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comparison 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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-1:000000000000 0:ab62b4ecd5b9
1 library(SticsRFiles)
2 library(SticsOnR)
3 library(dplyr)
4 library(stringr)
5 library(parallel)
6
7 print("==================================")
8
9 print(paste0("Cores=", detectCores()))
10
11 print("==================================")
12
13 native_wd_path <- getwd()
14
15 # Initializations: set path here
16
17 sms_path_V9 <- paste0(getwd(), "/Stics_Tests/branches/Stics_Tests_for_Stics_v92")
18
19 sms_idesticsr_path <- "/home/rstudio/IDESticsR"
20
21 invisible(sapply(list.files(file.path(sms_idesticsr_path),pattern = "*[R|r]$", full.names = TRUE), source))
22
23 javastics <- paste0(getwd(), "/JavaSTICS-1.41-stics-9.2")
24
25 path_typoFR <- file.path(sms_path_V9, "typo_usms_FR_14_12_2017_pour_tri_evaluation_officielle.csv")
26 path_typo <- file.path(sms_path_V9, "typo_usms.csv")
27
28 # Select corresponding USMs
29 plant_files <- NULL
30
31 USM_list_file <- paste0(native_wd_path,"/USMlist.csv")
32
33 UsmMetadata <- read.csv(USM_list_file,header=T, sep=";",stringsAsFactors = FALSE)
34
35 # to guess the plant
36 plant <- UsmMetadata$plant1[1]
37
38 if (plant == "corn") {plant <- "maize"}
39
40 USM_names <- UsmMetadata$usm
41
42 workspace <- paste0(native_wd_path, "/work")
43
44 res <- evaluate_SMS(sms_path=sms_path_V9, javastics=javastics, workspace=workspace,
45 workspace_prev=NULL,
46 workspace_ref=NULL, path_typo=path_typo,
47 eval_folder=paste0("eval_",plant), usms=USM_names,
48 param_values=NULL, plant=plant, plant_files=plant_files,
49 var_names=NULL,
50 nb_cores=1, do_create_workspace=TRUE,
51 do_run=TRUE, do_eval=TRUE, do_generate_report=TRUE,
52 report_path=file.path(paste0(native_wd_path, "/EvaluationReports"),str_to_title(plant)),
53 stics_eval_version=NULL, stics_ref_version=NULL,
54 sms_version=NULL)