com.esotericsoftware.kryo.io.Output Java Examples
The following examples show how to use
com.esotericsoftware.kryo.io.Output.
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Example #1
Source File: Serializer.java From Overchan-Android with GNU General Public License v3.0 | 6 votes |
private void serialize(String filename, Object obj) { synchronized (kryoLock) { File file = fileCache.create(filename); Output output = null; try { output = createOutput(new FileOutputStream(file)); kryo.writeObject(output, obj); } catch (Exception e) { Logger.e(TAG, e); } catch (OutOfMemoryError oom) { MainApplication.freeMemory(); Logger.e(TAG, oom); } finally { IOUtils.closeQuietly(output); } fileCache.put(file); } }
Example #2
Source File: TestDataFileSerialization.java From iceberg with Apache License 2.0 | 6 votes |
@Test public void testDataFileKryoSerialization() throws Exception { File data = temp.newFile(); Assert.assertTrue(data.delete()); Kryo kryo = new KryoSerializer(new SparkConf()).newKryo(); try (Output out = new Output(new FileOutputStream(data))) { kryo.writeClassAndObject(out, DATA_FILE); kryo.writeClassAndObject(out, DATA_FILE.copy()); } try (Input in = new Input(new FileInputStream(data))) { for (int i = 0; i < 2; i += 1) { Object obj = kryo.readClassAndObject(in); Assert.assertTrue("Should be a DataFile", obj instanceof DataFile); checkDataFile(DATA_FILE, (DataFile) obj); } } }
Example #3
Source File: FeatureSerializer.java From StormCV with Apache License 2.0 | 6 votes |
@Override protected void writeObject(Kryo kryo, Output output, Feature feature) throws Exception { output.writeString(feature.getName()); output.writeLong(feature.getDuration()); kryo.writeObject(output, feature.getSparseDescriptors()); float[][][] m = feature.getDenseDescriptors(); output.writeInt(m.length); // write x if(m.length == 0) return; output.writeInt(m[0].length); // write y output.writeInt(m[0][0].length); // write z for(int x=0; x<m.length; x++){ for(int y=0; y<m[0].length; y++){ for(int z=0; z<m[0][0].length; z++){ output.writeFloat(m[x][y][z]); } } } }
Example #4
Source File: AssemblyContigWithFineTunedAlignmentsUnitTest.java From gatk with BSD 3-Clause "New" or "Revised" License | 6 votes |
@Test(groups = "sv") public void testSerializationAndHashCode() { final AlignmentInterval one = fromSAMRecordString("asm002362:tig00002\t16\tchr2\t1422222\t60\t75M56I139M\t*\t0\t0\tATGCTGGGGAATTTGTGTGCTCCTTGGGTGGGGACGAGCATGGAAGGCGCGTGGGACTGAAGCCTTGAAGACCCCGCAGGCGCCTCTCCTGGACAGACCTCGTGCAGGCGCCTCTCCTGGACCGACCTCGTGCAGGCGCCTCTCCTGGACAGACCTCGTGCAGGCGCCTCTCCTGGACCGACCTCGTGCAGGCGCCGCGCTGGACCGACCTCGTGCAGGCGCCGCGCTGGGCCATGGGGAGAGCGAGAGCCTGGTGTGCCCCTCAGGGAC\t*\tSA:Z:chr2_KI270774v1_alt,105288,-,114M1I27M1I127M,56,13;\tMD:Z:214\tRG:Z:GATKSVContigAlignments\tNM:i:56\tAS:i:142\tXS:i:0\n", true); final AlignmentInterval two = fromSAMRecordString("asm002362:tig00002\t2064\tchr2_KI270774v1_alt\t105288\t56\t114M1I27M1I127M\t*\t0\t0\tATGCTGGGGAATTTGTGTGCTCCTTGGGTGGGGACGAGCATGGAAGGCGCGTGGGACTGAAGCCTTGAAGACCCCGCAGGCGCCTCTCCTGGACAGACCTCGTGCAGGCGCCTCTCCTGGACCGACCTCGTGCAGGCGCCTCTCCTGGACAGACCTCGTGCAGGCGCCTCTCCTGGACCGACCTCGTGCAGGCGCCGCGCTGGACCGACCTCGTGCAGGCGCCGCGCTGGGCCATGGGGAGAGCGAGAGCCTGGTGTGCCCCTCAGGGAC\t*\tSA:Z:chr2,1422222,-,75M56I139M,60,56;\tMD:Z:94C17G1G6T13T3G1G34A3T9T68T8\tRG:Z:GATKSVContigAlignments\tNM:i:13\tAS:i:179\tXS:i:142", true); final AlignedContig sourceTig = new