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DSpace core data model and service APIs.
/**
* 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.io.IOException;
import java.net.HttpURLConnection;
import java.net.URISyntaxException;
import java.sql.SQLException;
import java.util.ArrayList;
import java.util.Calendar;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import org.dspace.authorize.AuthorizeException;
import org.dspace.content.DSpaceObject;
import org.dspace.content.Item;
import org.dspace.content.MetadataValue;
import org.dspace.content.factory.ContentServiceFactory;
import org.dspace.content.service.DSpaceObjectService;
import org.dspace.content.service.ItemService;
import org.dspace.core.Context;
import org.dspace.identifier.ezid.EZIDRequest;
import org.dspace.identifier.ezid.EZIDRequestFactory;
import org.dspace.identifier.ezid.EZIDResponse;
import org.dspace.identifier.ezid.Transform;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
/**
* Provide service for DOIs through DataCite using the EZID service.
*
* Configuration of this class is is in two parts.
*
* Installation-specific configuration (credentials and the "shoulder" value
* which forms a prefix of the site's DOIs) is supplied from property files in
* [DSpace]/config**.
*
*
* - identifier.doi.ezid.shoulder
* - base of the site's DOIs. Example: 10.5072/FK2
* - identifier.doi.ezid.user
* - EZID username.
* - identifier.doi.ezid.password
* - EZID password.
* - identifier.doi.ezid.publisher
* - A default publisher, for Items not previously published. EZID requires a publisher.
*
*
* Then there are properties injected using Spring:
*
* - There is a Map (with the property name "crosswalk") from EZID metadata
* field names into DSpace field names, injected by Spring. Specify the
* fully-qualified names of all metadata fields to be looked up on a DSpace
* object and their values set on mapped fully-qualified names in the object's
* DataCite metadata.
*
* - A second map ("crosswalkTransform") provides Transform instances mapped
* from EZID metadata field names. This allows the crosswalk to rewrite field
* values where the form maintained by DSpace is not directly usable in EZID
* metadata.
*
* - Optional: A boolean property ("generateDataciteXML") that controls the
* creation and inclusion of DataCite xml schema during the metadata
* crosswalking. The default "DataCite" dissemination plugin uses
* DIM2DataCite.xsl for crosswalking. Default value: false.
*
* - Optional: A string property ("disseminationCrosswalkName") that can be
* used to set the name of the dissemination crosswalk plugin for metadata
* crosswalking. Default value: "DataCite".
*
*
* @author mwood
*/
public class EZIDIdentifierProvider
extends IdentifierProvider {
private static final Logger log = LoggerFactory.getLogger(EZIDIdentifierProvider.class);
// Configuration property names
static final String CFG_SHOULDER = "identifier.doi.ezid.shoulder";
static final String CFG_USER = "identifier.doi.ezid.user";
static final String CFG_PASSWORD = "identifier.doi.ezid.password";
static final String CFG_PUBLISHER = "identifier.doi.ezid.publisher";
// DataCite metadata field names
static final String DATACITE_PUBLISHER = "datacite.publisher";
static final String DATACITE_PUBLICATION_YEAR = "datacite.publicationyear";
// DSpace metadata field name elements
// XXX move these to MetadataSchema or some such
public static final String MD_SCHEMA = "dc";
public static final String DOI_ELEMENT = "identifier";
public static final String DOI_QUALIFIER = null;
private static final String DOI_SCHEME = "doi:";
protected boolean GENERATE_DATACITE_XML = false;
protected String DATACITE_XML_CROSSWALK = "DataCite";
/**
* Map DataCite metadata into local metadata.
*/
private Map crosswalk = new HashMap<>();
/**
* Converters to be applied to specific fields.
*/
private static Map transforms = new HashMap<>();
/**
* Factory for EZID requests.
*/
private EZIDRequestFactory requestFactory;
@Autowired(required = true)
protected ContentServiceFactory contentServiceFactory;
@Autowired(required = true)
protected ItemService itemService;
@Override
public boolean supports(Class identifier) {
return DOI.class.isAssignableFrom(identifier);
}
@Override
public boolean supports(String identifier) {
if (null == identifier) {
return false;
} else {
return identifier.startsWith(DOI_SCHEME);
} // XXX more thorough test?
