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Merged
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Jul 16, 2020
Merged

Updated TileDB-Java Examples - Replaced get/setCoordinates with setBuffer #184

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12 changes: 5 additions & 7 deletions src/main/java/examples/io/tiledb/java/api/DenseReadOrderedSubarray.java
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Original file line number Diff line number Diff line change
Expand Up @@ -39,20 +39,18 @@ public static void main(String[] args) throws Exception {
// Compute maximum buffer elements for the query results per attribute
Array my_dense_array = new Array(ctx, "my_dense_array");
NativeArray subarray = new NativeArray(ctx, new long[] {3l, 4l, 2l, 4l}, Long.class);
HashMap<String, Pair<Long, Long>> max_sizes = my_dense_array.maxBufferElements(subarray);

// Create query
Query query = new Query(my_dense_array, TILEDB_READ);
query.setLayout(TILEDB_ROW_MAJOR);
query.setSubarray(subarray);
query.setBuffer(
"a1", new NativeArray(ctx, max_sizes.get("a1").getSecond().intValue(), Integer.class));
int bufferSize = 1024;
query.setBuffer("a1", new NativeArray(ctx, bufferSize, Integer.class));
query.setBuffer(
"a2",
new NativeArray(ctx, max_sizes.get("a2").getFirst().intValue(), Long.class),
new NativeArray(ctx, max_sizes.get("a2").getSecond().intValue(), String.class));
query.setBuffer(
"a3", new NativeArray(ctx, max_sizes.get("a3").getSecond().intValue(), Float.class));
new NativeArray(ctx, bufferSize, Datatype.TILEDB_UINT64),
new NativeArray(ctx, bufferSize, String.class));
query.setBuffer("a3", new NativeArray(ctx, bufferSize, Float.class));

// Submit query
System.out.println("Query submitted: " + query.submit());
Expand Down
10 changes: 6 additions & 4 deletions src/main/java/examples/io/tiledb/java/api/DenseWriteUnordered.java
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Expand Up @@ -37,24 +37,26 @@ public static void main(String[] args) throws Exception {

// Prepare cell buffers
NativeArray a1_data = new NativeArray(ctx, new int[] {211, 213, 212, 208}, Integer.class);
NativeArray a2_offsets = new NativeArray(ctx, new long[] {0, 4, 6, 7}, Long.class);
NativeArray a2_offsets = new NativeArray(ctx, new long[] {0, 4, 6, 7}, Datatype.TILEDB_UINT64);
NativeArray buffer_var_a2 = new NativeArray(ctx, "wwwwyyxu", String.class);
NativeArray buffer_a3 =
new NativeArray(
ctx,
new float[] {211.1f, 211.2f, 213.1f, 213.2f, 212.1f, 212.2f, 208.1f, 208.2f},
Float.class);
NativeArray coords = new NativeArray(ctx, new long[] {4, 2, 3, 4, 3, 3, 3, 1}, Long.class);

NativeArray d1 = new NativeArray(ctx, new long[] {4, 3, 3, 3}, Long.class);
NativeArray d2 = new NativeArray(ctx, new long[] {2, 4, 3, 1}, Long.class);

// Create query
Array my_dense_array = new Array(ctx, "my_dense_array", TILEDB_WRITE);
Query query = new Query(my_dense_array);
query.setLayout(TILEDB_UNORDERED);
query.setSubarray(new NativeArray(ctx, new long[] {3, 4, 3, 4}, Long.class));
query.setBuffer("d1", d1);
query.setBuffer("d2", d2);
query.setBuffer("a1", a1_data);
query.setBuffer("a2", a2_offsets, buffer_var_a2);
query.setBuffer("a3", buffer_a3);
query.setCoordinates(coords);

// Submit query
query.submit();
Expand Down
10 changes: 5 additions & 5 deletions src/main/java/examples/io/tiledb/java/api/SparseCreate.java
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Expand Up @@ -41,19 +41,19 @@ public static void main(String[] args) throws Exception {
Context ctx = new Context();
// Create getDimensions
Dimension<Long> d1 =
new Dimension<Long>(ctx, "d1", Long.class, new Pair<Long, Long>(1l, 4l), 2l);
new Dimension<Long>(ctx, "d1", Datatype.TILEDB_INT64, new Pair(1l, 4l), 2l);
Dimension<Long> d2 =
new Dimension<Long>(ctx, "d2", Long.class, new Pair<Long, Long>(1l, 4l), 2l);
new Dimension<Long>(ctx, "d2", Datatype.TILEDB_INT64, new Pair(1l, 4l), 2l);
// Create getDomain
Domain domain = new Domain(ctx);
domain.addDimension(d1);
domain.addDimension(d2);

