Examples with JsonProcessingException org.apache.flink.shaded.jackson2.com.fasterxml.jackson.core.JsonProcessingException used on opensource projects

Example 96 with JsonProcessingException

use of org.apache.flink.shaded.jackson2.com.fasterxml.jackson.core.JsonProcessingException in project jackson-core by FasterXML.

the class GeneratorFailFromReaderTest method _testFailOnWritingStringFromNullReader.

private void _testFailOnWritingStringFromNullReader(JsonFactory f, boolean useReader) throws Exception {
    JsonGenerator gen;
    ByteArrayOutputStream bout = new ByteArrayOutputStream();
    if (useReader) {
        gen = f.createGenerator(ObjectWriteContext.empty(), new OutputStreamWriter(bout, "UTF-8"));
    } else {
        gen = f.createGenerator(ObjectWriteContext.empty(), bout, JsonEncoding.UTF8);
    }
    gen.writeStartObject();
    try {
        gen.writeFieldName("a");
        gen.writeString(null, -1);
        gen.flush();
        String json = bout.toString("UTF-8");
        fail("Should not have let " + gen.getClass().getName() + ".writeString() ': output = " + json);
    } catch (JsonProcessingException e) {
        verifyException(e, "null reader");
    }
    gen.close();
}

Example 97 with JsonProcessingException

use of org.apache.flink.shaded.jackson2.com.fasterxml.jackson.core.JsonProcessingException in project jackson-core by FasterXML.

the class GeneratorFailFromReaderTest method _testFailOnWritingStringFromReaderWithTooFewCharacters.

private void _testFailOnWritingStringFromReaderWithTooFewCharacters(JsonFactory f, boolean useReader) throws Exception {
    JsonGenerator gen;
    ByteArrayOutputStream bout = new ByteArrayOutputStream();
    if (useReader) {
        gen = f.createGenerator(ObjectWriteContext.empty(), new OutputStreamWriter(bout, "UTF-8"));
    } else {
        gen = f.createGenerator(ObjectWriteContext.empty(), bout, JsonEncoding.UTF8);
    }
    gen.writeStartObject();
    try {
        String testStr = "aaaaaaaaa";
        StringReader reader = new StringReader(testStr);
        gen.writeFieldName("a");
        gen.writeString(reader, testStr.length() + 1);
        gen.flush();
        String json = bout.toString("UTF-8");
        fail("Should not have let " + gen.getClass().getName() + ".writeString() ': output = " + json);
    } catch (JsonProcessingException e) {
        verifyException(e, "Didn't read enough from reader");
    }
    gen.close();
}

Example 98 with JsonProcessingException

use of org.apache.flink.shaded.jackson2.com.fasterxml.jackson.core.JsonProcessingException in project joynr by bmwcarit.

the class MyRadioConsumerApplication method run.

@SuppressWarnings("checkstyle:methodlength")
@Override
public void run() {
    DiscoveryQos discoveryQos = new DiscoveryQos();
    // As soon as the arbitration QoS is set on the proxy builder, discovery of suitable providers
    // is triggered. If the discovery process does not find matching providers within the
    // arbitration timeout duration it will be terminated and you will get an arbitration exception.
    discoveryQos.setDiscoveryTimeoutMs(10000);
    discoveryQos.setDiscoveryScope(discoveryScope);
    // Provider entries in the global capabilities directory are cached locally. Discovery will
    // consider entries in this cache valid if they are younger as the max age of cached
    // providers as defined in the QoS. All valid entries will be processed by the arbitrator when searching
    // for and arbitrating the "best" matching provider.
    // NOTE: Valid cache entries might prevent triggering a lookup in the global capabilities
    // directory. Therefore, not all providers registered with the global capabilities
    // directory might be taken into account during arbitration.
    discoveryQos.setCacheMaxAgeMs(Long.MAX_VALUE);
    // The discovery process outputs a list of matching providers. The arbitration strategy then
    // chooses one or more of them to be used by the proxy.
    discoveryQos.setArbitrationStrategy(ArbitrationStrategy.HighestPriority);
    // The provider will maintain at least a minimum interval idle time in milliseconds between
    // successive notifications, even if on-change notifications are enabled and the value changes more
    // often. This prevents the consumer from being flooded by updated values. The filtering happens on
    // the provider's side, thus also preventing excessive network traffic.
    int minInterval_ms = 0;
    // The provider will send notifications every maximum interval in milliseconds, even if the value didn't
    // change. It will send notifications more often if on-change notifications are enabled,
    // the value changes more often, and the minimum interval QoS does not prevent it. The maximum interval
    // can thus be seen as a sort of heart beat.
    int maxInterval_ms = 10000;
    // The provider will send notifications until the end date is reached. The consumer will not receive any
    // notifications (neither value notifications nor missed publication notifications) after
    // this date.
    long validityMs = 60000;
    // If no notification was received within the last alert interval, a missed publication
    // notification will be raised.
    int alertAfterInterval_ms = 20000;
    // Notification messages will be sent with this time-to-live. If a notification message can not be
    // delivered within its TTL, it will be deleted from the system.
    // NOTE: If a notification message is not delivered due to an expired TTL, it might raise a
    // missed publication notification (depending on the value of the alert interval QoS).
    int publicationTtl_ms = 5000;
    OnChangeWithKeepAliveSubscriptionQos subscriptionQos = new OnChangeWithKeepAliveSubscriptionQos();
    subscriptionQos.setMinIntervalMs(minInterval_ms).setMaxIntervalMs(maxInterval_ms).setValidityMs(validityMs);
    subscriptionQos.setAlertAfterIntervalMs(alertAfterInterval_ms).setPublicationTtlMs(publicationTtl_ms);
    ProxyBuilder<RadioProxy> proxyBuilder = runtime.getProxyBuilder(providerDomain, RadioProxy.class);
    try {
        // getting an attribute
        radioProxy = proxyBuilder.setMessagingQos(new MessagingQos()).setDiscoveryQos(discoveryQos).build();
        RadioStation currentStation = radioProxy.getCurrentStation();
        LOG.info(PRINT_BORDER + "ATTRIBUTE GET: current station: " + currentStation + PRINT_BORDER);
        // subscribe to an attribute
        subscriptionFutureCurrentStation = radioProxy.subscribeToCurrentStation(new AttributeSubscriptionAdapter<RadioStation>() {

