Merge pull request #11 from JuliaDataCubes/datasetconstructors

Give Dataset constructors an mode kwarg

Author: meggart

src/datasets/archgdal.jl

@@ -42,7 +42,7 @@ struct GDALDataset
     bands::OrderedDict{String}
 end
 
-function GDALDataset(filename)
+function GDALDataset(filename;mode="r")
     AG.read(filename) do r
         nb = AG.nraster(r)
         allbands = map(1:nb) do iband

src/datasets/datasetinterface.jl

@@ -76,17 +76,20 @@ backendlist = OrderedDict{Symbol, Any}(
 
 backendregex = Pair[]
 
-function to_dataset(g::String; driver=:all)
+function backendfrompath(g::String; driver = :all)
   if driver == :all
     for p in YAXArrayBase.backendregex
       if match(p[1],g) !== nothing
-        return to_dataset(p[2],g)
+        return p[2]
       end
     end
-    return to_dataset(g,driver=:zarr)
+    return last(first(backendregex))
   else
-    return to_dataset(backendlist[driver],g)
+    return backendlist[driver]
   end
 end
+
+to_dataset(g::String; driver=:all, kwargs...) = to_dataset(backendfrompath(g;driver),g,kwargs...)
+
 to_dataset(g; kwargs...) = g
-to_dataset(T::Type{<:Any}, g::String) = T(g)
+to_dataset(T::Type{<:Any}, g::String;kwargs...) = T(g;kwargs...)

src/datasets/netcdf.jl

@@ -14,7 +14,7 @@ struct NetCDFDataset
   filename::String
   mode::UInt16
 end
-NetCDFDataset(filename) = NetCDFDataset(filename,NC_NOWRITE)
+NetCDFDataset(filename;mode="r") = mode == "r" ? NetCDFDataset(filename,NC_NOWRITE) : NetCDFDataset(filename,NC_WRITE)
 
 import .NetCDF: AbstractDiskArray, readblock!, writeblock!, haschunks, eachchunk
 

src/datasets/zarr.jl

@@ -4,7 +4,7 @@ to_zarrtype, zopen, Compressor
 struct ZarrDataset
   g::ZGroup
 end
-ZarrDataset(g::String) = ZarrDataset(zopen(g))
+ZarrDataset(g::String;mode="r") = ZarrDataset(zopen(g,mode,fill_as_missing=true))
 
 get_var_dims(ds::ZarrDataset,name) = reverse(ds[name].attrs["_ARRAY_DIMENSIONS"])
 get_varnames(ds::ZarrDataset) = collect(keys(ds.g.arrays))
@@ -21,7 +21,7 @@ end
 function add_var(p::ZarrDataset, T::Type, varname, s, dimnames, attr;
   chunksize=s, kwargs...)
   attr2 = merge(attr,Dict("_ARRAY_DIMENSIONS"=>reverse(collect(dimnames))))
-  za = zcreate(T, p.g, varname, s...;attrs=attr2,chunks=chunksize,kwargs...)
+  za = zcreate(T, p.g, varname,s...;fill_as_missing=true,attrs=attr2,chunks=chunksize,kwargs...)
   za
 end
 

test/datasets.jl

@@ -24,7 +24,7 @@ end
 
 @testset "Reading Zarr" begin
 p = "gs://cmip6/CMIP6/HighResMIP/CMCC/CMCC-CM2-HR4/highresSST-present/r1i1p1f1/6hrPlev/psl/gn/v20170706/"
-ds_zarr = to_dataset(p)
+ds_zarr = to_dataset(p,driver=:zarr)
 vn = get_varnames(ds_zarr)
 @test sort(vn) == ["lat", "lat_bnds", "lon", "lon_bnds", "psl", "time", "time_bnds"]
 @test get_var_dims(ds_zarr, "psl") == ["lon", "lat", "time"]