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Port DS-3579_Context-mode-and-cache-management-CLI-commands to master

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This commit is contained in:
Tom Desair
2017-06-28 14:49:11 -07:00
parent 207a9e64be
commit 10e028918a
37 changed files with 398 additions and 388 deletions
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14
dspace-api/src/main/java/org/dspace/app/bulkedit/MetadataExport.java
View File

@@ -34,6 +34,8 @@ public class MetadataExport
protected ItemService itemService; protected ItemService itemService;
protected Context context;
/** Whether to export all metadata, or just normally edited metadata */ /** Whether to export all metadata, or just normally edited metadata */
protected boolean exportAll; protected boolean exportAll;
@@ -55,6 +57,7 @@ public class MetadataExport
// Store the export settings // Store the export settings
this.toExport = toExport; this.toExport = toExport;
this.exportAll = exportAll; this.exportAll = exportAll;
this.context = c;
} }
/** /**
@@ -73,6 +76,7 @@ public class MetadataExport
// Try to export the community // Try to export the community
this.toExport = buildFromCommunity(c, toExport, 0); this.toExport = buildFromCommunity(c, toExport, 0);
this.exportAll = exportAll; this.exportAll = exportAll;
this.context = c;
} }
catch (SQLException sqle) catch (SQLException sqle)
{ {
@@ -144,13 +148,19 @@ public class MetadataExport
{ {
try try
{ {
Context.Mode originalMode = context.getCurrentMode();
context.setMode(Context.Mode.READ_ONLY);
// Process each item // Process each item
DSpaceCSV csv = new DSpaceCSV(exportAll); DSpaceCSV csv = new DSpaceCSV(exportAll);
while (toExport.hasNext()) while (toExport.hasNext())
{ {
csv.addItem(toExport.next()); Item item = toExport.next();
csv.addItem(item);
context.uncacheEntity(item);
} }
context.setMode(originalMode);
// Return the results // Return the results
return csv; return csv;
} }
@@ -224,7 +234,7 @@ public class MetadataExport
String filename = line.getOptionValue('f'); String filename = line.getOptionValue('f');
// Create a context // Create a context
Context c = new Context(); Context c = new Context(Context.Mode.READ_ONLY);
c.turnOffAuthorisationSystem(); c.turnOffAuthorisationSystem();
// The things we'll export // The things we'll export

27
dspace-api/src/main/java/org/dspace/app/bulkedit/MetadataImport.java
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@@ -31,6 +31,7 @@ import org.dspace.eperson.EPerson;
import org.dspace.eperson.factory.EPersonServiceFactory; import org.dspace.eperson.factory.EPersonServiceFactory;
import org.dspace.handle.factory.HandleServiceFactory; import org.dspace.handle.factory.HandleServiceFactory;
import org.dspace.handle.service.HandleService; import org.dspace.handle.service.HandleService;
import org.dspace.workflow.WorkflowItem;
import org.dspace.workflow.WorkflowService; import org.dspace.workflow.WorkflowService;
import org.dspace.workflow.factory.WorkflowServiceFactory; import org.dspace.workflow.factory.WorkflowServiceFactory;
@@ -122,6 +123,9 @@ public class MetadataImport
// Make the changes // Make the changes
try try
{ {
Context.Mode originalMode = c.getCurrentMode();
c.setMode(Context.Mode.BATCH_EDIT);
// Process each change // Process each change
for (DSpaceCSVLine line : toImport) for (DSpaceCSVLine line : toImport)
{ {
@@ -134,11 +138,15 @@ public class MetadataImport
throw new MetadataImportException("'action' not allowed for new items!"); throw new MetadataImportException("'action' not allowed for new items!");
} }
WorkspaceItem wsItem = null;
WorkflowItem wfItem = null;
Item item = null;
// Is this a new item? // Is this a new item?
if (id != null) if (id != null)
{ {
// Get the item // Get the item
Item item = itemService.find(c, id); item = itemService.find(c, id);
if (item == null) if (item == null)
{ {
throw new MetadataImportException("Unknown item ID " + id); throw new MetadataImportException("Unknown item ID " + id);
@@ -345,8 +353,8 @@ public class MetadataImport
// Create the item // Create the item
String collectionHandle = line.get("collection").get(0); String collectionHandle = line.get("collection").get(0);
collection = (Collection) handleService.resolveToObject(c, collectionHandle); collection = (Collection) handleService.resolveToObject(c, collectionHandle);
WorkspaceItem wsItem = workspaceItemService.create(c, collection, useTemplate); wsItem = workspaceItemService.create(c, collection, useTemplate);
Item item = wsItem.getItem(); item = wsItem.getItem();
// Add the metadata to the item // Add the metadata to the item
for (BulkEditMetadataValue dcv : whatHasChanged.getAdds()) for (BulkEditMetadataValue dcv : whatHasChanged.getAdds())
@@ -364,9 +372,9 @@ public class MetadataImport
if(useWorkflow){ if(useWorkflow){
WorkflowService workflowService = WorkflowServiceFactory.getInstance().getWorkflowService(); WorkflowService workflowService = WorkflowServiceFactory.getInstance().getWorkflowService();
if (workflowNotify) { if (workflowNotify) {
workflowService.start(c, wsItem); wfItem = workflowService.start(c, wsItem);
} else { } else {
workflowService.startWithoutNotify(c, wsItem); wfItem = workflowService.startWithoutNotify(c, wsItem);
} }
} }
else else
@@ -394,7 +402,16 @@ public class MetadataImport
// Record the changes // Record the changes
changes.add(whatHasChanged); changes.add(whatHasChanged);
} }
if (change) {
//only clear cache if changes have been made.
c.uncacheEntity(wsItem);
c.uncacheEntity(wfItem);
c.uncacheEntity(item);
}
} }
c.setMode(originalMode);
} }
catch (MetadataImportException mie) catch (MetadataImportException mie)
{ {

96
dspace-api/src/main/java/org/dspace/app/harvest/Harvest.java
View File

@@ -7,36 +7,32 @@
*/ */
package org.dspace.app.harvest; package org.dspace.app.harvest;
import org.apache.commons.cli.*;
import org.dspace.authorize.AuthorizeException;
import org.dspace.content.Collection;
import org.dspace.content.DSpaceObject;
import org.dspace.content.Item;
import org.dspace.content.factory.ContentServiceFactory;
import org.dspace.content.service.CollectionService;
import org.dspace.content.service.ItemService;
import org.dspace.core.Constants;
import org.dspace.core.Context;
import org.dspace.eperson.EPerson;
import org.dspace.eperson.factory.EPersonServiceFactory;
import org.dspace.eperson.service.EPersonService;
import org.dspace.handle.factory.HandleServiceFactory;
import org.dspace.harvest.HarvestedCollection;
import org.dspace.harvest.HarvestingException;
import org.dspace.harvest.OAIHarvester;
import org.dspace.harvest.factory.HarvestServiceFactory;
import org.dspace.harvest.service.HarvestedCollectionService;
import java.io.IOException; import java.io.IOException;
import java.sql.SQLException; import java.sql.SQLException;
import java.util.Iterator; import java.util.Iterator;
import java.util.List; import java.util.List;
import java.util.UUID; import java.util.UUID;
import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.CommandLineParser;
import org.apache.commons.cli.HelpFormatter;
import org.apache.commons.cli.Options;
import org.apache.commons.cli.PosixParser;
import org.dspace.authorize.AuthorizeException;
import org.dspace.content.Collection;
import org.dspace.content.DSpaceObject;
import org.dspace.content.factory.ContentServiceFactory;
import org.dspace.content.service.CollectionService;
import org.dspace.content.service.ItemService;
import org.dspace.eperson.factory.EPersonServiceFactory;
import org.dspace.eperson.service.EPersonService;
import org.dspace.handle.factory.HandleServiceFactory;
import org.dspace.harvest.HarvestedCollection;
import org.dspace.content.Item;
import org.dspace.harvest.HarvestingException;
import org.dspace.harvest.OAIHarvester;
import org.dspace.core.Constants;
import org.dspace.core.Context;
import org.dspace.eperson.EPerson;
import org.dspace.harvest.factory.HarvestServiceFactory;
import org.dspace.harvest.service.HarvestedCollectionService;
/** /**
* Test class for harvested collections. * Test class for harvested collections.
* *
@@ -96,7 +92,7 @@ public class Harvest
{ {
HelpFormatter myhelp = new HelpFormatter(); HelpFormatter myhelp = new HelpFormatter();
myhelp.printHelp("Harvest\n", options); myhelp.printHelp("Harvest\n", options);
System.out.println("\nPING OAI server: Harvest -g -s oai_source -i oai_set_id"); System.out.println("\nPING OAI server: Harvest -g -a oai_source -i oai_set_id");
System.out.println("RUNONCE harvest with arbitrary options: Harvest -o -e eperson -c collection -t harvest_type -a oai_source -i oai_set_id -m metadata_format"); System.out.println("RUNONCE harvest with arbitrary options: Harvest -o -e eperson -c collection -t harvest_type -a oai_source -i oai_set_id -m metadata_format");
System.out.println("SETUP a collection for harvesting: Harvest -s -c collection -t harvest_type -a oai_source -i oai_set_id -m metadata_format"); System.out.println("SETUP a collection for harvesting: Harvest -s -c collection -t harvest_type -a oai_source -i oai_set_id -m metadata_format");
System.out.println("RUN harvest once: Harvest -r -e eperson -c collection"); System.out.println("RUN harvest once: Harvest -r -e eperson -c collection");
@@ -160,7 +156,7 @@ public class Harvest
// Instantiate our class // Instantiate our class
Harvest harvester = new Harvest(); Harvest harvester = new Harvest();
harvester.context = new Context(); harvester.context = new Context(Context.Mode.BATCH_EDIT);
// Check our options // Check our options
@@ -203,7 +199,7 @@ public class Harvest
System.out.println(" (run with -h flag for details)"); System.out.println(" (run with -h flag for details)");
System.exit(1); System.exit(1);
} }
List<HarvestedCollection> harvestedCollections = harvestedCollectionService.findAll(context); List<HarvestedCollection> harvestedCollections = harvestedCollectionService.findAll(context);
for (HarvestedCollection harvestedCollection : harvestedCollections) for (HarvestedCollection harvestedCollection : harvestedCollections)
{ {
@@ -247,7 +243,7 @@ public class Harvest
{ {
System.out.println("Error - a metadata key (commonly the prefix) must be specified for this collection"); System.out.println("Error - a metadata key (commonly the prefix) must be specified for this collection");
System.out.println(" (run with -h flag for details)"); System.out.println(" (run with -h flag for details)");
System.exit(1); System.exit(1);
} }
harvester.configureCollection(collection, harvestType, oaiSource, oaiSetID, metadataKey); harvester.configureCollection(collection, harvestType, oaiSource, oaiSetID, metadataKey);
@@ -270,10 +266,10 @@ public class Harvest
* the collection, if not, bail out. * the collection, if not, bail out.
*/ */
private Collection resolveCollection(String collectionID) { private Collection resolveCollection(String collectionID) {
DSpaceObject dso; DSpaceObject dso;
Collection targetCollection = null; Collection targetCollection = null;
try { try {
// is the ID a handle? // is the ID a handle?
if (collectionID != null) if (collectionID != null)
@@ -311,30 +307,30 @@ public class Harvest
catch (SQLException se) { catch (SQLException se) {
se.printStackTrace(); se.printStackTrace();
} }
return targetCollection; return targetCollection;
} }
private void configureCollection(String collectionID, int type, String oaiSource, String oaiSetId, String mdConfigId) { private void configureCollection(String collectionID, int type, String oaiSource, String oaiSetId, String mdConfigId) {
System.out.println("Running: configure collection"); System.out.println("Running: configure collection");
Collection collection = resolveCollection(collectionID); Collection collection = resolveCollection(collectionID);
System.out.println(collection.getID()); System.out.println(collection.getID());
try { try {
HarvestedCollection hc = harvestedCollectionService.find(context, collection); HarvestedCollection hc = harvestedCollectionService.find(context, collection);
if (hc == null) { if (hc == null) {
hc = harvestedCollectionService.create(context, collection); hc = harvestedCollectionService.create(context, collection);
} }
context.turnOffAuthorisationSystem(); context.turnOffAuthorisationSystem();
hc.setHarvestParams(type, oaiSource, oaiSetId, mdConfigId); hc.setHarvestParams(type, oaiSource, oaiSetId, mdConfigId);
hc.setHarvestStatus(HarvestedCollection.STATUS_READY); hc.setHarvestStatus(HarvestedCollection.STATUS_READY);
harvestedCollectionService.update(context, hc); harvestedCollectionService.update(context, hc);
context.restoreAuthSystemState(); context.restoreAuthSystemState();
context.complete(); context.complete();
} }
catch (Exception e) { catch (Exception e) {
System.out.println("Changes could not be committed"); System.out.println("Changes could not be committed");
e.printStackTrace(); e.printStackTrace();
@@ -358,8 +354,8 @@ public class Harvest
private void purgeCollection(String collectionID, String email) { private void purgeCollection(String collectionID, String email) {
System.out.println("Purging collection of all items and resetting last_harvested and harvest_message: " + collectionID); System.out.println("Purging collection of all items and resetting last_harvested and harvest_message: " + collectionID);
Collection collection = resolveCollection(collectionID); Collection collection = resolveCollection(collectionID);
try try
{ {
EPerson eperson = ePersonService.findByEmail(context, email); EPerson eperson = ePersonService.findByEmail(context, email);
context.setCurrentUser(eperson); context.setCurrentUser(eperson);
@@ -373,16 +369,16 @@ public class Harvest
Item item = it.next(); Item item = it.next();
System.out.println("Deleting: " + item.getHandle()); System.out.println("Deleting: " + item.getHandle());
collectionService.removeItem(context, collection, item); collectionService.removeItem(context, collection, item);
// Dispatch events every 50 items context.uncacheEntity(item);// Dispatch events every 50 items
if (i%50 == 0) { if (i%50 == 0) {
context.dispatchEvents(); context.dispatchEvents();
i=0; i=0;
} }
} }
HarvestedCollection hc = harvestedCollectionService.find(context, collection); HarvestedCollection hc = harvestedCollectionService.find(context, collection);
if (hc != null) { if (hc != null) {
hc.setLastHarvested(null); hc.setLastHarvested(null);
hc.setHarvestMessage(""); hc.setHarvestMessage("");
hc.setHarvestStatus(HarvestedCollection.STATUS_READY); hc.setHarvestStatus(HarvestedCollection.STATUS_READY);
hc.setHarvestStartTime(null); hc.setHarvestStartTime(null);
@@ -407,7 +403,7 @@ public class Harvest
*/ */
private void runHarvest(String collectionID, String email) { private void runHarvest(String collectionID, String email) {
System.out.println("Running: a harvest cycle on " + collectionID); System.out.println("Running: a harvest cycle on " + collectionID);
System.out.print("Initializing the harvester... "); System.out.print("Initializing the harvester... ");
OAIHarvester harvester = null; OAIHarvester harvester = null;
try { try {
@@ -425,7 +421,7 @@ public class Harvest
System.out.println(se.getMessage()); System.out.println(se.getMessage());
throw new IllegalStateException("Unable to access database", se); throw new IllegalStateException("Unable to access database", se);
} }
try { try {
// Harvest will not work for an anonymous user // Harvest will not work for an anonymous user
EPerson eperson = ePersonService.findByEmail(context, email); EPerson eperson = ePersonService.findByEmail(context, email);
@@ -468,7 +464,7 @@ public class Harvest
catch (Exception ex) { catch (Exception ex) {
System.out.println("failed. "); System.out.println("failed. ");
ex.printStackTrace(); ex.printStackTrace();
} }
} }
/** /**

