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changeset 7:2586f7dbcde1 draft

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"planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/af2d1fcb63a2ae897e02f11e82cc76c4f6e8ca5e/tools/REDELACSticsSimulator commit af2d1fcb63a2ae897e02f11e82cc76c4f6e8ca5e-dirty"
author siwaa
date Mon, 02 Oct 2023 13:51:01 +0000
parents 41f652e6616f
children 806bf835c109
files redelacSticsSimulator.R redelacSticsSimulator.bash redelacSticsSimulator.xml test-data/input/listeUSMsExp10.csv test-data/input/rotx10.zip
diffstat 5 files changed, 331 insertions(+), 41 deletions(-) [+]
line wrap: on
line diff
--- a/redelacSticsSimulator.R	Tue Sep 26 15:21:42 2023 +0000
+++ b/redelacSticsSimulator.R	Mon Oct 02 13:51:01 2023 +0000
@@ -3,9 +3,21 @@
 library(parallel)
 library(doParallel)
 library(readxl)
+library(tidyr)
+library(data.table)
+library(readr)
+library(dplyr)
+library(stringr)
+library(readr)
 
 sessionInfo()
 
+args = commandArgs(trailingOnly = TRUE)
+
+parallel <- (args[1] == "parallel")
+nbSlots <- as.integer(args[2])
+scenario <- args[3]
+
 workspace <- paste0(getwd(), "/WS")
 javastics_path <- getwd()
 default_config_path <- paste0(javastics_path, "/config")
@@ -14,15 +26,32 @@
 
 # List of successive USMs
 successive_usms_file <- ("successionPlan.csv")
-successive_usms_tab <- read.csv(file = file.path(workspace, successive_usms_file), sep =";")
+successive_usms_tab <-
+  read.csv(file = file.path(workspace, successive_usms_file),
+           sep = ";")
+
+# from succesions to simulate retrieving upcSol Cases
+
+successRef <- successive_usms_tab["Treatment"]
 
-args = commandArgs(trailingOnly = TRUE)
+successRef <- successRef %>%
+  separate(
+    col = Treatment,
+    into = c("upc", "sol", "systeme", "rotation", "tete_rotation", "horizon"),
+    sep = "-",
+    remove = FALSE
+  )
 
-parallel <- (args[1] == "parallel")
-nbSlots <- as.integer(args[2])
+successRef$upcSol <- paste0(successRef$upc, "-", successRef$sol)
+
+casesUpcSol <- unique(successRef$upcSol)
+
+systeme <- successRef$systeme[1]
+rotation <- successRef$rotation[1]
 
 if (parallel) {
   cl <- makeCluster(nbSlots)
+  print("Inside R, info on the cluster:")
   print(cl)
   registerDoParallel(cl)
   `%dordopar%` <- `%dopar%`
@@ -30,35 +59,242 @@
   `%dordopar%` <- `%do%`
 }
 
-result <- foreach(i=1:nrow(successive_usms_tab),
-                  .packages = c("foreach", "SticsRFiles", "SticsOnR") ) %dordopar% {
+successive_usms_tab_split <- list()
+
+for (j in  1:length(casesUpcSol)) {
+  splited <- strsplit(casesUpcSol[j], split = "-")[[1]]
+
+  upc <- splited[1]
+
+  sol <- splited[2]
+
+  successive_usms_tab_split[[j]] <-
+    successive_usms_tab[successRef$upcSol == casesUpcSol[j],]
+}
+
+result <- foreach(j = 1:length(casesUpcSol)) %:%
+  foreach(
+    i = 1:nrow(successive_usms_tab_split[[j]]),
+    .packages = c("foreach", "SticsRFiles", "SticsOnR")
+  ) %dordopar% {
+    if (parallel)
+      sink("./logPaRedelac.txt", append = TRUE)
+
+    nusms <- as.numeric(successive_usms_tab_split[[j]][i, 2])
 
