#23004

Committed 27 Aug 2024 08:33AM UTC coverage: 20.786%. First build

Build # #23004

Build Type

Pull #10790

github

Committed by

web-flow

Commit Message

Merge f6e1b0697 into a6b549840

Pull Request Pull Request #10790: fix: issues in exporters and citations for PermaLink/non-DOI PIDs

Run Details

24 of 38 new or added lines in 7 files covered. (63.16%)

17536 of 84363 relevant lines covered (20.79%)

0.21 hits per line

Source File
Press 'n' to go to next uncovered line, 'b' for previous

29.57

/src/main/java/edu/harvard/iq/dataverse/util/json/JsonPrinter.java

package edu.harvard.iq.dataverse.util.json;

import edu.harvard.iq.dataverse.*;
import edu.harvard.iq.dataverse.authorization.DataverseRole;
import edu.harvard.iq.dataverse.authorization.groups.impl.maildomain.MailDomainGroup;
import edu.harvard.iq.dataverse.authorization.providers.builtin.BuiltinUser;
import edu.harvard.iq.dataverse.api.Util;
import edu.harvard.iq.dataverse.authorization.Permission;
import edu.harvard.iq.dataverse.authorization.RoleAssigneeDisplayInfo;
import edu.harvard.iq.dataverse.authorization.groups.impl.explicit.ExplicitGroup;
import edu.harvard.iq.dataverse.authorization.groups.impl.ipaddress.IpGroup;
import edu.harvard.iq.dataverse.authorization.groups.impl.ipaddress.ip.IpAddress;
import edu.harvard.iq.dataverse.authorization.groups.impl.ipaddress.ip.IpAddressRange;
import edu.harvard.iq.dataverse.authorization.groups.impl.shib.ShibGroup;
import edu.harvard.iq.dataverse.authorization.providers.AuthenticationProviderRow;
import edu.harvard.iq.dataverse.authorization.users.AuthenticatedUser;
import edu.harvard.iq.dataverse.authorization.users.User;
import edu.harvard.iq.dataverse.branding.BrandingUtil;
import edu.harvard.iq.dataverse.dataaccess.DataAccess;
import edu.harvard.iq.dataverse.dataset.DatasetUtil;
import edu.harvard.iq.dataverse.datavariable.CategoryMetadata;
import edu.harvard.iq.dataverse.datavariable.DataVariable;
import edu.harvard.iq.dataverse.datavariable.SummaryStatistic;
import edu.harvard.iq.dataverse.datavariable.VarGroup;
import edu.harvard.iq.dataverse.datavariable.VariableCategory;
import edu.harvard.iq.dataverse.datavariable.VariableMetadata;
import edu.harvard.iq.dataverse.datavariable.VariableRange;
import edu.harvard.iq.dataverse.license.License;
import edu.harvard.iq.dataverse.globus.FileDetailsHolder;
import edu.harvard.iq.dataverse.harvest.client.HarvestingClient;
import edu.harvard.iq.dataverse.privateurl.PrivateUrl;
import edu.harvard.iq.dataverse.settings.SettingsServiceBean;
import edu.harvard.iq.dataverse.util.BundleUtil;
import edu.harvard.iq.dataverse.util.DatasetFieldWalker;
import static edu.harvard.iq.dataverse.util.json.NullSafeJsonBuilder.jsonObjectBuilder;

import edu.harvard.iq.dataverse.workflow.Workflow;
import edu.harvard.iq.dataverse.workflow.step.WorkflowStepData;

import java.util.*;
import jakarta.json.Json;
import jakarta.json.JsonArrayBuilder;
import jakarta.json.JsonObjectBuilder;

import java.util.function.BiConsumer;
import java.util.function.BinaryOperator;
import java.util.function.Function;
import java.util.function.Supplier;
import java.util.logging.Logger;
import java.util.stream.Collector;
import java.util.stream.Collectors;
import static java.util.stream.Collectors.toList;

import jakarta.ejb.EJB;
import jakarta.ejb.Singleton;
import jakarta.json.JsonArray;
import jakarta.json.JsonObject;
import java.math.BigDecimal;

/**
 * Convert objects to Json.
 *
 * @author michael
 */
@Singleton
public class JsonPrinter {

    private static final Logger logger = Logger.getLogger(JsonPrinter.class.getCanonicalName());

    @EJB
    static SettingsServiceBean settingsService;

    @EJB
    static DatasetFieldServiceBean datasetFieldService;

    public static void injectSettingsService(SettingsServiceBean ssb, DatasetFieldServiceBean dfsb) {
            settingsService = ssb;
            datasetFieldService = dfsb;
    }

    public JsonPrinter() {

    }

    public static final BriefJsonPrinter brief = new BriefJsonPrinter();

    public static JsonArrayBuilder asJsonArray(Collection<String> strings) {
        JsonArrayBuilder arr = Json.createArrayBuilder();
        for (String s : strings) {
            arr.add(s);
        }
        return arr;
    }

    public static JsonObjectBuilder json(User u) {
        RoleAssigneeDisplayInfo displayInfo = u.getDisplayInfo();
        return jsonObjectBuilder()
                .add("identifier", u.getIdentifier())
                .add("displayInfo", jsonObjectBuilder()
                        .add("Title", displayInfo.getTitle())
                        .add("email", displayInfo.getEmailAddress()));
    }

    public static JsonObjectBuilder json(AuthenticatedUser authenticatedUser) {
        NullSafeJsonBuilder builder = jsonObjectBuilder()
            .add("id", authenticatedUser.getId())
            .add("identifier", authenticatedUser.getIdentifier())
            .add("displayName", authenticatedUser.getDisplayInfo().getTitle())
            .add("firstName", authenticatedUser.getFirstName())
            .add("lastName", authenticatedUser.getLastName())
            .add("email", authenticatedUser.getEmail())
            .add("superuser", authenticatedUser.isSuperuser())
            .add("deactivated", authenticatedUser.isDeactivated())
            .add("deactivatedTime", authenticatedUser.getDeactivatedTime())
            .add("affiliation", authenticatedUser.getAffiliation())
            .add("position", authenticatedUser.getPosition())
            .add("persistentUserId", authenticatedUser.getAuthenticatedUserLookup().getPersistentUserId())
            .add("emailLastConfirmed", authenticatedUser.getEmailConfirmed())
            .add("createdTime", authenticatedUser.getCreatedTime())
            .add("lastLoginTime", authenticatedUser.getLastLoginTime())
            .add("lastApiUseTime", authenticatedUser.getLastApiUseTime())
            .add("authenticationProviderId", authenticatedUser.getAuthenticatedUserLookup().getAuthenticationProviderId());
        return builder;
    }

    public static JsonObjectBuilder json(RoleAssignment ra) {
        return jsonObjectBuilder()
                .add("id", ra.getId())
                .add("assignee", ra.getAssigneeIdentifier())
                .add("roleId", ra.getRole().getId())
                .add("_roleAlias", ra.getRole().getAlias())
                .add("privateUrlToken", ra.getPrivateUrlToken())
                .add("definitionPointId", ra.getDefinitionPoint().getId());
    }

    public static JsonArrayBuilder json(Set<Permission> permissions) {
        JsonArrayBuilder bld = Json.createArrayBuilder();
        permissions.forEach(p -> bld.add(p.name()));
        return bld;
    }

    public static JsonObjectBuilder json(DatasetLock lock) {
        return jsonObjectBuilder()
                .add("lockType", lock.getReason().toString())
                .add("date", lock.getStartTime().toString())
                .add("user", lock.getUser().getUserIdentifier())
                .add("dataset", lock.getDataset().getGlobalId().asString())
                .add("message", lock.getInfo());
    }

    public static JsonObjectBuilder json( RoleAssigneeDisplayInfo d ) {
        return jsonObjectBuilder()
                .add("title", d.getTitle())
                .add("email", d.getEmailAddress())
                .add("affiliation", d.getAffiliation());
    }

    public static JsonObjectBuilder json(IpGroup grp) {
         // collect single addresses
        List<String> singles = grp.getRanges().stream().filter( IpAddressRange::isSingleAddress )
                                .map( IpAddressRange::getBottom )
                                .map( IpAddress::toString ).collect(toList());
        // collect "real" ranges
        List<List<String>> ranges = grp.getRanges().stream().filter( rng -> !rng.isSingleAddress() )
                                .map( rng -> Arrays.asList(rng.getBottom().toString(), rng.getTop().toString()) )
                                .collect(toList());