2
dspace-api/src/main/java/org/dspace/app/itemexport/ItemExportCLITool.java
View File

@@ -176,7 +176,7 @@ public class ItemExportCLITool {
System.exit(1); System.exit(1);
} }
Context c = new Context(); Context c = new Context(Context.Mode.READ_ONLY);
c.turnOffAuthorisationSystem(); c.turnOffAuthorisationSystem();
if (myType == Constants.ITEM) if (myType == Constants.ITEM)

38
dspace-api/src/main/java/org/dspace/app/itemexport/ItemExportServiceImpl.java
View File

@@ -7,44 +7,28 @@
*/ */
package org.dspace.app.itemexport; package org.dspace.app.itemexport;
import java.io.BufferedOutputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.FileWriter;
import java.io.IOException;
import java.io.InputStream;
import java.io.PrintWriter;
import java.sql.SQLException;
import java.text.SimpleDateFormat;
import java.util.*;
import java.util.zip.ZipEntry;
import java.util.zip.ZipOutputStream;
import javax.mail.MessagingException;
import org.apache.commons.lang.StringUtils; import org.apache.commons.lang.StringUtils;
import org.apache.log4j.Logger; import org.apache.log4j.Logger;
import org.dspace.app.itemexport.service.ItemExportService; import org.dspace.app.itemexport.service.ItemExportService;
import org.dspace.content.*; import org.dspace.content.*;
import org.dspace.content.Collection; import org.dspace.content.Collection;
import org.dspace.content.service.BitstreamService; import org.dspace.content.service.BitstreamService;
import org.dspace.content.service.CommunityService; import org.dspace.content.service.CommunityService;
import org.dspace.content.service.ItemService; import org.dspace.content.service.ItemService;
import org.dspace.core.ConfigurationManager; import org.dspace.core.*;
import org.dspace.core.Constants;
import org.dspace.core.Context;
import org.dspace.core.I18nUtil;
import org.dspace.core.LogManager;
import org.dspace.core.Utils;
import org.dspace.core.Email;
import org.dspace.eperson.EPerson; import org.dspace.eperson.EPerson;
import org.dspace.eperson.service.EPersonService; import org.dspace.eperson.service.EPersonService;
import org.dspace.handle.service.HandleService; import org.dspace.handle.service.HandleService;
import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Autowired;
import javax.mail.MessagingException;
import java.io.*;
import java.sql.SQLException;
import java.text.SimpleDateFormat;
import java.util.*;
import java.util.zip.ZipEntry;
import java.util.zip.ZipOutputStream;
/** /**
* Item exporter to create simple AIPs for DSpace content. Currently exports * Item exporter to create simple AIPs for DSpace content. Currently exports
* individual items, or entire collections. For instructions on use, see * individual items, or entire collections. For instructions on use, see
@@ -129,7 +113,9 @@ public class ItemExportServiceImpl implements ItemExportService
} }
System.out.println("Exporting item to " + mySequenceNumber); System.out.println("Exporting item to " + mySequenceNumber);
exportItem(c, i.next(), fullPath, mySequenceNumber, migrate, excludeBitstreams); Item item = i.next();
exportItem(c, item, fullPath, mySequenceNumber, migrate, excludeBitstreams);
c.uncacheEntity(item);
mySequenceNumber++; mySequenceNumber++;
} }
} }

2
dspace-api/src/main/java/org/dspace/app/itemimport/ItemImportCLITool.java
View File

@@ -294,7 +294,7 @@ public class ItemImportCLITool {
myloader.setQuiet(isQuiet); myloader.setQuiet(isQuiet);
// create a context // create a context
Context c = new Context(); Context c = new Context(Context.Mode.BATCH_EDIT);
// find the EPerson, assign to context // find the EPerson, assign to context
EPerson myEPerson = null; EPerson myEPerson = null;

105
dspace-api/src/main/java/org/dspace/app/itemimport/ItemImportServiceImpl.java
View File