            @Override
            public void onReceive(RadioStation value) {
                LOG.info(PRINT_BORDER + "ATTRIBUTE SUBSCRIPTION: current station: " + value + PRINT_BORDER);
            }

            @Override
            public void onError(JoynrRuntimeException error) {
                LOG.info(PRINT_BORDER + "ATTRIBUTE SUBSCRIPTION: " + error + PRINT_BORDER);
            }
        }, subscriptionQos);
        // broadcast subscription
        // The provider will send a notification whenever the value changes.
        MulticastSubscriptionQos weakSignalBroadcastSubscriptionQos;
        // The consumer will be subscribed to the multicast until the end date is reached, after which the
        // consumer will be automatically unsubscribed, and will not receive any further notifications
        // this date.
        long wsbValidityMs = 60 * 1000;
        weakSignalBroadcastSubscriptionQos = new MulticastSubscriptionQos();
        weakSignalBroadcastSubscriptionQos.setValidityMs(wsbValidityMs);
        weakSignalFuture = subscribeToWeakSignal(weakSignalBroadcastSubscriptionQos);
        // susbcribe to weak signal with partition "GERMANY"
        weakSignalWithPartitionFuture = subscribeToWeakSignal(weakSignalBroadcastSubscriptionQos, "GERMANY");
        // selective broadcast subscription
        OnChangeSubscriptionQos newStationDiscoveredBroadcastSubscriptionQos;
        int nsdbMinIntervalMs = 2 * 1000;
        long nsdbValidityMs = 180 * 1000;
        int nsdbPublicationTtlMs = 5 * 1000;
        newStationDiscoveredBroadcastSubscriptionQos = new OnChangeSubscriptionQos();
        newStationDiscoveredBroadcastSubscriptionQos.setMinIntervalMs(nsdbMinIntervalMs).setValidityMs(nsdbValidityMs).setPublicationTtlMs(nsdbPublicationTtlMs);
        NewStationDiscoveredBroadcastFilterParameters newStationDiscoveredBroadcastFilterParams = new NewStationDiscoveredBroadcastFilterParameters();
        newStationDiscoveredBroadcastFilterParams.setHasTrafficService("true");
        // Munich
        GeoPosition positionOfInterest = new GeoPosition(48.1351250, 11.5819810);
        String positionOfInterestJson = null;
        try {
            positionOfInterestJson = objectMapper.writeValueAsString(positionOfInterest);
        } catch (JsonProcessingException e1) {
            LOG.error("Unable to write position of interest filter parameter to JSON", e1);
        }
        newStationDiscoveredBroadcastFilterParams.setPositionOfInterest(positionOfInterestJson);
        // 200 km
        newStationDiscoveredBroadcastFilterParams.setRadiusOfInterestArea("200000");
        radioProxy.subscribeToNewStationDiscoveredBroadcast(new RadioBroadcastInterface.NewStationDiscoveredBroadcastAdapter() {

