Mercurial > repos > siwaa > carboseq_s
changeset 16:5ed871d666b4 draft
"planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/be8c2ab794a3722ee6edc3c9f7e73ccc45806f31/toos/CarboSeqSimulator commit be8c2ab794a3722ee6edc3c9f7e73ccc45806f31-dirty"
| author | siwaa |
|---|---|
| date | Thu, 12 Dec 2024 14:38:52 +0000 |
| parents | de71663fbce4 |
| children | 56b0bf51585a |
| files | carboseqSimulator.xml run.r |
| diffstat | 2 files changed, 3 insertions(+), 178 deletions(-) [+] |
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--- a/carboseqSimulator.xml Tue Dec 10 09:14:52 2024 +0000 +++ b/carboseqSimulator.xml Thu Dec 12 14:38:52 2024 +0000 @@ -1,4 +1,4 @@ -<tool id="CarboSeqSimulator" name="CarboSeqSimulator" version="1.0.17"> +<tool id="CarboSeqSimulator" name="CarboSeqSimulator" version="1.0.18"> <description>To run the CarboSeq simulator</description> <requirements> <container type="singularity">docker://registry.forgemia.inra.fr/csopra/csopralibs:main</container> @@ -16,7 +16,8 @@ cp /usr/local/src/myscripts/start_server.sh . && cp -r /usr/local/src/myscripts/config_mappers . && cp -r /usr/local/src/myscripts/data . && - Rscript $__tool_directory__/run.r --srcDir=\$(realpath -s input) --srcOut=\$(realpath -s output) --semPath=\$(realpath -s .) --part=${semantifier} --NBCores=\${GALAXY_SLOTS:-4}&& + cp /usr/local/src/myscripts/scenarios/run-sim-perf/run.r . && + Rscript ./run.r --srcDir=\$(realpath -s input) --srcOut=\$(realpath -s output) --semPath=\$(realpath -s .) --part=${semantifier} --NBCores=\${GALAXY_SLOTS:-4}&& cp output/* ${output}" ]]> </command>
--- a/run.r Tue Dec 10 09:14:52 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,176 +0,0 @@ - -# help : Rscript % --url=https://coby.infosol.inrae.fr:7777/semantify --srcDir=~/CSCL/src/csoprapreprocessor/inst/extdata/carboseq/set001/ - -# Function to parse command-line arguments -parse_args <- function() { - args <- commandArgs(trailingOnly = TRUE) - - # Default values for optional parameters - url <- "https://coby.infosol.inrae.fr:8080/semantify/" - srcDir <- NULL - # srcDirOutput <- NULL - part <- "modeltoolbox_sem_remote" - DS <- T - NBCores <- 1 - semPath <- "." - # Parse arguments - for (arg in args) { - - if (grepl("^--url=", arg)) { - url <- sub("^--url=", "", arg) - } - - if (grepl("^--srcDir=", arg)) { - srcDir <- sub("^--srcDir=", "", arg) - } - - # if (grepl("^--srcDirOutput=", arg)) { - # srcDirOutput <- sub("^--srcDirOutput=", "", arg) - # } - if (grepl("^--part=", arg)) { - part <- sub("^--part=", "", arg) - } - - if (grepl("^--DS=", arg)) { - DS <- ifelse(sub("^--DS=", "", arg) == "TRUE", TRUE, FALSE) - } - - if (grepl("^--NBCores=", arg)) { - NBCores <- as.numeric(sub("^--NBCores=", "", arg)) - } - - if (grepl("^--srcOut=", arg)) { - srcOut <- sub("^--srcOut=", "", arg) - } - - if (grepl("^--semPath=", arg)) { - semPath <- sub("^--semPath=", "", arg) - } - } - - list( url = url, srcDir = srcDir, part = part, DS = DS, - NBCores = NBCores, srcOut = srcOut, semPath = semPath ) -} - -argus <- parse_args() - -url <- argus[["url"]] -srcDir <- argus[["srcDir"]] -# srcDirOutput <- argus[["srcDirOutput"]] -part <- argus[["part"]] -DS <- argus[["DS"]] -NBCores <- argus[["NBCores"]] - -srcOut <- argus[["srcOut"]] - -semPath <- argus[["semPath"]] - -if (!endsWith(srcOut, "/")) { - srcOut <- paste0(srcOut, "/") -} - -#if (is.null(srcDirOutput)) { -# srcDirOutput <- srcDir -# } - -# url="https://147.100.203.110/semantify " -# srcDir="~/tmp/testFiles/400Sites/" -# part="modeltoolbox" -# part="csoprapreprocessor" -# DS=TRUE -# NBCores=10 - -# MTB{{{ -if (part == "modeltoolbox") { -f0 <- function(){ - modeltoolbox::loadCSVs(maxCores = NBCores, cinputCalculator = "cinest", - preprocessorInputs = ppi) - modeltoolbox::runSims(maxCores = NBCores) - res <- modeltoolbox::readSocForcingsResults() - fileName <- "resRun.RData" - filePath <- file.path(srcOut, fileName) - save(res, file = filePath) -} -} -#}}} - -if (part == "modeltoolbox_sem_local") { - DS <- F - print("Setting DS to F. Will semantify outside of the csoprapreprocessor functions") - f0 <- function(){ - path <- this.path::this.dir() - print(path) - csopratools::semantify( - inputDir = srcDir, - outputDir = srcDir, - name = "carboseq", - # use = "service", - URL = url, - use = "java", - semantifierRootPath = semPath, - extFileNames = paste0(c("crop", "soil", "units"), ".csv") - ) - print("between semantify and load") - - ppi$srcDirOutput <- NULL # Hack - - modeltoolbox::loadCSVs(maxCores = NBCores, cinputCalculator = "cinest", - preprocessorInputs = ppi) - print("between load an sim") - modeltoolbox::runSims(maxCores = NBCores) - res <- modeltoolbox::getYearlySOCResults() - # res <- modeltoolbox::readSocForcingsResults() - fileName <- "resRun.RData" - filePath <- file.path(srcOut, fileName) - save(res, file = filePath) - } -} - -if (part == "modeltoolbox_sem_remote") { - DS <- F - print("Setting DS to F. Will semantify outside of the csoprapreprocessor functions") - f0 <- function(){ - path <- this.path::this.dir() - print(path) - setwd(path) - setwd("../..") - csopratools::semantify( - inputDir = srcDir, - outputDir = srcDir, - name = "carboseq", - use = "service", - URL = url, - extFileNames = paste0(c("crop", "soil", "units"), ".csv") - ) - - # ppi$srcDirOutput <- NULL # Hack - - modeltoolbox::loadCSVs(maxCores = NBCores, cinputCalculator = "cinest", - preprocessorInputs = ppi) - modeltoolbox::runSims(maxCores = NBCores) - res <- modeltoolbox::getYearlySOCResults() - # res <- modeltoolbox::readSocForcingsResults() - fileName <- "resRun.RData" - filePath <- file.path(srcOut, fileName) - save(res, file = filePath) - } -} - -ppi <- list( - weatherRetrievalMethod = "service", - srcDir = srcDir, - doSemantify = DS, - weatherRetrievalURL = "https://coby.infosol.inrae.fr:8080/spatial-data/temporal/climate", - semantifierServiceURL = url - ) - - -print(url) -print(srcDir) -# print(srcDirOutput) -print(srcOut) -print(DS) -print(NBCores) -print(f0) - -f0()