// Create and add getAttributes
Attribute a1 = new Attribute(ctx, "a1", Integer.class);
Attribute a2 = new Attribute(ctx, "a2", String.class);
Attribute a1 = new Attribute(ctx, "a1", Datatype.TILEDB_INT32);
Attribute a2 = new Attribute(ctx, "a2", Datatype.TILEDB_CHAR);
a2.setCellValNum(TILEDB_VAR_NUM);
Attribute a3 = new Attribute(ctx, "a3", Float.class);
Attribute a3 = new Attribute(ctx, "a3", Datatype.TILEDB_FLOAT32);
a3.setCellValNum(2);
a1.setFilterList(new FilterList(ctx).addFilter(new LZ4Filter(ctx)));
a2.setFilterList(new FilterList(ctx).addFilter(new GzipFilter(ctx)));
Expand Down
19 changes: 12 additions & 7 deletions src/main/java/examples/io/tiledb/java/api/SparseReadGlobal.java
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Expand Up @@ -35,7 +35,6 @@

package examples.io.tiledb.java.api;

import static io.tiledb.java.api.Constants.TILEDB_COORDS;
import static io.tiledb.java.api.Layout.TILEDB_GLOBAL_ORDER;
import static io.tiledb.java.api.QueryType.TILEDB_READ;

Expand Down Expand Up @@ -73,12 +72,16 @@ public static void main(String[] args) throws Exception {
"a1", new NativeArray(ctx, max_sizes.get("a1").getSecond().intValue(), Integer.class));
query.setBuffer(
"a2",
new NativeArray(ctx, max_sizes.get("a2").getFirst().intValue(), Long.class),
new NativeArray(ctx, max_sizes.get("a2").getFirst().intValue(), Datatype.TILEDB_UINT64),
new NativeArray(ctx, max_sizes.get("a2").getSecond().intValue(), String.class));
query.setBuffer(
"a3", new NativeArray(ctx, max_sizes.get("a3").getSecond().intValue(), Float.class));
query.setCoordinates(
new NativeArray(ctx, max_sizes.get(TILEDB_COORDS).getSecond().intValue(), Long.class));

query.setBuffer(
"d1", new NativeArray(ctx, max_sizes.get("d1").getSecond().intValue(), Long.class));

query.setBuffer(
"d2", new NativeArray(ctx, max_sizes.get("d2").getSecond().intValue(), Long.class));

// Submit query
System.out.println("Query submitted: " + query.submit());
Expand All @@ -89,11 +92,13 @@ public static void main(String[] args) throws Exception {
long[] a2_offsets = (long[]) query.getVarBuffer("a2");
byte[] a2_data = (byte[]) query.getBuffer("a2");
float[] a3_buff = (float[]) query.getBuffer("a3");
long[] coords = (long[]) query.getBuffer(TILEDB_COORDS);
long[] d1_buff = (long[]) query.getBuffer("d1");
long[] d2_buff = (long[]) query.getBuffer("d2");

System.out.println("Result num: " + a1_buff.length);
System.out.println(
String.format("%8s", TILEDB_COORDS)
"d1"
+ String.format("%9s", "d2")
+ String.format("%9s", "a1")
+ String.format("%11s", "a2")
+ String.format("%11s", "a3[0]")
Expand All @@ -102,7 +107,7 @@ public static void main(String[] args) throws Exception {
for (int i = 0; i < a1_buff.length; i++) {
int end = (i == a1_buff.length - 1) ? a2_data.length : (int) a2_offsets[i + 1];
System.out.println(
String.format("%8s", "(" + coords[2 * i] + ", " + coords[2 * i + 1] + ")")
String.format("%8s", "(" + d1_buff[2 * i] + ", " + d2_buff[2 * i] + ")")
+ String.format("%9s", a1_buff[i])
+ String.format(
"%11s", new String(Arrays.copyOfRange(a2_data, (int) a2_offsets[i], end)))
Expand Down
19 changes: 9 additions & 10 deletions src/main/java/examples/io/tiledb/java/api/SparseReadOrderedSubarray.java
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Expand Up @@ -51,23 +51,22 @@ public static void main(String[] args) throws Exception {

// Calculate maximum buffer elements for the query results per attribute
Array my_sparse_array = new Array(ctx, "my_sparse_array");
NativeArray subarray = new NativeArray(ctx, new long[] {3l, 4l, 2l, 4l}, Long.class);
HashMap<String, Pair<Long, Long>> max_sizes = my_sparse_array.maxBufferElements(subarray);
NativeArray subarray = new NativeArray(ctx, new long[] {3l, 4l, 2l, 4l}, Datatype.TILEDB_INT64);

long bufferSize = 1024;

