Don't allow missings in Zarr anymore

Author: meggart

src/datasets/zarr.jl

@@ -4,24 +4,33 @@ to_zarrtype, zopen, Compressor
 struct ZarrDataset
   g::ZGroup
 end
-ZarrDataset(g::String;mode="r") = ZarrDataset(zopen(g,mode,fill_as_missing=true))
+ZarrDataset(g::String;mode="r") = ZarrDataset(zopen(g,mode,fill_as_missing=false))
 
 get_var_dims(ds::ZarrDataset,name) = reverse(ds[name].attrs["_ARRAY_DIMENSIONS"])
 get_varnames(ds::ZarrDataset) = collect(keys(ds.g.arrays))
-get_var_attrs(ds::ZarrDataset, name) = ds[name].attrs
+function 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
 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), kwargs...)
-end
+# 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 add_var(p::ZarrDataset, T::Type, varname, s, dimnames, attr;
-  chunksize=s, kwargs...)
+  chunksize=s, fill_as_missing=false, kwargs...)
   attr2 = merge(attr,Dict("_ARRAY_DIMENSIONS"=>reverse(collect(dimnames))))
-  za = zcreate(T, p.g, varname,s...;fill_as_missing=true,attrs=attr2,chunks=chunksize,kwargs...)
+  fv = get(attr,"_FillValue",get(attr,"missing_value",default_fillvalue(T)))
+  za = zcreate(T, p.g, varname,s...;fill_as_missing,attrs=attr2,chunks=chunksize,kwargs...)
   za
 end
 
@@ -40,6 +49,6 @@ backendlist[:zarr] = ZarrDataset
 push!(backendregex, r"(.zarr$)|(.zarr/$)"=>ZarrDataset)
 
 allow_parallel_write(::ZarrDataset) = true
-allow_missings(::ZarrDataset) = true
+allow_missings(::ZarrDataset) = false
 to_dataset(g::ZGroup; kwargs...) = ZarrDataset(g)
 iscompressed(a::ZArray{<:Any,<:Any,<:Compressor}) = true