        JsonObjectBuilder bld = jsonObjectBuilder()
                .add("alias", grp.getPersistedGroupAlias() )
                .add("identifier", grp.getIdentifier())
                .add("id", grp.getId() )
                .add("name", grp.getDisplayName() )
                .add("description", grp.getDescription() );

        if ( ! singles.isEmpty() ) {
            bld.add("addresses", asJsonArray(singles) );
        }

        if ( ! ranges.isEmpty() ) {
            JsonArrayBuilder rangesBld = Json.createArrayBuilder();
            ranges.forEach( r -> rangesBld.add( Json.createArrayBuilder().add(r.get(0)).add(r.get(1))) );
            bld.add("ranges", rangesBld );
        }

        return bld;
    }

    public static JsonObjectBuilder json(ShibGroup grp) {
        return jsonObjectBuilder()
                .add("name", grp.getName())
                .add("attribute", grp.getAttribute())
                .add("pattern", grp.getPattern())
                .add("id", grp.getId());
    }

    public static JsonObjectBuilder json(MailDomainGroup grp) {
        JsonObjectBuilder bld = jsonObjectBuilder()
            .add("alias", grp.getPersistedGroupAlias() )
            .add("id", grp.getId() )
            .add("name", grp.getDisplayName() )
            .add("description", grp.getDescription() )
            .add("domains", asJsonArray(grp.getEmailDomainsAsList()) )
            .add("regex", grp.isRegEx());
        return bld;
    }

    public static JsonArrayBuilder rolesToJson(List<DataverseRole> role) {
        JsonArrayBuilder bld = Json.createArrayBuilder();
        for (DataverseRole r : role) {
            bld.add(JsonPrinter.json(r));
        }
        return bld;
    }

    public static <E extends Enum> JsonArrayBuilder enumsToJson(Collection<E> collection) {
        JsonArrayBuilder arr = Json.createArrayBuilder();
        for (E entry : collection) {
            arr.add(entry.name());
        }
        return arr;
    }

    public static JsonObjectBuilder json(DataverseRole role) {
        JsonObjectBuilder bld = jsonObjectBuilder()
                .add("alias", role.getAlias())
                .add("name", role.getName())
                .add("permissions", JsonPrinter.json(role.permissions()))
                .add("description", role.getDescription());
        if (role.getId() != null) {
            bld.add("id", role.getId());
        }
        if (role.getOwner() != null && role.getOwner().getId() != null) {
            bld.add("ownerId", role.getOwner().getId());
        }

        return bld;
    }

    public static JsonObjectBuilder json(Workflow wf){
        JsonObjectBuilder bld = jsonObjectBuilder();
        bld.add("name", wf.getName());
        if ( wf.getId() != null ) {
            bld.add("id", wf.getId());
        }

        if ( wf.getSteps()!=null && !wf.getSteps().isEmpty()) {
            JsonArrayBuilder arr = Json.createArrayBuilder();
            for ( WorkflowStepData stp : wf.getSteps() ) {
                arr.add( jsonObjectBuilder().add("stepType", stp.getStepType())
                                   .add("provider", stp.getProviderId())
                                   .add("parameters", mapToObject(stp.getStepParameters()))
                                   .add("requiredSettings", mapToObject(stp.getStepSettings())) );
            }
            bld.add("steps", arr );
        }

        return bld;
    }

    public static JsonObjectBuilder json(Dataverse dv) {
        return json(dv, false, false);
    }

    //TODO: Once we upgrade to Java EE 8 we can remove objects from the builder, and this email removal can be done in a better place.
    public static JsonObjectBuilder json(Dataverse dv, Boolean hideEmail, Boolean returnOwners) {
        JsonObjectBuilder bld = jsonObjectBuilder()
                .add("id", dv.getId())
                .add("alias", dv.getAlias())
                .add("name", dv.getName())
                .add("affiliation", dv.getAffiliation());
        if(!hideEmail) {
            bld.add("dataverseContacts", JsonPrinter.json(dv.getDataverseContacts()));
        }
        if (returnOwners){
            bld.add("isPartOf", getOwnersFromDvObject(dv));
        }
        bld.add("permissionRoot", dv.isPermissionRoot())
                .add("description", dv.getDescription())
                .add("dataverseType", dv.getDataverseType().name());
        if (dv.getOwner() != null) {
            bld.add("ownerId", dv.getOwner().getId());
        }
        if (dv.getCreateDate() != null) {
            bld.add("creationDate", Util.getDateTimeFormat().format(dv.getCreateDate()));
        }
        if (dv.getDataverseTheme() != null) {
            bld.add("theme", JsonPrinter.json(dv.getDataverseTheme()));
        }
        if(dv.getStorageDriverId() != null) {
                bld.add("storageDriverLabel", DataAccess.getStorageDriverLabelFor(dv.getStorageDriverId()));
        }
        if (dv.getFilePIDsEnabled() != null) {
            bld.add("filePIDsEnabled", dv.getFilePIDsEnabled());
        }
        bld.add("isReleased", dv.isReleased());

        List<DataverseFieldTypeInputLevel> inputLevels = dv.getDataverseFieldTypeInputLevels();
        if(!inputLevels.isEmpty()) {
            bld.add("inputLevels", JsonPrinter.jsonDataverseFieldTypeInputLevels(inputLevels));
        }

        return bld;
    }

    public static JsonArrayBuilder json(List<DataverseContact> dataverseContacts) {
        JsonArrayBuilder jsonArrayOfContacts = Json.createArrayBuilder();
        for (DataverseContact dataverseContact : dataverseContacts) {
            NullSafeJsonBuilder contactJsonObject = NullSafeJsonBuilder.jsonObjectBuilder();
            contactJsonObject.add("displayOrder", dataverseContact.getDisplayOrder());
            contactJsonObject.add("contactEmail", dataverseContact.getContactEmail());
            jsonArrayOfContacts.add(contactJsonObject);
        }
        return jsonArrayOfContacts;
    }

    public static JsonObjectBuilder getOwnersFromDvObject(DvObject dvObject){
        return getOwnersFromDvObject(dvObject, null);
    }

    public static JsonObjectBuilder getOwnersFromDvObject(DvObject dvObject, DatasetVersion dsv) {
        List <DvObject> ownerList = new ArrayList();
        dvObject = dvObject.getOwner(); // We're going to ignore the object itself
        //Get "root" to top of list
        while (dvObject != null) {
            ownerList.add(0, dvObject);
            dvObject = dvObject.getOwner();
        }
        //then work "inside out"
        JsonObjectBuilder saved = null;
        for (DvObject dvo : ownerList) {
            saved = addEmbeddedOwnerObject(dvo, saved, dsv);
        }
        return saved;
    }

    private static JsonObjectBuilder addEmbeddedOwnerObject(DvObject dvo, JsonObjectBuilder isPartOf, DatasetVersion dsv ) {
        JsonObjectBuilder ownerObject = jsonObjectBuilder();

        if (dvo.isInstanceofDataverse()) {
            ownerObject.add("type", "DATAVERSE");
            Dataverse in = (Dataverse) dvo;
            ownerObject.add("identifier", in.getAlias());
        }

        if (dvo.isInstanceofDataset()) {
            ownerObject.add("type", "DATASET");
            if (dvo.getGlobalId() != null) {
                ownerObject.add("persistentIdentifier", dvo.getGlobalId().asString());
            }
            ownerObject.add("identifier", dvo.getId());
            String versionString = dsv == null ? "" : dsv.getFriendlyVersionNumber();
            if (!versionString.isEmpty()){
               ownerObject.add("version", versionString);
            }
        }

        ownerObject.add("displayName", dvo.getDisplayName());

        if (isPartOf != null) {
            ownerObject.add("isPartOf", isPartOf);
        }

