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[DS-2701] dspace-oai 'the simple bits'

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This commit is contained in:
Mark H. Wood
2015-08-19 16:43:23 -04:00
parent dc96b2d3ee
commit 021fba9d40
13 changed files with 210 additions and 193 deletions
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81
dspace-oai/src/main/java/org/dspace/xoai/app/XOAI.java
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@@ -23,14 +23,11 @@ import org.apache.solr.client.solrj.SolrServer;
import org.apache.solr.client.solrj.SolrServerException; import org.apache.solr.client.solrj.SolrServerException;
import org.apache.solr.common.SolrDocumentList; import org.apache.solr.common.SolrDocumentList;
import org.apache.solr.common.SolrInputDocument; import org.apache.solr.common.SolrInputDocument;
import org.dspace.authorize.AuthorizeException; import org.dspace.authorize.service.AuthorizeService;
import org.dspace.authorize.AuthorizeServiceImpl;
import org.dspace.content.*; import org.dspace.content.*;
import org.dspace.core.ConfigurationManager; import org.dspace.core.ConfigurationManager;
import org.dspace.core.Constants; import org.dspace.core.Constants;
import org.dspace.core.Context; import org.dspace.core.Context;
import org.dspace.storage.rdbms.DatabaseManager;
import org.dspace.storage.rdbms.TableRowIterator;
import org.dspace.xoai.exceptions.CompilingException; import org.dspace.xoai.exceptions.CompilingException;
import org.dspace.xoai.services.api.cache.XOAICacheService; import org.dspace.xoai.services.api.cache.XOAICacheService;
import org.dspace.xoai.services.api.cache.XOAIItemCacheService; import org.dspace.xoai.services.api.cache.XOAIItemCacheService;
@@ -55,10 +52,12 @@ import java.text.ParseException;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.Arrays; import java.util.Arrays;
import java.util.Date; import java.util.Date;
import java.util.Iterator;
import java.util.List; import java.util.List;
import javax.inject.Inject;
import org.dspace.content.service.ItemService;
import static com.lyncode.xoai.dataprovider.core.Granularity.Second; import static com.lyncode.xoai.dataprovider.core.Granularity.Second;
import static org.dspace.content.Item.find;
import static org.dspace.xoai.util.ItemUtils.retrieveMetadata; import static org.dspace.xoai.util.ItemUtils.retrieveMetadata;
/** /**
@@ -68,9 +67,9 @@ import static org.dspace.xoai.util.ItemUtils.retrieveMetadata;
public class XOAI { public class XOAI {
private static Logger log = LogManager.getLogger(XOAI.class); private static Logger log = LogManager.getLogger(XOAI.class);
private Context context; private final Context context;
private boolean optimize; private boolean optimize;
private boolean verbose; private final boolean verbose;
private boolean clean; private boolean clean;
@Autowired @Autowired
@@ -87,15 +86,19 @@ public class XOAI {
private XOAIItemCacheService xoaiItemCacheService; private XOAIItemCacheService xoaiItemCacheService;
@Autowired @Autowired
private CollectionsService collectionsService; private CollectionsService collectionsService;
@Inject
private AuthorizeService authorizeService;
@Inject
private ItemService itemService;
private static List<String> getFileFormats(Item item) { private List<String> getFileFormats(Item item) {
List<String> formats = new ArrayList<String>(); List<String> formats = new ArrayList<>();
try { try {
for (Bundle b : item.getBundles("ORIGINAL")) { for (Bundle b : itemService.getBundles(item, "ORIGINAL")) {
for (Bitstream bs : b.getBitstreams()) { for (BundleBitstream bs : b.getBitstreams()) {
if (!formats.contains(bs.getFormat().getMIMEType())) { if (!formats.contains(bs.getBitstream().getFormat(context).getMIMEType())) {
formats.add(bs.getFormat().getMIMEType()); formats.add(bs.getBitstream().getFormat(context).getMIMEType());
} }
} }
} }
@@ -154,11 +157,7 @@ public class XOAI {
// Set last compilation date // Set last compilation date
xoaiLastCompilationCacheService.put(new Date()); xoaiLastCompilationCacheService.put(new Date());
return result; return result;
} catch (DSpaceSolrException ex) { } catch (DSpaceSolrException | SolrServerException | IOException ex) {
throw new DSpaceSolrIndexerException(ex.getMessage(), ex);
} catch (SolrServerException ex) {
throw new DSpaceSolrIndexerException(ex.getMessage(), ex);
} catch (IOException ex) {
throw new DSpaceSolrIndexerException(ex.getMessage(), ex); throw new DSpaceSolrIndexerException(ex.getMessage(), ex);
} }
} }
@@ -257,17 +256,20 @@ public class XOAI {
doc.addField("item.communities", doc.addField("item.communities",
"com_" + com.getHandle().replace("/", "_")); "com_" + com.getHandle().replace("/", "_"));
Metadatum[] allData = item.getMetadata(Item.ANY, Item.ANY, Item.ANY, List<MetadataValue> allData = itemService.getMetadata(item,
Item.ANY); Item.ANY, Item.ANY, Item.ANY, Item.ANY);
for (Metadatum dc : allData) { for (MetadataValue dc : allData) {
String key = "metadata." + dc.schema + "." + dc.element; MetadataField field = dc.getMetadataField();
if (dc.qualifier != null) { String key = "metadata."
key += "." + dc.qualifier; + field.getMetadataSchema().getName() + "."
+ field.getElement();
if (field.getQualifier() != null) {
key += "." + field.getQualifier();
} }
doc.addField(key, dc.value); doc.addField(key, dc.getValue());
if (dc.authority != null) { if (dc.getAuthority() != null) {
doc.addField(key + ".authority", dc.authority); doc.addField(key + ".authority", dc.getAuthority());
doc.addField(key + ".confidence", dc.confidence + ""); doc.addField(key + ".confidence", dc.getConfidence() + "");
} }
} }
@@ -276,10 +278,10 @@ public class XOAI {
} }
ByteArrayOutputStream out = new ByteArrayOutputStream(); ByteArrayOutputStream out = new ByteArrayOutputStream();
XmlOutputContext context = XmlOutputContext.emptyContext(out, Second); XmlOutputContext xmlContext = XmlOutputContext.emptyContext(out, Second);
retrieveMetadata(item).write(context); retrieveMetadata(item).write(xmlContext);
context.getWriter().flush(); xmlContext.getWriter().flush();
context.getWriter().close(); xmlContext.getWriter().close();
doc.addField("item.compile", out.toString()); doc.addField("item.compile", out.toString());
if (verbose) { if (verbose) {
@@ -294,7 +296,7 @@ public class XOAI {
boolean pub = false; boolean pub = false;
try { try {
//Check if READ access allowed on this Item //Check if READ access allowed on this Item
pub = AuthorizeManager.authorizeActionBoolean(context, item, Constants.READ); pub = authorizeService.authorizeActionBoolean(context, item, Constants.READ);
} catch (SQLException ex) { } catch (SQLException ex) {
log.error(ex.getMessage()); log.error(ex.getMessage());
} }
@@ -327,9 +329,7 @@ public class XOAI {
solrServerResolver.getServer().deleteByQuery("*:*"); solrServerResolver.getServer().deleteByQuery("*:*");
solrServerResolver.getServer().commit(); solrServerResolver.getServer().commit();
System.out.println("Index cleared"); System.out.println("Index cleared");
} catch (SolrServerException ex) { } catch (SolrServerException | IOException ex) {
throw new DSpaceSolrIndexerException(ex.getMessage(), ex);
} catch (IOException ex) {
throw new DSpaceSolrIndexerException(ex.getMessage(), ex); throw new DSpaceSolrIndexerException(ex.getMessage(), ex);
} }
} }
@@ -449,13 +449,13 @@ public class XOAI {
} }
private void compile() throws CompilingException { private void compile() throws CompilingException {
ItemIterator iterator; Iterator<Item> iterator;
try { try {
Date last = xoaiLastCompilationCacheService.get(); Date last = xoaiLastCompilationCacheService.get();
if (last == null) { if (last == null) {
System.out.println("Retrieving all items to be compiled"); System.out.println("Retrieving all items to be compiled");
iterator = Item.findAll(context); iterator = itemService.findAll(context);
} else { } else {
System.out.println("Retrieving items modified after " + last + " to be compiled"); System.out.println("Retrieving items modified after " + last + " to be compiled");
String query = "SELECT * FROM item WHERE last_modified>?"; String query = "SELECT * FROM item WHERE last_modified>?";
@@ -466,13 +466,10 @@ public class XOAI {
Item item = iterator.next(); Item item = iterator.next();
if (verbose) System.out.println("Compiling item with handle: " + item.getHandle()); if (verbose) System.out.println("Compiling item with handle: " + item.getHandle());
xoaiItemCacheService.put(item, retrieveMetadata(item)); xoaiItemCacheService.put(item, retrieveMetadata(item));
context.clearCache();
} }
xoaiLastCompilationCacheService.put(new Date()); xoaiLastCompilationCacheService.put(new Date());
} catch (SQLException e) { } catch (SQLException | IOException e) {
throw new CompilingException(e);
} catch (IOException e) {
throw new CompilingException(e); throw new CompilingException(e);
} }
System.out.println("Items compiled"); System.out.println("Items compiled");

