# Generating STICS text files from XML files

    library(SticsRFiles)

## Introduction

In this part information are focusing on functionalities related to generation of text input files for the STICS model.

Generated files will be directly usable for running the model with SticsOnR package functions. See the documentation here.

## Converting JavaSTICS workspace files

For using the model directly neither using the JavaSTICS graphical interface nor the `run_javastics` function interface, we provide a function, `gen_usms_xml2txt`, for converting JavaSTICS XML files to STICS text files from a JavaStics workspace.

Then, the model can be run using the `run_stics()` function from SticsOnR

Observation files may also be copied if they have a standard name corresponding to a usm name and a `.obs` extension. If not, they must be renamed to do so.

    # Specifying the JavaSTICS folder
    javastics_path <- "/path/to/JavaSTICS-1.5.2-STICS-10.1.0"

    # Specifying a workspace as a subfolder of JavaSTICS
    workspace_path <- "example"
    # or an absolute path to an external folder
    # workspace_path <- "/path/to/javastics/workspace"

    # Specifying an output folder path
    output_path <- "/path/to/output/folder"

## Converting files into separated folders (one per usm)

    ## Generating files for all the usms contained in the workspace

    # Into the workspace directory
    gen_usms_xml2txt(javastics_path,
                     workspace_path)
    #> ℹ USM 'SugarCane' successfully created
    #> ℹ USM 'potato' successfully created
    #> ℹ USM 'banana' successfully created
    #> ℹ USM 'sorghum' successfully created
    #> ℹ USM 'barley' successfully created
    #> ℹ USM 'sugarbeet' successfully created
    #> ℹ USM 'wheat' successfully created
    #> ℹ USM 'maize' successfully created
    #> ℹ USM 'soybean' successfully created
    #> ℹ USM 'lettuce' successfully created
    #> ℹ USM 'tomato' successfully created
    #> ℹ USM 'DurumWheat' successfully created
    #> ℹ USM 'rapeseed' successfully created
    #> ℹ USM 'sunflower' successfully created
    #> ℹ USM 'grass' successfully created
    #> ℹ USM 'BareSoil' successfully created
    #> ! Obs file not found for USM
    #> "demo_Wheat1": '/tmp/JavaSTICS-1.5.2-STICS-10.1.0/example/demo_Wheat1.obs'
    #> ℹ USM 'demo_Wheat1' successfully created
    #> ! Obs file not found for USM
    #> "demo_BareSoil2": '/tmp/JavaSTICS-1.5.2-STICS-10.1.0/example/demo_BareSoil2.obs'
    #> ℹ USM 'demo_BareSoil2' successfully created
    #> ! Obs file not found for USM
    #> "demo_maize3": '/tmp/JavaSTICS-1.5.2-STICS-10.1.0/example/demo_maize3.obs'
    #> ℹ USM 'demo_maize3' successfully created
    #> ! Obs file not found for USM
    #> "DurumWheat_4years": '/tmp/JavaSTICS-1.5.2-STICS-10.1.0/example/DurumWheat_4years.obs'
    #> ℹ USM 'DurumWheat_4years' successfully created
    #> ! Obs file not found for USM
    #> "maize_4years": '/tmp/JavaSTICS-1.5.2-STICS-10.1.0/example/maize_4years.obs'
    #> ℹ USM 'maize_4years' successfully created
    #> ℹ USM 'strawberry' successfully created
    #> ℹ USM 'pea' successfully created
    #> ℹ USM 'vine' successfully created
    #> ℹ USM 'fescue' successfully created
    #> ℹ USM 'flax' successfully created
    #> ! Obs file not found for USM
    #> "intercrop_pea_barley": '/tmp/JavaSTICS-1.5.2-STICS-10.1.0/example/intercrop_pea_barley.obs'
    #> ℹ USM 'intercrop_pea_barley' successfully created
    #> ℹ USM 'timothy' successfully created
    #> ℹ USM 'DurumWheat_snow' successfully created
    #> ℹ USM 'Turmeric' successfully created
    #> ℹ USM 'cc_BristleOat' successfully created
    #> ℹ USM 'cc_mustard' successfully created
    #> ℹ USM 'cc_ItalianRyegrass' successfully created
    #> ℹ USM 'cc_vetch' successfully created
    #> ℹ USM 'cc_CrimsonClover' successfully created
    #> ℹ USM 'proto_rice' successfully created

    # Into a specific output folder, with verbose mode turned off
    gen_usms_xml2txt(javastics_path,
                     workspace_path,
                     out_dir = output_path,
                     verbose = FALSE)

    ## Generating files for a subset of usms
    # Into the workspace directory
    gen_usms_xml2txt(javastics_path,
                     workspace_path,
                     usm = c("banana", "wheat"))
    #> ℹ USM 'banana' successfully created
    #> ℹ USM 'wheat' successfully created

    # Into a specific folder
    gen_usms_xml2txt(javastics_path,
                     workspace_path,
                     usm = c("banana", "wheat"),
                     out_dir = output_path)
    #> ℹ USM 'banana' successfully created
    #> ℹ USM 'wheat' successfully created

    ## Getting returned information about files generation
    gen_info <- gen_usms_xml2txt(javastics_path,
                                 workspace_path,
                                 usm = c("banana", "wheat"),
                                 out_dir = output_path)
    #> ℹ USM 'banana' successfully created
    #> ℹ USM 'wheat' successfully created

    gen_info
    #> $usms_path
    #> [1] "/path/to/output/folder/banana"
    #> [2] "/path/to/output/folder/wheat"
    #>
    #> $files
    #>  [1] "climat.txt"      "param.sol"       "ficini.txt"      "ficplt1.txt"
    #>  [5] "fictec1.txt"     "station.txt"     "new_travail.usm" "tempopar.sti"
    #>  [9] "tempoparv6.sti"  "ficplt2.txt"     "fictec2.txt"
    #>
    #> $copy_status
    #> [1] TRUE TRUE
    #>
    #> $obs_copy_status
    #> [1] TRUE TRUE
    #>
    #> $lai_copy_status
    #> [1] FALSE FALSE

## Converting files into one folder (overwriting case)

    # Generating files directly in the workspace or a specific folder
    # (no usm sub-folder)
    # In this case the model files are overwritten at each gen_usms_xml2txt call !
    # In the workspace
    gen_usms_xml2txt(javastics_path,
                     workspace_path,
                     usm = "banana",
                     dir_per_usm_flag = FALSE,
                     verbose = FALSE)

    # In a specific folder
    gen_usms_xml2txt(javastics_path,
                     workspace_path,
                     usm = "banana",
                     out_dir = output_path,
                     dir_per_usm_flag = FALSE,
                     verbose = FALSE)