Mercurial > repos > siwaa > redelac_stics_t

annotate redelacSticsTool.R @ 18:8293d67cd1a9 draft

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"planemo upload for repository https://forgemia.inra.fr/redelac commit b972382172a3923486a799d46efe363d21e8ea1d"
author siwaa
date Thu, 09 Jul 2026 07:09:47 +0000
parents fa4e7fd1d3f7
children 8848db582840
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1 library(SticsRFiles)
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2 library(SticsOnR)
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3 library(dplyr)
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4 library(lubridate)
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5 library(parallel)
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6 library(doParallel)
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7 library(doFuture)
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8 library(stringr)
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9 library(readxl)
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10 library(data.table)
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11 library(readr)
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12 library(tidyr)
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13 library(arrow)
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14 sessionInfo()
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16 args = commandArgs(trailingOnly = TRUE)
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18 startTime <- Sys.time()
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20 workspace <- paste0(getwd(), "/WS")
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21 javastics_path <- getwd()
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22 default_config_path <- paste0(javastics_path, "/config")
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24 txt_path <- paste0(getwd(), "/WS/txt_files")
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25 dir.create(txt_path, recursive = T)
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27 USMsFile <- "USMs.csv"
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28 TecFile <- "Tec.csv"
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29 IniFile <- "Ini.csv"
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30 StationFile <- "Station.csv"
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32 redelac <- (args[1] == "optim")
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33 parallel <- (args[2] == "parallel")
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34 print(paste("parallel:", parallel, args[2]))
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35 nbSlots <- as.integer(args[3])
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36 print(paste("nbslots:", nbSlots))
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37 scenario <- args[4]
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38 resulType <- args[5]
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40 parquetOut <- (resulType == "parquet" || resulType == "both" )
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41 baseOut <- (resulType == "rds+csv" || resulType == "both" )
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43 # USMs file loading
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45 usms_param <- read_params_table(file.path(workspace, USMsFile)) %>%
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46 select(
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47 usm_name,
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48 datedebut,
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49 datefin,
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50 finit,
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51 nomsol,
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52 fstation,
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53 fclim1,
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54 fclim2,
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55 culturean,
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56 nbplantes,
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57 codesimul,
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58 fplt_1,
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59 ftec_1,
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60 flai_1,
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61 fplt_2,
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62 ftec_2,
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63 flai_2
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64 )
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65
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66 # Tec files loading and generating xml
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67
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68 tec_param <- read_params_table(file.path(workspace, TecFile))
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69 columnToRemove <-
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70 names(tec_param[grep("juleclair|nbinfloecl", names(tec_param))])
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71 columnToKeep <-
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72 names(tec_param)[names(tec_param) %in% columnToRemove == FALSE]
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73
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74 tec_param <- subset(tec_param, select = columnToKeep)
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75
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76 gen_tec_xml(param_df = tec_param, out_dir = workspace)
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78 # Ini files loading and generating xml
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79
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80 ini_param <- read_params_table(file.path(workspace, IniFile))
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81
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82 gen_ini_xml(param_df = ini_param, out_dir = workspace)
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83
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84 # Station files loading and generating xml
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85
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86 sta_param <- read_params_table(file.path(workspace, StationFile))
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87
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88 gen_sta_xml(param_df = sta_param, out_dir = workspace)
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89
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90 if (parallel) {
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91 doFuture::registerDoFuture()
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92 future::plan(multisession, workers = nbSlots)
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93 `%dordopar%` <- `%dofuture%`
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94 } else {
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95 `%dordopar%` <- `%do%`
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96 }
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siwaa
parents:
diff changeset
97
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
98 beforeGenXmlTime <- Sys.time()
