Merge remote-tracking branch '4science-bitbucket/main' into CST-5587

This commit is contained in:
Luca Giamminonni
2022-06-17 13:28:31 +02:00
159 changed files with 22624 additions and 1598 deletions

View File

@@ -550,10 +550,17 @@
<groupId>com.ibm.icu</groupId>
<artifactId>icu4j</artifactId>
</dependency>
<!-- Codebase at https://github.com/OCLC-Research/oaiharvester2/ -->
<dependency>
<groupId>org.dspace</groupId>
<artifactId>oclc-harvester2</artifactId>
</dependency>
<!-- Xalan is REQUIRED by 'oclc-harvester2' listed above (OAI harvesting fails without it).
Please do NOT use Xalan in DSpace codebase as it is not well maintained. -->
<dependency>
<groupId>xalan</groupId>
<artifactId>xalan</artifactId>
</dependency>
<dependency>
<groupId>org.dspace</groupId>
<artifactId>dspace-services</artifactId>

View File

@@ -0,0 +1,170 @@
/**
* 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.app.bulkedit;
import java.sql.SQLException;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
import java.util.UUID;
import org.apache.commons.cli.ParseException;
import org.dspace.content.Item;
import org.dspace.content.MetadataDSpaceCsvExportServiceImpl;
import org.dspace.content.factory.ContentServiceFactory;
import org.dspace.content.service.CollectionService;
import org.dspace.content.service.CommunityService;
import org.dspace.content.service.MetadataDSpaceCsvExportService;
import org.dspace.core.Context;
import org.dspace.discovery.DiscoverQuery;
import org.dspace.discovery.IndexableObject;
import org.dspace.discovery.SearchService;
import org.dspace.discovery.SearchUtils;
import org.dspace.discovery.configuration.DiscoveryConfiguration;
import org.dspace.discovery.configuration.DiscoveryConfigurationService;
import org.dspace.discovery.indexobject.IndexableCollection;
import org.dspace.discovery.indexobject.IndexableCommunity;
import org.dspace.discovery.utils.DiscoverQueryBuilder;
import org.dspace.discovery.utils.parameter.QueryBuilderSearchFilter;
import org.dspace.eperson.factory.EPersonServiceFactory;
import org.dspace.eperson.service.EPersonService;
import org.dspace.scripts.DSpaceRunnable;
import org.dspace.sort.SortOption;
import org.dspace.utils.DSpace;
/**
* Metadata exporter to allow the batch export of metadata from a discovery search into a file
*
*/
public class MetadataExportSearch extends DSpaceRunnable<MetadataExportSearchScriptConfiguration> {
private static final String EXPORT_CSV = "exportCSV";
private boolean help = false;
private String identifier;
private String discoveryConfigName;
private String[] filterQueryStrings;
private boolean hasScope = false;
private String query;
private SearchService searchService;
private MetadataDSpaceCsvExportService metadataDSpaceCsvExportService;
private EPersonService ePersonService;
private DiscoveryConfigurationService discoveryConfigurationService;
private CommunityService communityService;
private CollectionService collectionService;
private DiscoverQueryBuilder queryBuilder;
@Override
public MetadataExportSearchScriptConfiguration getScriptConfiguration() {
return new DSpace().getServiceManager()
.getServiceByName("metadata-export-search", MetadataExportSearchScriptConfiguration.class);
}
@Override
public void setup() throws ParseException {
searchService = SearchUtils.getSearchService();
metadataDSpaceCsvExportService = new DSpace().getServiceManager()
.getServiceByName(
MetadataDSpaceCsvExportServiceImpl.class.getCanonicalName(),
MetadataDSpaceCsvExportService.class
);
ePersonService = EPersonServiceFactory.getInstance().getEPersonService();
discoveryConfigurationService = SearchUtils.getConfigurationService();
communityService = ContentServiceFactory.getInstance().getCommunityService();
collectionService = ContentServiceFactory.getInstance().getCollectionService();
queryBuilder = SearchUtils.getQueryBuilder();
if (commandLine.hasOption('h')) {
help = true;
return;
}
if (commandLine.hasOption('q')) {
query = commandLine.getOptionValue('q');
}
if (commandLine.hasOption('s')) {
hasScope = true;
identifier = commandLine.getOptionValue('s');
}
if (commandLine.hasOption('c')) {
discoveryConfigName = commandLine.getOptionValue('c');
}
if (commandLine.hasOption('f')) {
filterQueryStrings = commandLine.getOptionValues('f');
}
}
@Override
public void internalRun() throws Exception {
if (help) {
loghelpinfo();
printHelp();
return;
}
handler.logDebug("starting search export");
IndexableObject dso = null;
Context context = new Context();
context.setCurrentUser(ePersonService.find(context, this.getEpersonIdentifier()));
if (hasScope) {
dso = resolveScope(context, identifier);
}
DiscoveryConfiguration discoveryConfiguration =
discoveryConfigurationService.getDiscoveryConfiguration(discoveryConfigName);
List<QueryBuilderSearchFilter> queryBuilderSearchFilters = new ArrayList<>();
handler.logDebug("processing filter queries");
if (filterQueryStrings != null) {
for (String filterQueryString: filterQueryStrings) {
String field = filterQueryString.split(",", 2)[0];
String operator = filterQueryString.split("(,|=)", 3)[1];
String value = filterQueryString.split("=", 2)[1];
QueryBuilderSearchFilter queryBuilderSearchFilter =
new QueryBuilderSearchFilter(field, operator, value);
queryBuilderSearchFilters.add(queryBuilderSearchFilter);
}
}
handler.logDebug("building query");
DiscoverQuery discoverQuery =
queryBuilder.buildQuery(context, dso, discoveryConfiguration, query, queryBuilderSearchFilters,
"Item", 10, Long.getLong("0"), null, SortOption.DESCENDING);
handler.logDebug("creating iterator");
Iterator<Item> itemIterator = searchService.iteratorSearch(context, dso, discoverQuery);
handler.logDebug("creating dspacecsv");
DSpaceCSV dSpaceCSV = metadataDSpaceCsvExportService.export(context, itemIterator, true);
handler.logDebug("writing to file " + getFileNameOrExportFile());
handler.writeFilestream(context, getFileNameOrExportFile(), dSpaceCSV.getInputStream(), EXPORT_CSV);
context.restoreAuthSystemState();
context.complete();
}
protected void loghelpinfo() {
handler.logInfo("metadata-export");
}
protected String getFileNameOrExportFile() {
return "metadataExportSearch.csv";
}
public IndexableObject resolveScope(Context context, String id) throws SQLException {
UUID uuid = UUID.fromString(id);
IndexableObject scopeObj = new IndexableCommunity(communityService.find(context, uuid));
if (scopeObj.getIndexedObject() == null) {
scopeObj = new IndexableCollection(collectionService.find(context, uuid));
}
return scopeObj;
}
}

View File

@@ -0,0 +1,20 @@
/**
* 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.app.bulkedit;
/**
* The cli version of the {@link MetadataExportSearch} script
*/
public class MetadataExportSearchCli extends MetadataExportSearch {
@Override
protected String getFileNameOrExportFile() {
return commandLine.getOptionValue('n');
}
}

View File

@@ -0,0 +1,26 @@
/**
* 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.app.bulkedit;
import org.apache.commons.cli.Options;
/**
* This is the CLI version of the {@link MetadataExportSearchScriptConfiguration} class that handles the
* configuration for the {@link MetadataExportSearchCli} script
*/
public class MetadataExportSearchCliScriptConfiguration
extends MetadataExportSearchScriptConfiguration<MetadataExportSearchCli> {
@Override
public Options getOptions() {
Options options = super.getOptions();
options.addOption("n", "filename", true, "the filename to export to");
return super.getOptions();
}
}

View File

@@ -0,0 +1,62 @@
/**
* 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.app.bulkedit;
import org.apache.commons.cli.Options;
import org.dspace.core.Context;
import org.dspace.scripts.configuration.ScriptConfiguration;
/**
* The {@link ScriptConfiguration} for the {@link MetadataExportSearch} script
*/
public class MetadataExportSearchScriptConfiguration<T extends MetadataExportSearch> extends ScriptConfiguration<T> {
private Class<T> dspaceRunnableclass;
@Override
public Class<T> getDspaceRunnableClass() {
return dspaceRunnableclass;
}
@Override
public void setDspaceRunnableClass(Class<T> dspaceRunnableClass) {
this.dspaceRunnableclass = dspaceRunnableClass;
}
@Override
public boolean isAllowedToExecute(Context context) {
return true;
}
@Override
public Options getOptions() {
if (options == null) {
Options options = new Options();
options.addOption("q", "query", true,
"The discovery search string to will be used to match records. Not URL encoded");
options.getOption("q").setType(String.class);
options.addOption("s", "scope", true,
"UUID of a specific DSpace container (site, community or collection) to which the search has to be " +
"limited");
options.getOption("s").setType(String.class);
options.addOption("c", "configuration", true,
"The name of a Discovery configuration that should be used by this search");
options.getOption("c").setType(String.class);
options.addOption("f", "filter", true,
"Advanced search filter that has to be used to filter the result set, with syntax `<:filter-name>," +
"<:filter-operator>=<:filter-value>`. Not URL encoded. For example `author," +
"authority=5df05073-3be7-410d-8166-e254369e4166` or `title,contains=sample text`");
options.getOption("f").setType(String.class);
options.addOption("h", "help", false, "help");
super.options = options;
}
return options;
}
}

View File

@@ -925,11 +925,10 @@ public class MetadataImport extends DSpaceRunnable<MetadataImportScriptConfigura
rightItem = item;
}
// Create the relationship
int leftPlace = relationshipService.findNextLeftPlaceByLeftItem(c, leftItem);
int rightPlace = relationshipService.findNextRightPlaceByRightItem(c, rightItem);
Relationship persistedRelationship = relationshipService.create(c, leftItem, rightItem,
foundRelationshipType, leftPlace, rightPlace);
// Create the relationship, appending to the end
Relationship persistedRelationship = relationshipService.create(
c, leftItem, rightItem, foundRelationshipType, -1, -1
);
relationshipService.update(c, persistedRelationship);
}

View File

@@ -403,10 +403,8 @@ public class ItemImportServiceImpl implements ItemImportService, InitializingBea
}
// Create the relationship
int leftPlace = relationshipService.findNextLeftPlaceByLeftItem(c, leftItem);
int rightPlace = relationshipService.findNextRightPlaceByRightItem(c, rightItem);
Relationship persistedRelationship = relationshipService.create(
c, leftItem, rightItem, foundRelationshipType, leftPlace, rightPlace);
Relationship persistedRelationship =
relationshipService.create(c, leftItem, rightItem, foundRelationshipType, -1, -1);
// relationshipService.update(c, persistedRelationship);
System.out.println("\tAdded relationship (type: " + relationshipType + ") from " +

View File

@@ -227,7 +227,7 @@ public class ResearcherProfileServiceImpl implements ResearcherProfileService {
if (StringUtils.isBlank(profileType)) {
return false;
}
return profileType.equals(itemService.getEntityType(item));
return profileType.equals(itemService.getEntityTypeLabel(item));
}
@Override
@@ -251,7 +251,7 @@ public class ResearcherProfileServiceImpl implements ResearcherProfileService {
Iterator<Item> items = itemService.findByAuthorityValue(context, "dspace", "object", "owner", id.toString());
while (items.hasNext()) {
Item item = items.next();
String entityType = itemService.getEntityType(item);
String entityType = itemService.getEntityTypeLabel(item);
if (profileType.equals(entityType)) {
return item;
}

View File

@@ -0,0 +1,175 @@
/**
* 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.app.solrdatabaseresync;
import static org.dspace.discovery.indexobject.ItemIndexFactoryImpl.STATUS_FIELD;
import static org.dspace.discovery.indexobject.ItemIndexFactoryImpl.STATUS_FIELD_PREDB;
import java.io.IOException;
import java.sql.SQLException;
import java.util.Calendar;
import java.util.HashMap;
import java.util.Map;
import java.util.Optional;
import org.apache.commons.cli.ParseException;
import org.apache.logging.log4j.Logger;
import org.apache.solr.client.solrj.SolrQuery;
import org.apache.solr.client.solrj.SolrServerException;
import org.apache.solr.client.solrj.response.QueryResponse;
import org.apache.solr.common.SolrDocument;
import org.dspace.core.Context;
import org.dspace.discovery.IndexableObject;
import org.dspace.discovery.IndexingService;
import org.dspace.discovery.SearchServiceException;
import org.dspace.discovery.SearchUtils;
import org.dspace.discovery.SolrSearchCore;
import org.dspace.discovery.indexobject.IndexableItem;
import org.dspace.discovery.indexobject.factory.IndexObjectFactoryFactory;
import org.dspace.scripts.DSpaceRunnable;
import org.dspace.services.ConfigurationService;
import org.dspace.services.factory.DSpaceServicesFactory;
import org.dspace.util.SolrUtils;
import org.dspace.utils.DSpace;
/**
* {@link DSpaceRunnable} implementation to update solr items with "predb" status to either:
* - Delete them from solr if they're not present in the database
* - Remove their status if they're present in the database
*/
public class SolrDatabaseResyncCli extends DSpaceRunnable<SolrDatabaseResyncCliScriptConfiguration> {
/* Log4j logger */
private static final Logger log = org.apache.logging.log4j.LogManager.getLogger(SolrDatabaseResyncCli.class);
public static final String TIME_UNTIL_REINDEX_PROPERTY = "solr-database-resync.time-until-reindex";
private IndexingService indexingService;
private SolrSearchCore solrSearchCore;
private IndexObjectFactoryFactory indexObjectServiceFactory;
private ConfigurationService configurationService;
private int timeUntilReindex = 0;
private String maxTime;
@Override
public SolrDatabaseResyncCliScriptConfiguration getScriptConfiguration() {
return new DSpace().getServiceManager()
.getServiceByName("solr-database-resync", SolrDatabaseResyncCliScriptConfiguration.class);
}
public static void runScheduled() throws Exception {
SolrDatabaseResyncCli script = new SolrDatabaseResyncCli();
script.setup();
script.internalRun();
}
@Override
public void setup() throws ParseException {
indexingService = DSpaceServicesFactory.getInstance().getServiceManager()
.getServiceByName(IndexingService.class.getName(), IndexingService.class);
solrSearchCore = DSpaceServicesFactory.getInstance().getServiceManager()
.getServicesByType(SolrSearchCore.class).get(0);
indexObjectServiceFactory = IndexObjectFactoryFactory.getInstance();
configurationService = DSpaceServicesFactory.getInstance().getConfigurationService();
}
@Override
public void internalRun() throws Exception {
logInfoAndOut("Starting Item resync of Solr and Database...");
timeUntilReindex = getTimeUntilReindex();
maxTime = getMaxTime();
Context context = new Context();
try {
context.turnOffAuthorisationSystem();
performStatusUpdate(context);
} finally {
context.restoreAuthSystemState();
context.complete();
}
}
private void performStatusUpdate(Context context) throws SearchServiceException, SolrServerException, IOException {
SolrQuery solrQuery = new SolrQuery();
solrQuery.setQuery(STATUS_FIELD + ":" + STATUS_FIELD_PREDB);
solrQuery.addFilterQuery(SearchUtils.RESOURCE_TYPE_FIELD + ":" + IndexableItem.TYPE);
String dateRangeFilter = SearchUtils.LAST_INDEXED_FIELD + ":[* TO " + maxTime + "]";
logDebugAndOut("Date range filter used; " + dateRangeFilter);
solrQuery.addFilterQuery(dateRangeFilter);
solrQuery.addField(SearchUtils.RESOURCE_ID_FIELD);
solrQuery.addField(SearchUtils.RESOURCE_UNIQUE_ID);
QueryResponse response = solrSearchCore.getSolr().query(solrQuery, solrSearchCore.REQUEST_METHOD);
if (response != null) {
logInfoAndOut(response.getResults().size() + " items found to process");
for (SolrDocument doc : response.getResults()) {
String uuid = (String) doc.getFirstValue(SearchUtils.RESOURCE_ID_FIELD);
String uniqueId = (String) doc.getFirstValue(SearchUtils.RESOURCE_UNIQUE_ID);
logDebugAndOut("Processing item with UUID: " + uuid);
Optional<IndexableObject> indexableObject = Optional.empty();
try {
indexableObject = indexObjectServiceFactory
.getIndexableObjectFactory(uniqueId).findIndexableObject(context, uuid);
} catch (SQLException e) {
log.warn("An exception occurred when attempting to retrieve item with UUID \"" + uuid +
"\" from the database, removing related solr document", e);
}
try {
if (indexableObject.isPresent()) {
logDebugAndOut("Item exists in DB, updating solr document");
updateItem(context, indexableObject.get());
} else {
logDebugAndOut("Item doesn't exist in DB, removing solr document");
removeItem(context, uniqueId);
}
} catch (SQLException | IOException e) {
log.error(e.getMessage(), e);
}
}
}
indexingService.commit();
}
private void updateItem(Context context, IndexableObject indexableObject) throws SolrServerException, IOException {
Map<String,Object> fieldModifier = new HashMap<>(1);
fieldModifier.put("remove", STATUS_FIELD_PREDB);
indexingService.atomicUpdate(context, indexableObject.getUniqueIndexID(), STATUS_FIELD, fieldModifier);
}
private void removeItem(Context context, String uniqueId) throws IOException, SQLException {
indexingService.unIndexContent(context, uniqueId);
}
private String getMaxTime() {
Calendar cal = Calendar.getInstance();
if (timeUntilReindex > 0) {
cal.add(Calendar.MILLISECOND, -timeUntilReindex);
}
return SolrUtils.getDateFormatter().format(cal.getTime());
}
private int getTimeUntilReindex() {
return configurationService.getIntProperty(TIME_UNTIL_REINDEX_PROPERTY, 0);
}
private void logInfoAndOut(String message) {
log.info(message);
System.out.println(message);
}
private void logDebugAndOut(String message) {
log.debug(message);
System.out.println(message);
}
}

View File

@@ -0,0 +1,42 @@
/**
* 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.app.solrdatabaseresync;
import org.apache.commons.cli.Options;
import org.dspace.core.Context;
import org.dspace.scripts.configuration.ScriptConfiguration;
/**
* The {@link ScriptConfiguration} for the {@link SolrDatabaseResyncCli} script.
*/
public class SolrDatabaseResyncCliScriptConfiguration extends ScriptConfiguration<SolrDatabaseResyncCli> {
private Class<SolrDatabaseResyncCli> dspaceRunnableClass;
@Override
public Class<SolrDatabaseResyncCli> getDspaceRunnableClass() {
return dspaceRunnableClass;
}
@Override
public void setDspaceRunnableClass(Class<SolrDatabaseResyncCli> dspaceRunnableClass) {
this.dspaceRunnableClass = dspaceRunnableClass;
}
@Override
public boolean isAllowedToExecute(Context context) {
return true;
}
@Override
public Options getOptions() {
if (options == null) {
options = new Options();
}
return options;
}
}

View File

@@ -158,6 +158,11 @@ public class BundleServiceImpl extends DSpaceObjectServiceImpl<Bundle> implement
}
bundle.addBitstream(bitstream);
// If a bitstream is moved from one bundle to another it may be temporarily flagged as deleted
// (when removed from the original bundle)
if (bitstream.isDeleted()) {
bitstream.setDeleted(false);
}
bitstream.getBundles().add(bundle);

View File

@@ -621,8 +621,14 @@ public abstract class DSpaceObjectServiceImpl<T extends DSpaceObject> implements
});
for (MetadataValue metadataValue : metadataValues) {
//Retrieve & store the place for each metadata value
if (StringUtils.startsWith(metadataValue.getAuthority(), Constants.VIRTUAL_AUTHORITY_PREFIX) &&
((RelationshipMetadataValue) metadataValue).isUseForPlace()) {
if (
// For virtual MDVs with useForPlace=true,
// update both the place of the metadatum and the place of the Relationship.
// E.g. for an Author relationship,
// the place should be updated using the same principle as dc.contributor.author.
StringUtils.startsWith(metadataValue.getAuthority(), Constants.VIRTUAL_AUTHORITY_PREFIX)
&& ((RelationshipMetadataValue) metadataValue).isUseForPlace()
) {
int mvPlace = getMetadataValuePlace(fieldToLastPlace, metadataValue);
metadataValue.setPlace(mvPlace);
String authority = metadataValue.getAuthority();
@@ -635,8 +641,16 @@ public abstract class DSpaceObjectServiceImpl<T extends DSpaceObject> implements
}
relationshipService.update(context, relationship);
} else if (!StringUtils.startsWith(metadataValue.getAuthority(),
Constants.VIRTUAL_AUTHORITY_PREFIX)) {
} else if (
// Otherwise, just set the place of the metadatum
// ...unless the metadatum in question is a relation.* metadatum.
// This case is a leftover from when a Relationship is removed and copied to metadata.
// If we let its place change the order of any remaining Relationships will be affected.
// todo: this makes it so these leftover MDVs can't be reordered later on
!StringUtils.equals(
metadataValue.getMetadataField().getMetadataSchema().getName(), "relation"
)
) {
int mvPlace = getMetadataValuePlace(fieldToLastPlace, metadataValue);
metadataValue.setPlace(mvPlace);
}

View File

@@ -49,6 +49,7 @@ import org.dspace.content.service.BitstreamService;
import org.dspace.content.service.BundleService;
import org.dspace.content.service.CollectionService;
import org.dspace.content.service.CommunityService;
import org.dspace.content.service.EntityTypeService;
import org.dspace.content.service.InstallItemService;
import org.dspace.content.service.ItemService;
import org.dspace.content.service.MetadataSchemaService;
@@ -129,6 +130,9 @@ public class ItemServiceImpl extends DSpaceObjectServiceImpl<Item> implements It
@Autowired(required = true)
private RelationshipMetadataService relationshipMetadataService;
@Autowired(required = true)
private EntityTypeService entityTypeService;
@Autowired
private OrcidTokenService orcidTokenService;
@@ -265,6 +269,10 @@ public class ItemServiceImpl extends DSpaceObjectServiceImpl<Item> implements It
return itemDAO.findAll(context, true, true);
}
public Iterator<Item> findAllRegularItems(Context context) throws SQLException {
return itemDAO.findAllRegularItems(context);
};
@Override
public Iterator<Item> findBySubmitter(Context context, EPerson eperson) throws SQLException {
return itemDAO.findBySubmitter(context, eperson);
@@ -748,7 +756,7 @@ public class ItemServiceImpl extends DSpaceObjectServiceImpl<Item> implements It
+ item.getID()));
// Remove relationships
for (Relationship relationship : relationshipService.findByItem(context, item)) {
for (Relationship relationship : relationshipService.findByItem(context, item, -1, -1, false, false)) {
relationshipService.forceDelete(context, relationship, false, false);
}
@@ -1611,8 +1619,36 @@ prevent the generation of resource policy entry values with null dspace_object a
}
@Override
public String getEntityType(Item item) {
return getMetadataFirstValue(item, new MetadataFieldName("dspace.entity.type"), Item.ANY);
public String getEntityTypeLabel(Item item) {
List<MetadataValue> mdvs = getMetadata(item, "dspace", "entity", "type", Item.ANY, false);
if (mdvs.isEmpty()) {
return null;
}
if (mdvs.size() > 1) {
log.warn(
"Item with uuid {}, handle {} has {} entity types ({}), expected 1 entity type",
item.getID(), item.getHandle(), mdvs.size(),
mdvs.stream().map(MetadataValue::getValue).collect(Collectors.toList())
);
}
String entityType = mdvs.get(0).getValue();
if (StringUtils.isBlank(entityType)) {
return null;
}
return entityType;
}
@Override
public EntityType getEntityType(Context context, Item item) throws SQLException {
String entityTypeString = getEntityTypeLabel(item);
if (StringUtils.isBlank(entityTypeString)) {
return null;
}
return entityTypeService.findByEntityType(context, entityTypeString);
}
private void removeOrcidSynchronizationStuff(Context context, Item item) throws SQLException, AuthorizeException {

View File

@@ -89,6 +89,15 @@ public class Relationship implements ReloadableEntity<Integer> {
@Column(name = "rightward_value")
private String rightwardValue;
/**
* Whether the left and/or right side of a given relationship are the "latest".
* A side of a relationship is "latest" if the item on that side has either no other versions,
* or the item on that side is the most recent version that is relevant to the given relationship.
* This column affects what version of an item appears on search pages or the relationship listings of other items.
*/
@Column(name = "latest_version_status")
private LatestVersionStatus latestVersionStatus = LatestVersionStatus.BOTH;
/**
* Protected constructor, create object using:
* {@link org.dspace.content.service.RelationshipService#create(Context)} }
@@ -216,6 +225,39 @@ public class Relationship implements ReloadableEntity<Integer> {
this.rightwardValue = rightwardValue;
}
/**
* Getter for {@link #latestVersionStatus}.
* @return the latest version status of this relationship.
*/
public LatestVersionStatus getLatestVersionStatus() {
return latestVersionStatus;
}
/**
* Setter for {@link #latestVersionStatus}.
* @param latestVersionStatus the new latest version status for this relationship.
*/
public void setLatestVersionStatus(LatestVersionStatus latestVersionStatus) {
if (this.latestVersionStatus == latestVersionStatus) {
return; // no change or cache reset needed
}
this.latestVersionStatus = latestVersionStatus;
// on one item, relation.* fields will change
// on the other item, relation.*.latestForDiscovery will change
leftItem.setMetadataModified();
rightItem.setMetadataModified();
}
public enum LatestVersionStatus {
// NOTE: SQL migration expects BOTH to be the first constant in this enum!
BOTH, // both items in this relationship are the "latest"
LEFT_ONLY, // the left-hand item of this relationship is the "latest", but the right-hand item is not
RIGHT_ONLY // the right-hand item of this relationship is the "latest", but the left-hand item is not
// NOTE: one side of any given relationship should ALWAYS be the "latest"
}
/**
* Standard getter for the ID for this Relationship
* @return The ID of this relationship

View File

@@ -56,7 +56,9 @@ public interface RelationshipMetadataService {
* This method will retrieve the EntityType String from an item
* @param item The Item for which the entityType String will be returned
* @return A String value indicating the entityType
* @deprecated use {@link org.dspace.content.service.ItemService#getEntityTypeLabel(Item)} instead.
*/
@Deprecated
public String getEntityTypeStringFromMetadata(Item item);
}

View File

@@ -7,16 +7,24 @@
*/
package org.dspace.content;
import static org.dspace.content.RelationshipType.Tilted.LEFT;
import static org.dspace.content.RelationshipType.Tilted.RIGHT;
import java.sql.SQLException;
import java.util.HashMap;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
import java.util.Objects;
import java.util.stream.Collectors;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.Logger;
import org.dspace.content.dao.pojo.ItemUuidAndRelationshipId;
import org.dspace.content.service.ItemService;
import org.dspace.content.service.MetadataFieldService;
import org.dspace.content.service.RelationshipService;
import org.dspace.content.service.RelationshipTypeService;
import org.dspace.content.virtual.VirtualMetadataConfiguration;
import org.dspace.content.virtual.VirtualMetadataPopulator;
import org.dspace.core.Constants;
@@ -33,6 +41,12 @@ public class RelationshipMetadataServiceImpl implements RelationshipMetadataServ
@Autowired(required = true)
protected RelationshipService relationshipService;
@Autowired(required = true)
protected RelationshipTypeService relationshipTypeService;
@Autowired(required = true)
protected ItemService itemService;
@Autowired(required = true)
protected VirtualMetadataPopulator virtualMetadataPopulator;
@@ -44,12 +58,25 @@ public class RelationshipMetadataServiceImpl implements RelationshipMetadataServ
Context context = new Context();
List<RelationshipMetadataValue> fullMetadataValueList = new LinkedList<>();
try {
String entityType = getEntityTypeStringFromMetadata(item);
if (StringUtils.isNotBlank(entityType)) {
EntityType entityType = itemService.getEntityType(context, item);
if (entityType != null) {
// NOTE: The following code will add metadata fields of type relation.*.latestForDiscovery
// (e.g. relation.isAuthorOfPublication.latestForDiscovery).
// These fields contain the UUIDs of the items that have a relationship with current item,
// from the perspective of the other item. In other words, given a relationship with this item,
// the current item should have "latest status" in order for the other item to appear in
// relation.*.latestForDiscovery fields.
fullMetadataValueList.addAll(findLatestForDiscoveryMetadataValues(context, item, entityType));
// NOTE: The following code will, among other things,
// add metadata fields of type relation.* (e.g. relation.isAuthorOfPublication).
// These fields contain the UUIDs of the items that have a relationship with current item,
// from the perspective of this item. In other words, given a relationship with this item,
// the other item should have "latest status" in order to appear in relation.* fields.
List<Relationship> relationships = relationshipService.findByItem(context, item, -1, -1, true);
for (Relationship relationship : relationships) {
fullMetadataValueList
.addAll(findRelationshipMetadataValueForItemRelationship(context, item, entityType,
.addAll(findRelationshipMetadataValueForItemRelationship(context, item, entityType.getLabel(),
relationship, enableVirtualMetadata));
}
@@ -60,18 +87,92 @@ public class RelationshipMetadataServiceImpl implements RelationshipMetadataServ
return fullMetadataValueList;
}
public String getEntityTypeStringFromMetadata(Item item) {
List<MetadataValue> list = item.getMetadata();
for (MetadataValue mdv : list) {
if (StringUtils.equals(mdv.getMetadataField().getMetadataSchema().getName(), "dspace")
&& StringUtils.equals(mdv.getMetadataField().getElement(), "entity")
&& StringUtils.equals(mdv.getMetadataField().getQualifier(), "type")) {
return mdv.getValue();
/**
* Create the list of relation.*.latestForDiscovery virtual metadata values for the given item.
* @param context the DSpace context.
* @param item the item.
* @param itemEntityType the entity type of the item.
* @return a list (may be empty) of metadata values of type relation.*.latestForDiscovery.
*/
protected List<RelationshipMetadataValue> findLatestForDiscoveryMetadataValues(
Context context, Item item, EntityType itemEntityType
) throws SQLException {
final String schema = MetadataSchemaEnum.RELATION.getName();
final String qualifier = "latestForDiscovery";
List<RelationshipMetadataValue> mdvs = new LinkedList<>();
List<RelationshipType> relationshipTypes = relationshipTypeService.findByEntityType(context, itemEntityType);
for (RelationshipType relationshipType : relationshipTypes) {
// item is on left side of this relationship type
// NOTE: On the left item, we should index the uuids of the right items. If the relationship type is
// "tilted right", it means that we expect a huge amount of right items, so we don't index their uuids
// on the left item as a storage/performance improvement.
// As a consequence, when searching for related items (using discovery)
// on the pages of the right items you won't be able to find the left item.
if (relationshipType.getTilted() != RIGHT && relationshipType.getLeftType().equals(itemEntityType)) {
String element = relationshipType.getLeftwardType();
List<ItemUuidAndRelationshipId> data = relationshipService
.findByLatestItemAndRelationshipType(context, item, relationshipType, true);
mdvs.addAll(constructLatestForDiscoveryMetadataValues(context, schema, element, qualifier, data));
}
// item is on right side of this relationship type
// NOTE: On the right item, we should index the uuids of the left items. If the relationship type is
// "tilted left", it means that we expect a huge amount of left items, so we don't index their uuids
// on the right item as a storage/performance improvement.
// As a consequence, when searching for related items (using discovery)
// on the pages of the left items you won't be able to find the right item.
if (relationshipType.getTilted() != LEFT && relationshipType.getRightType().equals(itemEntityType)) {
String element = relationshipType.getRightwardType();
List<ItemUuidAndRelationshipId> data = relationshipService
.findByLatestItemAndRelationshipType(context, item, relationshipType, false);
mdvs.addAll(constructLatestForDiscoveryMetadataValues(context, schema, element, qualifier, data));
}
}
return mdvs;
}
/**
* Turn the given data into a list of relation.*.latestForDiscovery virtual metadata values.
* @param context the DSpace context.
* @param schema the schema for all metadata values.
* @param element the element for all metadata values.
* @param qualifier the qualifier for all metadata values.
* @param data a POJO containing the item uuid and relationship id.
* @return a list (may be empty) of metadata values of type relation.*.latestForDiscovery.
*/
protected List<RelationshipMetadataValue> constructLatestForDiscoveryMetadataValues(
Context context, String schema, String element, String qualifier, List<ItemUuidAndRelationshipId> data
) {
String mdf = new MetadataFieldName(schema, element, qualifier).toString();
return data.stream()
.map(datum -> {
RelationshipMetadataValue mdv = constructMetadataValue(context, mdf);
if (mdv == null) {
return null;
}
mdv.setAuthority(Constants.VIRTUAL_AUTHORITY_PREFIX + datum.getRelationshipId());
mdv.setValue(datum.getItemUuid().toString());
// NOTE: place has no meaning for relation.*.latestForDiscovery metadata fields
mdv.setPlace(-1);
mdv.setUseForPlace(false);
return mdv;
})
.filter(Objects::nonNull)
.collect(Collectors.toUnmodifiableList());
}
@Override
@Deprecated
public String getEntityTypeStringFromMetadata(Item item) {
return itemService.getEntityTypeLabel(item);
}
@Override
public List<RelationshipMetadataValue> findRelationshipMetadataValueForItemRelationship(
Context context, Item item, String entityType, Relationship relationship, boolean enableVirtualMetadata)