        return ownerObject;
    }

    public static JsonObjectBuilder json( DataverseTheme theme ) {
        final NullSafeJsonBuilder baseObject = jsonObjectBuilder()
                .add("id", theme.getId() )
                .add("logo", theme.getLogo())
                .add("tagline", theme.getTagline())
                .add("linkUrl", theme.getLinkUrl())
                .add("linkColor", theme.getLinkColor())
                .add("textColor", theme.getTextColor())
                .add("backgroundColor", theme.getBackgroundColor());
        if ( theme.getLogoAlignment() != null ) {
            baseObject.add("logoBackgroundColor", theme.getLogoBackgroundColor());
        }
        return baseObject;
    }

    public static JsonObjectBuilder json(BuiltinUser user) {
        return (user == null)
                ? null
                : jsonObjectBuilder()
                .add("id", user.getId())
                .add("userName", user.getUserName());
    }

    public static JsonObjectBuilder json(Dataset ds){
       return json(ds, false);
    }

    public static JsonObjectBuilder json(Dataset ds, Boolean returnOwners) {
        JsonObjectBuilder bld = jsonObjectBuilder()
                .add("id", ds.getId())
                .add("identifier", ds.getIdentifier())
                .add("persistentUrl", ds.getPersistentURL())
                .add("protocol", ds.getProtocol())
                .add("authority", ds.getAuthority())
                .add("separator", ds.getSeparator())
                .add("publisher", BrandingUtil.getInstallationBrandName())
                .add("publicationDate", ds.getPublicationDateFormattedYYYYMMDD())
                .add("storageIdentifier", ds.getStorageIdentifier());
        if (DvObjectContainer.isMetadataLanguageSet(ds.getMetadataLanguage())) {
            bld.add("metadataLanguage", ds.getMetadataLanguage());
        }
        if (returnOwners){
            bld.add("isPartOf", getOwnersFromDvObject(ds));
        }
        return bld;
    }

    public static JsonObjectBuilder json(FileDetailsHolder ds) {
        return Json.createObjectBuilder().add(ds.getStorageID() ,
                Json.createObjectBuilder()
                .add("id", ds.getStorageID() )
                .add("hash", ds.getHash())
                .add("mime",ds.getMime()));
    }

    public static JsonObjectBuilder json(DatasetVersion dsv, boolean includeFiles) {
        return json(dsv, null, includeFiles, false);
    }

    public static JsonObjectBuilder json(DatasetVersion dsv, List<String> anonymizedFieldTypeNamesList,
        boolean includeFiles, boolean returnOwners) {
        Dataset dataset = dsv.getDataset();
        JsonObjectBuilder bld = jsonObjectBuilder()
                .add("id", dsv.getId()).add("datasetId", dataset.getId())
                .add("datasetPersistentId", dataset.getGlobalId().asString())
                .add("storageIdentifier", dataset.getStorageIdentifier())
                .add("versionNumber", dsv.getVersionNumber())
                .add("versionMinorNumber", dsv.getMinorVersionNumber())
                .add("versionState", dsv.getVersionState().name())
                .add("latestVersionPublishingState", dataset.getLatestVersion().getVersionState().name())
                .add("versionNote", dsv.getVersionNote())
                .add("archiveNote", dsv.getArchiveNote())
                .add("deaccessionLink", dsv.getDeaccessionLink())
                .add("distributionDate", dsv.getDistributionDate())
                .add("productionDate", dsv.getProductionDate())
                .add("UNF", dsv.getUNF()).add("archiveTime", format(dsv.getArchiveTime()))
                .add("lastUpdateTime", format(dsv.getLastUpdateTime()))
                .add("releaseTime", format(dsv.getReleaseTime()))
                .add("createTime", format(dsv.getCreateTime()))
                .add("alternativePersistentId", dataset.getAlternativePersistentIdentifier())
                .add("publicationDate", dataset.getPublicationDateFormattedYYYYMMDD())
                .add("citationDate", dataset.getCitationDateFormattedYYYYMMDD());

        License license = DatasetUtil.getLicense(dsv);
        if (license != null) {
            bld.add("license", jsonLicense(dsv));
        } else {
            // Custom terms
            bld.add("termsOfUse", dsv.getTermsOfUseAndAccess().getTermsOfUse())
                    .add("confidentialityDeclaration", dsv.getTermsOfUseAndAccess().getConfidentialityDeclaration())
                    .add("specialPermissions", dsv.getTermsOfUseAndAccess().getSpecialPermissions())
                    .add("restrictions", dsv.getTermsOfUseAndAccess().getRestrictions())
                    .add("citationRequirements", dsv.getTermsOfUseAndAccess().getCitationRequirements())
                    .add("depositorRequirements", dsv.getTermsOfUseAndAccess().getDepositorRequirements())
                    .add("conditions", dsv.getTermsOfUseAndAccess().getConditions())
                    .add("disclaimer", dsv.getTermsOfUseAndAccess().getDisclaimer());
        }
        bld.add("termsOfAccess", dsv.getTermsOfUseAndAccess().getTermsOfAccess())
                .add("dataAccessPlace", dsv.getTermsOfUseAndAccess().getDataAccessPlace())
                .add("originalArchive", dsv.getTermsOfUseAndAccess().getOriginalArchive())
                .add("availabilityStatus", dsv.getTermsOfUseAndAccess().getAvailabilityStatus())
                .add("contactForAccess", dsv.getTermsOfUseAndAccess().getContactForAccess())
                .add("sizeOfCollection", dsv.getTermsOfUseAndAccess().getSizeOfCollection())
                .add("studyCompletion", dsv.getTermsOfUseAndAccess().getStudyCompletion())
                .add("fileAccessRequest", dsv.getTermsOfUseAndAccess().isFileAccessRequest());

        bld.add("metadataBlocks", (anonymizedFieldTypeNamesList != null) ?
                jsonByBlocks(dsv.getDatasetFields(), anonymizedFieldTypeNamesList)
                : jsonByBlocks(dsv.getDatasetFields())
        );
        if(returnOwners){
            bld.add("isPartOf", getOwnersFromDvObject(dataset));
        }
        if (includeFiles) {
            bld.add("files", jsonFileMetadatas(dsv.getFileMetadatas()));
        }

        return bld;
    }

    public static JsonObjectBuilder jsonDataFileList(List<DataFile> dataFiles){

        if (dataFiles==null){
            throw new NullPointerException("dataFiles cannot be null");
        }

        JsonObjectBuilder bld = jsonObjectBuilder();


        List<FileMetadata> dataFileList = dataFiles.stream()
                                    .map(x -> x.getFileMetadata())
                                    .collect(Collectors.toList());


        bld.add("files", jsonFileMetadatas(dataFileList));

        return bld;
    }

    /**
     * Export formats such as DDI require the citation to be included. See
     * https://github.com/IQSS/dataverse/issues/2579 for more on DDI export.
     *
     * @todo Instead of having this separate method, should "citation" be added
     * to the regular `json` method for DatasetVersion? Will anything break?
     * Unit tests for that method could not be found.
     */
    public static JsonObjectBuilder jsonWithCitation(DatasetVersion dsv, boolean includeFiles) {
        JsonObjectBuilder dsvWithCitation = JsonPrinter.json(dsv, includeFiles);
        dsvWithCitation.add("citation", dsv.getCitation());
        return dsvWithCitation;
    }

