Mercurial > repos > siwaa > redelac_stics_g

annotate redelacSticsInputGenerator.R @ 14:812bb8097dac draft

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"planemo upload for repository https://forgemia.inra.fr/redelac commit d16b9ecdb4dd51b69a6aaa4ab298b82455fe0267"
author siwaa
date Tue, 12 Dec 2023 10:38:20 +0000
parents f707c2fb725b
children 413cec4dfe5f
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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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8 sessionInfo()
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10 startTime <- Sys.time()
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12 workspace <- paste0(getwd(), "/WS")
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13 javastics_path <- getwd()
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15 txt_path <- paste0(getwd(), "/WS/txt_files")
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16 dir.create(txt_path, recursive = T)
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18 USMsFile <- "USMs.csv"
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19 TecFile <- "Tec.csv"
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20 IniFile <- "Ini.csv"
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21 StationFile <- "Station.csv"
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22
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23 args = commandArgs(trailingOnly = TRUE)
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25 redelac <- (args[1] == "optim")
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26 parallel <- (args[2] == "parallel")
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27 print(paste("parallel:", parallel, args[2]))
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28 nbSlots <- as.integer(args[3])
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29 print(paste("nbslots:", nbSlots))
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31 # USMs file loading
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33 usms_param <- read_params_table(file.path(workspace, USMsFile)) %>%
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34 select(
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35 usm_name,
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36 datedebut,
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37 datefin,
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38 finit,
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39 nomsol,
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40 fstation,
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41 fclim1,
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42 fclim2,
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43 culturean,
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44 nbplantes,
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45 codesimul,
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46 fplt_1,
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47 ftec_1,
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48 flai_1,
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49 fplt_2,
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50 ftec_2,
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51 flai_2
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52 )
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54 # Tec files loading and generating xml
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56 tec_param <- read_params_table(file.path(workspace, TecFile))
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57 columnToRemove <-
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58 names(tec_param[grep("juleclair|nbinfloecl", names(tec_param))])
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59 columnToKeep <-
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60 names(tec_param)[names(tec_param) %in% columnToRemove == FALSE]
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62 tec_param <- subset(tec_param, select = columnToKeep)
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64 gen_tec_xml(param_df = tec_param, out_dir = workspace)
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66 # Ini files loading and generating xml
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68 ini_param <- read_params_table(file.path(workspace, IniFile))
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70 gen_ini_xml(param_df = ini_param, out_dir = workspace)
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72 # Station files loading and generating xml
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74 sta_param <- read_params_table(file.path(workspace, StationFile))
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76 gen_sta_xml(param_df = sta_param, out_dir = workspace)
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78 if (parallel) {
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79 doFuture::registerDoFuture()
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80 future::plan(multisession, workers = nbSlots)
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81 }
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83 beforeGenXmlTime <- Sys.time()
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84
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85 gen_usms_xml(file = file.path(workspace, "usms.xml"),
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86 param_df = usms_param)
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87
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88 afterGenXmlTime <- Sys.time()
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89 durGenX <-
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90 lubridate::as.duration(lubridate::interval(beforeGenXmlTime,
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91 afterGenXmlTime))
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92 beforeGenTxtTime <- Sys.time()
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93
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94 gen_usms_xml2txt(
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95 javastics = javastics_path,
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96 workspace = workspace,
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97 out_dir = txt_path,
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98 usms_file = "usms.xml",
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99 redelac = redelac,
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100 parallel = parallel,
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101 verbose = FALSE
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102 )
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103
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104 afterGenTxtTime <- Sys.time()
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105 durGenT <-
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106 lubridate::as.duration(lubridate::interval(beforeGenTxtTime,
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107 afterGenTxtTime))
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108
7
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109 endTime <- Sys.time()
9
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110
7
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111 dur <-
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112 lubridate::as.period(lubridate::as.duration(lubridate::interval(startTime, endTime)))
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113 durGenXP <- lubridate::as.period(durGenX)
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114 durGenTP <- lubridate::as.period(durGenT)
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115
9
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116 print("REDELACSticsInputGenerator Report")
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117 print("=================================")
14
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118 print(paste("number of usms: ", nrow(usms_param)))
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119 print(paste("redelac optimization:", redelac))
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120 print(paste("process in parallel:", parallel))
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121 print(paste("nbslots:", nbSlots))
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122
7
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123 sprintf(
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124 'overall duration: %g jour(s) %g heure(s) %g minute(s) %g seconde(s)',
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125 lubridate::day(dur),
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126 lubridate::hour(dur),
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127 lubridate::minute(dur),
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128 lubridate::second(dur))
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129
7
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130 sprintf(
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131 'inside gen_usms_xml duration: %g jour(s) %g heure(s) %g minute(s) %g seconde(s)',
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132 lubridate::day(durGenXP),
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133 lubridate::hour(durGenXP),
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134 lubridate::minute(durGenXP),
9
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135 lubridate::second(durGenXP))
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136
7
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137 sprintf(
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138 'inside gen_usms_xml2txt duration: %g jour(s) %g heure(s) %g minute(s) %g seconde(s)',
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139 lubridate::day(durGenTP),
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140 lubridate::hour(durGenTP),
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141 lubridate::minute(durGenTP),
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142 lubridate::second(durGenTP))
10
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143 print("===================================================================================")