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

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Coar notify 7 part two merge main
This commit is contained in:
frabacche
2024-03-01 13:42:57 +01:00
committed by GitHub
parent 1bbe119435 3f8369e77c
commit e65d766f96
114 changed files with 1120 additions and 693 deletions
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18
dspace-api/src/main/java/org/dspace/administer/MetadataImporter.java
View File

@@ -21,6 +21,8 @@ import org.apache.commons.cli.CommandLineParser;
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.factory.ContentServiceFactory;
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 @@ import org.xml.sax.SAXException;
/**
* @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 @@ public class 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 class MetadataImporter {
* @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 @@ public class MetadataImporter {
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 @@ public class MetadataImporter {
// 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 @@ public class MetadataImporter {
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);
}

3
dspace-api/src/main/java/org/dspace/app/mediafilter/MediaFilterScriptConfiguration.java
View File

@@ -33,7 +33,8 @@ public class MediaFilterScriptConfiguration<T extends MediaFilterScript> extends
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");

13
dspace-api/src/main/java/org/dspace/app/mediafilter/MediaFilterServiceImpl.java
View File

@@ -132,12 +132,18 @@ public class MediaFilterServiceImpl implements MediaFilterService, InitializingB
@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 class MediaFilterServiceImpl implements MediaFilterService, InitializingB
@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 class MediaFilterServiceImpl implements MediaFilterService, InitializingB
}
// clear item objects from context cache and internal cache
c.uncacheEntity(currentItem);
// commit after each item to release DB resources
c.commit();
currentItem = null;
}
}

18
dspace-api/src/main/java/org/dspace/app/suggestion/openaire/PublicationLoaderRunnable.java
View File

@@ -12,6 +12,8 @@ import java.util.Iterator;
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.discovery.utils.parameter.QueryBuilderSearchFilter;
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 @@ import org.slf4j.LoggerFactory;
* 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 class PublicationLoaderRunnable
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 class PublicationLoaderRunnable
* 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 class PublicationLoaderRunnable
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,

7
dspace-api/src/main/java/org/dspace/app/util/AbstractDSpaceWebapp.java
View File

@@ -12,13 +12,13 @@ import java.sql.SQLException;
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 @@ import org.slf4j.LoggerFactory;
*/
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;

12
dspace-api/src/main/java/org/dspace/app/util/DCInput.java
View File

@@ -16,10 +16,10 @@ import java.util.regex.PatternSyntaxException;
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 @@ import org.slf4j.LoggerFactory;
*/
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 class DCInput {
}
//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 class DCInput {
|| "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 class DCInput {
* @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;
}

10
dspace-api/src/main/java/org/dspace/authenticate/AuthenticationServiceImpl.java
View File

@@ -15,6 +15,8 @@ import java.util.Iterator;
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;
@@ -22,8 +24,6 @@ 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 @@ import org.springframework.beans.factory.annotation.Autowired;
* 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 @@ public class AuthenticationServiceImpl implements AuthenticationService {
return bestRet;
}
@Override
public void updateLastActiveDate(Context context) {
EPerson me = context.getCurrentUser();
if (me != null) {

10
dspace-api/src/main/java/org/dspace/authenticate/OidcAuthenticationBean.java
View File

@@ -24,6 +24,8 @@ import javax.servlet.http.HttpServletRequest;
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;
@@ -31,8 +33,6 @@ 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 class OidcAuthenticationBean implements AuthenticationMethod {
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 class OidcAuthenticationBean implements AuthenticationMethod {
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 "";
}

9
dspace-api/src/main/java/org/dspace/authenticate/OrcidAuthenticationBean.java
View File

@@ -23,6 +23,8 @@ import javax.servlet.http.HttpServletResponse;
import org.apache.commons.collections4.CollectionUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.authorize.AuthorizeException;
import org.dspace.core.Context;
import org.dspace.eperson.EPerson;
@@ -39,8 +41,6 @@ import org.dspace.profile.service.ResearcherProfileService;
import org.dspace.services.ConfigurationService;
import org.orcid.jaxb.model.v3.release.record.Email;
import org.orcid.jaxb.model.v3.release.record.Person;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
/**
@@ -53,7 +53,7 @@ public class OrcidAuthenticationBean implements AuthenticationMethod {
public static final String ORCID_AUTH_ATTRIBUTE = "orcid-authentication";
private final static Logger LOGGER = LoggerFactory.getLogger(OrcidAuthenticationBean.class);
private final static Logger LOGGER = LogManager.getLogger();
private final static String LOGIN_PAGE_URL_FORMAT = "%s?client_id=%s&response_type=code&scope=%s&redirect_uri=%s";
@@ -282,7 +282,8 @@ public class OrcidAuthenticationBean implements AuthenticationMethod {
try {
return orcidClient.getPerson(token.getAccessToken(), token.getOrcid());
} catch (Exception ex) {
LOGGER.error("An error occurs retriving the ORCID record with id " + token.getOrcid(), ex);
LOGGER.error("An error occurs retriving the ORCID record with id {}",
token.getOrcid(), ex);
return null;
}
}

10
dspace-api/src/main/java/org/dspace/content/crosswalk/XSLTCrosswalk.java
View File

@@ -18,12 +18,12 @@ import javax.xml.transform.TransformerConfigurationException;
import javax.xml.transform.TransformerFactory;
import javax.xml.transform.stream.StreamSource;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.core.SelfNamedPlugin;
import org.dspace.services.ConfigurationService;
import org.dspace.services.factory.DSpaceServicesFactory;
import org.jdom2.Namespace;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/**
* Configurable XSLT-driven Crosswalk
@@ -88,7 +88,7 @@ public abstract class XSLTCrosswalk extends SelfNamedPlugin {
/**
* log4j category
*/
private static final Logger LOG = LoggerFactory.getLogger(XSLTCrosswalk.class);
private static final Logger LOG = LogManager.getLogger();
/**
* DSpace XML Namespace in JDOM form.
@@ -168,8 +168,8 @@ public abstract class XSLTCrosswalk extends SelfNamedPlugin {
transformFile.lastModified() > transformLastModified) {
try {
LOG.debug(
(transformer == null ? "Loading {} XSLT stylesheet from {}" : "Reloading {} XSLT stylesheet from " +
"{}"),
(transformer == null ? "Loading {} XSLT stylesheet from {}"
: "Reloading {} XSLT stylesheet from {}"),
getPluginInstanceName(), transformFile.toString());
Source transformSource

47
dspace-api/src/main/java/org/dspace/content/crosswalk/XSLTDisseminationCrosswalk.java
View File

@@ -23,6 +23,8 @@ import javax.xml.transform.Transformer;
import javax.xml.transform.TransformerException;
import org.apache.commons.lang3.ArrayUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.authorize.AuthorizeException;
import org.dspace.content.Collection;
import org.dspace.content.Community;
@@ -51,8 +53,6 @@ import org.jdom2.output.Format;
import org.jdom2.output.XMLOutputter;
import org.jdom2.transform.JDOMResult;
import org.jdom2.transform.JDOMSource;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/**
* Configurable XSLT-driven dissemination Crosswalk
@@ -88,7 +88,7 @@ public class XSLTDisseminationCrosswalk
/**
* log4j category
*/
private static final Logger LOG = LoggerFactory.getLogger(XSLTDisseminationCrosswalk.class);
private static final Logger LOG = LogManager.getLogger();
/**
* DSpace context, will be created if XSLTDisseminationCrosswalk had been started by command-line.
@@ -140,12 +140,13 @@ public class XSLTDisseminationCrosswalk
// right format for value of "schemaLocation" attribute.
schemaLocation = configurationService.getProperty(prefix + "schemaLocation");
if (schemaLocation == null) {
LOG.warn("No schemaLocation for crosswalk=" + myAlias + ", key=" + prefix + "schemaLocation");
LOG.warn("No schemaLocation for crosswalk={}, key={}schemaLocation", myAlias, prefix);
} else if (schemaLocation.length() > 0 && schemaLocation.indexOf(' ') < 0) {
// sanity check: schemaLocation should have space.
LOG.warn("Possible INVALID schemaLocation (no space found) for crosswalk=" +
myAlias + ", key=" + prefix + "schemaLocation" +
"\n\tCorrect format is \"{namespace} {schema-URL}\"");
LOG.warn("Possible INVALID schemaLocation (no space found) for crosswalk={},"
+ " key={}schemaLocation"
+ "\n\tCorrect format is \"{namespace} {schema-URL}\"",
myAlias, prefix);
}
// grovel for namespaces of the form:
@@ -172,7 +173,7 @@ public class XSLTDisseminationCrosswalk
try {
init();
} catch (CrosswalkInternalException e) {
LOG.error(e.toString());
LOG.error(e::toString);
}
return (Namespace[]) ArrayUtils.clone(namespaces);
}
@@ -187,7 +188,7 @@ public class XSLTDisseminationCrosswalk
try {
init();
} catch (CrosswalkInternalException e) {
LOG.error(e.toString());
LOG.error(e::toString);
}
return schemaLocation;
}
@@ -220,7 +221,7 @@ public class XSLTDisseminationCrosswalk
}
for (Map.Entry<String, String> parameter : parameters.entrySet()) {
LOG.debug("Setting parameter {} to {}", parameter.getKey(), parameter.getValue());
LOG.debug("Setting parameter {} to {}", parameter::getKey, parameter::getValue);
xform.setParameter(parameter.getKey(), parameter.getValue());
}
@@ -232,7 +233,7 @@ public class XSLTDisseminationCrosswalk
root.detach();
return root;
} catch (TransformerException e) {
LOG.error("Got error: " + e.toString());
LOG.error("Got error: ()", e::toString);
throw new CrosswalkInternalException("XSL translation failed: " + e.toString(), e);
}
}
@@ -278,13 +279,13 @@ public class XSLTDisseminationCrosswalk
.map(Element.class::cast).collect(Collectors.toList());
return elementList;
} catch (TransformerException e) {
LOG.error("Got error: " + e.toString());
LOG.error("Got error: {}", e::toString);
throw new CrosswalkInternalException("XSL translation failed: " + e.toString(), e);
}
}
/**
* Determine is this crosswalk can dessiminate the given object.
* Determine is this crosswalk can disseminate the given object.
*
* @see DisseminationCrosswalk
*/
@@ -304,7 +305,7 @@ public class XSLTDisseminationCrosswalk
try {
init();
} catch (CrosswalkInternalException e) {
LOG.error(e.toString());
LOG.error(e::toString);
}
return preferList;
}
@@ -312,7 +313,7 @@ public class XSLTDisseminationCrosswalk
/**
* Generate an intermediate representation of a DSpace object.
*
* @param dso The dspace object to build a representation of.
* @param dso The DSpace object to build a representation of.
* @param dcvs list of metadata
* @return element
*/
@@ -480,9 +481,7 @@ public class XSLTDisseminationCrosswalk
if (reason == null) {
return value;
} else {
if (LOG.isDebugEnabled()) {
LOG.debug("Filtering out non-XML characters in string, reason=" + reason);
}
LOG.debug("Filtering out non-XML characters in string, reason={}", reason);
StringBuilder result = new StringBuilder(value.length());
for (int i = 0; i < value.length(); ++i) {
char c = value.charAt(i);
@@ -567,11 +566,11 @@ public class XSLTDisseminationCrosswalk
System.err.println("=== Stack Trace ===");
e.printStackTrace(System.err);
System.err.println("=====================");
LOG.error("Caught: {}.", e.toString());
LOG.error(e.getMessage());
LOG.error("Caught: {}.", e::toString);
LOG.error(e::getMessage);
CharArrayWriter traceWriter = new CharArrayWriter(2048);
e.printStackTrace(new PrintWriter(traceWriter));
LOG.error(traceWriter.toString());
LOG.error(traceWriter::toString);
System.exit(1);
}
@@ -588,11 +587,11 @@ public class XSLTDisseminationCrosswalk
System.err.println("=== Stack Trace ===");
e.printStackTrace(System.err);
System.err.println("=====================");
LOG.error("Caught: {}.", e.toString());
LOG.error(e.getMessage());
LOG.error("Caught: {}.", e::toString);
LOG.error(e::getMessage);
CharArrayWriter traceWriter = new CharArrayWriter(2048);
e.printStackTrace(new PrintWriter(traceWriter));
LOG.error(traceWriter.toString());
LOG.error(traceWriter::toString);
System.exit(1);
}

29
dspace-api/src/main/java/org/dspace/content/dao/impl/BitstreamDAOImpl.java
View File

@@ -12,6 +12,7 @@ import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.UUID;
import javax.persistence.Query;
import javax.persistence.criteria.CriteriaBuilder;
import javax.persistence.criteria.CriteriaQuery;
@@ -26,6 +27,7 @@ import org.dspace.content.dao.BitstreamDAO;
import org.dspace.core.AbstractHibernateDSODAO;
import org.dspace.core.Constants;
import org.dspace.core.Context;
import org.dspace.core.UUIDIterator;
/**
* Hibernate implementation of the Database Access Object interface class for the Bitstream object.
@@ -76,7 +78,7 @@ public class BitstreamDAOImpl extends AbstractHibernateDSODAO<Bitstream> impleme
@Override
public Iterator<Bitstream> findByCommunity(Context context, Community community) throws SQLException {
Query query = createQuery(context, "select b from Bitstream b " +
Query query = createQuery(context, "select b.id from Bitstream b " +
"join b.bundles bitBundles " +
"join bitBundles.items item " +
"join item.collections itemColl " +
@@ -84,40 +86,45 @@ public class BitstreamDAOImpl extends AbstractHibernateDSODAO<Bitstream> impleme
"WHERE :community IN community");
query.setParameter("community", community);
return iterate(query);
@SuppressWarnings("unchecked")
List<UUID> uuids = query.getResultList();
return new UUIDIterator<Bitstream>(context, uuids, Bitstream.class, this);
}
@Override
public Iterator<Bitstream> findByCollection(Context context, Collection collection) throws SQLException {
Query query = createQuery(context, "select b from Bitstream b " +
Query query = createQuery(context, "select b.id from Bitstream b " +
"join b.bundles bitBundles " +
"join bitBundles.items item " +
"join item.collections c " +
"WHERE :collection IN c");
query.setParameter("collection", collection);
return iterate(query);
@SuppressWarnings("unchecked")
List<UUID> uuids = query.getResultList();
return new UUIDIterator<Bitstream>(context, uuids, Bitstream.class, this);
}
@Override
public Iterator<Bitstream> findByItem(Context context, Item item) throws SQLException {
Query query = createQuery(context, "select b from Bitstream b " +
Query query = createQuery(context, "select b.id from Bitstream b " +
"join b.bundles bitBundles " +
"join bitBundles.items item " +
"WHERE :item IN item");
query.setParameter("item", item);
return iterate(query);
@SuppressWarnings("unchecked")
List<UUID> uuids = query.getResultList();
return new UUIDIterator<Bitstream>(context, uuids, Bitstream.class, this);
}
@Override
public Iterator<Bitstream> findByStoreNumber(Context context, Integer storeNumber) throws SQLException {
Query query = createQuery(context, "select b from Bitstream b where b.storeNumber = :storeNumber");
Query query = createQuery(context, "select b.id from Bitstream b where b.storeNumber = :storeNumber");
query.setParameter("storeNumber", storeNumber);
return iterate(query);
@SuppressWarnings("unchecked")
List<UUID> uuids = query.getResultList();
return new UUIDIterator<Bitstream>(context, uuids, Bitstream.class, this);
}
@Override

87
dspace-api/src/main/java/org/dspace/content/dao/impl/ItemDAOImpl.java
View File

@@ -36,6 +36,7 @@ import org.dspace.contentreport.QueryOperator;
import org.dspace.contentreport.QueryPredicate;
import org.dspace.core.AbstractHibernateDSODAO;
import org.dspace.core.Context;
import org.dspace.core.UUIDIterator;
import org.dspace.eperson.EPerson;
import org.dspace.util.JpaCriteriaBuilderKit;
@@ -54,28 +55,34 @@ public class ItemDAOImpl extends AbstractHibernateDSODAO<Item> implements ItemDA
@Override
public Iterator<Item> findAll(Context context, boolean archived) throws SQLException {
Query query = createQuery(context, "FROM Item WHERE inArchive=:in_archive ORDER BY id");
Query query = createQuery(context, "SELECT i.id FROM Item i WHERE inArchive=:in_archive ORDER BY id");
query.setParameter("in_archive", archived);
return iterate(query);
@SuppressWarnings("unchecked")
List<UUID> uuids = query.getResultList();
return new UUIDIterator<Item>(context, uuids, Item.class, this);
}
@Override
public Iterator<Item> findAll(Context context, boolean archived, int limit, int offset) throws SQLException {
Query query = createQuery(context, "FROM Item WHERE inArchive=:in_archive ORDER BY id");
Query query = createQuery(context, "SELECT i.id FROM Item i WHERE inArchive=:in_archive ORDER BY id");
query.setParameter("in_archive", archived);
query.setFirstResult(offset);
query.setMaxResults(limit);
return iterate(query);
@SuppressWarnings("unchecked")
List<UUID> uuids = query.getResultList();
return new UUIDIterator<Item>(context, uuids, Item.class, this);
}
@Override
public Iterator<Item> findAll(Context context, boolean archived, boolean withdrawn) throws SQLException {
Query query = createQuery(context,
"FROM Item WHERE inArchive=:in_archive or withdrawn=:withdrawn ORDER BY id");
"SELECT i.id FROM Item i WHERE inArchive=:in_archive or withdrawn=:withdrawn ORDER BY id");
query.setParameter("in_archive", archived);
query.setParameter("withdrawn", withdrawn);
return iterate(query);
@SuppressWarnings("unchecked")
List<UUID> uuids = query.getResultList();
return new UUIDIterator<Item>(context, uuids, Item.class, this);
}
@Override
@@ -84,12 +91,14 @@ public class ItemDAOImpl extends AbstractHibernateDSODAO<Item> implements ItemDA
// It does not include workspace, workflow or template items.
Query query = createQuery(
context,
"SELECT i FROM Item as i " +
"SELECT i.id FROM Item as i " +
"LEFT JOIN Version as v ON i = v.item " +
"WHERE i.inArchive=true or i.withdrawn=true or (i.inArchive=false and v.id IS NOT NULL) " +
"ORDER BY i.id"
);
return iterate(query);
@SuppressWarnings("unchecked")
List<UUID> uuids = query.getResultList();
return new UUIDIterator<Item>(context, uuids, Item.class, this);
}
@Override
@@ -97,7 +106,7 @@ public class ItemDAOImpl extends AbstractHibernateDSODAO<Item> implements ItemDA
boolean withdrawn, boolean discoverable, Date lastModified)
throws SQLException {
StringBuilder queryStr = new StringBuilder();
queryStr.append("SELECT i FROM Item i");
queryStr.append("SELECT i.id FROM Item i");
queryStr.append(" WHERE (inArchive = :in_archive OR withdrawn = :withdrawn)");
queryStr.append(" AND discoverable = :discoverable");
@@ -113,16 +122,20 @@ public class ItemDAOImpl extends AbstractHibernateDSODAO<Item> implements ItemDA
if (lastModified != null) {
query.setParameter("last_modified", lastModified, TemporalType.TIMESTAMP);
}
return iterate(query);
@SuppressWarnings("unchecked")
List<UUID> uuids = query.getResultList();
return new UUIDIterator<Item>(context, uuids, Item.class, this);
}
@Override
public Iterator<Item> findBySubmitter(Context context, EPerson eperson) throws SQLException {
Query query = createQuery(context,
"FROM Item WHERE inArchive=:in_archive and submitter=:submitter ORDER BY id");
"SELECT i.id FROM Item i WHERE inArchive=:in_archive and submitter=:submitter ORDER BY id");
query.setParameter("in_archive", true);
query.setParameter("submitter", eperson);
return iterate(query);
@SuppressWarnings("unchecked")
List<UUID> uuids = query.getResultList();
return new UUIDIterator<Item>(context, uuids, Item.class, this);
}
@Override
@@ -131,16 +144,18 @@ public class ItemDAOImpl extends AbstractHibernateDSODAO<Item> implements ItemDA
if (!retrieveAllItems) {
return findBySubmitter(context, eperson);
}
Query query = createQuery(context, "FROM Item WHERE submitter=:submitter ORDER BY id");
Query query = createQuery(context, "SELECT i.id FROM Item i WHERE submitter=:submitter ORDER BY id");
query.setParameter("submitter", eperson);
return iterate(query);
@SuppressWarnings("unchecked")
List<UUID> uuids = query.getResultList();
return new UUIDIterator<Item>(context, uuids, Item.class, this);
}
@Override
public Iterator<Item> findBySubmitter(Context context, EPerson eperson, MetadataField metadataField, int limit)
throws SQLException {
StringBuilder query = new StringBuilder();
query.append("SELECT item FROM Item as item ");
query.append("SELECT item.id FROM Item as item ");
addMetadataLeftJoin(query, Item.class.getSimpleName().toLowerCase(), Collections.singletonList(metadataField));
query.append(" WHERE item.inArchive = :in_archive");
query.append(" AND item.submitter =:submitter");
@@ -152,13 +167,15 @@ public class ItemDAOImpl extends AbstractHibernateDSODAO<Item> implements ItemDA
hibernateQuery.setParameter("in_archive", true);
hibernateQuery.setParameter("submitter", eperson);
hibernateQuery.setMaxResults(limit);
return iterate(hibernateQuery);
@SuppressWarnings("unchecked")
List<UUID> uuids = hibernateQuery.getResultList();
return new UUIDIterator<Item>(context, uuids, Item.class, this);
}
@Override
public Iterator<Item> findByMetadataField(Context context, MetadataField metadataField, String value,
boolean inArchive) throws SQLException {
String hqlQueryString = "SELECT item FROM Item as item join item.metadata metadatavalue " +
String hqlQueryString = "SELECT item.id FROM Item as item join item.metadata metadatavalue " +
"WHERE item.inArchive=:in_archive AND metadatavalue.metadataField = :metadata_field";
if (value != null) {
hqlQueryString += " AND STR(metadatavalue.value) = :text_value";
@@ -170,7 +187,9 @@ public class ItemDAOImpl extends AbstractHibernateDSODAO<Item> implements ItemDA
if (value != null) {
query.setParameter("text_value", value);
}
return iterate(query);
@SuppressWarnings("unchecked")
List<UUID> uuids = query.getResultList();
return new UUIDIterator<Item>(context, uuids, Item.class, this);
}
@Override
@@ -276,20 +295,22 @@ public class ItemDAOImpl extends AbstractHibernateDSODAO<Item> implements ItemDA
public Iterator<Item> findByAuthorityValue(Context context, MetadataField metadataField, String authority,
boolean inArchive) throws SQLException {
Query query = createQuery(context,
"SELECT item FROM Item as item join item.metadata metadatavalue " +
"SELECT item.id FROM Item as item join item.metadata metadatavalue " +
"WHERE item.inArchive=:in_archive AND metadatavalue.metadataField = :metadata_field AND " +
"metadatavalue.authority = :authority ORDER BY item.id");
query.setParameter("in_archive", inArchive);
query.setParameter("metadata_field", metadataField);
query.setParameter("authority", authority);
return iterate(query);
@SuppressWarnings("unchecked")
List<UUID> uuids = query.getResultList();
return new UUIDIterator<Item>(context, uuids, Item.class, this);
}
@Override
public Iterator<Item> findArchivedByCollection(Context context, Collection collection, Integer limit,
Integer offset) throws SQLException {
Query query = createQuery(context,
"select i from Item i join i.collections c " +
"select i.id from Item i join i.collections c " +
"WHERE :collection IN c AND i.inArchive=:in_archive ORDER BY i.id");
query.setParameter("collection", collection);
query.setParameter("in_archive", true);
@@ -299,7 +320,9 @@ public class ItemDAOImpl extends AbstractHibernateDSODAO<Item> implements ItemDA
if (limit != null) {
query.setMaxResults(limit);
}
return iterate(query);
@SuppressWarnings("unchecked")
List<UUID> uuids = query.getResultList();
return new UUIDIterator<Item>(context, uuids, Item.class, this);
}
@Override
@@ -334,17 +357,18 @@ public class ItemDAOImpl extends AbstractHibernateDSODAO<Item> implements ItemDA
@Override
public Iterator<Item> findAllByCollection(Context context, Collection collection) throws SQLException {
Query query = createQuery(context,
"select i from Item i join i.collections c WHERE :collection IN c ORDER BY i.id");
"select i.id from Item i join i.collections c WHERE :collection IN c ORDER BY i.id");
query.setParameter("collection", collection);
return iterate(query);
@SuppressWarnings("unchecked")
List<UUID> uuids = query.getResultList();
return new UUIDIterator<Item>(context, uuids, Item.class, this);
}
@Override
public Iterator<Item> findAllByCollection(Context context, Collection collection, Integer limit, Integer offset)
throws SQLException {
Query query = createQuery(context,
"select i from Item i join i.collections c WHERE :collection IN c ORDER BY i.id");
"select i.id from Item i join i.collections c WHERE :collection IN c ORDER BY i.id");
query.setParameter("collection", collection);
if (offset != null) {
@@ -353,8 +377,9 @@ public class ItemDAOImpl extends AbstractHibernateDSODAO<Item> implements ItemDA
if (limit != null) {
query.setMaxResults(limit);
}
return iterate(query);
@SuppressWarnings("unchecked")
List<UUID> uuids = query.getResultList();
return new UUIDIterator<Item>(context, uuids, Item.class, this);
}
@Override
@@ -390,9 +415,11 @@ public class ItemDAOImpl extends AbstractHibernateDSODAO<Item> implements ItemDA
public Iterator<Item> findByLastModifiedSince(Context context, Date since)
throws SQLException {
Query query = createQuery(context,
"SELECT i FROM Item i WHERE last_modified > :last_modified ORDER BY id");
"SELECT i.id FROM Item i WHERE last_modified > :last_modified ORDER BY id");
query.setParameter("last_modified", since, TemporalType.TIMESTAMP);
return iterate(query);
@SuppressWarnings("unchecked")
List<UUID> uuids = query.getResultList();
return new UUIDIterator<Item>(context, uuids, Item.class, this);
}
@Override

