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Write reviewed SSSOM mapping sets into a Salmon Data Package

Source: R/sssom.R
write_sdp_sssom.Rd

Writes explicitly supplied SSSOM 1.1 mapping sets under metadata/semantic/ and records their paths, hashes, row counts, source versions, licenses, and writer provenance in metadata/semantic/mapping-sets.json. Bytes and manifest ordering are deterministic. This function does not turn semantic suggestions or variable decompositions into mappings; mapping_sets = NULL is therefore a no-op.

Usage

write_sdp_sssom(path, mapping_sets = NULL, overwrite = FALSE)

Arguments

path

Existing Salmon Data Package directory.

mapping_sets

NULL, one or more paths to reviewed .sssom.tsv files, or parsed objects returned by read_sssom_mapping_set().

overwrite

Logical; replace files managed by this writer when TRUE.

Value

The manifest path, invisibly, or NULL when mapping_sets is NULL.

Examples

# Supply a reviewed SSSOM file. This temporary set illustrates the format.
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)
sdp_path <- tempfile("sdp-")
dir.create(sdp_path)
write_sdp_sssom(sdp_path, mapping_file)
validate_sdp_sssom(sdp_path)
unlink(c(mapping_file, sdp_path), recursive = TRUE)