Move nested handling to io.ts

hms-dbmi · Mar 31, 2021 · 3cdabea · 3cdabea
1 parent e10b2ae
commit 3cdabea
Show file tree

Hide file tree

Showing 2 changed files with 22 additions and 14 deletions.
diff --git a/src/io.ts b/src/io.ts
@@ -18,6 +18,7 @@ import {
   loadMultiscales,
   MAGENTA_GREEN,
   MAX_CHANNELS,
+  nested,
   open,
   parseMatrix,
   range,
@@ -115,13 +116,29 @@ function loadMultiChannel(config: MultichannelConfig, data: ZarrPixelSource<stri
   };
 }
 
+function isNested(attrs: Ome.Attrs) {
+  let version;
+  if ('plate' in attrs) {
+    version = attrs.plate.version;
+  } else if ('omero' in attrs) {
+    version = attrs.multiscales[0].version;
+  } else if ('well' in attrs) {
+    version = attrs.well.version;
+  }
+  return version && version !== '0.1';
+}
+
 export async function createSourceData(config: ImageLayerConfig): Promise<SourceData> {
   const node = await open(config.source);
   let data: ZarrArray[];
 
   if (node instanceof ZarrGroup) {
     const attrs = (await node.attrs.asObject()) as Ome.Attrs;
 
+    if (isNested(attrs)) {
+      node.store = nested(node.store);
+    }
+
     if ('plate' in attrs) {
       return loadPlate(config, node, attrs.plate);
     }

diff --git a/src/utils.ts b/src/utils.ts
@@ -50,24 +50,15 @@ export async function loadMultiscales(grp: ZarrGroup, multiscales: Ome.Multiscal
 
 export function nested(store: ZarrArray['store']) {
   const get = (target: ZarrArray['store'], key: string | number | symbol) => {
-    if (key === 'getItem' || key === 'containsItem' || key === 'setItem') {
-      return (path: string, ...args: any[]) => {
+    if (key === 'getItem' || key === 'containsItem') {
+      return (path: string, ...args: unknown[]) => {
         if (path.endsWith('.zarray') || path.endsWith('.zattrs') || path.endsWith('.zgroup')) {
-          if (key === 'setItem') {
-            // TypeScript: setItem() needs 'value'
-            return target[key](path, args[0]);
-          } else {
-            return target[key](path, ...args);
-          }
+          return target[key](path, ...args);
         }
         const prefix = path.split('/');
-        const chunkKey = prefix.pop() as string;
+        const chunkKey = prefix.pop()!;
         const newPath = [...prefix, chunkKey.replaceAll('.', '/')].join('/');
-        if (key === 'setItem') {
-          return target[key](newPath, args[0]);
-        } else {
-          return target[key](newPath, ...args);
-        }
+        return target[key](newPath, ...args);
       };
     }
     return Reflect.get(target, key);