20
dspace-oai/src/main/java/org/dspace/xoai/filter/DSpaceAuthorizationFilter.java
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@@ -14,11 +14,13 @@ import java.util.List;
import org.apache.log4j.LogManager; import org.apache.log4j.LogManager;
import org.apache.log4j.Logger; import org.apache.log4j.Logger;
import org.dspace.authorize.AuthorizeManager; import org.dspace.authorize.factory.AuthorizeServiceFactory;
import org.dspace.authorize.service.AuthorizeService;
import org.dspace.content.Item; import org.dspace.content.Item;
import org.dspace.core.Constants; import org.dspace.core.Constants;
import org.dspace.core.Context; import org.dspace.core.Context;
import org.dspace.handle.HandleServiceImpl; import org.dspace.handle.factory.HandleServiceFactory;
import org.dspace.handle.service.HandleService;
import org.dspace.xoai.data.DSpaceItem; import org.dspace.xoai.data.DSpaceItem;
import org.dspace.xoai.filter.results.DatabaseFilterResult; import org.dspace.xoai.filter.results.DatabaseFilterResult;
import org.dspace.xoai.filter.results.SolrFilterResult; import org.dspace.xoai.filter.results.SolrFilterResult;
@@ -29,12 +31,18 @@ import org.dspace.xoai.filter.results.SolrFilterResult;
*/ */
public class DSpaceAuthorizationFilter extends DSpaceFilter public class DSpaceAuthorizationFilter extends DSpaceFilter
{ {
private static Logger log = LogManager.getLogger(DSpaceAuthorizationFilter.class); private static final Logger log = LogManager.getLogger(DSpaceAuthorizationFilter.class);
private static final AuthorizeService authorizeService
= AuthorizeServiceFactory.getInstance().getAuthorizeService();
private static final HandleService handleService
= HandleServiceFactory.getInstance().getHandleService();
@Override @Override
public DatabaseFilterResult buildDatabaseQuery(Context context) public DatabaseFilterResult buildDatabaseQuery(Context context)
{ {
List<Object> params = new ArrayList<Object>(); List<Object> params = new ArrayList<>();
return new DatabaseFilterResult("EXISTS (SELECT p.action_id FROM " return new DatabaseFilterResult("EXISTS (SELECT p.action_id FROM "
+ "resourcepolicy p, " + "bundle2bitstream b, " + "bundle bu, " + "resourcepolicy p, " + "bundle2bitstream b, " + "bundle bu, "
+ "item2bundle ib " + "WHERE " + "p.resource_type_id=0 AND " + "item2bundle ib " + "WHERE " + "p.resource_type_id=0 AND "
@@ -54,12 +62,12 @@ public class DSpaceAuthorizationFilter extends DSpaceFilter
String handle = DSpaceItem.parseHandle(item.getIdentifier()); String handle = DSpaceItem.parseHandle(item.getIdentifier());
if (handle == null) if (handle == null)
return false; return false;
Item dspaceItem = (Item) HandleManager.resolveToObject(context, handle); Item dspaceItem = (Item) handleService.resolveToObject(context, handle);
if (dspaceItem == null) if (dspaceItem == null)
return false; return false;
// Check if READ access allowed on Item // Check if READ access allowed on Item
pub = AuthorizeManager.authorizeActionBoolean(context, dspaceItem, Constants.READ); pub = authorizeService.authorizeActionBoolean(context, dspaceItem, Constants.READ);
} }
catch (SQLException ex) catch (SQLException ex)
{ {

