diff OTB_BandMath.R @ 0:0ed34e3202b9 draft

planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/OtbBandMath commit d85a00bfd9f603fd25ad0fc93736d0b1e395fe25

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/OTB_BandMath.R	Tue Mar 12 12:39:59 2024 +0000
@@ -0,0 +1,150 @@
+#Run with Rscript ./OTB_BandMath.R --file otb_band_math_test_input.txt --processingMemory 256 --mathExpression im1b3,im1b2,im1b1 --outputType png --outputFormat download --outputImage float --outputData otb_band_math_test_output.png
+
+library("httr2")
+library("jsonlite")
+library("getopt")
+
+args <- commandArgs(trailingOnly = TRUE)
+option_specification <- matrix(c(
+  'file', 'i1', 1, 'character',
+  'processingMemory', 'i2', 2, 'integer',
+  'mathExpression', 'i3', 2, 'character',
+  'outputType', 'i4', 2, 'character',
+  'outputFormat', 'i5', 1, 'character',
+  'outputImage', 'i6', 1, 'character',
+  'outputData', 'o', 1, 'character'
+), byrow = TRUE, ncol = 4)
+options <- getopt(option_specification)
+
+file <- options$file
+processingMemory <- options$processingMemory
+mathExpression <-options$mathExpression
+outputType <- paste0("image/", options$outputType)
+outputFormat <- options$outputFormat
+outputImage <- options$outputImage
+outputData <- options$outputData
+
+cat("\n file: ", file)
+cat("\n ram: ", processingMemory)
+cat("\n exp: ", mathExpression)
+cat("\n outputType: ", outputType)
+cat("\n outputFormat: ", outputFormat)
+cat("\n outputImage: ", outputImage)
+
+baseUrl <- "https://ospd.geolabs.fr:8300/ogc-api/"
+execute <- "processes/OTB.BandMath/execution"
+getStatus <- "jobs/"
+getResult <- "/results"
+
+file_urls <- readLines(file, warn = FALSE)
+
+il_list <- lapply(file_urls, function(url) {
+  list("href" = url)
+})
+
+json_data <- list(
+  "inputs" = list(
+    "il" = il_list,
+    "out" = outputImage,
+    "exp" = mathExpression,
+    "ram" = processingMemory
+  ),
+  "outputs" = list(
+    "out" = list(
+      "format" = list(
+        "mediaType" = outputType
+      ),
+      "transmissionMode" = "reference"
+    )
+  )
+)
+
+makeResponseBodyReadable <- function(body) {
+  hex <- c(body)
+  int_values <- as.integer(hex)
+  raw_vector <- as.raw(int_values)
+  readable_output <- rawToChar(raw_vector)
+  json_object <- jsonlite::fromJSON(readable_output)
+  return(json_object)
+}
+
+tryCatch({
+  #Request 1
+  resp1 <- request(paste0(baseUrl, execute)) %>%
+    req_headers(
+      'accept' = '/*',
+      'Prefer' = 'respond-async;return=representation',
+      'Content-Type' = 'application/json'
+    ) %>%
+    req_body_json(json_data) %>%
+    req_perform()
+
+  response <- makeResponseBodyReadable(resp1$body)
+  status_code1 <- resp1$status_code
+
+  if (status_code1 == 201) {
+    status <- "running"
+    attempt = 1
+    while (status == "running") {
+      #Request 2
+      #cat("\n",response$jobID)
+      resp2 <- request(paste0(baseUrl,getStatus,response$jobID)) %>%
+        req_headers(
+          'accept' = 'application/json'
+        ) %>%
+        req_perform()
+      status_code2 <- resp2$status_code
+      #cat("\n", status_code2)
+      if (status_code2 == 200) {
+        response2 <- makeResponseBodyReadable(resp2$body)
+        cat("\n", response2$status)
+        if (response2$status=="successful") {
+          status <- "successful"
+          #Request 3
+          resp3 <- request(paste0(baseUrl,getStatus, response2$jobID, getResult)) %>%
+            req_headers(
+              'accept' = 'application/json'
+            ) %>%
+            req_perform()
+          status_code3 <- resp3$status_code
+          if (status_code3 == 200) {
+            response3 <- makeResponseBodyReadable(resp3$body)
+            if (outputFormat == "download") {
+              options(timeout=300)
+              download.file(response3$out$href, destfile = outputData, mode = "wb")              
+            } else if (outputFormat == "getUrl") {
+              writeLines(response3$out$href, con = outputData)
+            }
+          } else if (status_code3 == 404) {
+            print("The requested URI was not found.")
+          } else if (status_code3 == 500) {
+            print("A server error occurred.")
+          } else {
+            print(paste("HTTP", status_code3, "Error:", resp3$status_message))
+          }
+        } else if (response2$status=="failed") {
+          status <- "failed"
+        }
+         #else {
+         # attempt <- attempt +1
+         # if (attempt == 200) {
+         #   status <- "failed"          
+         # }
+        #}        
+      } else {
+        status <- "failed"
+        print(paste("HTTP", status_code2, "Error:", resp2$status_message))
+      }
+      Sys.sleep(3)
+    }
+    print(status)
+  } else if (status_code1 == 400) {
+    print("A query parameter has an invalid value.")
+  } else if (status_code1 == 404) {
+    print("The requested URI was not found.")
+  } else if (status_code1 == 500) {
+    print("The requested URI was not found.")
+  } else {
+    print(paste("HTTP", status_code1, "Error:", resp1$status_message))
+  }
+})
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