Mercurial > repos > patrick_chabrier > carboseq_s

comparison run.r @ 11:32bda6e69c5a draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author patrick_chabrier
date Thu, 11 Jul 2024 09:40:46 +0000
parents 74a8deeedd19
children
comparison
equal deleted inserted replaced
10:28139f7f1dbc 11:32bda6e69c5a
3 # Function to parse command-line arguments 3 # Function to parse command-line arguments
4 parse_args <- function() { 4 parse_args <- function() {
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 url <- "http://localhost:8282/semantify"
10 srcDir <- NULL 9 srcDir <- NULL
11 part <- "modeltoolbox_sem_sep" 10 part <- "modeltoolbox_sem_sep"
12 DS <- T 11 DS <- T
13 NBCores <- 1 12 NBCores <- 1
14 # Parse arguments 13 # Parse arguments
34 } 33 }
35 34
36 if (grepl("^--srcOut=", arg)) { 35 if (grepl("^--srcOut=", arg)) {
37 srcOut <- sub("^--srcOut=", "", arg) 36 srcOut <- sub("^--srcOut=", "", arg)
38 } 37 }
38
39 if (grepl("^--semPath=", arg)) {
40 semPath <- sub("^--semPath=", "", arg)
41 }
39 42
40 } 43 }
41 44
42 list(url = url, srcDir = srcDir, part = part, DS = DS, NBCores = NBCores, srcOut = srcOut) 45 list(url = url, srcDir = srcDir, part = part, DS = DS, NBCores = NBCores, srcOut = srcOut, semPath = semPath)
43 } 46 }
44 47
45 argus <- parse_args() 48 argus <- parse_args()
46 url <- argus[["url"]] 49 url <- argus[["url"]]
47 srcDir <- argus[["srcDir"]] 50 srcDir <- argus[["srcDir"]]
48 part <- argus[["part"]] 51 part <- argus[["part"]]
49 DS <- argus[["DS"]] 52 DS <- argus[["DS"]]
50 NBCores <- argus[["NBCores"]] 53 NBCores <- argus[["NBCores"]]
51 54
52 srcOut <- argus[["srcOut"]] 55 srcOut <- argus[["srcOut"]]
56 semPath <- argus[["semPath"]]
53 57
54 if (!endsWith(srcOut, "/")) { 58 if (!endsWith(srcOut, "/")) {
55 srcOut <- paste0(srcOut, "/") 59 srcOut <- paste0(srcOut, "/")
56 } 60 }
57 61
79 83
80 if (part == "modeltoolbox_sem_sep") { 84 if (part == "modeltoolbox_sem_sep") {
81 DS <- F 85 DS <- F
82 print("Setting DS to F. Will semantify outside of the csoprapreprocessor functions") 86 print("Setting DS to F. Will semantify outside of the csoprapreprocessor functions")
83 f0 <- function(){ 87 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( 88 csopratools::semantify(
91 inputDir = srcDir, 89 inputDir = srcDir,
92 outputDir = srcDir, 90 outputDir = srcDir,
93 name = "carboseq", 91 name = "carboseq",
94 use = "service", 92 # use = "service",
95 URL = url, 93 URL = url,
96 # extFileNames = paste0(c("crop", "soil", "units"), ".csv") 94 use = "java",
97 extFileNames = list.files(srcDir) 95 semantifierRootPath = semPath,
96 extFileNames = paste0(c("crop", "soil", "units"), ".csv")
98 ) 97 )
99 print("between semantify and load") 98 print("between semantify and load")
100 modeltoolbox::loadCSVs(maxCores = NBCores, cinputCalculator = "cinest", 99 modeltoolbox::loadCSVs(maxCores = NBCores, cinputCalculator = "cinest",
101 preprocessorInputs = ppi) 100 preprocessorInputs = ppi)
102 print("between load an sim") 101 print("between load an sim")