Mercurial > repos > siwaa > redelac_stics_g

annotate redelacSticsInputGenerator.R @ 7:fb6f7d60508d draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"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
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
1 library(SticsRFiles)
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
2 library(dplyr)
7
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
3 library(lubridate)
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
4
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
5
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
6 startTime <- Sys.time()
0
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
7
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
8 workspace <- paste0(getwd(), "/WS")
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
9 javastics_path <- getwd()
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
10
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
11 txt_path <- paste0(getwd(), "/WS/txt_files")
7
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
12 dir.create(txt_path, recursive = T)
0
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
13
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
14 USMsFile <- "USMs.csv"
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
15 TecFile <- "Tec.csv"
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
16 IniFile <- "Ini.csv"
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
17 StationFile <- "Station.csv"
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
18
7
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
19 args = commandArgs(trailingOnly = TRUE)
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
20
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
21 genUSMsXmlOneAfterOther <- (args[1] == "usmx_one_after_other")
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
22
6
bb1ac57f8545 "planemo upload for repository https://forgemia.inra.fr/redelac commit 5c06627ff4fa4a31f7fae2cd625f32a29ed2d773"
siwaa
parents: 5
diff changeset
23 # USMs file loading
7
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
24
0
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
25 usms_param <- read_params_table(file.path(workspace, USMsFile)) %>%
7
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
26 select(
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
27 usm_name,
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
28 datedebut,
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
29 datefin,
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
30 finit,
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
31 nomsol,
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
32 fstation,
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
33 fclim1,
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
34 fclim2,
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
35 culturean,
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
36 nbplantes,
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
37 codesimul,
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
38 fplt_1,
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
39 ftec_1,
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
40 flai_1,
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
41 fplt_2,
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
42 ftec_2,
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
43 flai_2
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
44 )
0
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
45
6
bb1ac57f8545 "planemo upload for repository https://forgemia.inra.fr/redelac commit 5c06627ff4fa4a31f7fae2cd625f32a29ed2d773"
siwaa
parents: 5
diff changeset
46 # Tec files loading and generating xml
7
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
47
6
bb1ac57f8545 "planemo upload for repository https://forgemia.inra.fr/redelac commit 5c06627ff4fa4a31f7fae2cd625f32a29ed2d773"
siwaa
parents: 5
diff changeset
48 tec_param <- read_params_table(file.path(workspace, TecFile))
7
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
49 columnToRemove <-
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
50 names(tec_param[grep("juleclair|nbinfloecl", names(tec_param))])
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
51 columnToKeep <-
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
52 names(tec_param)[names(tec_param) %in% columnToRemove == FALSE]
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
53
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
54 tec_param <- subset(tec_param, select = columnToKeep)
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
55
3
e344100f3354 "planemo upload for repository https://forgemia.inra.fr/redelac commit ff64e62033c2485113100d60c38be73e59ef119c"
siwaa
parents: 0
diff changeset
56 gen_tec_xml(param_df = tec_param, out_dir = workspace)
0
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
57
6
bb1ac57f8545 "planemo upload for repository https://forgemia.inra.fr/redelac commit 5c06627ff4fa4a31f7fae2cd625f32a29ed2d773"
siwaa
parents: 5
diff changeset
58 # Ini files loading and generating xml
7
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
59
0
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
60 ini_param <- read_params_table(file.path(workspace, IniFile))
7
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
61
0
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
62 gen_ini_xml(param_df = ini_param, out_dir = workspace)
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
63
6
bb1ac57f8545 "planemo upload for repository https://forgemia.inra.fr/redelac commit 5c06627ff4fa4a31f7fae2cd625f32a29ed2d773"
siwaa
parents: 5
diff changeset
64 # Station files loading and generating xml
7
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
65
0
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
66 sta_param <- read_params_table(file.path(workspace, StationFile))
7
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
67
0
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
68 gen_sta_xml(param_df = sta_param, out_dir = workspace)
c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
siwaa
parents:
diff changeset
69
7
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
70 if (genUSMsXmlOneAfterOther) {
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
71 durGenX <- lubridate::as.duration(0)
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
72 durGenT <- lubridate::as.duration(0)
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
73
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
74 # looping on USMs
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
75 for (i in 1:nrow(usms_param)) {
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
76 row <- usms_param[i, ]
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
77
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
78 beforeGenXmlTimeI <- Sys.time()
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
79
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
