Update the metadata for an existing project database. Cannot update ID, R1, or R2, but can add new metadata columns. Creates a backup of the existing database prior to updating.
Usage
update_sample_metadata(
path = ".",
update_mapping_fn = NULL,
mapping_id = "ID",
mapping_taxon = "Taxon",
mapping_geome = "GEOME_BCID",
fetch_geome = TRUE,
mapping_gbif = "GBIF_ID",
fetch_gbif = TRUE,
mapping_ncbi = "BioSample",
fetch_ncbi = TRUE,
link_sources = FALSE
)Arguments
- path
Path to the project directory (default = current working directory)
- update_mapping_fn
Path to the update mapping CSV file. Must contain columns "ID" and "Taxon"
- mapping_id
Column name of the update mapping file to use as the primary key
- mapping_taxon
Column name of the update mapping file containing a Taxonomic identifier (eg, species name)
- mapping_geome
Name of the mapping-file column holding GEOME BCIDs
- fetch_geome
Fetch GEOME metadata for samples with a BCID during setup (default TRUE). Set FALSE when offline and run [fetch_geome()] later.
- mapping_gbif
Name of the mapping-file column holding GBIF occurrence IDs
- fetch_gbif
Fetch GBIF metadata for samples with a GBIF ID (default TRUE). Set FALSE when offline and run [fetch_gbif()] later.
- mapping_ncbi
Name of the mapping-file column holding NCBI BioSample or SRA accessions (optional). Must not be the sample ID column. Stored as `BioSample`. See `vignette("Specimen-Metadata")`.
- fetch_ncbi
Fetch NCBI metadata for samples with a BioSample value (default TRUE). Set FALSE when offline and run [fetch_ncbi()] later.
- link_sources
Follow links between GEOME, GBIF, and NCBI records for these samples (default FALSE). Linking also runs when the project setting is on; this argument does not change the setting. See `vignette("Specimen-Metadata")`.