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33abc10c11
DS-2119. EZID IdentifierProvider Metadata Mapping. In the interest of time, merging this despite a problem with the transform, for which I already have a solution. A separate PR will provide that solution.
667 lines
22 KiB
Java
667 lines
22 KiB
Java
/**
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* The contents of this file are subject to the license and copyright
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* detailed in the LICENSE and NOTICE files at the root of the source
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* tree and available online at
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*
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* http://www.dspace.org/license/
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*/
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package org.dspace.identifier;
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import java.io.IOException;
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import java.net.*;
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import java.sql.SQLException;
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import java.util.ArrayList;
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import java.util.Calendar;
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import java.util.HashMap;
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import java.util.List;
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import java.util.Map;
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import java.util.Map.Entry;
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import org.dspace.authorize.AuthorizeException;
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import org.dspace.content.Metadatum;
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import org.dspace.content.DSpaceObject;
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import org.dspace.content.Item;
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import org.dspace.content.ItemIterator;
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import org.dspace.core.Context;
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import org.dspace.identifier.ezid.EZIDRequest;
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import org.dspace.identifier.ezid.EZIDRequestFactory;
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import org.dspace.identifier.ezid.EZIDResponse;
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import org.dspace.identifier.ezid.Transform;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import org.springframework.beans.factory.annotation.Required;
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/**
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* Provide service for DOIs through DataCite using the EZID service.
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*
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* <p>Configuration of this class is is in two parts.</p>
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*
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* <p>Installation-specific configuration (credentials and the "shoulder" value
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* which forms a prefix of the site's DOIs) is supplied from property files in
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* [DSpace]/config**.</p>
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*
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* <dl>
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* <dt>identifier.doi.ezid.shoulder</dt>
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* <dd>base of the site's DOIs. Example: 10.5072/FK2</dd>
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* <dt>identifier.doi.ezid.user</dt>
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* <dd>EZID username.</dd>
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* <dt>identifier.doi.ezid.password</dt>
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* <dd>EZID password.</dd>
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* <dt>identifier.doi.ezid.publisher</dt>
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* <dd>A default publisher, for Items not previously published. EZID requires a publisher.</dd>
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* </dl>
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*
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* <p>Then there are properties injected using Spring:</p>
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* <ul>
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* <li>There is a Map (with the property name "crosswalk") from EZID metadata
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* field names into DSpace field names, injected by Spring. Specify the
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* fully-qualified names of all metadata fields to be looked up on a DSpace
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* object and their values set on mapped fully-qualified names in the object's
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* DataCite metadata.</li>
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*
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* <li>A second map ("crosswalkTransform") provides Transform instances mapped
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* from EZID metadata field names. This allows the crosswalk to rewrite field
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* values where the form maintained by DSpace is not directly usable in EZID
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* metadata.</li>
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*
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* <li>Optional: A boolean property ("generateDataciteXML") that controls the
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* creation and inclusion of DataCite xml schema during the metadata
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* crosswalking. The default "DataCite" dissemination plugin uses
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* DIM2DataCite.xsl for crosswalking. Default value: false.</li>
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*
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* <li>Optional: A string property ("disseminationCrosswalkName") that can be
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* used to set the name of the dissemination crosswalk plugin for metadata
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* crosswalking. Default value: "DataCite".</li>
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* </ul>
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*
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* @author mwood
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*/
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public class EZIDIdentifierProvider
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extends IdentifierProvider
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{
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private static final Logger log = LoggerFactory.getLogger(EZIDIdentifierProvider.class);
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// Configuration property names
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static final String CFG_SHOULDER = "identifier.doi.ezid.shoulder";
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static final String CFG_USER = "identifier.doi.ezid.user";
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static final String CFG_PASSWORD = "identifier.doi.ezid.password";
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static final String CFG_PUBLISHER = "identifier.doi.ezid.publisher";
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// DataCite metadata field names
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static final String DATACITE_PUBLISHER = "datacite.publisher";
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static final String DATACITE_PUBLICATION_YEAR = "datacite.publicationyear";
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// DSpace metadata field name elements
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// XXX move these to MetadataSchema or some such
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public static final String MD_SCHEMA = "dc";
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public static final String DOI_ELEMENT = "identifier";
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public static final String DOI_QUALIFIER = null;
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private static final String DOI_SCHEME = "doi:";
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protected boolean GENERATE_DATACITE_XML = false;
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protected String DATACITE_XML_CROSSWALK = "DataCite";
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/** Map DataCite metadata into local metadata. */
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private static Map<String, String> crosswalk = new HashMap<>();
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/** Converters to be applied to specific fields. */
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private static Map<String, Transform> transforms = new HashMap<>();
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/** Factory for EZID requests. */
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private static EZIDRequestFactory requestFactory;
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@Override
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public boolean supports(Class<? extends Identifier> identifier)
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{
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return DOI.class.isAssignableFrom(identifier);
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}
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@Override
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public boolean supports(String identifier)
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{
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if (null == identifier)
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{
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return false;
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}
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else
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{
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return identifier.startsWith(DOI_SCHEME);
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} // XXX more thorough test?
