Merge pull request #57 from chris-allan/nested-check

Fix nested support and add test case
glencoesoftware · Apr 12, 2021 · 919586c · 919586c
2 parents 55881d1 + 6971a02
commit 919586c
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diff --git a/build.gradle b/build.gradle
@@ -32,7 +32,7 @@ repositories {
 }
 
 dependencies {
-    implementation 'com.bc.zarr:jzarr:0.3.2'
+    implementation 'com.bc.zarr:jzarr:0.3.3-gs-SNAPSHOT'
     implementation 'info.picocli:picocli:4.2.0'
     implementation 'me.tongfei:progressbar:0.9.0'
     implementation 'ome:formats-bsd:6.4.0'

diff --git a/src/test/java/com/glencoesoftware/raw2ometiff/test/ConversionTest.java b/src/test/java/com/glencoesoftware/raw2ometiff/test/ConversionTest.java
@@ -20,6 +20,10 @@
 import java.util.List;
 import java.util.Map;
 
+import com.bc.zarr.ZarrArray;
+import com.bc.zarr.ZarrGroup;
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.ObjectMapper;
 import com.glencoesoftware.bioformats2raw.Converter;
 import com.glencoesoftware.pyramid.PyramidFromDirectoryWriter;
 
@@ -240,6 +244,13 @@ public void testDefaults() throws Exception {
     input = fake();
     assertBioFormats2Raw();
     assertTool();
+    ZarrArray series0 = ZarrGroup.open(output.resolve("0")).openArray("0");
+    Assert.assertTrue(series0.getNested());
+    // Also ensure we're using the latest .zarray metadata
+    ObjectMapper objectMapper = new ObjectMapper();
+    JsonNode root = objectMapper.readTree(
+        output.resolve("0/0/.zarray").toFile());
+    Assert.assertEquals("/", root.path("dimension_separator").asText());
     try (ImageReader reader = new ImageReader()) {
       reader.setFlattenedResolutions(false);
       reader.setId(outputOmeTiff.toString());