Mercurial > repos > siwaa > carboseq_s

comparison run.r @ 4:a069fc43b0b1 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/carboseq/record-projet-carboseq/-/tree/ed5816b24b0c91099c78cbb5bbbe835ae5c74cd7/toos/CarboSeqSimulator commit ed5816b24b0c91099c78cbb5bbbe835ae5c74cd7-dirty"
author siwaa
date Fri, 23 Aug 2024 13:19:04 +0000
parents 89c69fcbf561
children 366449cab681
comparison
equal deleted inserted replaced
3:d753f3430970 4:a069fc43b0b1
5 args <- commandArgs(trailingOnly = TRUE) 5 args <- commandArgs(trailingOnly = TRUE)
6 6
7 # Default values for optional parameters 7 # Default values for optional parameters
8 url <- "https://coby.infosol.inrae.fr:8080/semantify/" 8 url <- "https://coby.infosol.inrae.fr:8080/semantify/"
9 srcDir <- NULL 9 srcDir <- NULL
10 part <- "modeltoolbox_sem_sep" 10 part <- "modeltoolbox"
11 DS <- T 11 DS <- T
12 NBCores <- 1 12 NBCores <- 1
13 # Parse arguments 13 # Parse arguments
14 for (arg in args) { 14 for (arg in args) {
15 if (grepl("^--url=", arg)) { 15 if (grepl("^--url=", arg)) {
33 } 33 }
34 34
35 if (grepl("^--srcOut=", arg)) { 35 if (grepl("^--srcOut=", arg)) {
36 srcOut <- sub("^--srcOut=", "", arg) 36 srcOut <- sub("^--srcOut=", "", arg)
37 } 37 }
38
39 if (grepl("^--semPath=", arg)) {
40 semPath <- sub("^--semPath=", "", arg)
41 }
42 38
43 } 39 }
44 40
45 list(url = url, srcDir = srcDir, part = part, DS = DS, NBCores = NBCores, srcOut = srcOut, semPath = semPath) 41 list(url = url, srcDir = srcDir, part = part, DS = DS, NBCores = NBCores, srcOut = srcOut)
46 } 42 }
47 43
48 argus <- parse_args() 44 argus <- parse_args()
49 url <- argus[["url"]] 45 url <- argus[["url"]]
50 srcDir <- argus[["srcDir"]] 46 srcDir <- argus[["srcDir"]]
51 part <- argus[["part"]] 47 part <- argus[["part"]]
52 DS <- argus[["DS"]] 48 DS <- argus[["DS"]]
53 NBCores <- argus[["NBCores"]] 49 NBCores <- argus[["NBCores"]]
54 50
55 srcOut <- argus[["srcOut"]] 51 srcOut <- argus[["srcOut"]]
56 semPath <- argus[["semPath"]]
57 52
58 if (!endsWith(srcOut, "/")) { 53 if (!endsWith(srcOut, "/")) {
59 srcOut <- paste0(srcOut, "/") 54 srcOut <- paste0(srcOut, "/")
60 } 55 }
61 56
63 # srcDir="~/tmp/testFiles/400Sites/" 58 # srcDir="~/tmp/testFiles/400Sites/"
64 # part="modeltoolbox" 59 # part="modeltoolbox"
65 # part="csoprapreprocessor" 60 # part="csoprapreprocessor"
66 # DS=TRUE 61 # DS=TRUE
67 # NBCores=10 62 # NBCores=10
63
64 ppi <- list(
65 weatherRetrievalMethod = "service",
66 srcDir = srcDir,
67 doSemantify = DS,
68 weatherRetrievalURL = "https://147.100.203.110/climate",
69 semantifierServiceURL = url
70 )
68 71
69 72
70 # MTB{{{ 73 # MTB{{{
71 if (part == "modeltoolbox") { 74 if (part == "modeltoolbox") {
72 f0 <- function(){ 75 f0 <- function(){
79 save(res, file = filePath) 82 save(res, file = filePath)
80 } 83 }
81 } 84 }
82 #}}} 85 #}}}
83 86
84 if (part == "modeltoolbox_sem_sep") { 87 # prepro{{
85 DS <- F 88 if (part == "csoprapreprocessor") {
86 print("Setting DS to F. Will semantify outside of the csoprapreprocessor functions") 89 f0 <- function(){
87 f0 <- function(){ 90 path <- this.path::this.dir()
88 csopratools::semantify( 91 print(path)
89 inputDir = srcDir, 92 setwd(path)
90 outputDir = srcDir, 93 setwd("../..")
91 name = "carboseq", 94 source("src/csoprapreprocessor/src-utils.r")
92 # use = "service", 95 CsopPre$Tool$sourceCodeFiles()
93 URL = url, 96 CsopPre$runPreprocessor(name = "carboseq", maxCores = NBCores, preprocessorInputs = ppi)
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 } 97 }
109 98 }
110 ppi <- list( 99 #}}}
111 weatherRetrievalMethod = "service",
112 srcDir = srcDir,
113 doSemantify = DS,
114 weatherRetrievalURL = "https://147.100.203.110/climate",
115 semantifierServiceURL = url
116 )
117
118 100
119 print(url) 101 print(url)
120 print(srcDir) 102 print(srcDir)
121 print(srcOut) 103 print(srcOut)
122 print(DS) 104 print(DS)
123 print(NBCores) 105 print(NBCores)
124 print(f0) 106 print(f0)
125
126 f0() 107 f0()
127 108
128 109