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
99
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
100 #gen_usms_xml(file = file.path(workspace, "usms.xml"),
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
101 # param_df = usms_param)
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
102
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
103 chunckSize <- 1000
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
104 nbUSMs <- nrow(usms_param)
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
105
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
106 ids <- seq(1, nbUSMs, chunckSize)
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
107
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
108 foreach (i = ids,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
109 .options.future = list(packages = c("foreach", "SticsRFiles"))) %dordopar% {
15
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
110 usmsXfolder = file.path(workspace, paste0("UXF__", i))
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
111 dir.create(usmsXfolder)
1
ed9c49c6c6e1 "planemo upload for repository https://forgemia.inra.fr/redelac commit c398d524dabc89c0979403d2ff62970fc6c2b404"
siwaa
parents: 0
diff changeset
112 gen_usms_xml(file = file.path(usmsXfolder, paste0("usms__", i, ".xml")),
0
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
113 param_df = usms_param[i:min(i + chunckSize - 1, nbUSMs),])
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
114 }
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
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115
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
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116 afterGenXmlTime <- Sys.time()
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
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117 durGenX <-
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
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118 lubridate::as.duration(lubridate::interval(beforeGenXmlTime,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
119 afterGenXmlTime))
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
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120
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parents:
diff changeset
121 beforeGenTxtTime <- Sys.time()
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
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122
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
123 foreach (i = ids,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
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124 .options.future = list(packages = c("foreach", "SticsRFiles"))) %dordopar% {
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
125 gen_usms_xml2txt(
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
126 javastics = javastics_path,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
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127 workspace = workspace,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
128 out_dir = txt_path,
1
ed9c49c6c6e1 "planemo upload for repository https://forgemia.inra.fr/redelac commit c398d524dabc89c0979403d2ff62970fc6c2b404"
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parents: 0
diff changeset
129 usms_file = paste0("UXF__", i, "/usms__", i, ".xml"),
0
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
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130 redelac = redelac,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
diff changeset
131 parallel = parallel,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
diff changeset
132 verbose = FALSE
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
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133 )
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
134 }
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
135
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
136 afterGenTxtTime <- Sys.time()
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
137 durGenT <-
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
138 lubridate::as.duration(lubridate::interval(beforeGenTxtTime, afterGenTxtTime))
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
139
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
140 endTime <- Sys.time()
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
141
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
142 dur <-
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
143 lubridate::as.period(lubridate::as.duration(lubridate::interval(startTime, endTime)))
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
144 durGenXP <- lubridate::as.period(durGenX)
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
145 durGenTP <- lubridate::as.period(durGenT)
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
146
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parents:
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147 print("REDELACSticsInputGenerator Report")
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
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148 print("=================================")
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parents:
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149 print(paste("number of usms: ", nrow(usms_param)))
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
diff changeset
150 print(paste("redelac optimization:", redelac))
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
diff changeset
151 print(paste("process in parallel:", parallel))
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
152 print(paste("nbslots:", nbSlots))
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siwaa
parents:
diff changeset
153
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
154 sprintf(
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
diff changeset
155 'overall duration: %g jour(s) %g heure(s) %g minute(s) %g seconde(s)',
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
156 lubridate::day(dur),
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
157 lubridate::hour(dur),
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
diff changeset
158 lubridate::minute(dur),
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
159 lubridate::second(dur)
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
diff changeset
160 )
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
161
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
162 sprintf(
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
diff changeset
163 'inside gen_usms_xml duration: %g jour(s) %g heure(s) %g minute(s) %g seconde(s)',
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
164 lubridate::day(durGenXP),
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
165 lubridate::hour(durGenXP),
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
166 lubridate::minute(durGenXP),
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
167 lubridate::second(durGenXP)
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
diff changeset
168 )
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
169
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
diff changeset
170 sprintf(
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
diff changeset
171 'inside gen_usms_xml2txt duration: %g jour(s) %g heure(s) %g minute(s) %g seconde(s)',
