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Validate and report on a column of identifiers

Source: R/report.R
report_id.Rd

report_id() runs check_id() over a column and returns its result table with the extra class biobouncer_report, so it prints with a one-line summary of how many values are valid, repairable, invalid, or missing. It is the recommended entry point for inspecting and cleaning a column. Use repair_id() inside dplyr::mutate() to substitute the fixable values. For enforcing validity inside a framework, reach for the adapters such as id_predicate().

Usage

report_id(
  x,
  source_db,
  how = "pattern",
  species = NULL,
  version = NULL,
  refresh = FALSE,
  on_error = "raise"
)

# S3 method for class 'biobouncer_report'
summary(object, ...)

# S3 method for class 'biobouncer_report'
print(x, ...)

Arguments

x

A biobouncer_report, as returned by report_id().

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.

refresh

In remote checks, skip any cached response and refetch. Ignored by the offline modes.

on_error

How a per-id remote failure is handled. "raise" (the default) lets the failure unwind the whole call. "indeterminate" leaves just that id NA with the reason in its error column and checks the rest of the batch, so one unreachable id does not lose the others. Ignored by the offline modes.

object

A biobouncer_report, as returned by report_id().

...

Ignored.

Value

A tibble, as returned by check_id(), with the extra class biobouncer_report. Calling summary() on it returns a one-row tibble of counts.

See also

repair_id(), check_id().

Examples

report_id(c("MONDO:0005148", "mondo:5148"), "mondo")
#> # biobouncer report on mondo (pattern mode): 1 valid, 1 repairable, 0 invalid, 0 missing of 2
#> # A tibble: 2 × 9
#>   input        valid normalized suggestion source_db version species how   error
#>   <chr>        <lgl> <chr>      <chr>      <chr>     <chr>   <chr>   <chr> <chr>
#> 1 MONDO:00051… TRUE  MONDO:000… NA         mondo     NA      NA      patt… NA   
#> 2 mondo:5148   FALSE NA         MONDO:000… mondo     NA      NA      patt… NA