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annotate eval_only_stics_on_sms.R @ 0:ab62b4ecd5b9 draft default tip

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"planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 5e434da355bade7d12364ccbd84b53848e6fa4c5"
author siwaa
date Mon, 18 Jul 2022 10:54:39 +0000
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ab62b4ecd5b9 "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 5e434da355bade7d12364ccbd84b53848e6fa4c5"
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1 library(SticsRFiles)
ab62b4ecd5b9 "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 5e434da355bade7d12364ccbd84b53848e6fa4c5"
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2 library(SticsOnR)
ab62b4ecd5b9 "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 5e434da355bade7d12364ccbd84b53848e6fa4c5"
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3 library(dplyr)
ab62b4ecd5b9 "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 5e434da355bade7d12364ccbd84b53848e6fa4c5"
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4 library(stringr)
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5 library(parallel)
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7 print("==================================")
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9 print(paste0("Cores=", detectCores()))
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11 print("==================================")
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ab62b4ecd5b9 "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 5e434da355bade7d12364ccbd84b53848e6fa4c5"
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13 native_wd_path <- getwd()
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ab62b4ecd5b9 "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 5e434da355bade7d12364ccbd84b53848e6fa4c5"
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15 # Initializations: set path here
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17 sms_path_V9 <- paste0(getwd(), "/Stics_Tests/branches/Stics_Tests_for_Stics_v92")
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19 sms_idesticsr_path <- "/home/rstudio/IDESticsR"
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21 invisible(sapply(list.files(file.path(sms_idesticsr_path),pattern = "*[R|r]$", full.names = TRUE), source))
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23 javastics <- paste0(getwd(), "/JavaSTICS-1.41-stics-9.2")
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25 path_typoFR <- file.path(sms_path_V9, "typo_usms_FR_14_12_2017_pour_tri_evaluation_officielle.csv")
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26 path_typo <- file.path(sms_path_V9, "typo_usms.csv")
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28 # Select corresponding USMs
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29 plant_files <- NULL
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31 USM_list_file <- paste0(native_wd_path,"/USMlist.csv")
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33 UsmMetadata <- read.csv(USM_list_file,header=T, sep=";",stringsAsFactors = FALSE)
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35 # to guess the plant
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36 plant <- UsmMetadata$plant1[1]
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38 if (plant == "corn") {plant <- "maize"}
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40 USM_names <- UsmMetadata$usm
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42 workspace <- paste0(native_wd_path, "/work")
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44 res <- evaluate_SMS(sms_path=sms_path_V9, javastics=javastics, workspace=workspace,
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45 workspace_prev=NULL,
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46 workspace_ref=NULL, path_typo=path_typo,
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47 eval_folder=paste0("eval_",plant), usms=USM_names,
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48 param_values=NULL, plant=plant, plant_files=plant_files,
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49 var_names=NULL,
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50 nb_cores=1, do_create_workspace=TRUE,
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51 do_run=TRUE, do_eval=TRUE, do_generate_report=TRUE,
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52 report_path=file.path(paste0(native_wd_path, "/EvaluationReports"),str_to_title(plant)),
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53 stics_eval_version=NULL, stics_ref_version=NULL,
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54 sms_version=NULL)