13
dspace-api/src/main/java/org/dspace/content/packager/RoleIngester.java
View File

@@ -19,6 +19,8 @@ import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.parsers.ParserConfigurationException;
import org.apache.commons.codec.DecoderException;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.authorize.AuthorizeException;
import org.dspace.content.Collection;
import org.dspace.content.Community;
@@ -36,8 +38,6 @@ import org.dspace.eperson.PasswordHash;
import org.dspace.eperson.factory.EPersonServiceFactory;
import org.dspace.eperson.service.EPersonService;
import org.dspace.eperson.service.GroupService;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.w3c.dom.NamedNodeMap;
@@ -51,8 +51,7 @@ import org.xml.sax.SAXException;
* @author mwood
*/
public class RoleIngester implements PackageIngester {
private static final Logger log = LoggerFactory
.getLogger(RoleIngester.class);
private static final Logger log = LogManager.getLogger();
protected CommunityService communityService = ContentServiceFactory.getInstance().getCommunityService();
protected CollectionService collectionService = ContentServiceFactory.getInstance().getCollectionService();
@@ -217,10 +216,10 @@ public class RoleIngester implements PackageIngester {
// Community or Collection that doesn't currently exist in the
// system. So, log a warning & skip it for now.
log.warn(
"Skipping group named '" + name + "' as it seems to correspond to a Community or Collection that " +
"Skipping group named '{}' as it seems to correspond to a Community or Collection that " +
"does not exist in the system. " +
"If you are performing an AIP restore, you can ignore this warning as the " +
"Community/Collection AIP will likely create this group once it is processed.");
"Community/Collection AIP will likely create this group once it is processed.", name);
continue;
}
log.debug("Translated group name: {}", name);
@@ -307,7 +306,7 @@ public class RoleIngester implements PackageIngester {
// Always set the name: parent.createBlop() is guessing
groupService.setName(groupObj, name);
log.info("Created Group {}.", groupObj.getName());
log.info("Created Group {}.", groupObj::getName);
}
// Add EPeople to newly created Group

29
dspace-api/src/main/java/org/dspace/contentreport/QueryOperator.java
View File

@@ -8,7 +8,6 @@
package org.dspace.contentreport;
import java.util.Arrays;
import java.util.function.BiFunction;
import javax.persistence.criteria.CriteriaBuilder;
import javax.persistence.criteria.Expression;
import javax.persistence.criteria.Path;
@@ -21,10 +20,6 @@ import org.dspace.content.MetadataValue;
import org.dspace.content.MetadataValue_;
import org.dspace.util.DSpacePostgreSQLDialect;
import org.dspace.util.JpaCriteriaBuilderKit;
import org.hibernate.criterion.Criterion;
import org.hibernate.criterion.Property;
import org.hibernate.criterion.Restrictions;
import org.hibernate.type.StandardBasicTypes;
/**
* Operators available for creating predicates to query the
@@ -34,52 +29,36 @@ import org.hibernate.type.StandardBasicTypes;
public enum QueryOperator {
EXISTS("exists", true, false,
(val, regexClause) -> Property.forName("mv.value").isNotNull(),
(val, regexClause, jpaKit) -> jpaKit.criteriaBuilder().isNotNull(jpaKit.root().get(MetadataValue_.VALUE))),
DOES_NOT_EXIST("doesnt_exist", true, true,
(val, regexClause) -> EXISTS.buildPredicate(val, regexClause),
(val, regexClause, jpaKit) -> EXISTS.buildJpaPredicate(val, regexClause, jpaKit)),
EQUALS("equals", true, false,
(val, regexClause) -> Property.forName("mv.value").eq(val),
(val, regexClause, jpaKit) -> jpaKit.criteriaBuilder().equal(jpaKit.root().get(MetadataValue_.VALUE), val)),
DOES_NOT_EQUAL("not_equals", true, true,
(val, regexClause) -> EQUALS.buildPredicate(val, regexClause),
(val, regexClause, jpaKit) -> EQUALS.buildJpaPredicate(val, regexClause, jpaKit)),
LIKE("like", true, false,
(val, regexClause) -> Property.forName("mv.value").like(val),
(val, regexClause, jpaKit) -> jpaKit.criteriaBuilder().like(jpaKit.root().get(MetadataValue_.VALUE), val)),
NOT_LIKE("not_like", true, true,
(val, regexClause) -> LIKE.buildPredicate(val, regexClause),
(val, regexClause, jpaKit) -> LIKE.buildJpaPredicate(val, regexClause, jpaKit)),
CONTAINS("contains", true, false,
(val, regexClause) -> Property.forName("mv.value").like("%" + val + "%"),
(val, regexClause, jpaKit) -> LIKE.buildJpaPredicate("%" + val + "%", regexClause, jpaKit)),
DOES_NOT_CONTAIN("doesnt_contain", true, true,
(val, regexClause) -> CONTAINS.buildPredicate(val, regexClause),
(val, regexClause, jpaKit) -> CONTAINS.buildJpaPredicate(val, regexClause, jpaKit)),
MATCHES("matches", false, false,
(val, regexClause) -> Restrictions.sqlRestriction(regexClause, val, StandardBasicTypes.STRING),
(val, regexClause, jpaKit) -> regexPredicate(val, DSpacePostgreSQLDialect.REGEX_MATCHES, jpaKit)),
DOES_NOT_MATCH("doesnt_match", false, false,
(val, regexClause) -> Restrictions.not(Restrictions.sqlRestriction(
regexClause, val, StandardBasicTypes.STRING)),
(val, regexClause, jpaKit) -> regexPredicate(val, DSpacePostgreSQLDialect.REGEX_NOT_MATCHES, jpaKit));
private final String code;
/** Criteria builder for the old Hibernate API */
@Deprecated(forRemoval = true)
private final BiFunction<String, String, Criterion> criterionBuilder;
private final TriFunction<String, String, JpaCriteriaBuilderKit<MetadataValue>, Predicate> predicateBuilder;
private final boolean usesRegex;
private final boolean negate;
QueryOperator(String code, boolean usesRegex, boolean negate,
BiFunction<String, String, Criterion> criterionBuilder,
TriFunction<String, String, JpaCriteriaBuilderKit<MetadataValue>, Predicate> predicateBuilder) {
this.code = code;
this.usesRegex = usesRegex;
this.negate = negate;
this.criterionBuilder = criterionBuilder;
this.predicateBuilder = predicateBuilder;
}
@@ -96,10 +75,6 @@ public enum QueryOperator {
return negate;
}
public Criterion buildPredicate(String val, String regexClause) {
return criterionBuilder.apply(val, regexClause);
}
public Predicate buildJpaPredicate(String val, String regexClause, JpaCriteriaBuilderKit<MetadataValue> jpaKit) {
return predicateBuilder.apply(val, regexClause, jpaKit);
}
@@ -112,10 +87,6 @@ public enum QueryOperator {
.orElse(null);
}
public BiFunction<String, String, Criterion> getCriterionBuilder() {
return criterionBuilder;
}
private static Predicate regexPredicate(String val, String regexFunction,
JpaCriteriaBuilderKit<MetadataValue> jpaKit) {
// Source: https://stackoverflow.com/questions/24995881/use-regular-expressions-in-jpa-criteriabuilder

10
dspace-api/src/main/java/org/dspace/core/LicenseServiceImpl.java
View File

@@ -19,12 +19,12 @@ import java.io.OutputStreamWriter;
import java.io.PrintWriter;
import javax.servlet.http.HttpServletRequest;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.core.service.LicenseService;
import org.dspace.services.factory.DSpaceServicesFactory;
import org.dspace.services.model.Request;
import org.dspace.web.ContextUtil;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/**
* Encapsulate the deposit license.
@@ -32,7 +32,7 @@ import org.slf4j.LoggerFactory;
* @author mhwood
*/
public class LicenseServiceImpl implements LicenseService {
private final Logger log = LoggerFactory.getLogger(LicenseServiceImpl.class);
private final Logger log = LogManager.getLogger();
/**
* The default license
@@ -53,7 +53,7 @@ public class LicenseServiceImpl implements LicenseService {
out.print(newLicense);
out.close();
} catch (IOException e) {
log.warn("license_write: " + e.getLocalizedMessage());
log.warn("license_write: {}", e::getLocalizedMessage);
}
license = newLicense;
}
@@ -140,7 +140,7 @@ public class LicenseServiceImpl implements LicenseService {
br.close();
} catch (IOException e) {
log.error("Can't load license: " + licenseFile.toString(), e);
log.error("Can't load license {}: ", licenseFile.toString(), e);
// FIXME: Maybe something more graceful here, but with the
// configuration we can't do anything

10
dspace-api/src/main/java/org/dspace/core/NewsServiceImpl.java
View File

@@ -19,11 +19,11 @@ import java.io.PrintWriter;
import java.util.ArrayList;
import java.util.List;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.core.service.NewsService;
import org.dspace.services.ConfigurationService;
import org.dspace.services.factory.DSpaceServicesFactory;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
/**
@@ -32,7 +32,7 @@ import org.springframework.beans.factory.annotation.Autowired;
* @author mhwood
*/
public class NewsServiceImpl implements NewsService {
private final Logger log = LoggerFactory.getLogger(NewsServiceImpl.class);
private final Logger log = LogManager.getLogger();
private List<String> acceptableFilenames;
@@ -94,7 +94,7 @@ public class NewsServiceImpl implements NewsService {
ir.close();
fir.close();
} catch (IOException e) {
log.warn("news_read: " + e.getLocalizedMessage());
log.warn("news_read: {}", e::getLocalizedMessage);
}
return text.toString();
@@ -117,7 +117,7 @@ public class NewsServiceImpl implements NewsService {
out.print(news);
out.close();
} catch (IOException e) {
log.warn("news_write: " + e.getLocalizedMessage());
log.warn("news_write: {}", e::getLocalizedMessage);
}
return news;

63
dspace-api/src/main/java/org/dspace/core/UUIDIterator.java Normal file
View File

@@ -0,0 +1,63 @@
/**
* 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.core;
import java.sql.SQLException;
import java.util.Iterator;
import java.util.List;
import java.util.UUID;
import com.google.common.collect.AbstractIterator;
import org.dspace.content.DSpaceObject;
import org.springframework.beans.factory.annotation.Autowired;
/**
* Iterator implementation which allows to iterate over items and commit while
* iterating. Using an iterator over previous retrieved UUIDs the iterator doesn't
* get invalidated after a commit that would instead close the database ResultSet
*
* @author Andrea Bollini (andrea.bollini at 4science.com)
* @param <T> class type
*/
public class UUIDIterator<T extends DSpaceObject> extends AbstractIterator<T> {
private Class<T> clazz;
private Iterator<UUID> iterator;
@Autowired
private AbstractHibernateDSODAO<T> dao;
private Context ctx;
public UUIDIterator(Context ctx, List<UUID> uuids, Class<T> clazz, AbstractHibernateDSODAO<T> dao)
throws SQLException {
this.ctx = ctx;
this.clazz = clazz;
this.dao = dao;
this.iterator = uuids.iterator();
}
@Override
protected T computeNext() {
try {
if (iterator.hasNext()) {
T item = dao.findByID(ctx, clazz, iterator.next());
if (item != null) {
return item;
} else {
return computeNext();
}
} else {
return endOfData();
}
} catch (SQLException e) {
throw new RuntimeException(e);
}
}
}

14
dspace-api/src/main/java/org/dspace/ctask/general/ClamScan.java
View File

@@ -19,6 +19,8 @@ import java.sql.SQLException;
import java.util.ArrayList;
import java.util.List;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.authorize.AuthorizeException;
import org.dspace.content.Bitstream;
import org.dspace.content.Bundle;
@@ -29,8 +31,6 @@ import org.dspace.content.service.BitstreamService;
import org.dspace.curate.AbstractCurationTask;
import org.dspace.curate.Curator;
import org.dspace.curate.Suspendable;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/**
* ClamScan.java
@@ -58,7 +58,7 @@ public class ClamScan extends AbstractCurationTask {
protected final String SCAN_FAIL_MESSAGE = "Error encountered using virus service - check setup";
protected final String NEW_ITEM_HANDLE = "in workflow";
private static final Logger log = LoggerFactory.getLogger(ClamScan.class);
private static final Logger log = LogManager.getLogger();
protected String host = null;
protected int port = 0;
@@ -100,7 +100,7 @@ public class ClamScan extends AbstractCurationTask {
try {
Bundle bundle = itemService.getBundles(item, "ORIGINAL").get(0);
results = new ArrayList<String>();
results = new ArrayList<>();
for (Bitstream bitstream : bundle.getBitstreams()) {
InputStream inputstream = bitstreamService.retrieve(Curator.curationContext(), bitstream);
logDebugMessage("Scanning " + bitstream.getName() + " . . . ");
@@ -157,7 +157,7 @@ public class ClamScan extends AbstractCurationTask {
try {
socket.setSoTimeout(timeout);
} catch (SocketException e) {
log.error("Could not set socket timeout . . . " + timeout + "ms", e);
log.error("Could not set socket timeout . . . {}ms", timeout, e);
throw (new IOException(e));
}
try {
@@ -293,8 +293,6 @@ public class ClamScan extends AbstractCurationTask {
protected void logDebugMessage(String message) {
if (log.isDebugEnabled()) {
log.debug(message);
}
log.debug(message);
}
}

8
dspace-api/src/main/java/org/dspace/ctask/test/WorkflowReportTest.java
View File

@@ -10,11 +10,11 @@ package org.dspace.ctask.test;
import java.io.IOException;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.content.DSpaceObject;
import org.dspace.curate.AbstractCurationTask;
import org.dspace.curate.Curator;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/**
* Curation task which simply reports its invocation without changing anything.
@@ -24,13 +24,13 @@ import org.slf4j.LoggerFactory;
*/
public class WorkflowReportTest
extends AbstractCurationTask {
private static final Logger LOG = LoggerFactory.getLogger(WorkflowReportTest.class);
private static final Logger LOG = LogManager.getLogger();
@Override
public int perform(DSpaceObject dso)
throws IOException {
LOG.info("Class {} as task {} received 'perform' for object {}",
WorkflowReportTest.class.getSimpleName(), taskId, dso);
WorkflowReportTest.class::getSimpleName, () -> taskId, () -> dso);
curator.report(String.format(
"Class %s as task %s received 'perform' for object %s%n",
WorkflowReportTest.class.getSimpleName(), taskId, dso));

7
dspace-api/src/main/java/org/dspace/ctask/testing/PropertyParameterTestingTask.java
View File

@@ -10,12 +10,12 @@ package org.dspace.ctask.testing;
import java.io.IOException;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.content.DSpaceObject;
import org.dspace.core.Context;
import org.dspace.curate.AbstractCurationTask;
import org.dspace.curate.Curator;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/**
* Logs what it was asked to do, samples run parameters and task
@@ -32,8 +32,7 @@ import org.slf4j.LoggerFactory;
*/
public class PropertyParameterTestingTask
extends AbstractCurationTask {
private static final Logger LOG
= LoggerFactory.getLogger(PropertyParameterTestingTask.class);
private static final Logger LOG = LogManager.getLogger();
@Override
public void init(Curator curator, String taskId)

10
dspace-api/src/main/java/org/dspace/curate/LogReporter.java
View File

@@ -10,8 +10,8 @@ package org.dspace.curate;
import java.io.IOException;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
/**
* Write curation report records through the logging framework.
@@ -22,7 +22,7 @@ import org.slf4j.LoggerFactory;
*/
public class LogReporter
implements Reporter {
private static final Logger LOG = LoggerFactory.getLogger("curation");
private static final Logger LOG = LogManager.getLogger("curation");
private final StringBuilder buffer = new StringBuilder();
@Override
@@ -31,7 +31,7 @@ public class LogReporter
for (int pos = 0; pos < cs.length(); pos++) {
char c = cs.charAt(pos);
if (c == '\n') {
LOG.info(buffer.toString());
LOG.info(buffer::toString);
buffer.delete(0, buffer.length()); // Clear the buffer
} else {
buffer.append(c);
@@ -56,7 +56,7 @@ public class LogReporter
public void close()
throws Exception {
if (buffer.length() > 0) {
LOG.info(buffer.toString());
LOG.info(buffer::toString);
}
}
}

12
dspace-api/src/main/java/org/dspace/eperson/PasswordHash.java
View File

@@ -16,10 +16,10 @@ import java.util.Arrays;
import org.apache.commons.codec.DecoderException;
import org.apache.commons.codec.binary.Hex;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.services.ConfigurationService;
import org.dspace.services.factory.DSpaceServicesFactory;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/**
* For handling digested secrets (such as passwords).
@@ -31,7 +31,7 @@ import org.slf4j.LoggerFactory;
* @author mwood
*/
public class PasswordHash {
private static final Logger log = LoggerFactory.getLogger(PasswordHash.class);
private static final Logger log = LogManager.getLogger();
private static final ConfigurationService config
= DSpaceServicesFactory.getInstance().getConfigurationService();
private static final Charset UTF_8 = Charset.forName("UTF-8"); // Should always succeed: UTF-8 is required
@@ -133,7 +133,7 @@ public class PasswordHash {
try {
hash = digest(salt, algorithm, password);
} catch (NoSuchAlgorithmException e) {
log.error(e.getMessage());
log.error(e::getMessage);
hash = new byte[] {0};
}
}
@@ -149,7 +149,7 @@ public class PasswordHash {
try {
candidate = digest(salt, algorithm, secret);
} catch (NoSuchAlgorithmException e) {
log.error(e.getMessage());
log.error(e::getMessage);
return false;
}
return Arrays.equals(candidate, hash);
@@ -225,7 +225,7 @@ public class PasswordHash {
if (null == rng) {
rng = new SecureRandom();
log.info("Initialized a random number stream using {} provided by {}",
rng.getAlgorithm(), rng.getProvider());
rng::getAlgorithm, rng::getProvider);
rngUses = 0;
}

11
dspace-api/src/main/java/org/dspace/external/provider/impl/OrcidPublicationDataProvider.java vendored
View File

@@ -28,6 +28,8 @@ import org.apache.commons.collections.CollectionUtils;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.math.NumberUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.content.Item;
import org.dspace.content.MetadataFieldName;
import org.dspace.content.dto.MetadataValueDTO;
@@ -63,13 +65,11 @@ import org.orcid.jaxb.model.v3.release.record.WorkTitle;
import org.orcid.jaxb.model.v3.release.record.summary.WorkGroup;
import org.orcid.jaxb.model.v3.release.record.summary.WorkSummary;
import org.orcid.jaxb.model.v3.release.record.summary.Works;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
/**
* Implementation of {@link ExternalDataProvider} that search for all the works
* of the profile with the given orcid id that hava a source other than DSpace.
* of the profile with the given orcid id that have a source other than DSpace.
* The id of the external data objects returned by the methods of this class is
* the concatenation of the orcid id and the put code associated with the
* publication, separated by :: (example 0000-0000-0123-4567::123456)
@@ -79,7 +79,7 @@ import org.springframework.beans.factory.annotation.Autowired;
*/
public class OrcidPublicationDataProvider extends AbstractExternalDataProvider {
private final static Logger LOGGER = LoggerFactory.getLogger(OrcidPublicationDataProvider.class);
private final static Logger LOGGER = LogManager.getLogger();
/**
* Examples of valid ORCID IDs:
@@ -335,7 +335,8 @@ public class OrcidPublicationDataProvider extends AbstractExternalDataProvider {
try {
addMetadataValuesFromCitation(externalDataObject, work.getWorkCitation());
} catch (Exception e) {
LOGGER.error("An error occurs reading the following citation: " + work.getWorkCitation().getCitation(), e);
LOGGER.error("An error occurs reading the following citation: {}",
work.getWorkCitation().getCitation(), e);
}
return externalDataObject;

6
dspace-api/src/main/java/org/dspace/google/client/GoogleAnalyticsClientImpl.java
View File

@@ -19,9 +19,9 @@ import org.apache.http.client.methods.HttpPost;
import org.apache.http.entity.StringEntity;
import org.apache.http.impl.client.CloseableHttpClient;
import org.apache.http.impl.client.HttpClients;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.google.GoogleAnalyticsEvent;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/**
* Implementation of {@link GoogleAnalyticsClient}.
@@ -31,7 +31,7 @@ import org.slf4j.LoggerFactory;
*/
public class GoogleAnalyticsClientImpl implements GoogleAnalyticsClient {
private static final Logger LOGGER = LoggerFactory.getLogger(GoogleAnalyticsClientImpl.class);
private static final Logger LOGGER = LogManager.getLogger();
private final String keyPrefix;

56
dspace-api/src/main/java/org/dspace/identifier/DOIIdentifierProvider.java
View File