AlignedContig("asm002362:tig00002", "GTCCCTGAGGGGCACACCAGGCTCTCGCTCTCCCCATGGCCCAGCGCGGCGCCTGCACGAGGTCGGTCCAGCGCGGCGCCTGCACGAGGTCGGTCCAGGAGAGGCGCCTGCACGAGGTCTGTCCAGGAGAGGCGCCTGCACGAGGTCGGTCCAGGAGAGGCGCCTGCACGAGGTCTGTCCAGGAGAGGCGCCTGCGGGGTCTTCAAGGCTTCAGTCCCACGCGCCTTCCATGCTCGTCCCCACCCAAGGAGCACACAAATTCCCCAGCAT".getBytes(), Arrays.asList(one, two)); final List<AssemblyContigAlignmentsConfigPicker.GoodAndBadMappings> config = AssemblyContigAlignmentsConfigPicker.pickBestConfigurations(sourceTig, new HashSet<>(Collections.singletonList("chr2")), 0.); final AssemblyContigWithFineTunedAlignments tig = AssemblyContigAlignmentsConfigPicker.reConstructContigFromPickedConfiguration(new Tuple2<>(new Tuple2<>(sourceTig.getContigName(), sourceTig.getContigSequence()), config)).next(); final ByteArrayOutputStream bos = new ByteArrayOutputStream(); final Output out = new Output(bos); final Kryo kryo = new Kryo(); kryo.writeClassAndObject(out, tig); out.flush(); final ByteArrayInputStream bis = new ByteArrayInputStream(bos.toByteArray()); final Input in = new Input(bis); @SuppressWarnings("unchecked") final AssemblyContigWithFineTunedAlignments roundTrip = (AssemblyContigWithFineTunedAlignments) kryo.readClassAndObject(in); Assert.assertEquals(tig, roundTrip); Assert.assertEquals(tig.hashCode(), roundTrip.hashCode()); }
Example #5
Source File: IOTools.java From phrasal with GNU General Public License v3.0 | 6 votes |
/** * Serialize an object. * Only supports BIN and BIN_GZ SerializationMode. * * @param outputStream * @param o * @throws IOException */ public static void serialize(OutputStream outStream, Object o, SerializationMode mode) { try { if (mode == SerializationMode.BIN || mode == SerializationMode.BIN_GZ) { Kryo kryo = new Kryo(); kryo.setReferences(false); Output output = mode == SerializationMode.BIN_GZ ? new Output(new GZIPOutputStream( outStream)) : new Output(outStream); kryo.writeObject(output, o); output.close(); } else { logger.warn("Unsupported serialization mode: {} file: {}", mode); } } catch (KryoException | IOException e) { logger.error("Serialization exception", e); throw new RuntimeException(e); } }
Example #6
Source File: GenericSerde.java From attic-apex-malhar with Apache License 2.0 | 6 votes |
@Override public void serialize(T object, Output output) { Class type = object.getClass(); Serde serde = null; if (clazz == type) { serde = getDefaultSerde(type); } if (serde != null) { serde.serialize(object, output); return; } //delegate to kryo if (clazz == null) { kryo.writeClassAndObject(output, object); } else { kryo.writeObject(output, object); } }
Example #7
Source File: Kryo5Codec.java From redisson with Apache License 2.0 | 6 votes |
public Kryo5Codec(ClassLoader classLoader) { this.kryoPool = new Pool<Kryo>(true, false, 1024) { @Override protected Kryo create() { return createKryo(classLoader); } }; this.inputPool = new Pool<Input>(true, false, 512) { @Override protected Input create() { return new Input(8192); } }; this.outputPool = new Pool<Output>(true, false, 512) { @Override protected Output create() { return new Output(8192, -1); } }; }
Example #8
Source File: KryoSerializerImpl.java From utils with Apache License 2.0 | 6 votes |
public byte[] serialize(Object object) { byte[] result; if (object == null) { result = new byte[0]; return result; } ByteArrayOutputStream stream = new ByteArrayOutputStream(); try { Output output = new Output(stream); kryo.writeObject(output, object); output.close(); } catch (Exception e) { result = new byte[0]; } result = stream.toByteArray(); return result; }
