# HG changeset patch
# User siwaa
# Date 1695741702 0
# Node ID 41f652e6616f51632675af449b98b28713352658
# Parent  fa8e742b197b36f62e9bc0945d64648b1f009847
"planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/f8a7aebffe0c850bef03045efa3772aca6cd51c2/tools/REDELACSticsSimulator commit f8a7aebffe0c850bef03045efa3772aca6cd51c2-dirty"

diff -r fa8e742b197b -r 41f652e6616f redelacSticsSimulator.R
--- a/redelacSticsSimulator.R	Mon Aug 21 15:47:50 2023 +0000
+++ b/redelacSticsSimulator.R	Tue Sep 26 15:21:42 2023 +0000
@@ -4,35 +4,34 @@
 library(doParallel)
 library(readxl)
 
+sessionInfo()
+
 workspace <- paste0(getwd(), "/WS")
 javastics_path <- getwd()
 default_config_path <- paste0(javastics_path, "/config")
 
 txt_path <- paste0(getwd(), "/WS/txt_files")
 
-print("==================================")
-
-print(paste0("Cores=", detectCores()))
-print(paste0("javastics=", javastics_path))
-print(paste0("ws=", workspace))
-print(paste0("out_dir=", txt_path))
-
-print("==================================")
-
 # List of successive USMs
 successive_usms_file <- ("successionPlan.csv")
 successive_usms_tab <- read.csv(file = file.path(workspace, successive_usms_file), sep =";")
 
-#no_cores <- detectCores() - 1  
-#no_cores <- 10  
-#cl <- makeCluster(no_cores)  
-#registerDoParallel(cl)
+args = commandArgs(trailingOnly = TRUE)
+
+parallel <- (args[1] == "parallel")
+nbSlots <- as.integer(args[2])
 
-result <- list()
+if (parallel) {
+  cl <- makeCluster(nbSlots)
+  print(cl)
+  registerDoParallel(cl)
+  `%dordopar%` <- `%dopar%`
+} else {
+  `%dordopar%` <- `%do%`
+}
 
-#result <- foreach(i=1:nrow(successive_usms_tab),
-#                  .packages = c("SticsRFiles", "SticsOnR") ) %dopar% {
- for(i in 1:nrow(successive_usms_tab)) {
+result <- foreach(i=1:nrow(successive_usms_tab),
+                  .packages = c("foreach", "SticsRFiles", "SticsOnR") ) %dordopar% {
 
   nusms <- as.numeric(successive_usms_tab[i,2])
   
@@ -47,12 +46,11 @@
                                        successive = list_successive_usms)
   list_usms <- vec
 
-  singleResult = stics_wrapper(model_options = sim_options, situation = list_usms)
+  return(stics_wrapper(model_options = sim_options, situation = list_usms))
 
-  result = append(result, list(singleResult))
-                  }
+}
 
-#stopCluster(cl)
+if (parallel) stopCluster(cl)
 
 for (i in 1:nrow(successive_usms_tab)) { #i=1
   if (i == 1) {
diff -r fa8e742b197b -r 41f652e6616f redelacSticsSimulator.bash
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/redelacSticsSimulator.bash	Tue Sep 26 15:21:42 2023 +0000
@@ -0,0 +1,12 @@
+cp -r /home/rstudio/JavaSTICS-1.5.1-STICS-10.0.0 . &&
+unzip -qq $4 -d TMP &&
+export WSname=$(ls TMP) &&
+mv TMP/* JavaSTICS-1.5.1-STICS-10.0.0/WS &&
+cp $5 JavaSTICS-1.5.1-STICS-10.0.0/WS/successionPlan.csv &&
+cd JavaSTICS-1.5.1-STICS-10.0.0 &&
+Rscript --verbose $3/redelacSticsSimulator.R $1 $2 &&
+mv WS $WSname &&
+zip -qq -r $WSname $WSname &&
+cp $WSname.zip $6 &&
+cp results.RData $7
+             
diff -r fa8e742b197b -r 41f652e6616f redelacSticsSimulator.xml
--- a/redelacSticsSimulator.xml	Mon Aug 21 15:47:50 2023 +0000
+++ b/redelacSticsSimulator.xml	Tue Sep 26 15:21:42 2023 +0000
@@ -1,29 +1,18 @@
-<tool id="redelacSticsSimulator" name="redelacSticsSimulator" version="1.0.2">
+<tool id="redelacSticsSimulator" name="redelacSticsSimulator" version="1.0.3">
   <description>to run sequences paralelly [Stics-10.0.0]</description>
   <requirements>
-    <container type="singularity">docker://registry.forgemia.inra.fr/quaysofthestics/sticsquays/rstudio_stics:10.0.0</container>
+    <container type="singularity">docker://registry.forgemia.inra.fr/redelac/redelac-toolbox/sticsrpacks:28483bbc8a70159a36bccc30e2270284ea4388e3</container>
   </requirements>
   <command detect_errors="aggressive">
     <![CDATA[ 
-	     cp -r /home/rstudio/JavaSTICS-1.5.1-STICS-10.0.0/JavaSTICS-1.5.1-STICS-10.0.0 . &&
-	     rm JavaSTICS-1.5.1-STICS-10.0.0/bin/stics_modulo &&
-             cp $__tool_directory__/stics_modulo JavaSTICS-1.5.1-STICS-10.0.0/bin &&
-	     unzip -qq ${WorkSpace} -d TMP &&
-             export WSname=\$(ls TMP) &&
-	     mv TMP/* JavaSTICS-1.5.1-STICS-10.0.0/WS &&
-	     cp ${SuccessionPlan} JavaSTICS-1.5.1-STICS-10.0.0/WS/successionPlan.csv &&
-	     cd JavaSTICS-1.5.1-STICS-10.0.0 &&
-	     Rscript --verbose $__tool_directory__/redelacSticsSimulator.R \${GALAXY_SLOTS:-2}	&&
-             mv WS \$WSname &&
-	     zip -qq -r \$WSname \$WSname &&
-	     cp \$WSname.zip ${SimulatedWorkspace} &&
-	     cp results.RData ${SimulationResults}
+              bash $__tool_directory__/redelacSticsSimulator.bash ${parallel} \${GALAXY_SLOTS:-4} $__tool_directory__ ${Workspace} ${SuccessionPlan} ${SimulatedWorkspace} ${SimulationResults}
      ]]>
   </command>
   <inputs>
-    <param name="WorkSpace" type="data" format="zip" label="Select a stics Workspace(zip file)"/>
+    <param name="Workspace" type="data" format="zip" label="Select a stics Workspace(zip file)"/>
     <param name="SuccessionPlan" type="data" format="csv" label="Select a plan of succession (csv)"/>
     <param name="Tag" type="text" value="" label="Outputs tag"/>
+    <param name="parallel" type="boolean" checked="true" truevalue="parallel" falsevalue="sequential"/>
   </inputs>
   <outputs>
     <data format="zip" name="SimulatedWorkspace"
diff -r fa8e742b197b -r 41f652e6616f stics_modulo
Binary file stics_modulo has changed
diff -r fa8e742b197b -r 41f652e6616f version.txt
--- a/version.txt	Mon Aug 21 15:47:50 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-origin/plecharpent/debug/prairies               6b6441bd ndecalf and ndecalg are (as for bare soil)  now set to 0 at non perenial crops harvest, or perenial crop destruction
-