@@ -14,6 +14,8 @@ import java.util.Arrays;
import java.util.List;
import java.util.Objects;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.authorize.AuthorizeException;
import org.dspace.content.DSpaceObject;
import org.dspace.content.Item;
@@ -30,8 +32,6 @@ import org.dspace.identifier.doi.DOIIdentifierException;
import org.dspace.identifier.doi.DOIIdentifierNotApplicableException;
import org.dspace.identifier.service.DOIService;
import org.dspace.services.factory.DSpaceServicesFactory;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
/**
@@ -49,7 +49,7 @@ import org.springframework.beans.factory.annotation.Autowired;
* @author Kim Shepherd
*/
public class DOIIdentifierProvider extends FilteredIdentifierProvider {
private static final Logger log = LoggerFactory.getLogger(DOIIdentifierProvider.class);
private static final Logger log = LogManager.getLogger();
/**
* A DOIConnector connects the DOIIdentifierProvider to the API of the DOI
@@ -286,7 +286,7 @@ public class DOIIdentifierProvider extends FilteredIdentifierProvider {
try {
doiRow = loadOrCreateDOI(context, dso, doi, filter);
} catch (SQLException ex) {
log.error("Error in databse connection: " + ex.getMessage());
log.error("Error in databse connection: {}", ex::getMessage);
throw new RuntimeException("Error in database conncetion.", ex);
}
@@ -492,7 +492,7 @@ public class DOIIdentifierProvider extends FilteredIdentifierProvider {
if (doiService.findDOIByDSpaceObject(context, dso) != null) {
// We can skip the filter here since we know the DOI already exists for the item
log.debug("updateMetadata: found DOIByDSpaceObject: " +
log.debug("updateMetadata: found DOIByDSpaceObject: {}",
doiService.findDOIByDSpaceObject(context, dso).getDoi());
updateFilter = DSpaceServicesFactory.getInstance().getServiceManager().getServiceByName(
"always_true_filter", TrueFilter.class);
@@ -501,7 +501,7 @@ public class DOIIdentifierProvider extends FilteredIdentifierProvider {
DOI doiRow = loadOrCreateDOI(context, dso, doi, updateFilter);
if (PENDING.equals(doiRow.getStatus()) || MINTED.equals(doiRow.getStatus())) {
log.info("Not updating metadata for PENDING or MINTED doi: " + doi);
log.info("Not updating metadata for PENDING or MINTED doi: {}", doi);
return;
}
@@ -611,8 +611,8 @@ public class DOIIdentifierProvider extends FilteredIdentifierProvider {
try {
doi = getDOIByObject(context, dso);
} catch (SQLException e) {
log.error("Error while attemping to retrieve information about a DOI for "
+ contentServiceFactory.getDSpaceObjectService(dso).getTypeText(dso) + " with ID " + dso.getID() + ".");
log.error("Error while attemping to retrieve information about a DOI for {} with ID {}.",
contentServiceFactory.getDSpaceObjectService(dso).getTypeText(dso), dso.getID());
throw new RuntimeException("Error while attempting to retrieve " +
"information about a DOI for " + contentServiceFactory.getDSpaceObjectService(dso).getTypeText(dso) +
" with ID " + dso.getID() + ".", e);
@@ -624,7 +624,7 @@ public class DOIIdentifierProvider extends FilteredIdentifierProvider {
} catch (SQLException e) {
log.error("Error while creating new DOI for Object of " +
"ResourceType {} with id {}.", dso.getType(), dso.getID());
"ResourceType {} with id {}.", dso::getType, dso::getID);
throw new RuntimeException("Error while attempting to create a " +
"new DOI for " + contentServiceFactory.getDSpaceObjectService(dso).getTypeText(dso) + " with ID " +
dso.getID() + ".", e);
@@ -709,9 +709,9 @@ public class DOIIdentifierProvider extends FilteredIdentifierProvider {
doi = getDOIByObject(context, dso);
}
} catch (SQLException ex) {
log.error("Error while attemping to retrieve information about a DOI for " +
contentServiceFactory.getDSpaceObjectService(dso).getTypeText(dso) +
" with ID " + dso.getID() + ".", ex);
log.error("Error while attemping to retrieve information about a DOI for {} with ID {}.",
contentServiceFactory.getDSpaceObjectService(dso).getTypeText(dso),
dso.getID(), ex);
throw new RuntimeException("Error while attempting to retrieve " +
"information about a DOI for " + contentServiceFactory.getDSpaceObjectService(dso).getTypeText(dso) +
" with ID " + dso.getID() + ".", ex);
@@ -726,17 +726,17 @@ public class DOIIdentifierProvider extends FilteredIdentifierProvider {
doi = getDOIOutOfObject(dso);
}
} catch (AuthorizeException ex) {
log.error("Error while removing a DOI out of the metadata of an " +
contentServiceFactory.getDSpaceObjectService(dso).getTypeText(dso) +
" with ID " + dso.getID() + ".", ex);
log.error("Error while removing a DOI out of the metadata of an {} with ID {}.",
contentServiceFactory.getDSpaceObjectService(dso).getTypeText(dso),
dso.getID(), ex);
throw new RuntimeException("Error while removing a DOI out of the metadata of an " +
contentServiceFactory.getDSpaceObjectService(dso).getTypeText(dso) +
" with ID " + dso.getID() + ".", ex);
} catch (SQLException ex) {
log.error("Error while removing a DOI out of the metadata of an " +
contentServiceFactory.getDSpaceObjectService(dso).getTypeText(dso) +
" with ID " + dso.getID() + ".", ex);
log.error("Error while removing a DOI out of the metadata of an {} with ID {}.",
contentServiceFactory.getDSpaceObjectService(dso).getTypeText(dso),
dso.getID(), ex);
throw new RuntimeException("Error while removing a DOI out of the " +
"metadata of an " + contentServiceFactory.getDSpaceObjectService(dso).getTypeText(dso) +
" with ID " + dso.getID() + ".", ex);
@@ -779,8 +779,8 @@ public class DOIIdentifierProvider extends FilteredIdentifierProvider {
throw new DOIIdentifierException("Not authorized to delete DOI.",
ex, DOIIdentifierException.UNAUTHORIZED_METADATA_MANIPULATION);
} catch (SQLException ex) {
log.error("SQLException occurred while deleting a DOI out of an item: "
+ ex.getMessage());
log.error("SQLException occurred while deleting a DOI out of an item: {}",
ex::getMessage);
throw new RuntimeException("Error while deleting a DOI out of the " +
"metadata of an Item " + dso.getID(), ex);
}
@@ -826,8 +826,9 @@ public class DOIIdentifierProvider extends FilteredIdentifierProvider {
DOIIdentifierException.DOI_DOES_NOT_EXIST);
}
if (!TO_BE_DELETED.equals(doiRow.getStatus())) {
log.error("This identifier: {} couldn't be deleted. Delete it first from metadata.",
DOI.SCHEME + doiRow.getDoi());
log.error("This identifier: " + DOI.SCHEME
+ "{} couldn't be deleted. Delete it first from metadata.",
doiRow::getDoi);
throw new IllegalArgumentException("Couldn't delete this identifier:"
+ DOI.SCHEME + doiRow.getDoi()
+ ". Delete it first from metadata.");
@@ -863,7 +864,7 @@ public class DOIIdentifierProvider extends FilteredIdentifierProvider {
}
if (doiRow.getDSpaceObject() == null) {
log.error("Found DOI " + doi + " in database, but no assigned Object could be found.");
log.error("Found DOI {} in database, but no assigned Object could be found.", doi);
throw new IllegalStateException("Found DOI " + doi +
" in database, but no assigned Object could be found.");
}
@@ -890,8 +891,9 @@ public class DOIIdentifierProvider extends FilteredIdentifierProvider {
}
if (doiRow.getDoi() == null) {
log.error("A DOI with an empty doi column was found in the database. DSO-Type: " +
contentServiceFactory.getDSpaceObjectService(dso).getTypeText(dso) + ", ID: " + dso.getID() + ".");
log.error("A DOI with an empty doi column was found in the database. DSO-Type: {}, ID: {}.",
contentServiceFactory.getDSpaceObjectService(dso).getTypeText(dso),
dso.getID());
throw new IllegalStateException("A DOI with an empty doi column was found in the database. DSO-Type: " +
contentServiceFactory.getDSpaceObjectService(dso).getTypeText(dso) + ", ID: " + dso.getID() + ".");
}
@@ -1134,13 +1136,13 @@ public class DOIIdentifierProvider extends FilteredIdentifierProvider {
if (contentServiceFactory.getDSpaceObjectService(dso).getTypeText(dso).equals("ITEM")) {
try {
boolean result = filter.getResult(context, (Item) dso);
log.debug("Result of filter for " + dso.getHandle() + " is " + result);
log.debug("Result of filter for {} is {}", dso.getHandle(), result);
if (!result) {
throw new DOIIdentifierNotApplicableException("Item " + dso.getHandle() +
" was evaluated as 'false' by the item filter, not minting");
}
} catch (LogicalStatementException e) {
log.error("Error evaluating item with logical filter: " + e.getLocalizedMessage());
log.error("Error evaluating item with logical filter: {}", e::getLocalizedMessage);
throw new DOIIdentifierNotApplicableException(e);
}
} else {

17
dspace-api/src/main/java/org/dspace/identifier/DataCiteXMLCreator.java
View File

@@ -13,6 +13,8 @@ import java.sql.SQLException;
import java.util.HashMap;
import java.util.Map;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.authorize.AuthorizeException;
import org.dspace.content.DSpaceObject;
import org.dspace.content.crosswalk.CrosswalkException;
@@ -25,8 +27,6 @@ import org.dspace.services.ConfigurationService;
import org.dspace.utils.DSpace;
import org.jdom2.Element;
import org.jdom2.output.XMLOutputter;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/**
* Provide XML based metadata crosswalk for EZID Identifier provider module.
@@ -36,9 +36,9 @@ import org.slf4j.LoggerFactory;
public class DataCiteXMLCreator {
/**
* log4j category
* logging category
*/
private static final Logger LOG = LoggerFactory.getLogger(DataCiteXMLCreator.class);
private static final Logger LOG = LogManager.getLogger();
/**
* Name of crosswalk to convert metadata into DataCite Metadata Scheme.
@@ -70,9 +70,8 @@ public class DataCiteXMLCreator {
this.prepareXwalk();
if (!this.xwalk.canDisseminate(dso)) {
LOG.error("Crosswalk " + this.CROSSWALK_NAME
+ " cannot disseminate DSO with type " + dso.getType()
+ " and ID " + dso.getID() + ".");
LOG.error("Crosswalk {} cannot disseminate DSO with type {} and ID {}.",
this.CROSSWALK_NAME, dso.getType(), dso.getID());
return null;
}
@@ -98,8 +97,8 @@ public class DataCiteXMLCreator {
try {
root = xwalk.disseminateElement(context, dso, parameters);
} catch (CrosswalkException | IOException | SQLException | AuthorizeException e) {
LOG.error("Exception while crosswalking DSO with type "
+ dso.getType() + " and ID " + dso.getID() + ".", e);
LOG.error("Exception while crosswalking DSO with type {} and ID {}.",
dso.getType(), dso.getID(), e);
return null;
}

66
dspace-api/src/main/java/org/dspace/identifier/EZIDIdentifierProvider.java
View File

@@ -20,6 +20,8 @@ import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.authorize.AuthorizeException;
import org.dspace.content.DSpaceObject;
import org.dspace.content.Item;
@@ -32,8 +34,6 @@ import org.dspace.identifier.ezid.EZIDRequest;
import org.dspace.identifier.ezid.EZIDRequestFactory;
import org.dspace.identifier.ezid.EZIDResponse;
import org.dspace.identifier.ezid.Transform;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
/**
@@ -83,7 +83,7 @@ import org.springframework.beans.factory.annotation.Autowired;
*/
public class EZIDIdentifierProvider
extends IdentifierProvider {
private static final Logger log = LoggerFactory.getLogger(EZIDIdentifierProvider.class);
private static final Logger log = LogManager.getLogger();
// Configuration property names
static final String CFG_SHOULDER = "identifier.doi.ezid.shoulder";
@@ -184,7 +184,8 @@ public class EZIDIdentifierProvider
loadUser(), loadPassword());
response = request.create(identifier, crosswalkMetadata(context, object));
} catch (IdentifierException | IOException | URISyntaxException e) {
log.error("Identifier '{}' not registered: {}", identifier, e.getMessage());
log.error("Identifier '{}' not registered: {}",
() -> identifier, e::getMessage);
return;
}
@@ -201,7 +202,7 @@ public class EZIDIdentifierProvider
}
} else {
log.error("Identifier '{}' not registered -- EZID returned: {}",
identifier, response.getEZIDStatusValue());
() -> identifier, response::getEZIDStatusValue);
}
}
@@ -218,7 +219,8 @@ public class EZIDIdentifierProvider
metadata.put("_status", "reserved");
response = request.create(identifier, metadata);
} catch (IOException | URISyntaxException e) {
log.error("Identifier '{}' not registered: {}", identifier, e.getMessage());
log.error("Identifier '{}' not registered: {}",
() -> identifier, e::getMessage);
return;
}
@@ -233,7 +235,7 @@ public class EZIDIdentifierProvider
}
} else {
log.error("Identifier '{}' not registered -- EZID returned: {}",
identifier, response.getEZIDStatusValue());
() -> identifier, response::getEZIDStatusValue);
}
}
@@ -247,7 +249,7 @@ public class EZIDIdentifierProvider
try {
request = requestFactory.getInstance(loadAuthority(), loadUser(), loadPassword());
} catch (URISyntaxException ex) {
log.error(ex.getMessage());
log.error(ex::getMessage);
throw new IdentifierException("DOI request not sent: " + ex.getMessage());
}
@@ -256,18 +258,16 @@ public class EZIDIdentifierProvider
try {
response = request.mint(crosswalkMetadata(context, dso));
} catch (IOException | URISyntaxException ex) {
log.error("Failed to send EZID request: {}", ex.getMessage());
log.error("Failed to send EZID request: {}", ex::getMessage);
throw new IdentifierException("DOI request not sent: " + ex.getMessage());
}
// Good response?
if (HttpURLConnection.HTTP_CREATED != response.getHttpStatusCode()) {
log.error("EZID server responded: {} {}: {}",
new String[] {
String.valueOf(response.getHttpStatusCode()),
response.getHttpReasonPhrase(),
response.getEZIDStatusValue()
});
response::getHttpStatusCode,
response::getHttpReasonPhrase,
response::getEZIDStatusValue);
throw new IdentifierException("DOI not created: "
+ response.getHttpReasonPhrase()
+ ": "
@@ -285,7 +285,7 @@ public class EZIDIdentifierProvider
log.info("Created {}", doi);
return doi;
} else {
log.error("EZID responded: {}", response.getEZIDStatusValue());
log.error("EZID responded: {}", response::getEZIDStatusValue);
throw new IdentifierException("No DOI returned");
}
}
@@ -302,7 +302,7 @@ public class EZIDIdentifierProvider
MD_SCHEMA, DOI_ELEMENT, DOI_QUALIFIER,
idToDOI(identifier));
} catch (IdentifierException | SQLException | AuthorizeException | IOException ex) {
log.error(ex.getMessage());
log.error(ex::getMessage);
throw new IdentifierNotResolvableException(ex);
}
if (!found.hasNext()) {
@@ -360,24 +360,24 @@ public class EZIDIdentifierProvider
loadUser(), loadPassword());
response = request.delete(DOIToId(id.getValue()));
} catch (URISyntaxException e) {
log.error("Bad URI in metadata value: {}", e.getMessage());
log.error("Bad URI in metadata value: {}", e::getMessage);
remainder.add(id.getValue());
skipped++;
continue;
} catch (IOException e) {
log.error("Failed request to EZID: {}", e.getMessage());
log.error("Failed request to EZID: {}", e::getMessage);
remainder.add(id.getValue());
skipped++;
continue;
}
if (!response.isSuccess()) {
log.error("Unable to delete {} from DataCite: {}", id.getValue(),
response.getEZIDStatusValue());
log.error("Unable to delete {} from DataCite: {}", id::getValue,
response::getEZIDStatusValue);
remainder.add(id.getValue());
skipped++;
continue;
}
log.info("Deleted {}", id.getValue());
log.info("Deleted {}", id::getValue);
}
// delete from item
@@ -386,7 +386,7 @@ public class EZIDIdentifierProvider
dsoService.addMetadata(context, dso, MD_SCHEMA, DOI_ELEMENT, DOI_QUALIFIER, null, remainder);
dsoService.update(context, dso);
} catch (SQLException | AuthorizeException e) {
log.error("Failed to re-add identifiers: {}", e.getMessage());
log.error("Failed to re-add identifiers: {}", e::getMessage);
}
if (skipped > 0) {
@@ -415,25 +415,25 @@ public class EZIDIdentifierProvider
loadUser(), loadPassword());
response = request.delete(DOIToId(id.getValue()));
} catch (URISyntaxException e) {
log.error("Bad URI in metadata value {}: {}", id.getValue(), e.getMessage());
log.error("Bad URI in metadata value {}: {}", id::getValue, e::getMessage);
remainder.add(id.getValue());
skipped++;
continue;
} catch (IOException e) {
log.error("Failed request to EZID: {}", e.getMessage());
log.error("Failed request to EZID: {}", e::getMessage);
remainder.add(id.getValue());
skipped++;
continue;
}
if (!response.isSuccess()) {
log.error("Unable to delete {} from DataCite: {}", id.getValue(),
response.getEZIDStatusValue());
log.error("Unable to delete {} from DataCite: {}", id::getValue,
response::getEZIDStatusValue);
remainder.add(id.getValue());
skipped++;
continue;
}
log.info("Deleted {}", id.getValue());
log.info("Deleted {}", id::getValue);
}
// delete from item
@@ -442,7 +442,7 @@ public class EZIDIdentifierProvider
dsoService.addMetadata(context, dso, MD_SCHEMA, DOI_ELEMENT, DOI_QUALIFIER, null, remainder);
dsoService.update(context, dso);
} catch (SQLException | AuthorizeException e) {
log.error("Failed to re-add identifiers: {}", e.getMessage());
log.error("Failed to re-add identifiers: {}", e::getMessage);
}
if (skipped > 0) {
@@ -544,12 +544,10 @@ public class EZIDIdentifierProvider
mappedValue = xfrm.transform(value.getValue());
} catch (Exception ex) {
log.error("Unable to transform '{}' from {} to {}: {}",
new String[] {
value.getValue(),
value.toString(),
key,
ex.getMessage()
});
value::getValue,
value::toString,
() -> key,
ex::getMessage);
continue;
}
} else {

61
dspace-api/src/main/java/org/dspace/identifier/doi/DataCiteConnector.java
View File

@@ -33,6 +33,8 @@ import org.apache.http.impl.client.BasicCredentialsProvider;
import org.apache.http.impl.client.CloseableHttpClient;
import org.apache.http.impl.client.HttpClientBuilder;
import org.apache.http.util.EntityUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.authorize.AuthorizeException;
import org.dspace.content.DSpaceObject;
import org.dspace.content.crosswalk.CrosswalkException;
@@ -52,8 +54,6 @@ import org.jdom2.filter.ElementFilter;
import org.jdom2.input.SAXBuilder;
import org.jdom2.output.Format;
import org.jdom2.output.XMLOutputter;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
/**
@@ -62,7 +62,7 @@ import org.springframework.beans.factory.annotation.Autowired;
public class DataCiteConnector
implements DOIConnector {
private static final Logger log = LoggerFactory.getLogger(DataCiteConnector.class);
private static final Logger log = LogManager.getLogger();
// Configuration property names
static final String CFG_USER = "identifier.doi.user";
@@ -356,10 +356,8 @@ public class DataCiteConnector
.getDSpaceObjectService(dso);
if (!this.xwalk.canDisseminate(dso)) {
log.error("Crosswalk " + this.CROSSWALK_NAME
+ " cannot disseminate DSO with type " + dso.getType()
+ " and ID " + dso.getID() + ". Giving up reserving the DOI "
+ doi + ".");
log.error("Crosswalk {} cannot disseminate DSO with type {} and ID {}. Giving up reserving the DOI {}.",
this.CROSSWALK_NAME, dso.getType(), dso.getID(), doi);
throw new DOIIdentifierException("Cannot disseminate "
+ dSpaceObjectService.getTypeText(dso) + "/" + dso.getID()
+ " using crosswalk " + this.CROSSWALK_NAME + ".",
@@ -390,18 +388,18 @@ public class DataCiteConnector
try {
root = xwalk.disseminateElement(context, dso, parameters);
} catch (AuthorizeException ae) {
log.error("Caught an AuthorizeException while disseminating DSO "
+ "with type " + dso.getType() + " and ID " + dso.getID()
+ ". Giving up to reserve DOI " + doi + ".", ae);
log.error("Caught an AuthorizeException while disseminating DSO"
+ " with type {} and ID {}. Giving up to reserve DOI {}.",
dso.getType(), dso.getID(), doi, ae);
throw new DOIIdentifierException("AuthorizeException occured while "
+ "converting " + dSpaceObjectService.getTypeText(dso) + "/" + dso
.getID()
+ " using crosswalk " + this.CROSSWALK_NAME + ".", ae,
DOIIdentifierException.CONVERSION_ERROR);
} catch (CrosswalkException ce) {
log.error("Caught an CrosswalkException while reserving a DOI ("
+ doi + ") for DSO with type " + dso.getType() + " and ID "
+ dso.getID() + ". Won't reserve the doi.", ce);
log.error("Caught a CrosswalkException while reserving a DOI ({})"
+ " for DSO with type {} and ID {}. Won't reserve the doi.",
doi, dso.getType(), dso.getID(), ce);
throw new DOIIdentifierException("CrosswalkException occured while "
+ "converting " + dSpaceObjectService.getTypeText(dso) + "/" + dso
.getID()
@@ -421,9 +419,8 @@ public class DataCiteConnector
} else if (!metadataDOI.equals(doi.substring(DOI.SCHEME.length()))) {
log.error("While reserving a DOI, the "
+ "crosswalk to generate the metadata used another DOI than "
+ "the DOI we're reserving. Cannot reserve DOI " + doi
+ " for " + dSpaceObjectService.getTypeText(dso) + " "
+ dso.getID() + ".");
+ "the DOI we're reserving. Cannot reserve DOI {} for {} {}.",
doi, dSpaceObjectService.getTypeText(dso), dso.getID());
throw new IllegalStateException("An internal error occured while "
+ "generating the metadata. Unable to reserve doi, see logs "
+ "for further information.");
@@ -440,12 +437,12 @@ public class DataCiteConnector
// 400 -> invalid XML
case (400): {
log.warn("DataCite was unable to understand the XML we send.");
log.warn("DataCite Metadata API returned a http status code "
+ "400: " + resp.getContent());
log.warn("DataCite Metadata API returned a http status code"
+ " 400: {}", resp::getContent);
Format format = Format.getCompactFormat();
format.setEncoding("UTF-8");
XMLOutputter xout = new XMLOutputter(format);
log.info("We send the following XML:\n" + xout.outputString(root));
log.info("We send the following XML:\n{}", xout.outputString(root));
throw new DOIIdentifierException("Unable to reserve DOI " + doi
+ ". Please inform your administrator or take a look "
+ " into the log files.", DOIIdentifierException.BAD_REQUEST);
@@ -479,8 +476,8 @@ public class DataCiteConnector
resp = this.sendDOIPostRequest(doi,
handleService.resolveToURL(context, dso.getHandle()));
} catch (SQLException e) {
log.error("Caught SQL-Exception while resolving handle to URL: "
+ e.getMessage());
log.error("Caught SQL-Exception while resolving handle to URL: {}",
e::getMessage);
throw new RuntimeException(e);
}
@@ -492,7 +489,7 @@ public class DataCiteConnector
// 400 -> wrong domain, wrong prefix, wrong request body
case (400): {
log.warn("We send an irregular request to DataCite. While "
+ "registering a DOI they told us: " + resp.getContent());
+ "registering a DOI they told us: {}", resp::getContent);
throw new DOIIdentifierException("Currently we cannot register "
+ "DOIs. Please inform the administrator or take a look "
+ " in the DSpace log file.",
@@ -501,8 +498,8 @@ public class DataCiteConnector
// 412 Precondition failed: DOI was not reserved before registration!
case (412): {
log.error("We tried to register a DOI {} that has not been reserved "
+ "before! The registration agency told us: {}.", doi,
resp.getContent());
+ "before! The registration agency told us: {}.",
() -> doi, resp::getContent);
throw new DOIIdentifierException("There was an error in handling "
+ "of DOIs. The DOI we wanted to register had not been "
+ "reserved in advance. Please contact the administrator "
@@ -511,7 +508,7 @@ public class DataCiteConnector
}
// Catch all other http status code in case we forgot one.
default: {
log.warn("While registration of DOI {}, we got a http status code "
log.warn("While registering DOI {}, we got a http status code "
+ "{} and the message \"{}\".",
doi, Integer.toString(resp.statusCode), resp.getContent());
throw new DOIIdentifierException("Unable to parse an answer from "
@@ -564,8 +561,8 @@ public class DataCiteConnector
try {
EntityUtils.consume(reqEntity);
} catch (IOException ioe) {
log.info("Caught an IOException while releasing a HTTPEntity:"
+ ioe.getMessage());
log.info("Caught an IOException while releasing a HTTPEntity: {}",
ioe::getMessage);
}
}
}
@@ -668,8 +665,8 @@ public class DataCiteConnector
try {
EntityUtils.consume(reqEntity);
} catch (IOException ioe) {
log.info("Caught an IOException while releasing an HTTPEntity:"
+ ioe.getMessage());
log.info("Caught an IOException while releasing an HTTPEntity: {}",
ioe::getMessage);
}
}
}
@@ -768,7 +765,7 @@ public class DataCiteConnector
// 500 is documented and signals an internal server error
case (500): {
log.warn("Caught an http status code 500 while managing DOI "
+ "{}. Message was: " + content);
+ "{}. Message was: {}", doi, content);
throw new DOIIdentifierException("DataCite API has an internal error. "
+ "It is temporarily impossible to manage DOIs. "
+ "Further information can be found in DSpace log file.",
@@ -781,7 +778,7 @@ public class DataCiteConnector
return new DataCiteResponse(statusCode, content);
} catch (IOException e) {
log.warn("Caught an IOException: " + e.getMessage());
log.warn("Caught an IOException: {}", e::getMessage);
throw new RuntimeException(e);
} finally {
try {
@@ -790,7 +787,7 @@ public class DataCiteConnector
EntityUtils.consume(entity);
}
} catch (IOException e) {
log.warn("Can't release HTTP-Entity: " + e.getMessage());
log.warn("Can't release HTTP-Entity: {}", e::getMessage);
}
}
}