-  nusms <- as.numeric(successive_usms_tab[i,2])
-  
-  vec <- as.character(successive_usms_tab[i,c(3:(2+nusms))])
-  
-  list_successive_usms <- list(vec)
-  
-  sim_options <- stics_wrapper_options(javastics = javastics_path, 
-                                       stics_exe = paste0(javastics_path,"/bin/stics_modulo"),
-                                       workspace = txt_path, 
-                                       verbose = TRUE, 
-                                       successive = list_successive_usms)
-  list_usms <- vec
+    vec <-
+      as.character(successive_usms_tab_split[[j]][i, c(3:(2 + nusms))])
+
+    list_successive_usms <- list(vec)
+
+    sim_options <- stics_wrapper_options(
+      javastics = javastics_path,
+      stics_exe = paste0(javastics_path, "/bin/stics_modulo"),
+      workspace = txt_path,
+      verbose = TRUE,
+      successive = list_successive_usms
+    )
 
-  return(stics_wrapper(model_options = sim_options, situation = list_usms))
+    list_usms <- vec
+
+    cat(paste0("-->", successive_usms_tab_split[[j]][i, 1], "launched\n"))
+
+    return(stics_wrapper(model_options = sim_options, situation = list_usms))
 
+  }
+
+if (parallel) {
+  stopCluster(cl)
+  sink()
+  cat(read_file("./logPaRedelac.txt"))
 }
 
-if (parallel) stopCluster(cl)
+for (j in  1:length(casesUpcSol)) {
+  splited <- strsplit(casesUpcSol[j], split = "-")[[1]]
+
+  upc <- splited[1]
+
+  sol <- splited[2]
+
+  for (i in 1:nrow(successive_usms_tab_split[[j]])) {
+    #i=1
+    if (i == 1) {
+      simPCP <- result[[j]][[i]]
+    } else {
+      simPCP$sim_list <- c(simPCP$sim_list, result[[j]][[i]]$sim_list)
+    }
+
+  }
+
+  #agregation des sorties dans un dataframe
+  sim_df <-
+    rbindlist(simPCP$sim_list, use.names = TRUE, idcol = "usm")
 
-for (i in 1:nrow(successive_usms_tab)) { #i=1
-  if (i == 1) {
-    simPCP <- result[[i]]
-  } else {
-    simPCP$sim_list <- c(simPCP$sim_list, result[[i]]$sim_list)
+  #ajout des colonnes explicatives + de l'horizon temporel
+  sim_df <- sim_df %>%
+    separate(
+      col = usm,
+      into = c(
+        "upc",
+        "sol",
+        "systeme",
+        "rotation",
+        "tete_rotation",
+        "horizon",
+        "annee",
+        "culture"
+      ),
+      sep = "-",
+      remove = FALSE
+    )
+
+  #sauvegarde sous la forme d'un fichier rds
+
+  if (dir.exists(paste0(
+    workspace,
+    "/analyse_simulations_STICS/",
+    systeme,
+    "/",
+    rotation
+  )) == FALSE) {
+    dir.create(
+      paste0(
+        workspace,
+        "/analyse_simulations_STICS/",
+        systeme,
+        "/",
+        rotation
+      ),
+      recursive = TRUE
+    )
   }
 
-}
+  saveRDS(
+    sim_df,
+    paste0(
+      workspace,
+      "/analyse_simulations_STICS/",
+      systeme,
+      "/",
+      rotation,
+      "/outputs-",
+      rotation,
+      "-",
+      upc,
+      "-",
+      sol,
+      "-",
+      scenario,
+      ".rds"
+    )
+  )
+
+  successive_usms_tab_split[[j]]$Treatment <- NULL
+  successive_usms_tab_split[[j]]$Number_USM <- NULL
+
+  list_usms <-
+    unlist(unname(as.list(
+      transpose(successive_usms_tab_split[[j]])
+    )))
+  list_usms <- list_usms[!is.na(list_usms)]
+  list_usms <- list_usms[list_usms != '']
+
+  list_usms_yr1 <- successive_usms_tab_split[[j]]$USM_1
+
+  for (i in 1:length(list_usms)) {
+    if (i == 1) {
+      #ajout d'une condition sur l'existence du fichier "mod_rapport.sti" pour la concatenation
+      #en attendant que toutes les simulations tournent correctement
+      #if(exists(file.path(txt_path, list_usms[i], "mod_rapport.sti"))==TRUE){
+      rap_1 <-
+        read_delim(file.path(txt_path, list_usms[i], "mod_rapport.sti"),
+                   col_names = TRUE)
+      names_col <- colnames(rap_1)
+
+      rap_string <-
+        read_lines(file = file.path(txt_path, list_usms[i], "mod_rapport.sti"),
+                   skip = 1)
+
+      rap <- as_tibble(rap_string) %>%
+        separate(col = value,
+                 sep = ";",
+                 into = names_col) %>%
+        mutate(USM = list_usms[i])
+      # }
+
+    } else {
+      #if (list_usms[i] %in% list_usms_yr1) {
+      #ajout d'une condition sur l'existence du fichier "mod_rapport.sti" pour la concatenation
+      #en attendant que toutes les simulations tournent correctement
+      #if(exists(file.path(txt_path, list_usms[i], "mod_rapport.sti"))==TRUE){
+      rap_string <-
+        read_lines(file = file.path(txt_path, list_usms[i], "mod_rapport.sti"),
+                   skip = 1,)#}
 