// Create query
Query query = new Query(my_sparse_array, TILEDB_READ);
query.setLayout(TILEDB_ROW_MAJOR);
query.setSubarray(subarray);
query.setBuffer(
"a1", new NativeArray(ctx, max_sizes.get("a1").getSecond().intValue(), Integer.class));
query.setBuffer("d1", new NativeArray(ctx, bufferSize, Datatype.TILEDB_INT64));
query.setBuffer("d2", new NativeArray(ctx, bufferSize, Datatype.TILEDB_INT64));
query.setBuffer("a1", new NativeArray(ctx, bufferSize, Datatype.TILEDB_INT32));
query.setBuffer(
"a2",
new NativeArray(ctx, max_sizes.get("a2").getFirst().intValue(), Long.class),
new NativeArray(ctx, max_sizes.get("a2").getSecond().intValue(), String.class));
query.setBuffer(
"a3", new NativeArray(ctx, max_sizes.get("a3").getSecond().intValue(), Float.class));
query.setCoordinates(
new NativeArray(ctx, max_sizes.get(TILEDB_COORDS).getSecond().intValue(), Long.class));
new NativeArray(ctx, bufferSize, Datatype.TILEDB_INT64),
new NativeArray(ctx, bufferSize, Datatype.TILEDB_CHAR));
query.setBuffer("a3", new NativeArray(ctx, bufferSize, Datatype.TILEDB_FLOAT32));

// Submit query
System.out.println("Query submitted: " + query.submit());
Expand Down
24 changes: 13 additions & 11 deletions src/main/java/examples/io/tiledb/java/api/SparseWriteGlobal1.java
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Expand Up @@ -38,21 +38,20 @@
import static io.tiledb.java.api.Layout.TILEDB_GLOBAL_ORDER;
import static io.tiledb.java.api.QueryType.TILEDB_WRITE;

import io.tiledb.java.api.Array;
import io.tiledb.java.api.Context;
import io.tiledb.java.api.NativeArray;
import io.tiledb.java.api.Query;
import io.tiledb.java.api.*;

public class SparseWriteGlobal1 {
public static void main(String[] args) throws Exception {
// Create TileDB context
Context ctx = ctx = new Context();

// Prepare cell buffers
NativeArray a1_data = new NativeArray(ctx, new int[] {0, 1, 2, 3, 4, 5, 6, 7}, Integer.class);
NativeArray a1_data =
new NativeArray(ctx, new int[] {0, 1, 2, 3, 4, 5, 6, 7}, Datatype.TILEDB_INT32);
NativeArray a2_offsets =
new NativeArray(ctx, new long[] {0, 1, 3, 6, 10, 11, 13, 16}, Long.class);
NativeArray buffer_var_a2 = new NativeArray(ctx, "abbcccdddd" + "effggghhhh", String.class);
new NativeArray(ctx, new long[] {0, 1, 3, 6, 10, 11, 13, 16}, Datatype.TILEDB_UINT64);
NativeArray buffer_var_a2 =
new NativeArray(ctx, "abbcccdddd" + "effggghhhh", Datatype.TILEDB_CHAR);

NativeArray buffer_a3 =
new NativeArray(
Expand All @@ -63,18 +62,21 @@ public static void main(String[] args) throws Exception {
},
Float.class);

NativeArray coords_buff =
new NativeArray(
ctx, new long[] {1, 1, 1, 2, 1, 4, 2, 3, 3, 1, 4, 2, 3, 3, 3, 4}, Long.class);
NativeArray d1_buff =
new NativeArray(ctx, new long[] {1, 1, 1, 2, 3, 4, 3, 3}, Datatype.TILEDB_INT64);

NativeArray d2_buff =
new NativeArray(ctx, new long[] {1, 2, 4, 3, 1, 2, 3, 4}, Datatype.TILEDB_INT64);

// Create query
Array my_sparse_array = new Array(ctx, "my_sparse_array", TILEDB_WRITE);
Query query = new Query(my_sparse_array);
query.setLayout(TILEDB_GLOBAL_ORDER);
query.setBuffer("d1", d1_buff);
query.setBuffer("d2", d2_buff);
query.setBuffer("a1", a1_data);
query.setBuffer("a2", a2_offsets, buffer_var_a2);
query.setBuffer("a3", buffer_a3);
query.setCoordinates(coords_buff);