Example #9
Source File: FloatOperand.java From ytk-mp4j with MIT License | 6 votes |
public void write(Kryo kryo, Output output, ArrayMetaData<float[]> object) { try { float[] arrData = arrayMetaData.getArrData(); arrayMetaData.send(output); int arrSegNum = arrayMetaData.getSegNum(); for (int i = 0; i < arrSegNum; i++) { int from = arrayMetaData.getFrom(i); int to = arrayMetaData.getTo(i); for (int j = from; j < to; j++) { output.writeFloat(arrData[j]); } } } catch (IOException e) { LOG.error("double array write exception", e); System.exit(1); } }
Example #10
Source File: EventFields.java From accumulo-recipes with Apache License 2.0 | 6 votes |
@Override public void write(Kryo kryo, Output output, EventFields eventFields) { // Write out the number of entries; intSerializer.write(kryo, output, size); for (Entry<String, Set<FieldValue>> entry : map.entrySet()) { for(FieldValue fieldValue : entry.getValue()) { // Write the fields in the value stringSerializer.write(kryo, output, entry.getKey()); valueSerializer.write(kryo, output, fieldValue.getVisibility().getExpression().length > 0 ? fieldValue.getVisibility().flatten() : fieldValue.getVisibility().getExpression()); valueSerializer.write(kryo, output, fieldValue.getValue()); valueSerializer.write(kryo, output, fieldValue.getMetadata()); } } output.flush(); }
Example #11
Source File: PSTaxonomyDatabaseTest.java From gatk with BSD 3-Clause "New" or "Revised" License | 5 votes |
@Test public void testSerializeDeserialize() { final Map<String,Integer> accessionToTaxMap = new HashMap<>(); accessionToTaxMap.put("A",1); accessionToTaxMap.put("B",1); accessionToTaxMap.put("C",2); accessionToTaxMap.put("D",3); final PSTree tree = new PSTree(1); tree.addNode(2, "node2", 1, 0, "genus"); tree.addNode(3, "node3", 1, 0, "genus"); tree.addNode(4, "node4", 2, 200, "species"); tree.addNode(5, "node5", 2, 300, "species"); tree.addNode(6, "node6", 3, 100, "species"); final PSTaxonomyDatabase taxonomyDatabase = new PSTaxonomyDatabase(tree, accessionToTaxMap); final Kryo kryo = new Kryo(); final Output output = new Output(new ByteArrayOutputStream()); kryo.writeObject(output, taxonomyDatabase); final Input input = new Input(new ByteArrayInputStream(output.getBuffer())); final PSTaxonomyDatabase taxonomyDatabaseTest = kryo.readObject(input, PSTaxonomyDatabase.class); Assert.assertEquals(taxonomyDatabaseTest.tree, taxonomyDatabase.tree); Assert.assertEquals(taxonomyDatabaseTest.accessionToTaxId, taxonomyDatabase.accessionToTaxId); }
Example #12
Source File: ConcatMap.java From metron with Apache License 2.0 | 5 votes |
@Override public void write(Kryo kryo, Output output) { int numVariableMappings = variableMappings.isEmpty()?0:variableMappings.size(); output.writeShort(numVariableMappings); for(Map m : variableMappings) { byte[] b = m == null?new byte[]{}:SerDeUtils.toBytes(m); output.writeInt(b.length); if(b.length > 0) { output.writeBytes(b); } } }
Example #13
Source File: KryoSerializer.java From mobility-rpc with Apache License 2.0 | 5 votes |
@Override public byte[] serialize(Object object) { ByteArrayOutputStream baos = new ByteArrayOutputStream(); Output output = new Output(baos); kryo.writeClassAndObject(output, object); output.flush(); output.close(); return baos.toByteArray(); }
Example #14
