Mercurial > repos > siwaa > redelac_stics_g

annotate redelacSticsInputGenerator.R @ 16:f2fe11a20371 draft

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"planemo upload for repository https://forgemia.inra.fr/redelac commit 27e73ca1d96c6eea20bcad339e074aab0d206d4c"
author siwaa
date Mon, 22 Jan 2024 15:15:07 +0000
parents 413cec4dfe5f
children 4d0807472ad3
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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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6 library(doFuture)
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7 library(stringr)
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9 sessionInfo()
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11 startTime <- Sys.time()
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13 workspace <- paste0(getwd(), "/WS")
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14 javastics_path <- getwd()
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16 txt_path <- paste0(getwd(), "/WS/txt_files")
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17 dir.create(txt_path, recursive = T)
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19 USMsFile <- "USMs.csv"
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20 TecFile <- "Tec.csv"
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21 IniFile <- "Ini.csv"
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22 StationFile <- "Station.csv"
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23
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24 args = commandArgs(trailingOnly = TRUE)
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26 redelac <- (args[1] == "optim")
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27 parallel <- (args[2] == "parallel")
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28 print(paste("parallel:", parallel, args[2]))
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29 nbSlots <- as.integer(args[3])
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30 print(paste("nbslots:", nbSlots))
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32 # USMs file loading
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34 usms_param <- read_params_table(file.path(workspace, USMsFile)) %>%
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35 select(
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36 usm_name,
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37 datedebut,
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38 datefin,
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39 finit,
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40 nomsol,
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41 fstation,
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42 fclim1,
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43 fclim2,
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44 culturean,
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45 nbplantes,
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46 codesimul,
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47 fplt_1,
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48 ftec_1,
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49 flai_1,
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50 fplt_2,
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51 ftec_2,
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52 flai_2
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53 )
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55 # Tec files loading and generating xml
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57 tec_param <- read_params_table(file.path(workspace, TecFile))
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58 columnToRemove <-
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59 names(tec_param[grep("juleclair|nbinfloecl", names(tec_param))])
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60 columnToKeep <-
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61 names(tec_param)[names(tec_param) %in% columnToRemove == FALSE]
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63 tec_param <- subset(tec_param, select = columnToKeep)
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65 gen_tec_xml(param_df = tec_param, out_dir = workspace)
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67 # Ini files loading and generating xml
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69 ini_param <- read_params_table(file.path(workspace, IniFile))
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71 gen_ini_xml(param_df = ini_param, out_dir = workspace)
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73 # Station files loading and generating xml
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75 sta_param <- read_params_table(file.path(workspace, StationFile))
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77 gen_sta_xml(param_df = sta_param, out_dir = workspace)
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79 if (parallel) {
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80 doFuture::registerDoFuture()
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82 future::plan(multicore, workers = nbSlots)
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83 }
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85 beforeGenXmlTime <- Sys.time()
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87 #gen_usms_xml(file = file.path(workspace, "usms.xml"),
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88 # param_df = usms_param)
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89
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90 chunckSize <- 1000
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91 nbUSMs <- nrow(usms_param)
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93 ids <- seq(1, nbUSMs, chunckSize)
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94
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95 foreach (i = ids,
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96 .options.future = list(packages = c("foreach", "SticsRFiles"))) %dofuture% {
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97 gen_usms_xml(file = file.path(workspace, paste0("usms__", i, ".xml")),
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98 param_df = usms_param[i:min(i + chunckSize - 1, nbUSMs),])
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99 }
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101 afterGenXmlTime <- Sys.time()
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102 durGenX <-
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103 lubridate::as.duration(lubridate::interval(beforeGenXmlTime,
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104 afterGenXmlTime))
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105
14
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106 beforeGenTxtTime <- Sys.time()
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107
15
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108 foreach (i = ids,
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109 .options.future = list(packages = c("foreach", "SticsRFiles"))) %dofuture% {
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110 gen_usms_xml2txt(
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111 javastics = javastics_path,
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112 workspace = workspace,
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113 out_dir = txt_path,
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114 usms_file = paste0("usms__", i, ".xml"),
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115 redelac = redelac,
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116 parallel = parallel,
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117 verbose = FALSE
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118 )
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119 }
14
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120
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121 afterGenTxtTime <- Sys.time()
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122 durGenT <-
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123 lubridate::as.duration(lubridate::interval(beforeGenTxtTime, afterGenTxtTime))
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124
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125 afterGenTxtTime <- Sys.time()
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126 durGenT <-
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127 lubridate::as.duration(lubridate::interval(beforeGenTxtTime, afterGenTxtTime))
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128
7
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129 endTime <- Sys.time()
9
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130
7
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131 dur <-
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132 lubridate::as.period(lubridate::as.duration(lubridate::interval(startTime, endTime)))
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133 durGenXP <- lubridate::as.period(durGenX)
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134 durGenTP <- lubridate::as.period(durGenT)
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135
9
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136 print("REDELACSticsInputGenerator Report")
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137 print("=================================")
14
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138 print(paste("number of usms: ", nrow(usms_param)))
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139 print(paste("redelac optimization:", redelac))
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140 print(paste("process in parallel:", parallel))
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141 print(paste("nbslots:", nbSlots))
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142
7
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143 sprintf(
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144 'overall duration: %g jour(s) %g heure(s) %g minute(s) %g seconde(s)',
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145 lubridate::day(dur),
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146 lubridate::hour(dur),
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147 lubridate::minute(dur),
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148 lubridate::second(dur)
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149 )
9
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150
7
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151 sprintf(
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152 'inside gen_usms_xml duration: %g jour(s) %g heure(s) %g minute(s) %g seconde(s)',
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153 lubridate::day(durGenXP),
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154 lubridate::hour(durGenXP),
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155 lubridate::minute(durGenXP),
15
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156 lubridate::second(durGenXP)
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157 )
9
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158
7
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159 sprintf(
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160 'inside gen_usms_xml2txt duration: %g jour(s) %g heure(s) %g minute(s) %g seconde(s)',
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161 lubridate::day(durGenTP),
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162 lubridate::hour(durGenTP),
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163 lubridate::minute(durGenTP),
15
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164 lubridate::second(durGenTP)
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165 )
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166 print(
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167 "==================================================================================="
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168 )