Merge pull request DSpace#10014 from tdonohue/oai_dep_cleanup

Dependency cleanup for OAI-PMH and Log4j (removing log4j v1 bridge & settings which used it)
4Science · Nov 18, 2024 · 117859d · 117859d
2 parents 398c61f + 76b54b3
commit 117859d
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Showing 28 changed files with 107 additions and 133 deletions.
diff --git a/dspace-api/pom.xml b/dspace-api/pom.xml
@@ -703,7 +703,6 @@
         <dependency>
             <groupId>jakarta.inject</groupId>
             <artifactId>jakarta.inject-api</artifactId>
-            <version>2.0.1</version>
         </dependency>
 
         <!-- JAXB API and implementation (no longer bundled as of Java 11) -->

diff --git a/dspace-api/src/test/java/org/dspace/app/bulkedit/MetadataExportSearchIT.java b/dspace-api/src/test/java/org/dspace/app/bulkedit/MetadataExportSearchIT.java
@@ -23,7 +23,8 @@
 import com.google.common.io.Files;
 import com.opencsv.CSVReader;
 import com.opencsv.exceptions.CsvException;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.dspace.AbstractIntegrationTestWithDatabase;
 import org.dspace.app.launcher.ScriptLauncher;
 import org.dspace.app.scripts.handler.impl.TestDSpaceRunnableHandler;
@@ -51,7 +52,7 @@ public class MetadataExportSearchIT extends AbstractIntegrationTestWithDatabase
     private Item[] itemsSubject2 = new Item[numberItemsSubject2];
     private String filename;
     private Collection collection;
-    private Logger logger = Logger.getLogger(MetadataExportSearchIT.class);
+    private Logger logger = LogManager.getLogger(MetadataExportSearchIT.class);
     private ConfigurationService configurationService = DSpaceServicesFactory.getInstance().getConfigurationService();
     private SearchService searchService;
 

diff --git a/dspace-api/src/test/java/org/dspace/builder/OrcidHistoryBuilder.java b/dspace-api/src/test/java/org/dspace/builder/OrcidHistoryBuilder.java
@@ -11,7 +11,8 @@
 import java.sql.SQLException;
 import java.util.Date;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.dspace.content.Item;
 import org.dspace.core.Context;
 import org.dspace.orcid.OrcidHistory;
@@ -24,7 +25,7 @@
  */
 public class OrcidHistoryBuilder extends  AbstractBuilder<OrcidHistory, OrcidHistoryService> {
 
-    private static final Logger log = Logger.getLogger(OrcidHistoryBuilder.class);
+    private static final Logger log = LogManager.getLogger(OrcidHistoryBuilder.class);
 
     private OrcidHistory orcidHistory;
 

diff --git a/dspace-oai/pom.xml b/dspace-oai/pom.xml
@@ -65,9 +65,8 @@
 
         <!-- Java Injection -->
         <dependency>
-            <groupId>javax.inject</groupId>
-            <artifactId>javax.inject</artifactId>
-            <version>1</version>
+            <groupId>jakarta.inject</groupId>
+            <artifactId>jakarta.inject-api</artifactId>
         </dependency>
 
         <!-- Needed to support Spring @Configuration classes (to register servlets/beans with Spring Boot webapp) -->
@@ -99,22 +98,9 @@
                     <groupId>org.springframework.boot</groupId>
                     <artifactId>spring-boot-starter-web</artifactId>
                 </exclusion>
-                <!-- More recent version is pulled in via below dependencies -->
-                <exclusion>
-                    <groupId>org.parboiled</groupId>
-                    <artifactId>parboiled-java</artifactId>
-                </exclusion>
             </exclusions>
         </dependency>
 
