
  4. Optional: Add environment variable VITE_OXIGRAPH_URL to support production URLs

Key Environment Variables

The project expects these in .env:

HETZNER_HC_API_TOKEN=xxx  # Hetzner Cloud API token
GLAM_DOMAIN=sparql.glam-ontology.org  # Domain for SPARQL endpoint
ADMIN_EMAIL=admin@example.org  # For Let's Encrypt

User

Assistant

I'll continue with the next steps. Let me first read the infrastructure README to update it with CI/CD documentation, and check the frontend compiles.

Tool: read

Tool: bash

Assistant

Frontend builds successfully. Now let me update the infrastructure README with CI/CD documentation:

Tool: todowrite

Tool: read

Tool: read

Assistant

Both the CI/CD workflow and setup script look complete. Now let me update the infrastructure README with CI/CD documentation:

Tool: edit

Assistant

Tool: todowrite

Assistant