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Merge branch 'master' into configurable_entities

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This commit is contained in:
Tim Donohue
2018-12-06 17:05:31 +00:00
parent b44cf37d9d 301f804d44
commit ceed829800
568 changed files with 3990 additions and 2864 deletions
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1
LICENSES_THIRD_PARTY
View File

@@ -366,7 +366,6 @@ https://wiki.duraspace.org/display/DSPACE/Code+Contribution+Guidelines
* FindBugs-Annotations (com.google.code.findbugs:annotations:3.0.1u2 - http://findbugs.sourceforge.net/)
* MaxMind GeoIP Legacy API (com.maxmind.geoip:geoip-api:1.3.0 - https://github.com/maxmind/geoip-api-java)
* JHighlight (com.uwyn:jhighlight:1.0 - https://jhighlight.dev.java.net/)
* DSpace TM-Extractors Dependency (org.dspace.dependencies:dspace-tm-extractors:1.0.1 - http://projects.dspace.org/dspace-pom/dspace-tm-extractors)
* A Hibernate O/RM Module (org.hibernate:hibernate-core:4.2.21.Final - http://hibernate.org)
* A Hibernate O/RM Module (org.hibernate:hibernate-ehcache:4.2.21.Final - http://hibernate.org)
* Hibernate Commons Annotations (org.hibernate.common:hibernate-commons-annotations:4.0.2.Final - http://hibernate.org)

57
dspace-api/pom.xml
View File

@@ -343,14 +343,28 @@
<groupId>org.dspace</groupId>
<artifactId>mets</artifactId>
</dependency>
<dependency>
<groupId>org.dspace.dependencies</groupId>
<artifactId>dspace-tm-extractors</artifactId>
</dependency>
<dependency>
<groupId>org.apache.jena</groupId>
<artifactId>apache-jena-libs</artifactId>
<type>pom</type>
<exclusions>
<exclusion>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-core</artifactId>
</exclusion>
<exclusion>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
</exclusion>
<exclusion>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-log4j12</artifactId>
</exclusion>
<exclusion>
<groupId>log4j</groupId>
<artifactId>log4j</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>commons-cli</groupId>
@@ -364,10 +378,6 @@
<groupId>org.apache.commons</groupId>
<artifactId>commons-collections4</artifactId>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-collections4</artifactId>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-dbcp2</artifactId>
@@ -382,8 +392,8 @@
<artifactId>commons-io</artifactId>
</dependency>
<dependency>
<groupId>commons-lang</groupId>
<artifactId>commons-lang</artifactId>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
@@ -399,7 +409,7 @@
</dependency>
<dependency>
<groupId>javax.servlet</groupId>
<artifactId>servlet-api</artifactId>
<artifactId>javax.servlet-api</artifactId>
<scope>provided</scope>
</dependency>
<dependency>
@@ -417,8 +427,16 @@
<artifactId>jdom</artifactId>
</dependency>
<dependency>
<groupId>log4j</groupId>
<artifactId>log4j</artifactId>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-api</artifactId>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-1.2-api</artifactId>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-core</artifactId>
</dependency>
<dependency>
<groupId>oro</groupId>
@@ -531,6 +549,10 @@
<groupId>org.mockito</groupId>
<artifactId>mockito-core</artifactId>
</exclusion>
<exclusion>
<groupId>log4j</groupId>
<artifactId>log4j</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
@@ -548,6 +570,10 @@
<groupId>org.mockito</groupId>
<artifactId>mockito-core</artifactId>
</exclusion>
<exclusion>
<groupId>log4j</groupId>
<artifactId>log4j</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
@@ -575,8 +601,8 @@
</dependency>
<dependency>
<groupId>commons-configuration</groupId>
<artifactId>commons-configuration</artifactId>
<groupId>org.apache.commons</groupId>
<artifactId>commons-configuration2</artifactId>
</dependency>
<dependency>
<groupId>com.maxmind.geoip2</groupId>
@@ -615,7 +641,6 @@
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
<version>19.0</version>
</dependency>

2
dspace-api/src/main/java/org/dspace/administer/CreateAdministrator.java
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@@ -15,7 +15,7 @@ import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.CommandLineParser;
import org.apache.commons.cli.Options;
import org.apache.commons.cli.PosixParser;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.lang3.StringUtils;
import org.dspace.core.ConfigurationManager;
import org.dspace.core.Context;
import org.dspace.core.I18nUtil;

4
dspace-api/src/main/java/org/dspace/administer/RegistryLoader.java
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@@ -17,7 +17,7 @@ import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.parsers.ParserConfigurationException;
import javax.xml.transform.TransformerException;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.Logger;
import org.apache.xpath.XPathAPI;
import org.dspace.authorize.AuthorizeException;
import org.dspace.content.BitstreamFormat;
@@ -47,7 +47,7 @@ public class RegistryLoader {
/**
* log4j category
*/
private static Logger log = Logger.getLogger(RegistryLoader.class);
private static Logger log = org.apache.logging.log4j.LogManager.getLogger(RegistryLoader.class);
protected static BitstreamFormatService bitstreamFormatService = ContentServiceFactory.getInstance()
.getBitstreamFormatService();

6
dspace-api/src/main/java/org/dspace/app/bulkedit/MetadataImport.java
View File

@@ -26,8 +26,8 @@ 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.log4j.Logger;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.Logger;
import org.dspace.authority.AuthorityValue;
import org.dspace.authority.factory.AuthorityServiceFactory;
import org.dspace.authority.service.AuthorityValueService;
@@ -103,7 +103,7 @@ public class MetadataImport {
/**
* Logger
*/
protected static final Logger log = Logger.getLogger(MetadataImport.class);
protected static final Logger log = org.apache.logging.log4j.LogManager.getLogger(MetadataImport.class);
protected final AuthorityValueService authorityValueService;

5
dspace-api/src/main/java/org/dspace/app/checker/ChecksumChecker.java
View File

@@ -23,7 +23,8 @@ 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.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.checker.BitstreamDispatcher;
import org.dspace.checker.CheckerCommand;
import org.dspace.checker.HandleDispatcher;
@@ -48,7 +49,7 @@ import org.dspace.core.Utils;
* @author Nathan Sarr
*/
public final class ChecksumChecker {
private static final Logger LOG = Logger.getLogger(ChecksumChecker.class);
private static final Logger LOG = LogManager.getLogger(ChecksumChecker.class);
private static final BitstreamService bitstreamService = ContentServiceFactory.getInstance().getBitstreamService();

6
dspace-api/src/main/java/org/dspace/app/itemexport/ItemExportServiceImpl.java
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@@ -32,8 +32,8 @@ 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.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.Logger;
import org.dspace.app.itemexport.service.ItemExportService;
import org.dspace.content.Bitstream;
import org.dspace.content.Bundle;
@@ -98,7 +98,7 @@ public class ItemExportServiceImpl implements ItemExportService {
/**
* log4j logger
*/
private Logger log = Logger.getLogger(ItemExportServiceImpl.class);
private Logger log = org.apache.logging.log4j.LogManager.getLogger(ItemExportServiceImpl.class);
protected ItemExportServiceImpl() {

8
dspace-api/src/main/java/org/dspace/app/itemimport/ItemImportServiceImpl.java
View File

@@ -55,10 +55,10 @@ import gr.ekt.bteio.loaders.OAIPMHDataLoader;
import org.apache.commons.collections4.ComparatorUtils;
import org.apache.commons.io.FileDeleteStrategy;
import org.apache.commons.io.FileUtils;
import org.apache.commons.lang.RandomStringUtils;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.lang3.RandomStringUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.exception.ExceptionUtils;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.Logger;
import org.apache.xpath.XPathAPI;
import org.dspace.app.itemimport.service.ItemImportService;
import org.dspace.app.util.LocalSchemaFilenameFilter;
@@ -125,7 +125,7 @@ import org.xml.sax.SAXException;
* allow the registration of files (bitstreams) into DSpace.
*/
public class ItemImportServiceImpl implements ItemImportService, InitializingBean {
private final Logger log = Logger.getLogger(ItemImportServiceImpl.class);
private final Logger log = org.apache.logging.log4j.LogManager.getLogger(ItemImportServiceImpl.class);
@Autowired(required = true)
protected AuthorizeService authorizeService;

4
dspace-api/src/main/java/org/dspace/app/itemupdate/ItemArchive.java
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@@ -30,7 +30,7 @@ import javax.xml.transform.TransformerConfigurationException;
import javax.xml.transform.TransformerException;
import javax.xml.transform.TransformerFactory;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.Logger;
import org.dspace.app.util.LocalSchemaFilenameFilter;
import org.dspace.authorize.AuthorizeException;
import org.dspace.content.DSpaceObject;
@@ -47,7 +47,7 @@ import org.w3c.dom.Document;
* Encapsulates the Item in the context of the DSpace Archive Format
*/
public class ItemArchive {
private static final Logger log = Logger.getLogger(ItemArchive.class);
private static final Logger log = org.apache.logging.log4j.LogManager.getLogger(ItemArchive.class);
public static final String DUBLIN_CORE_XML = "dublin_core.xml";

2
dspace-api/src/main/java/org/dspace/app/itemupdate/MetadataUtilities.java
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@@ -28,7 +28,7 @@ import javax.xml.transform.TransformerException;
import javax.xml.transform.dom.DOMSource;
import javax.xml.transform.stream.StreamResult;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.xpath.XPathAPI;
import org.dspace.authorize.AuthorizeException;
import org.dspace.content.Item;

4
dspace-api/src/main/java/org/dspace/app/mediafilter/ExcelFilter.java
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@@ -11,7 +11,7 @@ import java.io.InputStream;
import java.nio.charset.StandardCharsets;
import org.apache.commons.io.IOUtils;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.Logger;
import org.apache.poi.POITextExtractor;
import org.apache.poi.extractor.ExtractorFactory;
import org.apache.poi.hssf.extractor.ExcelExtractor;
@@ -36,7 +36,7 @@ import org.dspace.content.Item;
*/
public class ExcelFilter extends MediaFilter {
private static Logger log = Logger.getLogger(ExcelFilter.class);
private static Logger log = org.apache.logging.log4j.LogManager.getLogger(ExcelFilter.class);
public String getFilteredName(String oldFilename) {
return oldFilename + ".txt";

2
dspace-api/src/main/java/org/dspace/app/mediafilter/MediaFilterCLITool.java
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@@ -22,7 +22,7 @@ import org.apache.commons.cli.Option;
import org.apache.commons.cli.OptionBuilder;
import org.apache.commons.cli.Options;
import org.apache.commons.cli.PosixParser;
import org.apache.commons.lang.ArrayUtils;
import org.apache.commons.lang3.ArrayUtils;
import org.dspace.app.mediafilter.factory.MediaFilterServiceFactory;
import org.dspace.app.mediafilter.service.MediaFilterService;
import org.dspace.content.Collection;

