Mercurial > repos > siwaa > redelac_stics_g

comparison redelacSticsInputGenerator.R @ 7:fb6f7d60508d draft

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"planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
author siwaa
date Thu, 20 Jul 2023 16:18:59 +0000
parents bb1ac57f8545
children 2a6d7d053ba7
comparison
equal deleted inserted replaced
6:bb1ac57f8545 7:fb6f7d60508d
1 library(SticsRFiles) 1 library(SticsRFiles)
2 library(dplyr) 2 library(dplyr)
3 library(lubridate)
4
5
6 startTime <- Sys.time()
3 7
4 workspace <- paste0(getwd(), "/WS") 8 workspace <- paste0(getwd(), "/WS")
5 javastics_path <- getwd() 9 javastics_path <- getwd()
6 10
7 txt_path <- paste0(getwd(), "/WS/txt_files") 11 txt_path <- paste0(getwd(), "/WS/txt_files")
8 dir.create(txt_path,recursive = T) 12 dir.create(txt_path, recursive = T)
9 13
10 USMsFile <- "USMs.csv" 14 USMsFile <- "USMs.csv"
11 TecFile <- "Tec.csv" 15 TecFile <- "Tec.csv"
12 IniFile <- "Ini.csv" 16 IniFile <- "Ini.csv"
13 StationFile <- "Station.csv" 17 StationFile <- "Station.csv"
14 18
19 args = commandArgs(trailingOnly = TRUE)
20
21 genUSMsXmlOneAfterOther <- (args[1] == "usmx_one_after_other")
22
15 # USMs file loading 23 # USMs file loading
24
16 usms_param <- read_params_table(file.path(workspace, USMsFile)) %>% 25 usms_param <- read_params_table(file.path(workspace, USMsFile)) %>%
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) 26 select(
27 usm_name,
28 datedebut,
29 datefin,
30 finit,
31 nomsol,
32 fstation,
33 fclim1,
34 fclim2,
35 culturean,
36 nbplantes,
37 codesimul,
38 fplt_1,
39 ftec_1,
40 flai_1,
41 fplt_2,
42 ftec_2,
43 flai_2
44 )
18 45
19 # Tec files loading and generating xml 46 # Tec files loading and generating xml
47
20 tec_param <- read_params_table(file.path(workspace, TecFile)) 48 tec_param <- read_params_table(file.path(workspace, TecFile))
21 columnToRemove <- names(tec_param[grep("juleclair|nbinfloecl", names(tec_param))]) 49 columnToRemove <-
22 columnToKeep <- names(tec_param)[names(tec_param) %in% columnToRemove == FALSE] 50 names(tec_param[grep("juleclair|nbinfloecl", names(tec_param))])
23 tec_param <- subset(tec_param, select=columnToKeep) 51 columnToKeep <-
52 names(tec_param)[names(tec_param) %in% columnToRemove == FALSE]
53
54 tec_param <- subset(tec_param, select = columnToKeep)
55
24 gen_tec_xml(param_df = tec_param, out_dir = workspace) 56 gen_tec_xml(param_df = tec_param, out_dir = workspace)
25 57
26 # Ini files loading and generating xml 58 # Ini files loading and generating xml
59
27 ini_param <- read_params_table(file.path(workspace, IniFile)) 60 ini_param <- read_params_table(file.path(workspace, IniFile))
61
28 gen_ini_xml(param_df = ini_param, out_dir = workspace) 62 gen_ini_xml(param_df = ini_param, out_dir = workspace)
29 63
30 # Station files loading and generating xml 64 # Station files loading and generating xml
65
31 sta_param <- read_params_table(file.path(workspace, StationFile)) 66 sta_param <- read_params_table(file.path(workspace, StationFile))
67
