--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/redelacSticsTool.R	Tue Feb 06 09:21:00 2024 +0000
@@ -0,0 +1,440 @@
+library(SticsRFiles)
+library(SticsOnR)
+library(dplyr)
+library(lubridate)
+library(parallel)
+library(doParallel)
+library(doFuture)
+library(stringr)
+library(readxl)
+library(data.table)
+library(readr)
+library(tidyr)
+
+sessionInfo()
+
+args = commandArgs(trailingOnly = TRUE)
+
+startTime <- Sys.time()
+
+workspace <- paste0(getwd(), "/WS")
+javastics_path <- getwd()
+default_config_path <- paste0(javastics_path, "/config")
+
+txt_path <- paste0(getwd(), "/WS/txt_files")
+dir.create(txt_path, recursive = T)
+
+USMsFile <- "USMs.csv"
+TecFile <- "Tec.csv"
+IniFile <- "Ini.csv"
+StationFile <- "Station.csv"
+
+redelac <- (args[1] == "optim")
+parallel <- (args[2] == "parallel")
+print(paste("parallel:", parallel, args[2]))
+nbSlots <- as.integer(args[3])
+print(paste("nbslots:", nbSlots))
+scenario <- args[4]
+
+# 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
+  )
+
+# 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)
+
+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)
+
+if (parallel) {
+  doFuture::registerDoFuture()
+  future::plan(multisession, workers = nbSlots)
+  `%dordopar%` <- `%dofuture%`
+} else {
+  `%dordopar%` <- `%do%`
+}
+
+beforeGenXmlTime <- Sys.time()
+
+#gen_usms_xml(file = file.path(workspace, "usms.xml"),
+#             param_df = usms_param)
+
+chunckSize <- 1000
+nbUSMs <- nrow(usms_param)
+
+ids <- seq(1, nbUSMs, chunckSize)
+
+foreach (i = ids,
+         .options.future = list(packages = c("foreach", "SticsRFiles"))) %dordopar% {
+           gen_usms_xml(file = file.path(workspace, paste0("usms__", i, ".xml")),
+                        param_df = usms_param[i:min(i + chunckSize - 1, nbUSMs),])
+         }
+
+afterGenXmlTime <- Sys.time()
+durGenX <-
+  lubridate::as.duration(lubridate::interval(beforeGenXmlTime,
+                                             afterGenXmlTime))
+
+beforeGenTxtTime <- Sys.time()
+
+foreach (i = ids,
+         .options.future = list(packages = c("foreach", "SticsRFiles"))) %dordopar% {
+           gen_usms_xml2txt(
+             javastics = javastics_path,
+             workspace = workspace,
+             out_dir = txt_path,
+             usms_file = paste0("usms__", i, ".xml"),
+             redelac = redelac,
+             parallel = parallel,
+             verbose = FALSE
+           )
+         }
+
+afterGenTxtTime <- Sys.time()
+durGenT <-
+  lubridate::as.duration(lubridate::interval(beforeGenTxtTime, afterGenTxtTime))
+
+afterGenTxtTime <- Sys.time()
+durGenT <-
+  lubridate::as.duration(lubridate::interval(beforeGenTxtTime, afterGenTxtTime))
+
+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("REDELACSticsInputGenerator Report")
+print("=================================")
+print(paste("number of usms: ", nrow(usms_param)))
+print(paste("redelac optimization:", redelac))
+print(paste("process in parallel:", parallel))
+print(paste("nbslots:", nbSlots))
+
+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)
+)
+print(
+  "==================================================================================="
+)
+
+
+#
+# Simulation part
+#
+
+# List of successive USMs
+successive_usms_file <- ("successionPlan.csv")
+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"]
+
+successRef <- successRef %>%
+  separate(
+    col = Treatment,
+    into = c("upc", "sol", "systeme", "rotation", "tete_rotation", "horizon"),
+    sep = "-",
+    remove = FALSE
+  )
+
+successRef$upcSol <- paste0(successRef$upc, "-", successRef$sol)
+
+casesUpcSol <- unique(successRef$upcSol)
+
+systeme <- successRef$systeme[1]
+rotation <- successRef$rotation[1]
+
+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$upcSol == casesUpcSol[j],]
+}
+
+result <- foreach(j = 1:length(casesUpcSol)) %:%
+  foreach(
+    i = 1:nrow(successive_usms_tab_split[[j]]),
+    .options.future = list(packages =c("foreach", "SticsRFiles", "SticsOnR"))
+
+  ) %dordopar% {
+
+    nusms <- as.numeric(successive_usms_tab_split[[j]][i, 2])
+
+    vec <-
+      as.character(successive_usms_tab_split[[j]][i, c(3:(2 + nusms))])
+
+    list_successive_usms <- list(vec)
+
+    sim_options <- stics_wrapper_options(
+      javastics = javastics_path,
+      stics_exe = paste0(javastics_path, "/bin/stics_modulo"),
+      workspace = txt_path,
+      verbose = TRUE,
+      successive = list_successive_usms
+    )
+
+    list_usms <- vec
+
+    cat(paste0("--> succession : ", successive_usms_tab_split[[j]][i, 1], " launched\n"))
+
+    return(stics_wrapper(model_options = sim_options, situation = list_usms))
+
+  }
+
+for (j in  1:length(casesUpcSol)) {
+  splited <- strsplit(casesUpcSol[j], split = "-")[[1]]
+
+  upc <- splited[1]
+
+  sol <- splited[2]
+
+  for (i in 1:nrow(successive_usms_tab_split[[j]])) {
+    #i=1
+    if (i == 1) {
+      simPCP <- result[[j]][[i]]
+    } else {
+      simPCP$sim_list <- c(simPCP$sim_list, result[[j]][[i]]$sim_list)
+    }
+
+  }
+
+  #agregation des sorties dans un dataframe
+  sim_df <-
+    rbindlist(simPCP$sim_list, use.names = TRUE, idcol = "usm")
+
+  #ajout des colonnes explicatives + de l'horizon temporel
+  sim_df <- sim_df %>%
+    separate(
+      col = usm,
+      into = c(
+        "upc",
+        "sol",
+        "systeme",
+        "rotation",
+        "tete_rotation",
+        "horizon",
+        "annee",
+        "culture"
+      ),
+      sep = "-",
+      remove = FALSE
+    )
+
+  #sauvegarde sous la forme d'un fichier rds
+
+  if (dir.exists(paste0(
+    workspace,
+    "/analyse_simulations_STICS/",
+    systeme,
+    "/",
+    rotation
+  )) == FALSE) {
+    dir.create(
+      paste0(
+        workspace,
+        "/analyse_simulations_STICS/",
+        systeme,
+        "/",
+        rotation
+      ),
+      recursive = TRUE
+    )
+  }
+
+  saveRDS(
+    sim_df,
+    paste0(
+      workspace,
+      "/analyse_simulations_STICS/",
+      systeme,
+      "/",
+      rotation,
+      "/outputs-",
+      rotation,
+      "-",
+      upc,
+      "-",
+      sol,
+      "-",
+      scenario,
+      ".rds"
+    )
+  )
+
+  successive_usms_tab_split[[j]]$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,)#}
+
+      # } 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