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Fix dspace-api module per new code style

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This commit is contained in:
Tim Donohue
2018-02-14 10:53:46 -06:00
parent 8ffc97f7f9
commit 8a48f782ea
1051 changed files with 53347 additions and 63373 deletions
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343
dspace-api/src/main/java/org/dspace/identifier/EZIDIdentifierProvider.java
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@@ -9,14 +9,21 @@
package org.dspace.identifier;
import java.io.IOException;
import java.net.*;
import java.net.HttpURLConnection;
import java.net.URISyntaxException;
import java.sql.SQLException;
import java.util.*;
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.MetadataValue;
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;
@@ -40,14 +47,14 @@ import org.springframework.beans.factory.annotation.Required;
* [DSpace]/config**.</p>
*
* <dl>
* <dt>identifier.doi.ezid.shoulder</dt>
* <dd>base of the site's DOIs. Example: 10.5072/FK2</dd>
* <dt>identifier.doi.ezid.user</dt>
* <dd>EZID username.</dd>
* <dt>identifier.doi.ezid.password</dt>
* <dd>EZID password.</dd>
* <dt>identifier.doi.ezid.publisher</dt>
* <dd>A default publisher, for Items not previously published. EZID requires a publisher.</dd>
* <dt>identifier.doi.ezid.shoulder</dt>
* <dd>base of the site's DOIs. Example: 10.5072/FK2</dd>
* <dt>identifier.doi.ezid.user</dt>
* <dd>EZID username.</dd>
* <dt>identifier.doi.ezid.password</dt>
* <dd>EZID password.</dd>
* <dt>identifier.doi.ezid.publisher</dt>
* <dd>A default publisher, for Items not previously published. EZID requires a publisher.</dd>
* </dl>
*
* <p>Then there are properties injected using Spring:</p>
@@ -57,17 +64,17 @@ import org.springframework.beans.factory.annotation.Required;
* 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.</li>
*
*
* <li>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.</li>
*
*
* <li>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.</li>
*
*
* <li>Optional: A string property ("disseminationCrosswalkName") that can be
* used to set the name of the dissemination crosswalk plugin for metadata
* crosswalking. Default value: "DataCite".</li>
@@ -76,8 +83,7 @@ import org.springframework.beans.factory.annotation.Required;
* @author mwood
*/
public class EZIDIdentifierProvider
extends IdentifierProvider
{
extends IdentifierProvider {
private static final Logger log = LoggerFactory.getLogger(EZIDIdentifierProvider.class);
// Configuration property names
@@ -102,13 +108,19 @@ public class EZIDIdentifierProvider
protected String DATACITE_XML_CROSSWALK = "DataCite";
/** Map DataCite metadata into local metadata. */
/**
* Map DataCite metadata into local metadata.
*/
private Map<String, String> crosswalk = new HashMap<>();
/** Converters to be applied to specific fields. */
/**
* Converters to be applied to specific fields.
*/
private static Map<String, Transform> transforms = new HashMap<>();
/** Factory for EZID requests. */
/**
* Factory for EZID requests.
*/
private EZIDRequestFactory requestFactory;
@Autowired(required = true)
@@ -118,36 +130,28 @@ public class EZIDIdentifierProvider
protected ItemService itemService;
@Override
public boolean supports(Class<? extends Identifier> identifier)
{
public boolean supports(Class<? extends Identifier> identifier) {
return DOI.class.isAssignableFrom(identifier);
}
@Override
public boolean supports(String identifier)
{
if (null == identifier)
{
public boolean supports(String identifier) {
if (null == identifier) {
return false;
}
else
{
} else {
return identifier.startsWith(DOI_SCHEME);
} // XXX more thorough test?