// Submit query
query.submit();
Expand Down
21 changes: 11 additions & 10 deletions src/main/java/examples/io/tiledb/java/api/SparseWriteGlobal2.java
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Expand Up @@ -38,10 +38,7 @@
import static io.tiledb.java.api.Layout.TILEDB_GLOBAL_ORDER;
import static io.tiledb.java.api.QueryType.TILEDB_WRITE;

import io.tiledb.java.api.Array;
import io.tiledb.java.api.Context;
import io.tiledb.java.api.NativeArray;
import io.tiledb.java.api.Query;
import io.tiledb.java.api.*;

public class SparseWriteGlobal2 {
public static void main(String[] args) throws Exception {
Expand All @@ -52,7 +49,7 @@ public static void main(String[] args) throws Exception {
// Prepare cell buffers - #1
NativeArray a1_data = new NativeArray(ctx, new int[] {0, 1, 2}, Integer.class);
NativeArray a2_offsets =
new NativeArray(ctx, new long[] {0, 1, 3, 6, 10, 11, 13, 16}, Long.class);
new NativeArray(ctx, new long[] {0, 1, 3, 6, 10, 11, 13, 16}, Datatype.TILEDB_UINT64);
NativeArray buffer_var_a2 = new NativeArray(ctx, "abbcccddddeffggghhhh", String.class);

NativeArray buffer_a3 =
Expand All @@ -64,35 +61,39 @@ public static void main(String[] args) throws Exception {
},
Float.class);

NativeArray coords_buff = new NativeArray(ctx, new long[] {1, 1, 1, 2}, Long.class);
NativeArray d1_buff = new NativeArray(ctx, new long[] {1, 1}, Long.class);
NativeArray d2_buff = new NativeArray(ctx, new long[] {1, 2}, Long.class);

// Create query
Array my_sparse_array = new Array(ctx, "my_sparse_array", TILEDB_WRITE);
Query query = new Query(my_sparse_array);
query.setLayout(TILEDB_GLOBAL_ORDER);
query.setBuffer("d1", d1_buff);
query.setBuffer("d2", d2_buff);
query.setBuffer("a1", a1_data);
query.setBuffer("a2", a2_offsets, buffer_var_a2);
query.setBuffer("a3", buffer_a3);
query.setCoordinates(coords_buff);

// Submit query
query.submit();

// Prepare cell buffers - #2

a1_data = new NativeArray(ctx, new int[] {3, 4, 5, 6, 7}, Integer.class);
a2_offsets = new NativeArray(ctx, new long[] {}, Long.class);
a2_offsets = new NativeArray(ctx, new long[] {}, Datatype.TILEDB_UINT64);
buffer_var_a2 = new NativeArray(ctx, "", String.class);

buffer_a3 = new NativeArray(ctx, new float[] {}, Float.class);
coords_buff = new NativeArray(ctx, new long[] {1, 4, 2, 3, 3, 1, 4, 2, 3, 3, 3, 4}, Long.class);
d1_buff = new NativeArray(ctx, new long[] {1, 2, 3, 4, 3, 3}, Long.class);
d2_buff = new NativeArray(ctx, new long[] {4, 3, 1, 2, 3, 4}, Long.class);

// Reset buffers
query.resetBuffers();
query.setBuffer("d1", d1_buff);
query.setBuffer("d2", d2_buff);
query.setBuffer("a1", a1_data);
query.setBuffer("a2", a2_offsets, buffer_var_a2);
query.setBuffer("a3", buffer_a3);
query.setCoordinates(coords_buff);

// Submit query - #2
query.submit();
Expand Down
23 changes: 12 additions & 11 deletions src/main/java/examples/io/tiledb/java/api/SparseWriteUnordered1.java
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Expand Up @@ -36,23 +36,21 @@
import static io.tiledb.java.api.Layout.TILEDB_UNORDERED;
import static io.tiledb.java.api.QueryType.TILEDB_WRITE;

import io.tiledb.java.api.Array;
import io.tiledb.java.api.Context;
import io.tiledb.java.api.NativeArray;
import io.tiledb.java.api.Query;
import io.tiledb.java.api.*;

public class SparseWriteUnordered1 {
public static void main(String[] args) throws Exception {
// Create TileDB context
Context ctx = ctx = new Context();

