getSpecialGroups(Context context, HttpServletRequest request)
* otherwise
*/
public default boolean areSpecialGroupsApplicable(Context context, HttpServletRequest request) {
- return getName().equals(context.getAuthenticationMethod());
+ return getName().equals(context.getAuthenticationMethod()) || isUsed(context, request);
}
/**
@@ -188,7 +188,7 @@ public default boolean areSpecialGroupsApplicable(Context context, HttpServletRe
* Meaning:
*
SUCCESS - authenticated OK.
*
BAD_CREDENTIALS - user exists, but credentials (e.g. passwd) don't match
- *
CERT_REQUIRED - not allowed to login this way without X.509 cert.
+ *
CERT_REQUIRED - not allowed to login this way without a cert.
*
NO_SUCH_USER - user not found using this method.
*
BAD_ARGS - user/pw not appropriate for this method
* @throws SQLException if database error
diff --git a/dspace-api/src/main/java/org/dspace/authenticate/AuthenticationServiceImpl.java b/dspace-api/src/main/java/org/dspace/authenticate/AuthenticationServiceImpl.java
index 2b07f73c489c..c0dde49b13a3 100644
--- a/dspace-api/src/main/java/org/dspace/authenticate/AuthenticationServiceImpl.java
+++ b/dspace-api/src/main/java/org/dspace/authenticate/AuthenticationServiceImpl.java
@@ -38,11 +38,11 @@
* Configuration
* The stack of authentication methods is defined by one property in the DSpace configuration:
*
- * plugin.sequence.org.dspace.eperson.AuthenticationMethod = a list of method class names
+ * plugin.sequence.org.dspace.authenticate.AuthenticationMethod = a list of method class names
* e.g.
- * plugin.sequence.org.dspace.eperson.AuthenticationMethod = \
- * org.dspace.eperson.X509Authentication, \
- * org.dspace.eperson.PasswordAuthentication
+ * plugin.sequence.org.dspace.authenticate.AuthenticationMethod = \
+ * org.dspace.authenticate.IPAuthentication, \
+ * org.dspace.authenticate.PasswordAuthentication
*
*
* The "stack" is always traversed in order, with the methods
@@ -110,6 +110,7 @@ protected int authenticateInternal(Context context,
}
if (ret == AuthenticationMethod.SUCCESS) {
updateLastActiveDate(context);
+ context.setAuthenticationMethod(aMethodStack.getName());
return ret;
}
if (ret < bestRet) {
diff --git a/dspace-api/src/main/java/org/dspace/authenticate/LDAPAuthentication.java b/dspace-api/src/main/java/org/dspace/authenticate/LDAPAuthentication.java
index 40b8f48078c9..9d7c09f1c314 100644
--- a/dspace-api/src/main/java/org/dspace/authenticate/LDAPAuthentication.java
+++ b/dspace-api/src/main/java/org/dspace/authenticate/LDAPAuthentication.java
@@ -203,7 +203,7 @@ public List getSpecialGroups(Context context, HttpServletRequest request)
* Meaning:
*
SUCCESS - authenticated OK.
*
BAD_CREDENTIALS - user exists, but credentials (e.g. passwd) don't match
- *
CERT_REQUIRED - not allowed to login this way without X.509 cert.
+ *
CERT_REQUIRED - not allowed to login this way without a cert.
*
NO_SUCH_USER - user not found using this method.
*
BAD_ARGS - user/pw not appropriate for this method
*/
diff --git a/dspace-api/src/main/java/org/dspace/authenticate/PasswordAuthentication.java b/dspace-api/src/main/java/org/dspace/authenticate/PasswordAuthentication.java
index 8e030305c957..035a235422a6 100644
--- a/dspace-api/src/main/java/org/dspace/authenticate/PasswordAuthentication.java
+++ b/dspace-api/src/main/java/org/dspace/authenticate/PasswordAuthentication.java
@@ -188,7 +188,7 @@ public List getSpecialGroups(Context context, HttpServletRequest request)
* Meaning:
*
SUCCESS - authenticated OK.
*
BAD_CREDENTIALS - user exists, but password doesn't match
- *
CERT_REQUIRED - not allowed to login this way without X.509 cert.
+ *
CERT_REQUIRED - not allowed to login this way without a cert.
*
NO_SUCH_USER - no EPerson with matching email address.
