No suitable parser found to handle request body type application/vnd.ms-excel.

[chuxinyuan]

Description

I want to upload the data in .csv format, but I had trouble deploying it to the server.

Code

plumber_run.R

library(plumber)
pr("plumber.R") %>%
  pr_run(host = "0.0.0.0", port = 8001)

plumber.R

#* @apiTitle  render report API

#* upload csv file
#* @post /upload
#* @parser multi
#* @parser csv
#* @param f:file
\(f) {
  data = read.csv(f[[1]])
  print(data)
}

Data

data = data.frame(
  name = c("AAA", "BBB", "CCC"),
  ID = c("001", "002", "003"),
  address = c("Peking", "New York", "Paris")
)
write.csv(data, "data.csv", row.names = FALSE)

Session info

R version 4.2.2 Patched (2022-11-10 r83330)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 12 (bookworm), RStudio 2022.7.1.554

Locale:
  LC_CTYPE=zh_CN.UTF-8       LC_NUMERIC=C               LC_TIME=zh_CN.UTF-8       
  LC_COLLATE=zh_CN.UTF-8     LC_MONETARY=zh_CN.UTF-8    LC_MESSAGES=en_US.UTF-8   
  LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
  LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

Package version:
  askpass_1.2.0     base64enc_0.1.3   bslib_0.7.0       cachem_1.1.0      cli_3.6.2        
  compiler_4.2.2    crayon_1.5.2      curl_5.2.1        data.table_1.15.4 digest_0.6.35    
  ellipsis_0.3.2    evaluate_0.23     fansi_1.0.6       fastmap_1.2.0     fontawesome_0.5.2
  fs_1.6.4          glue_1.7.0        graphics_4.2.2    grDevices_4.2.2   highr_0.11       
  htmltools_0.5.8.1 httpuv_1.6.15     httr_1.4.7        jquerylib_0.1.4   jsonlite_1.8.8   
  knitr_1.47        later_1.3.2       lifecycle_1.0.4   magrittr_2.0.3    memoise_2.0.1    
  methods_4.2.2     mime_0.12         openssl_2.2.0     pillar_1.9.0      pkgconfig_2.0.3  
  plumber_1.2.2     promises_1.3.0    purrr_1.0.2       R6_2.5.1          rapidoc_9.3.4    
  rappdirs_0.3.3    Rcpp_1.0.12       rlang_1.1.3       rmarkdown_2.27    rstudioapi_0.16.0
  sass_0.4.9        sodium_1.3.1      stats_4.2.2       stringi_1.8.4     swagger_5.17.14.1
  sys_3.4.2         tibble_3.2.1      tinytex_0.51      tools_4.2.2       utf8_1.2.4       
  utils_4.2.2       vctrs_0.6.5       webutils_1.2.0    xfun_0.44         yaml_2.3.8  

[thomasp85]

How are you sending the data? If you send the data as a .csv the body type should not be reported as application/vnd.ms-excel?

[schloerke]

Similar to

plumber/inst/plumber/09-content-type/plumber.R

Line 1 in 972a19b

#* @serializer contentType list(type="application/pdf")

, you'll need to set #* @serializer contentType list(type="application/vnd.ms-excel").

You'll also need to transform your output into an excel file before returning it in your function. (I do not know how to do this last step.)

[schloerke]

A possible approach which adds a xlsx serializer: #793 (comment)

# untested!

register_serializer(
  "xlsx",
  function(..., type = "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet") {
    if (!requireNamespace("writexl", quietly = TRUE)) {
      stop("The writexl package is not available but is required in order to use the writexl serializer",
           call. = FALSE)
  }

  serializer_write_file(
    # The temp file should end in `.xlsx`
    fileext = ".xlsx",
    # Pass through your content type
    type = type,
    write_fn = function(val, tmpfile) {
      writexl::write_xlsx(x = val, path =tmpfile, ...)
    }
  )
})

[r2evans]

@schloerke I thought serializer_* functions handled rendering output, not handling input which is what I think the issue is asking,

I want to upload the data in .csv format

@chuxinyuan I think you don't need to use read.csv at all, the use of @parser should handle that for you. (For this reprex, I created a CSV file with the top few rows of mtcars.)

