org.dspace.identifier.VersionedDOIIdentifierProvider Maven / Gradle / Ivy

Go to download
Show more of this group Show more artifacts with this name
Show all versions of dspace-api Show documentation
DSpace core data model and service APIs.
The newest version!
/**
 * The contents of this file are subject to the license and copyright
 * detailed in the LICENSE and NOTICE files at the root of the source
 * tree and available online at
 *
 * http://www.dspace.org/license/
 */
package org.dspace.identifier;

import java.sql.SQLException;
import java.util.ArrayList;
import java.util.List;

import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.authorize.AuthorizeException;
import org.dspace.content.DSpaceObject;
import org.dspace.content.Item;
import org.dspace.content.MetadataValue;
import org.dspace.content.logic.Filter;
import org.dspace.core.Context;
import org.dspace.identifier.doi.DOIConnector;
import org.dspace.identifier.doi.DOIIdentifierException;
import org.dspace.services.ConfigurationService;
import org.dspace.versioning.Version;
import org.dspace.versioning.VersionHistory;
import org.dspace.versioning.service.VersionHistoryService;
import org.dspace.versioning.service.VersioningService;
import org.springframework.beans.factory.InitializingBean;
import org.springframework.beans.factory.annotation.Autowired;

/**
 * @author Marsa Haoua
 * @author Pascal-Nicolas Becker (dspace at pascal dash becker dot de)
 */
public class VersionedDOIIdentifierProvider extends DOIIdentifierProvider implements InitializingBean {
    /**
     * log4j category
     */
    private static final Logger log = LogManager.getLogger(VersionedDOIIdentifierProvider.class);

    protected DOIConnector connector;

    static final char DOT = '.';
    protected static final String pattern = "\\d+\\" + String.valueOf(DOT) + "\\d+";

    @Autowired(required = true)
    protected VersioningService versioningService;
    @Autowired(required = true)
    protected VersionHistoryService versionHistoryService;

    /**
     * After all the properties are set check that the versioning is enabled
     *
     * @throws Exception throws an exception if this isn't the case
     */
    @Override
    public void afterPropertiesSet() throws Exception {
        if (!configurationService.getBooleanProperty("versioning.enabled", true)) {
            throw new RuntimeException("the " + VersionedDOIIdentifierProvider.class.getName() +
                    " is enabled, but the versioning is disabled.");
        }
    }

    @Override
    public String mint(Context context, DSpaceObject dso) throws IdentifierException {
        return mint(context, dso, this.filter);
    }

    @Override
    public String mint(Context context, DSpaceObject dso, Filter filter)
        throws IdentifierException {
        if (!(dso instanceof Item)) {
            throw new IdentifierException("Currently only Items are supported for DOIs.");
        }
        Item item = (Item) dso;

        VersionHistory history = null;
        try {
            history = versionHistoryService.findByItem(context, item);
        } catch (SQLException ex) {
            throw new RuntimeException("A problem occurred while accessing the database.", ex);
        }

        String doi = null;
        try {
            doi = getDOIByObject(context, dso);
            if (doi != null) {
                return doi;
            }
        } catch (SQLException ex) {
            log.error("Error while attempting to retrieve information about a DOI for "
                          + contentServiceFactory.getDSpaceObjectService(dso).getTypeText(dso)
                          + " with ID " + dso.getID() + ".", ex);
            throw new RuntimeException("Error while attempting to retrieve "
                                           + "information about a DOI for "
                                           + contentServiceFactory.getDSpaceObjectService(dso).getTypeText(dso)
                                           + " with ID " + dso.getID() + ".", ex);
        }

        // Make a call to the filter here to throw an exception instead of carrying on with removal + creation
        checkMintable(context, filter, dso);

        // check whether we have a DOI in the metadata and if we have to remove it
        String metadataDOI = getDOIOutOfObject(dso);
        if (metadataDOI != null) {
            // check whether doi and version number matches
            String bareDOI = getBareDOI(metadataDOI);
            int versionNumber;
            try {
                versionNumber = versionHistoryService.getVersion(context, history, item).getVersionNumber();
            } catch (SQLException ex) {
                throw new RuntimeException(ex);
            }
            String versionedDOI = bareDOI;
            if (versionNumber > 1) {
                versionedDOI = bareDOI
                    .concat(String.valueOf(DOT))
                    .concat(String.valueOf(versionNumber));
            }
            if (!metadataDOI.equalsIgnoreCase(versionedDOI)) {
                log.debug("Will remove DOI " + metadataDOI
                              + " from item metadata, as it should become " + versionedDOI + ".");
                // remove old versioned DOIs
                try {
                    removePreviousVersionDOIsOutOfObject(context, item, metadataDOI);
                } catch (AuthorizeException ex) {
                    throw new RuntimeException(
                        "Trying to remove an old DOI from a versioned item, but wasn't authorized to.", ex);
                }
            } else {
                log.debug("DOI " + doi + " matches version number " + versionNumber + ".");
                // ensure DOI exists in our database as well and return.
                // this also checks that the doi is not assigned to another dso already.
                try {
                    loadOrCreateDOI(context, dso, versionedDOI, filter);
                } catch (SQLException ex) {
                    log.error(
                        "A problem with the database connection occurred while processing DOI " + versionedDOI + ".",
                        ex);
                    throw new RuntimeException("A problem with the database connection occurred.", ex);
                }
                return versionedDOI;
            }
        }