    /**
     * Export formats such as DDI require the persistent identifier components
     * such as "protocol", "authority" and "identifier" to be included so we
     * create a JSON object we can convert to a DatasetDTO which can include a
     * DatasetVersionDTO, which has all the metadata fields we need to export.
     * See https://github.com/IQSS/dataverse/issues/2579 for more on DDI export.
     *
     * @todo Instead of having this separate method, should "datasetVersion" be
     * added to the regular `json` method for Dataset? Will anything break? Unit
     * tests for that method could not be found. If we keep this method as-is
     * should the method be renamed?
     */
    public static JsonObjectBuilder jsonAsDatasetDto(DatasetVersion dsv) {
        JsonObjectBuilder datasetDtoAsJson = JsonPrinter.json(dsv.getDataset());
        datasetDtoAsJson.add("datasetVersion", jsonWithCitation(dsv, true));
        return datasetDtoAsJson;
    }

    public static JsonArrayBuilder jsonFileMetadatas(Collection<FileMetadata> fmds) {
        JsonArrayBuilder filesArr = Json.createArrayBuilder();
        for (FileMetadata fmd : fmds) {
            filesArr.add(JsonPrinter.json(fmd));
        }

        return filesArr;
    }

    public static JsonObjectBuilder json(DatasetDistributor dist) {
        return jsonObjectBuilder()
                .add("displayOrder", dist.getDisplayOrder())
                .add("version", dist.getVersion())
                .add("abbreviation", JsonPrinter.json(dist.getAbbreviation()))
                .add("affiliation", JsonPrinter.json(dist.getAffiliation()))
                .add("logo", JsonPrinter.json(dist.getLogo()))
                .add("name", JsonPrinter.json(dist.getName()))
                .add("url", JsonPrinter.json(dist.getUrl()));
    }

    public static JsonObjectBuilder jsonByBlocks(List<DatasetField> fields) {
        return jsonByBlocks(fields, null);
    }

    public static JsonObjectBuilder jsonByBlocks(List<DatasetField> fields, List<String> anonymizedFieldTypeNamesList) {
        JsonObjectBuilder blocksBld = jsonObjectBuilder();

        for (Map.Entry<MetadataBlock, List<DatasetField>> blockAndFields : DatasetField.groupByBlock(fields).entrySet()) {
            MetadataBlock block = blockAndFields.getKey();
            blocksBld.add(block.getName(), JsonPrinter.json(block, blockAndFields.getValue(), anonymizedFieldTypeNamesList));
        }
        return blocksBld;
    }

    /**
     * Create a JSON object for the block and its fields. The fields are assumed
     * to belong to the block - there's no checking of that in the method.
     *
     * @param block
     * @param fields
     * @return JSON Object builder with the block and fields information.
     */
    public static JsonObjectBuilder json(MetadataBlock block, List<DatasetField> fields) {
        return json(block, fields, null);
    }

    public static JsonObjectBuilder json(MetadataBlock block, List<DatasetField> fields, List<String> anonymizedFieldTypeNamesList) {
        JsonObjectBuilder blockBld = jsonObjectBuilder();

        blockBld.add("displayName", block.getDisplayName());
        blockBld.add("name", block.getName());

        final JsonArrayBuilder fieldsArray = Json.createArrayBuilder();
        Map<Long, JsonObject> cvocMap = (datasetFieldService==null) ? new HashMap<Long, JsonObject>() :datasetFieldService.getCVocConf(true);
        DatasetFieldWalker.walk(fields, settingsService, cvocMap, new DatasetFieldsToJson(fieldsArray, anonymizedFieldTypeNamesList));

        blockBld.add("fields", fieldsArray);
        return blockBld;
    }

    public static JsonArrayBuilder json(List<MetadataBlock> metadataBlocks, boolean returnDatasetFieldTypes, boolean printOnlyDisplayedOnCreateDatasetFieldTypes) {
        return json(metadataBlocks, returnDatasetFieldTypes, printOnlyDisplayedOnCreateDatasetFieldTypes, null);
    }

    public static JsonArrayBuilder json(List<MetadataBlock> metadataBlocks, boolean returnDatasetFieldTypes, boolean printOnlyDisplayedOnCreateDatasetFieldTypes, Dataverse ownerDataverse) {
        JsonArrayBuilder arrayBuilder = Json.createArrayBuilder();
        for (MetadataBlock metadataBlock : metadataBlocks) {
            arrayBuilder.add(returnDatasetFieldTypes ? json(metadataBlock, printOnlyDisplayedOnCreateDatasetFieldTypes, ownerDataverse) : brief.json(metadataBlock));
        }
        return arrayBuilder;
    }

    public static String typeClassString(DatasetFieldType typ) {
        if (typ.isControlledVocabulary()) {
            return "controlledVocabulary";
        }
        if (typ.isCompound()) {
            return "compound";
        }
        return "primitive";
    }

    public static JsonObject json(DatasetField dfv) {
        if (dfv.isEmpty()) {
            return null;
        } else {
            JsonArrayBuilder fieldArray = Json.createArrayBuilder();
            Map<Long, JsonObject> cvocMap = (datasetFieldService==null) ? new HashMap<Long, JsonObject>() :datasetFieldService.getCVocConf(true);
            DatasetFieldWalker.walk(dfv, new DatasetFieldsToJson(fieldArray), cvocMap);
            JsonArray out = fieldArray.build();
            return out.getJsonObject(0);
        }
    }

    public static JsonObjectBuilder json(MetadataBlock metadataBlock) {
        return json(metadataBlock, false, null);
    }

    public static JsonObjectBuilder json(MetadataBlock metadataBlock, boolean printOnlyDisplayedOnCreateDatasetFieldTypes, Dataverse ownerDataverse) {
        JsonObjectBuilder jsonObjectBuilder = jsonObjectBuilder()
                .add("id", metadataBlock.getId())
                .add("name", metadataBlock.getName())
                .add("displayName", metadataBlock.getDisplayName())
                .add("displayOnCreate", metadataBlock.isDisplayOnCreate());

        Set<DatasetFieldType> datasetFieldTypes;

        if (ownerDataverse != null) {
            datasetFieldTypes = new TreeSet<>(datasetFieldService.findAllInMetadataBlockAndDataverse(
                    metadataBlock, ownerDataverse, printOnlyDisplayedOnCreateDatasetFieldTypes));
        } else {
            datasetFieldTypes = printOnlyDisplayedOnCreateDatasetFieldTypes
                    ? new TreeSet<>(datasetFieldService.findAllDisplayedOnCreateInMetadataBlock(metadataBlock))
                    : new TreeSet<>(metadataBlock.getDatasetFieldTypes());
        }

        JsonObjectBuilder fieldsBuilder = Json.createObjectBuilder();
        for (DatasetFieldType datasetFieldType : datasetFieldTypes) {
            fieldsBuilder.add(datasetFieldType.getName(), json(datasetFieldType, ownerDataverse));
        }

        jsonObjectBuilder.add("fields", fieldsBuilder);
        return jsonObjectBuilder;
    }

    public static JsonArrayBuilder jsonDatasetFieldTypes(List<DatasetFieldType> fields) {
        JsonArrayBuilder fieldsJson = Json.createArrayBuilder();
        for (DatasetFieldType field : fields) {
            fieldsJson.add(JsonPrinter.json(field));
        }
        return fieldsJson;
    }

    public static JsonObjectBuilder json(DatasetFieldType fld) {
        return json(fld, null);
    }

    public static JsonObjectBuilder json(DatasetFieldType fld, Dataverse ownerDataverse) {
        JsonObjectBuilder fieldsBld = jsonObjectBuilder();
        fieldsBld.add("name", fld.getName());
        fieldsBld.add("displayName", fld.getDisplayName());
        fieldsBld.add("displayOnCreate", fld.isDisplayOnCreate());
        fieldsBld.add("title", fld.getTitle());
        fieldsBld.add("type", fld.getFieldType().toString());
        fieldsBld.add("typeClass", typeClassString(fld));
        fieldsBld.add("watermark", fld.getWatermark());
        fieldsBld.add("description", fld.getDescription());
        fieldsBld.add("multiple", fld.isAllowMultiples());
        fieldsBld.add("isControlledVocabulary", fld.isControlledVocabulary());
        fieldsBld.add("displayFormat", fld.getDisplayFormat());
        fieldsBld.add("displayOrder", fld.getDisplayOrder());

        boolean requiredInOwnerDataverse = ownerDataverse != null && ownerDataverse.isDatasetFieldTypeRequiredAsInputLevel(fld.getId());
        fieldsBld.add("isRequired", requiredInOwnerDataverse || fld.isRequired());

        if (fld.isControlledVocabulary()) {
            // If the field has a controlled vocabulary,
            // add all values to the resulting JSON
            JsonArrayBuilder jab = Json.createArrayBuilder();
            for (ControlledVocabularyValue cvv : fld.getControlledVocabularyValues()) {
                jab.add(cvv.getStrValue());
            }
            fieldsBld.add("controlledVocabularyValues", jab);
        }

        if (!fld.getChildDatasetFieldTypes().isEmpty()) {
            JsonObjectBuilder subFieldsBld = jsonObjectBuilder();
            for (DatasetFieldType subFld : fld.getChildDatasetFieldTypes()) {
                subFieldsBld.add(subFld.getName(), JsonPrinter.json(subFld, ownerDataverse));
            }
            fieldsBld.add("childFields", subFieldsBld);
        }

        return fieldsBld;
    }

    public static JsonObjectBuilder json(FileMetadata fmd){
        return json(fmd, false, false);
    }

    public static JsonObjectBuilder json(FileMetadata fmd, boolean returnOwners, boolean printDatasetVersion) {
        NullSafeJsonBuilder builder = jsonObjectBuilder();