4
dspace-api/src/main/java/org/dspace/app/mediafilter/PDFFilter.java
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@@ -16,7 +16,7 @@ import java.io.InputStream;
import java.io.OutputStreamWriter;
import java.io.Writer;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.Logger;
import org.apache.pdfbox.pdmodel.PDDocument;
import org.apache.pdfbox.text.PDFTextStripper;
import org.dspace.content.Item;
@@ -30,7 +30,7 @@ import org.dspace.core.ConfigurationManager;
*/
public class PDFFilter extends MediaFilter {
private static Logger log = Logger.getLogger(PDFFilter.class);
private static Logger log = org.apache.logging.log4j.LogManager.getLogger(PDFFilter.class);
@Override
public String getFilteredName(String oldFilename) {

4
dspace-api/src/main/java/org/dspace/app/mediafilter/PowerPointFilter.java
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@@ -10,7 +10,7 @@ package org.dspace.app.mediafilter;
import java.io.ByteArrayInputStream;
import java.io.InputStream;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.Logger;
import org.apache.poi.POITextExtractor;
import org.apache.poi.extractor.ExtractorFactory;
import org.apache.poi.hslf.extractor.PowerPointExtractor;
@@ -23,7 +23,7 @@ import org.dspace.content.Item;
*/
public class PowerPointFilter extends MediaFilter {
private static Logger log = Logger.getLogger(PowerPointFilter.class);
private static Logger log = org.apache.logging.log4j.LogManager.getLogger(PowerPointFilter.class);
@Override
public String getFilteredName(String oldFilename) {

93
dspace-api/src/main/java/org/dspace/app/mediafilter/WordFilter.java
View File

@@ -1,93 +0,0 @@
/**
* The contents of this file are subject to the license and copyright
* detailed in the LICENSE and NOTICE files at the root of the source
* tree and available online at
*
* http://www.dspace.org/license/
*/
package org.dspace.app.mediafilter;
import java.io.ByteArrayInputStream;
import java.io.IOException;
import java.io.InputStream;
import org.apache.log4j.Logger;
import org.dspace.content.Item;
import org.textmining.extraction.TextExtractor;
import org.textmining.extraction.word.WordTextExtractorFactory;
/*
*
* to do: helpful error messages - can't find mediafilter.cfg - can't
* instantiate filter - bitstream format doesn't exist.
*
*/
public class WordFilter extends MediaFilter {
private static Logger log = Logger.getLogger(WordFilter.class);
@Override
public String getFilteredName(String oldFilename) {
return oldFilename + ".txt";
}
/**
* @return String bundle name
*/
@Override
public String getBundleName() {
return "TEXT";
}
/**
* @return String bitstreamformat
*/
@Override
public String getFormatString() {
return "Text";
}
/**
* @return String description
*/
@Override
public String getDescription() {
return "Extracted text";
}
/**
* @param currentItem item
* @param source source input stream
* @param verbose verbose mode
* @return InputStream the resulting input stream
* @throws Exception if error
*/
@Override
public InputStream getDestinationStream(Item currentItem, InputStream source, boolean verbose)
throws Exception {
// get input stream from bitstream
// pass to filter, get string back
try {
WordTextExtractorFactory factory = new WordTextExtractorFactory();
TextExtractor e = factory.textExtractor(source);
String extractedText = e.getText();
// if verbose flag is set, print out extracted text
// to STDOUT
if (verbose) {
System.out.println(extractedText);
}
// generate an input stream with the extracted text
byte[] textBytes = extractedText.getBytes();
ByteArrayInputStream bais = new ByteArrayInputStream(textBytes);
return bais; // will this work? or will the byte array be out of scope?
} catch (IOException ioe) {
System.out.println("Invalid Word Format");
log.error("Error detected - Word File format not recognized: "
+ ioe.getMessage(), ioe);
throw ioe;
}
}
}

6
dspace-api/src/main/java/org/dspace/app/requestitem/RequestItemHelpdeskStrategy.java
View File

@@ -9,8 +9,8 @@ package org.dspace.app.requestitem;
import java.sql.SQLException;
import org.apache.commons.lang.StringUtils;
import org.apache.log4j.Logger;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.Logger;
import org.dspace.content.Item;
import org.dspace.core.ConfigurationManager;
import org.dspace.core.Context;
@@ -31,7 +31,7 @@ import org.springframework.beans.factory.annotation.Autowired;
*/
public class RequestItemHelpdeskStrategy extends RequestItemSubmitterStrategy {
private Logger log = Logger.getLogger(RequestItemHelpdeskStrategy.class);
private Logger log = org.apache.logging.log4j.LogManager.getLogger(RequestItemHelpdeskStrategy.class);
@Autowired(required = true)
protected EPersonService ePersonService;

2
dspace-api/src/main/java/org/dspace/app/requestitem/RequestItemMetadataStrategy.java
View File

@@ -10,7 +10,7 @@ package org.dspace.app.requestitem;
import java.sql.SQLException;
import java.util.List;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.lang3.StringUtils;
import org.dspace.content.Item;
import org.dspace.content.MetadataValue;
import org.dspace.content.service.ItemService;

4
dspace-api/src/main/java/org/dspace/app/requestitem/RequestItemServiceImpl.java
View File

@@ -10,7 +10,7 @@ package org.dspace.app.requestitem;
import java.sql.SQLException;
import java.util.Date;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.Logger;
import org.dspace.app.requestitem.dao.RequestItemDAO;
import org.dspace.app.requestitem.service.RequestItemService;
import org.dspace.content.Bitstream;
@@ -28,7 +28,7 @@ import org.springframework.beans.factory.annotation.Autowired;
*/
public class RequestItemServiceImpl implements RequestItemService {
private final Logger log = Logger.getLogger(RequestItemServiceImpl.class);
private final Logger log = org.apache.logging.log4j.LogManager.getLogger(RequestItemServiceImpl.class);
@Autowired(required = true)
protected RequestItemDAO requestItemDAO;

6
dspace-api/src/main/java/org/dspace/app/sfx/SFXFileReaderServiceImpl.java
View File

@@ -15,8 +15,8 @@ import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.parsers.ParserConfigurationException;
import org.apache.commons.lang.StringUtils;
import org.apache.log4j.Logger;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.Logger;
import org.dspace.app.sfx.service.SFXFileReaderService;
import org.dspace.content.DCPersonName;
import org.dspace.content.Item;
@@ -58,7 +58,7 @@ public class SFXFileReaderServiceImpl implements SFXFileReaderService {
/**
* log4j logger
*/
private final Logger log = Logger.getLogger(SFXFileReaderServiceImpl.class);
private final Logger log = org.apache.logging.log4j.LogManager.getLogger(SFXFileReaderServiceImpl.class);
protected SFXFileReaderServiceImpl() {
}

2
dspace-api/src/main/java/org/dspace/app/sherpa/SHERPAResponse.java
View File

@@ -13,7 +13,7 @@ import java.util.List;
import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.lang3.StringUtils;
import org.dspace.app.util.XMLUtils;
import org.w3c.dom.Document;
import org.w3c.dom.Element;

6
dspace-api/src/main/java/org/dspace/app/sherpa/SHERPAService.java
View File

@@ -7,7 +7,7 @@
*/
package org.dspace.app.sherpa;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.http.HttpEntity;
import org.apache.http.HttpResponse;
import org.apache.http.HttpStatus;
@@ -16,7 +16,7 @@ import org.apache.http.client.methods.HttpGet;
import org.apache.http.client.utils.URIBuilder;
import org.apache.http.impl.client.CloseableHttpClient;
import org.apache.http.impl.client.HttpClientBuilder;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.Logger;
import org.dspace.core.ConfigurationManager;
public class SHERPAService {
@@ -29,7 +29,7 @@ public class SHERPAService {
/**
* log4j category
*/
private static final Logger log = Logger.getLogger(SHERPAService.class);
private static final Logger log = org.apache.logging.log4j.LogManager.getLogger(SHERPAService.class);
public SHERPAService() {
HttpClientBuilder builder = HttpClientBuilder.create();

6
dspace-api/src/main/java/org/dspace/app/sherpa/submit/SHERPASubmitService.java
View File

@@ -11,8 +11,8 @@ import java.util.LinkedHashSet;
import java.util.List;
import java.util.Set;
import org.apache.commons.lang.StringUtils;
import org.apache.log4j.Logger;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.Logger;
import org.dspace.app.sherpa.SHERPAResponse;
import org.dspace.app.sherpa.SHERPAService;
import org.dspace.content.Item;
@@ -27,7 +27,7 @@ public class SHERPASubmitService {
/**
* log4j logger
*/
private static Logger log = Logger.getLogger(SHERPASubmitService.class);
private static Logger log = org.apache.logging.log4j.LogManager.getLogger(SHERPASubmitService.class);
public void setConfiguration(SHERPASubmitConfigurationService configuration) {
this.configuration = configuration;

8
dspace-api/src/main/java/org/dspace/app/sitemap/GenerateSitemaps.java
View File

@@ -27,9 +27,9 @@ 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.ArrayUtils;
import org.apache.commons.lang.StringUtils;
import org.apache.log4j.Logger;
import org.apache.commons.lang3.ArrayUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.Logger;
import org.dspace.content.Collection;
import org.dspace.content.Community;
import org.dspace.content.Item;
@@ -52,7 +52,7 @@ public class GenerateSitemaps {
/**
* Logger
*/
private static Logger log = Logger.getLogger(GenerateSitemaps.class);
private static Logger log = org.apache.logging.log4j.LogManager.getLogger(GenerateSitemaps.class);
private static final CommunityService communityService = ContentServiceFactory.getInstance().getCommunityService();
private static final CollectionService collectionService =

2
dspace-api/src/main/java/org/dspace/app/statistics/StatisticsLoader.java
View File

@@ -21,7 +21,7 @@ import java.util.Set;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import org.apache.commons.lang.time.DateUtils;
import org.apache.commons.lang3.time.DateUtils;
import org.dspace.core.ConfigurationManager;
/**

2
dspace-api/src/main/java/org/dspace/app/util/DCInput.java
View File

@@ -13,7 +13,7 @@ import java.util.Map;
import java.util.regex.Pattern;
import java.util.regex.PatternSyntaxException;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.lang3.StringUtils;
import org.dspace.content.MetadataSchemaEnum;
import org.dspace.core.Utils;
import org.slf4j.Logger;

4
dspace-api/src/main/java/org/dspace/app/util/DSpaceContextListener.java
View File

@@ -16,14 +16,14 @@ import java.util.Enumeration;
import javax.servlet.ServletContextEvent;
import javax.servlet.ServletContextListener;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.Logger;
/**
* Class to initialize / cleanup resources used by DSpace when the web application
* is started or stopped.
*/
public class DSpaceContextListener implements ServletContextListener {
private static Logger log = Logger.getLogger(DSpaceContextListener.class);
private static Logger log = org.apache.logging.log4j.LogManager.getLogger(DSpaceContextListener.class);
/**
* Initialize any resources required by the application.

