datafmt.jl

## file formats ##

module DataFmt

importall Base
import Base: _default_delims

export countlines, readdlm, readcsv, writedlm, writecsv


const invalid_dlm = char(0xfffffffe)
const offs_chunk_size = 5000

countlines(nameorfile) = countlines(nameorfile, '\n')
function countlines(filename::AbstractString, eol::Char)
    open(filename) do io
        countlines(io, eol)
    end
end
function countlines(io::IO, eol::Char)
    if !isascii(eol)
        error("only ASCII line terminators are supported")
    end
    a = Array(UInt8, 8192)
    nl = 0
    preceded_by_eol = true
    while !eof(io)
        nb = readbytes!(io, a)
        for i=1:nb
            if char(a[i]) == eol
                preceded_by_eol = true
            elseif preceded_by_eol
                preceded_by_eol = false
                nl+=1
            end
        end
    end
    nl
end

readdlm(input, T::Type; opts...) = readdlm(input, invalid_dlm, T, '\n'; opts...)
readdlm(input, dlm::Char, T::Type; opts...) = readdlm(input, dlm, T, '\n'; opts...)

readdlm(input; opts...) = readdlm(input, invalid_dlm, '\n'; opts...)
readdlm(input, dlm::Char; opts...) = readdlm(input, dlm, '\n'; opts...)

readdlm(input, dlm::Char, eol::Char; opts...) = readdlm_auto(input, dlm, Float64, eol, true; opts...)
readdlm(input, dlm::Char, T::Type, eol::Char; opts...) = readdlm_auto(input, dlm, T, eol, false; opts...)

function readdlm_auto(input, dlm::Char, T::Type, eol::Char, auto::Bool; opts...)
    optsd = val_opts(opts)
    use_mmap = get(optsd, :use_mmap, @windows ? false : true)
    isa(input, AbstractString) && (fsz = filesize(input); input = use_mmap && (fsz > 0) && fsz < typemax(Int) ? as_mmap(input,fsz) : readall(input))
    sinp = isa(input, Vector{UInt8}) ? bytestring(input) :
           isa(input, IO) ? readall(input) :
           input
    readdlm_string(sinp, dlm, T, eol, auto, optsd)
end

function as_mmap(fname::AbstractString, fsz::Int64)
    open(fname) do io
        mmap_array(UInt8, (int(fsz),), io)
    end
end

function ascii_if_possible(sbuff::AbstractString)
    isascii(sbuff) ? convert(ASCIIString,sbuff) : sbuff
end

#
# Handlers act on events generated by the parser.
# Parser calls store_cell on the handler to pass events.
#
# DLMOffsets: Keep offsets (when result dimensions are not known)
# DLMStore: Store values directly into a result store (when result dimensions are known)
abstract DLMHandler

type DLMOffsets <: DLMHandler
    oarr::Vector{Vector{Int}}
    offidx::Int
    thresh::Int
    bufflen::Int

    function DLMOffsets(sbuff::AbstractString)
        offsets = Array(Array{Int,1}, 1)
        offsets[1] = Array(Int, offs_chunk_size)
        thresh = int(Base.Sys.total_memory() / sizeof(Int) / 5)
        new(offsets, 1, thresh, length(sbuff.data))
    end
end

function store_cell(dlmoffsets::DLMOffsets, row::Int, col::Int, quoted::Bool, startpos::Int, endpos::Int)
    offidx = dlmoffsets.offidx
    (offidx == 0) && return     # offset collection stopped to avoid choking on memory

    oarr = dlmoffsets.oarr
    offsets = oarr[end]
    if length(offsets) < offidx
        offlen = offs_chunk_size * length(oarr)
        if (offlen + offs_chunk_size) > dlmoffsets.thresh
            est_tot = int(offlen * dlmoffsets.bufflen / endpos)
            if (est_tot - offlen) > offs_chunk_size    # allow another chunk
                # abandon offset collection
                dlmoffsets.oarr = Vector{Int}[]
                dlmoffsets.offidx = 0
                return
            end
        end
        offsets = Array(Int, offs_chunk_size)
        push!(oarr, offsets)
        offidx = 1
    end
    offsets[offidx] = row
    offsets[offidx+1] = col
    offsets[offidx+2] = int(quoted)
    offsets[offidx+3] = startpos
    offsets[offidx+4] = endpos
    dlmoffsets.offidx = offidx + 5
    nothing
end