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
172 lubridate::day(durGenTP),
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
173 lubridate::hour(durGenTP),
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
174 lubridate::minute(durGenTP),
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
175 lubridate::second(durGenTP)
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parents:
diff changeset
176 )
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
177 print(
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
178 "==================================================================================="
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
diff changeset
179 )
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
180
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
181 #
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
diff changeset
182 # Simulation part
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
diff changeset
183 #
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
184
18
8293d67cd1a9 "planemo upload for repository https://forgemia.inra.fr/redelac commit b972382172a3923486a799d46efe363d21e8ea1d"
siwaa
parents: 17
diff changeset
185 beforeSimsTime <- Sys.time()
8293d67cd1a9 "planemo upload for repository https://forgemia.inra.fr/redelac commit b972382172a3923486a799d46efe363d21e8ea1d"
siwaa
parents: 17
diff changeset
186
0
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
diff changeset
187 # List of successive USMs
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
diff changeset
188 successive_usms_file <- ("successionPlan.csv")
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
diff changeset
189 successive_usms_tab <-
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
diff changeset
190 read.csv(file = file.path(workspace, successive_usms_file),
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
diff changeset
191 sep = ";")
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parents:
diff changeset
192
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parents:
diff changeset
193 # from succesions to simulate retrieving upcSol Cases
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194
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parents:
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195 successRef <- successive_usms_tab["Treatment"]
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parents:
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196
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parents:
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197 successRef <- successRef %>%
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parents:
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198 separate(
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parents:
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199 col = Treatment,
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parents:
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200 into = c("upc", "sol", "systeme", "rotation", "tete_rotation", "horizon"),
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parents:
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201 sep = "-",
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parents:
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202 remove = FALSE
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parents:
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203 )
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parents:
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204
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parents:
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205 successRef$upcSol <- paste0(successRef$upc, "-", successRef$sol)
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parents:
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206
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siwaa
parents:
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207 casesUpcSol <- unique(successRef$upcSol)
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parents:
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208
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siwaa
parents:
diff changeset
209 systeme <- successRef$systeme[1]
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siwaa
parents:
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210 rotation <- successRef$rotation[1]
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parents:
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211
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siwaa
parents:
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212 successive_usms_tab_split <- list()
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parents:
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213
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parents:
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214 for (j in 1:length(casesUpcSol)) {
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parents:
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215 splited <- strsplit(casesUpcSol[j], split = "-")[[1]]
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parents:
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216
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parents:
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217 upc <- splited[1]
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218
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parents:
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219 sol <- splited[2]
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parents:
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220
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parents:
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221 successive_usms_tab_split[[j]] <-
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parents:
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222 successive_usms_tab[successRef$upcSol == casesUpcSol[j],]
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parents:
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223 }
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parents:
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224
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parents:
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225 result <- foreach(j = 1:length(casesUpcSol)) %:%
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parents:
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226 foreach(
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parents:
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227 i = 1:nrow(successive_usms_tab_split[[j]]),
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parents:
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228 .options.future = list(packages =c("foreach", "SticsRFiles", "SticsOnR"))
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229
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230 ) %dordopar% {
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231
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parents:
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232 nusms <- as.numeric(successive_usms_tab_split[[j]][i, 2])
