--- a/run.r	Thu Jul 11 09:39:17 2024 +0000
+++ b/run.r	Thu Jul 11 09:40:46 2024 +0000
@@ -5,8 +5,7 @@
     args <- commandArgs(trailingOnly = TRUE)
     
     # Default values for optional parameters
-#	url <- "https://coby.infosol.inrae.fr:8080/semantify/"
-	url <- "http://localhost:8282/semantify"
+	url <- "https://coby.infosol.inrae.fr:8080/semantify/"
 	srcDir <- NULL
 	part <- "modeltoolbox_sem_sep"
 	DS <- T
@@ -36,10 +35,14 @@
 	if (grepl("^--srcOut=", arg)) {
             srcOut <- sub("^--srcOut=", "", arg)
         }
+	
+	if (grepl("^--semPath=", arg)) {
+            semPath <- sub("^--semPath=", "", arg)
+        }
 
     }
     
-    list(url = url, srcDir = srcDir, part = part, DS = DS, NBCores = NBCores, srcOut = srcOut)
+    list(url = url, srcDir = srcDir, part = part, DS = DS, NBCores = NBCores, srcOut = srcOut, semPath = semPath)
 }
 
 argus <- parse_args()
@@ -50,6 +53,7 @@
 NBCores <- argus[["NBCores"]]
 
 srcOut <- argus[["srcOut"]]
+semPath <- argus[["semPath"]]
 
 if (!endsWith(srcOut, "/")) {
   srcOut <- paste0(srcOut, "/")
@@ -81,20 +85,15 @@
 	DS <- F
 	print("Setting DS to F. Will semantify outside of the csoprapreprocessor functions")
 	f0 <- function(){
-#		path <- this.path::this.dir()
-#		print(path)
-#		setwd(path)
-#		setwd("../..")
-                print("before semantify")
-#		Sys.sleep(runif(n=1, min=30, max=60))
 		csopratools::semantify(
 			  inputDir = srcDir,
 			  outputDir = srcDir,
 			  name = "carboseq",
-			  use = "service", 
+			  # use = "service",
 			  URL = url,
-#			  extFileNames = paste0(c("crop", "soil", "units"), ".csv")
-			  extFileNames = list.files(srcDir)
+			  use = "java",
+			  semantifierRootPath =  semPath,
+			  extFileNames = paste0(c("crop", "soil", "units"), ".csv")
 		)
 		print("between semantify and load")
 		modeltoolbox::loadCSVs(maxCores = NBCores, cinputCalculator = "cinest",