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}
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@Override
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public String register(Context context, DSpaceObject dso)
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throws IdentifierException
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{
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log.debug("register {}", dso);
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Metadatum[] identifiers = dso.getMetadata(MD_SCHEMA, DOI_ELEMENT, DOI_QUALIFIER, null);
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for (Metadatum identifier : identifiers)
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{
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if ((null != identifier.value) && (identifier.value.startsWith(DOI_SCHEME)))
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{
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return identifier.value;
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}
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}
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String id = mint(context, dso);
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dso.addMetadata(MD_SCHEMA, DOI_ELEMENT, DOI_QUALIFIER, null, id);
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try {
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dso.update();
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context.commit();
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} catch (SQLException | AuthorizeException ex) {
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throw new IdentifierException("New identifier not stored", ex);
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}
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log.info("Registered {}", id);
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return id;
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}
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@Override
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public void register(Context context, DSpaceObject object, String identifier)
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{
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log.debug("register {} as {}", object, identifier);
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EZIDResponse response;
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try {
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EZIDRequest request = requestFactory.getInstance(loadAuthority(),
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loadUser(), loadPassword());
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response = request.create(identifier, crosswalkMetadata(object));
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} catch (IdentifierException | IOException | URISyntaxException e) {
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log.error("Identifier '{}' not registered: {}", identifier, e.getMessage());
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return;
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}
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if (response.isSuccess())
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{
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try {
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object.addMetadata(MD_SCHEMA, DOI_ELEMENT, DOI_QUALIFIER, null,
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idToDOI(identifier));
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object.update();
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context.commit();
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log.info("registered {}", identifier);
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} catch (SQLException | AuthorizeException | IdentifierException ex) {
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// TODO throw new IdentifierException("New identifier not stored", ex);
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log.error("New identifier not stored", ex);
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}
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}
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else
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{
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log.error("Identifier '{}' not registered -- EZID returned: {}",
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identifier, response.getEZIDStatusValue());
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}
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}
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@Override
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public void reserve(Context context, DSpaceObject dso, String identifier)
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throws IdentifierException
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{
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log.debug("reserve {}", identifier);
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EZIDResponse response;
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try {
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EZIDRequest request = requestFactory.getInstance(loadAuthority(),
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loadUser(), loadPassword());
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Map<String, String> metadata = crosswalkMetadata(dso);
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metadata.put("_status", "reserved");
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response = request.create(identifier, metadata);
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} catch (IOException | URISyntaxException e) {
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log.error("Identifier '{}' not registered: {}", identifier, e.getMessage());
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return;
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}
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if (response.isSuccess())
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{
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dso.addMetadata(MD_SCHEMA, DOI_ELEMENT, DOI_QUALIFIER, null, idToDOI(identifier));
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try {
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dso.update();
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context.commit();
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log.info("reserved {}", identifier);
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} catch (SQLException | AuthorizeException ex) {
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throw new IdentifierException("New identifier not stored", ex);
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}
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}
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else
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{
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log.error("Identifier '{}' not registered -- EZID returned: {}",
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identifier, response.getEZIDStatusValue());
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}
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}
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@Override
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public String mint(Context context, DSpaceObject dso)
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throws IdentifierException
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{
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log.debug("mint for {}", dso);
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// Compose the request
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EZIDRequest request;
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try {
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request = requestFactory.getInstance(loadAuthority(), loadUser(), loadPassword());
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} catch (URISyntaxException ex) {
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log.error(ex.getMessage());
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throw new IdentifierException("DOI request not sent: " + ex.getMessage());
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}
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// Send the request
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EZIDResponse response;
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try
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{
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response = request.mint(crosswalkMetadata(dso));
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} catch (IOException | URISyntaxException ex) {
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log.error("Failed to send EZID request: {}", ex.getMessage());
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throw new IdentifierException("DOI request not sent: " + ex.getMessage());
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}
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// Good response?