                // deprecated: .add("category", fmd.getCategory())
                // TODO: uh, figure out what to do here... it's deprecated
                // in a sense that there's no longer the category field in the
                // fileMetadata object; but there are now multiple, oneToMany file
                // categories - and we probably need to export them too!) -- L.A. 4.5
                // DONE: catgegories by name
                builder.add("description", fmd.getDescription())
                .add("label", fmd.getLabel()) // "label" is the filename
                .add("restricted", fmd.isRestricted())
                .add("directoryLabel", fmd.getDirectoryLabel())
                .add("version", fmd.getVersion())
                .add("datasetVersionId", fmd.getDatasetVersion().getId())
                .add("categories", getFileCategories(fmd))
                .add("dataFile", JsonPrinter.json(fmd.getDataFile(), fmd, false, returnOwners));

        if (printDatasetVersion) {
            builder.add("datasetVersion", json(fmd.getDatasetVersion(), false));
        }

        return builder;
    }

    public static JsonObjectBuilder json(AuxiliaryFile auxFile) {
        return jsonObjectBuilder()
               .add("formatTag", auxFile.getFormatTag())
                .add("formatVersion", auxFile.getFormatVersion()) // "label" is the filename
                .add("origin", auxFile.getOrigin())
                .add("isPublic", auxFile.getIsPublic())
                .add("type", auxFile.getType())
                .add("contentType", auxFile.getContentType())
                .add("fileSize", auxFile.getFileSize())
                .add("checksum", auxFile.getChecksum())
                .add("dataFile", JsonPrinter.json(auxFile.getDataFile()));
    }

    public static JsonObjectBuilder json(DataFile df) {
        return JsonPrinter.json(df, null, false);
    }

    public static JsonObjectBuilder json(DataFile df, FileMetadata fileMetadata, boolean forExportDataProvider){
        return json(df, fileMetadata, forExportDataProvider, false);
    }

    public static JsonObjectBuilder json(DataFile df, FileMetadata fileMetadata, boolean forExportDataProvider, boolean returnOwners) {
        // File names are no longer stored in the DataFile entity; 
        // (they are instead in the FileMetadata (as "labels") - this way 
        // the filename can change between versions... 
        // It does appear that for some historical purpose we still need the
        // filename in the file DTO (?)... We rely on it to be there for the 
        // DDI export, for example. So we need to make sure this is is the 
        // *correct* file name - i.e., that it comes from the right version. 
        // (TODO...? L.A. 4.5, Aug 7 2016)
        String fileName = null;

        if (fileMetadata == null){
            // Note that this may not necessarily grab the file metadata from the 
            // version *you want*! (L.A.)
            fileMetadata = df.getFileMetadata();
        }

        fileName = fileMetadata.getLabel();
        GlobalId filePid = df.getGlobalId();
        String pidURL = (filePid!=null)? filePid.asURL(): null;
        //For backward compatibility - prior to #8674, asString() returned "" for the value when no PID exists.
        String pidString = (filePid!=null)? filePid.asString(): "";

        JsonObjectBuilder embargo = df.getEmbargo() != null ? JsonPrinter.json(df.getEmbargo()) : null;
        JsonObjectBuilder retention = df.getRetention() != null ? JsonPrinter.json(df.getRetention()) : null;

        NullSafeJsonBuilder builder = jsonObjectBuilder()
                .add("id", df.getId())
                .add("persistentId", pidString)
                .add("pidURL", pidURL)
                .add("filename", fileName)
                .add("contentType", df.getContentType())
                .add("friendlyType", df.getFriendlyType())
                .add("filesize", df.getFilesize())
                .add("description", fileMetadata.getDescription())
                .add("categories", getFileCategories(fileMetadata))
                .add("embargo", embargo)
                .add("retention", retention)
                //.add("released", df.isReleased())
                .add("storageIdentifier", df.getStorageIdentifier())
                .add("originalFileFormat", df.getOriginalFileFormat())
                .add("originalFormatLabel", df.getOriginalFormatLabel())
                .add ("originalFileSize", df.getOriginalFileSize())
                .add("originalFileName", df.getOriginalFileName())
                .add("UNF", df.getUnf())
                //---------------------------------------------
                // For file replace: rootDataFileId, previousDataFileId
                //---------------------------------------------
                .add("rootDataFileId", df.getRootDataFileId())
                .add("previousDataFileId", df.getPreviousDataFileId())
                //---------------------------------------------
                // Checksum
                // * @todo Should we deprecate "md5" now that it's under
                // * "checksum" (which may also be a SHA-1 rather than an MD5)? - YES!
                //---------------------------------------------
                .add("md5", getMd5IfItExists(df.getChecksumType(), df.getChecksumValue()))
                .add("checksum", getChecksumTypeAndValue(df.getChecksumType(), df.getChecksumValue()))
                .add("tabularData", df.isTabularData())
                .add("tabularTags", getTabularFileTags(df))
                .add("creationDate", df.getCreateDateFormattedYYYYMMDD())
                .add("publicationDate",  df.getPublicationDateFormattedYYYYMMDD());
        Dataset dfOwner = df.getOwner();
        if (dfOwner != null) {
            builder.add("fileAccessRequest", dfOwner.isFileAccessRequest());
        }
        /*
         * The restricted state was not included prior to #9175 so to avoid backward
         * incompatability, it is now only added when generating json for the
         * InternalExportDataProvider fileDetails.
         */
        if (forExportDataProvider) {
            builder.add("restricted", df.isRestricted())
            .add("fileMetadataId", fileMetadata.getId())
            .add("dataTables", df.getDataTables().isEmpty() ? null : JsonPrinter.jsonDT(df.getDataTables()))
            .add("varGroups", fileMetadata.getVarGroups().isEmpty()
                    ? JsonPrinter.jsonVarGroup(fileMetadata.getVarGroups())
                    : null);
        }
        if (returnOwners){
            builder.add("isPartOf", getOwnersFromDvObject(df, fileMetadata.getDatasetVersion()));
        }
        return builder;
    }

    //Started from https://github.com/RENCI-NRIG/dataverse/, i.e. https://github.com/RENCI-NRIG/dataverse/commit/2b5a1225b42cf1caba85e18abfeb952171c6754a
    public static JsonArrayBuilder jsonDT(List<DataTable> ldt) {
        JsonArrayBuilder ldtArr = Json.createArrayBuilder();
        for(DataTable dt: ldt){
            ldtArr.add(JsonPrinter.json(dt));
        }
        return ldtArr;
    }

    public static JsonObjectBuilder json(DataTable dt) {
        return jsonObjectBuilder()
                .add("varQuantity", dt.getVarQuantity())
                .add("caseQuantity", dt.getCaseQuantity())
                .add("recordsPerCase", dt.getRecordsPerCase())
                .add("UNF", dt.getUnf())
                .add("dataVariables", JsonPrinter.jsonDV(dt.getDataVariables()))
                ;
    }

    public static JsonArrayBuilder jsonDV(List<DataVariable> dvl) {
        JsonArrayBuilder varArr = Json.createArrayBuilder();
        if(dvl!=null){
            for (DataVariable dv: dvl){
                varArr.add(JsonPrinter.json(dv));
            }
        }
        return varArr;
    }