View File

@@ -10,9 +10,11 @@ package org.dspace.content;
import java.sql.SQLException;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Comparator;
import java.util.HashMap;
import java.util.List;
import java.util.UUID;
import java.util.stream.Collectors;
import java.util.stream.Stream;
import org.apache.commons.collections4.CollectionUtils;
import org.apache.commons.lang3.StringUtils;
@@ -20,15 +22,19 @@ import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.authorize.AuthorizeException;
import org.dspace.authorize.service.AuthorizeService;
import org.dspace.content.Relationship.LatestVersionStatus;
import org.dspace.content.dao.RelationshipDAO;
import org.dspace.content.dao.pojo.ItemUuidAndRelationshipId;
import org.dspace.content.service.EntityTypeService;
import org.dspace.content.service.ItemService;
import org.dspace.content.service.RelationshipService;
import org.dspace.content.service.RelationshipTypeService;
import org.dspace.content.virtual.VirtualMetadataConfiguration;
import org.dspace.content.virtual.VirtualMetadataPopulator;
import org.dspace.core.Constants;
import org.dspace.core.Context;
import org.dspace.services.ConfigurationService;
import org.dspace.versioning.utils.RelationshipVersioningUtils;
import org.springframework.beans.factory.annotation.Autowired;
public class RelationshipServiceImpl implements RelationshipService {
@@ -55,6 +61,10 @@ public class RelationshipServiceImpl implements RelationshipService {
@Autowired
private RelationshipMetadataService relationshipMetadataService;
@Autowired
private RelationshipVersioningUtils relationshipVersioningUtils;
@Autowired
private VirtualMetadataPopulator virtualMetadataPopulator;
@@ -76,9 +86,10 @@ public class RelationshipServiceImpl implements RelationshipService {
@Override
public Relationship create(Context c, Item leftItem, Item rightItem, RelationshipType relationshipType,
int leftPlace, int rightPlace, String leftwardValue, String rightwardValue)
throws AuthorizeException, SQLException {
public Relationship create(
Context c, Item leftItem, Item rightItem, RelationshipType relationshipType, int leftPlace, int rightPlace,
String leftwardValue, String rightwardValue, LatestVersionStatus latestVersionStatus
) throws AuthorizeException, SQLException {
Relationship relationship = new Relationship();
relationship.setLeftItem(leftItem);
relationship.setRightItem(rightItem);
@@ -87,9 +98,21 @@ public class RelationshipServiceImpl implements RelationshipService {
relationship.setRightPlace(rightPlace);
relationship.setLeftwardValue(leftwardValue);
relationship.setRightwardValue(rightwardValue);
relationship.setLatestVersionStatus(latestVersionStatus);
return create(c, relationship);
}
@Override
public Relationship create(
Context c, Item leftItem, Item rightItem, RelationshipType relationshipType, int leftPlace, int rightPlace,
String leftwardValue, String rightwardValue
) throws AuthorizeException, SQLException {
return create(
c, leftItem, rightItem, relationshipType, leftPlace, rightPlace, leftwardValue, rightwardValue,
LatestVersionStatus.BOTH
);
}
@Override
public Relationship create(Context context, Relationship relationship) throws SQLException, AuthorizeException {
if (isRelationshipValidToCreate(context, relationship)) {
@@ -98,7 +121,7 @@ public class RelationshipServiceImpl implements RelationshipService {
// This order of execution should be handled in the creation (create, updateplace, update relationship)
// for a proper place allocation
Relationship relationshipToReturn = relationshipDAO.create(context, relationship);
updatePlaceInRelationship(context, relationshipToReturn);
updatePlaceInRelationship(context, relationshipToReturn, null, null, true, true);
update(context, relationshipToReturn);
updateItemsInRelationship(context, relationship);
return relationshipToReturn;
@@ -113,71 +136,388 @@ public class RelationshipServiceImpl implements RelationshipService {
}
@Override
public void updatePlaceInRelationship(Context context, Relationship relationship)
throws SQLException, AuthorizeException {
public Relationship move(
Context context, Relationship relationship, Integer newLeftPlace, Integer newRightPlace
) throws SQLException, AuthorizeException {
if (authorizeService.authorizeActionBoolean(context, relationship.getLeftItem(), Constants.WRITE) ||
authorizeService.authorizeActionBoolean(context, relationship.getRightItem(), Constants.WRITE)) {
// Don't do anything if neither the leftPlace nor rightPlace was updated
if (newLeftPlace != null || newRightPlace != null) {
// This order of execution should be handled in the creation (create, updateplace, update relationship)
// for a proper place allocation
updatePlaceInRelationship(context, relationship, newLeftPlace, newRightPlace, false, false);
update(context, relationship);
updateItemsInRelationship(context, relationship);
}
return relationship;
} else {
throw new AuthorizeException(
"You do not have write rights on this relationship's items");
}
}
@Override
public Relationship move(
Context context, Relationship relationship, Item newLeftItem, Item newRightItem
) throws SQLException, AuthorizeException {
// If the new Item is the same as the current Item, don't move
newLeftItem = newLeftItem != relationship.getLeftItem() ? newLeftItem : null;
newRightItem = newRightItem != relationship.getRightItem() ? newRightItem : null;
// Don't do anything if neither the leftItem nor rightItem was updated
if (newLeftItem != null || newRightItem != null) {
// First move the Relationship to the back within the current Item's lists
// This ensures that we won't have any gaps once we move the Relationship to a different Item
move(
context, relationship,
newLeftItem != null ? -1 : null,
newRightItem != null ? -1 : null
);
boolean insertLeft = false;
boolean insertRight = false;
// If Item has been changed, mark the previous Item as modified to make sure we discard the old relation.*
// metadata on the next update.
// Set the Relationship's Items to the new ones, appending to the end
if (newLeftItem != null) {
relationship.getLeftItem().setMetadataModified();
relationship.setLeftItem(newLeftItem);
relationship.setLeftPlace(-1);
insertLeft = true;
}
if (newRightItem != null) {
relationship.getRightItem().setMetadataModified();
relationship.setRightItem(newRightItem);
relationship.setRightPlace(-1);
insertRight = true;
}
// This order of execution should be handled in the creation (create, updateplace, update relationship)
// for a proper place allocation
updatePlaceInRelationship(context, relationship, null, null, insertLeft, insertRight);
update(context, relationship);
updateItemsInRelationship(context, relationship);
}
return relationship;
}
/**
* This method will update the place for the Relationship and all other relationships found by the items and
* relationship type of the given Relationship.
*
* @param context The relevant DSpace context
* @param relationship The Relationship object that will have its place updated and that will be used
* to retrieve the other relationships whose place might need to be updated.
* @param newLeftPlace If the Relationship in question is to be moved, the leftPlace it is to be moved to.
* Set this to null if the Relationship has not been moved, i.e. it has just been created,
* deleted or when its Items have been modified.
* @param newRightPlace If the Relationship in question is to be moved, the rightPlace it is to be moved to.
* Set this to null if the Relationship has not been moved, i.e. it has just been created,
* deleted or when its Items have been modified.
* @param insertLeft Whether the Relationship in question should be inserted into the left Item.
* Should be set to true when creating or moving to a different Item.
* @param insertRight Whether the Relationship in question should be inserted into the right Item.
* Should be set to true when creating or moving to a different Item.
* @throws SQLException If something goes wrong
* @throws AuthorizeException
* If the user is not authorized to update the Relationship or its Items
*/
private void updatePlaceInRelationship(
Context context, Relationship relationship,
Integer newLeftPlace, Integer newRightPlace, boolean insertLeft, boolean insertRight
) throws SQLException, AuthorizeException {
Item leftItem = relationship.getLeftItem();
// Max value is used to ensure that these will get added to the back of the list and thus receive the highest
// (last) place as it's set to a -1 for creation
if (relationship.getLeftPlace() == -1) {
relationship.setLeftPlace(Integer.MAX_VALUE);
}
Item rightItem = relationship.getRightItem();
if (relationship.getRightPlace() == -1) {
relationship.setRightPlace(Integer.MAX_VALUE);
}
List<Relationship> leftRelationships = findByItemAndRelationshipType(context,
leftItem,
relationship.getRelationshipType(), true);
List<Relationship> rightRelationships = findByItemAndRelationshipType(context,
rightItem,
relationship.getRelationshipType(),
false);
// These relationships are only deleted from the temporary lists incase they're present in them so that we can
// These list also include the non-latest. This is relevant to determine whether it's deleted.
// This can also imply there may be overlapping places, and/or the given relationship will overlap
// But the shift will allow this, and only happen when needed based on the latest status
List<Relationship> leftRelationships = findByItemAndRelationshipType(
context, leftItem, relationship.getRelationshipType(), true, -1, -1, false
);
List<Relationship> rightRelationships = findByItemAndRelationshipType(
context, rightItem, relationship.getRelationshipType(), false, -1, -1, false
);
// These relationships are only deleted from the temporary lists in case they're present in them so that we can
// properly perform our place calculation later down the line in this method.
if (leftRelationships.contains(relationship)) {
boolean deletedFromLeft = !leftRelationships.contains(relationship);
boolean deletedFromRight = !rightRelationships.contains(relationship);
leftRelationships.remove(relationship);
}
if (rightRelationships.contains(relationship)) {
rightRelationships.remove(relationship);
}
List<MetadataValue> leftMetadata = getSiblingMetadata(leftItem, relationship, true);
List<MetadataValue> rightMetadata = getSiblingMetadata(rightItem, relationship, false);
// For new relationships added to the end, this will be -1.
// For new relationships added at a specific position, this will contain that position.
// For existing relationships, this will contain the place before it was moved.
// For deleted relationships, this will contain the place before it was deleted.
int oldLeftPlace = relationship.getLeftPlace();
int oldRightPlace = relationship.getRightPlace();
boolean movedUpLeft = resolveRelationshipPlace(
relationship, true, leftRelationships, leftMetadata, oldLeftPlace, newLeftPlace
);
boolean movedUpRight = resolveRelationshipPlace(
relationship, false, rightRelationships, rightMetadata, oldRightPlace, newRightPlace
);
context.turnOffAuthorisationSystem();
//If useForPlace for the leftwardType is false for the relationshipType,
// we need to sort the relationships here based on leftplace.
if (!virtualMetadataPopulator.isUseForPlaceTrueForRelationshipType(relationship.getRelationshipType(), true)) {
if (!leftRelationships.isEmpty()) {
leftRelationships.sort(Comparator.comparingInt(Relationship::getLeftPlace));
for (int i = 0; i < leftRelationships.size(); i++) {
leftRelationships.get(i).setLeftPlace(i);
//only shift if the place is relevant for the latest relationships
if (relationshipVersioningUtils.otherSideIsLatest(true, relationship.getLatestVersionStatus())) {
shiftSiblings(
relationship, true, oldLeftPlace, movedUpLeft, insertLeft, deletedFromLeft,
leftRelationships, leftMetadata
);
}
relationship.setLeftPlace(leftRelationships.size());
} else {
relationship.setLeftPlace(0);
if (relationshipVersioningUtils.otherSideIsLatest(false, relationship.getLatestVersionStatus())) {
shiftSiblings(
relationship, false, oldRightPlace, movedUpRight, insertRight, deletedFromRight,
rightRelationships, rightMetadata
);
}
} else {
updateItem(context, leftItem);
}
//If useForPlace for the rightwardType is false for the relationshipType,
// we need to sort the relationships here based on the rightplace.
if (!virtualMetadataPopulator.isUseForPlaceTrueForRelationshipType(relationship.getRelationshipType(), false)) {
if (!rightRelationships.isEmpty()) {
rightRelationships.sort(Comparator.comparingInt(Relationship::getRightPlace));
for (int i = 0; i < rightRelationships.size(); i++) {
rightRelationships.get(i).setRightPlace(i);
}
relationship.setRightPlace(rightRelationships.size());
} else {
relationship.setRightPlace(0);
}
} else {
updateItem(context, rightItem);
}
context.restoreAuthSystemState();
}
/**
* Return the MDVs in the Item's MDF corresponding to the given Relationship.
* Return an empty list if the Relationship isn't mapped to any MDF
* or if the mapping is configured with useForPlace=false.
*
* This returns actual metadata (not virtual) which in the same metadata field as the useForPlace.
* For a publication with 2 author relationships and 3 plain text dc.contributor.author values,
* it would return the 3 plain text dc.contributor.author values.
* For a person related to publications, it would return an empty list.
*/
private List<MetadataValue> getSiblingMetadata(
Item item, Relationship relationship, boolean isLeft
) {
List<MetadataValue> metadata = new ArrayList<>();
if (virtualMetadataPopulator.isUseForPlaceTrueForRelationshipType(relationship.getRelationshipType(), isLeft)) {
HashMap<String, VirtualMetadataConfiguration> mapping;
if (isLeft) {
mapping = virtualMetadataPopulator.getMap().get(relationship.getRelationshipType().getLeftwardType());
} else {
mapping = virtualMetadataPopulator.getMap().get(relationship.getRelationshipType().getRightwardType());
}
if (mapping != null) {
for (String mdf : mapping.keySet()) {
metadata.addAll(
// Make sure we're only looking at database MDVs; if the relationship currently overlaps
// one of these, its virtual MDV will overwrite the database MDV in itemService.getMetadata()
// The relationship pass should be sufficient to move any sibling virtual MDVs.
item.getMetadata()
.stream()
.filter(mdv -> mdv.getMetadataField().toString().equals(mdf.replace(".", "_")))
.collect(Collectors.toList())
);
}
}
}
return metadata;
}
/**
* Set the left/right place of a Relationship
* - To a new place in case it's being moved
* - Resolve -1 to the actual last place based on the places of its sibling Relationships and/or MDVs
* and determine if it has been moved up in the list.
*
* Examples:
* - Insert a Relationship at place 3
* newPlace starts out as null and is not updated. Return movedUp=false
* - Insert a Relationship at place -1
* newPlace starts out as null and is resolved to e.g. 6. Update the Relationship and return movedUp=false
* - Move a Relationship from place 4 to 2
* Update the Relationship and return movedUp=false.
* - Move a Relationship from place 2 to -1
* newPlace starts out as -1 and is resolved to e.g. 5. Update the relationship and return movedUp=true.
* - Remove a relationship from place 1
* Return movedUp=false
*
* @param relationship the Relationship that's being updated
* @param isLeft whether to consider the left side of the Relationship.
* This method should be called twice, once with isLeft=true and once with isLeft=false.
* Make sure this matches the provided relationships/metadata/oldPlace/newPlace.
* @param relationships the list of sibling Relationships
* @param metadata the list of sibling MDVs
* @param oldPlace the previous place for this Relationship, in case it has been moved.
* Otherwise, the current place of a deleted Relationship
* or the place a Relationship has been inserted.
* @param newPlace The new place for this Relationship. Will be null on insert/delete.
* @return true if the Relationship was moved and newPlace > oldPlace
*/
private boolean resolveRelationshipPlace(
Relationship relationship, boolean isLeft,
List<Relationship> relationships, List<MetadataValue> metadata,
int oldPlace, Integer newPlace
) {
boolean movedUp = false;
if (newPlace != null) {
// We're moving an existing Relationship...
if (newPlace == -1) {
// ...to the end of the list
int nextPlace = getNextPlace(relationships, metadata, isLeft);
if (nextPlace == oldPlace) {
// If this Relationship is already at the end, do nothing.
newPlace = oldPlace;
} else {
// Subtract 1 from the next place since we're moving, not inserting and
// the total number of Relationships stays the same.
newPlace = nextPlace - 1;
}
}
if (newPlace > oldPlace) {
// ...up the list. We have to keep track of this in order to shift correctly later on
movedUp = true;
}
} else if (oldPlace == -1) {
// We're _not_ moving an existing Relationship. The newPlace is already set in the Relationship object.
// We only need to resolve it to the end of the list if it's set to -1, otherwise we can just keep it as is.
newPlace = getNextPlace(relationships, metadata, isLeft);
}
if (newPlace != null) {
setPlace(relationship, isLeft, newPlace);
}
return movedUp;
}
/**
* Return the index of the next place in a list of Relationships and Metadata.
* By not relying on the size of both lists we can support one-to-many virtual MDV mappings.
* @param isLeft whether to take the left or right place of each Relationship
*/
private int getNextPlace(List<Relationship> relationships, List<MetadataValue> metadata, boolean isLeft) {
return Stream.concat(
metadata.stream().map(MetadataValue::getPlace),
relationships.stream().map(r -> getPlace(r, isLeft))
).max(Integer::compare)
.map(integer -> integer + 1)
.orElse(0);
}
/**
* Adjust the left/right place of sibling Relationships and MDVs
*
* Examples: with sibling Relationships R,S,T and metadata a,b,c
* - Insert T at place 1 aRbSc -> a T RbSc
* Shift all siblings with place >= 1 one place to the right
* - Delete R from place 2 aT R bSc -> aTbSc
* Shift all siblings with place > 2 one place to the left
* - Move S from place 3 to place 2 (movedUp=false) aTb S c -> aT S bc
* Shift all siblings with 2 < place <= 3 one place to the right
* - Move T from place 1 to place 3 (movedUp=true) a T Sbc -> aSb T c
* Shift all siblings with 1 < place <= 3 one place to the left
*
* @param relationship the Relationship that's being updated
* @param isLeft whether to consider the left side of the Relationship.
* This method should be called twice, once with isLeft=true and once with isLeft=false.
* Make sure this matches the provided relationships/metadata/oldPlace/newPlace.
* @param oldPlace the previous place for this Relationship, in case it has been moved.
* Otherwise, the current place of a deleted Relationship
* or the place a Relationship has been inserted.
* @param movedUp if this Relationship has been moved up the list, e.g. from place 2 to place 4
* @param deleted whether this Relationship has been deleted
* @param relationships the list of sibling Relationships
* @param metadata the list of sibling MDVs
*/
private void shiftSiblings(
Relationship relationship, boolean isLeft, int oldPlace, boolean movedUp, boolean inserted, boolean deleted,
List<Relationship> relationships, List<MetadataValue> metadata
) {
int newPlace = getPlace(relationship, isLeft);
for (Relationship sibling : relationships) {
// NOTE: If and only if the other side of the relationship has "latest" status, the relationship will appear
// as a metadata value on the item at the current side (indicated by isLeft) of the relationship.
//
// Example: volume <----> issue (LEFT_ONLY)
// => LEFT_ONLY means that the volume has "latest" status, but the issue does NOT have "latest" status
// => the volume will appear in the metadata of the issue,
// but the issue will NOT appear in the metadata of the volume
//
// This means that the other side of the relationship has to have "latest" status, otherwise this
// relationship is NOT relevant for place calculation.
if (relationshipVersioningUtils.otherSideIsLatest(isLeft, sibling.getLatestVersionStatus())) {
int siblingPlace = getPlace(sibling, isLeft);
if (
(deleted && siblingPlace > newPlace)
// If the relationship was deleted, all relationships after it should shift left
// We must make the distinction between deletes and moves because for inserts oldPlace == newPlace
|| (movedUp && siblingPlace <= newPlace && siblingPlace > oldPlace)
// If the relationship was moved up e.g. from place 2 to 5, all relationships
// with place > 2 (the old place) and <= to 5 should shift left
) {
setPlace(sibling, isLeft, siblingPlace - 1);
} else if (
(inserted && siblingPlace >= newPlace)
// If the relationship was inserted, all relationships starting from that place should shift right
// We must make the distinction between inserts and moves because for inserts oldPlace == newPlace
|| (!movedUp && siblingPlace >= newPlace && siblingPlace < oldPlace)
// If the relationship was moved down e.g. from place 5 to 2, all relationships
// with place >= 2 and < 5 (the old place) should shift right
) {
setPlace(sibling, isLeft, siblingPlace + 1);
}
}
}
for (MetadataValue mdv : metadata) {
// NOTE: Plain text metadata values should ALWAYS be included in the place calculation,
// because they are by definition only visible/relevant to the side of the relationship
// that we are currently processing.
int mdvPlace = mdv.getPlace();
if (
(deleted && mdvPlace > newPlace)
// If the relationship was deleted, all metadata after it should shift left
// We must make the distinction between deletes and moves because for inserts oldPlace == newPlace
// If the reltionship was copied to metadata on deletion:
// - the plain text can be after the relationship (in which case it's moved forward again)
// - or before the relationship (in which case it remains in place)
|| (movedUp && mdvPlace <= newPlace && mdvPlace > oldPlace)
// If the relationship was moved up e.g. from place 2 to 5, all metadata
// with place > 2 (the old place) and <= to 5 should shift left
) {
mdv.setPlace(mdvPlace - 1);
} else if (
(inserted && mdvPlace >= newPlace)
// If the relationship was inserted, all relationships starting from that place should shift right
// We must make the distinction between inserts and moves because for inserts oldPlace == newPlace
|| (!movedUp && mdvPlace >= newPlace && mdvPlace < oldPlace)
// If the relationship was moved down e.g. from place 5 to 2, all relationships
// with place >= 2 and < 5 (the old place) should shift right
) {
mdv.setPlace(mdvPlace + 1);
}
}
}
private int getPlace(Relationship relationship, boolean isLeft) {
if (isLeft) {
return relationship.getLeftPlace();
} else {
return relationship.getRightPlace();
}
}
private void setPlace(Relationship relationship, boolean isLeft, int place) {
if (isLeft) {
relationship.setLeftPlace(place);
} else {
relationship.setRightPlace(place);
}
}
@Override
@@ -187,16 +527,6 @@ public class RelationshipServiceImpl implements RelationshipService {
itemService.update(context, relatedItem);
}
@Override
public int findNextLeftPlaceByLeftItem(Context context, Item item) throws SQLException {
return relationshipDAO.findNextLeftPlaceByLeftItem(context, item);
}
@Override
public int findNextRightPlaceByRightItem(Context context, Item item) throws SQLException {
return relationshipDAO.findNextRightPlaceByRightItem(context, item);
}
private boolean isRelationshipValidToCreate(Context context, Relationship relationship) throws SQLException {
RelationshipType relationshipType = relationship.getRelationshipType();
@@ -212,15 +542,19 @@ public class RelationshipServiceImpl implements RelationshipService {
logRelationshipTypeDetailsForError(relationshipType);
return false;
}
if (!verifyMaxCardinality(context, relationship.getLeftItem(),
if (!relationship.getLatestVersionStatus().equals(LatestVersionStatus.LEFT_ONLY)
&& !verifyMaxCardinality(context, relationship.getLeftItem(),
relationshipType.getLeftMaxCardinality(), relationshipType, true)) {
//If RIGHT_ONLY => it's a copied relationship, and the count can be ignored
log.warn("The relationship has been deemed invalid since the left item has more" +
" relationships than the left max cardinality allows after we'd store this relationship");
logRelationshipTypeDetailsForError(relationshipType);
return false;
}
if (!verifyMaxCardinality(context, relationship.getRightItem(),
if (!relationship.getLatestVersionStatus().equals(LatestVersionStatus.RIGHT_ONLY)
&& !verifyMaxCardinality(context, relationship.getRightItem(),
relationshipType.getRightMaxCardinality(), relationshipType, false)) {
//If LEFT_ONLY => it's a copied relationship, and the count can be ignored
log.warn("The relationship has been deemed invalid since the right item has more" +
" relationships than the right max cardinality allows after we'd store this relationship");
logRelationshipTypeDetailsForError(relationshipType);
@@ -279,10 +613,18 @@ public class RelationshipServiceImpl implements RelationshipService {
}
@Override
public List<Relationship> findByItem(Context context, Item item, Integer limit, Integer offset,
boolean excludeTilted) throws SQLException {
public List<Relationship> findByItem(
Context context, Item item, Integer limit, Integer offset, boolean excludeTilted
) throws SQLException {
return findByItem(context, item, limit, offset, excludeTilted, true);
}
List<Relationship> list = relationshipDAO.findByItem(context, item, limit, offset, excludeTilted);
@Override
public List<Relationship> findByItem(
Context context, Item item, Integer limit, Integer offset, boolean excludeTilted, boolean excludeNonLatest
) throws SQLException {
List<Relationship> list =
relationshipDAO.findByItem(context, item, limit, offset, excludeTilted, excludeNonLatest);
list.sort((o1, o2) -> {
int relationshipType = o1.getRelationshipType().getLeftwardType()
@@ -377,7 +719,7 @@ public class RelationshipServiceImpl implements RelationshipService {
if (authorizeService.authorizeActionBoolean(context, relationship.getLeftItem(), Constants.WRITE) ||
authorizeService.authorizeActionBoolean(context, relationship.getRightItem(), Constants.WRITE)) {
relationshipDAO.delete(context, relationship);
updatePlaceInRelationship(context, relationship);
updatePlaceInRelationship(context, relationship, null, null, false, false);
updateItemsInRelationship(context, relationship);
} else {
throw new AuthorizeException(
@@ -450,7 +792,7 @@ public class RelationshipServiceImpl implements RelationshipService {
+ item.getID() + " due to " + currentDepth + " depth");
return;
}
String entityTypeStringFromMetadata = relationshipMetadataService.getEntityTypeStringFromMetadata(item);
String entityTypeStringFromMetadata = itemService.getEntityTypeLabel(item);
EntityType actualEntityType = entityTypeService.findByEntityType(context, entityTypeStringFromMetadata);
// Get all types of relations for the current item
List<RelationshipType> relationshipTypes = relationshipTypeService.findByEntityType(context, actualEntityType);
@@ -510,6 +852,9 @@ public class RelationshipServiceImpl implements RelationshipService {
/**
* Converts virtual metadata from RelationshipMetadataValue objects to actual item metadata.
* The resulting MDVs are added in front or behind the Relationship's virtual MDVs.
* The Relationship's virtual MDVs may be shifted right, and all subsequent metadata will be shifted right.
* So this method ensures the places are still valid.
*
* @param context The relevant DSpace context
* @param relationship The relationship containing the left and right items
@@ -520,13 +865,20 @@ public class RelationshipServiceImpl implements RelationshipService {
boolean copyToRightItem)
throws SQLException, AuthorizeException {
if (copyToLeftItem) {
String entityTypeString = relationshipMetadataService
.getEntityTypeStringFromMetadata(relationship.getLeftItem());
String entityTypeString = itemService.getEntityTypeLabel(relationship.getLeftItem());
List<RelationshipMetadataValue> relationshipMetadataValues =
relationshipMetadataService.findRelationshipMetadataValueForItemRelationship(context,
relationship.getLeftItem(), entityTypeString, relationship, true);
for (RelationshipMetadataValue relationshipMetadataValue : relationshipMetadataValues) {
itemService.addAndShiftRightMetadata(context, relationship.getLeftItem(),
// This adds the plain text metadata values on the same spot as the virtual values.
// This will be overruled in org.dspace.content.DSpaceObjectServiceImpl.update
// in the line below but it's not important whether the plain text or virtual values end up on top.
// The virtual values will eventually be deleted, and the others shifted
// This is required because addAndShiftRightMetadata has issues on metadata fields containing
// relationship values which are not useForPlace, while the relationhip type has useForPlace
// E.g. when using addAndShiftRightMetadata on relation.isAuthorOfPublication, it will break the order
// from dc.contributor.author
itemService.addMetadata(context, relationship.getLeftItem(),
relationshipMetadataValue.getMetadataField().
getMetadataSchema().getName(),
relationshipMetadataValue.getMetadataField().getElement(),
@@ -535,16 +887,16 @@ public class RelationshipServiceImpl implements RelationshipService {
relationshipMetadataValue.getValue(), null, -1,
relationshipMetadataValue.getPlace());
}
//This will ensure the new values no longer overlap, but won't break the order
itemService.update(context, relationship.getLeftItem());
}
if (copyToRightItem) {
String entityTypeString = relationshipMetadataService
.getEntityTypeStringFromMetadata(relationship.getRightItem());
String entityTypeString = itemService.getEntityTypeLabel(relationship.getRightItem());
List<RelationshipMetadataValue> relationshipMetadataValues =
relationshipMetadataService.findRelationshipMetadataValueForItemRelationship(context,
relationship.getRightItem(), entityTypeString, relationship, true);
for (RelationshipMetadataValue relationshipMetadataValue : relationshipMetadataValues) {
itemService.addAndShiftRightMetadata(context, relationship.getRightItem(),
itemService.addMetadata(context, relationship.getRightItem(),
relationshipMetadataValue.getMetadataField().
getMetadataSchema().getName(),
relationshipMetadataValue.getMetadataField().getElement(),
@@ -638,22 +990,46 @@ public class RelationshipServiceImpl implements RelationshipService {
public List<Relationship> findByItemAndRelationshipType(Context context, Item item,
RelationshipType relationshipType)
throws SQLException {
return relationshipDAO.findByItemAndRelationshipType(context, item, relationshipType, -1, -1);
return findByItemAndRelationshipType(context, item, relationshipType, -1, -1, true);
}
@Override
public List<Relationship> findByItemAndRelationshipType(Context context, Item item,
RelationshipType relationshipType, int limit, int offset)
throws SQLException {
return relationshipDAO.findByItemAndRelationshipType(context, item, relationshipType, limit, offset);
return findByItemAndRelationshipType(context, item, relationshipType, limit, offset, true);
}
@Override
public List<Relationship> findByItemAndRelationshipType(Context context, Item item,
RelationshipType relationshipType, boolean isLeft,
int limit, int offset)
throws SQLException {
return relationshipDAO.findByItemAndRelationshipType(context, item, relationshipType, isLeft, limit, offset);
public List<Relationship> findByItemAndRelationshipType(
Context context, Item item, RelationshipType relationshipType, int limit, int offset, boolean excludeNonLatest
) throws SQLException {
return relationshipDAO
.findByItemAndRelationshipType(context, item, relationshipType, limit, offset, excludeNonLatest);
}
@Override
public List<Relationship> findByItemAndRelationshipType(
Context context, Item item, RelationshipType relationshipType, boolean isLeft, int limit, int offset
) throws SQLException {
return findByItemAndRelationshipType(context, item, relationshipType, isLeft, limit, offset, true);
}
@Override
public List<Relationship> findByItemAndRelationshipType(
Context context, Item item, RelationshipType relationshipType, boolean isLeft, int limit, int offset,
boolean excludeNonLatest
) throws SQLException {
return relationshipDAO
.findByItemAndRelationshipType(context, item, relationshipType, isLeft, limit, offset, excludeNonLatest);
}
@Override
public List<ItemUuidAndRelationshipId> findByLatestItemAndRelationshipType(
Context context, Item latestItem, RelationshipType relationshipType, boolean isLeft
) throws SQLException {
return relationshipDAO
.findByLatestItemAndRelationshipType(context, latestItem, relationshipType, isLeft);
}
@Override
@@ -690,7 +1066,14 @@ public class RelationshipServiceImpl implements RelationshipService {
@Override
public int countByItem(Context context, Item item) throws SQLException {
return relationshipDAO.countByItem(context, item);
return countByItem(context, item, false, true);
}
@Override
public int countByItem(
Context context, Item item, boolean excludeTilted, boolean excludeNonLatest
) throws SQLException {
return relationshipDAO.countByItem(context, item, excludeTilted, excludeNonLatest);
}
@Override
@@ -699,9 +1082,18 @@ public class RelationshipServiceImpl implements RelationshipService {
}
@Override
public int countByItemAndRelationshipType(Context context, Item item, RelationshipType relationshipType,
boolean isLeft) throws SQLException {
return relationshipDAO.countByItemAndRelationshipType(context, item, relationshipType, isLeft);
public int countByItemAndRelationshipType(
Context context, Item item, RelationshipType relationshipType, boolean isLeft
) throws SQLException {
return countByItemAndRelationshipType(context, item, relationshipType, isLeft, true);
}
@Override
public int countByItemAndRelationshipType(
Context context, Item item, RelationshipType relationshipType, boolean isLeft, boolean excludeNonLatest
) throws SQLException {
return relationshipDAO
.countByItemAndRelationshipType(context, item, relationshipType, isLeft, excludeNonLatest);
}
@Override

View File

@@ -128,20 +128,24 @@ public class WorkspaceItemServiceImpl implements WorkspaceItemService {
Optional<MetadataValue> colEntityType = getDSpaceEntityType(collection);
Optional<MetadataValue> templateItemEntityType = getDSpaceEntityType(templateItem);
if (colEntityType.isPresent() && templateItemEntityType.isPresent() &&
if (template && colEntityType.isPresent() && templateItemEntityType.isPresent() &&
!StringUtils.equals(colEntityType.get().getValue(), templateItemEntityType.get().getValue())) {
throw new IllegalStateException("The template item has entity type : (" +
templateItemEntityType.get().getValue() + ") different than collection entity type : " +
colEntityType.get().getValue());
}
if (colEntityType.isPresent() && templateItemEntityType.isEmpty()) {
if (template && colEntityType.isPresent() && templateItemEntityType.isEmpty()) {
MetadataValue original = colEntityType.get();
MetadataField metadataField = original.getMetadataField();
MetadataSchema metadataSchema = metadataField.getMetadataSchema();
// NOTE: dspace.entity.type = <blank> does not make sense
// the collection entity type is by default blank when a collection is first created
if (StringUtils.isNotBlank(original.getValue())) {
itemService.addMetadata(context, item, metadataSchema.getName(), metadataField.getElement(),
metadataField.getQualifier(), original.getLanguage(), original.getValue());
}
}
if (template && (templateItem != null)) {
List<MetadataValue> md = itemService.getMetadata(templateItem, Item.ANY, Item.ANY, Item.ANY, Item.ANY);

View File

@@ -32,8 +32,22 @@ public interface ItemDAO extends DSpaceObjectLegacySupportDAO<Item> {
public Iterator<Item> findAll(Context context, boolean archived, int limit, int offset) throws SQLException;
@Deprecated
public Iterator<Item> findAll(Context context, boolean archived, boolean withdrawn) throws SQLException;
/**
* Find all items that are:
* - NOT in the workspace
* - NOT in the workflow
* - NOT a template item for e.g. a collection
*
* This implies that the result also contains older versions of items and withdrawn items.
* @param context the DSpace context.
* @return iterator over all regular items.
* @throws SQLException if database error.
*/
public Iterator<Item> findAllRegularItems(Context context) throws SQLException;
/**
* Find all Items modified since a Date.
*

View File

@@ -14,6 +14,7 @@ import java.util.UUID;
import org.dspace.content.Item;
import org.dspace.content.Relationship;
import org.dspace.content.RelationshipType;
import org.dspace.content.dao.pojo.ItemUuidAndRelationshipId;
import org.dspace.core.Context;
import org.dspace.core.GenericDAO;
@@ -32,11 +33,15 @@ public interface RelationshipDAO extends GenericDAO<Relationship> {
* @param item The item that should be either a leftItem or a rightItem of all
* the Relationship objects in the returned list
* @param excludeTilted If true, excludes tilted relationships
* @param excludeNonLatest If true, excludes all relationships for which the other item has a more recent version
* that is relevant for this relationship
* @return The list of Relationship objects that contain either a left or a
* right item that is equal to the given item
* @throws SQLException If something goes wrong
*/
List<Relationship> findByItem(Context context, Item item, boolean excludeTilted) throws SQLException;
List<Relationship> findByItem(
Context context, Item item, boolean excludeTilted, boolean excludeNonLatest
) throws SQLException;
/**
* This method returns a list of Relationship objects that have the given Item object
@@ -47,34 +52,15 @@ public interface RelationshipDAO extends GenericDAO<Relationship> {
* @param limit paging limit
* @param offset paging offset
* @param excludeTilted If true, excludes tilted relationships
* @param excludeNonLatest If true, excludes all relationships for which the other item has a more recent version
* that is relevant for this relationship
* @return The list of Relationship objects that contain either a left or a
* right item that is equal to the given item
* @throws SQLException If something goes wrong
*/
List<Relationship> findByItem(Context context, Item item, Integer limit, Integer offset, boolean excludeTilted)
throws SQLException;
/**
* This method returns the next leftplace integer to use for a relationship with this item as the leftItem
*
* @param context The relevant DSpace context
* @param item The item to be matched on leftItem
* @return The next integer to be used for the leftplace of a relationship with the given item
* as a left item
* @throws SQLException If something goes wrong
*/
int findNextLeftPlaceByLeftItem(Context context, Item item) throws SQLException;
/**
* This method returns the next rightplace integer to use for a relationship with this item as the rightItem
*
* @param context The relevant DSpace context
* @param item The item to be matched on rightItem
* @return The next integer to be used for the rightplace of a relationship with the given item
* as a right item
* @throws SQLException If something goes wrong
*/
int findNextRightPlaceByRightItem(Context context, Item item) throws SQLException;
List<Relationship> findByItem(
Context context, Item item, Integer limit, Integer offset, boolean excludeTilted, boolean excludeNonLatest
) throws SQLException;
/**
* This method returns a list of Relationship objects for the given RelationshipType object.
@@ -108,34 +94,69 @@ public interface RelationshipDAO extends GenericDAO<Relationship> {
* It will construct a list of all Relationship objects that have the given RelationshipType object
* as the relationshipType property
* @param context The relevant DSpace context
* @param item item to filter by
* @param relationshipType The RelationshipType object to be checked on
* @param limit paging limit
* @param offset paging offset
* @param item item to filter by
* @param excludeNonLatest If true, excludes all relationships for which the other item has a more recent version
* that is relevant for this relationship
* @return A list of Relationship objects that have the given RelationshipType object as the
* relationshipType property
* @throws SQLException If something goes wrong
*/
List<Relationship> findByItemAndRelationshipType(Context context, Item item, RelationshipType relationshipType,
Integer limit, Integer offset) throws SQLException;
List<Relationship> findByItemAndRelationshipType(
Context context, Item item, RelationshipType relationshipType, Integer limit, Integer offset,
boolean excludeNonLatest
) throws SQLException;
/**
* This method returns a list of Relationship objects for the given RelationshipType object.
* It will construct a list of all Relationship objects that have the given RelationshipType object
* as the relationshipType property
* @param context The relevant DSpace context
* @param item item to filter by
* @param relationshipType The RelationshipType object to be checked on
* @param isLeft Is item left or right
* @param limit paging limit
* @param offset paging offset
* @param item item to filter by
* @param isLeft Is item left or right
* @param excludeNonLatest If true, excludes all relationships for which the other item has a more recent version
* that is relevant for this relationship
* @return A list of Relationship objects that have the given RelationshipType object as the
* relationshipType property
* @throws SQLException If something goes wrong
*/
List<Relationship> findByItemAndRelationshipType(Context context, Item item, RelationshipType relationshipType,
boolean isLeft, Integer limit, Integer offset)
throws SQLException;
List<Relationship> findByItemAndRelationshipType(
Context context, Item item, RelationshipType relationshipType, boolean isLeft, Integer limit, Integer offset,
boolean excludeNonLatest
) throws SQLException;
/**
* This method returns the UUIDs of all items that have a relationship with the given item, from the perspective
* of the other item. In other words, given a relationship with the given item, the given item should have
* "latest status" in order for the other item uuid to be returned.
*
* This method differs from the "excludeNonLatest" property in other methods,
* because in this method the current item should have "latest status" to return the other item,
* whereas with "excludeNonLatest" the other item should have "latest status" to be returned.
*
* This method is used to index items in solr; when searching for related items of one of the returned uuids,
* the given item should appear as a search result.
*
* NOTE: This method does not return {@link Relationship}s for performance, because doing so would eagerly fetch
* the items on both sides, which is unnecessary.
* NOTE: tilted relationships are NEVER excluded when fetching one relationship type.
* @param context the DSpace context.
* @param latestItem the target item; only relationships where this item has "latest status" should be considered.
* @param relationshipType the relationship type for which relationships should be selected.
* @param isLeft whether the entity type of the item occurs on the left or right side of the relationship type.
* This is redundant in most cases, but necessary because relationship types my have
* the same entity type on both sides.
* @return a list containing pairs of relationship ids and item uuids.
* @throws SQLException if something goes wrong.
*/
public List<ItemUuidAndRelationshipId> findByLatestItemAndRelationshipType(
Context context, Item latestItem, RelationshipType relationshipType, boolean isLeft
) throws SQLException;
/**
* This method returns a list of Relationship objects for the given typeName
@@ -186,11 +207,14 @@ public interface RelationshipDAO extends GenericDAO<Relationship> {
* @param context The relevant DSpace context
* @param item The item that should be either a leftItem or a rightItem of all
* the Relationship objects in the returned list
* @param excludeTilted if true, excludes tilted relationships
* @param excludeNonLatest if true, exclude relationships for which the opposite item is not the latest version
* that is relevant
* @return The list of Relationship objects that contain either a left or a
* right item that is equal to the given item
* @throws SQLException If something goes wrong
*/
int countByItem(Context context, Item item) throws SQLException;
int countByItem(Context context, Item item, boolean excludeTilted, boolean excludeNonLatest) throws SQLException;
/**
* Count total number of relationships (rows in relationship table) by an item and a relationship type and a boolean
@@ -199,12 +223,15 @@ public interface RelationshipDAO extends GenericDAO<Relationship> {
* @param context context
* @param relationshipType relationship type to filter by
* @param item item to filter by
* @param isLeft Indicating whether the counted Relationships should have the given Item on the left side or not
* @param isLeft indicating whether the counted Relationships should have the given Item on the left side
* @param excludeNonLatest if true, exclude relationships for which the opposite item is not the latest version
* that is relevant
* @return total count
* @throws SQLException if database error
*/
int countByItemAndRelationshipType(Context context, Item item, RelationshipType relationshipType, boolean isLeft)
throws SQLException;
int countByItemAndRelationshipType(
Context context, Item item, RelationshipType relationshipType, boolean isLeft, boolean excludeNonLatest
) throws SQLException;
/**
* Count total number of relationships (rows in relationship table) given a typeName

View File

@@ -79,6 +79,20 @@ public class ItemDAOImpl extends AbstractHibernateDSODAO<Item> implements ItemDA
return iterate(query);
}
@Override
public Iterator<Item> findAllRegularItems(Context context) throws SQLException {
// NOTE: This query includes archived items, withdrawn items and older versions of items.
// It does not include workspace, workflow or template items.
Query query = createQuery(
context,
"SELECT i FROM Item as i " +
"LEFT JOIN Version as v ON i = v.item " +
"WHERE i.inArchive=true or i.withdrawn=true or (i.inArchive=false and v.id IS NOT NULL) " +
"ORDER BY i.id"
);
return iterate(query);
}
@Override
public Iterator<Item> findAll(Context context, boolean archived,
boolean withdrawn, boolean discoverable, Date lastModified)

View File

@@ -11,17 +11,22 @@ import java.sql.SQLException;
import java.util.ArrayList;
import java.util.List;
import java.util.UUID;
import java.util.stream.Collectors;
import javax.persistence.Query;
import javax.persistence.Tuple;
import javax.persistence.criteria.CriteriaBuilder;
import javax.persistence.criteria.CriteriaQuery;
import javax.persistence.criteria.Predicate;
import javax.persistence.criteria.Root;
import org.dspace.content.Item;
import org.dspace.content.Item_;
import org.dspace.content.Relationship;
import org.dspace.content.RelationshipType;
import org.dspace.content.RelationshipType_;
import org.dspace.content.Relationship_;
import org.dspace.content.dao.RelationshipDAO;
import org.dspace.content.dao.pojo.ItemUuidAndRelationshipId;
import org.dspace.content.factory.ContentServiceFactory;
import org.dspace.content.service.RelationshipTypeService;
import org.dspace.core.AbstractHibernateDAO;
@@ -30,95 +35,152 @@ import org.dspace.core.Context;
public class RelationshipDAOImpl extends AbstractHibernateDAO<Relationship> implements RelationshipDAO {
@Override
public List<Relationship> findByItem(Context context, Item item, boolean excludeTilted) throws SQLException {
return findByItem(context, item, -1, -1, excludeTilted);
public List<Relationship> findByItem(
Context context, Item item, boolean excludeTilted, boolean excludeNonLatest
) throws SQLException {
return findByItem(context, item, -1, -1, excludeTilted, excludeNonLatest);
}
@Override
public List<Relationship> findByItem(Context context, Item item, Integer limit, Integer offset,
boolean excludeTilted) throws SQLException {
public List<Relationship> findByItem(
Context context, Item item, Integer limit, Integer offset, boolean excludeTilted, boolean excludeNonLatest
) throws SQLException {
CriteriaBuilder criteriaBuilder = getCriteriaBuilder(context);
CriteriaQuery criteriaQuery = getCriteriaQuery(criteriaBuilder, Relationship.class);
CriteriaQuery<Relationship> criteriaQuery = getCriteriaQuery(criteriaBuilder, Relationship.class);
Root<Relationship> relationshipRoot = criteriaQuery.from(Relationship.class);
criteriaQuery.select(relationshipRoot);
if (excludeTilted) {
// If this item is the left item,
// return relationships for types which are not tilted right (tilted is either left nor null)
// If this item is the right item,
// return relationships for types which are not tilted left (tilted is either right nor null)
criteriaQuery
.where(criteriaBuilder.or(
criteriaBuilder.and(
criteriaBuilder.equal(relationshipRoot.get(Relationship_.leftItem), item),
criteriaQuery.where(
criteriaBuilder.or(
criteriaBuilder.isNull(relationshipRoot.get(Relationship_.relationshipType)
.get(RelationshipType_.tilted)),
criteriaBuilder.notEqual(relationshipRoot
.get(Relationship_.relationshipType)
.get(RelationshipType_.tilted), RelationshipType.Tilted.RIGHT))),
criteriaBuilder.and(
criteriaBuilder.equal(relationshipRoot.get(Relationship_.rightItem), item),
criteriaBuilder.or(
criteriaBuilder.isNull(relationshipRoot.get(Relationship_.relationshipType)
.get(RelationshipType_.tilted)),
criteriaBuilder.notEqual(relationshipRoot
.get(Relationship_.relationshipType)
.get(RelationshipType_.tilted), RelationshipType.Tilted.LEFT)))));
} else {
criteriaQuery
.where(criteriaBuilder.or(criteriaBuilder.equal(relationshipRoot.get(Relationship_.leftItem), item),
criteriaBuilder.equal(relationshipRoot.get(Relationship_.rightItem), item)));
}
getLeftItemPredicate(criteriaBuilder, relationshipRoot, item, excludeTilted, excludeNonLatest),
getRightItemPredicate(criteriaBuilder, relationshipRoot, item, excludeTilted, excludeNonLatest)
)
);
return list(context, criteriaQuery, false, Relationship.class, limit, offset);
}
@Override
public int countByItem(Context context, Item item)
throws SQLException {
/**
* Get the predicate for a criteria query that selects relationships by their left item.
* @param criteriaBuilder the criteria builder.
* @param relationshipRoot the relationship root.
* @param item the item that is being searched for.
* @param excludeTilted if true, exclude tilted relationships.
* @param excludeNonLatest if true, exclude relationships for which the opposite item is not the latest version
* that is relevant.
* @return a predicate that satisfies the given restrictions.
*/
protected Predicate getLeftItemPredicate(
CriteriaBuilder criteriaBuilder, Root<Relationship> relationshipRoot, Item item,
boolean excludeTilted, boolean excludeNonLatest
) {
List<Predicate> predicates = new ArrayList<>();
// match relationships based on the left item
predicates.add(
criteriaBuilder.equal(relationshipRoot.get(Relationship_.leftItem), item)
);
if (excludeTilted) {
// if this item is the left item,
// return relationships for types which are NOT tilted right (tilted is either left nor null)
predicates.add(
criteriaBuilder.or(
criteriaBuilder.isNull(
relationshipRoot.get(Relationship_.relationshipType).get(RelationshipType_.tilted)
),
criteriaBuilder.notEqual(
relationshipRoot.get(Relationship_.relationshipType).get(RelationshipType_.tilted),
RelationshipType.Tilted.RIGHT
)
)
);
}
if (excludeNonLatest) {
// if this item is the left item,
// return relationships for which the right item is the "latest" version that is relevant.
predicates.add(
criteriaBuilder.notEqual(
relationshipRoot.get(Relationship_.LATEST_VERSION_STATUS),
Relationship.LatestVersionStatus.LEFT_ONLY
)
);
}
return criteriaBuilder.and(predicates.toArray(new Predicate[]{}));
}
/**
* Get the predicate for a criteria query that selects relationships by their right item.
* @param criteriaBuilder the criteria builder.
* @param relationshipRoot the relationship root.
* @param item the item that is being searched for.
* @param excludeTilted if true, exclude tilted relationships.
* @param excludeNonLatest if true, exclude relationships for which the opposite item is not the latest version
* that is relevant.
* @return a predicate that satisfies the given restrictions.
*/
protected Predicate getRightItemPredicate(
CriteriaBuilder criteriaBuilder, Root<Relationship> relationshipRoot, Item item,
boolean excludeTilted, boolean excludeNonLatest
) {
List<Predicate> predicates = new ArrayList<>();
// match relationships based on the right item
predicates.add(
criteriaBuilder.equal(relationshipRoot.get(Relationship_.rightItem), item)
);
if (excludeTilted) {
// if this item is the right item,
// return relationships for types which are NOT tilted left (tilted is either right nor null)
predicates.add(
criteriaBuilder.or(
criteriaBuilder.isNull(
relationshipRoot.get(Relationship_.relationshipType).get(RelationshipType_.tilted)
),
criteriaBuilder.notEqual(
relationshipRoot.get(Relationship_.relationshipType).get(RelationshipType_.tilted),
RelationshipType.Tilted.LEFT
)
)
);
}
if (excludeNonLatest) {
// if this item is the right item,
// return relationships for which the left item is the "latest" version that is relevant.
predicates.add(
criteriaBuilder.notEqual(
relationshipRoot.get(Relationship_.LATEST_VERSION_STATUS),
Relationship.LatestVersionStatus.RIGHT_ONLY
)
);
}
return criteriaBuilder.and(predicates.toArray(new Predicate[]{}));
}
@Override
public int countByItem(
Context context, Item item, boolean excludeTilted, boolean excludeNonLatest
) throws SQLException {
CriteriaBuilder criteriaBuilder = getCriteriaBuilder(context);
CriteriaQuery criteriaQuery = getCriteriaQuery(criteriaBuilder, Relationship.class);
Root<Relationship> relationshipRoot = criteriaQuery.from(Relationship.class);
criteriaQuery.select(relationshipRoot);
criteriaQuery
.where(criteriaBuilder.or(criteriaBuilder.equal(relationshipRoot.get(Relationship_.leftItem), item),
criteriaBuilder.equal(relationshipRoot.get(Relationship_.rightItem), item)));
criteriaQuery.where(
criteriaBuilder.or(
getLeftItemPredicate(criteriaBuilder, relationshipRoot, item, excludeTilted, excludeNonLatest),
getRightItemPredicate(criteriaBuilder, relationshipRoot, item, excludeTilted, excludeNonLatest)
)
);
return count(context, criteriaQuery, criteriaBuilder, relationshipRoot);
}
@Override
public int findNextLeftPlaceByLeftItem(Context context, Item item) throws SQLException {
CriteriaBuilder criteriaBuilder = getCriteriaBuilder(context);
CriteriaQuery criteriaQuery = getCriteriaQuery(criteriaBuilder, Relationship.class);
Root<Relationship> relationshipRoot = criteriaQuery.from(Relationship.class);
criteriaQuery.select(relationshipRoot);
criteriaQuery.where(criteriaBuilder.equal(relationshipRoot.get(Relationship_.leftItem), item));
List<Relationship> list = list(context, criteriaQuery, false, Relationship.class, -1, -1);
list.sort((o1, o2) -> o2.getLeftPlace() - o1.getLeftPlace());
if (!list.isEmpty()) {
return list.get(0).getLeftPlace() + 1;
} else {
return 0;
}
}
@Override
public int findNextRightPlaceByRightItem(Context context, Item item) throws SQLException {
CriteriaBuilder criteriaBuilder = getCriteriaBuilder(context);
CriteriaQuery criteriaQuery = getCriteriaQuery(criteriaBuilder, Relationship.class);
Root<Relationship> relationshipRoot = criteriaQuery.from(Relationship.class);
criteriaQuery.select(relationshipRoot);
criteriaQuery.where(criteriaBuilder.equal(relationshipRoot.get(Relationship_.rightItem), item));
List<Relationship> list = list(context, criteriaQuery, false, Relationship.class, -1, -1);
list.sort((o1, o2) -> o2.getRightPlace() - o1.getRightPlace());
if (!list.isEmpty()) {
return list.get(0).getRightPlace() + 1;
} else {
return 0;
}
}
@Override
public List<Relationship> findByRelationshipType(Context context, RelationshipType relationshipType)
throws SQLException {
@@ -140,49 +202,132 @@ public class RelationshipDAOImpl extends AbstractHibernateDAO<Relationship> impl
}
@Override
public List<Relationship> findByItemAndRelationshipType(Context context, Item item,
RelationshipType relationshipType, Integer limit,
Integer offset)
throws SQLException {
public List<Relationship> findByItemAndRelationshipType(
Context context, Item item, RelationshipType relationshipType, Integer limit, Integer offset,
boolean excludeNonLatest
) throws SQLException {
CriteriaBuilder criteriaBuilder = getCriteriaBuilder(context);
CriteriaQuery criteriaQuery = getCriteriaQuery(criteriaBuilder, Relationship.class);
Root<Relationship> relationshipRoot = criteriaQuery.from(Relationship.class);
criteriaQuery.select(relationshipRoot);
criteriaQuery
.where(criteriaBuilder.equal(relationshipRoot.get(Relationship_.relationshipType),
relationshipType), criteriaBuilder.or
(criteriaBuilder.equal(relationshipRoot.get(Relationship_.leftItem), item),
criteriaBuilder.equal(relationshipRoot.get(Relationship_.rightItem), item)));
criteriaQuery.where(
criteriaBuilder.equal(relationshipRoot.get(Relationship_.relationshipType), relationshipType),
criteriaBuilder.or(
getLeftItemPredicate(criteriaBuilder, relationshipRoot, item, false, excludeNonLatest),
getRightItemPredicate(criteriaBuilder, relationshipRoot, item, false, excludeNonLatest)
)
);
return list(context, criteriaQuery, true, Relationship.class, limit, offset);
}
@Override
public List<Relationship> findByItemAndRelationshipType(Context context, Item item,
RelationshipType relationshipType, boolean isLeft,
Integer limit, Integer offset)
throws SQLException {
public List<Relationship> findByItemAndRelationshipType(
Context context, Item item, RelationshipType relationshipType, boolean isLeft, Integer limit, Integer offset,
boolean excludeNonLatest
) throws SQLException {
CriteriaBuilder criteriaBuilder = getCriteriaBuilder(context);
CriteriaQuery criteriaQuery = getCriteriaQuery(criteriaBuilder, Relationship.class);
Root<Relationship> relationshipRoot = criteriaQuery.from(Relationship.class);
criteriaQuery.select(relationshipRoot);
if (isLeft) {
criteriaQuery
.where(criteriaBuilder.equal(relationshipRoot.get(Relationship_.relationshipType),
relationshipType),
criteriaBuilder.equal(relationshipRoot.get(Relationship_.leftItem), item));
criteriaQuery.where(
criteriaBuilder.equal(relationshipRoot.get(Relationship_.relationshipType), relationshipType),
getLeftItemPredicate(criteriaBuilder, relationshipRoot, item, false, excludeNonLatest)
);
criteriaQuery.orderBy(criteriaBuilder.asc(relationshipRoot.get(Relationship_.leftPlace)));
} else {
criteriaQuery
.where(criteriaBuilder.equal(relationshipRoot.get(Relationship_.relationshipType),
relationshipType),
criteriaBuilder.equal(relationshipRoot.get(Relationship_.rightItem), item));
criteriaQuery.where(
criteriaBuilder.equal(relationshipRoot.get(Relationship_.relationshipType), relationshipType),
getRightItemPredicate(criteriaBuilder, relationshipRoot, item, false, excludeNonLatest)
);
criteriaQuery.orderBy(criteriaBuilder.asc(relationshipRoot.get(Relationship_.rightPlace)));
}
return list(context, criteriaQuery, true, Relationship.class, limit, offset);
}
@Override
public List<ItemUuidAndRelationshipId> findByLatestItemAndRelationshipType(
Context context, Item latestItem, RelationshipType relationshipType, boolean isLeft
) throws SQLException {
final String relationshipIdAlias = "relationshipId";
final String itemUuidAlias = "itemUuid";
CriteriaBuilder criteriaBuilder = getCriteriaBuilder(context);
CriteriaQuery<Tuple> criteriaQuery = criteriaBuilder.createTupleQuery();
Root<Relationship> relationshipRoot = criteriaQuery.from(Relationship.class);
ArrayList<Predicate> predicates = new ArrayList<>();
// all relationships should have the specified relationship type
predicates.add(
criteriaBuilder.equal(relationshipRoot.get(Relationship_.relationshipType), relationshipType)
);
if (isLeft) {
// match relationships based on the left item
predicates.add(
criteriaBuilder.equal(relationshipRoot.get(Relationship_.leftItem), latestItem)
);
// the left item has to have "latest status" => accept BOTH and LEFT_ONLY
predicates.add(
criteriaBuilder.notEqual(
relationshipRoot.get(Relationship_.LATEST_VERSION_STATUS),
Relationship.LatestVersionStatus.RIGHT_ONLY
)
);
// return the UUIDs of the right item
criteriaQuery.multiselect(
relationshipRoot.get(Relationship_.id).alias(relationshipIdAlias),
relationshipRoot.get(Relationship_.rightItem).get(Item_.id).alias(itemUuidAlias)
);
} else {
// match relationships based on the right item
predicates.add(
criteriaBuilder.equal(relationshipRoot.get(Relationship_.rightItem), latestItem)
);
// the right item has to have "latest status" => accept BOTH and RIGHT_ONLY
predicates.add(
criteriaBuilder.notEqual(
relationshipRoot.get(Relationship_.LATEST_VERSION_STATUS),
Relationship.LatestVersionStatus.LEFT_ONLY
)
);
// return the UUIDs of the left item
criteriaQuery.multiselect(
relationshipRoot.get(Relationship_.id).alias(relationshipIdAlias),
relationshipRoot.get(Relationship_.leftItem).get(Item_.id).alias(itemUuidAlias)
);
}
// all predicates are chained with the AND operator
criteriaQuery.where(predicates.toArray(new Predicate[]{}));
// deduplicate result
criteriaQuery.distinct(true);
// execute query
Query query = this.getHibernateSession(context).createQuery(criteriaQuery);
query.setHint("org.hibernate.cacheable", true);
List<?> resultList = query.getResultList();
// convert types
return resultList.stream()
.map(Tuple.class::cast)
.map(t -> new ItemUuidAndRelationshipId(
(UUID) t.get(itemUuidAlias),
(Integer) t.get(relationshipIdAlias)
))
.collect(Collectors.toList());
}
@Override
public List<Relationship> findByTypeName(Context context, String typeName)
throws SQLException {
@@ -228,24 +373,26 @@ public class RelationshipDAOImpl extends AbstractHibernateDAO<Relationship> impl
}
@Override
public int countByItemAndRelationshipType(Context context, Item item, RelationshipType relationshipType,
boolean isLeft) throws SQLException {
public int countByItemAndRelationshipType(
Context context, Item item, RelationshipType relationshipType, boolean isLeft, boolean excludeNonLatest
) throws SQLException {
CriteriaBuilder criteriaBuilder = getCriteriaBuilder(context);
CriteriaQuery criteriaQuery = getCriteriaQuery(criteriaBuilder, Relationship.class);
Root<Relationship> relationshipRoot = criteriaQuery.from(Relationship.class);
criteriaQuery.select(relationshipRoot);
if (isLeft) {
criteriaQuery
.where(criteriaBuilder.equal(relationshipRoot.get(Relationship_.relationshipType),
relationshipType),
criteriaBuilder.equal(relationshipRoot.get(Relationship_.leftItem), item));
criteriaQuery.where(
criteriaBuilder.equal(relationshipRoot.get(Relationship_.relationshipType), relationshipType),
getLeftItemPredicate(criteriaBuilder, relationshipRoot, item, false, excludeNonLatest)
);
} else {
criteriaQuery
.where(criteriaBuilder.equal(relationshipRoot.get(Relationship_.relationshipType),
relationshipType),
criteriaBuilder.equal(relationshipRoot.get(Relationship_.rightItem), item));
criteriaQuery.where(
criteriaBuilder.equal(relationshipRoot.get(Relationship_.relationshipType), relationshipType),
getRightItemPredicate(criteriaBuilder, relationshipRoot, item, false, excludeNonLatest)
);
}
return count(context, criteriaQuery, criteriaBuilder, relationshipRoot);
}

View File

@@ -0,0 +1,37 @@
/**
* 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.content.dao.pojo;
import java.util.UUID;
import org.dspace.content.Relationship;
import org.dspace.content.dao.RelationshipDAO;
import org.springframework.lang.NonNull;
/**
* Used by {@link RelationshipDAO#findByLatestItemAndRelationshipType} to avoid creating {@link Relationship}s.
*/
public class ItemUuidAndRelationshipId {
private final UUID itemUuid;
private final int relationshipId;
public ItemUuidAndRelationshipId(@NonNull UUID itemUuid, @NonNull int relationshipId) {
this.itemUuid = itemUuid;
this.relationshipId = relationshipId;
}
public UUID getItemUuid() {
return this.itemUuid;
}
public int getRelationshipId() {
return this.relationshipId;
}
}

