List of usage examples for com.fasterxml.jackson.databind ObjectMapper setSerializationInclusion
public ObjectMapper setSerializationInclusion(JsonInclude.Include incl)
From source file:org.openmrs.module.fhir.swagger.SwaggerSpecificationCreator.java
private String createSwaggerSpecification() { String json = ""; try {/* w w w. jav a 2s . c o m*/ ObjectMapper mapper = new ObjectMapper(); mapper.configure(SerializationFeature.INDENT_OUTPUT, true); mapper.configure(SerializationFeature.WRITE_NULL_MAP_VALUES, true); mapper.setSerializationInclusion(Include.NON_NULL); mapper.getSerializerProvider().setNullKeySerializer(new NullSerializer()); json = mapper.writeValueAsString(swaggerSpecification); } catch (Exception exp) { log.error("Error while creating object mapper", exp); } return json; }
From source file:com.netflix.dyno.queues.redis.RedisDynoQueue.java
public RedisDynoQueue(String redisKeyPrefix, String queueName, Set<String> allShards, String shardName, ExecutorService dynoCallExecutor) { this.redisKeyPrefix = redisKeyPrefix; this.queueName = queueName; this.allShards = allShards.stream().collect(Collectors.toList()); this.shardName = shardName; this.messageStoreKey = redisKeyPrefix + ".MESSAGE." + queueName; this.myQueueShard = getQueueShardKey(queueName, shardName); ObjectMapper om = new ObjectMapper(); om.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); om.configure(DeserializationFeature.FAIL_ON_IGNORED_PROPERTIES, false); om.configure(DeserializationFeature.FAIL_ON_NULL_FOR_PRIMITIVES, false); om.setSerializationInclusion(Include.NON_NULL); om.setSerializationInclusion(Include.NON_EMPTY); om.disable(SerializationFeature.INDENT_OUTPUT); this.om = om; this.monitor = new QueueMonitor(queueName, shardName); this.prefetchedIds = new LinkedBlockingQueue<>(); this.executorService = dynoCallExecutor; Executors.newScheduledThreadPool(1).scheduleAtFixedRate(() -> processUnacks(), unackScheduleInMS, unackScheduleInMS, TimeUnit.MILLISECONDS); Executors.newScheduledThreadPool(1).scheduleAtFixedRate(() -> prefetchIds(), 0, 10, TimeUnit.MILLISECONDS); logger.info(RedisDynoQueue.class.getName() + " is ready to serve " + queueName); }
From source file:synapticloop.scaleway.api.ScalewayApiClient.java
/** * Serialize an object to JSON/* w w w . j a v a2 s . c om*/ * * @param object The object to serialize * @return The object serialized as a JSON String * @throws JsonProcessingException if there was an error serializing */ private String serializeObject(Object object) throws JsonProcessingException { ObjectMapper objectMapper = new ObjectMapper(); objectMapper.setSerializationInclusion(Include.NON_NULL); return (objectMapper.writeValueAsString(object)); }
From source file:org.opencb.cellbase.app.cli.VariantAnnotationCommandExecutor.java
private boolean runAnnotation() throws Exception { // Build indexes for custom files and/or population frequencies file getIndexes();// ww w . j av a 2s . c o m if (variantAnnotationCommandOptions.variant != null && !variantAnnotationCommandOptions.variant.isEmpty()) { List<Variant> variants = Variant.parseVariants(variantAnnotationCommandOptions.variant); if (local) { DBAdaptorFactory dbAdaptorFactory = new MongoDBAdaptorFactory(configuration); VariantAnnotationCalculator variantAnnotationCalculator = new VariantAnnotationCalculator( this.species, this.assembly, dbAdaptorFactory); List<QueryResult<VariantAnnotation>> annotationByVariantList = variantAnnotationCalculator .getAnnotationByVariantList(variants, queryOptions); ObjectMapper jsonObjectMapper = new ObjectMapper(); jsonObjectMapper.setSerializationInclusion(JsonInclude.Include.NON_NULL); jsonObjectMapper.configure(MapperFeature.REQUIRE_SETTERS_FOR_GETTERS, true); ObjectWriter objectWriter = jsonObjectMapper.writer(); Path outPath = Paths.get(variantAnnotationCommandOptions.output); FileUtils.checkDirectory(outPath.getParent()); BufferedWriter bufferedWriter = FileUtils.newBufferedWriter(outPath); for (QueryResult queryResult : annotationByVariantList) { bufferedWriter.write(objectWriter.writeValueAsString(queryResult.getResult())); bufferedWriter.newLine(); } bufferedWriter.close(); } return true; } // If a variant file is provided then we annotate it. Lines in the input file can be computationally // expensive to parse, i.e.: multisample vcf with thousands of samples. A specific task is created to enable // parallel parsing of these lines if (input != null) { DataReader dataReader = new StringDataReader(input); List<ParallelTaskRunner.TaskWithException<String, Variant, Exception>> variantAnnotatorTaskList = getStringTaskList(); DataWriter dataWriter = getDataWriter(output.toString()); ParallelTaskRunner.Config config = new ParallelTaskRunner.Config(numThreads, batchSize, QUEUE_CAPACITY, false); ParallelTaskRunner<String, Variant> runner = new ParallelTaskRunner<>(dataReader, variantAnnotatorTaskList, dataWriter, config); runner.run(); // For internal use only - will only be run when -Dpopulation-frequencies is activated writeRemainingPopFrequencies(); } else { // This will annotate the CellBase