Return neuron metadata from Cambridge seatables

This function is a generic building block for access to experimental/in progress neuron metadata. It is intended for internal use and the end user or developer is responsible for choosing the active CAVE dataset (see choose_segmentation).

Usage

cam_meta(
  ids = NULL,
  ignore.case = F,
  fixed = F,
  table = "aedes_main",
  base = NULL,
  version = NULL,
  timestamp = NULL,
  unique = FALSE,
  token = NULL,
  ...
)

Arguments

ids: Root ids (as character or int64 vector) or a query (see examples)
ignore.case: for queries whether to ignore the case
fixed: whether to treat queries as a fixed string
table: The name of the table to query
base: Optional name of the seatable base containing the table (sometimes the table may not be found or two bases contain a table with the same name).
version: Integer materialisation version. The special value of 'latest' means the most recent materialisation according to CAVE.
timestamp: A timestamp to normalise into an R or Python timestamp in UTC. The special value of 'now' means the current time in UTC.
unique: Whether to drop rows that have the same root_id. See details. There is no special logic in choosing which rows to drop, but the dropped rows are retained as an attribute on the table with a warning so that you can inspect.
token: Optional API token. When supplied, the FLYTABLE_TOKEN environment variable is temporarily set to this value for the duration of the call (and restored on exit) so you can authenticate against an alternative seatable instance without permanently overwriting your token. Typically used in combination with the fafbseg.flytable.url package option.
...: Additional arguments passed to flytable_cached_table (e.g. expiry, refresh) which can be used to control details of the cache strategy.

Value

A data frame with appropriate rows based on the ids argument.

Details

This function now uses flytable_cached_table for efficient row-wise caching of metadata. The defaults should be a good trade-off between cache speed and getting the latest updates, but you can set expiry = 0 if you want to ensure that you are as up to date as possible - this still only downloads new changes and is very fast (300ms vs 100ms for a pre-cached dataset with 14k rows).

Note that rows with status `duplicate` or `bad_nucleus` are dropped even before the `unique` argument is processed.

Examples

# implies type
if (FALSE) { # \dontrun{
cam_meta("MBON.+")
cam_meta("class:ALPN")
# ensure that root ids match the most recent materialisation
cam_meta("class:ALPN", version='latest')

with_aedes(cam_meta)

} # }