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

27
dspace-api/src/main/java/org/dspace/app/bulkedit/MetadataImport.java
View File

@@ -31,6 +31,7 @@ import org.dspace.eperson.EPerson;
import org.dspace.eperson.factory.EPersonServiceFactory;
import org.dspace.handle.factory.HandleServiceFactory;
import org.dspace.handle.service.HandleService;
import org.dspace.workflow.WorkflowItem;
import org.dspace.workflow.WorkflowService;
import org.dspace.workflow.factory.WorkflowServiceFactory;
@@ -122,6 +123,9 @@ public class MetadataImport
// Make the changes
try
{
Context.Mode originalMode = c.getCurrentMode();
c.setMode(Context.Mode.BATCH_EDIT);
// Process each change
for (DSpaceCSVLine line : toImport)
{
@@ -134,11 +138,15 @@ public class MetadataImport
throw new MetadataImportException("'action' not allowed for new items!");
}
WorkspaceItem wsItem = null;
WorkflowItem wfItem = null;
Item item = null;
// Is this a new item?
if (id != null)
{
// Get the item
Item item = itemService.find(c, id);
item = itemService.find(c, id);
if (item == null)
{
throw new MetadataImportException("Unknown item ID " + id);
@@ -345,8 +353,8 @@ public class MetadataImport
// Create the item
String collectionHandle = line.get("collection").get(0);
collection = (Collection) handleService.resolveToObject(c, collectionHandle);
WorkspaceItem wsItem = workspaceItemService.create(c, collection, useTemplate);
Item item = wsItem.getItem();
wsItem = workspaceItemService.create(c, collection, useTemplate);
item = wsItem.getItem();
// Add the metadata to the item
for (BulkEditMetadataValue dcv : whatHasChanged.getAdds())
@@ -364,9 +372,9 @@ public class MetadataImport
if(useWorkflow){
WorkflowService workflowService = WorkflowServiceFactory.getInstance().getWorkflowService();
if (workflowNotify) {
workflowService.start(c, wsItem);
wfItem = workflowService.start(c, wsItem);
} else {
workflowService.startWithoutNotify(c, wsItem);
wfItem = workflowService.startWithoutNotify(c, wsItem);
}
}
else
@@ -394,8 +402,17 @@ public class MetadataImport
// Record the changes
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)
{
throw mie;

50
dspace-api/src/main/java/org/dspace/app/harvest/Harvest.java
View File

@@ -7,36 +7,32 @@
*/
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.sql.SQLException;
import java.util.Iterator;
import java.util.List;
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.
*
@@ -96,7 +92,7 @@ public class Harvest
{
HelpFormatter myhelp = new HelpFormatter();
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("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");
@@ -160,7 +156,7 @@ public class Harvest
// Instantiate our class
Harvest harvester = new Harvest();
harvester.context = new Context();
harvester.context = new Context(Context.Mode.BATCH_EDIT);
// Check our options
@@ -373,7 +369,7 @@ public class Harvest
Item item = it.next();
System.out.println("Deleting: " + item.getHandle());
collectionService.removeItem(context, collection, item);
// Dispatch events every 50 items
context.uncacheEntity(item);// Dispatch events every 50 items
if (i%50 == 0) {
context.dispatchEvents();
i=0;

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

@@ -176,7 +176,7 @@ public class ItemExportCLITool {
System.exit(1);
}
Context c = new Context();
Context c = new Context(Context.Mode.READ_ONLY);
c.turnOffAuthorisationSystem();
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;
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.log4j.Logger;
import org.dspace.app.itemexport.service.ItemExportService;
import org.dspace.content.*;
import org.dspace.content.Collection;
import org.dspace.content.service.BitstreamService;
import org.dspace.content.service.CommunityService;
import org.dspace.content.service.ItemService;
import org.dspace.core.ConfigurationManager;
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.core.*;
import org.dspace.eperson.EPerson;
import org.dspace.eperson.service.EPersonService;
import org.dspace.handle.service.HandleService;
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
* 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);
exportItem(c, i.next(), fullPath, mySequenceNumber, migrate, excludeBitstreams);
Item item = i.next();
exportItem(c, item, fullPath, mySequenceNumber, migrate, excludeBitstreams);
c.uncacheEntity(item);
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);
// create a context
Context c = new Context();
Context c = new Context(Context.Mode.BATCH_EDIT);
// find the EPerson, assign to context
EPerson myEPerson = null;