            @Override
            public void onReceive(RadioStation discoveredStation, GeoPosition geoPosition) {
                LOG.info(PRINT_BORDER + "BROADCAST SUBSCRIPTION: new station discovered: " + discoveredStation + " at " + geoPosition + PRINT_BORDER);
            }
        }, newStationDiscoveredBroadcastSubscriptionQos, newStationDiscoveredBroadcastFilterParams);
        boolean success;
        try {
            // add favorite radio station
            RadioStation favoriteStation = new RadioStation("99.3 The Fox Rocks", false, Country.CANADA);
            success = radioProxy.addFavoriteStation(favoriteStation);
            LOG.info(PRINT_BORDER + "METHOD: added favorite station: " + favoriteStation + ": " + success + PRINT_BORDER);
            success = radioProxy.addFavoriteStation(favoriteStation);
        } catch (ApplicationException exception) {
            AddFavoriteStationErrorEnum error = exception.getError();
            switch(error) {
                case DUPLICATE_RADIOSTATION:
                    LOG.info(PRINT_BORDER + "METHOD: addFavoriteStation failed with the following excpected error: " + error);
                    break;
                default:
                    LOG.error(PRINT_BORDER + "METHOD: addFavoriteStation failed with an unexpected error: " + error);
                    break;
            }
        }
        try {
            // add favorite radio station
            RadioStation favoriteStation = new RadioStation("", false, Country.GERMANY);
            success = radioProxy.addFavoriteStation(favoriteStation);
            LOG.info(PRINT_BORDER + "METHOD: addFavoriteStation completed unexpected with the following output: " + success);
        } catch (ApplicationException exception) {
            String errorName = exception.getError().name();
            LOG.info(PRINT_BORDER + "METHOD: addFavoriteStation failed with the following unexpected ApplicationExcecption: " + errorName);
        } catch (ProviderRuntimeException exception) {
            String errorName = exception.getMessage();
            String expectation = errorName.equals(MyRadioProvider.MISSING_NAME) ? "expected" : "unexpected";
            LOG.info(PRINT_BORDER + "METHOD: addFavoriteStation failed with the following " + expectation + " exception: " + errorName);
        }
        // shuffle the stations
        radioProxy.shuffleStations();
        currentStation = radioProxy.getCurrentStation();
        LOG.info(PRINT_BORDER + "The current radio station after shuffling is: " + currentStation + PRINT_BORDER);
        // add favorite radio station async
        RadioStation radioStation = new RadioStation("99.4 AFN", false, Country.GERMANY);
        Future<Boolean> future = radioProxy.addFavoriteStation(new CallbackWithModeledError<Boolean, AddFavoriteStationErrorEnum>() {

            @Override
            public void onSuccess(Boolean result) {
                LOG.info(PRINT_BORDER + "ASYNC METHOD: added favorite station: callback onSuccess" + PRINT_BORDER);
            }

            @Override
            public void onFailure(JoynrRuntimeException error) {
                LOG.info(PRINT_BORDER + "ASYNC METHOD: added favorite station: callback onFailure: " + error.getMessage() + PRINT_BORDER);
            }

            @Override
            public void onFailure(AddFavoriteStationErrorEnum errorEnum) {
                switch(errorEnum) {
                    case DUPLICATE_RADIOSTATION:
                        LOG.info(PRINT_BORDER + "ASYNC METHOD: added favorite station failed: Duplicate Station!" + PRINT_BORDER);
                        break;
                    default:
                        LOG.error(PRINT_BORDER + "ASYNC METHOD: added favorite station failed: unknown errorEnum:" + errorEnum + PRINT_BORDER);
                        break;
                }
                LOG.info(PRINT_BORDER + "ASYNC METHOD: added favorite station: callback onFailure: " + errorEnum + PRINT_BORDER);
            }
        }, radioStation);
        try {
            long timeoutInMilliseconds = 8000;
            Boolean reply = future.get(timeoutInMilliseconds);
            LOG.info(PRINT_BORDER + "ASYNC METHOD: added favorite station: " + radioStation + ": " + reply + PRINT_BORDER);
        } catch (InterruptedException | JoynrRuntimeException | ApplicationException e) {
            LOG.info(PRINT_BORDER + "ASYNC METHOD: added favorite station: " + radioStation + ": " + e.getClass().getSimpleName() + "!");
        }
        ConsoleReader console;
        try {
            console = new ConsoleReader();
            int key;
            while ((key = console.readCharacter()) != 'q') {
                switch(key) {
                    case 's':
                        radioProxy.shuffleStations();
                        LOG.info("called shuffleStations");
                        break;
                    case 'm':
                        GetLocationOfCurrentStationReturned locationOfCurrentStation = radioProxy.getLocationOfCurrentStation();
                        LOG.info("called getLocationOfCurrentStation. country: " + locationOfCurrentStation.country + ", location: " + locationOfCurrentStation.location);
                        break;
                    default:
                        LOG.info("\n\nUSAGE press\n" + " q\tto quit\n" + " s\tto shuffle stations\n");
                        break;
                }
            }
        } catch (IOException e) {
            LOG.error("error reading input from console", e);
        }
    } catch (DiscoveryException e) {
        LOG.error("No provider found", e);
    } catch (JoynrCommunicationException e) {
        LOG.error("The message was not sent: ", e);
    }
}

Example 99 with JsonProcessingException

use of org.apache.flink.shaded.jackson2.com.fasterxml.jackson.core.JsonProcessingException in project mixcr by milaboratory.