@@ -14,21 +14,6 @@ import gr.ekt.bte.core.TransformationSpec;
import gr.ekt.bte.dataloader.FileDataLoader; import gr.ekt.bte.dataloader.FileDataLoader;
import gr.ekt.bteio.generators.DSpaceOutputGenerator; import gr.ekt.bteio.generators.DSpaceOutputGenerator;
import gr.ekt.bteio.loaders.OAIPMHDataLoader; import gr.ekt.bteio.loaders.OAIPMHDataLoader;
import java.io.*;
import java.net.URL;
import java.sql.SQLException;
import java.text.SimpleDateFormat;
import java.util.*;
import java.util.zip.ZipFile;
import java.util.zip.ZipEntry;
import javax.mail.MessagingException;
import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.parsers.ParserConfigurationException;
import javax.xml.transform.TransformerException;
import org.apache.commons.collections.ComparatorUtils; import org.apache.commons.collections.ComparatorUtils;
import org.apache.commons.io.FileDeleteStrategy; import org.apache.commons.io.FileDeleteStrategy;
import org.apache.commons.io.FileUtils; import org.apache.commons.io.FileUtils;
@@ -46,18 +31,14 @@ import org.dspace.authorize.service.ResourcePolicyService;
import org.dspace.content.*; import org.dspace.content.*;
import org.dspace.content.Collection; import org.dspace.content.Collection;
import org.dspace.content.service.*; import org.dspace.content.service.*;
import org.dspace.core.ConfigurationManager; import org.dspace.core.*;
import org.dspace.core.Constants;
import org.dspace.core.Context;
import org.dspace.core.Email;
import org.dspace.core.I18nUtil;
import org.dspace.core.LogManager;
import org.dspace.eperson.EPerson; import org.dspace.eperson.EPerson;
import org.dspace.eperson.Group; import org.dspace.eperson.Group;
import org.dspace.eperson.service.EPersonService; import org.dspace.eperson.service.EPersonService;
import org.dspace.eperson.service.GroupService; import org.dspace.eperson.service.GroupService;
import org.dspace.handle.service.HandleService; import org.dspace.handle.service.HandleService;
import org.dspace.utils.DSpace; import org.dspace.utils.DSpace;
import org.dspace.workflow.WorkflowItem;
import org.dspace.workflow.WorkflowService; import org.dspace.workflow.WorkflowService;
import org.springframework.beans.factory.InitializingBean; import org.springframework.beans.factory.InitializingBean;
import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Autowired;
@@ -67,6 +48,19 @@ import org.w3c.dom.Node;
import org.w3c.dom.NodeList; import org.w3c.dom.NodeList;
import org.xml.sax.SAXException; import org.xml.sax.SAXException;
import javax.mail.MessagingException;
import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.parsers.ParserConfigurationException;
import javax.xml.transform.TransformerException;
import java.io.*;
import java.net.URL;
import java.sql.SQLException;
import java.text.SimpleDateFormat;
import java.util.*;
import java.util.zip.ZipEntry;
import java.util.zip.ZipFile;
/** /**
* Import items into DSpace. The conventional use is upload files by copying * Import items into DSpace. The conventional use is upload files by copying
@@ -314,39 +308,39 @@ public class ItemImportServiceImpl implements ItemImportService, InitializingBea
Arrays.sort(dircontents, ComparatorUtils.naturalComparator()); Arrays.sort(dircontents, ComparatorUtils.naturalComparator());
for (int i = 0; i < dircontents.length; i++) for (int i = 0; i < dircontents.length; i++)
{
if (skipItems.containsKey(dircontents[i]))
{ {
if (skipItems.containsKey(dircontents[i])) System.out.println("Skipping import of " + dircontents[i]);
{ }
System.out.println("Skipping import of " + dircontents[i]); else
{
List<Collection> clist;
if (directoryFileCollections) {
String path = sourceDir + File.separatorChar + dircontents[i];
try {
List<Collection> cols = processCollectionFile(c, path, "collections");
if (cols == null) {
System.out.println("No collections specified for item " + dircontents[i] + ". Skipping.");
continue;
}
clist = cols;
}
catch (IllegalArgumentException e)
{
System.out.println(e.getMessage() + " Skipping." );
continue;
}
} }
else else
{ {
List<Collection> clist; clist = mycollections;
if (directoryFileCollections) {
String path = sourceDir + File.separatorChar + dircontents[i];
try {
List<Collection> cols = processCollectionFile(c, path, "collections");
if (cols == null) {
System.out.println("No collections specified for item " + dircontents[i] + ". Skipping.");
continue;
}
clist = cols;
}
catch (IllegalArgumentException e)
{
System.out.println(e.getMessage() + " Skipping." );
continue;
}
}
else
{
clist = mycollections;
}
addItem(c, clist, sourceDir, dircontents[i], mapOut, template);
System.out.println(i + " " + dircontents[i]);
} }
Item item =addItem(c, clist, sourceDir, dircontents[i], mapOut, template);c.uncacheEntity(item);
System.out.println(i + " " + dircontents[i]);
} }
}
} finally { } finally {
if(mapOut!=null) { if(mapOut!=null) {
@@ -416,7 +410,9 @@ public class ItemImportServiceImpl implements ItemImportService, InitializingBea
handleOut.close(); handleOut.close();
deleteItem(c, oldItem); deleteItem(c, oldItem);
addItem(c, mycollections, sourceDir, newItemName, null, template); Item newItem = addItem(c, mycollections, sourceDir, newItemName, null, template);
c.uncacheEntity(oldItem);
c.uncacheEntity(newItem);
} }
} }
@@ -447,6 +443,7 @@ public class ItemImportServiceImpl implements ItemImportService, InitializingBea
Item myitem = itemService.findByIdOrLegacyId(c, itemID); Item myitem = itemService.findByIdOrLegacyId(c, itemID);
System.out.println("Deleting item " + itemID); System.out.println("Deleting item " + itemID);
deleteItem(c, myitem); deleteItem(c, myitem);
c.uncacheEntity(myitem);
} }
} }
} }
@@ -473,6 +470,7 @@ public class ItemImportServiceImpl implements ItemImportService, InitializingBea
// create workspace item // create workspace item
Item myitem = null; Item myitem = null;
WorkspaceItem wi = null; WorkspaceItem wi = null;
WorkflowItem wfi = null;
if (!isTest) if (!isTest)
{ {
@@ -498,9 +496,9 @@ public class ItemImportServiceImpl implements ItemImportService, InitializingBea
{ {
// Should we send a workflow alert email or not? // Should we send a workflow alert email or not?
if (useWorkflowSendEmail) { if (useWorkflowSendEmail) {
workflowService.start(c, wi); wfi = workflowService.start(c, wi);
} else { } else {
workflowService.startWithoutNotify(c, wi); wfi = workflowService.startWithoutNotify(c, wi);
} }
// send ID to the mapfile // send ID to the mapfile
@@ -556,6 +554,10 @@ public class ItemImportServiceImpl implements ItemImportService, InitializingBea
mapOut.println(mapOutputString); mapOut.println(mapOutputString);
} }
//Clear intermediary objects from the cache
c.uncacheEntity(wi);
c.uncacheEntity(wfi);
return myitem; return myitem;
} }
@@ -593,6 +595,7 @@ public class ItemImportServiceImpl implements ItemImportService, InitializingBea
else else
{ {
deleteItem(c, myitem); deleteItem(c, myitem);
c.uncacheEntity(myitem);
} }
} }

