Amrex.jl

abstract type AbstractAmrex <: AbstractExtractor end

mutable struct Amrex <: AbstractAmrex
    app::String
    outputPrefix::String
    inputs::Array{String}
    outputs::Array{String}
    runlogFile::String

    Amrex(outputPrefix::String, runlogFile::String) = new(
        "Amrex",
        outputPrefix,
        ["max_step", "amr.check_int", "amr.plot_int", "amr.n_cell", "amr.max_level", "caseID"],
        ["plots_size", "checkpoints_size"],
        runlogFile,
    )
end


"""
    Parses an input file with entries key = value, returns all entries in a Dict
    # Arguments
    - `extractor::AbstractAmrex` : input type extending AbstractAmrex
    - `inputFile::String` : input file to be parsed, absolute path is preferred
"""
function _input_parser(extractor::AbstractAmrex, inputFile::String)::Dict{String,String}

    parameters = Dict{String,String}()
    # get file contents in a single iterable type, \n newline is removed 
    fileContents = readlines(inputFile)

    # go through each line
    for line in fileContents
        if isempty(line)
            continue
        end

        # remove comments marked with #
        result = findfirst("#", line)

        if isnothing(result) == false
            line = SubString(line, 1, result[1] - 1)
            if isempty(line)
                continue
            end
        end

        parameter = split(line, "=")
        parameters[strip(parameter[1])] = strip(parameter[2])

    end

    return parameters
end

"""
    Get actual independent variables for I/O characterization: 
    number of cells or ncells, output frequency or nplots, ncheckpoints, etc.    
    from input parameters 
    # Arguments
    - `extractor::AbstractAmrex` : input type extending AbstractAmrex
    - `parameters::Dict{Any,Any}` : input file to be parsed, absolute path is preferred
"""
function _get_independent_variables(extractor::AbstractAmrex, parameters)::Dict{String,Any}

    independentVariables = Dict{String,Any}()

    # Number of output events, 
    # get is the safe way. 3rd argument is a default fallback if key not found
    maxStepStr = get(parameters, "max_step", "")

    if maxStepStr != ""

        # safe string conversion to a type
        maxStep = parse(Int64, maxStepStr)

        plotIntStr = get(parameters, "amr.plot_int", "")
        if plotIntStr != ""
            plotFrequency = parse(Int64, plotIntStr)
            independentVariables["amr.plot_int"] = plotFrequency
            independentVariables["amr.nplot_files"] = floor(Int32, maxStep / plotFrequency)
        else
            throw(NoSuchFieldException("jexio Amrex: Can't find amr.plot_int"))
        end

        checkIntStr = get(parameters, "amr.check_int", "")
        if checkIntStr != ""
            checkpointFrequency = parse(Int64, checkIntStr)
            independentVariables["amr.check_int"] = checkpointFrequency
            independentVariables["amr.ncheck_files"] =
                floor(Int32, maxStep / checkpointFrequency)
        else
            throw(NoSuchFieldException("jexio Amrex: Can't find amr.check_int"))
        end

    end

    # Using the dot "." operator to apply it on an element-by-element basis (like a dot product)
    # input is a dictionary with key="amr.ncell" and value = {"nx" "ny" "nz"},  
    # output is nx*ny*nz
    # Example:  
    # input Dict[ "amr.n_cell" => ["16" "16"] ], if key not found return 0
    # >ncells
    #   256
    ncells = prod(parse.(Int64, split(get(parameters, "amr.n_cell", ["0"]))))
    independentVariables["amr.ncells"] = ncells

    maxLevel = get(parameters, "amr.max_level", "")
    independentVariables["amr.max_level"] = maxLevel == "" ? 1 : parse(Int32, maxLevel)

    regrid = get(parameters, "amr.regrid_int", "")
    independentVariables["amr.regrid_int"] = regrid == "" ? 1 : parse(Int32, regrid)

    return independentVariables

end


function _get_inputs_X(extractor::AbstractAmrex)

end