Add methods to construct a ZarrDataset from Zarr.jl objects

This commit allows the user to construct a ZarrDataset from a `Zarr.AbstractStore` or `Zarr.ZGroup`.

It also refactors the pipeline such that strings open stores, stores open ZGroups, and then ZGroups are finally wrapped in ZarrDataset.  This way, all of the infrastructure is reused and bugfixes are cleaner.

Author: asinghvi17

src/dataset.jl

@@ -135,33 +135,54 @@ function ZarrDataset(url::AbstractString,mode = "r";
                      )
 
     dimensions = OrderedDict{Symbol,Int}()
-    iswritable = false
 
-    if mode == "r"
+    zg = if mode == "r"
         zg = Zarr.zopen(url,mode)
-        if (zg.storage isa Zarr.HTTPStore) ||
-            (zg.storage isa Zarr.ConsolidatedStore{Zarr.HTTPStore})
+    elseif mode == "c"
+        store = Zarr.DirectoryStore(url)
+        zg = zgroup(store, "",attrs = Dict{String,Any}(attrib))
+    end
+    ZarrDataset(zg; mode, parentdataset, _omitcode, maskingvalue, attrib)
+end
+
+function ZarrDataset(store::Zarr.AbstractStore,mode = "r";
+                     parentdataset = nothing,
+                     _omitcode = [404,403],
+                     maskingvalue = missing,
+                     attrib = Dict(),
+                     )
+    return ZarrDataset(zopen(store, mode); mode, parentdataset, _omitcode, maskingvalue, attrib)
+end
+
+function ZarrDataset(zg::Zarr.ZGroup;
+                     mode = "r",
+                     parentdataset = nothing,
+                     _omitcode = [404,403],
+                     maskingvalue = missing,
+                     attrib = Dict(),
+                     )
+
+    dimensions = ZarrDatasets.OrderedDict{Symbol,Int}()
+    iswritable = false
+    if (zg.storage isa Zarr.HTTPStore) ||
+        (zg.storage isa Zarr.ConsolidatedStore{Zarr.HTTPStore})
             @debug "omit chunks on HTTP error" _omitcode
             Zarr.missing_chunk_return_code!(zg.storage,_omitcode)
         end
 
         for (varname,zarray) in zg.arrays
             for (dimname,dimlen) in zip(reverse(zarray.attrs["_ARRAY_DIMENSIONS"]),size(zarray))
-
                 dn = Symbol(dimname)
                 if haskey(dimensions,dn)
                     @assert dimensions[dn] == dimlen
                 else
                     dimensions[dn] = dimlen
                 end
-            end
         end
-    elseif mode == "c"
-        store = Zarr.DirectoryStore(url)
-        zg = zgroup(store, "",attrs = Dict{String,Any}(attrib))
-        iswritable = true
     end
-    ZarrDataset(parentdataset,zg,dimensions,iswritable,maskingvalue)
+
+    return ZarrDataset(parentdataset, zg, dimensions, mode == "r" ? false : zg.writeable, maskingvalue)
+
 end
 
 

test/runtests.jl

@@ -7,5 +7,6 @@ using ZarrDatasets
     include("test_write.jl")
     include("test_groups.jl")
     include("test_fillvalue.jl")
+    include("test_preexisting.jl")
     include("test_aqua.jl")
 end

test/test_preexisting.jl

@@ -0,0 +1,49 @@
+using ZarrDatasets
+using Test
+using Zarr
+
+# Test opening a ZarrDataset using a pre-existing Zarr store or group
+
+# First, 
+fname = tempname()
+mkdir(fname)
+gattrib = Dict("title" => "this is the title")
+ds = ZarrDataset(fname,"c",attrib = gattrib)
+
+ds.attrib["number"] = 1
+defDim(ds,"lon",3)
+defDim(ds,"lat",5)
+
+attrib = Dict(
+    "units" => "m/s",
+    "long_name" => "test",
+)
+
+
+varname = "var2"
+dimensionnames = ("lon","lat")
+vtype = Int32
+
+zv = defVar(ds,varname,vtype,dimensionnames, attrib = attrib)
+zv[:,:] = data = rand(Int32,3,5)
+
+zv.attrib["number"] = 12
+zv.attrib["standard_name"] = "test"
+ds.attrib["history"] = "test"
+close(ds)
+
+for ds in ZarrDataset.((Zarr.storefromstring(fname)[1], Zarr.zopen(fname), ))
+
+    zv = ds[varname]
+
+    @test zv.attrib["number"] == 12
+    @test zv.attrib["standard_name"] == "test"
+    @test ds.attrib["history"] == "test"
+
+    @test zv[:,:] == data
+
+    io = IOBuffer()
+    show(io,ds)
+    str = String(take!(io))
+    @test occursin("Global",str)
+end