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Verify all datasets listed in a manifest

Source: R/manifest.R
verify_manifest.Rd

Reads a manifest.yaml produced by update_manifest and, for every entry, confirms that (a) the file exists, (b) its SHA-256 checksum matches the recorded value, and (c) its row count matches. Supported formats for automatic row-count verification: CSV (.csv), SAS (.sas7bdat), and Excel (.xlsx, .xls). For other file types the row-count check is skipped and only the SHA-256 is verified.

Call this function at the top of every analysis script or Quarto document to ensure data integrity before any results are generated.

Usage

verify_manifest(
  manifest_path = "manifest.yaml",
  data_dir = NULL,
  stop_on_error = TRUE
)

Arguments

manifest_path

Character. Path to the manifest YAML file. Defaults to "manifest.yaml" in the current working directory.

data_dir

Character. Directory in which to look for the dataset files. When NULL (default) the directory containing manifest_path is used.

stop_on_error

Logical. If TRUE (default) the function calls stop() on the first failed check, preventing the analysis from proceeding. Set to FALSE to collect all errors and report them together as a warning.

Value

Invisibly returns a data frame with columns file, status ("OK" or "FAIL"), and message.

See also

update_manifest

Examples

if (FALSE) { # \dontrun{
# --- Typical usage: top of every analysis script or .qmd -----------
hvtiRutilities::verify_manifest(here::here("manifest.yaml"))
# cohort_20240115.csv    — SHA-256 match (n = 831)
# labs_20240115.sas7bdat — SHA-256 match (n = 1204)
# adjudication_20240115.xlsx — SHA-256 match (n = 47)

# --- Collect all failures instead of stopping on the first ---------
report <- verify_manifest(
  here::here("manifest.yaml"),
  stop_on_error = FALSE
)
report[report$status == "FAIL", ]
} # }