193
dspace-api/src/main/java/org/dspace/app/itemupdate/ItemUpdate.java
View File

@@ -7,21 +7,7 @@
*/ */
package org.dspace.app.itemupdate; package org.dspace.app.itemupdate;
import java.io.BufferedWriter; import org.apache.commons.cli.*;
import java.io.File;
import java.io.FilenameFilter;
import java.io.FileNotFoundException;
import java.io.FileWriter;
import java.io.IOException;
import java.io.PrintWriter;
import java.util.*;
import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.CommandLineParser;
import org.apache.commons.cli.HelpFormatter;
import org.apache.commons.cli.Option;
import org.apache.commons.cli.Options;
import org.apache.commons.cli.PosixParser;
import org.dspace.content.Item; import org.dspace.content.Item;
import org.dspace.content.factory.ContentServiceFactory; import org.dspace.content.factory.ContentServiceFactory;
import org.dspace.content.service.ItemService; import org.dspace.content.service.ItemService;
@@ -31,6 +17,9 @@ import org.dspace.eperson.EPerson;
import org.dspace.eperson.factory.EPersonServiceFactory; import org.dspace.eperson.factory.EPersonServiceFactory;
import org.dspace.eperson.service.EPersonService; import org.dspace.eperson.service.EPersonService;
import java.io.*;
import java.util.*;
/** /**
* *
* Provides some batch editing capabilities for items in DSpace: * Provides some batch editing capabilities for items in DSpace:
@@ -62,7 +51,7 @@ import org.dspace.eperson.service.EPersonService;
* *
*/ */
public class ItemUpdate { public class ItemUpdate {
public static final String SUPPRESS_UNDO_FILENAME = "suppress_undo"; public static final String SUPPRESS_UNDO_FILENAME = "suppress_undo";
public static final String CONTENTS_FILE = "contents"; public static final String CONTENTS_FILE = "contents";
@@ -70,7 +59,7 @@ public class ItemUpdate {
public static String HANDLE_PREFIX = null; public static String HANDLE_PREFIX = null;
public static final Map<String, String> filterAliases = new HashMap<String, String>(); public static final Map<String, String> filterAliases = new HashMap<String, String>();
public static boolean verbose = false; public static boolean verbose = false;
protected static final EPersonService epersonService = EPersonServiceFactory.getInstance().getEPersonService(); protected static final EPersonService epersonService = EPersonServiceFactory.getInstance().getEPersonService();
@@ -80,10 +69,10 @@ public class ItemUpdate {
{ {
filterAliases.put("ORIGINAL", "org.dspace.app.itemupdate.OriginalBitstreamFilter"); filterAliases.put("ORIGINAL", "org.dspace.app.itemupdate.OriginalBitstreamFilter");
filterAliases.put("ORIGINAL_AND_DERIVATIVES", "org.dspace.app.itemupdate.OriginalWithDerivativesBitstreamFilter"); filterAliases.put("ORIGINAL_AND_DERIVATIVES", "org.dspace.app.itemupdate.OriginalWithDerivativesBitstreamFilter");
filterAliases.put("TEXT", "org.dspace.app.itemupdate.DerivativeTextBitstreamFilter"); filterAliases.put("TEXT", "org.dspace.app.itemupdate.DerivativeTextBitstreamFilter");
filterAliases.put("THUMBNAIL", "org.dspace.app.itemupdate.ThumbnailBitstreamFilter"); filterAliases.put("THUMBNAIL", "org.dspace.app.itemupdate.ThumbnailBitstreamFilter");
} }
// File listing filter to check for folders // File listing filter to check for folders
static FilenameFilter directoryFilter = new FilenameFilter() static FilenameFilter directoryFilter = new FilenameFilter()
{ {
@@ -122,11 +111,11 @@ public class ItemUpdate {
Options options = new Options(); Options options = new Options();
//processing basis for determining items //processing basis for determining items
//item-specific changes with metadata in source directory with dublin_core.xml files //item-specific changes with metadata in source directory with dublin_core.xml files
options.addOption("s", "source", true, "root directory of source dspace archive "); options.addOption("s", "source", true, "root directory of source dspace archive ");
//actions on items //actions on items
options.addOption("a", "addmetadata", true, "add metadata specified for each item; multiples separated by semicolon ';'"); options.addOption("a", "addmetadata", true, "add metadata specified for each item; multiples separated by semicolon ';'");
options.addOption("d", "deletemetadata", true, "delete metadata specified for each item"); options.addOption("d", "deletemetadata", true, "delete metadata specified for each item");
@@ -138,13 +127,13 @@ public class ItemUpdate {
delBitstreamOption.setArgName("BitstreamFilter"); delBitstreamOption.setArgName("BitstreamFilter");
options.addOption(delBitstreamOption); options.addOption(delBitstreamOption);
//other params //other params
options.addOption("e", "eperson", true, "email of eperson doing the update"); options.addOption("e", "eperson", true, "email of eperson doing the update");
options.addOption("i", "itemfield", true, "optional metadata field that containing item identifier; default is dc.identifier.uri"); options.addOption("i", "itemfield", true, "optional metadata field that containing item identifier; default is dc.identifier.uri");
options.addOption("F", "filter-properties", true, "filter class name; only for deleting bitstream"); options.addOption("F", "filter-properties", true, "filter class name; only for deleting bitstream");
options.addOption("v", "verbose", false, "verbose logging"); options.addOption("v", "verbose", false, "verbose logging");
//special run states //special run states
options.addOption("t", "test", false, "test run - do not actually import items"); options.addOption("t", "test", false, "test run - do not actually import items");
options.addOption("P", "provenance", false, "suppress altering provenance field for bitstream changes"); options.addOption("P", "provenance", false, "suppress altering provenance field for bitstream changes");
options.addOption("h", "help", false, "help"); options.addOption("h", "help", false, "help");
@@ -156,12 +145,12 @@ public class ItemUpdate {
String metadataIndexName = null; String metadataIndexName = null;
Context context = null; Context context = null;
ItemUpdate iu = new ItemUpdate(); ItemUpdate iu = new ItemUpdate();
try try
{ {
CommandLine line = parser.parse(options, argv); CommandLine line = parser.parse(options, argv);
if (line.hasOption('h')) if (line.hasOption('h'))
{ {
HelpFormatter myhelp = new HelpFormatter(); HelpFormatter myhelp = new HelpFormatter();
@@ -173,10 +162,10 @@ public class ItemUpdate {
pr(" adding bitstreams: ItemUpdate -e jsmith@mit.edu -s sourcedir -A -i dc.identifier"); pr(" adding bitstreams: ItemUpdate -e jsmith@mit.edu -s sourcedir -A -i dc.identifier");
pr(" deleting bitstreams: ItemUpdate -e jsmith@mit.edu -s sourcedir -D ORIGINAL "); pr(" deleting bitstreams: ItemUpdate -e jsmith@mit.edu -s sourcedir -D ORIGINAL ");
pr(""); pr("");
System.exit(0); System.exit(0);
} }
if (line.hasOption('v')) if (line.hasOption('v'))
{ {
verbose = true; verbose = true;
@@ -190,85 +179,85 @@ public class ItemUpdate {
} }
iu.eperson = line.getOptionValue('e'); // db ID or email iu.eperson = line.getOptionValue('e'); // db ID or email
if (!line.hasOption('s')) // item specific changes from archive dir if (!line.hasOption('s')) // item specific changes from archive dir
{ {
pr("Missing source archive option"); pr("Missing source archive option");
System.exit(1); System.exit(1);
} }
String sourcedir = line.getOptionValue('s'); String sourcedir = line.getOptionValue('s');
if (line.hasOption('t')) //test if (line.hasOption('t')) //test
{ {
isTest = true; isTest = true;
pr("**Test Run** - not actually updating items."); pr("**Test Run** - not actually updating items.");
} }
if (line.hasOption('i')) if (line.hasOption('i'))
{ {
itemField = line.getOptionValue('i'); itemField = line.getOptionValue('i');
} }
if (line.hasOption('d')) if (line.hasOption('d'))
{ {
String[] targetFields = line.getOptionValues('d'); String[] targetFields = line.getOptionValues('d');
DeleteMetadataAction delMetadataAction = (DeleteMetadataAction) iu.actionMgr.getUpdateAction(DeleteMetadataAction.class); DeleteMetadataAction delMetadataAction = (DeleteMetadataAction) iu.actionMgr.getUpdateAction(DeleteMetadataAction.class);
delMetadataAction.addTargetFields(targetFields); delMetadataAction.addTargetFields(targetFields);
//undo is an add //undo is an add
for (String field : targetFields) for (String field : targetFields)
{ {
iu.undoActionList.add(" -a " + field + " "); iu.undoActionList.add(" -a " + field + " ");
} }
pr("Delete metadata for fields: "); pr("Delete metadata for fields: ");
for (String s : targetFields) for (String s : targetFields)
{ {
pr(" " + s); pr(" " + s);
} }
} }
if (line.hasOption('a')) if (line.hasOption('a'))
{ {
String[] targetFields = line.getOptionValues('a'); String[] targetFields = line.getOptionValues('a');
AddMetadataAction addMetadataAction = (AddMetadataAction) iu.actionMgr.getUpdateAction(AddMetadataAction.class); AddMetadataAction addMetadataAction = (AddMetadataAction) iu.actionMgr.getUpdateAction(AddMetadataAction.class);
addMetadataAction.addTargetFields(targetFields); addMetadataAction.addTargetFields(targetFields);
//undo is a delete followed by an add of a replace record for target fields //undo is a delete followed by an add of a replace record for target fields
for (String field : targetFields) for (String field : targetFields)
{ {
iu.undoActionList.add(" -d " + field + " "); iu.undoActionList.add(" -d " + field + " ");
} }
for (String field : targetFields) for (String field : targetFields)
{ {
iu.undoActionList.add(" -a " + field + " "); iu.undoActionList.add(" -a " + field + " ");
} }
pr("Add metadata for fields: "); pr("Add metadata for fields: ");
for (String s : targetFields) for (String s : targetFields)
{ {
pr(" " + s); pr(" " + s);
} }
} }
if (line.hasOption('D')) // undo not supported if (line.hasOption('D')) // undo not supported
{ {
pr("Delete bitstreams "); pr("Delete bitstreams ");
String[] filterNames = line.getOptionValues('D'); String[] filterNames = line.getOptionValues('D');
if ((filterNames != null) && (filterNames.length > 1)) if ((filterNames != null) && (filterNames.length > 1))
{ {
pr("Error: Only one filter can be a used at a time."); pr("Error: Only one filter can be a used at a time.");
System.exit(1); System.exit(1);
} }
String filterName = line.getOptionValue('D'); String filterName = line.getOptionValue('D');
pr("Filter argument: " + filterName); pr("Filter argument: " + filterName);
if (filterName == null) // indicates using delete_contents files if (filterName == null) // indicates using delete_contents files
{ {
DeleteBitstreamsAction delAction = (DeleteBitstreamsAction) iu.actionMgr.getUpdateAction(DeleteBitstreamsAction.class); DeleteBitstreamsAction delAction = (DeleteBitstreamsAction) iu.actionMgr.getUpdateAction(DeleteBitstreamsAction.class);
@@ -278,19 +267,19 @@ public class ItemUpdate {
{ {
// check if param is on ALIAS list // check if param is on ALIAS list
String filterClassname = filterAliases.get(filterName); String filterClassname = filterAliases.get(filterName);
if (filterClassname == null) if (filterClassname == null)
{ {
filterClassname = filterName; filterClassname = filterName;
} }
BitstreamFilter filter = null; BitstreamFilter filter = null;
try try
{ {
Class<?> cfilter = Class.forName(filterClassname); Class<?> cfilter = Class.forName(filterClassname);
pr("BitstreamFilter class to instantiate: " + cfilter.toString()); pr("BitstreamFilter class to instantiate: " + cfilter.toString());
filter = (BitstreamFilter) cfilter.newInstance(); //unfortunate cast, an erasure consequence filter = (BitstreamFilter) cfilter.newInstance(); //unfortunate cast, an erasure consequence
} }
catch(Exception e) catch(Exception e)
@@ -298,7 +287,7 @@ public class ItemUpdate {
pr("Error: Failure instantiating bitstream filter class: " + filterClassname); pr("Error: Failure instantiating bitstream filter class: " + filterClassname);
System.exit(1); System.exit(1);
} }
String filterPropertiesName = line.getOptionValue('F'); String filterPropertiesName = line.getOptionValue('F');
if (filterPropertiesName != null) //not always required if (filterPropertiesName != null) //not always required
{ {
@@ -309,7 +298,7 @@ public class ItemUpdate {
{ {
filterPropertiesName = sourcedir + File.separator + filterPropertiesName; filterPropertiesName = sourcedir + File.separator + filterPropertiesName;
} }
filter.initProperties(filterPropertiesName); filter.initProperties(filterPropertiesName);
} }
catch(Exception e) catch(Exception e)
@@ -318,52 +307,52 @@ public class ItemUpdate {
System.exit(1); System.exit(1);
} }
} }
DeleteBitstreamsByFilterAction delAction = DeleteBitstreamsByFilterAction delAction =
(DeleteBitstreamsByFilterAction) iu.actionMgr.getUpdateAction(DeleteBitstreamsByFilterAction.class); (DeleteBitstreamsByFilterAction) iu.actionMgr.getUpdateAction(DeleteBitstreamsByFilterAction.class);
delAction.setAlterProvenance(alterProvenance); delAction.setAlterProvenance(alterProvenance);
delAction.setBitstreamFilter(filter); delAction.setBitstreamFilter(filter);
//undo not supported //undo not supported
} }
} }
if (line.hasOption('A')) if (line.hasOption('A'))
{ {
pr("Add bitstreams "); pr("Add bitstreams ");
AddBitstreamsAction addAction = (AddBitstreamsAction) iu.actionMgr.getUpdateAction(AddBitstreamsAction.class); AddBitstreamsAction addAction = (AddBitstreamsAction) iu.actionMgr.getUpdateAction(AddBitstreamsAction.class);
addAction.setAlterProvenance(alterProvenance); addAction.setAlterProvenance(alterProvenance);
iu.undoActionList.add(" -D "); // delete_contents file will be written, no arg required iu.undoActionList.add(" -D "); // delete_contents file will be written, no arg required
} }
if (!iu.actionMgr.hasActions()) if (!iu.actionMgr.hasActions())
{ {
pr("Error - an action must be specified"); pr("Error - an action must be specified");
System.exit(1); System.exit(1);
} }
else else
{ {
pr("Actions to be performed: "); pr("Actions to be performed: ");
for (UpdateAction ua : iu.actionMgr) for (UpdateAction ua : iu.actionMgr)
{ {
pr(" " + ua.getClass().getName()); pr(" " + ua.getClass().getName());
} }
} }
pr("ItemUpdate - initializing run on " + (new Date()).toString()); pr("ItemUpdate - initializing run on " + (new Date()).toString());
context = new Context(); context = new Context(Context.Mode.BATCH_EDIT);
iu.setEPerson(context, iu.eperson); iu.setEPerson(context, iu.eperson);
context.turnOffAuthorisationSystem(); context.turnOffAuthorisationSystem();
HANDLE_PREFIX = ConfigurationManager.getProperty("handle.canonical.prefix"); HANDLE_PREFIX = ConfigurationManager.getProperty("handle.canonical.prefix");
if (HANDLE_PREFIX == null || HANDLE_PREFIX.length() == 0) if (HANDLE_PREFIX == null || HANDLE_PREFIX.length() == 0)
{ {
HANDLE_PREFIX = "http://hdl.handle.net/"; HANDLE_PREFIX = "http://hdl.handle.net/";
} }
iu.processArchive(context, sourcedir, itemField, metadataIndexName, alterProvenance, isTest); iu.processArchive(context, sourcedir, itemField, metadataIndexName, alterProvenance, isTest);
context.complete(); // complete all transactions context.complete(); // complete all transactions
} }
@@ -388,7 +377,7 @@ public class ItemUpdate {
else else
{ {
pr("End."); pr("End.");
} }
System.exit(status); System.exit(status);
} }
@@ -430,24 +419,24 @@ public class ItemUpdate {
File undoDir = null; //sibling directory of source archive File undoDir = null; //sibling directory of source archive
if (!suppressUndo && !isTest) if (!suppressUndo && !isTest)
{ {
undoDir = initUndoArchive(sourceDir); undoDir = initUndoArchive(sourceDir);
} }
int itemCount = 0; int itemCount = 0;
int successItemCount = 0; int successItemCount = 0;
for (String dirname : dircontents) for (String dirname : dircontents)
{ {
itemCount++; itemCount++;
pr(""); pr("");
pr("processing item " + dirname); pr("processing item " + dirname);
try try
{ {
ItemArchive itarch = ItemArchive.create(context, new File(sourceDir, dirname), itemField); ItemArchive itarch = ItemArchive.create(context, new File(sourceDir, dirname), itemField);
for (UpdateAction action : actionMgr) for (UpdateAction action : actionMgr)
{ {
pr("action: " + action.getClass().getName()); pr("action: " + action.getClass().getName());
@@ -461,28 +450,28 @@ public class ItemUpdate {
{ {
Item item = itarch.getItem(); Item item = itarch.getItem();
itemService.update(context, item); //need to update before commit itemService.update(context, item); //need to update before commit
} context.uncacheEntity(item);}
ItemUpdate.pr("Item " + dirname + " completed"); ItemUpdate.pr("Item " + dirname + " completed");
successItemCount++; successItemCount++;
} }
catch(Exception e) catch(Exception e)
{ {
pr("Exception processing item " + dirname + ": " + e.toString()); pr("Exception processing item " + dirname + ": " + e.toString());
e.printStackTrace(); e.printStackTrace();
} }
} }
if (!suppressUndo && !isTest) if (!suppressUndo && !isTest)
{ {
StringBuilder sb = new StringBuilder("dsrun org.dspace.app.itemupdate.ItemUpdate "); StringBuilder sb = new StringBuilder("dsrun org.dspace.app.itemupdate.ItemUpdate ");
sb.append(" -e ").append(this.eperson); sb.append(" -e ").append(this.eperson);
sb.append(" -s ").append(undoDir); sb.append(" -s ").append(undoDir);
if (itemField != null) if (itemField != null)
{ {
sb.append(" -i ").append(itemField); sb.append(" -i ").append(itemField);
} }
if (!alterProvenance) if (!alterProvenance)
{ {
sb.append(" -P "); sb.append(" -P ");
@@ -491,12 +480,12 @@ public class ItemUpdate {
{ {
sb.append(" -t "); sb.append(" -t ");
} }
for (String actionOption : undoActionList) for (String actionOption : undoActionList)
{ {
sb.append(actionOption); sb.append(actionOption);
} }
PrintWriter pw = null; PrintWriter pw = null;
try try
{ {
@@ -527,29 +516,29 @@ public class ItemUpdate {
*/ */
protected File initUndoArchive(File sourceDir) protected File initUndoArchive(File sourceDir)
throws FileNotFoundException, IOException throws FileNotFoundException, IOException
{ {
File parentDir = sourceDir.getCanonicalFile().getParentFile(); File parentDir = sourceDir.getCanonicalFile().getParentFile();
if (parentDir == null) if (parentDir == null)
{ {
throw new FileNotFoundException("Parent directory of archive directory not found; unable to write UndoArchive; no processing performed"); throw new FileNotFoundException("Parent directory of archive directory not found; unable to write UndoArchive; no processing performed");
} }
String sourceDirName = sourceDir.getName(); String sourceDirName = sourceDir.getName();
int seqNo = 1; int seqNo = 1;
File undoDir = new File(parentDir, "undo_" + sourceDirName + "_" + seqNo); File undoDir = new File(parentDir, "undo_" + sourceDirName + "_" + seqNo);
while (undoDir.exists()) while (undoDir.exists())
{ {
undoDir = new File(parentDir, "undo_" + sourceDirName+ "_" + ++seqNo); //increment undoDir = new File(parentDir, "undo_" + sourceDirName+ "_" + ++seqNo); //increment
} }
// create root directory // create root directory
if (!undoDir.mkdir()) if (!undoDir.mkdir())
{ {
pr("ERROR creating Undo Archive directory " + undoDir.getCanonicalPath()); pr("ERROR creating Undo Archive directory " + undoDir.getCanonicalPath());
throw new IOException("ERROR creating Undo Archive directory " + undoDir.getCanonicalPath()); throw new IOException("ERROR creating Undo Archive directory " + undoDir.getCanonicalPath());
} }
//Undo is suppressed to prevent undo of undo //Undo is suppressed to prevent undo of undo
File fSuppressUndo = new File(undoDir, ItemUpdate.SUPPRESS_UNDO_FILENAME); File fSuppressUndo = new File(undoDir, ItemUpdate.SUPPRESS_UNDO_FILENAME);
try try
@@ -561,9 +550,9 @@ public class ItemUpdate {
pr("ERROR creating Suppress Undo File " + e.toString()); pr("ERROR creating Suppress Undo File " + e.toString());
throw e; throw e;
} }
return undoDir; return undoDir;
} }
//private void write //private void write
/** /**
@@ -606,7 +595,7 @@ public class ItemUpdate {
* poor man's logging * poor man's logging
* As with ItemImport, API logging goes through log4j to the DSpace.log files * As with ItemImport, API logging goes through log4j to the DSpace.log files
* whereas the batch logging goes to the console to be captured there. * whereas the batch logging goes to the console to be captured there.
* *
* @param s String * @param s String
*/ */
static void pr(String s) static void pr(String s)
@@ -620,7 +609,7 @@ public class ItemUpdate {
*/ */
static void prv(String s) static void prv(String s)
{ {
if (verbose) if (verbose)
{ {
System.out.println(s); System.out.println(s);
} }