299
dspace-api/src/main/java/org/dspace/app/util/DailyFileAppender.java
View File

@@ -1,299 +0,0 @@
/**
* The contents of this file are subject to the license and copyright
* detailed in the LICENSE and NOTICE files at the root of the source
* tree and available online at
*
* http://www.dspace.org/license/
*/
package org.dspace.app.util;
import java.io.File;
import java.io.IOException;
import java.net.UnknownHostException;
import java.text.SimpleDateFormat;
import java.util.Calendar;
import java.util.Date;
import org.apache.commons.lang.time.DateUtils;
import org.apache.log4j.FileAppender;
import org.apache.log4j.helpers.LogLog;
import org.apache.log4j.spi.LoggingEvent;
/**
* Special log appender for log4j. Adds the current date (ie. year-mon) to
* the end of the file name, so that rolling on to the next log is simply
* a case of starting a new one - no renaming of old logs.
*
* This is advisable if you are using Windows, and have multiple applications
* (ie. dspace, dspace-oai, dspace-sword) that all want to write to the same log file,
* as each would otherwise try to rename the old files during rollover.
*
* An example log4j.properties (one log per month, retains three months of logs)
*
* log4j.rootCategory=INFO, A1
* log4j.appender.A1=org.dspace.app.util.DailyFileAppender
* log4j.appender.A1.File=@@log.dir@@/dspace.log
* log4j.appender.A1.DatePattern=yyyy-MM
* log4j.appender.A1.MaxLogs=3
* log4j.appender.A1.layout=org.apache.log4j.PatternLayout
* log4j.appender.A1.layout.ConversionPattern=%d %-5p %c @ %m%n
*/
public class DailyFileAppender extends FileAppender {
/**
* The fixed date pattern to be used if one is not specified.
*/
private static final String DATE_PATTERN = "yyyy-MM-dd";
/**
* The folder under which daily folders are created. This can be a absolute path
* or relative path also.
* e.g. JavaLogs/CPRILog or F:/LogFiles/CPRILog
*/
private String mstrFileName;
/**
* Used internally and contains the name of the date derived from current system date.
*/
private Date mstrDate = new Date(System.currentTimeMillis());
/**
* Holds the user specified DatePattern,
*/
private String mstrDatePattern = DATE_PATTERN;
private boolean mMonthOnly = false;
/**
* The date formatter object used for parsing the user specified DatePattern.
*/
private SimpleDateFormat mobjSDF;
private boolean mWithHostName = false;
private int mMaxLogs = 0;
/**
* Default constructor. This is required as the appender class is dynamically
* loaded.
*/
public DailyFileAppender() {
super();
}
/* (non-Javadoc)
* @see org.apache.log4j.FileAppender#activateOptions()
*/
@Override
public void activateOptions() {
setFileName();
cleanupOldFiles();
super.activateOptions();
}
/*------------------------------------------------------------------------------
* Getters
*----------------------------------------------------------------------------*/
public String getDatePattern() {
return this.mstrDatePattern;
}
@Override
public String getFile() {
return this.mstrFileName;
}
public boolean getWithHost() {
return mWithHostName;
}
public int getMaxLogs() {
return mMaxLogs;
}
/*------------------------------------------------------------------------------
* Setters
*----------------------------------------------------------------------------*/
public void setDatePattern(String pstrPattern) {
this.mstrDatePattern = checkPattern(pstrPattern);
if (mstrDatePattern.contains("dd") || mstrDatePattern.contains("DD")) {
mMonthOnly = false;
} else {
mMonthOnly = true;
}
}
@Override
public void setFile(String file) {
// Trim spaces from both ends. The users probably does not want
// trailing spaces in file names.
String val = file.trim();
mstrFileName = val;
}
public void setWithHost(boolean wh) {
mWithHostName = wh;
}
public void setMaxLogs(int ml) {
mMaxLogs = ml;
}
/*------------------------------------------------------------------------------
* Methods
*----------------------------------------------------------------------------*/
/* (non-Javadoc)
* @see org.apache.log4j.WriterAppender#subAppend(org.apache.log4j.spi.LoggingEvent)
*/
@Override
protected void subAppend(LoggingEvent pobjEvent) {
Date dtNow = new Date(System.currentTimeMillis());
boolean rollover = false;
if (mMonthOnly) {
Calendar now = Calendar.getInstance();
Calendar cur = Calendar.getInstance();
now.setTime(dtNow);
cur.setTime(mstrDate);
rollover = !(now.get(Calendar.YEAR) == cur.get(Calendar.YEAR) && now.get(Calendar.MONTH) == cur
.get(Calendar.MONTH));
} else {
rollover = !(DateUtils.isSameDay(dtNow, mstrDate));
}
if (rollover) {
try {
rollOver(dtNow);
} catch (IOException IOEx) {
LogLog.error("rollOver() failed!", IOEx);
}
}
super.subAppend(pobjEvent);
}
/*------------------------------------------------------------------------------
* Helpers
*----------------------------------------------------------------------------*/
/**
* The helper function to validate the DatePattern.
*
* @param pstrPattern The DatePattern to be validated.
* @return The validated date pattern or defautlt DATE_PATTERN
*/
private String checkPattern(String pstrPattern) {
String strRet = null;
SimpleDateFormat objFmt = new SimpleDateFormat(DATE_PATTERN);
try {
this.mobjSDF = new SimpleDateFormat(pstrPattern);
strRet = pstrPattern;
} catch (NullPointerException NPExIgnore) {
LogLog.error("Invalid DatePattern " + pstrPattern, NPExIgnore);
this.mobjSDF = objFmt;
strRet = DATE_PATTERN;
} catch (IllegalArgumentException IlArgExIgnore) {
LogLog.error("Invalid DatePattern " + pstrPattern, IlArgExIgnore);
this.mobjSDF = objFmt;
strRet = DATE_PATTERN;
} finally {
objFmt = null;
}
return strRet;
}
/**
* This function is responsible for performing the actual file rollover.
*
* @param pstrName The name of the new folder based on current system date.
* @throws IOException if IO error
*/
private static boolean deletingFiles = false;
private void cleanupOldFiles() {
// If we need to delete log files
if (mMaxLogs > 0 && !deletingFiles) {
deletingFiles = true;
// Determine the final file extension with the hostname
String hostFileExt = null;
try {
hostFileExt = "." + java.net.InetAddress.getLocalHost().getHostName();
} catch (UnknownHostException e) {
LogLog.error("Unable to retrieve host name");
}
try {
// Array to hold the logs we are going to keep
File[] logsToKeep = new File[mMaxLogs];
// Get a 'master' file handle, and the parent directory from it
File logMaster = new File(mstrFileName);
File logDir = logMaster.getParentFile();
if (logDir.isDirectory()) {
// Iterate all the files in that directory
File[] logArr = logDir.listFiles();
for (File curLog : logArr) {
LogLog.debug("Comparing '" + curLog.getAbsolutePath() + "' to '" + mstrFileName + "'");
String name = curLog.getAbsolutePath();
// First, see if we are not using hostname, or the log file ends with this host
if (!mWithHostName || (hostFileExt != null && name.endsWith(hostFileExt))) {
// Check that the file is indeed one we want (contains the master file name)
if (name.contains(mstrFileName)) {
// Iterate through the array of logs we are keeping
for (int i = 0; curLog != null && i < logsToKeep.length; i++) {
// Have we exhausted the 'to keep' array?
if (logsToKeep[i] == null) {
// Empty space, retain this log file
logsToKeep[i] = curLog;
curLog = null;
} else if (logsToKeep[i].getName().compareTo(curLog.getName()) < 0) {
// If the 'kept' file is older than the current one
// Replace tested entry with current file
File temp = logsToKeep[i];
logsToKeep[i] = curLog;
curLog = temp;
}
}
// If we have a 'current' entry at this point, it's a log we don't want
if (curLog != null) {
LogLog.debug("Deleting log " + curLog.getName());
if (!curLog.delete()) {
LogLog.error("Unable to delete log file");
}
}
}
}
}
}
} catch (Exception e) {
// Don't worry about exceptions
} finally {
deletingFiles = false;
}
}
}
private void rollOver(Date dtNow) throws IOException {
mstrDate = dtNow;
setFileName();
this.setFile(fileName, true, bufferedIO, bufferSize);
cleanupOldFiles();
}
private void setFileName() {
fileName = mstrFileName + "." + mobjSDF.format(mstrDate);
if (mWithHostName) {
try {
fileName += "." + java.net.InetAddress.getLocalHost().getHostName();
} catch (UnknownHostException e) {
LogLog.error("Unable to retrieve host name");
}
}
}
}

4
dspace-api/src/main/java/org/dspace/app/util/GoogleBitstreamComparator.java
View File

@@ -12,7 +12,7 @@ import java.util.Comparator;
import java.util.HashMap;
import java.util.Map;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.Logger;
import org.dspace.content.Bitstream;
import org.dspace.content.BitstreamFormat;
import org.dspace.content.factory.ContentServiceFactory;
@@ -24,7 +24,7 @@ import org.dspace.core.Context;
*/
public class GoogleBitstreamComparator implements Comparator<Bitstream> {
private final static Logger log = Logger.getLogger(GoogleBitstreamComparator.class);
private final static Logger log = org.apache.logging.log4j.LogManager.getLogger(GoogleBitstreamComparator.class);
HashMap<String, Integer> priorityMap = new HashMap<>();

4
dspace-api/src/main/java/org/dspace/app/util/GoogleMetadata.java
View File

@@ -26,7 +26,7 @@ import java.util.Properties;
import com.google.common.collect.ArrayListMultimap;
import com.google.common.collect.ListMultimap;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.Logger;
import org.dspace.authorize.factory.AuthorizeServiceFactory;
import org.dspace.content.Bitstream;
import org.dspace.content.Bundle;
@@ -51,7 +51,7 @@ import org.jdom.Element;
@SuppressWarnings("deprecation")
public class GoogleMetadata {
private final static Logger log = Logger.getLogger(GoogleMetadata.class);
private final static Logger log = org.apache.logging.log4j.LogManager.getLogger(GoogleMetadata.class);
protected static final String GOOGLE_PREFIX = "google.";

4
dspace-api/src/main/java/org/dspace/app/util/MetadataExposureServiceImpl.java
View File

@@ -14,7 +14,7 @@ import java.util.List;
import java.util.Map;
import java.util.Set;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.Logger;
import org.dspace.app.util.service.MetadataExposureService;
import org.dspace.authorize.service.AuthorizeService;
import org.dspace.core.Context;
@@ -58,7 +58,7 @@ import org.springframework.beans.factory.annotation.Autowired;
* @version $Revision: 3734 $
*/
public class MetadataExposureServiceImpl implements MetadataExposureService {
protected Logger log = Logger.getLogger(MetadataExposureServiceImpl.class);
protected Logger log = org.apache.logging.log4j.LogManager.getLogger(MetadataExposureServiceImpl.class);
protected Map<String, Set<String>> hiddenElementSets = null;
protected Map<String, Map<String, Set<String>>> hiddenElementMaps = null;