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if (HttpURLConnection.HTTP_CREATED != response.getHttpStatusCode())
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{
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log.error("EZID server responded: {} {}: {}",
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new String[] {
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String.valueOf(response.getHttpStatusCode()),
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response.getHttpReasonPhrase(),
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response.getEZIDStatusValue()
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});
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throw new IdentifierException("DOI not created: "
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+ response.getHttpReasonPhrase()
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+ ": "
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+ response.getEZIDStatusValue());
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}
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// Extract the DOI from the content blob
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if (response.isSuccess())
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{
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String value = response.getEZIDStatusValue();
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int end = value.indexOf('|'); // Following pipe is "shadow ARK"
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if (end < 0)
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{
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end = value.length();
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}
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String doi = value.substring(0, end).trim();
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log.info("Created {}", doi);
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return doi;
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}
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else
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{
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log.error("EZID responded: {}", response.getEZIDStatusValue());
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throw new IdentifierException("No DOI returned");
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}
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}
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@Override
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public DSpaceObject resolve(Context context, String identifier,
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String... attributes)
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throws IdentifierNotFoundException, IdentifierNotResolvableException
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{
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log.debug("resolve {}", identifier);
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ItemIterator found;
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try {
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found = Item.findByMetadataField(context,
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MD_SCHEMA, DOI_ELEMENT, DOI_QUALIFIER,
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idToDOI(identifier));
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} catch (IdentifierException | SQLException | AuthorizeException | IOException ex) {
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log.error(ex.getMessage());
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throw new IdentifierNotResolvableException(ex);
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}
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try {
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if (!found.hasNext())
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{
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throw new IdentifierNotFoundException("No object bound to " + identifier);
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}
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Item found1 = found.next();
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if (found.hasNext())
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{
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log.error("More than one object bound to {}!", identifier);
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}
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log.debug("Resolved to {}", found1);
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return found1;
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} catch (SQLException ex) {
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log.error(ex.getMessage());
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throw new IdentifierNotResolvableException(ex);
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}
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}
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@Override
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public String lookup(Context context, DSpaceObject object)
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throws IdentifierNotFoundException, IdentifierNotResolvableException
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{
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log.debug("lookup {}", object);
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Metadatum found = null;
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for (Metadatum candidate : object.getMetadata(MD_SCHEMA, DOI_ELEMENT, DOI_QUALIFIER, null))
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{
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if (candidate.value.startsWith(DOI_SCHEME))
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{
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found = candidate;
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break;
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}
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}
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if (null != found)
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{
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log.debug("Found {}", found.value);
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return found.value;
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}
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else
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{
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throw new IdentifierNotFoundException(object.getTypeText() + " "
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+ object.getID() + " has no DOI");
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}
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}
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@Override
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public void delete(Context context, DSpaceObject dso)
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throws IdentifierException
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{
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log.debug("delete {}", dso);
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// delete from EZID
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Metadatum[] metadata = dso.getMetadata(MD_SCHEMA, DOI_ELEMENT, DOI_QUALIFIER, null);
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List<String> remainder = new ArrayList<>();
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int skipped = 0;
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for (Metadatum id : metadata)
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{
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if (!id.value.startsWith(DOI_SCHEME))
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{
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remainder.add(id.value);
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continue;
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}
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EZIDResponse response;
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try {
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EZIDRequest request = requestFactory.getInstance(loadAuthority(),
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loadUser(), loadPassword());
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response = request.delete(DOIToId(id.value));
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} catch (URISyntaxException e) {
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log.error("Bad URI in metadata value: {}", e.getMessage());
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remainder.add(id.value);
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skipped++;
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continue;
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} catch (IOException e) {
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log.error("Failed request to EZID: {}", e.getMessage());
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remainder.add(id.value);
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skipped++;
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continue;
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}
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if (!response.isSuccess())
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{
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log.error("Unable to delete {} from DataCite: {}", id.value,
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response.getEZIDStatusValue());
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remainder.add(id.value);
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skipped++;
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continue;
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}
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log.info("Deleted {}", id.value);
