Merge pull request #181 from JuliaIO/sd/07

fixes for 0.7

Author: SimonDanisch

src/FileIO.jl

@@ -28,6 +28,7 @@ export DataFormat,
        metadata
 
 import Base.showerror
+using Base: RefValue
 
 include("query.jl")
 include("error_handling.jl")

src/loadsave.jl

@@ -1,11 +1,21 @@
 const sym2loader = Dict{Symbol,Vector{Symbol}}()
 const sym2saver  = Dict{Symbol,Vector{Symbol}}()
+const has_pkg3 = try
+    using Pkg3
+    true
+catch e
+    false
+end
 
-function is_installed(pkg::Symbol)
-    isdefined(Main, pkg) && isa(getfield(Main, pkg), Module) && return true # is a module defined in Main scope
-    path = Base.find_in_path(string(pkg)) # hacky way to determine if a Package is installed
-    path == nothing && return false
-    return isfile(path)
+if isdefined(Base, :find_in_path)
+    function is_installed(pkg::Symbol)
+        isdefined(Main, pkg) && isa(getfield(Main, pkg), Module) && return true # is a module defined in Main scope
+        path = Base.find_in_path(string(pkg)) # hacky way to determine if a Package is installed
+        path == nothing && return false
+        return isfile(path)
+    end
+elseif has_pkg3 && isdefined(Pkg3, :installed)
+    is_installed(pkg::Symbol) = get(Pkg3.installed(), string(pkg), nothing) != nothing
 end
 
 function checked_import(pkg::Symbol)

src/query.jl

@@ -245,43 +245,42 @@ written in known `Format`.  For example, `Stream{PNG}(io)` would
 indicate PNG format.  If known, the optional `filename` argument can
 be used to improve error messages, etc.
 """
-struct Stream{F<:DataFormat,IOtype<:IO} <: Formatted{F}
+struct Stream{F <: DataFormat, IOtype <: IO} <: Formatted{F}
     io::IOtype
-    filename::Nullable{String}
+    filename::Union{String, Nothing}
 end
 
-Stream{F<:DataFormat}(::Type{F}, io::IO) = Stream{F,typeof(io)}(io, Nullable{String}())
-Stream{F<:DataFormat}(::Type{F}, io::IO, filename::AbstractString) = Stream{F,typeof(io)}(io,String(filename))
-Stream{F<:DataFormat}(::Type{F}, io::IO, filename) = Stream{F,typeof(io)}(io,filename)
-Stream{F}(file::File{F}, io::IO) = Stream{F,typeof(io)}(io,filename(file))
+Stream{F<:DataFormat}(::Type{F}, io::IO) = Stream{F,typeof(io)}(io, nothing)
+Stream{F<:DataFormat}(::Type{F}, io::IO, filename::AbstractString) = Stream{F, typeof(io)}(io, String(filename))
+Stream{F<:DataFormat}(::Type{F}, io::IO, filename) = Stream{F, typeof(io)}(io, filename)
+Stream{F}(file::File{F}, io::IO) = Stream{F, typeof(io)}(io, filename(file))
 
 "`stream(s)` returns the stream associated with `Stream` `s`"
 stream(s::Stream) = s.io
 
 """
-`filename(stream)` returns a nullable-string of the filename
-associated with `Stream` `stream`.
+`filename(stream)` returns a string of the filename
+associated with `Stream` `stream`, or nothing if there is no file associated.
 """
 filename(s::Stream) = s.filename
 
 """
 `file_extension(file)` returns a nullable-string for the file extension associated with `Stream` `stream`.
 """
 function file_extension(f::Stream)
-    isnull(filename(f)) && return filename(f)
-    splitext(get(filename(f)))[2]
+    fname = filename(f)
+    (fname == nothing) && return nothing
+    splitext(fname)[2]
 end
 
 # Note this closes the stream. It's useful when you've opened
 # the file to check the magic bytes, but don't want to leave
 # a dangling stream.
 function file!{F}(strm::Stream{F})
     f = filename(strm)
-    if isnull(f)
-        error("filename unknown")
-    end
+    f == nothing && error("filename unknown")
     close(strm.io)
-    File{F}(get(f))
+    File{F}(f)
 end
 
