Mercurial > repos > patrick_chabrier > carboseq_s

comparison run.r @ 8:74a8deeedd19 draft

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author patrick_chabrier
date Thu, 04 Jul 2024 14:15:56 +0000
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children 32bda6e69c5a
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7:fe6b69ede424 8:74a8deeedd19
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 url <- "http://localhost:8282/semantify"
10 srcDir <- NULL
11 part <- "modeltoolbox_sem_sep"
12 DS <- T
13 NBCores <- 1
14 # Parse arguments
15 for (arg in args) {
16 if (grepl("^--url=", arg)) {
17 url <- sub("^--url=", "", arg)
18 }
19
20 if (grepl("^--srcDir=", arg)) {
21 srcDir <- sub("^--srcDir=", "", arg)
22 }
23
24 if (grepl("^--part=", arg)) {
25 part <- sub("^--part=", "", arg)
26 }
27
28 if (grepl("^--DS=", arg)) {
29 DS <- ifelse(sub("^--DS=", "", arg) == "TRUE", TRUE, FALSE)
30 }
31
32 if (grepl("^--NBCores=", arg)) {
33 NBCores <- as.numeric(sub("^--NBCores=", "", arg))
34 }
35
36 if (grepl("^--srcOut=", arg)) {
37 srcOut <- sub("^--srcOut=", "", arg)
38 }
39
40 }
41
42 list(url = url, srcDir = srcDir, part = part, DS = DS, NBCores = NBCores, srcOut = srcOut)
43 }
44
45 argus <- parse_args()
46 url <- argus[["url"]]
47 srcDir <- argus[["srcDir"]]
48 part <- argus[["part"]]
49 DS <- argus[["DS"]]
50 NBCores <- argus[["NBCores"]]
51
52 srcOut <- argus[["srcOut"]]
53
54 if (!endsWith(srcOut, "/")) {
55 srcOut <- paste0(srcOut, "/")
56 }
57
58 # url="https://147.100.203.110/semantify "
59 # srcDir="~/tmp/testFiles/400Sites/"
60 # part="modeltoolbox"
61 # part="csoprapreprocessor"
62 # DS=TRUE
63 # NBCores=10
64
65
66 # MTB{{{
67 if (part == "modeltoolbox") {
68 f0 <- function(){
69 modeltoolbox::loadCSVs(maxCores = NBCores, cinputCalculator = "cinest",
70 preprocessorInputs = ppi)
71 modeltoolbox::runSims(maxCores = NBCores)
72 res <- modeltoolbox::readSocForcingsResults()
73 fileName <- "resRun.RData"
74 filePath <- file.path(srcOut, fileName)
75 save(res, file = filePath)
76 }
77 }
78 #}}}
79
80 if (part == "modeltoolbox_sem_sep") {
81 DS <- F
82 print("Setting DS to F. Will semantify outside of the csoprapreprocessor functions")
83 f0 <- function(){
84 # path <- this.path::this.dir()
85 # print(path)
86 # setwd(path)
87 # setwd("../..")
88 print("before semantify")
89 # Sys.sleep(runif(n=1, min=30, max=60))
90 csopratools::semantify(
91 inputDir = srcDir,
92 outputDir = srcDir,
93 name = "carboseq",
94 use = "service",
95 URL = url,
96 # extFileNames = paste0(c("crop", "soil", "units"), ".csv")
97 extFileNames = list.files(srcDir)
98 )
99 print("between semantify and load")
100 modeltoolbox::loadCSVs(maxCores = NBCores, cinputCalculator = "cinest",
101 preprocessorInputs = ppi)
102 print("between load an sim")
103 modeltoolbox::runSims(maxCores = NBCores)
104 res <- modeltoolbox::getYearlySOCResults()
105 fileName <- "resRun.RData"
106 filePath <- file.path(srcOut, fileName)
107 save(res, file = filePath)
108 }
109 }
110
111 ppi <- list(
112 weatherRetrievalMethod = "service",
113 srcDir = srcDir,
114 doSemantify = DS,
115 weatherRetrievalURL = "https://147.100.203.110/climate",
116 semantifierServiceURL = url
117 )
118
119
120 print(url)
121 print(srcDir)
122 print(srcOut)
123 print(DS)
124 print(NBCores)
125 print(f0)
126
127 f0()
128
129