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Merged
meggart merged 3 commits into from
Jan 30, 2026
Merged

Zippedzarrs #49

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97dcc4f
Add possiblity to open zipped zarrs
meggart Jan 30, 2026
0544f24
update Project.toml
meggart Jan 30, 2026
3ba18fb
Fix bug
meggart Jan 30, 2026
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7 changes: 5 additions & 2 deletions Project.toml
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
name = "YAXArrayBase"
uuid = "90b8fcef-0c2d-428d-9c56-5f86629e9d14"
authors = ["Fabian Gans <fgans@bgc-jena.mpg.de>"]
version = "0.7.7"
version = "0.7.8"

[deps]
DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
Expand All @@ -18,21 +18,24 @@ DimensionalData = "0.27, 0.28, 0.29"
NetCDF = "0.11, 0.12"
Zarr = "0.8, 0.9"


[extensions]
ArchGDALExt = "ArchGDAL"
AxisArraysExt = "AxisArrays"
AxisKeysExt = "AxisKeys"
DimensionalDataExt = "DimensionalData"
NamedDimsExt = "NamedDims"
NetCDFExt = "NetCDF"
ZarrExt = "Zarr"
ZarrExt = ["Zarr", "ZipArchives", "DiskArrays"]

[weakdeps]
ArchGDAL = "c9ce4bd3-c3d5-55b8-8973-c0e20141b8c3"
AxisArrays = "39de3d68-74b9-583c-8d2d-e117c070f3a9"
AxisKeys = "94b1ba4f-4ee9-5380-92f1-94cde586c3c5"
DimensionalData = "0703355e-b756-11e9-17c0-8b28908087d0"
Downloads = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
DiskArrays = "3c3547ce-8d99-4f5e-a174-61eb10b00ae3"
NamedDims = "356022a1-0364-5f58-8944-0da4b18d706f"
NetCDF = "30363a11-5582-574a-97bb-aa9a979735b9"
Zarr = "0a941bbe-ad1d-11e8-39d9-ab76183a1d99"
ZipArchives = "49080126-0e18-4c2a-b176-c102e4b3760c"
148 changes: 96 additions & 52 deletions ext/ZarrExt.jl
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Original file line number Diff line number Diff line change
@@ -1,64 +1,108 @@
module ZarrExt
using YAXArrayBase
using Zarr: ZArray, ZGroup, zgroup, zcreate, to_zarrtype, zopen, Compressor
import YAXArrayBase: YAXArrayBase as YAB
export ZarrDataset

function __init__()
@debug "new driver key :zarr, updating backendlist."
YAB.backendlist[:zarr] = ZarrDataset
push!(YAB.backendregex, r"(.zarr$)|(.zarr/$)"=>ZarrDataset)
end
using YAXArrayBase
using Zarr: ZArray, ZGroup, zgroup, zcreate, to_zarrtype, zopen, Compressor, ZipStore
import DiskArrays: AbstractDiskArray, DiskArrays, Unchunked, Chunked, GridChunks
using ZipArchives: ZipReader
import YAXArrayBase: YAXArrayBase as YAB
export ZarrDataset

struct ZarrDataset
g::ZGroup
end
ZarrDataset(g::String;mode="r") = ZarrDataset(zopen(g,mode,fill_as_missing=false))

YAB.get_var_dims(ds::ZarrDataset,name) = reverse(ds[name].attrs["_ARRAY_DIMENSIONS"])
YAB.get_varnames(ds::ZarrDataset) = collect(keys(ds.g.arrays))
function YAB.get_var_attrs(ds::ZarrDataset, name)
#We add the fill value to the attributes to be consistent with NetCDF
a = ds[name]
if a.metadata.fill_value !== nothing
merge(ds[name].attrs,Dict("_FillValue"=>a.metadata.fill_value))
else
ds[name].attrs
end
function __init__()
@debug "new driver key :zarr, updating backendlist."
YAB.backendlist[:zarr] = ZarrDataset
push!(YAB.backendregex, r"(.zarr$)|(.zarr/$)|(zarr.zip$)" => ZarrDataset)
end

struct ZarrDataset
g::ZGroup
end
function ZarrDataset(g::String; mode="r")
store = if endswith(g, "zip")
ZipStore(ZipReader(SimpleFileDiskArray(g)))
else
g
end
YAB.get_global_attrs(ds::ZarrDataset) = ds.g.attrs
Base.getindex(ds::ZarrDataset, i) = ds.g[i]
Base.haskey(ds::ZarrDataset,k) = haskey(ds.g,k)