7
dspace-api/src/main/java/org/dspace/app/mediafilter/MediaFilterServiceImpl.java
View File

@@ -7,9 +7,6 @@
*/ */
package org.dspace.app.mediafilter; package org.dspace.app.mediafilter;
import java.io.InputStream;
import java.util.*;
import org.dspace.app.mediafilter.service.MediaFilterService; import org.dspace.app.mediafilter.service.MediaFilterService;
import org.dspace.authorize.service.AuthorizeService; import org.dspace.authorize.service.AuthorizeService;
import org.dspace.content.*; import org.dspace.content.*;
@@ -24,6 +21,9 @@ import org.dspace.services.ConfigurationService;
import org.springframework.beans.factory.InitializingBean; import org.springframework.beans.factory.InitializingBean;
import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Autowired;
import java.io.InputStream;
import java.util.*;
/** /**
* MediaFilterManager is the class that invokes the media/format filters over the * MediaFilterManager is the class that invokes the media/format filters over the
* repository's content. A few command line flags affect the operation of the * repository's content. A few command line flags affect the operation of the
@@ -161,6 +161,7 @@ public class MediaFilterServiceImpl implements MediaFilterService, InitializingB
++processed; ++processed;
} }
// clear item objects from context cache and internal cache // clear item objects from context cache and internal cache
c.uncacheEntity(currentItem);
currentItem = null; currentItem = null;
} }
} }

25
dspace-api/src/main/java/org/dspace/app/packager/Packager.java
View File

@@ -7,26 +7,14 @@
*/ */
package org.dspace.app.packager; package org.dspace.app.packager;
import java.io.BufferedReader; import org.apache.commons.cli.*;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStreamReader;
import java.sql.SQLException;
import java.util.List;
import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.CommandLineParser;
import org.apache.commons.cli.HelpFormatter;
import org.apache.commons.cli.Options;
import org.apache.commons.cli.PosixParser;
import org.dspace.authorize.AuthorizeException; import org.dspace.authorize.AuthorizeException;
import org.dspace.content.DSpaceObject; import org.dspace.content.DSpaceObject;
import org.dspace.content.crosswalk.CrosswalkException; import org.dspace.content.crosswalk.CrosswalkException;
import org.dspace.content.packager.PackageDisseminator; import org.dspace.content.packager.PackageDisseminator;
import org.dspace.content.packager.PackageException; import org.dspace.content.packager.PackageException;
import org.dspace.content.packager.PackageParameters;
import org.dspace.content.packager.PackageIngester; import org.dspace.content.packager.PackageIngester;
import org.dspace.content.packager.PackageParameters;
import org.dspace.core.Constants; import org.dspace.core.Constants;
import org.dspace.core.Context; import org.dspace.core.Context;
import org.dspace.core.factory.CoreServiceFactory; import org.dspace.core.factory.CoreServiceFactory;
@@ -36,6 +24,10 @@ import org.dspace.eperson.factory.EPersonServiceFactory;
import org.dspace.handle.factory.HandleServiceFactory; import org.dspace.handle.factory.HandleServiceFactory;
import org.dspace.workflow.WorkflowException; import org.dspace.workflow.WorkflowException;
import java.io.*;
import java.sql.SQLException;
import java.util.List;
/** /**
* Command-line interface to the Packager plugin. * Command-line interface to the Packager plugin.
* <p> * <p>
@@ -331,6 +323,7 @@ public class Packager
//If we are in REPLACE mode //If we are in REPLACE mode
if(pkgParams.replaceModeEnabled()) if(pkgParams.replaceModeEnabled())
{ {
context.setMode(Context.Mode.BATCH_EDIT);
PackageIngester sip = (PackageIngester) pluginService PackageIngester sip = (PackageIngester) pluginService
.getNamedPlugin(PackageIngester.class, myPackager.packageType); .getNamedPlugin(PackageIngester.class, myPackager.packageType);
if (sip == null) if (sip == null)
@@ -394,6 +387,8 @@ public class Packager
//else if normal SUBMIT mode (or basic RESTORE mode -- which is a special type of submission) //else if normal SUBMIT mode (or basic RESTORE mode -- which is a special type of submission)
else if (myPackager.submit || pkgParams.restoreModeEnabled()) else if (myPackager.submit || pkgParams.restoreModeEnabled())
{ {
context.setMode(Context.Mode.BATCH_EDIT);
PackageIngester sip = (PackageIngester) pluginService PackageIngester sip = (PackageIngester) pluginService
.getNamedPlugin(PackageIngester.class, myPackager.packageType); .getNamedPlugin(PackageIngester.class, myPackager.packageType);
if (sip == null) if (sip == null)
@@ -445,6 +440,8 @@ public class Packager
}// else, if DISSEMINATE mode }// else, if DISSEMINATE mode
else else
{ {
context.setMode(Context.Mode.READ_ONLY);
//retrieve specified package disseminator //retrieve specified package disseminator
PackageDisseminator dip = (PackageDisseminator) pluginService PackageDisseminator dip = (PackageDisseminator) pluginService
.getNamedPlugin(PackageDisseminator.class, myPackager.packageType); .getNamedPlugin(PackageDisseminator.class, myPackager.packageType);

41
dspace-api/src/main/java/org/dspace/app/sitemap/GenerateSitemaps.java
View File