4
dspace-api/src/main/java/org/dspace/app/util/OpenSearchServiceImpl.java
View File

@@ -20,7 +20,7 @@ import com.sun.syndication.feed.module.opensearch.OpenSearchModule;
import com.sun.syndication.feed.module.opensearch.entity.OSQuery;
import com.sun.syndication.feed.module.opensearch.impl.OpenSearchModuleImpl;
import com.sun.syndication.io.FeedException;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.Logger;
import org.dspace.app.util.service.OpenSearchService;
import org.dspace.content.DSpaceObject;
import org.dspace.core.Constants;
@@ -54,7 +54,7 @@ import org.w3c.dom.Document;
* @author Richard Rodgers
*/
public class OpenSearchServiceImpl implements OpenSearchService, InitializingBean {
private static final Logger log = Logger.getLogger(OpenSearchServiceImpl.class);
private static final Logger log = org.apache.logging.log4j.LogManager.getLogger(OpenSearchServiceImpl.class);
// are open search queries enabled?
protected boolean enabled = false;

4
dspace-api/src/main/java/org/dspace/app/util/OptimizeSelectCollection.java
View File

@@ -11,7 +11,7 @@ import java.sql.SQLException;
import java.util.ArrayList;
import java.util.List;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.Logger;
import org.dspace.content.Collection;
import org.dspace.content.factory.ContentServiceFactory;
import org.dspace.content.service.CollectionService;
@@ -28,7 +28,7 @@ import org.springframework.util.StopWatch;
* Invocation: dsrun org.dspace.app.util.OptimizeSelectCollection
*/
public class OptimizeSelectCollection {
private static final Logger log = Logger.getLogger(OptimizeSelectCollection.class);
private static final Logger log = org.apache.logging.log4j.LogManager.getLogger(OptimizeSelectCollection.class);
private static Context context;
private static ArrayList<EPerson> brokenPeople;

4
dspace-api/src/main/java/org/dspace/app/util/SubmissionConfig.java
View File

@@ -12,7 +12,7 @@ import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.Logger;
/**
* Class representing a single Item Submission config definition, organized into
@@ -44,7 +44,7 @@ public class SubmissionConfig implements Serializable {
/**
* log4j logger
*/
private static Logger log = Logger.getLogger(SubmissionConfig.class);
private static Logger log = org.apache.logging.log4j.LogManager.getLogger(SubmissionConfig.class);
/**
* Constructs a new Submission Configuration object, based on the XML

4
dspace-api/src/main/java/org/dspace/app/util/SubmissionConfigReader.java
View File

@@ -19,7 +19,7 @@ import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.parsers.FactoryConfigurationError;
import org.apache.commons.lang3.StringUtils;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.Logger;
import org.dspace.content.Collection;
import org.dspace.content.DSpaceObject;
import org.dspace.core.Context;
@@ -71,7 +71,7 @@ public class SubmissionConfigReader {
/**
* log4j logger
*/
private static Logger log = Logger.getLogger(SubmissionConfigReader.class);
private static Logger log = org.apache.logging.log4j.LogManager.getLogger(SubmissionConfigReader.class);
/**
* The fully qualified pathname of the directory containing the Item Submission Configuration file

8
dspace-api/src/main/java/org/dspace/app/util/SyndicationFeed.java
View File

@@ -34,9 +34,9 @@ import com.sun.syndication.feed.synd.SyndPerson;
import com.sun.syndication.feed.synd.SyndPersonImpl;
import com.sun.syndication.io.FeedException;
import com.sun.syndication.io.SyndFeedOutput;
import org.apache.commons.lang.ArrayUtils;
import org.apache.commons.lang.StringUtils;
import org.apache.log4j.Logger;
import org.apache.commons.lang3.ArrayUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.Logger;
import org.dspace.content.Bitstream;
import org.dspace.content.Bundle;
import org.dspace.content.Collection;
@@ -69,7 +69,7 @@ import org.w3c.dom.Document;
* @author Larry Stone
*/
public class SyndicationFeed {
protected final Logger log = Logger.getLogger(SyndicationFeed.class);
protected final Logger log = org.apache.logging.log4j.LogManager.getLogger(SyndicationFeed.class);
/**

6
dspace-api/src/main/java/org/dspace/app/util/Util.java
View File

@@ -23,8 +23,8 @@ import java.util.UUID;
import javax.servlet.http.HttpServletRequest;
import org.apache.commons.collections4.ListUtils;
import org.apache.commons.lang.StringUtils;
import org.apache.log4j.Logger;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.Logger;
import org.dspace.content.Collection;
import org.dspace.content.Item;
import org.dspace.content.MetadataValue;
@@ -44,7 +44,7 @@ public class Util {
// cache for source version result
private static String sourceVersion = null;
private static Logger log = Logger.getLogger(Util.class);
private static Logger log = org.apache.logging.log4j.LogManager.getLogger(Util.class);
/**
* Default constructor. Must be protected as org.dspace.xmlworkflow.WorkflowUtils extends it

4
dspace-api/src/main/java/org/dspace/app/util/WebAppServiceImpl.java
View File

@@ -18,7 +18,7 @@ import org.apache.http.HttpStatus;
import org.apache.http.client.HttpClient;
import org.apache.http.client.methods.HttpHead;
import org.apache.http.impl.client.DefaultHttpClient;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.Logger;
import org.dspace.app.util.dao.WebAppDAO;
import org.dspace.app.util.service.WebAppService;
import org.dspace.core.Context;
@@ -33,7 +33,7 @@ import org.springframework.beans.factory.annotation.Autowired;
*/
public class WebAppServiceImpl implements WebAppService {
private final Logger log = Logger.getLogger(WebAppServiceImpl.class);
private final Logger log = org.apache.logging.log4j.LogManager.getLogger(WebAppServiceImpl.class);
@Autowired(required = true)
protected WebAppDAO webAppDAO;

2
dspace-api/src/main/java/org/dspace/app/util/XMLUtils.java
View File

@@ -11,7 +11,7 @@ import java.util.ArrayList;
import java.util.LinkedList;
import java.util.List;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.lang3.StringUtils;
import org.w3c.dom.Element;
import org.w3c.dom.NodeList;

22
dspace-api/src/main/java/org/dspace/authenticate/IPAuthentication.java
View File

@@ -17,14 +17,15 @@ import java.util.UUID;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import org.apache.log4j.Logger;
import org.dspace.core.ConfigurationManager;
import org.apache.logging.log4j.Logger;
import org.dspace.core.Context;
import org.dspace.core.LogManager;
import org.dspace.core.factory.CoreServiceFactory;
import org.dspace.eperson.EPerson;
import org.dspace.eperson.Group;
import org.dspace.eperson.factory.EPersonServiceFactory;
import org.dspace.eperson.service.GroupService;
import org.dspace.service.ClientInfoService;
import org.dspace.services.factory.DSpaceServicesFactory;
/**
@@ -49,7 +50,7 @@ public class IPAuthentication implements AuthenticationMethod {
/**
* Our logger
*/
private static Logger log = Logger.getLogger(IPAuthentication.class);
private static Logger log = org.apache.logging.log4j.LogManager.getLogger(IPAuthentication.class);
/**
* Whether to look for x-forwarded headers for logging IP addresses
@@ -67,6 +68,7 @@ public class IPAuthentication implements AuthenticationMethod {
protected List<IPMatcher> ipNegativeMatchers;
protected GroupService groupService;
protected ClientInfoService clientInfoService;
/**
@@ -91,6 +93,7 @@ public class IPAuthentication implements AuthenticationMethod {
ipMatcherGroupIDs = new HashMap<>();
ipMatcherGroupNames = new HashMap<>();
groupService = EPersonServiceFactory.getInstance().getGroupService();
clientInfoService = CoreServiceFactory.getInstance().getClientInfoService();
List<String> propNames = DSpaceServicesFactory.getInstance().getConfigurationService()
.getPropertyKeys("authentication-ip");
@@ -169,18 +172,7 @@ public class IPAuthentication implements AuthenticationMethod {
List<Group> groups = new ArrayList<Group>();
// Get the user's IP address
String addr = request.getRemoteAddr();
if (useProxies == null) {
useProxies = ConfigurationManager.getBooleanProperty("useProxies", false);
}
if (useProxies && request.getHeader("X-Forwarded-For") != null) {
/* This header is a comma delimited list */
for (String xfip : request.getHeader("X-Forwarded-For").split(",")) {
if (!request.getHeader("X-Forwarded-For").contains(addr)) {
addr = xfip.trim();
}
}
}
String addr = clientInfoService.getClientIp(request);
for (IPMatcher ipm : ipMatchers) {
try {

4
dspace-api/src/main/java/org/dspace/authenticate/IPMatcher.java
View File

@@ -10,7 +10,7 @@ package org.dspace.authenticate;
import java.net.Inet6Address;
import java.net.UnknownHostException;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.Logger;
/**
* <p>
@@ -38,7 +38,7 @@ import org.apache.log4j.Logger;
* @version $Revision$
*/
public class IPMatcher {
private static Logger log = Logger.getLogger(IPMatcher.class);
private static Logger log = org.apache.logging.log4j.LogManager.getLogger(IPMatcher.class);
/**
* Network to match

6
dspace-api/src/main/java/org/dspace/authenticate/LDAPAuthentication.java
View File

@@ -28,8 +28,8 @@ import javax.naming.ldap.StartTlsResponse;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import org.apache.commons.lang.StringUtils;
import org.apache.log4j.Logger;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.Logger;
import org.dspace.authenticate.factory.AuthenticateServiceFactory;
import org.dspace.authenticate.service.AuthenticationService;
import org.dspace.authorize.AuthorizeException;
@@ -61,7 +61,7 @@ public class LDAPAuthentication
/**
* log4j category
*/
private static Logger log = Logger.getLogger(LDAPAuthentication.class);
private static Logger log = org.apache.logging.log4j.LogManager.getLogger(LDAPAuthentication.class);
protected AuthenticationService authenticationService = AuthenticateServiceFactory.getInstance()
.getAuthenticationService();

4
dspace-api/src/main/java/org/dspace/authenticate/PasswordAuthentication.java
View File

@@ -15,7 +15,7 @@ import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import org.apache.commons.lang3.StringUtils;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.Logger;
import org.dspace.core.Context;
import org.dspace.core.LogManager;
import org.dspace.eperson.EPerson;
@@ -49,7 +49,7 @@ public class PasswordAuthentication
/**
* log4j category
*/
private static Logger log = Logger.getLogger(PasswordAuthentication.class);
private static Logger log = org.apache.logging.log4j.LogManager.getLogger(PasswordAuthentication.class);
/**

6
dspace-api/src/main/java/org/dspace/authenticate/ShibAuthentication.java
View File

@@ -23,8 +23,8 @@ import java.util.UUID;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import org.apache.commons.lang.StringUtils;
import org.apache.log4j.Logger;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.Logger;
import org.dspace.authenticate.factory.AuthenticateServiceFactory;
import org.dspace.authorize.AuthorizeException;
import org.dspace.content.MetadataField;
@@ -70,7 +70,7 @@ public class ShibAuthentication implements AuthenticationMethod {
/**
* log4j category
*/
private static Logger log = Logger.getLogger(ShibAuthentication.class);
private static Logger log = org.apache.logging.log4j.LogManager.getLogger(ShibAuthentication.class);
/**
* Additional metadata mappings

6
dspace-api/src/main/java/org/dspace/authenticate/X509Authentication.java
View File

@@ -29,8 +29,8 @@ import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import javax.servlet.http.HttpSession;
import org.apache.commons.lang.ArrayUtils;
import org.apache.log4j.Logger;
import org.apache.commons.lang3.ArrayUtils;
import org.apache.logging.log4j.Logger;
import org.dspace.authenticate.factory.AuthenticateServiceFactory;
import org.dspace.authenticate.service.AuthenticationService;
import org.dspace.authorize.AuthorizeException;
@@ -105,7 +105,7 @@ public class X509Authentication implements AuthenticationMethod {
/**
* log4j category
*/
private static Logger log = Logger.getLogger(X509Authentication.class);
private static Logger log = org.apache.logging.log4j.LogManager.getLogger(X509Authentication.class);
/**
* public key of CA to check client certs against.

