Victorgiannakouris/ch648/support open at for arrays

build.gradle

@@ -9,7 +9,7 @@ plugins {
 }
 
 group 'io.tiledb'
-version '0.2.0-SNAPSHOT'
+version '0.2.1-SNAPSHOT'
 
 repositories {
     jcenter()

src/main/java/io/tiledb/java/api/Array.java

@@ -27,6 +27,7 @@
 import static io.tiledb.java.api.QueryType.*;
 
 import io.tiledb.libtiledb.*;
+import java.math.BigInteger;
 import java.util.HashMap;
 
 /**
@@ -73,6 +74,25 @@ public Array(Context ctx, String uri) throws TileDBError {
     openArray(ctx, uri, TILEDB_READ, EncryptionType.TILEDB_NO_ENCRYPTION, new byte[] {});
   }
 
+  /**
+   * Constructs an Array object opening the array for reading at a user-given timestamp
+   * (time-travelling).
+   *
+   * <pre><b>Example:</b>
+   * {@code
+   *   Context ctx = new Context();
+   *   Array array new Array(ctx, "s3://bucket-name/array-name");
+   * }</pre>
+   *
+   * @param ctx TileDB context
+   * @param uri The array URI
+   * @param timestamp The timestamp
+   * @exception TileDBError A TileDB exception
+   */
+  public Array(Context ctx, String uri, BigInteger timestamp) throws TileDBError {
+    openArray(ctx, uri, TILEDB_READ, EncryptionType.TILEDB_NO_ENCRYPTION, new byte[] {}, timestamp);
+  }
+
   /**
    * Constructs an Array object, opening the array for the given query type.
    *
@@ -119,6 +139,39 @@ public Array(
     openArray(ctx, uri, query_type, encryption_type, key);
   }
 
+  /**
+   * Constructs an Array object, opening the encrypted array for the given query type.
+   *
+   * <pre><b>Example:</b>
+   * {@code
+   * Context ctx = new Context();
+   * String key = "0123456789abcdeF0123456789abcdeF";
+   * Array array new Array(ctx, "s3://bucket-name/array-name",
+   *                       TILEDB_READ,
+   *                       TILEDB_AES_256_GCM,
+   *                       key.getBytes(StandardCharsets.UTF_8));
+   * }
+   * </pre>
+   *
+   * @param ctx TileDB context
+   * @param uri The array URI
+   * @param query_type Query type to open the array for
+   * @param encryption_type The encryption type to use
+   * @param key The encryption key to use
+   * @param timestamp The timestamp
+   * @throws TileDBError A TileDB exception
+   */
+  public Array(
+      Context ctx,
+      String uri,
+      QueryType query_type,
+      EncryptionType encryption_type,
+      byte[] key,
+      BigInteger timestamp)
+      throws TileDBError {
+    openArray(ctx, uri, query_type, encryption_type, key, timestamp);
+  }
+
   private synchronized void openArray(
       Context ctx, String uri, QueryType query_type, EncryptionType encryption_type, byte[] key)
       throws TileDBError {
@@ -155,6 +208,48 @@ private synchronized void openArray(
     this.arrayp = _arrayp;
   }
 
