ontoindex-cli 0.3.0

CLI for OntoIndex ontology indexing and querying
ontoindex-cli-0.3.0 is not a library.

OntoCode

CI Extension VS Code E2E License MSRV Rust edition

crates core parser catalog query cli lsp diagnostics downloads

Ontology-as-code for Git and VS Code — v0.3.0 ships today.

Browse OWL/RDF in VS Code, query and validate in CI, and index workspaces locally with a Rust engine. v0.3 adds ontology diagnostics in the Problems panel and explorer; editing, reasoning, and semantic diffs are on the roadmap.

Naming: OntoCode is the VS Code extension (product UI). OntoIndex is the Rust engine (ontoindex CLI, ontoindex-* crates, ontoindex-lsp). This repo contains both.

Choose your path

Use the CLI (OntoIndex)

cargo install ontoindex-cli
ontoindex query ./fixtures "SELECT * FROM classes"
ontoindex validate .

From a clone, cargo run -- runs the ontoindex binary (workspace default-member is ontoindex-cli).

Use VS Code (OntoCode Explorer)

  1. Install OntoCode from the Marketplace, or download a VSIX from GitHub Releases.
  2. Open a folder with .ttl, .owl, .rdf, or other supported ontology files.
  3. Use the OntoCode activity bar to browse entities and open the inspector.

Full install and troubleshooting: docs/vscode-install.md.

OntoCode Explorer preview

Two-layer architecture

OntoCode is designed as two products that ship together:

Layer What it is Status in v0.3.0
OntoCode VS Code extension (explorer, entity inspector, diagnostics, jump-to-source) Shipping — install VSIX or run from extension/
OntoIndex Rust library + CLI + LSP (scan, parse, catalog, query, validate, diagnostics) Shipping 
┌─────────────────────────────────────┐
│  OntoCode (v0.3)                    │
│  VS Code extension + explorer UI    │
└─────────────────┬───────────────────┘
                  │ ontoindex-lsp (stdio)
┌─────────────────▼───────────────────┐
│  OntoIndex (v0.3.0)                 │
│  Rust index, catalog, query, CLI, LSP │
└─────────────────┬───────────────────┘
                  │ Oxigraph / RDF parsers
┌─────────────────▼───────────────────┐
│  Your ontology repo                 │
│  .ttl .owl .rdf .jsonld …           │
└─────────────────────────────────────┘

OntoIndex is useful on its own today (CLI, CI, local analysis). The extension will call into the same engine via a language server rather than reimplementing ontology logic in TypeScript.

Why OntoCode?

Protégé is strong for traditional ontology editing, but most engineering teams live in Git, pull requests, and VS Code. OntoCode targets that workflow:

Shipped in v0.3 Planned (v1.0 target)
Browse ontologies in VS Code Hybrid authoring: forms + Manchester editor
Entity inspector and jump-to-source OWL axiom editing and patch write-back
Inline diagnostics (Problems panel + explorer) Query workbench, OntoLogos-backed reasoners + explanations
ontoindex validate and SELECT * FROM diagnostics for CI OBO format + ROBOT interop
SQL-like and SPARQL queries via CLI Semantic Git diff, LSP completion/rename
Local-first indexing SHACL validation (rudof)

Long-term goal: Protégé-competitive OWL 2 DL + OBO maintenance in VS Code — see PROTEGE_PARITY.md.

What's in v0.3.0 (Ontology Diagnostics)

v0.3 adds ontology linting and editor integration described in the v0.3 roadmap:

  • Catalog lint rules — parse errors, broken imports, undefined prefixes, duplicate/missing labels, orphan classes
  • diagnostics SQL table — SELECT * FROM diagnostics WHERE severity = 'error'
  • LSP publishDiagnostics — Problems panel updates after each workspace reindex
  • Diagnostics explorer — sidebar tree grouped by severity; click to jump to source
  • ontoindex validate — prints all diagnostics; non-zero exit on errors (CI-friendly)
  • Open-buffer parsing — unsaved edits show parse errors without saving

Exit criterion (works today):

  1. Open a repo with ontology files in VS Code
  2. See parse and lint issues in the Problems panel and Diagnostics sidebar
  3. Run ontoindex validate . or query the diagnostics table in CI

Also since v0.2 (OntoCode Explorer)

  • VS Code extension — OntoCode activity bar with ontology tree views
  • Entity inspector — IRI, labels, comments, parents, children, axioms
  • Jump to source — open Turtle/RDF files at entity declarations
  • ontoindex-lsp — hover, document/workspace symbols, go-to-definition

Install the extension

See docs/vscode-install.md (release VSIX, dev build, LSP troubleshooting) and extension/README.md.