53
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.bteio.generators.DSpaceOutputGenerator;
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.io.FileDeleteStrategy;
import org.apache.commons.io.FileUtils;
@@ -46,18 +31,14 @@ import org.dspace.authorize.service.ResourcePolicyService;
import org.dspace.content.*;
import org.dspace.content.Collection;
import org.dspace.content.service.*;
import org.dspace.core.ConfigurationManager;
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.core.*;
import org.dspace.eperson.EPerson;
import org.dspace.eperson.Group;
import org.dspace.eperson.service.EPersonService;
import org.dspace.eperson.service.GroupService;
import org.dspace.handle.service.HandleService;
import org.dspace.utils.DSpace;
import org.dspace.workflow.WorkflowItem;
import org.dspace.workflow.WorkflowService;
import org.springframework.beans.factory.InitializingBean;
import org.springframework.beans.factory.annotation.Autowired;
@@ -67,6 +48,19 @@ import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
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
@@ -343,7 +337,7 @@ public class ItemImportServiceImpl implements ItemImportService, InitializingBea
{
clist = mycollections;
}
addItem(c, clist, sourceDir, dircontents[i], mapOut, template);
Item item =addItem(c, clist, sourceDir, dircontents[i], mapOut, template);c.uncacheEntity(item);
System.out.println(i + " " + dircontents[i]);
}
}
@@ -416,7 +410,9 @@ public class ItemImportServiceImpl implements ItemImportService, InitializingBea
handleOut.close();
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);
System.out.println("Deleting item " + itemID);
deleteItem(c, myitem);
c.uncacheEntity(myitem);
}
}
}
@@ -473,6 +470,7 @@ public class ItemImportServiceImpl implements ItemImportService, InitializingBea
// create workspace item
Item myitem = null;
WorkspaceItem wi = null;
WorkflowItem wfi = null;
if (!isTest)
{
@@ -498,9 +496,9 @@ public class ItemImportServiceImpl implements ItemImportService, InitializingBea
{
// Should we send a workflow alert email or not?
if (useWorkflowSendEmail) {
workflowService.start(c, wi);
wfi = workflowService.start(c, wi);
} else {
workflowService.startWithoutNotify(c, wi);
wfi = workflowService.startWithoutNotify(c, wi);
}
// send ID to the mapfile
@@ -556,6 +554,10 @@ public class ItemImportServiceImpl implements ItemImportService, InitializingBea
mapOut.println(mapOutputString);
}
//Clear intermediary objects from the cache
c.uncacheEntity(wi);
c.uncacheEntity(wfi);
return myitem;
}
@@ -593,6 +595,7 @@ public class ItemImportServiceImpl implements ItemImportService, InitializingBea
else
{
deleteItem(c, myitem);
c.uncacheEntity(myitem);
}
}

23
dspace-api/src/main/java/org/dspace/app/itemupdate/ItemUpdate.java
View File

@@ -7,21 +7,7 @@
*/
package org.dspace.app.itemupdate;
import java.io.BufferedWriter;
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.apache.commons.cli.*;
import org.dspace.content.Item;
import org.dspace.content.factory.ContentServiceFactory;
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.service.EPersonService;
import java.io.*;
import java.util.*;
/**
*
* Provides some batch editing capabilities for items in DSpace:
@@ -353,7 +342,7 @@ public class ItemUpdate {
pr("ItemUpdate - initializing run on " + (new Date()).toString());
context = new Context();
context = new Context(Context.Mode.BATCH_EDIT);
iu.setEPerson(context, iu.eperson);
context.turnOffAuthorisationSystem();
@@ -461,7 +450,7 @@ public class ItemUpdate {
{
Item item = itarch.getItem();
itemService.update(context, item); //need to update before commit
}
context.uncacheEntity(item);}
ItemUpdate.pr("Item " + dirname + " completed");
successItemCount++;
}

