Assert that identifiers are valid

A checkmate-style assertion. Throws an error when any element of x is not a valid identifier for source_db, otherwise returns x invisibly.

Usage

assert_valid_id(
  x,
  source_db,
  how = "pattern",
  species = NULL,
  version = NULL,
  .var.name = checkmate::vname(x),
  add = NULL
)

Arguments

x

A vector of identifiers. Coerced to character.

source_db

Source key, for example "mondo". See sources().

how

Checking mode: "pattern" (offline, shape only), "cache" (offline existence against a snapshot), "remote" (live existence against the source API), or "existence" (cache when a snapshot is available for version, otherwise remote, or pattern for a source with no resolver).

species

Optional species context, echoed in the result. A name such as "homo_sapiens" or an NCBI taxon id such as 9606. When given, an id of a different species is invalid: Ensembl is checked from its id prefix (in pattern and remote modes), and UniProt from the entry's organism in remote mode. A species outside the source map is not checked.

version

Snapshot version. In cache mode it selects the snapshot and defaults to the latest installed one when omitted; it selects the snapshot for existence mode; ignored in pattern and remote modes.

.var.name

Name for x to use in error messages.

add

A checkmate AssertCollection to push messages onto, or NULL.

Value

x invisibly on success.

See also

check_valid_id(), test_valid_id().

Examples

assert_valid_id(c("MONDO:0005148", "MONDO:0018076"), "mondo")