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comparison redelacSticsSimulator.R @ 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 65c00476f417
comparison
equal deleted inserted replaced
6:41f652e6616f 7:2586f7dbcde1
1 library(SticsRFiles) 1 library(SticsRFiles)
2 library(SticsOnR) 2 library(SticsOnR)
3 library(parallel) 3 library(parallel)
4 library(doParallel) 4 library(doParallel)
5 library(readxl) 5 library(readxl)
6 library(tidyr)
7 library(data.table)
8 library(readr)
9 library(dplyr)
10 library(stringr)
11 library(readr)
6 12
7 sessionInfo() 13 sessionInfo()
14
15 args = commandArgs(trailingOnly = TRUE)
16
17 parallel <- (args[1] == "parallel")
18 nbSlots <- as.integer(args[2])
19 scenario <- args[3]
8 20
9 workspace <- paste0(getwd(), "/WS") 21 workspace <- paste0(getwd(), "/WS")
10 javastics_path <- getwd() 22 javastics_path <- getwd()
11 default_config_path <- paste0(javastics_path, "/config") 23 default_config_path <- paste0(javastics_path, "/config")
12 24
13 txt_path <- paste0(getwd(), "/WS/txt_files") 25 txt_path <- paste0(getwd(), "/WS/txt_files")
14 26
15 # List of successive USMs 27 # List of successive USMs
16 successive_usms_file <- ("successionPlan.csv") 28 successive_usms_file <- ("successionPlan.csv")
17 successive_usms_tab <- read.csv(file = file.path(workspace, successive_usms_file), sep =";") 29 successive_usms_tab <-
18 30 read.csv(file = file.path(workspace, successive_usms_file),
19 args = commandArgs(trailingOnly = TRUE) 31 sep = ";")
20 32
21 parallel <- (args[1] == "parallel") 33 # from succesions to simulate retrieving upcSol Cases
22 nbSlots <- as.integer(args[2]) 34
35 successRef <- successive_usms_tab["Treatment"]
36
37 successRef <- successRef %>%
38 separate(
39 col = Treatment,
40 into = c("upc", "sol", "systeme", "rotation", "tete_rotation", "horizon"),
41 sep = "-",
42 remove = FALSE
43 )
44
45 successRef$upcSol <- paste0(successRef$upc, "-", successRef$sol)
46
47 casesUpcSol <- unique(successRef$upcSol)
48
49 systeme <- successRef$systeme[1]
50 rotation <- successRef$rotation[1]
23 51
24 if (parallel) { 52 if (parallel) {
25 cl <- makeCluster(nbSlots) 53 cl <- makeCluster(nbSlots)
54 print("Inside R, info on the cluster:")
26 print(cl) 55 print(cl)
27 registerDoParallel(cl) 56 registerDoParallel(cl)
28 `%dordopar%` <- `%dopar%` 57 `%dordopar%` <- `%dopar%`
29 } else { 58 } else {
30 `%dordopar%` <- `%do%` 59 `%dordopar%` <- `%do%`
31 } 60 }
32 61
33 result <- foreach(i=1:nrow(successive_usms_tab), 62 successive_usms_tab_split <- list()
34 .packages = c("foreach", "SticsRFiles", "SticsOnR") ) %dordopar% { 63
35 64 for (j in 1:length(casesUpcSol)) {
36 nusms <- as.numeric(successive_usms_tab[i,2]) 65 splited <- strsplit(casesUpcSol[j], split = "-")[[1]]
37 66
38 vec <- as.character(successive_usms_tab[i,c(3:(2+nusms))]) 67 upc <- splited[1]
39 68
40 list_successive_usms <- list(vec) 69 sol <- splited[2]
41 70
42 sim_options <- stics_wrapper_options(javastics = javastics_path, 71 successive_usms_tab_split[[j]] <-