View File

@@ -21,6 +21,7 @@ import org.dspace.content.Bitstream;
import org.dspace.content.Bundle;
import org.dspace.content.Collection;
import org.dspace.content.Community;
import org.dspace.content.EntityType;
import org.dspace.content.Item;
import org.dspace.content.MetadataField;
import org.dspace.content.MetadataValue;
@@ -111,8 +112,22 @@ public interface ItemService
* @return an iterator over the items in the archive.
* @throws SQLException if database error
*/
@Deprecated
public Iterator<Item> findAllUnfiltered(Context context) throws SQLException;
/**
* Find all items that are:
* - NOT in the workspace
* - NOT in the workflow
* - NOT a template item for e.g. a collection
*
* This implies that the result also contains older versions of items and withdrawn items.
* @param context the DSpace context.
* @return iterator over all regular items.
* @throws SQLException if database error.
*/
public Iterator<Item> findAllRegularItems(Context context) throws SQLException;
/**
* Find all the items in the archive by a given submitter. The order is
* indeterminate. Only items with the "in archive" flag set are included.
@@ -813,12 +828,20 @@ public interface ItemService
*/
public List<MetadataValue> getMetadata(Item item, String schema, String element, String qualifier,
String lang, boolean enableVirtualMetadata);
/**
* Returns the item's entity type, if any.
*
* @param item the item
* @return the entity type as string, if any
* Retrieve the label of the entity type of the given item.
* @param item the item.
* @return the label of the entity type, taken from the item metadata, or null if not found.
*/
public String getEntityType(Item item);
public String getEntityTypeLabel(Item item);
/**
* Retrieve the entity type of the given item.
* @param context the DSpace context.
* @param item the item.
* @return the entity type of the given item, or null if not found.
*/
public EntityType getEntityType(Context context, Item item) throws SQLException;
}

View File

@@ -14,7 +14,9 @@ import java.util.UUID;
import org.dspace.authorize.AuthorizeException;
import org.dspace.content.Item;
import org.dspace.content.Relationship;
import org.dspace.content.Relationship.LatestVersionStatus;
import org.dspace.content.RelationshipType;
import org.dspace.content.dao.pojo.ItemUuidAndRelationshipId;
import org.dspace.core.Context;
import org.dspace.service.DSpaceCRUDService;
@@ -49,6 +51,25 @@ public interface RelationshipService extends DSpaceCRUDService<Relationship> {
List<Relationship> findByItem(Context context, Item item, Integer limit, Integer offset, boolean excludeTilted)
throws SQLException;
/**
* Retrieves the list of Relationships currently in the system for which the given Item is either
* a leftItem or a rightItem object
* @param context The relevant DSpace context
* @param item The Item that has to be the left or right item for the relationship to be
* included in the list
* @param limit paging limit
* @param offset paging offset
* @param excludeTilted If true, excludes tilted relationships
* @param excludeNonLatest If true, excludes all relationships for which the other item has a more recent version
* that is relevant for this relationship
* @return The list of relationships for which each relationship adheres to the above
* listed constraint
* @throws SQLException If something goes wrong
*/
List<Relationship> findByItem(
Context context, Item item, Integer limit, Integer offset, boolean excludeTilted, boolean excludeNonLatest
) throws SQLException;
/**
* Retrieves the full list of relationships currently in the system
* @param context The relevant DSpace context
@@ -79,30 +100,54 @@ public interface RelationshipService extends DSpaceCRUDService<Relationship> {
public Relationship create(Context context, Relationship relationship) throws SQLException, AuthorizeException;
/**
* This method returns the next leftplace integer to use for a relationship with this item as the leftItem
* Move the given relationship to a new leftPlace and/or rightPlace.
*
* This will
* 1. verify whether the move is authorized
* 2. move the relationship to the specified left/right place
* 3. update the left/right place of other relationships and/or metadata in order to resolve the move without
* leaving any gaps
*
* At least one of the new places should be non-null, otherwise no changes will be made.
*
* @param context The relevant DSpace context
* @param item The item that has to be the leftItem of a relationship for it to qualify
* @return The next integer to be used for the leftplace of a relationship with the given item
* as a left item
* @param relationship The Relationship to move
* @param newLeftPlace The value to set the leftPlace of this Relationship to
* @param newRightPlace The value to set the rightPlace of this Relationship to
* @return The moved relationship with updated place variables
* @throws SQLException If something goes wrong
* @throws AuthorizeException If the user is not authorized to update the Relationship or its Items
*/
int findNextLeftPlaceByLeftItem(Context context, Item item) throws SQLException;
Relationship move(Context context, Relationship relationship, Integer newLeftPlace, Integer newRightPlace)
throws SQLException, AuthorizeException;
/**
* This method returns the next rightplace integer to use for a relationship with this item as the rightItem
* Move the given relationship to a new leftItem and/or rightItem.
*
* This will
* 1. move the relationship to the last place in its current left or right Item. This ensures that we don't leave
* any gaps when moving the relationship to a new Item.
* If only one of the relationship's Items is changed,the order of relationships and metadatain the other
* will not be affected
* 2. insert the relationship into the new Item(s)
*
* At least one of the new Items should be non-null, otherwise no changes will be made.
*
* @param context The relevant DSpace context
* @param item The item that has to be the rightitem of a relationship for it to qualify
* @return The next integer to be used for the rightplace of a relationship with the given item
* as a right item
* @param relationship The Relationship to move
* @param newLeftItem The value to set the leftItem of this Relationship to
* @param newRightItem The value to set the rightItem of this Relationship to
* @return The moved relationship with updated left/right Items variables
* @throws SQLException If something goes wrong
* @throws AuthorizeException If the user is not authorized to update the Relationship or its Items
*/
int findNextRightPlaceByRightItem(Context context, Item item) throws SQLException;
Relationship move(Context context, Relationship relationship, Item newLeftItem, Item newRightItem)
throws SQLException, AuthorizeException;
/**
* This method returns a list of Relationships for which the leftItem or rightItem is equal to the given
* Item object and for which the RelationshipType object is equal to the relationshipType property
* NOTE: tilted relationships are NEVER excluded when fetching one relationship type
* @param context The relevant DSpace context
* @param item The Item object to be matched on the leftItem or rightItem for the relationship
* @param relationshipType The RelationshipType object that will be used to check the Relationship on
@@ -117,6 +162,7 @@ public interface RelationshipService extends DSpaceCRUDService<Relationship> {
/**
* This method returns a list of Relationships for which the leftItem or rightItem is equal to the given
* Item object and for which the RelationshipType object is equal to the relationshipType property
* NOTE: tilted relationships are NEVER excluded when fetching one relationship type
* @param context The relevant DSpace context
* @param item The Item object to be matched on the leftItem or rightItem for the relationship
* @param relationshipType The RelationshipType object that will be used to check the Relationship on
@@ -131,6 +177,24 @@ public interface RelationshipService extends DSpaceCRUDService<Relationship> {
/**
* This method returns a list of Relationships for which the leftItem or rightItem is equal to the given
* Item object and for which the RelationshipType object is equal to the relationshipType property
* NOTE: tilted relationships are NEVER excluded when fetching one relationship type
* @param context The relevant DSpace context
* @param item The Item object to be matched on the leftItem or rightItem for the relationship
* @param relationshipType The RelationshipType object that will be used to check the Relationship on
* @param excludeNonLatest If true, excludes all relationships for which the other item has a more recent version
* that is relevant for this relationship
* @return The list of Relationship objects that have the given Item object as leftItem or rightItem and
* for which the relationshipType property is equal to the given RelationshipType
* @throws SQLException If something goes wrong
*/
public List<Relationship> findByItemAndRelationshipType(
Context context, Item item, RelationshipType relationshipType, int limit, int offset, boolean excludeNonLatest
) throws SQLException;
/**
* This method returns a list of Relationships for which the leftItem or rightItem is equal to the given
* Item object and for which the RelationshipType object is equal to the relationshipType property
* NOTE: tilted relationships are NEVER excluded when fetching one relationship type
* @param context The relevant DSpace context
* @param item The Item object to be matched on the leftItem or rightItem for the relationship
* @param relationshipType The RelationshipType object that will be used to check the Relationship on
@@ -145,17 +209,51 @@ public interface RelationshipService extends DSpaceCRUDService<Relationship> {
throws SQLException;
/**
* This method will update the place for the Relationship and all other relationships found by the items and
* relationship type of the given Relationship. It will give this Relationship the last place in both the
* left and right place determined by querying for the list of leftRelationships and rightRelationships
* by the leftItem, rightItem and relationshipType of the given Relationship.
* This method returns a list of Relationships for which the leftItem or rightItem is equal to the given
* Item object and for which the RelationshipType object is equal to the relationshipType property
* NOTE: tilted relationships are NEVER excluded when fetching one relationship type
* @param context The relevant DSpace context
* @param relationship The Relationship object that will have it's place updated and that will be used
* to retrieve the other relationships whose place might need to be updated
* @param item The Item object to be matched on the leftItem or rightItem for the relationship
* @param relationshipType The RelationshipType object that will be used to check the Relationship on
* @param isLeft Is the item left or right
* @param excludeNonLatest If true, excludes all relationships for which the other item has a more recent version
* that is relevant for this relationship
* @return The list of Relationship objects that have the given Item object as leftItem or rightItem and
* for which the relationshipType property is equal to the given RelationshipType
* @throws SQLException If something goes wrong
*/
public void updatePlaceInRelationship(Context context, Relationship relationship)
throws SQLException, AuthorizeException;
public List<Relationship> findByItemAndRelationshipType(
Context context, Item item, RelationshipType relationshipType, boolean isLeft, int limit, int offset,
boolean excludeNonLatest
) throws SQLException;
/**
* This method returns the UUIDs of all items that have a relationship with the given item, from the perspective
* of the other item. In other words, given a relationship with the given item, the given item should have
* "latest status" in order for the other item uuid to be returned.
*
* This method differs from the "excludeNonLatest" property in other methods,
* because in this method the current item should have "latest status" to return the other item,
* whereas with "excludeNonLatest" the other item should have "latest status" to be returned.
*
* This method is used to index items in solr; when searching for related items of one of the returned uuids,
* the given item should appear as a search result.
*
* NOTE: This method does not return {@link Relationship}s for performance, because doing so would eagerly fetch
* the items on both sides, which is unnecessary.
* NOTE: tilted relationships are NEVER excluded when fetching one relationship type.
* @param context the DSpace context.
* @param latestItem the target item; only relationships where this item has "latest status" should be considered.
* @param relationshipType the relationship type for which relationships should be selected.
* @param isLeft whether the entity type of the item occurs on the left or right side of the relationship type.
* This is redundant in most cases, but necessary because relationship types my have
* the same entity type on both sides.
* @return a list containing pairs of relationship ids and item uuids.
* @throws SQLException if something goes wrong.
*/
public List<ItemUuidAndRelationshipId> findByLatestItemAndRelationshipType(
Context context, Item latestItem, RelationshipType relationshipType, boolean isLeft
) throws SQLException;
/**
* This method will update the given item's metadata order.
@@ -174,6 +272,7 @@ public interface RelationshipService extends DSpaceCRUDService<Relationship> {
/**
* This method returns a list of Relationship objects for which the relationshipType property is equal to the given
* RelationshipType object
* NOTE: tilted relationships are NEVER excluded when fetching one relationship type
* @param context The relevant DSpace context
* @param relationshipType The RelationshipType object that will be used to check the Relationship on
* @return The list of Relationship objects for which the given RelationshipType object is equal
@@ -185,6 +284,7 @@ public interface RelationshipService extends DSpaceCRUDService<Relationship> {
/**
* This method returns a list of Relationship objets for which the relationshipType property is equal to the given
* RelationshipType object
* NOTE: tilted relationships are NEVER excluded when fetching one relationship type
* @param context The relevant DSpace context
* @param relationshipType The RelationshipType object that will be used to check the Relationship on
* @param limit paging limit
@@ -206,18 +306,40 @@ public interface RelationshipService extends DSpaceCRUDService<Relationship> {
* @param rightPlace The rightPlace integer for the relationship
* @param leftwardValue The leftwardValue string for the relationship
* @param rightwardValue The rightwardValue string for the relationship
* @param latestVersionStatus The latestVersionStatus value for the relationship
* @return The created Relationship object with the given properties
* @throws AuthorizeException If something goes wrong
* @throws SQLException If something goes wrong
*/
Relationship create(Context c, Item leftItem, Item rightItem, RelationshipType relationshipType,
int leftPlace, int rightPlace, String leftwardValue, String rightwardValue)
throws AuthorizeException, SQLException;
Relationship create(
Context c, Item leftItem, Item rightItem, RelationshipType relationshipType, int leftPlace, int rightPlace,
String leftwardValue, String rightwardValue, LatestVersionStatus latestVersionStatus
) throws AuthorizeException, SQLException;
/**
* This method is used to construct a Relationship object with all it's variables,
* except the latest version status
* @param c The relevant DSpace context
* @param leftItem The leftItem Item object for the relationship
* @param rightItem The rightItem Item object for the relationship
* @param relationshipType The RelationshipType object for the relationship
* @param leftPlace The leftPlace integer for the relationship
* @param rightPlace The rightPlace integer for the relationship
* @param leftwardValue The leftwardValue string for the relationship
* @param rightwardValue The rightwardValue string for the relationship
* @return The created Relationship object with the given properties
* @throws AuthorizeException If something goes wrong
* @throws SQLException If something goes wrong
*/
Relationship create(
Context c, Item leftItem, Item rightItem, RelationshipType relationshipType, int leftPlace, int rightPlace,
String leftwardValue, String rightwardValue
) throws AuthorizeException, SQLException;
/**
* This method is used to construct a Relationship object with all it's variables,
* except the leftward and rightward labels
* except the leftward label, rightward label and latest version status
* @param c The relevant DSpace context
* @param leftItem The leftItem Item object for the relationship
* @param rightItem The rightItem Item object for the relationship
@@ -267,7 +389,7 @@ public interface RelationshipService extends DSpaceCRUDService<Relationship> {
/**
* Count total number of relationships (rows in relationship table) by a relationship type
*
* NOTE: tilted relationships are NEVER excluded when fetching one relationship type
* @param context context
* @param relationshipType relationship type to filter by
* @return total count
@@ -287,10 +409,25 @@ public interface RelationshipService extends DSpaceCRUDService<Relationship> {
*/
int countByItem(Context context, Item item) throws SQLException;
/**
* This method returns a count of Relationship objects that have the given Item object
* as a leftItem or a rightItem
* @param context The relevant DSpace context
* @param item The item that should be either a leftItem or a rightItem of all
* the Relationship objects in the returned list
* @param excludeTilted if true, excludes tilted relationships
* @param excludeNonLatest if true, exclude relationships for which the opposite item is not the latest version
* that is relevant
* @return The list of Relationship objects that contain either a left or a
* right item that is equal to the given item
* @throws SQLException If something goes wrong
*/
int countByItem(Context context, Item item, boolean excludeTilted, boolean excludeNonLatest) throws SQLException;
/**
* Count total number of relationships (rows in relationship table) by a relationship type and a boolean indicating
* whether the relationship should contain the item on the left side or not
*
* NOTE: tilted relationships are NEVER excluded when fetching one relationship type
* @param context context
* @param relationshipType relationship type to filter by
* @param isLeft Indicating whether the counted Relationships should have the given Item on the left side or not
@@ -300,6 +437,22 @@ public interface RelationshipService extends DSpaceCRUDService<Relationship> {
int countByItemAndRelationshipType(Context context, Item item, RelationshipType relationshipType, boolean isLeft)
throws SQLException;
/**
* Count total number of relationships (rows in relationship table) by a relationship type and a boolean indicating
* whether the relationship should contain the item on the left side or not
* NOTE: tilted relationships are NEVER excluded when fetching one relationship type
* @param context context
* @param relationshipType relationship type to filter by
* @param isLeft Indicating whether the counted Relationships should have the given Item on the left side
* @param excludeNonLatest If true, excludes all relationships for which the other item has a more recent version
* that is relevant for this relationship
* @return total count with the given parameters
* @throws SQLException if database error
*/
int countByItemAndRelationshipType(
Context context, Item item, RelationshipType relationshipType, boolean isLeft, boolean excludeNonLatest
) throws SQLException;
/**
* Count total number of relationships (rows in relationship table)
* by a relationship leftward or rightward typeName

View File

@@ -155,12 +155,11 @@ public abstract class AbstractHibernateDAO<T> implements GenericDAO<T> {
* @return A list of distinct results as depicted by the CriteriaQuery and parameters
* @throws SQLException
*/
public List<T> list(Context context, CriteriaQuery criteriaQuery, boolean cacheable, Class<T> clazz, int maxResults,
int offset) throws SQLException {
public List<T> list(
Context context, CriteriaQuery<T> criteriaQuery, boolean cacheable, Class<T> clazz, int maxResults, int offset
) throws SQLException {
criteriaQuery.distinct(true);
@SuppressWarnings("unchecked")
List<T> result = (List<T>) executeCriteriaQuery(context, criteriaQuery, cacheable, maxResults, offset);
return result;
return executeCriteriaQuery(context, criteriaQuery, cacheable, maxResults, offset);
}
/**
@@ -183,12 +182,12 @@ public abstract class AbstractHibernateDAO<T> implements GenericDAO<T> {
* @return A list of results determined by the CriteriaQuery and parameters
* @throws SQLException
*/
public List<T> list(Context context, CriteriaQuery criteriaQuery, boolean cacheable, Class<T> clazz, int maxResults,
int offset, boolean distinct) throws SQLException {
public List<T> list(
Context context, CriteriaQuery<T> criteriaQuery, boolean cacheable, Class<T> clazz, int maxResults, int offset,
boolean distinct
) throws SQLException {
criteriaQuery.distinct(distinct);
@SuppressWarnings("unchecked")
List<T> result = (List<T>) executeCriteriaQuery(context, criteriaQuery, cacheable, maxResults, offset);
return result;
return executeCriteriaQuery(context, criteriaQuery, cacheable, maxResults, offset);
}
/**

View File

@@ -259,12 +259,19 @@ public class Curation extends DSpaceRunnable<CurationScriptConfiguration> {
super.handler.logError("EPerson not found: " + currentUserUuid);
throw new IllegalArgumentException("Unable to find a user with uuid: " + currentUserUuid);
}
assignSpecialGroupsInContext();
this.context.setCurrentUser(eperson);
} catch (SQLException e) {
handler.handleException("Something went wrong trying to fetch eperson for uuid: " + currentUserUuid, e);
}
}
protected void assignSpecialGroupsInContext() throws SQLException {
for (UUID uuid : handler.getSpecialGroups()) {
context.setSpecialGroup(uuid);
}
}
/**
* Fills in some optional command line options.
* Checks if there are missing required options or invalid values for options.

View File

@@ -7,6 +7,7 @@
*/
package org.dspace.discovery;
import java.sql.SQLException;
import java.util.HashSet;
import java.util.Optional;
import java.util.Set;
@@ -37,6 +38,8 @@ public class IndexEventConsumer implements Consumer {
// collect Items, Collections, Communities that need indexing
private Set<IndexableObject> objectsToUpdate = new HashSet<>();
// collect freshly created Items that need indexing (requires pre-db status)
private Set<IndexableObject> createdItemsToUpdate = new HashSet<>();
// unique search IDs to delete
private Set<String> uniqueIdsToDelete = new HashSet<>();
@@ -65,6 +68,7 @@ public class IndexEventConsumer implements Consumer {
if (objectsToUpdate == null) {
objectsToUpdate = new HashSet<>();
uniqueIdsToDelete = new HashSet<>();
createdItemsToUpdate = new HashSet<>();
}
int st = event.getSubjectType();
@@ -143,6 +147,7 @@ public class IndexEventConsumer implements Consumer {
String detail = indexableObjectService.getType() + "-" + event.getSubjectID().toString();
uniqueIdsToDelete.add(detail);
}
objectsToUpdate.addAll(indexObjectServiceFactory.getIndexableObjects(ctx, subject));
}
break;
@@ -162,7 +167,7 @@ public class IndexEventConsumer implements Consumer {
// also update the object in order to index mapped/unmapped Items
if (subject != null &&
subject.getType() == Constants.COLLECTION && object.getType() == Constants.ITEM) {
objectsToUpdate.addAll(indexObjectServiceFactory.getIndexableObjects(ctx, object));
createdItemsToUpdate.addAll(indexObjectServiceFactory.getIndexableObjects(ctx, object));
}
}
break;
@@ -209,23 +214,11 @@ public class IndexEventConsumer implements Consumer {
}
// update the changed Items not deleted because they were on create list
for (IndexableObject iu : objectsToUpdate) {
/* we let all types through here and
* allow the search indexer to make
* decisions on indexing and/or removal
*/
iu.setIndexedObject(ctx.reloadEntity(iu.getIndexedObject()));
String uniqueIndexID = iu.getUniqueIndexID();
if (uniqueIndexID != null) {
try {
indexer.indexContent(ctx, iu, true, false);
log.debug("Indexed "
+ iu.getTypeText()
+ ", id=" + iu.getID()
+ ", unique_id=" + uniqueIndexID);
} catch (Exception e) {
log.error("Failed while indexing object: ", e);
}
indexObject(ctx, iu, false);
}
// update the created Items with a pre-db status
for (IndexableObject iu : createdItemsToUpdate) {
indexObject(ctx, iu, true);
}
} finally {
if (!objectsToUpdate.isEmpty() || !uniqueIdsToDelete.isEmpty()) {
@@ -235,6 +228,27 @@ public class IndexEventConsumer implements Consumer {
// "free" the resources
objectsToUpdate.clear();
uniqueIdsToDelete.clear();
createdItemsToUpdate.clear();
}
}
}
private void indexObject(Context ctx, IndexableObject iu, boolean preDb) throws SQLException {
/* we let all types through here and
* allow the search indexer to make
* decisions on indexing and/or removal
*/
iu.setIndexedObject(ctx.reloadEntity(iu.getIndexedObject()));
String uniqueIndexID = iu.getUniqueIndexID();
if (uniqueIndexID != null) {
try {
indexer.indexContent(ctx, iu, true, false, preDb);
log.debug("Indexed "
+ iu.getTypeText()
+ ", id=" + iu.getID()
+ ", unique_id=" + uniqueIndexID);
} catch (Exception e) {
log.error("Failed while indexing object: ", e);
}
}
}

View File

@@ -9,7 +9,9 @@ package org.dspace.discovery;
import java.io.IOException;
import java.sql.SQLException;
import java.util.Map;
import org.apache.solr.client.solrj.SolrServerException;
import org.dspace.core.Context;
/**
@@ -30,6 +32,17 @@ public interface IndexingService {
void indexContent(Context context, IndexableObject dso,
boolean force, boolean commit) throws SQLException, SearchServiceException;
/**
* Index a given DSO
* @param context The DSpace Context
* @param dso The DSpace Object to index
* @param force Force update even if not stale
* @param commit Commit the changes
* @param preDb Add a "preDB" status to the index (only applicable to Items)
*/
void indexContent(Context context, IndexableObject dso,
boolean force, boolean commit, boolean preDb) throws SQLException, SearchServiceException;
void unIndexContent(Context context, IndexableObject dso)
throws SQLException, IOException;
@@ -62,4 +75,15 @@ public interface IndexingService {
void optimize() throws SearchServiceException;
void buildSpellCheck() throws SearchServiceException, IOException;
/**
* Atomically update the index of a single field for an object
* @param context The DSpace context
* @param uniqueIndexId The unqiue index ID of the object to update the index for
* @param field The field to update
* @param fieldModifier The modifiers for the field to update. More information on how to atomically update a solr
* field using a field modifier can be found here: https://yonik.com/solr/atomic-updates/
*/
void atomicUpdate(Context context, String uniqueIndexId, String field, Map<String,Object> fieldModifier)
throws SolrServerException, IOException;
}

View File

@@ -8,6 +8,7 @@
package org.dspace.discovery;
import java.sql.SQLException;
import java.util.Iterator;
import java.util.List;
import org.dspace.content.Item;
@@ -38,6 +39,7 @@ public interface SearchService {
DiscoverResult search(Context context, DiscoverQuery query)
throws SearchServiceException;
/**
* Convenient method to call @see #search(Context, DSpaceObject,
* DiscoverQuery, boolean) with includeWithdrawn=false
@@ -52,6 +54,19 @@ public interface SearchService {
DiscoverResult search(Context context, IndexableObject dso, DiscoverQuery query)
throws SearchServiceException;
/**
* Convenience method to call @see #search(Context, DSpaceObject, DiscoverQuery) and getting an iterator for the
* results
*
* @param context DSpace context object
* @param dso a DSpace object to use as a scope of the search
* @param query the discovery query object
* @return an iterator iterating over all results from the search
* @throws SearchServiceException if search error
*/
Iterator<Item> iteratorSearch(Context context, IndexableObject dso, DiscoverQuery query)
throws SearchServiceException;
List<IndexableObject> search(Context context, String query, String orderfield, boolean ascending, int offset,
int max, String... filterquery);

View File

@@ -20,6 +20,7 @@ import org.dspace.content.Item;
import org.dspace.content.WorkspaceItem;
import org.dspace.discovery.configuration.DiscoveryConfiguration;
import org.dspace.discovery.configuration.DiscoveryConfigurationService;
import org.dspace.discovery.utils.DiscoverQueryBuilder;
import org.dspace.kernel.ServiceManager;
import org.dspace.services.factory.DSpaceServicesFactory;
import org.dspace.workflow.WorkflowItem;
@@ -170,4 +171,10 @@ public class SearchUtils {
DiscoveryConfiguration configurationExtra = getDiscoveryConfigurationByName(confName);
result.add(configurationExtra);
}
public static DiscoverQueryBuilder getQueryBuilder() {
ServiceManager manager = DSpaceServicesFactory.getInstance().getServiceManager();
return manager
.getServiceByName(DiscoverQueryBuilder.class.getName(), DiscoverQueryBuilder.class);
}
}

View File

@@ -8,6 +8,8 @@
package org.dspace.discovery;
import static java.util.stream.Collectors.joining;
import static org.dspace.discovery.indexobject.ItemIndexFactoryImpl.STATUS_FIELD;
import static org.dspace.discovery.indexobject.ItemIndexFactoryImpl.STATUS_FIELD_PREDB;
import java.io.IOException;
import java.io.PrintWriter;
@@ -118,8 +120,6 @@ public class SolrServiceImpl implements SearchService, IndexingService {
}
/**
* If the handle for the "dso" already exists in the index, and the "dso"
* has a lastModified timestamp that is newer than the document in the index
@@ -166,6 +166,24 @@ public class SolrServiceImpl implements SearchService, IndexingService {
indexableObjectService.writeDocument(context, indexableObject, solrInputDocument);
}
/**
* Update the given indexable object using a given service
* @param context The DSpace Context
* @param indexableObjectService The service to index the object with
* @param indexableObject The object to index
* @param preDB Add a "preDB" status to the document
*/
protected void update(Context context, IndexFactory indexableObjectService, IndexableObject indexableObject,
boolean preDB) throws IOException, SQLException, SolrServerException {
if (preDB) {
final SolrInputDocument solrInputDocument =
indexableObjectService.buildNewDocument(context, indexableObject);
indexableObjectService.writeDocument(context, indexableObject, solrInputDocument);
} else {
update(context, indexableObjectService, indexableObject);
}
}
/**
* unIndex removes an Item, Collection, or Community
*
@@ -454,6 +472,16 @@ public class SolrServiceImpl implements SearchService, IndexingService {
}
}
@Override
public void atomicUpdate(Context context, String uniqueIndexId, String field, Map<String, Object> fieldModifier)
throws SolrServerException, IOException {
SolrInputDocument solrInputDocument = new SolrInputDocument();
solrInputDocument.addField(SearchUtils.RESOURCE_UNIQUE_ID, uniqueIndexId);
solrInputDocument.addField(field, fieldModifier);
solrSearchCore.getSolr().add(solrInputDocument);
}
// //////////////////////////////////
// Private
// //////////////////////////////////
@@ -717,9 +745,14 @@ public class SolrServiceImpl implements SearchService, IndexingService {
}
@Override
public Iterator<Item> iteratorSearch(Context context, IndexableObject dso, DiscoverQuery query)
throws SearchServiceException {
return new SearchIterator(context, dso, query);
}
@Override
public DiscoverResult search(Context context, DiscoverQuery discoveryQuery )
public DiscoverResult search(Context context, DiscoverQuery discoveryQuery)
throws SearchServiceException {
try {
if (solrSearchCore.getSolr() == null) {
@@ -733,6 +766,72 @@ public class SolrServiceImpl implements SearchService, IndexingService {
}
}
/**
* This class implements an iterator over items that is specifically used to iterate over search results
*/
private class SearchIterator implements Iterator<Item> {
private Context context;
private DiscoverQuery discoverQuery;
private DiscoverResult discoverResult;
private IndexableObject dso;
private int absoluteCursor;
private int relativeCursor;
private int pagesize;
SearchIterator(Context context, DiscoverQuery discoverQuery) throws SearchServiceException {
this.context = context;
this.discoverQuery = discoverQuery;
this.absoluteCursor = discoverQuery.getStart();
initialise();
}
SearchIterator(Context context, IndexableObject dso, DiscoverQuery discoverQuery)
throws SearchServiceException {
this.context = context;
this.dso = dso;
this.discoverQuery = discoverQuery;
initialise();
}
private void initialise() throws SearchServiceException {
this.relativeCursor = 0;
if (discoverQuery.getMaxResults() != -1) {
pagesize = discoverQuery.getMaxResults();
} else {
pagesize = 10;
}
discoverQuery.setMaxResults(pagesize);
this.discoverResult = search(context, dso, discoverQuery);
}
@Override
public boolean hasNext() {
return absoluteCursor < discoverResult.getTotalSearchResults();
}
@Override
public Item next() {
//paginate getting results from the discoverquery.
if (relativeCursor == pagesize) {
// get a new page of results when the last element of the previous page has been read
int offset = absoluteCursor;
// reset the position counter for getting element relativecursor on a page
relativeCursor = 0;
discoverQuery.setStart(offset);
try {
discoverResult = search(context, dso, discoverQuery);
} catch (SearchServiceException e) {
log.error("error while getting search results", e);
}
}
// get the element at position relativecursor on a page
IndexableObject res = discoverResult.getIndexableObjects().get(relativeCursor);
relativeCursor++;
absoluteCursor++;
return (Item) res.getIndexedObject();
}
}
protected SolrQuery resolveToSolrQuery(Context context, DiscoverQuery discoveryQuery)
throws SearchServiceException {
SolrQuery solrQuery = new SolrQuery();
@@ -753,6 +852,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
solrQuery.addField(SearchUtils.RESOURCE_TYPE_FIELD);
solrQuery.addField(SearchUtils.RESOURCE_ID_FIELD);
solrQuery.addField(SearchUtils.RESOURCE_UNIQUE_ID);
solrQuery.addField(STATUS_FIELD);
if (discoveryQuery.isSpellCheck()) {
solrQuery.setParam(SpellingParams.SPELLCHECK_Q, query);
@@ -903,12 +1003,15 @@ public class SolrServiceImpl implements SearchService, IndexingService {
// Enables solr to remove documents related to items not on database anymore (Stale)
// if maxAttemps is greater than 0 cleanup the index on each step
if (maxAttempts >= 0) {
Object statusObj = doc.getFirstValue(STATUS_FIELD);
if (!(statusObj instanceof String && statusObj.equals(STATUS_FIELD_PREDB))) {
zombieDocs.add((String) doc.getFirstValue(SearchUtils.RESOURCE_UNIQUE_ID));
// avoid to process the response except if we are in the last allowed execution.
// When maxAttempts is 0 this will be just the first and last run as the
// executionCount is increased at the start of the loop it will be equals to 1
skipLoadingResponse = maxAttempts + 1 != executionCount;
}
}
continue;
}
if (!skipLoadingResponse) {
@@ -1389,6 +1492,28 @@ public class SolrServiceImpl implements SearchService, IndexingService {
}
}
@Override
public void indexContent(Context context, IndexableObject indexableObject, boolean force,
boolean commit, boolean preDb) throws SearchServiceException, SQLException {
if (preDb) {
try {
final IndexFactory indexableObjectFactory = indexObjectServiceFactory.
getIndexableObjectFactory(indexableObject);
if (force || requiresIndexing(indexableObject.getUniqueIndexID(), indexableObject.getLastModified())) {
update(context, indexableObjectFactory, indexableObject, true);
log.info(LogHelper.getHeader(context, "indexed_object", indexableObject.getUniqueIndexID()));
}
} catch (IOException | SQLException | SolrServerException | SearchServiceException e) {
log.error(e.getMessage(), e);
}
} else {
indexContent(context, indexableObject, force);
}
if (commit) {
commit();
}
}
@Override
public void commit() throws SearchServiceException {
try {

View File

@@ -70,10 +70,20 @@ public abstract class IndexFactoryImpl<T extends IndexableObject, S> implements
return doc;
}
@Override
public SolrInputDocument buildNewDocument(Context context, T indexableObject) throws SQLException, IOException {
return buildDocument(context, indexableObject);
}
@Override
public void writeDocument(Context context, T indexableObject, SolrInputDocument solrInputDocument)
throws SQLException, IOException, SolrServerException {
try {
writeDocument(solrInputDocument, null);
} catch (Exception e) {
log.error("Error occurred while writing SOLR document for {} object {}",
indexableObject.getType(), indexableObject.getID(), e);
}
}
/**

View File

@@ -10,7 +10,6 @@ package org.dspace.discovery.indexobject;
import java.io.IOException;
import java.sql.SQLException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Date;
import java.util.HashMap;
import java.util.HashSet;
@@ -43,7 +42,6 @@ import org.dspace.content.service.WorkspaceItemService;
import org.dspace.core.Context;
import org.dspace.core.LogHelper;
import org.dspace.discovery.FullTextContentStreams;
import org.dspace.discovery.IndexableObject;
import org.dspace.discovery.SearchUtils;
import org.dspace.discovery.configuration.DiscoveryConfiguration;
import org.dspace.discovery.configuration.DiscoveryConfigurationParameters;
@@ -64,6 +62,9 @@ import org.dspace.handle.service.HandleService;
import org.dspace.services.factory.DSpaceServicesFactory;
import org.dspace.util.MultiFormatDateParser;
import org.dspace.util.SolrUtils;
import org.dspace.versioning.Version;
import org.dspace.versioning.VersionHistory;
import org.dspace.versioning.service.VersionHistoryService;
import org.dspace.xmlworkflow.storedcomponents.XmlWorkflowItem;
import org.dspace.xmlworkflow.storedcomponents.service.XmlWorkflowItemService;
import org.springframework.beans.factory.annotation.Autowired;
@@ -78,6 +79,8 @@ public class ItemIndexFactoryImpl extends DSpaceObjectIndexFactoryImpl<Indexable
private static final Logger log = org.apache.logging.log4j.LogManager.getLogger(ItemIndexFactoryImpl.class);
public static final String VARIANTS_STORE_SEPARATOR = "###";
public static final String STORE_SEPARATOR = "\n|||\n";
public static final String STATUS_FIELD = "database_status";
public static final String STATUS_FIELD_PREDB = "predb";
@Autowired
@@ -96,11 +99,13 @@ public class ItemIndexFactoryImpl extends DSpaceObjectIndexFactoryImpl<Indexable
protected WorkflowItemIndexFactory workflowItemIndexFactory;
@Autowired
protected WorkspaceItemIndexFactory workspaceItemIndexFactory;
@Autowired
protected VersionHistoryService versionHistoryService;
@Override
public Iterator<IndexableItem> findAll(Context context) throws SQLException {
Iterator<Item> items = itemService.findAllUnfiltered(context);
Iterator<Item> items = itemService.findAllRegularItems(context);
return new Iterator<IndexableItem>() {
@Override
public boolean hasNext() {
@@ -139,6 +144,7 @@ public class ItemIndexFactoryImpl extends DSpaceObjectIndexFactoryImpl<Indexable
doc.addField("withdrawn", item.isWithdrawn());
doc.addField("discoverable", item.isDiscoverable());
doc.addField("lastModified", SolrUtils.getDateFormatter().format(item.getLastModified()));
doc.addField("latestVersion", isLatestVersion(context, item));
EPerson submitter = item.getSubmitter();
if (submitter != null) {
@@ -169,6 +175,51 @@ public class ItemIndexFactoryImpl extends DSpaceObjectIndexFactoryImpl<Indexable
return doc;
}
/**
* Check whether the given item is the latest version.
* If the latest item cannot be determined, because either the version history or the latest version is not present,
* assume the item is latest.
* @param context the DSpace context.
* @param item the item that should be checked.
* @return true if the item is the latest version, false otherwise.
*/
protected boolean isLatestVersion(Context context, Item item) throws SQLException {
VersionHistory history = versionHistoryService.findByItem(context, item);
if (history == null) {
// not all items have a version history
// if an item does not have a version history, it is by definition the latest version
return true;
}
// start with the very latest version of the given item (may still be in workspace)
Version latestVersion = versionHistoryService.getLatestVersion(context, history);
// find the latest version of the given item that is archived
while (latestVersion != null && !latestVersion.getItem().isArchived()) {
latestVersion = versionHistoryService.getPrevious(context, history, latestVersion);
}
// could not find an archived version of the given item
if (latestVersion == null) {
// this scenario should never happen, but let's err on the side of showing too many items vs. to little
// (see discovery.xml, a lot of discovery configs filter out all items that are not the latest version)
return true;
}
// sanity check
assert latestVersion.getItem().isArchived();
return item.equals(latestVersion.getItem());
}
@Override
public SolrInputDocument buildNewDocument(Context context, IndexableItem indexableItem)
throws SQLException, IOException {
SolrInputDocument doc = buildDocument(context, indexableItem);
doc.addField(STATUS_FIELD, STATUS_FIELD_PREDB);
return doc;
}
@Override
public void addDiscoveryFields(SolrInputDocument doc, Context context, Item item,
List<DiscoveryConfiguration> discoveryConfigurations)
@@ -713,26 +764,31 @@ public class ItemIndexFactoryImpl extends DSpaceObjectIndexFactoryImpl<Indexable
}
@Override
public List getIndexableObjects(Context context, Item object) throws SQLException {
List<IndexableObject> results = new ArrayList<>();
if (object.isArchived() || object.isWithdrawn()) {
// We only want to index an item as an item if it is not in workflow
results.addAll(Arrays.asList(new IndexableItem(object)));
} else {
// Check if we have a workflow / workspace item
final WorkspaceItem workspaceItem = workspaceItemService.findByItem(context, object);
if (workspaceItem != null) {
results.addAll(workspaceItemIndexFactory.getIndexableObjects(context, workspaceItem));
} else {
// Check if we a workflow item
final XmlWorkflowItem xmlWorkflowItem = xmlWorkflowItemService.findByItem(context, object);
if (xmlWorkflowItem != null) {
results.addAll(workflowItemIndexFactory.getIndexableObjects(context, xmlWorkflowItem));
}
}
public List getIndexableObjects(Context context, Item item) throws SQLException {
if (item.isArchived() || item.isWithdrawn()) {
// we only want to index an item as an item if it is not in workflow
return List.of(new IndexableItem(item));
}
return results;
final WorkspaceItem workspaceItem = workspaceItemService.findByItem(context, item);
if (workspaceItem != null) {
// a workspace item is linked to the given item
return List.copyOf(workspaceItemIndexFactory.getIndexableObjects(context, workspaceItem));
}
final XmlWorkflowItem xmlWorkflowItem = xmlWorkflowItemService.findByItem(context, item);
if (xmlWorkflowItem != null) {
// a workflow item is linked to the given item
return List.copyOf(workflowItemIndexFactory.getIndexableObjects(context, xmlWorkflowItem));
}
if (!isLatestVersion(context, item)) {
// the given item is an older version of another item
return List.of(new IndexableItem(item));
}
// nothing to index
return List.of();
}
@Override

View File

@@ -46,6 +46,14 @@ public interface IndexFactory<T extends IndexableObject, S> {
*/
SolrInputDocument buildDocument(Context context, T indexableObject) throws SQLException, IOException;
/**
* Create solr document with all the shared fields initialized.
* Can contain special fields required for "new" documents vs regular buildDocument
* @param indexableObject the indexableObject that we want to index
* @return initialized solr document
*/
SolrInputDocument buildNewDocument(Context context, T indexableObject) throws SQLException, IOException;
/**
* Write the provided document to the solr core
* @param context DSpace context object