4
dspace-api/src/main/java/org/dspace/authority/AuthoritySolrServiceImpl.java
View File

@@ -12,7 +12,7 @@ import java.net.MalformedURLException;
import java.util.ArrayList;
import java.util.List;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.Logger;
import org.apache.solr.client.solrj.SolrQuery;
import org.apache.solr.client.solrj.SolrServerException;
import org.apache.solr.client.solrj.impl.HttpSolrServer;
@@ -30,7 +30,7 @@ import org.dspace.core.ConfigurationManager;
*/
public class AuthoritySolrServiceImpl implements AuthorityIndexingService, AuthoritySearchService {
private static final Logger log = Logger.getLogger(AuthoritySolrServiceImpl.class);
private static final Logger log = org.apache.logging.log4j.LogManager.getLogger(AuthoritySolrServiceImpl.class);
protected AuthoritySolrServiceImpl() {

4
dspace-api/src/main/java/org/dspace/authority/AuthorityTypes.java
View File

@@ -12,7 +12,7 @@ import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.Logger;
/**
* This class contains a list of active authority types.
@@ -32,7 +32,7 @@ public class AuthorityTypes {
/**
* log4j logger
*/
private static Logger log = Logger.getLogger(AuthorityTypes.class);
private static Logger log = org.apache.logging.log4j.LogManager.getLogger(AuthorityTypes.class);
protected List<AuthorityValue> types = new ArrayList<AuthorityValue>();

6
dspace-api/src/main/java/org/dspace/authority/AuthorityValue.java
View File

@@ -14,8 +14,8 @@ import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.apache.commons.lang.StringUtils;
import org.apache.log4j.Logger;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.Logger;
import org.apache.solr.common.SolrDocument;
import org.apache.solr.common.SolrInputDocument;
import org.dspace.authorize.AuthorizeException;
@@ -234,7 +234,7 @@ public class AuthorityValue {
/**
* log4j logger
*/
private static Logger log = Logger.getLogger(AuthorityValue.class);
private static Logger log = org.apache.logging.log4j.LogManager.getLogger(AuthorityValue.class);
@Override
public String toString() {

6
dspace-api/src/main/java/org/dspace/authority/AuthorityValueServiceImpl.java
View File

@@ -13,8 +13,8 @@ import java.util.List;
import java.util.Map;
import java.util.UUID;
import org.apache.commons.lang.StringUtils;
import org.apache.log4j.Logger;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.Logger;
import org.apache.solr.client.solrj.SolrQuery;
import org.apache.solr.client.solrj.response.QueryResponse;
import org.apache.solr.common.SolrDocument;
@@ -34,7 +34,7 @@ import org.springframework.beans.factory.annotation.Autowired;
*/
public class AuthorityValueServiceImpl implements AuthorityValueService {
private final Logger log = Logger.getLogger(AuthorityValueServiceImpl.class);
private final Logger log = org.apache.logging.log4j.LogManager.getLogger(AuthorityValueServiceImpl.class);
@Autowired(required = true)
protected AuthorityTypes authorityTypes;

4
dspace-api/src/main/java/org/dspace/authority/PersonAuthorityValue.java
View File

@@ -12,8 +12,8 @@ import java.util.Collection;
import java.util.List;
import java.util.Map;
import org.apache.commons.lang.ObjectUtils;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.lang3.ObjectUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.solr.common.SolrDocument;
import org.apache.solr.common.SolrInputDocument;

4
dspace-api/src/main/java/org/dspace/authority/UpdateAuthorities.java
View File

@@ -19,7 +19,7 @@ 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.logging.log4j.Logger;
import org.dspace.authority.factory.AuthorityServiceFactory;
import org.dspace.authority.service.AuthorityValueService;
import org.dspace.content.Item;
@@ -40,7 +40,7 @@ public class UpdateAuthorities {
/**
* log4j logger
*/
private static Logger log = Logger.getLogger(UpdateAuthorities.class);
private static Logger log = org.apache.logging.log4j.LogManager.getLogger(UpdateAuthorities.class);
protected PrintWriter print = null;

4
dspace-api/src/main/java/org/dspace/authority/indexer/AuthorityConsumer.java
View File

@@ -12,7 +12,7 @@ import java.util.HashSet;
import java.util.Set;
import java.util.UUID;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.Logger;
import org.dspace.authority.factory.AuthorityServiceFactory;
import org.dspace.authority.service.AuthorityService;
import org.dspace.content.DSpaceObject;
@@ -33,7 +33,7 @@ import org.dspace.event.Event;
*/
public class AuthorityConsumer implements Consumer {
private final Logger log = Logger.getLogger(AuthorityConsumer.class);
private final Logger log = org.apache.logging.log4j.LogManager.getLogger(AuthorityConsumer.class);
/**
* A set of all item IDs installed which need their authority updated

4
dspace-api/src/main/java/org/dspace/authority/indexer/AuthorityIndexClient.java
View File

@@ -12,7 +12,7 @@ import java.util.Iterator;
import java.util.List;
import java.util.Map;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.Logger;
import org.dspace.authority.AuthorityValue;
import org.dspace.authority.factory.AuthorityServiceFactory;
import org.dspace.authority.service.AuthorityService;
@@ -29,7 +29,7 @@ import org.dspace.core.Context;
*/
public class AuthorityIndexClient {
private static Logger log = Logger.getLogger(AuthorityIndexClient.class);
private static Logger log = org.apache.logging.log4j.LogManager.getLogger(AuthorityIndexClient.class);
protected static final AuthorityService authorityService =
AuthorityServiceFactory.getInstance().getAuthorityService();

6
dspace-api/src/main/java/org/dspace/authority/indexer/DSpaceAuthorityIndexer.java
View File

@@ -13,8 +13,8 @@ import java.util.List;
import java.util.Map;
import org.apache.commons.collections4.CollectionUtils;
import org.apache.commons.lang.StringUtils;
import org.apache.log4j.Logger;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.Logger;
import org.dspace.authority.AuthorityValue;
import org.dspace.authority.service.AuthorityValueService;
import org.dspace.authorize.AuthorizeException;
@@ -45,7 +45,7 @@ import org.springframework.beans.factory.annotation.Autowired;
*/
public class DSpaceAuthorityIndexer implements AuthorityIndexerInterface, InitializingBean {
private static final Logger log = Logger.getLogger(DSpaceAuthorityIndexer.class);
private static final Logger log = org.apache.logging.log4j.LogManager.getLogger(DSpaceAuthorityIndexer.class);
/**
* The list of metadata fields which are to be indexed *

11
dspace-api/src/main/java/org/dspace/authority/orcid/Orcidv2.java
View File

@@ -15,12 +15,13 @@ import java.net.URLEncoder;
import java.util.ArrayList;
import java.util.List;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.http.HttpResponse;
import org.apache.http.client.HttpClient;
import org.apache.http.client.methods.HttpPost;
import org.apache.http.impl.client.HttpClientBuilder;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.authority.AuthorityValue;
import org.dspace.authority.SolrAuthorityInterface;
import org.dspace.authority.orcid.xml.XMLtoBio;
@@ -35,7 +36,7 @@ import org.orcid.jaxb.model.record_v2.Person;
*/
public class Orcidv2 implements SolrAuthorityInterface {
private static Logger log = Logger.getLogger(Orcidv2.class);
private static Logger log = LogManager.getLogger(Orcidv2.class);
public RESTConnector restConnector;
private String OAUTHUrl;
@@ -46,7 +47,9 @@ public class Orcidv2 implements SolrAuthorityInterface {
private String accessToken;
/**
* Initialize the accessToken that is required for all subsequent calls to ORCID
* Initialize the accessToken that is required for all subsequent calls to ORCID.
*
* @throws java.io.IOException passed through from HTTPclient.
*/
public void init() throws IOException {
if (StringUtils.isNotBlank(accessToken) && StringUtils.isNotBlank(clientSecret)) {

2
dspace-api/src/main/java/org/dspace/authority/orcid/Orcidv2AuthorityValue.java
View File

@@ -15,7 +15,7 @@ import java.util.List;
import java.util.Map;
import java.util.UUID;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.solr.common.SolrDocument;
import org.apache.solr.common.SolrInputDocument;
import org.dspace.authority.AuthorityValue;

5
dspace-api/src/main/java/org/dspace/authority/orcid/xml/Converter.java
View File

@@ -14,10 +14,9 @@ import javax.xml.bind.JAXBContext;
import javax.xml.bind.JAXBException;
import javax.xml.bind.Unmarshaller;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.Logger;
import org.xml.sax.SAXException;
/**
* @param <T> type
* @author Antoine Snyers (antoine at atmire.com)
@@ -30,7 +29,7 @@ public abstract class Converter<T> {
/**
* log4j logger
*/
private static Logger log = Logger.getLogger(Converter.class);
private static Logger log = org.apache.logging.log4j.LogManager.getLogger(Converter.class);
public abstract T convert(InputStream document);

6
dspace-api/src/main/java/org/dspace/authority/orcid/xml/XMLtoBio.java
View File

@@ -12,7 +12,7 @@ import java.net.URISyntaxException;
import java.util.ArrayList;
import java.util.List;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.Logger;
import org.dspace.authority.orcid.Orcidv2;
import org.dspace.utils.DSpace;
import org.orcid.jaxb.model.common_v2.OrcidId;
@@ -21,8 +21,6 @@ import org.orcid.jaxb.model.search_v2.Result;
import org.orcid.jaxb.model.search_v2.Search;
import org.xml.sax.SAXException;
/**
* @author Antoine Snyers (antoine at atmire.com)
* @author Kevin Van de Velde (kevin at atmire dot com)
@@ -34,7 +32,7 @@ public class XMLtoBio extends Converter {
/**
* log4j logger
*/
private static Logger log = Logger.getLogger(XMLtoBio.class);
private static Logger log = org.apache.logging.log4j.LogManager.getLogger(XMLtoBio.class);
@Override
public List<Person> convert(InputStream xml) {

