CLI reference (Strixonomy v0.27)¶

The strixonomy binary indexes ontology workspaces and exposes query, validation, patch, and reasoning commands.

Install (pin latest tagged release):

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

From a git clone, use cargo run -- instead of strixonomy.

Commands at a glance¶

Global output formats¶

Several commands accept --format text|json|csv (where noted). Default is text.

Commands¶

new¶

Create a new Turtle or OBO ontology file with owl:Ontology header metadata.

strixonomy new ./people.ttl --ontology-iri 'http://example.org/people'
strixonomy new ./terms.obo --ontology-iri 'http://purl.obolibrary.org/obo/demo.owl' --force

Exit: 0 on success; non-zero if the path exists (without --force) or IRI validation fails.

index¶

Scan and index ontology files in a workspace. Prints catalog statistics only — use for CI scripts and machine-readable output.

strixonomy index [workspace]
strixonomy index ./ontologies --format json

Default workspace: . (current directory).

Exit: 0 on success; non-zero on index failure.

inspect¶

Index the workspace and print catalog statistics plus a diagnostic summary (counts and up to 10 sample messages). Use for a quick human health check; run validate for full diagnostic listing and CI gating.

strixonomy inspect fixtures
strixonomy inspect /path/to/ontologies --format json

Expected output (text, fixtures/): ontology/class/property counts (e.g. multiple classes including Person).

query¶

Run a SQL-like query against virtual tables. See SQL reference.

strixonomy query fixtures "SELECT short_name, labels FROM classes"
strixonomy query . "SELECT code, message FROM diagnostics WHERE severity = 'error'" --format json

Expected output (text, fixtures/): tab-separated columns plus rows (e.g. Person in short_name).

Exit: 0 on success; non-zero on parse/unsupported SQL/I/O errors.

sparql¶

Run SPARQL against indexed triples. See SPARQL reference.

strixonomy sparql fixtures "SELECT ?s ?p ?o WHERE { ?s ?p ?o } LIMIT 10"

Exit: 0 on success; non-zero on failure. Results truncate at 100,000 rows.

dl-query¶

Run a Protégé-style DL Query (Manchester class expression). See DL Query.

strixonomy dl-query "Person and hasPet some Dog" --workspace fixtures --profile dl
strixonomy dl-query "Person" --mode asserted --format json

Exit: 0 on success; non-zero on parse/reasoner error.

validate¶

Index workspace and fail if diagnostic errors exist (warnings allowed).

strixonomy validate .
strixonomy validate /path/to/ontologies

Expected output (text, clean workspace): diagnostic summary with exit code 0 (warnings allowed).

Exit: 0 when no errors; non-zero otherwise. Stable for CI — ci-integration.md.

patch¶

Apply Turtle (.ttl), OBO (.obo), RDF/XML (.owl/.rdf), and OWL/XML (.owx) patch operations from a JSON file. See patch reference and patch examples. For a one-page format matrix (index/query vs write-back), see Supported formats. XML caveats: OWL/XML write-back.

strixonomy patch ./ontology.ttl patches.json --preview
strixonomy patch ./ontology.ttl patches.json
strixonomy patch ./ontology.owl patches.json

Exit: 0 on success; non-zero on invalid patch or unsupported format/op.

robot¶

Run ROBOT CLI subcommands. Requires Java and robot on PATH (or --robot-path). See ROBOT interop guide.

strixonomy robot validate path/to/ontology.owl
strixonomy robot merge --inputs a.owl --inputs b.owl --output merged.owl
strixonomy robot report path/to/ontology.owl --report report.tsv

Optional --robot-path overrides the robot executable (same as VS Code strixonomy.robotPath).

Exit: matches ROBOT exit code (0 on success).

classify¶

Run OWL classification via OntoLogos 1.0.0.

strixonomy classify ./ontologies --profile el
strixonomy classify . --profile rl --format json

Expected output (json): consistent: true, unsatisfiable: [], profile_used, duration_ms when ontology is consistent.