// Prepare cell buffers
NativeArray a1_data = new NativeArray(ctx, new int[] {7, 5, 0, 6, 4, 3, 1, 2}, Integer.class);
NativeArray a1_data =
new NativeArray(ctx, new int[] {7, 5, 0, 6, 4, 3, 1, 2}, Datatype.TILEDB_INT32);
NativeArray a2_offsets =
new NativeArray(ctx, new long[] {0, 4, 6, 7, 10, 11, 15, 17}, Long.class);
new NativeArray(ctx, new long[] {0, 4, 6, 7, 10, 11, 15, 17}, Datatype.TILEDB_UINT64);
NativeArray buffer_var_a2 =
new NativeArray(
ctx, "hhhh" + "ff" + "a" + "ggg" + "e" + "dddd" + "bb" + "ccc", String.class);
ctx, "hhhh" + "ff" + "a" + "ggg" + "e" + "dddd" + "bb" + "ccc", Datatype.TILEDB_CHAR);

NativeArray buffer_a3 =
new NativeArray(
Expand All @@ -63,18 +61,21 @@ public static void main(String[] args) throws Exception {
},
Float.class);

NativeArray coords_buff =
new NativeArray(
ctx, new long[] {3, 4, 4, 2, 1, 1, 3, 3, 3, 1, 2, 3, 1, 2, 1, 4}, Long.class);
NativeArray d1_buff =
new NativeArray(ctx, new long[] {3, 4, 1, 3, 3, 2, 1, 1}, Datatype.TILEDB_INT64);

NativeArray d2_buff =
new NativeArray(ctx, new long[] {4, 2, 1, 3, 1, 3, 2, 4}, Datatype.TILEDB_INT64);

// Create query
Array my_sparse_array = new Array(ctx, "my_sparse_array", TILEDB_WRITE);
Query query = new Query(my_sparse_array);
query.setLayout(TILEDB_UNORDERED);
query.setBuffer("d1", d1_buff);
query.setBuffer("d2", d2_buff);
query.setBuffer("a1", a1_data);
query.setBuffer("a2", a2_offsets, buffer_var_a2);
query.setBuffer("a3", buffer_a3);
query.setCoordinates(coords_buff);

// Submit query
query.submit();
Expand Down
19 changes: 10 additions & 9 deletions src/main/java/examples/io/tiledb/java/api/SparseWriteUnordered1Again.java
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Expand Up @@ -37,37 +37,38 @@
import static io.tiledb.java.api.Layout.TILEDB_UNORDERED;
import static io.tiledb.java.api.QueryType.TILEDB_WRITE;

import io.tiledb.java.api.Array;
import io.tiledb.java.api.Context;
import io.tiledb.java.api.NativeArray;
import io.tiledb.java.api.Query;
import io.tiledb.java.api.*;

public class SparseWriteUnordered1Again {
public static void main(String[] args) throws Exception {
// Create TileDB context
Context ctx = ctx = new Context();

// Prepare cell buffers
NativeArray a1_data = new NativeArray(ctx, new int[] {107, 104, 106, 105}, Integer.class);
NativeArray a2_offsets = new NativeArray(ctx, new long[] {0, 3, 4, 5}, Long.class);
NativeArray buffer_var_a2 = new NativeArray(ctx, "yyy" + "u" + "w" + "vvvv", String.class);
NativeArray a1_data =
new NativeArray(ctx, new int[] {107, 104, 106, 105}, Datatype.TILEDB_INT32);
NativeArray a2_offsets = new NativeArray(ctx, new long[] {0, 3, 4, 5}, Datatype.TILEDB_UINT64);
NativeArray buffer_var_a2 =
new NativeArray(ctx, "yyy" + "u" + "w" + "vvvv", Datatype.TILEDB_CHAR);

NativeArray buffer_a3 =
new NativeArray(
ctx,
new float[] {107.1f, 107.2f, 104.1f, 104.2f, 106.1f, 106.2f, 105.1f, 105.2f},
Float.class);

NativeArray coords_buff = new NativeArray(ctx, new long[] {3, 4, 3, 2, 3, 3, 4, 1}, Long.class);
NativeArray d1_buff = new NativeArray(ctx, new long[] {3, 3, 3, 4}, Datatype.TILEDB_INT64);
NativeArray d2_buff = new NativeArray(ctx, new long[] {4, 2, 3, 1}, Datatype.TILEDB_INT64);

// Create query
Array my_sparse_array = new Array(ctx, "my_sparse_array", TILEDB_WRITE);
Query query = new Query(my_sparse_array);
query.setLayout(TILEDB_UNORDERED);
query.setBuffer("d1", d1_buff);
query.setBuffer("d2", d2_buff);
query.setBuffer("a1", a1_data);
query.setBuffer("a2", a2_offsets, buffer_var_a2);
query.setBuffer("a3", buffer_a3);
query.setCoordinates(coords_buff);

// Submit query
query.submit();
Expand Down
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