*
BAD_ARGS - missing username, or user matched but cannot login.
* @throws SQLException if database error
@@ -213,7 +213,7 @@ public int authenticate(Context context,
// cannot login this way
return BAD_ARGS;
} else if (eperson.getRequireCertificate()) {
- // this user can only login with x.509 certificate
+ // this user can only login with a certificate
log.warn(LogHelper.getHeader(context, "authenticate",
"rejecting PasswordAuthentication because " + username + " requires " +
"certificate."));
diff --git a/dspace-api/src/main/java/org/dspace/authenticate/ShibAuthentication.java b/dspace-api/src/main/java/org/dspace/authenticate/ShibAuthentication.java
index 24d8266012d4..13a5ae6d0dfd 100644
--- a/dspace-api/src/main/java/org/dspace/authenticate/ShibAuthentication.java
+++ b/dspace-api/src/main/java/org/dspace/authenticate/ShibAuthentication.java
@@ -160,7 +160,7 @@ public class ShibAuthentication implements AuthenticationMethod {
* SUCCESS - authenticated OK.
* BAD_CREDENTIALS - user exists, but credentials (e.g. passwd)
* don't match
- * CERT_REQUIRED - not allowed to login this way without X.509 cert.
+ * CERT_REQUIRED - not allowed to login this way without a cert.
*
* NO_SUCH_USER - user not found using this method.
* BAD_ARGS - user/pw not appropriate for this method
@@ -417,8 +417,7 @@ public boolean allowSetPassword(Context context,
* Predicate, is this an implicit authentication method. An implicit method
* gets credentials from the environment (such as an HTTP request or even
* Java system properties) rather than the explicit username and password.
- * For example, a method that reads the X.509 certificates in an HTTPS
- * request is implicit.
+ * For example, a method that provides IP-based authentication is implicit.
*
* @return true if this method uses implicit authentication.
*/
@@ -871,7 +870,7 @@ protected void updateEPerson(Context context, HttpServletRequest request, EPerso
String[] nameParts = MetadataFieldName.parse(field);
ePersonService.setMetadataSingleValue(context, eperson,
- nameParts[0], nameParts[1], nameParts[2], value, null);
+ nameParts[0], nameParts[1], nameParts[2], null, value);
log.debug("Updated the eperson's '{}' metadata using header: '{}' = '{}'.",
field, header, value);
}
@@ -917,7 +916,7 @@ protected int swordCompatibility(Context context, String username, String passwo
" is not allowed to login.");
return BAD_ARGS;
} else if (eperson.getRequireCertificate()) {
- // this user can only login with x.509 certificate
+ // this user can only login with a certificate
log.error(
"Shibboleth-based password authentication failed for user " + username + " because the eperson object" +
" requires a certificate to authenticate..");
diff --git a/dspace-api/src/main/java/org/dspace/authenticate/X509Authentication.java b/dspace-api/src/main/java/org/dspace/authenticate/X509Authentication.java
deleted file mode 100644
index 55843c710760..000000000000
--- a/dspace-api/src/main/java/org/dspace/authenticate/X509Authentication.java
+++ /dev/null
@@ -1,616 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.authenticate;
-
-import java.io.BufferedInputStream;
-import java.io.FileInputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.security.GeneralSecurityException;
-import java.security.KeyStore;
-import java.security.Principal;
-import java.security.PublicKey;
-import java.security.cert.Certificate;
-import java.security.cert.CertificateException;
-import java.security.cert.CertificateFactory;
-import java.security.cert.X509Certificate;
-import java.sql.SQLException;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.Enumeration;
-import java.util.List;
-import java.util.StringTokenizer;
-
-import jakarta.servlet.http.HttpServletRequest;
-import jakarta.servlet.http.HttpServletResponse;
-import jakarta.servlet.http.HttpSession;
-import org.apache.commons.lang3.ArrayUtils;
-import org.apache.logging.log4j.Logger;
-import org.dspace.authenticate.factory.AuthenticateServiceFactory;
-import org.dspace.authenticate.service.AuthenticationService;
-import org.dspace.authorize.AuthorizeException;
-import org.dspace.core.Context;
-import org.dspace.core.LogHelper;
-import org.dspace.eperson.EPerson;
-import org.dspace.eperson.Group;
-import org.dspace.eperson.factory.EPersonServiceFactory;
-import org.dspace.eperson.service.EPersonService;
-import org.dspace.eperson.service.GroupService;
-import org.dspace.services.ConfigurationService;
-import org.dspace.services.factory.DSpaceServicesFactory;
-
-/**
- * Implicit authentication method that gets credentials from the X.509 client
- * certificate supplied by the HTTPS client when connecting to this server. The
- * email address in that certificate is taken as the authenticated user name
- * with no further checking, so be sure your HTTP server (e.g. Tomcat) is
- * configured correctly to accept only client certificates it can validate.
