Merge pull request #37 from cmhulbert/fix/compressor

Fix/compressor
saalfeldlab · Mar 4, 2024 · 0afb158 · 0afb158
2 parents 6c9182c + 43f9c44
commit 0afb158
Show file tree

Hide file tree

Showing 6 changed files with 167 additions and 164 deletions.
diff --git a/pom.xml b/pom.xml
@@ -138,7 +138,7 @@
 
 		<json-simple.version>1.1.1</json-simple.version>
 
-		<n5.version>3.1.3</n5.version>
+		<n5.version>3.2.0</n5.version>
 		<n5-zstandard.version>1.0.2</n5-zstandard.version>
 
 	</properties>

diff --git a/src/main/java/org/janelia/saalfeldlab/n5/zarr/ZarrCompressor.java b/src/main/java/org/janelia/saalfeldlab/n5/zarr/ZarrCompressor.java
@@ -35,6 +35,8 @@
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
 
+import com.google.gson.JsonNull;
+import com.google.gson.JsonSerializer;
 import org.janelia.saalfeldlab.n5.Bzip2Compression;
 import org.janelia.saalfeldlab.n5.Compression;
 import org.janelia.saalfeldlab.n5.GzipCompression;
@@ -265,12 +267,12 @@ public Bzip2Compression getCompression() {
 		}
 	}
 
-	public static class Raw extends RawCompression implements ZarrCompressor {
-
+	class Raw implements ZarrCompressor {
+		public Raw() {}
 		@Override
 		public RawCompression getCompression() {
 
-			return this;
+			return new RawCompression();
 		}
 	}
 
@@ -294,4 +296,6 @@ public ZarrCompressor deserialize(final JsonElement json, final Type typeOfT, fi
 			return context.deserialize(json, compressorClass);
 		}
 	}
+
+	JsonSerializer<Raw> rawNullAdapter = (src, typeOfSrc, context) -> JsonNull.INSTANCE;
 }
diff --git a/src/main/java/org/janelia/saalfeldlab/n5/zarr/ZarrKeyValueReader.java b/src/main/java/org/janelia/saalfeldlab/n5/zarr/ZarrKeyValueReader.java
@@ -149,6 +149,21 @@ public ZarrKeyValueReader(
 			final boolean cacheMeta)
 			throws N5Exception {
 
+		this(checkVersion, keyValueAccess, basePath, gsonBuilder, mapN5DatasetAttributes, mergeAttributes, cacheMeta, true);
+	}
+
+	protected ZarrKeyValueReader(
+			final boolean checkVersion,
+			final KeyValueAccess keyValueAccess,
+			final String basePath,
+			final GsonBuilder gsonBuilder,
+			final boolean mapN5DatasetAttributes,
+			final boolean mergeAttributes,
+			final boolean cacheMeta,
+			final boolean checkRootExists
+	) {
+
+
 		this.keyValueAccess = keyValueAccess;
 		this.gson = registerGson(gsonBuilder);
 		this.cacheMeta = cacheMeta;
@@ -169,6 +184,10 @@ public ZarrKeyValueReader(
 			cache = newCache();
 		else
 			cache = null;
+
+ 		if( checkRootExists && !exists("/"))
+			throw new N5Exception.N5IOException("No container exists at " + basePath );
+
 	}
 
 	/**
@@ -837,6 +856,7 @@ protected static GsonBuilder addTypeAdapters(final GsonBuilder gsonBuilder) {
 
 		gsonBuilder.registerTypeAdapter(DataType.class, new DataType.JsonAdapter());
 		gsonBuilder.registerTypeAdapter(ZarrCompressor.class, ZarrCompressor.jsonAdapter);
+		gsonBuilder.registerTypeAdapter(ZarrCompressor.Raw.class, ZarrCompressor.rawNullAdapter);
 		gsonBuilder.registerTypeHierarchyAdapter(Compression.class, CompressionAdapter.getJsonAdapter());
 		gsonBuilder.registerTypeAdapter(Compression.class, CompressionAdapter.getJsonAdapter());
 		gsonBuilder.registerTypeAdapter(ZArrayAttributes.class, ZArrayAttributes.jsonAdapter);

diff --git a/src/main/java/org/janelia/saalfeldlab/n5/zarr/ZarrKeyValueWriter.java b/src/main/java/org/janelia/saalfeldlab/n5/zarr/ZarrKeyValueWriter.java
@@ -120,7 +120,8 @@ public ZarrKeyValueWriter(
 				gsonBuilder,
 				mapN5DatasetAttributes,
 				mergeAttributes,
-				cacheAttributes);
+				cacheAttributes,
+				false);
 		this.dimensionSeparator = dimensionSeparator;
 		Version version = null;
 		if (exists("/")) {