annotate ogc_api_processes_wrapper.R @ 2:bcb6009d5af7 draft default tip

planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit e03f4d27ec44d873aacdf406d7a26ec8038e9b05

library("httr2")
library("jsonlite")
library("getopt")

cat("start generic wrapper service \n")

getParameters <- function(){
    con <- file("inputs.json", "r")
    line <- readLines(con, n = 1)
    json <- fromJSON(line)
    close(con)
    return(json$conditional_process)
}

parseResponseBody <- function(body) {
  hex <- c(body)
  intValues <- as.integer(hex)
  rawVector <- as.raw(intValues)
  readableOutput <- rawToChar(rawVector)
  jsonObject <- jsonlite::fromJSON(readableOutput)
  return(jsonObject)
}

getOutputs <- function(inputs, output, server) {
    url <- paste(paste(server, "/processes/", sep = ""), inputs$select_process, sep = "")
    request <- request(url)
    response <- req_perform(request)
    responseBody <- parseResponseBody(response$body)
    outputs <- list()

    for (x in 1:length(responseBody$outputs)) {
        outputformatName <- paste(names(responseBody$outputs[x]), "_outformat", sep="")
        output_item <- list()

        for (p in names(inputs)) {
            if(p == outputformatName){
                format <- list("mediaType" = inputs[[outputformatName]])
                output_item$format <- format
            }
        }
        output_item$transmissionMode <- "reference"
        outputs[[x]] <- output_item
    }

    names(outputs) <- names(responseBody$outputs)
    return(outputs)
}

executeProcess <- function(url, process, requestBodyData, output) {
    url <- paste(paste(paste(url, "processes/", sep = ""), process, sep = ""), "/execution", sep = "")
    response <- request(url) %>%
    req_headers(
      "accept" = "/*",
      "Prefer" = "respond-async;return=representation",
      "Content-Type" = "application/json"
    ) %>%
    req_body_json(requestBodyData) %>%
    req_perform()

    cat("\n Process executed")
    cat("\n status: ", response$status_code)
    cat("\n jobID: ", parseResponseBody(response$body)$jobID, "\n")

    jobID <- parseResponseBody(response$body)$jobID

    return(jobID)
}

checkJobStatus <- function(server, jobID) {
  response <- request(paste0(server, "jobs/", jobID)) %>%
    req_headers(
        'accept' = 'application/json'
    ) %>%
    req_perform()
  jobStatus <- parseResponseBody(response$body)$status
  jobProgress <- parseResponseBody(response$body)$progress
  cat(paste0("\n status: ", jobStatus, ", progress: ", jobProgress))
  return(jobStatus)
}

getStatusCode <- function(server, jobID) {
  url <- paste0(server, "jobs/", jobID)
  response <- request(url) %>%
      req_headers(
        'accept' = 'application/json'
      ) %>%
      req_perform()
  return(response$status_code)
}

getResult <- function (server, jobID) {
  response <- request(paste0(server, "jobs/", jobID, "/results")) %>%
    req_headers(
      'accept' = 'application/json'
    ) %>%
    req_perform()
  return(response)
}

retrieveResults <- function(server, jobID, outputData) {
    status_code <- getStatusCode(server, jobID)
    if(status_code == 200){
        status <- "running"
        cat(status)
        while(status == "running"){
            jobStatus <- checkJobStatus(server, jobID)
            if (jobStatus == "successful") {
                status <- jobStatus
                result <- getResult(server, jobID)
                if (result$status_code == 200) {
                  resultBody <- parseResponseBody(result$body)
                  urls <- unname(unlist(lapply(resultBody, function(x) x$href)))
                  urls_with_newline <- paste(urls, collapse = "\n")
                  con <- file(outputData, "w")
                  writeLines(urls_with_newline, con = con)
                  close(con)
                }
            } else if (jobStatus == "failed") {
              status <- jobStatus
            }
        Sys.sleep(3)
        }
        cat("\n done \n")
    } else if (status_code1 == 400) {
    print("A query parameter has an invalid value.")
  } else if (status_code1 == 404) {
    print("The requested URI was not found.")
  } else if (status_code1 == 500) {
    print("The requested URI was not found.")
  } else {
    print(paste("HTTP", status_code1, "Error:", resp1$status_message))
  }
}

is_url <- function(x) {
  grepl("^https?://", x)
}

server <- "https://ospd.geolabs.fr:8300/ogc-api/"

inputParameters <- getParameters()

args <- commandArgs(trailingOnly = TRUE)
outputLocation <- args[2]

outputs <- getOutputs(inputParameters, outputLocation, server)

for (key in names(inputParameters)) {
  print(inputParameters[[key]])
  if (is.character(inputParameters[[key]]) && (endsWith(inputParameters[[key]], ".dat") || endsWith(inputParameters[[key]], ".txt"))) { 
    con <- file(inputParameters[[key]], "r")
    url_list <- list()
    while (length(line <- readLines(con, n = 1)) > 0) {
      if (is_url(line)) {
        url_list <- c(url_list, list(list(href = trimws(line))))
      }
    }
    close(con)
    inputParameters[[key]] <- url_list
  }
}

jsonData <- list(
  "inputs" = inputParameters,
  "outputs" = outputs
)

jobID <- executeProcess(server, inputParameters$select_process, jsonData, outputLocation)

retrieveResults(server, jobID, outputLocation)