        try {
            if (history != null) {
                // versioning is currently supported for items only
                // if we have a history, we have a item
                doi = makeIdentifierBasedOnHistory(context, dso, history, filter);
            } else {
                doi = loadOrCreateDOI(context, dso, null, filter).getDoi();
            }
        } catch (SQLException ex) {
            log.error("SQLException while creating a new DOI: ", ex);
            throw new IdentifierException(ex);
        } catch (AuthorizeException ex) {
            log.error("AuthorizationException while creating a new DOI: ", ex);
            throw new IdentifierException(ex);
        }
        return doi.startsWith(DOI.SCHEME) ? doi : DOI.SCHEME + doi;
    }

    @Override
    public void register(Context context, DSpaceObject dso, String identifier) throws IdentifierException {
        register(context, dso, identifier, this.filter);
    }

    @Override
    public String register(Context context, DSpaceObject dso, Filter filter)
            throws IdentifierException {
        if (!(dso instanceof Item)) {
            // DOIs are currently assigned only to Items
            return null;
        }

        String doi = mint(context, dso, filter);

        register(context, dso, doi, filter);

        return doi;
    }

    @Override
    public void register(Context context, DSpaceObject dso, String identifier, Filter filter)
        throws IdentifierException {
        if (!(dso instanceof Item)) {
            throw new IdentifierException("Currently only Items are supported for DOIs.");
        }
        Item item = (Item) dso;

        if (StringUtils.isEmpty(identifier)) {
            identifier = mint(context, dso, filter);
        }
        String doiIdentifier = doiService.formatIdentifier(identifier);

        DOI doi = null;

        // search DOI in our db
        try {
            doi = loadOrCreateDOI(context, dso, doiIdentifier, filter);
        } catch (SQLException ex) {
            log.error("Error in database connection: " + ex.getMessage(), ex);
            throw new RuntimeException("Error in database connection.", ex);
        }

        if (DELETED.equals(doi.getStatus()) ||
            TO_BE_DELETED.equals(doi.getStatus())) {
            throw new DOIIdentifierException("You tried to register a DOI that "
                                                 + "is marked as DELETED.", DOIIdentifierException.DOI_IS_DELETED);
        }

        // Check status of DOI
        if (IS_REGISTERED.equals(doi.getStatus())) {
            return;
        }

        String metadataDOI = getDOIOutOfObject(dso);
        if (!StringUtils.isEmpty(metadataDOI)
            && !metadataDOI.equalsIgnoreCase(doiIdentifier)) {
            // remove doi of older version from the metadata
            try {
                removePreviousVersionDOIsOutOfObject(context, item, metadataDOI);
            } catch (AuthorizeException ex) {
                throw new RuntimeException(
                    "Trying to remove an old DOI from a versioned item, but wasn't authorized to.", ex);
            }
        }

        // change status of DOI
        doi.setStatus(TO_BE_REGISTERED);
        try {
            doiService.update(context, doi);
        } catch (SQLException ex) {
            log.warn("SQLException while changing status of DOI {} to be registered.", ex);
            throw new RuntimeException(ex);
        }
    }

    protected String getBareDOI(String identifier)
        throws DOIIdentifierException {
        doiService.formatIdentifier(identifier);
        String doiPrefix = DOI.SCHEME.concat(getPrefix())
                                     .concat(String.valueOf(SLASH))
                                     .concat(getNamespaceSeparator());
        String doiPostfix = identifier.substring(doiPrefix.length());
        if (doiPostfix.matches(pattern) && doiPostfix.lastIndexOf(DOT) != -1) {
            return doiPrefix.concat(doiPostfix.substring(0, doiPostfix.lastIndexOf(DOT)));
        }
        // if the pattern does not match, we are already working on a bare handle.
        return identifier;
    }

    protected String getDOIPostfix(String identifier)
        throws DOIIdentifierException {