the class FieldExtractors method getFields.

public static synchronized Field[] getFields() {
    if (descriptors == null) {
        List<Field> descriptorsList = new ArrayList<>();
        // Number of targets
        descriptorsList.add(new PL_O("-targets", "Export number of targets", "Number of targets", "numberOfTargets") {

            @Override
            protected String extract(VDJCObject object) {
                return Integer.toString(object.numberOfTargets());
            }
        });
        // Best hits
        for (final GeneType type : GeneType.values()) {
            char l = type.getLetter();
            descriptorsList.add(new PL_O("-" + Character.toLowerCase(l) + "Hit", "Export best " + l + " hit", "Best " + l + " hit", "best" + l + "Hit") {

                @Override
                protected String extract(VDJCObject object) {
                    VDJCHit bestHit = object.getBestHit(type);
                    if (bestHit == null)
                        return NULL;
                    return bestHit.getGene().getName();
                }
            });
        }
        // Best gene
        for (final GeneType type : GeneType.values()) {
            char l = type.getLetter();
            descriptorsList.add(new PL_O("-" + Character.toLowerCase(l) + "Gene", "Export best " + l + " hit gene name (e.g. TRBV12-3 for TRBV12-3*00)", "Best " + l + " gene", "best" + l + "Gene") {

                @Override
                protected String extract(VDJCObject object) {
                    VDJCHit bestHit = object.getBestHit(type);
                    if (bestHit == null)
                        return NULL;
                    return bestHit.getGene().getGeneName();
                }
            });
        }
        // Best family
        for (final GeneType type : GeneType.values()) {
            char l = type.getLetter();
            descriptorsList.add(new PL_O("-" + Character.toLowerCase(l) + "Family", "Export best " + l + " hit family name (e.g. TRBV12 for TRBV12-3*00)", "Best " + l + " family", "best" + l + "Family") {

                @Override
                protected String extract(VDJCObject object) {
                    VDJCHit bestHit = object.getBestHit(type);
                    if (bestHit == null)
                        return NULL;
                    return bestHit.getGene().getFamilyName();
                }
            });
        }
        // Best hit score
        for (final GeneType type : GeneType.values()) {
            char l = type.getLetter();
            descriptorsList.add(new PL_O("-" + Character.toLowerCase(l) + "HitScore", "Export score for best " + l + " hit", "Best " + l + " hit score", "best" + l + "HitScore") {

                @Override
                protected String extract(VDJCObject object) {
                    VDJCHit bestHit = object.getBestHit(type);
                    if (bestHit == null)
                        return NULL;
                    return String.valueOf(bestHit.getScore());
                }
            });
        }
        // All hits
        for (final GeneType type : GeneType.values()) {
            char l = type.getLetter();
            descriptorsList.add(new PL_O("-" + Character.toLowerCase(l) + "HitsWithScore", "Export all " + l + " hits with score", "All " + l + " hits", "all" + l + "HitsWithScore") {

                @Override
                protected String extract(VDJCObject object) {
                    VDJCHit[] hits = object.getHits(type);
                    if (hits.length == 0)
                        return "";
                    StringBuilder sb = new StringBuilder();
                    for (int i = 0; ; i++) {
                        sb.append(hits[i].getGene().getName()).append("(").append(SCORE_FORMAT.format(hits[i].getScore())).append(")");
                        if (i == hits.length - 1)
                            break;
                        sb.append(",");
                    }
                    return sb.toString();
                }
            });
        }
        // All hits without score
        for (final GeneType type : GeneType.values()) {
            char l = type.getLetter();
            descriptorsList.add(new PL_O("-" + Character.toLowerCase(l) + "Hits", "Export all " + l + " hits", "All " + l + " Hits", "all" + l + "Hits") {

                @Override
                protected String extract(VDJCObject object) {
                    VDJCHit[] hits = object.getHits(type);
                    if (hits.length == 0)
                        return "";
                    StringBuilder sb = new StringBuilder();
                    for (int i = 0; ; i++) {
                        sb.append(hits[i].getGene().getName());
                        if (i == hits.length - 1)
                            break;
                        sb.append(",");
                    }
                    return sb.toString();
                }
            });
        }
        // All gene names
        for (final GeneType type : GeneType.values()) {
            char l = type.getLetter();
            descriptorsList.add(new StringExtractor("-" + Character.toLowerCase(l) + "Genes", "Export all " + l + " gene names (e.g. TRBV12-3 for TRBV12-3*00)", "All " + l + " genes", "all" + l + "Genes", type) {

                @Override
                String extractStringForHit(VDJCHit hit) {
                    return hit.getGene().getGeneName();
                }
            });
        }
        // All families
        for (final GeneType type : GeneType.values()) {
            char l = type.getLetter();
            descriptorsList.add(new StringExtractor("-" + Character.toLowerCase(l) + "Families", "Export all " + l + " gene family anmes (e.g. TRBV12 for TRBV12-3*00)", "All " + l + " families", "all" + l + "Families", type) {

