refactoring

Author: normanrz

pom.xml

@@ -21,26 +21,27 @@
             <artifactId>jackson-databind</artifactId>
             <version>${jackson.version}</version>
         </dependency>
-        <dependency>
-            <groupId>com.fasterxml.jackson.core</groupId>
-            <artifactId>jackson-annotations</artifactId>
-            <version>${jackson.version}</version>
-        </dependency>
-        <dependency>
-            <groupId>com.fasterxml.jackson.core</groupId>
-            <artifactId>jackson-core</artifactId>
-            <version>${jackson.version}</version>
-        </dependency>
         <dependency>
             <groupId>com.fasterxml.jackson.datatype</groupId>
             <artifactId>jackson-datatype-jdk8</artifactId>
             <version>${jackson.version}</version>
         </dependency>
+        <dependency>
+            <groupId>org.lasersonlab</groupId>
+            <artifactId>jblosc</artifactId>
+            <version>1.0.1</version>
+        </dependency>
         <dependency>
             <groupId>com.squareup.okhttp</groupId>
             <artifactId>okhttp</artifactId>
             <version>2.7.5</version>
         </dependency>
+        <dependency>
+            <groupId>junit</groupId>
+            <artifactId>junit</artifactId>
+            <version>4.13.1</version>
+            <scope>test</scope>
+        </dependency>
     </dependencies>
 
 </project>

src/main/java/dev/zarr/zarrjava/indexing/Indexer.java

@@ -0,0 +1,37 @@
+package dev.zarr.zarrjava.indexing;
+
+import java.util.Arrays;
+
+public class Indexer {
+    public static long[][] computeChunkCoords(long[] shape, int[] chunkShape, int[] bufferShape, long[] offset) {
+        final int depth = shape.length;
+        long[] start = new long[depth];
+        long[] end = new long[depth];
+        int numChunks = 1;
+        for (int i = 0; i < depth; i++) {
+            final int staIdx = (int)(offset[i] / chunkShape[i]);
+            final int endIdx = (int)((offset[i] + bufferShape[i] - 1) / chunkShape[i]);
+            numChunks *= (endIdx - staIdx + 1);
+            start[i] = staIdx;
+            end[i] = endIdx;
+        }
+
+        final long[][] chunkIndices = new long[numChunks][];
+
+        final long[] currentIdx = Arrays.copyOf(start, depth);
+        for (int i = 0; i < chunkIndices.length; i++) {
+            chunkIndices[i] = Arrays.copyOf(currentIdx, depth);
+            int depthIdx = depth - 1;
+            while (depthIdx >= 0) {
+                if (currentIdx[depthIdx] >= end[depthIdx]) {
+                    currentIdx[depthIdx] = start[depthIdx];
+                    depthIdx--;
+                } else {
+                    currentIdx[depthIdx]++;
+                    depthIdx = -1;
+                }
+            }
+        }
+        return chunkIndices;
+    }
+}

src/main/java/dev/zarr/zarrjava/indexing/OpenSlice.java

@@ -0,0 +1,36 @@
+package dev.zarr.zarrjava.indexing;
+
+public class OpenSlice {
+    public Long start;
+    public Long end;
+
+    public OpenSlice(long start, long end) {
+        this.start = start;
+        this.end = end;
+    }
+
+    public StrictSlice normalize(long length) {
+        long _start = 0;
+        long _end = 0;
+        if (start != null) {
+            _start = start;
+            if (_start < 0) {
+                _start += length;
+                if (_start < 0) {
+                    _start = 0;
+                }
+            }
+        }
+        if (end != null) {
+            _end = end;
+            if (_end < 0) {
+                _end += length;
+                if (_end < 0) {
+                    _end = 0;
+                }
+            }
+        }
+        return new StrictSlice(_start, _end);
+    }
+
+}

src/main/java/dev/zarr/zarrjava/indexing/Selector.java

@@ -0,0 +1,21 @@
+package dev.zarr.zarrjava.indexing;
+
+public class Selector {
+    public OpenSlice[] value;
+    public Selector(int ndim) {
+        value = new OpenSlice[ndim];
+    }
+
+    public void assertDimensions(int ndim) {
+        assert ndim == value.length;
+    }
+
+    public StrictSlice[] normalize(long[] shape) {
+        assert shape.length == value.length;
+        StrictSlice[] output = new StrictSlice[shape.length];
+        for (int i = 0; i < shape.length; i++) {
+            output[i] = value[i].normalize(shape[i]);
+        }
+        return output;
+    }
+}

src/main/java/dev/zarr/zarrjava/indexing/StrictSlice.java

@@ -0,0 +1,11 @@
+package dev.zarr.zarrjava.indexing;
+
+public class StrictSlice {
+    public long start;
+    public long end;
+
+    public StrictSlice(long start, long end) {
+        this.start = start;
+        this.end = end;
+    }
+}