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233
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parents:
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234 vec <-
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parents:
diff changeset
235 as.character(successive_usms_tab_split[[j]][i, c(3:(2 + nusms))])
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parents:
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236
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parents:
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237 list_successive_usms <- list(vec)
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parents:
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238
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siwaa
parents:
diff changeset
239 sim_options <- stics_wrapper_options(
5
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240 stics_exe = "stics_modulo",
0
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parents:
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241 workspace = txt_path,
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242 verbose = TRUE,
5
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243 force = TRUE,
0
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parents:
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244 successive = list_successive_usms
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245 )
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parents:
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246
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parents:
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247 list_usms <- vec
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248
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parents:
diff changeset
249 cat(paste0("--> succession : ", successive_usms_tab_split[[j]][i, 1], " launched\n"))
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parents:
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250
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siwaa
parents:
diff changeset
251 return(stics_wrapper(model_options = sim_options, situation = list_usms))
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parents:
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252
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parents:
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253 }
18
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parents: 17
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254
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255 afterSimsTime <- Sys.time()
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diff changeset
256 durSimsT <-
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diff changeset
257 lubridate::as.duration(lubridate::interval(beforeSimsTime, afterSimsTime))
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258 durSimsTP <- lubridate::as.period(durSimsT)
0
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259
18
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parents: 17
diff changeset
260 sprintf(
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parents: 17
diff changeset
261 'Simulations duration: %g jour(s) %g heure(s) %g minute(s) %g seconde(s)',
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diff changeset
262 lubridate::day(durSimsTP),
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parents: 17
diff changeset
263 lubridate::hour(durSimsTP),
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parents: 17
diff changeset
264 lubridate::minute(durSimsTP),
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diff changeset
265 lubridate::second(durSimsTP)
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parents: 17
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266 )
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267 print(
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diff changeset
268 "==================================================================================="
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parents: 17
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269 )
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270
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parents: 17
diff changeset
271 #
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diff changeset
272 # Output part
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diff changeset
273 #
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274
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diff changeset
275 beforeOutputsTime <- Sys.time()
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276
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diff changeset
277 #for (j in 1:length(casesUpcSol)) {
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278
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diff changeset
279 foreach(
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diff changeset
280 j = 1:length(casesUpcSol),
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diff changeset
281 .options.future = list(packages =c("foreach", "tidyr", "arrow")
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diff changeset
282 ) %dordopar% {
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diff changeset
283
0
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parents:
diff changeset
284 splited <- strsplit(casesUpcSol[j], split = "-")[[1]]
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285
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parents:
diff changeset
286 upc <- splited[1]
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287
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parents:
diff changeset
288 sol <- splited[2]
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parents:
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289
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parents:
diff changeset
290 for (i in 1:nrow(successive_usms_tab_split[[j]])) {
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
291 #i=1
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
292 if (i == 1) {
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
293 simPCP <- result[[j]][[i]]
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
294 } else {
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
295 simPCP$sim_list <- c(simPCP$sim_list, result[[j]][[i]]$sim_list)
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
296 }
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
297
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
298 }
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
299
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
300 #agregation des sorties dans un dataframe
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
301 sim_df <-
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
302 rbindlist(simPCP$sim_list, use.names = TRUE, idcol = "usm")
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
303
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
304 #ajout des colonnes explicatives + de l'horizon temporel
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
305 sim_df <- sim_df %>%
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
306 separate(
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