Source File: PriorityQueueSerializer.java From flink with Apache License 2.0 | 5 votes |
public void write(Kryo k, Output o, PriorityQueue<?> q) { k.writeClassAndObject(o, getComparator(q)); o.writeInt(q.size(), true); for (Object a : q) { k.writeClassAndObject(o, a); o.flush(); } }
Example #15
Source File: KryoValuesSerializer.java From jstorm with Apache License 2.0 | 5 votes |
private void serializeStrings(List<Object> values, Output out) { out.writeInt(values.size(), true); for (Object o : values) { String str = (String) o; out.writeString(str); } }
Example #16
Source File: SerializationUtil.java From dubbox with Apache License 2.0 | 5 votes |
public static byte[] serialize(Object obj) { if (obj == null) { return null; } Output output = new Output(1024, -1); kryos.get().writeClassAndObject(output, obj); return output.getBuffer(); }
Example #17
Source File: BreakpointComplications.java From gatk with BSD 3-Clause "New" or "Revised" License | 5 votes |
protected void serialize(final Kryo kryo, final Output output) { super.serialize(kryo, output); output.writeString(dupSeqRepeatUnitRefSpan.getContig()); output.writeInt(dupSeqRepeatUnitRefSpan.getStart()); output.writeInt(dupSeqRepeatUnitRefSpan.getEnd()); output.writeInt(dupSeqRepeatNumOnRef); output.writeInt(dupSeqRepeatNumOnCtg); dupSeqStrandOnRef.forEach(s -> output.writeInt(s.ordinal())); dupSeqStrandOnCtg.forEach(s -> output.writeInt(s.ordinal())); }
Example #18
Source File: Journal.java From attic-apex-core with Apache License 2.0 | 5 votes |
final void write(Recoverable op) { if (replayMode.get()) { throw new IllegalStateException("Request to write while journal is replaying operations"); } Integer classId = RecoverableOperation.getId(op.getClass()); if (classId == null) { throw new IllegalArgumentException("Class not registered " + op.getClass()); } while (true) { final Output out = output.get(); if (out != null) { // need to atomically write id, operation and flush the output stream synchronized (out) { try { LOG.debug("WAL write {}", RecoverableOperation.get(classId)); out.writeInt(classId); op.write(out); out.flush(); break; } catch (KryoException e) { // check that no other threads sneaked between get() and synchronized block and set output stream to a new // stream or null leading to the current stream being closed if (output.get() == out) { throw e; } } } } else { LOG.warn("Journal output stream is null. Skipping write to the WAL."); break; } } }
Example #19
Source File: IpPrefixSerializer.java From onos with Apache License 2.0 | 5 votes |
@Override public void write(Kryo kryo, Output output, IpPrefix object) { byte[] octs = object.address().toOctets(); output.writeInt(octs.length); output.writeBytes(octs); output.writeInt(object.prefixLength()); }
Example #20
Source File: ArrayMetaData.java From ytk-mp4j with MIT License | 5 votes |
@Override public void send(Output output) throws IOException { output.writeInt(srcRank); output.writeInt(destRank); output.writeInt(step); output.writeInt(sum); output.writeInt(segNum); for (int i = 0; i < segNum; i++) { output.writeInt(ranks.get(i)); output.writeInt(segFroms.get(i)); output.writeInt(segTos.get(i)); } output.flush(); }
Example #21
Source File: KryoNamespace.java From onos with Apache License 2.0 | 5 votes |