15
dspace-oai/src/main/java/org/dspace/xoai/filter/DSpaceSetSpecFilter.java
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@@ -8,6 +8,7 @@
package org.dspace.xoai.filter; package org.dspace.xoai.filter;
import com.lyncode.xoai.dataprovider.core.ReferenceSet; import com.lyncode.xoai.dataprovider.core.ReferenceSet;
import java.sql.SQLException;
import org.apache.commons.lang.StringUtils; import org.apache.commons.lang.StringUtils;
import org.apache.log4j.LogManager; import org.apache.log4j.LogManager;
import org.apache.log4j.Logger; import org.apache.log4j.Logger;
@@ -21,6 +22,8 @@ import org.dspace.xoai.services.api.database.CollectionsService;
import org.dspace.xoai.services.api.database.HandleResolver; import org.dspace.xoai.services.api.database.HandleResolver;
import java.util.List; import java.util.List;
import java.util.UUID;
import org.dspace.xoai.services.api.database.HandleResolverException;
/** /**
* *
@@ -28,11 +31,11 @@ import java.util.List;
*/ */
public class DSpaceSetSpecFilter extends DSpaceFilter public class DSpaceSetSpecFilter extends DSpaceFilter
{ {
private static Logger log = LogManager.getLogger(DSpaceSetSpecFilter.class); private static final Logger log = LogManager.getLogger(DSpaceSetSpecFilter.class);
private String setSpec; private final String setSpec;
private HandleResolver handleResolver; private final HandleResolver handleResolver;
private CollectionsService collectionsService; private final CollectionsService collectionsService;
public DSpaceSetSpecFilter(CollectionsService collectionsService, HandleResolver handleResolver, String spec) public DSpaceSetSpecFilter(CollectionsService collectionsService, HandleResolver handleResolver, String spec)
{ {
@@ -66,14 +69,14 @@ public class DSpaceSetSpecFilter extends DSpaceFilter
{ {
DSpaceObject dso = handleResolver.resolve(setSpec.replace("com_", "").replace("_", "/")); DSpaceObject dso = handleResolver.resolve(setSpec.replace("com_", "").replace("_", "/"));
if(dso != null){ if(dso != null){
List<Integer> list = collectionsService.getAllSubCollections(dso.getID()); List<UUID> list = collectionsService.getAllSubCollections(dso.getID());
String subCollections = StringUtils.join(list.iterator(), ","); String subCollections = StringUtils.join(list.iterator(), ",");
return new DatabaseFilterResult( return new DatabaseFilterResult(
"EXISTS (SELECT tmp.* FROM collection2item tmp WHERE tmp.resource_id=i.item_id AND collection_id IN (" "EXISTS (SELECT tmp.* FROM collection2item tmp WHERE tmp.resource_id=i.item_id AND collection_id IN ("
+ subCollections + "))"); + subCollections + "))");
} }
} }
catch (Exception e) catch (HandleResolverException | SQLException e)
{ {
log.error(e.getMessage(), e); log.error(e.getMessage(), e);
} }

7
dspace-oai/src/main/java/org/dspace/xoai/filter/DSpaceWithdrawnFilter.java
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@@ -31,7 +31,7 @@ public class DSpaceWithdrawnFilter extends DSpaceFilter {
@Override @Override
public DatabaseFilterResult buildDatabaseQuery(Context context) public DatabaseFilterResult buildDatabaseQuery(Context context)
{ {
List<Object> params = new ArrayList<Object>(); List<Object> params = new ArrayList<>();
String filter = "i.withdrawn=TRUE"; String filter = "i.withdrawn=TRUE";
if(DatabaseManager.isOracle()) if(DatabaseManager.isOracle())
@@ -48,10 +48,7 @@ public class DSpaceWithdrawnFilter extends DSpaceFilter {
// we can properly respond with a "deleted" status via OAI-PMH. // we can properly respond with a "deleted" status via OAI-PMH.
// Don't worry, this does NOT make the metadata public for withdrawn items, // Don't worry, this does NOT make the metadata public for withdrawn items,
// it merely provides an item "tombstone" via OAI-PMH. // it merely provides an item "tombstone" via OAI-PMH.
if (item.isDeleted()) return item.isDeleted();
return true;
else
return false;
} }
@Override @Override

3
dspace-oai/src/main/java/org/dspace/xoai/services/api/database/CollectionsService.java
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@@ -13,9 +13,10 @@ import org.dspace.content.Item;
import java.sql.SQLException; import java.sql.SQLException;
import java.util.List; import java.util.List;
import java.util.UUID;
public interface CollectionsService { public interface CollectionsService {
List<Integer> getAllSubCollections(int communityId) throws SQLException; List<UUID> getAllSubCollections(UUID communityId) throws SQLException;
List<Community> flatParentCommunities(Collection collection) throws SQLException; List<Community> flatParentCommunities(Collection collection) throws SQLException;
List<Community> flatParentCommunities(Community community) throws SQLException; List<Community> flatParentCommunities(Community community) throws SQLException;
List<Community> flatParentCommunities(Item item) throws SQLException; List<Community> flatParentCommunities(Item item) throws SQLException;

8
dspace-oai/src/main/java/org/dspace/xoai/services/api/database/DatabaseQuery.java
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@@ -16,11 +16,11 @@ import java.util.ArrayList;
import java.util.List; import java.util.List;
public class DatabaseQuery { public class DatabaseQuery {
private static Logger log = Logger.getLogger(DatabaseQuery.class); private static final Logger log = Logger.getLogger(DatabaseQuery.class);
private String query; private String query;
private List<Object> parameters; private final List<Object> parameters;
private Context context; private final Context context;
private Integer total; private Integer total;
private String countQuery; private String countQuery;
@@ -28,7 +28,7 @@ public class DatabaseQuery {
public DatabaseQuery(Context context) { public DatabaseQuery(Context context) {
this.context = context; this.context = context;
this.parameters = new ArrayList<Object>(); this.parameters = new ArrayList<>();
} }
public String getQuery() { public String getQuery() {

