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Generate a synthetic column of identifiers

Source: R/synthetic.R
synthesize_ids.Rd

synthesize_ids() builds a small "messy column" for a source: a mix of well-formed ids, repairable ids (a wrong-case or unpadded form that suggests a valid one), hard-invalid ids, and missing cells. Every value is labeled by running the checker, so the labels are always correct and match what the Python synthesize() produces for the same source. It works in pattern mode (the shape) for any source and in cache mode (the snapshot) for a source that ships one. It is useful for exercising a validation pipeline (feed the column to report_id(), repair_id(), or an adapter) without hand-writing test data. The generation is deterministic and offline.

Usage

synthesize_ids(
  source_db,
  how = "pattern",
  version = NULL,
  n_valid = 2,
  n_repairable = 1,
  n_invalid = 1,
  missing = 1,
  seed = 0
)

Arguments

source_db

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

how

Checking mode to label against: "pattern" (the shape, any source) or "cache" (the snapshot; the source must ship one).

version

In cache mode, the snapshot version. Defaults to "sample".

n_valid

How many well-formed or in-snapshot ids to include. A source with no numeric part yields just the example.

n_repairable

How many repairable ids (a wrong-case or unpadded form that suggests a valid id, or in cache mode a retired id that maps to a successor). ec, hgvs, and hgnc have no pattern-mode repairable form, so they yield none there.

n_invalid

How many hard-invalid ids (neither valid nor suggestible).

missing

How many missing cells (NA).

seed

Shifts the numeric variants, for a different but still deterministic column (pattern mode).

Value

A tibble with the columns input, category ("valid", "repairable", "invalid", or "missing"), and the valid, normalized, and suggestion the checker returned for that input. Categories a source cannot produce are simply absent.

See also

report_id(), check_id().

Examples

synthesize_ids("mondo")
#> # A tibble: 5 × 5
#>   input          category   valid normalized    suggestion   
#>   <chr>          <chr>      <lgl> <chr>         <chr>        
#> 1 MONDO:0005148  valid      TRUE  MONDO:0005148 NA           
#> 2 mondo:0005148  repairable FALSE NA            MONDO:0005148
#> 3 MONDO:0005148! invalid    FALSE NA            NA           
#> 4 NA             missing    NA    NA            NA           
#> 5 MONDO:0005149  valid      TRUE  MONDO:0005149 NA