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FAQ

Common questions about Strixonomy IDE and Strixonomy engine. For step-by-step fixes, see Troubleshooting.

If you’re stuck or want to report a bug, see Support and contact.

Naming and products

What is the difference between the Strixonomy IDE and the Strixonomy engine?

  • Strixonomy IDE — VS Code/Cursor extension (explorer, inspector, Query Workbench, Manchester editor, diagnostics).
  • Strixonomy engine — Rust semantic workspace (strixonomy crate, strixonomy-* crates, strixonomy CLI, strixonomy-lsp).

Full table and legacy names: Product identity.

History: OntoIndex → OntoCore (engine) + OntoCode (IDE) → Strixonomy (v0.27). See v0.9 migration and v0.27 migration. This repository contains both the IDE and the engine.

Is the API stable?

Pre-1.0. Published crates are at 0.27.x. Library APIs, LSP JSON, and SQL table columns may change between minor releases until v1.0. Pin versions in CI with cargo install strixonomy-cli --locked --version 0.27.0. See API stability. Upgrading from 0.17.x? See v0.18 migration. Upgrading from 0.16.x? See v0.17 migration. Upgrading from 0.15.x? See v0.16 migration. Upgrading from 0.14.x (or earlier)? Start at the migration index. The validate and classify exit codes are documented in workspace-limits.md.

What ships in the current release?

See What ships today for the canonical capability matrix.

Production readiness

Is Strixonomy production-ready?

Pilot-ready for many OWL/OBO workflows in VS Code and CI — not a full Protégé replacement for every profile. Use What ships today and Known limitations for the capability matrix, Production readiness for pilot vs production tiers, and Protégé decision guide for gap analysis. Pin releases in CI (--version 0.27.0) and review API stability before embedding Rust libraries.

Installation

Which version should I install?

Pin to the tagged release in docs/TAGGED_RELEASE (currently 0.27.0). See Versions and channels for Marketplace vs GitHub Releases vs crates.io vs Read the Docs latest.

Why might Marketplace lag GitHub Releases?

Marketplace publish is always manual after the release workflow. Open VSX publishes automatically when OVSX_PAT is configured on the release workflow; either store may still lag the GitHub tag by hours or longer. Prefer the GitHub Release VSIX when you need a specific tag immediately.

Can I edit Protégé .owl / RDF/XML in place?

Yes (v0.21+), with caveats. RDF/XML (.owl/.rdf) and OWL/XML (.owx) support Entity Inspector and strixonomy patch write-back via full-document re-serialize (semantic fidelity, not Protégé byte-identical). Prefer Turtle when you need byte-stable diffs, full Manchester, or Turtle-first refactor ops; rename / merge / replace also apply to XML and OBO. Details: Supported formats and OWL/XML and RDF/XML write-back.

SQL or SPARQL — which should I use?

Use catalog SQL for simple tabular listing (classes, properties). Prefer SPARQL for graph patterns, filters, and joins. Catalog SQL is a subset — not full SQL.

What is the workspace runtime (v0.20)?

Host-owned registry for open ontologies (active target, dirty/save, semantic undo, session restore under .ide/session.json). See migration v0.20.

I ran cargo install strixonomy-cli and strixonomy query ./fixtures failed.

The fixtures/ directory exists only in a git clone. Use your own ontology path:

strixonomy query /path/to/your/ontologies "SELECT * FROM classes"

See Install CLI & CI (detail). Always pin with --version 0.27.0 in CI so you do not surprise-upgrade.

Do I need Rust to use VS Code?

No. Install the extension from the Marketplace, Open VSX (Cursor), or a release VSIX. The language server is bundled.

Can I install without cargo?

Yes. Download release binaries and VSIX from GitHub Releases. Linux x64 CLI tarballs are published; macOS/Windows CLI uses cargo install. See release-integrity.md.

I ran cargo install strixonomy and something went wrong.

Install the CLI with cargo install strixonomy-cli (binary name strixonomy). The strixonomy crates.io package is the library façade, not the CLI. See Product identity.

VS Code

The explorer is empty.

  1. Run Strixonomy: Index Workspace from the Command Palette.
  2. Check View → Output → Strixonomy Language Server for errors.
  3. Confirm the folder contains supported files (.ttl, .owl, etc.).

How do I run SQL or SPARQL in VS Code?

Command Palette → Strixonomy: Open Query Workbench. See Query Workbench.

Does Strixonomy support Protégé-style DL Query?

Partially (v0.24+). Query Workbench DL mode runs Manchester class expressions with Instances / Subclasses / Superclasses / Equivalents tabs (also CLI strixonomy dl-query and LSP strixonomy/dlQuery). It is Protégé-inspired, not HermiT-identical — see DL Query honesty. SQL and SPARQL modes remain separate.

How do I edit complex axioms?

Select a class in a .ttl file → Entity Inspector → Edit in Manchester or Add Manchester axiom. See Manchester editor.

I cannot edit in the Entity Inspector.

Write-back applies to Turtle (.ttl), OBO (.obo), RDF/XML (.owl/.rdf), and OWL/XML (.owx). For the full matrix (index/query vs write-back), see Supported formats. JSON-LD and line-oriented RDF are read-only in the inspector. See OBO authoring and OWL/XML write-back.

How do multi-root VS Code workspaces work?

Since v0.10, the language server indexes all workspace folders on open. If you run Strixonomy: Index Workspace with multiple roots, VS Code may prompt you to pick a folder — automatic indexing still uses every registered root.

failed to start language server

  • Check Output → Strixonomy Language Server and uninstall duplicate Strixonomy versions.
  • Strixonomy’s bundled language server works in trusted and Restricted Mode. Do not Trust the workspace unless you configured strixonomy.lspPath or strixonomy.robotPath.
  • Set strixonomy.lspPath to a local strixonomy-lsp binary (cargo install strixonomy-lsp --locked --version 0.27.0) when debugging a custom build — trusted workspaces only.
  • See vscode-install.md and Troubleshooting (symptom table).

