Troubleshooting¶

Common problems and fixes for Strixonomy (VS Code) and Strixonomy (CLI/LSP).

For quick answers, see also FAQ.

Where to start (symptom → guide)¶

Need help beyond this page? See Support and contact.

flowchart TD
  start[Something went wrong]
  start --> vscode{VS Code or CLI?}
  vscode -->|VS Code| empty{Explorer empty?}
  vscode -->|CLI| cliFix[Use absolute ontology path not fixtures/]
  empty -->|Yes| indexWs[Index Workspace + check Output panel]
  empty -->|No| edit{Cannot edit?}
  edit -->|Yes| formatCheck{ttl obo owl rdf or owx?}
  formatCheck -->|No| readOnly[JSON-LD TriG N-Triples stay read-only]
  formatCheck -->|Yes| reindex[Index Workspace + check parse status + Supported formats]
  edit -->|No| reasoner{Reasoner issue?}
  reasoner -->|Yes| reasonerGuide[Reasoner guide + lighter profile]
  reasoner -->|No| faq[FAQ + errors reference]

VS Code: explorer empty or stale¶

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, .obo, .owl, .rdf, .jsonld, .nt, .nq, .trig).
4. Multi-root workspace: since v0.10 all folders are indexed — confirm each root contains ontology files and check Output → Strixonomy Language Server for per-root errors.

VS Code: language server failed to start¶

1. Check Output → Strixonomy Language Server for the exact error.
2. Uninstall duplicate Strixonomy extension versions.
3. Strixonomy’s bundled language server works in trusted and Restricted Mode. Do not Trust the workspace unless you configured strixonomy.lspPath or strixonomy.robotPath (Restricted Mode ignores those settings).
4. Set strixonomy.lspPath to a local strixonomy-lsp binary (cargo install strixonomy-lsp --locked --version 0.27.0) — trusted workspaces only.
5. See Install VS Code.

VS Code: cannot edit in inspector¶

• Write-back applies to Turtle (.ttl), OBO (.obo), RDF/XML (.owl/.rdf), and OWL/XML (.owx) (v0.21+). See Supported formats. JSON-LD and line-oriented RDF are read-only. XML is semantic re-serialize — OWL/XML write-back.
• Entity must be declared in an indexed editable file (.ttl, .obo, .owl/.rdf, or .owx) in the workspace.
• See OBO authoring and OWL/XML write-back.

VS Code: patch or Manchester apply did not stick¶

Patches write the source file on disk first (.ttl, .obo, .owl/.rdf, or .owx), then update the language server’s open-buffer copy. XML formats are semantic re-serialize — see OWL/XML and RDF/XML write-back:

1. If the editor still shows old text, accept or re-apply the workspace edit, or reload the file from disk.
2. If you had unsaved local edits that conflicted, review the file on disk — the server applied against its buffer/disk snapshot.
3. If re-index fails after a successful write, the catalog may be stale. Run Strixonomy: Index Workspace.
4. Check View → Output → Strixonomy Language Server and errors reference.

CLI: install or version not found¶

Symptom: cargo install strixonomy-cli --locked --version X.Y.Z fails with “could not find version” or GitHub Release curl returns 404.

Cause: Documentation on main may describe an unreleased minor while crates.io and GitHub Releases only publish tagged versions.

Fix:

1. Pin the latest tagged release from docs/TAGGED_RELEASE (currently 0.27.0):

cargo install strixonomy-cli --locked --version 0.27.0

1. For release tarballs, download assets from the matching tag (e.g. v0.27.0). Prefer the tagged release over docs that may preview a future minor on main.

2. Ensure Cargo’s bin directory is on your PATH — see Install CLI.

Marketplace / Open VSX extension versions may lag a brand-new GitHub tag briefly — check the installed extension version in Extensions, or install the release VSIX from GitHub Releases.

CLI: strixonomy query ./fixtures fails¶

The fixtures/ directory exists only in a git clone, not after cargo install:

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

CLI: install and PATH¶

CLI: validate exits non-zero¶

Exit code 0 only when there are no diagnostic errors (warnings are allowed). Query errors:

strixonomy query /path/to/ontologies "SELECT code, severity, message FROM diagnostics WHERE severity = 'error'"

See CI integration.

Queries return no rows or wrong data¶

1. Re-index: strixonomy validate or VS Code Index Workspace.
2. Confirm SQL table name and column names — SQL reference.
3. SPARQL runs over indexed triples — prefix declarations must be valid in source files.

Results truncated at 100,000 rows¶

Both SQL and SPARQL cap results at 100,000 rows with silent truncation. In the Query Workbench or LSP responses, check truncated: true. Narrow your query with WHERE or SPARQL LIMIT.

See workspace limits.

Patch JSON errors¶

Workspace too large¶

Indexing may fail above workspace limits (file count, size, triple caps). For very large terminologies, use CLI batch workflows on a subset.

Graphs, OBO, ROBOT, and semantic diff¶

Reasoner¶

See Reasoner guide.

Still stuck?¶

• FAQ
• Errors reference
• Report an issue