}
@Override
public String register(Context context, DSpaceObject dso)
throws IdentifierException
{
throws IdentifierException {
log.debug("register {}", dso);
DSpaceObjectService<DSpaceObject> dsoService = contentServiceFactory.getDSpaceObjectService(dso);
List<MetadataValue> identifiers = dsoService.getMetadata(dso, MD_SCHEMA, DOI_ELEMENT, DOI_QUALIFIER, null);
for (MetadataValue identifier : identifiers)
{
if ((null != identifier.getValue()) && (identifier.getValue().startsWith(DOI_SCHEME)))
{
for (MetadataValue identifier : identifiers) {
if ((null != identifier.getValue()) && (identifier.getValue().startsWith(DOI_SCHEME))) {
return identifier.getValue();
}
}
@@ -164,50 +168,45 @@ public class EZIDIdentifierProvider
}
@Override
public void register(Context context, DSpaceObject object, String identifier)
{
public void register(Context context, DSpaceObject object, String identifier) {
log.debug("register {} as {}", object, identifier);
EZIDResponse response;
try {
EZIDRequest request = requestFactory.getInstance(loadAuthority(),
loadUser(), loadPassword());
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())
{
if (response.isSuccess()) {
try {
DSpaceObjectService<DSpaceObject> dsoService = contentServiceFactory.getDSpaceObjectService(object);
dsoService.addMetadata(context, object, MD_SCHEMA, DOI_ELEMENT, DOI_QUALIFIER, null,
idToDOI(identifier));
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
{
} else {
log.error("Identifier '{}' not registered -- EZID returned: {}",
identifier, response.getEZIDStatusValue());
identifier, response.getEZIDStatusValue());
}
}
@Override
public void reserve(Context context, DSpaceObject dso, String identifier)
throws IdentifierException
{
throws IdentifierException {
log.debug("reserve {}", identifier);
EZIDResponse response;
try {
EZIDRequest request = requestFactory.getInstance(loadAuthority(),
loadUser(), loadPassword());
loadUser(), loadPassword());
Map<String, String> metadata = crosswalkMetadata(context, dso);
metadata.put("_status", "reserved");
response = request.create(identifier, metadata);
@@ -216,8 +215,7 @@ public class EZIDIdentifierProvider
return;
}
if (response.isSuccess())
{
if (response.isSuccess()) {
DSpaceObjectService<DSpaceObject> dsoService = contentServiceFactory.getDSpaceObjectService(dso);
try {
dsoService.addMetadata(context, dso, MD_SCHEMA, DOI_ELEMENT, DOI_QUALIFIER, null, idToDOI(identifier));
@@ -226,18 +224,15 @@ public class EZIDIdentifierProvider
} catch (SQLException | AuthorizeException ex) {
throw new IdentifierException("New identifier not stored", ex);
}
}
else
{
} else {
log.error("Identifier '{}' not registered -- EZID returned: {}",
identifier, response.getEZIDStatusValue());
identifier, response.getEZIDStatusValue());
}
}
@Override
public String mint(Context context, DSpaceObject dso)
throws IdentifierException
{
throws IdentifierException {
log.debug("mint for {}", dso);
// Compose the request
@@ -251,8 +246,7 @@ public class EZIDIdentifierProvider
// Send the request
EZIDResponse response;
try
{
try {
response = request.mint(crosswalkMetadata(context, dso));
} catch (IOException | URISyntaxException ex) {
log.error("Failed to send EZID request: {}", ex.getMessage());
@@ -260,35 +254,30 @@ public class EZIDIdentifierProvider
}
// 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());
}
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())
{
// 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)
{
if (end < 0) {
end = value.length();
}
String doi = value.substring(0, end).trim();
log.info("Created {}", doi);
return doi;
}
else
{
} else {
log.error("EZID responded: {}", response.getEZIDStatusValue());
throw new IdentifierException("No DOI returned");
}
@@ -296,27 +285,24 @@ public class EZIDIdentifierProvider
@Override
public DSpaceObject resolve(Context context, String identifier,
String... attributes)
throws IdentifierNotFoundException, IdentifierNotResolvableException
{
String... attributes)
throws IdentifierNotFoundException, IdentifierNotResolvableException {
log.debug("resolve {}", identifier);
Iterator<Item> found;
try {
found = itemService.findByMetadataField(context,
MD_SCHEMA, DOI_ELEMENT, DOI_QUALIFIER,
idToDOI(identifier));
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())
{
if (!found.hasNext()) {
throw new IdentifierNotFoundException("No object bound to " + identifier);
}
Item found1 = found.next();
if (found.hasNext())
{
if (found.hasNext()) {
log.error("More than one object bound to {}!", identifier);
}
log.debug("Resolved to {}", found1);
@@ -325,36 +311,29 @@ public class EZIDIdentifierProvider
@Override
public String lookup(Context context, DSpaceObject object)
throws IdentifierNotFoundException, IdentifierNotResolvableException
{
throws IdentifierNotFoundException, IdentifierNotResolvableException {
