Verify selected HTTP semantic IRIs in a Salmon Data Package — verify_sdp_semantic

Collects exact HTTP(S) identifiers from selected SDP semantic metadata, including manifest-bound reviewed SSSOM mappings. Candidate suggestions, arbitrary data URLs, and non-HTTP identifiers are excluded. GET requests follow redirects and stop after complete final response headers, with a 30-second timeout across connection and redirects. The final body is not retained or required for HTTP resolution. Only HTTP 408, 429, 5xx, and classified transient transport failures are retried, with at most three attempts per IRI. All IRIs are checked before any failure aborts.

Usage

verify_sdp_semantic_iris(
  path,
  report_path = file.path(path, "reproducibility", "provenance",
    "semantic-iri-dereference.csv"),
  requester = .ms_semantic_iri_request,
  sleep_fn = Sys.sleep
)

Arguments

path: Existing Salmon Data Package directory.
report_path: CSV output path. Defaults to reproducibility/provenance/semantic-iri-dereference.csv inside path.
requester: GET function receiving one exact IRI and returning a list with integer status and character final_url. Intended for offline tests.
sleep_fn: Delay function, receiving seconds. Intended for offline tests.

Value

Invisibly, a tibble with iri, status, final_url, error, and attempts, one row for each unique exact HTTP semantic IRI. On failure, the complete CSV is written before an aggregate error is raised.

Details

The report is written even if verification fails. Its stable row order and bytes allow a publication workflow to checksum the file. A successful dereference proves HTTP resolution only, not that an ontology term is an appropriate semantic choice.

Examples

if (FALSE) { # \dontrun{
# This makes live HTTP requests to every selected semantic IRI.
verify_sdp_semantic_iris("path/to/package")
} # }