 # Implement standard I/O operations for File and Stream
@@ -329,9 +328,9 @@ skipmagic(io, magic::Function) = nothing
 skipmagic{N}(io, magic::NTuple{N,UInt8}) = seek(io, length(magic))
 function skipmagic(io, magic::Tuple)
     lengths = map(length, magic)
-    all(x->lengths[1] == x, lengths) && return seek(io, lengths[1]) # it doesn't matter what magic bytes get skipped as they all have the same length
+    all(x-> lengths[1] == x, lengths) && return seek(io, lengths[1]) # it doesn't matter what magic bytes get skipped as they all have the same length
     magic = [magic...]
-    sort!(magic, lt=(a,b)-> length(a)>= length(b)) # start with longest first, to avoid overlapping magic bytes
+    sort!(magic, lt = (a,b)-> length(a) >= length(b)) # start with longest first, to avoid overlapping magic bytes
     seekend(io)
     len = position(io)
     seekstart(io)
@@ -397,9 +396,9 @@ hasfunction(s::Tuple) = false #has magic
 `query(io, [filename])` returns a `Stream` object with information about the
 format inferred from the magic bytes.
 """
-query(io::IO, filename) = query(io, Nullable(String(filename)))
+query(io::IO, filename) = query(io, String(filename))
 
-function query(io::IO, filename::Nullable{String}=Nullable{String}())
+function query(io::IO, filename::Union{Nothing, String} = nothing)
     magic = Vector{UInt8}(0)
     pos = position(io)
     for p in magic_list
@@ -408,7 +407,7 @@ function query(io::IO, filename::Nullable{String}=Nullable{String}())
         while length(m) > length(magic)
             if eof(io)
                 seek(io, pos)
-                return Stream{unknown_df,typeof(io)}(io, filename)
+                return Stream{unknown_df, typeof(io)}(io, filename)
             end
             push!(magic, read(io, UInt8))
         end
@@ -421,8 +420,14 @@ function query(io::IO, filename::Nullable{String}=Nullable{String}())
         for p in magic_func
             seek(io, pos)
             f = first(p)
-            if f(io)
-                return Stream{DataFormat{last(p)},typeof(io)}(seek(io, pos), filename)
+            try
+                if f(io)
+                    return Stream{DataFormat{last(p)},typeof(io)}(seek(io, pos), filename)
+                end
+            catch e
+                println("There was an error in magick function $f")
+                println("Please open an issue at FileIO.jl. Error:")
+                println(e)
             end
         end
         seek(io, pos)

src/registry.jl

@@ -160,21 +160,19 @@ add_format(format"FLAC","fLaC",".flac",[:FLAC])
 ### Complex cases
 
 # bedGraph: the complication is that the magic bytes may start at any location within an indeterminate header.
-const bedgraph_magic = UInt8[0x74, 0x79, 0x70, 0x65, 0x3D, 0x62, 0x65, 0x64, 0x47, 0x72, 0x61, 0x70, 0x68]
 function detect_bedgraph(io)
-    position(io) == 0 || return false
-
-    line = ""
-
+    bedgraph_magic = b"type=bedGraph"
     # Check lines for magic bytes.
-    while !eof(io) && !ismatch(r"^\s*([A-Za-z]+\S*)\s+(\d+)\s+(\d+)\s+(\S*\d)\s*$", line) # Note: regex is used to limit the search by exiting the loop when a line matches the bedGraph track format.
-        line = readline(io, chomp=false)
-
-        if contains(line, String(bedgraph_magic)) # Note: String(bedgraph_magic) = "type=bedGraph"
-            return true
+    pos = 1
+    while !eof(io)
+        r = read(io, UInt8)
+        if bedgraph_magic[pos] == r
+            pos >= length(bedgraph_magic) && return true
+            pos += 1
+        else
+            pos = 1
         end
     end
-
     return false
 end
 add_format(format"bedGraph", detect_bedgraph, [".bedgraph"], [:BedgraphFiles])
@@ -235,28 +233,27 @@ end
 add_format(format"HDF5", detecthdf5, [".h5", ".hdf5"], [:HDF5])
 