Exit: 0 when consistent (no unsatisfiable classes); non-zero on unsatisfiable classes or reasoner error.

JSON includes: profile_used, consistent, unsatisfiable, warnings, duration_ms, inferred hierarchy fields.

See Reasoner guide and workspace-limits.md.

explain¶

Explain unsatisfiability for a class IRI (requires OntoLogos explain support).

strixonomy explain ./ontologies --class 'http://example.org#Invalid' --profile el
strixonomy explain . --class 'http://example.org#Invalid' --format json

Exit: 0 when explanation produced; non-zero if class not found or explanation unavailable.

realize¶

Realize individuals (inferred types) for a workspace (ABox). Default profile is rl.

strixonomy realize ./ontologies --profile rl
strixonomy realize fixtures --profile dl --format json

Expected output (text): one line per individual with types=[…] and most_specific=[…].

Exit: 0 on success; non-zero on reasoner error.

See Reasoner guide and realize cookbook.

check-instance¶

Check whether an individual is an instance of a class.

strixonomy check-instance fixtures \
  --individual 'http://example.org/people#alice' \
  --class 'http://example.org/people#Person' \
  --profile rl

strixonomy check-instance . \
  --individual 'http://example.org/people#alice' \
  --class 'http://example.org/people#Person' \
  --format json

Exit: 0 when entailed; non-zero when not entailed or on reasoner error.

LSP note: Realization is a CLI / CI command today (strixonomy realize). Instance checks are available via LSP strixonomy/checkInstance. There is no LSP realize method — use the CLI in automation.

SWRL (no CLI subcommand)¶

refactor¶

Workspace refactoring (rename / merge / replace across formats where remaps apply; move / extract / import ops are Turtle-first). See Refactoring guide.

refactor usages¶

List usages of an entity IRI across the workspace.

strixonomy refactor usages fixtures 'http://example.org/people#Person'
strixonomy refactor usages . 'http://example.org/people#Person' --format json

Exit: 0 on success; non-zero on index failure.

refactor rename¶

Rename an entity IRI across indexed ontology files (Turtle + format remaps for RDF/XML, OWL/XML, OBO).

strixonomy refactor rename fixtures \
  --from 'http://example.org/people#Person' \
  --to 'http://example.org/people#Human' \
  --preview

strixonomy refactor rename fixtures \
  --from 'http://example.org/people#Person' \
  --to 'http://example.org/people#Human'

refactor merge¶

Merge one entity into another (rewrite references to the keep IRI; drop the merge declaration).

strixonomy refactor merge fixtures \
  --keep 'http://example.org/people#Person' \
  --merge 'http://example.org/people#Human' \
  --preview

refactor replace¶

Replace references to one entity with another (keeps source declaration when the target already exists).

strixonomy refactor replace fixtures \
  --from 'http://example.org/people#OldName' \
  --to 'http://example.org/people#NewName' \
  --preview

refactor migrate-namespace¶

Replace a namespace base IRI across Turtle files (@prefix and term IRIs).

strixonomy refactor migrate-namespace fixtures \
  --from 'http://example.org/people#' \
  --to 'http://example.org/v2/people#' \
  --preview

refactor move¶

Move an entity block to another Turtle file.

strixonomy refactor move fixtures 'http://example.org/people#Student' \
  --to ./students.ttl \
  --preview

refactor extract¶

Extract selected entities into a new module file.

strixonomy refactor extract fixtures \
  --entities 'http://example.org/people#Person,http://example.org/people#Student' \
  --out ./core.ttl \
  --leave-stub \
  --locality \
  --preview

refactor merge-ontologies¶

Merge one or more Turtle ontology files into a target Turtle file.