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}
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// delete from item
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dso.clearMetadata(MD_SCHEMA, DOI_ELEMENT, DOI_QUALIFIER, null);
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dso.addMetadata(MD_SCHEMA, DOI_ELEMENT, DOI_QUALIFIER, null,
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remainder.toArray(new String[remainder.size()]));
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try {
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dso.update();
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context.commit();
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} catch (SQLException | AuthorizeException e) {
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log.error("Failed to re-add identifiers: {}", e.getMessage());
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}
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if (skipped > 0)
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{
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throw new IdentifierException(skipped + " identifiers could not be deleted.");
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}
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}
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@Override
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public void delete(Context context, DSpaceObject dso, String identifier)
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throws IdentifierException
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{
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log.debug("delete {} from {}", identifier, dso);
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Metadatum[] metadata = dso.getMetadata(MD_SCHEMA, DOI_ELEMENT, DOI_QUALIFIER, null);
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List<String> remainder = new ArrayList<>();
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int skipped = 0;
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for (Metadatum id : metadata)
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{
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if (!id.value.equals(idToDOI(identifier)))
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{
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remainder.add(id.value);
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continue;
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}
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EZIDResponse response;
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try {
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EZIDRequest request = requestFactory.getInstance(loadAuthority(),
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loadUser(), loadPassword());
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response = request.delete(DOIToId(id.value));
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} catch (URISyntaxException e) {
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log.error("Bad URI in metadata value {}: {}", id.value, e.getMessage());
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remainder.add(id.value);
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skipped++;
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continue;
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} catch (IOException e) {
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log.error("Failed request to EZID: {}", e.getMessage());
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remainder.add(id.value);
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skipped++;
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continue;
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}
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if (!response.isSuccess())
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{
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log.error("Unable to delete {} from DataCite: {}", id.value,
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response.getEZIDStatusValue());
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remainder.add(id.value);
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skipped++;
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continue;
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}
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log.info("Deleted {}", id.value);
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}
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// delete from item
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dso.clearMetadata(MD_SCHEMA, DOI_ELEMENT, DOI_QUALIFIER, null);
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dso.addMetadata(MD_SCHEMA, DOI_ELEMENT, DOI_QUALIFIER, null,
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remainder.toArray(new String[remainder.size()]));
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try {
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dso.update();
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context.commit();
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} catch (SQLException | AuthorizeException e) {
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log.error("Failed to re-add identifiers: {}", e.getMessage());
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}
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if (skipped > 0)
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{
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throw new IdentifierException(identifier + " could not be deleted.");
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}
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}
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/**
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* Format a naked identifier as a DOI with our configured authority prefix.
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*
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* @throws IdentifierException if authority prefix is not configured.
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*/
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String idToDOI(String id)
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throws IdentifierException
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{
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return "doi:" + loadAuthority() + id;
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}
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/**
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* Remove scheme and our configured authority prefix from a doi: URI string.
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* @return naked local identifier.
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* @throws IdentifierException if authority prefix is not configured.
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*/
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String DOIToId(String DOI)
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throws IdentifierException
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{
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String prefix = "doi:" + loadAuthority();
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if (DOI.startsWith(prefix))
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{
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return DOI.substring(prefix.length());
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}
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else
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{
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return DOI;
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}
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}
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/**
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* Get configured value of EZID username.
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* @throws IdentifierException
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*/
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private String loadUser()
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throws IdentifierException
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{
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String user = configurationService.getProperty(CFG_USER);
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if (null != user)
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{
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return user;
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}
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else
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{
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throw new IdentifierException("Unconfigured: define " + CFG_USER);
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}
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}
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/**
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* Get configured value of EZID password.
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* @throws IdentifierException
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*/
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private String loadPassword()
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throws IdentifierException
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{
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String password = configurationService.getProperty(CFG_PASSWORD);
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if (null != password)
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{
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return password;
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}
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else
|
|
{
|
|
throw new IdentifierException("Unconfigured: define " + CFG_PASSWORD);
|
|
}
|
|
}
|
|
|
|
/**
|
|
* Get configured value of EZID "shoulder".
