Mercurial > repos > siwaa > carboseq_s

comparison run.r @ 1:89c69fcbf561 draft

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"planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
author siwaa
date Fri, 09 Aug 2024 15:09:48 +0000
parents
children a069fc43b0b1
comparison
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0:fb1b9308807f 1:89c69fcbf561
1 # help : Rscript % --url=https://coby.infosol.inrae.fr:7777/semantify --srcDir=~/CSCL/src/csoprapreprocessor/inst/extdata/carboseq/set001/
2
3 # Function to parse command-line arguments
4 parse_args <- function() {
5 args <- commandArgs(trailingOnly = TRUE)
6
7 # Default values for optional parameters
8 url <- "https://coby.infosol.inrae.fr:8080/semantify/"
9 srcDir <- NULL
10 part <- "modeltoolbox_sem_sep"
11 DS <- T
12 NBCores <- 1
13 # Parse arguments
14 for (arg in args) {
15 if (grepl("^--url=", arg)) {
16 url <- sub("^--url=", "", arg)
17 }
18
19 if (grepl("^--srcDir=", arg)) {
20 srcDir <- sub("^--srcDir=", "", arg)
21 }
22
23 if (grepl("^--part=", arg)) {
24 part <- sub("^--part=", "", arg)
25 }
26
27 if (grepl("^--DS=", arg)) {
28 DS <- ifelse(sub("^--DS=", "", arg) == "TRUE", TRUE, FALSE)
29 }
30
31 if (grepl("^--NBCores=", arg)) {
32 NBCores <- as.numeric(sub("^--NBCores=", "", arg))
33 }
34
35 if (grepl("^--srcOut=", arg)) {
36 srcOut <- sub("^--srcOut=", "", arg)
37 }
38
39 if (grepl("^--semPath=", arg)) {
40 semPath <- sub("^--semPath=", "", arg)
41 }
42
43 }
44
45 list(url = url, srcDir = srcDir, part = part, DS = DS, NBCores = NBCores, srcOut = srcOut, semPath = semPath)
46 }
47
48 argus <- parse_args()
49 url <- argus[["url"]]
50 srcDir <- argus[["srcDir"]]
51 part <- argus[["part"]]
52 DS <- argus[["DS"]]
53 NBCores <- argus[["NBCores"]]
54
55 srcOut <- argus[["srcOut"]]
56 semPath <- argus[["semPath"]]
57
58 if (!endsWith(srcOut, "/")) {
59 srcOut <- paste0(srcOut, "/")
60 }
61
62 # url="https://147.100.203.110/semantify "
63 # srcDir="~/tmp/testFiles/400Sites/"
64 # part="modeltoolbox"
65 # part="csoprapreprocessor"
66 # DS=TRUE
67 # NBCores=10
68
69
70 # MTB{{{
71 if (part == "modeltoolbox") {
72 f0 <- function(){
73 modeltoolbox::loadCSVs(maxCores = NBCores, cinputCalculator = "cinest",
74 preprocessorInputs = ppi)
75 modeltoolbox::runSims(maxCores = NBCores)
76 res <- modeltoolbox::readSocForcingsResults()
77 fileName <- "resRun.RData"
78 filePath <- file.path(srcOut, fileName)
79 save(res, file = filePath)
80 }
81 }
82 #}}}
83
84 if (part == "modeltoolbox_sem_sep") {
85 DS <- F
86 print("Setting DS to F. Will semantify outside of the csoprapreprocessor functions")
87 f0 <- function(){
88 csopratools::semantify(
89 inputDir = srcDir,
90 outputDir = srcDir,
91 name = "carboseq",
92 # use = "service",
93 URL = url,
94 use = "java",
95 semantifierRootPath = semPath,
96 extFileNames = paste0(c("crop", "soil", "units"), ".csv")
97 )
98 print("between semantify and load")
99 modeltoolbox::loadCSVs(maxCores = NBCores, cinputCalculator = "cinest",
100 preprocessorInputs = ppi)
101 print("between load an sim")
102 modeltoolbox::runSims(maxCores = NBCores)
103 res <- modeltoolbox::getYearlySOCResults()
104 fileName <- "resRun.RData"
105 filePath <- file.path(srcOut, fileName)
106 save(res, file = filePath)
107 }
108 }
109
110 ppi <- list(
111 weatherRetrievalMethod = "service",
112 srcDir = srcDir,
113 doSemantify = DS,
114 weatherRetrievalURL = "https://147.100.203.110/climate",
115 semantifierServiceURL = url
116 )
117
118
119 print(url)
120 print(srcDir)
121 print(srcOut)
122 print(DS)
123 print(NBCores)
124 print(f0)
125
126 f0()
127
128