# HG changeset patch
# User siwaa
# Date 1689869939 0
# Node ID fb6f7d60508df45d1b90bcf21233d1c4acd2e5b9
# Parent  bb1ac57f8545413775ef9287f9cbb4d39994b33f
"planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"

diff -r bb1ac57f8545 -r fb6f7d60508d redelacSticsInputGenerator.R
--- a/redelacSticsInputGenerator.R	Fri Jul 07 10:19:22 2023 +0000
+++ b/redelacSticsInputGenerator.R	Thu Jul 20 16:18:59 2023 +0000
@@ -1,48 +1,164 @@
 library(SticsRFiles)
 library(dplyr)
+library(lubridate)
+
+
+startTime <- Sys.time()
 
 workspace <- paste0(getwd(), "/WS")
 javastics_path <- getwd()
 
 txt_path <- paste0(getwd(), "/WS/txt_files")
-dir.create(txt_path,recursive = T)
+dir.create(txt_path, recursive = T)
 
 USMsFile <- "USMs.csv"
 TecFile <- "Tec.csv"
 IniFile <- "Ini.csv"
 StationFile <- "Station.csv"
 
+args = commandArgs(trailingOnly = TRUE)
+
+genUSMsXmlOneAfterOther <- (args[1] == "usmx_one_after_other")
+
 # USMs file loading
+
 usms_param <- read_params_table(file.path(workspace, USMsFile)) %>%
-  select(usm_name,datedebut,datefin,finit,nomsol,fstation,fclim1,fclim2,culturean,nbplantes,codesimul,fplt_1,ftec_1,flai_1,fplt_2,ftec_2,flai_2)
+  select(
+    usm_name,
+    datedebut,
+    datefin,
+    finit,
+    nomsol,
+    fstation,
+    fclim1,
+    fclim2,
+    culturean,
+    nbplantes,
+    codesimul,
+    fplt_1,
+    ftec_1,
+    flai_1,
+    fplt_2,
+    ftec_2,
+    flai_2
+  )
 
 # Tec files loading and generating xml
+
 tec_param <- read_params_table(file.path(workspace, TecFile))
-columnToRemove <- names(tec_param[grep("juleclair|nbinfloecl", names(tec_param))])
-columnToKeep <- names(tec_param)[names(tec_param) %in% columnToRemove == FALSE]
-tec_param <- subset(tec_param, select=columnToKeep)
+columnToRemove <-
+  names(tec_param[grep("juleclair|nbinfloecl", names(tec_param))])
+columnToKeep <-
+  names(tec_param)[names(tec_param) %in% columnToRemove == FALSE]
+
+tec_param <- subset(tec_param, select = columnToKeep)
+
 gen_tec_xml(param_df = tec_param, out_dir = workspace)
 
 # Ini files loading and generating xml
+
 ini_param <- read_params_table(file.path(workspace, IniFile))
+
 gen_ini_xml(param_df = ini_param, out_dir = workspace)
 
 # Station files loading and generating xml
+
 sta_param <- read_params_table(file.path(workspace, StationFile))
+
 gen_sta_xml(param_df = sta_param, out_dir = workspace)
 
-
-# looping on USMs
-for(i in 1:nrow(usms_param)) {
-   row <- usms_param[i,]
-
-   # generating xml
-   gen_usms_xml(file = file.path(workspace, "usms.xml"), param_df = row)
+if (genUSMsXmlOneAfterOther) {
+  durGenX <- lubridate::as.duration(0)
+  durGenT <- lubridate::as.duration(0)
+  
+  # looping on USMs
+  for (i in 1:nrow(usms_param)) {
+    row <- usms_param[i, ]
+    
+    beforeGenXmlTimeI <- Sys.time()
+    
+    gen_usms_xml(file = file.path(workspace, "usms.xml"),
+                 param_df = row)
+    
+    afterGenXmlTimeI <- Sys.time()
+    durGenXI <-
+      lubridate::as.duration(lubridate::interval(beforeGenXmlTimeI,
+                                                 afterGenXmlTimeI))
+    
+    # one after the other generating txt folder
+    
+    beforeGenTxtTimeI <- Sys.time()
+    
+    gen_usms_xml2txt(
+      javastics = javastics_path,
+      workspace = workspace,
+      out_dir = txt_path,
+      verbose = TRUE
+    )
+    
+    afterGenTxtTimeI <- Sys.time()
+    durGenTI <-
+      lubridate::as.duration(lubridate::interval(beforeGenTxtTimeI,
+                                                 afterGenTxtTimeI))
+    
+    durGenX <- durGenX + durGenXI
+    durGenT <- durGenT + durGenTI
+  }
+} else {
+  beforeGenXmlTime <- Sys.time()
+  
+  gen_usms_xml(file = file.path(workspace, "usms.xml"),
+               param_df = usms_param)
+  
+  afterGenXmlTime <- Sys.time()
+  durGenX <-
+    lubridate::as.duration(lubridate::interval(beforeGenXmlTime,
+                                               afterGenXmlTime))
+  
+  beforeGenTxtTime <- Sys.time()
+  
+  gen_usms_xml2txt(
+    javastics = javastics_path,
+    workspace = workspace,
+    out_dir = txt_path,
+    verbose = TRUE
+  )
+  
+  afterGenTxtTime <- Sys.time()
+  durGenT <-
+    lubridate::as.duration(lubridate::interval(beforeGenTxtTime,
+                                               afterGenTxtTime))
+  
+}
 