Variation collection if (cellBaseAnnotation) { // TODO: enable this query in the parseQuery method within VariantMongoDBAdaptor // Query query = new Query("$match", // new Document("annotation.consequenceTypes", new Document("$exists", 0))); // Query query = new Query(); QueryOptions options = new QueryOptions("include", "chromosome,start,reference,alternate,type"); List<ParallelTaskRunner.TaskWithException<Variant, Variant, Exception>> variantAnnotatorTaskList = getVariantTaskList(); ParallelTaskRunner.Config config = new ParallelTaskRunner.Config(numThreads, batchSize, QUEUE_CAPACITY, false); for (String chromosome : chromosomeList) { logger.info("Annotating chromosome {}", chromosome); Query query = new Query("chromosome", chromosome); DataReader dataReader = new VariationDataReader(dbAdaptorFactory.getVariationDBAdaptor(species), query, options); DataWriter dataWriter = getDataWriter( output.toString() + "/" + VARIATION_ANNOTATION_FILE_PREFIX + chromosome + ".json.gz"); ParallelTaskRunner<Variant, Variant> runner = new ParallelTaskRunner<Variant, Variant>( dataReader, variantAnnotatorTaskList, dataWriter, config); runner.run(); } } } if (customFiles != null || populationFrequenciesFile != null) { closeIndexes(); } logger.info("Variant annotation finished."); return false; }
From source file:org.redisson.config.ConfigSupport.java
private ObjectMapper createMapper(JsonFactory mapping) { ObjectMapper mapper = new ObjectMapper(mapping); mapper.addMixIn(MasterSlaveServersConfig.class, MasterSlaveServersConfigMixIn.class); mapper.addMixIn(SingleServerConfig.class, SingleSeverConfigMixIn.class); mapper.addMixIn(Config.class, ConfigMixIn.class); mapper.addMixIn(CodecProvider.class, ClassMixIn.class); mapper.addMixIn(ResolverProvider.class, ClassMixIn.class); mapper.addMixIn(Codec.class, ClassMixIn.class); mapper.addMixIn(RedissonNodeInitializer.class, ClassMixIn.class); mapper.addMixIn(LoadBalancer.class, ClassMixIn.class); FilterProvider filterProvider = new SimpleFilterProvider().addFilter("classFilter", SimpleBeanPropertyFilter.filterOutAllExcept()); mapper.setFilterProvider(filterProvider); mapper.setSerializationInclusion(Include.NON_NULL); return mapper; }
From source file:de.brendamour.jpasskit.signing.PKAbstractSIgningUtil.java
protected ObjectWriter configureObjectMapper(final ObjectMapper jsonObjectMapper) { jsonObjectMapper.configure(SerializationFeature.WRITE_DATES_AS_TIMESTAMPS, false); jsonObjectMapper.setDateFormat(new ISO8601DateFormat()); SimpleFilterProvider filters = new SimpleFilterProvider(); // haven't found out, how to stack filters. Copying the validation one for now. filters.addFilter("validateFilter", SimpleBeanPropertyFilter.serializeAllExcept("valid", "validationErrors")); filters.addFilter("pkPassFilter", SimpleBeanPropertyFilter.serializeAllExcept("valid", "validationErrors", "foregroundColorAsObject", "backgroundColorAsObject", "labelColorAsObject", "passThatWasSet")); filters.addFilter("barcodeFilter", SimpleBeanPropertyFilter.serializeAllExcept("valid", "validationErrors", "messageEncodingAsString")); filters.addFilter("charsetFilter", SimpleBeanPropertyFilter.filterOutAllExcept("name")); jsonObjectMapper.setSerializationInclusion(Include.NON_NULL); jsonObjectMapper.addMixIn(Object.class, ValidateFilterMixIn.class); jsonObjectMapper.addMixIn(PKPass.class, PkPassFilterMixIn.class); jsonObjectMapper.addMixIn(PKBarcode.class, BarcodeFilterMixIn.class); jsonObjectMapper.addMixIn(Charset.class, CharsetFilterMixIn.class); return jsonObjectMapper.writer(filters); }
From source file:com.nesscomputing.jackson.NessObjectMapperProvider.java
@Override public ObjectMapper get() { final ObjectMapper mapper = new ObjectMapper(jsonFactory); // Set the features for (Map.Entry<Enum<?>, Boolean> entry : featureMap.entrySet()) { final Enum<?> key = entry.getKey(); if (key instanceof JsonGenerator.Feature) { mapper.configure(((JsonGenerator.Feature) key), entry.getValue()); } else if (key instanceof JsonParser.Feature) { mapper.configure(((JsonParser.Feature) key), entry.getValue()); } else if (key instanceof SerializationFeature) { mapper.configure(((SerializationFeature) key), entry.getValue()); } else if (key instanceof DeserializationFeature) { mapper.configure(((DeserializationFeature) key), entry.getValue()); } else if (key instanceof MapperFeature) { mapper.configure(((MapperFeature) key), entry.getValue()); } else {/* www.java 2s. co m*/ throw new IllegalArgumentException("Can not configure ObjectMapper with " + key.name()); } } for (Module module : modules) { mapper.registerModule(module); } // by default, don't serialize null values. mapper.setSerializationInclusion(Include.NON_NULL); return mapper; }
From source file:com.thinkbiganalytics.metadata.rest.client.MetadataClient.java
private ObjectMapper createObjectMapper() { ObjectMapper mapper = new ObjectMapper(); mapper.registerModule(new JodaModule()); // TODO Module dependency is causing a conflict somehow. // mapper.registerModule(new JavaTimeModule()); mapper.setSerializationInclusion(Include.NON_NULL); return mapper; }