log.debug("lookup {}", object);
MetadataValue found = null;
DSpaceObjectService<DSpaceObject> dsoService = contentServiceFactory.getDSpaceObjectService(object);
for (MetadataValue candidate : dsoService.getMetadata(object, MD_SCHEMA, DOI_ELEMENT, DOI_QUALIFIER, null))
{
if (candidate.getValue().startsWith(DOI_SCHEME))
{
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)
{
if (null != found) {
log.debug("Found {}", found.getValue());
return found.getValue();
}
else
{
} else {
throw new IdentifierNotFoundException(dsoService.getTypeText(object) + " "
+ object.getID() + " has no DOI");
+ object.getID() + " has no DOI");
}
}
@Override
public void delete(Context context, DSpaceObject dso)
throws IdentifierException
{
throws IdentifierException {
log.debug("delete {}", dso);
// delete from EZID
@@ -362,10 +341,8 @@ public class EZIDIdentifierProvider
List<MetadataValue> metadata = dsoService.getMetadata(dso, MD_SCHEMA, DOI_ELEMENT, DOI_QUALIFIER, null);
List<String> remainder = new ArrayList<>();
int skipped = 0;
for (MetadataValue id : metadata)
{
if (!id.getValue().startsWith(DOI_SCHEME))
{
for (MetadataValue id : metadata) {
if (!id.getValue().startsWith(DOI_SCHEME)) {
remainder.add(id.getValue());
continue;
}
@@ -373,7 +350,7 @@ public class EZIDIdentifierProvider
EZIDResponse response;
try {
EZIDRequest request = requestFactory.getInstance(loadAuthority(),
loadUser(), loadPassword());
loadUser(), loadPassword());
response = request.delete(DOIToId(id.getValue()));
} catch (URISyntaxException e) {
log.error("Bad URI in metadata value: {}", e.getMessage());
@@ -386,10 +363,9 @@ public class EZIDIdentifierProvider
skipped++;
continue;
}
if (!response.isSuccess())
{
if (!response.isSuccess()) {
log.error("Unable to delete {} from DataCite: {}", id.getValue(),
response.getEZIDStatusValue());
response.getEZIDStatusValue());
remainder.add(id.getValue());
skipped++;
continue;
@@ -406,26 +382,22 @@ public class EZIDIdentifierProvider
log.error("Failed to re-add identifiers: {}", e.getMessage());
}
if (skipped > 0)
{
if (skipped > 0) {
throw new IdentifierException(skipped + " identifiers could not be deleted.");
}
}
@Override
public void delete(Context context, DSpaceObject dso, String identifier)
throws IdentifierException
{
throws IdentifierException {
log.debug("delete {} from {}", identifier, dso);
DSpaceObjectService<DSpaceObject> dsoService = contentServiceFactory.getDSpaceObjectService(dso);
List<MetadataValue> metadata = dsoService.getMetadata(dso, MD_SCHEMA, DOI_ELEMENT, DOI_QUALIFIER, null);
List<String> remainder = new ArrayList<>();
int skipped = 0;
for (MetadataValue id : metadata)
{
if (!id.getValue().equals(idToDOI(identifier)))
{
for (MetadataValue id : metadata) {
if (!id.getValue().equals(idToDOI(identifier))) {
remainder.add(id.getValue());
continue;
}
@@ -433,7 +405,7 @@ public class EZIDIdentifierProvider
EZIDResponse response;
try {
EZIDRequest request = requestFactory.getInstance(loadAuthority(),
loadUser(), loadPassword());
loadUser(), loadPassword());
response = request.delete(DOIToId(id.getValue()));
} catch (URISyntaxException e) {
log.error("Bad URI in metadata value {}: {}", id.getValue(), e.getMessage());
@@ -447,10 +419,9 @@ public class EZIDIdentifierProvider
continue;
}
if (!response.isSuccess())
{
if (!response.isSuccess()) {
log.error("Unable to delete {} from DataCite: {}", id.getValue(),
response.getEZIDStatusValue());
response.getEZIDStatusValue());
remainder.add(id.getValue());
skipped++;
continue;
@@ -467,92 +438,78 @@ public class EZIDIdentifierProvider
log.error("Failed to re-add identifiers: {}", e.getMessage());
}
if (skipped > 0)
{
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
{
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
{
throws IdentifierException {
String prefix = "doi:" + loadAuthority();
if (DOI.startsWith(prefix))
{
if (DOI.startsWith(prefix)) {
return DOI.substring(prefix.length());
}
else
{
} else {
return DOI;
}
}
/**
* Get configured value of EZID username.
*
* @throws IdentifierException if identifier error
*/
private String loadUser()
throws IdentifierException
{
throws IdentifierException {
String user = configurationService.getProperty(CFG_USER);
if (null != user)
{
if (null != user) {
return user;
}
else
{
} else {
throw new IdentifierException("Unconfigured: define " + CFG_USER);
}
}
/**
* Get configured value of EZID password.
*
* @throws IdentifierException if identifier error
*/
private String loadPassword()
throws IdentifierException
{
throws IdentifierException {
String password = configurationService.getProperty(CFG_PASSWORD);
if (null != password)
{
if (null != password) {
return password;
}
else
{
} else {
throw new IdentifierException("Unconfigured: define " + CFG_PASSWORD);
}
}
/**
* Get configured value of EZID "shoulder".