+  private synchronized void openArray(
+      Context ctx,
+      String uri,
+      QueryType query_type,
+      EncryptionType encryption_type,
+      byte[] key,
+      BigInteger timestamp)
+      throws TileDBError {
+    SWIGTYPE_p_p_tiledb_array_t _arraypp = tiledb.new_tiledb_array_tpp();
+    try {
+      ctx.handleError(tiledb.tiledb_array_alloc(ctx.getCtxp(), uri, _arraypp));
+    } catch (TileDBError err) {
+      tiledb.delete_tiledb_array_tpp(_arraypp);
+      throw err;
+    }
+    SWIGTYPE_p_tiledb_array_t _arrayp = tiledb.tiledb_array_tpp_value(_arraypp);
+    ArraySchema _schema;
+    try (NativeArray keyArray = new NativeArray(ctx, key, Byte.class)) {
+      try {
+        ctx.handleError(
+            tiledb.tiledb_array_open_at_with_key(
+                ctx.getCtxp(),
+                _arrayp,
+                query_type.toSwigEnum(),
+                encryption_type.toSwigEnum(),
+                keyArray.toVoidPointer(),
+                keyArray.getSize(),
+                timestamp));
+      } catch (TileDBError err) {
+        tiledb.delete_tiledb_array_tpp(_arraypp);
+        throw err;
+      }
+      _schema = new ArraySchema(ctx, uri, encryption_type, key);
+    }
+    this.ctx = ctx;
+    this.uri = uri;
+    this.query_type = query_type;
+    this.schema = _schema;
+    this.arraypp = _arraypp;
+    this.arrayp = _arrayp;
+  }
+
   private void checkIsOpen() throws TileDBError {
     if (arrayp == null) {
       throw new TileDBError("TileDB Array " + uri + " is closed");

src/test/java/io/tiledb/java/api/ArrayTest.java

@@ -1,13 +1,21 @@
 package io.tiledb.java.api;
 
+import static io.tiledb.java.api.Layout.TILEDB_ROW_MAJOR;
+import static io.tiledb.java.api.QueryType.TILEDB_READ;
+import static io.tiledb.java.api.QueryType.TILEDB_WRITE;
+
+import java.math.BigInteger;
 import java.nio.charset.StandardCharsets;
+import java.sql.Timestamp;
+import java.util.Arrays;
 import org.junit.*;
 import org.junit.rules.TemporaryFolder;
 
 public class ArrayTest {
 
   private Context ctx;
   private String arrayURI;
+  private String attributeName;
   private byte[] key;
 
   @Rule public TemporaryFolder temp = new TemporaryFolder();
@@ -16,6 +24,7 @@ public class ArrayTest {
   public void setup() throws Exception {
     ctx = new Context();
     arrayURI = temp.getRoot().toString();
+    attributeName = "a1";
     String keyString = "0123456789abcdeF0123456789abcdeF";
     key = keyString.getBytes(StandardCharsets.US_ASCII);
   }
@@ -31,7 +40,7 @@ public ArraySchema schemaCreate() throws Exception {
     Domain domain = new Domain(ctx);
     domain.addDimension(d1);
 
-    Attribute a1 = new Attribute(ctx, "a1", Integer.class);
+    Attribute a1 = new Attribute(ctx, attributeName, Long.class);
     ArraySchema schema = new ArraySchema(ctx, ArrayType.TILEDB_DENSE);
     schema.setTileOrder(Layout.TILEDB_ROW_MAJOR);
     schema.setCellOrder(Layout.TILEDB_ROW_MAJOR);
@@ -41,6 +50,59 @@ public ArraySchema schemaCreate() throws Exception {
     return schema;
   }
 
