KNB download CSV

knb-download-poc.R

library(dataone)

# Download a CSV-formatted data file from the KNB 
# repository, and convert it to a data.frame
get_dataframe <- function(pid) {
  d1c <- D1Client("PROD", "urn:node:KNB")
  data_raw <- getObject(d1c@mn, pid)
  data_char <- rawToChar(data_raw)
  csv_text <- textConnection(data_char)
  df <- read.csv(csv_text, stringsAsFactors = FALSE)
  return(df)
}

# data_url <- "https://knb.ecoinformatics.org/knb/d1/mn/v2/object/urn%3Auuid%3A4c9bdb65-e58b-41bc-8f80-10f59ee332e9"

# be sure to set your DataONE auth token first (but don't check it into scripts) for access to private data
# options(dataone_token = "eyJhbGciOiJSUzI1NiJ9.eyJzdWIi...........lZNw")
pid <- "urn:uuid:4c9bdb65-e58b-41bc-8f80-10f59ee332e9"
df <- get_dataframe(pid)
head(df)