@@ -7,28 +7,9 @@
*/ */
package org.dspace.app.sitemap; package org.dspace.app.sitemap;
import java.io.BufferedReader; import org.apache.commons.cli.*;
import java.io.File;
import java.io.IOException;
import java.io.InputStreamReader;
import java.io.UnsupportedEncodingException;
import java.net.HttpURLConnection;
import java.net.MalformedURLException;
import java.net.URL;
import java.net.URLEncoder;
import java.sql.SQLException;
import java.util.Date;
import java.util.Iterator;
import java.util.List;
import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.CommandLineParser;
import org.apache.commons.cli.HelpFormatter;
import org.apache.commons.cli.Options;
import org.apache.commons.cli.ParseException;
import org.apache.commons.cli.PosixParser;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.lang.ArrayUtils; import org.apache.commons.lang.ArrayUtils;
import org.apache.commons.lang.StringUtils;
import org.apache.log4j.Logger; import org.apache.log4j.Logger;
import org.dspace.content.Collection; import org.dspace.content.Collection;
import org.dspace.content.Community; import org.dspace.content.Community;
@@ -42,6 +23,16 @@ import org.dspace.core.LogManager;
import org.dspace.services.ConfigurationService; import org.dspace.services.ConfigurationService;
import org.dspace.services.factory.DSpaceServicesFactory; import org.dspace.services.factory.DSpaceServicesFactory;
import java.io.*;
import java.net.HttpURLConnection;
import java.net.MalformedURLException;
import java.net.URL;
import java.net.URLEncoder;
import java.sql.SQLException;
import java.util.Date;
import java.util.Iterator;
import java.util.List;
/** /**
* Command-line utility for generating HTML and Sitemaps.org protocol Sitemaps. * Command-line utility for generating HTML and Sitemaps.org protocol Sitemaps.
* *
@@ -188,7 +179,7 @@ public class GenerateSitemaps
+ "?map=", null); + "?map=", null);
} }
Context c = new Context(); Context c = new Context(Context.Mode.READ_ONLY);
List<Community> comms = communityService.findAll(c); List<Community> comms = communityService.findAll(c);
@@ -201,6 +192,8 @@ public class GenerateSitemaps
if (makeSitemapOrg) { if (makeSitemapOrg) {
sitemapsOrg.addURL(url, null); sitemapsOrg.addURL(url, null);
} }
c.uncacheEntity(comm);
} }
List<Collection> colls = collectionService.findAll(c); List<Collection> colls = collectionService.findAll(c);
@@ -214,6 +207,8 @@ public class GenerateSitemaps
if (makeSitemapOrg) { if (makeSitemapOrg) {
sitemapsOrg.addURL(url, null); sitemapsOrg.addURL(url, null);
} }
c.uncacheEntity(coll);
} }
Iterator<Item> allItems = itemService.findAll(c); Iterator<Item> allItems = itemService.findAll(c);
@@ -234,6 +229,8 @@ public class GenerateSitemaps
sitemapsOrg.addURL(url, lastMod); sitemapsOrg.addURL(url, lastMod);
} }
c.uncacheEntity(i);
itemCount++; itemCount++;
} }

1
dspace-api/src/main/java/org/dspace/authority/indexer/DSpaceAuthorityIndexer.java
View File

@@ -145,6 +145,7 @@ public class DSpaceAuthorityIndexer implements AuthorityIndexerInterface, Initia
} else { } else {
// 3. iterate over the items // 3. iterate over the items
context.uncacheEntity(currentItem);
if (itemIterator.hasNext()) { if (itemIterator.hasNext()) {
currentItem = itemIterator.next(); currentItem = itemIterator.next();

2
dspace-api/src/main/java/org/dspace/authorize/AuthorizeServiceImpl.java
View File

@@ -460,7 +460,6 @@ public class AuthorizeServiceImpl implements AuthorizeService
return groupService.isMember(c, Group.ADMIN); return groupService.isMember(c, Group.ADMIN);
} }
} }
@Override @Override
public boolean isAdmin(Context c, EPerson e) throws SQLException public boolean isAdmin(Context c, EPerson e) throws SQLException
{ {
@@ -478,7 +477,6 @@ public class AuthorizeServiceImpl implements AuthorizeService
return groupService.isMember(c, e, Group.ADMIN); return groupService.isMember(c, e, Group.ADMIN);
} }
} }
public boolean isCommunityAdmin(Context c) throws SQLException public boolean isCommunityAdmin(Context c) throws SQLException
{ {
EPerson e = c.getCurrentUser(); EPerson e = c.getCurrentUser();

11
dspace-api/src/main/java/org/dspace/checker/CheckerCommand.java
View File

@@ -7,11 +7,6 @@
*/ */
package org.dspace.checker; package org.dspace.checker;
import java.io.IOException;
import java.sql.SQLException;
import java.util.Date;
import java.util.Map;
import org.apache.commons.collections.MapUtils; import org.apache.commons.collections.MapUtils;
import org.apache.log4j.Logger; import org.apache.log4j.Logger;
import org.dspace.checker.factory.CheckerServiceFactory; import org.dspace.checker.factory.CheckerServiceFactory;
@@ -23,6 +18,11 @@ import org.dspace.core.Context;
import org.dspace.storage.bitstore.factory.StorageServiceFactory; import org.dspace.storage.bitstore.factory.StorageServiceFactory;
import org.dspace.storage.bitstore.service.BitstreamStorageService; import org.dspace.storage.bitstore.service.BitstreamStorageService;
import java.io.IOException;
import java.sql.SQLException;
import java.util.Date;
import java.util.Map;
/** /**
* <p> * <p>
* Main class for the checksum checker tool, which calculates checksums for each * Main class for the checksum checker tool, which calculates checksums for each
@@ -127,6 +127,7 @@ public final class CheckerCommand
collector.collect(context, info); collector.collect(context, info);
} }
context.uncacheEntity(bitstream);
bitstream = dispatcher.next(); bitstream = dispatcher.next();
} }
} }

25
dspace-api/src/main/java/org/dspace/checker/DailyReportEmailer.java
View File

@@ -7,20 +7,7 @@
*/ */
package org.dspace.checker; package org.dspace.checker;
import java.io.File; import org.apache.commons.cli.*;
import java.io.FileWriter;
import java.io.IOException;
import java.sql.SQLException;
import java.util.Date;
import java.util.GregorianCalendar;
import javax.mail.MessagingException;
import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.CommandLineParser;
import org.apache.commons.cli.HelpFormatter;
import org.apache.commons.cli.Options;
import org.apache.commons.cli.ParseException;
import org.apache.commons.cli.PosixParser;
import org.apache.log4j.Logger; import org.apache.log4j.Logger;
import org.dspace.checker.factory.CheckerServiceFactory; import org.dspace.checker.factory.CheckerServiceFactory;
import org.dspace.checker.service.SimpleReporterService; import org.dspace.checker.service.SimpleReporterService;
@@ -28,6 +15,14 @@ import org.dspace.core.ConfigurationManager;
import org.dspace.core.Context; import org.dspace.core.Context;
import org.dspace.core.Email; import org.dspace.core.Email;
import javax.mail.MessagingException;
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import java.sql.SQLException;
import java.util.Date;
import java.util.GregorianCalendar;
/** /**
* <p> * <p>
* The email reporter creates and sends emails to an administrator. This only * The email reporter creates and sends emails to an administrator. This only
@@ -168,7 +163,7 @@ public class DailyReportEmailer
try try
{ {
context = new Context(); context = new Context(Context.Mode.READ_ONLY);
// the number of bitstreams in report // the number of bitstreams in report
int numBitstreams = 0; int numBitstreams = 0;

2
dspace-api/src/main/java/org/dspace/content/Collection.java
View File

@@ -13,8 +13,6 @@ import org.dspace.content.service.CollectionService;
import org.dspace.core.*; import org.dspace.core.*;
import org.dspace.eperson.Group; import org.dspace.eperson.Group;
import org.hibernate.annotations.CacheConcurrencyStrategy; import org.hibernate.annotations.CacheConcurrencyStrategy;
import org.hibernate.annotations.Sort;
import org.hibernate.annotations.SortType;
import org.hibernate.proxy.HibernateProxyHelper; import org.hibernate.proxy.HibernateProxyHelper;
import javax.persistence.*; import javax.persistence.*;

2
dspace-api/src/main/java/org/dspace/content/Community.java
View File

@@ -15,8 +15,6 @@ import org.dspace.content.service.CommunityService;
import org.dspace.core.*; import org.dspace.core.*;
import org.dspace.eperson.Group; import org.dspace.eperson.Group;
import org.hibernate.annotations.CacheConcurrencyStrategy; import org.hibernate.annotations.CacheConcurrencyStrategy;
import org.hibernate.annotations.Sort;
import org.hibernate.annotations.SortType;
import org.hibernate.proxy.HibernateProxyHelper; import org.hibernate.proxy.HibernateProxyHelper;
import javax.persistence.*; import javax.persistence.*;

3
dspace-api/src/main/java/org/dspace/content/MetadataValueServiceImpl.java
View File

@@ -21,6 +21,7 @@ import org.springframework.beans.factory.annotation.Autowired;
import java.io.IOException; import java.io.IOException;
import java.sql.SQLException; import java.sql.SQLException;
import java.util.Iterator;
import java.util.List; import java.util.List;
/** /**
@@ -98,7 +99,7 @@ public class MetadataValueServiceImpl implements MetadataValueService {
} }
@Override @Override
public List<MetadataValue> findByValueLike(Context context, String value) throws SQLException { public Iterator<MetadataValue> findByValueLike(Context context, String value) throws SQLException {
return metadataValueDAO.findByValueLike(context, value); return metadataValueDAO.findByValueLike(context, value);
} }

3
dspace-api/src/main/java/org/dspace/content/dao/MetadataValueDAO.java
View File

@@ -13,6 +13,7 @@ import org.dspace.core.Context;
import org.dspace.core.GenericDAO; import org.dspace.core.GenericDAO;
import java.sql.SQLException; import java.sql.SQLException;
import java.util.Iterator;
import java.util.List; import java.util.List;
/** /**
@@ -26,7 +27,7 @@ public interface MetadataValueDAO extends GenericDAO<MetadataValue> {
public List<MetadataValue> findByField(Context context, MetadataField fieldId) throws SQLException; public List<MetadataValue> findByField(Context context, MetadataField fieldId) throws SQLException;
public List<MetadataValue> findByValueLike(Context context, String value) throws SQLException; public Iterator<MetadataValue> findByValueLike(Context context, String value) throws SQLException;
public void deleteByMetadataField(Context context, MetadataField metadataField) throws SQLException; public void deleteByMetadataField(Context context, MetadataField metadataField) throws SQLException;

15
dspace-api/src/main/java/org/dspace/content/dao/impl/MetadataValueDAOImpl.java
View File

@@ -18,6 +18,7 @@ import org.hibernate.Query;
import org.hibernate.criterion.Restrictions; import org.hibernate.criterion.Restrictions;
import java.sql.SQLException; import java.sql.SQLException;
import java.util.Iterator;
import java.util.List; import java.util.List;
/** /**
@@ -48,14 +49,14 @@ public class MetadataValueDAOImpl extends AbstractHibernateDAO<MetadataValue> im
} }
@Override @Override
public List<MetadataValue> findByValueLike(Context context, String value) throws SQLException { public Iterator<MetadataValue> findByValueLike(Context context, String value) throws SQLException {
Criteria criteria = createCriteria(context, MetadataValue.class); String queryString = "SELECT m FROM MetadataValue m JOIN m.metadataField f " +
criteria.add( "WHERE m.value like concat('%', concat(:searchString,'%')) ORDER BY m.id ASC";
Restrictions.like("value", "%" + value + "%")
);
criteria.setFetchMode("metadataField", FetchMode.JOIN);
return list(criteria); Query query = createQuery(context, queryString);
query.setString("searchString", value);
return iterate(query);
} }
@Override @Override

3
dspace-api/src/main/java/org/dspace/content/service/MetadataValueService.java
View File