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

@@ -7,9 +7,6 @@
*/
package org.dspace.app.mediafilter;
import java.io.InputStream;
import java.util.*;
import org.dspace.app.mediafilter.service.MediaFilterService;
import org.dspace.authorize.service.AuthorizeService;
import org.dspace.content.*;
@@ -24,6 +21,9 @@ import org.dspace.services.ConfigurationService;
import org.springframework.beans.factory.InitializingBean;
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
* repository's content. A few command line flags affect the operation of the
@@ -161,6 +161,7 @@ public class MediaFilterServiceImpl implements MediaFilterService, InitializingB
++processed;
}
// clear item objects from context cache and internal cache
c.uncacheEntity(currentItem);
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;
import java.io.BufferedReader;
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.apache.commons.cli.*;
import org.dspace.authorize.AuthorizeException;
import org.dspace.content.DSpaceObject;
import org.dspace.content.crosswalk.CrosswalkException;
import org.dspace.content.packager.PackageDisseminator;
import org.dspace.content.packager.PackageException;
import org.dspace.content.packager.PackageParameters;
import org.dspace.content.packager.PackageIngester;
import org.dspace.content.packager.PackageParameters;
import org.dspace.core.Constants;
import org.dspace.core.Context;
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.workflow.WorkflowException;
import java.io.*;
import java.sql.SQLException;
import java.util.List;
/**
* Command-line interface to the Packager plugin.
* <p>
@@ -331,6 +323,7 @@ public class Packager
//If we are in REPLACE mode
if(pkgParams.replaceModeEnabled())
{
context.setMode(Context.Mode.BATCH_EDIT);
PackageIngester sip = (PackageIngester) pluginService
.getNamedPlugin(PackageIngester.class, myPackager.packageType);
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 (myPackager.submit || pkgParams.restoreModeEnabled())
{
context.setMode(Context.Mode.BATCH_EDIT);
PackageIngester sip = (PackageIngester) pluginService
.getNamedPlugin(PackageIngester.class, myPackager.packageType);
if (sip == null)
@@ -445,6 +440,8 @@ public class Packager
}// else, if DISSEMINATE mode
else
{
context.setMode(Context.Mode.READ_ONLY);
//retrieve specified package disseminator
PackageDisseminator dip = (PackageDisseminator) pluginService
.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;
import java.io.BufferedReader;
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.cli.*;
import org.apache.commons.lang.ArrayUtils;
import org.apache.commons.lang.StringUtils;
import org.apache.log4j.Logger;
import org.dspace.content.Collection;
import org.dspace.content.Community;
@@ -42,6 +23,16 @@ import org.dspace.core.LogManager;
import org.dspace.services.ConfigurationService;
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.
*
@@ -188,7 +179,7 @@ public class GenerateSitemaps
+ "?map=", null);
}
Context c = new Context();
Context c = new Context(Context.Mode.READ_ONLY);
List<Community> comms = communityService.findAll(c);
@@ -201,6 +192,8 @@ public class GenerateSitemaps
if (makeSitemapOrg) {
sitemapsOrg.addURL(url, null);
}
c.uncacheEntity(comm);
}
List<Collection> colls = collectionService.findAll(c);
@@ -214,6 +207,8 @@ public class GenerateSitemaps
if (makeSitemapOrg) {
sitemapsOrg.addURL(url, null);
}
c.uncacheEntity(coll);
}
Iterator<Item> allItems = itemService.findAll(c);
@@ -234,6 +229,8 @@ public class GenerateSitemaps
sitemapsOrg.addURL(url, lastMod);
}
c.uncacheEntity(i);
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 {
// 3. iterate over the items
context.uncacheEntity(currentItem);
if (itemIterator.hasNext()) {
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);
}
}
@Override
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);
}
}
public boolean isCommunityAdmin(Context c) throws SQLException
{
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;
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.log4j.Logger;
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.service.BitstreamStorageService;
import java.io.IOException;
import java.sql.SQLException;
import java.util.Date;
import java.util.Map;
/**
* <p>
* Main class for the checksum checker tool, which calculates checksums for each
@@ -127,6 +127,7 @@ public final class CheckerCommand
collector.collect(context, info);
}
context.uncacheEntity(bitstream);
bitstream = dispatcher.next();
}
}

