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Return all DVID body annotations

Source: R/annotations.R
manc_dvid_annotations.Rd

Return all DVID body annotations

Usage

manc_dvid_annotations(
  ids = NULL,
  node = "neutu",
  rval = c("data.frame", "list"),
  columns_show = NULL,
  cache = FALSE
)

Arguments

ids

A set of body ids in any form understandable to manc_ids

node

A DVID node as returned by manc_dvid_node. The default is to return the current active (unlocked) node being used through neutu.

rval

Whether to return a fully parsed data.frame (the default) or an R list. The data.frame is easier to work with but typically includes NAs for many values that would be missing in the list.

columns_show

Whether to show all columns, or just with '_user', or '_time' suffix. Accepted options are: 'user', 'time', 'all'.

cache

Whether to cache the result of this call for 5 minutes.

Value

A tibble containing with columns including

  • bodyid as a numeric value

  • status

  • user

  • naming_user

  • instance

  • status_user

  • comment

NB only one bodyid is used regardless of whether the key-value returned has 0, 1 or 2 bodyid fields. When the ids are specified, missing ids will have a row containing the bodyid in question and then all other columns will be NA.

Details

See this Slack post from Stuart Berg for details.

Note that the original api call was <rootuuid>:master, but I have now just changed this to <neutu-uuid> as returned by manc_dvid_node. This was because the range query stopped working 16 May 2021, probably because of a bad node.

Examples

# \donttest{
mdf=manc_dvid_annotations()
#> Error in manc_dvid_node("neutu"): The package option malevnc.dataset is unset. Please set or manually reload package!
head(mdf)
#> Error: object 'mdf' not found
table(mdf$status)
#> Error: object 'mdf' not found

manc_dvid_annotations('DNp01')
#> Error in neuprint_login(server = server, dataset = dataset, token = token,     ...): Sorry you must specify a neuprint server! See ?neuprint_login for details!

if (FALSE) { # \dontrun{
# compare live body annotations with version in clio
mdf.clio=manc_dvid_annotations('clio')
waldo::compare(mdf.clio, mdf)
} # }
# }