7
dspace-oai/src/main/java/org/dspace/xoai/services/impl/context/DSpaceContextService.java
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@@ -14,7 +14,6 @@ import org.springframework.web.context.request.RequestContextHolder;
import org.springframework.web.context.request.ServletRequestAttributes; import org.springframework.web.context.request.ServletRequestAttributes;
import javax.servlet.http.HttpServletRequest; import javax.servlet.http.HttpServletRequest;
import java.sql.SQLException;
public class DSpaceContextService implements ContextService { public class DSpaceContextService implements ContextService {
private static final String OAI_CONTEXT = "OAI_CONTEXT"; private static final String OAI_CONTEXT = "OAI_CONTEXT";
@@ -24,11 +23,7 @@ public class DSpaceContextService implements ContextService {
HttpServletRequest request = ((ServletRequestAttributes) RequestContextHolder.currentRequestAttributes()).getRequest(); HttpServletRequest request = ((ServletRequestAttributes) RequestContextHolder.currentRequestAttributes()).getRequest();
Object value = request.getAttribute(OAI_CONTEXT); Object value = request.getAttribute(OAI_CONTEXT);
if (value == null || !(value instanceof Context)) { if (value == null || !(value instanceof Context)) {
try { request.setAttribute(OAI_CONTEXT, new Context());
request.setAttribute(OAI_CONTEXT, new Context());
} catch (SQLException e) {
throw new ContextServiceException(e);
}
} }
return (Context) request.getAttribute(OAI_CONTEXT); return (Context) request.getAttribute(OAI_CONTEXT);
} }

47
dspace-oai/src/main/java/org/dspace/xoai/services/impl/database/DSpaceCollectionsService.java
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@@ -19,18 +19,24 @@ import java.util.ArrayList;
import java.util.LinkedList; import java.util.LinkedList;
import java.util.List; import java.util.List;
import java.util.Queue; import java.util.Queue;
import java.util.UUID;
import org.dspace.content.factory.ContentServiceFactory;
import org.dspace.content.service.CommunityService;
public class DSpaceCollectionsService implements CollectionsService { public class DSpaceCollectionsService implements CollectionsService {
private ContextService contextService; private ContextService contextService;
private static final CommunityService communityService
= ContentServiceFactory.getInstance().getCommunityService();
public List<Integer> getAllSubCollections(int communityId) @Override
public List<UUID> getAllSubCollections(UUID communityId)
throws SQLException throws SQLException
{ {
Queue<Community> comqueue = new LinkedList<Community>(); Queue<Community> comqueue = new LinkedList<>();
List<Integer> list = new ArrayList<Integer>(); List<UUID> list = new ArrayList<>();
try { try {
comqueue.add(Community.find(contextService.getContext(), communityId)); comqueue.add(communityService.find(contextService.getContext(), communityId));
} catch (ContextServiceException e) { } catch (ContextServiceException e) {
throw new SQLException(e); throw new SQLException(e);
} }
@@ -40,26 +46,27 @@ public class DSpaceCollectionsService implements CollectionsService {
for (Community sub : c.getSubcommunities()) for (Community sub : c.getSubcommunities())
comqueue.add(sub); comqueue.add(sub);
for (Collection col : c.getCollections()) for (Collection col : c.getCollections())
if (!list.contains(col)) if (!list.contains(col.getID()))
list.add(col.getID()); list.add(col.getID());
} }
return list; return list;
} }
@Override
public List<Community> flatParentCommunities(Collection c) public List<Community> flatParentCommunities(Collection c)
throws SQLException throws SQLException
{ {
Queue<Community> queue = new LinkedList<Community>(); Queue<Community> queue = new LinkedList<>();
List<Community> result = new ArrayList<Community>(); List<Community> result = new ArrayList<>();
for (Community com : c.getCommunities()) for (Community com : c.getCommunities())
queue.add(com); queue.add(com);
while (!queue.isEmpty()) while (!queue.isEmpty())
{ {
Community p = queue.poll(); Community p = queue.poll();
Community par = p.getParentCommunity(); List<Community> par = p.getParentCommunities();
if (par != null) if (par != null)
queue.add(par); queue.addAll(par);
if (!result.contains(p)) if (!result.contains(p))
result.add(p); result.add(p);
} }
@@ -67,20 +74,21 @@ public class DSpaceCollectionsService implements CollectionsService {
return result; return result;
} }
@Override
public List<Community> flatParentCommunities(Community c) public List<Community> flatParentCommunities(Community c)
throws SQLException throws SQLException
{ {
Queue<Community> queue = new LinkedList<Community>(); Queue<Community> queue = new LinkedList<>();
List<Community> result = new ArrayList<Community>(); List<Community> result = new ArrayList<>();
queue.add(c); queue.add(c);
while (!queue.isEmpty()) while (!queue.isEmpty())
{ {
Community p = queue.poll(); Community p = queue.poll();
Community par = p.getParentCommunity(); List<Community> par = p.getParentCommunities();
if (par != null) if (par != null)
queue.add(par); queue.addAll(par);
if (!result.contains(p)) if (!result.contains(p))
result.add(p); result.add(p);
} }
@@ -88,21 +96,22 @@ public class DSpaceCollectionsService implements CollectionsService {
return result; return result;
} }
@Override
public List<Community> flatParentCommunities(Item c) public List<Community> flatParentCommunities(Item c)
throws SQLException throws SQLException
{ {
Queue<Community> queue = new LinkedList<Community>(); Queue<Community> queue = new LinkedList<>();
List<Community> result = new ArrayList<Community>(); List<Community> result = new ArrayList<>();
for (Community com : c.getCommunities()) for (Collection com : c.getCollections())
queue.add(com); queue.addAll(com.getCommunities());
while (!queue.isEmpty()) while (!queue.isEmpty())
{ {
Community p = queue.poll(); Community p = queue.poll();
Community par = p.getParentCommunity(); List<Community> par = p.getParentCommunities();
if (par != null) if (par != null)
queue.add(par); queue.addAll(par);
if (!result.contains(p)) if (!result.contains(p))
result.add(p); result.add(p);
} }

6
dspace-oai/src/main/java/org/dspace/xoai/services/impl/database/DSpaceDatabaseQueryResolver.java
View File