-        <!-- Newer version, necessary to align with newer version of ASM in parent POM
-             This is needed by both jtwig-spring-boot-starter and our tests. -->
-        <dependency>
-            <groupId>org.parboiled</groupId>
-            <artifactId>parboiled-java</artifactId>
-            <version>1.3.1</version>
-        </dependency>
-
         <!-- Internal -->
         <dependency>
             <groupId>org.dspace</groupId>
@@ -137,19 +123,6 @@
             <groupId>org.apache.logging.log4j</groupId>
             <artifactId>log4j-core</artifactId>
         </dependency>
-        <dependency>
-            <groupId>org.apache.logging.log4j</groupId>
-            <artifactId>log4j-web</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>org.apache.logging.log4j</groupId>
-            <artifactId>log4j-slf4j-impl</artifactId>
-            <scope>runtime</scope>
-        </dependency>
-        <dependency>
-            <groupId>org.apache.logging.log4j</groupId>
-            <artifactId>log4j-1.2-api</artifactId>
-        </dependency>
 
         <!-- Testing -->
         <dependency>

diff --git a/dspace-oai/src/main/java/org/dspace/xoai/app/CCElementItemCompilePlugin.java b/dspace-oai/src/main/java/org/dspace/xoai/app/CCElementItemCompilePlugin.java
@@ -11,7 +11,7 @@
 
 import com.lyncode.xoai.dataprovider.xml.xoai.Element;
 import com.lyncode.xoai.dataprovider.xml.xoai.Metadata;
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.dspace.content.Item;
 import org.dspace.core.Context;
 import org.dspace.license.factory.LicenseServiceFactory;

diff --git a/dspace-oai/src/main/java/org/dspace/xoai/app/XOAI.java b/dspace-oai/src/main/java/org/dspace/xoai/app/XOAI.java
@@ -9,7 +9,7 @@
 
 import static com.lyncode.xoai.dataprovider.core.Granularity.Second;
 import static java.util.Objects.nonNull;
-import static org.apache.commons.lang.StringUtils.EMPTY;
+import static org.apache.commons.lang3.StringUtils.EMPTY;
 import static org.apache.solr.common.params.CursorMarkParams.CURSOR_MARK_PARAM;
 import static org.apache.solr.common.params.CursorMarkParams.CURSOR_MARK_START;
 import static org.dspace.xoai.util.ItemUtils.retrieveMetadata;

diff --git a/dspace-oai/src/main/java/org/dspace/xoai/filter/ItemsWithBitstreamFilter.java b/dspace-oai/src/main/java/org/dspace/xoai/filter/ItemsWithBitstreamFilter.java
@@ -9,8 +9,8 @@
 
 import java.sql.SQLException;
 
-import org.apache.log4j.LogManager;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.dspace.content.Bundle;
 import org.dspace.content.Item;
 import org.dspace.handle.factory.HandleServiceFactory;

diff --git a/dspace-oai/src/test/java/org/dspace/xoai/tests/integration/xoai/PipelineTest.java b/dspace-oai/src/test/java/org/dspace/xoai/tests/integration/xoai/PipelineTest.java
@@ -13,13 +13,14 @@
 import static org.hamcrest.MatcherAssert.assertThat;
 
 import java.io.InputStream;
+import java.nio.charset.Charset;
 import javax.xml.transform.TransformerFactory;
 import javax.xml.transform.stream.StreamSource;
 
 import com.lyncode.xoai.util.XSLPipeline;
+import org.apache.commons.io.IOUtils;
 import org.dspace.xoai.tests.support.XmlMatcherBuilder;
 import org.junit.Test;
-import org.parboiled.common.FileUtils;
 
 public class PipelineTest {
     private static TransformerFactory factory = TransformerFactory.newInstance();
@@ -28,9 +29,9 @@ public class PipelineTest {
     public void pipelineTest() throws Exception {
         InputStream input = PipelineTest.class.getClassLoader().getResourceAsStream("item.xml");
         InputStream xslt = PipelineTest.class.getClassLoader().getResourceAsStream("oai_dc.xsl");
-        String output = FileUtils.readAllText(new XSLPipeline(input, true)
-                                                  .apply(factory.newTemplates(new StreamSource(xslt)))
-                                                  .getTransformed());
+        String output = IOUtils.toString(new XSLPipeline(input, true)
+                                             .apply(factory.newTemplates(new StreamSource(xslt)))
+                                             .getTransformed(), Charset.defaultCharset());
 