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

@@ -7,20 +7,7 @@
*/
package org.dspace.checker;
import java.io.File;
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.commons.cli.*;
import org.apache.log4j.Logger;
import org.dspace.checker.factory.CheckerServiceFactory;
import org.dspace.checker.service.SimpleReporterService;
@@ -28,6 +15,14 @@ import org.dspace.core.ConfigurationManager;
import org.dspace.core.Context;
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>
* The email reporter creates and sends emails to an administrator. This only
@@ -168,7 +163,7 @@ public class DailyReportEmailer
try
{
context = new Context();
context = new Context(Context.Mode.READ_ONLY);
// the number of bitstreams in report
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.eperson.Group;
import org.hibernate.annotations.CacheConcurrencyStrategy;
import org.hibernate.annotations.Sort;
import org.hibernate.annotations.SortType;
import org.hibernate.proxy.HibernateProxyHelper;
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.eperson.Group;
import org.hibernate.annotations.CacheConcurrencyStrategy;
import org.hibernate.annotations.Sort;
import org.hibernate.annotations.SortType;
import org.hibernate.proxy.HibernateProxyHelper;
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.sql.SQLException;
import java.util.Iterator;
import java.util.List;
/**
@@ -98,7 +99,7 @@ public class MetadataValueServiceImpl implements MetadataValueService {
}
@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);
}

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 java.sql.SQLException;
import java.util.Iterator;
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> 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;

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 java.sql.SQLException;
import java.util.Iterator;
import java.util.List;
/**
@@ -48,14 +49,14 @@ public class MetadataValueDAOImpl extends AbstractHibernateDAO<MetadataValue> im
}
@Override
public List<MetadataValue> findByValueLike(Context context, String value) throws SQLException {
Criteria criteria = createCriteria(context, MetadataValue.class);
criteria.add(
Restrictions.like("value", "%" + value + "%")
);
criteria.setFetchMode("metadataField", FetchMode.JOIN);
public Iterator<MetadataValue> findByValueLike(Context context, String value) throws SQLException {
String queryString = "SELECT m FROM MetadataValue m JOIN m.metadataField f " +
"WHERE m.value like concat('%', concat(:searchString,'%')) ORDER BY m.id ASC";
return list(criteria);
Query query = createQuery(context, queryString);
query.setString("searchString", value);
return iterate(query);
}
@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.sql.SQLException;
import java.util.Iterator;
import java.util.List;
/**
@@ -82,7 +83,7 @@ public interface MetadataValueService {
*/
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;

7
dspace-api/src/main/java/org/dspace/core/Context.java
View File

@@ -362,9 +362,14 @@ public class Context
try
{
// 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,
// otherwise, commit any changes made as part of the transaction
if(isReadOnly()) {
abort();
} else {
commit();
}
}
finally
{
if(dbConnection != null)

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

@@ -7,16 +7,7 @@
*/
package org.dspace.curate;
import java.io.BufferedReader;
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.apache.commons.cli.*;
import org.dspace.content.factory.ContentServiceFactory;
import org.dspace.core.Context;
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.service.EPersonService;
import java.io.BufferedReader;
import java.io.FileReader;
import java.util.Iterator;
/**
* CurationCli provides command-line access to Curation tools and processes.
*
@@ -142,7 +137,7 @@ public class CurationCli
}
EPersonService ePersonService = EPersonServiceFactory.getInstance().getEPersonService();
Context c = new Context();
Context c = new Context(Context.Mode.BATCH_EDIT);
if (ePersonName != null)
{
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;
}
Iterator<Item> iter = itemService.findByCollection(curationContext(), coll);
Context context = curationContext();
Iterator<Item> iter = itemService.findByCollection(context, coll);
while (iter.hasNext())
{
if (! tr.run(iter.next()))
Item item = iter.next();
boolean shouldContinue = tr.run(item);
context.uncacheEntity(item);
if (!shouldContinue)
{
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;
try
{
context = new Context();
context = new Context(Context.Mode.BATCH_EDIT);
context.turnOffAuthorisationSystem();
Date now = new Date();
@@ -149,10 +149,12 @@ public class EmbargoCLITool {
Iterator<Item> ii = embargoService.findItemsByLiftMetadata(context);
while (ii.hasNext())
{
if (processOneItem(context, ii.next(), line, now))
Item item = ii.next();
if (processOneItem(context, item, line, now))
{
status = 1;
}
context.uncacheEntity(item);
}
}
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;
try {
context = new Context();
context = new Context(Context.Mode.READ_ONLY);
processDaily(context, test);
context.complete();
} catch (Exception e) {