 function detect_stlascii(io)
+    pos = position(io)
     try
-        position(io) != 0 && (seekstart(io); return false)
         seekend(io)
         len = position(io)
-        seekstart(io)
+        seek(io, pos)
         len < 80 && return false
         header = read(io, 80) # skip header
-        seekstart(io)
+        seek(io, pos)
         header[1:6] == b"solid " && !detect_stlbinary(io)
     finally
-        seekstart(io)
+        seek(io, pos)
     end
 end
 
 function detect_stlbinary(io)
-    size_header = 80+sizeof(UInt32)
-    size_triangleblock = (4*3*sizeof(Float32)) + sizeof(UInt16)
-
-    position(io) != 0 && (seekstart(io); return false)
+    size_header = 80 + sizeof(UInt32)
+    size_triangleblock = (4 * 3 * sizeof(Float32)) + sizeof(UInt16)
+    pos = position(io)
     seekend(io)
     len = position(io)
-    seekstart(io)
+    seek(io, pos)
     len < size_header && return false
 
     skip(io, 80) # skip header
@@ -267,7 +264,6 @@ function detect_stlbinary(io)
     attrib_byte_count = read(io, UInt16) # read last attrib_byte
     attrib_byte_count != zero(UInt16) && (seekstart(io); return false) # should be zero as not used
     result = eof(io) # if end of file, we have a stl!
-    seekstart(io)
     return result
 end
 add_format(format"STL_ASCII", detect_stlascii, [".stl", ".STL"], [:MeshIO])

test/error_handling.jl

@@ -1,4 +1,11 @@
 println("these tests will print warnings: ")
+
+if VERSION > v"0.6.9"
+    const fetch07 = fetch
+else
+    const fetch07 = wait
+end
+
 @testset "Not installed" begin
     eval(Base, :(is_interactive = true)) # for interactive error handling
 
@@ -9,11 +16,11 @@ println("these tests will print warnings: ")
     rserr, wrerr = redirect_stderr()
     ref = @async save("test.not_installed", nothing)
     println(wr, "y")
-    @test_throws CompositeException wait(ref) #("unknown package NotInstalled")
+    @test_throws CompositeException fetch07(ref) #("unknown package NotInstalled")
     ref = @async save("test.not_installed", nothing)
     println(wr, "invalid") #test invalid input
     println(wr, "n") # don't install
-    wait(ref)
+    fetch07(ref)
     @test istaskdone(ref)
 
     close(rs);close(wr);close(rserr);close(wrerr)

test/loadsave.jl

@@ -175,8 +175,8 @@ add_saver(format"DUMMY", :Dummy)
         f = File(format"DUMMY", fnrel)
         @test !(isabspath(filename(f)))
         open(f) do s
-            @test isabspath(get(filename(s)))
-            @test endswith(get(filename(s)),fn)
+            @test isabspath(filename(s))
+            @test endswith(filename(s), fn)
         end
     end
 
@@ -192,8 +192,8 @@ add_saver(format"DUMMY", :Dummy)
         f = File(format"DUMMY", fnrel)
         @test !(isabspath(filename(f)))
         open(f) do s
-            @test isabspath(get(filename(s)))
-            @test endswith(get(filename(s)),fn2)
+            @test isabspath(filename(s))
+            @test endswith(filename(s),fn2)
         end
     end
     rm(fn2)

test/query.jl

@@ -93,12 +93,12 @@ try
         io = IOBuffer()
         s = Stream(format"JUNK", io)
         @test typeof(s) == Stream{DataFormat{:JUNK},IOBuffer}
-        @test isnull(filename(s))
+        @test filename(s) == nothing
         @test_throws Exception FileIO.file!(s)
         s = Stream(format"JUNK", io, "junk.jnk")
-        @test get(filename(s)) == "junk.jnk"
-        s = Stream(format"JUNK", io, Nullable("junk2.jnk"))
-        @test get(filename(s)) == "junk2.jnk"
+        @test filename(s) == "junk.jnk"
+        s = Stream(format"JUNK", io, "junk2.jnk")
+        @test filename(s) == "junk2.jnk"
     end
 
     @testset "query" begin
@@ -122,7 +122,7 @@ try
         q = query(io)
         @test typeof(q) == Stream{format"JUNK",typeof(io)}
         @test !(unknown(q))
-        @test isnull(file_extension(q))
+        @test file_extension(q) == nothing
 
         # File with correct extension
         str = String(take!(io))