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Write reviewed EML 2.2.0 metadata from a Salmon Data Package

Source: R/eml-export.R
write_eml_from_sdp.Rd

Builds deterministic EML 2.2.0 XML from a strictly valid Salmon Data Package and an explicit EML mapping sidecar. The sidecar is required because EML concepts such as measurement scale, structured parties, dataset-level method narrative, and rights cannot be inferred defensibly from the canonical SDP tables. Method and protocol placements are read from the sdp-0.3.0 fields — tables.csv (method_iri, protocol_iri, protocol_citation) and dataset.csv (protocol_iri, protocol_citation) — and emitted as method steps; row-varying procedures actually used by the data are resolved through codes.csv term_iri and listed in a dedicated method step. A legacy metadata/methods.csv registry is an error: run migrate_sdp_methods() first.

Usage

write_eml_from_sdp(
  path,
  output_path = NULL,
  mapping_path = NULL,
  overwrite = FALSE,
  supplementary_objects = NULL,
  require_revision_key = FALSE,
  knb_environment = "production"
)

Arguments

path

Directory containing a Salmon Data Package.

output_path

Output XML path. Defaults to metadata/eml.xml inside path.

mapping_path

Reviewed YAML mapping. Defaults to metadata/eml-mapping.yml inside path.

overwrite

Logical; replace a different existing output only when TRUE. An identical existing file is treated as an idempotent success.

supplementary_objects

Optional data frame describing canonical SDP archives or expanded artifacts to expose as EML otherEntity elements. Required columns are path, pid, format_id, checksum, object_name, entity_name, and description; optional size, when supplied, must match the file. entity_type may distinguish an expanded artifact from an archive. Objects use lowercase SHA-256 checksums and safe relative object_name paths; only application/zip objects receive compressionMethod = zip. publish_sdp_to_knb() supplies this plan automatically; ordinary standalone EML export leaves the argument NULL.

require_revision_key

Logical; when TRUE, require a reviewed publication.revision_key in the EML mapping sidecar. The key creates a new deterministic metadata package ID without changing the series ID.

knb_environment

KNB deposit environment the document is written for: "production" (the default) or "test". It selects the DataONE member node whose object URLs the EML distribution elements point at, and is folded into the deterministic package and series identifiers so a test identifier can never be mistaken for a production one. Accepted exactly; there is no partial matching and no custom endpoint. The default is "production" because this function writes the package's reviewed metadata/eml.xml; publish_sdp_to_knb() supplies its own environment and writes a test document to a separate path, leaving the reviewed production record untouched.

Value

Invisibly returns a list containing the XML text, normalized output path, EML version, metadata package ID, stable series ID, validation result, revision key, deterministic data and supplementary-object plans, the complete method registry (methods), and the subset asserted in EML (used_methods).

Details

Measurement attributes receive exactly two semantic annotations in the initial profile. Both reviewed OWL measurement-datum classes and SKOS compound-variable concepts use Dublin Core Terms subject with the reviewed term_iri, followed by QUDT hasUnit using the reviewed unit_iri. The broader topic predicate is intentional: an OWL class is not necessarily an OBOE MeasurementType, and schema-valid EML must not silently assert that unsupported range. The exporter deliberately does not project incomplete I-ADOPT roles or procedure annotations into EML.

Examples

if (FALSE) { # \dontrun{
write_eml_from_sdp("path/to/reviewed-sdp")
} # }