Mercurial > repos > siwaa > redelac_stics_g

annotate redelacSticsInputGenerator.R @ 0:c7d424481b03 draft

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"planemo upload for repository https://forgemia.inra.fr/redelac"
author siwaa
date Wed, 07 Jun 2023 06:08:27 +0000
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children e344100f3354
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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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3
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4 workspace <- paste0(getwd(), "/WS")
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5 javastics_path <- getwd()
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6
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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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9
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10 gen_usms_xml2txt(javastics = javastics_path,
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11 workspace = workspace,
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12 out_dir = txt_path,
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13 check = FALSE)
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14
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15 USMsFile <- "USMs.csv"
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16 TecFile <- "Tec.csv"
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17 IniFile <- "Ini.csv"
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18 StationFile <- "Station.csv"
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20 # Generate STICS xml files------------------------------------------------------------------------------
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22 # USMs file
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23 usms_param <- read_params_table(file.path(workspace, USMsFile)) %>%
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
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24 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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25 gen_usms_xml(file = file.path(workspace, "usms.xml"), param_df = usms_param)
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27 # Tec files
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28 tec_param <- read_params_table(file.path(workspace, TecFile))
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29 gen_tec_xml(param_table = tec_param, out_path = workspace)
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30
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31 # Ini files
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32 ini_param <- read_params_table(file.path(workspace, IniFile))
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33 gen_ini_xml(param_df = ini_param, out_dir = workspace)
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34
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35 # Sta files
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36 sta_param <- read_params_table(file.path(workspace, StationFile))
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37 gen_sta_xml(param_df = sta_param, out_dir = workspace)
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39 # Generate STICS txt files------------------------------------------------------------------------------
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40 # List of USMs
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41 list_usms <- SticsRFiles::get_usms_list(file = file.path(workspace,"usms.xml"))
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43 ### Generate txt files into individual folders
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44
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45 # generate text files
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46 gen_usms_xml2txt(javastics = javastics_path,
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47 workspace = workspace,
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48 out_dir = txt_path,
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49 verbose = TRUE,
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50 usm = list_usms,
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51 check=FALSE) #je mets l'option a FALSE car sinon j'ai soit disant des fichiers climatiques manquants du type 14050.198,14050.199,14050.2 (pas de lecture des z?ros)
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