-   # generating txt folder
-   gen_usms_xml2txt(javastics = javastics_path,
-	            workspace = workspace, 
-                    out_dir = txt_path,
-                    verbose = TRUE)
-}
-    
+endTime <- Sys.time()
+dur <-
+  lubridate::as.period(lubridate::as.duration(lubridate::interval(startTime, endTime)))
+durGenXP <- lubridate::as.period(durGenX)
+durGenTP <- lubridate::as.period(durGenT)
+
+print("REDELAC Report")
+print("==============")
+print(paste0("number of usms: ", nrow(usms_param)))
+print(paste("usms.xml one after the other:", genUSMsXmlOneAfterOther))
+sprintf(
+  'overall duration: %g jour(s) %g heure(s) %g minute(s) %g seconde(s)',
+  lubridate::day(dur),
+  lubridate::hour(dur),
+  lubridate::minute(dur),
+  lubridate::second(dur)
+)
+sprintf(
+  'inside gen_usms_xml duration: %g jour(s) %g heure(s) %g minute(s) %g seconde(s)',
+  lubridate::day(durGenXP),
+  lubridate::hour(durGenXP),
+  lubridate::minute(durGenXP),
+  lubridate::second(durGenXP)
+)
+sprintf(
+  'inside gen_usms_xml2txt duration: %g jour(s) %g heure(s) %g minute(s) %g seconde(s)',
+  lubridate::day(durGenTP),
+  lubridate::hour(durGenTP),
+  lubridate::minute(durGenTP),
+  lubridate::second(durGenTP)
+)
diff -r bb1ac57f8545 -r fb6f7d60508d redelacSticsInputGenerator.bash
--- a/redelacSticsInputGenerator.bash	Fri Jul 07 10:19:22 2023 +0000
+++ b/redelacSticsInputGenerator.bash	Thu Jul 20 16:18:59 2023 +0000
@@ -1,20 +1,20 @@
 cp -r /home/rstudio/JavaSTICS-1.5.1-STICS-10.0.0/JavaSTICS-1.5.1-STICS-10.0.0 . &&
 rm -rf JavaSTICS-1.5.1-STICS-10.0.0/config &&
-cp -r $1/config JavaSTICS-1.5.1-STICS-10.0.0 &&
-unzip $2 -d TMP &&
+cp -r $2/config JavaSTICS-1.5.1-STICS-10.0.0 &&
+unzip -q $3 -d TMP &&
 export WSname=$(ls TMP) &&
 mv TMP/* JavaSTICS-1.5.1-STICS-10.0.0/WS &&
 cp JavaSTICS-1.5.1-STICS-10.0.0/config/param_gen.xml JavaSTICS-1.5.1-STICS-10.0.0/WS &&
 cp JavaSTICS-1.5.1-STICS-10.0.0/config/param_newform.xml JavaSTICS-1.5.1-STICS-10.0.0/WS &&
-unzip $3 -d TMPbis &&
+unzip -q $4 -d TMPbis &&
 mv TMPbis/*/* JavaSTICS-1.5.1-STICS-10.0.0/WS &&
-cp $4 JavaSTICS-1.5.1-STICS-10.0.0/WS/USMs.csv &&
-cp $5 JavaSTICS-1.5.1-STICS-10.0.0/WS/Tec.csv &&
-cp $6 JavaSTICS-1.5.1-STICS-10.0.0/WS/Ini.csv &&
-cp $7 JavaSTICS-1.5.1-STICS-10.0.0/WS/Station.csv &&
+cp $5 JavaSTICS-1.5.1-STICS-10.0.0/WS/USMs.csv &&
+cp $6 JavaSTICS-1.5.1-STICS-10.0.0/WS/Tec.csv &&
+cp $7 JavaSTICS-1.5.1-STICS-10.0.0/WS/Ini.csv &&
+cp $8 JavaSTICS-1.5.1-STICS-10.0.0/WS/Station.csv &&
 cd JavaSTICS-1.5.1-STICS-10.0.0 &&
-Rscript --verbose $1/redelacSticsInputGenerator.R &&
+Rscript --verbose $2/redelacSticsInputGenerator.R $1 &&
 rm WS/1* &&
 mv WS $WSname &&
-zip -r $WSname $WSname &&
+zip -q -r $WSname $WSname &&
 cp $WSname.zip $8
diff -r bb1ac57f8545 -r fb6f7d60508d redelacSticsInputGenerator.xml
--- a/redelacSticsInputGenerator.xml	Fri Jul 07 10:19:22 2023 +0000
+++ b/redelacSticsInputGenerator.xml	Thu Jul 20 16:18:59 2023 +0000
@@ -5,8 +5,8 @@
   </requirements>
   <command detect_errors="aggressive">
     <![CDATA[
-	     bash $__tool_directory__/redelacSticsInputGenerator.bash $__tool_directory__ ${Workspace} ${Climat} ${USMs} ${Tec} ${Ini} ${Station} ${GeneratedWorkspace}
-     ]]>
+	     bash $__tool_directory__/redelacSticsInputGenerator.bash ${IterUsmX} $__tool_directory__ ${Workspace} ${Climat} ${USMs} ${Tec} ${Ini} ${Station} ${GeneratedWorkspace}
+     ]]>{
   </command>
   <inputs>
     <param name="Workspace" type="data" format="zip" label="Select a stics Workspace (zip file)"/>
@@ -16,6 +16,7 @@
     <param name="Ini" type="data" format="csv" label="Select the Ini sheet (csv)"/>
     <param name="Station" type="data" format="csv" label="Select the Station sheet (csv)"/>
     <param name="Tag" type="text" value="" label="Outputs tag"/>
+    <param name="IterUsmX" type="boolean" checked="true" truevalue="usmx_one_after_other" falsevalue="usmx_at_once"/>
   </inputs>
   <outputs>
     <data format="zip" name="GeneratedWorkspace"