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comparison run.r @ 7:366449cab681 draft

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"planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
author siwaa
date Thu, 29 Aug 2024 14:58:19 +0000
parents a069fc43b0b1
children 5fdc9d0c223b
comparison
equal deleted inserted replaced
6:f9183e245cdb 7:366449cab681
1
1 # help : Rscript % --url=https://coby.infosol.inrae.fr:7777/semantify --srcDir=~/CSCL/src/csoprapreprocessor/inst/extdata/carboseq/set001/ 2 # help : Rscript % --url=https://coby.infosol.inrae.fr:7777/semantify --srcDir=~/CSCL/src/csoprapreprocessor/inst/extdata/carboseq/set001/
2 3
3 # Function to parse command-line arguments 4 # Function to parse command-line arguments
4 parse_args <- function() { 5 parse_args <- function() {
5 args <- commandArgs(trailingOnly = TRUE) 6 args <- commandArgs(trailingOnly = TRUE)
6 7
7 # Default values for optional parameters 8 # Default values for optional parameters
8 url <- "https://coby.infosol.inrae.fr:8080/semantify/" 9 url <- "https://coby.infosol.inrae.fr:8080/semantify/"
9 srcDir <- NULL 10 srcDir <- NULL
10 part <- "modeltoolbox" 11 # srcDirOutput <- NULL
12 part <- "modeltoolbox_sem_remote"
11 DS <- T 13 DS <- T
12 NBCores <- 1 14 NBCores <- 1
15 semPath <- "."
13 # Parse arguments 16 # Parse arguments
14 for (arg in args) { 17 for (arg in args) {
18
15 if (grepl("^--url=", arg)) { 19 if (grepl("^--url=", arg)) {
16 url <- sub("^--url=", "", arg) 20 url <- sub("^--url=", "", arg)
17 } 21 }
18 22
19 if (grepl("^--srcDir=", arg)) { 23 if (grepl("^--srcDir=", arg)) {
20 srcDir <- sub("^--srcDir=", "", arg) 24 srcDir <- sub("^--srcDir=", "", arg)
21 } 25 }
22 26
23 if (grepl("^--part=", arg)) { 27 # if (grepl("^--srcDirOutput=", arg)) {
28 # srcDirOutput <- sub("^--srcDirOutput=", "", arg)
29 # }
30 if (grepl("^--part=", arg)) {
24 part <- sub("^--part=", "", arg) 31 part <- sub("^--part=", "", arg)
25 } 32 }
26 33
27 if (grepl("^--DS=", arg)) { 34 if (grepl("^--DS=", arg)) {
28 DS <- ifelse(sub("^--DS=", "", arg) == "TRUE", TRUE, FALSE) 35 DS <- ifelse(sub("^--DS=", "", arg) == "TRUE", TRUE, FALSE)
29 } 36 }
30 37
31 if (grepl("^--NBCores=", arg)) { 38 if (grepl("^--NBCores=", arg)) {
32 NBCores <- as.numeric(sub("^--NBCores=", "", arg)) 39 NBCores <- as.numeric(sub("^--NBCores=", "", arg))
33 } 40 }
34 41
35 if (grepl("^--srcOut=", arg)) { 42 if (grepl("^--srcOut=", arg)) {
36 srcOut <- sub("^--srcOut=", "", arg) 43 srcOut <- sub("^--srcOut=", "", arg)
37 } 44 }
38 45
46 if (grepl("^--semPath=", arg)) {
47 semPath <- sub("^--semPath=", "", arg)
48 }
39 } 49 }
40 50
41 list(url = url, srcDir = srcDir, part = part, DS = DS, NBCores = NBCores, srcOut = srcOut) 51 list( url = url, srcDir = srcDir, part = part, DS = DS,
52 NBCores = NBCores, srcOut = srcOut, semPath = semPath )
42 } 53 }
43 54
44 argus <- parse_args() 55 argus <- parse_args()
56
45 url <- argus[["url"]] 57 url <- argus[["url"]]
46 srcDir <- argus[["srcDir"]] 58 srcDir <- argus[["srcDir"]]
59 # srcDirOutput <- argus[["srcDirOutput"]]
47 part <- argus[["part"]] 60 part <- argus[["part"]]
48 DS <- argus[["DS"]] 61 DS <- argus[["DS"]]
49 NBCores <- argus[["NBCores"]] 62 NBCores <- argus[["NBCores"]]
50 63
51 srcOut <- argus[["srcOut"]] 64 srcOut <- argus[["srcOut"]]
52 65
66 semPath <- argus[["semPath"]]
67
53 if (!endsWith(srcOut, "/")) { 68 if (!endsWith(srcOut, "/")) {
54 srcOut <- paste0(srcOut, "/") 69 srcOut <- paste0(srcOut, "/")
55 } 70 }
71
72 #if (is.null(srcDirOutput)) {
