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Re-probe every spatial file a mif points at

Source: R/mif_to_disk.R
verify_mif.Rd

Checks that each file still has the row count and columns the mif expects, and reports the first that does not.

open_mif() does this automatically, but two cases are not covered by it. A mif built with create_mif(spatial_list = <parquet paths>) references your files directly and has no manifest, so there is nothing to validate at construction and nothing stops those files changing afterwards. And a long-running session holds a store open across hours of computation, during which the files can be replaced underneath it. In both cases the recorded row count goes stale, and because the metrics index cells by position a stale count means markers attached to the wrong cells rather than an error.

Usage

verify_mif(mif)

Arguments

mif

object of class mif. In-memory mifs have nothing to verify and pass trivially, so this is safe to call unconditionally.

Value

invisibly TRUE; errors naming the first sample that fails.

See also

mif_to_disk(), open_mif()

Examples

x <- create_mif(clinical_data = spatialTIME::example_clinical,
  sample_data = spatialTIME::example_summary,
  spatial_list = spatialTIME::example_spatial[1],
  patient_id = "deidentified_id", sample_id = "deidentified_sample")
store <- file.path(tempdir(), "verify.mif")
xd <- mif_to_disk(x, store, overwrite = TRUE)
verify_mif(xd)
unlink(store, recursive = TRUE)