    // TODO: add sumstat and variable categories, check formats
    public static JsonObjectBuilder json(DataVariable dv) {
    return jsonObjectBuilder()
            .add("id", dv.getId())
            .add("name", dv.getName())
            .add("label", dv.getLabel())
            .add("weighted", dv.isWeighted())
            .add("variableIntervalType", dv.getIntervalLabel())
            .add("variableFormatType", dv.getType().name()) // varFormat
            .add("formatCategory", dv.getFormatCategory())
            .add("format", dv.getFormat())
            .add("isOrderedCategorical", dv.isOrderedCategorical())
            .add("fileOrder", dv.getFileOrder())
            .add("UNF",dv.getUnf())
            .add("fileStartPosition", dv.getFileStartPosition())
            .add("fileEndPosition", dv.getFileEndPosition())
            .add("recordSegmentNumber", dv.getRecordSegmentNumber())
            .add("numberOfDecimalPoints",dv.getNumberOfDecimalPoints())
            .add("variableMetadata",jsonVarMetadata(dv.getVariableMetadatas()))
            .add("invalidRanges", dv.getInvalidRanges().isEmpty() ? null : JsonPrinter.jsonInvalidRanges(dv.getInvalidRanges()))
            .add("summaryStatistics", dv.getSummaryStatistics().isEmpty() ? null : JsonPrinter.jsonSumStat(dv.getSummaryStatistics()))
            .add("variableCategories", dv.getCategories().isEmpty() ? null : JsonPrinter.jsonCatStat(dv.getCategories()))
            ;
    }

    private static JsonArrayBuilder jsonInvalidRanges(Collection<VariableRange> invalidRanges) {
        JsonArrayBuilder invRanges = Json.createArrayBuilder();
        JsonObjectBuilder job = Json.createObjectBuilder();
        for (VariableRange vr: invalidRanges){
            job.add("beginValue", vr.getBeginValue())
            .add("hasBeginValueType", vr.getBeginValueType()!=null)
            .add("isBeginValueTypePoint", vr.isBeginValueTypePoint())
            .add("isBeginValueTypeMin", vr.isBeginValueTypeMin())
            .add("isBeginValueTypeMinExcl", vr.isBeginValueTypeMinExcl())
            .add("isBeginValueTypeMax", vr.isBeginValueTypeMax())
            .add("isBeginValueTypeMaxExcl", vr.isBeginValueTypeMaxExcl())
            .add("endValue", vr.getEndValue())
            .add("hasEndValueType", vr.getEndValueType()!=null)
            .add("endValueTypeMax", vr.isEndValueTypeMax())
            .add("endValueTypeMaxExcl", vr.isEndValueTypeMaxExcl());

            invRanges.add(job);
        }
        return invRanges;
    }

    private static JsonObjectBuilder jsonSumStat(Collection<SummaryStatistic> sumStat){
        //JsonArrayBuilder sumStatArr = Json.createArrayBuilder();
        JsonObjectBuilder sumStatObj = Json.createObjectBuilder();
        for (SummaryStatistic stat: sumStat){
            String label = stat.getTypeLabel()==null ? "unknown":stat.getTypeLabel();
            sumStatObj.add(label, stat.getValue());
        }
        return sumStatObj;
    }


    private static JsonArrayBuilder jsonCatStat(Collection<VariableCategory> catStat){
        JsonArrayBuilder catArr = Json.createArrayBuilder();

        for (VariableCategory stat: catStat){
            JsonObjectBuilder catStatObj = Json.createObjectBuilder();
            catStatObj.add("label", stat.getLabel())
                      .add("value", stat.getValue())
                      .add("isMissing", stat.isMissing());
            if(stat.getFrequency()!=null){
                catStatObj.add("frequency", stat.getFrequency());
            }
            catArr.add(catStatObj);
        }
        return catArr;
    }

    private static JsonArrayBuilder jsonVarGroup(List<VarGroup> varGroups) {
        JsonArrayBuilder vgArr = Json.createArrayBuilder();
        for (VarGroup vg : varGroups) {
            JsonObjectBuilder vgJson = jsonObjectBuilder().add("id", vg.getId()).add("label", vg.getLabel());
            JsonArrayBuilder jab = Json.createArrayBuilder();
            for (DataVariable dvar : vg.getVarsInGroup()) {
                jab.add(dvar.getId());
            }
            vgJson.add("dataVariableIds", jab);
            vgArr.add(vgJson);
        }
        return vgArr;
    }

    private static JsonArrayBuilder jsonVarMetadata(Collection<VariableMetadata> varMetadatas) {
        JsonArrayBuilder vmArr = Json.createArrayBuilder();
        for (VariableMetadata vm : varMetadatas) {
            JsonObjectBuilder vmJson = jsonObjectBuilder()
                    .add("id", vm.getId())
                    .add("fileMetadataId", vm.getFileMetadata().getId())
                    .add("label", vm.getLabel())
                    .add("isWeightVar", vm.isIsweightvar())
                    .add("isWeighted",vm.isWeighted())
                    .add("weightVariableId", (vm.getWeightvariable()==null) ? null : vm.getWeightvariable().getId())
                    .add("literalQuestion", vm.getLiteralquestion())
                    .add("interviewInstruction", vm.getInterviewinstruction())
                    .add("postQuestion", vm.getPostquestion())
                    .add("universe", vm.getUniverse())
                    .add("notes", vm.getNotes())
                    .add("categoryMetadatas",json(vm.getCategoriesMetadata()));
            JsonArrayBuilder jab = Json.createArrayBuilder();
        }
        return vmArr;
    }

    private static JsonArrayBuilder json(Collection<CategoryMetadata> categoriesMetadata) {
        JsonArrayBuilder cmArr = Json.createArrayBuilder();
        for(CategoryMetadata cm: categoriesMetadata) {
            JsonObjectBuilder job = jsonObjectBuilder()
                    .add("wFreq", cm.getWfreq())
                    .add("categoryValue", cm.getCategory().getValue());
            cmArr.add(job);
        }
        return cmArr;
    }

    public static JsonObjectBuilder json(HarvestingClient harvestingClient) {
        if (harvestingClient == null) {
            return null;
        }

        return jsonObjectBuilder().add("nickName", harvestingClient.getName()).
                add("dataverseAlias", harvestingClient.getDataverse().getAlias()).
                add("type", harvestingClient.getHarvestType()).
                add("style", harvestingClient.getHarvestStyle()).
                add("harvestUrl", harvestingClient.getHarvestingUrl()).
                add("archiveUrl", harvestingClient.getArchiveUrl()).
                add("archiveDescription", harvestingClient.getArchiveDescription()).
                add("metadataFormat", harvestingClient.getMetadataPrefix()).
                add("set", harvestingClient.getHarvestingSet()).
                add("schedule", harvestingClient.isScheduled() ? harvestingClient.getScheduleDescription() : "none").
                add("status", harvestingClient.isHarvestingNow() ? "inProgress" : "inActive").
                add("customHeaders", harvestingClient.getCustomHttpHeaders()).
                add("allowHarvestingMissingCVV", harvestingClient.getAllowHarvestingMissingCVV()).
                add("lastHarvest", harvestingClient.getLastHarvestTime() == null ? null : harvestingClient.getLastHarvestTime().toString()).
                add("lastResult", harvestingClient.getLastResult()).
                add("lastSuccessful", harvestingClient.getLastSuccessfulHarvestTime() == null ? null : harvestingClient.getLastSuccessfulHarvestTime().toString()).
                add("lastNonEmpty", harvestingClient.getLastNonEmptyHarvestTime() == null ? null : harvestingClient.getLastNonEmptyHarvestTime().toString()).
                add("lastDatasetsHarvested", harvestingClient.getLastHarvestedDatasetCount()). // == null ? "N/A" : harvestingClient.getLastHarvestedDatasetCount().toString()).
                add("lastDatasetsDeleted", harvestingClient.getLastDeletedDatasetCount()). // == null ? "N/A" : harvestingClient.getLastDeletedDatasetCount().toString()).
                add("lastDatasetsFailed", harvestingClient.getLastFailedDatasetCount()); // == null ? "N/A" : harvestingClient.getLastFailedDatasetCount().toString());
    }