16
dspace-api/src/main/java/org/dspace/identifier/ezid/EZIDRequest.java
View File

@@ -27,10 +27,10 @@ import org.apache.http.entity.StringEntity;
import org.apache.http.impl.client.BasicCredentialsProvider;
import org.apache.http.impl.client.CloseableHttpClient;
import org.apache.http.impl.client.HttpClientBuilder;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.identifier.DOI;
import org.dspace.identifier.IdentifierException;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/**
* A request to EZID concerning a given (or expected) identifier.
@@ -38,7 +38,7 @@ import org.slf4j.LoggerFactory;
* @author Mark H. Wood
*/
public class EZIDRequest {
private static final Logger log = LoggerFactory.getLogger(EZIDRequest.class);
private static final Logger log = LogManager.getLogger();
private static final String ID_PATH = "/id/" + DOI.SCHEME;
@@ -149,7 +149,7 @@ public class EZIDRequest {
// GET path
HttpGet request;
URI uri = new URI(scheme, host, path + ID_PATH + authority + name, null);
log.debug("EZID lookup {}", uri.toASCIIString());
log.debug("EZID lookup {}", uri::toASCIIString);
request = new HttpGet(uri);
HttpResponse response = client.execute(request, httpContext);
return new EZIDResponse(response);
@@ -172,7 +172,7 @@ public class EZIDRequest {
// PUT path [+metadata]
HttpPut request;
URI uri = new URI(scheme, host, path + ID_PATH + authority + '/' + name, null);
log.debug("EZID create {}", uri.toASCIIString());
log.debug("EZID create {}", uri::toASCIIString);
request = new HttpPut(uri);
if (null != metadata) {
request.setEntity(new StringEntity(formatMetadata(metadata), UTF_8));
@@ -196,7 +196,7 @@ public class EZIDRequest {
// POST path [+metadata]
HttpPost request;
URI uri = new URI(scheme, host, path + SHOULDER_PATH + authority, null);
log.debug("EZID mint {}", uri.toASCIIString());
log.debug("EZID mint {}", uri::toASCIIString);
request = new HttpPost(uri);
if (null != metadata) {
request.setEntity(new StringEntity(formatMetadata(metadata), UTF_8));
@@ -225,7 +225,7 @@ public class EZIDRequest {
// POST path +metadata
HttpPost request;
URI uri = new URI(scheme, host, path + ID_PATH + authority + name, null);
log.debug("EZID modify {}", uri.toASCIIString());
log.debug("EZID modify {}", uri::toASCIIString);
request = new HttpPost(uri);
request.setEntity(new StringEntity(formatMetadata(metadata), UTF_8));
HttpResponse response = client.execute(request, httpContext);
@@ -246,7 +246,7 @@ public class EZIDRequest {
// DELETE path
HttpDelete request;
URI uri = new URI(scheme, host, path + ID_PATH + authority + name, null);
log.debug("EZID delete {}", uri.toASCIIString());
log.debug("EZID delete {}", uri::toASCIIString);
request = new HttpDelete(uri);
HttpResponse response = client.execute(request, httpContext);
return new EZIDResponse(response);

18
dspace-api/src/main/java/org/dspace/identifier/ezid/EZIDResponse.java
View File

@@ -19,15 +19,15 @@ import org.apache.http.HttpEntity;
import org.apache.http.HttpResponse;
import org.apache.http.ParseException;
import org.apache.http.util.EntityUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.identifier.IdentifierException;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/**
* Decoded response data evoked by a request made to EZID.
*/
public class EZIDResponse {
private static final Logger log = LoggerFactory.getLogger(EZIDResponse.class);
private static final Logger log = LogManager.getLogger();
private static final String UTF_8 = "UTF-8";
@@ -35,7 +35,7 @@ public class EZIDResponse {
private final String statusValue;
private final Map<String, String> attributes = new HashMap<String, String>();
private final Map<String, String> attributes = new HashMap<>();
private final HttpResponse response;
@@ -49,12 +49,8 @@ public class EZIDResponse {
String body;
try {
body = EntityUtils.toString(responseBody, UTF_8);
} catch (IOException ex) {
log.error(ex.getMessage());
throw new IdentifierException("EZID response not understood: "
+ ex.getMessage());
} catch (ParseException ex) {
log.error(ex.getMessage());
} catch (IOException | ParseException ex) {
log.error(ex::getMessage);
throw new IdentifierException("EZID response not understood: "
+ ex.getMessage());
}
@@ -124,7 +120,7 @@ public class EZIDResponse {
* @return all keys found in the response.
*/
public List<String> getKeys() {
List<String> keys = new ArrayList<String>();
List<String> keys = new ArrayList<>();
for (String key : attributes.keySet()) {
keys.add(key);
}

12
dspace-api/src/main/java/org/dspace/orcid/consumer/OrcidQueueConsumer.java
View File

@@ -22,6 +22,8 @@ import java.util.stream.Collectors;
import java.util.stream.Stream;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.content.DSpaceObject;
import org.dspace.content.Item;
import org.dspace.content.MetadataFieldName;
@@ -45,8 +47,6 @@ import org.dspace.orcid.service.OrcidTokenService;
import org.dspace.profile.OrcidProfileSyncPreference;
import org.dspace.services.ConfigurationService;
import org.dspace.services.factory.DSpaceServicesFactory;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/**
* The consumer to fill the ORCID queue. The addition to the queue is made for
@@ -56,7 +56,7 @@ import org.slf4j.LoggerFactory;
* be synchronized (based on the preferences set by the user)</li>
* <li>are publications/fundings related to profile items linked to orcid (based
* on the preferences set by the user)</li>
*
*
* </ul>
*
* @author Luca Giamminonni (luca.giamminonni at 4science.it)
@@ -64,7 +64,7 @@ import org.slf4j.LoggerFactory;
*/
public class OrcidQueueConsumer implements Consumer {
private static final Logger LOGGER = LoggerFactory.getLogger(OrcidQueueConsumer.class);
private static final Logger LOGGER = LogManager.getLogger();
private OrcidQueueService orcidQueueService;
@@ -82,7 +82,7 @@ public class OrcidQueueConsumer implements Consumer {
private RelationshipService relationshipService;
private List<UUID> alreadyConsumedItems = new ArrayList<>();
private final List<UUID> alreadyConsumedItems = new ArrayList<>();
@Override
public void initialize() throws Exception {
@@ -263,7 +263,7 @@ public class OrcidQueueConsumer implements Consumer {
if (StringUtils.isBlank(putCode)) {
LOGGER.warn("The orcid history record with id {} should have a not blank put code",
historyRecord.getID());
historyRecord::getID);
continue;
}

6
dspace-api/src/main/java/org/dspace/orcid/model/factory/impl/OrcidFundingFactory.java
View File

@@ -18,6 +18,8 @@ import java.util.Optional;
import java.util.stream.Collectors;
import java.util.stream.Stream;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.content.Item;
import org.dspace.content.MetadataValue;
import org.dspace.content.Relationship;
@@ -44,8 +46,6 @@ import org.orcid.jaxb.model.v3.release.record.Funding;
import org.orcid.jaxb.model.v3.release.record.FundingContributor;
import org.orcid.jaxb.model.v3.release.record.FundingContributors;
import org.orcid.jaxb.model.v3.release.record.FundingTitle;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
/**
@@ -57,7 +57,7 @@ import org.springframework.beans.factory.annotation.Autowired;
*/
public class OrcidFundingFactory implements OrcidEntityFactory {
private static final Logger LOGGER = LoggerFactory.getLogger(OrcidFundingFactory.class);
private static final Logger LOGGER = LogManager.getLogger();
@Autowired
private ItemService itemService;

8
dspace-api/src/main/java/org/dspace/orcid/model/factory/impl/OrcidWorkFactory.java
View File

@@ -19,6 +19,8 @@ import java.util.Optional;
import java.util.stream.Collectors;
import org.apache.commons.lang3.EnumUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.content.Item;
import org.dspace.content.MetadataValue;
import org.dspace.content.service.ItemService;
@@ -42,8 +44,6 @@ import org.orcid.jaxb.model.v3.release.record.ExternalIDs;
import org.orcid.jaxb.model.v3.release.record.Work;
import org.orcid.jaxb.model.v3.release.record.WorkContributors;
import org.orcid.jaxb.model.v3.release.record.WorkTitle;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
/**
@@ -55,7 +55,7 @@ import org.springframework.beans.factory.annotation.Autowired;
*/
public class OrcidWorkFactory implements OrcidEntityFactory {
private static final Logger LOGGER = LoggerFactory.getLogger(OrcidWorkFactory.class);
private static final Logger LOGGER = LogManager.getLogger();
@Autowired
private ItemService itemService;
@@ -164,7 +164,7 @@ public class OrcidWorkFactory implements OrcidEntityFactory {
*/
private List<ExternalID> getWorkSelfExternalIds(Context context, Item item) {
List<ExternalID> selfExternalIds = new ArrayList<ExternalID>();
List<ExternalID> selfExternalIds = new ArrayList<>();
Map<String, String> externalIdentifierFields = fieldMapping.getExternalIdentifierFields();

8
dspace-api/src/main/java/org/dspace/orcid/script/OrcidBulkPush.java
View File

@@ -20,6 +20,8 @@ import java.util.stream.Collectors;
import org.apache.commons.cli.ParseException;
import org.apache.commons.lang3.exception.ExceptionUtils;
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.eperson.EPerson;
@@ -36,8 +38,6 @@ import org.dspace.scripts.DSpaceRunnable;
import org.dspace.services.ConfigurationService;
import org.dspace.services.factory.DSpaceServicesFactory;
import org.dspace.utils.DSpace;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/**
* Script that perform the bulk synchronization with ORCID registry of all the
@@ -48,7 +48,7 @@ import org.slf4j.LoggerFactory;
*/
public class OrcidBulkPush extends DSpaceRunnable<OrcidBulkPushScriptConfiguration<OrcidBulkPush>> {
private static final Logger LOGGER = LoggerFactory.getLogger(OrcidBulkPush.class);
private static final Logger LOGGER = LogManager.getLogger();
private OrcidQueueService orcidQueueService;
@@ -63,7 +63,7 @@ public class OrcidBulkPush extends DSpaceRunnable<OrcidBulkPushScriptConfigurati
/**
* Cache that stores the synchronization mode set for a specific profile item.
*/
private Map<Item, OrcidSynchronizationMode> synchronizationModeByProfileItem = new HashMap<>();
private final Map<Item, OrcidSynchronizationMode> synchronizationModeByProfileItem = new HashMap<>();
private boolean ignoreMaxAttempts = false;

14
dspace-api/src/main/java/org/dspace/orcid/service/impl/OrcidHistoryServiceImpl.java
View File

@@ -24,6 +24,8 @@ import java.util.Optional;
import org.apache.commons.collections.CollectionUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.http.HttpStatus;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.content.Item;
import org.dspace.content.MetadataFieldName;
import org.dspace.content.MetadataValue;
@@ -48,8 +50,6 @@ import org.dspace.orcid.service.OrcidHistoryService;
import org.dspace.orcid.service.OrcidProfileSectionFactoryService;
import org.dspace.orcid.service.OrcidTokenService;
import org.orcid.jaxb.model.v3.release.record.Activity;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
/**
@@ -61,7 +61,7 @@ import org.springframework.beans.factory.annotation.Autowired;
*/
public class OrcidHistoryServiceImpl implements OrcidHistoryService {
private static final Logger LOGGER = LoggerFactory.getLogger(OrcidHistoryServiceImpl.class);
private static final Logger LOGGER = LogManager.getLogger();
@Autowired
private OrcidHistoryDAO orcidHistoryDAO;
@@ -134,7 +134,7 @@ public class OrcidHistoryServiceImpl implements OrcidHistoryService {
@Override
public Map<Item, String> findLastPutCodes(Context context, Item entity) throws SQLException {
Map<Item, String> profileItemAndPutCodeMap = new HashMap<Item, String>();
Map<Item, String> profileItemAndPutCodeMap = new HashMap<>();
List<OrcidHistory> orcidHistoryRecords = findByEntity(context, entity);
for (OrcidHistory orcidHistoryRecord : orcidHistoryRecords) {
@@ -187,10 +187,12 @@ public class OrcidHistoryServiceImpl implements OrcidHistoryService {
} catch (OrcidValidationException ex) {
throw ex;
} catch (OrcidClientException ex) {
LOGGER.error("An error occurs during the orcid synchronization of ORCID queue " + orcidQueue, ex);
LOGGER.error("An error occurs during the orcid synchronization of ORCID queue {}",
orcidQueue, ex);
return createHistoryRecordFromOrcidError(context, orcidQueue, operation, ex);
} catch (RuntimeException ex) {
LOGGER.warn("An unexpected error occurs during the orcid synchronization of ORCID queue " + orcidQueue, ex);
LOGGER.warn("An unexpected error occurs during the orcid synchronization of ORCID queue {}",
orcidQueue, ex);
return createHistoryRecordFromGenericError(context, orcidQueue, operation, ex);
}

8
dspace-api/src/main/java/org/dspace/profile/ResearcherProfileServiceImpl.java
View File

@@ -27,6 +27,8 @@ import javax.annotation.PostConstruct;
import org.apache.commons.collections4.CollectionUtils;
import org.apache.commons.lang.StringUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.app.exception.ResourceAlreadyExistsException;
import org.dspace.authorize.AuthorizeException;
import org.dspace.authorize.service.AuthorizeService;
@@ -53,8 +55,6 @@ import org.dspace.profile.service.AfterResearcherProfileCreationAction;
import org.dspace.profile.service.ResearcherProfileService;
import org.dspace.services.ConfigurationService;
import org.dspace.util.UUIDUtils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.util.Assert;
@@ -66,7 +66,7 @@ import org.springframework.util.Assert;
*/
public class ResearcherProfileServiceImpl implements ResearcherProfileService {
private static Logger log = LoggerFactory.getLogger(ResearcherProfileServiceImpl.class);
private static final Logger log = LogManager.getLogger();
@Autowired
private ItemService itemService;
@@ -310,7 +310,7 @@ public class ResearcherProfileServiceImpl implements ResearcherProfileService {
if (isNotProfileCollection(collection)) {
log.warn("The configured researcher-profile.collection.uuid "
+ "has an invalid entity type, expected " + getProfileType());
+ "has an invalid entity type, expected {}", this::getProfileType);
return Optional.empty();
}

6
dspace-api/src/main/java/org/dspace/qaevent/action/QAReinstateRequestAction.java
View File

@@ -9,14 +9,14 @@ package org.dspace.qaevent.action;
import java.sql.SQLException;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.authorize.AuthorizeException;
import org.dspace.content.Item;
import org.dspace.content.service.ItemService;
import org.dspace.core.Context;
import org.dspace.qaevent.QualityAssuranceAction;
import org.dspace.qaevent.service.dto.QAMessageDTO;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
/**
@@ -27,7 +27,7 @@ import org.springframework.beans.factory.annotation.Autowired;
*/
public class QAReinstateRequestAction implements QualityAssuranceAction {
private static final Logger log = LoggerFactory.getLogger(QAReinstateRequestAction.class);
private static final Logger log = LogManager.getLogger();
@Autowired
private ItemService itemService;

8
dspace-api/src/main/java/org/dspace/qaevent/action/QAWithdrawnRequestAction.java
View File

@@ -9,25 +9,25 @@ package org.dspace.qaevent.action;
import java.sql.SQLException;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.authorize.AuthorizeException;
import org.dspace.content.Item;
import org.dspace.content.service.ItemService;
import org.dspace.core.Context;
import org.dspace.qaevent.QualityAssuranceAction;
import org.dspace.qaevent.service.dto.QAMessageDTO;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
/**
* QAWithdrawnRequestAction is an implementation of the QualityAssuranceAction interface.
* It is responsible for applying a correction to withdraw a specified item.
*
*
* @author Mykhaylo Boychuk (mykhaylo.boychuk@4science.com)
*/
public class QAWithdrawnRequestAction implements QualityAssuranceAction {
private static final Logger log = LoggerFactory.getLogger(QAWithdrawnRequestAction.class);
private static final Logger log = LogManager.getLogger();
@Autowired
private ItemService itemService;

8
dspace-api/src/main/java/org/dspace/qaevent/service/impl/QAEventServiceImpl.java
View File

@@ -78,7 +78,7 @@ import org.springframework.beans.factory.annotation.Qualifier;
*/
public class QAEventServiceImpl implements QAEventService {
private static final Logger log = LogManager.getLogger(QAEventServiceImpl.class);
private static final Logger log = LogManager.getLogger();
public static final String QAEVENTS_SOURCES = "qaevents.sources";
@@ -405,8 +405,8 @@ public class QAEventServiceImpl implements QAEventService {
email.addArgument(parsJson(qaEvent.getMessage()));
email.send();
} catch (Exception e) {
log.warn("Error during sending email of Withdrawn/Reinstate request for item with uuid:"
+ qaEvent.getTarget(), e);
log.warn("Error during sending email of Withdrawn/Reinstate request for item with uuid: {}",
qaEvent.getTarget(), e);
}
}
@@ -416,7 +416,7 @@ public class QAEventServiceImpl implements QAEventService {
JsonNode jsonNode = objectMapper.readTree(jsonString);
return jsonNode.get("reason").asText();
} catch (Exception e) {
log.warn("Unable to parse the JSON:" + jsonString);
log.warn("Unable to parse the JSON: {}", jsonString);
return jsonString;
}
}

8
dspace-api/src/main/java/org/dspace/scripts/ScriptServiceImpl.java
View File

@@ -12,19 +12,19 @@ import java.util.Comparator;
import java.util.List;
import java.util.stream.Collectors;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.core.Context;
import org.dspace.kernel.ServiceManager;
import org.dspace.scripts.configuration.ScriptConfiguration;
import org.dspace.scripts.service.ScriptService;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
/**
* The implementation for the {@link ScriptService}
*/
public class ScriptServiceImpl implements ScriptService {
private static final Logger log = LoggerFactory.getLogger(ScriptServiceImpl.class);
private static final Logger log = LogManager.getLogger();
@Autowired
private ServiceManager serviceManager;
@@ -48,7 +48,7 @@ public class ScriptServiceImpl implements ScriptService {
try {
return (DSpaceRunnable) scriptToExecute.getDspaceRunnableClass().getDeclaredConstructor().newInstance();
} catch (InvocationTargetException | NoSuchMethodException e) {
log.error(e.getMessage(), e);
log.error(e::getMessage, e);
throw new RuntimeException(e);
}
}

19
dspace-api/src/main/java/org/dspace/service/impl/ClientInfoServiceImpl.java
View File

@@ -15,12 +15,12 @@ import javax.servlet.http.HttpServletRequest;
import com.google.common.net.InetAddresses;
import org.apache.commons.lang3.ArrayUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.core.Utils;
import org.dspace.service.ClientInfoService;
import org.dspace.services.ConfigurationService;
import org.dspace.statistics.util.IPTable;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
/**
@@ -32,16 +32,16 @@ public class ClientInfoServiceImpl implements ClientInfoService {
private static final String X_FORWARDED_FOR_HEADER = "X-Forwarded-For";
private static final Logger log = LoggerFactory.getLogger(ClientInfoServiceImpl.class);
private static final Logger log = LogManager.getLogger();
private Boolean useProxiesEnabled;
private ConfigurationService configurationService;
private final ConfigurationService configurationService;
/**
* Sparse HashTable structure to hold IP address ranges of trusted proxies
*/
private IPTable trustedProxies;
private final IPTable trustedProxies;
@Autowired(required = true)
public ClientInfoServiceImpl(ConfigurationService configurationService) {
@@ -84,7 +84,7 @@ public class ClientInfoServiceImpl implements ClientInfoService {
public boolean isUseProxiesEnabled() {
if (useProxiesEnabled == null) {
useProxiesEnabled = configurationService.getBooleanProperty("useProxies", true);
log.info("Proxies (useProxies) enabled? " + useProxiesEnabled);
log.info("Proxies (useProxies) enabled? {}", useProxiesEnabled);
}
return useProxiesEnabled;
@@ -163,6 +163,7 @@ public class ClientInfoServiceImpl implements ClientInfoService {
* @param ipAddress IP address to check for
* @return true if trusted, false otherwise
*/
@Override
public boolean isRequestFromTrustedProxy(String ipAddress) {
try {
return trustedProxies != null && trustedProxies.contains(ipAddress);
@@ -205,15 +206,15 @@ public class ClientInfoServiceImpl implements ClientInfoService {
}
/**
* Anonymize the given IP address by setting the last specified bytes to 0
* @param ipAddress the ip address to be anonymize
* Anonymize the given IP address by setting the last specified bytes to 0.
* @param ipAddress the ip address to be anonymized
* @param bytes the number of bytes to be set to 0
* @return the modified ip address
*/
private String anonymizeIpAddress(String ipAddress, int bytes) {
if (bytes > 4) {
log.warn("It is not possible to anonymize " + bytes + " bytes of an IPv4 address.");
log.warn("It is not possible to anonymize {} bytes of an IPv4 address.", bytes);
return ipAddress;
}