        String doiPrefix = DOI.SCHEME.concat(getPrefix()).concat(String.valueOf(SLASH)).concat(getNamespaceSeparator());
        String doiPostfix = null;
        if (null != identifier) {
            doiPostfix = identifier.substring(doiPrefix.length());
        }
        return doiPostfix;
    }

    protected String makeIdentifierBasedOnHistory(Context context, DSpaceObject dso, VersionHistory history)
            throws AuthorizeException, SQLException, DOIIdentifierException, IdentifierNotApplicableException {
        return makeIdentifierBasedOnHistory(context, dso, history, this.filter);
    }

    // Should never return null!
    protected String makeIdentifierBasedOnHistory(Context context, DSpaceObject dso, VersionHistory history,
                                                  Filter filter)
        throws AuthorizeException, SQLException, DOIIdentifierException, IdentifierNotApplicableException {
        // Mint foreach new version an identifier like: 12345/100.versionNumber
        // use the bare handle (g.e. 12345/100) for the first version.

        // currently versioning is supported for items only
        if (!(dso instanceof Item)) {
            throw new IllegalArgumentException(
                "Cannot create versioned handle for objects other then item: Currently versioning supports items only" +
                    ".");
        }
        Item item = (Item) dso;
        Version version = versionHistoryService.getVersion(context, history, item);

        String previousVersionDOI = null;
        for (Version v : versioningService.getVersionsByHistory(context, history)) {
            previousVersionDOI = getDOIByObject(context, v.getItem());
            if (null != previousVersionDOI) {
                break;
            }
        }

        if (previousVersionDOI == null) {
            // Before continuing with any new DOI creation, apply the filter
            checkMintable(context, filter, dso);

            // We need to generate a new DOI.
            DOI doi = doiService.create(context);

            // as we reuse the DOI ID, we do not have to check whether the DOI exists already.
            String identifier = this.getPrefix() + "/" + this.getNamespaceSeparator() +
                doi.getID().toString();

            if (version.getVersionNumber() > 1) {
                identifier = identifier.concat(String.valueOf(DOT).concat(String.valueOf(version.getVersionNumber())));
            }

            doi.setDoi(identifier);
            doi.setDSpaceObject(dso);
            doi.setStatus(null);
            doiService.update(context, doi);
            return doi.getDoi();
        }

        String identifier = getBareDOI(previousVersionDOI);

        if (version.getVersionNumber() > 1) {
            identifier = identifier.concat(String.valueOf(DOT)).concat(
                String.valueOf(versionHistoryService.getVersion(context, history, item).getVersionNumber()));
        }

        loadOrCreateDOI(context, dso, identifier, filter);
        return identifier;
    }

    void removePreviousVersionDOIsOutOfObject(Context c, Item item, String oldDoi)
        throws IdentifierException, AuthorizeException {
        if (StringUtils.isEmpty(oldDoi)) {
            throw new IllegalArgumentException("Old DOI must be neither empty nor null!");
        }

        String bareDoi = getBareDOI(doiService.formatIdentifier(oldDoi));
        String bareDoiRef = doiService.DOIToExternalForm(bareDoi);

        List identifiers = itemService
            .getMetadata(item, MD_SCHEMA, DOI_ELEMENT, DOI_QUALIFIER, Item.ANY);
        // We have to remove all DOIs referencing previous versions. To do that,
        // we store all identifiers we do not know in an array list, clear
        // dc.identifier.uri and add the safed identifiers.
        // The list of identifiers to safe won't get larger then the number of
        // existing identifiers.
        ArrayList newIdentifiers = new ArrayList<>(identifiers.size());
        boolean changed = false;
        for (MetadataValue identifier : identifiers) {
            if (!StringUtils.startsWithIgnoreCase(identifier.getValue(), bareDoiRef)) {
                newIdentifiers.add(identifier.getValue());
            } else {
                changed = true;
            }
        }
        // reset the metadata if necessary.
        if (changed) {
            try {
                itemService.clearMetadata(c, item, MD_SCHEMA, DOI_ELEMENT, DOI_QUALIFIER, Item.ANY);
                // Checks if Array newIdentifiers is empty to avoid adding null values to the metadata field.
                if (!newIdentifiers.isEmpty()) {
                    itemService.addMetadata(c, item, MD_SCHEMA, DOI_ELEMENT, DOI_QUALIFIER, null, newIdentifiers);
                }
                itemService.update(c, item);
            } catch (SQLException ex) {
                throw new RuntimeException("A problem with the database connection occurred.", ex);
            }
        }
    }

    @Override
    @Autowired(required = true)
    public void setDOIConnector(DOIConnector connector) {
        super.setDOIConnector(connector);
        this.connector = connector;
    }

    @Override
    @Autowired(required = true)
    public void setConfigurationService(ConfigurationService configurationService) {
        super.setConfigurationService(configurationService);
        this.configurationService = configurationService;
    }

}