4
dspace-api/src/main/java/org/dspace/authority/rest/RESTConnector.java
View File

@@ -15,7 +15,7 @@ import org.apache.http.HttpResponse;
import org.apache.http.client.HttpClient;
import org.apache.http.client.methods.HttpGet;
import org.apache.http.impl.client.HttpClientBuilder;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.Logger;
/**
* @author Antoine Snyers (antoine at atmire.com)
@@ -28,7 +28,7 @@ public class RESTConnector {
/**
* log4j logger
*/
private static Logger log = Logger.getLogger(RESTConnector.class);
private static Logger log = org.apache.logging.log4j.LogManager.getLogger(RESTConnector.class);
private String url;

6
dspace-api/src/main/java/org/dspace/authority/util/EnumUtils.java
View File

@@ -7,8 +7,8 @@
*/
package org.dspace.authority.util;
import org.apache.commons.lang.StringUtils;
import org.apache.log4j.Logger;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.Logger;
/**
* @author Antoine Snyers (antoine at atmire.com)
@@ -21,7 +21,7 @@ public class EnumUtils {
/**
* log4j logger
*/
private static Logger log = Logger.getLogger(EnumUtils.class);
private static Logger log = org.apache.logging.log4j.LogManager.getLogger(EnumUtils.class);
/**
* Default constructor

4
dspace-api/src/main/java/org/dspace/authority/util/XMLUtils.java
View File

@@ -17,7 +17,7 @@ import javax.xml.parsers.ParserConfigurationException;
import javax.xml.transform.TransformerException;
import javax.xml.xpath.XPathExpressionException;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.Logger;
import org.apache.xpath.XPathAPI;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
@@ -36,7 +36,7 @@ public class XMLUtils {
/**
* log4j logger
*/
private static Logger log = Logger.getLogger(XMLUtils.class);
private static Logger log = org.apache.logging.log4j.LogManager.getLogger(XMLUtils.class);
/**
* Default constructor

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

@@ -16,7 +16,7 @@ import java.util.List;
import java.util.UUID;
import org.apache.commons.collections4.CollectionUtils;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.lang3.StringUtils;
import org.dspace.authorize.service.AuthorizeService;
import org.dspace.authorize.service.ResourcePolicyService;
import org.dspace.content.Bitstream;

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

@@ -23,7 +23,7 @@ import javax.persistence.Table;
import javax.persistence.Temporal;
import javax.persistence.TemporalType;
import org.apache.commons.lang.ObjectUtils;
import org.apache.commons.lang3.ObjectUtils;
import org.dspace.content.DSpaceObject;
import org.dspace.core.Context;
import org.dspace.core.ReloadableEntity;

6
dspace-api/src/main/java/org/dspace/authorize/ResourcePolicyServiceImpl.java
View File

@@ -15,8 +15,8 @@ import java.util.List;
import java.util.Set;
import org.apache.commons.collections4.CollectionUtils;
import org.apache.commons.lang.ObjectUtils;
import org.apache.log4j.Logger;
import org.apache.commons.lang3.ObjectUtils;
import org.apache.logging.log4j.Logger;
import org.dspace.authorize.dao.ResourcePolicyDAO;
import org.dspace.authorize.service.ResourcePolicyService;
import org.dspace.content.DSpaceObject;
@@ -38,7 +38,7 @@ public class ResourcePolicyServiceImpl implements ResourcePolicyService {
/**
* log4j logger
*/
private static Logger log = Logger.getLogger(ResourcePolicyServiceImpl.class);
private static Logger log = org.apache.logging.log4j.LogManager.getLogger(ResourcePolicyServiceImpl.class);
@Autowired(required = true)
protected ContentServiceFactory contentServiceFactory;

4
dspace-api/src/main/java/org/dspace/browse/BrowseEngine.java
View File

@@ -12,7 +12,7 @@ import java.util.ArrayList;
import java.util.List;
import org.apache.commons.lang3.StringUtils;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.Logger;
import org.dspace.content.Collection;
import org.dspace.content.Community;
import org.dspace.content.Item;
@@ -34,7 +34,7 @@ public class BrowseEngine {
/**
* the logger for this class
*/
private static final Logger log = Logger.getLogger(BrowseEngine.class);
private static final Logger log = org.apache.logging.log4j.LogManager.getLogger(BrowseEngine.class);
/**
* the browse scope which is the basis for our browse

4
dspace-api/src/main/java/org/dspace/browse/ItemCountDAOSolr.java
View File

@@ -11,7 +11,7 @@ import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.Logger;
import org.dspace.content.Collection;
import org.dspace.content.Community;
import org.dspace.content.DSpaceObject;
@@ -36,7 +36,7 @@ public class ItemCountDAOSolr implements ItemCountDAO {
/**
* Log4j logger
*/
private static Logger log = Logger.getLogger(ItemCountDAOSolr.class);
private static Logger log = org.apache.logging.log4j.LogManager.getLogger(ItemCountDAOSolr.class);
/**
* DSpace context

4
dspace-api/src/main/java/org/dspace/browse/ItemCounter.java
View File

@@ -9,7 +9,7 @@ package org.dspace.browse;
import java.sql.SQLException;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.Logger;
import org.dspace.content.Collection;
import org.dspace.content.Community;
import org.dspace.content.DSpaceObject;
@@ -37,7 +37,7 @@ public class ItemCounter {
/**
* Log4j logger
*/
private static Logger log = Logger.getLogger(ItemCounter.class);
private static Logger log = org.apache.logging.log4j.LogManager.getLogger(ItemCounter.class);
/**
* DAO to use to store and retrieve data

2
dspace-api/src/main/java/org/dspace/browse/ItemListConfig.java
View File

@@ -12,7 +12,7 @@ import java.util.HashMap;
import java.util.Map;
import java.util.StringTokenizer;
import org.apache.commons.lang.ArrayUtils;
import org.apache.commons.lang3.ArrayUtils;
import org.dspace.services.ConfigurationService;
import org.dspace.services.factory.DSpaceServicesFactory;

4
dspace-api/src/main/java/org/dspace/browse/LocaleOrderingFilter.java
View File

@@ -12,7 +12,7 @@ import java.util.Locale;
import com.ibm.icu.text.CollationElementIterator;
import com.ibm.icu.text.Collator;
import com.ibm.icu.text.RuleBasedCollator;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.Logger;
import org.dspace.core.ConfigurationManager;
import org.dspace.text.filter.TextFilter;
@@ -32,7 +32,7 @@ import org.dspace.text.filter.TextFilter;
* @author Graham Triggs
*/
public class LocaleOrderingFilter implements TextFilter {
private static Logger log = Logger.getLogger(LocaleOrderingFilter.class);
private static Logger log = org.apache.logging.log4j.LogManager.getLogger(LocaleOrderingFilter.class);
/**
* Uses a Locale dependent Collator to generate a sort string

4
dspace-api/src/main/java/org/dspace/browse/SolrBrowseDAO.java
View File

@@ -16,7 +16,7 @@ import java.util.List;
import java.util.UUID;
import org.apache.commons.lang3.StringUtils;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.Logger;
import org.dspace.authorize.factory.AuthorizeServiceFactory;
import org.dspace.authorize.service.AuthorizeService;
import org.dspace.content.DSpaceObject;
@@ -68,7 +68,7 @@ public class SolrBrowseDAO implements BrowseDAO {
/**
* Log4j log
*/
private static final Logger log = Logger.getLogger(SolrBrowseDAO.class);
private static final Logger log = org.apache.logging.log4j.LogManager.getLogger(SolrBrowseDAO.class);
/**
* The DSpace context

4
dspace-api/src/main/java/org/dspace/checker/CheckerCommand.java
View File

@@ -13,7 +13,7 @@ import java.util.Date;
import java.util.Map;
import org.apache.commons.collections4.MapUtils;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.Logger;
import org.dspace.checker.factory.CheckerServiceFactory;
import org.dspace.checker.service.ChecksumHistoryService;
import org.dspace.checker.service.ChecksumResultService;
@@ -42,7 +42,7 @@ public final class CheckerCommand {
/**
* Usual Log4J logger.
*/
private static final Logger LOG = Logger.getLogger(CheckerCommand.class);
private static final Logger LOG = org.apache.logging.log4j.LogManager.getLogger(CheckerCommand.class);
private Context context;

4
dspace-api/src/main/java/org/dspace/checker/CheckerConsumer.java
View File

@@ -7,7 +7,7 @@
*/
package org.dspace.checker;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.Logger;
import org.dspace.checker.factory.CheckerServiceFactory;
import org.dspace.checker.service.ChecksumHistoryService;
import org.dspace.content.Bitstream;
@@ -26,7 +26,7 @@ public class CheckerConsumer implements Consumer {
/**
* log4j logger
*/
private static Logger log = Logger.getLogger(CheckerConsumer.class);
private static Logger log = org.apache.logging.log4j.LogManager.getLogger(CheckerConsumer.class);
protected ChecksumHistoryService checksumHistoryService = CheckerServiceFactory.getInstance()
.getChecksumHistoryService();

4
dspace-api/src/main/java/org/dspace/checker/DailyReportEmailer.java
View File

@@ -21,7 +21,7 @@ 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.logging.log4j.Logger;
import org.dspace.checker.factory.CheckerServiceFactory;
import org.dspace.checker.service.SimpleReporterService;
import org.dspace.core.ConfigurationManager;
@@ -43,7 +43,7 @@ public class DailyReportEmailer {
/**
* log4j logger.
*/
private static Logger log = Logger.getLogger(DailyReportEmailer.class);
private static Logger log = org.apache.logging.log4j.LogManager.getLogger(DailyReportEmailer.class);
/**
* Default constructor.

