Merge pull request #436 from 4Science/coar-notify-7-part-two-merge-main

Coar notify 7 part two merge main

dspace-api/src/main/java/org/dspace/administer/MetadataImporter.java

@@ -21,6 +21,8 @@
 import org.apache.commons.cli.DefaultParser;
 import org.apache.commons.cli.Options;
 import org.apache.commons.cli.ParseException;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.dspace.authorize.AuthorizeException;
 import org.dspace.content.MetadataField;
 import org.dspace.content.MetadataSchema;
@@ -30,8 +32,6 @@
 import org.dspace.content.service.MetadataFieldService;
 import org.dspace.content.service.MetadataSchemaService;
 import org.dspace.core.Context;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
 import org.w3c.dom.Document;
 import org.w3c.dom.Node;
 import org.w3c.dom.NodeList;
@@ -40,9 +40,9 @@
 /**
  * @author Richard Jones
  *
- * This class takes an xml document as passed in the arguments and
+ * This class takes an XML document as passed in the arguments and
  * uses it to create metadata elements in the Metadata Registry if
- * they do not already exist
+ * they do not already exist.
  *
  * The format of the XML file is as follows:
  *
@@ -69,7 +69,7 @@ public class MetadataImporter {
     /**
      * logging category
      */
-    private static final Logger log = LoggerFactory.getLogger(MetadataImporter.class);
+    private static final Logger log = LogManager.getLogger();
 
     /**
      * Default constructor
@@ -89,6 +89,7 @@ private MetadataImporter() { }
      * @throws SAXException                 if parser error
      * @throws NonUniqueMetadataException   if duplicate metadata
      * @throws RegistryImportException      if import fails
+     * @throws XPathExpressionException     passed through
      **/
     public static void main(String[] args)
         throws ParseException, SQLException, IOException, TransformerException,
@@ -125,6 +126,7 @@ public static void main(String[] args)
      * @throws SAXException                 if parser error
      * @throws NonUniqueMetadataException   if duplicate metadata
      * @throws RegistryImportException      if import fails
+     * @throws XPathExpressionException     passed through
      */
     public static void loadRegistry(String file, boolean forceUpdate)
         throws SQLException, IOException, TransformerException, ParserConfigurationException, AuthorizeException,
@@ -203,7 +205,7 @@ private static void loadSchema(Context context, Node node, boolean updateExistin
 
         if (s == null) {
             // Schema does not exist - create
-            log.info("Registering Schema " + name + " (" + namespace + ")");
+            log.info("Registering Schema {}({})", name, namespace);
             metadataSchemaService.create(context, name, namespace);
         } else {
             // Schema exists - if it's the same namespace, allow the type imports to continue
@@ -215,7 +217,7 @@ private static void loadSchema(Context context, Node node, boolean updateExistin
             // It's a different namespace - have we been told to update?
             if (updateExisting) {
                 // Update the existing schema namespace and continue to type import
-                log.info("Updating Schema " + name + ": New namespace " + namespace);
+                log.info("Updating Schema {}: New namespace {}", name, namespace);
                 s.setNamespace(namespace);
                 metadataSchemaService.update(context, s);
             } else {
@@ -274,7 +276,7 @@ private static void loadType(Context context, Node node)
         if (qualifier == null) {
             fieldName = schema + "." + element;
         }
-        log.info("Registering metadata field " + fieldName);
+        log.info("Registering metadata field {}", fieldName);
         MetadataField field = metadataFieldService.create(context, schemaObj, element, qualifier, scopeNote);
         metadataFieldService.update(context, field);
     }

dspace-api/src/main/java/org/dspace/app/mediafilter/MediaFilterScriptConfiguration.java

@@ -33,7 +33,8 @@ public Options getOptions() {
         options.addOption("v", "verbose", false, "print all extracted text and other details to STDOUT");
         options.addOption("q", "quiet", false, "do not print anything except in the event of errors.");
         options.addOption("f", "force", false, "force all bitstreams to be processed");
-        options.addOption("i", "identifier", true, "ONLY process bitstreams belonging to identifier");
+        options.addOption("i", "identifier", true,
+            "ONLY process bitstreams belonging to the provided handle identifier");
         options.addOption("m", "maximum", true, "process no more than maximum items");
         options.addOption("h", "help", false, "help");
 