function result(dlmoffsets::DLMOffsets)
    trimsz = (dlmoffsets.offidx-1)%offs_chunk_size
    ((trimsz > 0) || (dlmoffsets.offidx == 1)) && resize!(dlmoffsets.oarr[end], trimsz)
    dlmoffsets.oarr
end

type DLMStore{T,S<:AbstractString} <: DLMHandler
    hdr::Array{AbstractString, 2}
    data::Array{T, 2}

    nrows::Int
    ncols::Int
    lastrow::Int
    lastcol::Int
    hdr_offset::Int
    sbuff::S
    auto::Bool
    eol::Char
    tmp64::Array{Float64,1}
end

function DLMStore{T,S<:AbstractString}(::Type{T}, dims::NTuple{2,Integer}, has_header::Bool, sbuff::S, auto::Bool, eol::Char)
    (nrows,ncols) = dims
    ((nrows == 0) || (ncols == 0)) && error("Empty input")
    ((nrows < 0) || (ncols < 0)) && error("Invalid dimensions")
    hdr_offset = has_header ? 1 : 0
    DLMStore{T,S}(fill(SubString(sbuff,1,0), 1, ncols), Array(T, nrows-hdr_offset, ncols), nrows, ncols, 0, 0, hdr_offset, sbuff, auto, eol, Array(Float64,1))
end

function store_cell{T,S<:AbstractString}(dlmstore::DLMStore{T,S}, row::Int, col::Int, quoted::Bool, startpos::Int, endpos::Int)
    drow = row - dlmstore.hdr_offset

    ncols = dlmstore.ncols
    lastcol = dlmstore.lastcol
    lastrow = dlmstore.lastrow
    cells::Array{T,2} = dlmstore.data
    sbuff::S = dlmstore.sbuff
    tmp64 = dlmstore.tmp64

    endpos = prevind(sbuff, nextind(sbuff,endpos))
    (endpos > 0) && ('\n' == dlmstore.eol) && ('\r' == char(sbuff[endpos])) && (endpos = prevind(sbuff, endpos))
    sval = quoted ? SubString(sbuff, startpos+1, endpos-1) : SubString(sbuff, startpos, endpos)

    if drow > 0
        # fill missing elements
        while ((drow - lastrow) > 1) || ((drow > lastrow > 0) && (lastcol < ncols))
            if (lastcol == ncols) || (lastrow == 0)
                lastcol = 0
                lastrow += 1
            end
            for cidx in (lastcol+1):ncols
                if (T <: AbstractString) || (T == Any)
                    cells[lastrow,cidx] = SubString(sbuff, 1, 0)
                elseif ((T <: Number) || (T <: Char)) && dlmstore.auto
                    throw(TypeError(:store_cell, "", Any, T))
                else
                    error("missing value at row $lastrow column $cidx")
                end
            end
            lastcol = ncols
        end

        # fill data
        if quoted && ('"' in sval)
            fail = colval(replace(sval, r"\"\"", "\""), cells, drow, col, tmp64)
        else
            fail = colval(sval, cells, drow, col, tmp64)
        end
        if fail
            ((T <: Number) && dlmstore.auto) ? throw(TypeError(:store_cell, "", Any, T)) : error("file entry \"$(sval)\" cannot be converted to $T")
        end

        dlmstore.lastrow = drow
        dlmstore.lastcol = col
    else
        # fill header
        colval((quoted && ('"' in sval)) ? replace(sval, r"\"\"", "\"") : sval, dlmstore.hdr, 1, col, tmp64)
    end

