annotate aquainfra_ogc_api_processes.R @ 0:3073e68373a5 draft default tip

planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit d07f89c8f6d6ee44c05de6b1b8047b387e76cad6

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

cat("start generic wrapper service \n")

remove_null_values <- function(x) {
  # Check if the input is a list
  if (is.list(x)) {
    # Remove NULL values and apply the function recursively to sublists
    x <- lapply(x, remove_null_values)
    x <- x[!sapply(x, is.null)]
  }
  return(x)
}

getParameters <- function() {
  con <- file("inputs.json", "r")
  lines <- readLines(con)
  close(con)
  
  json_string <- paste(lines, collapse = "\n")
  json_data <- fromJSON(json_string)
  
  # Remove NULL values from json_data
  cleaned_json_data <- remove_null_values(json_data)
  return(cleaned_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) {
  url <-
    paste(paste(paste(url, "processes/", sep = ""), process, sep = ""), "/execution", sep = "")
  requestBodyData$inputs$select_process <- NULL
  
  body <- list()
  body$inputs <- requestBodyData$inputs
  
  response <- request(url) %>%
    req_headers("Content-Type" = "application/json",
                "Prefer" = "respond-async") %>%
    req_body_json(body) %>%
    req_perform()
  
  cat("\n Process executed")
  cat("\n status: ", response$status_code)
  #if ( process == "barplot-trend-results") {
  #  process = "batplot-trend-results"
  #}
  #href <- parseResponseBody(response$body)$outputs[[gsub("-", "_", process)]]$href
  jobId <- parseResponseBody(response$body)$jobID
  
  return(jobId)
}

checkJobStatus <- function(server, process, jobID) {
  url <- paste0(server, "jobs/", jobID)
  response <- request(url) %>%
    req_perform()
  jobStatus <- parseResponseBody(response$body)$status
  jobProgress <- parseResponseBody(response$body)$progress
  return(jobStatus)
}

getStatusCode <- function(server, process, jobID) {
  url <- paste0(server, "jobs/", jobID)
  print(url)
  response <- request(url) %>%
    req_perform()
  status_code <- response$status_code
  return(status_code)
}

getResult <- function (server, process, jobID) {
  response <-
    request(paste0(server, "jobs/", jobID, "/results?f=json")) %>%
    req_perform()
  return(response)
}

# Recursive function to search for href in a nested list
findHref <- function(obj) {
  hrefs <- c()  # Initialize an empty vector to store hrefs
  
  if (is.list(obj)) {
    # If the object is a list, loop through its elements
    for (name in names(obj)) {
      element <- obj[[name]]
      
      if (is.list(element)) {
        # Recursively search if the element is another list
        hrefs <- c(hrefs, findHref(element))
      } else if (name == "href") {
        # If the element has a name "href", capture its value
        hrefs <- c(hrefs, element)
      }
    }
  }
  return(hrefs)
}

retrieveResults <- function(server, process, jobID, outputData) {
  status_code <- getStatusCode(server, process, jobID)
  print(status_code)
  
  if (status_code == 200) {
    status <- "running"
    
    while (status == "running") {
      jobStatus <- checkJobStatus(server, process, jobID)
      print(jobStatus)
      
      if (jobStatus == "successful") {
        status <- jobStatus
        result <- getResult(server, process, jobID)
        
        if (result$status_code == 200) {
          resultBody <- parseResponseBody(result$body)
          print(resultBody)
          
          # Call the recursive function to find all hrefs
          hrefs <- findHref(resultBody)
          
          if (length(hrefs) > 0) {
            # Collapse the URLs with a newline
            urls_with_newline <- paste(hrefs, collapse = "\n")
            print(urls_with_newline)
            
            # Write the URLs to a file
            con <- file(outputData, "w")
            writeLines(urls_with_newline, con = con)
            close(con)
          } else {
            print("No hrefs found.")
          }
        }
      } 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))
  }
}



saveResult <- function(href, outputData) {
  con <- file(outputData, "w")
    writeLines(href, con = con)
  close(con)
}

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

server <- "https://aqua.igb-berlin.de/pygeoapi-dev/"

print("--> Retrieve parameters")
inputParameters <- getParameters()
#print(inputParameters)
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)
    print("--------------------------------------------------------------------1")
    print(length(lines))
    close(con)
    if (!length(lines) > 1 && endsWith(lines, ".jp2") && startsWith(lines, "https")) {
      print("--------------------------------------------------------------------2")
      tmp <- list()
      tmp$href <- lines
      tmp$type <- "image/jp2"
      inputParameters[[key]] <- tmp
    }
    else if (!length(lines) > 1 && endsWith(lines, ".zip") && startsWith(lines, "https")) {
      print("--------------------------------------------------------------------3")
      json_string <- paste(lines, collapse = "\n")
      inputParameters[[key]] <- json_string
    } else if (!length(lines) > 1 && (endsWith(lines, ".xlsx") || endsWith(lines, ".csv") || grepl("f=csv", lines)) && startsWith(lines, "https")) {
      print("--------------------------------------------------------------------4")
      json_string <- paste(lines, collapse = "\n")
      inputParameters[[key]] <- json_string
    } else if (inputParameters$select_process == "plot-image" ||
               inputParameters$select_process == "reproject-image") {
      print("--------------------------------------------------------------------5")
      tmp <- list()
      tmp$href <- lines
      tmp$type <- "image/tiff; application=geotiff"
      if (inputParameters$select_process == "reproject-image") {
        tmp$type <- "image/tiff; subtype=geotiff"
      }
      inputParameters[[key]] <- tmp
    } else {
      print("-----------------------------------6")
      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(value)
      } 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
    print("-------------------------")
    print(convertedValues)
    print("-------------------------")
    convertedKeys <- append(convertedKeys, convertedKey)
  } else {
    print("-------------------------")
    print(key)
    print(inputParameters[[key]])
    if (!is.null(inputParameters[[key]])) {
      convertedKeys <- append(convertedKeys, key)
    }
    print("-------------------------")
    
  }
}
print(inputParameters)
names(inputParameters) <- convertedKeys
#print(inputParameters)
print("--> Inputs parsed")

print("--> Prepare process execution")
jsonData <- list("inputs" = inputParameters,
                 "outputs" = outputs)

print("--> Execute process")
jobId <- executeProcess(server, inputParameters$select_process, jsonData)
print("--> Process executed")

print("--> Retrieve results")
retrieveResults(server, inputParameters$select_process, jobId, outputLocation)
print("--> Results retrieved")