Merge branch 'main' into accept-missing-configuration-for-chunkKeyEncoding

Author: brokkoli71

src/main/java/dev/zarr/zarrjava/core/Group.java

@@ -64,14 +64,14 @@ public static Group open(String path) throws IOException, ZarrException {
     }
 
     @Nullable
-    public abstract Node get(String key) throws ZarrException;
+    public abstract Node get(String key) throws ZarrException, IOException;
 
     public Stream<Node> list() {
         return storeHandle.list()
             .map(key -> {
                 try {
                     return get(key);
-                } catch (ZarrException e) {
+                } catch (Exception e) {
                     throw new RuntimeException(e);
                 }
             })

src/main/java/dev/zarr/zarrjava/store/MemoryStore.java

@@ -0,0 +1,88 @@
+package dev.zarr.zarrjava.store;
+
+import javax.annotation.Nonnull;
+import javax.annotation.Nullable;
+import java.nio.ByteBuffer;
+import java.util.*;
+import java.util.concurrent.ConcurrentHashMap;
+import java.util.stream.Stream;
+
+public class MemoryStore implements Store, Store.ListableStore {
+  private final Map<List<String>, byte[]> map = new ConcurrentHashMap<>();
+
+  List<String> resolveKeys(String[] keys) {
+    ArrayList<String> resolvedKeys = new ArrayList<>();
+    for(String key:keys){
+      if(key.startsWith("/")){
+        key = key.substring(1);
+      }
+      resolvedKeys.addAll(Arrays.asList(key.split("/")));
+    }
+    return resolvedKeys;
+  }
+
+  @Override
+  public boolean exists(String[] keys) {
+    return map.containsKey(resolveKeys(keys));
+  }
+
+  @Nullable
+  @Override
+  public ByteBuffer get(String[] keys) {
+      return get(keys, 0);
+  }
+
+  @Nullable
+  @Override
+  public ByteBuffer get(String[] keys, long start) {
+    return get(keys, start, -1);
+  }
+
+  @Nullable
+  @Override
+  public ByteBuffer get(String[] keys, long start, long end) {
+    byte[] bytes = map.get(resolveKeys(keys));
+    if (bytes == null) return null;
+    if (end < 0) end = bytes.length;
+    if (end > Integer.MAX_VALUE) throw new IllegalArgumentException("End index too large");
+    return ByteBuffer.wrap(bytes, (int) start, (int) end);
+  }
+
+
+  @Override
+  public void set(String[] keys, ByteBuffer bytes) {
+    map.put(resolveKeys(keys), bytes.array());
+  }
+
+  @Override
+  public void delete(String[] keys) {
+    map.remove(resolveKeys(keys));
+  }
+
+  public Stream<String> list(String[] keys) {
+    List<String> prefix = resolveKeys(keys);
+    Set<String> allKeys = new HashSet<>();
+
+    for (List<String> k : map.keySet()) {
+      if (k.size() <= prefix.size() || ! k.subList(0, prefix.size()).equals(prefix))
+        continue;
+      for (int i = 0; i < k.size(); i++) {
+        List<String> subKey = k.subList(0, i+1);
+        allKeys.add(String.join("/", subKey));
+      }
+    }
+    return allKeys.stream();
+  }
+
+  @Nonnull
+  @Override
+  public StoreHandle resolve(String... keys) {
+    return new StoreHandle(this, keys);
+  }
+
+  @Override
+  public String toString() {
+    return String.format("<MemoryStore {%s}>", hashCode());
+  }
+}
+

src/main/java/dev/zarr/zarrjava/v2/Array.java

@@ -5,6 +5,7 @@
 import dev.zarr.zarrjava.ZarrException;
 import dev.zarr.zarrjava.core.Attributes;
 import dev.zarr.zarrjava.store.FilesystemStore;
+import dev.zarr.zarrjava.store.MemoryStore;
 import dev.zarr.zarrjava.store.StoreHandle;
 import dev.zarr.zarrjava.utils.Utils;
 import dev.zarr.zarrjava.core.codec.CodecPipeline;
@@ -87,6 +88,16 @@ public static Array open(String path) throws IOException, ZarrException {
       return open(Paths.get(path));
     }
 
+  /**
+   * Creates a new Zarr array with the provided metadata in an in-memory store
+   *
+   * @param arrayMetadata the metadata of the Zarr array
+   * @throws IOException if the metadata cannot be serialized
+   * @throws ZarrException if the Zarr array cannot be created
+   */
+  public static Array create(ArrayMetadata arrayMetadata) throws ZarrException, IOException {
+    return create(new StoreHandle(new MemoryStore()), arrayMetadata);
+  }
   /**
    * Creates a new Zarr array with the provided metadata at a specified storage location. This
    * method will raise an exception if a Zarr array already exists at the specified storage

src/main/java/dev/zarr/zarrjava/v2/Group.java

@@ -5,13 +5,15 @@
 import dev.zarr.zarrjava.ZarrException;
 import dev.zarr.zarrjava.core.Attributes;
 import dev.zarr.zarrjava.store.FilesystemStore;
+import dev.zarr.zarrjava.store.MemoryStore;
 import dev.zarr.zarrjava.store.StoreHandle;
 import dev.zarr.zarrjava.utils.Utils;
 
 import javax.annotation.Nonnull;
 import javax.annotation.Nullable;
 import java.io.IOException;
 import java.nio.ByteBuffer;
+import java.nio.file.NoSuchFileException;
 import java.nio.file.Path;
 import java.nio.file.Paths;
 import java.util.function.Function;
@@ -26,6 +28,12 @@ protected Group(@Nonnull StoreHandle storeHandle, @Nonnull GroupMetadata groupMe
     this.metadata = groupMetadata;
   }
 
