Mercurial > repos > siwaa > redelac_stics_g

annotate redelacSticsInputGenerator.R @ 6:bb1ac57f8545 draft

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"planemo upload for repository https://forgemia.inra.fr/redelac commit 5c06627ff4fa4a31f7fae2cd625f32a29ed2d773"
author siwaa
date Fri, 07 Jul 2023 10:19:22 +0000
parents 4f8d87b9c246
children fb6f7d60508d
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c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
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1 library(SticsRFiles)
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2 library(dplyr)
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4 workspace <- paste0(getwd(), "/WS")
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5 javastics_path <- getwd()
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7 txt_path <- paste0(getwd(), "/WS/txt_files")
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8 dir.create(txt_path,recursive = T)
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10 USMsFile <- "USMs.csv"
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11 TecFile <- "Tec.csv"
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12 IniFile <- "Ini.csv"
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13 StationFile <- "Station.csv"
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15 # USMs file loading
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16 usms_param <- read_params_table(file.path(workspace, USMsFile)) %>%
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17 select(usm_name,datedebut,datefin,finit,nomsol,fstation,fclim1,fclim2,culturean,nbplantes,codesimul,fplt_1,ftec_1,flai_1,fplt_2,ftec_2,flai_2)
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19 # Tec files loading and generating xml
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20 tec_param <- read_params_table(file.path(workspace, TecFile))
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21 columnToRemove <- names(tec_param[grep("juleclair|nbinfloecl", names(tec_param))])
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22 columnToKeep <- names(tec_param)[names(tec_param) %in% columnToRemove == FALSE]
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23 tec_param <- subset(tec_param, select=columnToKeep)
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24 gen_tec_xml(param_df = tec_param, out_dir = workspace)
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26 # Ini files loading and generating xml
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27 ini_param <- read_params_table(file.path(workspace, IniFile))
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28 gen_ini_xml(param_df = ini_param, out_dir = workspace)
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30 # Station files loading and generating xml
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31 sta_param <- read_params_table(file.path(workspace, StationFile))
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32 gen_sta_xml(param_df = sta_param, out_dir = workspace)
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35 # looping on USMs
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36 for(i in 1:nrow(usms_param)) {
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37 row <- usms_param[i,]
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39 # generating xml
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40 gen_usms_xml(file = file.path(workspace, "usms.xml"), param_df = row)
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42 # generating txt folder
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43 gen_usms_xml2txt(javastics = javastics_path,
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44 workspace = workspace,
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45 out_dir = txt_path,
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46 verbose = TRUE)
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47 }
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