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Download OBO Foundry Ontology File

download_obo_ontology.Rd

Downloads the current version of one or more ontologies from the OBO Foundry.

Usage

download_obo_ontology(ontology_id, dest_dir, on_failure = "warn", ...)

Arguments

ontology_id

A character vector of OBO Foundry ontology identifier(s) (lowercase, as found on http://www.obofoundry.org/). For reference, ontology identifiers are also provided in obofoundry_metadata within this package.

dest_dir

Path to directory where files will be saved.

on_failure

A string indicating how to handle download failure:

  • "warn" - produce a warning; includes exit codes for debugging

  • "abort" - abort execution

  • "list_failed" - list URLs that failed (output format differs, see Value)

  • "warn-list_failed" - combination of "warn" and "list_failed"

  • "skip" - do nothing

...

Additional arguments passed on to utils::download.file().

Value

Unless on_failure includes "list_failed", the successfully downloaded dest_file(s); otherwise, a 2-vector list where successful = dest_file(s) and failed = url(s).