         assertThat(output, oai_dc().withXPath("/oai_dc:dc/dc:title", equalTo("Teste")));
 

diff --git a/dspace-rdf/pom.xml b/dspace-rdf/pom.xml
@@ -89,10 +89,6 @@
             <groupId>org.apache.logging.log4j</groupId>
             <artifactId>log4j-core</artifactId>
         </dependency>
-	<dependency>
-	  <groupId>org.apache.logging.log4j</groupId>
-	  <artifactId>log4j-web</artifactId>
-	</dependency>
 
         <dependency>
             <groupId>org.apache.commons</groupId>

diff --git a/dspace-server-webapp/src/main/java/org/dspace/app/rest/converter/SearchEventConverter.java b/dspace-server-webapp/src/main/java/org/dspace/app/rest/converter/SearchEventConverter.java
@@ -13,7 +13,8 @@
 import java.util.List;
 
 import jakarta.servlet.http.HttpServletRequest;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.dspace.app.rest.model.PageRest;
 import org.dspace.app.rest.model.SearchEventRest;
 import org.dspace.app.rest.model.SearchResultsRest;
@@ -31,7 +32,7 @@
 @Component
 public class SearchEventConverter {
     /* Log4j logger */
-    private static final Logger log = Logger.getLogger(SearchEventConverter.class);
+    private static final Logger log = LogManager.getLogger(SearchEventConverter.class);
 
     @Autowired
     private ScopeResolver scopeResolver;

diff --git a/...n/java/org/dspace/app/rest/signposting/processor/bitstream/BitstreamLinksetProcessor.java b/...n/java/org/dspace/app/rest/signposting/processor/bitstream/BitstreamLinksetProcessor.java
@@ -10,7 +10,8 @@
 import java.util.List;
 
 import jakarta.servlet.http.HttpServletRequest;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.dspace.app.rest.signposting.model.LinksetNode;
 import org.dspace.app.rest.signposting.model.LinksetRelationType;
 import org.dspace.content.Bitstream;
@@ -25,7 +26,7 @@
  */
 public class BitstreamLinksetProcessor extends BitstreamSignpostingProcessor {
 
-    private static final Logger log = Logger.getLogger(BitstreamLinksetProcessor.class);
+    private static final Logger log = LogManager.getLogger(BitstreamLinksetProcessor.class);
 
     private final BitstreamService bitstreamService;
 

diff --git a/...ava/org/dspace/app/rest/signposting/processor/bitstream/BitstreamParentItemProcessor.java b/...ava/org/dspace/app/rest/signposting/processor/bitstream/BitstreamParentItemProcessor.java
@@ -10,7 +10,8 @@
 import java.util.List;
 
 import jakarta.servlet.http.HttpServletRequest;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.dspace.app.rest.signposting.model.LinksetNode;
 import org.dspace.app.rest.signposting.model.LinksetRelationType;
 import org.dspace.content.Bitstream;
@@ -28,7 +29,7 @@
  */
 public class BitstreamParentItemProcessor extends BitstreamSignpostingProcessor {
 
-    private static final Logger log = Logger.getLogger(BitstreamParentItemProcessor.class);
+    private static final Logger log = LogManager.getLogger(BitstreamParentItemProcessor.class);
 
     private final BitstreamService bitstreamService;
 

diff --git a/...main/java/org/dspace/app/rest/signposting/processor/bitstream/BitstreamTypeProcessor.java b/...main/java/org/dspace/app/rest/signposting/processor/bitstream/BitstreamTypeProcessor.java
@@ -11,7 +11,8 @@
 
 import jakarta.servlet.http.HttpServletRequest;
 import org.apache.commons.lang3.StringUtils;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.dspace.app.rest.signposting.model.LinksetNode;
 import org.dspace.app.rest.signposting.model.LinksetRelationType;
 import org.dspace.content.Bitstream;
@@ -28,7 +29,7 @@
  */
 public class BitstreamTypeProcessor extends BitstreamSignpostingProcessor {
 
