Check that identifiers are valid

A checkmate-style check function. Returns TRUE when every element of x is a valid identifier for source_db, otherwise a message describing the failure. A missing element (NA) is not a failure. Pairs with assert_valid_id() and test_valid_id().

Usage

check_valid_id(x, source_db, how = "pattern", species = NULL, version = 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.

Value

TRUE if all elements are valid, otherwise a message string.

See also

assert_valid_id(), test_valid_id(), is_valid_id().

Examples

check_valid_id(c("MONDO:0005148", "MONDO:0018076"), "mondo")
#> [1] TRUE
check_valid_id("mondo:5148", "mondo")
#> [1] "Must be valid mondo identifiers (pattern mode), but 1 of 1 failed, for example 'mondo:5148'"