307 col = usm,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
308 into = c(
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
309 "upc",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
310 "sol",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
311 "systeme",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
312 "rotation",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
313 "tete_rotation",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
314 "horizon",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
315 "annee",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
316 "culture"
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
317 ),
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
318 sep = "-",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
319 remove = FALSE
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
320 )
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
321
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
322 #sauvegarde sous la forme d'un fichier rds
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
323
15
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
324 if (baseOut) {
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
325
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
326 if (dir.exists(paste0(
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
327 workspace,
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
328 "/analyse_simulations_STICS/",
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
329 systeme,
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
330 "/",
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
331 rotation
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
332 )) == FALSE) {
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
333 dir.create(
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
334 paste0(
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
335 workspace,
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
336 "/analyse_simulations_STICS/",
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
337 systeme,
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
338 "/",
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
339 rotation
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
340 ),
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
341 recursive = TRUE
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
342 )
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
343 }
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
344
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
345 saveRDS(
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
346 sim_df,
0
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
347 paste0(
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
348 workspace,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
349 "/analyse_simulations_STICS/",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
350 systeme,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
351 "/",
15
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
352 rotation,
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
353 "/outputs-",
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
354 rotation,
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
355 "-",
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
356 upc,
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
357 "-",
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
358 sol,
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
359 "-",
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
360 scenario,
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
361 ".rds"
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
362 )
0
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
363 )
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
364 }
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
365
15
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
366 if (parquetOut) {
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
367
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
368 if (dir.exists(paste0(
0
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
369 workspace,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
370 "/analyse_simulations_STICS/",
15
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
371 "/donnees_parquet_outputs/"
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
372 )) == FALSE) {
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
373 dir.create(
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
374 paste0(
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
375 workspace,
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
376 "/analyse_simulations_STICS/",
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
377 "/donnees_parquet_outputs/"
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
378 ),
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
379 recursive = TRUE
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
380 )
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
381 }
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
382
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
383 write_parquet(
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
384 sim_df,
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
385 paste0(
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
386 workspace,
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
387 "/analyse_simulations_STICS/",
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
388 "/donnees_parquet_outputs/",
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
389 "outputs-",
17
fa4e7fd1d3f7 "planemo upload for repository https://forgemia.inra.fr/redelac commit d102b73678f095281635bf5f00d86a4a77a1ae9e"
siwaa
parents: 16
diff changeset
390 systeme,
fa4e7fd1d3f7 "planemo upload for repository https://forgemia.inra.fr/redelac commit d102b73678f095281635bf5f00d86a4a77a1ae9e"
siwaa
parents: 16
diff changeset
391 "-",
15
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
392 rotation,
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
393 "-",
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
394 upc,
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
395 "-",
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
396 sol,
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
397 "-",
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
398 scenario,
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
399 ".parquet"
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
400
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
401 ))
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
402 }
0
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
403
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
404 successive_usms_tab_split[[j]]$Treatment <- NULL
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
405 successive_usms_tab_split[[j]]$Number_USM <- NULL
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
406
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
407 list_usms <-
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
408 unlist(unname(as.list(
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
409 transpose(successive_usms_tab_split[[j]])
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
410 )))