80 gen_usms_xml(file = file.path(workspace, "usms.xml"),
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
81 param_df = row)
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
82
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
83 afterGenXmlTimeI <- Sys.time()
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
84 durGenXI <-
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
85 lubridate::as.duration(lubridate::interval(beforeGenXmlTimeI,
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
86 afterGenXmlTimeI))
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
87
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
88 # one after the other generating txt folder
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
89
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
90 beforeGenTxtTimeI <- Sys.time()
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
91
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
92 gen_usms_xml2txt(
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
93 javastics = javastics_path,
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
94 workspace = workspace,
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
95 out_dir = txt_path,
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
96 verbose = TRUE
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
97 )
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
98
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
99 afterGenTxtTimeI <- Sys.time()
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
100 durGenTI <-
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
101 lubridate::as.duration(lubridate::interval(beforeGenTxtTimeI,
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
102 afterGenTxtTimeI))
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
103
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
104 durGenX <- durGenX + durGenXI
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
105 durGenT <- durGenT + durGenTI
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
106 }
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
107 } else {
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
108 beforeGenXmlTime <- Sys.time()
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
109
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
110 gen_usms_xml(file = file.path(workspace, "usms.xml"),
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
111 param_df = usms_param)
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
112
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
113 afterGenXmlTime <- Sys.time()
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
114 durGenX <-
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
115 lubridate::as.duration(lubridate::interval(beforeGenXmlTime,
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
116 afterGenXmlTime))
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
117
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
118 beforeGenTxtTime <- Sys.time()
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
119
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
120 gen_usms_xml2txt(
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
121 javastics = javastics_path,
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
122 workspace = workspace,
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
123 out_dir = txt_path,
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
124 verbose = TRUE
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
125 )
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
126
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
127 afterGenTxtTime <- Sys.time()
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
128 durGenT <-
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
129 lubridate::as.duration(lubridate::interval(beforeGenTxtTime,
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
130 afterGenTxtTime))
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
131
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
132 }
5
4f8d87b9c246 "planemo upload for repository https://forgemia.inra.fr/redelac commit b3a95e69b8c2496ff3ec12c854404798d8bc55b1"
siwaa
parents: 3
diff changeset
133
7
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
134 endTime <- Sys.time()
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
135 dur <-
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
136 lubridate::as.period(lubridate::as.duration(lubridate::interval(startTime, endTime)))
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
137 durGenXP <- lubridate::as.period(durGenX)
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
138 durGenTP <- lubridate::as.period(durGenT)
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
139
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
140 print("REDELAC Report")
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
141 print("==============")
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
142 print(paste0("number of usms: ", nrow(usms_param)))
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
143 print(paste("usms.xml one after the other:", genUSMsXmlOneAfterOther))
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
144 sprintf(
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
145 'overall duration: %g jour(s) %g heure(s) %g minute(s) %g seconde(s)',
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
146 lubridate::day(dur),
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
147 lubridate::hour(dur),
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
148 lubridate::minute(dur),
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
149 lubridate::second(dur)
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
150 )
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
151 sprintf(
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
152 'inside gen_usms_xml duration: %g jour(s) %g heure(s) %g minute(s) %g seconde(s)',
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
153 lubridate::day(durGenXP),
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
154 lubridate::hour(durGenXP),
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
155 lubridate::minute(durGenXP),
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
156 lubridate::second(durGenXP)
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
157 )
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
158 sprintf(
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
159 'inside gen_usms_xml2txt duration: %g jour(s) %g heure(s) %g minute(s) %g seconde(s)',
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
160 lubridate::day(durGenTP),
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
161 lubridate::hour(durGenTP),
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
162 lubridate::minute(durGenTP),
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
163 lubridate::second(durGenTP)
fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 6
diff changeset
164 )