#* @post /upload
#* @param f:file
#* @parser multi
#* @parser csv
function(req, res, f) {
  browser() # for demonstration
  data <- f[[1]]
  data
}

Execution:

print(f)
# $out.csv
# # A tibble: 3 × 11
#     mpg   cyl  disp    hp  drat    wt  qsec    vs    am  gear  carb
#   <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
# 1  21       6   160   110  3.9   2.62  16.5     0     1     4     4
# 2  21       6   160   110  3.9   2.88  17.0     0     1     4     4
# 3  22.8     4   108    93  3.85  2.32  18.6     1     1     4     1

So you can use f[[1]] directly to access the already-parsed data frame.

FYI, the command-line for uploading the file (for this test):

curl -X 'POST' 'http://127.0.0.1:9999/v1/upload' -F '[email protected];type=text/csv'

Alternatively, if you want to be able to work with the raw CSV string, remove the @parsers and use read.csv(text = f[[1]]):

A simple reprex:

#* @post /upload
#* @param f:file
function(req, res, f) {
  browser()
  data <- read.csv(text = f[[1]])
  data
}

Execution:

print(f)
# $out.csv
# [1] "mpg,cyl,disp,hp,drat,wt,qsec,vs,am,gear,carb\n21,6,160,110,3.9,2.62,16.46,0,1,4,4\n21,6,160,110,3.9,2.875,17.02,0,1,4,4\n22.8,4,108,93,3.85,2.32,18.61,1,1,4,1\n"

data <- read.csv(f[[1]])
# Warning in file(file, "rt") :
#   cannot open file 'mpg,cyl,disp,hp,drat,wt,qsec,vs,am,gear,carb
# 21,6,160,110,3.9,2.62,16.46,0,1,4,4
# 21,6,160,110,3.9,2.875,17.02,0,1,4,4
# 22.8,4,108,93,3.85,2.32,18.61,1,1,4,1
# ': No such file or directory
# Error in file(file, "rt") : cannot open the connection

data <- read.csv(text = f[[1]])
print(data)
#    mpg cyl disp  hp drat    wt  qsec vs am gear carb
# 1 21.0   6  160 110 3.90 2.620 16.46  0  1    4    4
# 2 21.0   6  160 110 3.90 2.875 17.02  0  1    4    4
# 3 22.8   4  108  93 3.85 2.320 18.61  1  1    4    1

... and then do with data as you need.

[r2evans]

A possible approach which adds a xlsx serializer: #793 (comment)

untested!

register_serializer(
"xlsx",
function(..., type = "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet") {
if (!requireNamespace("writexl", quietly = TRUE)) {
stop("The writexl package is not available but is required in order to use the writexl serializer",
call. = FALSE)
}

serializer_write_file(
# The temp file should end in .xlsx
fileext = ".xlsx",
# Pass through your content type
type = type,
write_fn = function(val, tmpfile) {
writexl::write_xlsx(x = val, path =tmpfile, ...)
}
)
})

@schloerke seems like a simple PR with this code might be welcome? (Unrelated to this issue.)

[schloerke]

@r2evans Yes, Thomas and I both mis-read as we were just talking about serializers. Thank you! **Re-opening

---

@schloerke seems like a simple PR with this code might be welcome? (Unrelated to this issue.)

@r2evans Yes, can you please make a PR?

[schloerke]

@chuxinyuan I believe you want something similar to...

# untested

parser_xlsx <- function(...) {
  parser_read_file(function(tmpfile) {
    read_xl:: read_excel(tmpfile, ...)
  })
}

plumber::register_parser("xlsx", parser_xlsx, fixed = "application/vnd.ms-excel", regex = "^application/vnd\.ms-excel")

---

@r2evans When a parser can be paired with a serializer, it makes for a good combo. Can I ask for you to include it as well? Thank you!

[r2evans]

Can I ask for you to include it as well?

Already working on it :-)