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
411 list_usms <- list_usms[!is.na(list_usms)]
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
412 list_usms <- list_usms[list_usms != '']
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
413
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
414 list_usms_yr1 <- successive_usms_tab_split[[j]]$USM_1
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
415
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
416 for (i in 1:length(list_usms)) {
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
417 if (i == 1) {
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
418 #ajout d'une condition sur l'existence du fichier "mod_rapport.sti" pour la concatenation
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
419 #en attendant que toutes les simulations tournent correctement
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
420 #if(exists(file.path(txt_path, list_usms[i], "mod_rapport.sti"))==TRUE){
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
421 rap_1 <-
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
422 read_delim(file.path(txt_path, list_usms[i], "mod_rapport.sti"),
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
423 col_names = TRUE)
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
424 names_col <- colnames(rap_1)
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
425
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
426 rap_string <-
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
427 read_lines(file = file.path(txt_path, list_usms[i], "mod_rapport.sti"),
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
428 skip = 1)
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
429
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
430 rap <- as_tibble(rap_string) %>%
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
431 separate(col = value,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
432 sep = ";",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
433 into = names_col) %>%
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
434 mutate(USM = list_usms[i])
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
435 # }
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
436
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
437 } else {
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
438 #if (list_usms[i] %in% list_usms_yr1) {
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
439 #ajout d'une condition sur l'existence du fichier "mod_rapport.sti" pour la concatenation
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
440 #en attendant que toutes les simulations tournent correctement
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
441 #if(exists(file.path(txt_path, list_usms[i], "mod_rapport.sti"))==TRUE){
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
442 rap_string <-
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
443 read_lines(file = file.path(txt_path, list_usms[i], "mod_rapport.sti"),
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
444 skip = 1,)#}
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
445
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
446 # } else {
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
447 #ajout d'une condition sur l'existence du fichier "mod_rapport.sti" pour la concatenation
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
448 #en attendant que toutes les simulations tournent correctement
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
449 #if(exists(file.path(txt_path, list_usms[i], "mod_rapport.sti"))==TRUE){
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
450 # rap_string <-
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
451 # read_file(file = file.path(txt_path, list_usms[i], "mod_rapport.sti"))#}
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
452 # }
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
453 rap_i <- as_tibble(rap_string) %>%
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
454 separate(col = value,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
455 sep = ";",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
456 into = names_col) %>%
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
457 mutate(USM = list_usms[i])
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
458
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
459 rap <- bind_rows(rap, rap_i)
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
460
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
461 }
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
462
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
463 }
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
464 rm(rap_1, names_col, rap_string, rap_i)
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
465
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
466 rap <- rap %>%
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
467 select(USM, everything()) %>%
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
468 mutate(P_usm = str_replace_all(P_usm, " ", "")) %>%
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
469 mutate(wlieu = str_replace_all(wlieu, " ", "")) %>%
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
470 mutate(stade = str_replace_all(stade, " ", "")) %>%
5
e0d592bb516e "planemo upload for repository https://forgemia.inra.fr/redelac commit 1b434482800e773a592b5fc6f472e7df465e91ce"
siwaa
parents: 1
diff changeset
471 mutate(nomversion = str_replace_all(P_usm, " ", "")) %>%
e0d592bb516e "planemo upload for repository https://forgemia.inra.fr/redelac commit 1b434482800e773a592b5fc6f472e7df465e91ce"
siwaa
parents: 1
diff changeset
472 mutate(across(4:10, as.numeric)) %>%
e0d592bb516e "planemo upload for repository https://forgemia.inra.fr/redelac commit 1b434482800e773a592b5fc6f472e7df465e91ce"
siwaa
parents: 1
diff changeset
473 mutate(across(14:ncol(rap), as.numeric)) %>%
0
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
474 separate(
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
475 col = USM,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
476 into = c(
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
477 "upc",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
478 "sol",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
479 "systeme",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
480 "rotation",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
481 "tete_rotation",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
482 "horizon",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
483 "annee",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
484 "culture"
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
485 ),
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
486 sep = "-",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
487 remove = FALSE
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
488 )
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
489
15
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
490 if (baseOut) {
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
491
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
492 write_delim(
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
493 x = rap,
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
494 file = paste0(