                @Override
                String extractStringForHit(VDJCHit hit) {
                    return hit.getGene().getFamilyName();
                }
            });
        }
        // Best alignment
        for (final GeneType type : GeneType.values()) {
            char l = type.getLetter();
            descriptorsList.add(new PL_O("-" + Character.toLowerCase(l) + "Alignment", "Export best " + l + " alignment", "Best " + l + " alignment", "best" + l + "Alignment") {

                @Override
                protected String extract(VDJCObject object) {
                    VDJCHit bestHit = object.getBestHit(type);
                    if (bestHit == null)
                        return NULL;
                    StringBuilder sb = new StringBuilder();
                    for (int i = 0; ; i++) {
                        Alignment<NucleotideSequence> alignment = bestHit.getAlignment(i);
                        if (alignment == null)
                            sb.append(NULL);
                        else
                            sb.append(alignment.toCompactString());
                        if (i == object.numberOfTargets() - 1)
                            break;
                        sb.append(",");
                    }
                    return sb.toString();
                }
            });
        }
        // All alignments
        for (final GeneType type : GeneType.values()) {
            char l = type.getLetter();
            descriptorsList.add(new PL_O("-" + Character.toLowerCase(l) + "Alignments", "Export all " + l + " alignments", "All " + l + " alignments", "all" + l + "Alignments") {

                @Override
                protected String extract(VDJCObject object) {
                    VDJCHit[] hits = object.getHits(type);
                    if (hits.length == 0)
                        return "";
                    StringBuilder sb = new StringBuilder();
                    for (int j = 0; ; ++j) {
                        for (int i = 0; ; i++) {
                            Alignment<NucleotideSequence> alignment = hits[j].getAlignment(i);
                            if (alignment == null)
                                sb.append(NULL);
                            else
                                sb.append(alignment.toCompactString());
                            if (i == object.numberOfTargets() - 1)
                                break;
                            sb.append(',');
                        }
                        if (j == hits.length - 1)
                            break;
                        sb.append(';');
                    }
                    return sb.toString();
                }
            });
        }
        descriptorsList.add(new FeatureExtractors.NSeqExtractor("-nFeature", "Export nucleotide sequence of specified gene feature", "N. Seq. ", "nSeq") {

            @Override
            public String convert(NSequenceWithQuality seq) {
                return seq.getSequence().toString();
            }
        });
        descriptorsList.add(new FeatureExtractors.NSeqExtractor("-qFeature", "Export quality string of specified gene feature", "Qual. ", "qual") {

            @Override
            public String convert(NSequenceWithQuality seq) {
                return seq.getQuality().toString();
            }
        });
        descriptorsList.add(new FeatureExtractors.WithHeader("-aaFeature", "Export amino acid sequence of specified gene feature", 1, new String[] { "AA. Seq. " }, new String[] { "aaSeq" }) {

            @Override
            protected String extractValue(VDJCObject object, GeneFeature[] parameters) {
                GeneFeature geneFeature = parameters[parameters.length - 1];
                NSequenceWithQuality feature = object.getFeature(geneFeature);
                if (feature == null)
                    return NULL;
                int targetId = object.getTargetContainingFeature(geneFeature);
                TranslationParameters tr = targetId == -1 ? TranslationParameters.FromLeftWithIncompleteCodon : object.getPartitionedTarget(targetId).getPartitioning().getTranslationParameters(geneFeature);
                if (tr == null)
                    return NULL;
                return AminoAcidSequence.translate(feature.getSequence(), tr).toString();
            }
        });
        // descriptorsList.add(new FeatureExtractorDescriptor("-aaFeatureFromLeft", "Export amino acid sequence of " +
        // "specified gene feature starting from the leftmost nucleotide (differs from -aaFeature only for " +
        // "sequences which length are not multiple of 3)", "AA. Seq.", "aaSeq") {
        // @Override
        // public String convert(NSequenceWithQuality seq) {
        // return AminoAcidSequence.translate(seq.getSequence(), FromLeftWithoutIncompleteCodon).toString();
        // }
        // });
        // 
        // descriptorsList.add(new FeatureExtractorDescriptor("-aaFeatureFromRight", "Export amino acid sequence of " +
        // "specified gene feature starting from the rightmost nucleotide (differs from -aaFeature only for " +
        // "sequences which length are not multiple of 3)", "AA. Seq.", "aaSeq") {
        // @Override
        // public String convert(NSequenceWithQuality seq) {
        // return AminoAcidSequence.translate(seq.getSequence(), FromRightWithoutIncompleteCodon).toString();
        // }
        // });
        descriptorsList.add(new FeatureExtractors.NSeqExtractor("-minFeatureQuality", "Export minimal quality of specified gene feature", "Min. qual. ", "minQual") {