@@ -15,6 +15,7 @@ import org.dspace.core.Context;
import java.io.IOException; import java.io.IOException;
import java.sql.SQLException; import java.sql.SQLException;
import java.util.Iterator;
import java.util.List; import java.util.List;
/** /**
@@ -82,7 +83,7 @@ public interface MetadataValueService {
*/ */
public void delete(Context context, MetadataValue metadataValue) throws SQLException; public void delete(Context context, MetadataValue metadataValue) throws SQLException;
public List<MetadataValue> findByValueLike(Context context, String value) throws SQLException; public Iterator<MetadataValue> findByValueLike(Context context, String value) throws SQLException;
public void deleteByMetadataField(Context context, MetadataField metadataField) throws SQLException; public void deleteByMetadataField(Context context, MetadataField metadataField) throws SQLException;

9
dspace-api/src/main/java/org/dspace/core/Context.java
View File

@@ -362,8 +362,13 @@ public class Context
try try
{ {
// As long as we have a valid, writeable database connection, // As long as we have a valid, writeable database connection,
// commit any changes made as part of the transaction // rollback any changes if we are in read-only mode,
commit(); // otherwise, commit any changes made as part of the transaction
if(isReadOnly()) {
abort();
} else {
commit();
}
} }
finally finally
{ {

17
dspace-api/src/main/java/org/dspace/curate/CurationCli.java
View File

@@ -7,16 +7,7 @@
*/ */
package org.dspace.curate; package org.dspace.curate;
import java.io.BufferedReader; import org.apache.commons.cli.*;
import java.io.FileReader;
import java.util.Iterator;
import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.CommandLineParser;
import org.apache.commons.cli.HelpFormatter;
import org.apache.commons.cli.Options;
import org.apache.commons.cli.PosixParser;
import org.dspace.content.factory.ContentServiceFactory; import org.dspace.content.factory.ContentServiceFactory;
import org.dspace.core.Context; import org.dspace.core.Context;
import org.dspace.core.factory.CoreServiceFactory; import org.dspace.core.factory.CoreServiceFactory;
@@ -25,6 +16,10 @@ import org.dspace.eperson.EPerson;
import org.dspace.eperson.factory.EPersonServiceFactory; import org.dspace.eperson.factory.EPersonServiceFactory;
import org.dspace.eperson.service.EPersonService; import org.dspace.eperson.service.EPersonService;
import java.io.BufferedReader;
import java.io.FileReader;
import java.util.Iterator;
/** /**
* CurationCli provides command-line access to Curation tools and processes. * CurationCli provides command-line access to Curation tools and processes.
* *
@@ -142,7 +137,7 @@ public class CurationCli
} }
EPersonService ePersonService = EPersonServiceFactory.getInstance().getEPersonService(); EPersonService ePersonService = EPersonServiceFactory.getInstance().getEPersonService();
Context c = new Context(); Context c = new Context(Context.Mode.BATCH_EDIT);
if (ePersonName != null) if (ePersonName != null)
{ {
EPerson ePerson = ePersonService.findByEmail(c, ePersonName); EPerson ePerson = ePersonService.findByEmail(c, ePersonName);

8
dspace-api/src/main/java/org/dspace/curate/Curator.java
View File

@@ -512,10 +512,14 @@ public class Curator
{ {
return false; return false;
} }
Iterator<Item> iter = itemService.findByCollection(curationContext(), coll); Context context = curationContext();
Iterator<Item> iter = itemService.findByCollection(context, coll);
while (iter.hasNext()) while (iter.hasNext())
{ {
if (! tr.run(iter.next())) Item item = iter.next();
boolean shouldContinue = tr.run(item);
context.uncacheEntity(item);
if (!shouldContinue)
{ {
return false; return false;
} }

6
dspace-api/src/main/java/org/dspace/embargo/EmbargoCLITool.java
View File

@@ -115,7 +115,7 @@ public class EmbargoCLITool {
Context context = null; Context context = null;
try try
{ {
context = new Context(); context = new Context(Context.Mode.BATCH_EDIT);
context.turnOffAuthorisationSystem(); context.turnOffAuthorisationSystem();
Date now = new Date(); Date now = new Date();
@@ -149,10 +149,12 @@ public class EmbargoCLITool {
Iterator<Item> ii = embargoService.findItemsByLiftMetadata(context); Iterator<Item> ii = embargoService.findItemsByLiftMetadata(context);
while (ii.hasNext()) while (ii.hasNext())
{ {
if (processOneItem(context, ii.next(), line, now)) Item item = ii.next();
if (processOneItem(context, item, line, now))
{ {
status = 1; status = 1;
} }
context.uncacheEntity(item);
} }
} }
context.complete(); context.complete();

2
dspace-api/src/main/java/org/dspace/eperson/SubscribeCLITool.java
View File

@@ -302,7 +302,7 @@ public class SubscribeCLITool {
Context context = null; Context context = null;
try { try {
context = new Context(); context = new Context(Context.Mode.READ_ONLY);
processDaily(context, test); processDaily(context, test);
context.complete(); context.complete();
} catch (Exception e) { } catch (Exception e) {

2
dspace-api/src/main/java/org/dspace/eperson/service/GroupService.java
View File

@@ -169,7 +169,7 @@ public interface GroupService extends DSpaceObjectService<Group>, DSpaceObjectLe
* @throws SQLException if database error * @throws SQLException if database error
*/ */
public boolean isMember(Context context, EPerson epersonToCheck, String groupName) throws SQLException; public boolean isMember(Context context, EPerson epersonToCheck, String groupName) throws SQLException;
/** /**
* fast check to see if an eperson is a member called with eperson id, does * fast check to see if an eperson is a member called with eperson id, does
* database lookup without instantiating all of the epeople objects and is * database lookup without instantiating all of the epeople objects and is

6
dspace-api/src/main/java/org/dspace/handle/HandleServiceImpl.java
View File

@@ -231,6 +231,10 @@ public class HandleServiceImpl implements HandleService
// can verify during a restore whether the same *type* of resource // can verify during a restore whether the same *type* of resource
// is reusing this handle! // is reusing this handle!
handle.setDSpaceObject(null); handle.setDSpaceObject(null);
//Also remove the handle from the DSO list to keep a consistent model
dso.getHandles().remove(handle);
handleDAO.save(context, handle); handleDAO.save(context, handle);
if (log.isDebugEnabled()) if (log.isDebugEnabled())
@@ -241,7 +245,7 @@ public class HandleServiceImpl implements HandleService
} }
else else
{ {
log.warn("Cannot find Handle entry to unbind for object " + Constants.typeText[dso.getType()] + " id=" + dso.getID()); log.trace("Cannot find Handle entry to unbind for object " + Constants.typeText[dso.getType()] + " id=" + dso.getID() + ". Handle could have been unbinded before.");
} }
} }

27
dspace-api/src/main/java/org/dspace/handle/UpdateHandlePrefix.java
View File

@@ -7,10 +7,6 @@
*/ */
package org.dspace.handle; package org.dspace.handle;
import java.io.BufferedReader;
import java.io.InputStreamReader;
import java.sql.SQLException;
import java.util.List;
import org.apache.log4j.Logger; import org.apache.log4j.Logger;
import org.dspace.content.MetadataValue; import org.dspace.content.MetadataValue;
import org.dspace.content.factory.ContentServiceFactory; import org.dspace.content.factory.ContentServiceFactory;
@@ -19,6 +15,13 @@ import org.dspace.core.Context;
import org.dspace.discovery.IndexClient; import org.dspace.discovery.IndexClient;
import org.dspace.handle.factory.HandleServiceFactory; import org.dspace.handle.factory.HandleServiceFactory;
import org.dspace.handle.service.HandleService; import org.dspace.handle.service.HandleService;
import org.dspace.services.ConfigurationService;
import org.dspace.services.factory.DSpaceServicesFactory;
import java.io.BufferedReader;
import java.io.InputStreamReader;
import java.sql.SQLException;
import java.util.Iterator;
/** /**
* A script to update the handle values in the database. This is typically used * A script to update the handle values in the database. This is typically used
@@ -32,6 +35,7 @@ public class UpdateHandlePrefix
{ {
private static final Logger log = Logger.getLogger(UpdateHandlePrefix.class); private static final Logger log = Logger.getLogger(UpdateHandlePrefix.class);
private static final ConfigurationService configurationService = DSpaceServicesFactory.getInstance().getConfigurationService();
/** /**
* When invoked as a command-line tool, updates handle prefix * When invoked as a command-line tool, updates handle prefix
@@ -94,12 +98,19 @@ public class UpdateHandlePrefix
System.out.print("Updating metadatavalues table... "); System.out.print("Updating metadatavalues table... ");
MetadataValueService metadataValueService = ContentServiceFactory.getInstance().getMetadataValueService(); MetadataValueService metadataValueService = ContentServiceFactory.getInstance().getMetadataValueService();
List<MetadataValue> metadataValues = metadataValueService.findByValueLike(context, "http://hdl.handle.net/");
int updMeta = metadataValues.size(); String handlePrefix = configurationService.getProperty("handle.canonical.prefix");
for (MetadataValue metadataValue : metadataValues) { Iterator<MetadataValue> metadataValues = metadataValueService.findByValueLike(context, handlePrefix);
metadataValue.setValue(metadataValue.getValue().replace("http://hdl.handle.net/" + oldH, "http://hdl.handle.net/" + newH));
int updMeta = 0;
while(metadataValues.hasNext()) {
MetadataValue metadataValue = metadataValues.next();
metadataValue.setValue(metadataValue.getValue().replace(handlePrefix + oldH, handlePrefix + newH));
metadataValueService.update(context, metadataValue, true); metadataValueService.update(context, metadataValue, true);
context.uncacheEntity(metadataValue);
updMeta++;
} }
System.out.println( System.out.println(
updMeta + " metadata value" + ((updMeta > 1) ? "s" : "") + " updated" updMeta + " metadata value" + ((updMeta > 1) ? "s" : "") + " updated"
); );

9
dspace-api/src/main/java/org/dspace/harvest/OAIHarvester.java
View File

@@ -646,8 +646,13 @@ public class OAIHarvester {
log.info(String.format("Item %s (%s) has been ingested (item %d of %d). The whole process took: %d ms.", log.info(String.format("Item %s (%s) has been ingested (item %d of %d). The whole process took: %d ms.",
item.getHandle(), item.getID(), currentRecord, totalListSize, timeTaken)); item.getHandle(), item.getID(), currentRecord, totalListSize, timeTaken));
// Stop ignoring authorization //Clear the context cache
ourContext.restoreAuthSystemState(); ourContext.uncacheEntity(wi);
ourContext.uncacheEntity(hi);
ourContext.uncacheEntity(item);
// Stop ignoring authorization
ourContext.restoreAuthSystemState();
} }

29
dspace-api/src/main/java/org/dspace/identifier/doi/DOIOrganiser.java
View File