View File

@@ -5,7 +5,7 @@
*
* http://www.dspace.org/license/
*/
package org.dspace.app.rest.utils;
package org.dspace.discovery.utils;
import static java.util.Collections.emptyList;
import static java.util.Collections.singletonList;
@@ -19,10 +19,6 @@ import java.util.Objects;
import org.apache.commons.collections4.CollectionUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.Logger;
import org.dspace.app.rest.converter.query.SearchQueryConverter;
import org.dspace.app.rest.exception.DSpaceBadRequestException;
import org.dspace.app.rest.exception.InvalidSearchRequestException;
import org.dspace.app.rest.parameter.SearchFilter;
import org.dspace.core.Context;
import org.dspace.core.LogHelper;
import org.dspace.discovery.DiscoverFacetField;
@@ -32,6 +28,7 @@ import org.dspace.discovery.DiscoverQuery;
import org.dspace.discovery.FacetYearRange;
import org.dspace.discovery.IndexableObject;
import org.dspace.discovery.SearchService;
import org.dspace.discovery.SearchServiceException;
import org.dspace.discovery.configuration.DiscoveryConfiguration;
import org.dspace.discovery.configuration.DiscoveryConfigurationParameters;
import org.dspace.discovery.configuration.DiscoveryHitHighlightFieldConfiguration;
@@ -40,17 +37,11 @@ import org.dspace.discovery.configuration.DiscoverySearchFilterFacet;
import org.dspace.discovery.configuration.DiscoverySortConfiguration;
import org.dspace.discovery.configuration.DiscoverySortFieldConfiguration;
import org.dspace.discovery.indexobject.factory.IndexFactory;
import org.dspace.discovery.utils.parameter.QueryBuilderSearchFilter;
import org.dspace.services.ConfigurationService;
import org.springframework.beans.factory.InitializingBean;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.data.domain.Pageable;
import org.springframework.data.domain.Sort;
import org.springframework.stereotype.Component;
/**
* This class builds the queries for the /search and /facet endpoints.
*/
@Component
public class DiscoverQueryBuilder implements InitializingBean {
private static final Logger log = org.apache.logging.log4j.LogManager.getLogger(DiscoverQueryBuilder.class);
@@ -80,19 +71,24 @@ public class DiscoverQueryBuilder implements InitializingBean {
* @param query the query string for this discovery query
* @param searchFilters the search filters for this discovery query
* @param dsoType only include search results with this type
* @param page the pageable for this discovery query
* @param pageSize the page size for this discovery query
* @param offset the offset for this discovery query
* @param sortProperty the sort property for this discovery query
* @param sortDirection the sort direction for this discovery query
*/
public DiscoverQuery buildQuery(Context context, IndexableObject scope,
DiscoveryConfiguration discoveryConfiguration,
String query, List<SearchFilter> searchFilters,
String dsoType, Pageable page)
throws DSpaceBadRequestException {
String query, List<QueryBuilderSearchFilter> searchFilters,
String dsoType, Integer pageSize, Long offset, String sortProperty,
String sortDirection) throws SearchServiceException {
List<String> dsoTypes = dsoType != null ? singletonList(dsoType) : emptyList();
return buildQuery(context, scope, discoveryConfiguration, query, searchFilters, dsoTypes, page);
return buildQuery(context, scope, discoveryConfiguration, query, searchFilters, dsoTypes, pageSize, offset,
sortProperty, sortDirection);
}
/**
* Build a discovery query
*
@@ -102,13 +98,17 @@ public class DiscoverQueryBuilder implements InitializingBean {
* @param query the query string for this discovery query
* @param searchFilters the search filters for this discovery query
* @param dsoTypes only include search results with one of these types
* @param page the pageable for this discovery query
* @param pageSize the page size for this discovery query
* @param offset the offset for this discovery query
* @param sortProperty the sort property for this discovery query
* @param sortDirection the sort direction for this discovery query
*/
public DiscoverQuery buildQuery(Context context, IndexableObject scope,
DiscoveryConfiguration discoveryConfiguration,
String query, List<SearchFilter> searchFilters,
List<String> dsoTypes, Pageable page)
throws DSpaceBadRequestException {
String query, List<QueryBuilderSearchFilter> searchFilters,
List<String> dsoTypes, Integer pageSize, Long offset, String sortProperty,
String sortDirection)
throws IllegalArgumentException, SearchServiceException {
DiscoverQuery queryArgs = buildCommonDiscoverQuery(context, discoveryConfiguration, query, searchFilters,
dsoTypes);
@@ -117,8 +117,8 @@ public class DiscoverQueryBuilder implements InitializingBean {
addFaceting(context, scope, queryArgs, discoveryConfiguration);
//Configure pagination and sorting
configurePagination(page, queryArgs);
configureSorting(page, queryArgs, discoveryConfiguration.getSearchSortConfiguration());
configurePagination(pageSize, offset, queryArgs);
configureSorting(sortProperty, sortDirection, queryArgs, discoveryConfiguration.getSearchSortConfiguration());
addDiscoveryHitHighlightFields(discoveryConfiguration, queryArgs);
return queryArgs;
@@ -147,19 +147,21 @@ public class DiscoverQueryBuilder implements InitializingBean {
* @param query the query string for this discovery query
* @param searchFilters the search filters for this discovery query
* @param dsoType only include search results with this type
* @param page the pageable for this discovery query
* @param pageSize the page size for this discovery query
* @param offset the offset for this discovery query
* @param facetName the facet field
*/
public DiscoverQuery buildFacetQuery(Context context, IndexableObject scope,
DiscoveryConfiguration discoveryConfiguration,
String prefix, String query, List<SearchFilter> searchFilters,
String dsoType, Pageable page, String facetName)
throws DSpaceBadRequestException {
String prefix, String query, List<QueryBuilderSearchFilter> searchFilters,
String dsoType, Integer pageSize, Long offset, String facetName)
throws IllegalArgumentException {
List<String> dsoTypes = dsoType != null ? singletonList(dsoType) : emptyList();
return buildFacetQuery(
context, scope, discoveryConfiguration, prefix, query, searchFilters, dsoTypes, page, facetName);
context, scope, discoveryConfiguration, prefix, query, searchFilters, dsoTypes, pageSize, offset,
facetName);
}
/**
@@ -172,49 +174,52 @@ public class DiscoverQueryBuilder implements InitializingBean {
* @param query the query string for this discovery query
* @param searchFilters the search filters for this discovery query
* @param dsoTypes only include search results with one of these types
* @param page the pageable for this discovery query
* @param pageSize the page size for this discovery query
* @param offset the offset for this discovery query
* @param facetName the facet field
*/
public DiscoverQuery buildFacetQuery(Context context, IndexableObject scope,
DiscoveryConfiguration discoveryConfiguration,
String prefix, String query, List<SearchFilter> searchFilters,
List<String> dsoTypes, Pageable page, String facetName)
throws DSpaceBadRequestException {
String prefix, String query, List<QueryBuilderSearchFilter> searchFilters,
List<String> dsoTypes, Integer pageSize, Long offset, String facetName)
throws IllegalArgumentException {
DiscoverQuery queryArgs = buildCommonDiscoverQuery(context, discoveryConfiguration, query, searchFilters,
dsoTypes);
//When all search criteria are set, configure facet results
addFacetingForFacets(context, scope, prefix, queryArgs, discoveryConfiguration, facetName, page);
addFacetingForFacets(context, scope, prefix, queryArgs, discoveryConfiguration, facetName, pageSize);
//We don' want any search results, we only want facet values
queryArgs.setMaxResults(0);
//Configure pagination
configurePaginationForFacets(page, queryArgs);
configurePaginationForFacets(offset, queryArgs);
return queryArgs;
}
private void configurePaginationForFacets(Pageable page, DiscoverQuery queryArgs) {
if (page != null) {
queryArgs.setFacetOffset(Math.toIntExact(page.getOffset()));
private void configurePaginationForFacets(Long offset, DiscoverQuery queryArgs) {
if (offset != null) {
queryArgs.setFacetOffset(Math.toIntExact(offset));
}
}
private DiscoverQuery addFacetingForFacets(Context context, IndexableObject scope, String prefix,
DiscoverQuery queryArgs, DiscoveryConfiguration discoveryConfiguration, String facetName, Pageable page)
throws DSpaceBadRequestException {
DiscoverQuery queryArgs, DiscoveryConfiguration discoveryConfiguration,
String facetName, Integer pageSize)
throws IllegalArgumentException {
DiscoverySearchFilterFacet facet = discoveryConfiguration.getSidebarFacet(facetName);
if (facet != null) {
queryArgs.setFacetMinCount(1);
int pageSize = Math.min(pageSizeLimit, page.getPageSize());
pageSize = pageSize != null ? Math.min(pageSizeLimit, pageSize) : pageSizeLimit;
fillFacetIntoQueryArgs(context, scope, prefix, queryArgs, facet, pageSize);
} else {
throw new DSpaceBadRequestException(facetName + " is not a valid search facet");
throw new IllegalArgumentException(facetName + " is not a valid search facet");
}
return queryArgs;
@@ -241,18 +246,18 @@ public class DiscoverQueryBuilder implements InitializingBean {
int facetLimit = pageSize + 1;
//This should take care of the sorting for us
queryArgs.addFacetField(new DiscoverFacetField(facet.getIndexFieldName(), facet.getType(), facetLimit,
facet.getSortOrderSidebar(), StringUtils.trimToNull(prefix)));
facet.getSortOrderSidebar(),
StringUtils.trimToNull(prefix)));
}
}
private DiscoverQuery buildCommonDiscoverQuery(Context context, DiscoveryConfiguration discoveryConfiguration,
String query,
List<SearchFilter> searchFilters, List<String> dsoTypes)
throws DSpaceBadRequestException {
List<QueryBuilderSearchFilter> searchFilters, List<String> dsoTypes)
throws IllegalArgumentException {
DiscoverQuery queryArgs = buildBaseQueryForConfiguration(discoveryConfiguration);
//Add search filters
queryArgs.addFilterQueries(convertFilters(context, discoveryConfiguration, searchFilters));
queryArgs.addFilterQueries(convertFiltersToString(context, discoveryConfiguration, searchFilters));
//Set search query
if (StringUtils.isNotBlank(query)) {
@@ -274,30 +279,17 @@ public class DiscoverQueryBuilder implements InitializingBean {
queryArgs.setDiscoveryConfigurationName(discoveryConfiguration.getId());
queryArgs.addFilterQueries(discoveryConfiguration.getDefaultFilterQueries()
.toArray(
new String[discoveryConfiguration.getDefaultFilterQueries()
new String[discoveryConfiguration
.getDefaultFilterQueries()
.size()]));
return queryArgs;
}
private void configureSorting(Pageable page, DiscoverQuery queryArgs,
DiscoverySortConfiguration searchSortConfiguration) throws DSpaceBadRequestException {
String sortBy = null;
String sortOrder = null;
//Read the Pageable object if there is one
if (page != null) {
Sort sort = page.getSort();
if (sort != null && sort.iterator().hasNext()) {
Sort.Order order = sort.iterator().next();
sortBy = order.getProperty();
sortOrder = order.getDirection().name();
}
}
if (StringUtils.isNotBlank(sortBy) && !isConfigured(sortBy, searchSortConfiguration)) {
throw new InvalidSearchRequestException(
"The field: " + sortBy + "is not configured for the configuration!");
}
private void configureSorting(String sortProperty, String sortDirection, DiscoverQuery queryArgs,
DiscoverySortConfiguration searchSortConfiguration)
throws IllegalArgumentException, SearchServiceException {
String sortBy = sortProperty;
String sortOrder = sortDirection;
//Load defaults if we did not receive values
if (sortBy == null) {
@@ -307,6 +299,12 @@ public class DiscoverQueryBuilder implements InitializingBean {
sortOrder = getDefaultSortDirection(searchSortConfiguration, sortOrder);
}
if (StringUtils.isNotBlank(sortBy) && !isConfigured(sortBy, searchSortConfiguration)) {
throw new SearchServiceException(
"The field: " + sortBy + "is not configured for the configuration!");
}
//Update Discovery query
DiscoverySortFieldConfiguration sortFieldConfiguration = searchSortConfiguration
.getSortFieldConfiguration(sortBy);
@@ -320,11 +318,11 @@ public class DiscoverQueryBuilder implements InitializingBean {
} else if ("desc".equalsIgnoreCase(sortOrder)) {
queryArgs.setSortField(sortField, DiscoverQuery.SORT_ORDER.desc);
} else {
throw new DSpaceBadRequestException(sortOrder + " is not a valid sort order");
throw new IllegalArgumentException(sortOrder + " is not a valid sort order");
}
} else {
throw new DSpaceBadRequestException(sortBy + " is not a valid sort field");
throw new IllegalArgumentException(sortBy + " is not a valid sort field");
}
}
@@ -354,59 +352,24 @@ public class DiscoverQueryBuilder implements InitializingBean {
return sortBy;
}
private void configurePagination(Pageable page, DiscoverQuery queryArgs) {
if (page != null) {
queryArgs.setMaxResults(Math.min(pageSizeLimit, page.getPageSize()));
queryArgs.setStart(Math.toIntExact(page.getOffset()));
} else {
queryArgs.setMaxResults(pageSizeLimit);
queryArgs.setStart(0);
}
private void configurePagination(Integer size, Long offset, DiscoverQuery queryArgs) {
queryArgs.setMaxResults(size != null ? Math.min(pageSizeLimit, size) : pageSizeLimit);
queryArgs.setStart(offset != null ? Math.toIntExact(offset) : 0);
}
private String getDsoType(String dsoType) throws DSpaceBadRequestException {
private String getDsoType(String dsoType) throws IllegalArgumentException {
for (IndexFactory indexFactory : indexableFactories) {
if (StringUtils.equalsIgnoreCase(indexFactory.getType(), dsoType)) {
return indexFactory.getType();
}
}
throw new DSpaceBadRequestException(dsoType + " is not a valid DSpace Object type");
throw new IllegalArgumentException(dsoType + " is not a valid DSpace Object type");
}
public void setIndexableFactories(List<IndexFactory> indexableFactories) {
this.indexableFactories = indexableFactories;
}
private String[] convertFilters(Context context, DiscoveryConfiguration discoveryConfiguration,
List<SearchFilter> searchFilters) throws DSpaceBadRequestException {
ArrayList<String> filterQueries = new ArrayList<>(CollectionUtils.size(searchFilters));
SearchQueryConverter searchQueryConverter = new SearchQueryConverter();
List<SearchFilter> transformedFilters = searchQueryConverter.convert(searchFilters);
try {
for (SearchFilter searchFilter : CollectionUtils.emptyIfNull(transformedFilters)) {
DiscoverySearchFilter filter = discoveryConfiguration.getSearchFilter(searchFilter.getName());
if (filter == null) {
throw new DSpaceBadRequestException(searchFilter.getName() + " is not a valid search filter");
}
DiscoverFilterQuery filterQuery = searchService.toFilterQuery(context,
filter.getIndexFieldName(),
searchFilter.getOperator(),
searchFilter.getValue(),
discoveryConfiguration);
if (filterQuery != null) {
filterQueries.add(filterQuery.getFilterQuery());
}
}
} catch (SQLException e) {
throw new DSpaceBadRequestException("There was a problem parsing the search filters.", e);
}
return filterQueries.toArray(new String[filterQueries.size()]);
}
private DiscoverQuery addFaceting(Context context, IndexableObject scope, DiscoverQuery queryArgs,
DiscoveryConfiguration discoveryConfiguration) {
@@ -427,4 +390,34 @@ public class DiscoverQueryBuilder implements InitializingBean {
return queryArgs;
}
private String[] convertFiltersToString(Context context, DiscoveryConfiguration discoveryConfiguration,
List<QueryBuilderSearchFilter> searchFilters)
throws IllegalArgumentException {
ArrayList<String> filterQueries = new ArrayList<>(CollectionUtils.size(searchFilters));
try {
for (QueryBuilderSearchFilter searchFilter : CollectionUtils.emptyIfNull(searchFilters)) {
DiscoverySearchFilter filter = discoveryConfiguration.getSearchFilter(searchFilter.getName());
if (filter == null) {
throw new IllegalArgumentException(searchFilter.getName() + " is not a valid search filter");
}
DiscoverFilterQuery filterQuery = searchService.toFilterQuery(context,
filter.getIndexFieldName(),
searchFilter.getOperator(),
searchFilter.getValue(),
discoveryConfiguration);
if (filterQuery != null) {
filterQueries.add(filterQuery.getFilterQuery());
}
}
} catch (SQLException e) {
throw new IllegalArgumentException("There was a problem parsing the search filters.", e);
}
return filterQueries.toArray(new String[filterQueries.size()]);
}
}

View File

@@ -0,0 +1,70 @@
/**
* 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.discovery.utils.parameter;
import java.util.Objects;
import org.apache.commons.lang3.StringUtils;
/**
* Representation for a Discovery search filter
*/
public class QueryBuilderSearchFilter {
private String name;
private String operator;
private String value;
public QueryBuilderSearchFilter(final String name, final String operator, final String value) {
this.name = name;
this.operator = operator;
this.value = value;
}
public String getName() {
return name;
}
public String getOperator() {
return operator;
}
public String getValue() {
return value;
}
public String toString() {
return "QueryBuilderSearchFilter{" +
"name='" + name + '\'' +
", operator='" + operator + '\'' +
", value='" + value + '\'' +
'}';
}
public boolean equals(Object object) {
if (object instanceof QueryBuilderSearchFilter) {
QueryBuilderSearchFilter obj = (QueryBuilderSearchFilter) object;
if (!StringUtils.equals(obj.getName(), getName())) {
return false;
}
if (!StringUtils.equals(obj.getOperator(), getOperator())) {
return false;
}
if (!StringUtils.equals(obj.getValue(), getValue())) {
return false;
}
return true;
}
return false;
}
public int hashCode() {
return Objects.hash(name, operator, value);
}
}

View File

@@ -0,0 +1,37 @@
/**
* 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.importer.external.cinii;
import java.util.Map;
import javax.annotation.Resource;
import org.dspace.importer.external.metadatamapping.AbstractMetadataFieldMapping;
/**
* An implementation of {@link AbstractMetadataFieldMapping}
* Responsible for defining the mapping of the Cinii metadatum fields on the DSpace metadatum fields
*
* @author Pasquale Cavallo (pasquale.cavallo at 4science dot it)
*/
public class CiniiFieldMapping extends AbstractMetadataFieldMapping {
/**
* Defines which metadatum is mapped on which metadatum. Note that while the key must be unique it
* only matters here for postprocessing of the value. The mapped MetadatumContributor has full control over
* what metadatafield is generated.
*
* @param metadataFieldMap The map containing the link between retrieve metadata and metadata that will be set to
* the item.
*/
@Override
@Resource(name = "ciniiMetadataFieldMap")
public void setMetadataFieldMap(Map metadataFieldMap) {
super.setMetadataFieldMap(metadataFieldMap);
}
}

View File

@@ -0,0 +1,447 @@
/**
* 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.importer.external.cinii;
import java.io.IOException;
import java.io.StringReader;
import java.net.URISyntaxException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.HashMap;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
import java.util.Objects;
import java.util.concurrent.Callable;
import javax.el.MethodNotFoundException;
import org.apache.commons.collections.CollectionUtils;
import org.apache.commons.lang.StringUtils;
import org.apache.http.HttpException;
import org.apache.http.client.utils.URIBuilder;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.content.Item;
import org.dspace.importer.external.datamodel.ImportRecord;
import org.dspace.importer.external.datamodel.Query;
import org.dspace.importer.external.exception.MetadataSourceException;
import org.dspace.importer.external.liveimportclient.service.LiveImportClient;
import org.dspace.importer.external.metadatamapping.MetadatumDTO;
import org.dspace.importer.external.service.AbstractImportMetadataSourceService;
import org.dspace.importer.external.service.components.QuerySource;
import org.dspace.services.ConfigurationService;
import org.jdom2.Attribute;
import org.jdom2.Document;
import org.jdom2.Element;
import org.jdom2.JDOMException;
import org.jdom2.Namespace;
import org.jdom2.filter.Filters;
import org.jdom2.input.SAXBuilder;
import org.jdom2.xpath.XPathExpression;
import org.jdom2.xpath.XPathFactory;
import org.springframework.beans.factory.annotation.Autowired;
/**
* Implements a data source for querying Cinii
*
* @author Mykhaylo Boychuk (mykhaylo.boychuk at 4science.com)
*/
public class CiniiImportMetadataSourceServiceImpl extends AbstractImportMetadataSourceService<Element>
implements QuerySource {
private final static Logger log = LogManager.getLogger();
private String url;
private String urlSearch;
@Autowired
private LiveImportClient liveImportClient;
@Autowired
private ConfigurationService configurationService;
@Override
public String getImportSource() {
return "cinii";
}
@Override
public void init() throws Exception {}
@Override
public ImportRecord getRecord(String id) throws MetadataSourceException {
List<ImportRecord> records = retry(new SearchByIdCallable(id));
return CollectionUtils.isNotEmpty(records) ? records.get(0) : null;
}
@Override
public int getRecordsCount(String query) throws MetadataSourceException {
return retry(new CountByQueryCallable(query));
}
@Override
public int getRecordsCount(Query query) throws MetadataSourceException {
return retry(new CountByQueryCallable(query));
}
@Override
public Collection<ImportRecord> getRecords(String query, int start, int count) throws MetadataSourceException {
return retry(new SearchByQueryCallable(query, count, start));
}
@Override
public Collection<ImportRecord> getRecords(Query query) throws MetadataSourceException {
return retry(new SearchByQueryCallable(query));
}
@Override
public ImportRecord getRecord(Query query) throws MetadataSourceException {
List<ImportRecord> records = retry(new SearchByIdCallable(query));
return CollectionUtils.isNotEmpty(records) ? records.get(0) : null;
}
@Override
public Collection<ImportRecord> findMatchingRecords(Query query) throws MetadataSourceException {
return retry(new FindMatchingRecordCallable(query));
}
@Override
public Collection<ImportRecord> findMatchingRecords(Item item) throws MetadataSourceException {
throw new MethodNotFoundException("This method is not implemented for Cinii");
}
public String getUrl() {
return url;
}
public void setUrl(String url) {
this.url = url;
}
public String getUrlSearch() {
return urlSearch;
}
public void setUrlSearch(String urlSearch) {
this.urlSearch = urlSearch;
}
/**
* This class is a Callable implementation to get CiNii entries based on
* query object.
*
* This Callable use as query value the string queryString passed to constructor.
* If the object will be construct through Query.class instance, a Query's map entry with key "query" will be used.
* Pagination is supported too, using the value of the Query's map with keys "start" and "count".
*
* @author Mykhaylo Boychuk (mykhaylo.boychuk at 4science.com)
*/
private class SearchByQueryCallable implements Callable<List<ImportRecord>> {
private Query query;
private SearchByQueryCallable(String queryString, Integer maxResult, Integer start) {
query = new Query();
query.addParameter("query", queryString);
query.addParameter("count", maxResult);
query.addParameter("start", start);
}
private SearchByQueryCallable(Query query) {
this.query = query;
}
@Override
public List<ImportRecord> call() throws Exception {
List<ImportRecord> records = new LinkedList<ImportRecord>();
Integer count = query.getParameterAsClass("count", Integer.class);
Integer start = query.getParameterAsClass("start", Integer.class);
String queryString = query.getParameterAsClass("query", String.class);
String appId = configurationService.getProperty("cinii.appid");
List<String> ids = getCiniiIds(appId, count, null, null, null, start, queryString);
if (CollectionUtils.isNotEmpty(ids)) {
for (String id : ids) {
List<ImportRecord> tmp = search(id, appId);
if (CollectionUtils.isNotEmpty(tmp)) {
tmp.forEach(x -> x.addValue(createIdentifier(id)));
}
records.addAll(tmp);
}
}
return records;
}
}
/**
* This class is a Callable implementation to get an CiNii entry using CiNii ID
*
* @author Mykhaylo Boychuk (mykhaylo.boychuk at 4science.com)
*/
private class SearchByIdCallable implements Callable<List<ImportRecord>> {
private Query query;
private SearchByIdCallable(Query query) {
this.query = query;
}
private SearchByIdCallable(String id) {
this.query = new Query();
query.addParameter("id", id);
}
@Override
public List<ImportRecord> call() throws Exception {
String appId = configurationService.getProperty("cinii.appid");
String id = query.getParameterAsClass("id", String.class);
List<ImportRecord> importRecord = search(id, appId);
if (CollectionUtils.isNotEmpty(importRecord)) {
importRecord.forEach(x -> x.addValue(createIdentifier(id)));
}
return importRecord;
}
}
/**
* This class is a Callable implementation to search CiNii entries
* using author, title and year.
* Pagination is supported too, using the value of the Query's map with keys "start" and "count".
*
* @author Mykhaylo Boychuk (mykhaylo.boychuk at 4science.com)
*/
private class FindMatchingRecordCallable implements Callable<List<ImportRecord>> {
private Query query;
private FindMatchingRecordCallable(Query q) {
query = q;
}
@Override
public List<ImportRecord> call() throws Exception {
List<ImportRecord> records = new LinkedList<ImportRecord>();
String title = query.getParameterAsClass("title", String.class);
String author = query.getParameterAsClass("author", String.class);
Integer year = query.getParameterAsClass("year", Integer.class);
Integer maxResult = query.getParameterAsClass("maxResult", Integer.class);
Integer start = query.getParameterAsClass("start", Integer.class);
String appId = configurationService.getProperty("cinii.appid");
List<String> ids = getCiniiIds(appId, maxResult, author, title, year, start, null);
if (CollectionUtils.isNotEmpty(ids)) {
for (String id : ids) {
List<ImportRecord> importRecords = search(id, appId);
if (CollectionUtils.isNotEmpty(importRecords)) {
importRecords.forEach(x -> x.addValue(createIdentifier(id)));
}
records.addAll(importRecords);
}
}
return records;
}
}
/**
* This class is a Callable implementation to count the number
* of entries for an CiNii query.
*
* @author Mykhaylo Boychuk (mykhaylo.boychuk at 4science.com)
*/
private class CountByQueryCallable implements Callable<Integer> {
private Query query;
private CountByQueryCallable(String queryString) {
query = new Query();
query.addParameter("query", queryString);
}
private CountByQueryCallable(Query query) {
this.query = query;
}
@Override
public Integer call() throws Exception {
String appId = configurationService.getProperty("cinii.appid");
String queryString = query.getParameterAsClass("query", String.class);
return countCiniiElement(appId, null, null, null, null, null, queryString);
}
}
/**
* Get metadata by searching CiNii RDF API with CiNii NAID
*
* @param id CiNii NAID to search by
* @param appId registered application identifier for the API
* @return record metadata
* @throws IOException A general class of exceptions produced by failed or interrupted I/O operations.
* @throws HttpException Represents a XML/HTTP fault and provides access to the HTTP status code.
*/
protected List<ImportRecord> search(String id, String appId)
throws IOException, HttpException {
try {
List<ImportRecord> records = new LinkedList<ImportRecord>();
URIBuilder uriBuilder = new URIBuilder(this.url + id + ".rdf?appid=" + appId);
Map<String, Map<String, String>> params = new HashMap<String, Map<String,String>>();
String response = liveImportClient.executeHttpGetRequest(1000, uriBuilder.toString(), params);
List<Element> elements = splitToRecords(response);
for (Element record : elements) {
records.add(transformSourceRecords(record));
}
return records;
} catch (URISyntaxException e) {
log.error(e.getMessage(), e);
throw new RuntimeException(e.getMessage(), e);
}
}
private List<Element> splitToRecords(String recordsSrc) {
try {
SAXBuilder saxBuilder = new SAXBuilder();
Document document = saxBuilder.build(new StringReader(recordsSrc));
Element root = document.getRootElement();
return root.getChildren();
} catch (JDOMException | IOException e) {
log.error(e.getMessage(), e);
throw new RuntimeException(e.getMessage(), e);
}
}
/**
* Returns a list of uri links (for example:https://cir.nii.ac.jp/crid/123456789)
* to the searched CiNii articles
*
* @param appId Application ID
* @param maxResult The number of search results per page
* @param author Author name
* @param title Article name
* @param year Year of publication
* @param start Start number for the acquired search result list
* @param query Keyword to be searched
*/
private List<String> getCiniiIds(String appId, Integer maxResult, String author, String title,
Integer year, Integer start, String query) {
try {
List<String> ids = new ArrayList<>();
URIBuilder uriBuilder = new URIBuilder(this.urlSearch);
uriBuilder.addParameter("format", "rss");
if (StringUtils.isNotBlank(appId)) {
uriBuilder.addParameter("appid", appId);
}
if (Objects.nonNull(maxResult) && maxResult != 0) {
uriBuilder.addParameter("count", maxResult.toString());
}
if (Objects.nonNull(start)) {
uriBuilder.addParameter("start", start.toString());
}
if (StringUtils.isNotBlank(title)) {
uriBuilder.addParameter("title", title);
}
if (StringUtils.isNotBlank(author)) {
uriBuilder.addParameter("author", author);
}
if (StringUtils.isNotBlank(query)) {
uriBuilder.addParameter("q", query);
}
if (Objects.nonNull(year) && year != -1 && year != 0) {
uriBuilder.addParameter("year_from", String.valueOf(year));
uriBuilder.addParameter("year_to", String.valueOf(year));
}
Map<String, Map<String, String>> params = new HashMap<String, Map<String,String>>();
String response = liveImportClient.executeHttpGetRequest(1000, uriBuilder.toString(), params);
int url_len = this.url.length() - 1;
SAXBuilder saxBuilder = new SAXBuilder();
Document document = saxBuilder.build(new StringReader(response));
Element root = document.getRootElement();
List<Namespace> namespaces = Arrays.asList(
Namespace.getNamespace("ns", "http://purl.org/rss/1.0/"),
Namespace.getNamespace("rdf", "http://www.w3.org/1999/02/22-rdf-syntax-ns#"));
XPathExpression<Attribute> xpath = XPathFactory.instance().compile("//ns:item/@rdf:about",
Filters.attribute(), null, namespaces);
List<Attribute> recordsList = xpath.evaluate(root);
for (Attribute item : recordsList) {
String value = item.getValue();
if (value.length() > url_len) {
ids.add(value.substring(url_len + 1));
}
}
return ids;
} catch (JDOMException | IOException | URISyntaxException e) {
log.error(e.getMessage(), e);
throw new RuntimeException(e.getMessage(), e);
}
}
/**
* Returns the total number of CiNii articles returned by a specific query
*
* @param appId Application ID
* @param maxResult The number of search results per page
* @param author Author name
* @param title Article name
* @param year Year of publication
* @param start Start number for the acquired search result list
* @param query Keyword to be searched
*/
private Integer countCiniiElement(String appId, Integer maxResult, String author, String title,
Integer year, Integer start, String query) {
try {
URIBuilder uriBuilder = new URIBuilder(this.urlSearch);
uriBuilder.addParameter("format", "rss");
uriBuilder.addParameter("appid", appId);
if (Objects.nonNull(maxResult) && maxResult != 0) {
uriBuilder.addParameter("count", maxResult.toString());
}
if (Objects.nonNull(start)) {
uriBuilder.addParameter("start", start.toString());
}
if (StringUtils.isNotBlank(title)) {
uriBuilder.addParameter("title", title);
}
if (StringUtils.isNotBlank(author)) {
uriBuilder.addParameter("author", author);
}
if (StringUtils.isNotBlank(query)) {
uriBuilder.addParameter("q", query);
}
if (Objects.nonNull(year) && year != -1 && year != 0) {
uriBuilder.addParameter("year_from", String.valueOf(year));
uriBuilder.addParameter("year_to", String.valueOf(year));
}
Map<String, Map<String, String>> params = new HashMap<String, Map<String,String>>();
String response = liveImportClient.executeHttpGetRequest(1000, uriBuilder.toString(), params);
SAXBuilder saxBuilder = new SAXBuilder();
Document document = saxBuilder.build(new StringReader(response));
Element root = document.getRootElement();
List<Namespace> namespaces = Arrays
.asList(Namespace.getNamespace("opensearch", "http://a9.com/-/spec/opensearch/1.1/"));
XPathExpression<Element> xpath = XPathFactory.instance().compile("//opensearch:totalResults",
Filters.element(), null, namespaces);
List<Element> nodes = xpath.evaluate(root);
if (nodes != null && !nodes.isEmpty()) {
return Integer.parseInt(((Element) nodes.get(0)).getText());
}
return 0;
} catch (JDOMException | IOException | URISyntaxException e) {
log.error(e.getMessage(), e);
throw new RuntimeException(e.getMessage(), e);
}
}
private MetadatumDTO createIdentifier(String id) {
MetadatumDTO metadatumDTO = new MetadatumDTO();
metadatumDTO.setSchema("dc");
metadatumDTO.setElement("identifier");
metadatumDTO.setQualifier("other");
metadatumDTO.setValue(id);
return metadatumDTO;
}
}

View File

@@ -74,7 +74,8 @@ public class LiveImportClientImpl implements LiveImportClient {
HttpResponse httpResponse = httpClient.execute(method);
if (isNotSuccessfull(httpResponse)) {
throw new RuntimeException();
throw new RuntimeException("The request failed with: " + getStatusCode(httpResponse) + " code, reason= "
+ httpResponse.getStatusLine().getReasonPhrase());
}
InputStream inputStream = httpResponse.getEntity().getContent();
return IOUtils.toString(inputStream, Charset.defaultCharset());

View File

@@ -0,0 +1,173 @@
/**
* 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.importer.external.metadatamapping.contributor;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashMap;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
import java.util.Objects;
import org.apache.commons.lang.StringUtils;
import org.dspace.importer.external.metadatamapping.MetadataFieldConfig;
import org.dspace.importer.external.metadatamapping.MetadatumDTO;
import org.jaxen.JaxenException;
import org.jdom2.Element;
import org.jdom2.Namespace;
/**
* Scopus specific implementation of {@link MetadataContributor}
* Responsible for generating the ScopusID, orcid, author name and affiliationID
* from the retrieved item.
*
* @author Boychuk Mykhaylo (boychuk.mykhaylo at 4science dot it)
*/
public class AuthorMetadataContributor extends SimpleXpathMetadatumContributor {
private static final Namespace NAMESPACE = Namespace.getNamespace("http://www.w3.org/2005/Atom");
private MetadataFieldConfig orcid;
private MetadataFieldConfig scopusId;
private MetadataFieldConfig authname;
private MetadataFieldConfig affiliation;
private Map<String, String> affId2affName = new HashMap<String, String>();
/**
* Retrieve the metadata associated with the given object.
* Depending on the retrieved node (using the query),
* different types of values will be added to the MetadatumDTO list.
*
* @param element A class to retrieve metadata from.
* @return A collection of import records. Only the ScopusID, orcid, author name and affiliation
* of the found records may be put in the record.
*/
@Override
public Collection<MetadatumDTO> contributeMetadata(Element element) {
List<MetadatumDTO> values = new LinkedList<>();
List<MetadatumDTO> metadatums = null;
fillAffillation(element);
try {
List<Element> nodes = element.getChildren("author", NAMESPACE);
for (Element el : nodes) {
metadatums = getMetadataOfAuthors(el);
if (Objects.nonNull(metadatums)) {
for (MetadatumDTO metadatum : metadatums) {
values.add(metadatum);
}
}
}
} catch (JaxenException e) {
throw new RuntimeException(e);
}
return values;
}
/**
* Retrieve the the ScopusID, orcid, author name and affiliationID
* metadata associated with the given element object.
* If the value retrieved from the element is empty
* it is set PLACEHOLDER_PARENT_METADATA_VALUE
*
* @param element A class to retrieve metadata from
* @throws JaxenException If Xpath evaluation failed
*/
private List<MetadatumDTO> getMetadataOfAuthors(Element element) throws JaxenException {
List<MetadatumDTO> metadatums = new ArrayList<MetadatumDTO>();
Element authname = element.getChild("authname", NAMESPACE);
Element scopusId = element.getChild("authid", NAMESPACE);
Element orcid = element.getChild("orcid", NAMESPACE);
Element afid = element.getChild("afid", NAMESPACE);
addMetadatum(metadatums, getMetadata(getElementValue(authname), this.authname));
addMetadatum(metadatums, getMetadata(getElementValue(scopusId), this.scopusId));
addMetadatum(metadatums, getMetadata(getElementValue(orcid), this.orcid));
addMetadatum(metadatums, getMetadata(StringUtils.isNotBlank(afid.getValue())
? this.affId2affName.get(afid.getValue()) : null, this.affiliation));
return metadatums;
}
private void addMetadatum(List<MetadatumDTO> list, MetadatumDTO metadatum) {
if (Objects.nonNull(metadatum)) {
list.add(metadatum);
}
}
private String getElementValue(Element element) {
if (Objects.nonNull(element)) {
return element.getValue();
}
return StringUtils.EMPTY;
}
private MetadatumDTO getMetadata(String value, MetadataFieldConfig metadaConfig) {
if (StringUtils.isBlank(value)) {
return null;
}
MetadatumDTO metadata = new MetadatumDTO();
metadata.setElement(metadaConfig.getElement());
metadata.setQualifier(metadaConfig.getQualifier());
metadata.setSchema(metadaConfig.getSchema());
metadata.setValue(value);
return metadata;
}
private void fillAffillation(Element element) {
try {
List<Element> nodes = element.getChildren("affiliation", NAMESPACE);
for (Element el : nodes) {
fillAffiliation2Name(el);
}
} catch (JaxenException e) {
throw new RuntimeException(e);
}
}
private void fillAffiliation2Name(Element element) throws JaxenException {
Element affilationName = element.getChild("affilname", NAMESPACE);
Element affilationId = element.getChild("afid", NAMESPACE);
if (Objects.nonNull(affilationId) && Objects.nonNull(affilationName)) {
affId2affName.put(affilationId.getValue(), affilationName.getValue());
}
}
public MetadataFieldConfig getAuthname() {
return authname;
}
public void setAuthname(MetadataFieldConfig authname) {
this.authname = authname;
}
public MetadataFieldConfig getOrcid() {
return orcid;
}
public void setOrcid(MetadataFieldConfig orcid) {
this.orcid = orcid;
}
public MetadataFieldConfig getScopusId() {
return scopusId;
}
public void setScopusId(MetadataFieldConfig scopusId) {
this.scopusId = scopusId;
}
public MetadataFieldConfig getAffiliation() {
return affiliation;
}
public void setAffiliation(MetadataFieldConfig affiliation) {
this.affiliation = affiliation;
}
}

View File

@@ -0,0 +1,110 @@
/**
* 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.importer.external.metadatamapping.contributor;
import java.util.ArrayList;
import java.util.Collection;
import java.util.LinkedList;
import java.util.List;
import java.util.Objects;
import org.apache.commons.lang3.StringUtils;
import org.dspace.importer.external.metadatamapping.MetadataFieldConfig;
import org.dspace.importer.external.metadatamapping.MetadatumDTO;
import org.jdom2.Element;
import org.jdom2.Namespace;
/**
* Scopus specific implementation of {@link MetadataContributor}
* Responsible for generating the Scopus startPage and endPage from the retrieved item.
*
* @author Boychuk Mykhaylo (boychuk.mykhaylo at 4science.com)
*/
public class PageRangeXPathMetadataContributor extends SimpleXpathMetadatumContributor {
private MetadataFieldConfig startPageMetadata;
private MetadataFieldConfig endPageMetadata;
/**
* Retrieve the metadata associated with the given Element object.
* Depending on the retrieved node (using the query),
* StartPage and EndPage values will be added to the MetadatumDTO list
*
* @param el A class to retrieve metadata from.
* @return A collection of import records. Only the StartPage and EndPage
* of the found records may be put in the record.
*/
@Override
public Collection<MetadatumDTO> contributeMetadata(Element el) {
List<MetadatumDTO> values = new LinkedList<>();
List<MetadatumDTO> metadatums = null;
for (String ns : prefixToNamespaceMapping.keySet()) {
List<Element> nodes = el.getChildren(query, Namespace.getNamespace(ns));
for (Element element : nodes) {
metadatums = getMetadatum(element.getValue());
if (Objects.nonNull(metadatums)) {
for (MetadatumDTO metadatum : metadatums) {
values.add(metadatum);
}
}
}
}
return values;
}
private List<MetadatumDTO> getMetadatum(String value) {
List<MetadatumDTO> metadatums = new ArrayList<MetadatumDTO>();
if (StringUtils.isBlank(value)) {
return null;
}
String [] range = value.split("-");
if (range.length == 2) {
metadatums.add(setStartPage(range));
metadatums.add(setEndPage(range));
} else if (range.length != 0) {
metadatums.add(setStartPage(range));
}
return metadatums;
}
private MetadatumDTO setEndPage(String[] range) {
MetadatumDTO endPage = new MetadatumDTO();
endPage.setValue(range[1]);
endPage.setElement(endPageMetadata.getElement());
endPage.setQualifier(endPageMetadata.getQualifier());
endPage.setSchema(endPageMetadata.getSchema());
return endPage;
}
private MetadatumDTO setStartPage(String[] range) {
MetadatumDTO startPage = new MetadatumDTO();
startPage.setValue(range[0]);
startPage.setElement(startPageMetadata.getElement());
startPage.setQualifier(startPageMetadata.getQualifier());
startPage.setSchema(startPageMetadata.getSchema());
return startPage;
}
public MetadataFieldConfig getStartPageMetadata() {
return startPageMetadata;
}
public void setStartPageMetadata(MetadataFieldConfig startPageMetadata) {
this.startPageMetadata = startPageMetadata;
}
public MetadataFieldConfig getEndPageMetadata() {
return endPageMetadata;
}
public void setEndPageMetadata(MetadataFieldConfig endPageMetadata) {
this.endPageMetadata = endPageMetadata;
}
}

View File

@@ -0,0 +1,66 @@
/**
* 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.importer.external.metadatamapping.contributor;
import java.util.Collection;
import java.util.LinkedList;
import java.util.List;
import java.util.Objects;
import org.dspace.importer.external.metadatamapping.MetadataFieldConfig;
import org.dspace.importer.external.metadatamapping.MetadatumDTO;
import org.jdom2.Element;
import org.jdom2.Namespace;
/**
* This contributor replace specific character in the metadata value.
* It is useful for some provider (e.g. Scopus) which use containing "/" character.
* Actually, "/" will never encode by framework in URL building. In the same ways, if we
* encode "/" -> %2F, it will be encoded by framework and become %252F.
*
* @author Boychuk Mykhaylo (boychuk.mykhaylo at 4science.com)
*/
public class ReplaceCharacterXPathMetadataContributor extends SimpleXpathMetadatumContributor {
private char characterToBeReplaced;
private char characterToReplaceWith;
@Override
public Collection<MetadatumDTO> contributeMetadata(Element element) {
List<MetadatumDTO> values = new LinkedList<>();
for (String ns : prefixToNamespaceMapping.keySet()) {
List<Element> nodes = element.getChildren(query, Namespace.getNamespace(ns));
for (Element el : nodes) {
values.add(getMetadatum(field, el.getValue()));
}
}
return values;
}
private MetadatumDTO getMetadatum(MetadataFieldConfig field, String value) {
MetadatumDTO dcValue = new MetadatumDTO();
if (Objects.isNull(field)) {
return null;
}
dcValue.setValue(value == null ? null : value.replace(characterToBeReplaced, characterToReplaceWith));
dcValue.setElement(field.getElement());
dcValue.setQualifier(field.getQualifier());
dcValue.setSchema(field.getSchema());
return dcValue;
}
public void setCharacterToBeReplaced(int characterToBeReplaced) {
this.characterToBeReplaced = (char)characterToBeReplaced;
}
public void setCharacterToReplaceWith(int characterToReplaceWith) {
this.characterToReplaceWith = (char)characterToReplaceWith;
}
}

View File

@@ -0,0 +1,65 @@
/**
* 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.importer.external.metadatamapping.contributor;
import java.util.ArrayList;
import java.util.Collection;
import java.util.LinkedList;
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.importer.external.metadatamapping.MetadatumDTO;
import org.jdom2.Element;
import org.jdom2.Namespace;
import org.jdom2.filter.Filters;
import org.jdom2.xpath.XPathExpression;
import org.jdom2.xpath.XPathFactory;
/**
* This contributor is able to concat multi value.
* Given a certain path, if it contains several nodes,
* the values of nodes will be concatenated into a single one.
* The concrete example we can see in the file wos-responce.xml in the <abstract_text> node,
* which may contain several <p> paragraphs,
* this Contributor allows concatenating all <p> paragraphs. to obtain a single one.
*
* @author Boychuk Mykhaylo (boychuk.mykhaylo at 4Science dot it)
*/
public class SimpleConcatContributor extends SimpleXpathMetadatumContributor {
private final static Logger log = LogManager.getLogger();
@Override
public Collection<MetadatumDTO> contributeMetadata(Element t) {
List<MetadatumDTO> values = new LinkedList<>();
StringBuilder text = new StringBuilder();
List<Namespace> namespaces = new ArrayList<Namespace>();
for (String ns : prefixToNamespaceMapping.keySet()) {
namespaces.add(Namespace.getNamespace(prefixToNamespaceMapping.get(ns), ns));
}
XPathExpression<Object> xpath = XPathFactory.instance().compile(query, Filters.fpassthrough(), null,namespaces);
List<Object> nodes = xpath.evaluate(t);
for (Object el : nodes) {
if (el instanceof Element) {
Element element = (Element) el;
if (StringUtils.isNotBlank(element.getText())) {
text.append(element.getText());
}
} else {
log.warn("node of type: " + el.getClass());
}
}
if (StringUtils.isNotBlank(text.toString())) {
values.add(metadataFieldMapping.toDCValue(field, text.toString()));
}
return values;
}
}

View File

@@ -0,0 +1,75 @@
/**
* 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.importer.external.metadatamapping.contributor;
import java.util.ArrayList;
import java.util.Collection;
import java.util.LinkedList;
import java.util.List;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.importer.external.metadatamapping.MetadatumDTO;
import org.jdom2.Element;
import org.jdom2.Namespace;
import org.jdom2.filter.Filters;
import org.jdom2.xpath.XPathExpression;
import org.jdom2.xpath.XPathFactory;
/**
* Web of Science specific implementation of {@link MetadataContributor}.
* This contributor can perform research on multi-paths.
* For example, to populate the subject metadata, in the Web of Science response
* the values are contained in different paths,
* so this Contributor allows you to collect the values by configuring the paths in the paths list.
*
* @author Boychuk Mykhaylo (boychuk.mykhaylo at 4Science dot it)
*/
public class SimpleMultiplePathContributor extends SimpleXpathMetadatumContributor {
private final static Logger log = LogManager.getLogger();
private List<String> paths;
public SimpleMultiplePathContributor() {}
public SimpleMultiplePathContributor(List<String> paths) {
this.paths = paths;
}
@Override
public Collection<MetadatumDTO> contributeMetadata(Element t) {
List<MetadatumDTO> values = new LinkedList<>();
for (String path : this.paths) {
List<Namespace> namespaces = new ArrayList<Namespace>();
for (String ns : prefixToNamespaceMapping.keySet()) {
namespaces.add(Namespace.getNamespace(prefixToNamespaceMapping.get(ns), ns));
}
XPathExpression<Object> xpath = XPathFactory.instance().compile(path, Filters.fpassthrough(), null,
namespaces);
List<Object> nodes = xpath.evaluate(t);
for (Object el : nodes) {
if (el instanceof Element) {
values.add(metadataFieldMapping.toDCValue(field, ((Element) el).getText()));
} else {
log.warn("node of type: " + el.getClass());
}
}
}
return values;
}
public List<String> getPaths() {
return paths;
}
public void setPaths(List<String> paths) {
this.paths = paths;
}
}

View File

@@ -0,0 +1,69 @@
/**
* 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.importer.external.metadatamapping.contributor;
import java.util.ArrayList;
import java.util.Collection;
import java.util.LinkedList;
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.importer.external.metadatamapping.MetadatumDTO;
import org.jdom2.Element;
import org.jdom2.Namespace;
import org.jdom2.filter.Filters;
import org.jdom2.xpath.XPathExpression;
import org.jdom2.xpath.XPathFactory;
/**
* This contributor checks for each node returned for the supplied path
* if node contains supplied attribute - the value of the current node is taken if exist.
*
* @author Boychuk Mykhaylo (boychuk.mykhaylo at 4Science dot com)
*/
public class SimpleXpathMetadatumAndAttributeContributor extends SimpleXpathMetadatumContributor {
private final static Logger log = LogManager.getLogger();
private String attribute;
@Override
public Collection<MetadatumDTO> contributeMetadata(Element t) {
List<MetadatumDTO> values = new LinkedList<>();
List<Namespace> namespaces = new ArrayList<Namespace>();
for (String ns : prefixToNamespaceMapping.keySet()) {
namespaces.add(Namespace.getNamespace(prefixToNamespaceMapping.get(ns), ns));
}
XPathExpression<Object> xpath = XPathFactory.instance().compile(query, Filters.fpassthrough(), null,
namespaces);
List<Object> nodes = xpath.evaluate(t);
for (Object el : nodes) {
if (el instanceof Element) {
Element element = (Element) el;
String attributeValue = element.getAttributeValue(this.attribute);
if (StringUtils.isNotBlank(attributeValue)) {
values.add(metadataFieldMapping.toDCValue(this.field, attributeValue));
}
} else {
log.warn("node of type: " + el.getClass());
}
}
return values;
}
public String getAttribute() {
return attribute;
}
public void setAttribute(String attribute) {
this.attribute = attribute;
}
}

View File

@@ -34,10 +34,10 @@ import org.springframework.beans.factory.annotation.Autowired;
*/
public class SimpleXpathMetadatumContributor implements MetadataContributor<Element> {
protected MetadataFieldConfig field;
private static final Logger log = org.apache.logging.log4j.LogManager.getLogger();
protected MetadataFieldConfig field;
/**
* Return prefixToNamespaceMapping
*
@@ -171,4 +171,5 @@ public class SimpleXpathMetadatumContributor implements MetadataContributor<Elem
}
return values;
}
}

View File

@@ -0,0 +1,160 @@
/**
* 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.importer.external.metadatamapping.contributor;
import java.util.ArrayList;
import java.util.Collection;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
import javax.annotation.Resource;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.importer.external.metadatamapping.MetadataFieldConfig;
import org.dspace.importer.external.metadatamapping.MetadataFieldMapping;
import org.dspace.importer.external.metadatamapping.MetadatumDTO;
import org.jdom2.Element;
import org.jdom2.Namespace;
import org.jdom2.filter.Filters;
import org.jdom2.xpath.XPathExpression;
import org.jdom2.xpath.XPathFactory;
/**
* Web Of Science specific implementation of {@link MetadataContributor}
* This contributor checks for each node returned for the given path if the node contains "this.attribute"
* and then checks if the attribute value is one of the values configured
* in the "this.attributeValue2metadata" map, if the value of the current known is taken.
* If "this.firstChild" is true, it takes the value of the child of the known.
* The mapping and configuration of this class can be found in the following wos-integration.xml file.
*
* @author Boychuk Mykhaylo (boychuk.mykhaylo at 4Science dot it)
*/
public class WosAttribute2ValueContributor implements MetadataContributor<Element> {
private final static Logger log = LogManager.getLogger();
private String query;
private String attribute;
private boolean firstChild;
private String childName;
private Map<String, String> prefixToNamespaceMapping;
private Map<String, MetadataFieldConfig> attributeValue2metadata;
private MetadataFieldMapping<Element, MetadataContributor<Element>> metadataFieldMapping;
public WosAttribute2ValueContributor() {}
public WosAttribute2ValueContributor(String query,
Map<String, String> prefixToNamespaceMapping,
Map<String, MetadataFieldConfig> attributeValue2metadata) {
this.query = query;
this.prefixToNamespaceMapping = prefixToNamespaceMapping;
this.attributeValue2metadata = attributeValue2metadata;
}
@Override
public Collection<MetadatumDTO> contributeMetadata(Element t) {
List<MetadatumDTO> values = new LinkedList<>();
List<Namespace> namespaces = new ArrayList<Namespace>();
for (String ns : prefixToNamespaceMapping.keySet()) {
namespaces.add(Namespace.getNamespace(prefixToNamespaceMapping.get(ns), ns));
}
XPathExpression<Object> xpath = XPathFactory.instance().compile(query, Filters.fpassthrough(), null,
namespaces);
List<Object> nodes = xpath.evaluate(t);
for (Object el : nodes) {
if (el instanceof Element) {
Element element = (Element) el;
String attributeValue = element.getAttributeValue(this.attribute);
setField(attributeValue, element, values);
} else {
log.warn("node of type: " + el.getClass());
}
}
return values;
}
private void setField(String attributeValue, Element el, List<MetadatumDTO> values) {
for (String id : attributeValue2metadata.keySet()) {
if (StringUtils.equals(id, attributeValue)) {
if (this.firstChild) {
String value = el.getChild(this.childName).getValue();
values.add(metadataFieldMapping.toDCValue(attributeValue2metadata.get(id), value));
} else {
values.add(metadataFieldMapping.toDCValue(attributeValue2metadata.get(id), el.getText()));
}
}
}
}
public MetadataFieldMapping<Element, MetadataContributor<Element>> getMetadataFieldMapping() {
return metadataFieldMapping;
}
public void setMetadataFieldMapping(
MetadataFieldMapping<Element, MetadataContributor<Element>> metadataFieldMapping) {
this.metadataFieldMapping = metadataFieldMapping;
}
@Resource(name = "isiFullprefixMapping")
public void setPrefixToNamespaceMapping(Map<String, String> prefixToNamespaceMapping) {
this.prefixToNamespaceMapping = prefixToNamespaceMapping;
}
public Map<String, String> getPrefixToNamespaceMapping() {
return prefixToNamespaceMapping;
}
public String getAttribute() {
return attribute;
}
public void setAttribute(String attribute) {
this.attribute = attribute;
}
public Map<String, MetadataFieldConfig> getAttributeValue2metadata() {
return attributeValue2metadata;
}
public void setAttributeValue2metadata(Map<String, MetadataFieldConfig> attributeValue2metadata) {
this.attributeValue2metadata = attributeValue2metadata;
}
public String getQuery() {
return query;
}
public void setQuery(String query) {
this.query = query;
}
public boolean isFirstChild() {
return firstChild;
}
public void setFirstChild(boolean firstChild) {
this.firstChild = firstChild;
}
public String getChildName() {
return childName;
}
public void setChildName(String childName) {
this.childName = childName;
}
}

