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Harmonize environmental media strings to canonical CONCERT media terms

Source: R/media_harmonizer.R
harmonize_media.Rd

Maps a character vector of raw environmental media strings against the generated CONCERT media vocabulary cache (amos_media.rds). Resolution order: (1) user assertions; (2) active bundled auto assertions; (3) unambiguous phrase fallback for partial matches; (4) media_unmatched flag for everything else. Pending source-table aliases are not auto-resolved.

Usage

harmonize_media(
  raw_media,
  orig_row_id = seq_along(raw_media),
  media_map = NULL
)

Arguments

raw_media

Character vector of media strings to harmonize.

orig_row_id

Integer vector of row IDs corresponding to each element of raw_media. Defaults to seq_along(raw_media) for direct column processing.

media_map

Optional tibble with columns term, canonical_term, envo_id, media_category, source, active, and assertion_mode. When NULL (default), falls back to the bundled generated media cache via get_media_table(). Pass a merged map from load_media_map() to enable user-defined mappings (MEDIT-03, D-14). If the tibble uses canonical instead of canonical_term (display schema), the column is translated internally before lookup.

Value

A row-preserving tibble retaining these original columns:

orig_row_id

Integer row position for join-by-position merge.

raw_media

Original input string, preserved for audit.

canonical_media

Canonical CONCERT media term, or NA_character_ if unmatched.

envo_id

ENVO identifier for the matched term, or NA_character_.

media_category

Top-level routing value: "aqueous", "air", "solid", or NA_character_.

media_flag

One of: "" (exact match), "parent_walk", "media_unmatched".

Additional fields retain published term_id, parent_id, preferred_label, rank, definition, physical_phase, physical_state, is_water_based, concert_unit_route, ontology_node_id, ontology_path, source, assertion_mode, confidence, confidence_tier, and artifact_version. CURIE capitalization is preserved. routing_status is available, unavailable for a known identity without a route, or unmatched. A successful identity match does not require a route.