Merge pull request #203 from melissalinkert/jzarr-switch

Update to new jzarr 0.4.2

build.gradle

@@ -18,21 +18,12 @@ repositories {
     maven {
         url 'https://artifacts.glencoesoftware.com/artifactory/ome.releases'
     }
-    maven {
-        url 'https://repo.glencoesoftware.com/repository/n5-zarr-snapshots/'
-    }
-    maven {
-        url 'https://repo.glencoesoftware.com/repository/jzarr-snapshots'
-    }
     maven {
         url 'https://artifacts.glencoesoftware.com/artifactory/ome.external'
     }
     maven {
         url 'https://artifacts.glencoesoftware.com/artifactory/scijava-thirdparty'
     }
-    maven {
-        url 'https://artifacts.glencoesoftware.com/artifactory/jzarr-releases'
-    }
     maven {
         name 'Unidata'
         url 'https://artifacts.glencoesoftware.com/artifactory/unidata-releases'
@@ -49,7 +40,7 @@ dependencies {
     implementation 'ome:formats-gpl:7.0.0'
     implementation 'info.picocli:picocli:4.6.1'
     implementation 'com.univocity:univocity-parsers:2.8.4'
-    implementation 'com.bc.zarr:jzarr:0.3.5'
+    implementation 'dev.zarr:jzarr:0.4.2'
     // implementation 'org.carlspring.cloud.aws:s3fs-nio:1.0-SNAPSHOT'
     // implementation 'io.nextflow:nxf-s3fs:1.1.0'
     implementation 'org.lasersonlab:s3fs:2.2.3'

src/test/java/com/glencoesoftware/bioformats2raw/test/ZarrTest.java

@@ -24,6 +24,7 @@
 import java.util.stream.Stream;
 
 import com.bc.zarr.DataType;
+import com.bc.zarr.DimensionSeparator;
 import com.bc.zarr.ZarrArray;
 import com.bc.zarr.ZarrGroup;
 import com.fasterxml.jackson.databind.JsonNode;
@@ -267,10 +268,8 @@ public void testDefaultLayoutIsSetAndIsNested() throws Exception {
 
     ZarrArray series0 = ZarrGroup.open(output.resolve("0")).openArray("0");
 
-    // no getter for DimensionSeparator in ZarrArray
-    // check that the correct separator was used by checking
-    // that the expected first chunk file exists
-    assertTrue(output.resolve("0/0/0/0/0/0/0").toFile().exists());
+    // check that the correct separator was used
+    assertEquals(series0.getDimensionSeparator(), DimensionSeparator.SLASH);
 
     // Also ensure we're using the latest .zarray metadata
     ObjectMapper objectMapper = new ObjectMapper();