+  /**
+   * Opens an existing Zarr group at a specified storage location.
+   *
+   * @param storeHandle the storage location of the Zarr group
+   * @throws IOException if the metadata cannot be read
+   */
   public static Group open(@Nonnull StoreHandle storeHandle) throws IOException {
     ObjectMapper mapper = makeObjectMapper();
     GroupMetadata metadata = mapper.readValue(
@@ -40,77 +48,221 @@ public static Group open(@Nonnull StoreHandle storeHandle) throws IOException {
     return new Group(storeHandle, metadata);
   }
 
+  /**
+   * Opens an existing Zarr group at a specified storage location.
+   *
+   * @param path the storage location of the Zarr group
+   * @throws IOException if the metadata cannot be read
+   */
   public static Group open(Path path) throws IOException {
       return open(new StoreHandle(new FilesystemStore(path)));
     }
 
-    public static Group open(String path) throws IOException {
+  /**
+   * Opens an existing Zarr group at a specified storage location.
+   *
+   * @param path the storage location of the Zarr group
+   * @throws IOException if the metadata cannot be read
+   */
+  public static Group open(String path) throws IOException {
       return open(Paths.get(path));
     }
 
+  /**
+   * Creates a new Zarr group with the provided metadata in an in-memory store.
+   *
+   * @param groupMetadata the metadata of the Zarr group
+   * @throws IOException if the metadata cannot be serialized
+   */
+  public static Group create(@Nonnull GroupMetadata groupMetadata) throws IOException {
+    return new Group(new MemoryStore().resolve(), groupMetadata).writeMetadata();
+  }
+
+  /**
+   * Creates a new Zarr group with the provided metadata at a specified storage location.
+   *
+   * @param storeHandle the storage location of the Zarr group
+   * @param groupMetadata the metadata of the Zarr group
+   * @throws IOException if the metadata cannot be serialized
+   */
   public static Group create(
       @Nonnull StoreHandle storeHandle, @Nonnull GroupMetadata groupMetadata
   ) throws IOException {
-    ObjectWriter objectWriter = makeObjectWriter();
-    ByteBuffer metadataBytes = ByteBuffer.wrap(objectWriter.writeValueAsBytes(groupMetadata));
-    storeHandle.resolve(ZGROUP).set(metadataBytes);
-    if (groupMetadata.attributes != null) {
-      StoreHandle attrsHandle = storeHandle.resolve(ZATTRS);
-      ByteBuffer attrsBytes = ByteBuffer.wrap(
-          objectWriter.writeValueAsBytes(groupMetadata.attributes));
-      attrsHandle.set(attrsBytes);
-    }
-    return new Group(storeHandle, groupMetadata);
+    return new Group(storeHandle, groupMetadata).writeMetadata();
   }
 
+  /**
+   * Creates a new Zarr group with default metadata at a specified storage location.
+   *
+   * @param storeHandle the storage location of the Zarr group
+   * @throws IOException if the metadata cannot be serialized
+   * @throws ZarrException if the metadata is invalid
+   */
   public static Group create(@Nonnull StoreHandle storeHandle) throws IOException, ZarrException {
     return create(storeHandle, new GroupMetadata());
   }
 
+  /**
+   * Creates a new Zarr group with the provided attributes at a specified storage location.
+   *
+   * @param storeHandle the storage location of the Zarr group
+   * @param attributes the attributes of the Zarr group
+   * @throws IOException if the metadata cannot be serialized
+   * @throws ZarrException if the attributes are invalid
+   */
   public static Group create(@Nonnull StoreHandle storeHandle, Attributes attributes) throws IOException, ZarrException {
     return create(storeHandle, new GroupMetadata(attributes));
   }
 
+  /**
+   * Creates a new Zarr group with default metadata at a specified storage location.
+   *
+   * @param path the storage location of the Zarr group
+   * @throws IOException if the metadata cannot be serialized
+   * @throws ZarrException if the metadata is invalid
+   */
   public static Group create(Path path) throws IOException, ZarrException {
     return create(new StoreHandle(new FilesystemStore(path)));
   }
 
+  /**
+   * Creates a new Zarr group with the provided attributes at a specified storage location.
+   *
+   * @param path the storage location of the Zarr group
+   * @param attributes the attributes of the Zarr group
+   * @throws IOException if the metadata cannot be serialized
+   * @throws ZarrException if the attributes are invalid
+   */
   public static Group create(Path path, Attributes attributes) throws IOException, ZarrException {
     return create(new StoreHandle(new FilesystemStore(path)), attributes);
   }
 