    nothing
end

function result{T}(dlmstore::DLMStore{T})
    nrows = dlmstore.nrows - dlmstore.hdr_offset
    ncols = dlmstore.ncols
    lastcol = dlmstore.lastcol
    lastrow = dlmstore.lastrow
    cells = dlmstore.data
    sbuff = dlmstore.sbuff

    if (lastcol < ncols) || (lastrow < nrows)
        while lastrow <= nrows
            (lastcol == ncols) && (lastcol = 0; lastrow += 1)
            for cidx in (lastcol+1):ncols
                if (T <: AbstractString) || (T == Any)
                    cells[lastrow,cidx] = SubString(sbuff, 1, 0)
                elseif ((T <: Number) || (T <: Char)) && dlmstore.auto
                    throw(TypeError(:store_cell, "", Any, T))
                else
                    error("missing value at row $lastrow column $cidx")
                end
            end
            lastcol = ncols
            (lastrow == nrows) && break
        end
        dlmstore.lastrow = lastrow
        dlmstore.lastcol = ncols
    end
    (dlmstore.hdr_offset > 0) ? (dlmstore.data, dlmstore.hdr) : dlmstore.data
end


function readdlm_string(sbuff::AbstractString, dlm::Char, T::Type, eol::Char, auto::Bool, optsd::Dict)
    ign_empty = (dlm == invalid_dlm)
    quotes = get(optsd, :quotes, true)
    comments = get(optsd, :comments, true)
    comment_char = get(optsd, :comment_char, '#')
    dims = get(optsd, :dims, nothing)

    has_header = get(optsd, :header, get(optsd, :has_header, false))
    haskey(optsd, :has_header) && (optsd[:has_header] != has_header) && error("conflicting values for header and has_header")

    skipstart = get(optsd, :skipstart, 0)
    (skipstart >= 0) || error("invalid value for skipstart")

    skipblanks = get(optsd, :skipblanks, true)

    offset_handler = (dims == nothing) ? DLMOffsets(sbuff) : DLMStore(T, dims, has_header, sbuff, auto, eol)

    for retry in 1:2
        try
            dims = dlm_parse(sbuff, eol, dlm, '"', comment_char, ign_empty, quotes, comments, skipstart, skipblanks, offset_handler)
            break
        catch ex
            if isa(ex, TypeError) && (ex.func == :store_cell)
                T = ex.expected
            elseif get(optsd, :ignore_invalid_chars, false)
                sbuff = ascii_if_possible(convert(typeof(sbuff), sbuff.data, ""))
            else
                rethrow(ex)
            end
            offset_handler = (dims == nothing) ? DLMOffsets(sbuff) : DLMStore(T, dims, has_header, sbuff, auto, eol)
        end
    end

    isa(offset_handler, DLMStore) && (return result(offset_handler))

    offsets = result(offset_handler)
    !isempty(offsets) && (return dlm_fill(T, offsets, dims, has_header, sbuff, auto, eol))

    optsd[:dims] = dims
    return readdlm_string(sbuff, dlm, T, eol, auto, optsd)
end

const valid_opts = [:header, :has_header, :ignore_invalid_chars, :use_mmap, :quotes, :comments, :dims, :comment_char, :skipstart, :skipblanks]
const valid_opt_types = [Bool, Bool, Bool, Bool, Bool, Bool, NTuple{2,Integer}, Char, Integer, Bool]
const deprecated_opts = Dict(:has_header => :header)
function val_opts(opts)
    d = Dict{Symbol,Union(Bool,NTuple{2,Integer},Char,Integer)}()
    for (opt_name, opt_val) in opts
        !in(opt_name, valid_opts) && error("unknown option $opt_name")
        opt_typ = valid_opt_types[findfirst(valid_opts, opt_name)]
        !isa(opt_val, opt_typ) && error("$opt_name should be of type $opt_typ")
        d[opt_name] = opt_val
        haskey(deprecated_opts, opt_name) && warn("$opt_name is deprecated, use $(deprecated_opts[opt_name]) instead")
    end
    d
end