@@ -39,8 +39,8 @@ public class DSpaceDatabaseQueryResolver implements DatabaseQueryResolver {
@Override @Override
public DatabaseQuery buildQuery(List<ScopedFilter> filters, int offset, int length) throws DatabaseQueryException { public DatabaseQuery buildQuery(List<ScopedFilter> filters, int offset, int length) throws DatabaseQueryException {
List<Object> parameters = new ArrayList<Object>(); List<Object> parameters = new ArrayList<>();
List<Object> countParameters = new ArrayList<Object>(); List<Object> countParameters = new ArrayList<>();
String query = "SELECT i.* FROM item i "; String query = "SELECT i.* FROM item i ";
String countQuery = "SELECT COUNT(*) as count FROM item i"; String countQuery = "SELECT COUNT(*) as count FROM item i";
@@ -98,7 +98,7 @@ public class DSpaceDatabaseQueryResolver implements DatabaseQueryResolver {
} }
private String buildCondition (List<ScopedFilter> filters, List<Object> parameters) throws ContextServiceException { private String buildCondition (List<ScopedFilter> filters, List<Object> parameters) throws ContextServiceException {
List<String> whereCond = new ArrayList<String>(); List<String> whereCond = new ArrayList<>();
for (ScopedFilter filter : filters) for (ScopedFilter filter : filters)
whereCond.add(this.buildQuery(filter.getCondition(), filter.getScope(), parameters)); whereCond.add(this.buildQuery(filter.getCondition(), filter.getScope(), parameters));

25
dspace-oai/src/main/java/org/dspace/xoai/services/impl/database/DSpaceHandlerResolver.java
View File

@@ -7,28 +7,27 @@
*/ */
package org.dspace.xoai.services.impl.database; package org.dspace.xoai.services.impl.database;
import java.sql.SQLException;
import javax.inject.Inject;
import org.dspace.content.DSpaceObject; import org.dspace.content.DSpaceObject;
import org.dspace.handle.HandleServiceImpl; import org.dspace.handle.service.HandleService;
import org.dspace.xoai.services.api.context.ContextService; import org.dspace.xoai.services.api.context.ContextService;
import org.dspace.xoai.services.api.context.ContextServiceException; import org.dspace.xoai.services.api.context.ContextServiceException;
import org.dspace.xoai.services.api.database.HandleResolver; import org.dspace.xoai.services.api.database.HandleResolver;
import org.dspace.xoai.services.api.database.HandleResolverException; import org.dspace.xoai.services.api.database.HandleResolverException;
import org.springframework.beans.factory.annotation.Autowired;
import java.sql.SQLException;
public class DSpaceHandlerResolver implements HandleResolver { public class DSpaceHandlerResolver implements HandleResolver {
@Autowired @Inject
private ContextService contextService; private ContextService contextService;
@Inject
private HandleService handleService;
@Override @Override
public DSpaceObject resolve(String handle) throws HandleResolverException { public DSpaceObject resolve(String handle) throws HandleResolverException {
try { try {
return HandleServiceImpl.resolveToObject(contextService.getContext(), handle); return handleService.resolveToObject(contextService.getContext(), handle);
} catch (ContextServiceException e) { } catch (ContextServiceException | SQLException e) {
throw new HandleResolverException(e);
} catch (SQLException e) {
throw new HandleResolverException(e); throw new HandleResolverException(e);
} }
} }
@@ -36,10 +35,8 @@ public class DSpaceHandlerResolver implements HandleResolver {
@Override @Override
public String getHandle(DSpaceObject object) throws HandleResolverException { public String getHandle(DSpaceObject object) throws HandleResolverException {
try { try {
return HandleServiceImpl.findHandle(contextService.getContext(), object); return handleService.findHandle(contextService.getContext(), object);
} catch (SQLException e) { } catch (SQLException | ContextServiceException e) {
throw new HandleResolverException(e);
} catch (ContextServiceException e) {
throw new HandleResolverException(e); throw new HandleResolverException(e);
} }
} }

25
dspace-oai/src/main/java/org/dspace/xoai/services/impl/xoai/DSpaceItemDatabaseRepository.java
View File

@@ -39,6 +39,8 @@ import java.sql.SQLException;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.List; import java.util.List;
import java.util.regex.Pattern; import java.util.regex.Pattern;
import org.dspace.handle.factory.HandleServiceFactory;
import org.dspace.handle.service.HandleService;
/** /**
* *
@@ -48,7 +50,10 @@ import java.util.regex.Pattern;
public class DSpaceItemDatabaseRepository extends DSpaceItemRepository public class DSpaceItemDatabaseRepository extends DSpaceItemRepository
{ {
private static Logger log = LogManager.getLogger(DSpaceItemDatabaseRepository.class); private static final Logger log = LogManager.getLogger(DSpaceItemDatabaseRepository.class);
private static final HandleService handleService
= HandleServiceFactory.getInstance().getHandleService();
private XOAIItemCacheService cacheService; private XOAIItemCacheService cacheService;
private boolean useCache; private boolean useCache;
@@ -79,11 +84,11 @@ public class DSpaceItemDatabaseRepository extends DSpaceItemRepository
private List<ReferenceSet> getSets(org.dspace.content.Item item) private List<ReferenceSet> getSets(org.dspace.content.Item item)
{ {
List<ReferenceSet> sets = new ArrayList<ReferenceSet>(); List<ReferenceSet> sets = new ArrayList<>();
List<Community> coms = new ArrayList<Community>(); List<Community> coms = new ArrayList<>();
try try
{ {
Collection[] itemCollections = item.getCollections(); List<Collection> itemCollections = item.getCollections();
for (Collection col : itemCollections) for (Collection col : itemCollections)
{ {
ReferenceSet s = new DSpaceSet(col); ReferenceSet s = new DSpaceSet(col);
@@ -113,7 +118,7 @@ public class DSpaceItemDatabaseRepository extends DSpaceItemRepository
String parts[] = id.split(Pattern.quote(":")); String parts[] = id.split(Pattern.quote(":"));
if (parts.length == 3) if (parts.length == 3)
{ {
DSpaceObject obj = HandleServiceImpl.resolveToObject(context.getContext(), DSpaceObject obj = handleService.resolveToObject(context.getContext(),
parts[2]); parts[2]);
if (obj == null) if (obj == null)
throw new IdDoesNotExistException(); throw new IdDoesNotExistException();
@@ -129,13 +134,9 @@ public class DSpaceItemDatabaseRepository extends DSpaceItemRepository
log.debug(e.getMessage(), e); log.debug(e.getMessage(), e);
throw new IdDoesNotExistException(); throw new IdDoesNotExistException();
} }
catch (SQLException e) catch (SQLException | IOException | ContextServiceException e)
{ {
throw new OAIException(e); throw new OAIException(e);
} catch (IOException e) {
throw new OAIException(e);
} catch (ContextServiceException e) {
throw new OAIException(e);
} }
throw new IdDoesNotExistException(); throw new IdDoesNotExistException();
} }
@@ -145,7 +146,7 @@ public class DSpaceItemDatabaseRepository extends DSpaceItemRepository
public ListItemsResults getItems(List<ScopedFilter> filters, int offset, public ListItemsResults getItems(List<ScopedFilter> filters, int offset,
int length) throws OAIException int length) throws OAIException
{ {
List<Item> list = new ArrayList<Item>(); List<Item> list = new ArrayList<>();
try try
{ {
DatabaseQuery databaseQuery = queryResolver.buildQuery(filters, offset, length); DatabaseQuery databaseQuery = queryResolver.buildQuery(filters, offset, length);
@@ -179,7 +180,7 @@ public class DSpaceItemDatabaseRepository extends DSpaceItemRepository
List<ScopedFilter> filters, int offset, int length) throws OAIException List<ScopedFilter> filters, int offset, int length) throws OAIException
{ {
List<ItemIdentifier> list = new ArrayList<ItemIdentifier>(); List<ItemIdentifier> list = new ArrayList<>();
try try
{ {
DatabaseQuery databaseQuery = queryResolver.buildQuery(filters, offset, length); DatabaseQuery databaseQuery = queryResolver.buildQuery(filters, offset, length);