32 gen_sta_xml(param_df = sta_param, out_dir = workspace) 68 gen_sta_xml(param_df = sta_param, out_dir = workspace)
33 69
70 if (genUSMsXmlOneAfterOther) {
71 durGenX <- lubridate::as.duration(0)
72 durGenT <- lubridate::as.duration(0)
73
74 # looping on USMs
75 for (i in 1:nrow(usms_param)) {
76 row <- usms_param[i, ]
77
78 beforeGenXmlTimeI <- Sys.time()
79
80 gen_usms_xml(file = file.path(workspace, "usms.xml"),
81 param_df = row)
82
83 afterGenXmlTimeI <- Sys.time()
84 durGenXI <-
85 lubridate::as.duration(lubridate::interval(beforeGenXmlTimeI,
86 afterGenXmlTimeI))
87
88 # one after the other generating txt folder
89
90 beforeGenTxtTimeI <- Sys.time()
91
92 gen_usms_xml2txt(
93 javastics = javastics_path,
94 workspace = workspace,
95 out_dir = txt_path,
96 verbose = TRUE
97 )
98
99 afterGenTxtTimeI <- Sys.time()
100 durGenTI <-
101 lubridate::as.duration(lubridate::interval(beforeGenTxtTimeI,
102 afterGenTxtTimeI))
103
104 durGenX <- durGenX + durGenXI
105 durGenT <- durGenT + durGenTI
106 }
107 } else {
108 beforeGenXmlTime <- Sys.time()
109
110 gen_usms_xml(file = file.path(workspace, "usms.xml"),
111 param_df = usms_param)
112
113 afterGenXmlTime <- Sys.time()
114 durGenX <-
115 lubridate::as.duration(lubridate::interval(beforeGenXmlTime,
116 afterGenXmlTime))
117
118 beforeGenTxtTime <- Sys.time()
119
120 gen_usms_xml2txt(
121 javastics = javastics_path,
122 workspace = workspace,
123 out_dir = txt_path,
124 verbose = TRUE
125 )
126
127 afterGenTxtTime <- Sys.time()
128 durGenT <-
129 lubridate::as.duration(lubridate::interval(beforeGenTxtTime,
130 afterGenTxtTime))
131
132 }
34 133
35 # looping on USMs 134 endTime <- Sys.time()
36 for(i in 1:nrow(usms_param)) { 135 dur <-
37 row <- usms_param[i,] 136 lubridate::as.period(lubridate::as.duration(lubridate::interval(startTime, endTime)))
137 durGenXP <- lubridate::as.period(durGenX)
138 durGenTP <- lubridate::as.period(durGenT)
38 139
39 # generating xml 140 print("REDELAC Report")
40 gen_usms_xml(file = file.path(workspace, "usms.xml"), param_df = row) 141 print("==============")
41 142 print(paste0("number of usms: ", nrow(usms_param)))
42 # generating txt folder 143 print(paste("usms.xml one after the other:", genUSMsXmlOneAfterOther))
43 gen_usms_xml2txt(javastics = javastics_path, 144 sprintf(
44 workspace = workspace, 145 'overall duration: %g jour(s) %g heure(s) %g minute(s) %g seconde(s)',
45 out_dir = txt_path, 146 lubridate::day(dur),
46 verbose = TRUE) 147 lubridate::hour(dur),
47 } 148 lubridate::minute(dur),
48 149 lubridate::second(dur)
150 )
151 sprintf(
152 'inside gen_usms_xml duration: %g jour(s) %g heure(s) %g minute(s) %g seconde(s)',
153 lubridate::day(durGenXP),
154 lubridate::hour(durGenXP),
155 lubridate::minute(durGenXP),
156 lubridate::second(durGenXP)
157 )
158 sprintf(
159 'inside gen_usms_xml2txt duration: %g jour(s) %g heure(s) %g minute(s) %g seconde(s)',
160 lubridate::day(durGenTP),
161 lubridate::hour(durGenTP),
162 lubridate::minute(durGenTP),
163 lubridate::second(durGenTP)
164 )