strixonomy refactor merge-ontologies fixtures \
  --sources ./a.ttl --sources ./b.ttl \
  --target ./combined.ttl \
  --preview

refactor flatten-imports / cleanup-imports¶

Inline imported Turtle axioms (flatten) or remove unused owl:imports (cleanup heuristic).

strixonomy refactor flatten-imports fixtures --file ./root.ttl --preview
strixonomy refactor cleanup-imports fixtures --file ./root.ttl --preview

Exit (rename / merge / replace / migrate / move / extract / ontology ops): 0 on success; non-zero on invalid request, path jail violation, or I/O failure. With --preview, files are not written.

diff¶

Semantic catalog diff between git refs, directories, or indexed snapshots. See Semantic diff guide.

strixonomy diff HEAD..WORKTREE
strixonomy diff --left-ref main --right-ref feature --format markdown
strixonomy diff --left-ref HEAD --right-ref WORKTREE --breaking-only
strixonomy diff --left-ref ./baseline --right-ref ./candidate
strixonomy diff main..feature --pr-summary

Ref tokens (CLI vs LSP): The CLI compares git refs and directories on disk only. Use WORKTREE for the working-tree catalog built from disk. To compare against the indexed in-memory catalog (LSP / VS Code), use strixonomy/semanticDiff with INDEXED or CATALOG (legacy alias: WORKSPACE). Passing WORKSPACE / INDEXED / CATALOG to the CLI returns an error directing you to the LSP or WORKTREE.

Exit: 0 on success; non-zero on git/parse/I/O errors.

Troubleshooting: If you see provide --left-ref or a git range, pass a range or both refs. Do not use --left / --right — those flags do not exist.

docs¶

Export Markdown or HTML documentation from an indexed workspace. See Documentation export guide.

strixonomy docs ./fixtures --format markdown --output /tmp/onto-docs
strixonomy docs . --format html --output ./docs-out \
  --ontology-id http://example.org/people

Markdown index.md includes Class hierarchy and Property index sections (v0.13+).

Exit: 0 on success; non-zero on index, plugin export, or I/O failure.

plugins¶

Discover, inspect, enable/disable, and run workspace plugins from .strixonomy/plugins/*.toml. See Plugin authoring guide (SDK 1.0).

plugins list¶

strixonomy plugins list [workspace]
strixonomy plugins list . --format json

Result (text): one line per plugin (id, kind, version). Result (json): array of plugin descriptors (includes lifecycle fields such as state, enabled, depends_on, activation when present).

Exit: 0 on success; non-zero on discovery/host failure.

plugins info¶

strixonomy plugins info <plugin_id> [workspace]
strixonomy plugins info strixonomy.naming-validator . --format json

Shows lifecycle and dependency info: state, activation, enabled, depends_on, manifest_path.

Exit: 0 on success; non-zero if the plugin id is unknown or host discovery fails.

plugins enable / plugins disable¶

strixonomy plugins enable <plugin_id> [workspace]
strixonomy plugins disable <plugin_id> [workspace]

enable activates the plugin (and dependents per activation policy). disable cascade-deactivates dependents.

Exit: 0 on success; non-zero on host/policy failure.

plugins run¶

strixonomy plugins run <plugin_id> [--action <name>] [--step <name>] [--query <text>] [--iri <iri>] [workspace]
strixonomy plugins run strixonomy.naming-validator --action validate .
strixonomy plugins run my.query --action query.run --query 'SELECT short_name FROM classes' .

Exit: 0 on success; non-zero on host/action failure or plugin-reported failure.

workflow¶

Run an external workflow plugin subprocess (e.g. owlmake scaffold).

strixonomy workflow --plugin owlmake --step qc [workspace]

Exit: 0 when the workflow reports success; non-zero when the plugin fails or subprocess exits unsuccessfully.

Related¶

• Plugin authoring guide
• Refactoring guide
• Examples: refactoring
• Install CLI & CI (detail)
• CI integration
• Errors reference
• What ships today