}
@Override
public String register(Context context, DSpaceObject dso)
throws IdentifierException {
log.debug("register {}", dso);
if (!(dso instanceof Item)) {
// DOI are currently assigned only to Item
return null;
}
DSpaceObjectService dsoService = contentServiceFactory.getDSpaceObjectService(dso);
List identifiers = dsoService.getMetadata(dso, MD_SCHEMA, DOI_ELEMENT, DOI_QUALIFIER, null);
for (MetadataValue identifier : identifiers) {
if ((null != identifier.getValue()) && (identifier.getValue().startsWith(DOI_SCHEME))) {
return identifier.getValue();
}
}
String id = mint(context, dso);
try {
dsoService.addMetadata(context, dso, MD_SCHEMA, DOI_ELEMENT, DOI_QUALIFIER, null, id);
dsoService.update(context, dso);
} catch (SQLException | AuthorizeException ex) {
throw new IdentifierException("New identifier not stored", ex);
}
log.info("Registered {}", id);
return id;
}
@Override
public void register(Context context, DSpaceObject object, String identifier) {
log.debug("register {} as {}", object, identifier);
if (!(object instanceof Item)) {
// DOI are currently assigned only to Item
return;
}
EZIDResponse response;
try {
EZIDRequest request = requestFactory.getInstance(loadAuthority(),
loadUser(), loadPassword());
response = request.create(identifier, crosswalkMetadata(context, object));
} catch (IdentifierException | IOException | URISyntaxException e) {
log.error("Identifier '{}' not registered: {}", identifier, e.getMessage());
return;
}
if (response.isSuccess()) {
try {
DSpaceObjectService dsoService = contentServiceFactory.getDSpaceObjectService(object);
dsoService.addMetadata(context, object, MD_SCHEMA, DOI_ELEMENT, DOI_QUALIFIER, null,
idToDOI(identifier));
dsoService.update(context, object);
log.info("registered {}", identifier);
} catch (SQLException | AuthorizeException | IdentifierException ex) {
// TODO throw new IdentifierException("New identifier not stored", ex);
log.error("New identifier not stored", ex);
}
} else {
log.error("Identifier '{}' not registered -- EZID returned: {}",
identifier, response.getEZIDStatusValue());
}
}
@Override
public void reserve(Context context, DSpaceObject dso, String identifier)
throws IdentifierException {
log.debug("reserve {}", identifier);
EZIDResponse response;
try {
EZIDRequest request = requestFactory.getInstance(loadAuthority(),
loadUser(), loadPassword());
Map metadata = crosswalkMetadata(context, dso);
metadata.put("_status", "reserved");
response = request.create(identifier, metadata);
} catch (IOException | URISyntaxException e) {
log.error("Identifier '{}' not registered: {}", identifier, e.getMessage());
return;
}
if (response.isSuccess()) {
DSpaceObjectService dsoService = contentServiceFactory.getDSpaceObjectService(dso);
try {
dsoService.addMetadata(context, dso, MD_SCHEMA, DOI_ELEMENT, DOI_QUALIFIER, null, idToDOI(identifier));
dsoService.update(context, dso);
log.info("reserved {}", identifier);
} catch (SQLException | AuthorizeException ex) {
throw new IdentifierException("New identifier not stored", ex);
}
} else {
log.error("Identifier '{}' not registered -- EZID returned: {}",
identifier, response.getEZIDStatusValue());
}
}
@Override
public String mint(Context context, DSpaceObject dso)
throws IdentifierException {
log.debug("mint for {}", dso);
// Compose the request
EZIDRequest request;
try {
request = requestFactory.getInstance(loadAuthority(), loadUser(), loadPassword());
} catch (URISyntaxException ex) {
log.error(ex.getMessage());
throw new IdentifierException("DOI request not sent: " + ex.getMessage());
}
// Send the request
EZIDResponse response;
try {
response = request.mint(crosswalkMetadata(context, dso));
} catch (IOException | URISyntaxException ex) {
log.error("Failed to send EZID request: {}", ex.getMessage());
throw new IdentifierException("DOI request not sent: " + ex.getMessage());
}
// Good response?
