Validate SDP SSSOM artifacts — validate_sdp

Validates either one SSSOM 1.1 embedded-TSV file or an SDP directory. For an SDP directory, the function validates metadata/semantic/mapping-sets.json, safe relative paths, byte hashes, row counts, metadata provenance, and every referenced mapping set.

Usage

validate_sdp_sssom(path)

Arguments

path: Path to an SDP directory or one .sssom.tsv mapping set.

Value

TRUE, invisibly, when validation succeeds; otherwise an error.

Examples

# Validate a self-contained mapping set before placing it in an SDP.
mapping_file <- tempfile(fileext = ".sssom.tsv")
writeLines(c(
  '#sssom_version: "1.1"',
  "#curie_map:",
  "#  exa: https://example.org/ontology-a/",
  "#  exb: https://example.org/ontology-b/",
  "#mapping_set_id: https://example.org/mappings/demo",
  "#mapping_set_version: 1",
  "#license: https://creativecommons.org/licenses/by/4.0/",
  "#subject_source: https://example.org/ontology-a/",
  "#subject_source_version: 1",
  "#object_source: https://example.org/ontology-b/",
  "#object_source_version: 1",
  paste("subject_id", "subject_label", "predicate_id", "object_id",
        "object_label", "mapping_justification", sep = "\t"),
  paste("exa:spawner-count", "Spawner count", "skos:exactMatch",
        "exb:spawner-count", "Spawner count",
        "semapv:ManualMappingCuration", sep = "\t")
), mapping_file, useBytes = TRUE)
validate_sdp_sssom(mapping_file)
unlink(mapping_file)