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Write ordered measurement decompositions into a Salmon Data Package

Source: R/measurement-decompositions.R
write_sdp_measurement_decompositions.Rd

Writes explicit decomposition rows to metadata/semantic/measurement-decompositions.csv and binds the exact deterministic bytes to measurement-decompositions.json. The writer never infers components, splits labels, or converts decompositions into SSSOM mappings. Supplying decompositions = NULL is an explicit no-op.

Usage

write_sdp_measurement_decompositions(
  path,
  decompositions = NULL,
  overwrite = FALSE
)

Arguments

path

Existing Salmon Data Package directory.

decompositions

NULL or a non-empty data frame matching the ordered measurement-decomposition schema.

overwrite

Logical; replace artifacts managed by this writer when TRUE.

Value

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

Details

Each row has the following closed schema:

  • dataset_id, table_id, and column_name bind the decomposition to one measurement row in metadata/column_dictionary.csv.

  • measurement_concept_iri must exactly equal that dictionary row's term_iri.

  • component_order is a positive, contiguous, per-measurement sequence.

  • component_role is one of property, entity, constraint, method, or unit; repeated roles are allowed.

  • component_status is matched or gap. A matched row requires an absolute component_iri. A gap requires a blank component_iri plus a non-empty component_label and rationale.

  • component_relation and related_component_order are normally blank. value_of_dimension links a matched constraint value to an earlier matched constraint dimension in the same measurement; for example, an age-1 class can target its freshwater-age dimension without flattening the two constraints.

  • source, source_version, source_url, and provenance identify the pinned source and review evidence. component_label and rationale preserve caller-supplied text; they are never tokenized or inferred.

Every non-empty dictionary property_iri, entity_iri, constraint_iri, method_iri, and unit_iri must appear as a matched component of the same role. Semicolon-separated dictionary constraints are checked separately. Additional same-role components and explicit gaps stay only in this artifact, leaving the frozen SDP dictionary columns unchanged. This is an ordered SDP semantic profile informed by I-ADOPT roles, not a claim of native I-ADOPT conformance.