Load JLD2 from IOBuffer

[cwiese]

I am not finding a method to load a JLD from IOBuffer. This seems basic for saving and loading to cloud like S3 or Azure Blob storage (which is my case). I would like to avoid reading from a REST call and saving locally - just to load using a filename. Perhaps I am missing something?

[JonasIsensee]

Hi @cwiese ,
it's not possible to load JLD2 files directly from IOBuffers. ( it has to be seekable)
JLD2 is based on the HDF5 format and therefore a hierarchical file format. This requires non-linear access during both reading and writing.
I typically load remote files either by copy (duh) or using a file system abstraction (sshfs).

I also remember this discussion #233

It should absolutely be possible to add this feature to JLD2
by implementing a more general buffered reader that reads linearly from file and holds an incremental copy in memory.
(Note, the "table of contents" is typically located at the end of a file, so this will be rather inefficient, if bandwidth / file size is a concern)

[bartvanerp]

Ran into the same issue today when loading from AWS S3. I think it would be a nice addition to this package. For other people who will encounter this same limitation, I wanted to share my snippet of code to help them save time. The code basically hacks around the issue by saving locally as described above:

function load(x::Vector{UInt8}, format::String)

    # create temp folder
    mkdir(".tmp")

    # write to file
    write(".tmp/file." * format, x)

    # load object
    y = load(".tmp/file." * format)

    # remove temp folder
    rm(".tmp"; recursive=true)

    # return object
    return y

end

object = load(s3("GET", "/your-bucket/file.jld2"), "jld2")

[stevengj]

it's not possible to load JLD2 files directly from IOBuffers. ( it has to be seekable)

An IOBuffer is seekable! (It's just a wrapper around an array, so random access is no problem.)

For example:

julia> buf = IOBuffer("foo bar")
IOBuffer(data=UInt8[...], readable=true, writable=false, seekable=true, append=false, size=7, maxsize=Inf, ptr=1, mark=-1)

julia> seek(buf, 4)
IOBuffer(data=UInt8[...], readable=true, writable=false, seekable=true, append=false, size=7, maxsize=Inf, ptr=5, mark=-1)

julia> read(buf, Char)
'b': ASCII/Unicode U+0062 (category Ll: Letter, lowercase)

julia> seek(buf, 1)
IOBuffer(data=UInt8[...], readable=true, writable=false, seekable=true, append=false, size=7, maxsize=Inf, ptr=2, mark=-1)

julia> read(buf, Char)
'o': ASCII/Unicode U+006F (category Ll: Letter, lowercase)

The main thing seems to be to implement the analogue of https://github.com/JuliaIO/JLD2.jl/blob/ad988caea3e2da874aaf0140ef37165e6189b64b/src/mmapio.jl for IOBuffer streams (which are effectively already "memory-mapped").

[JonasIsensee]

@stevengj You are right. This should definitely be possible to implement.

I wonder if it would make sense to implement a more general internal io buffer that can also wrap non-seekable IO objects (just read) and then buffer internally.
If made cleverly, this could allow reading from e.g. compression streams.

[JonasIsensee]

Implemented in #535