+  public void insertArbitraryValuesMeth(Array array, NativeArray a_data) throws TileDBError {
+    // Create query
+    try (Query query = new Query(array, TILEDB_WRITE)) {
+      query.setLayout(TILEDB_ROW_MAJOR).setBuffer(attributeName, a_data);
+      query.submit();
+    }
+    array.close();
+  }
+
+  public void insertArbitraryValues(NativeArray a_data) throws TileDBError {
+    Array array = new Array(ctx, arrayURI, TILEDB_WRITE);
+    insertArbitraryValuesMeth(array, a_data);
+    array.close();
+  }
+
+  public void insertArbitraryValuesEncrypted(NativeArray a_data) throws TileDBError {
+    Array array = new Array(ctx, arrayURI, TILEDB_WRITE, EncryptionType.TILEDB_AES_256_GCM, key);
+    insertArbitraryValuesMeth(array, a_data);
+    array.close();
+  }
+
+  public long[] readArray(Array array) throws TileDBError {
+    NativeArray sub_array = new NativeArray(ctx, new long[] {1, 4, 1, 2}, Long.class);
+    // Create query
+    Query query = new Query(array, TILEDB_READ);
+    query.setLayout(TILEDB_ROW_MAJOR);
+    query.setSubarray(sub_array);
+    query.setBuffer(attributeName, new NativeArray(ctx, 10, Long.class));
+
+    // Submit query
+    query.submit();
+
+    long[] a_buff = (long[]) query.getBuffer(attributeName);
+
+    query.close();
+    array.close();
+
+    return a_buff;
+  }
+
+  public long[] readArray() throws TileDBError {
+    return readArray(new Array(ctx, arrayURI));
+  }
+
+  public long[] readArrayAt(BigInteger timestamp) throws TileDBError {
+    return readArray(new Array(ctx, arrayURI, timestamp));
+  }
+
+  public long[] readArrayAtEncrypted(BigInteger timestamp) throws TileDBError {
+    return readArray(
+        new Array(ctx, arrayURI, TILEDB_READ, EncryptionType.TILEDB_AES_256_GCM, key, timestamp));
+  }
+
   @Test
   public void testArrayExists() throws Exception {
     // Test that we can create an array
@@ -97,4 +159,54 @@ public void testLoadingEncryptedArrayWrongKeyLenErrors() throws Exception {
             EncryptionType.TILEDB_AES_256_GCM,
             keyString.getBytes(StandardCharsets.US_ASCII));
   }
+
+  @Test
+  public void testArrayOpenAt() throws Exception {
+    Array.create(arrayURI, schemaCreate());
+
+    long[] array_a = new long[] {1, 2, 3, 6};
+    insertArbitraryValues(new NativeArray(ctx, array_a, Long.class));
+    long ts_a = new Timestamp(System.currentTimeMillis()).toInstant().toEpochMilli();
+
+    Thread.sleep(1000);
+
+    long[] array_b = new long[] {1, 1, 1, 1};
+    insertArbitraryValues(new NativeArray(ctx, array_b, Long.class));
+    long ts_b = new Timestamp(System.currentTimeMillis()).toInstant().toEpochMilli();
+
+    Thread.sleep(1000);
+
+    long[] array_c = new long[] {0, 0, 0, 0};
+    insertArbitraryValues(new NativeArray(ctx, array_c, Long.class));
+    long ts_c = new Timestamp(System.currentTimeMillis()).toInstant().toEpochMilli();
+
+    assert Arrays.equals(readArrayAt(BigInteger.valueOf(ts_a)), array_a);
+    assert Arrays.equals(readArrayAt(BigInteger.valueOf(ts_b)), array_b);
+    assert Arrays.equals(readArrayAt(BigInteger.valueOf(ts_c)), array_c);
+  }
+
+  @Test
+  public void testArrayOpenAtEncrypted() throws Exception {
+    Array.create(arrayURI, schemaCreate(), EncryptionType.TILEDB_AES_256_GCM, key);
+
+    long[] array_a = new long[] {1, 2, 3, 6};
+    insertArbitraryValuesEncrypted(new NativeArray(ctx, array_a, Long.class));
+    long ts_a = new Timestamp(System.currentTimeMillis()).toInstant().toEpochMilli();
+
+    Thread.sleep(1000);
+
+    long[] array_b = new long[] {1, 1, 1, 1};
+    insertArbitraryValuesEncrypted(new NativeArray(ctx, array_b, Long.class));
+    long ts_b = new Timestamp(System.currentTimeMillis()).toInstant().toEpochMilli();
+
+    Thread.sleep(1000);
+
+    long[] array_c = new long[] {0, 0, 0, 0};
+    insertArbitraryValuesEncrypted(new NativeArray(ctx, array_c, Long.class));
+    long ts_c = new Timestamp(System.currentTimeMillis()).toInstant().toEpochMilli();
+
+    assert Arrays.equals(readArrayAtEncrypted(BigInteger.valueOf(ts_a)), array_a);
+    assert Arrays.equals(readArrayAtEncrypted(BigInteger.valueOf(ts_b)), array_b);
+    assert Arrays.equals(readArrayAtEncrypted(BigInteger.valueOf(ts_c)), array_c);
+  }
 }