43 stics_exe = paste0(javastics_path,"/bin/stics_modulo"), 72 successive_usms_tab[successRef$upcSol == casesUpcSol[j],]
44 workspace = txt_path,
45 verbose = TRUE,
46 successive = list_successive_usms)
47 list_usms <- vec
48
49 return(stics_wrapper(model_options = sim_options, situation = list_usms))
50
51 } 73 }
52 74
53 if (parallel) stopCluster(cl) 75 result <- foreach(j = 1:length(casesUpcSol)) %:%
54 76 foreach(
55 for (i in 1:nrow(successive_usms_tab)) { #i=1 77 i = 1:nrow(successive_usms_tab_split[[j]]),
56 if (i == 1) { 78 .packages = c("foreach", "SticsRFiles", "SticsOnR")
57 simPCP <- result[[i]] 79 ) %dordopar% {
58 } else { 80 if (parallel)
59 simPCP$sim_list <- c(simPCP$sim_list, result[[i]]$sim_list) 81 sink("./logPaRedelac.txt", append = TRUE)
82
83 nusms <- as.numeric(successive_usms_tab_split[[j]][i, 2])
84
85 vec <-
86 as.character(successive_usms_tab_split[[j]][i, c(3:(2 + nusms))])
87
88 list_successive_usms <- list(vec)
89
90 sim_options <- stics_wrapper_options(
91 javastics = javastics_path,
92 stics_exe = paste0(javastics_path, "/bin/stics_modulo"),
93 workspace = txt_path,
94 verbose = TRUE,
95 successive = list_successive_usms
96 )
97
98 list_usms <- vec
99
100 cat(paste0("-->", successive_usms_tab_split[[j]][i, 1], "launched\n"))
101
102 return(stics_wrapper(model_options = sim_options, situation = list_usms))
103
60 } 104 }
61 105
106 if (parallel) {
107 stopCluster(cl)
108 sink()
109 cat(read_file("./logPaRedelac.txt"))
62 } 110 }
63 111
64 save(simPCP, file = "results.RData") 112 for (j in 1:length(casesUpcSol)) {
113 splited <- strsplit(casesUpcSol[j], split = "-")[[1]]
114
115 upc <- splited[1]
116
117 sol <- splited[2]
118
119 for (i in 1:nrow(successive_usms_tab_split[[j]])) {
120 #i=1
121 if (i == 1) {
122 simPCP <- result[[j]][[i]]
123 } else {
124 simPCP$sim_list <- c(simPCP$sim_list, result[[j]][[i]]$sim_list)
125 }
126
127 }
128
129 #agregation des sorties dans un dataframe
130 sim_df <-
131 rbindlist(simPCP$sim_list, use.names = TRUE, idcol = "usm")
132
133 #ajout des colonnes explicatives + de l'horizon temporel
134 sim_df <- sim_df %>%
135 separate(
136 col = usm,
137 into = c(
138 "upc",
139 "sol",
140 "systeme",
141 "rotation",
142 "tete_rotation",
143 "horizon",
144 "annee",
145 "culture"
146 ),
147 sep = "-",
148 remove = FALSE
149 )
150
151 #sauvegarde sous la forme d'un fichier rds
152
153 if (dir.exists(paste0(
154 workspace,
155 "/analyse_simulations_STICS/",
156 systeme,
157 "/",
158 rotation
159 )) == FALSE) {
160 dir.create(
161 paste0(
162 workspace,
163 "/analyse_simulations_STICS/",
164 systeme,
165 "/",
166 rotation
167 ),
168 recursive = TRUE
169 )
170 }
171
172 saveRDS(
173 sim_df,
174 paste0(
175 workspace,
176 "/analyse_simulations_STICS/",
177 systeme,
178 "/",
179 rotation,
180 "/outputs-",
181 rotation,
182 "-",
183 upc,
184 "-",
185 sol,
186 "-",
187 scenario,
188 ".rds"
189 )
190 )
191
192 successive_usms_tab_split[[j]]$Treatment <- NULL