-save(simPCP, file = "results.RData")
+      # } else {
+      #ajout d'une condition sur l'existence du fichier "mod_rapport.sti" pour la concatenation
+      #en attendant que toutes les simulations tournent correctement
+      #if(exists(file.path(txt_path, list_usms[i], "mod_rapport.sti"))==TRUE){
+      #   rap_string <-
+      #     read_file(file = file.path(txt_path, list_usms[i], "mod_rapport.sti"))#}
+      # }
+      rap_i <- as_tibble(rap_string) %>%
+        separate(col = value,
+                 sep = ";",
+                 into = names_col) %>%
+        mutate(USM = list_usms[i])
+
+      rap <- bind_rows(rap, rap_i)
+
+    }
+
+  }
+  rm(rap_1, names_col, rap_string, rap_i)
+
+  rap <- rap %>%
+    select(USM, everything()) %>%
+    mutate(P_usm = str_replace_all(P_usm, " ", "")) %>%
+    mutate(wlieu = str_replace_all(wlieu, " ", "")) %>%
+    mutate(stade = str_replace_all(stade, " ", "")) %>%
+    mutate(nomversion = str_replace_all(nomversion, " ", "")) %>%
+    mutate(across(3:9, as.numeric)) %>%
+    mutate(across(13:ncol(rap), as.numeric)) %>%
+    #separate(col=P_usm,into=c("upc","sol","systeme","rotation","tete_rotation","horizon","annee","culture"),sep="-",remove = FALSE)
+    separate(
+      col = USM,
+      into = c(
+        "upc",
+        "sol",
+        "systeme",
+        "rotation",
+        "tete_rotation",
+        "horizon",
+        "annee",
+        "culture"
+      ),
+      sep = "-",
+      remove = FALSE
+    )
+
+  write_delim(
+    x = rap,
+    file = paste0(
+      workspace,
+      "/analyse_simulations_STICS/",
+      systeme,
+      "/",
+      rotation,
+      "/report-",
+      rotation,
+      "-",
+      upc,
+      "-",
+      sol,
+      "-",
+      scenario,
+      ".csv"
+    ),
+    delim = ";"
+  )
+
+}
\ No newline at end of file
--- a/redelacSticsSimulator.bash	Tue Sep 26 15:21:42 2023 +0000
+++ b/redelacSticsSimulator.bash	Mon Oct 02 13:51:01 2023 +0000
@@ -1,12 +1,31 @@
 cp -r /home/rstudio/JavaSTICS-1.5.1-STICS-10.0.0 . &&
-unzip -qq $4 -d TMP &&
+/usr/bin/time -p -o ./bashlog unzip -qq $5 -d TMP &&
+echo "Step 0, time to unzip the Workspace:" &&
+echo "====================================" && 
+cat ./bashlog &&
+echo "====================================" && 
 export WSname=$(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 &&
+cp $6 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 &&
+/usr/bin/time -p -o ./bashlog Rscript --verbose $4/redelacSticsSimulator.R $1 $2 $3 &&
+echo "Step 1, time to run the R script:" &&
+echo "=================================" && 
+cat ./bashlog &&
+echo "=================================" && 
+cd WS &&
+/usr/bin/time -p -o ./bashlog zip -qq -r analyse_simulations_STICS analyse_simulations_STICS &&
+echo "Step 2, time to zip the results:" &&
+echo "================================" && 
+cat ./bashlog &&
+echo "================================" && 
+cp analyse_simulations_STICS.zip $8 &&
+rm -rf analyse_simulations_STICS &&
+cd .. &&
 mv WS $WSname &&
-zip -qq -r $WSname $WSname &&
-cp $WSname.zip $6 &&
-cp results.RData $7
-             
+/usr/bin/time -p -o ./bashlog zip -qq -r $WSname $WSname &&
+echo "Step 3, time to zip the Workspace:" &&
+echo "==================================" && 
+cat ./bashlog &&
+echo "==================================" && 
+cp $WSname.zip $7
--- a/redelacSticsSimulator.xml	Tue Sep 26 15:21:42 2023 +0000