/** * Serializes given object to byte array using Kryo instance in pool. * * @param obj Object to serialize * @param bufferSize maximum size of serialized bytes * @return serialized bytes */ public byte[] serialize(final Object obj, final int bufferSize) { ByteArrayOutputStream outputStream = new ByteArrayOutputStream(bufferSize); Output out = new Output(outputStream); return pool.run(kryo -> { kryo.writeClassAndObject(out, obj); out.flush(); return outputStream.toByteArray(); }); }
Example #22
Source File: AlignedAssemblyUnitTest.java From gatk with BSD 3-Clause "New" or "Revised" License | 5 votes |
@Test(dataProvider="AlignedAssemblySerializationTest", groups = "sv") public void testAlignedAssemblySerialization(final Integer assemblyID, final AlignedAssembly expectedAssembly) { final ByteArrayOutputStream bos = new ByteArrayOutputStream(); final Output out = new Output(bos); final Kryo kryo = new Kryo(); kryo.writeClassAndObject(out, expectedAssembly); out.flush(); final ByteArrayInputStream bis = new ByteArrayInputStream(bos.toByteArray()); final Input in = new Input(bis); @SuppressWarnings("unchecked") final AlignedAssembly roundTrip = (AlignedAssembly) kryo.readClassAndObject(in); Assert.assertEquals(roundTrip, expectedAssembly); }
Example #23
Source File: VertexValueWritable.java From hgraphdb with Apache License 2.0 | 5 votes |
@Override public void write(final DataOutput output) throws IOException { Kryo kryo = new Kryo(); kryo.register(HBaseVertex.class, new HBaseVertexSerializer()); ByteArrayOutputStream baos = new ByteArrayOutputStream(); Output out = new Output(baos); kryo.writeObject(out, this.vertex); out.close(); final byte[] serialized = baos.toByteArray(); WritableUtils.writeCompressedByteArray(output, serialized); Writable writable = value != null ? value : NullWritable.get(); Text.writeString(output, writable.getClass().getName()); writable.write(output); }
Example #24
Source File: KryoSerializer.java From spork with Apache License 2.0 | 5 votes |
public static byte[] serialize(Object object) { ByteArrayOutputStream stream = new ByteArrayOutputStream(); Output output = new Output(stream); Utilities.runtimeSerializationKryo.get().writeObject(output, object); output.close(); // close() also calls flush() return stream.toByteArray(); }
Example #25
Source File: OffHeapPartitionTest.java From cubedb with GNU General Public License v3.0 | 5 votes |
@Test public void serDeTest() throws IOException { final Kryo kryo = new Kryo(); File destination = File.createTempFile("partition_", ".gz"); final Output output = new Output(new GZIPOutputStream(new FileOutputStream(destination))); int numColumns = 6; int numValues = 6; OffHeapPartition p = createPartition(); List<DataRow> data = TestUtils.genMultiColumnData("f1", numColumns, numValues); data.addAll(TestUtils.genMultiColumnData("f2", numColumns, numValues)); p.insertData(data); log.info("Writing partition with {} records to {}", data.size(), destination.getAbsolutePath()); long t0 = System.nanoTime(); kryo.writeObject(output, p); output.close(); long t1 = System.nanoTime(); log.info("Took {} ms to write {} records", (t1 - t0) / 1000000, data.size()); // Now reading the file Input input = new Input(new GZIPInputStream(new FileInputStream(destination))); t0 = System.nanoTime(); OffHeapPartition newP = kryo.readObject(input, OffHeapPartition.class); t1 = System.nanoTime(); assertEquals(p.getNumRecords(), newP.getNumRecords()); long cP = TestUtils.checkMatchMultiFilter( p, "c", "f1_0", "f1_0_0", "f1_0", "f1_0_1", "f1_0", "f1_0_2"); // , long cNp = TestUtils.checkMatchMultiFilter( newP, "c", "f1_0", "f1_0_0", "f1_0", "f1_0_1", "f1_0", "f1_0_2"); // , assertEquals(cP, cNp); log.info("Took {} ms to read {} records", (t1 - t0) / 1000000, data.size()); log.info("{}", newP.getStats()); destination.deleteOnExit(); }