View File

@@ -0,0 +1,71 @@
/**
* 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.importer.external.metadatamapping.contributor;
import java.util.ArrayList;
import java.util.Collection;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
import org.apache.commons.lang3.StringUtils;
import org.dspace.importer.external.metadatamapping.MetadataFieldConfig;
import org.dspace.importer.external.metadatamapping.MetadatumDTO;
import org.jdom2.Element;
import org.jdom2.Namespace;
import org.jdom2.filter.Filters;
import org.jdom2.xpath.XPathExpression;
import org.jdom2.xpath.XPathFactory;
/**
* This contributor can retrieve the identifiers
* configured in "this.identifire2field" from the Web of Science response.
* The mapping and configuration of this class can be found in the following wos-integration.xml file.
*
* @author Boychuk Mykhaylo (boychuk.mykhaylo at 4Science dot it)
*/
public class WosIdentifierContributor extends SimpleXpathMetadatumContributor {
protected Map<String, MetadataFieldConfig> identifier2field;
@Override
public Collection<MetadatumDTO> contributeMetadata(Element element) {
List<MetadatumDTO> values = new LinkedList<>();
List<Namespace> namespaces = new ArrayList<>();
for (String ns : prefixToNamespaceMapping.keySet()) {
namespaces.add(Namespace.getNamespace(prefixToNamespaceMapping.get(ns), ns));
}
XPathExpression<Element> xpath =
XPathFactory.instance().compile(query, Filters.element(), null, namespaces);
List<Element> nodes = xpath.evaluate(element);
for (Element el : nodes) {
String type = el.getAttributeValue("type");
setIdentyfier(type, el, values);
}
return values;
}
private void setIdentyfier(String type, Element el, List<MetadatumDTO> values) {
for (String id : identifier2field.keySet()) {
if (StringUtils.equals(id, type)) {
String value = el.getAttributeValue("value");
values.add(metadataFieldMapping.toDCValue(identifier2field.get(id), value));
}
}
}
public Map<String, MetadataFieldConfig> getIdentifier2field() {
return identifier2field;
}
public void setIdentifier2field(Map<String, MetadataFieldConfig> identifier2field) {
this.identifier2field = identifier2field;
}
}

View File

@@ -0,0 +1,68 @@
/**
* 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.importer.external.metadatamapping.contributor;
import java.util.ArrayList;
import java.util.Collection;
import java.util.LinkedList;
import java.util.List;
import java.util.Objects;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.importer.external.metadatamapping.MetadatumDTO;
import org.jdom2.Element;
import org.jdom2.Namespace;
import org.jdom2.filter.Filters;
import org.jdom2.xpath.XPathExpression;
import org.jdom2.xpath.XPathFactory;
/**
* Web Of Science specific implementation of {@link MetadataContributor}
*
* @author Boychuk Mykhaylo (boychuk.mykhaylo at 4Science dot it)
*/
public class WosIdentifierRidContributor extends SimpleXpathMetadatumContributor {
private final static Logger log = LogManager.getLogger();
@Override
public Collection<MetadatumDTO> contributeMetadata(Element t) {
List<MetadatumDTO> values = new LinkedList<>();
List<Namespace> namespaces = new ArrayList<Namespace>();
for (String ns : prefixToNamespaceMapping.keySet()) {
namespaces.add(Namespace.getNamespace(prefixToNamespaceMapping.get(ns), ns));
}
XPathExpression<Object> xpath = XPathFactory.instance().compile(query, Filters.fpassthrough(), null,
namespaces);
List<Object> nodes = xpath.evaluate(t);
for (Object el : nodes) {
if (el instanceof Element) {
Element element = ((Element) el).getChild("name");
if (Objects.nonNull(element)) {
String type = element.getAttributeValue("role");
setIdentyfier(type, element, values);
}
} else {
log.warn("node of type: " + el.getClass());
}
}
return values;
}
private void setIdentyfier(String type, Element el, List<MetadatumDTO> values) {
if (StringUtils.equals("researcher_id", type)) {
String value = el.getAttributeValue("r_id");
if (StringUtils.isNotBlank(value)) {
values.add(metadataFieldMapping.toDCValue(this.field, value));
}
}
}
}

View File

@@ -14,23 +14,23 @@ import java.io.InputStreamReader;
import java.io.Reader;
import java.io.StringReader;
import java.util.Collection;
import java.util.HashMap;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
import java.util.Objects;
import java.util.concurrent.Callable;
import javax.ws.rs.client.Client;
import javax.ws.rs.client.ClientBuilder;
import javax.ws.rs.client.Invocation;
import javax.ws.rs.client.WebTarget;
import javax.ws.rs.core.MediaType;
import javax.ws.rs.core.Response;
import com.google.common.io.CharStreams;
import org.apache.commons.lang3.StringUtils;
import org.apache.http.client.utils.URIBuilder;
import org.dspace.content.Item;
import org.dspace.importer.external.datamodel.ImportRecord;
import org.dspace.importer.external.datamodel.Query;
import org.dspace.importer.external.exception.FileMultipleOccurencesException;
import org.dspace.importer.external.exception.FileSourceException;
import org.dspace.importer.external.exception.MetadataSourceException;
import org.dspace.importer.external.liveimportclient.service.LiveImportClient;
import org.dspace.importer.external.service.AbstractImportMetadataSourceService;
import org.dspace.importer.external.service.components.FileSource;
import org.dspace.importer.external.service.components.QuerySource;
@@ -41,6 +41,7 @@ import org.jdom2.filter.Filters;
import org.jdom2.input.SAXBuilder;
import org.jdom2.xpath.XPathExpression;
import org.jdom2.xpath.XPathFactory;
import org.springframework.beans.factory.annotation.Autowired;
/**
* Implements a data source for querying PubMed Central
@@ -51,13 +52,16 @@ import org.jdom2.xpath.XPathFactory;
public class PubmedImportMetadataSourceServiceImpl extends AbstractImportMetadataSourceService<Element>
implements QuerySource, FileSource {
private String baseAddress;
private String urlFetch;
private String urlSearch;
// it is protected so that subclass can mock it for testing
protected WebTarget pubmedWebTarget;
private int attempt = 3;
private List<String> supportedExtensions;
@Autowired
private LiveImportClient liveImportClient;
/**
* Set the file extensions supported by this metadata service
*
@@ -187,29 +191,7 @@ public class PubmedImportMetadataSourceServiceImpl extends AbstractImportMetadat
* @throws Exception on generic exception
*/
@Override
public void init() throws Exception {
Client client = ClientBuilder.newClient();
WebTarget webTarget = client.target(baseAddress);
pubmedWebTarget = webTarget.queryParam("db", "pubmed");
}
/**
* Return the baseAddress set to this object
*
* @return The String object that represents the baseAddress of this object
*/
public String getBaseAddress() {
return baseAddress;
}
/**
* Set the baseAddress to this object
*
* @param baseAddress The String object that represents the baseAddress of this object
*/
public void setBaseAddress(String baseAddress) {
this.baseAddress = baseAddress;
}
public void init() throws Exception {}
private class GetNbRecords implements Callable<Integer> {
@@ -226,23 +208,26 @@ public class PubmedImportMetadataSourceServiceImpl extends AbstractImportMetadat
@Override
public Integer call() throws Exception {
WebTarget getRecordIdsTarget = pubmedWebTarget
.queryParam("term", query.getParameterAsClass("query", String.class));
getRecordIdsTarget = getRecordIdsTarget.path("esearch.fcgi");
Invocation.Builder invocationBuilder = getRecordIdsTarget.request(MediaType.TEXT_PLAIN_TYPE);
Response response = invocationBuilder.get();
String responseString = response.readEntity(String.class);
String count = getSingleElementValue(responseString, "Count");
return Integer.parseInt(count);
}
URIBuilder uriBuilder = new URIBuilder(urlSearch);
uriBuilder.addParameter("db", "pubmed");
uriBuilder.addParameter("term", query.getParameterAsClass("query", String.class));
Map<String, Map<String, String>> params = new HashMap<String, Map<String,String>>();
String response = StringUtils.EMPTY;
int countAttempt = 0;
while (StringUtils.isBlank(response) && countAttempt <= attempt) {
countAttempt++;
response = liveImportClient.executeHttpGetRequest(1000, uriBuilder.toString(), params);
}
if (StringUtils.isBlank(response)) {
throw new RuntimeException("After " + attempt
+ " attempts to contact the PubMed service, a correct answer could not be received."
+ " The request was made with this URL:" + uriBuilder.toString());
}
return Integer.parseInt(getSingleElementValue(response, "Count"));
}
}
private String getSingleElementValue(String src, String elementName) {
String value = null;
@@ -286,41 +271,61 @@ public class PubmedImportMetadataSourceServiceImpl extends AbstractImportMetadat
Integer start = query.getParameterAsClass("start", Integer.class);
Integer count = query.getParameterAsClass("count", Integer.class);
if (count == null || count < 0) {
if (Objects.isNull(count) || count < 0) {
count = 10;
}
if (start == null || start < 0) {
if (Objects.isNull(start) || start < 0) {
start = 0;
}
List<ImportRecord> records = new LinkedList<ImportRecord>();
WebTarget getRecordIdsTarget = pubmedWebTarget.queryParam("term", queryString);
getRecordIdsTarget = getRecordIdsTarget.queryParam("retstart", start);
getRecordIdsTarget = getRecordIdsTarget.queryParam("retmax", count);
getRecordIdsTarget = getRecordIdsTarget.queryParam("usehistory", "y");
getRecordIdsTarget = getRecordIdsTarget.path("esearch.fcgi");
URIBuilder uriBuilder = new URIBuilder(urlSearch);
uriBuilder.addParameter("db", "pubmed");
uriBuilder.addParameter("retstart", start.toString());
uriBuilder.addParameter("retmax", count.toString());
uriBuilder.addParameter("usehistory", "y");
uriBuilder.addParameter("term", queryString);
Map<String, Map<String, String>> params = new HashMap<String, Map<String,String>>();
String response = StringUtils.EMPTY;
int countAttempt = 0;
while (StringUtils.isBlank(response) && countAttempt <= attempt) {
countAttempt++;
response = liveImportClient.executeHttpGetRequest(1000, uriBuilder.toString(), params);
}
Invocation.Builder invocationBuilder = getRecordIdsTarget.request(MediaType.TEXT_PLAIN_TYPE);
if (StringUtils.isBlank(response)) {
throw new RuntimeException("After " + attempt
+ " attempts to contact the PubMed service, a correct answer could not be received."
+ " The request was made with this URL:" + uriBuilder.toString());
}
Response response = invocationBuilder.get();
String responseString = response.readEntity(String.class);
String queryKey = getSingleElementValue(response, "QueryKey");
String webEnv = getSingleElementValue(response, "WebEnv");
String queryKey = getSingleElementValue(responseString, "QueryKey");
String webEnv = getSingleElementValue(responseString, "WebEnv");
URIBuilder uriBuilder2 = new URIBuilder(urlFetch);
uriBuilder2.addParameter("db", "pubmed");
uriBuilder2.addParameter("retstart", start.toString());
uriBuilder2.addParameter("retmax", count.toString());
uriBuilder2.addParameter("WebEnv", webEnv);
uriBuilder2.addParameter("query_key", queryKey);
uriBuilder2.addParameter("retmode", "xml");
Map<String, Map<String, String>> params2 = new HashMap<String, Map<String,String>>();
String response2 = StringUtils.EMPTY;
countAttempt = 0;
while (StringUtils.isBlank(response2) && countAttempt <= attempt) {
countAttempt++;
response2 = liveImportClient.executeHttpGetRequest(1000, uriBuilder2.toString(), params2);
}
WebTarget getRecordsTarget = pubmedWebTarget.queryParam("WebEnv", webEnv);
getRecordsTarget = getRecordsTarget.queryParam("query_key", queryKey);
getRecordsTarget = getRecordsTarget.queryParam("retmode", "xml");
getRecordsTarget = getRecordsTarget.path("efetch.fcgi");
getRecordsTarget = getRecordsTarget.queryParam("retmax", count);
getRecordsTarget = getRecordsTarget.queryParam("retstart", start);
if (StringUtils.isBlank(response2)) {
throw new RuntimeException("After " + attempt
+ " attempts to contact the PubMed service, a correct answer could not be received."
+ " The request was made with this URL:" + uriBuilder2.toString());
}
invocationBuilder = getRecordsTarget.request(MediaType.TEXT_PLAIN_TYPE);
response = invocationBuilder.get();
List<Element> elements = splitToRecords(response.readEntity(String.class));
List<Element> elements = splitToRecords(response2);
for (Element record : elements) {
records.add(transformSourceRecords(record));
@@ -361,23 +366,29 @@ public class PubmedImportMetadataSourceServiceImpl extends AbstractImportMetadat
@Override
public ImportRecord call() throws Exception {
String id = query.getParameterAsClass("id", String.class);
WebTarget getRecordTarget = pubmedWebTarget.queryParam("id", id);
getRecordTarget = getRecordTarget.queryParam("retmode", "xml");
getRecordTarget = getRecordTarget.path("efetch.fcgi");
URIBuilder uriBuilder = new URIBuilder(urlFetch);
uriBuilder.addParameter("db", "pubmed");
uriBuilder.addParameter("retmode", "xml");
uriBuilder.addParameter("id", query.getParameterAsClass("id", String.class));
Invocation.Builder invocationBuilder = getRecordTarget.request(MediaType.TEXT_PLAIN_TYPE);
Response response = invocationBuilder.get();
List<Element> elements = splitToRecords(response.readEntity(String.class));
if (elements.isEmpty()) {
return null;
Map<String, Map<String, String>> params = new HashMap<String, Map<String,String>>();
String response = StringUtils.EMPTY;
int countAttempt = 0;
while (StringUtils.isBlank(response) && countAttempt <= attempt) {
countAttempt++;
response = liveImportClient.executeHttpGetRequest(1000, uriBuilder.toString(), params);
}
return transformSourceRecords(elements.get(0));
if (StringUtils.isBlank(response)) {
throw new RuntimeException("After " + attempt
+ " attempts to contact the PubMed service, a correct answer could not be received."
+ " The request was made with this URL:" + uriBuilder.toString());
}
List<Element> elements = splitToRecords(response);
return elements.isEmpty() ? null : transformSourceRecords(elements.get(0));
}
}
@@ -396,40 +407,57 @@ public class PubmedImportMetadataSourceServiceImpl extends AbstractImportMetadat
@Override
public Collection<ImportRecord> call() throws Exception {
WebTarget getRecordIdsTarget = pubmedWebTarget
.queryParam("term", query.getParameterAsClass("term", String.class));
getRecordIdsTarget = getRecordIdsTarget
.queryParam("field", query.getParameterAsClass("field", String.class));
getRecordIdsTarget = getRecordIdsTarget.queryParam("usehistory", "y");
getRecordIdsTarget = getRecordIdsTarget.path("esearch.fcgi");
URIBuilder uriBuilder = new URIBuilder(urlSearch);
uriBuilder.addParameter("db", "pubmed");
uriBuilder.addParameter("usehistory", "y");
uriBuilder.addParameter("term", query.getParameterAsClass("term", String.class));
uriBuilder.addParameter("field", query.getParameterAsClass("field", String.class));
Invocation.Builder invocationBuilder = getRecordIdsTarget.request(MediaType.TEXT_PLAIN_TYPE);
Response response = invocationBuilder.get();
String responseString = response.readEntity(String.class);
String queryKey = getSingleElementValue(responseString, "QueryKey");
String webEnv = getSingleElementValue(responseString, "WebEnv");
WebTarget getRecordsTarget = pubmedWebTarget.queryParam("WebEnv", webEnv);
getRecordsTarget = getRecordsTarget.queryParam("query_key", queryKey);
getRecordsTarget = getRecordsTarget.queryParam("retmode", "xml");
getRecordsTarget = getRecordsTarget.path("efetch.fcgi");
invocationBuilder = getRecordsTarget.request(MediaType.TEXT_PLAIN_TYPE);
response = invocationBuilder.get();
String xml = response.readEntity(String.class);
return parseXMLString(xml);
}
Map<String, Map<String, String>> params = new HashMap<String, Map<String,String>>();
String response = StringUtils.EMPTY;
int countAttempt = 0;
while (StringUtils.isBlank(response) && countAttempt <= attempt) {
countAttempt++;
response = liveImportClient.executeHttpGetRequest(1000, uriBuilder.toString(), params);
}
if (StringUtils.isBlank(response)) {
throw new RuntimeException("After " + attempt
+ " attempts to contact the PubMed service, a correct answer could not be received."
+ " The request was made with this URL:" + uriBuilder.toString());
}
String webEnv = getSingleElementValue(response, "WebEnv");
String queryKey = getSingleElementValue(response, "QueryKey");
URIBuilder uriBuilder2 = new URIBuilder(urlFetch);
uriBuilder2.addParameter("db", "pubmed");
uriBuilder2.addParameter("retmode", "xml");
uriBuilder2.addParameter("WebEnv", webEnv);
uriBuilder2.addParameter("query_key", queryKey);
Map<String, Map<String, String>> params2 = new HashMap<String, Map<String,String>>();
String response2 = StringUtils.EMPTY;
countAttempt = 0;
while (StringUtils.isBlank(response2) && countAttempt <= attempt) {
countAttempt++;
response2 = liveImportClient.executeHttpGetRequest(1000, uriBuilder2.toString(), params2);
}
if (StringUtils.isBlank(response2)) {
throw new RuntimeException("After " + attempt
+ " attempts to contact the PubMed service, a correct answer could not be received."
+ " The request was made with this URL:" + uriBuilder2.toString());
}
return parseXMLString(response2);
}
}
@Override
public List<ImportRecord> getRecords(InputStream inputStream) throws FileSourceException {
String xml = null;
try (Reader reader = new InputStreamReader(inputStream, "UTF-8")) {
xml = CharStreams.toString(reader);
String xml = CharStreams.toString(reader);
return parseXMLString(xml);
} catch (IOException e) {
throw new FileSourceException ("Cannot read XML from InputStream", e);
@@ -456,4 +484,21 @@ public class PubmedImportMetadataSourceServiceImpl extends AbstractImportMetadat
}
return records;
}
public String getUrlFetch() {
return urlFetch;
}
public void setUrlFetch(String urlFetch) {
this.urlFetch = urlFetch;
}
public String getUrlSearch() {
return urlSearch;
}
public void setUrlSearch(String urlSearch) {
this.urlSearch = urlSearch;
}
}

View File

@@ -0,0 +1,37 @@
/**
* 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.importer.external.pubmedeurope;
import java.util.Map;
import javax.annotation.Resource;
import org.dspace.importer.external.metadatamapping.AbstractMetadataFieldMapping;
/**
* An implementation of {@link AbstractMetadataFieldMapping}
* Responsible for defining the mapping of the PubmedEurope metadatum fields on the DSpace metadatum fields
*
* @author Pasquale Cavallo (pasquale.cavallo at 4science dot it)
*/
public class PubmedEuropeFieldMapping extends AbstractMetadataFieldMapping {
/**
* Defines which metadatum is mapped on which metadatum. Note that while the key must be unique it
* only matters here for postprocessing of the value. The mapped MetadatumContributor has full control over
* what metadatafield is generated.
*
* @param metadataFieldMap The map containing the link between retrieve metadata and metadata that will be set to
* the item.
*/
@Override
@Resource(name = "pubmedEuropeMetadataFieldMap")
public void setMetadataFieldMap(Map metadataFieldMap) {
super.setMetadataFieldMap(metadataFieldMap);
}
}

View File

@@ -0,0 +1,419 @@
/**
* 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.importer.external.pubmedeurope;
import java.io.IOException;
import java.io.StringReader;
import java.net.URISyntaxException;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Objects;
import java.util.concurrent.Callable;
import javax.el.MethodNotFoundException;
import org.apache.commons.lang3.StringUtils;
import org.apache.http.HttpException;
import org.apache.http.client.ClientProtocolException;
import org.apache.http.client.utils.URIBuilder;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.content.Item;
import org.dspace.importer.external.datamodel.ImportRecord;
import org.dspace.importer.external.datamodel.Query;
import org.dspace.importer.external.exception.MetadataSourceException;
import org.dspace.importer.external.liveimportclient.service.LiveImportClient;
import org.dspace.importer.external.service.AbstractImportMetadataSourceService;
import org.dspace.importer.external.service.components.QuerySource;
import org.jaxen.JaxenException;
import org.jdom2.Document;
import org.jdom2.Element;
import org.jdom2.JDOMException;
import org.jdom2.filter.Filters;
import org.jdom2.input.SAXBuilder;
import org.jdom2.xpath.XPathExpression;
import org.jdom2.xpath.XPathFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.util.CollectionUtils;
/**
* Implements a data source for querying PubMed Europe
*
* @author Mykhaylo Boychuk (mykhaylo.boychuk at 4science.com)
*/
public class PubmedEuropeMetadataSourceServiceImpl extends AbstractImportMetadataSourceService<Element>
implements QuerySource {
private final static Logger log = LogManager.getLogger();
private String url;
@Autowired
private LiveImportClient liveImportClient;
@Override
public String getImportSource() {
return "pubmedeu";
}
/**
* Get a single record from the PubMed Europe.
*
* @param id Identifier for the record
* @return The first matching record
* @throws MetadataSourceException If the underlying methods throw any exception.
*/
@Override
public ImportRecord getRecord(String id) throws MetadataSourceException {
List<ImportRecord> records = retry(new SearchByIdCallable(id));
return CollectionUtils.isEmpty(records) ? null : records.get(0);
}
/**
* Find the number of records matching a query;
*
* @param query a query string to base the search on.
* @return the sum of the matching records over this import source
* @throws MetadataSourceException if the underlying methods throw any exception.
*/
@Override
public int getRecordsCount(String query) throws MetadataSourceException {
return retry(new CountByQueryCallable(query));
}
/**
* Find the number of records matching a query;
*
* @param query A query string to base the search on.
* @return The sum of the matching records over this import source
* @throws MetadataSourceException If the underlying methods throw any exception.
*/
@Override
public int getRecordsCount(Query query) throws MetadataSourceException {
return retry(new CountByQueryCallable(query));
}
/**
* Find records matching a string query.
*
* @param query A query string to base the search on.
* @param start Offset to start at
* @param count Number of records to retrieve.
* @return A set of records. Fully transformed.
* @throws MetadataSourceException If the underlying methods throw any exception.
*/
@Override
public Collection<ImportRecord> getRecords(String query, int start, int count) throws MetadataSourceException {
return retry(new SearchByQueryCallable(query, count, start));
}
/**
* Find records based on a object query.
*
* @param query A query object to base the search on.
* @return A set of records. Fully transformed.
* @throws MetadataSourceException If the underlying methods throw any exception.
*/
@Override
public Collection<ImportRecord> getRecords(Query query) throws MetadataSourceException {
return retry(new SearchByQueryCallable(query));
}
/**
* Get a single record from the PubMed Europe.
*
* @param query A query matching a single record
* @return The first matching record
* @throws MetadataSourceException If the underlying methods throw any exception.
*/
@Override
public ImportRecord getRecord(Query query) throws MetadataSourceException {
List<ImportRecord> records = retry(new SearchByIdCallable(query));
return CollectionUtils.isEmpty(records) ? null : records.get(0);
}
/**
* Finds records based on query object.
*
* @param query A query object to base the search on.
* @return A collection of import records.
* @throws MetadataSourceException If the underlying methods throw any exception.
*/
@Override
public Collection<ImportRecord> findMatchingRecords(Query query) throws MetadataSourceException {
return retry(new FindMatchingRecordCallable(query));
}
@Override
public Collection<ImportRecord> findMatchingRecords(Item item) throws MetadataSourceException {
throw new MethodNotFoundException("This method is not implemented for PubMed Europe");
}
@Override
public void init() throws Exception {}
public List<ImportRecord> getByPubmedEuropeID(String pubmedID, Integer start, Integer size)
throws IOException, HttpException {
String query = "(EXT_ID:" + pubmedID + ")";
return search(query, size < 1 ? 1 : size, start);
}
/**
* This class is a Callable implementation to get PubMed Europe entries based on
* query object.
*
* This Callable use as query value the string queryString passed to constructor.
* If the object will be construct through Query.class instance, a Query's map entry with key "query" will be used.
* Pagination is supported too, using the value of the Query's map with keys "start" and "count".
*
* @author Mykhaylo Boychuk (mykhaylo.boychuk at 4science.com)
*/
private class SearchByQueryCallable implements Callable<List<ImportRecord>> {
private Query query;
private SearchByQueryCallable(String queryString, Integer maxResult, Integer start) {
query = new Query();
query.addParameter("query", queryString);
query.addParameter("count", maxResult);
query.addParameter("start", start);
}
private SearchByQueryCallable(Query query) {
this.query = query;
}
@Override
public List<ImportRecord> call() throws Exception {
Integer count = query.getParameterAsClass("count", Integer.class);
Integer start = query.getParameterAsClass("start", Integer.class);
String queryString = query.getParameterAsClass("query", String.class);
return search(queryString, count, start);
}
}
/**
* This class is a Callable implementation to get an PubMed Europe entry using PubMed Europe ID
*
* @author Mykhaylo Boychuk (mykhaylo.boychuk at 4science.com)
*/
private class SearchByIdCallable implements Callable<List<ImportRecord>> {
private Query query;
private SearchByIdCallable(Query query) {
this.query = query;
}
private SearchByIdCallable(String id) {
this.query = new Query();
query.addParameter("id", id);
}
@Override
public List<ImportRecord> call() throws Exception {
return getByPubmedEuropeID(query.getParameterAsClass("id", String.class), 1 ,0);
}
}
/**
* This class is a Callable implementation to search PubMed Europe entries
* using author, title and year.
* Pagination is supported too, using the value of the Query's map with keys "start" and "count".
*
* @author Mykhaylo Boychuk (mykhaylo.boychuk at 4science.com)
*/
public class FindMatchingRecordCallable implements Callable<List<ImportRecord>> {
private Query query;
private FindMatchingRecordCallable(Query q) {
query = q;
}
@Override
public List<ImportRecord> call() throws Exception {
String title = query.getParameterAsClass("title", String.class);
String author = query.getParameterAsClass("author", String.class);
Integer year = query.getParameterAsClass("year", Integer.class);
Integer maxResult = query.getParameterAsClass("maxResult", Integer.class);
Integer start = query.getParameterAsClass("start", Integer.class);
return search(title, author, year, maxResult, start);
}
}
/**
* This class is a Callable implementation to count the number
* of entries for an PubMed Europe query.
*
* @author Mykhaylo Boychuk (mykhaylo.boychuk at 4science.com)
*/
private class CountByQueryCallable implements Callable<Integer> {
private Query query;
private CountByQueryCallable(String queryString) {
query = new Query();
query.addParameter("query", queryString);
}
private CountByQueryCallable(Query query) {
this.query = query;
}
@Override
public Integer call() throws Exception {
try {
return count(query.getParameterAsClass("query", String.class));
} catch (Exception e) {
throw new RuntimeException();
}
}
}
/**
* Returns the total number of PubMed Europe publications returned by a specific query
*
* @param query A keyword or combination of keywords to be searched
* @throws URISyntaxException If URI syntax error
* @throws ClientProtocolException The client protocol exception
* @throws IOException If IO error
* @throws JaxenException If Xpath evaluation failed
*/
public Integer count(String query) throws URISyntaxException, ClientProtocolException, IOException, JaxenException {
try {
Map<String, Map<String, String>> params = new HashMap<String, Map<String,String>>();
String response = liveImportClient.executeHttpGetRequest(1000, buildURI(1, query), params);
SAXBuilder saxBuilder = new SAXBuilder();
Document document = saxBuilder.build(new StringReader(response));
Element root = document.getRootElement();
Element element = root.getChild("hitCount");
return Integer.parseInt(element.getValue());
} catch (JDOMException e) {
log.error(e.getMessage(), e);
throw new RuntimeException(e.getMessage(), e);
}
}
public List<ImportRecord> search(String title, String author, int year, int count, int start)
throws IOException {
StringBuffer query = new StringBuffer();
query.append("(");
if (StringUtils.isNotBlank(title)) {
query.append("TITLE:").append(title);
query.append(")");
}
if (StringUtils.isNotBlank(author)) {
// Search for a surname and (optionally) initial(s) in publication author lists
// AUTH:einstein, AUTH:”Smith AB”
String splitRegex = "(\\s*,\\s+|\\s*;\\s+|\\s*;+|\\s*,+|\\s+)";
String[] authors = author.split(splitRegex);
if (query.length() > 0) {
query.append(" AND ");
}
query.append("(");
int countAuthors = 0;
for (String auth : authors) {
countAuthors++;
query.append("AUTH:\"").append(auth).append("\"");
if (countAuthors < authors.length) {
query.append(" AND ");
}
}
query.append(")");
}
if (year != -1) {
if (query.length() > 0) {
query.append(" AND ");
}
query.append("( PUB_YEAR:").append(year).append(")");
}
query.append(")");
return search(query.toString(), count, start);
}
/**
* Returns a list of PubMed Europe publication records
*
* @param query A keyword or combination of keywords to be searched
* @param size The number of search results per page
* @param start Start number for the acquired search result list
* @throws IOException If IO error
*/
public List<ImportRecord> search(String query, Integer size, Integer start) throws IOException {
List<ImportRecord> results = new ArrayList<>();
try {
URIBuilder uriBuilder = new URIBuilder(this.url);
uriBuilder.addParameter("format", "xml");
uriBuilder.addParameter("resulttype", "core");
uriBuilder.addParameter("pageSize", String.valueOf(size));
uriBuilder.addParameter("query", query);
Map<String, Map<String, String>> params = new HashMap<String, Map<String,String>>();
boolean lastPage = false;
int skipped = 0;
while (!lastPage || results.size() < size) {
String response = liveImportClient.executeHttpGetRequest(1000, uriBuilder.toString(), params);
String cursorMark = StringUtils.EMPTY;
if (StringUtils.isNotBlank(response)) {
SAXBuilder saxBuilder = new SAXBuilder();
Document document = saxBuilder.build(new StringReader(response));
XPathFactory xpfac = XPathFactory.instance();
XPathExpression<Element> xPath = xpfac.compile("//responseWrapper/resultList/result",
Filters.element());
List<Element> records = xPath.evaluate(document);
if (records.size() > 0) {
for (Element item : records) {
if (start > skipped) {
skipped++;
} else {
results.add(transformSourceRecords(item));
}
}
} else {
lastPage = true;
break;
}
Element root = document.getRootElement();
Element nextCursorMark = root.getChild("nextCursorMark");
cursorMark = Objects.nonNull(nextCursorMark) ? nextCursorMark.getValue() : StringUtils.EMPTY;
}
if (StringUtils.isNotBlank(cursorMark)) {
uriBuilder.setParameter("cursorMar", cursorMark);
} else {
lastPage = true;
}
}
} catch (URISyntaxException | JDOMException e) {
log.error(e.getMessage(), e);
throw new RuntimeException(e.getMessage(), e);
}
return results;
}
private String buildURI(Integer pageSize, String query) throws URISyntaxException {
URIBuilder uriBuilder = new URIBuilder(this.url);
uriBuilder.addParameter("format", "xml");
uriBuilder.addParameter("resulttype", "core");
uriBuilder.addParameter("pageSize", String.valueOf(pageSize));
uriBuilder.addParameter("query", query);
return uriBuilder.toString();
}
public String getUrl() {
return url;
}
public void setUrl(String url) {
this.url = url;
}
}

View File

@@ -0,0 +1,38 @@
/**
* 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.importer.external.scopus.service;
import java.util.Map;
import javax.annotation.Resource;
import org.dspace.importer.external.metadatamapping.AbstractMetadataFieldMapping;
/**
* An implementation of {@link AbstractMetadataFieldMapping}
* Responsible for defining the mapping of the Scopus metadatum fields on the DSpace metadatum fields
*
* @author Pasquale Cavallo (pasquale.cavallo at 4science dot it)
*/
public class ScopusFieldMapping extends AbstractMetadataFieldMapping {
/**
* Defines which metadatum is mapped on which metadatum. Note that while the key must be unique it
* only matters here for postprocessing of the value. The mapped MetadatumContributor has full control over
* what metadatafield is generated.
*
* @param metadataFieldMap The map containing the link between retrieve metadata and metadata that will be set to
* the item.
*/
@Override
@Resource(name = "scopusMetadataFieldMap")
public void setMetadataFieldMap(Map metadataFieldMap) {
super.setMetadataFieldMap(metadataFieldMap);
}
}

View File

@@ -0,0 +1,421 @@
/**
* 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.importer.external.scopus.service;
import static org.dspace.importer.external.liveimportclient.service.LiveImportClientImpl.URI_PARAMETERS;
import java.io.IOException;
import java.io.StringReader;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Objects;
import java.util.concurrent.Callable;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import javax.el.MethodNotFoundException;
import org.apache.commons.lang3.StringUtils;
import org.dspace.content.Item;
import org.dspace.importer.external.datamodel.ImportRecord;
import org.dspace.importer.external.datamodel.Query;
import org.dspace.importer.external.exception.MetadataSourceException;
import org.dspace.importer.external.liveimportclient.service.LiveImportClient;
import org.dspace.importer.external.service.AbstractImportMetadataSourceService;
import org.dspace.importer.external.service.DoiCheck;
import org.dspace.importer.external.service.components.QuerySource;
import org.jdom2.Document;
import org.jdom2.Element;
import org.jdom2.JDOMException;
import org.jdom2.Namespace;
import org.jdom2.filter.Filters;
import org.jdom2.input.SAXBuilder;
import org.jdom2.xpath.XPathExpression;
import org.jdom2.xpath.XPathFactory;
import org.springframework.beans.factory.annotation.Autowired;
/**
* Implements a data source for querying Scopus
*
* @author Mykhaylo Boychuk (mykhaylo.boychuk at 4science dot com)
*/
public class ScopusImportMetadataSourceServiceImpl extends AbstractImportMetadataSourceService<Element>
implements QuerySource {
private int timeout = 1000;
int itemPerPage = 25;
private String url;
private String apiKey;
private String instKey;
private String viewMode;
@Autowired
private LiveImportClient liveImportClient;
public LiveImportClient getLiveImportClient() {
return liveImportClient;
}
public void setLiveImportClient(LiveImportClient liveImportClient) {
this.liveImportClient = liveImportClient;
}
@Override
public void init() throws Exception {}
/**
* The string that identifies this import implementation. Preferable a URI
*
* @return the identifying uri
*/
@Override
public String getImportSource() {
return "scopus";
}
@Override
public int getRecordsCount(String query) throws MetadataSourceException {
if (isEID(query)) {
return retry(new FindByIdCallable(query)).size();
}
if (DoiCheck.isDoi(query)) {
query = DoiCheck.purgeDoiValue(query);
}
return retry(new SearchNBByQueryCallable(query));
}
@Override
public int getRecordsCount(Query query) throws MetadataSourceException {
if (isEID(query.toString())) {
return retry(new FindByIdCallable(query.toString())).size();
}
if (DoiCheck.isDoi(query.toString())) {
query.addParameter("query", DoiCheck.purgeDoiValue(query.toString()));
}
return retry(new SearchNBByQueryCallable(query));
}
@Override
public Collection<ImportRecord> getRecords(String query, int start,
int count) throws MetadataSourceException {
if (isEID(query)) {
return retry(new FindByIdCallable(query));
}
if (DoiCheck.isDoi(query)) {
query = DoiCheck.purgeDoiValue(query);
}
return retry(new SearchByQueryCallable(query, count, start));
}
@Override
public Collection<ImportRecord> getRecords(Query query)
throws MetadataSourceException {
if (isEID(query.toString())) {
return retry(new FindByIdCallable(query.toString()));
}
if (DoiCheck.isDoi(query.toString())) {
query.addParameter("query", DoiCheck.purgeDoiValue(query.toString()));
}
return retry(new SearchByQueryCallable(query));
}
@Override
public ImportRecord getRecord(Query query) throws MetadataSourceException {
List<ImportRecord> records = null;
if (DoiCheck.isDoi(query.toString())) {
query.addParameter("query", DoiCheck.purgeDoiValue(query.toString()));
}
if (isEID(query.toString())) {
records = retry(new FindByIdCallable(query.toString()));
} else {
records = retry(new SearchByQueryCallable(query));
}
return records == null || records.isEmpty() ? null : records.get(0);
}
@Override
public Collection<ImportRecord> findMatchingRecords(Item item)
throws MetadataSourceException {
throw new MethodNotFoundException("This method is not implemented for Scopus");
}
@Override
public ImportRecord getRecord(String id) throws MetadataSourceException {
List<ImportRecord> records = retry(new FindByIdCallable(id));
return records == null || records.isEmpty() ? null : records.get(0);
}
@Override
public Collection<ImportRecord> findMatchingRecords(Query query)
throws MetadataSourceException {
if (isEID(query.toString())) {
return retry(new FindByIdCallable(query.toString()));
}
if (DoiCheck.isDoi(query.toString())) {
query.addParameter("query", DoiCheck.purgeDoiValue(query.toString()));
}
return retry(new FindByQueryCallable(query));
}
private boolean isEID(String query) {
Pattern pattern = Pattern.compile("2-s2\\.0-\\d+");
Matcher match = pattern.matcher(query);
if (match.matches()) {
return true;
}
return false;
}
/**
* This class implements a callable to get the numbers of result
*/
private class SearchNBByQueryCallable implements Callable<Integer> {
private String query;
private SearchNBByQueryCallable(String queryString) {
this.query = queryString;
}
private SearchNBByQueryCallable(Query query) {
this.query = query.getParameterAsClass("query", String.class);
}
@Override
public Integer call() throws Exception {
if (StringUtils.isNotBlank(apiKey)) {
// Execute the request.
Map<String, Map<String, String>> params = new HashMap<String, Map<String,String>>();
Map<String, String> requestParams = getRequestParameters(query, null, null, null);
params.put(URI_PARAMETERS, requestParams);
String response = liveImportClient.executeHttpGetRequest(timeout, url, params);
SAXBuilder saxBuilder = new SAXBuilder();
Document document = saxBuilder.build(new StringReader(response));
Element root = document.getRootElement();
List<Namespace> namespaces = Arrays.asList(
Namespace.getNamespace("opensearch", "http://a9.com/-/spec/opensearch/1.1/"));
XPathExpression<Element> xpath = XPathFactory.instance()
.compile("opensearch:totalResults", Filters.element(), null, namespaces);
Element count = xpath.evaluateFirst(root);
try {
return Integer.parseInt(count.getText());
} catch (NumberFormatException e) {
return null;
}
}
return null;
}
}
/**
* This class is a Callable implementation to get a Scopus entry using EID
*
* @author Mykhaylo Boychuk (mykhaylo.boychuk at 4science.com)
*/
private class FindByIdCallable implements Callable<List<ImportRecord>> {
private String eid;
private FindByIdCallable(String eid) {
this.eid = eid;
}
@Override
public List<ImportRecord> call() throws Exception {
List<ImportRecord> results = new ArrayList<>();
String queryString = "EID(" + eid.replace("!", "/") + ")";
if (StringUtils.isNotBlank(apiKey)) {
Map<String, Map<String, String>> params = new HashMap<String, Map<String,String>>();
Map<String, String> requestParams = getRequestParameters(queryString, viewMode, null, null);
params.put(URI_PARAMETERS, requestParams);
String response = liveImportClient.executeHttpGetRequest(timeout, url, params);
List<Element> elements = splitToRecords(response);
for (Element record : elements) {
results.add(transformSourceRecords(record));
}
}
return results;
}
}
/**
* This class implements a callable to get the items based on query parameters
*/
private class FindByQueryCallable implements Callable<List<ImportRecord>> {
private String title;
private String author;
private Integer year;
private Integer start;
private Integer count;
private FindByQueryCallable(Query query) {
this.title = query.getParameterAsClass("title", String.class);
this.year = query.getParameterAsClass("year", Integer.class);
this.author = query.getParameterAsClass("author", String.class);
this.start = query.getParameterAsClass("start", Integer.class) != null ?
query.getParameterAsClass("start", Integer.class) : 0;
this.count = query.getParameterAsClass("count", Integer.class) != null ?
query.getParameterAsClass("count", Integer.class) : 20;
}
@Override
public List<ImportRecord> call() throws Exception {
List<ImportRecord> results = new ArrayList<>();
String queryString = "";
StringBuffer query = new StringBuffer();
if (StringUtils.isNotBlank(title)) {
query.append("title(").append(title).append("");
}
if (StringUtils.isNotBlank(author)) {
// [FAU]
if (query.length() > 0) {
query.append(" AND ");
}
query.append("AUTH(").append(author).append(")");
}
if (year != -1) {
// [DP]
if (query.length() > 0) {
query.append(" AND ");
}
query.append("PUBYEAR IS ").append(year);
}
queryString = query.toString();
if (apiKey != null && !apiKey.equals("")) {
Map<String, Map<String, String>> params = new HashMap<String, Map<String,String>>();
Map<String, String> requestParams = getRequestParameters(queryString, viewMode, start, count);
params.put(URI_PARAMETERS, requestParams);
String response = liveImportClient.executeHttpGetRequest(timeout, url, params);
List<Element> elements = splitToRecords(response);
for (Element record : elements) {
results.add(transformSourceRecords(record));
}
}
return results;
}
}
/**
* Find records matching a string query.
*
* @param query A query string to base the search on.
* @param start Offset to start at
* @param count Number of records to retrieve.
* @return A set of records. Fully transformed.
*
* @author Mykhaylo Boychuk (mykhaylo.boychuk at 4science.com)
*/
private class SearchByQueryCallable implements Callable<List<ImportRecord>> {
private Query query;
private SearchByQueryCallable(String queryString, Integer maxResult, Integer start) {
query = new Query();
query.addParameter("query", queryString);
query.addParameter("start", start);
query.addParameter("count", maxResult);
}
private SearchByQueryCallable(Query query) {
this.query = query;
}
@Override
public List<ImportRecord> call() throws Exception {
List<ImportRecord> results = new ArrayList<>();
String queryString = query.getParameterAsClass("query", String.class);
Integer start = query.getParameterAsClass("start", Integer.class);
Integer count = query.getParameterAsClass("count", Integer.class);
if (StringUtils.isNotBlank(apiKey)) {
Map<String, Map<String, String>> params = new HashMap<String, Map<String,String>>();
Map<String, String> requestParams = getRequestParameters(queryString, viewMode, start, count);
params.put(URI_PARAMETERS, requestParams);
String response = liveImportClient.executeHttpGetRequest(timeout, url, params);
List<Element> elements = splitToRecords(response);
for (Element record : elements) {
results.add(transformSourceRecords(record));
}
}
return results;
}
}
private Map<String, String> getRequestParameters(String query, String viewMode, Integer start, Integer count) {
Map<String, String> params = new HashMap<String, String>();
params.put("httpAccept", "application/xml");
params.put("apiKey", apiKey);
params.put("query", query);
if (StringUtils.isNotBlank(instKey)) {
params.put("insttoken", instKey);
}
if (StringUtils.isNotBlank(viewMode)) {
params.put("view", viewMode);
}
params.put("start", (Objects.nonNull(start) ? start + "" : "0"));
params.put("count", (Objects.nonNull(count) ? count + "" : "20"));
return params;
}
private List<Element> splitToRecords(String recordsSrc) {
try {
SAXBuilder saxBuilder = new SAXBuilder();
Document document = saxBuilder.build(new StringReader(recordsSrc));
Element root = document.getRootElement();
List<Element> records = root.getChildren("entry",Namespace.getNamespace("http://www.w3.org/2005/Atom"));
return records;
} catch (JDOMException | IOException e) {
return new ArrayList<Element>();
}
}
public String getUrl() {
return url;
}
public void setUrl(String url) {
this.url = url;
}
public String getViewMode() {
return viewMode;
}
public void setViewMode(String viewMode) {
this.viewMode = viewMode;
}
public String getApiKey() {
return apiKey;
}
public String getInstKey() {
return instKey;
}
public void setApiKey(String apiKey) {
this.apiKey = apiKey;
}
public void setInstKey(String instKey) {
this.instKey = instKey;
}
}

View File

@@ -0,0 +1,37 @@
/**
* 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.importer.external.wos.service;
import java.util.Map;
import javax.annotation.Resource;
import org.dspace.importer.external.metadatamapping.AbstractMetadataFieldMapping;
/**
* An implementation of {@link AbstractMetadataFieldMapping}
* Responsible for defining the mapping of the Web of Science metadatum fields on the DSpace metadatum fields
*
* @author Boychuk Mykhaylo (boychuk.mykhaylo at 4science dot it)
*/
@SuppressWarnings("rawtypes")
public class WOSFieldMapping extends AbstractMetadataFieldMapping {
/**
* Defines which metadatum is mapped on which metadatum. Note that while the key must be unique it
* only matters here for postprocessing of the value. The mapped MetadatumContributor has full control over
* what metadatafield is generated.
*
* @param metadataFieldMap The map containing the link between retrieve
* metadata and metadata that will be set to the item.
*/
@Override
@SuppressWarnings("unchecked")
@Resource(name = "wosMetadataFieldMap")
public void setMetadataFieldMap(Map metadataFieldMap) {
super.setMetadataFieldMap(metadataFieldMap);
}
}