    public static String format(Date d) {
        return (d == null) ? null : Util.getDateTimeFormat().format(d);
    }

    private static JsonArrayBuilder getFileCategories(FileMetadata fmd) {
        if (fmd == null) {
            return null;
        }
        List<String> categories = fmd.getCategoriesByName();
        if (categories == null || categories.isEmpty()) {
            return null;
        }
        JsonArrayBuilder fileCategories = Json.createArrayBuilder();
        for (String category : categories) {
            fileCategories.add(category);
        }
        return fileCategories;
    }

    public static JsonArrayBuilder getTabularFileTags(DataFile df) {
        if (df == null) {
            return null;
        }
        List<DataFileTag> tags = df.getTags();
        if (tags == null || tags.isEmpty()) {
            return null;
        }
        JsonArrayBuilder tabularTags = Json.createArrayBuilder();
        for (DataFileTag tag : tags) {
            String label = tag.getTypeLabel();
            if (label != null) {
                tabularTags.add(label);
            }
        }
        return tabularTags;
    }

    private static class DatasetFieldsToJson implements DatasetFieldWalker.Listener {

        Deque<JsonObjectBuilder> objectStack = new LinkedList<>();
        Deque<JsonArrayBuilder> valueArrStack = new LinkedList<>();
        List<String> anonymizedFieldTypeNamesList = null;
        DatasetFieldsToJson(JsonArrayBuilder result) {
            valueArrStack.push(result);
        }

        DatasetFieldsToJson(JsonArrayBuilder result, List<String> anonymizedFieldTypeNamesList) {
            this(result);
            this.anonymizedFieldTypeNamesList = anonymizedFieldTypeNamesList;
        }

        @Override
        public void startField(DatasetField f) {
            objectStack.push(jsonObjectBuilder());
            // Invariant: all values are multiple. Differentiation between multiple and single is done at endField.
            valueArrStack.push(Json.createArrayBuilder());

            DatasetFieldType typ = f.getDatasetFieldType();
            objectStack.peek().add("typeName", typ.getName());
            objectStack.peek().add("multiple", typ.isAllowMultiples());
            objectStack.peek().add("typeClass", typeClassString(typ));
        }

        @Override
        public void addExpandedValuesArray(DatasetField f) {
            // Invariant: all values are multiple. Differentiation between multiple and single is done at endField.
            valueArrStack.push(Json.createArrayBuilder());
        }

        @Override
        public void endField(DatasetField f) {
            JsonObjectBuilder jsonField = objectStack.pop();
            JsonArray expandedValues = valueArrStack.pop().build();
            JsonArray jsonValues = valueArrStack.pop().build();
            if (!jsonValues.isEmpty()) {
                String datasetFieldName = f.getDatasetFieldType().getName();
                if (anonymizedFieldTypeNamesList != null && anonymizedFieldTypeNamesList.contains(datasetFieldName)) {
                    anonymizeField(jsonField);
                } else {
                    jsonField.add("value",
                            f.getDatasetFieldType().isAllowMultiples() ? jsonValues
                                    : jsonValues.get(0));
                    if (!expandedValues.isEmpty()) {
                        jsonField.add("expandedvalue",
                                f.getDatasetFieldType().isAllowMultiples() ? expandedValues
                                        : expandedValues.get(0));
                    }
                }
                valueArrStack.peek().add(jsonField);
            }
        }

        @Override
        public void externalVocabularyValue(DatasetFieldValue dsfv, JsonObject cvocEntry) {
            if (dsfv.getValue() != null) {
                if (cvocEntry.containsKey("retrieval-filtering")) {
                    JsonObject value = datasetFieldService.getExternalVocabularyValue(dsfv.getValue());
                    if (value!=null) {
                        valueArrStack.peek().add(value);
                    }
                }
            }
        }

        @Override
        public void primitiveValue(DatasetFieldValue dsfv) {
            if (dsfv.getValue() != null) {
                valueArrStack.peek().add(dsfv.getValue());
            }
        }

        @Override
        public void controlledVocabularyValue(ControlledVocabularyValue cvv) {
            valueArrStack.peek().add(cvv.getStrValue());
        }

        @Override
        public void startCompoundValue(DatasetFieldCompoundValue dsfcv) {
            valueArrStack.push(Json.createArrayBuilder());
        }

        @Override
        public void endCompoundValue(DatasetFieldCompoundValue dsfcv) {
            JsonArray jsonValues = valueArrStack.pop().build();
            if (!jsonValues.isEmpty()) {
                JsonObjectBuilder jsonField = jsonObjectBuilder();
                for (JsonObject jobj : jsonValues.getValuesAs(JsonObject.class)) {
                    jsonField.add(jobj.getString("typeName"), jobj);
                }
                valueArrStack.peek().add(jsonField);
            }
        }

        private void anonymizeField(JsonObjectBuilder jsonField) {
            jsonField.add("typeClass", "primitive");
            jsonField.add("value", BundleUtil.getStringFromBundle("dataset.anonymized.withheld"));
            jsonField.add("multiple", false);
        }
    }

    public static JsonObjectBuilder json(AuthenticationProviderRow aRow) {
        return jsonObjectBuilder()
                        .add("id", aRow.getId())
                        .add("factoryAlias", aRow.getFactoryAlias() )
                        .add("title", aRow.getTitle())
                        .add("subtitle",aRow.getSubtitle())
                        .add("factoryData", aRow.getFactoryData())
                        .add("enabled", aRow.isEnabled())
                ;
    }

    public static JsonObjectBuilder json(PrivateUrl privateUrl) {
        return jsonObjectBuilder()
                // We provide the token here as a convenience even though it is also in the role assignment.
                .add("token", privateUrl.getToken())
                .add("link", privateUrl.getLink())
                .add("roleAssignment", json(privateUrl.getRoleAssignment()));
    }

    public static JsonObjectBuilder json( ExplicitGroup eg ) {
        JsonArrayBuilder ras = Json.createArrayBuilder();
            for (String u : eg.getContainedRoleAssgineeIdentifiers()) {
                ras.add(u);
            }
            return jsonObjectBuilder()
                    .add("identifier", eg.getIdentifier())
                    .add("groupAliasInOwner", eg.getGroupAliasInOwner())
                    .add("owner", eg.getOwner().getId())
                    .add("description", eg.getDescription())
                    .add("displayName", eg.getDisplayName())
                    .add("containedRoleAssignees", ras);
    }

    public static JsonArrayBuilder jsonDataverseFacets(List<DataverseFacet> dataverseFacets) {
        JsonArrayBuilder dataverseFacetsJson = Json.createArrayBuilder();
        for(DataverseFacet facet: dataverseFacets) {
            dataverseFacetsJson.add(json(facet));
        }
        return dataverseFacetsJson;
    }

    public static JsonObjectBuilder json(DataverseFacet aFacet) {
        return jsonObjectBuilder()
                    .add("id", String.valueOf(aFacet.getId())) // TODO should just be id I think
                    .add("displayName", aFacet.getDatasetFieldType().getDisplayName())
                    .add("name", aFacet.getDatasetFieldType().getName());
    }

    public static JsonObjectBuilder json(Embargo embargo) {
        return jsonObjectBuilder().add("dateAvailable", embargo.getDateAvailable().toString()).add("reason",
                embargo.getReason());
    }

    public static JsonObjectBuilder json(Retention retention) {
        return jsonObjectBuilder().add("dateUnavailable", retention.getDateUnavailable().toString()).add("reason",
                retention.getReason());
    }

    public static JsonObjectBuilder json(License license) {
        return jsonObjectBuilder()
            .add("id", license.getId())
            .add("name", license.getName())
            .add("shortDescription", license.getShortDescription())
            .add("uri", license.getUri().toString())
            .add("iconUrl", license.getIconUrl() == null ? null : license.getIconUrl().toString())
            .add("active", license.isActive())
            .add("isDefault", license.isDefault())
            .add("sortOrder", license.getSortOrder());
    }

    public static Collector<String, JsonArrayBuilder, JsonArrayBuilder> stringsToJsonArray() {
        return new Collector<String, JsonArrayBuilder, JsonArrayBuilder>() {

