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Return neurojson body annotations via the Clio interface

Source: R/bodies.R
dyak_body_annotations.Rd

Return neurojson body annotations via the Clio interface

Usage

dyak_body_annotations(
  ids = NULL,
  query = NULL,
  json = FALSE,
  config = NULL,
  show.extra = c("none", "user", "time", "all"),
  cache = FALSE,
  test = FALSE,
  ...,
  dataset = dyak_default_dataset()
)

Arguments

ids

A set of body ids in any form understandable to manc_ids

query

A json query string (see examples or documentation) or an R list with field names as elements.

json

Whether to return unparsed JSON rather than an R list (default FALSE).

config

An optional httr::config (expert use only, must include a bearer token)

show.extra

Extra columns to show with user/timestamp information.

cache

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

test

Whether to unset the clio-store test server (default FALSE)

...

Additional arguments passed to pbapply::pblapply().

dataset

The name of the dataset as reported in Clio e.g. yakuba, yakuba-vnc etc. yakuba, yakuba-vnc and yakubavnc are treated as aliases for the main yakuba dataset.

Value

A data frame with metadata.

Details

In comparison with dyak_neuprint_meta(), this provides access to up to the second annotations; it is also presently faster than that call. Compared with dyak_neuprint_meta(), it does not produce a stable set of columns, only returning those that exist for the given query ids.

See also

malevnc::manc_body_annotations()

Examples

# \donttest{
dyak_body_annotations("DNa02")
#> Error in (function (path, body = NULL, server = NULL, conf = NULL, parse.json = TRUE,     include_headers = TRUE, simplifyVector = FALSE, app = NULL,     ...) {    if (is.null(app))         app = paste0("neuprintr/", utils::packageVersion("neuprintr"))    req <- if (is.null(body)) {        httr::GET(url = file.path(server, path, fsep = "/"),             config = conf, httr::user_agent(app), ...)    }    else {        httr::POST(url = file.path(server, path, fsep = "/"),             body = body, config = conf, httr::user_agent(app),             ...)    }    neuprint_error_check(req)    if (parse.json) {        parsed = neuprint_parse_json(req, simplifyVector = simplifyVector)        if (length(parsed) == 2 && isTRUE(names(parsed)[2] ==             "error")) {            stop("neuPrint error: ", parsed$error)        }        if (include_headers) {            fields_to_include = c("url", "headers")            attributes(parsed) = c(attributes(parsed), req[fields_to_include])        }        parsed    }    else req})(path = path, body = body, server = server, conf = conf, parse.json = parse.json,     include_headers = include_headers, simplifyVector = simplifyVector,     app = app): Unauthorized (HTTP 401). Failed to process url: https://neuprint-yakuba.janelia.org/api/dbmeta/datasets with neuPrint error: invalid or expired jwt.
# }