if (HttpURLConnection.HTTP_CREATED != response.getHttpStatusCode()) {
log.error("EZID server responded: {} {}: {}",
new String[] {
String.valueOf(response.getHttpStatusCode()),
response.getHttpReasonPhrase(),
response.getEZIDStatusValue()
});
throw new IdentifierException("DOI not created: "
+ response.getHttpReasonPhrase()
+ ": "
+ response.getEZIDStatusValue());
}
// Extract the DOI from the content blob
if (response.isSuccess()) {
String value = response.getEZIDStatusValue();
int end = value.indexOf('|'); // Following pipe is "shadow ARK"
if (end < 0) {
end = value.length();
}
String doi = value.substring(0, end).trim();
log.info("Created {}", doi);
return doi;
} else {
log.error("EZID responded: {}", response.getEZIDStatusValue());
throw new IdentifierException("No DOI returned");
}
}
@Override
public DSpaceObject resolve(Context context, String identifier,
String... attributes)
throws IdentifierNotFoundException, IdentifierNotResolvableException {
log.debug("resolve {}", identifier);
Iterator- found;
try {
found = itemService.findByMetadataField(context,
MD_SCHEMA, DOI_ELEMENT, DOI_QUALIFIER,
idToDOI(identifier));
} catch (IdentifierException | SQLException | AuthorizeException | IOException ex) {
log.error(ex.getMessage());
throw new IdentifierNotResolvableException(ex);
}
if (!found.hasNext()) {
throw new IdentifierNotFoundException("No object bound to " + identifier);
}
Item found1 = found.next();
if (found.hasNext()) {
log.error("More than one object bound to {}!", identifier);
}
log.debug("Resolved to {}", found1);
return found1;
}
@Override
public String lookup(Context context, DSpaceObject object)
throws IdentifierNotFoundException, IdentifierNotResolvableException {
log.debug("lookup {}", object);
MetadataValue found = null;
DSpaceObjectService
dsoService = contentServiceFactory.getDSpaceObjectService(object);
for (MetadataValue candidate : dsoService.getMetadata(object, MD_SCHEMA, DOI_ELEMENT, DOI_QUALIFIER, null)) {
if (candidate.getValue().startsWith(DOI_SCHEME)) {
found = candidate;
break;
}
}
if (null != found) {
log.debug("Found {}", found.getValue());
return found.getValue();
} else {
throw new IdentifierNotFoundException(dsoService.getTypeText(object) + " "
+ object.getID() + " has no DOI");
}
}
@Override
public void delete(Context context, DSpaceObject dso)
throws IdentifierException {
log.debug("delete {}", dso);
// delete from EZID
DSpaceObjectService dsoService = contentServiceFactory.getDSpaceObjectService(dso);
List metadata = dsoService.getMetadata(dso, MD_SCHEMA, DOI_ELEMENT, DOI_QUALIFIER, null);
List remainder = new ArrayList<>();
int skipped = 0;
for (MetadataValue id : metadata) {
if (!id.getValue().startsWith(DOI_SCHEME)) {
remainder.add(id.getValue());
continue;
}
EZIDResponse response;
try {
EZIDRequest request = requestFactory.getInstance(loadAuthority(),
loadUser(), loadPassword());
response = request.delete(DOIToId(id.getValue()));
} catch (URISyntaxException e) {
log.error("Bad URI in metadata value: {}", e.getMessage());
remainder.add(id.getValue());
skipped++;
continue;
} catch (IOException e) {
log.error("Failed request to EZID: {}", e.getMessage());
remainder.add(id.getValue());
skipped++;
continue;
}
if (!response.isSuccess()) {
log.error("Unable to delete {} from DataCite: {}", id.getValue(),
response.getEZIDStatusValue());
remainder.add(id.getValue());
skipped++;
continue;
}
log.info("Deleted {}", id.getValue());
}
// delete from item
try {
dsoService.clearMetadata(context, dso, MD_SCHEMA, DOI_ELEMENT, DOI_QUALIFIER, null);
dsoService.addMetadata(context, dso, MD_SCHEMA, DOI_ELEMENT, DOI_QUALIFIER, null, remainder);
dsoService.update(context, dso);
} catch (SQLException | AuthorizeException e) {
log.error("Failed to re-add identifiers: {}", e.getMessage());
}
if (skipped > 0) {
throw new IdentifierException(skipped + " identifiers could not be deleted.");
}
}
@Override
public void delete(Context context, DSpaceObject dso, String identifier)
throws IdentifierException {
log.debug("delete {} from {}", identifier, dso);
DSpaceObjectService dsoService = contentServiceFactory.getDSpaceObjectService(dso);
List metadata = dsoService.getMetadata(dso, MD_SCHEMA, DOI_ELEMENT, DOI_QUALIFIER, null);
List remainder = new ArrayList<>();
int skipped = 0;
for (MetadataValue id : metadata) {
if (!id.getValue().equals(idToDOI(identifier))) {
remainder.add(id.getValue());
continue;
}
EZIDResponse response;
try {
EZIDRequest request = requestFactory.getInstance(loadAuthority(),
loadUser(), loadPassword());
response = request.delete(DOIToId(id.getValue()));
} catch (URISyntaxException e) {
log.error("Bad URI in metadata value {}: {}", id.getValue(), e.getMessage());
remainder.add(id.getValue());
skipped++;
continue;
} catch (IOException e) {
log.error("Failed request to EZID: {}", e.getMessage());
remainder.add(id.getValue());
skipped++;
continue;
}
if (!response.isSuccess()) {
log.error("Unable to delete {} from DataCite: {}", id.getValue(),
response.getEZIDStatusValue());
remainder.add(id.getValue());
skipped++;
continue;
}
log.info("Deleted {}", id.getValue());
}
// delete from item
try {
dsoService.clearMetadata(context, dso, MD_SCHEMA, DOI_ELEMENT, DOI_QUALIFIER, null);
dsoService.addMetadata(context, dso, MD_SCHEMA, DOI_ELEMENT, DOI_QUALIFIER, null, remainder);
dsoService.update(context, dso);
} catch (SQLException | AuthorizeException e) {
log.error("Failed to re-add identifiers: {}", e.getMessage());
}
if (skipped > 0) {
throw new IdentifierException(identifier + " could not be deleted.");
}
}
/**
* Format a naked identifier as a DOI with our configured authority prefix.
