jq: add zarr functions

src/main/resources/n5.jq

@@ -290,6 +290,8 @@ def scaleTransform( $scales ): { "type" : "scale", "scale" : $scales };
 
 def toTreePath: ltrimstr( "/") | split("/") | map_values( ["children", . ] ) | flatten;
 
+def fromTreePath: if (length == 0) then "" else [.[range(1;length;2)]] | join("/") end;
+
 def getSubTree( $path ): getpath( $path | toTreePath );
 
 def moveSubTree( $srcPath; $dstPath ): getSubTree( $srcPath ) as $subTree | setpath( $dstPath | toTreePath; $subTree ) 

src/main/resources/zarr.jq

@@ -0,0 +1,56 @@
+def cleanPath: . | sub("^\\.(?<x>.*)\\/.+"; "\(.x)"; "g");
+
+def containsExactString($query): reduce .[] as $i (false; . or ($i == $query));
+
+def hasAllKeys($queryKeys):  keys as $keys |
+    reduce ($queryKeys | .[] ) as $k (true; . and ( $keys | containsExactString($k)));
+
+def inExact($arr): reduce ($arr | .[]) as $v ([., false]; [.[0], .[1] or ($v == .[0])]) | .[1];
+
+def zarrArrayKeys: ["zarr_format", "shape", "chunks", "dtype", "compressor", "fill_value", "order", 
+    "dimension_separator", "filters"];
+
+def zarrGroupKeys: ["zarr_format"];
+
+def isZarrArray: type == "object" and hasAllKeys( zarrArrayKeys );
+
+def zarrArrayObj: zarrArrayKeys as $za | with_entries(select(.key | inExact( $za )));
+
+def zarrArrayAttrs: zarrArrayKeys as $za | with_entries(select(.key | inExact( $za ) | not));
+
+def zarrGroupObj: { "zarr_format" : .zarr_format };
+
+def zarrGroupAttrs: zarrGroupKeys as $zg | with_entries(select(.key | inExact( $zg ) | not));
+
+def zarrAttrs: . as $obj |
+    if ($obj | isZarrArray) then 
+    {
+        ".zarray" : ($obj | zarrArrayObj),
+        ".zattrs" : ($obj | zarrArrayAttrs)
+    }
+    else 
+    {
+        ".zgroup" : ($obj | zarrGroupObj),
+        ".zattrs" : ($obj | zarrGroupAttrs)
+    }
+    end;
+
+def hasAttributes: type == "object" and has("attributes");
+
+def zomTreePath: ltrimstr( "/") | split("/") | map_values( ["members", . ] ) | flatten;
+
+def zomAdd( $path; $attrs; $suffix ):
+    ($path | zomTreePath | . + $suffix) as $p |
+    getpath( $p ) as $currentAttrs |
+    setpath( $p; $currentAttrs + $attrs );
+
+def zomAddFiles: 
+    reduce inputs as $i ({}; 
+        input_filename as $f |
+        ($f | cleanPath) as $p |
+        if ($f | endswith(".zattrs")) then
+            zomAdd( ($p | cleanPath); $i; ["attributes"] )
+        else
+            zomAdd( ($p | cleanPath); $i; [] )
+        end);
+