8
dspace-api/src/main/java/org/dspace/statistics/util/SpiderDetector.java
View File

@@ -13,8 +13,6 @@ import java.util.Set;
import javax.servlet.http.HttpServletRequest;
import org.dspace.statistics.factory.StatisticsServiceFactory;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/**
* SpiderDetector delegates static methods to SpiderDetectorService, which is used to find IP's that are spiders...
@@ -26,11 +24,9 @@ import org.slf4j.LoggerFactory;
*/
public class SpiderDetector {
private static final Logger log = LoggerFactory.getLogger(SpiderDetector.class);
//Service where all methods get delegated to, this is instantiated by a spring-bean defined in core-services.xml
private static SpiderDetectorService spiderDetectorService = StatisticsServiceFactory.getInstance()
.getSpiderDetectorService();
private static final SpiderDetectorService spiderDetectorService
= StatisticsServiceFactory.getInstance().getSpiderDetectorService();
/**
* Default constructor

26
dspace-api/src/main/java/org/dspace/statistics/util/SpiderDetectorServiceImpl.java
View File

@@ -21,10 +21,10 @@ import javax.servlet.http.HttpServletRequest;
import org.apache.commons.configuration2.ex.ConversionException;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.service.ClientInfoService;
import org.dspace.services.ConfigurationService;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
/**
@@ -39,18 +39,18 @@ import org.springframework.beans.factory.annotation.Autowired;
*/
public class SpiderDetectorServiceImpl implements SpiderDetectorService {
private static final Logger log = LoggerFactory.getLogger(SpiderDetectorServiceImpl.class);
private static final Logger log = LogManager.getLogger();
private Boolean useCaseInsensitiveMatching;
private final List<Pattern> agents
= Collections.synchronizedList(new ArrayList<Pattern>());
= Collections.synchronizedList(new ArrayList<>());
private final List<Pattern> domains
= Collections.synchronizedList(new ArrayList<Pattern>());
= Collections.synchronizedList(new ArrayList<>());
private ConfigurationService configurationService;
private ClientInfoService clientInfoService;
private final ConfigurationService configurationService;
private final ClientInfoService clientInfoService;
/**
* Sparse HashTable structure to hold IP address ranges.
@@ -63,6 +63,7 @@ public class SpiderDetectorServiceImpl implements SpiderDetectorService {
this.clientInfoService = clientInfoService;
}
@Override
public IPTable getTable() {
return table;
}
@@ -79,6 +80,7 @@ public class SpiderDetectorServiceImpl implements SpiderDetectorService {
* @param agent User-Agent header value, or null.
* @return true if the client matches any spider characteristics list.
*/
@Override
public boolean isSpider(String clientIP, String proxyIPs, String hostname, String agent) {
// See if any agent patterns match
if (null != agent) {
@@ -144,6 +146,7 @@ public class SpiderDetectorServiceImpl implements SpiderDetectorService {
* @return a vector full of patterns
* @throws IOException could not happen since we check the file be4 we use it
*/
@Override
public Set<String> readPatterns(File patternFile)
throws IOException {
Set<String> patterns = new HashSet<>();
@@ -191,7 +194,7 @@ public class SpiderDetectorServiceImpl implements SpiderDetectorService {
patterns = readPatterns(file);
} catch (IOException ex) {
log.error("Patterns not read from {}: {}",
file.getPath(), ex.getMessage());
file::getPath, ex::getMessage);
continue;
}
//If case insensitive matching is enabled, lowercase the patterns so they can be lowercase matched
@@ -203,10 +206,10 @@ public class SpiderDetectorServiceImpl implements SpiderDetectorService {
}
log.info("Loaded pattern file: {}", file.getPath());
log.info("Loaded pattern file: {}", file::getPath);
}
} else {
log.info("No patterns loaded from {}", patternsDir.getPath());
log.info("No patterns loaded from {}", patternsDir::getPath);
}
}
@@ -216,6 +219,7 @@ public class SpiderDetectorServiceImpl implements SpiderDetectorService {
* @param request
* @return true|false if the request was detected to be from a spider.
*/
@Override
public boolean isSpider(HttpServletRequest request) {
return isSpider(request.getRemoteAddr(),
request.getHeader("X-Forwarded-For"),
@@ -229,6 +233,7 @@ public class SpiderDetectorServiceImpl implements SpiderDetectorService {
* @param ip
* @return if is spider IP
*/
@Override
public boolean isSpider(String ip) {
if (table == null) {
loadSpiderIpAddresses();
@@ -248,6 +253,7 @@ public class SpiderDetectorServiceImpl implements SpiderDetectorService {
/*
* loader to populate the table from files.
*/
@Override
public synchronized void loadSpiderIpAddresses() {
if (table == null) {

6
dspace-api/src/main/java/org/dspace/storage/rdbms/RegistryUpdater.java
View File

@@ -14,6 +14,8 @@ import javax.xml.parsers.ParserConfigurationException;
import javax.xml.transform.TransformerException;
import javax.xml.xpath.XPathExpressionException;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.administer.MetadataImporter;
import org.dspace.administer.RegistryImportException;
import org.dspace.administer.RegistryLoader;
@@ -24,8 +26,6 @@ import org.dspace.services.ConfigurationService;
import org.dspace.services.factory.DSpaceServicesFactory;
import org.flywaydb.core.api.callback.Callback;
import org.flywaydb.core.api.callback.Event;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.xml.sax.SAXException;
/**
@@ -52,7 +52,7 @@ public class RegistryUpdater implements Callback {
/**
* logging category
*/
private static final Logger log = LoggerFactory.getLogger(RegistryUpdater.class);
private static final Logger log = LogManager.getLogger();
/**
* Method to actually update our registries from latest configuration files.

7
dspace-api/src/main/java/org/dspace/storage/rdbms/xmlworkflow/V5_0_2014_11_04__Enable_XMLWorkflow_Migration.java
View File

@@ -14,8 +14,6 @@ import org.dspace.storage.rdbms.DatabaseUtils;
import org.dspace.storage.rdbms.migration.MigrationUtils;
import org.flywaydb.core.api.migration.BaseJavaMigration;
import org.flywaydb.core.api.migration.Context;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/**
* This class automatically migrates your DSpace Database to use the
@@ -35,11 +33,6 @@ import org.slf4j.LoggerFactory;
*/
public class V5_0_2014_11_04__Enable_XMLWorkflow_Migration
extends BaseJavaMigration {
/**
* logging category
*/
private static final Logger log = LoggerFactory.getLogger(V5_0_2014_11_04__Enable_XMLWorkflow_Migration.class);
// Size of migration script run
Integer migration_file_size = -1;

21
dspace-api/src/main/java/org/dspace/usage/TabFileUsageEventListener.java
View File

@@ -15,16 +15,16 @@ import java.io.PrintWriter;
import java.text.SimpleDateFormat;
import java.util.Date;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.core.Constants;
import org.dspace.services.ConfigurationService;
import org.dspace.services.model.Event;
import org.dspace.utils.DSpace;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/**
* Serialize {@link UsageEvent} data to a file as Tab delimited. In dspace.cfg
* specify the path to the file as the value of
* Serialize {@link UsageEvent} data to a file as Tab delimited.
* In {@code dspace.cfg} specify the path to the file as the value of
* {@code usageEvent.tabFileLogger.file}. If that path is not absolute, it
* will be interpreted as relative to the directory named in {@code log.dir}.
* If no name is configured, it defaults to "usage-events.tsv". If the file is
@@ -38,8 +38,7 @@ public class TabFileUsageEventListener
/**
* log category.
*/
private static final Logger errorLog = LoggerFactory
.getLogger(TabFileUsageEventListener.class);
private static final Logger errorLog = LogManager.getLogger();
/**
* ISO 8601 Basic string format for record timestamps.
@@ -77,11 +76,11 @@ public class TabFileUsageEventListener
try {
eventLog = new PrintWriter(new OutputStreamWriter(
new FileOutputStream(logFile, true)));
errorLog.debug("Writing to {}", logFile.getAbsolutePath());
errorLog.debug("Writing to {}", logFile::getAbsolutePath);
} catch (FileNotFoundException e) {
errorLog.error("{} cannot open file, will not log events: {}",
TabFileUsageEventListener.class.getName(),
e.getMessage());
TabFileUsageEventListener.class::getName,
e::getMessage);
throw new IllegalArgumentException("Cannot open event log file", e);
}
@@ -104,9 +103,7 @@ public class TabFileUsageEventListener
init();
}
if (errorLog.isDebugEnabled()) {
errorLog.debug("got: {}", event.toString());
}
errorLog.debug("got: {}", event::toString);
if (!(event instanceof UsageEvent)) {
return;

11
dspace-api/src/main/java/org/dspace/util/FrontendUrlService.java
View File

@@ -14,6 +14,8 @@ import static org.apache.commons.lang3.StringUtils.lowerCase;
import java.util.List;
import java.util.Optional;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.content.Bitstream;
import org.dspace.content.Item;
import org.dspace.core.Context;
@@ -22,18 +24,16 @@ import org.dspace.discovery.DiscoverResult;
import org.dspace.discovery.SearchService;
import org.dspace.discovery.SearchServiceException;
import org.dspace.services.ConfigurationService;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Component;
/**
* Service class for generation of front-end urls.
* Service class for generation of front-end URLs.
*/
@Component
public class FrontendUrlService {
private static final Logger log = LoggerFactory.getLogger(FrontendUrlService.class);
private static final Logger log = LogManager.getLogger();
@Autowired
private ConfigurationService configurationService;
@@ -80,7 +80,8 @@ public class FrontendUrlService {
}
}
} catch (SearchServiceException e) {
log.error("Failed getting entitytype through solr for item " + item.getID() + ": " + e.getMessage());
log.error("Failed getting entitytype through solr for item {}: {}",
item::getID, e::getMessage);
}
return Optional.empty();
}

12
dspace-api/src/main/java/org/dspace/util/MultiFormatDateParser.java
View File

@@ -23,9 +23,9 @@ import java.util.regex.Pattern;
import java.util.regex.PatternSyntaxException;
import javax.inject.Inject;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.servicemanager.DSpaceKernelInit;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/**
* Attempt to parse date strings in a variety of formats. This uses an external
@@ -38,7 +38,7 @@ import org.slf4j.LoggerFactory;
* @author mwood
*/
public class MultiFormatDateParser {
private static final Logger log = LoggerFactory.getLogger(MultiFormatDateParser.class);
private static final Logger log = LogManager.getLogger();
/**
* A list of rules, each binding a regular expression to a date format.
@@ -71,7 +71,7 @@ public class MultiFormatDateParser {
pattern = Pattern.compile(rule.getKey(), Pattern.CASE_INSENSITIVE);
} catch (PatternSyntaxException ex) {
log.error("Skipping format with unparseable pattern '{}'",
rule.getKey());
rule::getKey);
continue;
}
@@ -80,7 +80,7 @@ public class MultiFormatDateParser {
format = new SimpleDateFormat(rule.getValue());
} catch (IllegalArgumentException ex) {
log.error("Skipping uninterpretable date format '{}'",
rule.getValue());
rule::getValue);
continue;
}
format.setCalendar(Calendar.getInstance(UTC_ZONE));
@@ -107,7 +107,7 @@ public class MultiFormatDateParser {
}
} catch (ParseException ex) {
log.info("Date string '{}' matched pattern '{}' but did not parse: {}",
new String[] {dateString, candidate.format.toPattern(), ex.getMessage()});
() -> dateString, candidate.format::toPattern, ex::getMessage);
continue;
}
return result;

237
dspace-api/src/test/java/org/dspace/app/mediafilter/MediaFilterIT.java Normal file
View File

@@ -0,0 +1,237 @@
/**
* 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 static org.junit.Assert.assertTrue;
import java.io.IOException;
import java.io.InputStream;
import java.sql.SQLException;
import java.util.Iterator;
import java.util.List;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.dspace.AbstractIntegrationTestWithDatabase;
import org.dspace.authorize.AuthorizeException;
import org.dspace.builder.BitstreamBuilder;
import org.dspace.builder.CollectionBuilder;
import org.dspace.builder.CommunityBuilder;
import org.dspace.builder.ItemBuilder;
import org.dspace.content.Bitstream;
import org.dspace.content.Bundle;
import org.dspace.content.Collection;
import org.dspace.content.Community;
import org.dspace.content.DSpaceObject;
import org.dspace.content.Item;
import org.dspace.content.factory.ContentServiceFactory;
import org.dspace.content.service.BitstreamService;
import org.dspace.content.service.ItemService;
import org.junit.Before;
import org.junit.Test;
/**
* Tests of {@link MediaFilterScript}.
*
* @author Andrea Bollini <andrea.bollini at 4science.com>
*/
public class MediaFilterIT extends AbstractIntegrationTestWithDatabase {
private ItemService itemService = ContentServiceFactory.getInstance().getItemService();
private BitstreamService bitstreamService = ContentServiceFactory.getInstance().getBitstreamService();
protected Community topComm1;
protected Community topComm2;
protected Community childComm1_1;
protected Community childComm1_2;
protected Collection col1_1;
protected Collection col1_2;
protected Collection col1_1_1;
protected Collection col1_1_2;
protected Collection col1_2_1;
protected Collection col1_2_2;
protected Collection col2_1;
protected Item item1_1_a;
protected Item item1_1_b;
protected Item item1_2_a;
protected Item item1_2_b;
protected Item item1_1_1_a;
protected Item item1_1_1_b;
protected Item item1_1_2_a;
protected Item item1_1_2_b;
protected Item item1_2_1_a;
protected Item item1_2_1_b;
protected Item item1_2_2_a;
protected Item item1_2_2_b;
protected Item item2_1_a;
protected Item item2_1_b;
@Before
public void setup() throws IOException, SQLException, AuthorizeException {
context.turnOffAuthorisationSystem();
topComm1 = CommunityBuilder.createCommunity(context).withName("Parent Community1").build();
topComm2 = CommunityBuilder.createCommunity(context).withName("Parent Community2").build();
childComm1_1 = CommunityBuilder.createCommunity(context).withName("Child Community1_1")
.addParentCommunity(context, topComm1).build();
childComm1_2 = CommunityBuilder.createCommunity(context).withName("Child Community1_2")
.addParentCommunity(context, topComm1).build();
col1_1 = CollectionBuilder.createCollection(context, topComm1).withName("Collection 1_1").build();
col1_2 = CollectionBuilder.createCollection(context, topComm1).withName("Collection 1_2").build();
col1_1_1 = CollectionBuilder.createCollection(context, childComm1_1).withName("Collection 1_1_1").build();
col1_1_2 = CollectionBuilder.createCollection(context, childComm1_1).withName("Collection 1_1_2").build();
col1_2_1 = CollectionBuilder.createCollection(context, childComm1_2).withName("Collection 1_1_1").build();
col1_2_2 = CollectionBuilder.createCollection(context, childComm1_2).withName("Collection 1_2").build();
col2_1 = CollectionBuilder.createCollection(context, topComm2).withName("Collection 2_1").build();
// Create two items in each collection, one with the test.csv file and one with the test.txt file
item1_1_a = ItemBuilder.createItem(context, col1_1).withTitle("Item 1_1_a").withIssueDate("2017-10-17").build();
item1_1_b = ItemBuilder.createItem(context, col1_1).withTitle("Item 1_1_b").withIssueDate("2017-10-17").build();
item1_1_1_a = ItemBuilder.createItem(context, col1_1_1).withTitle("Item 1_1_1_a").withIssueDate("2017-10-17")
.build();
item1_1_1_b = ItemBuilder.createItem(context, col1_1_1).withTitle("Item 1_1_1_b").withIssueDate("2017-10-17")
.build();
item1_1_2_a = ItemBuilder.createItem(context, col1_1_2).withTitle("Item 1_1_2_a").withIssueDate("2017-10-17")
.build();
item1_1_2_b = ItemBuilder.createItem(context, col1_1_2).withTitle("Item 1_1_2_b").withIssueDate("2017-10-17")
.build();
item1_2_a = ItemBuilder.createItem(context, col1_2).withTitle("Item 1_2_a").withIssueDate("2017-10-17").build();
item1_2_b = ItemBuilder.createItem(context, col1_2).withTitle("Item 1_2_b").withIssueDate("2017-10-17").build();
item1_2_1_a = ItemBuilder.createItem(context, col1_2_1).withTitle("Item 1_2_1_a").withIssueDate("2017-10-17")
.build();
item1_2_1_b = ItemBuilder.createItem(context, col1_2_1).withTitle("Item 1_2_1_b").withIssueDate("2017-10-17")
.build();
item1_2_2_a = ItemBuilder.createItem(context, col1_2_2).withTitle("Item 1_2_2_a").withIssueDate("2017-10-17")
.build();
item1_2_2_b = ItemBuilder.createItem(context, col1_2_2).withTitle("Item 1_2_2_b").withIssueDate("2017-10-17")
.build();
item2_1_a = ItemBuilder.createItem(context, col2_1).withTitle("Item 2_1_a").withIssueDate("2017-10-17").build();
item2_1_b = ItemBuilder.createItem(context, col2_1).withTitle("Item 2_1_b").withIssueDate("2017-10-17").build();
addBitstream(item1_1_a, "test.csv");
addBitstream(item1_1_b, "test.txt");
addBitstream(item1_2_a, "test.csv");
addBitstream(item1_2_b, "test.txt");
addBitstream(item1_1_1_a, "test.csv");
addBitstream(item1_1_1_b, "test.txt");
addBitstream(item1_1_2_a, "test.csv");
addBitstream(item1_1_2_b, "test.txt");
addBitstream(item1_2_1_a, "test.csv");
addBitstream(item1_2_1_b, "test.txt");
addBitstream(item1_2_2_a, "test.csv");
addBitstream(item1_2_2_b, "test.txt");
addBitstream(item2_1_a, "test.csv");
addBitstream(item2_1_b, "test.txt");
context.restoreAuthSystemState();
}
private void addBitstream(Item item, String filename) throws SQLException, AuthorizeException, IOException {
BitstreamBuilder.createBitstream(context, item, getClass().getResourceAsStream(filename)).withName(filename)
.guessFormat().build();
}
@Test
public void mediaFilterScriptAllItemsTest() throws Exception {
performMediaFilterScript(null);
Iterator<Item> items = itemService.findAll(context);
while (items.hasNext()) {
Item item = items.next();
checkItemHasBeenProcessed(item);
}
}
@Test
public void mediaFilterScriptIdentifiersTest() throws Exception {
// process the item 1_1_a and verify that no other items has been processed using the "closer" one
performMediaFilterScript(item1_1_a);
checkItemHasBeenProcessed(item1_1_a);
checkItemHasBeenNotProcessed(item1_1_b);
// process the collection 1_1_1 and verify that items in another collection has not been processed
performMediaFilterScript(col1_1_1);
checkItemHasBeenProcessed(item1_1_1_a);
checkItemHasBeenProcessed(item1_1_1_b);
checkItemHasBeenNotProcessed(item1_1_2_a);
checkItemHasBeenNotProcessed(item1_1_2_b);
// process a top community with only collections
performMediaFilterScript(topComm2);
checkItemHasBeenProcessed(item2_1_a);
checkItemHasBeenProcessed(item2_1_b);
// verify that the other items have not been processed yet
checkItemHasBeenNotProcessed(item1_1_b);
checkItemHasBeenNotProcessed(item1_2_a);
checkItemHasBeenNotProcessed(item1_2_b);
checkItemHasBeenNotProcessed(item1_1_2_a);
checkItemHasBeenNotProcessed(item1_1_2_b);
checkItemHasBeenNotProcessed(item1_2_1_a);
checkItemHasBeenNotProcessed(item1_2_1_b);
checkItemHasBeenNotProcessed(item1_2_2_a);
checkItemHasBeenNotProcessed(item1_2_2_b);
// process a more structured community and verify that all the items at all levels are processed
performMediaFilterScript(topComm1);
// items that were already processed should stay processed
checkItemHasBeenProcessed(item1_1_a);
checkItemHasBeenProcessed(item1_1_1_a);
checkItemHasBeenProcessed(item1_1_1_b);
// residual items should have been processed as well now
checkItemHasBeenProcessed(item1_1_b);
checkItemHasBeenProcessed(item1_2_a);
checkItemHasBeenProcessed(item1_2_b);
checkItemHasBeenProcessed(item1_1_2_a);
checkItemHasBeenProcessed(item1_1_2_b);
checkItemHasBeenProcessed(item1_2_1_a);
checkItemHasBeenProcessed(item1_2_1_b);
checkItemHasBeenProcessed(item1_2_2_a);
checkItemHasBeenProcessed(item1_2_2_b);
}
private void checkItemHasBeenNotProcessed(Item item) throws IOException, SQLException, AuthorizeException {
List<Bundle> textBundles = item.getBundles("TEXT");
assertTrue("The item " + item.getName() + " should NOT have the TEXT bundle", textBundles.size() == 0);
}
private void checkItemHasBeenProcessed(Item item) throws IOException, SQLException, AuthorizeException {
String expectedFileName = StringUtils.endsWith(item.getName(), "_a") ? "test.csv.txt" : "test.txt.txt";
String expectedContent = StringUtils.endsWith(item.getName(), "_a") ? "data3,3" : "quick brown fox";
List<Bundle> textBundles = item.getBundles("TEXT");
assertTrue("The item " + item.getName() + " has NOT the TEXT bundle", textBundles.size() == 1);
List<Bitstream> bitstreams = textBundles.get(0).getBitstreams();
assertTrue("The item " + item.getName() + " has NOT exactly 1 bitstream in the TEXT bundle",
bitstreams.size() == 1);
assertTrue("The text bistream in the " + item.getName() + " is NOT named properly [" + expectedFileName + "]",
StringUtils.equals(bitstreams.get(0).getName(), expectedFileName));
assertTrue("The text bistream in the " + item.getName() + " doesn't contain the proper content ["
+ expectedContent + "]", StringUtils.contains(getContent(bitstreams.get(0)), expectedContent));
}
private CharSequence getContent(Bitstream bitstream) throws IOException, SQLException, AuthorizeException {
try (InputStream input = bitstreamService.retrieve(context, bitstream)) {
return IOUtils.toString(input, "UTF-8");
}
}
private void performMediaFilterScript(DSpaceObject dso) throws Exception {
if (dso != null) {
runDSpaceScript("filter-media", "-i", dso.getHandle());
} else {
runDSpaceScript("filter-media");
}
// reload our items to see the changes
item1_1_a = context.reloadEntity(item1_1_a);
item1_1_b = context.reloadEntity(item1_1_b);
item1_2_a = context.reloadEntity(item1_2_a);
item1_2_b = context.reloadEntity(item1_2_b);
item1_1_1_a = context.reloadEntity(item1_1_1_a);
item1_1_1_b = context.reloadEntity(item1_1_1_b);
item1_1_2_a = context.reloadEntity(item1_1_2_a);
item1_1_2_b = context.reloadEntity(item1_1_2_b);
item1_2_1_a = context.reloadEntity(item1_2_1_a);
item1_2_1_b = context.reloadEntity(item1_2_1_b);
item1_2_2_a = context.reloadEntity(item1_2_2_a);
item1_2_2_b = context.reloadEntity(item1_2_2_b);
item2_1_a = context.reloadEntity(item2_1_a);
item2_1_b = context.reloadEntity(item2_1_b);
}
}

