ROBOT interop¶

OntoIndex v0.8.0 wraps the ROBOT CLI for validate, merge, and report workflows. ROBOT runs as an external Java process — OntoIndex does not embed a JVM.

Canonical capability matrix: What ships today.

Prerequisites¶

Requirement	Notes
Java	ROBOT requires a JRE on the agent or developer machine
`robot` on PATH	Or set an explicit path (see below)
OntoIndex 0.8.0+	`ontoindex robot` subcommand or LSP `ontoindex/runRobot`

Install ROBOT from robot.obolibrary.org.

CLI¶

# Validate
ontoindex robot validate path/to/ontology.owl

# Merge
ontoindex robot merge --inputs a.owl --inputs b.owl --output merged.owl

# Report
ontoindex robot report path/to/ontology.owl --report report.tsv

Override the executable:

ontoindex robot validate demo.obo --robot-path /opt/robot/robot.jar

Full flag reference: CLI reference.

VS Code¶

Set ontocode.robotPath in settings to the robot executable or JAR when it is not on PATH. Trusted workspaces only (ignored in Restricted Mode).

LSP clients can call ontoindex/runRobot — see LSP API.

CI recipe¶

- name: Install OntoIndex
  run: cargo install ontoindex-cli --locked --version 0.8.0

- name: OntoIndex validate
  run: ontoindex validate ./ontologies

- name: ROBOT validate
  run: ontoindex robot validate ./ontologies/core.owl

Example with OBO fixtures: examples/obo-workflow/.

Security note¶

ROBOT spawns a child process with user-supplied arguments. Run in trusted CI agents only; do not expose runRobot over an unauthenticated network LSP bridge.