SubmissionController has 27 methods (exceeds 20 allowed). Consider refactoring.

Open

@RepositoryRestController
@ExposesResourceFor(SubmissionEnvelope.class)
@RequiredArgsConstructor
@Getter
public class SubmissionController {

QueueConfig has 27 methods (exceeds 20 allowed). Consider refactoring.

Open

@Configuration
public class QueueConfig implements RabbitListenerConfigurer {
    @Bean Queue queueFileUpdate() { return new Queue(Constants.Queues.FILE_UPDATE, false); }

    @Bean Queue queueBundleUpdate() { return new Queue(Constants.Routing.UPDATE_SUBMITTED, true); }

Method cleanupLinksToSubmissionMetadata has 56 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    private void cleanupLinksToSubmissionMetadata(SubmissionEnvelope submissionEnvelope) {
        long startTime = System.currentTimeMillis();

        processRepository.findBySubmissionEnvelope(submissionEnvelope)
                         .forEach(p -> {

Method findByCriteria has 52 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    @Override
    public Page<Project> findByCriteria(List<MetadataCriteria> criteriaList, Boolean andCriteria, Pageable pageable) {
        Query query = new Query();
        
        List<Criteria> criterias = new ArrayList<>();

Method allowedStateTransitions has 34 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    public static List<SubmissionState> allowedStateTransitions(SubmissionState fromState) {
        List<SubmissionState> allowedStates = new ArrayList<>();
        switch (fromState) {
            case PENDING:
                allowedStates.add(SubmissionState.DRAFT);

Method allManifestsIterator has 28 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    private Iterator<BundleManifest> allManifestsIterator() {
        Iterator<BundleManifest> manifestsIterator = new Iterator<BundleManifest>() {
            Pageable pageable = new PageRequest(0, 5000);
            Page<BundleManifest> pagedBundleManifests = null;
            Queue<BundleManifest> bundleManifests;

Method bundleManifestsForDocuments has 26 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    public Map<String, Set<MetadataDocument>> bundleManifestsForDocuments(Collection<MetadataDocument> documents) {

        Map<String, Set<MetadataDocument>> hits = new HashMap<>();

        long fileStartTime = System.currentTimeMillis();

Method allManifestsIterator has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

Open

    private Iterator<BundleManifest> allManifestsIterator() {
        Iterator<BundleManifest> manifestsIterator = new Iterator<BundleManifest>() {
            Pageable pageable = new PageRequest(0, 5000);
            Page<BundleManifest> pagedBundleManifests = null;
            Queue<BundleManifest> bundleManifests;

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Method querySchemas has 6 arguments (exceeds 4 allowed). Consider refactoring.

Open

    Page<Schema> querySchemas(@Param("high-level-entity") String highLevelEntity,
                              @Param("concrete-entity") String concreteEntity,
                              @Param("domain-entity") String domainEntity,
                              @Param("sub-domain-entity") String subDomainEntity,
                              @Param("schema-version") String schemaVersion,

Method getFeatureCompatibilityVersion has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

    static ServerVersion getFeatureCompatibilityVersion(MongoDatabase db) {
        Document response = db.runCommand(new Document("getParameter", 1).append("featureCompatibilityVersion", 1));
        if (response.containsKey("ok") && response.containsKey("featureCompatibilityVersion")) {
            if (getServerVersion(db).compareTo(getVersionFromString("3.6")) < 0)
                return  getVersionFromString(response.getString("featureCompatibilityVersion"));

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Method findByCriteria has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

    @Override
    public Page<Project> findByCriteria(List<MetadataCriteria> criteriaList, Boolean andCriteria, Pageable pageable) {
        Query query = new Query();
        
        List<Criteria> criterias = new ArrayList<>();

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Avoid too many return statements within this method.

Open

            return Optional.ofNullable(bundleManifest.getFileBiomaterialMap());

Method entityMapFromManifest has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.

Open

    private Optional<Map<String, Collection<String>>> entityMapFromManifest(EntityType entityType, BundleManifest bundleManifest) {
        if(entityType.equals(EntityType.BIOMATERIAL)) {
            return Optional.ofNullable(bundleManifest.getFileBiomaterialMap());
        } else if(entityType.equals(EntityType.FILE)) {
            return Optional.ofNullable(bundleManifest.getFileFilesMap());

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Method handleFileStagedEvent has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.

Open

    @RabbitListener(queues = Constants.Queues.FILE_STAGED)
    public void handleFileStagedEvent(FileMessage fileMessage) {
        if(!StringUtils.isEmpty(fileMessage.getContentType())
                && fileMessage.getMediaType().isPresent()
                && fileMessage.getMediaType().get().equals(FileMediaTypes.HCA_DATA_FILE)){

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