Does strixonomy.autoIndexOnOpen do anything?

It is a legacy setting. Indexing is driven by the language server on workspace open.

CLI and queries

What SQL is supported?

A catalog SQL (subset): single-table SELECT, FROM, WHERE with =, !=, AND, OR, and boolean columns. No JOIN, GROUP BY, ORDER BY, or LIMIT. See sql-reference.md and Known limitations.

How do I run SPARQL?

strixonomy sparql /path/to/ontologies "SELECT ?s ?p ?o WHERE { ?s ?p ?o } LIMIT 10"

See sparql-reference.md.

What happens at 100,000 result rows?

Both SQL and SPARQL truncate at 100,000 rows (no error). LSP responses include truncated: true when the cap is hit. See workspace-limits.md.

What does strixonomy validate check?

Parse errors plus catalog lint rules: broken imports, undefined prefixes, duplicate/missing labels, orphan classes. See sql-reference.md (diagnostics table).

Authoring and patches

Which formats can I edit?

Turtle (.ttl), OBO (.obo), RDF/XML (.owl/.rdf), and OWL/XML (.owx) for write-back. JSON-LD and line-oriented RDF can be indexed and queried but are read-only in the inspector. See Supported formats.

Where is the patch JSON format documented?

patch-reference.md with copy-paste examples.

Security and licenses

Is ontology content uploaded anywhere?

No. Strixonomy IDE and Strixonomy engine are local-first by default. See security.md.

What about LGPL (horned-owl)?

strixonomy-owl links horned-owl (LGPL-3.0) for Turtle axiom modeling and write-back. See design/LICENSES.md.

Can I expose strixonomy-lsp on the network?

No. The LSP has no authentication. Use stdio with a trusted editor only. See security.md.

Reasoning

How do I run the reasoner in VS Code?

Run Strixonomy: Run Reasoner from the Command Palette, then use Strixonomy: Set Hierarchy Mode for asserted / inferred / combined. See Reasoner guide.

How do I classify in CI?

strixonomy classify /path/to/ontologies --profile el --format json

Exits non-zero when unsatisfiable classes are found. See CI integration and workspace-limits.md.

Why does dl or auto fail?

If classification fails, check that your ontology is within workspace limits and that constructs are supported by Ontologos 1.x for the selected profile. Use el, rl, or rdfs for lighter-weight profiles when DL is not required.

Why is explanation empty for a class?

Explanations require an unsatisfiable class and a prior reasoner run (or successful classify). On the DL profile, explanations are DL-first; EL/RL/RDFS alternatives depend on OntoLogos coverage for that profile.

Roadmap

When did full DL reasoning ship?

EL/RL/RDFS shipped in v0.6.0 (Ontologos 0.9.0). Full OWL 2 DL classification (dl / auto) is available in v0.9.0+ via Ontologos 1.x. Results are not certified identical to Protégé + HermiT — use dual-tool checks for critical audits. ABox realization, instance checking, and SWRL authoring/validation ship in v0.23. See Reasoner guide.

How does this compare to Protégé?

Strixonomy targets OWL/OBO workflows in VS Code: browse and edit Turtle, OBO, RDF/XML, and OWL/XML; SQL/SPARQL and DL Query; EL–DL reasoning; refactoring; graph views; Turtle completion; diagnostic quick fixes; Manage Imports; property chain editing; semantic diff (CLI, LSP, and VS Code panel); and Plugin SDK 1.0 (frozen TOML + subprocess wire — Plugin policy). Gaps vs Protégé today include byte-identical XML layout, full DL axiom catalog for all formats, and a curated plugin marketplace / production owlmake (product 1.0). For a decision framework see Protégé vs Strixonomy; for the live capability matrix see What ships today and Known limitations. The historical v0.18 checklist under design/PROTEGE_PARITY.md is not current. For a first-week adoption path, see Migrating from Protégé.

OBO and graphs

Can I edit .obo files in the inspector?

Yes (v0.13+). OBO terms can be edited in the Entity Inspector and via strixonomy patch on .obo files. RDF/XML and OWL/XML are also writable (v0.21+). JSON-LD and line-oriented RDF remain read-only. See OBO workflow guide and Supported formats.

How do I open ontology graphs?

Use Strixonomy: Open Class Graph (and related commands). See Graph view.

Does ROBOT require Java?

Yes. strixonomy robot and LSP runRobot spawn the external robot CLI. See ROBOT interop guide.

Which panels use React vs legacy HTML?

As of v0.10, production webview panels are React: Entity Inspector, graph panels, Query Workbench, Manchester editor, Refactor Preview, Semantic Diff, Reasoner Results, and Explanation. Legacy HTML panels were removed in v0.9.

Contributing

Do I need cargo test --workspace for a docs-only PR?

No. Use the testing matrix and scoped PR template checkboxes. Docs-only changes need MkDocs preview (./scripts/serve-docs.sh or ./scripts/build-docs.sh) — not a full Rust build. See scripts/README.md.

When should I run ./scripts/run-ci-local.sh?

Before PRs that change CI scripts, release packaging, or broad Rust/extension surfaces — or when you want full Actions parity. Expect 30–60+ minutes cold. Skip it for docs-only PRs.

I edited React webviews but F5 still shows the old UI — why?

npm run watch in extension/ rebuilds the host only. Run npm run build:webview or npm run compile after webview-ui/ changes — Extension development.