Example usage for com.fasterxml.jackson.databind ObjectMapper writer

Introduction

In this page you can find the example usage for com.fasterxml.jackson.databind ObjectMapper writer.

Prototype

public ObjectWriter writer() 

Source Link

Document

Convenience method for constructing ObjectWriter with default settings.

Usage

From source file:org.geppetto.frontend.controllers.ConnectionHandler.java

/**
 * Adds watch lists with variables to be watched
 * //from  w  w  w .  java2  s  . com
 * @param requestID
 * @param jsonLists
 * @throws GeppettoExecutionException
 * @throws GeppettoInitializationException
 */
public void setWatchedVariables(String requestID, List<String> variables, long experimentID, long projectId,
        boolean watch) throws GeppettoExecutionException, GeppettoInitializationException {

    IGeppettoProject geppettoProject = retrieveGeppettoProject(projectId);
    IExperiment experiment = retrieveExperiment(experimentID, geppettoProject);

    if (geppettoProject.isVolatile()) {
        info(requestID, Resources.VOLATILE_PROJECT.toString());
        return;
    } else {
        try {
            geppettoManager.setWatchedVariables(variables, experiment, geppettoProject, watch);
        } catch (GeppettoExecutionException | GeppettoAccessException e) {
            error(e, "Error setting watched variables");
        }

        // serialize watch-lists
        ObjectMapper mapper = new ObjectMapper();
        String serializedLists;

        try {
            serializedLists = mapper.writer().writeValueAsString(variables);

            // send to the client the watch lists were added
            websocketConnection.sendMessage(requestID, OutboundMessages.WATCHED_VARIABLES_SET, serializedLists);
        } catch (JsonProcessingException e) {
            error(e, "There was an error serializing the watched lists");
        }
    }

}

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From source file:org.opencb.cellbase.app.cli.DownloadCommandExecutor.java

private void writeVersionDataFile(Map versionData, Path outputFilePath) {
    try {//from  w  w  w  . ja  v a2s  .c o  m
        OutputStream os = Files.newOutputStream(outputFilePath);
        BufferedWriter bw = new BufferedWriter(new OutputStreamWriter(os));
        ObjectMapper jsonObjectMapper = new ObjectMapper();
        ObjectWriter jsonObjectWriter = jsonObjectMapper.writer();
        bw.write(jsonObjectWriter.writeValueAsString(versionData) + "\n");
        bw.close();
    } catch (IOException e) {
        e.printStackTrace();
    }

}

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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();/*from ww  w . ja v  a 2s .  com*/

    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;
}

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From source file:org.opencb.cellbase.app.cli.VariantAnnotationCommandExecutor.java

private void indexPopulationFrequencies(RocksDB db) {
    ObjectMapper jsonObjectMapper = new ObjectMapper();
    jsonObjectMapper.configure(MapperFeature.REQUIRE_SETTERS_FOR_GETTERS, true);
    ObjectWriter jsonObjectWriter = jsonObjectMapper.writer();

    try {/* w  w  w .j  a  v  a  2s  . co  m*/
        DataReader<Variant> dataReader = new JsonVariantReader(populationFrequenciesFile.toString());
        dataReader.open();
        dataReader.pre();
        int lineCounter = 0;
        List<Variant> variant = dataReader.read();
        while (variant != null) {
            db.put(VariantAnnotationUtils.buildVariantId(variant.get(0).getChromosome(),
                    variant.get(0).getStart(), variant.get(0).getReference(), variant.get(0).getAlternate())
                    .getBytes(), jsonObjectWriter.writeValueAsBytes(variant.get(0).getImpl()));
            lineCounter++;
            if (lineCounter % 100000 == 0) {
                logger.info("{} lines indexed", lineCounter);
            }
            variant = dataReader.read();
        }
        dataReader.post();
        dataReader.close();
    } catch (IOException | RocksDBException e) {
        e.printStackTrace();
    }
}