            @Override
            public String convert(NSequenceWithQuality seq) {
                return "" + seq.getQuality().minValue();
            }
        });
        descriptorsList.add(new FeatureExtractors.NSeqExtractor("-avrgFeatureQuality", "Export average quality of specified gene feature", "Mean. qual. ", "meanQual") {

            @Override
            public String convert(NSequenceWithQuality seq) {
                return "" + seq.getQuality().meanValue();
            }
        });
        descriptorsList.add(new FeatureExtractors.NSeqExtractor("-lengthOf", "Exports length of specified gene feature.", "Length of ", "lengthOf") {

            @Override
            public String convert(NSequenceWithQuality seq) {
                return "" + seq.size();
            }
        });
        descriptorsList.add(new FeatureExtractors.MutationsExtractor("-nMutations", "Extract nucleotide mutations for specific gene feature; relative to germline sequence.", 1, new String[] { "N. Mutations in " }, new String[] { "nMutations" }) {

            @Override
            String convert(Mutations<NucleotideSequence> mutations, NucleotideSequence seq1, NucleotideSequence seq2, TranslationParameters tr) {
                return mutations.encode(",");
            }
        });
        descriptorsList.add(new FeatureExtractors.MutationsExtractor("-nMutationsRelative", "Extract nucleotide mutations for specific gene feature relative to another feature.", 2, new String[] { "N. Mutations in ", " relative to " }, new String[] { "nMutationsIn", "Relative" }) {

            @Override
            String convert(Mutations<NucleotideSequence> mutations, NucleotideSequence seq1, NucleotideSequence seq2, TranslationParameters tr) {
                return mutations.encode(",");
            }
        });
        final class AAMutations extends FeatureExtractors.MutationsExtractor {

            AAMutations(String command, String description, int nArgs, String[] hPrefix, String[] sPrefix) {
                super(command, description, nArgs, hPrefix, sPrefix);
            }

            @Override
            String convert(Mutations<NucleotideSequence> mutations, NucleotideSequence seq1, NucleotideSequence seq2, TranslationParameters tr) {
                if (tr == null)
                    return "-";
                Mutations<AminoAcidSequence> aaMuts = MutationsUtil.nt2aa(seq1, mutations, tr);
                if (aaMuts == null)
                    return "-";
                return aaMuts.encode(",");
            }
        }
        descriptorsList.add(new AAMutations("-aaMutations", "Extract amino acid mutations for specific gene feature", 1, new String[] { "AA. Mutations in " }, new String[] { "aaMutations" }));
        descriptorsList.add(new AAMutations("-aaMutationsRelative", "Extract amino acid mutations for specific gene feature relative to another feature.", 2, new String[] { "AA. Mutations in ", " relative to " }, new String[] { "aaMutationsIn", "Relative" }));
        final class MutationsDetailed extends FeatureExtractors.MutationsExtractor {

            MutationsDetailed(String command, String description, int nArgs, String[] hPrefix, String[] sPrefix) {
                super(command, description, nArgs, hPrefix, sPrefix);
            }

            @Override
            String convert(Mutations<NucleotideSequence> mutations, NucleotideSequence seq1, NucleotideSequence seq2, TranslationParameters tr) {
                if (tr == null)
                    return "-";
                MutationsUtil.MutationNt2AADescriptor[] descriptors = MutationsUtil.nt2aaDetailed(seq1, mutations, tr, 10);
                if (descriptors == null)
                    return "-";
                StringBuilder sb = new StringBuilder();
                for (int i = 0; i < descriptors.length; i++) {
                    sb.append(descriptors[i]);
                    if (i == descriptors.length - 1)
                        break;
                    sb.append(",");
                }
                return sb.toString();
            }
        }
        String detailedMutationsFormat = "Format <nt_mutation>:<aa_mutation_individual>:<aa_mutation_cumulative>, where <aa_mutation_individual> is an expected amino acid " + "mutation given no other mutations have occurred, and <aa_mutation_cumulative> amino acid mutation is the observed amino acid " + "mutation combining effect from all other. WARNING: format may change in following versions.";
        descriptorsList.add(new MutationsDetailed("-mutationsDetailed", "Detailed list of nucleotide and corresponding amino acid mutations. " + detailedMutationsFormat, 1, new String[] { "Detailed mutations in " }, new String[] { "mutationsDetailedIn" }));
        descriptorsList.add(new MutationsDetailed("-mutationsDetailedRelative", "Detailed list of nucleotide and corresponding amino acid mutations written, positions relative to specified gene feature. " + detailedMutationsFormat, 2, new String[] { "Detailed mutations in ", " relative to " }, new String[] { "mutationsDetailedIn", "Relative" }));
        descriptorsList.add(new ExtractReferencePointPosition());
        descriptorsList.add(new ExtractDefaultReferencePointsPositions());
        descriptorsList.add(new PL_A("-readId", "Export id of read corresponding to alignment", "Read id", "readId") {

            @Override
            protected String extract(VDJCAlignments object) {
                return "" + object.getMinReadId();
            }

