download deployment metadata — get

downloads, restructures & formats metadata, appends dive/CTD start and end datetimes (for QC), & fills in missing required metadata - eg. release_datetime, release_longitude/latitude's with data from the GPS (if present) or Argos location file.

get_metadata(
  source = "smru",
  tag_mfr = "smru",
  tag_data = NULL,
  cid = NULL,
  user = NULL,
  pwd = NULL,
  dropIDs = NULL,
  file = NULL,
  meta.args,
  subset.ids = NULL,
  wc.meta = NULL,
  QCmode = NULL,
  build.meta = FALSE,
  server.check = TRUE,
  path2mdb = NULL,
  p2mdbtools = NULL,
  prov.dir = NULL,
  prov.name = NULL
)

Arguments

source: the source of the deployment metadata, current options are imos, otn, smru, or atn. If source = 'imos' or source = 'atn' then metadata are obtained from user-provided .CSV file via the config.json file. If sourcce = 'smru' then metadata are built from a combination of SMRU server details & deployment details in the config.json file.
tag_mfr: the tag manufacturer, current options are smru or wc cid SMRU campaign ids
tag_data: a list of either smru data tables or wc files as output by pull_data.
cid: SMRU campaign id must be provided when the tag_mfr is smru
user: SMRU data server username as a quoted string - to be used only if metadata are to be built from SMRU server details (source = 'smru').
pwd: SMRU data server password as a quoted string - to be used only if metadata are to be built from SMRU server details (source = 'smru').
dropIDs: SMRU refs or WC ids to be dropped from QC
file: path to metadata .csv file, if provided then metadata will be read from the provided source
meta.args: optional metadata fields to be passed from config file when downloading tag metadata from SMRU server. Typically used only when no metadata filepath is provided in the config file.
subset.ids: a character vector of comma-separated (no spaces) WC UUID's to be included in the QC. Ignored if tag_mfr != "wc".
wc.meta: an R data.frame of Wildlife Computers tag deployment metadata obtained via download_data(). Typically used only when no metadata filepath is provided in the config file.
QCmode: "nrt" or "dm". For IMOS metadata in delayed-mode QC, the tag identifiers are checked against the SMRU data server (see smru_clean_meta_imos())
build.meta: logical; delayed-mode QC only. Build the metadata of deployments missing from the metadata file from the SMRU data server, the .mdb deployments table, the Argos locations and meta.args
server.check: logical; delayed-mode QC of IMOS metadata only. Check ptt, body, WMO ID and tag type against the SMRU data server (default TRUE). FALSE takes them from the metadata file unchecked; build.meta must then be FALSE. Set by "server.check" in the config setup block
path2mdb, p2mdbtools: the .mdb folder and the mdbtools path (used when build.meta = TRUE)
prov.dir: near real-time QC of SMRU tags without a metadata file: the folder of the provisional metadata files, <cid>_metadata_provisional.csv (see smru_meta_provisional()); or near real-time QC of Wildlife Computers tags without a metadata file: the folder of <prov.name>_metadata_provisional.csv (see wc_meta_provisional()). NULL (default) builds the metadata from the SMRU server or the Wildlife Computers Portal on every run
prov.name: Wildlife Computers only: the provisional metadata file name stem (the config file name without "config_" and ".json")