45
dspace-oai/src/main/java/org/dspace/xoai/services/impl/xoai/DSpaceSetRepository.java
View File

@@ -16,7 +16,6 @@ import org.dspace.content.Collection;
import org.dspace.content.Community; import org.dspace.content.Community;
import org.dspace.content.DSpaceObject; import org.dspace.content.DSpaceObject;
import org.dspace.core.Context; import org.dspace.core.Context;
import org.dspace.handle.HandleServiceImpl;
import org.dspace.storage.rdbms.DatabaseManager; import org.dspace.storage.rdbms.DatabaseManager;
import org.dspace.storage.rdbms.TableRow; import org.dspace.storage.rdbms.TableRow;
import org.dspace.storage.rdbms.TableRowIterator; import org.dspace.storage.rdbms.TableRowIterator;
@@ -26,6 +25,11 @@ import java.io.Serializable;
import java.sql.SQLException; import java.sql.SQLException;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.List; import java.util.List;
import org.dspace.content.factory.ContentServiceFactory;
import org.dspace.content.service.CollectionService;
import org.dspace.content.service.CommunityService;
import org.dspace.handle.factory.HandleServiceFactory;
import org.dspace.handle.service.HandleService;
/** /**
* *
@@ -35,6 +39,15 @@ public class DSpaceSetRepository implements SetRepository
{ {
private static final Logger log = LogManager.getLogger(DSpaceSetRepository.class); private static final Logger log = LogManager.getLogger(DSpaceSetRepository.class);
private static final CommunityService communityService
= ContentServiceFactory.getInstance().getCommunityService();
private static final CollectionService collectionService
= ContentServiceFactory.getInstance().getCollectionService();
private static final HandleService handleService
= HandleServiceFactory.getInstance().getHandleService();
private final Context _context; private final Context _context;
public DSpaceSetRepository(Context context) public DSpaceSetRepository(Context context)
@@ -84,9 +97,9 @@ public class DSpaceSetRepository implements SetRepository
*/ */
private List<Set> community(int offset, int length) private List<Set> community(int offset, int length)
{ {
List<Set> array = new ArrayList<Set>(); List<Set> array = new ArrayList<>();
StringBuffer query = new StringBuffer("SELECT community_id FROM community ORDER BY community_id"); StringBuffer query = new StringBuffer("SELECT community_id FROM community ORDER BY community_id");
List<Serializable> params = new ArrayList<Serializable>(); List<Serializable> params = new ArrayList<>();
DatabaseManager.applyOffsetAndLimit(query,params,offset,length); DatabaseManager.applyOffsetAndLimit(query,params,offset,length);
@@ -99,7 +112,7 @@ public class DSpaceSetRepository implements SetRepository
{ {
TableRow row = iterator.next(); TableRow row = iterator.next();
int communityID = row.getIntColumn("community_id"); int communityID = row.getIntColumn("community_id");
Community community = Community.find(_context, communityID); Community community = communityService.find(_context, communityID);
array.add(DSpaceSet.newDSpaceCommunitySet( array.add(DSpaceSet.newDSpaceCommunitySet(
community.getHandle(), community.getName())); community.getHandle(), community.getName()));
i++; i++;
@@ -122,9 +135,9 @@ public class DSpaceSetRepository implements SetRepository
*/ */
private List<Set> collection(int offset, int length) private List<Set> collection(int offset, int length)
{ {
List<Set> array = new ArrayList<Set>(); List<Set> array = new ArrayList<>();
StringBuffer query = new StringBuffer("SELECT collection_id FROM collection ORDER BY collection_id"); StringBuffer query = new StringBuffer("SELECT collection_id FROM collection ORDER BY collection_id");
List<Serializable> params = new ArrayList<Serializable>(); List<Serializable> params = new ArrayList<>();
DatabaseManager.applyOffsetAndLimit(query,params,offset,length); DatabaseManager.applyOffsetAndLimit(query,params,offset,length);
@@ -137,7 +150,7 @@ public class DSpaceSetRepository implements SetRepository
{ {
TableRow row = iterator.next(); TableRow row = iterator.next();
int collectionID = row.getIntColumn("collection_id"); int collectionID = row.getIntColumn("collection_id");
Collection collection = Collection.find(_context, collectionID); Collection collection = collectionService.find(_context, collectionID);
array.add(DSpaceSet.newDSpaceCollectionSet( array.add(DSpaceSet.newDSpaceCollectionSet(
collection.getHandle(), collection.getHandle(),
collection.getName())); collection.getName()));
@@ -156,7 +169,7 @@ public class DSpaceSetRepository implements SetRepository
{ {
// Only database sets (virtual sets are added by lyncode common library) // Only database sets (virtual sets are added by lyncode common library)
log.debug("Querying sets. Offset: " + offset + " - Length: " + length); log.debug("Querying sets. Offset: " + offset + " - Length: " + length);
List<Set> array = new ArrayList<Set>(); List<Set> array = new ArrayList<>();
int communityCount = this.getCommunityCount(); int communityCount = this.getCommunityCount();
log.debug("Communities: " + communityCount); log.debug("Communities: " + communityCount);
int collectionCount = this.getCollectionCount(); int collectionCount = this.getCollectionCount();
@@ -198,13 +211,11 @@ public class DSpaceSetRepository implements SetRepository
{ {
try try
{ {
DSpaceObject dso = HandleServiceImpl.resolveToObject(_context, DSpaceObject dso = handleService.resolveToObject(_context,
setSpec.replace("col_", "").replace("_", "/")); setSpec.replace("col_", "").replace("_", "/"));
if (dso == null || !(dso instanceof Collection)) return !(dso == null || !(dso instanceof Collection));
return false;
return true;
} }
catch (Exception ex) catch (IllegalStateException | SQLException ex)
{ {
log.error(ex.getMessage(), ex); log.error(ex.getMessage(), ex);
} }
@@ -213,13 +224,11 @@ public class DSpaceSetRepository implements SetRepository
{ {
try try
{ {
DSpaceObject dso = HandleServiceImpl.resolveToObject(_context, DSpaceObject dso = handleService.resolveToObject(_context,
setSpec.replace("com_", "").replace("_", "/")); setSpec.replace("com_", "").replace("_", "/"));
if (dso == null || !(dso instanceof Community)) return !(dso == null || !(dso instanceof Community));
return false;
return true;
} }
catch (Exception ex) catch (IllegalStateException | SQLException ex)
{ {
log.error(ex.getMessage(), ex); log.error(ex.getMessage(), ex);
} }

