Mercurial > repos > siwaa > redelac_stics_g

annotate redelacSticsInputGenerator.R @ 10:f707c2fb725b draft

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"planemo upload for repository https://forgemia.inra.fr/redelac commit af2d1fcb63a2ae897e02f11e82cc76c4f6e8ca5e"
author siwaa
date Mon, 02 Oct 2023 13:49:57 +0000
parents 2a6d7d053ba7
children 812bb8097dac
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1 library(SticsRFiles)
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2 library(dplyr)
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3 library(lubridate)
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4 library(parallel)
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5 library(doParallel)
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7 sessionInfo()
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9 startTime <- Sys.time()
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11 workspace <- paste0(getwd(), "/WS")
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12 javastics_path <- getwd()
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14 txt_path <- paste0(getwd(), "/WS/txt_files")
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15 dir.create(txt_path, recursive = T)
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17 USMsFile <- "USMs.csv"
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18 TecFile <- "Tec.csv"
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19 IniFile <- "Ini.csv"
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20 StationFile <- "Station.csv"
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21
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22 args = commandArgs(trailingOnly = TRUE)
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24 genUSMsXmlOneAfterOther <- (args[1] == "usmx_one_after_other")
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25 parallel <- (args[2] == "parallel")
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26 nbSlots <- as.integer(args[3])
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28 # USMs file loading
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30 usms_param <- read_params_table(file.path(workspace, USMsFile)) %>%
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31 select(
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32 usm_name,
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33 datedebut,
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34 datefin,
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35 finit,
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36 nomsol,
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37 fstation,
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38 fclim1,
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39 fclim2,
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40 culturean,
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41 nbplantes,
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42 codesimul,
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43 fplt_1,
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44 ftec_1,
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45 flai_1,
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46 fplt_2,
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47 ftec_2,
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48 flai_2
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49 )
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51 # Tec files loading and generating xml
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53 tec_param <- read_params_table(file.path(workspace, TecFile))
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54 columnToRemove <-
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55 names(tec_param[grep("juleclair|nbinfloecl", names(tec_param))])
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56 columnToKeep <-
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57 names(tec_param)[names(tec_param) %in% columnToRemove == FALSE]
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59 tec_param <- subset(tec_param, select = columnToKeep)
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61 gen_tec_xml(param_df = tec_param, out_dir = workspace)
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63 # Ini files loading and generating xml
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65 ini_param <- read_params_table(file.path(workspace, IniFile))
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67 gen_ini_xml(param_df = ini_param, out_dir = workspace)
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69 # Station files loading and generating xml
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71 sta_param <- read_params_table(file.path(workspace, StationFile))
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73 gen_sta_xml(param_df = sta_param, out_dir = workspace)
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74
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75 if (genUSMsXmlOneAfterOther) {
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76
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77 durGenX <- lubridate::as.duration(0)
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78 durGenT <- lubridate::as.duration(0)
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79
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80 if (parallel) {
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81 cl <- makeCluster(nbSlots)
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82 print(cl)
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83 registerDoParallel(cl)
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84 `%dordopar%` <- `%dopar%`
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85 } else {
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86 `%dordopar%` <- `%do%`
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87 }
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88
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89 # looping on USMs
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90 loopRes <- foreach::foreach(i = 1:nrow(usms_param),
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91 .packages = c("SticsRFiles", "lubridate")) %dordopar% {
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92
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93 beforeGenXmlTimeI <- Sys.time()
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94
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95 usmxFileName = paste0("usms", as.character(i) , ".xml")
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96
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97 usmxFilePath = file.path(workspace, usmxFileName)
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98
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99 gen_usms_xml(file = usmxFilePath,
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100 param_df = usms_param[i, ])
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101
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102 afterGenXmlTimeI <- Sys.time()
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103 durGenXI <-
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104 lubridate::as.duration(lubridate::interval(beforeGenXmlTimeI,
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105 afterGenXmlTimeI))
9
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106
7
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107 # one after the other generating txt folder
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108
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109 beforeGenTxtTimeI <- Sys.time()
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110
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111 gen_usms_xml2txt(
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112 usms_file = usmxFileName,
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113 javastics = javastics_path,
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114 workspace = workspace,
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115 out_dir = txt_path,
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116 verbose = TRUE
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117 )
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118
7
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119 afterGenTxtTimeI <- Sys.time()
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120 durGenTI <-
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121 lubridate::as.duration(lubridate::interval(beforeGenTxtTimeI,
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122 afterGenTxtTimeI))
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123
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124 return(c(durGenXI, durGenTI))
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125 }
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126
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127 if (parallel) stopCluster(cl)
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128
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129 durDS <- as.data.frame(do.call(rbind, loopRes))
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130 durGenX <- sum(durDS[1])
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131 durGenT <- sum(durDS[2])
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132
7
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133 } else {
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134
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135 beforeGenXmlTime <- Sys.time()
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136
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137 gen_usms_xml(file = file.path(workspace, "usms.xml"),
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138 param_df = usms_param)
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139
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140 afterGenXmlTime <- Sys.time()
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141 durGenX <-
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142 lubridate::as.duration(lubridate::interval(beforeGenXmlTime,
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143 afterGenXmlTime))
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144
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145 beforeGenTxtTime <- Sys.time()
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146
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147 gen_usms_xml2txt(
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148 javastics = javastics_path,
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149 workspace = workspace,
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150 out_dir = txt_path,
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151 verbose = TRUE
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152 )
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153
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154 afterGenTxtTime <- Sys.time()
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155 durGenT <-
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156 lubridate::as.duration(lubridate::interval(beforeGenTxtTime,
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157 afterGenTxtTime))
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158
7
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159 }
5
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160
7
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161 endTime <- Sys.time()
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162
7
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163 dur <-
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164 lubridate::as.period(lubridate::as.duration(lubridate::interval(startTime, endTime)))
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165 durGenXP <- lubridate::as.period(durGenX)
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166 durGenTP <- lubridate::as.period(durGenT)
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167
9
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168 print("REDELACSticsInputGenerator Report")
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169 print("=================================")
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170 print(paste0("number of usms: ", nrow(usms_param)))
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171 print(paste("usms.xml one after the other:", genUSMsXmlOneAfterOther))
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172
7
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173 sprintf(
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174 'overall duration: %g jour(s) %g heure(s) %g minute(s) %g seconde(s)',
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175 lubridate::day(dur),
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176 lubridate::hour(dur),
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177 lubridate::minute(dur),
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178 lubridate::second(dur))
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179
7
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180 sprintf(
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181 'inside gen_usms_xml duration: %g jour(s) %g heure(s) %g minute(s) %g seconde(s)',
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182 lubridate::day(durGenXP),
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183 lubridate::hour(durGenXP),
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184 lubridate::minute(durGenXP),
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185 lubridate::second(durGenXP))
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186
7
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187 sprintf(
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188 'inside gen_usms_xml2txt duration: %g jour(s) %g heure(s) %g minute(s) %g seconde(s)',
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189 lubridate::day(durGenTP),
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190 lubridate::hour(durGenTP),
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191 lubridate::minute(durGenTP),
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192 lubridate::second(durGenTP))
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193 print("===================================================================================")