73 # srcDirOutput <- srcDir
74 # }
56 75
57 # url="https://147.100.203.110/semantify " 76 # url="https://147.100.203.110/semantify "
58 # srcDir="~/tmp/testFiles/400Sites/" 77 # srcDir="~/tmp/testFiles/400Sites/"
59 # part="modeltoolbox" 78 # part="modeltoolbox"
60 # part="csoprapreprocessor" 79 # part="csoprapreprocessor"
61 # DS=TRUE 80 # DS=TRUE
62 # NBCores=10 81 # 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 )
71
72 82
73 # MTB{{{ 83 # MTB{{{
74 if (part == "modeltoolbox") { 84 if (part == "modeltoolbox") {
75 f0 <- function(){ 85 f0 <- function(){
76 modeltoolbox::loadCSVs(maxCores = NBCores, cinputCalculator = "cinest", 86 modeltoolbox::loadCSVs(maxCores = NBCores, cinputCalculator = "cinest",
82 save(res, file = filePath) 92 save(res, file = filePath)
83 } 93 }
84 } 94 }
85 #}}} 95 #}}}
86 96
87 # prepro{{ 97 if (part == "modeltoolbox_sem_local") {
88 if (part == "csoprapreprocessor") { 98 DS <- F
89 f0 <- function(){ 99 print("Setting DS to F. Will semantify outside of the csoprapreprocessor functions")
90 path <- this.path::this.dir() 100 f0 <- function(){
91 print(path) 101 path <- this.path::this.dir()
92 setwd(path) 102 print(path)
93 setwd("../..") 103 csopratools::semantify(
94 source("src/csoprapreprocessor/src-utils.r") 104 inputDir = srcDir,
95 CsopPre$Tool$sourceCodeFiles() 105 outputDir = srcDir,
96 CsopPre$runPreprocessor(name = "carboseq", maxCores = NBCores, preprocessorInputs = ppi) 106 name = "carboseq",
107 # use = "service",
108 URL = url,
109 use = "java",
110 semantifierRootPath = semPath,
111 extFileNames = paste0(c("crop", "soil", "units"), ".csv")
112 )
113 print("between semantify and load")
114
115 ppi$srcDirOutput <- NULL # Hack
116
117 modeltoolbox::loadCSVs(maxCores = NBCores, cinputCalculator = "cinest",
118 preprocessorInputs = ppi)
119 print("between load an sim")
120 modeltoolbox::runSims(maxCores = NBCores)
121 # res <- modeltoolbox::getYearlySOCResults()
122 res <- modeltoolbox::readSocForcingsResults()
123 fileName <- "resRun.RData"
124 filePath <- file.path(srcOut, fileName)
125 save(res, file = filePath)
126 }
97 } 127 }
128
129 if (part == "modeltoolbox_sem_remote") {
130 DS <- F
131 print("Setting DS to F. Will semantify outside of the csoprapreprocessor functions")
132 f0 <- function(){
133 path <- this.path::this.dir()
134 print(path)
135 setwd(path)
136 setwd("../..")
137 csopratools::semantify(
138 inputDir = srcDir,
139 outputDir = srcDir,
140 name = "carboseq",
141 use = "service",
142 URL = url,
143 extFileNames = paste0(c("crop", "soil", "units"), ".csv")
144 )
145
146 # ppi$srcDirOutput <- NULL # Hack
147
148 modeltoolbox::loadCSVs(maxCores = NBCores, cinputCalculator = "cinest",
149 preprocessorInputs = ppi)
150 modeltoolbox::runSims(maxCores = NBCores)
151 # res <- modeltoolbox::getYearlySOCResults()
152 res <- modeltoolbox::readSocForcingsResults()
153 fileName <- "resRun.RData"
154 filePath <- file.path(srcOut, fileName)
155 save(res, file = filePath)
156 }
98 } 157 }
99 #}}} 158
159 ppi <- list(
160 weatherRetrievalMethod = "service",
161 srcDir = srcDir,
162 # srcDirOutput = srcDirOutput,
163 doSemantify = DS,
164 weatherRetrievalURL = "https://coby.infosol.inrae.fr:8080/climate",
165 semantifierServiceURL = url
166 )
167
100 168
101 print(url) 169 print(url)
102 print(srcDir) 170 print(srcDir)
171 # print(srcDirOutput)
103 print(srcOut) 172 print(srcOut)
104 print(DS) 173 print(DS)
105 print(NBCores) 174 print(NBCores)
106 print(f0) 175 print(f0)
176
107 f0() 177 f0()
108
109