Skip to contents

Project an uploaded file into the core obs / sample shape

Source: R/ctd_upload.R
ctd_upload_to_core.Rd

Once this has run, every QC rule in metadata/qc_rules/ applies unchanged.

Usage

ctd_upload_to_core(
  d,
  mapping,
  header = list(),
  dataset_key = "upload",
  cruise_key = NULL,
  site_key = NULL,
  cast_id = NULL
)

Arguments

d

the parsed upload

mapping

output of ctd_map_columns()

header

the Sea-Bird header list, if any

dataset_key

stamped on every row

cruise_key, site_key, cast_id

override the header-derived values

Value

list with sample, obs (both data frames) and n_sentinel

Details

The two source-specific repairs the pipeline already knows about are applied here too, because a new file is exactly where they arrive: the -99 sentinel (and -9.99e-29) are deleted rather than carried as readings, and quality codes stored as "9.0" by a double-to-string cast are stripped textually — not via an integer cast, which would round an unexpected "9.5".