Example #26
Source File: KryoTranscoder.java From cas4.0.x-server-wechat with Apache License 2.0 | 5 votes |
@Override public CachedData encode(final Object obj) { final ByteArrayOutputStream byteStream = new ByteArrayOutputStream(); final Output output = new Output(byteStream); kryo.writeClassAndObject(output, obj); output.flush(); IOUtils.closeQuietly(output); final byte[] bytes = byteStream.toByteArray(); return new CachedData(0, bytes, bytes.length); }
Example #27
Source File: TreeSerializationTest.java From swblocks-decisiontree with Apache License 2.0 | 5 votes |
@Test public void treeNode() { final Result<DecisionTreeRuleSet> result = (new CommisionRuleSetSupplier()).get(); EhSupport.ensure(result.isSuccess(), "Could not create decision tree"); final DecisionTreeRuleSet ruleSet = result.getData(); final TreeNode node = DecisionTreeFactory.constructDecisionTree(ruleSet, DecisionTreeType.SINGLE); final Kryo kryo = new Kryo(); // no default no-arg constructors kryo.setInstantiatorStrategy(new StdInstantiatorStrategy()); final InstantiatorStrategy defaultInstantiatorStrategy = new Kryo.DefaultInstantiatorStrategy(); kryo.getRegistration(ArrayList.class) .setInstantiator(defaultInstantiatorStrategy.newInstantiatorOf(ArrayList.class)); kryo.getRegistration(HashSet.class) .setInstantiator(defaultInstantiatorStrategy.newInstantiatorOf(HashSet.class)); UnmodifiableCollectionsSerializer.registerSerializers(kryo); final ByteArrayOutputStream out = new ByteArrayOutputStream(); final Output output = new Output(out); kryo.writeObject(output, node); output.flush(); output.close(); final ByteArrayInputStream inputStream = new ByteArrayInputStream(out.toByteArray()); final Input kryoInput = new Input(inputStream); final TreeNode tree = kryo.readObject(kryoInput, BaseTreeNode.class); final SingleDecisionTreeFactoryTest test = new SingleDecisionTreeFactoryTest(); test.checkTreeNode(tree, ruleSet); assertEquals(node, tree); }
Example #28
Source File: AvroKryoSerializerUtils.java From flink with Apache License 2.0 | 5 votes |
@Override public void write(Kryo kryo, Output output, LocalDate localDate) { output.writeInt(localDate.getYear()); output.writeInt(localDate.getMonthOfYear()); output.writeInt(localDate.getDayOfMonth()); final Chronology chronology = localDate.getChronology(); if (chronology != null && chronology != ISOChronology.getInstanceUTC()) { throw new RuntimeException("Unsupported chronology: " + chronology); } }
Example #29
Source File: ImmutableCollectionSerializers.java From dremio-oss with Apache License 2.0 | 5 votes |
@Override public void write(final Kryo kryo, final Output output, final ImmutableList<Object> object) { output.writeInt(object.size(), true); final UnmodifiableIterator iterator = object.iterator(); while (iterator.hasNext()) { final Object value = iterator.next(); kryo.writeClassAndObject(output, value); } }
Example #30
Source File: ImmutableListSerializer.java From onos with Apache License 2.0 | 5 votes |
@Override public void write(Kryo kryo, Output output, ImmutableList<?> object) { output.writeInt(object.size()); for (Object e : object) { kryo.writeClassAndObject(output, e); } }