+  /**
+   * Creates a new Zarr group with default metadata at a specified storage location.
+   *
+   * @param path the storage location of the Zarr group
+   * @throws IOException if the metadata cannot be serialized
+   * @throws ZarrException if the metadata is invalid
+   */
   public static Group create(String path) throws IOException, ZarrException {
     return create(Paths.get(path));
   }
 
+  /**
+   * Creates a new Zarr group with the provided attributes at a specified storage location.
+   *
+   * @param path the storage location of the Zarr group
+   * @param attributes the attributes of the Zarr group
+   * @throws IOException if the metadata cannot be serialized
+   * @throws ZarrException if the attributes are invalid
+   */
   public static Group create(String path, Attributes attributes) throws IOException, ZarrException {
     return create(Paths.get(path), attributes);
   }
 
+  /**
+   * Retrieves a node (group or array) at the specified key within the current group.
+   *
+   * @param key the key of the node to retrieve
+   * @return the node at the specified key, or null if it does not exist
+   * @throws ZarrException if the node cannot be opened
+   * @throws IOException if there is an error accessing the storage
+   */
   @Nullable
-  public Node get(String key) throws ZarrException {
+  public Node get(String key) throws ZarrException, IOException {
     StoreHandle keyHandle = storeHandle.resolve(key);
     try {
       return Node.open(keyHandle);
-    } catch (IOException e) {
+    } catch (NoSuchFileException e) {
         return null;
     }
   }
 
+  /**
+   * Creates a new subgroup with default metadata at the specified key.
+   *
+   * @param key the key of the new Zarr group within the current group
+   * @return the created subgroup
+   * @throws IOException if the metadata cannot be serialized
+   * @throws ZarrException if the group cannot be created
+   */
   public Group createGroup(String key) throws IOException, ZarrException {
     return Group.create(storeHandle.resolve(key));
   }
 
+  /**
+   * Creates a new array with the provided metadata at the specified key.
+   *
+   * @param key the key of the new Zarr array within the current group
+   * @param arrayMetadata the metadata of the Zarr array
+   * @return the created array
+   * @throws IOException if the metadata cannot be serialized
+   * @throws ZarrException if the array cannot be created
+   */
   public Array createArray(String key, ArrayMetadata arrayMetadata)
       throws IOException, ZarrException {
     return Array.create(storeHandle.resolve(key), arrayMetadata);
   }
 
+  /**
+   * Creates a new array with the provided metadata at the specified key.
+   *
+   * @param key the key of the new Zarr array within the current group
+   * @param arrayMetadataBuilderMapper a function that modifies the array metadata
+   * @return the created array
+   * @throws IOException if the metadata cannot be serialized
+   * @throws ZarrException if the array cannot be created
+   */
   public Array createArray(String key, Function<ArrayMetadataBuilder, ArrayMetadataBuilder> arrayMetadataBuilderMapper)
-      throws IOException, ZarrException {
+          throws IOException, ZarrException {
     return Array.create(storeHandle.resolve(key), arrayMetadataBuilderMapper, false);
   }
 
+  private Group writeMetadata() throws IOException {
+    return writeMetadata(this.metadata);
+  }
+
+  private Group writeMetadata(GroupMetadata newGroupMetadata) throws IOException {
+    ObjectWriter objectWriter = makeObjectWriter();
+    ByteBuffer metadataBytes = ByteBuffer.wrap(objectWriter.writeValueAsBytes(newGroupMetadata));
+    storeHandle.resolve(ZGROUP).set(metadataBytes);
+    if (newGroupMetadata.attributes != null) {
+      StoreHandle attrsHandle = storeHandle.resolve(ZATTRS);
+      ByteBuffer attrsBytes = ByteBuffer.wrap(
+          objectWriter.writeValueAsBytes(newGroupMetadata.attributes));
+      attrsHandle.set(attrsBytes);
+    }
+    this.metadata = newGroupMetadata;
+    return this;
+  }
+
+  /**
+   * Sets new attributes for the group, replacing any existing attributes.
+   *
+   * @param newAttributes the new attributes to set
+   * @return the updated group
+   * @throws ZarrException if the new attributes are invalid
+   * @throws IOException if the metadata cannot be serialized
+   */
+  public Group setAttributes(Attributes newAttributes) throws ZarrException, IOException {
+    GroupMetadata newGroupMetadata = new GroupMetadata(newAttributes);
+    return writeMetadata(newGroupMetadata);
+  }
+
+  /**
+   * Updates the attributes of the group using a mapper function.
+   *
+   * @param attributeMapper a function that takes the current attributes and returns the updated attributes
+   * @return the updated group
+   * @throws ZarrException if the new attributes are invalid
+   * @throws IOException if the metadata cannot be serialized
+   */
+  public Group updateAttributes(Function<Attributes, Attributes> attributeMapper)
+          throws ZarrException, IOException {
+    return setAttributes(attributeMapper.apply(metadata.attributes));
+  }
+
+
   @Override
   public String toString() {
     return String.format("<v2.Group {%s}>", storeHandle);