114
dspace-oai/src/main/java/org/dspace/xoai/util/ItemUtils.java
View File

@@ -13,7 +13,6 @@ import com.lyncode.xoai.util.Base64Utils;
import org.apache.log4j.LogManager; import org.apache.log4j.LogManager;
import org.apache.log4j.Logger; import org.apache.log4j.Logger;
import org.dspace.authorize.AuthorizeException; import org.dspace.authorize.AuthorizeException;
import org.dspace.content.Bitstream;
import org.dspace.content.Bundle; import org.dspace.content.Bundle;
import org.dspace.content.Metadatum; import org.dspace.content.Metadatum;
import org.dspace.content.Item; import org.dspace.content.Item;
@@ -28,6 +27,11 @@ import java.io.IOException;
import java.io.InputStream; import java.io.InputStream;
import java.sql.SQLException; import java.sql.SQLException;
import java.util.List; import java.util.List;
import org.dspace.content.BundleBitstream;
import org.dspace.content.MetadataField;
import org.dspace.content.MetadataValue;
import org.dspace.content.factory.ContentServiceFactory;
import org.dspace.content.service.ItemService;
/** /**
* *
@@ -36,8 +40,10 @@ import java.util.List;
@SuppressWarnings("deprecation") @SuppressWarnings("deprecation")
public class ItemUtils public class ItemUtils
{ {
private static Logger log = LogManager private static final Logger log = LogManager.getLogger(ItemUtils.class);
.getLogger(ItemUtils.class);
private static final ItemService itemService
= ContentServiceFactory.getInstance().getItemService();
private static Element getElement(List<Element> list, String name) private static Element getElement(List<Element> list, String name)
{ {
@@ -69,38 +75,40 @@ public class ItemUtils
// read all metadata into Metadata Object // read all metadata into Metadata Object
metadata = new Metadata(); metadata = new Metadata();
Metadatum[] vals = item.getMetadata(Item.ANY, Item.ANY, Item.ANY, Item.ANY); List<MetadataValue> vals = itemService.getMetadata(item, Item.ANY, Item.ANY, Item.ANY, Item.ANY);
for (Metadatum val : vals) for (MetadataValue val : vals)
{ {
MetadataField field = val.getMetadataField();
Element valueElem = null; Element valueElem = null;
Element schema = getElement(metadata.getElement(), val.schema); Element schema = getElement(metadata.getElement(), field.getMetadataSchema().getName());
if (schema == null) if (schema == null)
{ {
schema = create(val.schema); schema = create(field.getMetadataSchema().getName());
metadata.getElement().add(schema); metadata.getElement().add(schema);
} }
valueElem = schema; valueElem = schema;
// Has element.. with XOAI one could have only schema and value // Has element.. with XOAI one could have only schema and value
if (val.element != null && !val.element.equals("")) if (field.getElement() != null && !field.getElement().equals(""))
{ {
Element element = getElement(schema.getElement(), Element element = getElement(schema.getElement(),
val.element); field.getElement());
if (element == null) if (element == null)
{ {
element = create(val.element); element = create(field.getElement());
schema.getElement().add(element); schema.getElement().add(element);
} }
valueElem = element; valueElem = element;
// Qualified element? // Qualified element?
if (val.qualifier != null && !val.qualifier.equals("")) if (field.getQualifier() != null && !field.getQualifier().equals(""))
{ {
Element qualifier = getElement(element.getElement(), Element qualifier = getElement(element.getElement(),
val.qualifier); field.getQualifier());
if (qualifier == null) if (qualifier == null)
{ {
qualifier = create(val.qualifier); qualifier = create(field.getQualifier());
element.getElement().add(qualifier); element.getElement().add(qualifier);
} }
valueElem = qualifier; valueElem = qualifier;
@@ -108,13 +116,13 @@ public class ItemUtils
} }
// Language? // Language?
if (val.language != null && !val.language.equals("")) if (val.getLanguage() != null && !val.getLanguage().equals(""))
{ {
Element language = getElement(valueElem.getElement(), Element language = getElement(valueElem.getElement(),
val.language); val.getLanguage());
if (language == null) if (language == null)
{ {
language = create(val.language); language = create(val.getLanguage());
valueElem.getElement().add(language); valueElem.getElement().add(language);
} }
valueElem = language; valueElem = language;
@@ -131,11 +139,11 @@ public class ItemUtils
valueElem = language; valueElem = language;
} }
valueElem.getField().add(createValue("value", val.value)); valueElem.getField().add(createValue("value", val.getValue()));
if (val.authority != null) { if (val.getAuthority() != null) {
valueElem.getField().add(createValue("authority", val.authority)); valueElem.getField().add(createValue("authority", val.getAuthority()));
if (val.confidence != Choices.CF_NOVALUE) if (val.getConfidence() != Choices.CF_NOVALUE)
valueElem.getField().add(createValue("confidence", val.confidence + "")); valueElem.getField().add(createValue("confidence", val.getConfidence() + ""));
} }
} }
// Done! Metadata has been read! // Done! Metadata has been read!
@@ -143,7 +151,7 @@ public class ItemUtils