# function add_var(p::ZarrDataset, T::Type{>:Missing}, varname, s, dimnames, attr; kwargs...)
# S = Base.nonmissingtype(T)
# add_var(p,S, varname, s, dimnames, attr; fill_value = defaultfillval(S), fill_as_missing=true, kwargs...)
# end

function YAB.add_var(p::ZarrDataset, T::Type, varname, s, dimnames, attr;
chunksize=s, fill_as_missing=false, kwargs...)
attr2 = merge(attr,Dict("_ARRAY_DIMENSIONS"=>reverse(collect(dimnames))))
fv = get(attr,"_FillValue",get(attr,"missing_value",YAB.defaultfillval(T)))
za = zcreate(T, p.g, varname,s...;fill_value = fv,fill_as_missing,attrs=attr2,chunks=chunksize,kwargs...)
za
ZarrDataset(zopen(store, mode, fill_as_missing=false))
end

YAB.get_var_dims(ds::ZarrDataset, name) = reverse(ds[name].attrs["_ARRAY_DIMENSIONS"])
YAB.get_varnames(ds::ZarrDataset) = collect(keys(ds.g.arrays))
function YAB.get_var_attrs(ds::ZarrDataset, name)
#We add the fill value to the attributes to be consistent with NetCDF
a = ds[name]
if a.metadata.fill_value !== nothing
merge(ds[name].attrs, Dict("_FillValue" => a.metadata.fill_value))
else
ds[name].attrs
end
end
YAB.get_global_attrs(ds::ZarrDataset) = ds.g.attrs
Base.getindex(ds::ZarrDataset, i) = ds.g[i]
Base.haskey(ds::ZarrDataset, k) = haskey(ds.g, k)

#Special case for init with Arrays
function YAB.add_var(p::ZarrDataset, a::AbstractArray, varname, dimnames, attr;
kwargs...)
T = to_zarrtype(a)
b = add_var(p,T,varname,size(a),dimnames,attr;kwargs...)
b .= a
a
# function add_var(p::ZarrDataset, T::Type{>:Missing}, varname, s, dimnames, attr; kwargs...)
# S = Base.nonmissingtype(T)
# add_var(p,S, varname, s, dimnames, attr; fill_value = defaultfillval(S), fill_as_missing=true, kwargs...)
# end

function YAB.add_var(p::ZarrDataset, T::Type, varname, s, dimnames, attr;
chunksize=s, fill_as_missing=false, kwargs...)
attr2 = merge(attr, Dict("_ARRAY_DIMENSIONS" => reverse(collect(dimnames))))
fv = get(attr, "_FillValue", get(attr, "missing_value", YAB.defaultfillval(T)))
attr3 = filter(attr2) do (k, v)
!isa(v, AbstractFloat) || !isnan(v)
end
za = zcreate(T, p.g, varname, s...; fill_value=fv, fill_as_missing, attrs=attr3, chunks=chunksize, kwargs...)
za
end

#Special case for init with Arrays
function YAB.add_var(p::ZarrDataset, a::AbstractArray, varname, dimnames, attr;
kwargs...)
T = to_zarrtype(a)
b = add_var(p, T, varname, size(a), dimnames, attr; kwargs...)
b .= a
a
end

YAB.create_empty(::Type{ZarrDataset}, path, gatts=Dict()) = ZarrDataset(zgroup(path, attrs=gatts))

YAB.create_empty(::Type{ZarrDataset}, path, gatts=Dict()) = ZarrDataset(zgroup(path, attrs=gatts))


YAB.allow_parallel_write(::ZarrDataset) = true
YAB.allow_missings(::ZarrDataset) = false
YAB.to_dataset(g::ZGroup; kwargs...) = ZarrDataset(g)
YAB.iscompressed(a::ZArray{<:Any,<:Any,<:Compressor}) = true


#Add ability to read zipped zarrs


struct SimpleFileDiskArray{C<:Union{Int,Nothing}} <: AbstractDiskArray{UInt8,1}
file::String
s::Int
chunksize::C
end
Base.size(s::SimpleFileDiskArray) = (s.s,)
function SimpleFileDiskArray(filename; chunksize=nothing)
isfile(filename) || throw(ArgumentError("File $filename does not exist"))
s = filesize(filename)
SimpleFileDiskArray(filename, s, chunksize)
end
function DiskArrays.readblock!(a::SimpleFileDiskArray, aout, i::AbstractUnitRange)
open(a.file) do f
seek(f, first(i) - 1)
read!(f, aout)
end
end
DiskArrays.haschunks(a::SimpleFileDiskArray) = a.chunksize === nothing ? Unchunked() : Chunked()
function DiskArrays.eachchunk(a::SimpleFileDiskArray)
if a.chunksize === nothing
DiskArrays.estimate_chunksize(a)
else
GridChunks((a.s,), (a.chunksize,))
end
end


YAB.allow_parallel_write(::ZarrDataset) = true
YAB.allow_missings(::ZarrDataset) = false
YAB.to_dataset(g::ZGroup; kwargs...) = ZarrDataset(g)
YAB.iscompressed(a::ZArray{<:Any,<:Any,<:Compressor}) = true

end
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