Mercurial > repos > siwaa > redelac_stics_g

comparison 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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-1:000000000000 0:c7d424481b03
1 library(SticsRFiles)
2 library(dplyr)
3
4 workspace <- paste0(getwd(), "/WS")
5 javastics_path <- getwd()
6
7 txt_path <- paste0(getwd(), "/WS/txt_files")
8 dir.create(txt_path,recursive = T)
9
10 gen_usms_xml2txt(javastics = javastics_path,
11 workspace = workspace,
12 out_dir = txt_path,
13 check = FALSE)
14
15 USMsFile <- "USMs.csv"
16 TecFile <- "Tec.csv"
17 IniFile <- "Ini.csv"
18 StationFile <- "Station.csv"
19
20 # Generate STICS xml files------------------------------------------------------------------------------
21
22 # USMs file
23 usms_param <- read_params_table(file.path(workspace, USMsFile)) %>%
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)
25 gen_usms_xml(file = file.path(workspace, "usms.xml"), param_df = usms_param)
26
27 # Tec files
28 tec_param <- read_params_table(file.path(workspace, TecFile))
29 gen_tec_xml(param_table = tec_param, out_path = workspace)
30
31 # Ini files
32 ini_param <- read_params_table(file.path(workspace, IniFile))
33 gen_ini_xml(param_df = ini_param, out_dir = workspace)
34
35 # Sta files
36 sta_param <- read_params_table(file.path(workspace, StationFile))
37 gen_sta_xml(param_df = sta_param, out_dir = workspace)
38
39 # Generate STICS txt files------------------------------------------------------------------------------
40 # List of USMs
41 list_usms <- SticsRFiles::get_usms_list(file = file.path(workspace,"usms.xml"))
42
43 ### Generate txt files into individual folders
44
45 # generate text files
46 gen_usms_xml2txt(javastics = javastics_path,
47 workspace = workspace,
48 out_dir = txt_path,
49 verbose = TRUE,
50 usm = list_usms,
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)
52