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

@@ -132,12 +132,18 @@ public void applyFiltersAllItems(Context context) throws Exception {
     @Override
     public void applyFiltersCommunity(Context context, Community community)
         throws Exception {   //only apply filters if community not in skip-list
+        // ensure that the community is attached to the current hibernate session
+        // as we are committing after each item (handles, sub-communties and
+        // collections are lazy attributes)
+        community = context.reloadEntity(community);
         if (!inSkipList(community.getHandle())) {
             List<Community> subcommunities = community.getSubcommunities();
             for (Community subcommunity : subcommunities) {
                 applyFiltersCommunity(context, subcommunity);
             }
-
+            // ensure that the community is attached to the current hibernate session
+            // as we are committing after each item
+            community = context.reloadEntity(community);
             List<Collection> collections = community.getCollections();
             for (Collection collection : collections) {
                 applyFiltersCollection(context, collection);
@@ -148,6 +154,9 @@ public void applyFiltersCommunity(Context context, Community community)
     @Override
     public void applyFiltersCollection(Context context, Collection collection)
         throws Exception {
+        // ensure that the collection is attached to the current hibernate session
+        // as we are committing after each item (handles are lazy attributes)
+        collection = context.reloadEntity(collection);
         //only apply filters if collection not in skip-list
         if (!inSkipList(collection.getHandle())) {
             Iterator<Item> itemIterator = itemService.findAllByCollection(context, collection);
@@ -171,6 +180,8 @@ public void applyFiltersItem(Context c, Item item) throws Exception {
             }
             // clear item objects from context cache and internal cache
             c.uncacheEntity(currentItem);
+            // commit after each item to release DB resources
+            c.commit();
             currentItem = null;
         }
     }

dspace-api/src/main/java/org/dspace/app/suggestion/openaire/PublicationLoaderRunnable.java

@@ -12,6 +12,8 @@
 import java.util.List;
 
 import org.apache.commons.cli.ParseException;
+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.discovery.DiscoverQuery;
@@ -23,8 +25,6 @@
 import org.dspace.scripts.DSpaceRunnable;
 import org.dspace.sort.SortOption;
 import org.dspace.utils.DSpace;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
 
 /**
  * Runner responsible to import metadata about authors from OpenAIRE to Solr.
@@ -33,13 +33,13 @@
  * with this UUID will be used.
  * Invocation without any parameter results in massive import, processing all
  * authors registered in DSpace.
- * 
+ *
  * @author Alessandro Martelli (alessandro.martelli at 4science.it)
  */
 public class PublicationLoaderRunnable
     extends DSpaceRunnable<PublicationLoaderScriptConfiguration<PublicationLoaderRunnable>> {
 
-    private static final Logger LOGGER = LoggerFactory.getLogger(PublicationLoaderRunnable.class);
+    private static final Logger LOGGER = LogManager.getLogger();
 
     private PublicationLoader oairePublicationLoader = null;
 
@@ -63,9 +63,9 @@ public void setup() throws ParseException {
 
         profile = commandLine.getOptionValue("s");
         if (profile == null) {
-            LOGGER.info("No argument for -s, process all profile");
+            LOGGER.info("No argument for -s, process all profiles");
         } else {
-            LOGGER.info("Process eperson item with UUID " + profile);
+            LOGGER.info("Process eperson item with UUID {}", profile);
         }
     }
 
@@ -87,7 +87,7 @@ public void internalRun() throws Exception {
      * the researcher with this UUID will be chosen. If the uuid doesn't match any
      * researcher, the method returns an empty array list. If uuid is null, all
      * research will be return.
-     * 
+     *
      * @param  profileUUID uuid of the researcher. If null, all researcher will be
      *                     returned.
      * @return             the researcher with specified UUID or all researchers
@@ -96,10 +96,10 @@ public void internalRun() throws Exception {
     private Iterator<Item> getResearchers(String profileUUID) {
         SearchService searchService = new DSpace().getSingletonService(SearchService.class);
         DiscoverQueryBuilder queryBuilder = SearchUtils.getQueryBuilder();
-        List<QueryBuilderSearchFilter> filters = new ArrayList<QueryBuilderSearchFilter>();
+        List<QueryBuilderSearchFilter> filters = new ArrayList<>();
         String query = "*:*";
         if (profileUUID != null) {
-            query = "search.resourceid:" + profileUUID.toString();
+            query = "search.resourceid:" + profileUUID;
         }
         try {
             DiscoverQuery discoverQuery = queryBuilder.buildQuery(context, null,

dspace-api/src/main/java/org/dspace/app/util/AbstractDSpaceWebapp.java

@@ -12,13 +12,13 @@
 import java.sql.Timestamp;
 import java.util.Date;
 
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.dspace.app.util.factory.UtilServiceFactory;
 import org.dspace.app.util.service.WebAppService;
 import org.dspace.core.Context;
 import org.dspace.services.ConfigurationService;
 import org.dspace.services.factory.DSpaceServicesFactory;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
 
 /**
  * Represent a DSpace application while it is running.  This helps us report
@@ -29,11 +29,10 @@
  */
 abstract public class AbstractDSpaceWebapp
     implements DSpaceWebappMXBean {
-    private static final Logger log = LoggerFactory.getLogger(AbstractDSpaceWebapp.class);
+    private static final Logger log = LogManager.getLogger();
 
     protected final WebAppService webAppService = UtilServiceFactory.getInstance().getWebAppService();
 
-
     protected String kind;
 
     protected Date started;

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

@@ -16,10 +16,10 @@
 import javax.annotation.Nullable;
 
 import org.apache.commons.lang3.StringUtils;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.dspace.content.MetadataSchemaEnum;
 import org.dspace.core.Utils;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
 