*
* @throws IdentifierException if identifier error
*/
private String loadAuthority()
throws IdentifierException
{
throws IdentifierException {
String shoulder = configurationService.getProperty(CFG_SHOULDER);
if (null != shoulder)
{
if (null != shoulder) {
return shoulder;
}
else
{
} else {
throw new IdentifierException("Unconfigured: define " + CFG_SHOULDER);
}
}
@@ -560,43 +517,35 @@ public class EZIDIdentifierProvider
/**
* Map selected DSpace metadata to fields recognized by DataCite.
*/
Map<String, String> crosswalkMetadata(Context context, DSpaceObject dso)
{
if ((null == dso) || !(dso instanceof Item))
{
Map<String, String> 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<String, String> mapped = new HashMap<>();
for (Entry<String, String> datum : crosswalk.entrySet())
{
for (Entry<String, String> datum : crosswalk.entrySet()) {
List<MetadataValue> values = itemService.getMetadataByMetadataString(item, datum.getValue());
if (null != values)
{
for (MetadataValue value : values)
{
if (null != values) {
for (MetadataValue value : values) {
String key = datum.getKey();
String mappedValue;
Transform xfrm = transforms.get(key);
if (null != xfrm)
{
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()
});
new String[] {
value.getValue(),
value.toString(),
key,
ex.getMessage()
});
continue;
}
}
else
{
} else {
mappedValue = value.getValue();
}
mapped.put(key, mappedValue);
@@ -604,8 +553,7 @@ public class EZIDIdentifierProvider
}
}
if (GENERATE_DATACITE_XML == true)
{
if (GENERATE_DATACITE_XML == true) {
DataCiteXMLCreator xmlGen = new DataCiteXMLCreator();
xmlGen.setDisseminationCrosswalkName(DATACITE_XML_CROSSWALK);
String xmlString = xmlGen.getXMLString(context, dso);
@@ -615,8 +563,7 @@ public class EZIDIdentifierProvider
// Supply a default publisher, if the Item has none.
if (!mapped.containsKey(DATACITE_PUBLISHER)
&& !mapped.containsKey("datacite"))
{
&& !mapped.containsKey("datacite")) {
String publisher = configurationService.getPropertyAsType(CFG_PUBLISHER, "unknown");
log.info("Supplying default publisher: {}", publisher);
mapped.put(DATACITE_PUBLISHER, publisher);
@@ -624,8 +571,7 @@ public class EZIDIdentifierProvider
// Supply current year as year of publication, if the Item has none.
if (!mapped.containsKey(DATACITE_PUBLICATION_YEAR)
&& !mapped.containsKey("datacite"))
{
&& !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);
@@ -633,15 +579,12 @@ public class EZIDIdentifierProvider
// Supply _target link back to this object
String handle = dso.getHandle();
if (null == handle)
{
if (null == handle) {
log.warn("{} #{} has no handle -- location not set.",
contentServiceFactory.getDSpaceObjectService(dso).getTypeText(dso), dso.getID());
}
else
{
contentServiceFactory.getDSpaceObjectService(dso).getTypeText(dso), dso.getID());
} else {
String url = configurationService.getProperty("dspace.url")
+ "/handle/" + item.getHandle();
+ "/handle/" + item.getHandle();
log.info("Supplying location: {}", url);
mapped.put("_target", url);
}
@@ -653,12 +596,10 @@ public class EZIDIdentifierProvider
* 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
* @param aCrosswalk map of metadata fields to EZID keys
*/
@Required
public void setCrosswalk(Map<String, String> aCrosswalk)
{
public void setCrosswalk(Map<String, String> aCrosswalk) {
crosswalk = aCrosswalk;
}
@@ -670,27 +611,22 @@ public class EZIDIdentifierProvider
* 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
* @param transformMap map of metadata fields to EZID transformation classes
*/
public void setCrosswalkTransform(Map<String, Transform> transformMap)
{
public void setCrosswalkTransform(Map<String, Transform> transformMap) {
transforms = transformMap;
}
public void setGenerateDataciteXML(boolean GENERATE_DATACITE_XML)
{
public void setGenerateDataciteXML(boolean GENERATE_DATACITE_XML) {
this.GENERATE_DATACITE_XML = GENERATE_DATACITE_XML;
}
public void setDisseminationCrosswalkName(String DATACITE_XML_CROSSWALK)
{
public void setDisseminationCrosswalkName(String DATACITE_XML_CROSSWALK) {
this.DATACITE_XML_CROSSWALK = DATACITE_XML_CROSSWALK;
}
@Required
public void setRequestFactory(EZIDRequestFactory aRequestFactory)
{
public void setRequestFactory(EZIDRequestFactory aRequestFactory) {
requestFactory = aRequestFactory;
}
@@ -700,9 +636,10 @@ public class EZIDIdentifierProvider
/**
* 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){
protected void setItemService(ItemService itemService) {
this.itemService = itemService;
}
}