From a8f86d0e450ea7b2a835fa1352f8fd561e0574bf Mon Sep 17 00:00:00 2001 From: vicravel Date: Thu, 21 Nov 2019 20:29:19 +0200 Subject: [PATCH 1/7] added openArray() implementation with timestamp argument --- src/main/java/io/tiledb/java/api/Array.java | 57 +++++++++++++++++++++ 1 file changed, 57 insertions(+) diff --git a/src/main/java/io/tiledb/java/api/Array.java b/src/main/java/io/tiledb/java/api/Array.java index 150c5a0a..bc1810d0 100644 --- a/src/main/java/io/tiledb/java/api/Array.java +++ b/src/main/java/io/tiledb/java/api/Array.java @@ -27,6 +27,8 @@ import static io.tiledb.java.api.QueryType.*; import io.tiledb.libtiledb.*; + +import java.math.BigInteger; import java.util.HashMap; /** @@ -73,6 +75,23 @@ 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. + * + * 
Example:
+   * {@code
+   *   Context ctx = new Context();
+   *   Array array new Array(ctx, "s3://bucket-name/array-name");
+   * }
+ * + * @param ctx TileDB context + * @param uri The array URI + * @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. * @@ -155,6 +174,44 @@ 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"); From 47796ba814bdb68e77484a9c05ebefe41e275d43 Mon Sep 17 00:00:00 2001 From: vicravel Date: Thu, 21 Nov 2019 21:15:22 +0200 Subject: [PATCH 2/7] improved docs --- src/main/java/io/tiledb/java/api/Array.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/main/java/io/tiledb/java/api/Array.java b/src/main/java/io/tiledb/java/api/Array.java index bc1810d0..1f09edd2 100644 --- a/src/main/java/io/tiledb/java/api/Array.java +++ b/src/main/java/io/tiledb/java/api/Array.java @@ -76,7 +76,7 @@ public Array(Context ctx, String uri) throws TileDBError { } /** - * Constructs an Array object opening the array for reading. + * Constructs an Array object opening the array for reading at a user-given timestamp (time-travelling). * * 
Example:
    * {@code
@@ -86,6 +86,7 @@ public Array(Context ctx, String uri) throws TileDBError {
    *
    * @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 {

From 6c74c173b9d168a30c54509602d53b186e1d6347 Mon Sep 17 00:00:00 2001
From: gsvic 
Date: Fri, 13 Dec 2019 13:51:15 +0200
Subject: [PATCH 3/7] Added Array constructor for opening encrypted arrays at a
 specific timestamp

---
 src/main/java/io/tiledb/java/api/Array.java | 36 ++++++++++++++++++++-
 1 file changed, 35 insertions(+), 1 deletion(-)

diff --git a/src/main/java/io/tiledb/java/api/Array.java b/src/main/java/io/tiledb/java/api/Array.java
index 1f09edd2..a567a51e 100644
--- a/src/main/java/io/tiledb/java/api/Array.java
+++ b/src/main/java/io/tiledb/java/api/Array.java
@@ -76,7 +76,8 @@ public Array(Context ctx, String uri) throws TileDBError {
   }
 
   /**
-   * Constructs an Array object opening the array for reading at a user-given timestamp (time-travelling).
+   * Constructs an Array object opening the array for reading at a user-given timestamp
+   * (time-travelling).
    *
    * 
Example:
    * {@code
@@ -139,6 +140,39 @@ public Array(
     openArray(ctx, uri, query_type, encryption_type, key);
   }
 
+  /**
+   * Constructs an Array object, opening the encrypted array for the given query type.
+   *
+   * 
Example:
+   * {@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));
+   * }
+   * 

+   *
+   * @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 {

From 06415d7b3524bc88803b356161ad8b9159303461 Mon Sep 17 00:00:00 2001
From: gsvic 
Date: Fri, 13 Dec 2019 14:11:12 +0200
Subject: [PATCH 4/7] Updated Array format

---
 src/main/java/io/tiledb/java/api/Array.java | 27 ++++++++++++---------
 1 file changed, 15 insertions(+), 12 deletions(-)

diff --git a/src/main/java/io/tiledb/java/api/Array.java b/src/main/java/io/tiledb/java/api/Array.java
index a567a51e..8f8e4f9d 100644
--- a/src/main/java/io/tiledb/java/api/Array.java
+++ b/src/main/java/io/tiledb/java/api/Array.java
@@ -27,7 +27,6 @@
 import static io.tiledb.java.api.QueryType.*;
 
 import io.tiledb.libtiledb.*;
-
 import java.math.BigInteger;
 import java.util.HashMap;
 