14
dspace-api/src/test/java/org/dspace/builder/BitstreamBuilder.java
View File

@@ -21,6 +21,7 @@ import org.dspace.content.Item;
import org.dspace.content.MetadataField;
import org.dspace.content.MetadataValue;
import org.dspace.content.factory.ContentServiceFactory;
import org.dspace.content.service.BitstreamFormatService;
import org.dspace.content.service.DSpaceObjectService;
import org.dspace.content.service.MetadataValueService;
import org.dspace.core.Constants;
@@ -168,6 +169,19 @@ public class BitstreamBuilder extends AbstractDSpaceObjectBuilder<Bitstream> {
return this;
}
/**
* Guess the bitstream format as during the submission via the
* {@link BitstreamFormatService#guessFormat(Context, Bitstream)}
*
* @return the BitstreamBuilder with the format set according to
* {@link BitstreamFormatService#guessFormat(Context, Bitstream)}
* @throws SQLException
*/
public BitstreamBuilder guessFormat() throws SQLException {
bitstream.setFormat(context, bitstreamFormatService.guessFormat(context, bitstream));
return this;
}
public BitstreamBuilder withFormat(String format) throws SQLException {
bitstreamService.addMetadata(context, bitstream, "dc", "format", null, null, format);

6
dspace-api/src/test/java/org/dspace/curate/CuratorReportTest.java
View File

@@ -14,6 +14,8 @@ import java.util.ArrayList;
import java.util.List;
import java.util.regex.Pattern;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.AbstractUnitTest;
import org.dspace.authorize.AuthorizeException;
import org.dspace.content.Community;
@@ -27,8 +29,6 @@ import org.junit.Assert;
import org.junit.Before;
import org.junit.BeforeClass;
import org.junit.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/**
* Drive the Curator and check results.
@@ -37,7 +37,7 @@ import org.slf4j.LoggerFactory;
*/
public class CuratorReportTest
extends AbstractUnitTest {
Logger LOG = LoggerFactory.getLogger(CuratorReportTest.class);
Logger LOG = LogManager.getLogger();
public CuratorReportTest() {
}

6
dspace-iiif/pom.xml
View File

@@ -28,6 +28,12 @@
<dependencies>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-api</artifactId>
<version>${log4j.version}</version>
</dependency>
<!-- Needed to support Spring @Configuration classes (to register servlets/beans with Spring Boot webapp) -->
<dependency>
<groupId>org.springframework.boot</groupId>

10
dspace-server-webapp/pom.xml
View File

@@ -421,7 +421,7 @@
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter</artifactId>
<version>${spring-boot.version}</version>
<version>${spring-boot.version}</version>
<exclusions>
<exclusion>
<groupId>org.springframework.boot</groupId>
@@ -433,7 +433,13 @@
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-log4j2</artifactId>
<version>${spring-boot.version}</version>
<version>${spring-boot.version}</version>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-api</artifactId>
<version>${log4j.version}</version>
</dependency>
<!-- DSpace dependencies -->

4
dspace-server-webapp/src/main/java/org/dspace/app/rest/AuthenticationRestController.java
View File

@@ -36,8 +36,6 @@ import org.dspace.app.rest.utils.ContextUtil;
import org.dspace.app.rest.utils.Utils;
import org.dspace.core.Context;
import org.dspace.service.ClientInfoService;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.InitializingBean;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.data.domain.Page;
@@ -64,8 +62,6 @@ import org.springframework.web.bind.annotation.RestController;
@RestController
public class AuthenticationRestController implements InitializingBean {
private static final Logger log = LoggerFactory.getLogger(AuthenticationRestController.class);
@Autowired
DiscoverableEndpointsService discoverableEndpointsService;

15
dspace-server-webapp/src/main/java/org/dspace/app/rest/OidcRestController.java
View File

@@ -14,11 +14,11 @@ import javax.annotation.PostConstruct;
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.app.rest.model.AuthnRest;
import org.dspace.core.Utils;
import org.dspace.services.ConfigurationService;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.hateoas.Link;
import org.springframework.web.bind.annotation.RequestMapping;
@@ -27,7 +27,7 @@ import org.springframework.web.bind.annotation.RequestParam;
import org.springframework.web.bind.annotation.RestController;
/**
* Rest controller that handles redirect after OIDC authentication succeded.
* Rest controller that handles redirect after OIDC authentication succeeded.
*
* @author Luca Giamminonni (luca.giamminonni at 4science.it)
*/
@@ -35,7 +35,7 @@ import org.springframework.web.bind.annotation.RestController;
@RequestMapping(value = "/api/" + AuthnRest.CATEGORY + "/oidc")
public class OidcRestController {
private static final Logger log = LoggerFactory.getLogger(OidcRestController.class);
private static final Logger log = LogManager.getLogger();
@Autowired
private ConfigurationService configurationService;
@@ -66,11 +66,12 @@ public class OidcRestController {
}
if (StringUtils.equalsAnyIgnoreCase(redirectHostName, allowedHostNames.toArray(new String[0]))) {
log.debug("OIDC redirecting to " + redirectUrl);
log.debug("OIDC redirecting to {}", redirectUrl);
response.sendRedirect(redirectUrl); // lgtm [java/unvalidated-url-redirection]
} else {
log.error("Invalid OIDC redirectURL=" + redirectUrl +
". URL doesn't match hostname of server or UI!");
log.error("Invalid OIDC redirectURL={}."
+ " URL doesn't match hostname of server or UI!",
redirectUrl);
response.sendError(HttpServletResponse.SC_BAD_REQUEST,
"Invalid redirectURL! Must match server or ui hostname.");
}

4
dspace-server-webapp/src/main/java/org/dspace/app/rest/WebApplication.java
View File

@@ -24,8 +24,6 @@ import org.dspace.app.solrdatabaseresync.SolrDatabaseResyncCli;
import org.dspace.app.util.DSpaceContextListener;
import org.dspace.google.GoogleAsyncEventListener;
import org.dspace.utils.servlet.DSpaceWebappServletFilter;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.cache.annotation.EnableCaching;
import org.springframework.context.annotation.Bean;
@@ -55,8 +53,6 @@ import org.springframework.web.servlet.config.annotation.WebMvcConfigurer;
@Configuration
public class WebApplication {
private static final Logger log = LoggerFactory.getLogger(WebApplication.class);
@Autowired
private ApplicationConfig configuration;

9
dspace-server-webapp/src/main/java/org/dspace/app/rest/authorization/impl/CanClaimItemFeature.java
View File

@@ -11,6 +11,8 @@ import java.sql.SQLException;
import java.util.UUID;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.app.rest.authorization.AuthorizationFeature;
import org.dspace.app.rest.authorization.AuthorizationFeatureDocumentation;
import org.dspace.app.rest.model.BaseObjectRest;
@@ -22,8 +24,6 @@ import org.dspace.content.service.ItemService;
import org.dspace.core.Context;
import org.dspace.eperson.EPerson;
import org.dspace.profile.service.ResearcherProfileService;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Component;
@@ -43,7 +43,7 @@ public class CanClaimItemFeature implements AuthorizationFeature {
public static final String NAME = "canClaimItem";
private static final Logger LOG = LoggerFactory.getLogger(CanClaimItemFeature.class);
private static final Logger LOG = LogManager.getLogger();
@Autowired
private ItemService itemService;
@@ -72,7 +72,8 @@ public class CanClaimItemFeature implements AuthorizationFeature {
try {
return researcherProfileService.findById(context, context.getCurrentUser().getID()) == null;
} catch (SQLException | AuthorizeException e) {
LOG.warn("Error while checking if eperson has a ResearcherProfileAssociated: {}", e.getMessage(), e);
LOG.warn("Error while checking if eperson has a ResearcherProfileAssociated: {}",
e.getMessage(), e);
return false;
}
}

4
dspace-server-webapp/src/main/java/org/dspace/app/rest/filter/DSpaceRequestContextFilter.java
View File

@@ -17,8 +17,6 @@ import javax.servlet.ServletResponse;
import org.dspace.app.rest.utils.ContextUtil;
import org.dspace.core.Context;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/**
* A Servlet Filter whose only role is to clean up open Context objects in
@@ -29,8 +27,6 @@ import org.slf4j.LoggerFactory;
* @see ContextUtil
*/
public class DSpaceRequestContextFilter implements Filter {
private static final Logger log = LoggerFactory.getLogger(DSpaceRequestContextFilter.class);
@Override
public void init(FilterConfig filterConfig) throws ServletException {
//noop

6
dspace-server-webapp/src/main/java/org/dspace/app/rest/login/impl/ResearcherProfileAutomaticClaim.java
View File

@@ -18,6 +18,8 @@ import java.util.stream.Collectors;
import org.apache.commons.collections4.CollectionUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.app.rest.login.PostLoggedInAction;
import org.dspace.authorize.AuthorizeException;
import org.dspace.content.Item;
@@ -27,8 +29,6 @@ import org.dspace.core.Context;
import org.dspace.eperson.EPerson;
import org.dspace.eperson.service.EPersonService;
import org.dspace.profile.service.ResearcherProfileService;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.util.Assert;
@@ -43,7 +43,7 @@ import org.springframework.util.Assert;
*/
public class ResearcherProfileAutomaticClaim implements PostLoggedInAction {
private final static Logger LOGGER = LoggerFactory.getLogger(ResearcherProfileAutomaticClaim.class);
private final static Logger LOGGER = LogManager.getLogger();
@Autowired
private ResearcherProfileService researcherProfileService;

5
dspace-server-webapp/src/main/java/org/dspace/app/rest/model/LDNMessageEntityRest.java
View File

@@ -60,6 +60,11 @@ public class LDNMessageEntityRest extends BaseObjectRest<String> {
return NAME;
}
@Override
public String getTypePlural() {
return NAME_PLURALS;
}
@Override
public String getCategory() {
return CATEGORY;

16
dspace-server-webapp/src/main/java/org/dspace/app/rest/repository/AuthorizationRestRepository.java
View File

@@ -18,6 +18,8 @@ import java.util.UUID;
import java.util.stream.Collectors;
import org.apache.commons.lang3.ObjectUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.app.rest.Parameter;
import org.dspace.app.rest.SearchRestMethod;
import org.dspace.app.rest.authorization.Authorization;
@@ -34,8 +36,6 @@ import org.dspace.core.Context;
import org.dspace.discovery.SearchServiceException;
import org.dspace.eperson.EPerson;
import org.dspace.eperson.service.EPersonService;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.data.domain.Page;
import org.springframework.data.domain.Pageable;
@@ -52,7 +52,7 @@ import org.springframework.stereotype.Component;
@Component(AuthorizationRest.CATEGORY + "." + AuthorizationRest.PLURAL_NAME)
public class AuthorizationRestRepository extends DSpaceRestRepository<AuthorizationRest, String> {
private static final Logger log = LoggerFactory.getLogger(AuthorizationRestRepository.class);
private static final Logger log = LogManager.getLogger();
@Autowired
private AuthorizationFeatureService authorizationFeatureService;
@@ -79,7 +79,7 @@ public class AuthorizationRestRepository extends DSpaceRestRepository<Authorizat
try {
featureName = authorizationRestUtil.getFeatureName(id);
} catch (IllegalArgumentException e) {
log.warn(e.getMessage(), e);
log.warn(e::getMessage, e);
return null;
}
try {
@@ -87,7 +87,7 @@ public class AuthorizationRestRepository extends DSpaceRestRepository<Authorizat
try {
object = authorizationRestUtil.getObject(context, id);
} catch (IllegalArgumentException e) {
log.warn("Object informations not found in the specified id " + id, e);
log.warn("Object informations not found in the specified id {}", id, e);
return null;
}
@@ -104,7 +104,7 @@ public class AuthorizationRestRepository extends DSpaceRestRepository<Authorizat
try {
user = authorizationRestUtil.getEperson(context, id);
} catch (IllegalArgumentException e) {
log.warn("Invalid eperson informations in the specified id " + id, e);
log.warn("Invalid eperson informations in the specified id {}", id, e);
return null;
}
EPerson currUser = context.getCurrentUser();
@@ -136,7 +136,7 @@ public class AuthorizationRestRepository extends DSpaceRestRepository<Authorizat
/**
* It returns the list of matching available authorizations granted to the specified eperson or to the anonymous
* user. Only administrators and the user identified by the epersonUuid parameter can access this method
*
*
* @param uri
* the uri of the object to check the authorization against
* @param epersonUuid
@@ -283,7 +283,7 @@ public class AuthorizationRestRepository extends DSpaceRestRepository<Authorizat
/**
* Return the user specified in the request parameter if valid
*
*
* @param context
* @param epersonUuid
* @return

2
dspace-server-webapp/src/main/java/org/dspace/app/rest/repository/LDNMessageRestRepository.java
View File

@@ -30,7 +30,7 @@ import org.springframework.stereotype.Component;
* @author Stefano Maffei(stefano.maffei at 4science.com)
*/
@Component(LDNMessageEntityRest.CATEGORY + "." + LDNMessageEntityRest.NAME)
@Component(LDNMessageEntityRest.CATEGORY + "." + LDNMessageEntityRest.NAME_PLURALS)
public class LDNMessageRestRepository extends DSpaceRestRepository<LDNMessageEntityRest, String> {
@Autowired

8
dspace-server-webapp/src/main/java/org/dspace/app/rest/security/AdminRestPermissionEvaluatorPlugin.java
View File

@@ -10,6 +10,8 @@ package org.dspace.app.rest.security;
import java.io.Serializable;
import java.sql.SQLException;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.app.rest.utils.ContextUtil;
import org.dspace.authorize.service.AuthorizeService;
import org.dspace.core.Context;
@@ -17,8 +19,6 @@ import org.dspace.eperson.EPerson;
import org.dspace.eperson.service.EPersonService;
import org.dspace.services.RequestService;
import org.dspace.services.model.Request;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.core.Ordered;
import org.springframework.core.annotation.Order;
@@ -34,7 +34,7 @@ import org.springframework.stereotype.Component;
@Order(value = Ordered.HIGHEST_PRECEDENCE)
public class AdminRestPermissionEvaluatorPlugin extends RestObjectPermissionEvaluatorPlugin {
private static final Logger log = LoggerFactory.getLogger(RestObjectPermissionEvaluatorPlugin.class);
private static final Logger log = LogManager.getLogger();
@Autowired
private AuthorizeService authorizeService;
@@ -69,7 +69,7 @@ public class AdminRestPermissionEvaluatorPlugin extends RestObjectPermissionEval
}
} catch (SQLException e) {
log.error(e.getMessage(), e);
log.error(e::getMessage, e);
}
return false;
}

10
dspace-server-webapp/src/main/java/org/dspace/app/rest/security/AuthorizeServicePermissionEvaluatorPlugin.java
View File

@@ -11,6 +11,8 @@ import java.io.Serializable;
import java.sql.SQLException;
import java.util.UUID;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.app.rest.utils.ContextUtil;
import org.dspace.authorize.service.AuthorizeService;
import org.dspace.content.DSpaceObject;
@@ -24,21 +26,19 @@ import org.dspace.eperson.service.EPersonService;
import org.dspace.services.RequestService;
import org.dspace.services.model.Request;
import org.dspace.util.UUIDUtils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.security.core.Authentication;
import org.springframework.stereotype.Component;
/**
* DSpaceObjectPermissionEvaluatorPlugin will check persmissions based on the DSpace {@link AuthorizeService}.
* DSpaceObjectPermissionEvaluatorPlugin will check permissions based on the DSpace {@link AuthorizeService}.
* This service will validate if the authenticated user is allowed to perform an action on the given DSpace Object
* based on the resource policies attached to that DSpace object.
*/
@Component
public class AuthorizeServicePermissionEvaluatorPlugin extends RestObjectPermissionEvaluatorPlugin {
private static final Logger log = LoggerFactory.getLogger(AuthorizeServicePermissionEvaluatorPlugin.class);
private static final Logger log = LogManager.getLogger();
@Autowired
private AuthorizeService authorizeService;
@@ -106,7 +106,7 @@ public class AuthorizeServicePermissionEvaluatorPlugin extends RestObjectPermiss
}
} catch (SQLException e) {
log.error(e.getMessage(), e);
log.error(e::getMessage, e);
}
return false;

8
dspace-server-webapp/src/main/java/org/dspace/app/rest/security/BitstreamMetadataReadPermissionEvaluatorPlugin.java
View File

@@ -11,6 +11,8 @@ import java.io.Serializable;
import java.sql.SQLException;
import java.util.UUID;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.app.rest.repository.BitstreamRestRepository;
import org.dspace.app.rest.utils.ContextUtil;
import org.dspace.app.rest.utils.DSpaceObjectUtils;
@@ -24,8 +26,6 @@ import org.dspace.core.Constants;
import org.dspace.core.Context;
import org.dspace.services.RequestService;
import org.dspace.services.model.Request;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.security.core.Authentication;
import org.springframework.stereotype.Component;
@@ -39,7 +39,7 @@ import org.springframework.stereotype.Component;
@Component
public class BitstreamMetadataReadPermissionEvaluatorPlugin extends RestObjectPermissionEvaluatorPlugin {
private static final Logger log = LoggerFactory.getLogger(BitstreamMetadataReadPermissionEvaluatorPlugin.class);
private static final Logger log = LogManager.getLogger();
@Autowired
private RequestService requestService;
@@ -66,7 +66,7 @@ public class BitstreamMetadataReadPermissionEvaluatorPlugin extends RestObjectPe
return this.metadataReadPermissionOnBitstream(context, (Bitstream) dso);
}
} catch (SQLException e) {
log.error(e.getMessage(), e);
log.error(e::getMessage, e);
}
}
return false;

10
dspace-server-webapp/src/main/java/org/dspace/app/rest/security/ClaimedTaskRestPermissionEvaluatorPlugin.java
View File

@@ -11,6 +11,8 @@ import java.io.Serializable;
import java.sql.SQLException;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.app.rest.model.ClaimedTaskRest;
import org.dspace.app.rest.utils.ContextUtil;
import org.dspace.core.Context;
@@ -20,8 +22,6 @@ import org.dspace.services.RequestService;
import org.dspace.services.model.Request;
import org.dspace.xmlworkflow.storedcomponents.ClaimedTask;
import org.dspace.xmlworkflow.storedcomponents.service.ClaimedTaskService;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.security.core.Authentication;
import org.springframework.stereotype.Component;
@@ -29,13 +29,13 @@ import org.springframework.stereotype.Component;
/**
* An authenticated user is allowed to interact with a claimed task only if they own it
* claim.
*
*
* @author Andrea Bollini (andrea.bollini at 4science.it)
*/
@Component
public class ClaimedTaskRestPermissionEvaluatorPlugin extends RestObjectPermissionEvaluatorPlugin {
private static final Logger log = LoggerFactory.getLogger(ClaimedTaskRestPermissionEvaluatorPlugin.class);
private static final Logger log = LogManager.getLogger();
@Autowired
private RequestService requestService;
@@ -74,7 +74,7 @@ public class ClaimedTaskRestPermissionEvaluatorPlugin extends RestObjectPermissi
}
} catch (SQLException e) {
log.error(e.getMessage(), e);
log.error(e::getMessage, e);
}
return false;
}

7
dspace-server-webapp/src/main/java/org/dspace/app/rest/security/CustomLogoutHandler.java
View File

@@ -10,10 +10,10 @@ package org.dspace.app.rest.security;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.app.rest.utils.ContextUtil;
import org.dspace.core.Context;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.security.core.Authentication;
import org.springframework.security.web.authentication.logout.LogoutHandler;
@@ -28,7 +28,7 @@ import org.springframework.stereotype.Component;
@Component
public class CustomLogoutHandler implements LogoutHandler {
private static final Logger log = LoggerFactory.getLogger(CustomLogoutHandler.class);
private static final Logger log = LogManager.getLogger();
@Autowired
private RestAuthenticationService restAuthenticationService;
@@ -40,6 +40,7 @@ public class CustomLogoutHandler implements LogoutHandler {
* @param httpServletResponse
* @param authentication
*/
@Override
public void logout(HttpServletRequest httpServletRequest, HttpServletResponse httpServletResponse,
Authentication authentication) {
try {

13
dspace-server-webapp/src/main/java/org/dspace/app/rest/security/DSpaceObjectAdminPermissionEvaluatorPlugin.java
View File

@@ -12,6 +12,8 @@ import java.sql.SQLException;
import java.util.UUID;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.app.rest.utils.ContextUtil;
import org.dspace.app.rest.utils.DSpaceObjectUtils;
import org.dspace.authorize.service.AuthorizeService;
@@ -19,20 +21,19 @@ import org.dspace.content.DSpaceObject;
import org.dspace.core.Context;
import org.dspace.services.RequestService;
import org.dspace.services.model.Request;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.security.core.Authentication;
import org.springframework.stereotype.Component;
/**
* {@link RestPermissionEvaluatorPlugin} class that evaluate admin permission against a generic DSpace Object
*
* {@link RestPermissionEvaluatorPlugin} class that evaluate admin permission against a generic DSpace Object.
*
* @author Mykhaylo Boychuk (4science.it)
*/
@Component
public class DSpaceObjectAdminPermissionEvaluatorPlugin extends RestObjectPermissionEvaluatorPlugin {
private static final Logger log = LoggerFactory.getLogger(DSpaceObjectAdminPermissionEvaluatorPlugin.class);
private static final Logger log = LogManager.getLogger();
public static final String DSPACE_OBJECT = "dspaceObject";
@@ -64,7 +65,7 @@ public class DSpaceObjectAdminPermissionEvaluatorPlugin extends RestObjectPermis
DSpaceObject dso = dspaceObjectUtil.findDSpaceObject(context, dsoUuid);
return authorizeService.isAdmin(context, dso);
} catch (SQLException e) {
log.error(e.getMessage(), e);
log.error(e::getMessage, e);
}
return false;
}

17
dspace-server-webapp/src/main/java/org/dspace/app/rest/security/EPersonRestAuthenticationProvider.java
View File