            @Override
            public Supplier<JsonArrayBuilder> supplier() {
                return () -> Json.createArrayBuilder();
            }

            @Override
            public BiConsumer<JsonArrayBuilder, String> accumulator() {
                return (JsonArrayBuilder b, String s) -> b.add(s);
            }

            @Override
            public BinaryOperator<JsonArrayBuilder> combiner() {
                return (jab1, jab2) -> {
                    JsonArrayBuilder retVal = Json.createArrayBuilder();
                    jab1.build().forEach(retVal::add);
                    jab2.build().forEach(retVal::add);
                    return retVal;
                };
            }

            @Override
            public Function<JsonArrayBuilder, JsonArrayBuilder> finisher() {
                return Function.identity();
            }

            @Override
            public Set<Collector.Characteristics> characteristics() {
                return EnumSet.of(Collector.Characteristics.IDENTITY_FINISH);
            }
        };
    }

    public static JsonObjectBuilder json(Map<String, Long> map) {
        JsonObjectBuilder jsonObjectBuilder = Json.createObjectBuilder();
        for (Map.Entry<String, Long> mapEntry : map.entrySet()) {
            jsonObjectBuilder.add(mapEntry.getKey(), mapEntry.getValue());
        }
        return jsonObjectBuilder;
    }

    public static JsonObjectBuilder jsonFileCountPerAccessStatusMap(Map<FileSearchCriteria.FileAccessStatus, Long> map) {
        JsonObjectBuilder jsonObjectBuilder = Json.createObjectBuilder();
        for (Map.Entry<FileSearchCriteria.FileAccessStatus, Long> mapEntry : map.entrySet()) {
            jsonObjectBuilder.add(mapEntry.getKey().toString(), mapEntry.getValue());
        }
        return jsonObjectBuilder;
    }

    public static JsonObjectBuilder jsonFileCountPerTabularTagNameMap(Map<DataFileTag.TagType, Long> map) {
        JsonObjectBuilder jsonObjectBuilder = Json.createObjectBuilder();
        for (Map.Entry<DataFileTag.TagType, Long> mapEntry : map.entrySet()) {
            jsonObjectBuilder.add(mapEntry.getKey().toString(), mapEntry.getValue());
        }
        return jsonObjectBuilder;
    }

    public static Collector<JsonObjectBuilder, ArrayList<JsonObjectBuilder>, JsonArrayBuilder> toJsonArray() {
        return new Collector<JsonObjectBuilder, ArrayList<JsonObjectBuilder>, JsonArrayBuilder>() {

            @Override
            public Supplier<ArrayList<JsonObjectBuilder>> supplier() {
                return () -> new ArrayList<>();
            }

            @Override
            public BiConsumer<ArrayList<JsonObjectBuilder>, JsonObjectBuilder> accumulator() {
                return (t, u) ->t.add(u);
            }

            @Override
            public BinaryOperator<ArrayList<JsonObjectBuilder>> combiner() {
                return (jab1, jab2) -> {
                    jab1.addAll(jab2);
                    return jab1;
                };
            }

            @Override
            public Function<ArrayList<JsonObjectBuilder>, JsonArrayBuilder> finisher() {
                return (l) -> {
                  JsonArrayBuilder bld = Json.createArrayBuilder();
                  l.forEach( bld::add );
                  return bld;
                };
            }

            @Override
            public Set<Collector.Characteristics> characteristics() {
                return Collections.emptySet();
            }
        };
    }

    public static String getMd5IfItExists(DataFile.ChecksumType checksumType, String checksumValue) {
        if (DataFile.ChecksumType.MD5.equals(checksumType)) {
            return checksumValue;
        } else {
            return null;
        }
    }

    public static JsonObjectBuilder getChecksumTypeAndValue(DataFile.ChecksumType checksumType, String checksumValue) {
        if (checksumType != null) {
            return Json.createObjectBuilder()
                    .add("type", checksumType.toString())
                    .add("value", checksumValue);
        } else {
            return null;
        }
    }

    /**
     * Takes a map, returns a Json object for this map.
     * If map is {@code null}, returns {@code null}.
     * @param in the map to be translated
     * @return a Json Builder of the map, or {@code null}.
     */
    public static JsonObjectBuilder mapToObject(Map<String,String> in) {
        if ( in == null ) return null;
        JsonObjectBuilder b = jsonObjectBuilder();
        in.keySet().forEach( k->b.add(k, in.get(k)) );
        return b;
    }


    /**
     * Get signposting from Dataset
     * @param ds the designated Dataset
     * @return json linkset
     */
    public static JsonObjectBuilder jsonLinkset(Dataset ds) {
        return jsonObjectBuilder()
                .add("anchor", ds.getPersistentURL())
                .add("cite-as", Json.createArrayBuilder().add(jsonObjectBuilder().add("href", ds.getPersistentURL())))
                .add("type", Json.createArrayBuilder().add(jsonObjectBuilder().add("href", "https://schema.org/AboutPage")))
                .add("author", ds.getPersistentURL())
                .add("protocol", ds.getProtocol())
                .add("authority", ds.getAuthority())
                .add("publisher", BrandingUtil.getInstallationBrandName())
                .add("publicationDate", ds.getPublicationDateFormattedYYYYMMDD())
                .add("storageIdentifier", ds.getStorageIdentifier());
    }

    private static JsonObjectBuilder jsonLicense(DatasetVersion dsv) {
        JsonObjectBuilder licenseJsonObjectBuilder = jsonObjectBuilder()
                .add("name", DatasetUtil.getLicenseName(dsv))
                .add("uri", DatasetUtil.getLicenseURI(dsv));
        String licenseIconUri = DatasetUtil.getLicenseIcon(dsv);
        if (licenseIconUri != null) {
            licenseJsonObjectBuilder.add("iconUri", licenseIconUri);
        }
        return licenseJsonObjectBuilder;
    }

    public static JsonArrayBuilder jsonDataverseFieldTypeInputLevels(List<DataverseFieldTypeInputLevel> inputLevels) {
        JsonArrayBuilder jsonArrayOfInputLevels = Json.createArrayBuilder();
        for (DataverseFieldTypeInputLevel inputLevel : inputLevels) {
            NullSafeJsonBuilder inputLevelJsonObject = NullSafeJsonBuilder.jsonObjectBuilder();
            inputLevelJsonObject.add("datasetFieldTypeName", inputLevel.getDatasetFieldType().getName());
            inputLevelJsonObject.add("required", inputLevel.isRequired());
            inputLevelJsonObject.add("include", inputLevel.isInclude());
            jsonArrayOfInputLevels.add(inputLevelJsonObject);
        }
        return jsonArrayOfInputLevels;
    }

    public static JsonArrayBuilder jsonDataverseInputLevels(List<DataverseFieldTypeInputLevel> inputLevels) {
        JsonArrayBuilder inputLevelsArrayBuilder = Json.createArrayBuilder();
        for (DataverseFieldTypeInputLevel inputLevel : inputLevels) {
            inputLevelsArrayBuilder.add(jsonDataverseInputLevel(inputLevel));
        }
        return inputLevelsArrayBuilder;
    }

    private static JsonObjectBuilder jsonDataverseInputLevel(DataverseFieldTypeInputLevel inputLevel) {
        JsonObjectBuilder jsonObjectBuilder = Json.createObjectBuilder();
        jsonObjectBuilder.add("datasetFieldTypeName", inputLevel.getDatasetFieldType().getName());
        jsonObjectBuilder.add("required", inputLevel.isRequired());
        jsonObjectBuilder.add("include", inputLevel.isInclude());
        return jsonObjectBuilder;
    }
}

IQSS / dataverse / #23004

Source File Press 'n' to go to next uncovered line, 'b' for previous

Source File
Press 'n' to go to next uncovered line, 'b' for previous