function dlm_fill(T::DataType, offarr::Vector{Vector{Int}}, dims::NTuple{2,Integer}, has_header::Bool, sbuff::AbstractString, auto::Bool, eol::Char)
    idx = 1
    offidx = 1
    offsets = offarr[1]
    try
        dh = DLMStore(T, dims, has_header, sbuff, auto, eol)
        while idx <= length(offsets)
            row = offsets[idx]
            col = offsets[idx+1]
            quoted = bool(offsets[idx+2])
            startpos = offsets[idx+3]
            endpos = offsets[idx+4]

            ((idx += 5) > offs_chunk_size) && (offidx < length(offarr)) && (idx = 1; offsets = offarr[offidx += 1])

            store_cell(dh, row, col, quoted, startpos, endpos)
        end
        return result(dh)
    catch ex
        isa(ex, TypeError) && (ex.func == :store_cell) && (return dlm_fill(ex.expected, offarr, dims, has_header, sbuff, auto, eol))
        rethrow(ex)
    end
end


colval{T<:Bool, S<:AbstractString}(sval::S, cells::Array{T,2}, row::Int, col::Int, tmp64::Array{Float64,1}) = ((sval=="true") && (cells[row,col]=true; return false); (sval=="false") && (cells[row,col]=false; return false); true)
colval{T<:Number, S<:AbstractString}(sval::S, cells::Array{T,2}, row::Int, col::Int, tmp64::Array{Float64,1}) = (float64_isvalid(sval, tmp64) ? ((cells[row,col] = tmp64[1]); false) : true)
colval{T<:AbstractString, S<:AbstractString}(sval::S, cells::Array{T,2}, row::Int, col::Int, tmp64::Array{Float64,1}) = ((cells[row,col] = sval); false)
colval{S<:AbstractString}(sval::S, cells::Array{Any,2}, row::Int, col::Int, tmp64::Array{Float64,1}) = ((cells[row,col] = float64_isvalid(sval, tmp64) ? tmp64[1] : sval); false)
colval{T<:Char, S<:AbstractString}(sval::S, cells::Array{T,2}, row::Int, col::Int, tmp64::Array{Float64,1}) = ((length(sval) == 1) ? ((cells[row,col] = next(sval,1)[1]); false) : true)
colval{S<:AbstractString}(sval::S, cells::Array, row::Int, col::Int, tmp64::Array{Float64,1}) = true

dlm_parse(s::ASCIIString, eol::Char, dlm::Char, qchar::Char, cchar::Char, ign_adj_dlm::Bool, allow_quote::Bool, allow_comments::Bool, skipstart::Int, skipblanks::Bool, dh::DLMHandler) =  begin
    dlm_parse(s.data, uint8(uint32(eol)), uint8(uint32(dlm)), uint8(uint32(qchar)), uint8(uint32(cchar)),
              ign_adj_dlm, allow_quote, allow_comments, skipstart, skipblanks, dh)
end

function dlm_parse{T,D}(dbuff::T, eol::D, dlm::D, qchar::D, cchar::D, ign_adj_dlm::Bool, allow_quote::Bool, allow_comments::Bool, skipstart::Int, skipblanks::Bool, dh::DLMHandler)
    all_ascii = (D <: UInt8) || (isascii(eol) && isascii(dlm) && (!allow_quote || isascii(qchar)) && (!allow_comments || isascii(cchar)))
    (T <: UTF8String) && all_ascii && (return dlm_parse(dbuff.data, uint8(eol), uint8(dlm), uint8(qchar), uint8(cchar), ign_adj_dlm, allow_quote, allow_comments, skipstart, skipblanks, dh))
    ncols = nrows = col = 0
    is_default_dlm = (dlm == uint32(invalid_dlm) % D)
    error_str = ""
    # 0: begin field, 1: quoted field, 2: unquoted field, 3: second quote (could either be end of field or escape character), 4: comment, 5: skipstart
    state = (skipstart > 0) ? 5 : 0
    is_eol = is_dlm = is_cr = is_quote = is_comment = expct_col = false
    idx = 1
    try
        slen = sizeof(dbuff)
        col_start_idx = 1
        was_cr = false
        while idx <= slen
            val,idx = next(dbuff, idx)
            if (is_eol = (char(val) == char(eol)))
                is_dlm = is_comment = is_cr = is_quote = false
            elseif (is_dlm = (is_default_dlm ? in(char(val), _default_delims) : (char(val) == char(dlm))))
                is_comment = is_cr = is_quote = false
            elseif (is_quote = (char(val) == char(qchar)))
                is_comment = is_cr = false
            elseif (is_comment = (char(val) == char(cchar)))
                is_cr = false
            else
                is_cr = (char(eol) == '\n') && (char(val) == '\r')
            end