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From source file:org.opencb.cellbase.app.cli.VariantAnnotationCommandExecutor.java

private void indexCustomVcfFile(int customFileNumber, RocksDB db) {
    ObjectMapper jsonObjectMapper = new ObjectMapper();
    ObjectWriter jsonObjectWriter = jsonObjectMapper.writer();

    try {/*from  w  w  w.  j a va2  s  .co  m*/
        VCFFileReader vcfFileReader = new VCFFileReader(customFiles.get(customFileNumber).toFile(), false);
        Iterator<VariantContext> iterator = vcfFileReader.iterator();
        VariantContextToVariantConverter converter = new VariantContextToVariantConverter("", "",
                vcfFileReader.getFileHeader().getSampleNamesInOrder());
        VariantNormalizer normalizer = new VariantNormalizer(true, false, true);
        int lineCounter = 0;
        while (iterator.hasNext()) {
            VariantContext variantContext = iterator.next();
            // Reference positions will not be indexed
            if (variantContext.getAlternateAlleles().size() > 0) {
                List<Variant> variantList = normalizer
                        .normalize(converter.apply(Collections.singletonList(variantContext)), true);
                for (Variant variant : variantList) {
                    db.put((variant.getChromosome() + "_" + variant.getStart() + "_" + variant.getReference()
                            + "_" + variant.getAlternate()).getBytes(),
                            jsonObjectWriter.writeValueAsBytes(parseInfoAttributes(variant, customFileNumber)));
                }
            }
            lineCounter++;
            if (lineCounter % 100000 == 0) {
                logger.info("{} lines indexed", lineCounter);
            }
        }
        vcfFileReader.close();
    } catch (IOException | RocksDBException | NonStandardCompliantSampleField e) {
        e.printStackTrace();
        System.exit(1);
    }
}

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From source file:org.opencb.cellbase.lib.impl.GeneMongoDBAdaptor.java

@Override
public QueryResult<Gene> get(Query query, QueryOptions options) {
    Bson bson = parseQuery(query);//w  ww . j  a va  2 s .co  m
    options = addPrivateExcludeOptions(options);

    if (postDBFilteringParametersEnabled(query)) {
        QueryResult<Document> nativeQueryResult = postDBFiltering(query, mongoDBCollection.find(bson, options));
        QueryResult<Gene> queryResult = new QueryResult<Gene>(nativeQueryResult.getId(),
                nativeQueryResult.getDbTime(), nativeQueryResult.getNumResults(),
                nativeQueryResult.getNumTotalResults(), nativeQueryResult.getWarningMsg(),
                nativeQueryResult.getErrorMsg(), null);
        ObjectMapper jsonObjectMapper = new ObjectMapper();
        jsonObjectMapper.setSerializationInclusion(JsonInclude.Include.NON_EMPTY);
        jsonObjectMapper.configure(MapperFeature.REQUIRE_SETTERS_FOR_GETTERS, true);
        ObjectWriter objectWriter = jsonObjectMapper.writer();
        queryResult.setResult(nativeQueryResult.getResult().stream().map(document -> {
            try {
                return this.objectMapper.readValue(objectWriter.writeValueAsString(document), Gene.class);
            } catch (IOException e) {
                e.printStackTrace();
                return null;
            }
        }).collect(Collectors.toList()));
        return queryResult;
    } else {
        return mongoDBCollection.find(bson, null, Gene.class, options);
    }
}

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From source file:org.opencb.opencga.app.cli.main.OpenCGAMainOld.java

private StringBuilder createOutput(OptionsParser.CommonOptions commonOptions, List list, StringBuilder sb)
        throws JsonProcessingException {
    if (sb == null) {
        sb = new StringBuilder();
    }//from  w  ww  .  ja  v  a  2 s . c  o  m
    String idSeparator = null;
    switch (commonOptions.outputFormat) {
    case IDS:
        idSeparator = idSeparator == null ? "\n" : idSeparator;
    case ID_CSV:
        idSeparator = idSeparator == null ? "," : idSeparator;
    case ID_LIST:
        idSeparator = idSeparator == null ? "," : idSeparator; {
        if (!list.isEmpty()) {
            try {
                Iterator iterator = list.iterator();