4
dspace-api/src/main/java/org/dspace/checker/HandleDispatcher.java
View File

@@ -12,7 +12,7 @@ import java.util.ArrayList;
import java.util.Arrays;
import java.util.Iterator;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.Logger;
import org.dspace.content.Bitstream;
import org.dspace.content.DSpaceObject;
import org.dspace.content.factory.ContentServiceFactory;
@@ -35,7 +35,7 @@ public class HandleDispatcher implements BitstreamDispatcher {
/**
* Log 4j logger.
*/
private static final Logger LOG = Logger.getLogger(HandleDispatcher.class);
private static final Logger LOG = org.apache.logging.log4j.LogManager.getLogger(HandleDispatcher.class);
protected Context context;

4
dspace-api/src/main/java/org/dspace/checker/MostRecentChecksum.java
View File

@@ -19,8 +19,8 @@ import javax.persistence.Temporal;
import javax.persistence.TemporalType;
import javax.persistence.Transient;
import org.apache.commons.lang.builder.EqualsBuilder;
import org.apache.commons.lang.builder.HashCodeBuilder;
import org.apache.commons.lang3.builder.EqualsBuilder;
import org.apache.commons.lang3.builder.HashCodeBuilder;
import org.dspace.content.Bitstream;
/**

5
dspace-api/src/main/java/org/dspace/checker/MostRecentChecksumServiceImpl.java
View File

@@ -11,7 +11,7 @@ import java.sql.SQLException;
import java.util.Date;
import java.util.List;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.Logger;
import org.dspace.checker.dao.MostRecentChecksumDAO;
import org.dspace.checker.service.ChecksumResultService;
import org.dspace.checker.service.MostRecentChecksumService;
@@ -28,7 +28,8 @@ import org.springframework.beans.factory.annotation.Autowired;
* @author kevinvandevelde at atmire.com
*/
public class MostRecentChecksumServiceImpl implements MostRecentChecksumService {
private static final Logger log = Logger.getLogger(MostRecentChecksumServiceImpl.class);
private static final Logger log =
org.apache.logging.log4j.LogManager.getLogger(MostRecentChecksumServiceImpl.class);
@Autowired(required = true)
protected MostRecentChecksumDAO mostRecentChecksumDAO;

4
dspace-api/src/main/java/org/dspace/checker/ResultsLogger.java
View File

@@ -12,7 +12,7 @@ import java.text.DateFormat;
import java.text.SimpleDateFormat;
import java.util.Date;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.Logger;
import org.dspace.content.Bitstream;
import org.dspace.core.Context;
import org.dspace.core.I18nUtil;
@@ -30,7 +30,7 @@ public class ResultsLogger implements ChecksumResultsCollector {
/**
* Usual Log4J logger.
*/
private static final Logger LOG = Logger.getLogger(ResultsLogger.class);
private static final Logger LOG = org.apache.logging.log4j.LogManager.getLogger(ResultsLogger.class);
/**
* Utility date format.

4
dspace-api/src/main/java/org/dspace/checker/ResultsPruner.java
View File

@@ -19,7 +19,7 @@ import java.util.Properties;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.Logger;
import org.dspace.checker.factory.CheckerServiceFactory;
import org.dspace.checker.service.ChecksumHistoryService;
import org.dspace.core.ConfigurationManager;
@@ -40,7 +40,7 @@ public final class ResultsPruner {
/**
* Default logger.
*/
private static final Logger LOG = Logger.getLogger(ResultsPruner.class);
private static final Logger LOG = org.apache.logging.log4j.LogManager.getLogger(ResultsPruner.class);
/**
* Factory method for the default results pruner configuration using

4
dspace-api/src/main/java/org/dspace/content/BitstreamFormatServiceImpl.java
View File

@@ -12,7 +12,7 @@ import java.util.Collections;
import java.util.List;
import org.apache.commons.collections4.CollectionUtils;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.Logger;
import org.dspace.authorize.AuthorizeException;
import org.dspace.authorize.service.AuthorizeService;
import org.dspace.content.dao.BitstreamFormatDAO;
@@ -33,7 +33,7 @@ public class BitstreamFormatServiceImpl implements BitstreamFormatService {
/**
* log4j logger
*/
private static Logger log = Logger.getLogger(BitstreamFormat.class);
private static Logger log = org.apache.logging.log4j.LogManager.getLogger(BitstreamFormat.class);
@Autowired(required = true)
protected BitstreamFormatDAO bitstreamFormatDAO;

8
dspace-api/src/main/java/org/dspace/content/BitstreamServiceImpl.java
View File

@@ -15,8 +15,8 @@ import java.util.List;
import java.util.UUID;
import org.apache.commons.collections4.CollectionUtils;
import org.apache.commons.lang.StringUtils;
import org.apache.log4j.Logger;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.Logger;
import org.dspace.authorize.AuthorizeException;
import org.dspace.authorize.service.AuthorizeService;
import org.dspace.content.dao.BitstreamDAO;
@@ -43,7 +43,7 @@ public class BitstreamServiceImpl extends DSpaceObjectServiceImpl<Bitstream> imp
/**
* log4j logger
*/
private static Logger log = Logger.getLogger(BitstreamServiceImpl.class);
private static Logger log = org.apache.logging.log4j.LogManager.getLogger(BitstreamServiceImpl.class);
@Autowired(required = true)
@@ -103,6 +103,8 @@ public class BitstreamServiceImpl extends DSpaceObjectServiceImpl<Bitstream> imp
clonedBitstream.setSizeBytes(bitstream.getSizeBytes());
clonedBitstream.setChecksum(bitstream.getChecksum());
clonedBitstream.setChecksumAlgorithm(bitstream.getChecksumAlgorithm());
clonedBitstream.setFormat(bitstream.getBitstreamFormat());
try {
//Update our bitstream but turn off the authorization system since permissions
//haven't been set at this point in time.

6
dspace-api/src/main/java/org/dspace/content/BundleServiceImpl.java
View File

@@ -16,8 +16,8 @@ import java.util.List;
import java.util.UUID;
import org.apache.commons.collections4.CollectionUtils;
import org.apache.commons.lang.StringUtils;
import org.apache.log4j.Logger;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.Logger;
import org.dspace.authorize.AuthorizeConfiguration;
import org.dspace.authorize.AuthorizeException;
import org.dspace.authorize.ResourcePolicy;
@@ -45,7 +45,7 @@ public class BundleServiceImpl extends DSpaceObjectServiceImpl<Bundle> implement
/**
* log4j logger
*/
private static Logger log = Logger.getLogger(Bundle.class);
private static Logger log = org.apache.logging.log4j.LogManager.getLogger(Bundle.class);
@Autowired(required = true)
protected BundleDAO bundleDAO;

6
dspace-api/src/main/java/org/dspace/content/CollectionServiceImpl.java
View File

@@ -20,8 +20,8 @@ import java.util.MissingResourceException;
import java.util.UUID;
import org.apache.commons.collections4.CollectionUtils;
import org.apache.commons.lang.StringUtils;
import org.apache.log4j.Logger;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.Logger;
import org.dspace.app.util.AuthorizeUtil;
import org.dspace.authorize.AuthorizeConfiguration;
import org.dspace.authorize.AuthorizeException;
@@ -61,7 +61,7 @@ public class CollectionServiceImpl extends DSpaceObjectServiceImpl<Collection> i
/**
* log4j category
*/
private static final Logger log = Logger.getLogger(CollectionServiceImpl.class);
private static final Logger log = org.apache.logging.log4j.LogManager.getLogger(CollectionServiceImpl.class);
@Autowired(required = true)
protected CollectionDAO collectionDAO;

6
dspace-api/src/main/java/org/dspace/content/Community.java
View File

@@ -23,8 +23,8 @@ import javax.persistence.OneToOne;
import javax.persistence.Table;
import javax.persistence.Transient;
import org.apache.commons.lang.builder.HashCodeBuilder;
import org.apache.log4j.Logger;
import org.apache.commons.lang3.builder.HashCodeBuilder;
import org.apache.logging.log4j.Logger;
import org.dspace.content.comparator.NameAscendingComparator;
import org.dspace.content.factory.ContentServiceFactory;
import org.dspace.content.service.CommunityService;
@@ -52,7 +52,7 @@ public class Community extends DSpaceObject implements DSpaceObjectLegacySupport
/**
* log4j category
*/
private static final Logger log = Logger.getLogger(Community.class);
private static final Logger log = org.apache.logging.log4j.LogManager.getLogger(Community.class);
@Column(name = "community_id", insertable = false, updatable = false)
private Integer legacyId;

6
dspace-api/src/main/java/org/dspace/content/CommunityServiceImpl.java
View File

@@ -17,8 +17,8 @@ import java.util.MissingResourceException;
import java.util.UUID;
import org.apache.commons.collections4.CollectionUtils;
import org.apache.commons.lang.StringUtils;
import org.apache.log4j.Logger;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.Logger;
import org.dspace.app.util.AuthorizeUtil;
import org.dspace.authorize.AuthorizeConfiguration;
import org.dspace.authorize.AuthorizeException;
@@ -51,7 +51,7 @@ public class CommunityServiceImpl extends DSpaceObjectServiceImpl<Community> imp
/**
* log4j category
*/
private static Logger log = Logger.getLogger(CommunityServiceImpl.class);
private static Logger log = org.apache.logging.log4j.LogManager.getLogger(CommunityServiceImpl.class);
@Autowired(required = true)
protected CommunityDAO communityDAO;

4
dspace-api/src/main/java/org/dspace/content/DCDate.java
View File

@@ -18,7 +18,7 @@ import java.util.Locale;
import java.util.Map;
import java.util.TimeZone;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.Logger;
// FIXME: Not very robust - assumes dates will always be valid
@@ -45,7 +45,7 @@ public class DCDate {
/**
* Logger
*/
private static Logger log = Logger.getLogger(DCDate.class);
private static Logger log = org.apache.logging.log4j.LogManager.getLogger(DCDate.class);
// UTC timezone
private static final TimeZone utcZone = TimeZone.getTimeZone("UTC");

8
dspace-api/src/main/java/org/dspace/content/DSpaceObjectServiceImpl.java
View File

@@ -17,9 +17,9 @@ import java.util.Map;
import java.util.StringTokenizer;
import org.apache.commons.collections4.CollectionUtils;
import org.apache.commons.lang.ArrayUtils;
import org.apache.commons.lang.StringUtils;
import org.apache.log4j.Logger;
import org.apache.commons.lang3.ArrayUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.Logger;
import org.dspace.authorize.AuthorizeException;
import org.dspace.content.authority.Choices;
import org.dspace.content.authority.service.ChoiceAuthorityService;
@@ -48,7 +48,7 @@ public abstract class DSpaceObjectServiceImpl<T extends DSpaceObject> implements
/**
* log4j category
*/
private static final Logger log = Logger.getLogger(DSpaceObjectServiceImpl.class);
private static final Logger log = org.apache.logging.log4j.LogManager.getLogger(DSpaceObjectServiceImpl.class);
@Autowired(required = true)
protected ChoiceAuthorityService choiceAuthorityService;

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

@@ -15,7 +15,7 @@ import java.util.List;
import java.util.Map;
import java.util.Set;
import org.apache.commons.lang.builder.HashCodeBuilder;
import org.apache.commons.lang3.builder.HashCodeBuilder;
import org.dspace.content.factory.ContentServiceFactory;
import org.dspace.content.service.ItemService;
import org.dspace.sort.OrderFormat;

6
dspace-api/src/main/java/org/dspace/content/ItemServiceImpl.java
View File

@@ -20,8 +20,8 @@ import java.util.Map;
import java.util.UUID;
import org.apache.commons.collections4.CollectionUtils;
import org.apache.commons.lang.StringUtils;
import org.apache.log4j.Logger;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.Logger;
import org.dspace.app.util.AuthorizeUtil;
import org.dspace.authorize.AuthorizeConfiguration;
import org.dspace.authorize.AuthorizeException;
@@ -68,7 +68,7 @@ public class ItemServiceImpl extends DSpaceObjectServiceImpl<Item> implements It
/**
* log4j category
*/
private static final Logger log = Logger.getLogger(Item.class);
private static final Logger log = org.apache.logging.log4j.LogManager.getLogger(Item.class);
@Autowired(required = true)
protected ItemDAO itemDAO;

