playgrounds/HttrPlayground.R

In OuhscBbmc/REDCapR: Interaction Between R and REDCap

rm(list=ls(all=TRUE))  #Clear the variables from previous runs.

library(httr)

redcap_uri <- "https://www.redcapplugins.org/redcap_v6.5.0/API/"
token <- "D96029BFCE8FFE76737BFC33C2BCC72E" #For `UnitTestPhiFree` account and the simple project (pid 27) on Vandy's test server.


redcap_uri <- "https://bbmc.ouhsc.edu/redcap/api/"
token <- "9A81268476645C4E5F03428B8AC3AA7B"

raw_or_label <- "raw"
export_data_access_groups_string <- "true"
records_collapsed <- "1,2,5"
fields_collapsed <- NULL
events_collapsed <- NULL

config_options <- list(cainfo = system.file("cacert.pem", package="openssl"))
# config_options <- RCurl::curlOptions(ssl.verifypeer = FALSE)
config_options <- httr::config(ssl_verifypeer=FALSE)
# config_options <- list()

post_body <- list(
  token = token,
  content = 'record',
  format = 'csv',
  type = 'flat',
  rawOrLabel = raw_or_label,
  exportDataAccessGroups = export_data_access_groups_string,
  records = records_collapsed,
  fields = fields_collapsed,
  events = events_collapsed
)

result <- httr::POST(
  url = redcap_uri,
  body = post_body,
  config = config_options
)


result$status_code
result$headers$status
result$headers$statusmessage
raw_text <- httr::content(result, "text")

result <- httr::POST(
  url    = "https://httpbin.org/post",
  body   = "A simple text string",
  config = httr::config(ssl_verifypeer=FALSE)
)
httr::content(result, "text")

ds <- utils::read.csv(text=raw_text) #Convert the raw text to a dataset.

#
# raw_text2 <- RCurl::postForm(
#   uri = redcap_uri
#   , token = token
#   , content = 'record'
#   , format = 'csv'
#   , type = 'flat'
#   , rawOrLabel = raw_or_label
#   , exportDataAccessGroups = export_data_access_groups_string
#   , records = records_collapsed
#   , fields = fields_collapsed
#   , .opts = RCurl::curlOptions(ssl.verifypeer = FALSE)
# )
# ds2 <- utils::read.csv(text=raw_text2) #Convert the raw text to a dataset.

# result <- redcap_read_oneshot(redcap_uri="https://bbmc.ouhsc.edu/redcap/api/", token = "9A81268476645C4E5F03428B8AC3AA7B")
# dput(result$data)
dsToWrite <- structure(list(record_id = 1:5, name_first = c("Nutmeg", "Tumtum",
  "Marcus", "Trudy", "John Lee"), name_last = c("Nutmouse", "Nutmouse",
  "Wood", "DAG", "Walker"), address = c("14 Rose Cottage St.\nKenning UK, 323232",
  "14 Rose Cottage Blvd.\nKenning UK 34243", "243 Hill St.\nGuthrie OK 73402",
  "342 Elm\nDuncanville TX, 75116", "Hotel Suite\nNew Orleans LA, 70115"
  ), telephone = c("(432) 456-4848", "(234) 234-2343", "(433) 435-9865",
  "(987) 654-3210", "(333) 333-4444"), email = c("nutty@mouse.com",
  "tummy@mouse.comm", "mw@mwood.net", "peroxide@blonde.com", "left@hippocket.com"
  ), dob = c("2003-08-30", "2003-03-10", "1934-04-09", "1952-11-02",
  "1955-04-15"), age = c(10L, 10L, 79L, 61L, 58L), ethnicity = c(1L,
  1L, 0L, 1L, 1L), race = c(2L, 6L, 4L, 4L, 4L), sex = c(0L, 1L,
  1L, 0L, 1L), height = c(5, 6, 180, 165, 193.04), weight = c(1L,
  1L, 80L, 54L, 104L), bmi = c(400, 277.8, 24.7, 19.8, 27.9), comments = c("Character in a book, with some guessing",
  "A mouse character from a good book", "completely made up", "This record doesn't have a DAG assigned\n\nSo call up Trudy on the telephone\nSend her a letter in the mail",
  "Had a hand for trouble and a eye for cash\n\nHe had a gold watch chain and a black mustache"
  ), demographics_complete = c(2L, 2L, 2L, 2L, 2L)), .Names = c("record_id",
  "name_first", "name_last", "address", "telephone", "email", "dob",
  "age", "ethnicity", "race", "sex", "height", "weight", "bmi",
  "comments", "demographics_complete"), class = "data.frame", row.names = c(NA,
  -5L))
dsToWrite$age <- NULL; dsToWrite$bmi <- NULL #Drop the calculated fields
# dsToWrite <- dsToWrite[1:3, ]
# result <- REDCapR::redcap_write_oneshot(ds=dsToWrite, redcap_uri="https://bbmc.ouhsc.edu/redcap/api/", token = "9A81268476645C4E5F03428B8AC3AA7B")

con <-  base::textConnection(object='csvElements', open='w', local=TRUE)
utils::write.csv(dsToWrite, con, row.names = FALSE, na="")
close(con)

csv <- paste(csvElements, collapse="\n")
csvForPostman <- gsub(pattern="[\\]", replacement="", x=csv)
csvForPostman

post_body <- list(
  token = token,
  content = 'record',
  format = 'csv',
  type = 'flat',
  rawOrLabel = raw_or_label,
  exportDataAccessGroups = export_data_access_groups_string,
  records = records_collapsed,
  fields = fields_collapsed,

  #These next values separate the import from the export API call
  data = csv,
  overwriteBehavior = 'overwrite', #overwriteBehavior: *normal* - blank/empty values will be ignored [default]; *overwrite* - blank/empty values are valid and will overwrite data
  returnContent = 'ids',
  returnFormat = 'csv'
)

result <- httr::POST(
  url = redcap_uri,
  body = post_body,
  .opts = config_options
)
result

status_code <- result$status_code
status_message <- result$headers$statusmessage
return_content <- httr::content(result, type="text")

# returnContent <- RCurl::postForm(
#   uri = redcap_uri,
#   token = token,
#   content = 'record',
#   format = 'csv',
#   type = 'flat',
#   returnContent = "ids",
#   overwriteBehavior = 'overwrite', #overwriteBehavior: *normal* - blank/empty values will be ignored [default]; *overwrite* - blank/empty values are valid and will overwrite data
#   data = csv,
#   .opts = curl_options
# )

(was_successful <- !httr::http_error("https://bbmc.ouhsc.edu/redcap/plugins/redcapr/no_auth_test.php"))

RCurl::httpHEAD(url = "https://bbmc.ouhsc.edu/redcap/plugins/redcapr/no_auth_test.php", .opts = RCurl::curlOptions(ssl.verifypeer = FALSE))
RCurl::httpGET(url = "https://bbmc.ouhsc.edu/redcap/plugins/redcapr/no_auth_test.php", .opts = RCurl::curlOptions(ssl.verifypeer = FALSE))


cert_location <- system.file("cacert.pem", package="openssl")
file.exists(cert_location)
httr::url_ok("https://bbmc.ouhsc.edu/redcap/plugins/redcapr/no_auth_test.php", config=list(cainfo=cert_location, sslversion=3))