View File

@@ -0,0 +1,329 @@
/**
* 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.importer.external.wos.service;
import static org.dspace.importer.external.liveimportclient.service.LiveImportClientImpl.HEADER_PARAMETERS;
import java.io.IOException;
import java.io.StringReader;
import java.net.URLEncoder;
import java.nio.charset.StandardCharsets;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.concurrent.Callable;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import javax.el.MethodNotFoundException;
import org.apache.commons.collections.CollectionUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.content.Item;
import org.dspace.importer.external.datamodel.ImportRecord;
import org.dspace.importer.external.datamodel.Query;
import org.dspace.importer.external.exception.MetadataSourceException;
import org.dspace.importer.external.liveimportclient.service.LiveImportClient;
import org.dspace.importer.external.service.AbstractImportMetadataSourceService;
import org.dspace.importer.external.service.DoiCheck;
import org.dspace.importer.external.service.components.QuerySource;
import org.jdom2.Document;
import org.jdom2.Element;
import org.jdom2.JDOMException;
import org.jdom2.filter.Filters;
import org.jdom2.input.SAXBuilder;
import org.jdom2.xpath.XPathExpression;
import org.jdom2.xpath.XPathFactory;
import org.springframework.beans.factory.annotation.Autowired;
/**
* Implements a data source for querying Web of Science.
*
* @author Boychuk Mykhaylo (boychuk.mykhaylo at 4Science dot it)
*/
public class WOSImportMetadataSourceServiceImpl extends AbstractImportMetadataSourceService<Element>
implements QuerySource {
private final static Logger log = LogManager.getLogger();
private static final String AI_PATTERN = "^AI=(.*)";
private static final Pattern ISI_PATTERN = Pattern.compile("^\\d{15}$");
private int timeout = 1000;
private String url;
private String urlSearch;
private String apiKey;
@Autowired
private LiveImportClient liveImportClient;
@Override
public void init() throws Exception {}
/**
* The string that identifies this import implementation. Preferable a URI
*
* @return the identifying uri
*/
@Override
public String getImportSource() {
return "wos";
}
@Override
public Collection<ImportRecord> getRecords(String query, int start, int count) throws MetadataSourceException {
return retry(new SearchByQueryCallable(query, count, start));
}
@Override
public Collection<ImportRecord> getRecords(Query query) throws MetadataSourceException {
return retry(new SearchByQueryCallable(query));
}
@Override
public ImportRecord getRecord(Query query) throws MetadataSourceException {
List<ImportRecord> records = retry(new SearchByQueryCallable(query));
return records == null || records.isEmpty() ? null : records.get(0);
}
@Override
public ImportRecord getRecord(String id) throws MetadataSourceException {
List<ImportRecord> records = retry(new FindByIdCallable(id));
return records == null || records.isEmpty() ? null : records.get(0);
}
@Override
public int getRecordsCount(String query) throws MetadataSourceException {
return retry(new SearchNBByQueryCallable(query));
}
@Override
public int getRecordsCount(Query query) throws MetadataSourceException {
throw new MethodNotFoundException("This method is not implemented for WOS");
}
@Override
public Collection<ImportRecord> findMatchingRecords(Item item) throws MetadataSourceException {
throw new MethodNotFoundException("This method is not implemented for WOS");
}
@Override
public Collection<ImportRecord> findMatchingRecords(Query query) throws MetadataSourceException {
throw new MethodNotFoundException("This method is not implemented for WOS");
}
/**
* This class implements a callable to get the numbers of result
*/
private class SearchNBByQueryCallable implements Callable<Integer> {
private String query;
private SearchNBByQueryCallable(String queryString) {
this.query = queryString;
}
private SearchNBByQueryCallable(Query query) {
this.query = query.getParameterAsClass("query", String.class);
}
@Override
public Integer call() throws Exception {
if (StringUtils.isNotBlank(apiKey)) {
String queryString = URLEncoder.encode(checkQuery(query), StandardCharsets.UTF_8);
String url = urlSearch + queryString + "&count=1&firstRecord=1";
Map<String, Map<String, String>> params = new HashMap<String, Map<String,String>>();
params.put(HEADER_PARAMETERS, getRequestParameters());
String response = liveImportClient.executeHttpGetRequest(timeout, url, params);
SAXBuilder saxBuilder = new SAXBuilder();
Document document = saxBuilder.build(new StringReader(response));
Element root = document.getRootElement();
XPathExpression<Element> xpath = XPathFactory.instance().compile("//*[@name=\"RecordsFound\"]",
Filters.element(), null);
Element tot = xpath.evaluateFirst(root);
return Integer.valueOf(tot.getValue());
}
return null;
}
}
/**
* This class is a Callable implementation to get a Web of Science entry using Doi
*
* @author Mykhaylo Boychuk (mykhaylo.boychuk at 4science.com)
*/
private class FindByIdCallable implements Callable<List<ImportRecord>> {
private String doi;
private FindByIdCallable(String doi) {
this.doi = URLEncoder.encode(doi, StandardCharsets.UTF_8);
}
@Override
public List<ImportRecord> call() throws Exception {
List<ImportRecord> results = new ArrayList<>();
if (StringUtils.isNotBlank(apiKey)) {
String urlString = url + this.doi + "?databaseId=WOS&lang=en&count=10&firstRecord=1";
Map<String, Map<String, String>> params = new HashMap<String, Map<String,String>>();
params.put(HEADER_PARAMETERS, getRequestParameters());
String response = liveImportClient.executeHttpGetRequest(timeout, urlString, params);
List<Element> elements = splitToRecords(response);
for (Element record : elements) {
results.add(transformSourceRecords(record));
}
}
return results;
}
}
/**
* Find records matching a string query.
*
* @param query A query string to base the search on.
* @param start Offset to start at
* @param count Number of records to retrieve.
* @return A set of records. Fully transformed.
*
* @author Mykhaylo Boychuk (mykhaylo.boychuk at 4science.com)
*/
private class SearchByQueryCallable implements Callable<List<ImportRecord>> {
private Query query;
private SearchByQueryCallable(String queryString, Integer maxResult, Integer start) {
query = new Query();
query.addParameter("query", queryString);
query.addParameter("start", start);
query.addParameter("count", maxResult);
}
private SearchByQueryCallable(Query query) {
this.query = query;
}
@Override
public List<ImportRecord> call() throws Exception {
List<ImportRecord> results = new ArrayList<>();
String queryString = checkQuery(query.getParameterAsClass("query", String.class));
Integer start = query.getParameterAsClass("start", Integer.class);
Integer count = query.getParameterAsClass("count", Integer.class);
if (StringUtils.isNotBlank(apiKey)) {
Map<String, Map<String, String>> params = new HashMap<String, Map<String,String>>();
params.put(HEADER_PARAMETERS, getRequestParameters());
String url = urlSearch + URLEncoder.encode(queryString, StandardCharsets.UTF_8)
+ "&count=" + count + "&firstRecord=" + (start + 1);
String response = liveImportClient.executeHttpGetRequest(timeout, url, params);
List<Element> omElements = splitToRecords(response);
for (Element el : omElements) {
results.add(transformSourceRecords(el));
}
}
return results;
}
}
private Map<String, String> getRequestParameters() {
Map<String, String> params = new HashMap<String, String>();
params.put("Accept", "application/xml");
params.put("X-ApiKey", this.apiKey);
return params;
}
/**
* This method check if the query contain
* "AI=(...)" Author Identifier or a DOI "DO=(query)"
* or Accession Number "UT=(query)".
* Otherwise the value is placed in TS=(query) tag
* that searches for topic terms in the following fields within a document:
* Title, Abstract, Author keywords, Keywords Plus
*
* @param query
*/
private String checkQuery(String query) {
Pattern risPattern = Pattern.compile(AI_PATTERN);
Matcher risMatcher = risPattern.matcher(query.trim());
if (risMatcher.matches()) {
return query;
}
if (DoiCheck.isDoi(query)) {
// FIXME: workaround to be removed once fixed by the community the double post of query param
if (query.startsWith(",")) {
query = query.substring(1);
}
return "DO=(" + query + ")";
} else if (isIsi(query)) {
return "UT=(" + query + ")";
}
StringBuilder queryBuilder = new StringBuilder("TS=(");
queryBuilder.append(query).append(")");
return queryBuilder.toString();
}
private boolean isIsi(String query) {
if (query.startsWith("WOS:")) {
return true;
}
Matcher matcher = ISI_PATTERN.matcher(query.trim());
return matcher.matches();
}
private List<Element> splitToRecords(String recordsSrc) {
try {
SAXBuilder saxBuilder = new SAXBuilder();
Document document = saxBuilder.build(new StringReader(recordsSrc));
Element root = document.getRootElement();
String cData = XPathFactory.instance().compile("//*[@name=\"Records\"]",
Filters.element(), null).evaluate(root).get(0).getValue().trim();
Document intDocument = saxBuilder.build(new StringReader(cData));
XPathExpression<Element> xPath = XPathFactory.instance().compile("*", Filters.element(), null);
List<Element> records = xPath.evaluate(intDocument.getRootElement());
if (CollectionUtils.isNotEmpty(records)) {
return records;
}
} catch (JDOMException | IOException e) {
log.error(e.getMessage());
return new ArrayList<Element>();
}
return new ArrayList<Element>();
}
public String getUrl() {
return url;
}
public void setUrl(String url) {
this.url = url;
}
public String getUrlSearch() {
return urlSearch;
}
public void setUrlSearch(String urlSearch) {
this.urlSearch = urlSearch;
}
public String getApiKey() {
return apiKey;
}
public void setApiKey(String apiKey) {
this.apiKey = apiKey;
}
}

View File

@@ -10,6 +10,7 @@ package org.dspace.scripts;
import java.util.ArrayList;
import java.util.Date;
import java.util.List;
import javax.persistence.CascadeType;
import javax.persistence.Column;
import javax.persistence.Entity;
import javax.persistence.EnumType;
@@ -33,6 +34,7 @@ import org.dspace.content.Bitstream;
import org.dspace.content.ProcessStatus;
import org.dspace.core.ReloadableEntity;
import org.dspace.eperson.EPerson;
import org.dspace.eperson.Group;
/**
* This class is the DB Entity representation of the Process object to be stored in the Database
@@ -77,6 +79,17 @@ public class Process implements ReloadableEntity<Integer> {
)
private List<Bitstream> bitstreams;
/*
* Special Groups associated with this Process
*/
@ManyToMany(fetch = FetchType.LAZY, cascade = {CascadeType.PERSIST})
@JoinTable(
name = "process2group",
joinColumns = {@JoinColumn(name = "process_id")},
inverseJoinColumns = {@JoinColumn(name = "group_id")}
)
private List<Group> groups;
@Column(name = "creation_time", nullable = false)
@Temporal(TemporalType.TIMESTAMP)
private Date creationTime;
@@ -211,6 +224,21 @@ public class Process implements ReloadableEntity<Integer> {
return creationTime;
}
/**
* This method sets the special groups associated with the Process.
*/
public List<Group> getGroups() {
return groups;
}
/**
* This method will return special groups associated with the Process.
* @return The special groups of this process.
*/
public void setGroups(List<Group> groups) {
this.groups = groups;
}
/**
* Return <code>true</code> if <code>other</code> is the same Process
* as this object, <code>false</code> otherwise

View File

@@ -21,6 +21,7 @@ import java.util.Comparator;
import java.util.Date;
import java.util.HashSet;
import java.util.List;
import java.util.Optional;
import java.util.Set;
import java.util.regex.Pattern;
@@ -43,6 +44,7 @@ import org.dspace.core.Constants;
import org.dspace.core.Context;
import org.dspace.core.LogHelper;
import org.dspace.eperson.EPerson;
import org.dspace.eperson.Group;
import org.dspace.eperson.service.EPersonService;
import org.dspace.scripts.service.ProcessService;
import org.springframework.beans.factory.annotation.Autowired;
@@ -74,13 +76,21 @@ public class ProcessServiceImpl implements ProcessService {
@Override
public Process create(Context context, EPerson ePerson, String scriptName,
List<DSpaceCommandLineParameter> parameters) throws SQLException {
List<DSpaceCommandLineParameter> parameters,
final Set<Group> specialGroups) throws SQLException {
Process process = new Process();
process.setEPerson(ePerson);
process.setName(scriptName);
process.setParameters(DSpaceCommandLineParameter.concatenate(parameters));
process.setCreationTime(new Date());
Optional.ofNullable(specialGroups)
.ifPresent(sg -> {
// we use a set to be sure no duplicated special groups are stored with process
Set<Group> specialGroupsSet = new HashSet<>(sg);
process.setGroups(new ArrayList<>(specialGroupsSet));
});
Process createdProcess = processDAO.create(context, process);
log.info(LogHelper.getHeader(context, "process_create",
"Process has been created for eperson with email " + ePerson.getEmail()

View File

@@ -10,7 +10,9 @@ package org.dspace.scripts.handler;
import java.io.IOException;
import java.io.InputStream;
import java.sql.SQLException;
import java.util.List;
import java.util.Optional;
import java.util.UUID;
import org.apache.commons.cli.Options;
import org.dspace.authorize.AuthorizeException;
@@ -114,4 +116,12 @@ public interface DSpaceRunnableHandler {
*/
public void writeFilestream(Context context, String fileName, InputStream inputStream, String type)
throws IOException, SQLException, AuthorizeException;
/**
* This method will return a List of UUIDs for the special groups
* associated with the processId contained by specific implementations of this interface.
* Otherwise, it returns an empty collection.
* @return List containing UUIDs of Special Groups of the associated Process.
*/
public List<UUID> getSpecialGroups();
}

View File

@@ -10,7 +10,10 @@ package org.dspace.scripts.handler.impl;
import java.io.File;
import java.io.IOException;
import java.io.InputStream;
import java.util.Collections;
import java.util.List;
import java.util.Optional;
import java.util.UUID;
import org.apache.commons.cli.HelpFormatter;
import org.apache.commons.cli.Options;
@@ -113,4 +116,9 @@ public class CommandLineDSpaceRunnableHandler implements DSpaceRunnableHandler {
File file = new File(fileName);
FileUtils.copyInputStreamToFile(inputStream, file);
}
@Override
public List<UUID> getSpecialGroups() {
return Collections.emptyList();
}
}

View File

@@ -11,11 +11,13 @@ import java.io.IOException;
import java.io.InputStream;
import java.sql.SQLException;
import java.util.List;
import java.util.Set;
import org.dspace.authorize.AuthorizeException;
import org.dspace.content.Bitstream;
import org.dspace.core.Context;
import org.dspace.eperson.EPerson;
import org.dspace.eperson.Group;
import org.dspace.scripts.DSpaceCommandLineParameter;
import org.dspace.scripts.Process;
import org.dspace.scripts.ProcessLogLevel;
@@ -32,11 +34,14 @@ public interface ProcessService {
* @param ePerson The ePerson for which this process will be created on
* @param scriptName The script name to be used for the process
* @param parameters The parameters to be used for the process
* @param specialGroups Allows to set special groups, associated with application context when process is created,
* other than the ones derived from the eperson membership.
* @return The created process
* @throws SQLException If something goes wrong
*/
public Process create(Context context, EPerson ePerson, String scriptName,
List<DSpaceCommandLineParameter> parameters) throws SQLException;
List<DSpaceCommandLineParameter> parameters,
final Set<Group> specialGroups) throws SQLException;
/**
* This method will retrieve a Process object from the Database with the given ID

View File

@@ -21,6 +21,7 @@ import org.dspace.content.Item;
import org.dspace.content.MetadataField;
import org.dspace.content.MetadataSchema;
import org.dspace.content.MetadataValue;
import org.dspace.content.RelationshipMetadataValue;
import org.dspace.content.service.BitstreamService;
import org.dspace.content.service.BundleService;
import org.dspace.content.service.ItemService;
@@ -55,14 +56,24 @@ public abstract class AbstractVersionProvider {
MetadataSchema metadataSchema = metadataField.getMetadataSchema();
String unqualifiedMetadataField = metadataSchema.getName() + "." + metadataField.getElement();
if (getIgnoredMetadataFields().contains(metadataField.toString('.')) ||
getIgnoredMetadataFields().contains(unqualifiedMetadataField + "." + Item.ANY)) {
//Skip this metadata field
getIgnoredMetadataFields().contains(unqualifiedMetadataField + "." + Item.ANY) ||
aMd instanceof RelationshipMetadataValue) {
//Skip this metadata field (ignored and/or virtual)
continue;
}
itemService
.addMetadata(context, itemNew, metadataField, aMd.getLanguage(), aMd.getValue(), aMd.getAuthority(),
aMd.getConfidence());
itemService.addMetadata(
context,
itemNew,
metadataField.getMetadataSchema().getName(),
metadataField.getElement(),
metadataField.getQualifier(),
aMd.getLanguage(),
aMd.getValue(),
aMd.getAuthority(),
aMd.getConfidence(),
aMd.getPlace()
);
}
}

View File

@@ -15,7 +15,9 @@ import org.apache.logging.log4j.Logger;
import org.dspace.authorize.AuthorizeException;
import org.dspace.authorize.ResourcePolicy;
import org.dspace.content.Item;
import org.dspace.content.Relationship;
import org.dspace.content.WorkspaceItem;
import org.dspace.content.service.RelationshipService;
import org.dspace.content.service.WorkspaceItemService;
import org.dspace.core.Context;
import org.dspace.identifier.IdentifierException;
@@ -44,6 +46,8 @@ public class DefaultItemVersionProvider extends AbstractVersionProvider implemen
protected VersioningService versioningService;
@Autowired(required = true)
protected IdentifierService identifierService;
@Autowired(required = true)
protected RelationshipService relationshipService;
@Override
public Item createNewItemAndAddItInWorkspace(Context context, Item nativeItem) {
@@ -89,10 +93,18 @@ public class DefaultItemVersionProvider extends AbstractVersionProvider implemen
}
}
/**
* Copy all data (minus a few exceptions) from the old item to the new item.
* @param c the DSpace context.
* @param itemNew the new version of the item.
* @param previousItem the old version of the item.
* @return the new version of the item, with data from the old item.
*/
@Override
public Item updateItemState(Context c, Item itemNew, Item previousItem) {
try {
copyMetadata(c, itemNew, previousItem);
copyRelationships(c, itemNew, previousItem);
createBundlesAndAddBitstreams(c, itemNew, previousItem);
try {
identifierService.reserve(c, itemNew);
@@ -114,4 +126,49 @@ public class DefaultItemVersionProvider extends AbstractVersionProvider implemen
throw new RuntimeException(e.getMessage(), e);
}
}
/**
* Copy all relationships of the old item to the new item.
* At this point in the lifecycle of the item-version (before archival), only the opposite item receives
* "latest" status. On item archival of the item-version, the "latest" status of the relevant relationships
* will be updated.
* @param context the DSpace context.
* @param newItem the new version of the item.
* @param oldItem the old version of the item.
*/
protected void copyRelationships(
Context context, Item newItem, Item oldItem
) throws SQLException, AuthorizeException {
List<Relationship> oldRelationships = relationshipService.findByItem(context, oldItem, -1, -1, false, true);
for (Relationship oldRelationship : oldRelationships) {
if (oldRelationship.getLeftItem().equals(oldItem)) {
// current item is on left side of this relationship
relationshipService.create(
context,
newItem, // new item
oldRelationship.getRightItem(),
oldRelationship.getRelationshipType(),
oldRelationship.getLeftPlace(),
oldRelationship.getRightPlace(),
oldRelationship.getLeftwardValue(),
oldRelationship.getRightwardValue(),
Relationship.LatestVersionStatus.RIGHT_ONLY // only mark the opposite side as "latest" for now
);
} else if (oldRelationship.getRightItem().equals(oldItem)) {
// current item is on right side of this relationship
relationshipService.create(
context,
oldRelationship.getLeftItem(),
newItem, // new item
oldRelationship.getRelationshipType(),
oldRelationship.getLeftPlace(),
oldRelationship.getRightPlace(),
oldRelationship.getLeftwardValue(),
oldRelationship.getRightwardValue(),
Relationship.LatestVersionStatus.LEFT_ONLY // only mark the opposite side as "latest" for now
);
}
}
}
}

View File

@@ -22,5 +22,12 @@ public interface ItemVersionProvider {
public void deleteVersionedItem(Context c, Version versionToDelete, VersionHistory history) throws SQLException;
/**
* Copy all data (minus a few exceptions) from the old item to the new item.
* @param c the DSpace context.
* @param itemNew the new version of the item.
* @param previousItem the old version of the item.
* @return the new version of the item, with data from the old item.
*/
public Item updateItemState(Context c, Item itemNew, Item previousItem);
}

View File

@@ -7,39 +7,66 @@
*/
package org.dspace.versioning;
import java.util.HashSet;
import java.util.Set;
import static org.dspace.versioning.utils.RelationshipVersioningUtils.LatestVersionStatusChangelog.NO_CHANGES;
import java.sql.SQLException;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import java.util.stream.Collectors;
import org.apache.commons.collections4.CollectionUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.content.EntityType;
import org.dspace.content.Item;
import org.dspace.content.Relationship;
import org.dspace.content.RelationshipType;
import org.dspace.content.factory.ContentServiceFactory;
import org.dspace.content.service.EntityTypeService;
import org.dspace.content.service.ItemService;
import org.dspace.content.service.RelationshipService;
import org.dspace.content.service.RelationshipTypeService;
import org.dspace.core.Constants;
import org.dspace.core.Context;
import org.dspace.discovery.IndexEventConsumer;
import org.dspace.event.Consumer;
import org.dspace.event.Event;
import org.dspace.versioning.factory.VersionServiceFactory;
import org.dspace.versioning.service.VersionHistoryService;
import org.dspace.versioning.service.VersioningService;
import org.dspace.versioning.utils.RelationshipVersioningUtils;
import org.dspace.versioning.utils.RelationshipVersioningUtils.LatestVersionStatusChangelog;
/**
* When a new version of an item is published, unarchive the previous version and
* update {@link Relationship#latestVersionStatus} of the relevant relationships.
*
* @author Fabio Bolognesi (fabio at atmire dot com)
* @author Mark Diggory (markd at atmire dot com)
* @author Ben Bosman (ben at atmire dot com)
*/
public class VersioningConsumer implements Consumer {
private static Set<Item> itemsToProcess;
private static final Logger log = LogManager.getLogger(VersioningConsumer.class);
private Set<Item> itemsToProcess;
private VersionHistoryService versionHistoryService;
private VersioningService versioningService;
private ItemService itemService;
private EntityTypeService entityTypeService;
private RelationshipTypeService relationshipTypeService;
private RelationshipService relationshipService;
private RelationshipVersioningUtils relationshipVersioningUtils;
@Override
public void initialize() throws Exception {
versionHistoryService = VersionServiceFactory.getInstance().getVersionHistoryService();
versioningService = VersionServiceFactory.getInstance().getVersionService();
itemService = ContentServiceFactory.getInstance().getItemService();
entityTypeService = ContentServiceFactory.getInstance().getEntityTypeService();
relationshipTypeService = ContentServiceFactory.getInstance().getRelationshipTypeService();
relationshipService = ContentServiceFactory.getInstance().getRelationshipService();
relationshipVersioningUtils = VersionServiceFactory.getInstance().getRelationshipVersioningUtils();
}
@Override
@@ -49,35 +76,397 @@ public class VersioningConsumer implements Consumer {
@Override
public void consume(Context ctx, Event event) throws Exception {
if (itemsToProcess == null) {
itemsToProcess = new HashSet<Item>();
itemsToProcess = new HashSet<>();
}
int st = event.getSubjectType();
int et = event.getEventType();
// only items
if (event.getSubjectType() != Constants.ITEM) {
return;
}
if (st == Constants.ITEM && et == Event.INSTALL) {
// only install events
if (event.getEventType() != Event.INSTALL) {
return;
}
// get the item (should be archived)
Item item = (Item) event.getSubject(ctx);
if (item != null && item.isArchived()) {
if (item == null || !item.isArchived()) {
return;
}
// get version history
VersionHistory history = versionHistoryService.findByItem(ctx, item);
if (history != null) {
Version latest = versionHistoryService.getLatestVersion(ctx, history);
Version previous = versionHistoryService.getPrevious(ctx, history, latest);
if (previous != null) {
Item previousItem = previous.getItem();
if (previousItem != null) {
previousItem.setArchived(false);
itemsToProcess.add(previousItem);
if (history == null) {
return;
}
// get latest version
Version latestVersion = versionHistoryService.getLatestVersion(ctx, history);
if (latestVersion == null) {
return;
}
// get previous version
Version previousVersion = versionHistoryService.getPrevious(ctx, history, latestVersion);
if (previousVersion == null) {
return;
}
// get latest item
Item latestItem = latestVersion.getItem();
if (latestItem == null) {
String msg = String.format(
"Illegal state: Obtained version history of item with uuid %s, handle %s, but the latest item is null",
item.getID(), item.getHandle()
);
log.error(msg);
throw new IllegalStateException(msg);
}
// get previous item
Item previousItem = previousVersion.getItem();
if (previousItem == null) {
return;
}
// unarchive previous item
unarchiveItem(ctx, previousItem);
// update relationships
updateRelationships(ctx, latestItem, previousItem);
}
protected void unarchiveItem(Context ctx, Item item) {
item.setArchived(false);
itemsToProcess.add(item);
//Fire a new modify event for our previous item
//Due to the need to reindex the item in the search
//and browse index we need to fire a new event
ctx.addEvent(new Event(Event.MODIFY,
previousItem.getType(), previousItem.getID(),
null, itemService.getIdentifiers(ctx, previousItem)));
ctx.addEvent(new Event(
Event.MODIFY, item.getType(), item.getID(), null, itemService.getIdentifiers(ctx, item)
));
}
/**
* Update {@link Relationship#latestVersionStatus} of the relationships of both the old version and the new version
* of the item.
*
* This method will first locate all relationships that are eligible for an update,
* then it will try to match each of those relationships on the old version of given item
* with a relationship on the new version.
*
* One of the following scenarios will happen:
* - if a match is found, then the "latest" status on the side of given item is transferred from
* the old relationship to the new relationship. This implies that on the page of the third-party item,
* the old version of given item will NOT be shown anymore and the new version of given item will appear.
* Both versions of the given item still show the third-party item on their pages.
* - if a relationship only exists on the new version of given item, then this method does nothing.
* The status of those relationships should already have been set to "latest" on both sides during relationship
* creation.
* - if a relationship only exists on the old version of given item, then we assume that the relationship is no
* longer relevant to / has been removed from the new version of the item. The "latest" status is removed from
* the side of the given item. This implies that on the page of the third-party item,
* the relationship with given item will no longer be listed. The old version of given item still lists
* the third-party item and the new version doesn't.
* @param ctx the DSpace context.
* @param latestItem the new version of the item.
* @param previousItem the old version of the item.
*/
protected void updateRelationships(Context ctx, Item latestItem, Item previousItem) {
// check that the entity types of both items match
if (!doEntityTypesMatch(latestItem, previousItem)) {
return;
}
// get the entity type (same for both items)
EntityType entityType = getEntityType(ctx, latestItem);
if (entityType == null) {
return;
}
// get all relationship types that are linked to the given entity type
List<RelationshipType> relationshipTypes = getRelationshipTypes(ctx, entityType);
if (CollectionUtils.isEmpty(relationshipTypes)) {
return;
}
for (RelationshipType relationshipType : relationshipTypes) {
List<Relationship> latestItemRelationships = getAllRelationships(ctx, latestItem, relationshipType);
if (latestItemRelationships == null) {
continue;
}
List<Relationship> previousItemRelationships = getAllRelationships(ctx, previousItem, relationshipType);
if (previousItemRelationships == null) {
continue;
}
// NOTE: no need to loop through latestItemRelationships, because if no match can be found
// (meaning a relationship is only present on the new version of the item), then it's
// a newly added relationship and its status should have been set to BOTH during creation.
for (Relationship previousItemRelationship : previousItemRelationships) {
// determine on which side of the relationship the latest and previous item should be
boolean isLeft = previousItem.equals(previousItemRelationship.getLeftItem());
boolean isRight = previousItem.equals(previousItemRelationship.getRightItem());
if (isLeft == isRight) {
Item leftItem = previousItemRelationship.getLeftItem();
Item rightItem = previousItemRelationship.getRightItem();
String msg = String.format(
"Illegal state: could not determine side of item with uuid %s, handle %s in " +
"relationship with id %s, rightward name %s between " +
"left item with uuid %s, handle %s and right item with uuid %s, handle %s",
previousItem.getID(), previousItem.getHandle(), previousItemRelationship.getID(),
previousItemRelationship.getRelationshipType().getRightwardType(),
leftItem.getID(), leftItem.getHandle(), rightItem.getID(), rightItem.getHandle()
);
log.error(msg);
throw new IllegalStateException(msg);
}
// get the matching relationship on the latest item
Relationship latestItemRelationship =
getMatchingRelationship(latestItem, isLeft, previousItemRelationship, latestItemRelationships);
// the other side of the relationship should be "latest", otherwise the relationship could not have been
// copied to the new item in the first place (by DefaultVersionProvider#copyRelationships)
if (relationshipVersioningUtils.otherSideIsLatest(
isLeft, previousItemRelationship.getLatestVersionStatus()
)) {
// Set the previous version of the item to non-latest. This implies that the previous version
// of the item will not be shown anymore on the page of the third-party item. That makes sense,
// because either the relationship has been deleted from the new version of the item (no match),
// or the matching relationship (linked to new version) will receive "latest" status in
// the next step.
LatestVersionStatusChangelog changelog =
relationshipVersioningUtils.updateLatestVersionStatus(previousItemRelationship, isLeft, false);
reindexRelationship(ctx, changelog, previousItemRelationship);
}
if (latestItemRelationship != null) {
// Set the new version of the item to latest if the relevant relationship exists (match found).
// This implies that the new version of the item will appear on the page of the third-party item.
// The old version of the item will not appear anymore on the page of the third-party item,
// see previous step.
LatestVersionStatusChangelog changelog =
relationshipVersioningUtils.updateLatestVersionStatus(latestItemRelationship, isLeft, true);
reindexRelationship(ctx, changelog, latestItemRelationship);
}
}
}
}
/**
* If the {@link Relationship#latestVersionStatus} of the relationship has changed,
* an "item modified" event should be fired for both the left and right item of the relationship.
* On one item the relation.* fields will change. On the other item the relation.*.latestForDiscovery will change.
* The event will cause the items to be re-indexed by the {@link IndexEventConsumer}.
* @param ctx the DSpace context.
* @param changelog indicates which side of the relationship has changed.
* @param relationship the relationship.
*/
protected void reindexRelationship(
Context ctx, LatestVersionStatusChangelog changelog, Relationship relationship
) {
if (changelog == NO_CHANGES) {
return;
}
// on one item, relation.* fields will change
// on the other item, relation.*.latestForDiscovery will change
// reindex left item
Item leftItem = relationship.getLeftItem();
itemsToProcess.add(leftItem);
ctx.addEvent(new Event(
Event.MODIFY, leftItem.getType(), leftItem.getID(), null, itemService.getIdentifiers(ctx, leftItem)
));
// reindex right item
Item rightItem = relationship.getRightItem();
itemsToProcess.add(rightItem);
ctx.addEvent(new Event(
Event.MODIFY, rightItem.getType(), rightItem.getID(), null, itemService.getIdentifiers(ctx, rightItem)
));
}
/**
* Given two items, check if their entity types match.
* If one or both items don't have an entity type, comparing is pointless and this method will return false.
* @param latestItem the item that represents the most recent version.
* @param previousItem the item that represents the second-most recent version.
* @return true if the entity types of both items are non-null and equal, false otherwise.
*/
protected boolean doEntityTypesMatch(Item latestItem, Item previousItem) {
String latestItemEntityType = itemService.getEntityTypeLabel(latestItem);
String previousItemEntityType = itemService.getEntityTypeLabel(previousItem);
// check if both items have an entity type
if (latestItemEntityType == null || previousItemEntityType == null) {
if (previousItemEntityType != null) {
log.warn(
"Inconsistency: Item with uuid {}, handle {} has NO entity type, " +
"but the previous version of that item with uuid {}, handle {} has entity type {}",
latestItem.getID(), latestItem.getHandle(),
previousItem.getID(), previousItem.getHandle(), previousItemEntityType
);
}
// one or both items do not have an entity type, so comparing is pointless
return false;
}
// check if the entity types are equal
if (!StringUtils.equals(latestItemEntityType, previousItemEntityType)) {
log.warn(
"Inconsistency: Item with uuid {}, handle {} has entity type {}, " +
"but the previous version of that item with uuid {}, handle {} has entity type {}",
latestItem.getID(), latestItem.getHandle(), latestItemEntityType,
previousItem.getID(), previousItem.getHandle(), previousItemEntityType
);
return false;
}
// success - the entity types of both items are non-null and equal
log.info(
"Item with uuid {}, handle {} and the previous version of that item with uuid {}, handle {} " +
"have the same entity type: {}",
latestItem.getID(), latestItem.getHandle(), previousItem.getID(), previousItem.getHandle(),
latestItemEntityType
);
return true;
}
/**
* Get the entity type (stored in metadata field dspace.entity.type) of any item.
* @param item the item.
* @return the entity type.
*/
protected EntityType getEntityType(Context ctx, Item item) {
try {
return itemService.getEntityType(ctx, item);
} catch (SQLException e) {
log.error(
"Exception occurred when trying to obtain entity type with label {} of item with uuid {}, handle {}",
itemService.getEntityTypeLabel(item), item.getID(), item.getHandle(), e
);
return null;
}
}
/**
* Get all relationship types that have the given entity type on their left and/or right side.
* @param ctx the DSpace context.
* @param entityType the entity type for which all relationship types should be found.
* @return a list of relationship types (possibly empty), or null in case of error.
*/
protected List<RelationshipType> getRelationshipTypes(Context ctx, EntityType entityType) {
try {
return relationshipTypeService.findByEntityType(ctx, entityType);
} catch (SQLException e) {
log.error(
"Exception occurred when trying to obtain relationship types via entity type with id {}, label {}",
entityType.getID(), entityType.getLabel(), e
);
return null;
}
}
/**
* Get all relationships of the given type linked to the given item.
* @param ctx the DSpace context.
* @param item the item.
* @param relationshipType the relationship type.
* @return a list of relationships (possibly empty), or null in case of error.
*/
protected List<Relationship> getAllRelationships(Context ctx, Item item, RelationshipType relationshipType) {
try {
return relationshipService.findByItemAndRelationshipType(ctx, item, relationshipType, -1, -1, false);
} catch (SQLException e) {
log.error(
"Exception occurred when trying to obtain relationships of type with id {}, rightward name {} " +
"for item with uuid {}, handle {}",
relationshipType.getID(), relationshipType.getRightwardType(), item.getID(), item.getHandle(), e
);
return null;
}
}
/**
* From a list of relationships, find the relationship with the correct relationship type and items.
* If isLeft is true, the provided item should be on the left side of the relationship.
* If isLeft is false, the provided item should be on the right side of the relationship.
* In both cases, the other item is taken from the given relationship.
* @param latestItem the item that should either be on the left or right side of the returned relationship (if any).
* @param isLeft decide on which side of the relationship the provided item should be.
* @param previousItemRelationship the relationship from which the type and the other item are read.
* @param relationships the list of relationships that we'll search through.
* @return the relationship that satisfies the requirements (can only be one or zero).
*/
protected Relationship getMatchingRelationship(
Item latestItem, boolean isLeft, Relationship previousItemRelationship, List<Relationship> relationships
) {
Item leftItem = previousItemRelationship.getLeftItem();
RelationshipType relationshipType = previousItemRelationship.getRelationshipType();
Item rightItem = previousItemRelationship.getRightItem();
if (isLeft) {
return getMatchingRelationship(latestItem, relationshipType, rightItem, relationships);
} else {
return getMatchingRelationship(leftItem, relationshipType, latestItem, relationships);
}
}
/**
* Find the relationship with the given left item, relation type and right item, from a list of relationships.
* @param expectedLeftItem the relationship that we're looking for has this item on the left side.
* @param expectedRelationshipType the relationship that we're looking for has this relationship type.
* @param expectedRightItem the relationship that we're looking for has this item on the right side.
* @param relationships the list of relationships that we'll search through.
* @return the relationship that satisfies the requirements (can only be one or zero).
*/
protected Relationship getMatchingRelationship(
Item expectedLeftItem, RelationshipType expectedRelationshipType, Item expectedRightItem,
List<Relationship> relationships
) {
Integer expectedRelationshipTypeId = expectedRelationshipType.getID();
List<Relationship> matchingRelationships = relationships.stream()
.filter(relationship -> {
int relationshipTypeId = relationship.getRelationshipType().getID();
boolean leftItemMatches = expectedLeftItem.equals(relationship.getLeftItem());
boolean relationshipTypeMatches = expectedRelationshipTypeId == relationshipTypeId;
boolean rightItemMatches = expectedRightItem.equals(relationship.getRightItem());
return leftItemMatches && relationshipTypeMatches && rightItemMatches;
})
.distinct()
.collect(Collectors.toUnmodifiableList());
if (matchingRelationships.isEmpty()) {
return null;
}
// NOTE: this situation should never occur because the relationship table has a unique constraint
// over the "left_id", "type_id" and "right_id" columns
if (matchingRelationships.size() > 1) {
String msg = String.format(
"Illegal state: expected 0 or 1 relationship, but found %s relationships (ids: %s) " +
"of type with id %s, rightward name %s " +
"between left item with uuid %s, handle %s and right item with uuid %s, handle %s",
matchingRelationships.size(),
matchingRelationships.stream().map(Relationship::getID).collect(Collectors.toUnmodifiableList()),
expectedRelationshipTypeId, expectedRelationshipType.getRightwardType(),
expectedLeftItem.getID(), expectedLeftItem.getHandle(),
expectedRightItem.getID(), expectedRightItem.getHandle()
);
log.error(msg);
throw new IllegalStateException(msg);
}
return matchingRelationships.get(0);
}
@Override

View File

@@ -10,6 +10,7 @@ package org.dspace.versioning.factory;
import org.dspace.services.factory.DSpaceServicesFactory;
import org.dspace.versioning.service.VersionHistoryService;
import org.dspace.versioning.service.VersioningService;
import org.dspace.versioning.utils.RelationshipVersioningUtils;
/**
* Abstract factory to get services for the versioning package, use VersionServiceFactory.getInstance() to retrieve
@@ -23,6 +24,8 @@ public abstract class VersionServiceFactory {
public abstract VersioningService getVersionService();
public abstract RelationshipVersioningUtils getRelationshipVersioningUtils();
public static VersionServiceFactory getInstance() {
return DSpaceServicesFactory.getInstance().getServiceManager()
.getServiceByName("versionServiceFactory", VersionServiceFactory.class);

View File

@@ -9,6 +9,7 @@ package org.dspace.versioning.factory;
import org.dspace.versioning.service.VersionHistoryService;
import org.dspace.versioning.service.VersioningService;
import org.dspace.versioning.utils.RelationshipVersioningUtils;
import org.springframework.beans.factory.annotation.Autowired;
/**
@@ -25,6 +26,9 @@ public class VersionServiceFactoryImpl extends VersionServiceFactory {
@Autowired(required = true)
protected VersioningService versionService;
@Autowired(required = true)
protected RelationshipVersioningUtils relationshipVersioningUtils;
@Override
public VersionHistoryService getVersionHistoryService() {
return versionHistoryService;
@@ -34,4 +38,10 @@ public class VersionServiceFactoryImpl extends VersionServiceFactory {
public VersioningService getVersionService() {
return versionService;
}
@Override
public RelationshipVersioningUtils getRelationshipVersioningUtils() {
return relationshipVersioningUtils;
}
}

View File

@@ -0,0 +1,114 @@
/**
* 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.versioning.utils;
import static org.dspace.versioning.utils.RelationshipVersioningUtils.LatestVersionStatusChangelog.LEFT_SIDE_CHANGED;
import static org.dspace.versioning.utils.RelationshipVersioningUtils.LatestVersionStatusChangelog.NO_CHANGES;
import static org.dspace.versioning.utils.RelationshipVersioningUtils.LatestVersionStatusChangelog.RIGHT_SIDE_CHANGED;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.content.Relationship;
import org.dspace.content.Relationship.LatestVersionStatus;
/**
* Class with utility methods to manipulate relationships that are linked to versioned items.
* Specifically focussed on the "latest version status" of relationships,
* which controls which related items are relevant (visible) to any given item.
*/
public class RelationshipVersioningUtils {
private static final Logger log = LogManager.getLogger(RelationshipVersioningUtils.class);
/**
* Given a latest version status, check if the other side is "latest".
* If we look from the left, this implies BOTH and RIGHT_ONLY return true.
* If we look from the right, this implies BOTH and LEFT_ONLY return true.
* @param isLeft whether we should look from the left or right side.
* @param latestVersionStatus the latest version status.
* @return true if the other side has "latest" status, false otherwise.
*/
public boolean otherSideIsLatest(boolean isLeft, LatestVersionStatus latestVersionStatus) {
if (latestVersionStatus == LatestVersionStatus.BOTH) {
return true;
}
return latestVersionStatus == (isLeft ? LatestVersionStatus.RIGHT_ONLY : LatestVersionStatus.LEFT_ONLY);
}
public enum LatestVersionStatusChangelog {
NO_CHANGES,
LEFT_SIDE_CHANGED,
RIGHT_SIDE_CHANGED
}
/**
* Update {@link Relationship#latestVersionStatus} of the given relationship.
* If isLatest = true, this method will never throw IllegalStateException.
* If isLatest = false, you should make sure that the selected side of given relationship
* currently has "latest" status, otherwise IllegalStateException will be thrown.
* @param relationship the relationship.
* @param updateLeftSide whether the status of the left item or the right item should be updated.
* @param isLatest to what the status should be set.
* @throws IllegalStateException if the operation would result in both the left side and the right side
* being set to non-latest.
*/
public LatestVersionStatusChangelog updateLatestVersionStatus(
Relationship relationship, boolean updateLeftSide, boolean isLatest
) throws IllegalStateException {
LatestVersionStatus lvs = relationship.getLatestVersionStatus();
boolean leftSideIsLatest = lvs == LatestVersionStatus.BOTH || lvs == LatestVersionStatus.LEFT_ONLY;
boolean rightSideIsLatest = lvs == LatestVersionStatus.BOTH || lvs == LatestVersionStatus.RIGHT_ONLY;
if (updateLeftSide) {
if (leftSideIsLatest == isLatest) {
return NO_CHANGES; // no change needed
}
leftSideIsLatest = isLatest;
} else {
if (rightSideIsLatest == isLatest) {
return NO_CHANGES; // no change needed
}
rightSideIsLatest = isLatest;
}
LatestVersionStatus newVersionStatus;
if (leftSideIsLatest && rightSideIsLatest) {
newVersionStatus = LatestVersionStatus.BOTH;
} else if (leftSideIsLatest) {
newVersionStatus = LatestVersionStatus.LEFT_ONLY;
} else if (rightSideIsLatest) {
newVersionStatus = LatestVersionStatus.RIGHT_ONLY;
} else {
String msg = String.format(
"Illegal state: cannot set %s item to latest = false, because relationship with id %s, " +
"rightward name %s between left item with uuid %s, handle %s and right item with uuid %s, handle %s " +
"has latest version status set to %s",
updateLeftSide ? "left" : "right", relationship.getID(),
relationship.getRelationshipType().getRightwardType(),
relationship.getLeftItem().getID(), relationship.getLeftItem().getHandle(),
relationship.getRightItem().getID(), relationship.getRightItem().getHandle(), lvs
);
log.error(msg);
throw new IllegalStateException(msg);
}
log.info(
"set latest version status from {} to {} for relationship with id {}, rightward name {} " +
"between left item with uuid {}, handle {} and right item with uuid {}, handle {}",
lvs, newVersionStatus, relationship.getID(), relationship.getRelationshipType().getRightwardType(),
relationship.getLeftItem().getID(), relationship.getLeftItem().getHandle(),
relationship.getRightItem().getID(), relationship.getRightItem().getHandle()
);
relationship.setLatestVersionStatus(newVersionStatus);
return updateLeftSide ? LEFT_SIDE_CHANGED : RIGHT_SIDE_CHANGED;
}
}

View File

@@ -0,0 +1,10 @@
--
-- 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/
--
-- NOTE: default 0 ensures that existing relations have "latest_version_status" set to "both" (first constant in enum, see Relationship class)
ALTER TABLE relationship ADD COLUMN IF NOT EXISTS latest_version_status INTEGER DEFAULT 0 NOT NULL;

View File

@@ -0,0 +1,18 @@
--
-- 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/
--
-------------------------------------------------------------------------------
-- Table to store Groups related to a Process on its creation
-------------------------------------------------------------------------------
CREATE TABLE Process2Group
(
process_id INTEGER REFERENCES Process(process_id),
group_id UUID REFERENCES epersongroup (uuid) ON DELETE CASCADE,
CONSTRAINT PK_Process2Group PRIMARY KEY (process_id, group_id)
);

View File

@@ -0,0 +1,10 @@
--
-- 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/
--
-- NOTE: default 0 ensures that existing relations have "latest_version_status" set to "both" (first constant in enum, see Relationship class)
ALTER TABLE relationship ADD latest_version_status INTEGER DEFAULT 0 NOT NULL;

View File

@@ -0,0 +1,18 @@
--
-- 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/
--
-------------------------------------------------------------------------------
-- Table to store Groups related to a Process on its creation
-------------------------------------------------------------------------------
CREATE TABLE Process2Group
(
process_id INTEGER REFERENCES Process(process_id),
group_id UUID REFERENCES epersongroup (uuid) ON DELETE CASCADE,
CONSTRAINT PK_Process2Group PRIMARY KEY (process_id, group_id)
);

View File

@@ -0,0 +1,10 @@
--
-- 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/
--
-- NOTE: default 0 ensures that existing relations have "latest_version_status" set to "both" (first constant in enum, see Relationship class)
ALTER TABLE relationship ADD COLUMN IF NOT EXISTS latest_version_status INTEGER DEFAULT 0 NOT NULL;

View File

@@ -0,0 +1,18 @@
--
-- 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/
--
-------------------------------------------------------------------------------
-- Table to store Groups related to a Process on its creation
-------------------------------------------------------------------------------
CREATE TABLE Process2Group
(
process_id INTEGER REFERENCES Process(process_id),
group_id UUID REFERENCES epersongroup (uuid) ON DELETE CASCADE,
CONSTRAINT PK_Process2Group PRIMARY KEY (process_id, group_id)
);

View File

@@ -43,11 +43,11 @@
class="org.dspace.importer.external.arxiv.metadatamapping.ArXivFieldMapping">
</bean>
<bean id="pubmedImportService"
class="org.dspace.importer.external.pubmed.service.PubmedImportMetadataSourceServiceImpl">
<property name="metadataFieldMapping" ref="pubmedMetadataFieldMapping"/>
<property name="baseAddress" value="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/"/>
<property name="urlFetch" value="${pubmed.url.fetch}"/>
<property name="urlSearch" value="${pubmed.url.search}"/>
<property name="generateQueryForItem" ref="pubmedService"></property>
<property name="supportedExtensions">
<list>
@@ -56,7 +56,6 @@
</property>
</bean>
<bean id="pubmedMetadataFieldMapping"
class="org.dspace.importer.external.pubmed.metadatamapping.PubmedFieldMapping">
</bean>
@@ -120,6 +119,7 @@
<property name="url" value="${crossref.url}"/>
</bean>
<bean id="CrossRefMetadataFieldMapping" class="org.dspace.importer.external.crossref.CrossRefFieldMapping"/>
<bean id="EpoImportService" class="org.dspace.importer.external.epo.service.EpoImportMetadataSourceServiceImpl" scope="singleton">
<property name="metadataFieldMapping" ref="epoMetadataFieldMapping"/>
<property name="consumerKey" value="${epo.consumerKey}" />
@@ -133,6 +133,15 @@
</bean>
<bean id="epoMetadataFieldMapping" class="org.dspace.importer.external.epo.service.EpoFieldMapping"/>
<bean id="ScopusImportService" class="org.dspace.importer.external.scopus.service.ScopusImportMetadataSourceServiceImpl" scope="singleton">
<property name="metadataFieldMapping" ref="scopusMetadataFieldMapping"/>
<property name="url" value="${scopus.url}"/>
<property name="apiKey" value="${scopus.apiKey}"/>
<property name="instKey" value="${scopus.instToken}"/>
<property name="viewMode" value="${scopus.search-api.viewMode}"/>
</bean>
<bean id="scopusMetadataFieldMapping" class="org.dspace.importer.external.scopus.service.ScopusFieldMapping"/>
<bean id="vufindImportService" class="org.dspace.importer.external.vufind.VuFindImportMetadataSourceServiceImpl" scope="singleton">
<!-- Set to empty to use the default set of fields -->
<constructor-arg type="java.lang.String" value=""/>
@@ -148,6 +157,27 @@
</bean>
<bean id="scieloMetadataFieldMapping" class="org.dspace.importer.external.scielo.service.ScieloFieldMapping"/>
<bean id="WosImportService" class="org.dspace.importer.external.wos.service.WOSImportMetadataSourceServiceImpl" scope="singleton">
<property name="metadataFieldMapping" ref="wosMetadataFieldMapping"/>
<property name="apiKey" value="${wos.apiKey}"/>
<property name="url" value="${wos.url}"/>
<property name="urlSearch" value="${wos.url.search}"/>
</bean>
<bean id="wosMetadataFieldMapping" class="org.dspace.importer.external.wos.service.WOSFieldMapping"/>
<bean id="PubmedEuropeImportService" class="org.dspace.importer.external.pubmedeurope.PubmedEuropeMetadataSourceServiceImpl" scope="singleton">
<property name="metadataFieldMapping" ref="PubmedEuropeMetadataFieldMapping"/>
<property name="url" value="${pubmedeurope.url}"/>
</bean>
<bean id="PubmedEuropeMetadataFieldMapping" class="org.dspace.importer.external.pubmedeurope.PubmedEuropeFieldMapping"/>
<bean id="CiniiImportService" class="org.dspace.importer.external.cinii.CiniiImportMetadataSourceServiceImpl" scope="singleton">
<property name="metadataFieldMapping" ref="CiniiMetadataFieldMapping"/>
<property name="url" value="${cinii.url}"/>
<property name="urlSearch" value="${cinii.url.search}"/>
</bean>
<bean id="CiniiMetadataFieldMapping" class="org.dspace.importer.external.cinii.CiniiFieldMapping"/>
<bean id="ADSImportService" class="org.dspace.importer.external.ads.ADSImportMetadataSourceServiceImpl" scope="singleton">
<property name="apiKey" value="${ads.key}" />
<property name="url" value="${ads.url}" />