            @Override
            public FieldExtractor<VDJCAlignments> create(OutputMode outputMode, String[] args) {
                System.out.println("WARNING: -readId is deprecated. Use -readIds");
                return super.create(outputMode, args);
            }
        });
        descriptorsList.add(new PL_A("-readIds", "Export id of read corresponding to alignment", "Read id", "readId") {

            @Override
            protected String extract(VDJCAlignments object) {
                long[] readIds = object.getReadIds();
                StringBuilder sb = new StringBuilder();
                for (int i = 0; ; i++) {
                    sb.append(readIds[i]);
                    if (i == readIds.length - 1)
                        return sb.toString();
                    sb.append(",");
                }
            }
        });
        descriptorsList.add(new ExtractSequence(VDJCAlignments.class, "-sequence", "Export aligned sequence (initial read), or 2 sequences in case of paired-end reads", "Read(s) sequence", "readSequence"));
        descriptorsList.add(new ExtractSequenceQuality(VDJCAlignments.class, "-quality", "Export initial read quality, or 2 qualities in case of paired-end reads", "Read(s) sequence qualities", "readQuality"));
        descriptorsList.add(new PL_C("-cloneId", "Unique clone identifier", "Clone ID", "cloneId") {

            @Override
            protected String extract(Clone object) {
                return "" + object.getId();
            }
        });
        descriptorsList.add(new PL_C("-count", "Export clone count", "Clone count", "cloneCount") {

            @Override
            protected String extract(Clone object) {
                return "" + object.getCount();
            }
        });
        descriptorsList.add(new PL_C("-fraction", "Export clone fraction", "Clone fraction", "cloneFraction") {

            @Override
            protected String extract(Clone object) {
                return "" + object.getFraction();
            }
        });
        descriptorsList.add(new ExtractSequence(Clone.class, "-sequence", "Export aligned sequence (initial read), or 2 sequences in case of paired-end reads", "Clonal sequence(s)", "clonalSequence"));
        descriptorsList.add(new ExtractSequenceQuality(Clone.class, "-quality", "Export initial read quality, or 2 qualities in case of paired-end reads", "Clonal sequence quality(s)", "clonalSequenceQuality"));
        descriptorsList.add(new PL_A("-descrR1", "Export description line from initial .fasta or .fastq file " + "of the first read (only available if --save-description was used in align command)", "Description R1", "descrR1") {

            @Override
            protected String extract(VDJCAlignments object) {
                List<SequenceRead> reads = object.getOriginalReads();
                if (reads == null)
                    throw new IllegalArgumentException("Error for option \'-descrR1\':\n" + "No description available for read: either re-run align action with -OsaveOriginalReads=true option " + "or don't use \'-descrR1\' in exportAlignments");
                return reads.get(0).getRead(0).getDescription();
            }

            @Override
            public FieldExtractor<VDJCAlignments> create(OutputMode outputMode, String[] args) {
                System.out.println("WARNING: -descrR1 is deprecated. Use -descrsR1");
                return super.create(outputMode, args);
            }
        });
        descriptorsList.add(new PL_A("-descrR2", "Export description line from initial .fasta or .fastq file " + "of the second read (only available if --save-description was used in align command)", "Description R2", "descrR2") {

            @Override
            protected String extract(VDJCAlignments object) {
                List<SequenceRead> reads = object.getOriginalReads();
                if (reads == null)
                    throw new IllegalArgumentException("Error for option \'-descrR1\':\n" + "No description available for read: either re-run align action with -OsaveOriginalReads=true option " + "or don't use \'-descrR1\' in exportAlignments");
                SequenceRead read = reads.get(0);
                if (read.numberOfReads() < 2)
                    throw new IllegalArgumentException("Error for option \'-descrR2\':\n" + "No description available for second read: your input data was single-end");
                return read.getRead(1).getDescription();
            }

            @Override
            public FieldExtractor<VDJCAlignments> create(OutputMode outputMode, String[] args) {
                System.out.println("WARNING: -descrR2 is deprecated. Use -descrsR2");
                return super.create(outputMode, args);
            }
        });
        descriptorsList.add(new PL_A("-descrsR1", "Export description lines from initial .fasta or .fastq file " + "of the first reads (only available if -OsaveOriginalReads=true was used in align command)", "Descriptions R1", "descrsR1") {

            @Override
            protected String extract(VDJCAlignments object) {
                List<SequenceRead> reads = object.getOriginalReads();
                if (reads == null)
                    throw new IllegalArgumentException("Error for option \'-descrR1\':\n" + "No description available for read: either re-run align action with -OsaveOriginalReads option " + "or don't use \'-descrR1\' in exportAlignments");
                StringBuilder sb = new StringBuilder();
                for (int i = 0; ; i++) {
                    sb.append(reads.get(i).getRead(0).getDescription());
                    if (i == reads.size() - 1)
                        return sb.toString();
                    sb.append(",");
                }
            }
        });
        descriptorsList.add(new PL_A("-descrsR2", "Export description lines from initial .fasta or .fastq file " + "of the second reads (only available if -OsaveOriginalReads=true was used in align command)", "Descriptions R2", "descrsR2") {

