Add indents for JSON files for readbility (#167)

* Add indents for .zgroup file

* Add indents for .zattrs and .zarray

* Make indenting JSON an optional kargs

* Update src/ZGroup.jl

Co-authored-by: Anshul Singhvi <[email protected]>

* Update src/Storage/Storage.jl

Co-authored-by: Anshul Singhvi <[email protected]>

* Update src/Storage/Storage.jl

Co-authored-by: Anshul Singhvi <[email protected]>

* Update src/ZArray.jl

Co-authored-by: Anshul Singhvi <[email protected]>

* Fix syntax error

---------

Co-authored-by: Anshul Singhvi <[email protected]>

Author: calvinchai

src/Storage/Storage.jl

@@ -95,9 +95,15 @@ function getattrs(s::AbstractStore, p)
     JSON.parse(replace(String(maybecopy(atts)),": NaN,"=>": \"NaN\","))
   end
 end
-function writeattrs(s::AbstractStore, p, att::Dict)
+function writeattrs(s::AbstractStore, p, att::Dict; indent_json::Bool= false)
   b = IOBuffer()
-  JSON.print(b,att)
+
+  if indent_json
+    JSON.print(b,att,4)
+  else
+    JSON.print(b,att)
+  end
+
   s[p,".zattrs"] = take!(b)
   att
 end
@@ -110,9 +116,15 @@ isinitialized(s::AbstractStore, p, i) = isinitialized(s,_concatpath(p,i))
 isinitialized(s::AbstractStore, i) = s[i] !== nothing
 
 getmetadata(s::AbstractStore, p,fill_as_missing) = Metadata(String(maybecopy(s[p,".zarray"])),fill_as_missing)
-function writemetadata(s::AbstractStore, p, m::Metadata)
+function writemetadata(s::AbstractStore, p, m::Metadata; indent_json::Bool= false)
   met = IOBuffer()
-  JSON.print(met,m)
+
+  if indent_json
+    JSON.print(met,m,4)
+  else
+    JSON.print(met,m)
+  end
+  
   s[p,".zarray"] = take!(met)
   m
 end

src/ZArray.jl

@@ -310,6 +310,7 @@ Creates a new empty zarr array with element type `T` and array dimensions `dims`
 * `compressor=BloscCompressor()` compressor type and properties
 * `attrs=Dict()` a dict containing key-value pairs with metadata attributes associated to the array
 * `writeable=true` determines if the array is opened in read-only or write mode
+* `indent_json=false` determines if indents are added to format the json files `.zarray` and `.zattrs`.  This makes them more readable, but increases file size.
 """
 function zcreate(::Type{T}, dims::Integer...;
   name="",
@@ -334,6 +335,7 @@ function zcreate(::Type{T},storage::AbstractStore,
   filters = filterfromtype(T), 
   attrs=Dict(),
   writeable=true,
+  indent_json=false
   ) where T
 
   length(dims) == length(chunks) || throw(DimensionMismatch("Dims must have the same length as chunks"))
@@ -353,9 +355,9 @@ function zcreate(::Type{T},storage::AbstractStore,
 
   isemptysub(storage,path) || error("$storage $path is not empty")
 
-  writemetadata(storage, path, metadata)
+  writemetadata(storage, path, metadata, indent_json=indent_json)
 
-  writeattrs(storage, path, attrs)
+  writeattrs(storage, path, attrs, indent_json=indent_json)
 
   ZArray{T2, N, typeof(compressor), typeof(storage)}(
   metadata, storage, path, attrs, writeable)

src/ZGroup.jl

@@ -128,13 +128,19 @@ end
 
 Create a new zgroup in the store `s`
 """
-function zgroup(s::AbstractStore, path::String=""; attrs=Dict())
+function zgroup(s::AbstractStore, path::String=""; attrs=Dict(), indent_json::Bool= false)
     d = Dict("zarr_format"=>2)
     isemptysub(s, path) || error("Store is not empty")
     b = IOBuffer()
-    JSON.print(b,d)
+    
+    if indent_json
+      JSON.print(b,d,4)
+    else
+      JSON.print(b,d)
+    end
+
     s[path,".zgroup"]=take!(b)
-    writeattrs(s,path,attrs)
+    writeattrs(s,path,attrs, indent_json=indent_json)
     ZGroup(s, path, Dict{String,ZArray}(), Dict{String,ZGroup}(), attrs,true)
 end