@@ -19,6 +19,8 @@ import javax.annotation.PostConstruct;
import javax.servlet.http.HttpServletRequest;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.app.rest.login.PostLoggedInAction;
import org.dspace.app.rest.utils.ContextUtil;
import org.dspace.authenticate.AuthenticationMethod;
@@ -28,8 +30,6 @@ import org.dspace.core.Context;
import org.dspace.core.LogHelper;
import org.dspace.eperson.EPerson;
import org.dspace.services.RequestService;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.security.authentication.AuthenticationProvider;
import org.springframework.security.authentication.BadCredentialsException;
@@ -40,7 +40,7 @@ import org.springframework.security.core.authority.SimpleGrantedAuthority;
import org.springframework.stereotype.Component;
/**
* This class is responsible for authenticating a user via REST
* This class is responsible for authenticating a user via REST.
*
* @author Frederic Van Reet (frederic dot vanreet at atmire dot com)
* @author Tom Desair (tom dot desair at atmire dot com)
@@ -48,7 +48,7 @@ import org.springframework.stereotype.Component;
@Component
public class EPersonRestAuthenticationProvider implements AuthenticationProvider {
private static final Logger log = LoggerFactory.getLogger(EPersonRestAuthenticationProvider.class);
private static final Logger log = LogManager.getLogger();
public static final String MANAGE_ACCESS_GROUP = "MANAGE_ACCESS_GROUP";
@@ -144,9 +144,8 @@ public class EPersonRestAuthenticationProvider implements AuthenticationProvider
}
} else {
log.info(LogHelper.getHeader(newContext, "failed_login", "email="
+ name + ", result="
+ authenticateResult));
log.info(LogHelper.getHeader(newContext, "failed_login",
"email={}, result={}"), name, authenticateResult);
throw new BadCredentialsException("Login failed");
}
}
@@ -155,7 +154,7 @@ public class EPersonRestAuthenticationProvider implements AuthenticationProvider
try {
newContext.complete();
} catch (SQLException e) {
log.error(e.getMessage() + " occurred while trying to close", e);
log.error("{} occurred while trying to close", e.getMessage(), e);
}
}
}
@@ -182,7 +181,7 @@ public class EPersonRestAuthenticationProvider implements AuthenticationProvider
return new DSpaceAuthentication(ePerson, getGrantedAuthorities(context));
} else {
log.info(LogHelper.getHeader(context, "failed_login", "No eperson with an non-blank e-mail address found"));
log.info(LogHelper.getHeader(context, "failed_login", "No eperson with a non-blank e-mail address found"));
throw new BadCredentialsException("Login failed");
}
}

10
dspace-server-webapp/src/main/java/org/dspace/app/rest/security/EPersonRestPermissionEvaluatorPlugin.java
View File

@@ -14,6 +14,8 @@ import java.util.UUID;
import javax.servlet.http.HttpServletRequest;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.app.rest.model.patch.Operation;
import org.dspace.app.rest.model.patch.Patch;
import org.dspace.app.rest.repository.patch.operation.DSpaceObjectMetadataPatchUtils;
@@ -27,8 +29,6 @@ import org.dspace.core.Context;
import org.dspace.eperson.EPerson;
import org.dspace.services.RequestService;
import org.dspace.services.model.Request;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.security.core.Authentication;
import org.springframework.stereotype.Component;
@@ -40,7 +40,7 @@ import org.springframework.stereotype.Component;
@Component
public class EPersonRestPermissionEvaluatorPlugin extends RestObjectPermissionEvaluatorPlugin {
private static final Logger log = LoggerFactory.getLogger(EPersonRestPermissionEvaluatorPlugin.class);
private static final Logger log = LogManager.getLogger();
@Autowired
AuthorizeService authorizeService;
@@ -84,7 +84,7 @@ public class EPersonRestPermissionEvaluatorPlugin extends RestObjectPermissionEv
return true;
}
} catch (SQLException e) {
log.error(e.getMessage(), e);
log.error(e::getMessage, e);
}
@@ -100,7 +100,7 @@ public class EPersonRestPermissionEvaluatorPlugin extends RestObjectPermissionEv
Request currentRequest = requestService.getCurrentRequest();
if (currentRequest != null) {
HttpServletRequest httpServletRequest = currentRequest.getHttpServletRequest();
if (operations.size() > 0
if (!operations.isEmpty()
&& StringUtils.equalsIgnoreCase(operations.get(0).getOp(), PatchOperation.OPERATION_ADD)
&& StringUtils.equalsIgnoreCase(operations.get(0).getPath(),
EPersonPasswordAddOperation.OPERATION_PASSWORD_CHANGE)

8
dspace-server-webapp/src/main/java/org/dspace/app/rest/security/GroupRestPermissionEvaluatorPlugin.java
View File

@@ -11,6 +11,8 @@ import java.io.Serializable;
import java.sql.SQLException;
import java.util.UUID;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.app.rest.utils.ContextUtil;
import org.dspace.app.util.AuthorizeUtil;
import org.dspace.authorize.service.AuthorizeService;
@@ -22,8 +24,6 @@ import org.dspace.eperson.service.EPersonService;
import org.dspace.eperson.service.GroupService;
import org.dspace.services.RequestService;
import org.dspace.services.model.Request;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.security.core.Authentication;
import org.springframework.stereotype.Component;
@@ -35,7 +35,7 @@ import org.springframework.stereotype.Component;
@Component
public class GroupRestPermissionEvaluatorPlugin extends RestObjectPermissionEvaluatorPlugin {
private static final Logger log = LoggerFactory.getLogger(GroupRestPermissionEvaluatorPlugin.class);
private static final Logger log = LogManager.getLogger();
@Autowired
private RequestService requestService;
@@ -87,7 +87,7 @@ public class GroupRestPermissionEvaluatorPlugin extends RestObjectPermissionEval
}
} catch (SQLException e) {
log.error(e.getMessage(), e);
log.error(e::getMessage, e);
}
return false;
}

10
dspace-server-webapp/src/main/java/org/dspace/app/rest/security/OrcidQueueAndHistoryRestPermissionEvaluatorPlugin.java
View File

@@ -11,6 +11,8 @@ import java.io.Serializable;
import java.sql.SQLException;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.app.rest.utils.ContextUtil;
import org.dspace.content.Item;
import org.dspace.content.service.ItemService;
@@ -22,21 +24,19 @@ import org.dspace.orcid.service.OrcidHistoryService;
import org.dspace.orcid.service.OrcidQueueService;
import org.dspace.services.RequestService;
import org.dspace.services.model.Request;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.security.core.Authentication;
import org.springframework.stereotype.Component;
/**
* Class that evaluate DELETE and READ permissions
*
*
* @author Mykhaylo Boychuk (mykhaylo.boychuk at 4science.it)
*/
@Component
public class OrcidQueueAndHistoryRestPermissionEvaluatorPlugin extends RestObjectPermissionEvaluatorPlugin {
private static final Logger log = LoggerFactory.getLogger(OrcidQueueAndHistoryRestPermissionEvaluatorPlugin.class);
private static final Logger log = LogManager.getLogger();
public static final String ORCID_QUEUE = "ORCID_QUEUE";
public static final String ORCID_HISTORY = "ORCID_HISTORY";
@@ -97,7 +97,7 @@ public class OrcidQueueAndHistoryRestPermissionEvaluatorPlugin extends RestObjec
.anyMatch(authority -> currentUser.getID().toString().equals(authority));
} catch (SQLException e) {
log.error(e.getMessage(), e);
log.error(e::getMessage, e);
}
return false;

8
dspace-server-webapp/src/main/java/org/dspace/app/rest/security/OrcidQueueSearchRestPermissionEvaluatorPlugin.java
View File

@@ -13,6 +13,8 @@ import java.util.List;
import java.util.UUID;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.app.rest.utils.ContextUtil;
import org.dspace.content.Item;
import org.dspace.content.MetadataValue;
@@ -21,8 +23,6 @@ import org.dspace.core.Context;
import org.dspace.eperson.EPerson;
import org.dspace.services.RequestService;
import org.dspace.services.model.Request;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.security.core.Authentication;
import org.springframework.stereotype.Component;
@@ -36,7 +36,7 @@ import org.springframework.stereotype.Component;
@Component
public class OrcidQueueSearchRestPermissionEvaluatorPlugin extends RestObjectPermissionEvaluatorPlugin {
private static final Logger log = LoggerFactory.getLogger(OrcidQueueAndHistoryRestPermissionEvaluatorPlugin.class);
private static final Logger log = LogManager.getLogger();
public static final String ORCID_QUEUE_SEARCH = "ORCID_QUEUE_SEARCH";
@@ -75,7 +75,7 @@ public class OrcidQueueSearchRestPermissionEvaluatorPlugin extends RestObjectPer
return true;
}
} catch (SQLException e) {
log.error(e.getMessage(), e);
log.error(e::getMessage, e);
}
return false;
}

8
dspace-server-webapp/src/main/java/org/dspace/app/rest/security/PoolTaskRestPermissionEvaluatorPlugin.java
View File

@@ -12,6 +12,8 @@ import java.io.Serializable;
import java.sql.SQLException;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.app.rest.model.PoolTaskRest;
import org.dspace.app.rest.utils.ContextUtil;
import org.dspace.authorize.AuthorizeException;
@@ -23,8 +25,6 @@ import org.dspace.services.model.Request;
import org.dspace.xmlworkflow.storedcomponents.PoolTask;
import org.dspace.xmlworkflow.storedcomponents.XmlWorkflowItem;
import org.dspace.xmlworkflow.storedcomponents.service.PoolTaskService;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.security.core.Authentication;
import org.springframework.stereotype.Component;
@@ -37,7 +37,7 @@ import org.springframework.stereotype.Component;
@Component
public class PoolTaskRestPermissionEvaluatorPlugin extends RestObjectPermissionEvaluatorPlugin {
private static final Logger log = LoggerFactory.getLogger(PoolTaskRestPermissionEvaluatorPlugin.class);
private static final Logger log = LogManager.getLogger();
@Autowired
private RequestService requestService;
@@ -79,7 +79,7 @@ public class PoolTaskRestPermissionEvaluatorPlugin extends RestObjectPermissionE
return true;
}
} catch (SQLException | AuthorizeException | IOException e) {
log.error(e.getMessage(), e);
log.error(e::getMessage, e);
}
return false;
}

8
dspace-server-webapp/src/main/java/org/dspace/app/rest/security/ProcessRestPermissionEvaluatorPlugin.java
View File

@@ -11,6 +11,8 @@ import java.io.Serializable;
import java.sql.SQLException;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.app.rest.model.ProcessRest;
import org.dspace.app.rest.utils.ContextUtil;
import org.dspace.authorize.service.AuthorizeService;
@@ -19,8 +21,6 @@ import org.dspace.scripts.Process;
import org.dspace.scripts.service.ProcessService;
import org.dspace.services.RequestService;
import org.dspace.services.model.Request;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.security.core.Authentication;
import org.springframework.stereotype.Component;
@@ -33,7 +33,7 @@ import org.springframework.stereotype.Component;
@Component
public class ProcessRestPermissionEvaluatorPlugin extends RestObjectPermissionEvaluatorPlugin {
private static final Logger log = LoggerFactory.getLogger(ProcessRestPermissionEvaluatorPlugin.class);
private static final Logger log = LogManager.getLogger();
@Autowired
private RequestService requestService;
@@ -66,7 +66,7 @@ public class ProcessRestPermissionEvaluatorPlugin extends RestObjectPermissionEv
return true;
}
} catch (SQLException e) {
log.error(e.getMessage(), e);
log.error(e::getMessage, e);
}
return false;
}

6
dspace-server-webapp/src/main/java/org/dspace/app/rest/security/QAEventRestPermissionEvaluatorPlugin.java
View File

@@ -11,6 +11,8 @@ import java.io.Serializable;
import java.util.Objects;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.app.rest.model.QAEventRest;
import org.dspace.app.rest.utils.ContextUtil;
import org.dspace.content.QAEvent;
@@ -19,8 +21,6 @@ import org.dspace.qaevent.service.QAEventSecurityService;
import org.dspace.qaevent.service.QAEventService;
import org.dspace.services.RequestService;
import org.dspace.services.model.Request;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.security.core.Authentication;
import org.springframework.stereotype.Component;
@@ -33,7 +33,7 @@ import org.springframework.stereotype.Component;
@Component
public class QAEventRestPermissionEvaluatorPlugin extends RestObjectPermissionEvaluatorPlugin {
private static final Logger log = LoggerFactory.getLogger(QAEventRestPermissionEvaluatorPlugin.class);
private static final Logger log = LogManager.getLogger();
@Autowired
private QAEventService qaEventService;

6
dspace-server-webapp/src/main/java/org/dspace/app/rest/security/QASourceRestPermissionEvaluatorPlugin.java
View File

@@ -11,6 +11,8 @@ import java.io.Serializable;
import java.util.Objects;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.app.rest.model.QASourceRest;
import org.dspace.app.rest.model.QATopicRest;
import org.dspace.app.rest.utils.ContextUtil;
@@ -19,8 +21,6 @@ import org.dspace.qaevent.QATopic;
import org.dspace.qaevent.service.QAEventSecurityService;
import org.dspace.services.RequestService;
import org.dspace.services.model.Request;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.security.core.Authentication;
import org.springframework.stereotype.Component;
@@ -33,7 +33,7 @@ import org.springframework.stereotype.Component;
@Component
public class QASourceRestPermissionEvaluatorPlugin extends RestObjectPermissionEvaluatorPlugin {
private static final Logger log = LoggerFactory.getLogger(QASourceRestPermissionEvaluatorPlugin.class);
private static final Logger log = LogManager.getLogger();
@Autowired
private QAEventSecurityService qaEventSecurityService;

10
dspace-server-webapp/src/main/java/org/dspace/app/rest/security/ReadAuthorizationPermissionEvaluatorPlugin.java
View File

@@ -11,6 +11,8 @@ import java.io.Serializable;
import java.sql.SQLException;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.app.rest.authorization.AuthorizationRestUtil;
import org.dspace.app.rest.model.AuthorizationRest;
import org.dspace.app.rest.utils.ContextUtil;
@@ -19,21 +21,19 @@ import org.dspace.core.Context;
import org.dspace.eperson.EPerson;
import org.dspace.services.RequestService;
import org.dspace.services.model.Request;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.security.core.Authentication;
import org.springframework.stereotype.Component;
/**
* {@link RestPermissionEvaluatorPlugin} class that evaluate READ permissions for an Authorization
*
*
* @author Andrea Bollini (andrea.bollini at 4science.it)
*/
@Component
public class ReadAuthorizationPermissionEvaluatorPlugin extends RestObjectPermissionEvaluatorPlugin {
private static final Logger log = LoggerFactory.getLogger(ReadAuthorizationPermissionEvaluatorPlugin.class);
private static final Logger log = LogManager.getLogger();
@Autowired
AuthorizeService authorizeService;
@@ -75,7 +75,7 @@ public class ReadAuthorizationPermissionEvaluatorPlugin extends RestObjectPermis
}
}
} catch (SQLException e) {
log.error(e.getMessage(), e);
log.error(e::getMessage, e);
}
return false;

8
dspace-server-webapp/src/main/java/org/dspace/app/rest/security/ResourcePolicyAdminPermissionEvalutatorPlugin.java
View File

@@ -11,6 +11,8 @@ import java.io.Serializable;
import java.sql.SQLException;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.app.rest.model.ResourcePolicyRest;
import org.dspace.app.rest.utils.ContextUtil;
import org.dspace.authorize.ResourcePolicy;
@@ -20,8 +22,6 @@ import org.dspace.content.DSpaceObject;
import org.dspace.core.Context;
import org.dspace.services.RequestService;
import org.dspace.services.model.Request;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.data.rest.webmvc.ResourceNotFoundException;
import org.springframework.security.core.Authentication;
@@ -36,7 +36,7 @@ import org.springframework.stereotype.Component;
@Component
public class ResourcePolicyAdminPermissionEvalutatorPlugin extends RestObjectPermissionEvaluatorPlugin {
private static final Logger log = LoggerFactory.getLogger(ResourcePolicyRestPermissionEvaluatorPlugin.class);
private static final Logger log = LogManager.getLogger();
public static final String RESOURCE_POLICY_PATCH = "resourcepolicy";
@@ -74,7 +74,7 @@ public class ResourcePolicyAdminPermissionEvalutatorPlugin extends RestObjectPer
DSpaceObject dso = resourcePolicy.getdSpaceObject();
return authorizeService.isAdmin(context, dso);
} catch (SQLException e) {
log.error(e.getMessage(), e);
log.error(e::getMessage, e);
}
return false;
}

12
dspace-server-webapp/src/main/java/org/dspace/app/rest/security/ResourcePolicyRestPermissionEvaluatorPlugin.java
View File

@@ -11,6 +11,8 @@ import java.io.Serializable;
import java.sql.SQLException;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.app.rest.model.ResourcePolicyRest;
import org.dspace.app.rest.utils.ContextUtil;
import org.dspace.authorize.service.AuthorizeService;
@@ -20,21 +22,19 @@ import org.dspace.eperson.EPerson;
import org.dspace.eperson.service.EPersonService;
import org.dspace.services.RequestService;
import org.dspace.services.model.Request;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.security.core.Authentication;
import org.springframework.stereotype.Component;
/**
* {@link RestPermissionEvaluatorPlugin} class that evaluate READ, WRITE and DELETE permissions over a ResourcePolicy
*
* {@link RestPermissionEvaluatorPlugin} class that evaluate READ, WRITE and DELETE permissions over a ResourcePolicy.
*
* @author Mykhaylo Boychuk (4science.it)
*/
@Component
public class ResourcePolicyRestPermissionEvaluatorPlugin extends RestObjectPermissionEvaluatorPlugin {
private static final Logger log = LoggerFactory.getLogger(ResourcePolicyRestPermissionEvaluatorPlugin.class);
private static final Logger log = LogManager.getLogger();
@Autowired
AuthorizeService authorizeService;
@@ -78,7 +78,7 @@ public class ResourcePolicyRestPermissionEvaluatorPlugin extends RestObjectPermi
return true;
}
} catch (SQLException e) {
log.error(e.getMessage(), e);
log.error(e::getMessage, e);
}
return false;

25
dspace-server-webapp/src/main/java/org/dspace/app/rest/security/StatelessAuthenticationFilter.java
View File

@@ -16,6 +16,8 @@ import javax.servlet.ServletException;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.app.rest.utils.ContextUtil;
import org.dspace.authorize.AuthorizeException;
import org.dspace.authorize.factory.AuthorizeServiceFactory;
@@ -28,8 +30,6 @@ import org.dspace.services.ConfigurationService;
import org.dspace.services.RequestService;
import org.dspace.services.factory.DSpaceServicesFactory;
import org.dspace.util.UUIDUtils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.security.access.AccessDeniedException;
import org.springframework.security.authentication.AuthenticationManager;
import org.springframework.security.core.Authentication;
@@ -47,21 +47,24 @@ import org.springframework.security.web.authentication.www.BasicAuthenticationFi
*/
public class StatelessAuthenticationFilter extends BasicAuthenticationFilter {
private static final Logger log = LoggerFactory.getLogger(StatelessAuthenticationFilter.class);
private static final Logger log = LogManager.getLogger();
private static final String ON_BEHALF_OF_REQUEST_PARAM = "X-On-Behalf-Of";
private RestAuthenticationService restAuthenticationService;
private final RestAuthenticationService restAuthenticationService;
private EPersonRestAuthenticationProvider authenticationProvider;
private final EPersonRestAuthenticationProvider authenticationProvider;
private RequestService requestService;
private final RequestService requestService;
private AuthorizeService authorizeService = AuthorizeServiceFactory.getInstance().getAuthorizeService();
private final AuthorizeService authorizeService
= AuthorizeServiceFactory.getInstance().getAuthorizeService();
private EPersonService ePersonService = EPersonServiceFactory.getInstance().getEPersonService();
private final EPersonService ePersonService
= EPersonServiceFactory.getInstance().getEPersonService();
private ConfigurationService configurationService = DSpaceServicesFactory.getInstance().getConfigurationService();
private final ConfigurationService configurationService
= DSpaceServicesFactory.getInstance().getConfigurationService();
public StatelessAuthenticationFilter(AuthenticationManager authenticationManager,
RestAuthenticationService restAuthenticationService,
@@ -124,7 +127,7 @@ public class StatelessAuthenticationFilter extends BasicAuthenticationFilter {
// parse the token.
EPerson eperson = restAuthenticationService.getAuthenticatedEPerson(request, res, context);
if (eperson != null) {
log.debug("Found authentication data in request for EPerson {}", eperson.getEmail());
log.debug("Found authentication data in request for EPerson {}", eperson::getEmail);
//Pass the eperson ID to the request service
requestService.setCurrentUserId(eperson.getID());
@@ -174,7 +177,7 @@ public class StatelessAuthenticationFilter extends BasicAuthenticationFilter {
requestService.setCurrentUserId(epersonUuid);
context.switchContextUser(onBehalfOfEPerson);
log.debug("Found 'on-behalf-of' authentication data in request for EPerson {}",
onBehalfOfEPerson.getEmail());
onBehalfOfEPerson::getEmail);
return new DSpaceAuthentication(onBehalfOfEPerson,
authenticationProvider.getGrantedAuthorities(context));
} else {

10
dspace-server-webapp/src/main/java/org/dspace/app/rest/security/StatelessLoginFilter.java
View File

@@ -13,8 +13,8 @@ import javax.servlet.ServletException;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.springframework.security.authentication.AuthenticationManager;
import org.springframework.security.core.Authentication;
import org.springframework.security.core.AuthenticationException;
@@ -23,7 +23,7 @@ import org.springframework.security.web.util.matcher.AntPathRequestMatcher;
/**
* This class will filter /api/authn/login requests to try and authenticate them. Keep in mind, this filter runs *after*
* StatelessAuthenticationFilter (which looks for authentication data in the request itself). So, in some scenarios
* {@link StatelessAuthenticationFilter} (which looks for authentication data in the request itself). So, in some scenarios
* (e.g. after a Shibboleth login) the StatelessAuthenticationFilter does the actual authentication, and this Filter
* just ensures the auth token (JWT) is sent back in an Authorization header.
*
@@ -31,7 +31,7 @@ import org.springframework.security.web.util.matcher.AntPathRequestMatcher;
* @author Tom Desair (tom dot desair at atmire dot com)
*/
public class StatelessLoginFilter extends AbstractAuthenticationProcessingFilter {
private static final Logger log = LoggerFactory.getLogger(StatelessLoginFilter.class);
private static final Logger log = LogManager.getLogger();
protected AuthenticationManager authenticationManager;
@@ -97,7 +97,7 @@ public class StatelessLoginFilter extends AbstractAuthenticationProcessingFilter
Authentication auth) throws IOException, ServletException {
DSpaceAuthentication dSpaceAuthentication = (DSpaceAuthentication) auth;
log.debug("Authentication successful for EPerson {}", dSpaceAuthentication.getName());
log.debug("Authentication successful for EPerson {}", dSpaceAuthentication::getName);
restAuthenticationService.addAuthenticationDataForUser(req, res, dSpaceAuthentication, false);
}

10
dspace-server-webapp/src/main/java/org/dspace/app/rest/security/SubscriptionRestPermissionEvaluatorPlugin.java
View File

