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Set Clio body annotations

Source: R/bodies.R
yakuba_annotate_body.Rd

Set Clio body annotations

Usage

yakuba_annotate_body(
  x,
  test = TRUE,
  version = NULL,
  write_empty_fields = FALSE,
  designated_user = NULL,
  protect = c("user"),
  chunksize = 50,
  check_types = TRUE,
  ...,
  dataset = dyak_default_dataset()
)

Arguments

x

A data frame, list or JSON string containing body annotations. End users are strongly recommended to use data frames.

test

Whether to use the test Clio store (recommended until you are sure that you know what you are doing).

version

Optional Clio version to associate with this annotation. The default NULL uses the current version returned by the API.

write_empty_fields

When x is a data frame, this controls whether empty fields in x overwrite fields in the Clio database.

designated_user

Optional alternate user recorded in Clio for the annotation.

protect

Vector of fields that will not be overwritten if they already have a value in Clio. Set to TRUE to protect all fields and to FALSE to overwrite all fields for which you provide data.

chunksize

When you have many bodies to annotate the request will by default be sent 50 records at a time to avoid timeouts. Set to Inf to insist that all records are sent in a single request.

check_types

Whether to verify data-frame column types against the active yakuba Clio schema.

...

Additional parameters passed to pbapply::pbsapply().

dataset

The name of the dataset as reported in Clio or neuprint.

Value

NULL invisibly on success. Errors out on failure.

Details

Details of the Clio body annotation system are provided in malevnc::manc_annotate_body(). It can take some time to apply annotations, so requests are chunked by default in groups of 50.

A single column called position or 3 columns named x, y, z or X, Y, Z in any form accepted by nat::xyzmatrix() will be converted to a position stored with each record. This is recommended when creating records.

When protect=TRUE no data in Clio will be overwritten, only new data will be added. When protect=FALSE all fields will be overwritten by new data for each non-empty value in x. If write_empty_fields=TRUE then even empty fields in x will overwrite fields in the database.

Validation

Validation depends on how you provide your input data. If x is a data frame then each row is checked for some basics including the presence of a bodyid, and empty fields are removed. We also check field types against the active yakuba Clio schema by default.

Users

Clio records a user and timestamp for every modification to fields in a record. By default your email address from the Clio token will be used. You can specify an alternate user with the designated_user argument; see malevnc::manc_annotate_body() for details.

See also

malevnc::manc_annotate_body()

Examples

if (FALSE) { # \dontrun{
ids <- dyak_ids("DNa02", as_character = FALSE)
yakuba_annotate_body(
  data.frame(bodyid = ids[1], group = min(ids)),
  test = TRUE
)
} # }