            if 2 == state   # unquoted field
                if is_dlm
                    state = 0
                    col += 1
                    store_cell(dh, nrows+1, col, false, col_start_idx, idx-2)
                    col_start_idx = idx
                    !ign_adj_dlm && (expct_col = true)
                elseif is_eol
                    nrows += 1
                    col += 1
                    store_cell(dh, nrows, col, false, col_start_idx, idx - (was_cr ? 3 : 2))
                    col_start_idx = idx
                    ncols = max(ncols, col)
                    col = 0
                    state = 0
                elseif (is_comment && allow_comments)
                    nrows += 1
                    col += 1
                    store_cell(dh, nrows, col, false, col_start_idx, idx - 2)
                    ncols = max(ncols, col)
                    col = 0
                    state = 4
                end
            elseif 1 == state   # quoted field
                is_quote && (state = 3)
            elseif 4 == state   # comment line
                if is_eol
                    col_start_idx = idx
                    state = 0
                end
            elseif 0 == state   # begin field
                if is_quote
                    state = (allow_quote && !was_cr) ? 1 : 2
                    expct_col = false
                elseif is_dlm
                    if !ign_adj_dlm
                        expct_col = true
                        col += 1
                        store_cell(dh, nrows+1, col, false, col_start_idx, idx-2)
                    end
                    col_start_idx = idx
                elseif is_eol
                    if (col > 0) || !skipblanks
                        nrows += 1
                        if expct_col
                            col += 1
                            store_cell(dh, nrows, col, false, col_start_idx, idx - (was_cr ? 3 : 2))
                        end
                        ncols = max(ncols, col)
                        col = 0
                    end
                    col_start_idx = idx
                    expct_col = false
                elseif is_comment && allow_comments
                    if col > 0
                        nrows += 1
                        if expct_col
                            col += 1
                            store_cell(dh, nrows, col, false, col_start_idx, idx - 2)
                        end
                        ncols = max(ncols, col)
                        col = 0
                    end
                    expct_col = false
                    state = 4
                elseif !is_cr
                    state = 2
                    expct_col = false
                end
            elseif 3 == state   # second quote
                if is_quote && !was_cr
                    state = 1
                elseif is_dlm && !was_cr
                    state = 0
                    col += 1
                    store_cell(dh, nrows+1, col, true, col_start_idx, idx-2)
                    col_start_idx = idx
                    !ign_adj_dlm && (expct_col = true)
                elseif is_eol
                    nrows += 1
                    col += 1
                    store_cell(dh, nrows, col, true, col_start_idx, idx - (was_cr ? 3 : 2))
                    col_start_idx = idx
                    ncols = max(ncols, col)
                    col = 0
                    state = 0
                elseif is_comment && allow_comments && !was_cr
                    nrows += 1
                    col += 1
                    store_cell(dh, nrows, col, true, col_start_idx, idx - 2)
                    ncols = max(ncols, col)
                    col = 0
                    state = 4
                elseif (is_cr && was_cr) || !is_cr
                    error_str = escape_string("unexpected character '$(char(val))' after quoted field at row $(nrows+1) column $(col+1)")
                    break
                end
            elseif 5 == state # skip start
                if is_eol
                    col_start_idx = idx
                    skipstart -= 1
                    (0 == skipstart) && (state = 0)
                end
            end
            was_cr = is_cr
        end