+++ b/redelacSticsSimulator.xml	Mon Oct 02 13:51:01 2023 +0000
@@ -1,28 +1,52 @@
-<tool id="redelacSticsSimulator" name="redelacSticsSimulator" version="1.0.3">
+<tool id="redelacSticsSimulator" name="redelacSticsSimulator" version="1.0.4">
   <description>to run sequences paralelly [Stics-10.0.0]</description>
   <requirements>
-    <container type="singularity">docker://registry.forgemia.inra.fr/redelac/redelac-toolbox/sticsrpacks:28483bbc8a70159a36bccc30e2270284ea4388e3</container>
+    <container type="singularity">docker://registry.forgemia.inra.fr/redelac/redelac-toolbox/sticsrpacks:69b14ab2616cfea4afc36e6974d66e12ac20480b</container>
   </requirements>
   <command detect_errors="aggressive">
     <![CDATA[ 
-              bash $__tool_directory__/redelacSticsSimulator.bash ${parallel} \${GALAXY_SLOTS:-4} $__tool_directory__ ${Workspace} ${SuccessionPlan} ${SimulatedWorkspace} ${SimulationResults}
+              bash $__tool_directory__/redelacSticsSimulator.bash ${parallel} \${GALAXY_SLOTS:-4} ${Scenario} $__tool_directory__ ${Workspace} ${SuccessionPlan} ${SimulatedWorkspace} ${SimulationResults}
      ]]>
   </command>
   <inputs>
     <param name="Workspace" type="data" format="zip" label="Select a stics Workspace(zip file)"/>
     <param name="SuccessionPlan" type="data" format="csv" label="Select a plan of succession (csv)"/>
-    <param name="Tag" type="text" value="" label="Outputs tag"/>
+    <param name="Scenario" type="text" value="scenarioName" label="Scenario Name"/>
     <param name="parallel" type="boolean" checked="true" truevalue="parallel" falsevalue="sequential"/>
   </inputs>
   <outputs>
     <data format="zip" name="SimulatedWorkspace"
-          label="SticsSimulatedWorkspace${Tag}">
+          label="SticsSimulatedWorkspace">
     </data>
-    <data format="rdata" name="SimulationResults"
-          label="SticsOnResults${Tag}">
+    <data format="zip" name="SimulationResults"
+          label="SticsOnResults">
     </data>
   </outputs>
   <tests>
+    <test>
+      <param name="parallel" value="true" ftype="boolean" />
+      <param name="Workspace" value="input/rotx10.zip" ftype="zip" />
+      <param name="SuccessionPlan" value="input/listeUSMsExp10.csv" ftype="csv" />    
+      <output name="SimulationResults" ftype="zip" >
+	<assert_contents>
+	  <has_archive_member path="analyse_simulations_STICS\/1\/2\/report-2-806_1893-637_NGC1-scenarioName.csv">
+	    <has_text text="806_1893-637_NGC1-1-2-BT-NA-1973-BT" />
+	    	  </has_archive_member>
+	</assert_contents>	  
+      </output>
+    </test>
+    <test>
+      <param name="parallel" value="false" ftype="boolean" />
+      <param name="Workspace" value="input/rotx10.zip" ftype="zip" />
+      <param name="SuccessionPlan" value="input/listeUSMsExp10.csv" ftype="csv" />    
+      <output name="SimulationResults" ftype="zip" >
+	<assert_contents>
+	  <has_archive_member path="analyse_simulations_STICS\/1\/2\/report-2-806_1893-637_NGC1-scenarioName.csv">
+	    <has_text text="806_1893-637_NGC1-1-2-BT-NA-1973-BT" />
+	    	  </has_archive_member>
+	</assert_contents>	  
+      </output>
+    </test>
   </tests>
   <help>
 *The usage of this tool is restricted to the user of the stics_authorized group.*
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input/listeUSMsExp10.csv	Mon Oct 02 13:51:01 2023 +0000
@@ -0,0 +1,11 @@
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