*
* @throws IdentifierException if authority prefix is not configured.
*/
String idToDOI(String id)
throws IdentifierException {
return "doi:" + loadAuthority() + id;
}
/**
* Remove scheme and our configured authority prefix from a doi: URI string.
*
* @return naked local identifier.
* @throws IdentifierException if authority prefix is not configured.
*/
String DOIToId(String DOI)
throws IdentifierException {
String prefix = "doi:" + loadAuthority();
if (DOI.startsWith(prefix)) {
return DOI.substring(prefix.length());
} else {
return DOI;
}
}
/**
* Get configured value of EZID username.
*
* @throws IdentifierException if identifier error
*/
private String loadUser()
throws IdentifierException {
String user = configurationService.getProperty(CFG_USER);
if (null != user) {
return user;
} else {
throw new IdentifierException("Unconfigured: define " + CFG_USER);
}
}
/**
* Get configured value of EZID password.
*
* @throws IdentifierException if identifier error
*/
private String loadPassword()
throws IdentifierException {
String password = configurationService.getProperty(CFG_PASSWORD);
if (null != password) {
return password;
} else {
throw new IdentifierException("Unconfigured: define " + CFG_PASSWORD);
}
}
/**
* Get configured value of EZID "shoulder".
*
* @throws IdentifierException if identifier error
*/
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.
*/
Map crosswalkMetadata(Context context, 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 mapped = new HashMap<>();
for (Entry datum : crosswalk.entrySet()) {
List values = itemService.getMetadataByMetadataString(item, datum.getValue());
if (null != values) {
for (MetadataValue value : values) {
String key = datum.getKey();
String mappedValue;
Transform xfrm = transforms.get(key);
if (null != xfrm) {
try {
mappedValue = xfrm.transform(value.getValue());
} catch (Exception ex) {
log.error("Unable to transform '{}' from {} to {}: {}",
new String[] {
value.getValue(),
value.toString(),
key,
ex.getMessage()
});
continue;
}
} else {
mappedValue = value.getValue();
}
mapped.put(key, mappedValue);
}
}
}
if (GENERATE_DATACITE_XML == true) {
DataCiteXMLCreator xmlGen = new DataCiteXMLCreator();
xmlGen.setDisseminationCrosswalkName(DATACITE_XML_CROSSWALK);
String xmlString = xmlGen.getXMLString(context, dso);
log.debug("Generated DataCite XML: {}", xmlString);
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);
}
// Supply _target link back to this object
String handle = dso.getHandle();
if (null == handle) {
log.warn("{} #{} has no handle -- location not set.",
contentServiceFactory.getDSpaceObjectService(dso).getTypeText(dso), dso.getID());
} else {
String url = configurationService.getProperty("dspace.ui.url")
+ "/handle/" + item.getHandle();
log.info("Supplying location: {}", url);
mapped.put("_target", url);
}
return mapped;
}
/**
* Provide a map from DSO metadata keys to EZID keys. This will drive the
* generation of EZID metadata for the minting of new identifiers.
*
* @param aCrosswalk map of metadata fields to EZID keys
*/
@Autowired(required = true)
public void setCrosswalk(Map aCrosswalk) {
crosswalk = aCrosswalk;
}
public Map getCrosswalk() {
return crosswalk;
}
/**
* Provide a map from DSO metadata keys to classes which can transform their
* values to something acceptable to EZID.
*
* @param transformMap map of metadata fields to EZID transformation classes
*/
public void setCrosswalkTransform(Map 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;
}
@Autowired(required = true)
public void setRequestFactory(EZIDRequestFactory aRequestFactory) {
requestFactory = aRequestFactory;
}
public EZIDRequestFactory getRequestFactory() {
return requestFactory;
}
/**
* Method should never be used aside from the unit tests where we can cannot autowire this class.
*
* @param itemService itemService instance
*/
protected void setItemService(ItemService itemService) {
this.itemService = itemService;
}
}
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