-    private static final Logger log = Logger.getLogger(BitstreamTypeProcessor.class);
+    private static final Logger log = LogManager.getLogger(BitstreamTypeProcessor.class);
 
     @Autowired
     private SimpleMapConverter mapConverterDSpaceToSchemaOrgUri;

diff --git a/...app/src/main/java/org/dspace/app/rest/signposting/processor/item/ItemAuthorProcessor.java b/...app/src/main/java/org/dspace/app/rest/signposting/processor/item/ItemAuthorProcessor.java
@@ -16,7 +16,8 @@
 import java.util.List;
 
 import jakarta.servlet.http.HttpServletRequest;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.dspace.app.rest.signposting.model.LinksetNode;
 import org.dspace.app.rest.signposting.model.LinksetRelationType;
 import org.dspace.content.Item;
@@ -37,7 +38,7 @@ public class ItemAuthorProcessor extends ItemSignpostingProcessor {
     /**
      * log4j category
      */
-    private static final Logger log = Logger.getLogger(ItemAuthorProcessor.class);
+    private static final Logger log = LogManager.getLogger(ItemAuthorProcessor.class);
 
     private final ItemService itemService;
 

diff --git a/...n/java/org/dspace/app/rest/signposting/processor/item/ItemContentBitstreamsProcessor.java b/...n/java/org/dspace/app/rest/signposting/processor/item/ItemContentBitstreamsProcessor.java
@@ -11,7 +11,8 @@
 import java.util.List;
 
 import jakarta.servlet.http.HttpServletRequest;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.dspace.app.rest.signposting.model.LinksetNode;
 import org.dspace.app.rest.signposting.model.LinksetRelationType;
 import org.dspace.content.Bitstream;
@@ -33,7 +34,7 @@ public class ItemContentBitstreamsProcessor extends ItemSignpostingProcessor {
     /**
      * log4j category
      */
-    private static final Logger log = Logger.getLogger(ItemContentBitstreamsProcessor.class);
+    private static final Logger log = LogManager.getLogger(ItemContentBitstreamsProcessor.class);
 
     public ItemContentBitstreamsProcessor(FrontendUrlService frontendUrlService) {
         super(frontendUrlService);

diff --git a/...rc/main/java/org/dspace/app/rest/signposting/processor/item/ItemDescribedbyProcessor.java b/...rc/main/java/org/dspace/app/rest/signposting/processor/item/ItemDescribedbyProcessor.java
@@ -10,7 +10,8 @@
 import java.util.List;
 
 import jakarta.servlet.http.HttpServletRequest;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.dspace.app.rest.signposting.model.LinksetNode;
 import org.dspace.app.rest.signposting.model.LinksetRelationType;
 import org.dspace.content.Item;
@@ -23,7 +24,7 @@
  */
 public class ItemDescribedbyProcessor extends ItemSignpostingProcessor {
 
-    private static final Logger log = Logger.getLogger(ItemDescribedbyProcessor.class);
+    private static final Logger log = LogManager.getLogger(ItemDescribedbyProcessor.class);
 
     private final ConfigurationService configurationService;
 

diff --git a/...pp/src/main/java/org/dspace/app/rest/signposting/processor/item/ItemLicenseProcessor.java b/...pp/src/main/java/org/dspace/app/rest/signposting/processor/item/ItemLicenseProcessor.java
@@ -11,7 +11,8 @@
 
 import jakarta.servlet.http.HttpServletRequest;
 import org.apache.commons.lang3.StringUtils;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.dspace.app.rest.signposting.model.LinksetNode;
 import org.dspace.app.rest.signposting.model.LinksetRelationType;
 import org.dspace.content.Item;
@@ -25,7 +26,7 @@
  */
 public class ItemLicenseProcessor extends ItemSignpostingProcessor {
 
