Handle 0.5-dev version

ome · Jun 14, 2024 · f6de93d · f6de93d
1 parent 6940281
commit f6de93d
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Showing 4 changed files with 22 additions and 31 deletions.
diff --git a/src/App.svelte b/src/App.svelte
@@ -6,7 +6,7 @@
   import Modal from "svelte-simple-modal";
   import SplashScreen from "./SplashScreen.svelte";
 
-  import { getZarrJson } from "./utils";
+  import { getZarrGroupAttrs } from "./utils";
   import CheckMark from "./CheckMark.svelte";
 
   const searchParams = new URLSearchParams(window.location.search);
@@ -22,7 +22,7 @@
   if (source) {
     // load JSON to be validated...
     console.log("Loading JSON... " + source);
-    promise = getZarrJson(source);
+    promise = getZarrGroupAttrs(source);
   }
 </script>
 

diff --git a/src/JsonValidator/MultiscaleArrays/ZarrArray/index.svelte b/src/JsonValidator/MultiscaleArrays/ZarrArray/index.svelte
@@ -31,7 +31,7 @@
   <p>Path <a href="{source + "/" + path} ">{path}</a></p>
 
   {#await promise}
-    <div>loading array .zarray ...</div>
+    <div>loading array data ...</div>
   {:then zarray}
     <table>
       <tr>

diff --git a/src/JsonValidator/index.svelte b/src/JsonValidator/index.svelte
@@ -11,7 +11,6 @@
     CURRENT_VERSION,
     getSchemaUrlsForJson,
     validate,
-    getNgffData,
     getJson,
     getVersion,
     getDataType,
@@ -24,7 +23,6 @@
   const msVersion = getVersion(rootAttrs);
 
   const dtype = getDataType(rootAttrs);
-  const ngffData = getNgffData(rootAttrs);
   const schemaUrls = getSchemaUrlsForJson(rootAttrs);
   console.log("index.svelte schemaUrls", schemaUrls)
   const promise = validate(rootAttrs);
@@ -82,12 +80,12 @@
   {/await}
 </article>
 
-{#if ngffData.multiscales}
-  <MultiscaleArrays {source} rootAttrs={ngffData} />
-{:else if ngffData.plate}
-  <Plate {source} rootAttrs={ngffData} />
-{:else if ngffData.well}
-  <Well {source} rootAttrs={ngffData} />
+{#if rootAttrs.multiscales}
+  <MultiscaleArrays {source} rootAttrs={rootAttrs} />
+{:else if rootAttrs.plate}
+  <Plate {source} rootAttrs={rootAttrs} />
+{:else if rootAttrs.well}
+  <Well {source} rootAttrs={rootAttrs} />
 {/if}
 
 <style>

diff --git a/src/utils.js b/src/utils.js
@@ -14,6 +14,8 @@ export function getSchemaUrl(schemaName, version) {
   if (version == "0.5") {
     // TEMP: use open PR branch
     return `https://raw.githubusercontent.com/normanrz/ngff/spec-rfc2/latest/schemas/${schemaName}.schema`;
+  } else if (version == "0.5-dev") {
+    return `https://raw.githubusercontent.com/d-v-b/ngff/multiple_zarr_versions/0.5-dev1/schemas/${schemaName}.schema`;
   }
   return `https://raw.githubusercontent.com/ome/ngff/main/${version}/schemas/${schemaName}.schema`;
 }
@@ -80,11 +82,17 @@ export function getZarrArrayAttrsFileName(ngffVersion) {
   return "zarr.json";
 }
 
+export async function getZarrGroupAttrs(zarr_dir) {
+  let rawJson = await getZarrJson(zarr_dir, ".zattrs");
+  let groupAttrs = rawJson.attributes || rawJson;
+  return groupAttrs;
+}
+
 export async function getZarrArrayJson(zarr_dir) {
   return getZarrJson(zarr_dir, ".zarray");
 }
 
-export async function getZarrJson(zarr_dir, alternative=".zattrs") {
+async function getZarrJson(zarr_dir, alternative=".zattrs") {
   let zarrJson;
   let msg;
   // try to load v2 /.zattrs or v3 /zarr.json
@@ -143,30 +151,15 @@ export async function getSchema(schemaUrl) {
   return schemas[schemaUrl];
 }
 
-export function getNgffData(jsonData) {
-  // Handle nesting of NGFF data under namespace key for v0.5+
-  if (jsonData.attributes) {
-    for(let v=0; v<NAMESPACED_VERSIONS.length; v++) {
-      let key = getNamespacedKey(NAMESPACED_VERSIONS[v]);
-      if (jsonData.attributes.hasOwnProperty(key)) {
-        return jsonData.attributes[key];
-      }
-    }
-  }
-  return jsonData;
-}
-
-export function getVersion(jsonData) {
-  let ngffData = getNgffData(jsonData);
-  // TODO: v0.5 won't likely have version at multiscales[0].version
-  console.log("getVersion", jsonData, ngffData);
+export function getVersion(ngffData) {
   let version = ngffData.multiscales
     ? ngffData.multiscales[0].version
     : ngffData.plate
     ? ngffData.plate.version
     : ngffData.well
     ? ngffData.well.version
     : undefined;
+  console.log("version", version);
   return version;
 }
 
@@ -188,8 +181,7 @@ export function getSchemaName(jsonData) {
   return names[0];
 }
 
-export function getSchemaNames(jsonData) {
-  let ngffData = getNgffData(jsonData);
+export function getSchemaNames(ngffData) {
   let names = [];
   if (ngffData.multiscales) {
     names.push("image");
@@ -207,6 +199,7 @@ export function getSchemaNames(jsonData) {
 }
 
 export function getSchemaUrlsForJson(rootAttrs) {
+  console.log('getSchemaUrlsForJson rootAttrs', rootAttrs)
   const msVersion = getVersion(rootAttrs);
   const version = msVersion || CURRENT_VERSION;
   // for v0.5 onwards, rootAttrs is nested under attributes.namespace...