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
495 workspace,
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
496 "/analyse_simulations_STICS/",
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
497 systeme,
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
498 "/",
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
499 rotation,
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
500 "/report-",
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
501 rotation,
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
502 "-",
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
503 upc,
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
504 "-",
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
505 sol,
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
506 "-",
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
507 scenario,
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
508 ".csv"
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
509 ),
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
510 delim = ";"
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
511 )
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
512 }
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
513
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
514 if (parquetOut) {
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
515
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
516 if (dir.exists(paste0(
0
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
517 workspace,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
518 "/analyse_simulations_STICS/",
15
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
519 "/donnees_parquet_report/"
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
520 )) == FALSE) {
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
521 dir.create(
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
522 paste0(
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
523 workspace,
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
524 "/analyse_simulations_STICS/",
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
525 "/donnees_parquet_report/"
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
526 ),
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
527 recursive = TRUE
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
528 )
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
529 }
0
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
530
15
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
531 write_parquet(
16
816fbce5cf58 "planemo upload for repository https://forgemia.inra.fr/redelac commit cfb92a37e4cb2054f9d8caa5bd8f46c9f4a7be68"
siwaa
parents: 15
diff changeset
532 rap,
15
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
533 paste0(
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
534 workspace,
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
535 "/analyse_simulations_STICS/",
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
536 "/donnees_parquet_report/",
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
537 "report-",
17
fa4e7fd1d3f7 "planemo upload for repository https://forgemia.inra.fr/redelac commit d102b73678f095281635bf5f00d86a4a77a1ae9e"
siwaa
parents: 16
diff changeset
538 systeme,
fa4e7fd1d3f7 "planemo upload for repository https://forgemia.inra.fr/redelac commit d102b73678f095281635bf5f00d86a4a77a1ae9e"
siwaa
parents: 16
diff changeset
539 "-",
15
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
540 rotation,
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
541 "-",
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
542 upc,
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
543 "-",
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
544 sol,
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
545 "-",
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
546 scenario,
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
547 ".parquet"
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
548
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
549 ))
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
550 }
18
8293d67cd1a9 "planemo upload for repository https://forgemia.inra.fr/redelac commit b972382172a3923486a799d46efe363d21e8ea1d"
siwaa
parents: 17
diff changeset
551 }
8293d67cd1a9 "planemo upload for repository https://forgemia.inra.fr/redelac commit b972382172a3923486a799d46efe363d21e8ea1d"
siwaa
parents: 17
diff changeset
552
8293d67cd1a9 "planemo upload for repository https://forgemia.inra.fr/redelac commit b972382172a3923486a799d46efe363d21e8ea1d"
siwaa
parents: 17
diff changeset
553 afterOutputsTime <- Sys.time()
8293d67cd1a9 "planemo upload for repository https://forgemia.inra.fr/redelac commit b972382172a3923486a799d46efe363d21e8ea1d"
siwaa
parents: 17
diff changeset
554 durOutT <-
8293d67cd1a9 "planemo upload for repository https://forgemia.inra.fr/redelac commit b972382172a3923486a799d46efe363d21e8ea1d"
siwaa
parents: 17
diff changeset
555 lubridate::as.duration(lubridate::interval(beforeOutputsTime, afterOutputsTime))
8293d67cd1a9 "planemo upload for repository https://forgemia.inra.fr/redelac commit b972382172a3923486a799d46efe363d21e8ea1d"
siwaa
parents: 17
diff changeset
556 durOutTP <- lubridate::as.period(durOutT)
8293d67cd1a9 "planemo upload for repository https://forgemia.inra.fr/redelac commit b972382172a3923486a799d46efe363d21e8ea1d"
siwaa
parents: 17
diff changeset
557
8293d67cd1a9 "planemo upload for repository https://forgemia.inra.fr/redelac commit b972382172a3923486a799d46efe363d21e8ea1d"
siwaa
parents: 17
diff changeset
558 sprintf(
8293d67cd1a9 "planemo upload for repository https://forgemia.inra.fr/redelac commit b972382172a3923486a799d46efe363d21e8ea1d"
siwaa
parents: 17
diff changeset
559 'outputs generating duration: %g jour(s) %g heure(s) %g minute(s) %g seconde(s)',
8293d67cd1a9 "planemo upload for repository https://forgemia.inra.fr/redelac commit b972382172a3923486a799d46efe363d21e8ea1d"
siwaa
parents: 17
diff changeset
560 lubridate::day(durOutTP),
8293d67cd1a9 "planemo upload for repository https://forgemia.inra.fr/redelac commit b972382172a3923486a799d46efe363d21e8ea1d"
siwaa
parents: 17
diff changeset
561 lubridate::hour(durOutTP),
8293d67cd1a9 "planemo upload for repository https://forgemia.inra.fr/redelac commit b972382172a3923486a799d46efe363d21e8ea1d"
siwaa
parents: 17
diff changeset
562 lubridate::minute(durOutTP),
8293d67cd1a9 "planemo upload for repository https://forgemia.inra.fr/redelac commit b972382172a3923486a799d46efe363d21e8ea1d"
siwaa
parents: 17
diff changeset
563 lubridate::second(durOutTP)
8293d67cd1a9 "planemo upload for repository https://forgemia.inra.fr/redelac commit b972382172a3923486a799d46efe363d21e8ea1d"
siwaa
parents: 17
diff changeset
564 )
8293d67cd1a9 "planemo upload for repository https://forgemia.inra.fr/redelac commit b972382172a3923486a799d46efe363d21e8ea1d"
siwaa
parents: 17
diff changeset
565 print(
8293d67cd1a9 "planemo upload for repository https://forgemia.inra.fr/redelac commit b972382172a3923486a799d46efe363d21e8ea1d"
siwaa
parents: 17
diff changeset
566 "==================================================================================="
8293d67cd1a9 "planemo upload for repository https://forgemia.inra.fr/redelac commit b972382172a3923486a799d46efe363d21e8ea1d"
siwaa
parents: 17
diff changeset
567 )