|
|
* @throws IdentifierException
|
|
*/
|
|
private String loadAuthority()
|
|
throws IdentifierException
|
|
{
|
|
String shoulder = configurationService.getProperty(CFG_SHOULDER);
|
|
if (null != shoulder)
|
|
{
|
|
return shoulder;
|
|
}
|
|
else
|
|
{
|
|
throw new IdentifierException("Unconfigured: define " + CFG_SHOULDER);
|
|
}
|
|
}
|
|
|
|
/**
|
|
* Map selected DSpace metadata to fields recognized by DataCite.
|
|
*/
|
|
private Map<String, String> crosswalkMetadata(DSpaceObject dso)
|
|
{
|
|
if ((null == dso) || !(dso instanceof Item))
|
|
{
|
|
throw new IllegalArgumentException("Must be an Item");
|
|
}
|
|
Item item = (Item) dso; // TODO generalize to DSO when all DSOs have metadata.
|
|
|
|
Map<String, String> mapped = new HashMap<>();
|
|
|
|
for (Entry<String, String> datum : crosswalk.entrySet())
|
|
{
|
|
Metadatum[] values = item.getMetadataByMetadataString(datum.getValue());
|
|
if (null != values)
|
|
{
|
|
for (Metadatum value : values)
|
|
{
|
|
String key = datum.getKey();
|
|
String mappedValue;
|
|
Transform xfrm = transforms.get(key);
|
|
if (null != xfrm)
|
|
{
|
|
try {
|
|
mappedValue = xfrm.transform(value.value);
|
|
} catch (Exception ex) {
|
|
log.error("Unable to transform '{}' from {} to {}: {}",
|
|
new String[] {
|
|
value.value,
|
|
value.toString(),
|
|
key,
|
|
ex.getMessage()
|
|
});
|
|
continue;
|
|
}
|
|
}
|
|
else
|
|
{
|
|
mappedValue = value.value;
|
|
}
|
|
mapped.put(key, mappedValue);
|
|
}
|
|
}
|
|
}
|
|
|
|
if (GENERATE_DATACITE_XML == true)
|
|
{
|
|
DataCiteXMLCreator xmlGen = new DataCiteXMLCreator();
|
|
xmlGen.setDisseminationCrosswalkName(DATACITE_XML_CROSSWALK);
|
|
String xmlString = xmlGen.getXMLString(dso);
|
|
mapped.put("datacite", xmlString);
|
|
}
|
|
|
|
// Supply a default publisher, if the Item has none.
|
|
if (!mapped.containsKey(DATACITE_PUBLISHER)
|
|
&& !mapped.containsKey("datacite"))
|
|
{
|
|
String publisher = configurationService.getPropertyAsType(CFG_PUBLISHER, "unknown");
|
|
log.info("Supplying default publisher: {}", publisher);
|
|
mapped.put(DATACITE_PUBLISHER, publisher);
|
|
}
|
|
|
|
// Supply current year as year of publication, if the Item has none.
|
|
if (!mapped.containsKey(DATACITE_PUBLICATION_YEAR)
|
|
&& !mapped.containsKey("datacite"))
|
|
{
|
|
String year = String.valueOf(Calendar.getInstance().get(Calendar.YEAR));
|
|
log.info("Supplying default publication year: {}", year);
|
|
mapped.put(DATACITE_PUBLICATION_YEAR, year);
|
|
}
|
|
|
|
// TODO find a way to get a current direct URL to the object and set _target
|
|
// mapped.put("_target", url);
|
|
|
|
return mapped;
|
|
}
|
|
|
|
@Required
|
|
public void setCrosswalk(Map<String, String> aCrosswalk)
|
|
{
|
|
crosswalk = aCrosswalk;
|
|
}
|
|
|
|
public void setCrosswalkTransform(Map<String, Transform> transformMap)
|
|
{
|
|
transforms = transformMap;
|
|
}
|
|
|
|
public void setGenerateDataciteXML(boolean GENERATE_DATACITE_XML)
|
|
{
|
|
this.GENERATE_DATACITE_XML = GENERATE_DATACITE_XML;
|
|
}
|
|
|
|
public void setDisseminationCrosswalkName(String DATACITE_XML_CROSSWALK)
|
|
{
|
|
this.DATACITE_XML_CROSSWALK = DATACITE_XML_CROSSWALK;
|
|
}
|
|
|
|
@Required
|
|
public static void setRequestFactory(EZIDRequestFactory aRequestFactory)
|
|
{
|
|
requestFactory = aRequestFactory;
|
|
}
|
|
}
|