Url attributes

src/main/java/org/janelia/saalfeldlab/n5/AbstractGsonReader.java

@@ -1,16 +1,16 @@
 /**
  * Copyright (c) 2017, Stephan Saalfeld
  * All rights reserved.
- *
+ * <p>
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:
- *
+ * <p>
  * 1. Redistributions of source code must retain the above copyright notice,
- *    this list of conditions and the following disclaimer.
+ * this list of conditions and the following disclaimer.
  * 2. Redistributions in binary form must reproduce the above copyright notice,
- *    this list of conditions and the following disclaimer in the documentation
- *    and/or other materials provided with the distribution.
- *
+ * this list of conditions and the following disclaimer in the documentation
+ * and/or other materials provided with the distribution.
+ * <p>
  * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
  * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
  * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
@@ -25,14 +25,18 @@
  */
 package org.janelia.saalfeldlab.n5;
 
+import com.google.gson.Gson;
+import com.google.gson.GsonBuilder;
+import com.google.gson.JsonElement;
+import com.google.gson.JsonObject;
+import com.google.gson.reflect.TypeToken;
+
 import java.io.IOException;
 import java.lang.reflect.Type;
+import java.net.URISyntaxException;
 import java.util.Arrays;
 import java.util.HashMap;
-
-import com.google.gson.Gson;
-import com.google.gson.GsonBuilder;
-import com.google.gson.JsonElement;
+import java.util.Map;
 
 /**
  * Abstract base class implementing {@link N5Reader} with JSON attributes
@@ -41,7 +45,9 @@
  * @author Stephan Saalfeld
  * @author Igor Pisarev
  * @author Philipp Hanslovsky
+ * @author Caleb Hulbert
  */
+@Deprecated
 public abstract class AbstractGsonReader implements GsonAttributesParser, N5Reader {
 
 	protected final Gson gson;
@@ -52,6 +58,7 @@ public abstract class AbstractGsonReader implements GsonAttributesParser, N5Read
 	 *
 	 * @param gsonBuilder
 	 */
+	@Deprecated
 	public AbstractGsonReader(final GsonBuilder gsonBuilder) {
 
 		gsonBuilder.registerTypeAdapter(DataType.class, new DataType.JsonAdapter());
@@ -64,40 +71,48 @@ public AbstractGsonReader(final GsonBuilder gsonBuilder) {
 	 * Constructs an {@link AbstractGsonReader} with a default
 	 * {@link GsonBuilder}.
 	 */
+	@Deprecated
 	public AbstractGsonReader() {
 
 		this(new GsonBuilder());
 	}
 
 	@Override
+	@Deprecated
 	public Gson getGson() {
 
 		return gson;
 	}
 
 	@Override
+	@Deprecated
 	public DatasetAttributes getDatasetAttributes(final String pathName) throws IOException {
 
-		final HashMap<String, JsonElement> map = getAttributes(pathName);
+		final JsonElement root = getAttributes(pathName);
 		final Gson gson = getGson();
 
-		final long[] dimensions = GsonAttributesParser.parseAttribute(map, DatasetAttributes.dimensionsKey, long[].class, gson);
+		if (root == null || !root.isJsonObject())
+			return null;
+
+		final JsonObject rootObject = root.getAsJsonObject();
+
+		final long[] dimensions = GsonN5Reader.readAttribute(rootObject, DatasetAttributes.dimensionsKey, long[].class, gson);
 		if (dimensions == null)
 			return null;
 
-		final DataType dataType = GsonAttributesParser.parseAttribute(map, DatasetAttributes.dataTypeKey, DataType.class, gson);
+		final DataType dataType = GsonN5Reader.readAttribute(rootObject, DatasetAttributes.dataTypeKey, DataType.class, gson);
 		if (dataType == null)
 			return null;
 
-		int[] blockSize = GsonAttributesParser.parseAttribute(map, DatasetAttributes.blockSizeKey, int[].class, gson);
+		int[] blockSize = GsonN5Reader.readAttribute(rootObject, DatasetAttributes.blockSizeKey, int[].class, gson);
 		if (blockSize == null)
 			blockSize = Arrays.stream(dimensions).mapToInt(a -> (int)a).toArray();
 
-		Compression compression = GsonAttributesParser.parseAttribute(map, DatasetAttributes.compressionKey, Compression.class, gson);
+		Compression compression = GsonN5Reader.readAttribute(rootObject, DatasetAttributes.compressionKey, Compression.class, gson);
 
 		/* version 0 */
 		if (compression == null) {
-			switch (GsonAttributesParser.parseAttribute(map, DatasetAttributes.compressionTypeKey, String.class, gson)) {
+			switch (GsonN5Reader.readAttribute(rootObject, DatasetAttributes.compressionTypeKey, String.class, gson)) {
 			case "raw":
 				compression = new RawCompression();
 				break;
@@ -120,22 +135,43 @@ public DatasetAttributes getDatasetAttributes(final String pathName) throws IOEx
 	}
 
 	@Override
+	@Deprecated
 	public <T> T getAttribute(
 			final String pathName,
 			final String key,
 			final Class<T> clazz) throws IOException {
 
-		final HashMap<String, JsonElement> map = getAttributes(pathName);
-		return GsonAttributesParser.parseAttribute(map, key, clazz, getGson());
+		return getAttribute(pathName, key, TypeToken.get(clazz).getType());
 	}
 
 	@Override
+	@Deprecated
 	public <T> T getAttribute(
 			final String pathName,
 			final String key,
 			final Type type) throws IOException {
 
-		final HashMap<String, JsonElement> map = getAttributes(pathName);
-		return GsonAttributesParser.parseAttribute(map, key, type, getGson());
+		final String normalizedGroupPath;
+		final String normalizedAttributePath;
+		try {
+			final N5URL n5url = N5URL.from(null, pathName, key);
+			normalizedGroupPath = n5url.normalizeGroupPath();
+			normalizedAttributePath = n5url.normalizeAttributePath();
+		} catch (URISyntaxException e) {
+			throw new IOException(e);
+		}
+		return GsonN5Reader.readAttribute(getAttributes(normalizedGroupPath), normalizedAttributePath, type, gson);
+	}
+	@Deprecated
+	public HashMap<String, JsonElement> getAttributesMap(String pathName) throws IOException {
+
+		return GsonAttributesParser.super.getAttributesMap(getAttributes(pathName));
+	}
+
+	@Override
+	@Deprecated
+	public Map<String, Class<?>> listAttributes(String pathName) throws IOException {
+
+		return GsonN5Reader.listAttributes(getAttributes(pathName));
 	}
 }