@@ -8,28 +8,12 @@
package org.dspace.identifier.doi; package org.dspace.identifier.doi;
import java.io.IOException; import org.apache.commons.cli.*;
import java.io.PrintStream;
import java.sql.SQLException;
import java.util.*;
import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.CommandLineParser;
import org.apache.commons.cli.HelpFormatter;
import org.apache.commons.cli.Option;
import org.apache.commons.cli.OptionBuilder;
import org.apache.commons.cli.Options;
import org.apache.commons.cli.ParseException;
import org.apache.commons.cli.PosixParser;
import org.apache.log4j.Logger; import org.apache.log4j.Logger;
import org.dspace.content.DSpaceObject; import org.dspace.content.DSpaceObject;
import org.dspace.content.factory.ContentServiceFactory; import org.dspace.content.factory.ContentServiceFactory;
import org.dspace.content.service.ItemService; import org.dspace.content.service.ItemService;
import org.dspace.core.ConfigurationManager; import org.dspace.core.*;
import org.dspace.core.Constants;
import org.dspace.core.Context;
import org.dspace.core.Email;
import org.dspace.core.I18nUtil;
import org.dspace.handle.factory.HandleServiceFactory; import org.dspace.handle.factory.HandleServiceFactory;
import org.dspace.handle.service.HandleService; import org.dspace.handle.service.HandleService;
import org.dspace.identifier.DOI; import org.dspace.identifier.DOI;
@@ -39,6 +23,11 @@ import org.dspace.identifier.factory.IdentifierServiceFactory;
import org.dspace.identifier.service.DOIService; import org.dspace.identifier.service.DOIService;
import org.dspace.utils.DSpace; import org.dspace.utils.DSpace;
import java.io.IOException;
import java.io.PrintStream;
import java.sql.SQLException;
import java.util.*;
/** /**
* *
@@ -203,6 +192,7 @@ public class DOIOrganiser {
for (DOI doi : dois) { for (DOI doi : dois) {
organiser.reserve(doi); organiser.reserve(doi);
context.uncacheEntity(doi);
} }
} catch (SQLException ex) { } catch (SQLException ex) {
System.err.println("Error in database connection:" + ex.getMessage()); System.err.println("Error in database connection:" + ex.getMessage());
@@ -223,6 +213,7 @@ public class DOIOrganiser {
for (DOI doi : dois) for (DOI doi : dois)
{ {
organiser.register(doi); organiser.register(doi);
context.uncacheEntity(doi);
} }
} catch (SQLException ex) { } catch (SQLException ex) {
System.err.println("Error in database connection:" + ex.getMessage()); System.err.println("Error in database connection:" + ex.getMessage());
@@ -247,6 +238,7 @@ public class DOIOrganiser {
for (DOI doi : dois) for (DOI doi : dois)
{ {
organiser.update(doi); organiser.update(doi);
context.uncacheEntity(doi);
} }
} catch (SQLException ex) { } catch (SQLException ex) {
System.err.println("Error in database connection:" + ex.getMessage()); System.err.println("Error in database connection:" + ex.getMessage());
@@ -270,6 +262,7 @@ public class DOIOrganiser {
DOI doi = iterator.next(); DOI doi = iterator.next();
iterator.remove(); iterator.remove();
organiser.delete(doi.getDoi()); organiser.delete(doi.getDoi());
context.uncacheEntity(doi);
} }
} catch (SQLException ex) { } catch (SQLException ex) {
System.err.println("Error in database connection:" + ex.getMessage()); System.err.println("Error in database connection:" + ex.getMessage());

33
dspace-api/src/main/java/org/dspace/rdf/RDFizer.java
View File

@@ -9,29 +9,11 @@
package org.dspace.rdf; package org.dspace.rdf;
import com.hp.hpl.jena.rdf.model.Model; import com.hp.hpl.jena.rdf.model.Model;
import java.io.PrintWriter; import org.apache.commons.cli.*;
import java.sql.SQLException;
import java.util.Iterator;
import java.util.List;
import java.util.Set;
import java.util.UUID;
import java.util.concurrent.CopyOnWriteArraySet;
import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.CommandLineParser;
import org.apache.commons.cli.HelpFormatter;
import org.apache.commons.cli.Option;
import org.apache.commons.cli.OptionBuilder;
import org.apache.commons.cli.Options;
import org.apache.commons.cli.ParseException;
import org.apache.commons.cli.PosixParser;
import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.StringUtils;
import org.apache.log4j.Logger; import org.apache.log4j.Logger;
import org.dspace.authorize.AuthorizeException; import org.dspace.authorize.AuthorizeException;
import org.dspace.content.Collection; import org.dspace.content.*;
import org.dspace.content.Community;
import org.dspace.content.DSpaceObject;
import org.dspace.content.Item;
import org.dspace.content.Site;
import org.dspace.content.factory.ContentServiceFactory; import org.dspace.content.factory.ContentServiceFactory;
import org.dspace.content.service.CommunityService; import org.dspace.content.service.CommunityService;
import org.dspace.content.service.ItemService; import org.dspace.content.service.ItemService;
@@ -44,6 +26,14 @@ import org.dspace.rdf.storage.RDFStorage;
import org.dspace.services.ConfigurationService; import org.dspace.services.ConfigurationService;
import org.dspace.services.factory.DSpaceServicesFactory; import org.dspace.services.factory.DSpaceServicesFactory;
import java.io.PrintWriter;
import java.sql.SQLException;
import java.util.Iterator;
import java.util.List;
import java.util.Set;
import java.util.UUID;
import java.util.concurrent.CopyOnWriteArraySet;
/** /**
* This class manages the handling of RDF data in DSpace. It generates * This class manages the handling of RDF data in DSpace. It generates
* identifiers, it loads data, it manages the conversion of DSpace Objects into * identifiers, it loads data, it manages the conversion of DSpace Objects into
@@ -465,8 +455,9 @@ public class RDFizer {
// } // }
callback.callback(dso); callback.callback(dso);
report("Processed " + contentServiceFactory.getDSpaceObjectService(dso).getTypeText(dso) + " " + dso.getID() report("Processed " + contentServiceFactory.getDSpaceObjectService(dso).getTypeText(dso) + " " + dso.getID()
+ " (handle " + dso.getHandle() + ")."); + " (handle " + dso.getHandle() + ").");
context.uncacheEntity(dso);
} }
protected boolean isProcessed(DSpaceObject dso) protected boolean isProcessed(DSpaceObject dso)

2
dspace-api/src/main/java/org/dspace/storage/bitstore/BitStoreMigrate.java
View File

@@ -68,7 +68,7 @@ public class BitStoreMigrate {
System.exit(0); System.exit(0);
} }
Context context = new Context(); Context context = new Context(Context.Mode.BATCH_EDIT);
context.turnOffAuthorisationSystem(); context.turnOffAuthorisationSystem();
if(line.hasOption('p')) { if(line.hasOption('p')) {

11
dspace-api/src/main/java/org/dspace/storage/bitstore/BitstreamStorageServiceImpl.java
View File

@@ -223,7 +223,7 @@ public class BitstreamStorageServiceImpl implements BitstreamStorageService, Ini
try try
{ {
context = new Context(); context = new Context(Context.Mode.BATCH_EDIT);
context.turnOffAuthorisationSystem(); context.turnOffAuthorisationSystem();
List<Bitstream> storage = bitstreamService.findDeletedBitstreams(context); List<Bitstream> storage = bitstreamService.findDeletedBitstreams(context);
@@ -254,6 +254,7 @@ public class BitstreamStorageServiceImpl implements BitstreamStorageService, Ini
} }
bitstreamService.expunge(context, bitstream); bitstreamService.expunge(context, bitstream);
} }
context.uncacheEntity(bitstream);
continue; continue;
} }
@@ -262,7 +263,8 @@ public class BitstreamStorageServiceImpl implements BitstreamStorageService, Ini
if (isRecent(Long.valueOf(receivedMetadata.get("modified").toString()))) if (isRecent(Long.valueOf(receivedMetadata.get("modified").toString())))
{ {
log.debug("file is recent"); log.debug("file is recent");
continue; context.uncacheEntity(bitstream);
continue;
} }
if (deleteDbRecords) if (deleteDbRecords)
@@ -281,6 +283,7 @@ public class BitstreamStorageServiceImpl implements BitstreamStorageService, Ini
} }
if (isRegisteredBitstream(bitstream.getInternalId())) { if (isRegisteredBitstream(bitstream.getInternalId())) {
context.uncacheEntity(bitstream);
continue; // do not delete registered bitstreams continue; // do not delete registered bitstreams
} }
@@ -310,6 +313,8 @@ public class BitstreamStorageServiceImpl implements BitstreamStorageService, Ini
{ {
context.dispatchEvents(); context.dispatchEvents();
} }
context.uncacheEntity(bitstream);
} }
System.out.print("Committing changes to the database..."); System.out.print("Committing changes to the database...");
@@ -393,6 +398,8 @@ public class BitstreamStorageServiceImpl implements BitstreamStorageService, Ini
} }
processedCounter++; processedCounter++;
context.uncacheEntity(bitstream);
//modulo //modulo
if ((processedCounter % batchCommitSize) == 0) { if ((processedCounter % batchCommitSize) == 0) {
log.info("Migration Commit Checkpoint: " + processedCounter); log.info("Migration Commit Checkpoint: " + processedCounter);

3
dspace-api/src/main/java/org/dspace/workflow/WorkflowItem.java
View File

@@ -9,12 +9,13 @@ package org.dspace.workflow;
import org.dspace.content.InProgressSubmission; import org.dspace.content.InProgressSubmission;
import org.dspace.core.ReloadableEntity;
/** /**
* Interface representing a workflowitem, each workflowItem implementation must implement this interface. * Interface representing a workflowitem, each workflowItem implementation must implement this interface.
* *
* @author kevinvandevelde at atmire.com * @author kevinvandevelde at atmire.com
*/ */
public interface WorkflowItem extends InProgressSubmission { public interface WorkflowItem extends InProgressSubmission, ReloadableEntity<Integer> {
} }

2
dspace-api/src/main/java/org/dspace/workflowbasic/BasicWorkflowItem.java
View File

@@ -25,7 +25,7 @@ import java.sql.SQLException;
*/ */
@Entity @Entity
@Table(name = "workflowitem") @Table(name = "workflowitem")
public class BasicWorkflowItem implements WorkflowItem, ReloadableEntity<Integer> public class BasicWorkflowItem implements WorkflowItem
{ {
@Id @Id

3
dspace-api/src/test/java/org/dspace/content/VersioningTest.java
View File

@@ -166,9 +166,10 @@ public class VersioningTest extends AbstractUnitTest {
@Test @Test
public void testVersionDelete() throws Exception { public void testVersionDelete() throws Exception {
context.turnOffAuthorisationSystem(); context.turnOffAuthorisationSystem();
String handle = versionedItem.getHandle();
versionService.removeVersion(context, versionedItem); versionService.removeVersion(context, versionedItem);
assertThat("Test_version_delete", itemService.find(context, versionedItem.getID()), nullValue()); assertThat("Test_version_delete", itemService.find(context, versionedItem.getID()), nullValue());
assertThat("Test_version_handle_delete", handleService.resolveToObject(context, versionedItem.getHandle()), nullValue()); assertThat("Test_version_handle_delete", handleService.resolveToObject(context, handle), nullValue());
context.restoreAuthSystemState(); context.restoreAuthSystemState();
} }
} }