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

@@ -0,0 +1,26 @@
+package dev.zarr.zarrjava.store;
+
+import dev.zarr.zarrjava.indexing.Selector;
+
+public class BufferValueHandle extends ValueHandle {
+
+    byte[] bytes;
+    public BufferValueHandle(byte[] bytes) {
+        this.bytes=bytes;
+    }
+
+    @Override
+    public ValueHandle get(Selector selector) {
+        return null;
+    }
+
+    @Override
+    public void set(Selector selector, ValueHandle value) {
+
+    }
+
+    @Override
+    public byte[] toBytes() {
+        return bytes;
+    }
+}

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

@@ -0,0 +1,36 @@
+package dev.zarr.zarrjava.store;
+
+import dev.zarr.zarrjava.indexing.Selector;
+
+import java.util.Optional;
+
+public class FileValueHandle extends ValueHandle {
+    Store store;
+    String key;
+
+    public FileValueHandle(Store store, String key) {
+        this.store = store;
+        this.key = key;
+    }
+
+    @Override
+    public ValueHandle get(Selector selector) {
+        if (selector.value.length != 1) throw new AssertionError();
+        Optional<BufferValueHandle> valueHandle =
+                store.get(key, selector.value[0]).map(BufferValueHandle::new);
+        if (valueHandle.isPresent()) {
+            return valueHandle.get();
+        }
+        return new NoneHandle();
+    }
+
+    @Override
+    public void set(Selector selector, ValueHandle value) {
+
+    }
+
+    @Override
+    public byte[] toBytes() {
+        return store.get(key, null).orElse(null);
+    }
+}

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

@@ -1,5 +1,7 @@
 package dev.zarr.zarrjava.store;
 
+import dev.zarr.zarrjava.indexing.OpenSlice;
+
 import java.io.IOException;
 import java.nio.ByteBuffer;
 import java.nio.channels.SeekableByteChannel;
@@ -22,8 +24,10 @@ public FilesystemStore(String path) {
     }
 
     @Override
-    public Optional<byte[]> get(String key, ByteRange byteRange) {
+    public Optional<byte[]> get(String key, OpenSlice byteRange) {
         Path keyPath = fileSystem.getPath(this.path, key);
+
+        System.out.println(keyPath);
         if (byteRange == null) {
             try {
                 byte[] bytes = Files.readAllBytes(keyPath);
@@ -60,7 +64,7 @@ public Optional<byte[]> get(String key, ByteRange byteRange) {
     }
 
     @Override
-    public void set(String key, byte[] bytes, ByteRange byteRange) {
+    public void set(String key, byte[] bytes, OpenSlice byteRange) {
         Path keyPath = fileSystem.getPath(this.path, key);
         try {
             Files.createDirectories(keyPath.getParent());
@@ -102,4 +106,5 @@ public List<String> list(String key) {
     public String toString() {
         return fileSystem.getPath(this.path).toUri().toString().replaceAll("\\/$", "");
     }
+
 }

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

@@ -4,6 +4,7 @@
 import com.squareup.okhttp.OkHttpClient;
 import com.squareup.okhttp.Request;
 import com.squareup.okhttp.Response;
+import dev.zarr.zarrjava.indexing.OpenSlice;
 
 import java.io.IOException;
 import java.util.List;
@@ -19,12 +20,12 @@ public HttpStore(String path) {
         this.path = path;
     }
 
-    private String getRangeHeader(ByteRange byteRange) {
+    private String getRangeHeader(OpenSlice byteRange) {
         if (byteRange.start != null) {
             if (byteRange.start < 0) {
                 return String.format("bytes=-%d", -byteRange.start);
             } else if (byteRange.end != null && byteRange.end > 0) {
-                return String.format("bytes=%d-%d", byteRange.start, byteRange.end);
+                return String.format("bytes=%d-%d", byteRange.start, byteRange.end + 1);
             } else {
                 return String.format("bytes=%d", byteRange.start);
             }
@@ -33,7 +34,7 @@ private String getRangeHeader(ByteRange byteRange) {
     }
 
     @Override
-    public Optional<byte[]> get(String key, ByteRange byteRange) {
+    public Optional<byte[]> get(String key, OpenSlice byteRange) {
         Request.Builder builder = new Request.Builder()
                 .url(path + "/" + key);
 
@@ -53,7 +54,7 @@ public Optional<byte[]> get(String key, ByteRange byteRange) {
     }
 
     @Override
-    public void set(String key, byte[] bytes, ByteRange byteRange) {
+    public void set(String key, byte[] bytes, OpenSlice byteRange) {
         throw new UnsupportedOperationException("Not implemented");
     }
 

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

@@ -0,0 +1,19 @@
+package dev.zarr.zarrjava.store;
+
+import dev.zarr.zarrjava.indexing.Selector;
+
+public class NoneHandle extends ValueHandle{
+    @Override
+    public ValueHandle get(Selector selector) {
+        return this;
+    }
+
+    @Override
+    public void set(Selector selector, ValueHandle value) {
+    }
+
+    @Override
+    public byte[] toBytes() {
+        return null;
+    }
+}