        if isempty(error_str)
            if 1 == state       # quoted field
                error_str = "truncated column at row $(nrows+1) column $(col+1)"
            elseif (2 == state) || (3 == state) || ((0 == state) && is_dlm)   # unquoted field, second quote, or begin field with last character as delimiter
                col += 1
                nrows += 1
                store_cell(dh, nrows, col, (3 == state), col_start_idx, idx-1)
                ncols = max(ncols, col)
            end
        end
    catch ex
        if isa(ex, TypeError) && (ex.func == :store_cell)
            rethrow(ex)
        else
            error("at row $(nrows+1), column $col : $ex)")
        end
    end
    !isempty(error_str) && error(error_str)

    return (nrows, ncols)
end

readcsv(io; opts...)          = readdlm(io, ','; opts...)
readcsv(io, T::Type; opts...) = readdlm(io, ',', T; opts...)

# todo: keyword argument for # of digits to print
writedlm_cell(io::IO, elt::FloatingPoint, dlm, quotes) = print_shortest(io, elt)
function writedlm_cell{T}(io::IO, elt::AbstractString, dlm::T, quotes::Bool)
    if quotes && !isempty(elt) && (('"' in elt) || ('\n' in elt) || ((T <: Char) ? (dlm in elt) : contains(elt, dlm)))
        print(io, '"', replace(elt, r"\"", "\"\""), '"')
    else
        print(io, elt)
    end
end
writedlm_cell(io::IO, elt, dlm, quotes) = print(io, elt)
function writedlm(io::IO, a::AbstractVecOrMat, dlm; opts...)
    optsd = val_opts(opts)
    quotes = get(optsd, :quotes, true)
    pb = PipeBuffer()
    nr = size(a,1)
    nc = size(a,2)
    for i = 1:nr
        for j = 1:nc
            writedlm_cell(pb, a[i,j], dlm, quotes)
            j == nc ? write(pb,'\n') : print(pb,dlm)
        end
        (nb_available(pb) > (16*1024)) && write(io, takebuf_array(pb))
    end
    write(io, takebuf_array(pb))
    nothing
end

writedlm{T}(io::IO, a::AbstractArray{T,0}, dlm; opts...) = writedlm(io, reshape(a,1), dlm; opts...)

#=
function writedlm_ndarray(io::IO, a::AbstractArray, dlm; opts...)
    tail = size(a)[3:end]
    function print_slice(idxs...)
        writedlm(io, sub(a, 1:size(a,1), 1:size(a,2), idxs...), dlm; opts...)
        if idxs != tail
            print(io, "\n")
        end
    end
    cartesianmap(print_slice, tail)
end
=#

function writedlm(io::IO, itr, dlm; opts...)
    optsd = val_opts(opts)
    quotes = get(optsd, :quotes, true)
    pb = PipeBuffer()
    for row in itr
        state = start(row)
        while !done(row, state)
            (x, state) = next(row, state)
            writedlm_cell(pb, x, dlm, quotes)
            done(row, state) ? write(pb,'\n') : print(pb,dlm)
        end
        (nb_available(pb) > (16*1024)) && write(io, takebuf_array(pb))
    end
    write(io, takebuf_array(pb))
    nothing
end

function writedlm(fname::AbstractString, a, dlm; opts...)
    open(fname, "w") do io
        writedlm(io, a, dlm; opts...)
    end
end

writedlm(io, a; opts...) = writedlm(io, a, '\t'; opts...)
writecsv(io, a; opts...) = writedlm(io, a, ','; opts...)

writemime(io::IO, ::MIME"text/csv", a::AbstractVecOrMat) = writedlm(io, a, ',')
writemime(io::IO, ::MIME"text/tab-separated-values", a::AbstractVecOrMat) = writedlm(io, a, '\t')

end # module DataFmt