I am trying to upload an image to a website. Below is the successful curl function:
curl --location --request POST 'http://xxxxx?laboratoryResultVisibleId=LR-116807&assayAttribute=Trace&onBehalfOf=minnie' \
--header 'Authorization: Basic U1JWR0JMLUdEQklPTDpQZjgyNTE5Mw==' \
--form 'imageFile=#/C:/Users/minnie/Downloads/plot.png'
I am writing my R code as follows:
username <- "minnie"
url <- "http://xxxxx"
auth <- authenticate(user='abc', password='xyz', type="basic")
header <- list(username)
names(header) <- "X-On-Behalf-Of"
filepath <- "C:/Users/minnie/Downloads/plot.png"
post_zip <- httr::POST(
url = url,
auth,
body = list(
laboratoryResultVisibleId = 'LR-116807',
assayAttribute = 'Trace',
file = httr::upload_file(filepath),
userid = username
),
httr::add_headers("Content-Type"="multipart/form-data")
)
post_zip
content(post_zip, "text")
and I got the following feedback:
Response [http://xxxxx]
Date: 2020-11-18 22:30
Status: 200
Content-Type: application/json;charset=UTF-8
Size: 43 B
> content(post_zip, "text")
[1] "{\"success\":false,\"message\":\"No File found\"}"
It seems that no file has been found. Any clue? Thank you so much for your help :-)
I feel like this has something to do with http vs https, can you try changing to https?
The problem resides in the file path. We should use the file.path () function in R to let the server know it is a file path, rather than a character string.
filepath <- file.path(getwd(), "plot.png")
post_zip <- httr::POST(
url = url,
auth,
body = list(
laboratoryResultVisibleId = 'LR-116807',
assayAttribute = 'Trace',
imageFile = httr::upload_file(filepath),
userid = username
),
httr::add_headers("Content-Type"="multipart/form-data")
)
post_zip
content(post_zip, "text")
Related
I am currently trying to upload a CSV file to a proprietary service via httr::POST(). Unfortunately the Admins are not experienced in R and can give only little support.
This is an example on how it should look like in the command line:
curl -X POST --header 'Content-Type: multipart/form-data' \
-F file=#"member-1-test.csv.gz" 'https://some/api/endpoint'
So, in the following code I just try to stick with the example (and additionally provide a token).
> library(tidyverse)
> library(httr)
# Provide some test data with characters specifically quoted
> test_file <- tibble::tribble(
~keytype, ~key, ~action, ~segment,
6,"\"https://www.google.com\"", 0, 37372818,
6,"\"https://www.sport1.de\"" , 0, 37372818
)
> data.table::fwrite(test_file, "test.csv", quote = FALSE)
> file <- upload_file(path = "C:/R/projects/DefaultWorkingDirectory/test.csv")
> res <- POST(
url = "https://some/api/endpoint",
body = list(file = file),
add_headers(.headers = c('Content-Type' = "multipart/form-data", "Authorization" = token))
)
This gives me the follwing error:
> res
Response [https://some/api/endpoint]
Date: 2020-11-18 09:35
Status: 503
Content-Type: text/plain
Size: 95 B
> content(res, encoding = "UTF8")
"upstream connect error or disconnect/reset before headers. reset reason: connection termination"
Any help or guidance on how to move forward with this issue is very much appreciated. Thanks!
Directly after posting the question it was already solved by one of the Admins :)
The issue was that the encoding needs to be set to "multipart" and that a specific content type needs to be provided which is similar to JSON but needs to be added to the "Accept"-header field.
Here the answer for any future references:
> res <- POST(
url = "https://some/api/endpoint",
body = list(
file = upload_file("test.csv")
),
add_headers(c(
"Authorization" = token,
"Accept" = "specific_format_for_the_application"
)),
encode = "multipart",
verbose()
)
As a follow on from: How translate this curl command into a R curl call?
I can successful do a curl request but the returned result looks to be in a binary format, but the content should be ASCII. How do I write it out as an ASCII file?
require(httr)
headers = c(
`Content-Type` = 'text/csv'
)
data = upload_file('data/data.csv')
res <- httr::POST(url = 'https://some.url.com/invocations', httr::add_headers(.headers=headers), body = data)
content(res, "text")
works and if the output is JSON then
content(res, "parsed")
works too.
Hi I try to translate this curl instruction using httr
curl -H "Authorization: Token f2210dacd9c6ccb8133606d94ff8e61d99b477fd" -F file=#test.txt -F filename=test.txt -F parent_dir=/ http://cloud.seafile.com:8082/upload-api/73c5d117-3bcf-48a0-aa2a-3f48d5274ae3
Without the -F parameter the instruction is :
httr::POST(
url = "http://cloud.seafile.com:8082/upload-api/73c5d117-3bcf-48a0-aa2a-3f48d5274ae3",
add_headers(Authorization = "Token f2210dacd9c6ccb8133606d94ff8e61d99b477fd")
)
)
I think I have to use the httr::upload_file function but I didn't manage to use this without error.
