# R script for programtic access to Revigo. Run it with (last output file name is optional):
# Rscript revigo.R example.csv result.csv

library(httr)
library(stringi)

args = commandArgs(trailingOnly=TRUE)

# Read user data from a file
fileName <- args[1] #"example.csv"
userData <- readChar(fileName,file.info(fileName)$size)

# Default output file name is result.csv
if (length(args)>=2) {
    fileNameOutput <- args[2]
} else {
    fileNameOutput <- "result.csv"
}

# Submit job to Revigo
httr::POST(
  url = "http://revigo.irb.hr/Revigo",
  body = list(
    cutoff = "0.7",
    valueType = "pvalue",
    speciesTaxon = "0",
    measure = "SIMREL",
    goList = userData
  ),
  # application/x-www-form-urlencoded
  encode = "form"
) -> res

dat <- httr::content(res, as="text", encoding="UTF-8")

# Write results to a file
dat <- stri_replace_all_fixed(dat, "\r", "")
cat(dat, file=fileNameOutput, fill = FALSE)