Java tutorial
package org.gbif.registry.ws.util; import org.gbif.api.model.common.DOI; import org.gbif.api.model.common.User; import org.gbif.api.model.occurrence.Download; import org.gbif.api.model.registry.Dataset; import org.gbif.api.model.registry.DatasetOccurrenceDownloadUsage; import org.gbif.api.model.registry.Organization; import org.gbif.api.model.registry.eml.KeywordCollection; import org.gbif.api.model.registry.eml.geospatial.GeospatialCoverage; import org.gbif.api.vocabulary.IdentifierType; import org.gbif.api.vocabulary.Language; import org.gbif.doi.metadata.datacite.DataCiteMetadata; import org.gbif.doi.metadata.datacite.DateType; import org.gbif.doi.metadata.datacite.DescriptionType; import org.gbif.doi.metadata.datacite.RelatedIdentifierType; import org.gbif.doi.metadata.datacite.RelationType; import org.gbif.doi.metadata.datacite.ResourceType; import org.gbif.doi.service.InvalidMetadataException; import org.gbif.doi.service.datacite.DataCiteValidator; import org.gbif.occurrence.query.HumanFilterBuilder; import org.gbif.occurrence.query.TitleLookup; import java.net.URI; import java.util.Calendar; import java.util.Date; import java.util.GregorianCalendar; import java.util.List; import java.util.Set; import javax.xml.bind.JAXBException; import com.beust.jcommander.internal.Sets; import com.google.common.annotations.VisibleForTesting; import com.google.common.base.Joiner; import com.google.common.base.Preconditions; import com.google.common.base.Strings; import org.apache.commons.lang.time.DateFormatUtils; import org.apache.commons.lang3.StringUtils; import org.slf4j.Logger; import org.slf4j.LoggerFactory; public class DataCiteConverter { private static final Logger LOG = LoggerFactory.getLogger(DataCiteConverter.class); private static final String DOWNLOAD_TITLE = "GBIF Occurrence Download"; private static final String GBIF_PUBLISHER = "The Global Biodiversity Information Facility"; private static final String RIGHTS = "The data included in this download are provided to the user under a Creative Commons BY-NC 4.0 license which means that you are free to use, share, and adapt the data provided that you give reasonable and appropriate credit (attribution) and that you do not use the material for commercial purposes (non-commercial).\n\nData from some individual datasets included in this download may be licensed under less restrictive terms; review the details below."; private static final String RIGHTS_URL = "http://creativecommons.org/licenses/by-nc/4.0"; private static final String ENGLISH = Language.ENGLISH.getIso3LetterCode(); private static final String DWAC_FORMAT = "Darwin Core Archive"; private static String fdate(Date date) { return DateFormatUtils.ISO_DATE_FORMAT.format(date); } /** * Convert a dataset and publisher object into a datacite metadata instance. * DataCite requires at least the following properties: * <ul> * <li>Identifier</li> * <li>Creator</li> * <li>Title</li> * <li>Publisher</li> * <li>PublicationYear</li> * </ul> * * As the publicationYear property is often not available from newly created datasets, this converter uses the current * year as the default in case no created timestamp or pubdate exists. */ public static DataCiteMetadata convert(Dataset d, Organization publisher) { // always add required metadata DataCiteMetadata.Builder<java.lang.Void> b = DataCiteMetadata.builder().withTitles() .withTitle(DataCiteMetadata.Titles.Title.builder().withValue(d.getTitle()).build()).end() .withPublisher(publisher.getTitle()) // default to this year, e.g. when creating new datasets. This field is required! .withPublicationYear(getYear(new Date())).withResourceType() .withResourceTypeGeneral(ResourceType.DATASET).withValue(d.getType().name()).end().withCreators() .addCreator().withCreatorName(publisher.getTitle()).withNameIdentifier() .withValue(publisher.getKey().toString()).withSchemeURI("gbif.org").withNameIdentifierScheme("GBIF") .end().end().end().withRelatedIdentifiers().end(); if (d.getCreated() != null) { b.withPublicationYear(getYear(d.getModified())).withDates().addDate().withDateType(DateType.CREATED) .withValue(fdate(d.getCreated())).end().addDate().withDateType(DateType.UPDATED) .withValue(fdate(d.getModified())).end().end().withCreators().addCreator() .withCreatorName(d.getCreatedBy()).withNameIdentifier().withValue(d.getCreatedBy()) .withSchemeURI("gbif.org").withNameIdentifierScheme("GBIF").end().end().end(); } if (d.getPubDate() != null) { // use pub date for publication year if it exists b.withPublicationYear(getYear(d.getPubDate())); } if (d.getModified() != null) { b.withDates().addDate().withDateType(DateType.UPDATED).withValue(fdate(d.getModified())); } if (d.getDoi() != null) { b.withIdentifier().withIdentifierType(IdentifierType.DOI.name()).withValue(d.getDoi().getDoiName()); if (d.getKey() != null) { b.withAlternateIdentifiers().addAlternateIdentifier().withAlternateIdentifierType("UUID") .withValue(d.getKey().toString()); } } else if (d.getKey() != null) { b.withIdentifier().withIdentifierType("UUID").withValue(d.getKey().toString()); } if (!Strings.isNullOrEmpty(d.getDescription())) { b.withDescriptions().addDescription().addContent(d.getDescription()) .withDescriptionType(DescriptionType.ABSTRACT); } if (d.getDataLanguage() != null) { b.withLanguage(d.getDataLanguage().getIso3LetterCode()); } if (!Strings.isNullOrEmpty(d.getRights())) { b.withRightsList().addRights().withValue(d.getRights()).end(); } Set<DataCiteMetadata.Subjects.Subject> subjects = Sets.newHashSet(); for (KeywordCollection kcol : d.getKeywordCollections()) { for (String k : kcol.getKeywords()) { if (!Strings.isNullOrEmpty(k)) { DataCiteMetadata.Subjects.Subject s = DataCiteMetadata.Subjects.Subject.builder().withValue(k) .build(); if (!Strings.isNullOrEmpty(kcol.getThesaurus())) { s.setSubjectScheme(kcol.getThesaurus()); } subjects.add(s); } } } for (GeospatialCoverage gc : d.getGeographicCoverages()) { if (gc.getBoundingBox() != null) { b.withGeoLocations().addGeoLocation().addGeoLocationBox(gc.getBoundingBox().getMinLatitude(), gc.getBoundingBox().getMinLongitude(), gc.getBoundingBox().getMaxLatitude(), gc.getBoundingBox().getMaxLongitude()); } } return b.build(); } public static String truncateDescription(DOI doi, String xml, URI target) throws InvalidMetadataException { try { DataCiteMetadata dm = DataCiteValidator.fromXml(xml); String description = Joiner.on("\n").join(dm.getDescriptions().getDescription().get(0).getContent()); dm.setDescriptions(DataCiteMetadata.Descriptions.builder().addDescription() .withDescriptionType(DescriptionType.ABSTRACT).withLang(ENGLISH) .addContent(StringUtils.substringBefore(description, "constituent datasets:") + String.format("constituent datasets:\nPlease see %s for full list.", target)) .end().build()); return DataCiteValidator.toXml(doi, dm); } catch (JAXBException e) { throw new InvalidMetadataException("Failed to deserialize datacite xml for DOI " + doi, e); } } @VisibleForTesting protected static String getYear(Date date) { if (date == null) { return null; } Calendar cal = new GregorianCalendar(); cal.setTime(date); return String.valueOf(cal.get(Calendar.YEAR)); } /** * Convert a download and its dataset usages into a datacite metadata instance. */ public static DataCiteMetadata convert(Download d, User creator, List<DatasetOccurrenceDownloadUsage> usedDatasets, TitleLookup titleLookup) { Preconditions.checkNotNull(d.getDoi(), "Download DOI required to build valid DOI metadata"); Preconditions.checkNotNull(d.getCreated(), "Download created date required to build valid DOI metadata"); Preconditions.checkNotNull(creator, "Download creator required to build valid DOI metadata"); Preconditions.checkNotNull(d.getRequest(), "Download request required to build valid DOI metadata"); // always add required metadata DataCiteMetadata.Builder<java.lang.Void> b = DataCiteMetadata.builder().withIdentifier() .withIdentifierType(IdentifierType.DOI.name()).withValue(d.getDoi().getDoiName()).end().withTitles() .withTitle(DataCiteMetadata.Titles.Title.builder().withValue(DOWNLOAD_TITLE).build()).end() .withSubjects().addSubject().withValue("GBIF").withLang(ENGLISH).end().addSubject() .withValue("biodiversity").withLang(ENGLISH).end().addSubject().withValue("species occurrences") .withLang(ENGLISH).end().end().withCreators().addCreator().withCreatorName(creator.getName()).end() .end().withPublisher(GBIF_PUBLISHER).withPublicationYear(getYear(d.getCreated())).withResourceType() .withResourceTypeGeneral(ResourceType.DATASET).end().withAlternateIdentifiers() .addAlternateIdentifier().withAlternateIdentifierType("GBIF").withValue(d.getKey()).end().end() .withDates().addDate().withDateType(DateType.CREATED).withValue(fdate(d.getCreated())).end() .addDate().withDateType(DateType.UPDATED).withValue(fdate(d.getModified())).end().end() .withFormats().addFormat(DWAC_FORMAT).end().withSizes().addSize(Long.toString(d.getSize())).end() .withRightsList().addRights(DataCiteMetadata.RightsList.Rights.builder().withValue(RIGHTS) .withRightsURI(RIGHTS_URL).build()) .end(); String query = new HumanFilterBuilder(titleLookup).humanFilterString(d.getRequest().getPredicate()); final DataCiteMetadata.Descriptions.Description.Builder db = b.withDescriptions().addDescription() .withDescriptionType(DescriptionType.ABSTRACT).withLang(ENGLISH) .addContent(String.format( "A dataset containing %s species occurrences available in GBIF matching the query: %s.", d.getTotalRecords(), query)) .addContent(String.format("The dataset includes %s records from %s constituent datasets:", d.getTotalRecords(), d.getNumberDatasets())); if (!usedDatasets.isEmpty()) { final DataCiteMetadata.RelatedIdentifiers.Builder<?> relBuilder = b.withRelatedIdentifiers(); for (DatasetOccurrenceDownloadUsage du : usedDatasets) { if (du.getDatasetDOI() != null) { relBuilder.addRelatedIdentifier().withRelationType(RelationType.REFERENCES) .withValue(du.getDatasetDOI().getDoiName()) .withRelatedIdentifierType(RelatedIdentifierType.DOI).end(); } if (!Strings.isNullOrEmpty(du.getDatasetTitle())) { db.addContent("\n " + du.getNumberRecords() + " records from " + du.getDatasetTitle() + "."); } } } return b.build(); } }