            @Override
            protected String extract(VDJCAlignments object) {
                List<SequenceRead> reads = object.getOriginalReads();
                if (reads == null)
                    throw new IllegalArgumentException("Error for option \'-descrR1\':\n" + "No description available for read: either re-run align action with -OsaveOriginalReads option " + "or don't use \'-descrR1\' in exportAlignments");
                StringBuilder sb = new StringBuilder();
                for (int i = 0; ; i++) {
                    SequenceRead read = reads.get(i);
                    if (read.numberOfReads() < 2)
                        throw new IllegalArgumentException("Error for option \'-descrsR2\':\n" + "No description available for second read: your input data was single-end");
                    sb.append(read.getRead(1).getDescription());
                    if (i == reads.size() - 1)
                        return sb.toString();
                    sb.append(",");
                }
            }
        });
        descriptorsList.add(new PL_A("-readHistory", "Export read history", "Read history", "readHistory") {

            @Override
            protected String extract(VDJCAlignments object) {
                try {
                    return GlobalObjectMappers.toOneLine(object.getHistory());
                } catch (JsonProcessingException ex) {
                    throw new RuntimeException(ex);
                }
            }
        });
        for (final GeneType type : GeneType.values()) {
            String c = Character.toLowerCase(type.getLetter()) + "IdentityPercents";
            descriptorsList.add(new PL_O("-" + c, type.getLetter() + " alignment identity percents", type.getLetter() + " alignment identity percents", c) {

                @Override
                protected String extract(VDJCObject object) {
                    VDJCHit[] hits = object.getHits(type);
                    if (hits == null)
                        return NULL;
                    StringBuilder sb = new StringBuilder();
                    sb.append("");
                    for (int i = 0; ; i++) {
                        sb.append(hits[i].getIdentity());
                        if (i == hits.length - 1)
                            return sb.toString();
                        sb.append(",");
                    }
                }
            });
        }
        for (final GeneType type : GeneType.values()) {
            String c = Character.toLowerCase(type.getLetter()) + "BestIdentityPercent";
            descriptorsList.add(new PL_O("-" + c, type.getLetter() + "best alignment identity percent", type.getLetter() + "best alignment identity percent", c) {

                @Override
                protected String extract(VDJCObject object) {
                    VDJCHit hit = object.getBestHit(type);
                    if (hit == null)
                        return NULL;
                    return Float.toString(hit.getIdentity());
                }
            });
        }
        descriptorsList.add(new PL_O("-chains", "Chains", "Chains", "Chains") {

            @Override
            protected String extract(VDJCObject object) {
                return object.commonChains().toString();
            }
        });
        descriptorsList.add(new PL_O("-topChains", "Top chains", "Top chains", "topChains") {

            @Override
            protected String extract(VDJCObject object) {
                return object.commonTopChains().toString();
            }
        });
        descriptors = descriptorsList.toArray(new Field[descriptorsList.size()]);
    }
    return descriptors;
}

Example 100 with JsonProcessingException

use of org.apache.flink.shaded.jackson2.com.fasterxml.jackson.core.JsonProcessingException in project muikku by otavanopisto.

the class MetaRESTService method getResources.

@GET
@Path("/resources")
@RESTPermit(handling = Handling.UNSECURED)
public Response getResources(@Context Request request, @QueryParam("format") String format) {
    EntityTag tag = new EntityTag(ETAG);
    ResponseBuilder builder = request.evaluatePreconditions(tag);
    if (builder != null) {
        return builder.build();
    }
    List<String> resources = new ArrayList<>();
    ResourceMethodRegistry registry = (ResourceMethodRegistry) dispatcher.getRegistry();
    Set<Entry<String, java.util.List<org.jboss.resteasy.core.ResourceInvoker>>> entries = registry.getBounded().entrySet();
    for (Entry<String, java.util.List<org.jboss.resteasy.core.ResourceInvoker>> entry : entries) {
        String path = entry.getKey();
        resources.add(path);
    }
    CacheControl cacheControl = new CacheControl();
    cacheControl.setMaxAge(-1);
    cacheControl.setPrivate(false);
    cacheControl.setMustRevalidate(false);
    Collections.sort(resources);
    if (StringUtils.isNotBlank(format) && "js".equals(format)) {
        try {
            return Response.ok(String.format("var META_RESOURCES = %s", new ObjectMapper().writeValueAsString(resources)), "text/javascript").cacheControl(cacheControl).tag(tag).build();
        } catch (JsonProcessingException e) {
            return Response.status(Status.INTERNAL_SERVER_ERROR).entity(e.getMessage()).build();
        }
    } else {
        return Response.ok(resources).cacheControl(cacheControl).tag(tag).build();
    }
}