Mercurial > repos > siwaa > redelac_stics_g

comparison 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
comparison
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5:4f8d87b9c246 6:bb1ac57f8545
10 USMsFile <- "USMs.csv" 10 USMsFile <- "USMs.csv"
11 TecFile <- "Tec.csv" 11 TecFile <- "Tec.csv"
12 IniFile <- "Ini.csv" 12 IniFile <- "Ini.csv"
13 StationFile <- "Station.csv" 13 StationFile <- "Station.csv"
14 14
15 # Generate STICS xml files------------------------------------------------------------------------------ 15 # USMs file loading
16
17 # USMs file
18 usms_param <- read_params_table(file.path(workspace, USMsFile)) %>% 16 usms_param <- read_params_table(file.path(workspace, USMsFile)) %>%
19 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) 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)
20 18
21 # Tec files 19 # Tec files loading and generating xml
22 tec_param <- read_params_table(file.path(workspace, TecFile)) %>% 20 tec_param <- read_params_table(file.path(workspace, TecFile))
23 select(!c(annee, date_min, date_max, Date_res_1, Date_res_2, Type_res_1, Type_res_2, Date_trav_1, Date_trav_2, Date_trav_3, Type_trav_1, Type_trav_2 ,Type_trav_3, plante_sem, date_sem, starts_with("nom_vari"), date_ferti_1, date_ferti_2, date_ferti_3, type_eng_1, type_eng_2, type_eng_3, date_rec, date_des, juleclair, nbinfloecl)) 21 columnToRemove <- names(tec_param[grep("juleclair|nbinfloecl", names(tec_param))])
22 columnToKeep <- names(tec_param)[names(tec_param) %in% columnToRemove == FALSE]
23 tec_param <- subset(tec_param, select=columnToKeep)
24 gen_tec_xml(param_df = tec_param, out_dir = workspace) 24 gen_tec_xml(param_df = tec_param, out_dir = workspace)
25 25
26 # Ini files 26 # Ini files loading and generating xml
27 ini_param <- read_params_table(file.path(workspace, IniFile)) 27 ini_param <- read_params_table(file.path(workspace, IniFile))
28 gen_ini_xml(param_df = ini_param, out_dir = workspace) 28 gen_ini_xml(param_df = ini_param, out_dir = workspace)
29 29
30 # Sta files 30 # Station files loading and generating xml
31 sta_param <- read_params_table(file.path(workspace, StationFile)) 31 sta_param <- read_params_table(file.path(workspace, StationFile))
32 gen_sta_xml(param_df = sta_param, out_dir = workspace) 32 gen_sta_xml(param_df = sta_param, out_dir = workspace)
33 33
34 # Generate STICS txt files------------------------------------------------------------------------------
35 # List of USMs
36 34
37 ### Generate txt files into individual folders 35 # looping on USMs
38
39 for(i in 1:nrow(usms_param)) { 36 for(i in 1:nrow(usms_param)) {
40 row <- usms_param[i,] 37 row <- usms_param[i,]
41 # do stuff with row 38
42 39 # generating xml
43 gen_usms_xml(file = file.path(workspace, "usms.xml"), param_df = row) 40 gen_usms_xml(file = file.path(workspace, "usms.xml"), param_df = row)
44 41
42 # generating txt folder
45 gen_usms_xml2txt(javastics = javastics_path, 43 gen_usms_xml2txt(javastics = javastics_path,
46 workspace = workspace, 44 workspace = workspace,
47 out_dir = txt_path, 45 out_dir = txt_path,
48 verbose = TRUE) 46 verbose = TRUE)
49 } 47 }