Merge pull request #2 from meggart/netcdf_nohandles

Make NetCDF dataset not return handles

Manifest.toml

@@ -13,6 +13,11 @@ version = "0.17.11"
 deps = ["Printf"]
 uuid = "ade2ca70-3891-5945-98fb-dc099432e06a"
 
+[[DiskArrays]]
+git-tree-sha1 = "3bfd0eb19711297e1b3656b7d4709f7b4b240195"
+uuid = "3c3547ce-8d99-4f5e-a174-61eb10b00ae3"
+version = "0.2.4"
+
 [[Distributed]]
 deps = ["Random", "Serialization", "Sockets"]
 uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b"

Project.toml

@@ -1,17 +1,17 @@
 name = "YAXArrayBase"
 uuid = "90b8fcef-0c2d-428d-9c56-5f86629e9d14"
 authors = ["Fabian Gans <fgans@bgc-jena.mpg.de>"]
-version = "0.1.0"
+version = "0.2.0"
 
 [deps]
 DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
 Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
 Requires = "ae029012-a4dd-5104-9daa-d747884805df"
 
 [compat]
-julia = "^1"
 DataStructures = "0.17, 0.18"
 Requires = "1"
+julia = "^1"
 
 [extras]
 ArchGDAL = "c9ce4bd3-c3d5-55b8-8973-c0e20141b8c3"

src/datasets/netcdf.jl

@@ -16,24 +16,44 @@ struct NetCDFDataset
 end
 NetCDFDataset(filename) = NetCDFDataset(filename,NC_NOWRITE)
 
+import .NetCDF: AbstractDiskArray, readblock!, writeblock!, haschunks, eachchunk
+
+struct NetCDFVariable{T,N} <: AbstractDiskArray{T,N}
+  filename::String
+  varname::String
+  size::NTuple{N,Int}
+end
+#Define method forwarding for DiskArray methods
+for m in [:haschunks, :eachchunk]
+  eval(:(function $(m)(v::NetCDFVariable,args...;kwargs...)
+    NetCDF.open(a->$(m)(a,args...;kwargs...), v.filename, v.varname)
+end
+))
+end
+writeblock!(v::NetCDFVariable, aout, r::AbstractUnitRange...) = NetCDF.open(a->writeblock!(a,aout,r...), v.filename, v.varname, mode=NC_WRITE)
+readblock!(v::NetCDFVariable, aout, r::AbstractUnitRange...) = NetCDF.open(a->readblock!(a,aout,r...), v.filename, v.varname)
+
+Base.size(v::NetCDFVariable) = v.size
+
 get_var_dims(ds::NetCDFDataset,name) = NetCDF.open(v->map(i->i.name,v[name].dim),ds.filename)
 get_varnames(ds::NetCDFDataset) = NetCDF.open(v->collect(keys(v.vars)),ds.filename)
 get_var_attrs(ds::NetCDFDataset, name) = NetCDF.open(v->v[name].atts,ds.filename)
 function Base.getindex(ds::NetCDFDataset, i)
-  NetCDF.open(ds.filename,i,mode=ds.mode)
+  s,et = NetCDF.open(j->(size(j),eltype(j)),ds.filename,i)
+  NetCDFVariable{et,length(s)}(ds.filename, i, s)
 end
 Base.haskey(ds::NetCDFDataset,k) = NetCDF.open(nc->haskey(nc.vars,k),ds.filename)
 
 function add_var(p::NetCDFDataset, T::Type, varname, s, dimnames, attr;
   chunksize=s, compress = -1)
   dimsdescr = Iterators.flatten(zip(dimnames,s))
   nccreate(p.filename, varname, dimsdescr..., atts = attr, t=T, chunksize=chunksize, compress=compress)
-  NetCDF.open(p.filename,varname,mode=p.mode)
+  NetCDFVariable{T,length(s)}(p.filename,varname,s)
 end
 
 function create_empty(::Type{NetCDFDataset}, path)
   NetCDF.create(path, NcVar[])
-  NetCDFDataset(path,NC_WRITE)
+  NetCDFDataset(path)
 end
 
 allow_parallel_write(::NetCDFDataset) = false