Element bundles = create("bundles"); Element bundles = create("bundles");
metadata.getElement().add(bundles); metadata.getElement().add(bundles);
Bundle[] bs; List<Bundle> bs;
try try
{ {
bs = item.getBundles(); bs = item.getBundles();
@@ -156,31 +164,31 @@ public class ItemUtils
Element bitstreams = create("bitstreams"); Element bitstreams = create("bitstreams");
bundle.getElement().add(bitstreams); bundle.getElement().add(bitstreams);
Bitstream[] bits = b.getBitstreams(); List<BundleBitstream> bits = b.getBitstreams();
for (Bitstream bit : bits) for (BundleBitstream bit : bits)
{ {
Element bitstream = create("bitstream"); Element bitstream = create("bitstream");
bitstreams.getElement().add(bitstream); bitstreams.getElement().add(bitstream);
String url = ""; String url = "";
String bsName = bit.getName(); String bsName = bit.getBitstream().getName();
String sid = String.valueOf(bit.getSequenceID()); String sid = String.valueOf(bit.getBitstream().getSequenceID());
String baseUrl = ConfigurationManager.getProperty("oai", String baseUrl = ConfigurationManager.getProperty("oai",
"bitstream.baseUrl"); "bitstream.baseUrl");
String handle = null; String handle = null;
// get handle of parent Item of this bitstream, if there // get handle of parent Item of this bitstream, if there
// is one: // is one:
Bundle[] bn = bit.getBundles(); List<BundleBitstream> bn = bit.getBitstream().getBundles();
if (bn.length > 0) if (!bn.isEmpty())
{ {
Item bi[] = bn[0].getItems(); List<Item> bi = bn.get(0).getBundle().getItems();
if (bi.length > 0) if (!bi.isEmpty())
{ {
handle = bi[0].getHandle(); handle = bi.get(0).getHandle();
} }
} }
if (bsName == null) if (bsName == null)
{ {
String ext[] = bit.getFormat().getExtensions(); String ext[] = bit.getBitstream().getFormat().getExtensions();
bsName = "bitstream_" + sid bsName = "bitstream_" + sid
+ (ext.length > 0 ? ext[0] : ""); + (ext.length > 0 ? ext[0] : "");
} }
@@ -196,11 +204,11 @@ public class ItemUtils
url = URLUtils.encode(bsName); url = URLUtils.encode(bsName);
} }
String cks = bit.getChecksum(); String cks = bit.getBitstream().getChecksum();
String cka = bit.getChecksumAlgorithm(); String cka = bit.getBitstream().getChecksumAlgorithm();
String oname = bit.getSource(); String oname = bit.getBitstream().getSource();
String name = bit.getName(); String name = bit.getBitstream().getName();
String description = bit.getDescription(); String description = bit.getBitstream().getDescription();
if (name != null) if (name != null)
bitstream.getField().add( bitstream.getField().add(
@@ -212,17 +220,17 @@ public class ItemUtils
bitstream.getField().add( bitstream.getField().add(
createValue("description", description)); createValue("description", description));
bitstream.getField().add( bitstream.getField().add(
createValue("format", bit.getFormat() createValue("format", bit.getBitstream().getFormat()
.getMIMEType())); .getMIMEType()));
bitstream.getField().add( bitstream.getField().add(
createValue("size", "" + bit.getSize())); createValue("size", "" + bit.getBitstream().getSize()));
bitstream.getField().add(createValue("url", url)); bitstream.getField().add(createValue("url", url));
bitstream.getField().add( bitstream.getField().add(
createValue("checksum", cks)); createValue("checksum", cks));
bitstream.getField().add( bitstream.getField().add(
createValue("checksumAlgorithm", cka)); createValue("checksumAlgorithm", cka));
bitstream.getField().add( bitstream.getField().add(
createValue("sid", bit.getSequenceID() createValue("sid", bit.getBitstream().getSequenceID()
+ "")); + ""));
} }
} }
@@ -257,21 +265,21 @@ public class ItemUtils
// Licensing info // Licensing info
Element license = create("license"); Element license = create("license");
Bundle[] licBundles; List<Bundle> licBundles;
try try
{ {
licBundles = item.getBundles(Constants.LICENSE_BUNDLE_NAME); licBundles = itemService.getBundles(item, Constants.LICENSE_BUNDLE_NAME);
if (licBundles.length > 0) if (!licBundles.isEmpty())
{ {
Bundle licBundle = licBundles[0]; Bundle licBundle = licBundles.get(0);
Bitstream[] licBits = licBundle.getBitstreams(); List<BundleBitstream> licBits = licBundle.getBitstreams();
if (licBits.length > 0) if (!licBits.isEmpty())
{ {
Bitstream licBit = licBits[0]; BundleBitstream licBit = licBits.get(0);
InputStream in; InputStream in;
try try
{ {
in = licBit.retrieve(); in = licBit.getBitstream().retrieve();
ByteArrayOutputStream out = new ByteArrayOutputStream(); ByteArrayOutputStream out = new ByteArrayOutputStream();
Utils.bufferedCopy(in, out); Utils.bufferedCopy(in, out);
license.getField().add( license.getField().add(
@@ -279,15 +287,7 @@ public class ItemUtils
Base64Utils.encode(out.toString()))); Base64Utils.encode(out.toString())));
metadata.getElement().add(license); metadata.getElement().add(license);
} }
catch (AuthorizeException e) catch (AuthorizeException | IOException | SQLException e)
{
log.warn(e.getMessage(), e);
}
catch (IOException e)
{
log.warn(e.getMessage(), e);
}
catch (SQLException e)
{ {
log.warn(e.getMessage(), e); log.warn(e.getMessage(), e);
} }