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