193 successive_usms_tab_split[[j]]$Number_USM <- NULL
194
195 list_usms <-
196 unlist(unname(as.list(
197 transpose(successive_usms_tab_split[[j]])
198 )))
199 list_usms <- list_usms[!is.na(list_usms)]
200 list_usms <- list_usms[list_usms != '']
201
202 list_usms_yr1 <- successive_usms_tab_split[[j]]$USM_1
203
204 for (i in 1:length(list_usms)) {
205 if (i == 1) {
206 #ajout d'une condition sur l'existence du fichier "mod_rapport.sti" pour la concatenation
207 #en attendant que toutes les simulations tournent correctement
208 #if(exists(file.path(txt_path, list_usms[i], "mod_rapport.sti"))==TRUE){
209 rap_1 <-
210 read_delim(file.path(txt_path, list_usms[i], "mod_rapport.sti"),
211 col_names = TRUE)
212 names_col <- colnames(rap_1)
213
214 rap_string <-
215 read_lines(file = file.path(txt_path, list_usms[i], "mod_rapport.sti"),
216 skip = 1)
217
218 rap <- as_tibble(rap_string) %>%
219 separate(col = value,
220 sep = ";",
221 into = names_col) %>%
222 mutate(USM = list_usms[i])
223 # }
224
225 } else {
226 #if (list_usms[i] %in% list_usms_yr1) {
227 #ajout d'une condition sur l'existence du fichier "mod_rapport.sti" pour la concatenation
228 #en attendant que toutes les simulations tournent correctement
229 #if(exists(file.path(txt_path, list_usms[i], "mod_rapport.sti"))==TRUE){
230 rap_string <-
231 read_lines(file = file.path(txt_path, list_usms[i], "mod_rapport.sti"),
232 skip = 1,)#}
233
234 # } else {
235 #ajout d'une condition sur l'existence du fichier "mod_rapport.sti" pour la concatenation
236 #en attendant que toutes les simulations tournent correctement
237 #if(exists(file.path(txt_path, list_usms[i], "mod_rapport.sti"))==TRUE){
238 # rap_string <-
239 # read_file(file = file.path(txt_path, list_usms[i], "mod_rapport.sti"))#}
240 # }
241 rap_i <- as_tibble(rap_string) %>%
242 separate(col = value,
243 sep = ";",
244 into = names_col) %>%
245 mutate(USM = list_usms[i])
246
247 rap <- bind_rows(rap, rap_i)
248
249 }
250
251 }
252 rm(rap_1, names_col, rap_string, rap_i)
253
254 rap <- rap %>%
255 select(USM, everything()) %>%
256 mutate(P_usm = str_replace_all(P_usm, " ", "")) %>%
257 mutate(wlieu = str_replace_all(wlieu, " ", "")) %>%
258 mutate(stade = str_replace_all(stade, " ", "")) %>%
259 mutate(nomversion = str_replace_all(nomversion, " ", "")) %>%
260 mutate(across(3:9, as.numeric)) %>%
261 mutate(across(13:ncol(rap), as.numeric)) %>%
262 #separate(col=P_usm,into=c("upc","sol","systeme","rotation","tete_rotation","horizon","annee","culture"),sep="-",remove = FALSE)
263 separate(
264 col = USM,
265 into = c(
266 "upc",
267 "sol",
268 "systeme",
269 "rotation",
270 "tete_rotation",
271 "horizon",
272 "annee",
273 "culture"
274 ),
275 sep = "-",
276 remove = FALSE
277 )
278
279 write_delim(
280 x = rap,
281 file = paste0(
282 workspace,
283 "/analyse_simulations_STICS/",
284 systeme,
285 "/",
286 rotation,
287 "/report-",
288 rotation,
289 "-",
290 upc,
291 "-",
292 sol,
293 "-",
294 scenario,
295 ".csv"
296 ),
297 delim = ";"
298 )
299
300 }