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Migrate an sdp-0.2.0 package's method metadata to sdp-0.3.0

Source: R/sdp-methods.R
migrate_sdp_methods.Rd

sdp-0.3.0 removed the metadata/methods.csv registry and the column-dictionary method_iri field. This tool relocates what can be relocated mechanically and stops and reports on anything that needs a judgement call, rather than guessing:

Usage

migrate_sdp_methods(path, dry_run = FALSE)

Arguments

path

Existing Salmon Data Package directory.

dry_run

Logical; when TRUE, report what would change without touching any file.

Value

Invisibly, a list report: tables (the table-level method placements applied), dropped_review (unresolved REVIEW: bindings dropped), and registry (the legacy registry rows, for relocating labels/descriptions to the shared vocabulary and citations to protocol_citation).

Details

  • A method_iri shared by every bound measurement column of a table becomes that table's tables.csv$method_iri.

  • Columns of one table bound to different methods stop the migration: you decide whether to split the table, cite a protocol, or move the method into the data as a code column (see the methods section of the SDP specification).

  • REVIEW:-marked values are dropped, not migrated, and reported.

  • Registry labels and descriptions are reported, not relocated — they belong in the shared vocabulary. A registry method_version or citation is offered in the report as protocol_citation material.

The rewrite is atomic: either every affected metadata file is updated and metadata/methods.csv removed, or nothing changes.

Examples

example_sdp <- system.file("extdata", package = "metasalmon")
migration_plan <- migrate_sdp_methods(example_sdp, dry_run = TRUE)
#> Nothing to migrate: no method bindings and no metadata/methods.csv.
names(migration_plan)
#> [1] "tables"         "dropped_review" "registry"