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
// is reusing this handle!
handle.setDSpaceObject(null);
//Also remove the handle from the DSO list to keep a consistent model
dso.getHandles().remove(handle);
handleDAO.save(context, handle);
if (log.isDebugEnabled())
@@ -241,7 +245,7 @@ public class HandleServiceImpl implements HandleService
}
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;
import java.io.BufferedReader;
import java.io.InputStreamReader;
import java.sql.SQLException;
import java.util.List;
import org.apache.log4j.Logger;
import org.dspace.content.MetadataValue;
import org.dspace.content.factory.ContentServiceFactory;
@@ -19,6 +15,13 @@ import org.dspace.core.Context;
import org.dspace.discovery.IndexClient;
import org.dspace.handle.factory.HandleServiceFactory;
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
@@ -32,6 +35,7 @@ public class UpdateHandlePrefix
{
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
@@ -94,12 +98,19 @@ public class UpdateHandlePrefix
System.out.print("Updating metadatavalues table... ");
MetadataValueService metadataValueService = ContentServiceFactory.getInstance().getMetadataValueService();
List<MetadataValue> metadataValues = metadataValueService.findByValueLike(context, "http://hdl.handle.net/");
int updMeta = metadataValues.size();
for (MetadataValue metadataValue : metadataValues) {
metadataValue.setValue(metadataValue.getValue().replace("http://hdl.handle.net/" + oldH, "http://hdl.handle.net/" + newH));
String handlePrefix = configurationService.getProperty("handle.canonical.prefix");
Iterator<MetadataValue> metadataValues = metadataValueService.findByValueLike(context, handlePrefix);
int updMeta = 0;
while(metadataValues.hasNext()) {
MetadataValue metadataValue = metadataValues.next();
metadataValue.setValue(metadataValue.getValue().replace(handlePrefix + oldH, handlePrefix + newH));
metadataValueService.update(context, metadataValue, true);
context.uncacheEntity(metadataValue);
updMeta++;
}
System.out.println(
updMeta + " metadata value" + ((updMeta > 1) ? "s" : "") + " updated"
);

5
dspace-api/src/main/java/org/dspace/harvest/OAIHarvester.java
View File

@@ -646,6 +646,11 @@ public class OAIHarvester {
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));
//Clear the context cache
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;
import java.io.IOException;
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.commons.cli.*;
import org.apache.log4j.Logger;
import org.dspace.content.DSpaceObject;
import org.dspace.content.factory.ContentServiceFactory;
import org.dspace.content.service.ItemService;
import org.dspace.core.ConfigurationManager;
import org.dspace.core.Constants;
import org.dspace.core.Context;
import org.dspace.core.Email;
import org.dspace.core.I18nUtil;
import org.dspace.core.*;
import org.dspace.handle.factory.HandleServiceFactory;
import org.dspace.handle.service.HandleService;
import org.dspace.identifier.DOI;
@@ -39,6 +23,11 @@ import org.dspace.identifier.factory.IdentifierServiceFactory;
import org.dspace.identifier.service.DOIService;
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) {
organiser.reserve(doi);
context.uncacheEntity(doi);
}
} catch (SQLException ex) {
System.err.println("Error in database connection:" + ex.getMessage());
@@ -223,6 +213,7 @@ public class DOIOrganiser {
for (DOI doi : dois)
{
organiser.register(doi);
context.uncacheEntity(doi);
}
} catch (SQLException ex) {
System.err.println("Error in database connection:" + ex.getMessage());
@@ -247,6 +238,7 @@ public class DOIOrganiser {
for (DOI doi : dois)
{
organiser.update(doi);
context.uncacheEntity(doi);
}
} catch (SQLException ex) {
System.err.println("Error in database connection:" + ex.getMessage());
@@ -270,6 +262,7 @@ public class DOIOrganiser {
DOI doi = iterator.next();
iterator.remove();
organiser.delete(doi.getDoi());
context.uncacheEntity(doi);
}
} catch (SQLException ex) {
System.err.println("Error in database connection:" + ex.getMessage());

