Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Allow compressed data in R data files #308

Merged
merged 1 commit into from
Mar 7, 2021
Merged

Allow compressed data in R data files #308

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
44 changes: 39 additions & 5 deletions src/registry.jl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -22,14 +22,45 @@ add_format(format"GZIP", [0x1f, 0x8b], ".gz", [:Libz => UUID("2ec943e9-cfe8-584d
add_format(format"BSON",(),".bson", [:BSON => UUID("fbb218c0-5317-5bc6-957e-2ee96dd4b1f0")])
add_format(format"JLSO", (), ".jlso", [:JLSO => UUID("9da8a3cd-07a3-59c0-a743-3fdc52c30d11")])

function detect_compressed(io, len=getlength(io); formats=["GZIP", "BZIP2", "XZ", "LZ4"])
seekstart(io)
len < 2 && return false
b1 = read(io, UInt8)
b2 = read(io, UInt8)
if "GZIP" ∈ formats
b1 == 0x1f && b2 == 0x8b && return true
end
len < 3 && return false
b3 = read(io, UInt8)
if "BZIP2" ∈ formats
b1 == 0x42 && b2 == 0x5A && b3 == 68 && return true
end
len < 4 && return false
b4 = read(io, UInt8)
if "LZ4" ∈ formats
b1 == 0x04 && b2 == 0x22 && b3 == 0x4D && b4 == 0x18 && return true
end
len < 5 && return false
b5 = read(io, UInt8)
len < 6 && return false
b6 = read(io, UInt8)
if "XZ" ∈ formats
b1 == 0xFD && b2 == 0x37 && b3 == 0x7A && b4 == 0x58 && b5 == 0x5A && b6 == 0x00 && return true
end
return false
end

# test for RD?n magic sequence at the beginning of R data input stream
function detect_rdata(io)
seekstart(io)
read(io, UInt8) == UInt8('R') &&
read(io, UInt8) == UInt8('D') &&
read(io, UInt8) in (UInt8('A'), UInt8('B'), UInt8('X')) &&
read(io, UInt8) in (UInt8('2'), UInt8('3')) &&
(c = read(io, UInt8); c == UInt8('\n') || (c == UInt8('\r') && read(io, UInt8) == UInt8('\n')))
b = read(io, UInt8)
if b == UInt8('R')
return read(io, UInt8) == UInt8('D') &&
read(io, UInt8) in (UInt8('A'), UInt8('B'), UInt8('X')) &&
read(io, UInt8) in (UInt8('2'), UInt8('3')) &&
(c = read(io, UInt8); c == UInt8('\n') || (c == UInt8('\r') && read(io, UInt8) == UInt8('\n')))
end
return detect_compressed(io; formats=["GZIP", "BZIP2", "XZ"])
end

add_format(format"RData", detect_rdata, [".rda", ".RData", ".rdata"], [idRData, LOAD])
Expand All @@ -38,6 +69,9 @@ function detect_rdata_single(io)
seekstart(io)
res = read(io, UInt8) in (UInt8('A'), UInt8('B'), UInt8('X')) &&
(c = read(io, UInt8); c == UInt8('\n') || (c == UInt8('\r') && read(io, UInt8) == UInt8('\n')))
if !res
res = detect_compressed(io; formats=["GZIP", "BZIP2", "XZ"])
end
seekstart(io)
return res
end
Expand Down
Binary file added test/files/iris.rda
View file
Open in desktop
Binary file not shown.
3 changes: 3 additions & 0 deletions test/query.jl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -384,6 +384,9 @@ let file_dir = joinpath(@__DIR__, "files"), file_path = Path(file_dir)
# 6 for /r/n and 5 for /n
@test (position(io) in (5, 6))
end
# A GZipped file
q = query(joinpath(file_dir, "iris.rda"))
@test typeof(q) <: File{format"RData"}
end
@testset "RDS detection" begin
q = query(joinpath(file_dir, "minimal_ascii.rds"))
Expand Down