Validate a Key Resources Table — validate

Runs the registered validation rules over a table and returns a krt_validation_report. Structural rules check schema conformance offline; semantic rules check cross-field consistency and, when resolve = TRUE, identifier existence. Conditional packs (cell-line authentication, organism metadata, ethics/consent) apply only when the relevant resource types are present; they are minimal checks, not full ICLAC or ARRIVE assessments.

Usage

validate_krt(
  x,
  profile = NULL,
  layers = c("structural", "semantic"),
  resolve = FALSE,
  severity = NULL,
  attach = FALSE
)

Arguments

x: A krt_tbl.
profile: Profile whose severity overrides apply (default the table's profile).
layers: Which layers to run: "structural", "semantic", or both.
resolve: If TRUE, semantic rules may perform online existence checks (off by default; never on CRAN).
severity: Optional named list mapping rule_id to a severity (or "off"), overriding rule and profile defaults.
attach: If TRUE, return the table with the findings stored in its validation slot instead of returning the report.

Value

A krt_validation_report, or the krt_tbl when attach = TRUE.

Details

Each finding's severity is resolved from the rule default, then any profile override, then any per-rule value in severity. A severity of "off" disables the rule.

Examples

validate_krt(krt_example)
#> <krt_validation_report> profile: generic | VALID | 0 findings
#>   errors: 0  warnings: 0  notes: 0  info: 0
validate_krt(krt_example, layers = "structural")
#> <krt_validation_report> profile: generic | VALID | 0 findings
#>   errors: 0  warnings: 0  notes: 0  info: 0