View File

@@ -145,6 +145,8 @@ useProxies = true
proxies.trusted.ipranges = 7.7.7.7
proxies.trusted.include_ui_ip = true
csvexport.dir = dspace-server-webapp/src/test/data/dspaceFolder/exports
# For the tests we have to disable this health indicator because there isn't a mock server and the calculated status was DOWN
management.health.solrOai.enabled = false

View File

@@ -59,22 +59,26 @@
</bean>
<bean id="pubmedLiveImportDataProvider" class="org.dspace.external.provider.impl.LiveImportDataProvider">
<property name="metadataSource" ref="mockPubmedImportService"/>
<property name="metadataSource" ref="pubmedImportService"/>
<property name="sourceIdentifier" value="pubmed"/>
<property name="recordIdMetadata" value="dc.identifier.other"/>
<property name="supportedEntityTypes">
<list>
<value>Publication</value>
<value>none</value>
</list>
</property>
</bean>
<bean id="mockPubmedImportService"
class="org.dspace.external.provider.impl.MockPubmedImportMetadataSourceServiceImpl">
<property name="metadataFieldMapping" ref="pubmedMetadataFieldMapping"/>
<property name="baseAddress" value="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/"/>
<property name="supportedExtensions">
<bean id="scopusLiveImportDataProvider" class="org.dspace.external.provider.impl.LiveImportDataProvider">
<property name="metadataSource" ref="ScopusImportService"/>
<property name="sourceIdentifier" value="scopus"/>
<property name="recordIdMetadata" value="dc.identifier.scopus"/>
<property name="supportedEntityTypes">
<list>
<value>xml</value>
<value>Publication</value>
</list>
</property>
</bean>
</beans>

View File

@@ -22,6 +22,11 @@
<property name="dspaceRunnableClass" value="org.dspace.app.bulkedit.MetadataExportCli"/>
</bean>
<bean id="metadata-export-search" class="org.dspace.app.bulkedit.MetadataExportSearchCliScriptConfiguration">
<property name="description" value="export metadata from a discovery search" />
<property name="dspaceRunnableClass" value="org.dspace.app.bulkedit.MetadataExportSearchCli" />
</bean>
<bean id="curate"
class="org.dspace.curate.CurationCliScriptConfiguration">
<property name="description"
@@ -45,6 +50,11 @@
<property name="dspaceRunnableClass" value="org.dspace.app.mediafilter.MediaFilterScript"/>
</bean>
<bean id="solr-database-resync" class="org.dspace.app.solrdatabaseresync.SolrDatabaseResyncCliScriptConfiguration">
<property name="description" value="Update the database status of Items in solr"/>
<property name="dspaceRunnableClass" value="org.dspace.app.solrdatabaseresync.SolrDatabaseResyncCli"/>
</bean>
<bean id="another-mock-script" class="org.dspace.scripts.MockDSpaceRunnableScriptConfiguration" scope="prototype">
<property name="description" value="Mocking a script for testing purposes" />
<property name="dspaceRunnableClass" value="org.dspace.scripts.impl.MockDSpaceRunnableScript"/>

View File

@@ -0,0 +1,253 @@
/**
* 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.app.bulkedit;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;
import java.io.File;
import java.io.IOException;
import java.io.Reader;
import java.nio.charset.Charset;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import com.google.common.io.Files;
import com.opencsv.CSVReader;
import com.opencsv.exceptions.CsvException;
import org.apache.log4j.Logger;
import org.dspace.AbstractIntegrationTestWithDatabase;
import org.dspace.app.launcher.ScriptLauncher;
import org.dspace.app.scripts.handler.impl.TestDSpaceRunnableHandler;
import org.dspace.builder.CollectionBuilder;
import org.dspace.builder.CommunityBuilder;
import org.dspace.builder.ItemBuilder;
import org.dspace.content.Collection;
import org.dspace.content.Community;
import org.dspace.content.Item;
import org.dspace.discovery.DiscoverQuery;
import org.dspace.discovery.SearchService;
import org.dspace.discovery.SearchUtils;
import org.dspace.services.ConfigurationService;
import org.dspace.services.factory.DSpaceServicesFactory;
import org.junit.Before;
import org.junit.Ignore;
import org.junit.Test;
@Ignore
public class MetadataExportSearchIT extends AbstractIntegrationTestWithDatabase {
private String subject1 = "subject1";
private String subject2 = "subject2";
private int numberItemsSubject1 = 30;
private int numberItemsSubject2 = 2;
private Item[] itemsSubject1 = new Item[numberItemsSubject1];
private Item[] itemsSubject2 = new Item[numberItemsSubject2];
private String filename;
private Collection collection;
private Logger logger = Logger.getLogger(MetadataExportSearchIT.class);
private ConfigurationService configurationService = DSpaceServicesFactory.getInstance().getConfigurationService();
private SearchService searchService = SearchUtils.getSearchService();
@Override
@Before
public void setUp() throws Exception {
super.setUp();
// dummy search so that the SearchService gets called in a test context first
DiscoverQuery query = new DiscoverQuery();
query.setMaxResults(0);
searchService.search(context, query);
context.turnOffAuthorisationSystem();
Community community = CommunityBuilder.createCommunity(context).build();
collection = CollectionBuilder.createCollection(context, community).build();
filename = configurationService.getProperty("dspace.dir")
+ testProps.get("test.exportcsv").toString();
for (int i = 0; i < numberItemsSubject1; i++) {
itemsSubject1[i] = ItemBuilder.createItem(context, collection)
.withTitle(String.format("%s item %d", subject1, i))
.withSubject(subject1)
.withIssueDate("2020-09-" + i)
.build();
}
for (int i = 0; i < numberItemsSubject2; i++) {
itemsSubject2[i] = ItemBuilder.createItem(context, collection)
.withTitle(String.format("%s item %d", subject2, i))
.withSubject(subject2)
.withIssueDate("2021-09-" + i)
.build();
}
context.restoreAuthSystemState();
}
private void checkItemsPresentInFile(String filename, Item[] items) throws IOException, CsvException {
File file = new File(filename);
Reader reader = Files.newReader(file, Charset.defaultCharset());
CSVReader csvReader = new CSVReader(reader);
List<String[]> lines = csvReader.readAll();
//length + 1 is because of 1 row extra for the headers
assertEquals(items.length + 1, lines.size());
List<String> ids = new ArrayList<>();
//ignoring the first row as this only contains headers;
logger.debug("checking content of lines");
for (int i = 1; i < lines.size(); i++) {
logger.debug(String.join(", ", lines.get(i)));
ids.add(lines.get(i)[0]);
}
for (Item item : items) {
assertTrue(ids.contains(item.getID().toString()));
}
}
@Test
public void metadateExportSearchQueryTest() throws Exception {
int result = runDSpaceScript("metadata-export-search", "-q", "subject:" + subject1, "-n", filename);
assertEquals(0, result);
checkItemsPresentInFile(filename, itemsSubject1);
result = runDSpaceScript("metadata-export-search", "-q", "subject: " + subject2, "-n", filename);
assertEquals(0, result);
checkItemsPresentInFile(filename, itemsSubject2);
}
@Test
public void exportMetadataSearchSpecificContainerTest() throws Exception {
context.turnOffAuthorisationSystem();
Community community2 = CommunityBuilder.createCommunity(context).build();
Collection collection2 = CollectionBuilder.createCollection(context, community2).build();
int numberItemsDifferentCollection = 15;
Item[] itemsDifferentCollection = new Item[numberItemsDifferentCollection];
for (int i = 0; i < numberItemsDifferentCollection; i++) {
itemsDifferentCollection[i] = ItemBuilder.createItem(context, collection2)
.withTitle("item different collection " + i)
.withSubject(subject1)
.build();
}
//creating some items with a different subject to make sure the query still works
for (int i = 0; i < 5; i++) {
ItemBuilder.createItem(context, collection2)
.withTitle("item different collection, different subject " + i)
.withSubject(subject2)
.build();
}
context.restoreAuthSystemState();
int result = runDSpaceScript(
"metadata-export-search", "-q", "subject: " + subject1, "-s", collection2.getID().toString(), "-n", filename
);
assertEquals(0, result);
checkItemsPresentInFile(filename, itemsDifferentCollection);
}
@Test
public void exportMetadataSearchFilter() throws Exception {
int result = runDSpaceScript("metadata-export-search", "-f", "subject,equals=" + subject1, "-n", filename);
assertEquals(0, result);
checkItemsPresentInFile(filename, itemsSubject1);
}
@Test
public void exportMetadataSearchFilterDate() throws Exception {
int result = runDSpaceScript(
"metadata-export-search", "-f", "dateIssued,equals=[2000 TO 2020]", "-n", filename
);
assertEquals(0, result);
checkItemsPresentInFile(filename, itemsSubject1);
}
@Test
public void exportMetadataSearchMultipleFilters() throws Exception {
int result = runDSpaceScript(
"metadata-export-search", "-f", "subject,equals=" + subject1, "-f",
"title,equals=" + String.format("%s item %d", subject1, 0), "-n", filename
);
assertEquals(0, result);
Item[] expectedResult = Arrays.copyOfRange(itemsSubject1, 0, 1);
checkItemsPresentInFile(filename, expectedResult);
}
@Test
public void exportMetadataSearchEqualsFilterTest()
throws Exception {
context.turnOffAuthorisationSystem();
Item wellBeingItem = ItemBuilder.createItem(context, collection)
.withTitle("test item well-being")
.withSubject("well-being")
.build();
ItemBuilder.createItem(context, collection)
.withTitle("test item financial well-being")
.withSubject("financial well-being")
.build();
context.restoreAuthSystemState();
int result = runDSpaceScript("metadata-export-search", "-f", "subject,equals=well-being", "-n", filename);
assertEquals(0, result);
Item[] expectedResult = new Item[] {wellBeingItem};
checkItemsPresentInFile(filename, expectedResult);
}
@Test
public void exportMetadataSearchInvalidDiscoveryQueryTest() throws Exception {
int result = runDSpaceScript("metadata-export-search", "-q", "blabla", "-n", filename);
assertEquals(0, result);
Item[] items = {};
checkItemsPresentInFile(filename, items);
}
@Test
public void exportMetadataSearchNoResultsTest() throws Exception {
int result = runDSpaceScript(
"metadata-export-search", "-f", "subject,equals=notExistingSubject", "-n", filename
);
assertEquals(0, result);
Item[] items = {};
checkItemsPresentInFile(filename, items);
}
@Test
public void exportMetadataSearchNonExistinFacetsTest() throws Exception {
TestDSpaceRunnableHandler testDSpaceRunnableHandler = new TestDSpaceRunnableHandler();
String[] args = new String[] {"metadata-export-search", "-f", "nonExisting,equals=" + subject1, "-f",
"title,equals=" + String.format("%s item %d", subject1, 0), "-n", filename};
int result = ScriptLauncher.handleScript(
args, ScriptLauncher.getConfig(kernelImpl), testDSpaceRunnableHandler, kernelImpl
);
assertEquals(0, result); // exception should be handled, so the script should finish with 0
Exception exception = testDSpaceRunnableHandler.getException();
assertNotNull(exception);
assertEquals("nonExisting is not a valid search filter", exception.getMessage());
}
}

View File

@@ -19,6 +19,7 @@ import java.util.List;
import org.apache.commons.cli.ParseException;
import org.apache.commons.collections4.IteratorUtils;
import org.apache.commons.lang3.ArrayUtils;
import org.apache.commons.lang3.StringUtils;
import org.dspace.AbstractIntegrationTestWithDatabase;
import org.dspace.app.launcher.ScriptLauncher;
@@ -93,10 +94,10 @@ public class MetadataImportIT extends AbstractIntegrationTestWithDatabase {
}
@Test
public void metadataImportIntoCollectionWithEntityTypeTest() throws Exception {
public void metadataImportIntoCollectionWithEntityTypeWithTemplateEnabledTest() throws Exception {
String[] csv = {"id,collection,dc.title,dc.contributor.author",
"+," + publicationCollection.getHandle() + ",\"Test Import 1\"," + "\"Donald, SmithImported\""};
performImportScript(csv);
performImportScript(csv, true);
Item importedItem = findItemByName("Test Import 1");
assertTrue(StringUtils.equals(itemService.getMetadata(importedItem, "dc", "contributor", "author", Item.ANY)
.get(0).getValue(), "Donald, SmithImported"));
@@ -110,6 +111,24 @@ public class MetadataImportIT extends AbstractIntegrationTestWithDatabase {
context.restoreAuthSystemState();
}
@Test
public void metadataImportIntoCollectionWithEntityTypeWithTemplateDisabledTest() throws Exception {
String[] csv = {"id,collection,dc.title,dc.contributor.author",
"+," + publicationCollection.getHandle() + ",\"Test Import 1\"," + "\"Donald, SmithImported\""};
performImportScript(csv, false);
Item importedItem = findItemByName("Test Import 1");
assertTrue(StringUtils.equals(itemService.getMetadata(importedItem, "dc", "contributor", "author", Item.ANY)
.get(0).getValue(), "Donald, SmithImported"));
assertEquals(0, itemService.getMetadata(importedItem, "dspace", "entity", "type", Item.ANY)
.size());
eperson = ePersonService.findByEmail(context, eperson.getEmail());
assertEquals(importedItem.getSubmitter(), eperson);
context.turnOffAuthorisationSystem();
itemService.delete(context, itemService.find(context, importedItem.getID()));
context.restoreAuthSystemState();
}
@Test(expected = ParseException.class)
public void metadataImportWithoutEPersonParameterTest()
throws IllegalAccessException, InstantiationException, ParseException {
@@ -227,12 +246,16 @@ public class MetadataImportIT extends AbstractIntegrationTestWithDatabase {
return importedItem;
}
public void performImportScript(String[] csv) throws Exception {
performImportScript(csv, false);
}
/**
* Import mocked CSVs to test item creation behavior, deleting temporary file afterward.
* @param csv content for test file.
* @throws java.lang.Exception passed through.
*/
public void performImportScript(String[] csv) throws Exception {
public void performImportScript(String[] csv, boolean useTemplate) throws Exception {
File csvFile = File.createTempFile("dspace-test-import", "csv");
BufferedWriter out = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(csvFile), "UTF-8"));
for (String csvLine : csv) {
@@ -243,6 +266,9 @@ public class MetadataImportIT extends AbstractIntegrationTestWithDatabase {
String fileLocation = csvFile.getAbsolutePath();
try {
String[] args = new String[] {"metadata-import", "-f", fileLocation, "-e", eperson.getEmail(), "-s"};
if (useTemplate) {
args = ArrayUtils.add(args, "-t");
}
TestDSpaceRunnableHandler testDSpaceRunnableHandler = new TestDSpaceRunnableHandler();
ScriptLauncher
.handleScript(args, ScriptLauncher.getConfig(kernelImpl), testDSpaceRunnableHandler, kernelImpl);

View File

@@ -0,0 +1,154 @@
/**
* 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.app.solrdatabaseresync;
import static org.dspace.discovery.indexobject.ItemIndexFactoryImpl.STATUS_FIELD;
import static org.dspace.discovery.indexobject.ItemIndexFactoryImpl.STATUS_FIELD_PREDB;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotEquals;
import java.util.List;
import org.apache.commons.collections.CollectionUtils;
import org.apache.solr.client.solrj.SolrQuery;
import org.apache.solr.client.solrj.response.QueryResponse;
import org.apache.solr.common.SolrDocumentList;
import org.dspace.AbstractIntegrationTestWithDatabase;
import org.dspace.app.launcher.ScriptLauncher;
import org.dspace.app.scripts.handler.impl.TestDSpaceRunnableHandler;
import org.dspace.builder.CollectionBuilder;
import org.dspace.builder.CommunityBuilder;
import org.dspace.builder.ItemBuilder;
import org.dspace.content.Collection;
import org.dspace.content.Item;
import org.dspace.content.factory.ContentServiceFactory;
import org.dspace.content.service.CollectionService;
import org.dspace.discovery.MockSolrSearchCore;
import org.dspace.kernel.ServiceManager;
import org.dspace.services.ConfigurationService;
import org.dspace.services.factory.DSpaceServicesFactory;
import org.junit.Before;
import org.junit.Test;
public class SolrDatabaseResyncIT extends AbstractIntegrationTestWithDatabase {
private final ConfigurationService configurationService =
DSpaceServicesFactory.getInstance().getConfigurationService();
private final CollectionService collectionService =
ContentServiceFactory.getInstance().getCollectionService();
private MockSolrSearchCore searchService;
private Collection col;
private Item item1;
private Item item2;
@Before
public void setUp() throws Exception {
super.setUp();
configurationService.setProperty("solr-database-resync.time-until-reindex", 1);
ServiceManager serviceManager = DSpaceServicesFactory.getInstance().getServiceManager();
searchService = serviceManager.getServiceByName(null, MockSolrSearchCore.class);
context.turnOffAuthorisationSystem();
parentCommunity = CommunityBuilder.createCommunity(context).withName("Parent Community").build();
col = CollectionBuilder.createCollection(context, parentCommunity).withName("Collection").build();
item1 = ItemBuilder.createItem(context, col)
.withTitle("Public item 1")
.withIssueDate("2010-10-17")
.withAuthor("Smith, Donald")
.withSubject("ExtraEntry")
.build();
item2 = ItemBuilder.createItem(context, col)
.withTitle("Public item 2")
.withIssueDate("2011-08-13")
.withAuthor("Smith, Maria")
.withSubject("TestingForMore")
.build();
context.setDispatcher("noindex");
}
@Test
public void solrPreDBStatusExistingItemTest() throws Exception {
// Items were created, they should contain a predb status in solr
assertHasPreDBStatus(item1);
assertHasPreDBStatus(item2);
performSolrDatabaseResyncScript();
// Database status script was performed, their predb status should be removed
assertHasNoPreDBStatus(item1);
assertHasNoPreDBStatus(item2);
context.restoreAuthSystemState();
}
@Test
public void solrPreDBStatusRemovedItemTest() throws Exception {
// Items were created, they should contain a predb status in solr
assertHasPreDBStatus(item1);
assertHasPreDBStatus(item2);
collectionService.delete(context, col);
// Items were deleted, they should still contain a predb status in solr for now
assertHasPreDBStatus(item1);
assertHasPreDBStatus(item2);
performSolrDatabaseResyncScript();
// Database status script was performed, their solr document should have been removed
assertNoSolrDocument(item1);
assertNoSolrDocument(item2);
context.restoreAuthSystemState();
}
public void assertHasNoPreDBStatus(Item item) throws Exception {
assertNotEquals(STATUS_FIELD_PREDB, getStatus(item));
}
public void assertHasPreDBStatus(Item item) throws Exception {
assertEquals(STATUS_FIELD_PREDB, getStatus(item));
}
public void assertNoSolrDocument(Item item) throws Exception {
SolrDocumentList solrDocumentList = getSolrDocumentList(item);
assertEquals(0, solrDocumentList.size());
}
public String getStatus(Item item) throws Exception {
SolrDocumentList solrDocumentList = getSolrDocumentList(item);
List fieldValues = ((List) solrDocumentList.get(0).getFieldValues(STATUS_FIELD));
if (CollectionUtils.isNotEmpty(fieldValues)) {
return (String) fieldValues.get(0);
} else {
return null;
}
}
public SolrDocumentList getSolrDocumentList(Item item) throws Exception {
SolrQuery solrQuery = new SolrQuery();
solrQuery.setQuery("search.resourceid:" + item.getID());
QueryResponse queryResponse = searchService.getSolr().query(solrQuery);
return queryResponse.getResults();
}
public void performSolrDatabaseResyncScript() throws Exception {
String[] args = new String[] {"solr-database-resync"};
TestDSpaceRunnableHandler testDSpaceRunnableHandler = new TestDSpaceRunnableHandler();
ScriptLauncher
.handleScript(args, ScriptLauncher.getConfig(kernelImpl), testDSpaceRunnableHandler, kernelImpl);
}
}

View File

@@ -57,7 +57,7 @@ public class ItemBuilder extends AbstractDSpaceObjectBuilder<Item> {
this.context = context;
try {
workspaceItem = workspaceItemService.create(context, col, false);
workspaceItem = workspaceItemService.create(context, col, true);
item = workspaceItem.getItem();
} catch (Exception e) {
return handleException(e);

View File

@@ -12,11 +12,13 @@ import java.sql.SQLException;
import java.text.ParseException;
import java.text.SimpleDateFormat;
import java.util.List;
import java.util.Set;
import org.dspace.authorize.AuthorizeException;
import org.dspace.content.ProcessStatus;
import org.dspace.core.Context;
import org.dspace.eperson.EPerson;
import org.dspace.eperson.Group;
import org.dspace.scripts.DSpaceCommandLineParameter;
import org.dspace.scripts.Process;
import org.dspace.scripts.service.ProcessService;
@@ -33,14 +35,22 @@ public class ProcessBuilder extends AbstractBuilder<Process, ProcessService> {
List<DSpaceCommandLineParameter> parameters)
throws SQLException {
ProcessBuilder processBuilder = new ProcessBuilder(context);
return processBuilder.create(context, ePerson, scriptName, parameters);
return processBuilder.create(context, ePerson, scriptName, parameters, null);
}
public static ProcessBuilder createProcess(Context context, EPerson ePerson, String scriptName,
List<DSpaceCommandLineParameter> parameters,
Set<Group> specialGroups)
throws SQLException {
ProcessBuilder processBuilder = new ProcessBuilder(context);
return processBuilder.create(context, ePerson, scriptName, parameters, specialGroups);
}
private ProcessBuilder create(Context context, EPerson ePerson, String scriptName,
List<DSpaceCommandLineParameter> parameters)
List<DSpaceCommandLineParameter> parameters, final Set<Group> specialGroups)
throws SQLException {
this.context = context;
this.process = processService.create(context, ePerson, scriptName, parameters);
this.process = processService.create(context, ePerson, scriptName, parameters, specialGroups);
this.process.setProcessStatus(ProcessStatus.SCHEDULED);
return this;
}

View File

@@ -107,18 +107,26 @@ public class RelationshipBuilder extends AbstractBuilder<Relationship, Relations
}
public static RelationshipBuilder createRelationshipBuilder(Context context, Item leftItem, Item rightItem,
RelationshipType relationshipType) {
RelationshipType relationshipType, int leftPlace, int rightPlace) {
RelationshipBuilder relationshipBuilder = new RelationshipBuilder(context);
return relationshipBuilder.create(context, leftItem, rightItem, relationshipType);
return relationshipBuilder.create(context, leftItem, rightItem, relationshipType, leftPlace, rightPlace);
}
public static RelationshipBuilder createRelationshipBuilder(Context context, Item leftItem, Item rightItem,
RelationshipType relationshipType) {
return createRelationshipBuilder(context, leftItem, rightItem, relationshipType, -1, -1);
}
private RelationshipBuilder create(Context context, Item leftItem, Item rightItem,
RelationshipType relationshipType) {
RelationshipType relationshipType, int leftPlace, int rightPlace) {
this.context = context;
try {
relationship = relationshipService.create(context, leftItem, rightItem, relationshipType, 0, 0);
//place -1 will add it to the end
relationship = relationshipService.create(context, leftItem, rightItem, relationshipType,
leftPlace, rightPlace);
} catch (SQLException | AuthorizeException e) {
log.warn("Failed to create relationship", e);
}
@@ -140,4 +148,10 @@ public class RelationshipBuilder extends AbstractBuilder<Relationship, Relations
relationship.setLeftPlace(leftPlace);
return this;
}
public RelationshipBuilder withLatestVersionStatus(Relationship.LatestVersionStatus latestVersionStatus) {
relationship.setLatestVersionStatus(latestVersionStatus);
return this;
}
}

View File

@@ -8,6 +8,7 @@
package org.dspace.content;
import static org.hamcrest.CoreMatchers.equalTo;
import static org.hamcrest.CoreMatchers.nullValue;
import static org.hamcrest.MatcherAssert.assertThat;
import java.util.List;
@@ -71,19 +72,28 @@ public class LeftTiltedRelationshipMetadataServiceIT extends RelationshipMetadat
//request the virtual metadata of the publication only
List<RelationshipMetadataValue> leftList = relationshipMetadataService
.getRelationshipMetadata(leftItem, true);
assertThat(leftList.size(), equalTo(2));
assertThat(leftList.get(0).getValue(), equalTo("familyName, firstName"));
assertThat(leftList.get(0).getMetadataField().getMetadataSchema().getName(), equalTo("dc"));
assertThat(leftList.get(0).getMetadataField().getElement(), equalTo("contributor"));
assertThat(leftList.get(0).getMetadataField().getQualifier(), equalTo("author"));
assertThat(leftList.size(), equalTo(3));
assertThat(leftList.get(0).getValue(), equalTo(String.valueOf(rightItem.getID())));
assertThat(leftList.get(0).getMetadataField().getMetadataSchema().getName(),
equalTo(MetadataSchemaEnum.RELATION.getName()));
assertThat(leftList.get(0).getMetadataField().getElement(), equalTo("isAuthorOfPublication"));
assertThat(leftList.get(0).getMetadataField().getQualifier(), equalTo("latestForDiscovery"));
assertThat(leftList.get(0).getAuthority(), equalTo("virtual::" + relationship.getID()));
assertThat(leftList.get(1).getValue(), equalTo(String.valueOf(rightItem.getID())));
assertThat(leftList.get(1).getMetadataField().getMetadataSchema().getName(),
equalTo(MetadataSchemaEnum.RELATION.getName()));
assertThat(leftList.get(1).getMetadataField().getElement(), equalTo("isAuthorOfPublication"));
assertThat(leftList.get(1).getValue(), equalTo("familyName, firstName"));
assertThat(leftList.get(1).getMetadataField().getMetadataSchema().getName(), equalTo("dc"));
assertThat(leftList.get(1).getMetadataField().getElement(), equalTo("contributor"));
assertThat(leftList.get(1).getMetadataField().getQualifier(), equalTo("author"));
assertThat(leftList.get(1).getAuthority(), equalTo("virtual::" + relationship.getID()));
assertThat(leftList.get(2).getValue(), equalTo(String.valueOf(rightItem.getID())));
assertThat(leftList.get(2).getMetadataField().getMetadataSchema().getName(),
equalTo(MetadataSchemaEnum.RELATION.getName()));
assertThat(leftList.get(2).getMetadataField().getElement(), equalTo("isAuthorOfPublication"));
assertThat(leftList.get(2).getMetadataField().getQualifier(), nullValue());
assertThat(leftList.get(2).getAuthority(), equalTo("virtual::" + relationship.getID()));
// rightItem is the author
List<MetadataValue> rightRelationshipMetadataList = itemService
.getMetadata(rightItem, MetadataSchemaEnum.RELATION.getName(), "isPublicationOfAuthor", null, Item.ANY);

View File

@@ -8,6 +8,7 @@
package org.dspace.content;
import static org.hamcrest.CoreMatchers.equalTo;
import static org.hamcrest.CoreMatchers.nullValue;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNull;
@@ -186,19 +187,28 @@ public class RelationshipMetadataServiceIT extends AbstractIntegrationTestWithDa
//request the virtual metadata of the publication only
List<RelationshipMetadataValue> leftList = relationshipMetadataService
.getRelationshipMetadata(leftItem, true);
assertThat(leftList.size(), equalTo(2));
assertThat(leftList.get(0).getValue(), equalTo("familyName, firstName"));
assertThat(leftList.get(0).getMetadataField().getMetadataSchema().getName(), equalTo("dc"));
assertThat(leftList.get(0).getMetadataField().getElement(), equalTo("contributor"));
assertThat(leftList.get(0).getMetadataField().getQualifier(), equalTo("author"));
assertThat(leftList.size(), equalTo(3));
assertThat(leftList.get(0).getValue(), equalTo(String.valueOf(rightItem.getID())));
assertThat(leftList.get(0).getMetadataField().getMetadataSchema().getName(),
equalTo(MetadataSchemaEnum.RELATION.getName()));
assertThat(leftList.get(0).getMetadataField().getElement(), equalTo("isAuthorOfPublication"));
assertThat(leftList.get(0).getMetadataField().getQualifier(), equalTo("latestForDiscovery"));
assertThat(leftList.get(0).getAuthority(), equalTo("virtual::" + relationship.getID()));
assertThat(leftList.get(1).getValue(), equalTo(String.valueOf(rightItem.getID())));
assertThat(leftList.get(1).getMetadataField().getMetadataSchema().getName(),
equalTo(MetadataSchemaEnum.RELATION.getName()));
assertThat(leftList.get(1).getMetadataField().getElement(), equalTo("isAuthorOfPublication"));
assertThat(leftList.get(1).getValue(), equalTo("familyName, firstName"));
assertThat(leftList.get(1).getMetadataField().getMetadataSchema().getName(), equalTo("dc"));
assertThat(leftList.get(1).getMetadataField().getElement(), equalTo("contributor"));
assertThat(leftList.get(1).getMetadataField().getQualifier(), equalTo("author"));
assertThat(leftList.get(1).getAuthority(), equalTo("virtual::" + relationship.getID()));
assertThat(leftList.get(2).getValue(), equalTo(String.valueOf(rightItem.getID())));
assertThat(leftList.get(2).getMetadataField().getMetadataSchema().getName(),
equalTo(MetadataSchemaEnum.RELATION.getName()));
assertThat(leftList.get(2).getMetadataField().getElement(), equalTo("isAuthorOfPublication"));
assertThat(leftList.get(2).getMetadataField().getQualifier(), nullValue());
assertThat(leftList.get(2).getAuthority(), equalTo("virtual::" + relationship.getID()));
// rightItem is the author
List<MetadataValue> rightRelationshipMetadataList = itemService
.getMetadata(rightItem, MetadataSchemaEnum.RELATION.getName(), "isPublicationOfAuthor", null, Item.ANY);
@@ -208,12 +218,21 @@ public class RelationshipMetadataServiceIT extends AbstractIntegrationTestWithDa
//request the virtual metadata of the publication
List<RelationshipMetadataValue> rightList = relationshipMetadataService
.getRelationshipMetadata(rightItem, true);
assertThat(rightList.size(), equalTo(1));
assertThat(rightList.size(), equalTo(2));
assertThat(rightList.get(0).getValue(), equalTo(String.valueOf(leftItem.getID())));
assertThat(rightList.get(0).getMetadataField().getMetadataSchema().getName(),
equalTo(MetadataSchemaEnum.RELATION.getName()));
assertThat(rightList.get(0).getMetadataField().getElement(), equalTo("isPublicationOfAuthor"));
assertThat(rightList.get(0).getMetadataField().getQualifier(), equalTo("latestForDiscovery"));
assertThat(rightList.get(0).getAuthority(), equalTo("virtual::" + relationship.getID()));
assertThat(rightList.get(1).getValue(), equalTo(String.valueOf(leftItem.getID())));
assertThat(rightList.get(1).getMetadataField().getMetadataSchema().getName(),
equalTo(MetadataSchemaEnum.RELATION.getName()));
assertThat(rightList.get(1).getMetadataField().getElement(), equalTo("isPublicationOfAuthor"));
assertThat(rightList.get(1).getMetadataField().getQualifier(), nullValue());
assertThat(rightList.get(1).getAuthority(), equalTo("virtual::" + relationship.getID()));
}
@Test
@@ -380,34 +399,52 @@ public class RelationshipMetadataServiceIT extends AbstractIntegrationTestWithDa
//request the virtual metadata of the journal issue
List<RelationshipMetadataValue> issueRelList =
relationshipMetadataService.getRelationshipMetadata(leftItem, true);
assertThat(issueRelList.size(), equalTo(2));
assertThat(issueRelList.get(0).getValue(), equalTo("30"));
assertThat(issueRelList.get(0).getMetadataField().getMetadataSchema().getName(), equalTo("publicationvolume"));
assertThat(issueRelList.get(0).getMetadataField().getElement(), equalTo("volumeNumber"));
assertThat(issueRelList.get(0).getMetadataField().getQualifier(), equalTo(null));
assertThat(issueRelList.size(), equalTo(3));
assertThat(issueRelList.get(0).getValue(), equalTo(String.valueOf(rightItem.getID())));
assertThat(issueRelList.get(0).getMetadataField().getMetadataSchema().getName(),
equalTo(MetadataSchemaEnum.RELATION.getName()));
assertThat(issueRelList.get(0).getMetadataField().getElement(), equalTo("isJournalVolumeOfIssue"));
assertThat(issueRelList.get(0).getMetadataField().getQualifier(), equalTo("latestForDiscovery"));
assertThat(issueRelList.get(0).getAuthority(), equalTo("virtual::" + relationship.getID()));
assertThat(issueRelList.get(1).getValue(), equalTo(String.valueOf(rightItem.getID())));
assertThat(issueRelList.get(1).getMetadataField().getMetadataSchema().getName(),
equalTo(MetadataSchemaEnum.RELATION.getName()));
assertThat(issueRelList.get(1).getMetadataField().getElement(), equalTo("isJournalVolumeOfIssue"));
assertThat(issueRelList.get(1).getValue(), equalTo("30"));
assertThat(issueRelList.get(1).getMetadataField().getMetadataSchema().getName(), equalTo("publicationvolume"));
assertThat(issueRelList.get(1).getMetadataField().getElement(), equalTo("volumeNumber"));
assertThat(issueRelList.get(1).getMetadataField().getQualifier(), equalTo(null));
assertThat(issueRelList.get(1).getAuthority(), equalTo("virtual::" + relationship.getID()));
assertThat(issueRelList.get(2).getValue(), equalTo(String.valueOf(rightItem.getID())));
assertThat(issueRelList.get(2).getMetadataField().getMetadataSchema().getName(),
equalTo(MetadataSchemaEnum.RELATION.getName()));
assertThat(issueRelList.get(2).getMetadataField().getElement(), equalTo("isJournalVolumeOfIssue"));
assertThat(issueRelList.get(2).getMetadataField().getQualifier(), nullValue());
assertThat(issueRelList.get(2).getAuthority(), equalTo("virtual::" + relationship.getID()));
//request the virtual metadata of the journal volume
List<RelationshipMetadataValue> volumeRelList =
relationshipMetadataService.getRelationshipMetadata(rightItem, true);
assertThat(volumeRelList.size(), equalTo(2));
assertThat(volumeRelList.get(0).getValue(), equalTo("2"));
assertThat(volumeRelList.get(0).getMetadataField().getMetadataSchema().getName(), equalTo("publicationissue"));
assertThat(volumeRelList.get(0).getMetadataField().getElement(), equalTo("issueNumber"));
assertThat(volumeRelList.get(0).getMetadataField().getQualifier(), equalTo(null));
assertThat(volumeRelList.size(), equalTo(3));
assertThat(volumeRelList.get(0).getValue(), equalTo(String.valueOf(leftItem.getID())));
assertThat(volumeRelList.get(0).getMetadataField().getMetadataSchema().getName(),
equalTo(MetadataSchemaEnum.RELATION.getName()));
assertThat(volumeRelList.get(0).getMetadataField().getElement(), equalTo("isIssueOfJournalVolume"));
assertThat(volumeRelList.get(0).getMetadataField().getQualifier(), equalTo("latestForDiscovery"));
assertThat(volumeRelList.get(0).getAuthority(), equalTo("virtual::" + relationship.getID()));
assertThat(volumeRelList.get(1).getValue(), equalTo(String.valueOf(leftItem.getID())));
assertThat(volumeRelList.get(1).getMetadataField().getMetadataSchema().getName(),
equalTo(MetadataSchemaEnum.RELATION.getName()));
assertThat(volumeRelList.get(1).getMetadataField().getElement(), equalTo("isIssueOfJournalVolume"));
assertThat(volumeRelList.get(1).getValue(), equalTo("2"));
assertThat(volumeRelList.get(1).getMetadataField().getMetadataSchema().getName(), equalTo("publicationissue"));
assertThat(volumeRelList.get(1).getMetadataField().getElement(), equalTo("issueNumber"));
assertThat(volumeRelList.get(1).getMetadataField().getQualifier(), equalTo(null));
assertThat(volumeRelList.get(1).getAuthority(), equalTo("virtual::" + relationship.getID()));
assertThat(volumeRelList.get(2).getValue(), equalTo(String.valueOf(leftItem.getID())));
assertThat(volumeRelList.get(2).getMetadataField().getMetadataSchema().getName(),
equalTo(MetadataSchemaEnum.RELATION.getName()));
assertThat(volumeRelList.get(2).getMetadataField().getElement(), equalTo("isIssueOfJournalVolume"));
assertThat(volumeRelList.get(2).getMetadataField().getQualifier(), nullValue());
assertThat(volumeRelList.get(2).getAuthority(), equalTo("virtual::" + relationship.getID()));
}
@Test
@@ -614,45 +651,6 @@ public class RelationshipMetadataServiceIT extends AbstractIntegrationTestWithDa
.size(), equalTo(1));
}
@Test
public void testGetNextRightPlace() throws Exception {
assertThat(relationshipService.findNextRightPlaceByRightItem(context, rightItem), equalTo(0));
initPublicationAuthor();
assertThat(relationshipService.findNextRightPlaceByRightItem(context, rightItem), equalTo(1));
context.turnOffAuthorisationSystem();
Item secondItem = ItemBuilder.createItem(context, col).build();
RelationshipBuilder.createRelationshipBuilder(context, secondItem, rightItem,
isAuthorOfPublicationRelationshipType).build();
context.restoreAuthSystemState();
assertThat(relationshipService.findNextRightPlaceByRightItem(context, rightItem), equalTo(2));
}
@Test
public void testGetNextLeftPlace() throws Exception {
assertThat(relationshipService.findNextLeftPlaceByLeftItem(context, leftItem), equalTo(0));
initPublicationAuthor();
assertThat(relationshipService.findNextLeftPlaceByLeftItem(context, leftItem), equalTo(1));
context.turnOffAuthorisationSystem();
Item secondAuthor = ItemBuilder.createItem(context, col2)
.withPersonIdentifierFirstName("firstName")
.withPersonIdentifierLastName("familyName").build();
RelationshipBuilder.createRelationshipBuilder(context, leftItem, secondAuthor,
isAuthorOfPublicationRelationshipType).build();
context.restoreAuthSystemState();
assertThat(relationshipService.findNextLeftPlaceByLeftItem(context, leftItem), equalTo(2));
}
@Test
public void testGetVirtualMetadata() throws SQLException, AuthorizeException {
// Journal, JournalVolume, JournalIssue, Publication items, related to each other using the relationship types

View File

@@ -24,12 +24,14 @@ import org.dspace.content.virtual.VirtualMetadataPopulator;
import org.dspace.core.Constants;
import org.dspace.core.Context;
import org.dspace.services.ConfigurationService;
import org.dspace.versioning.utils.RelationshipVersioningUtils;
import org.junit.Before;
import org.junit.Test;
import org.junit.runner.RunWith;
import org.mockito.InjectMocks;
import org.mockito.Mock;
import org.mockito.Mockito;
import org.mockito.Spy;
import org.mockito.junit.MockitoJUnitRunner;
@RunWith(MockitoJUnitRunner.class)
@@ -71,6 +73,9 @@ public class RelationshipServiceImplTest {
@Mock
private ConfigurationService configurationService;
@Spy
private RelationshipVersioningUtils relationshipVersioningUtils;
@Before
public void init() {
relationshipsList = new ArrayList<>();
@@ -112,9 +117,6 @@ public class RelationshipServiceImplTest {
relationshipTest.add(getRelationship(bob, cindy, hasMother,1,0));
when(relationshipService.findByItem(context, cindy, -1, -1, false)).thenReturn(relationshipTest);
// Mock the state of objects utilized in findByItem() to meet the success criteria of the invocation
when(relationshipDAO.findByItem(context, cindy, -1, -1, false)).thenReturn(relationshipTest);
List<Relationship> results = relationshipService.findByItem(context, cindy);
assertEquals("TestFindByItem 0", relationshipTest, results);
for (int i = 0; i < relationshipTest.size(); i++) {
@@ -122,32 +124,6 @@ public class RelationshipServiceImplTest {
}
}
@Test
public void testFindLeftPlaceByLeftItem() throws Exception {
// Declare objects utilized in unit test
Item item = mock(Item.class);
// Mock DAO to return mocked left place as 0
when(relationshipDAO.findNextLeftPlaceByLeftItem(context, item)).thenReturn(0);
// The left place reported from out mocked item should match the DAO's report of the left place
assertEquals("TestFindLeftPlaceByLeftItem 0", relationshipDAO.findNextLeftPlaceByLeftItem(context, item),
relationshipService.findNextLeftPlaceByLeftItem(context, item));
}
@Test
public void testFindRightPlaceByRightItem() throws Exception {
// Declare objects utilized in unit test
Item item = mock(Item.class);
// Mock lower level DAO to return mocked right place as 0
when(relationshipDAO.findNextRightPlaceByRightItem(context, item)).thenReturn(0);
// The right place reported from out mocked item should match the DAO's report of the right place
assertEquals("TestFindRightPlaceByRightItem 0", relationshipDAO.findNextRightPlaceByRightItem(context, item),
relationshipService.findNextRightPlaceByRightItem(context, item));
}
@Test
public void testFindByItemAndRelationshipType() throws Exception {
// Declare objects utilized in unit test

View File

@@ -8,6 +8,7 @@
package org.dspace.content;
import static org.hamcrest.CoreMatchers.equalTo;
import static org.hamcrest.CoreMatchers.nullValue;
import static org.hamcrest.MatcherAssert.assertThat;
import java.util.List;
@@ -88,18 +89,27 @@ public class RightTiltedRelationshipMetadataServiceIT extends RelationshipMetada
//request the virtual metadata of the journal volume
List<RelationshipMetadataValue> volumeRelList =
relationshipMetadataService.getRelationshipMetadata(rightItem, true);
assertThat(volumeRelList.size(), equalTo(2));
assertThat(volumeRelList.get(0).getValue(), equalTo("2"));
assertThat(volumeRelList.get(0).getMetadataField().getMetadataSchema().getName(), equalTo("publicationissue"));
assertThat(volumeRelList.get(0).getMetadataField().getElement(), equalTo("issueNumber"));
assertThat(volumeRelList.get(0).getMetadataField().getQualifier(), equalTo(null));
assertThat(volumeRelList.size(), equalTo(3));
assertThat(volumeRelList.get(0).getValue(), equalTo(String.valueOf(leftItem.getID())));
assertThat(volumeRelList.get(0).getMetadataField().getMetadataSchema().getName(),
equalTo(MetadataSchemaEnum.RELATION.getName()));
assertThat(volumeRelList.get(0).getMetadataField().getElement(), equalTo("isIssueOfJournalVolume"));
assertThat(volumeRelList.get(0).getMetadataField().getQualifier(), equalTo("latestForDiscovery"));
assertThat(volumeRelList.get(0).getAuthority(), equalTo("virtual::" + relationship.getID()));
assertThat(volumeRelList.get(1).getValue(), equalTo(String.valueOf(leftItem.getID())));
assertThat(volumeRelList.get(1).getMetadataField().getMetadataSchema().getName(),
equalTo(MetadataSchemaEnum.RELATION.getName()));
assertThat(volumeRelList.get(1).getMetadataField().getElement(), equalTo("isIssueOfJournalVolume"));
assertThat(volumeRelList.get(1).getValue(), equalTo("2"));
assertThat(volumeRelList.get(1).getMetadataField().getMetadataSchema().getName(), equalTo("publicationissue"));
assertThat(volumeRelList.get(1).getMetadataField().getElement(), equalTo("issueNumber"));
assertThat(volumeRelList.get(1).getMetadataField().getQualifier(), equalTo(null));
assertThat(volumeRelList.get(1).getAuthority(), equalTo("virtual::" + relationship.getID()));
assertThat(volumeRelList.get(2).getValue(), equalTo(String.valueOf(leftItem.getID())));
assertThat(volumeRelList.get(2).getMetadataField().getMetadataSchema().getName(),
equalTo(MetadataSchemaEnum.RELATION.getName()));
assertThat(volumeRelList.get(2).getMetadataField().getElement(), equalTo("isIssueOfJournalVolume"));
assertThat(volumeRelList.get(2).getMetadataField().getQualifier(), nullValue());
assertThat(volumeRelList.get(2).getAuthority(), equalTo("virtual::" + relationship.getID()));
}
}

File diff suppressed because it is too large Load Diff

View File

@@ -138,28 +138,6 @@ public class RelationshipDAOImplTest extends AbstractIntegrationTest {
-1, -1, false));
}
/**
* Test findNextLeftPlaceByLeftItem should return 0 given our test left Item itemOne.
*
* @throws Exception
*/
@Test
public void testFindNextLeftPlaceByLeftItem() throws Exception {
assertEquals("TestNextLeftPlaceByLeftItem 0", 1, relationshipService.findNextLeftPlaceByLeftItem(context,
itemOne));
}
/**
* Test findNextRightPlaceByRightItem should return 0 given our test right Item itemTwo.
*
* @throws Exception
*/
@Test
public void testFindNextRightPlaceByRightItem() throws Exception {
assertEquals("TestNextRightPlaceByRightItem 0", 1, relationshipService.findNextRightPlaceByRightItem(context,
itemTwo));
}
/**
* Test findByRelationshipType should return our defined relationshipsList given our test RelationshipType
* relationshipType