@@ -210,9 +209,13 @@ private synchronized void openArray(
   }
 
   private synchronized void openArray(
-          Context ctx, String uri, QueryType query_type, EncryptionType encryption_type, byte[] key,
-          BigInteger timestamp)
-          throws TileDBError {
+      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));
@@ -225,14 +228,14 @@ private synchronized void openArray(
     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));
+            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;

From 65b53f89163ea30a09ade1143619607e695ce783 Mon Sep 17 00:00:00 2001
From: gsvic 
Date: Fri, 13 Dec 2019 17:49:07 +0200
Subject: [PATCH 5/7] Unit Tests Added

---
 .../java/io/tiledb/java/api/ArrayTest.java    | 117 +++++++++++++++++-
 1 file changed, 116 insertions(+), 1 deletion(-)

diff --git a/src/test/java/io/tiledb/java/api/ArrayTest.java b/src/test/java/io/tiledb/java/api/ArrayTest.java
index 7f0dd341..c6754155 100644
--- a/src/test/java/io/tiledb/java/api/ArrayTest.java
+++ b/src/test/java/io/tiledb/java/api/ArrayTest.java
@@ -1,13 +1,23 @@
 package io.tiledb.java.api;
 
+import java.math.BigInteger;
 import java.nio.charset.StandardCharsets;
+import java.sql.Timestamp;
+import java.util.Arrays;
+import java.util.HashMap;
+
 import org.junit.*;
 import org.junit.rules.TemporaryFolder;
 
+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;
+
 public class ArrayTest {
 
   private Context ctx;
   private String arrayURI;
+  private String attributeName;
   private byte[] key;
 
   @Rule public TemporaryFolder temp = new TemporaryFolder();
@@ -16,6 +26,7 @@ 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 +42,7 @@ 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 +52,58 @@ 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 +160,56 @@ 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);
+  }
 }

From 2d8098db9d1955ff816289ede6846742af61727d Mon Sep 17 00:00:00 2001
From: gsvic 
Date: Fri, 13 Dec 2019 18:23:07 +0200
Subject: [PATCH 6/7] Change version to 0.2.1-SNAPSHOT

---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 523a8c52..6df44c3f 100644
--- a/build.gradle
+++ b/build.gradle
@@ -9,7 +9,7 @@ plugins {
 }
 
 group 'io.tiledb'
-version '0.2.0-SNAPSHOT'
+version '0.2.1-SNAPSHOT'
 
 repositories {
     jcenter()

From ae6367a500b60728dafd82e5b28d9bce948e6ab8 Mon Sep 17 00:00:00 2001
From: gsvic 
Date: Fri, 13 Dec 2019 18:30:07 +0200
Subject: [PATCH 7/7] Formated ArrayTest.java

---
 .../java/io/tiledb/java/api/ArrayTest.java    | 19 ++++++++-----------
 1 file changed, 8 insertions(+), 11 deletions(-)

diff --git a/src/test/java/io/tiledb/java/api/ArrayTest.java b/src/test/java/io/tiledb/java/api/ArrayTest.java
index c6754155..d7e84cb0 100644
--- a/src/test/java/io/tiledb/java/api/ArrayTest.java
+++ b/src/test/java/io/tiledb/java/api/ArrayTest.java
@@ -1,18 +1,16 @@
 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 java.util.HashMap;
-
 import org.junit.*;
 import org.junit.rules.TemporaryFolder;
 
-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;
-
 public class ArrayTest {
 
   private Context ctx;
@@ -96,12 +94,13 @@ public long[] readArray() throws TileDBError {
     return readArray(new Array(ctx, arrayURI));
   }
 
-  public long[] readArrayAt(BigInteger timestamp) throws TileDBError{
+  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));
+  public long[] readArrayAtEncrypted(BigInteger timestamp) throws TileDBError {
+    return readArray(
+        new Array(ctx, arrayURI, TILEDB_READ, EncryptionType.TILEDB_AES_256_GCM, key, timestamp));
   }
 
   @Test
@@ -181,7 +180,6 @@ public void testArrayOpenAt() throws Exception {
     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);
@@ -207,7 +205,6 @@ public void testArrayOpenAtEncrypted() throws Exception {
     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);