diff ogc_api_processes_wrapper.R @ 0:afede0916f0a draft default tip

planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ogc_api_processes_wrapper.R	Fri Jun 07 11:37:33 2024 +0000
@@ -0,0 +1,239 @@
+library("httr2")
+library("jsonlite")
+library("getopt")
+
+cat("start generic wrapper service \n")
+
+getParameters <- function(){
+    con <- file("inputs.json", "r")
+    lines <- readLines(con)
+    close(con)
+
+    json_string <- paste(lines, collapse = "\n")
+    json_data <- fromJSON(json_string)
+    return(json_data$conditional_process)
+}
+
+parseResponseBody <- function(body) {
+  hex <- c(body)
+  intValues <- as.integer(hex)
+  rawVector <- as.raw(intValues)
+  readableOutput <- rawToChar(rawVector)
+  jsonObject <- jsonlite::fromJSON(readableOutput)
+  return(jsonObject)
+}
+
+getOutputs <- function(inputs, output, server) {
+    url <- paste(paste(server, "/processes/", sep = ""), inputs$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, cookie) {
+    url <- paste(paste(paste(url, "processes/", sep = ""), process, sep = ""), "/execution", sep = "")
+    requestBodyData$inputs$cookie <- NULL
+    requestBodyData$inputs$select_process <- NULL
+    
+    requestBodyData$inputs$s3_access_key <- requestBodyData$inputs$user_credentials$s3_access_key
+    requestBodyData$inputs$s3_secret_key <- requestBodyData$inputs$user_credentials$s3_secret_key
+    requestBodyData$inputs$user_credentials <- NULL
+
+    body <- list()
+    body$inputs <- requestBodyData$inputs
+    body$mode <- "async"
+    body$response <- "document"
+    
+    response <- request(url) %>%
+      req_headers(
+        "Accept" = "application/json",
+        "Content-Type" = "application/json",
+        "Cookie" = cookie
+      ) %>%
+      req_body_json(body) %>%
+      req_perform()
+
+    cat("\n Process executed")
+    cat("\n status: ", response$status_code)
+    cat("\n jobID: ", parseResponseBody(response$body)$jobID, "\n")
+
+    jobID <- parseResponseBody(response$body)$jobID
+
+    return(jobID)
+}
+
+checkJobStatus <- function(server, process, jobID, cookie) {
+  url <- paste0(server, "processes/", process, "/jobs/", jobID)
+  response <- request(url) %>%
+    req_headers(
+      "Cookie" = cookie
+    ) %>%
+    req_perform()
+  jobStatus <- parseResponseBody(response$body)$status
+  jobProgress <- parseResponseBody(response$body)$progress
+  return(jobStatus)
+}
+
+getStatusCode <- function(server, process, jobID, cookie) {
+  url <- paste0(server, "processes/", process, "/jobs/", jobID)
+  response <- request(url) %>%
+    req_headers(
+      "Cookie" = cookie
+    ) %>%
+    req_perform()
+  status_code <- response$status_code
+  return(status_code)
+}
+
+getResult <- function (server, process, jobID, cookie) {
+  response <- request(paste0(server, "processes/", process, "/jobs/", jobID, "/results")) %>%
+    req_headers(
+      "Cookie" = cookie
+    ) %>%
+    req_perform()
+  return(response)
+}
+
+retrieveResults <- function(server, process, jobID, outputData, cookie) {
+    status_code <- getStatusCode(server, process, jobID, cookie)
+    if(status_code == 200){
+        status <- "running"
+        while(status == "running"){
+            jobStatus <- checkJobStatus(server, process, jobID, cookie)
+            print(jobStatus)
+            if (jobStatus == "succeeded") {
+                status <- jobStatus
+                result <- getResult(server, process, jobID, cookie)
+                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://hirondelle.crim.ca/weaver/"
+
+print("--> Retrieve parameters")
+inputParameters <- getParameters()
+print("--> Parameters retrieved")
+
+args <- commandArgs(trailingOnly = TRUE)
+outputLocation <- args[2]
+
+print("--> Retrieve outputs")
+outputs <- getOutputs(inputParameters, outputLocation, server)
+print("--> Outputs retrieved")
+
+print("--> Parse inputs")
+convertedKeys <- c()
+for (key in names(inputParameters)) {
+  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))))
+    #  }
+    #}
+    con <- file(inputParameters[[key]], "r")
+    lines <- readLines(con)
+    close(con)
+    json_string <- paste(lines, collapse = "\n")
+    json_data <- fromJSON(json_string)
+
+    inputParameters[[key]] <- json_data
+    convertedKeys <- append(convertedKeys, key)
+  }
+  else if (grepl("_Array_", key)) {
+    keyParts <- strsplit(key, split = "_")[[1]]
+    type <- keyParts[length(keyParts)]
+    values <- inputParameters[[key]]
+    value_list <- strsplit(values, split = ",")
+
+    convertedValues <- c()
+
+    for (value in value_list) {
+      if(type == "integer") {
+        value <- as.integer(value)
+      } else if (type == "numeric") {
+        value <- as.numeric(balue)
+      } else if (type == "character") {
+        value <- as.character(value)
+      }
+    convertedValues <- append(convertedValues, value)
+
+    convertedKey <- ""
+    for (part in keyParts) {
+      if(part == "Array") {
+        break
+      }
+      convertedKey <- paste(convertedKey, paste(part, "_", sep=""), sep="")
+    }
+    convertedKey <- substr(convertedKey, 1, nchar(convertedKey)-1)
+}
+
+    inputParameters[[key]] <- convertedValues
+    convertedKeys <- append(convertedKeys, convertedKey)
+  } else {
+    convertedKeys <- append(convertedKeys, key)
+  }
+}
+
+names(inputParameters) <- convertedKeys
+print("--> Inputs parsed")
+
+print("--> Prepare process execution")
+jsonData <- list(
+  "inputs" = inputParameters,
+  "outputs" = outputs
+)
+
+cookie <- inputParameters$cookie
+
+print("--> Execute process")
+jobID <- executeProcess(server, inputParameters$select_process, jsonData, cookie)
+print("--> Process executed")
+
+print("--> Retrieve results")
+retrieveResults(server, inputParameters$select_process, jobID, outputLocation, cookie)
+print("--> Results retrieved")
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