View File

@@ -0,0 +1,485 @@
/**
* 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.content.service;
import static org.hamcrest.CoreMatchers.equalTo;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.fail;
import java.sql.SQLException;
import java.util.Comparator;
import java.util.List;
import java.util.stream.Collectors;
import org.apache.logging.log4j.Logger;
import org.dspace.AbstractIntegrationTestWithDatabase;
import org.dspace.authorize.AuthorizeException;
import org.dspace.builder.CollectionBuilder;
import org.dspace.builder.CommunityBuilder;
import org.dspace.builder.EntityTypeBuilder;
import org.dspace.builder.ItemBuilder;
import org.dspace.builder.RelationshipBuilder;
import org.dspace.builder.RelationshipTypeBuilder;
import org.dspace.content.Collection;
import org.dspace.content.Community;
import org.dspace.content.EntityType;
import org.dspace.content.Item;
import org.dspace.content.MetadataValue;
import org.dspace.content.Relationship;
import org.dspace.content.RelationshipType;
import org.dspace.content.WorkspaceItem;
import org.dspace.content.factory.ContentServiceFactory;
import org.dspace.versioning.Version;
import org.dspace.versioning.factory.VersionServiceFactory;
import org.dspace.versioning.service.VersioningService;
import org.junit.Before;
import org.junit.Test;
public class ItemServiceTest extends AbstractIntegrationTestWithDatabase {
private static final Logger log = org.apache.logging.log4j.LogManager.getLogger(ItemServiceTest.class);
protected RelationshipService relationshipService = ContentServiceFactory.getInstance().getRelationshipService();
protected RelationshipTypeService relationshipTypeService = ContentServiceFactory.getInstance()
.getRelationshipTypeService();
protected EntityTypeService entityTypeService = ContentServiceFactory.getInstance().getEntityTypeService();
protected CommunityService communityService = ContentServiceFactory.getInstance().getCommunityService();
protected CollectionService collectionService = ContentServiceFactory.getInstance().getCollectionService();
protected ItemService itemService = ContentServiceFactory.getInstance().getItemService();
protected InstallItemService installItemService = ContentServiceFactory.getInstance().getInstallItemService();
protected WorkspaceItemService workspaceItemService = ContentServiceFactory.getInstance().getWorkspaceItemService();
protected MetadataValueService metadataValueService = ContentServiceFactory.getInstance().getMetadataValueService();
protected VersioningService versioningService = VersionServiceFactory.getInstance().getVersionService();
Community community;
Collection collection1;
Item item;
String authorQualifier = "author";
String contributorElement = "contributor";
String dcSchema = "dc";
String subjectElement = "subject";
String descriptionElement = "description";
String abstractQualifier = "abstract";
/**
* This method will be run before every test as per @Before. It will
* initialize resources required for the tests.
*/
@Before
@Override
public void setUp() throws Exception {
super.setUp();
try {
context.turnOffAuthorisationSystem();
community = CommunityBuilder.createCommunity(context)
.build();
collection1 = CollectionBuilder.createCollection(context, community)
.withEntityType("Publication")
.build();
WorkspaceItem is = workspaceItemService.create(context, collection1, false);
item = installItemService.installItem(context, is);
context.restoreAuthSystemState();
} catch (AuthorizeException ex) {
log.error("Authorization Error in init", ex);
fail("Authorization Error in init: " + ex.getMessage());
} catch (SQLException ex) {
log.error("SQL Error in init", ex);
fail("SQL Error in init: " + ex.getMessage());
}
}
@Test
public void InsertAndMoveMetadataShiftPlaceTest() throws Exception {
context.turnOffAuthorisationSystem();
// Here we add the first set of metadata to the item
itemService.addMetadata(context, item, dcSchema, contributorElement, authorQualifier, null, "test, one");
itemService.addMetadata(context, item, dcSchema, contributorElement, authorQualifier, null, "test, two");
itemService.addMetadata(context, item, dcSchema, contributorElement, authorQualifier, null, "test, three");
context.restoreAuthSystemState();
// The code below performs the mentioned assertions to ensure the place is correct
List<MetadataValue> list = itemService
.getMetadata(item, dcSchema, contributorElement, authorQualifier, Item.ANY);
assertThat(list.size(), equalTo(3));
assertMetadataValue(authorQualifier, contributorElement, dcSchema, "test, one", null, 0, list.get(0));
assertMetadataValue(authorQualifier, contributorElement, dcSchema, "test, two", null, 1, list.get(1));
assertMetadataValue(authorQualifier, contributorElement, dcSchema, "test, three", null, 2, list.get(2));
context.turnOffAuthorisationSystem();
// This is where we add metadata at place=1
itemService.addAndShiftRightMetadata(
context, item, dcSchema, contributorElement, authorQualifier, null, "test, four", null, -1, 1
);
// Here we retrieve the list of metadata again to perform the assertions on the places below as mentioned
list = itemService.getMetadata(item, dcSchema, contributorElement, authorQualifier, Item.ANY)
.stream()
.sorted(Comparator.comparingInt(MetadataValue::getPlace))
.collect(Collectors.toList());
assertThat(list.size(), equalTo(4));
assertMetadataValue(authorQualifier, contributorElement, dcSchema, "test, one", null, 0, list.get(0));
assertMetadataValue(authorQualifier, contributorElement, dcSchema, "test, four", null, 1, list.get(1));
assertMetadataValue(authorQualifier, contributorElement, dcSchema, "test, two", null, 2, list.get(2));
assertMetadataValue(authorQualifier, contributorElement, dcSchema, "test, three", null, 3, list.get(3));
// And move metadata from place=2 to place=0
itemService.moveMetadata(context, item, dcSchema, contributorElement, authorQualifier, 2, 0);
context.restoreAuthSystemState();
// Here we retrieve the list of metadata again to perform the assertions on the places below as mentioned
list = itemService.getMetadata(item, dcSchema, contributorElement, authorQualifier, Item.ANY)
.stream()
.sorted(Comparator.comparingInt(MetadataValue::getPlace))
.collect(Collectors.toList());
assertThat(list.size(), equalTo(4));
assertMetadataValue(authorQualifier, contributorElement, dcSchema, "test, two", null, 0, list.get(0));
assertMetadataValue(authorQualifier, contributorElement, dcSchema, "test, one", null, 1, list.get(1));
assertMetadataValue(authorQualifier, contributorElement, dcSchema, "test, four", null, 2, list.get(2));
assertMetadataValue(authorQualifier, contributorElement, dcSchema, "test, three", null, 3, list.get(3));
}
@Test
public void InsertAndMoveMetadataShiftPlaceTest_complex() throws Exception {
context.turnOffAuthorisationSystem();
// Here we add the first set of metadata to the item
itemService.addMetadata(context, item, dcSchema, contributorElement, authorQualifier, null, "test, one");
// NOTE: dc.subject should NOT affect dc.contributor.author
itemService.addMetadata(context, item, dcSchema, subjectElement, null, null, "test, sub1");
// NOTE: dc.subject should NOT affect dc.contributor.author
itemService.addMetadata(context, item, dcSchema, subjectElement, null, null, "test, sub2");
itemService.addMetadata(context, item, dcSchema, contributorElement, authorQualifier, null, "test, two");
itemService.addMetadata(context, item, dcSchema, contributorElement, authorQualifier, null, "test, three");
// NOTE: dc.description.abstract should NOT affect dc.contributor.author
itemService.addMetadata(context, item, dcSchema, descriptionElement, abstractQualifier, null, "test, abs1");
context.restoreAuthSystemState();
// The code below performs the mentioned assertions to ensure the place is correct
List<MetadataValue> list1 = itemService
.getMetadata(item, dcSchema, contributorElement, authorQualifier, Item.ANY);
assertThat(list1.size(), equalTo(3));
assertMetadataValue(authorQualifier, contributorElement, dcSchema, "test, one", null, 0, list1.get(0));
assertMetadataValue(authorQualifier, contributorElement, dcSchema, "test, two", null, 1, list1.get(1));
assertMetadataValue(authorQualifier, contributorElement, dcSchema, "test, three", null, 2, list1.get(2));
List<MetadataValue> list2 = itemService
.getMetadata(item, dcSchema, subjectElement, null, Item.ANY);
assertThat(list2.size(), equalTo(2));
assertMetadataValue(null, subjectElement, dcSchema, "test, sub1", null, 0, list2.get(0));
assertMetadataValue(null, subjectElement, dcSchema, "test, sub2", null, 1, list2.get(1));
List<MetadataValue> list3 = itemService
.getMetadata(item, dcSchema, descriptionElement, abstractQualifier, Item.ANY);
assertThat(list3.size(), equalTo(1));
assertMetadataValue(abstractQualifier, descriptionElement, dcSchema, "test, abs1", null, 0, list3.get(0));
context.turnOffAuthorisationSystem();
// This is where we add metadata at place=1
itemService.addAndShiftRightMetadata(
context, item, dcSchema, contributorElement, authorQualifier, null, "test, four", null, -1, 1
);
// Here we retrieve the list of metadata again to perform the assertions on the places below as mentioned
List<MetadataValue> list4 = itemService
.getMetadata(item, dcSchema, contributorElement, authorQualifier, Item.ANY)
.stream()
.sorted(Comparator.comparingInt(MetadataValue::getPlace))
.collect(Collectors.toList());
assertThat(list4.size(), equalTo(4));
assertMetadataValue(authorQualifier, contributorElement, dcSchema, "test, one", null, 0, list4.get(0));
assertMetadataValue(authorQualifier, contributorElement, dcSchema, "test, four", null, 1, list4.get(1));
assertMetadataValue(authorQualifier, contributorElement, dcSchema, "test, two", null, 2, list4.get(2));
assertMetadataValue(authorQualifier, contributorElement, dcSchema, "test, three", null, 3, list4.get(3));
List<MetadataValue> list5 = itemService
.getMetadata(item, dcSchema, subjectElement, null, Item.ANY);
assertThat(list5.size(), equalTo(2));
assertMetadataValue(null, subjectElement, dcSchema, "test, sub1", null, 0, list5.get(0));
assertMetadataValue(null, subjectElement, dcSchema, "test, sub2", null, 1, list5.get(1));
List<MetadataValue> list6 = itemService
.getMetadata(item, dcSchema, descriptionElement, abstractQualifier, Item.ANY);
assertThat(list3.size(), equalTo(1));
assertMetadataValue(abstractQualifier, descriptionElement, dcSchema, "test, abs1", null, 0, list6.get(0));
// And move metadata from place=2 to place=0
itemService.moveMetadata(context, item, dcSchema, contributorElement, authorQualifier, 2, 0);
context.restoreAuthSystemState();
// Here we retrieve the list of metadata again to perform the assertions on the places below as mentioned
List<MetadataValue> list7 = itemService
.getMetadata(item, dcSchema, contributorElement, authorQualifier, Item.ANY)
.stream()
.sorted(Comparator.comparingInt(MetadataValue::getPlace))
.collect(Collectors.toList());
assertThat(list7.size(), equalTo(4));
assertMetadataValue(authorQualifier, contributorElement, dcSchema, "test, two", null, 0, list7.get(0));
assertMetadataValue(authorQualifier, contributorElement, dcSchema, "test, one", null, 1, list7.get(1));
assertMetadataValue(authorQualifier, contributorElement, dcSchema, "test, four", null, 2, list7.get(2));
assertMetadataValue(authorQualifier, contributorElement, dcSchema, "test, three", null, 3, list7.get(3));
List<MetadataValue> list8 = itemService
.getMetadata(item, dcSchema, subjectElement, null, Item.ANY);
assertThat(list8.size(), equalTo(2));
assertMetadataValue(null, subjectElement, dcSchema, "test, sub1", null, 0, list8.get(0));
assertMetadataValue(null, subjectElement, dcSchema, "test, sub2", null, 1, list8.get(1));
List<MetadataValue> list9 = itemService
.getMetadata(item, dcSchema, descriptionElement, abstractQualifier, Item.ANY);
assertThat(list9.size(), equalTo(1));
assertMetadataValue(abstractQualifier, descriptionElement, dcSchema, "test, abs1", null, 0, list9.get(0));
}
@Test
public void InsertAndMoveMetadataOnePlaceForwardTest() throws Exception {
context.turnOffAuthorisationSystem();
// Here we add the first set of metadata to the item
itemService.addMetadata(context, item, dcSchema, contributorElement, authorQualifier, null, "test, one");
itemService.addMetadata(context, item, dcSchema, contributorElement, authorQualifier, null, "test, two");
itemService.addMetadata(context, item, dcSchema, contributorElement, authorQualifier, null, "test, three");
context.restoreAuthSystemState();
// The code below performs the mentioned assertions to ensure the place is correct
List<MetadataValue> list = itemService
.getMetadata(item, dcSchema, contributorElement, authorQualifier, Item.ANY);
assertThat(list.size(), equalTo(3));
assertMetadataValue(authorQualifier, contributorElement, dcSchema, "test, one", null, 0, list.get(0));
assertMetadataValue(authorQualifier, contributorElement, dcSchema, "test, two", null, 1, list.get(1));
assertMetadataValue(authorQualifier, contributorElement, dcSchema, "test, three", null, 2, list.get(2));
context.turnOffAuthorisationSystem();
// This is where we add metadata at place=1
itemService.addAndShiftRightMetadata(
context, item, dcSchema, contributorElement, authorQualifier, null, "test, four", null, -1, 1
);
// Here we retrieve the list of metadata again to perform the assertions on the places below as mentioned
list = itemService.getMetadata(item, dcSchema, contributorElement, authorQualifier, Item.ANY)
.stream()
.sorted(Comparator.comparingInt(MetadataValue::getPlace))
.collect(Collectors.toList());
assertThat(list.size(), equalTo(4));
assertMetadataValue(authorQualifier, contributorElement, dcSchema, "test, one", null, 0, list.get(0));
assertMetadataValue(authorQualifier, contributorElement, dcSchema, "test, four", null, 1, list.get(1));
assertMetadataValue(authorQualifier, contributorElement, dcSchema, "test, two", null, 2, list.get(2));
assertMetadataValue(authorQualifier, contributorElement, dcSchema, "test, three", null, 3, list.get(3));
// And move metadata from place=1 to place=2
itemService.moveMetadata(context, item, dcSchema, contributorElement, authorQualifier, 1, 2);
context.restoreAuthSystemState();
// Here we retrieve the list of metadata again to perform the assertions on the places below as mentioned
list = itemService.getMetadata(item, dcSchema, contributorElement, authorQualifier, Item.ANY)
.stream()
.sorted(Comparator.comparingInt(MetadataValue::getPlace))
.collect(Collectors.toList());
assertThat(list.size(), equalTo(4));
assertMetadataValue(authorQualifier, contributorElement, dcSchema, "test, one", null, 0, list.get(0));
assertMetadataValue(authorQualifier, contributorElement, dcSchema, "test, two", null, 1, list.get(1));
assertMetadataValue(authorQualifier, contributorElement, dcSchema, "test, four", null, 2, list.get(2));
assertMetadataValue(authorQualifier, contributorElement, dcSchema, "test, three", null, 3, list.get(3));
}
@Test
public void InsertAndMoveMetadataOnePlaceForwardTest_complex() throws Exception {
context.turnOffAuthorisationSystem();
// NOTE: dc.description.abstract should NOT affect dc.contributor.author
itemService.addMetadata(context, item, dcSchema, descriptionElement, abstractQualifier, null, "test, abs1");
// Here we add the first set of metadata to the item
itemService.addMetadata(context, item, dcSchema, contributorElement, authorQualifier, null, "test, one");
// NOTE: dc.subject should NOT affect dc.contributor.author
itemService.addMetadata(context, item, dcSchema, subjectElement, null, null, "test, sub1");
itemService.addMetadata(context, item, dcSchema, contributorElement, authorQualifier, null, "test, two");
itemService.addMetadata(context, item, dcSchema, contributorElement, authorQualifier, null, "test, three");
// NOTE: dc.subject should NOT affect dc.contributor.author
itemService.addMetadata(context, item, dcSchema, subjectElement, null, null, "test, sub2");
context.restoreAuthSystemState();
// The code below performs the mentioned assertions to ensure the place is correct
List<MetadataValue> list1 = itemService
.getMetadata(item, dcSchema, contributorElement, authorQualifier, Item.ANY);
assertThat(list1.size(), equalTo(3));
assertMetadataValue(authorQualifier, contributorElement, dcSchema, "test, one", null, 0, list1.get(0));
assertMetadataValue(authorQualifier, contributorElement, dcSchema, "test, two", null, 1, list1.get(1));
assertMetadataValue(authorQualifier, contributorElement, dcSchema, "test, three", null, 2, list1.get(2));
List<MetadataValue> list2 = itemService
.getMetadata(item, dcSchema, subjectElement, null, Item.ANY);
assertThat(list2.size(), equalTo(2));
assertMetadataValue(null, subjectElement, dcSchema, "test, sub1", null, 0, list2.get(0));
assertMetadataValue(null, subjectElement, dcSchema, "test, sub2", null, 1, list2.get(1));
List<MetadataValue> list3 = itemService
.getMetadata(item, dcSchema, descriptionElement, abstractQualifier, Item.ANY);
assertThat(list3.size(), equalTo(1));
assertMetadataValue(abstractQualifier, descriptionElement, dcSchema, "test, abs1", null, 0, list3.get(0));
context.turnOffAuthorisationSystem();
// This is where we add metadata at place=1
itemService.addAndShiftRightMetadata(
context, item, dcSchema, contributorElement, authorQualifier, null, "test, four", null, -1, 1
);
// Here we retrieve the list of metadata again to perform the assertions on the places below as mentioned
List<MetadataValue> list4 = itemService
.getMetadata(item, dcSchema, contributorElement, authorQualifier, Item.ANY)
.stream()
.sorted(Comparator.comparingInt(MetadataValue::getPlace))
.collect(Collectors.toList());
assertThat(list4.size(), equalTo(4));
assertMetadataValue(authorQualifier, contributorElement, dcSchema, "test, one", null, 0, list4.get(0));
assertMetadataValue(authorQualifier, contributorElement, dcSchema, "test, four", null, 1, list4.get(1));
assertMetadataValue(authorQualifier, contributorElement, dcSchema, "test, two", null, 2, list4.get(2));
assertMetadataValue(authorQualifier, contributorElement, dcSchema, "test, three", null, 3, list4.get(3));
List<MetadataValue> list5 = itemService
.getMetadata(item, dcSchema, subjectElement, null, Item.ANY);
assertThat(list5.size(), equalTo(2));
assertMetadataValue(null, subjectElement, dcSchema, "test, sub1", null, 0, list5.get(0));
assertMetadataValue(null, subjectElement, dcSchema, "test, sub2", null, 1, list5.get(1));
List<MetadataValue> list6 = itemService
.getMetadata(item, dcSchema, descriptionElement, abstractQualifier, Item.ANY);
assertThat(list6.size(), equalTo(1));
assertMetadataValue(abstractQualifier, descriptionElement, dcSchema, "test, abs1", null, 0, list6.get(0));
// And move metadata from place=1 to place=2
itemService.moveMetadata(context, item, dcSchema, contributorElement, authorQualifier, 1, 2);
context.restoreAuthSystemState();
// Here we retrieve the list of metadata again to perform the assertions on the places below as mentioned
List<MetadataValue> list7 = itemService
.getMetadata(item, dcSchema, contributorElement, authorQualifier, Item.ANY)
.stream()
.sorted(Comparator.comparingInt(MetadataValue::getPlace))
.collect(Collectors.toList());
assertThat(list7.size(), equalTo(4));
assertMetadataValue(authorQualifier, contributorElement, dcSchema, "test, one", null, 0, list7.get(0));
assertMetadataValue(authorQualifier, contributorElement, dcSchema, "test, two", null, 1, list7.get(1));
assertMetadataValue(authorQualifier, contributorElement, dcSchema, "test, four", null, 2, list7.get(2));
assertMetadataValue(authorQualifier, contributorElement, dcSchema, "test, three", null, 3, list7.get(3));
List<MetadataValue> list8 = itemService
.getMetadata(item, dcSchema, subjectElement, null, Item.ANY);
assertThat(list8.size(), equalTo(2));
assertMetadataValue(null, subjectElement, dcSchema, "test, sub1", null, 0, list8.get(0));
assertMetadataValue(null, subjectElement, dcSchema, "test, sub2", null, 1, list8.get(1));
List<MetadataValue> list9 = itemService
.getMetadata(item, dcSchema, descriptionElement, abstractQualifier, Item.ANY);
assertThat(list9.size(), equalTo(1));
assertMetadataValue(abstractQualifier, descriptionElement, dcSchema, "test, abs1", null, 0, list9.get(0));
}
@Test
public void testDeleteItemWithMultipleVersions() throws Exception {
context.turnOffAuthorisationSystem();
EntityType publicationEntityType = EntityTypeBuilder.createEntityTypeBuilder(context, "Publication")
.build();
EntityType personEntityType = EntityTypeBuilder.createEntityTypeBuilder(context, "Person")
.build();
RelationshipType isAuthorOfPublication = RelationshipTypeBuilder.createRelationshipTypeBuilder(
context, publicationEntityType, personEntityType, "isAuthorOfPublication", "isPublicationOfAuthor",
null, null, null, null
)
.withCopyToLeft(false)
.withCopyToRight(false)
.build();
Collection collection2 = CollectionBuilder.createCollection(context, community)
.withEntityType("Person")
.build();
Item publication1 = ItemBuilder.createItem(context, collection1)
.withTitle("publication 1")
// NOTE: entity type comes from collection
.build();
Item person1 = ItemBuilder.createItem(context, collection2)
.withTitle("person 2")
// NOTE: entity type comes from collection
.build();
RelationshipBuilder.createRelationshipBuilder(context, publication1, person1, isAuthorOfPublication);
// create a new version, which results in a non-latest relationship attached person 1.
Version newVersion = versioningService.createNewVersion(context, publication1);
Item newPublication1 = newVersion.getItem();
WorkspaceItem newPublication1WSI = workspaceItemService.findByItem(context, newPublication1);
installItemService.installItem(context, newPublication1WSI);
context.dispatchEvents();
// verify person1 has a non-latest relationship, which should also be removed
List<Relationship> relationships1 = relationshipService.findByItem(context, person1, -1, -1, false, true);
assertEquals(1, relationships1.size());
List<Relationship> relationships2 = relationshipService.findByItem(context, person1, -1, -1, false, false);
assertEquals(2, relationships2.size());
itemService.delete(context, person1);
context.restoreAuthSystemState();
}
private void assertMetadataValue(String authorQualifier, String contributorElement, String dcSchema, String value,
String authority, int place, MetadataValue metadataValue) {
assertThat(metadataValue.getValue(), equalTo(value));
assertThat(metadataValue.getMetadataField().getMetadataSchema().getName(), equalTo(dcSchema));
assertThat(metadataValue.getMetadataField().getElement(), equalTo(contributorElement));
assertThat(metadataValue.getMetadataField().getQualifier(), equalTo(authorQualifier));
assertThat(metadataValue.getAuthority(), equalTo(authority));
assertThat(metadataValue.getPlace(), equalTo(place));
}
}

View File

@@ -8,13 +8,18 @@
package org.dspace.discovery;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;
import java.io.IOException;
import java.sql.SQLException;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
import javax.servlet.http.HttpServletRequest;
import org.dspace.AbstractIntegrationTestWithDatabase;
import org.dspace.app.launcher.ScriptLauncher;
import org.dspace.app.scripts.handler.impl.TestDSpaceRunnableHandler;
import org.dspace.authorize.AuthorizeException;
import org.dspace.builder.ClaimedTaskBuilder;
import org.dspace.builder.CollectionBuilder;
@@ -86,6 +91,12 @@ public class DiscoveryIT extends AbstractIntegrationTestWithDatabase {
MetadataAuthorityService metadataAuthorityService = ContentAuthorityServiceFactory.getInstance()
.getMetadataAuthorityService();
@Override
public void setUp() throws Exception {
super.setUp();
configurationService.setProperty("solr-database-resync.time-until-reindex", 1);
}
@Test
public void solrRecordsAfterDepositOrDeletionOfWorkspaceItemTest() throws Exception {
context.turnOffAuthorisationSystem();
@@ -371,7 +382,8 @@ public class DiscoveryIT extends AbstractIntegrationTestWithDatabase {
collectionService.delete(context, col1);
context.restoreAuthSystemState();
assertSearchQuery(IndexableCollection.TYPE, 2);
assertSearchQuery(IndexableItem.TYPE, 2);
// Deleted item contained within totalFound due to predb status (SolrDatabaseResyncCli takes care of this)
assertSearchQuery(IndexableItem.TYPE, 2, 3, 0, -1);
}
@Test
@@ -453,6 +465,10 @@ public class DiscoveryIT extends AbstractIntegrationTestWithDatabase {
assertSearchQuery(IndexableCollection.TYPE, 2, 2, 0, -1);
// check Item type with start=0 and limit=2, we expect: indexableObjects=2, totalFound=6
assertSearchQuery(IndexableItem.TYPE, 2, 6, 0, 2);
// Run SolrDatabaseResyncCli, updating items with "preDB" status and removing stale items
performSolrDatabaseResyncScript();
// check Item type with start=2 and limit=4, we expect: indexableObjects=1, totalFound=3
assertSearchQuery(IndexableItem.TYPE, 1, 3, 2, 4);
// check Item type with start=0 and limit=default, we expect: indexableObjects=3, totalFound=3
@@ -639,10 +655,79 @@ public class DiscoveryIT extends AbstractIntegrationTestWithDatabase {
// check Item type with start=0 and limit=default,
// we expect: indexableObjects=3, totalFound=6 (3 stale objects here)
assertSearchQuery(IndexableItem.TYPE, 3, 6, 0, -1);
// as the previous query hit the stale objects running a new query should lead to a clean situation
// Run SolrDatabaseResyncCli, updating items with "preDB" status and removing stale items
performSolrDatabaseResyncScript();
// as SolrDatabaseResyncCli removed the stale objects, running a new query should lead to a clean situation
assertSearchQuery(IndexableItem.TYPE, 3, 3, 0, -1);
}
@Test
public void iteratorSearchServiceTest() throws SearchServiceException {
String subject1 = "subject1";
String subject2 = "subject2";
int numberItemsSubject1 = 30;
int numberItemsSubject2 = 2;
Item[] itemsSubject1 = new Item[numberItemsSubject1];
Item[] itemsSubject2 = new Item[numberItemsSubject2];
context.turnOffAuthorisationSystem();
Community community = CommunityBuilder.createCommunity(context).build();
Collection collection = CollectionBuilder.createCollection(context, community).build();
for (int i = 0; i < numberItemsSubject1; i++) {
itemsSubject1[i] = ItemBuilder.createItem(context, collection)
.withTitle("item subject 1 number" + i)
.withSubject(subject1)
.build();
}
for (int i = 0; i < numberItemsSubject2; i++) {
itemsSubject2[i] = ItemBuilder.createItem(context, collection)
.withTitle("item subject 2 number " + i)
.withSubject(subject2)
.build();
}
Collection collection2 = CollectionBuilder.createCollection(context, community).build();
ItemBuilder.createItem(context, collection2)
.withTitle("item collection2")
.withSubject(subject1)
.build();
context.restoreAuthSystemState();
DiscoverQuery discoverQuery = new DiscoverQuery();
discoverQuery.addFilterQueries("subject:" + subject1);
Iterator<Item> itemIterator =
searchService.iteratorSearch(context, new IndexableCollection(collection), discoverQuery);
int counter = 0;
List<Item> foundItems = new ArrayList<>();
while (itemIterator.hasNext()) {
foundItems.add(itemIterator.next());
counter++;
}
for (Item item : itemsSubject1) {
assertTrue(foundItems.contains(item));
}
assertEquals(numberItemsSubject1, counter);
discoverQuery = new DiscoverQuery();
discoverQuery.addFilterQueries("subject:" + subject2);
itemIterator = searchService.iteratorSearch(context, null, discoverQuery);
counter = 0;
foundItems = new ArrayList<>();
while (itemIterator.hasNext()) {
foundItems.add(itemIterator.next());
counter++;
}
assertEquals(numberItemsSubject2, counter);
for (Item item : itemsSubject2) {
assertTrue(foundItems.contains(item));
}
}
private void assertSearchQuery(String resourceType, int size) throws SearchServiceException {
assertSearchQuery(resourceType, size, size, 0, -1);
}
@@ -739,6 +824,13 @@ public class DiscoveryIT extends AbstractIntegrationTestWithDatabase {
context.setCurrentUser(previousUser);
}
public void performSolrDatabaseResyncScript() throws Exception {
String[] args = new String[] {"solr-database-resync"};
TestDSpaceRunnableHandler testDSpaceRunnableHandler = new TestDSpaceRunnableHandler();
ScriptLauncher
.handleScript(args, ScriptLauncher.getConfig(kernelImpl), testDSpaceRunnableHandler, kernelImpl);
}
private void abort(XmlWorkflowItem workflowItem)
throws SQLException, AuthorizeException, IOException, SearchServiceException {
final EPerson previousUser = context.getCurrentUser();

View File

@@ -5,7 +5,7 @@
*
* http://www.dspace.org/license/
*/
package org.dspace.app.rest.utils;
package org.dspace.discovery.utils;
import static java.util.Collections.emptyList;
import static org.dspace.discovery.configuration.DiscoveryConfigurationParameters.SORT.COUNT;
@@ -16,10 +16,10 @@ import static org.hamcrest.Matchers.allOf;
import static org.hamcrest.Matchers.contains;
import static org.hamcrest.Matchers.containsInAnyOrder;
import static org.hamcrest.Matchers.empty;
import static org.hamcrest.Matchers.emptyOrNullString;
import static org.hamcrest.Matchers.equalTo;
import static org.hamcrest.Matchers.hasSize;
import static org.hamcrest.Matchers.is;
import static org.hamcrest.Matchers.isEmptyOrNullString;
import static org.junit.Assert.assertThat;
import static org.mockito.ArgumentMatchers.any;
import static org.mockito.ArgumentMatchers.anyInt;
@@ -35,9 +35,6 @@ import java.util.LinkedList;
import java.util.List;
import java.util.function.Function;
import org.dspace.app.rest.exception.DSpaceBadRequestException;
import org.dspace.app.rest.exception.InvalidSearchRequestException;
import org.dspace.app.rest.parameter.SearchFilter;
import org.dspace.core.Context;
import org.dspace.discovery.DiscoverFacetField;
import org.dspace.discovery.DiscoverFilterQuery;
@@ -45,6 +42,7 @@ import org.dspace.discovery.DiscoverHitHighlightingField;
import org.dspace.discovery.DiscoverQuery;
import org.dspace.discovery.FacetYearRange;
import org.dspace.discovery.IndexableObject;
import org.dspace.discovery.SearchServiceException;
import org.dspace.discovery.SolrServiceImpl;
import org.dspace.discovery.configuration.DiscoveryConfiguration;
import org.dspace.discovery.configuration.DiscoveryConfigurationParameters;
@@ -56,6 +54,7 @@ import org.dspace.discovery.configuration.DiscoverySortFieldConfiguration;
import org.dspace.discovery.configuration.HierarchicalSidebarFacetConfiguration;
import org.dspace.discovery.indexobject.IndexableItem;
import org.dspace.discovery.indexobject.factory.IndexFactory;
import org.dspace.discovery.utils.parameter.QueryBuilderSearchFilter;
import org.dspace.services.ConfigurationService;
import org.hamcrest.FeatureMatcher;
import org.hamcrest.Matcher;
@@ -65,8 +64,7 @@ import org.junit.runner.RunWith;
import org.mockito.InjectMocks;
import org.mockito.Mock;
import org.mockito.junit.MockitoJUnitRunner;
import org.springframework.data.domain.PageRequest;
import org.springframework.data.domain.Sort;
/**
* Unit tests for {@link DiscoverQueryBuilder}
@@ -94,8 +92,14 @@ public class DiscoverQueryBuilderTest {
private DiscoveryConfiguration discoveryConfiguration;
private String query;
private SearchFilter searchFilter;
private PageRequest page;
private int pageSize = 10;
private long offset = 10;
private String sortProperty = "dc.title";
private String sortDirection = "ASC";
private QueryBuilderSearchFilter searchFilter;
@Before
public void setUp() throws Exception {
@@ -109,14 +113,16 @@ public class DiscoverQueryBuilderTest {
.then(invocation -> invocation.getArguments()[0] + "_sort");
when(searchService
.getFacetYearRange(eq(context), nullable(IndexableObject.class), any(DiscoverySearchFilterFacet.class),
.getFacetYearRange(eq(context), nullable(IndexableObject.class),
any(DiscoverySearchFilterFacet.class),
any(), any(DiscoverQuery.class)))
.then(invocation -> new FacetYearRange((DiscoverySearchFilterFacet) invocation.getArguments()[2]));
when(searchService.toFilterQuery(any(Context.class), any(String.class), any(String.class), any(String.class),
any(DiscoveryConfiguration.class)))
.then(invocation -> new DiscoverFilterQuery((String) invocation.getArguments()[1],
invocation.getArguments()[1] + ":\"" + invocation.getArguments()[3] + "\"",
invocation.getArguments()[1] + ":\"" + invocation
.getArguments()[3] + "\"",
(String) invocation.getArguments()[3]));
discoveryConfiguration = new DiscoveryConfiguration();
@@ -177,9 +183,8 @@ public class DiscoverQueryBuilderTest {
discoveryConfiguration.setSidebarFacets(Arrays.asList(subjectFacet, dateFacet, hierarchyFacet));
discoveryConfiguration.setSearchFilters(Arrays.asList(subjectFacet, dateFacet, hierarchyFacet));
searchFilter = new QueryBuilderSearchFilter("subject", "equals", "Java");
query = "my test case";
searchFilter = new SearchFilter("subject", "equals", "Java");
page = PageRequest.of(1, 10, Sort.Direction.ASC, "dc.title");
queryBuilder.afterPropertiesSet();
}
@@ -188,7 +193,8 @@ public class DiscoverQueryBuilderTest {
public void testBuildQuery() throws Exception {
DiscoverQuery discoverQuery = queryBuilder
.buildQuery(context, scope, discoveryConfiguration, query, Arrays.asList(searchFilter), "item", page);
.buildQuery(context, scope, discoveryConfiguration, query, Collections.singletonList(searchFilter),
"item", pageSize, offset, sortProperty, sortDirection);
assertThat(discoverQuery.getFilterQueries(), containsInAnyOrder("archived:true", "subject:\"Java\""));
assertThat(discoverQuery.getQuery(), is(query));
@@ -214,10 +220,11 @@ public class DiscoverQueryBuilderTest {
@Test
public void testBuildQueryDefaults() throws Exception {
DiscoverQuery discoverQuery =
queryBuilder.buildQuery(context, null, discoveryConfiguration, null, null, emptyList(), null);
queryBuilder.buildQuery(context, null, discoveryConfiguration, null, null, emptyList(), null, null,
null, null);
assertThat(discoverQuery.getFilterQueries(), containsInAnyOrder("archived:true"));
assertThat(discoverQuery.getQuery(), is(emptyOrNullString()));
assertThat(discoverQuery.getQuery(), isEmptyOrNullString());
assertThat(discoverQuery.getDSpaceObjectFilters(), is(empty()));
//Note this should actually be "dc.date.accessioned_dt" but remember that our searchService is just a stupid
// mock
@@ -241,13 +248,12 @@ public class DiscoverQueryBuilderTest {
@Test
public void testSortByScore() throws Exception {
page = PageRequest.of(2, 10, Sort.Direction.ASC, "SCORE");
DiscoverQuery discoverQuery =
queryBuilder.buildQuery(context, null, discoveryConfiguration, null, null, emptyList(), page);
queryBuilder.buildQuery(context, null, discoveryConfiguration, null, null, emptyList(), 10, 20L,
"SCORE", "ASC");
assertThat(discoverQuery.getFilterQueries(), containsInAnyOrder("archived:true"));
assertThat(discoverQuery.getQuery(), is(emptyOrNullString()));
assertThat(discoverQuery.getQuery(), isEmptyOrNullString());
assertThat(discoverQuery.getDSpaceObjectFilters(), is(empty()));
//Note this should actually be "dc.date.accessioned_dt" but remember that our searchService is just a stupid
// mock
@@ -269,48 +275,50 @@ public class DiscoverQueryBuilderTest {
));
}
@Test(expected = DSpaceBadRequestException.class)
@Test(expected = IllegalArgumentException.class)
public void testInvalidDSOType() throws Exception {
queryBuilder
.buildQuery(context, scope, discoveryConfiguration, query, Arrays.asList(searchFilter), "TEST", page);
.buildQuery(context, scope, discoveryConfiguration, query, Collections.singletonList(searchFilter),
"TEST", pageSize, offset, sortProperty, sortDirection);
}
@Test(expected = InvalidSearchRequestException.class)
@Test(expected = SearchServiceException.class)
public void testInvalidSortField() throws Exception {
page = PageRequest.of(2, 10, Sort.Direction.ASC, "test");
queryBuilder
.buildQuery(context, scope, discoveryConfiguration, query, Arrays.asList(searchFilter), "ITEM", page);
.buildQuery(context, scope, discoveryConfiguration, query, Collections.singletonList(searchFilter),
"ITEM", pageSize, 20L, "test", sortDirection);
}
@Test(expected = DSpaceBadRequestException.class)
@Test(expected = IllegalArgumentException.class)
public void testInvalidSearchFilter1() throws Exception {
searchFilter = new SearchFilter("test", "equals", "Smith, Donald");
searchFilter = new QueryBuilderSearchFilter("test", "equals", "Smith, Donald");
queryBuilder
.buildQuery(context, scope, discoveryConfiguration, query, Arrays.asList(searchFilter), "ITEM", page);
.buildQuery(context, scope, discoveryConfiguration, query, Arrays.asList(searchFilter), "ITEM",
pageSize, offset, sortProperty, sortDirection);
}
@Test(expected = DSpaceBadRequestException.class)
@Test(expected = IllegalArgumentException.class)
public void testInvalidSearchFilter2() throws Exception {
when(searchService.toFilterQuery(any(Context.class), any(String.class), any(String.class), any(String.class),
any(DiscoveryConfiguration.class)))
.thenThrow(SQLException.class);
queryBuilder
.buildQuery(context, scope, discoveryConfiguration, query, Arrays.asList(searchFilter), "ITEM", page);
.buildQuery(context, scope, discoveryConfiguration, query, Arrays.asList(searchFilter), "ITEM",
pageSize, offset, sortProperty, sortDirection);
}
@Test
public void testBuildFacetQuery() throws Exception {
DiscoverQuery discoverQuery = queryBuilder.buildFacetQuery(context, scope, discoveryConfiguration,
"prefix", query,
Arrays.asList(searchFilter), "item", page,
"subject");
DiscoverQuery discoverQuery = queryBuilder.buildFacetQuery(context, scope, discoveryConfiguration, "prefix",
query, Collections.singletonList(searchFilter),
"item", pageSize, offset, "subject");
assertThat(discoverQuery.getFilterQueries(), containsInAnyOrder("archived:true", "subject:\"Java\""));
assertThat(discoverQuery.getQuery(), is(query));
assertThat(discoverQuery.getDSpaceObjectFilters(), contains(IndexableItem.TYPE));
assertThat(discoverQuery.getSortField(), is(emptyOrNullString()));
assertThat(discoverQuery.getSortField(), isEmptyOrNullString());
assertThat(discoverQuery.getMaxResults(), is(0));
assertThat(discoverQuery.getStart(), is(0));
assertThat(discoverQuery.getFacetMinCount(), is(1));
@@ -321,10 +329,10 @@ public class DiscoverQueryBuilderTest {
));
}
@Test(expected = DSpaceBadRequestException.class)
@Test(expected = IllegalArgumentException.class)
public void testInvalidSearchFacet() throws Exception {
queryBuilder.buildFacetQuery(context, scope, discoveryConfiguration, null, query,
Arrays.asList(searchFilter), "item", page, "test");
Collections.singletonList(searchFilter), "item", pageSize, offset, "test");
}
public Matcher<DiscoverFacetField> discoverFacetFieldMatcher(DiscoverFacetField expected) {

View File

@@ -1,87 +0,0 @@
/**
* 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.external.provider.impl;
import static org.mockito.Mockito.when;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.Reader;
import java.io.UncheckedIOException;
import java.nio.charset.StandardCharsets;
import javax.ws.rs.client.Invocation;
import javax.ws.rs.client.WebTarget;
import javax.ws.rs.core.MediaType;
import javax.ws.rs.core.Response;
import org.dspace.importer.external.pubmed.service.PubmedImportMetadataSourceServiceImpl;
import org.mockito.ArgumentCaptor;
import org.mockito.ArgumentMatchers;
import org.mockito.Mockito;
import org.mockito.invocation.InvocationOnMock;
import org.mockito.stubbing.Answer;
import org.springframework.util.FileCopyUtils;
/**
* we override the init method to mock the rest call to pubmed the following
* mock definitions will allow to answer to efetch or esearch requests using the
* test resource files (pubmed-esearch.fcgi.xml or pubmed-efetch.fcgi.xml)
*
* @author Andrea Bollini (andrea.bollini at 4science.it)
*
*/
public class MockPubmedImportMetadataSourceServiceImpl extends PubmedImportMetadataSourceServiceImpl {
@Override
public void init() throws Exception {
pubmedWebTarget = Mockito.mock(WebTarget.class);
ArgumentCaptor<String> valueCapture = ArgumentCaptor.forClass(String.class);
when(pubmedWebTarget.queryParam(ArgumentMatchers.any(), ArgumentMatchers.any()))
.thenAnswer(new Answer<WebTarget>() {
@Override
public WebTarget answer(InvocationOnMock invocation) throws Throwable {
return pubmedWebTarget;
}
});
when(pubmedWebTarget.path(valueCapture.capture())).thenAnswer(new Answer<WebTarget>() {
@Override
public WebTarget answer(InvocationOnMock invocation) throws Throwable {
return pubmedWebTarget;
}
});
when(pubmedWebTarget.request(ArgumentMatchers.any(MediaType.class)))
.thenAnswer(new Answer<Invocation.Builder>() {
@Override
public Invocation.Builder answer(InvocationOnMock invocation) throws Throwable {
Invocation.Builder builder = Mockito.mock(Invocation.Builder.class);
when(builder.get()).thenAnswer(new Answer<Response>() {
@Override
public Response answer(InvocationOnMock invocation) throws Throwable {
Response response = Mockito.mock(Response.class);
when(response.readEntity(ArgumentMatchers.eq(String.class))).then(new Answer<String>() {
@Override
public String answer(InvocationOnMock invocation) throws Throwable {
String resourceName = "pubmed-" + valueCapture.getValue() + ".xml";
InputStream resource = getClass().getResourceAsStream(resourceName);
try (Reader reader = new InputStreamReader(resource, StandardCharsets.UTF_8)) {
return FileCopyUtils.copyToString(reader);
} catch (IOException e) {
throw new UncheckedIOException(e);
}
}
});
return response;
}
});
return builder;
};
});
}
}

View File

@@ -0,0 +1,90 @@
/**
* 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.process;
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertTrue;
import java.util.HashSet;
import java.util.LinkedList;
import java.util.List;
import java.util.Set;
import java.util.UUID;
import org.dspace.AbstractIntegrationTestWithDatabase;
import org.dspace.builder.GroupBuilder;
import org.dspace.builder.ProcessBuilder;
import org.dspace.eperson.Group;
import org.dspace.eperson.factory.EPersonServiceFactory;
import org.dspace.eperson.service.GroupService;
import org.dspace.scripts.Process;
import org.dspace.scripts.factory.ScriptServiceFactory;
import org.dspace.scripts.service.ProcessService;
import org.junit.Test;
/**
* This class will aim to test Process related use cases
*
* @author Mykhaylo Boychuk (mykhaylo.boychuk at 4science.it)
*/
public class ProcessIT extends AbstractIntegrationTestWithDatabase {
protected ProcessService processService = ScriptServiceFactory.getInstance().getProcessService();
protected GroupService groupService = EPersonServiceFactory.getInstance().getGroupService();
@Test
public void checkProcessGroupsTest() throws Exception {
context.turnOffAuthorisationSystem();
Group groupA = GroupBuilder.createGroup(context)
.withName("Group A")
.addMember(admin)
.build();
Set<Group> groupSet = new HashSet<>();
groupSet.add(groupA);
Process processA = ProcessBuilder.createProcess(context, admin, "mock-script",
new LinkedList<>(),
groupSet).build();
context.restoreAuthSystemState();
Process process = processService.find(context, processA.getID());
List<Group> groups = process.getGroups();
boolean isPresent = groups.stream().anyMatch(g -> g.getID().equals(groupA.getID()));
assertTrue(isPresent);
}
@Test
public void removeOneGroupTest() throws Exception {
context.turnOffAuthorisationSystem();
Group groupA = GroupBuilder.createGroup(context)
.withName("Group A")
.addMember(admin).build();
Set<Group> groupSet = new HashSet<>();
groupSet.add(groupA);
UUID groupUuid = groupA.getID();
Process processA = ProcessBuilder.createProcess(context, admin, "mock-script", new LinkedList<>(),
groupSet).build();
context.restoreAuthSystemState();
groupService.delete(context, groupA);
context.commit();
context.reloadEntity(groupA);
processA = context.reloadEntity(processA);
Process process = processService.find(context, processA.getID());
List<Group> groups = process.getGroups();
boolean isPresent = groups.stream().anyMatch(g -> g.getID().equals(groupUuid));
assertFalse(isPresent);
}
}

View File

@@ -0,0 +1,53 @@
/**
* 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.util;
import static org.hamcrest.Matchers.allOf;
import static org.hamcrest.Matchers.hasProperty;
import static org.hamcrest.Matchers.is;
import static org.hamcrest.Matchers.nullValue;
import org.dspace.content.Item;
import org.dspace.content.Relationship.LatestVersionStatus;
import org.dspace.content.RelationshipType;
import org.hamcrest.Matcher;
/**
* Methods for testing relationships and their behavior with versioned items.
*/
public class RelationshipVersioningTestUtils {
private RelationshipVersioningTestUtils() {}
public static Matcher<Object> isRel(
Item leftItem, RelationshipType relationshipType, Item rightItem, LatestVersionStatus latestVersionStatus,
int leftPlace, int rightPlace
) {
return isRel(leftItem, relationshipType, rightItem, latestVersionStatus, null, null, leftPlace, rightPlace);
}
public static Matcher<Object> isRel(
Item leftItem, RelationshipType relationshipType, Item rightItem, LatestVersionStatus latestVersionStatus,
String leftwardValue, String rightwardValue, int leftPlace, int rightPlace
) {
return allOf(
hasProperty("leftItem", is(leftItem)),
// NOTE: this is a painful one... class RelationshipType does not implement the equals method, so we cannot
// rely on object equality and have to compare ids instead. It has to be in capital letters,
// because the getter has been implemented inconsistently (#id vs #setId() vs #getID()).
hasProperty("relationshipType", hasProperty("ID", is(relationshipType.getID()))),
hasProperty("rightItem", is(rightItem)),
hasProperty("leftPlace", is(leftPlace)),
hasProperty("rightPlace", is(rightPlace)),
hasProperty("leftwardValue", leftwardValue == null ? nullValue() : is(leftwardValue)),
hasProperty("rightwardValue", rightwardValue == null ? nullValue() : is(rightwardValue)),
hasProperty("latestVersionStatus", is(latestVersionStatus))
);
}
}

View File

@@ -20,6 +20,7 @@ import org.dspace.app.rest.utils.DSpaceAPIRequestLoggingFilter;
import org.dspace.app.rest.utils.DSpaceConfigurationInitializer;
import org.dspace.app.rest.utils.DSpaceKernelInitializer;
import org.dspace.app.sitemap.GenerateSitemaps;
import org.dspace.app.solrdatabaseresync.SolrDatabaseResyncCli;
import org.dspace.app.util.DSpaceContextListener;
import org.dspace.utils.servlet.DSpaceWebappServletFilter;
import org.slf4j.Logger;
@@ -71,6 +72,11 @@ public class Application extends SpringBootServletInitializer {
GenerateSitemaps.generateSitemapsScheduled();
}
@Scheduled(cron = "${solr-database-resync.cron:-}")
public void solrDatabaseResync() throws Exception {
SolrDatabaseResyncCli.runScheduled();
}
/**
* Override the default SpringBootServletInitializer.configure() method,
* passing it this Application class.

Some files were not shown because too many files have changed in this diff Show More