@@ -17,6 +17,8 @@ import java.sql.SQLException;
import java.util.Objects;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.app.rest.utils.ContextUtil;
import org.dspace.authorize.service.AuthorizeService;
import org.dspace.core.Context;
@@ -25,21 +27,19 @@ import org.dspace.eperson.Subscription;
import org.dspace.eperson.service.SubscribeService;
import org.dspace.services.RequestService;
import org.dspace.services.model.Request;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.security.core.Authentication;
import org.springframework.stereotype.Component;
/**
* {@link RestPermissionEvaluatorPlugin} class that evaluate READ, WRITE and DELETE permissions over a Subscription
*
*
* @author Mykhaylo Boychuk (mykhaylo.boychuk at 4science.com)
*/
@Component
public class SubscriptionRestPermissionEvaluatorPlugin extends RestObjectPermissionEvaluatorPlugin {
private static final Logger log = LoggerFactory.getLogger(SubscriptionRestPermissionEvaluatorPlugin.class);
private static final Logger log = LogManager.getLogger();
@Autowired
private RequestService requestService;
@@ -76,7 +76,7 @@ public class SubscriptionRestPermissionEvaluatorPlugin extends RestObjectPermiss
Subscription subscription = subscribeService.findById(context, Integer.parseInt(targetId.toString()));
return Objects.nonNull(subscription) ? currentUser.equals(subscription.getEPerson()) : false;
} catch (SQLException e) {
log.error(e.getMessage(), e);
log.error(e::getMessage, e);
}
return false;
}

8
dspace-server-webapp/src/main/java/org/dspace/app/rest/security/TemplateItemRestPermissionEvaluatorPlugin.java
View File

@@ -12,6 +12,8 @@ import java.sql.SQLException;
import java.util.UUID;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.app.rest.model.TemplateItemRest;
import org.dspace.app.rest.utils.ContextUtil;
import org.dspace.authorize.service.AuthorizeService;
@@ -21,8 +23,6 @@ import org.dspace.core.Context;
import org.dspace.eperson.EPerson;
import org.dspace.services.RequestService;
import org.dspace.services.model.Request;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.security.core.Authentication;
import org.springframework.stereotype.Component;
@@ -35,7 +35,7 @@ import org.springframework.stereotype.Component;
@Component
public class TemplateItemRestPermissionEvaluatorPlugin extends RestObjectPermissionEvaluatorPlugin {
private static final Logger log = LoggerFactory.getLogger(TemplateItemRestPermissionEvaluatorPlugin.class);
private static final Logger log = LogManager.getLogger();
@Autowired
private RequestService requestService;
@@ -76,7 +76,7 @@ public class TemplateItemRestPermissionEvaluatorPlugin extends RestObjectPermiss
return true;
}
} catch (SQLException e) {
log.error(e.getMessage(), e);
log.error(e::getMessage, e);
}
return false;
}

8
dspace-server-webapp/src/main/java/org/dspace/app/rest/security/UsageReportRestPermissionEvaluatorPlugin.java
View File

@@ -13,6 +13,8 @@ import java.util.Objects;
import java.util.UUID;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.app.rest.model.UsageReportRest;
import org.dspace.app.rest.utils.ContextUtil;
import org.dspace.app.rest.utils.DSpaceObjectUtils;
@@ -22,8 +24,6 @@ import org.dspace.core.Context;
import org.dspace.services.ConfigurationService;
import org.dspace.services.RequestService;
import org.dspace.services.model.Request;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.security.core.Authentication;
import org.springframework.stereotype.Component;
@@ -36,7 +36,7 @@ import org.springframework.stereotype.Component;
@Component
public class UsageReportRestPermissionEvaluatorPlugin extends RestObjectPermissionEvaluatorPlugin {
private static final Logger log = LoggerFactory.getLogger(UsageReportRestPermissionEvaluatorPlugin.class);
private static final Logger log = LogManager.getLogger();
@Autowired
private ConfigurationService configurationService;
@@ -95,7 +95,7 @@ public class UsageReportRestPermissionEvaluatorPlugin extends RestObjectPermissi
}
return authorizeService.authorizeActionBoolean(context, dso, restPermission.getDspaceApiActionId());
} catch (SQLException e) {
log.error(e.getMessage(), e);
log.error(e::getMessage, e);
}
}
return false;

8
dspace-server-webapp/src/main/java/org/dspace/app/rest/security/VersionHistoryRestPermissionEvaluatorPlugin.java
View File

@@ -11,6 +11,8 @@ import java.io.Serializable;
import java.sql.SQLException;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.app.rest.model.VersionHistoryRest;
import org.dspace.app.rest.utils.ContextUtil;
import org.dspace.authorize.service.AuthorizeService;
@@ -18,8 +20,6 @@ import org.dspace.core.Context;
import org.dspace.services.ConfigurationService;
import org.dspace.services.RequestService;
import org.dspace.services.model.Request;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.security.core.Authentication;
import org.springframework.stereotype.Component;
@@ -31,7 +31,7 @@ import org.springframework.stereotype.Component;
@Component
public class VersionHistoryRestPermissionEvaluatorPlugin extends RestObjectPermissionEvaluatorPlugin {
private static final Logger log = LoggerFactory.getLogger(VersionHistoryRestPermissionEvaluatorPlugin.class);
private static final Logger log = LogManager.getLogger();
@Autowired
private RequestService requestService;
@@ -62,7 +62,7 @@ public class VersionHistoryRestPermissionEvaluatorPlugin extends RestObjectPermi
}
return true;
} catch (SQLException e) {
log.error(e.getMessage(), e);
log.error(e::getMessage, e);
}
return false;
}

11
dspace-server-webapp/src/main/java/org/dspace/app/rest/security/VersionRestPatchPermissionEvaluatorPlugin.java
View File

@@ -6,11 +6,14 @@
* http://www.dspace.org/license/
*/
package org.dspace.app.rest.security;
import java.io.Serializable;
import java.sql.SQLException;
import java.util.UUID;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.app.rest.model.VersionRest;
import org.dspace.app.rest.utils.ContextUtil;
import org.dspace.authorize.service.AuthorizeService;
@@ -19,21 +22,19 @@ import org.dspace.services.RequestService;
import org.dspace.services.model.Request;
import org.dspace.versioning.Version;
import org.dspace.versioning.service.VersioningService;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.security.core.Authentication;
import org.springframework.stereotype.Component;
/**
* This class evaluate ADMIN permissions to patch operation over a Version.
*
*
* @author Mykhaylo Boychuk (mykhaylo.boychuk at 4science.it)
*/
@Component
public class VersionRestPatchPermissionEvaluatorPlugin extends RestObjectPermissionEvaluatorPlugin {
private static final Logger log = LoggerFactory.getLogger(VersionRestPatchPermissionEvaluatorPlugin.class);
private static final Logger log = LogManager.getLogger();
@Autowired
private RequestService requestService;
@@ -78,7 +79,7 @@ public class VersionRestPatchPermissionEvaluatorPlugin extends RestObjectPermiss
return true;
}
} catch (SQLException e) {
log.error(e.getMessage(), e);
log.error(e::getMessage, e);
}
return false;
}

10
dspace-server-webapp/src/main/java/org/dspace/app/rest/security/VersionRestPermissionEvaluatorPlugin.java
View File

@@ -12,6 +12,8 @@ import java.sql.SQLException;
import java.util.Objects;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.app.rest.model.VersionRest;
import org.dspace.app.rest.utils.ContextUtil;
import org.dspace.authorize.service.AuthorizeService;
@@ -21,20 +23,18 @@ import org.dspace.services.RequestService;
import org.dspace.services.model.Request;
import org.dspace.versioning.Version;
import org.dspace.versioning.service.VersioningService;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.security.core.Authentication;
import org.springframework.stereotype.Component;
/**
* This class acts as a PermissionEvaluator to decide whether a given request to a Versioning endpoint is allowed to
* pass through or not
* pass through or not.
*/
@Component
public class VersionRestPermissionEvaluatorPlugin extends RestObjectPermissionEvaluatorPlugin {
private static final Logger log = LoggerFactory.getLogger(VersionRestPermissionEvaluatorPlugin.class);
private static final Logger log = LogManager.getLogger();
@Autowired
private RequestService requestService;
@@ -77,7 +77,7 @@ public class VersionRestPermissionEvaluatorPlugin extends RestObjectPermissionEv
}
} catch (SQLException e) {
log.error(e.getMessage(), e);
log.error(e::getMessage, e);
}
return false;
}

10
dspace-server-webapp/src/main/java/org/dspace/app/rest/security/WorkflowRestPermissionEvaluatorPlugin.java
View File

@@ -12,6 +12,8 @@ import java.io.Serializable;
import java.sql.SQLException;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.app.rest.model.WorkflowItemRest;
import org.dspace.app.rest.utils.ContextUtil;
import org.dspace.authorize.AuthorizeException;
@@ -25,8 +27,6 @@ import org.dspace.xmlworkflow.storedcomponents.XmlWorkflowItem;
import org.dspace.xmlworkflow.storedcomponents.service.ClaimedTaskService;
import org.dspace.xmlworkflow.storedcomponents.service.PoolTaskService;
import org.dspace.xmlworkflow.storedcomponents.service.XmlWorkflowItemService;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.security.core.Authentication;
import org.springframework.stereotype.Component;
@@ -34,13 +34,13 @@ import org.springframework.stereotype.Component;
/**
* An authenticated user is allowed to interact with workflow item only if they belong to a task that they own or could
* claim.
*
*
* @author Andrea Bollini (andrea.bollini at 4science.it)
*/
@Component
public class WorkflowRestPermissionEvaluatorPlugin extends RestObjectPermissionEvaluatorPlugin {
private static final Logger log = LoggerFactory.getLogger(WorkflowRestPermissionEvaluatorPlugin.class);
private static final Logger log = LogManager.getLogger();
@Autowired
private RequestService requestService;
@@ -99,7 +99,7 @@ public class WorkflowRestPermissionEvaluatorPlugin extends RestObjectPermissionE
}
} catch (SQLException | AuthorizeException | IOException e) {
log.error(e.getMessage(), e);
log.error(e::getMessage, e);
}
return false;
}

12
dspace-server-webapp/src/main/java/org/dspace/app/rest/security/WorkspaceItemRestPermissionEvaluatorPlugin.java
View File

@@ -11,6 +11,8 @@ import java.io.Serializable;
import java.sql.SQLException;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.app.rest.model.WorkspaceItemRest;
import org.dspace.app.rest.utils.ContextUtil;
import org.dspace.authorize.service.AuthorizeService;
@@ -21,21 +23,19 @@ import org.dspace.eperson.EPerson;
import org.dspace.services.RequestService;
import org.dspace.services.model.Request;
import org.dspace.supervision.service.SupervisionOrderService;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.security.core.Authentication;
import org.springframework.stereotype.Component;
/**
* {@link RestPermissionEvaluatorPlugin} class that evaluate READ, WRITE and DELETE permissions over a WorkspaceItem
*
* {@link RestPermissionEvaluatorPlugin} class that evaluate READ, WRITE and DELETE permissions over a WorkspaceItem.
*
* @author Mykhaylo Boychuk (mykhaylo.boychuk at 4science.it)
*/
@Component
public class WorkspaceItemRestPermissionEvaluatorPlugin extends RestObjectPermissionEvaluatorPlugin {
private static final Logger log = LoggerFactory.getLogger(WorkspaceItemRestPermissionEvaluatorPlugin.class);
private static final Logger log = LogManager.getLogger();
@Autowired
private RequestService requestService;
@@ -100,7 +100,7 @@ public class WorkspaceItemRestPermissionEvaluatorPlugin extends RestObjectPermis
}
} catch (SQLException e) {
log.error(e.getMessage(), e);
log.error(e::getMessage, e);
}
return false;

11
dspace-server-webapp/src/main/java/org/dspace/app/rest/security/jwt/AuthenticationMethodClaimProvider.java
View File

@@ -12,10 +12,10 @@ import java.text.ParseException;
import javax.servlet.http.HttpServletRequest;
import com.nimbusds.jwt.JWTClaimsSet;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.authenticate.service.AuthenticationService;
import org.dspace.core.Context;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Component;
@@ -27,15 +27,17 @@ public class AuthenticationMethodClaimProvider implements JWTClaimProvider {
public static final String AUTHENTICATION_METHOD = "authenticationMethod";
private static final Logger log = LoggerFactory.getLogger(AuthenticationMethodClaimProvider.class);
private static final Logger log = LogManager.getLogger();
@Autowired
private AuthenticationService authenticationService;
@Override
public String getKey() {
return AUTHENTICATION_METHOD;
}
@Override
public Object getValue(final Context context, final HttpServletRequest request) {
if (context.getAuthenticationMethod() != null) {
return context.getAuthenticationMethod();
@@ -43,12 +45,13 @@ public class AuthenticationMethodClaimProvider implements JWTClaimProvider {
return authenticationService.getAuthenticationMethod(context, request);
}
@Override
public void parseClaim(final Context context, final HttpServletRequest request, final JWTClaimsSet jwtClaimsSet)
throws SQLException {
try {
context.setAuthenticationMethod(jwtClaimsSet.getStringClaim(AUTHENTICATION_METHOD));
} catch (ParseException e) {
log.error(e.getMessage(), e);
log.error(e::getMessage, e);
}
}
}

13
dspace-server-webapp/src/main/java/org/dspace/app/rest/security/jwt/JWTTokenHandler.java
View File

@@ -33,14 +33,14 @@ import com.nimbusds.jwt.SignedJWT;
import com.nimbusds.jwt.util.DateUtils;
import org.apache.commons.codec.binary.Base64;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.authorize.AuthorizeException;
import org.dspace.core.Context;
import org.dspace.eperson.EPerson;
import org.dspace.eperson.service.EPersonService;
import org.dspace.service.ClientInfoService;
import org.dspace.services.ConfigurationService;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.security.access.AccessDeniedException;
import org.springframework.security.crypto.keygen.BytesKeyGenerator;
@@ -59,7 +59,7 @@ public abstract class JWTTokenHandler {
private static final int MAX_CLOCK_SKEW_SECONDS = 60;
private static final String AUTHORIZATION_TOKEN_PARAMETER = "authentication-token";
private static final Logger log = LoggerFactory.getLogger(JWTTokenHandler.class);
private static final Logger log = LogManager.getLogger();
@Autowired
private List<JWTClaimProvider> jwtClaimProviders;
@@ -135,7 +135,7 @@ public abstract class JWTTokenHandler {
// As long as the JWT is valid, parse all claims and return the EPerson
if (isValidToken(request, signedJWT, jwtClaimsSet, ePerson)) {
log.debug("Received valid token for username: " + ePerson.getEmail());
log.debug("Received valid token for username: {}", ePerson::getEmail);
for (JWTClaimProvider jwtClaimProvider : jwtClaimProviders) {
jwtClaimProvider.parseClaim(context, request, jwtClaimsSet);
@@ -143,7 +143,7 @@ public abstract class JWTTokenHandler {
return ePerson;
} else {
log.warn(getIpAddress(request) + " tried to use an expired or non-valid token");
log.warn("{} tried to use an expired or non-valid token", getIpAddress(request));
return null;
}
}
@@ -155,7 +155,8 @@ public abstract class JWTTokenHandler {
* @param request current Request
* @param previousLoginDate date of last login (before this one)
* @return string version of signed JWT
* @throws JOSEException
* @throws JOSEException passed through.
* @throws SQLException passed through.
*/
public String createTokenForEPerson(Context context, HttpServletRequest request, Date previousLoginDate)
throws JOSEException, SQLException {

6
dspace-server-webapp/src/main/java/org/dspace/app/rest/security/jwt/JWTTokenRestAuthenticationServiceImpl.java
View File

@@ -18,6 +18,8 @@ import javax.ws.rs.core.HttpHeaders;
import com.nimbusds.jose.JOSEException;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.app.rest.model.wrapper.AuthenticationToken;
import org.dspace.app.rest.security.DSpaceAuthentication;
import org.dspace.app.rest.security.RestAuthenticationService;
@@ -27,8 +29,6 @@ import org.dspace.authenticate.service.AuthenticationService;
import org.dspace.core.Context;
import org.dspace.eperson.EPerson;
import org.dspace.eperson.service.EPersonService;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.InitializingBean;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.annotation.Lazy;
@@ -47,7 +47,7 @@ import org.springframework.stereotype.Component;
@Component
public class JWTTokenRestAuthenticationServiceImpl implements RestAuthenticationService, InitializingBean {
private static final Logger log = LoggerFactory.getLogger(RestAuthenticationService.class);
private static final Logger log = LogManager.getLogger();
private static final String AUTHORIZATION_COOKIE = "Authorization-cookie";
private static final String AUTHORIZATION_HEADER = "Authorization";
private static final String AUTHORIZATION_TYPE = "Bearer";

9
dspace-server-webapp/src/main/java/org/dspace/app/rest/security/jwt/SpecialGroupClaimProvider.java
View File

@@ -17,11 +17,11 @@ import javax.servlet.http.HttpServletRequest;
import com.nimbusds.jwt.JWTClaimsSet;
import org.apache.commons.collections4.CollectionUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.authenticate.service.AuthenticationService;
import org.dspace.core.Context;
import org.dspace.eperson.Group;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Component;
@@ -34,17 +34,19 @@ import org.springframework.stereotype.Component;
@Component
public class SpecialGroupClaimProvider implements JWTClaimProvider {
private static final Logger log = LoggerFactory.getLogger(SpecialGroupClaimProvider.class);
private static final Logger log = LogManager.getLogger();
public static final String SPECIAL_GROUPS = "sg";
@Autowired
private AuthenticationService authenticationService;
@Override
public String getKey() {
return SPECIAL_GROUPS;
}
@Override
public Object getValue(Context context, HttpServletRequest request) {
List<Group> groups = new ArrayList<>();
try {
@@ -57,6 +59,7 @@ public class SpecialGroupClaimProvider implements JWTClaimProvider {
return groupIds;
}
@Override
public void parseClaim(Context context, HttpServletRequest request, JWTClaimsSet jwtClaimsSet) {
try {
List<String> groupIds = jwtClaimsSet.getStringListClaim(SPECIAL_GROUPS);

35
dspace-server-webapp/src/main/java/org/dspace/app/rest/security/package-info.java Normal file
View File

@@ -0,0 +1,35 @@
/**
* 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/
*/
/**
* DSpace-specific concepts and behaviors to support Spring Security.
* These may be used by Spring EL expressions in Spring Security annotations.
*
* <p>{@code hasPermission} terms are evaluated by
* {@link DSpacePermissionEvaluator}, an implementation of Spring's
* {@link PermissionEvaluator}. It tests access to specific model objects
* (Item, EPerson etc.) using those objects' policies. It is injected with a
* collection of {@link RestPermissionEvaluatorPlugin}s which do the work.
*
* <p>{@code hasAuthority} terms are implemented by {@link GrantedAuthority}
* implementations such as {@link EPersonRestAuthenticationProvider}. These
* test for authorization properties of the session itself, such as membership
* in the site administrators group.
*
* <p>{@code *PermissionEvaluatorPlugin} classes test permission for specific
* types of objects. They implement {@link RestPermissionEvaluatorPlugin}.
*
* <p>Other classes TBD:
* <ul>
* <li>*Filter</li>
* <li>*Configuration</li>
* </ul>
*/
package org.dspace.app.rest.security;
import org.springframework.security.access.PermissionEvaluator;
import org.springframework.security.core.GrantedAuthority;

8
dspace-server-webapp/src/main/java/org/dspace/app/rest/submit/factory/impl/AccessConditionReplacePatchOperation.java
View File

@@ -17,6 +17,8 @@ import java.util.Objects;
import javax.servlet.http.HttpServletRequest;
import org.apache.commons.lang.StringUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.app.rest.exception.UnprocessableEntityException;
import org.dspace.app.rest.model.AccessConditionDTO;
import org.dspace.app.rest.model.patch.JsonValueEvaluator;
@@ -31,8 +33,6 @@ import org.dspace.submit.model.AccessConditionConfiguration;
import org.dspace.submit.model.AccessConditionConfigurationService;
import org.dspace.submit.model.AccessConditionOption;
import org.dspace.util.TimeHelpers;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
/**
@@ -42,7 +42,7 @@ import org.springframework.beans.factory.annotation.Autowired;
*/
public class AccessConditionReplacePatchOperation extends ReplacePatchOperation<AccessConditionDTO> {
private static final Logger log = LoggerFactory.getLogger(AccessConditionReplacePatchOperation.class);
private static final Logger log = LogManager.getLogger();
@Autowired
private ResourcePolicyService resourcePolicyService;
@@ -157,7 +157,7 @@ public class AccessConditionReplacePatchOperation extends ReplacePatchOperation<
try {
return pattern.parse(date);
} catch (ParseException e) {
log.error(e.getMessage(), e);
log.error(e::getMessage, e);
}
}
throw new UnprocessableEntityException("Provided format of date:" + date + " is not supported!");

4
dspace-server-webapp/src/main/java/org/dspace/app/rest/utils/DSpaceConfigurationInitializer.java
View File

@@ -11,8 +11,6 @@ import org.apache.commons.configuration2.Configuration;
import org.apache.commons.configuration2.spring.ConfigurationPropertySource;
import org.dspace.services.ConfigurationService;
import org.dspace.services.factory.DSpaceServicesFactory;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.context.ApplicationContextInitializer;
import org.springframework.context.ConfigurableApplicationContext;
@@ -29,8 +27,6 @@ import org.springframework.context.ConfigurableApplicationContext;
*/
public class DSpaceConfigurationInitializer implements ApplicationContextInitializer<ConfigurableApplicationContext> {
private static final Logger log = LoggerFactory.getLogger(DSpaceConfigurationInitializer.class);
@Override
public void initialize(final ConfigurableApplicationContext applicationContext) {
// Load DSpace Configuration service (requires kernel already initialized)

7
dspace-server-webapp/src/main/java/org/dspace/app/rest/utils/DSpaceKernelInitializer.java
View File

@@ -12,13 +12,13 @@ import javax.naming.Context;
import javax.naming.InitialContext;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.kernel.DSpaceKernel;
import org.dspace.kernel.DSpaceKernelManager;
import org.dspace.servicemanager.DSpaceKernelImpl;
import org.dspace.servicemanager.DSpaceKernelInit;
import org.dspace.servicemanager.config.DSpaceConfigurationService;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.context.ApplicationContextInitializer;
import org.springframework.context.ApplicationListener;
import org.springframework.context.ConfigurableApplicationContext;
@@ -31,7 +31,7 @@ import org.springframework.core.env.ConfigurableEnvironment;
*/
public class DSpaceKernelInitializer implements ApplicationContextInitializer<ConfigurableApplicationContext> {
private static final Logger log = LoggerFactory.getLogger(DSpaceKernelInitializer.class);
private static final Logger log = LogManager.getLogger();
private transient DSpaceKernel dspaceKernel;
@@ -119,6 +119,7 @@ public class DSpaceKernelInitializer implements ApplicationContextInitializer<Co
this.kernel = kernel;
}
@Override
public void onApplicationEvent(final ContextClosedEvent event) {
if (this.kernel != null) {
this.kernel.destroy();

6
dspace-server-webapp/src/main/java/org/dspace/app/rest/utils/HttpHeadersInitializer.java
View File

@@ -19,9 +19,9 @@ import javax.servlet.http.HttpServletRequest;
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.apache.tomcat.util.http.FastHttpDateFormat;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.http.HttpHeaders;
/**
@@ -32,7 +32,7 @@ import org.springframework.http.HttpHeaders;
*/
public class HttpHeadersInitializer {
protected final Logger log = LoggerFactory.getLogger(this.getClass());
protected final Logger log = LogManager.getLogger();
private static final String MULTIPART_BOUNDARY = "MULTIPART_BYTERANGES";
private static final String CONTENT_TYPE_MULTITYPE_WITH_BOUNDARY = "multipart/byteranges; boundary=" +

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