-    private static final Logger log = Logger.getLogger(ItemLicenseProcessor.class);
+    private static final Logger log = LogManager.getLogger(ItemLicenseProcessor.class);
 
     private final CreativeCommonsService creativeCommonsService =
             LicenseServiceFactory.getInstance().getCreativeCommonsService();

diff --git a/...pp/src/main/java/org/dspace/app/rest/signposting/processor/item/ItemLinksetProcessor.java b/...pp/src/main/java/org/dspace/app/rest/signposting/processor/item/ItemLinksetProcessor.java
@@ -10,7 +10,8 @@
 import java.util.List;
 
 import jakarta.servlet.http.HttpServletRequest;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.dspace.app.rest.signposting.model.LinksetNode;
 import org.dspace.app.rest.signposting.model.LinksetRelationType;
 import org.dspace.content.Item;
@@ -23,7 +24,7 @@
  */
 public class ItemLinksetProcessor extends ItemSignpostingProcessor {
 
-    private static final Logger log = Logger.getLogger(ItemLinksetProcessor.class);
+    private static final Logger log = LogManager.getLogger(ItemLinksetProcessor.class);
 
     private final ConfigurationService configurationService;
 

diff --git a/...ebapp/src/main/java/org/dspace/app/rest/signposting/processor/item/ItemTypeProcessor.java b/...ebapp/src/main/java/org/dspace/app/rest/signposting/processor/item/ItemTypeProcessor.java
@@ -11,7 +11,8 @@
 
 import jakarta.servlet.http.HttpServletRequest;
 import org.apache.commons.lang3.StringUtils;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.dspace.app.rest.signposting.model.LinksetNode;
 import org.dspace.app.rest.signposting.model.LinksetRelationType;
 import org.dspace.content.Item;
@@ -27,7 +28,7 @@
  */
 public class ItemTypeProcessor extends ItemSignpostingProcessor {
 
-    private static final Logger log = Logger.getLogger(ItemTypeProcessor.class);
+    private static final Logger log = LogManager.getLogger(ItemTypeProcessor.class);
     private static final String ABOUT_PAGE_URI = "https://schema.org/AboutPage";
 
     @Autowired

diff --git a/...webapp/src/main/java/org/dspace/app/rest/signposting/service/impl/LinksetServiceImpl.java b/...webapp/src/main/java/org/dspace/app/rest/signposting/service/impl/LinksetServiceImpl.java
@@ -13,7 +13,8 @@
 import java.util.List;
 
 import jakarta.servlet.http.HttpServletRequest;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.dspace.app.rest.security.BitstreamMetadataReadPermissionEvaluatorPlugin;
 import org.dspace.app.rest.signposting.model.LinksetNode;
 import org.dspace.app.rest.signposting.processor.bitstream.BitstreamSignpostingProcessor;
@@ -37,7 +38,7 @@
 @Service
 public class LinksetServiceImpl implements LinksetService {
 
-    private static final Logger log = Logger.getLogger(LinksetServiceImpl.class);
+    private static final Logger log = LogManager.getLogger(LinksetServiceImpl.class);
 
     @Autowired
     protected ItemService itemService;

diff --git a/...r-webapp/src/main/java/org/dspace/app/rest/submit/step/validation/CclicenseValidator.java b/...r-webapp/src/main/java/org/dspace/app/rest/submit/step/validation/CclicenseValidator.java
@@ -12,8 +12,8 @@
 import java.sql.SQLException;
 import java.util.ArrayList;
 import java.util.List;
-import javax.inject.Inject;
 
+import jakarta.inject.Inject;
 import org.dspace.app.rest.model.ErrorRest;
 import org.dspace.app.rest.submit.SubmissionService;
 import org.dspace.app.util.DCInputsReaderException;

diff --git a/dspace-sword/pom.xml b/dspace-sword/pom.xml
@@ -91,10 +91,6 @@
             <groupId>org.apache.logging.log4j</groupId>
             <artifactId>log4j-core</artifactId>
         </dependency>
-        <dependency>
-            <groupId>org.apache.logging.log4j</groupId>
-            <artifactId>log4j-web</artifactId>
-        </dependency>
 
         <dependency>
             <groupId>xom</groupId>