31
dspace-api/src/main/java/org/dspace/rdf/RDFizer.java
View File

@@ -9,29 +9,11 @@
package org.dspace.rdf;
import com.hp.hpl.jena.rdf.model.Model;
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;
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.cli.*;
import org.apache.commons.lang3.StringUtils;
import org.apache.log4j.Logger;
import org.dspace.authorize.AuthorizeException;
import org.dspace.content.Collection;
import org.dspace.content.Community;
import org.dspace.content.DSpaceObject;
import org.dspace.content.Item;
import org.dspace.content.Site;
import org.dspace.content.*;
import org.dspace.content.factory.ContentServiceFactory;
import org.dspace.content.service.CommunityService;
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.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
* identifiers, it loads data, it manages the conversion of DSpace Objects into
@@ -467,6 +457,7 @@ public class RDFizer {
callback.callback(dso);
report("Processed " + contentServiceFactory.getDSpaceObjectService(dso).getTypeText(dso) + " " + dso.getID()
+ " (handle " + dso.getHandle() + ").");
context.uncacheEntity(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);
}
Context context = new Context();
Context context = new Context(Context.Mode.BATCH_EDIT);
context.turnOffAuthorisationSystem();
if(line.hasOption('p')) {

9
dspace-api/src/main/java/org/dspace/storage/bitstore/BitstreamStorageServiceImpl.java
View File

@@ -223,7 +223,7 @@ public class BitstreamStorageServiceImpl implements BitstreamStorageService, Ini
try
{
context = new Context();
context = new Context(Context.Mode.BATCH_EDIT);
context.turnOffAuthorisationSystem();
List<Bitstream> storage = bitstreamService.findDeletedBitstreams(context);
@@ -254,6 +254,7 @@ public class BitstreamStorageServiceImpl implements BitstreamStorageService, Ini
}
bitstreamService.expunge(context, bitstream);
}
context.uncacheEntity(bitstream);
continue;
}
@@ -262,6 +263,7 @@ public class BitstreamStorageServiceImpl implements BitstreamStorageService, Ini
if (isRecent(Long.valueOf(receivedMetadata.get("modified").toString())))
{
log.debug("file is recent");
context.uncacheEntity(bitstream);
continue;
}
@@ -281,6 +283,7 @@ public class BitstreamStorageServiceImpl implements BitstreamStorageService, Ini
}
if (isRegisteredBitstream(bitstream.getInternalId())) {
context.uncacheEntity(bitstream);
continue; // do not delete registered bitstreams
}
@@ -310,6 +313,8 @@ public class BitstreamStorageServiceImpl implements BitstreamStorageService, Ini
{
context.dispatchEvents();
}
context.uncacheEntity(bitstream);
}
System.out.print("Committing changes to the database...");
@@ -393,6 +398,8 @@ public class BitstreamStorageServiceImpl implements BitstreamStorageService, Ini
}
processedCounter++;
context.uncacheEntity(bitstream);
//modulo
if ((processedCounter % batchCommitSize) == 0) {
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.core.ReloadableEntity;
/**
* Interface representing a workflowitem, each workflowItem implementation must implement this interface.
*
* @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
@Table(name = "workflowitem")
public class BasicWorkflowItem implements WorkflowItem, ReloadableEntity<Integer>
public class BasicWorkflowItem implements WorkflowItem
{
@Id

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

@@ -166,9 +166,10 @@ public class VersioningTest extends AbstractUnitTest {
@Test
public void testVersionDelete() throws Exception {
context.turnOffAuthorisationSystem();
String handle = versionedItem.getHandle();
versionService.removeVersion(context, versionedItem);
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();
}
}