 /**
  * Class representing a line in an input form.
@@ -28,7 +28,7 @@
  */
 public class DCInput {
 
-    private static final Logger log = LoggerFactory.getLogger(DCInput.class);
+    private static final Logger log = LogManager.getLogger();
 
     /**
      * the DC element name
@@ -183,7 +183,7 @@ public DCInput(Map<String, String> fieldMap, Map<String, List<String>> listMap)
         }
 
         //check if the input have a language tag
-        language = Boolean.valueOf(fieldMap.get("language"));
+        language = Boolean.parseBoolean(fieldMap.get("language"));
         valueLanguageList = new ArrayList<>();
         if (language) {
             String languageNameTmp = fieldMap.get("value-pairs-name");
@@ -219,7 +219,7 @@ public DCInput(Map<String, String> fieldMap, Map<String, List<String>> listMap)
             || "yes".equalsIgnoreCase(closedVocabularyStr);
 
         // parsing of the <type-bind> element (using the colon as split separator)
-        typeBind = new ArrayList<String>();
+        typeBind = new ArrayList<>();
         String typeBindDef = fieldMap.get("type-bind");
         if (typeBindDef != null && typeBindDef.trim().length() > 0) {
             String[] types = typeBindDef.split(",");
@@ -523,7 +523,7 @@ public boolean isClosedVocabulary() {
      * @return true when there is no type restriction or typeName is allowed
      */
     public boolean isAllowedFor(String typeName) {
-        if (typeBind.size() == 0) {
+        if (typeBind.isEmpty()) {
             return true;
         }
 

dspace-api/src/main/java/org/dspace/authenticate/AuthenticationServiceImpl.java

@@ -15,15 +15,15 @@
 import java.util.List;
 import javax.servlet.http.HttpServletRequest;
 
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.dspace.authenticate.service.AuthenticationService;
 import org.dspace.authorize.AuthorizeException;
 import org.dspace.core.Context;
 import org.dspace.core.factory.CoreServiceFactory;
 import org.dspace.eperson.EPerson;
 import org.dspace.eperson.Group;
 import org.dspace.eperson.service.EPersonService;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 
 /**
@@ -49,15 +49,14 @@
  * specified first (in the configuration) thus getting highest priority.
  *
  * @author Larry Stone
- * @version $Revision$
  * @see AuthenticationMethod
  */
 public class AuthenticationServiceImpl implements AuthenticationService {
 
     /**
-     * SLF4J logging category
+     * Logging category
      */
-    private final Logger log = (Logger) LoggerFactory.getLogger(AuthenticationServiceImpl.class);
+    private final Logger log = LogManager.getLogger();
 
     @Autowired(required = true)
     protected EPersonService ePersonService;
@@ -121,6 +120,7 @@ protected int authenticateInternal(Context context,
         return bestRet;
     }
 
+    @Override
     public void updateLastActiveDate(Context context) {
         EPerson me = context.getCurrentUser();
         if (me != null) {

dspace-api/src/main/java/org/dspace/authenticate/OidcAuthenticationBean.java

@@ -24,15 +24,15 @@
 import javax.servlet.http.HttpServletResponse;
 
 import org.apache.commons.lang3.StringUtils;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.dspace.authenticate.oidc.OidcClient;
 import org.dspace.authenticate.oidc.model.OidcTokenResponseDTO;
 import org.dspace.core.Context;
 import org.dspace.eperson.EPerson;
 import org.dspace.eperson.Group;
 import org.dspace.eperson.service.EPersonService;
 import org.dspace.services.ConfigurationService;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 
 /**
@@ -51,7 +51,7 @@ public class OidcAuthenticationBean implements AuthenticationMethod {
 
     private final static String LOGIN_PAGE_URL_FORMAT = "%s?client_id=%s&response_type=code&scope=%s&redirect_uri=%s";
 
-    private static final Logger LOGGER = LoggerFactory.getLogger(OidcAuthenticationBean.class);
+    private static final Logger LOGGER = LogManager.getLogger();
 
     private static final String OIDC_AUTHENTICATED = "oidc.authenticated";
 
@@ -174,7 +174,7 @@ public String loginPageURL(Context context, HttpServletRequest request, HttpServ
                 final Entry<String, String> entry = iterator.next();
 
                 if (isBlank(entry.getValue())) {
-                    LOGGER.error(" * {} is missing", entry.getKey());
+                    LOGGER.error(" * {} is missing", entry::getKey);
                 }
             }
             return "";
@@ -183,7 +183,7 @@ public String loginPageURL(Context context, HttpServletRequest request, HttpServ
         try {
             return format(LOGIN_PAGE_URL_FORMAT, authorizeUrl, clientId, scopes, encode(redirectUri, "UTF-8"));
         } catch (UnsupportedEncodingException e) {
-            LOGGER.error(e.getMessage(), e);
+            LOGGER.error(e::getMessage, e);
             return "";
         }