# 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 2. ✅ Search Functionality (Already Existed) Search was already implemented (filtering classes/properties by name, URI, or description). 3. ✅ 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. 4. ✅ 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 5. ✅ 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 ``` ``` Tool: read ``` ``` Tool: read ``` --- ## Assistant Now let me check the existing Oxigraph scripts and the indexed-db storage module to understand the current architecture: ``` Tool: read ``` ``` Tool: read ``` ``` Tool: glob ``` --- ## Assistant ``` Tool: read ``` ``` Tool: grep ``` --- ## 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 ``` --- ## Assistant ``` Tool: write ``` --- ## Assistant ``` Tool: todowrite ``` --- ## Assistant ``` Tool: write ``` --- ## Assistant ``` Tool: todowrite ``` --- ## Assistant ``` Tool: write ``` --- ## Assistant ``` Tool: todowrite ``` --- ## Assistant ``` Tool: edit ``` --- ## Assistant ``` Tool: todowrite ``` --- ## Assistant Now let me create the Infrastructure as Code for Hetzner. I'll create a complete Terraform setup: ``` Tool: list ``` --- ## Assistant ``` Tool: bash ``` --- ## Assistant ``` Tool: write ``` --- ## Assistant ``` Tool: write ``` --- ## Assistant ``` Tool: write ``` --- ## Assistant --- ## User continue --- ## Assistant ``` Tool: write ``` --- ## Assistant ``` Tool: write ``` --- ## Assistant ``` Tool: write ``` --- ## Assistant Now let's create a deployment script to help sync data to the server: ``` Tool: write ``` --- ## Assistant ``` Tool: bash ``` --- ## Assistant Now let's add `.gitignore` for the Terraform directory and add infrastructure to the main `.gitignore`: ``` Tool: write ``` --- ## Assistant ``` Tool: read ``` --- ## Assistant ``` Tool: edit ``` --- ## Assistant ``` Tool: todowrite ``` --- ## Assistant Let me verify the files were created correctly and provide a summary: ``` Tool: bash ``` --- ## Assistant ``` Tool: bash ``` --- ## Assistant 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) 5. **`infrastructure/README.md`** (NEW) - Architecture diagram - Setup instructions - Cost estimates (~€8.45/month) 6. **`infrastructure/terraform/main.tf`** (NEW) - Hetzner server (CX21: 2 vCPU, 4GB RAM) - Persistent volume (50GB SSD) - Firewall rules - SSH key management 7. **`infrastructure/terraform/variables.tf`** (NEW) - Configurable: server type, location, domain, email - SSH access restrictions - Oxigraph version 8. **`infrastructure/terraform/outputs.tf`** (NEW) - Server IP, SPARQL endpoints, SSH command - DNS record instructions - Cost estimation 9. **`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 10. **`infrastructure/terraform/terraform.tfvars.example`** (NEW) - Example configuration 11. **`infrastructure/deploy-data.sh`** (NEW) - Script to sync ontology/LinkML/UML files to server - Loads data into Oxigraph ### Usage **Local Development:** ```bash # Start Oxigraph locally cd frontend && ./scripts/start-oxigraph.sh # Start frontend dev server npm run dev # Visit http://localhost:5173/database ``` **Production Deployment:** ```bash 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 ``` --- ## Assistant ``` Tool: bash ``` --- ## Assistant ``` Tool: write ``` --- ## Assistant ``` Tool: todowrite ``` --- ## Assistant Now let me create a local deployment script that can use the Hetzner API token from .env: ``` Tool: write ``` --- ## Assistant ``` Tool: bash ``` --- ## Assistant ``` Tool: todowrite ``` --- ## Assistant Now let me update the Terraform configuration to support remote state and add a backend configuration for CI/CD: ``` Tool: write ``` --- ## Assistant Now let me create a setup script for generating SSH keys for CI/CD: ``` Tool: write ``` --- ## Assistant ``` Tool: bash ``` --- ## Assistant ``` Tool: todowrite ``` --- ## Assistant 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 ---