Send http GET or POST request to a CATMAID server

catmaid_fetch carries out a GET operation when body=NULL, POST otherwise. The http status code of the response will be checked - if invalid an error will be thrown.

catmaid_fetch(
  path,
  body = NULL,
  conn = NULL,
  parse.json = TRUE,
  include_headers = TRUE,
  simplifyVector = FALSE,
  ...
)

Arguments

path

The path on the CATMAID server relative to the CATMAID root

body

The (optional) body of the post request, usually in the form of a named list. See the POST documentation for full details.

conn

A catmaid_connection objection returned by catmaid_login. If NULL (the default) a new connection object will be generated using the values of the catmaid.* package options as described in the help for catmaid_login.

parse.json

Whether or not to parse a JSON response to an R object (default TRUE)

include_headers

Whether to include basic headers from the http request as attributes on the parsed JSON object (default TRUE) when parse.json=TRUE.

simplifyVector

Whether to use jsonlite::simplifyVector

...

Additional arguments passed to the httr::GET or httr::POST function

Value

When parse.json=FALSE an object of class response otherwise the raw R object generated by calling jsonlite::fromJSON on the body of the response.

See also

catmaid_login, GET, POST

Examples

if (FALSE) {
## Make a catmaid_connection object to use for these requests
conn=catmaid_login()

## fetch a demo skeleton using a GET request
# raw response
skel.response=catmaid_fetch("1/10418394/0/0/compact-skeleton", conn=conn)
# list object
skel=catmaid_fetch("1/10418394/0/0/compact-skeleton", conn=conn)

## Get the names of two skeletons using a POST request
# NB that the skids[n] elements are quoted when constructing the list since 
# they are not valid R names.
catmaid_fetch("/1/skeleton/neuronnames", conn=conn,
  body=list(pid=1, 'skids[1]'=10418394, 'skids[2]'=4453485))

## get all skeletons with more than 1000 nodes
skids=as.integer(catmaid_fetch("/1/skeletons/?nodecount_gt=1000"))

## fetch user history since 1st April 2016
uh = catmaid_fetch('1/stats/history?start_date=2016-04-01', 
  simplifyVector = T, include_headers = F)
uh$date=as.Date(uh$date,"%Y%m%d")
library(dplyr)
# select top 10 users by nodes added
top10=uh %>% 
  group_by(name) %>% 
  summarise(total=sum(count)) %>% 
  arrange(desc(total)) %>%
  top_n(10)
# plot cumulative nodes traced
library(ggplot2)
uh %>% 
  group_by(name) %>%
  mutate(ccount = cumsum(count)) %>%
  filter(name %in% top10$name) %>% 
  ggplot(aes(date, ccount, col = name)) + geom_line()

## demonstrate that bad urls will result in an error
catmaid_fetch("/1/rhubarb/crumble")
}