4
dspace-api/src/main/java/org/dspace/content/MetadataFieldServiceImpl.java
View File

@@ -12,7 +12,7 @@ import java.sql.SQLException;
import java.util.List;
import org.apache.commons.collections4.CollectionUtils;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.Logger;
import org.dspace.authorize.AuthorizeException;
import org.dspace.authorize.service.AuthorizeService;
import org.dspace.content.dao.MetadataFieldDAO;
@@ -33,7 +33,7 @@ public class MetadataFieldServiceImpl implements MetadataFieldService {
/**
* log4j logger
*/
private static Logger log = Logger.getLogger(MetadataFieldServiceImpl.class);
private static Logger log = org.apache.logging.log4j.LogManager.getLogger(MetadataFieldServiceImpl.class);
@Autowired(required = true)
protected MetadataFieldDAO metadataFieldDAO;

4
dspace-api/src/main/java/org/dspace/content/MetadataSchemaServiceImpl.java
View File

@@ -10,7 +10,7 @@ package org.dspace.content;
import java.sql.SQLException;
import java.util.List;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.Logger;
import org.dspace.authorize.AuthorizeException;
import org.dspace.authorize.service.AuthorizeService;
import org.dspace.content.dao.MetadataSchemaDAO;
@@ -31,7 +31,7 @@ public class MetadataSchemaServiceImpl implements MetadataSchemaService {
/**
* log4j logger
*/
private static Logger log = Logger.getLogger(MetadataSchemaServiceImpl.class);
private static Logger log = org.apache.logging.log4j.LogManager.getLogger(MetadataSchemaServiceImpl.class);
@Autowired(required = true)
protected AuthorizeService authorizeService;

4
dspace-api/src/main/java/org/dspace/content/MetadataValueServiceImpl.java
View File

@@ -12,7 +12,7 @@ import java.sql.SQLException;
import java.util.Iterator;
import java.util.List;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.Logger;
import org.dspace.authorize.AuthorizeException;
import org.dspace.authorize.service.AuthorizeService;
import org.dspace.content.dao.MetadataValueDAO;
@@ -33,7 +33,7 @@ import org.springframework.beans.factory.annotation.Autowired;
*/
public class MetadataValueServiceImpl implements MetadataValueService {
private static final Logger log = Logger.getLogger(MetadataValueServiceImpl.class);
private static final Logger log = org.apache.logging.log4j.LogManager.getLogger(MetadataValueServiceImpl.class);
@Autowired(required = true)
protected AuthorizeService authorizeService;

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

@@ -25,7 +25,7 @@ import javax.persistence.OneToOne;
import javax.persistence.SequenceGenerator;
import javax.persistence.Table;
import org.apache.commons.lang.builder.HashCodeBuilder;
import org.apache.commons.lang3.builder.HashCodeBuilder;
import org.dspace.core.Context;
import org.dspace.core.ReloadableEntity;
import org.dspace.eperson.EPerson;

4
dspace-api/src/main/java/org/dspace/content/WorkspaceItemServiceImpl.java
View File

@@ -13,7 +13,7 @@ import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.Logger;
import org.dspace.app.util.DCInputsReaderException;
import org.dspace.app.util.Util;
import org.dspace.authorize.AuthorizeException;
@@ -40,7 +40,7 @@ import org.springframework.beans.factory.annotation.Autowired;
*/
public class WorkspaceItemServiceImpl implements WorkspaceItemService {
private static final Logger log = Logger.getLogger(WorkspaceItemServiceImpl.class);
private static final Logger log = org.apache.logging.log4j.LogManager.getLogger(WorkspaceItemServiceImpl.class);
@Autowired(required = true)
protected WorkspaceItemDAO workspaceItemDAO;

4
dspace-api/src/main/java/org/dspace/content/authority/ChoiceAuthorityServiceImpl.java
View File

@@ -14,7 +14,7 @@ import java.util.Map;
import java.util.Set;
import org.apache.commons.lang3.StringUtils;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.Logger;
import org.dspace.app.util.DCInput;
import org.dspace.app.util.DCInputSet;
import org.dspace.app.util.DCInputsReader;
@@ -49,7 +49,7 @@ import org.springframework.beans.factory.annotation.Autowired;
* @see ChoiceAuthority
*/
public final class ChoiceAuthorityServiceImpl implements ChoiceAuthorityService {
private Logger log = Logger.getLogger(ChoiceAuthorityServiceImpl.class);
private Logger log = org.apache.logging.log4j.LogManager.getLogger(ChoiceAuthorityServiceImpl.class);
// map of field key to authority plugin
protected Map<String, ChoiceAuthority> controller = new HashMap<String, ChoiceAuthority>();

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

@@ -7,7 +7,7 @@
*/
package org.dspace.content.authority;
import org.apache.commons.lang.ArrayUtils;
import org.apache.commons.lang3.ArrayUtils;
/**
* Record class to hold a set of Choices returned by an authority in response

6
dspace-api/src/main/java/org/dspace/content/authority/DCInputAuthority.java
View File

@@ -12,8 +12,8 @@ import java.util.Arrays;
import java.util.Iterator;
import java.util.List;
import org.apache.commons.lang.ArrayUtils;
import org.apache.log4j.Logger;
import org.apache.commons.lang3.ArrayUtils;
import org.apache.logging.log4j.Logger;
import org.dspace.app.util.DCInputsReader;
import org.dspace.app.util.DCInputsReaderException;
import org.dspace.content.Collection;
@@ -42,7 +42,7 @@ import org.dspace.core.SelfNamedPlugin;
* fields.
*/
public class DCInputAuthority extends SelfNamedPlugin implements ChoiceAuthority {
private static Logger log = Logger.getLogger(DCInputAuthority.class);
private static Logger log = org.apache.logging.log4j.LogManager.getLogger(DCInputAuthority.class);
private String values[] = null;
private String labels[] = null;

8
dspace-api/src/main/java/org/dspace/content/authority/DSpaceControlledVocabulary.java
View File

@@ -16,9 +16,9 @@ import javax.xml.xpath.XPathConstants;
import javax.xml.xpath.XPathExpressionException;
import javax.xml.xpath.XPathFactory;
import org.apache.commons.lang.ArrayUtils;
import org.apache.commons.lang.StringUtils;
import org.apache.log4j.Logger;
import org.apache.commons.lang3.ArrayUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.Logger;
import org.dspace.content.Collection;
import org.dspace.core.SelfNamedPlugin;
import org.dspace.services.ConfigurationService;
@@ -56,7 +56,7 @@ import org.xml.sax.InputSource;
public class DSpaceControlledVocabulary extends SelfNamedPlugin implements ChoiceAuthority {
private static Logger log = Logger.getLogger(DSpaceControlledVocabulary.class);
private static Logger log = org.apache.logging.log4j.LogManager.getLogger(DSpaceControlledVocabulary.class);
protected static String xpathTemplate = "//node[contains(translate(@label,'ABCDEFGHIJKLMNOPQRSTUVWXYZ'," +
"'abcdefghijklmnopqrstuvwxyz'),'%s')]";
protected static String idTemplate = "//node[@id = '%s']";

7
dspace-api/src/main/java/org/dspace/content/authority/InputFormSelfRegisterWrapperAuthority.java
View File

@@ -13,8 +13,8 @@ import java.util.HashSet;
import java.util.Map;
import java.util.Set;
import org.apache.commons.lang.StringUtils;
import org.apache.log4j.Logger;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.Logger;
import org.dspace.app.util.DCInputsReader;
import org.dspace.app.util.DCInputsReaderException;
import org.dspace.content.Collection;
@@ -32,7 +32,8 @@ import org.dspace.content.Collection;
*/
public class InputFormSelfRegisterWrapperAuthority implements ChoiceAuthority {
private static Logger log = Logger.getLogger(InputFormSelfRegisterWrapperAuthority.class);
private static Logger log =
org.apache.logging.log4j.LogManager.getLogger(InputFormSelfRegisterWrapperAuthority.class);
private Map<String, ChoiceAuthority> delegates = new HashMap<String, ChoiceAuthority>();

4
dspace-api/src/main/java/org/dspace/content/authority/LCNameAuthority.java
View File

@@ -22,7 +22,7 @@ import org.apache.http.client.HttpClient;
import org.apache.http.client.methods.HttpGet;
import org.apache.http.client.utils.URIBuilder;
import org.apache.http.impl.client.DefaultHttpClient;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.Logger;
import org.dspace.content.Collection;
import org.dspace.content.DCPersonName;
import org.dspace.core.ConfigurationManager;
@@ -57,7 +57,7 @@ import org.xml.sax.helpers.DefaultHandler;
* @version $Revision $
*/
public class LCNameAuthority implements ChoiceAuthority {
private static final Logger log = Logger.getLogger(LCNameAuthority.class);
private static final Logger log = org.apache.logging.log4j.LogManager.getLogger(LCNameAuthority.class);
// get these from configuration
protected static String url = null;

4
dspace-api/src/main/java/org/dspace/content/authority/MetadataAuthorityServiceImpl.java
View File

@@ -15,7 +15,7 @@ import java.util.List;
import java.util.Map;
import org.apache.commons.lang3.StringUtils;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.Logger;
import org.dspace.app.util.DCInput;
import org.dspace.app.util.DCInputSet;
import org.dspace.app.util.DCInputsReader;
@@ -57,7 +57,7 @@ import org.springframework.beans.factory.annotation.Autowired;
* @see Choices
*/
public class MetadataAuthorityServiceImpl implements MetadataAuthorityService {
private static Logger log = Logger.getLogger(MetadataAuthorityServiceImpl.class);
private static Logger log = org.apache.logging.log4j.LogManager.getLogger(MetadataAuthorityServiceImpl.class);
@Autowired(required = true)
protected MetadataFieldService metadataFieldService;

4
dspace-api/src/main/java/org/dspace/content/authority/SHERPARoMEOProtocol.java
View File

@@ -19,7 +19,7 @@ import org.apache.http.client.methods.HttpGet;
import org.apache.http.client.utils.URLEncodedUtils;
import org.apache.http.impl.client.DefaultHttpClient;
import org.apache.http.message.BasicNameValuePair;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.Logger;
import org.dspace.content.Collection;
import org.dspace.core.ConfigurationManager;
import org.xml.sax.Attributes;
@@ -50,7 +50,7 @@ import org.xml.sax.helpers.DefaultHandler;
* @see SHERPARoMEOJournalTitle
*/
public abstract class SHERPARoMEOProtocol implements ChoiceAuthority {
private static final Logger log = Logger.getLogger(SHERPARoMEOProtocol.class);
private static final Logger log = org.apache.logging.log4j.LogManager.getLogger(SHERPARoMEOProtocol.class);
// contact URL from configuration
private static String url = null;

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