Do you have any idea how I can do that ?
Regards
Here is how to construct this curl request with httr package. I used httpbin.org to test the request sent.
You'll use POST filling the body with a list. encode argument controls how this list will be handle and by default it is the correct multipart you need.
res <- httr::POST(
url = "http://httpbin.org/post",
httr::add_headers(Authorization = "Token f2210dacd9c6ccb8133606d94ff8e61d99b477fd"),
# Add the file and metadata as body using a list. Default encode is ok
body = list(
file = httr::upload_file("test.txt"),
filename = "test.txt",
parent_dir = "/"
)
)
httr_ouput <- httr::content(res)
One way to check this is ok is to compare output with the curl command you know is working
out <- sys::exec_internal(
'curl -H "Authorization: Token f2210dacd9c6ccb8133606d94ff8e61d99b477fd" -F file=#test.txt -F filename=test.txt -F parent_dir=/ http://httpbin.org/post'
)
curl_output <- jsonlite::fromJSON(rawToChar(out$stdout))
#compare body
identical(curl_output$files, httr_ouput$files)
#> TRUE
identical(curl_output$form, httr_ouput$form)
#> TRUE
You can also do it with the crul package, another wrapper above curl; The logic is identical
con <- crul::HttpClient$new(
url = "http://httpbin.org/post"
)
crul_req <- con$post(
body = list(
file = crul::upload("test.txt"),
filename = "test.ext",
parent_dir = "/"
)
)
crul_output <- jsonlite::fromJSON(crul_req$parse())
I am trying to transcribe some sound files to text using bing speech-to-text.
The following command works in command line (using git bash on Windows 10):
curl -v -X POST "https://speech.platform.bing.com/speech/recognition/interactive/
cognitiveservices/v1?language=<LANG>&format=detailed" -H "Transfer-Encoding:
chunked" -H "Ocp-Apim-Subscription-Key: <MY KEY>" -H "Content-type:
audio/wav; codec=audio/pcm; samplerate=16000" --data-binary #<MY .WAV-FILE>
I've tried this, but it doesnt work:
httr::POST(url = myURL,
add_headers("Ocp-Apim-Subscription-Key" = key,
"Content-type" = "audio/wav; codec=audio/pcm; samplerate=16000",
"Transfer-Encoding" = "chunked"),
body = (list("file" = upload_file("PATH_TO_FILE.wav"))),
verbose())
It returns this output:
Response
[https://speech.platform.bing.com/speech/recognition/dictation/
cognitiveservices/v1?language=<LANG>&format=detailed]
Date: 2017-11-29 13:29
Status: 200
Content-Type: text/plain
Size: 75 B
I believe that the request is related to the interpretation of the .wav file, and that I need to somehow add the '--data-binary' tag to the httr-request. I can see that my "content-type" is plain text, although i've specified. Furthermore: the API documentation specifies that i need to prefix my wav-file with an at-sign.
Any help would be much appreciated.
cheers.
EDIT: Link to API documentation
https://learn.microsoft.com/da-dk/azure/cognitive-services/speech/getstarted/getstartedrest?tabs=curl#tabpanel_AFC9x30-dR_curl
I figured it out.
The key is to set the proper MIME type in the body. Not setting this MIME type can result in wrongful interpretation on the receiving end, even though we get a response 200 back.
body <- list(file = httr::upload_file(
paste0(path, "/", f),
type = "audio/wav; codec=audio/pcm; samplerate=16000"))
where paste0(path, "/", f) is a path to an audio file.
myURL <- sprintf('https://speech.platform.bing.com/speech/recognition/%s/cognitiveservices/v1?language=%s&format=%s',
"dictation",
"da-DK",
"detailed")
rs <- httr::POST(
url = myURL,
httr::add_headers(.headers = c("Ocp-Apim-Subscription-Key" = key)),
httr::add_headers(.headers = c("Transfer-Encoding" = "chunked")),
body = body)
I'm looking to send a PUT command to a server from R. The following unix commandline snippet works fine:
curl -i -k -u "username:pass" -X PUT -d "description=test+test+test" https://somewebsite.com/application
I've tried various iterations on httpPUT(), and I'm now working with the inner function getURLContent:
curl_opts = curlOptions(username = "username", password = "pass", httpauth=AUTH_BASIC, ssl.verifypeer = FALSE, headerfunction=h$update)
url=paste("https://somewebsite.com/", "application", sep="")
info <- "description=test+test+test"
val <- charToRaw(info)
getURLContent(url, infilesize = length(val), readfunction = val, upload = TRUE, customrequest = "PUT", .opts=curl_opts)
The server is sending back a search like response, as if I did not actually post the data. Any thoughts on how to recreate the curl commandline PUT in RCurl?
Thanks!