                Object next = iterator.next();
                if (next instanceof QueryResult) {
                    createOutput(commonOptions, (QueryResult) next, sb);
                } else {
                    sb.append(getId(next));
                }
                while (iterator.hasNext()) {
                    next = iterator.next();
                    if (next instanceof QueryResult) {
                        sb.append(idSeparator);
                        createOutput(commonOptions, (QueryResult) next, sb);
                    } else {
                        sb.append(idSeparator).append(getId(next));
                    }
                }
            } catch (NoSuchMethodException | IllegalAccessException | InvocationTargetException e) {
                e.printStackTrace();
            }
        }
        break;
    }
    case NAME_ID_MAP: {
        if (!list.isEmpty()) {
            try {
                Iterator iterator = list.iterator();
                Object object = iterator.next();
                if (object instanceof QueryResult) {
                    createOutput(commonOptions, (QueryResult) object, sb);
                } else {
                    sb.append(getName(object)).append(":").append(getId(object));
                }
                while (iterator.hasNext()) {
                    object = iterator.next();
                    if (object instanceof QueryResult) {
                        sb.append(",");
                        createOutput(commonOptions, (QueryResult) object, sb);
                    } else {
                        sb.append(",").append(getName(object)).append(":").append(getId(object));
                    }
                }
            } catch (InvocationTargetException | NoSuchMethodException | IllegalAccessException e) {
                e.printStackTrace();
            }
        }
        break;
    }
    case RAW:
        if (list != null) {
            for (Object o : list) {
                sb.append(String.valueOf(o));
            }
        }
        break;
    default:
        logger.warn("Unsupported output format \"{}\" for that query", commonOptions.outputFormat);
    case PRETTY_JSON:
    case PLAIN_JSON:
        JsonFactory factory = new JsonFactory();
        ObjectMapper objectMapper = new ObjectMapper(factory);
        objectMapper.setSerializationInclusion(JsonInclude.Include.NON_NULL);
        //                objectMapper.setSerializationInclusion(JsonInclude.Include.NON_EMPTY);
        objectMapper.setSerializationInclusion(JsonInclude.Include.NON_DEFAULT);
        ObjectWriter objectWriter = commonOptions.outputFormat == OptionsParser.OutputFormat.PRETTY_JSON
                ? objectMapper.writerWithDefaultPrettyPrinter()
                : objectMapper.writer();

        if (list != null && !list.isEmpty()) {
            Iterator iterator = list.iterator();
            sb.append(objectWriter.writeValueAsString(iterator.next()));
            while (iterator.hasNext()) {
                sb.append("\n").append(objectWriter.writeValueAsString(iterator.next()));
            }
        }
        break;
    }
    return sb;
}

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From source file:org.opentestsystem.delivery.logging.EventLoggerBase.java

public EventLoggerBase(final ObjectMapper objectMapper) {
    this.writer = objectMapper.writer();
    extraFields.put(BaseEventData.HTTP_REQUEST_UUID.name(), UUID.randomUUID());
}

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From source file:org.ownchan.server.persistence.typehandler.auto.PersistableJsonDataTypeHandler.java

public PersistableJsonDataTypeHandler() {
    ObjectMapper objectMapper = new ObjectMapper();
    this.reader = objectMapper.reader();
    this.writer = objectMapper.writer();
}

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From source file:piecework.ui.InlinePageModelSerializer.java

public InlinePageModelSerializer(UserInterfaceSettings settings, Object t, Class<?> type, Entity user,
        ObjectMapper objectMapper) {
    this.settings = settings;
    this.t = t;/* www .j av  a  2 s. c  o m*/
    this.type = type;
    PageContext pageContext = new PageContext.Builder().applicationTitle(settings.getApplicationTitle())
            .assetsUrl(settings.getAssetsUrl()).user(user).build();

    String pageContextAsJson;
    String modelAsJson;
    boolean isExplanation;
    try {
        pageContextAsJson = objectMapper.writer().writeValueAsString(pageContext);
        modelAsJson = objectMapper.writer().writeValueAsString(t);
        isExplanation = type != null && type.equals(Explanation.class);
    } catch (Exception e) {
        LOG.error("Unable to construct json", e);
        pageContextAsJson = "";
        modelAsJson = "";
        isExplanation = false;
    }
    this.pageContextAsJson = pageContextAsJson;
    this.modelAsJson = modelAsJson;
    this.isExplanation = isExplanation;
}

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