What's in v0.1.0 (OntoIndex foundation)

This release delivers the Rust backend described in the v0.1 roadmap:

  • Workspace scanner — recursive discovery, .gitignore support, content hashing
  • RDF/OWL parsing — Turtle, RDF/XML, OWL, JSON-LD, N-Triples, N-Quads, TriG via Oxigraph
  • Semantic catalog — ontologies, classes, properties, individuals, annotations, axioms, namespaces, imports
  • SQL-like queries — SELECT, FROM, WHERE, projections, CSV/JSON export
  • SPARQL — query indexed triples directly
  • CLI — ontoindex index, query, sparql, validate, inspect

Exit criterion (works today):

cargo run -- query ./fixtures "SELECT * FROM classes"

Quick start

# Build
cargo build --release

# Index and inspect a workspace
cargo run -- inspect fixtures

# Query classes
cargo run -- query fixtures "SELECT * FROM classes"

# Filter results
cargo run -- query fixtures "SELECT short_name, labels FROM classes WHERE short_name = 'Person'"

# SPARQL
cargo run -- sparql fixtures "SELECT ?s ?p ?o WHERE { ?s ?p ?o } LIMIT 5"

# Validate (non-zero exit on diagnostic errors — CI-friendly)
cargo run -- validate fixtures

# Query diagnostics
cargo run -- query fixtures "SELECT code, severity, message FROM diagnostics"

# JSON output
cargo run -- query fixtures "SELECT * FROM classes" --format json

Install the CLI from crates.io (binary name: ontoindex):

cargo install ontoindex-cli
ontoindex query ./fixtures "SELECT * FROM classes"

Or build from source after cloning this repository.

Planned VS Code experience (v0.4+)

Specs and wireframes live in docs/design/. Upcoming OntoCode UI includes:

  • Class/property/individual authoring (v0.4)
  • SPARQL and SQL query panels (v0.5+)
  • Reasoner integration and graph visualization
  • Semantic Git diff viewer

The extension is a thin TypeScript shell over ontoindex-lsp and the OntoIndex crates — not a second ontology stack.

Roadmap

Version Deliverable
v0.1 OntoIndex: scanner, parser, catalog, CLI
v0.2 VS Code extension, explorer, entity inspector, LSP
v0.3.0 (current) Diagnostics — Problems panel, diagnostics SQL table, ontoindex validate
v0.4a–b Simple write-back + Horned-OWL (ontoindex-owl)
v0.5 Query workbench + Manchester MVP
v0.6 Reasoning via OntoLogos 0.9.0 (EL, RL, inferred hierarchy)
v0.7–v0.7b Graphs + OBO/ROBOT interop
v0.8–v0.9 Full Manchester, refactoring, semantic diff; ontologos-watch hook
v1.0 Protégé-competitive OWL + OBO in VS Code — DL via OntoLogos 1.0.0 (parity checklist)

See ROADMAP.md, PLAN.md, and PROTEGE_PARITY.md for the full product plan.

Built on

OntoIndex delegates to mature Rust libraries — see DEPENDENCY_MATRIX.md.

Layer Crates
RDF / SPARQL Oxigraph
SQL queries sqlparser
OWL axioms (planned) horned-owl, horned-functional
Reasoning (planned) OntoLogos
OBO (planned) fastobo
LSP lsp-server, lsp-types

Policy: ADR-0016. Third-party licenses: LICENSES.md.

Repository layout

crates/
├── ontoindex-core      # types, workspace scanner
├── ontoindex-parser    # RDF parsing and entity extraction
├── ontoindex-catalog   # index builder and semantic catalog
├── ontoindex-diagnostics # lint rules and diagnostic collection
├── ontoindex-query     # SQL-like and SPARQL engines
├── ontoindex-cli       # `ontoindex` binary
└── ontoindex-lsp       # language server for OntoCode
extension/              # VS Code extension (OntoCode Explorer)
fixtures/               # sample ontology for tests
scripts/                # extension packaging helpers
docs/                   # user guides (install, SQL, LSP API)
docs/design/  # product specs, ADRs, wireframes, backlog
examples/               # Rust examples and query cookbook
tests/                  # integration and golden snapshot tests

Virtual tables

Table Description
ontologies Indexed ontology documents
classes OWL/RDFS classes
object_properties OWL object properties
data_properties OWL datatype properties
annotation_properties OWL annotation properties
individuals OWL named individuals
entities All extracted entities
annotations Label/comment and other annotation triples
axioms Extracted axioms (e.g. SubClassOf)
namespaces Namespace prefixes
imports Ontology imports
diagnostics Lint and parse diagnostics (v0.3)
properties Union of all property kinds

Column schemas, SQL limits, and examples: docs/sql-reference.md. LSP methods: docs/lsp-api.md.

Development

See CONTRIBUTING.md. Quick checks:

cargo build -p ontoindex-lsp --bins
cargo test --workspace
cd extension && npm ci && npm test
cargo fmt --all
cargo clippy --all-targets -- -D warnings

Update golden snapshots:

ONTOINDEX_UPDATE_GOLDEN=1 cargo test golden_classes

Releasing

Published crates (v0.3.0):

Crate crates.io
ontoindex-core https://crates.io/crates/ontoindex-core
ontoindex-parser https://crates.io/crates/ontoindex-parser
ontoindex-diagnostics https://crates.io/crates/ontoindex-diagnostics
ontoindex-catalog https://crates.io/crates/ontoindex-catalog
ontoindex-query https://crates.io/crates/ontoindex-query
ontoindex-lsp https://crates.io/crates/ontoindex-lsp
ontoindex-cli https://crates.io/crates/ontoindex-cli

Push a tag matching [workspace.package].version in Cargo.toml (e.g. v0.3.0):

git tag v0.3.0
git push origin v0.3.0

The release workflow verifies packages, runs tests, publishes workspace crates to crates.io in dependency order, and creates a GitHub Release with the ontoindex Linux binary, per-platform ontoindex-lsp archives, and a multi-platform VSIX (Linux, macOS, Windows). Requires the CARGO_REGISTRY_TOKEN repository secret.

See CHANGELOG.md for release notes. Verify downloads: docs/release-integrity.md. Security: SECURITY.md.

License

MIT OR Apache-2.0