- *
- * See the AuthenticationMethod interface for more details.
- *
- * Configuration:
- *
- *
- * x509.keystore.path =
- *
- * path to Java keystore file
- *
- * keystore.password =
- *
- * password to access the keystore
- *
- * ca.cert =
- *
- * path to certificate file for CA whose client certs to accept.
- *
- * autoregister =
- *
- * "true" if E-Person is created automatically for unknown new users.
- *
- * groups =
- *
- * comma-delimited list of special groups to add user to if authenticated.
- *
- * emaildomain =
- *
- * email address domain (after the 'at' symbol) to match before allowing
- * membership in special groups.
- *
- *
- *
- * Only one of the "keystore.path" or "ca.cert"
- * options is required. If you supply a keystore, then all of the "trusted"
- * certificates in the keystore represent CAs whose client certificates will be
- * accepted. The ca.cert option only allows a single CA to be
- * named.
- *
- * You can configure both a keystore and a CA cert, and both will be
- * used.
- *
- * The autoregister configuration parameter determines what the
- * canSelfRegister() method returns. It also allows an EPerson
- * record to be created automatically when the presented certificate is
- * acceptable but there is no corresponding EPerson.
- *
- * @author Larry Stone
- * @version $Revision$
- */
-public class X509Authentication implements AuthenticationMethod {
-
- /**
- * log4j category
- */
- private static Logger log = org.apache.logging.log4j.LogManager.getLogger(X509Authentication.class);
-
- /**
- * public key of CA to check client certs against.
- */
- private static PublicKey caPublicKey = null;
-
- /**
- * key store for CA certs if we use that
- */
- private static KeyStore caCertKeyStore = null;
-
- private static String loginPageTitle = null;
-
- private static String loginPageURL = null;
-
- protected AuthenticationService authenticationService = AuthenticateServiceFactory.getInstance()
- .getAuthenticationService();
- protected EPersonService ePersonService = EPersonServiceFactory.getInstance().getEPersonService();
- protected GroupService groupService = EPersonServiceFactory.getInstance().getGroupService();
- protected ConfigurationService configurationService =
- DSpaceServicesFactory.getInstance().getConfigurationService();
-
- private static final String X509_AUTHENTICATED = "x509.authenticated";
-
-
- /**
- * Initialization: Set caPublicKey and/or keystore. This loads the
- * information needed to check if a client cert presented is valid and
- * acceptable.
- */
- static {
- ConfigurationService configurationService =
- DSpaceServicesFactory.getInstance().getConfigurationService();
- /*
- * allow identification of alternative entry points for certificate
- * authentication when selected by the user rather than implicitly.
- */
- loginPageTitle = configurationService
- .getProperty("authentication-x509.chooser.title.key");
- loginPageURL = configurationService
- .getProperty("authentication-x509.chooser.uri");
-
- String keystorePath = configurationService
- .getProperty("authentication-x509.keystore.path");
- String keystorePassword = configurationService
- .getProperty("authentication-x509.keystore.password");
- String caCertPath = configurationService
- .getProperty("authentication-x509.ca.cert");
-
- // First look for keystore full of trusted certs.
- if (keystorePath != null) {
- FileInputStream fis = null;
- if (keystorePassword == null) {
- keystorePassword = "";
- }
- try {
- KeyStore ks = KeyStore.getInstance("JKS");
- fis = new FileInputStream(keystorePath);
- ks.load(fis, keystorePassword.toCharArray());
- caCertKeyStore = ks;
- } catch (IOException e) {
- log
- .error("X509Authentication: Failed to load CA keystore, file="
- + keystorePath + ", error=" + e.toString());
- } catch (GeneralSecurityException e) {
- log
- .error("X509Authentication: Failed to extract CA keystore, file="
- + keystorePath + ", error=" + e.toString());
- } finally {
- if (fis != null) {
- try {
- fis.close();
- } catch (IOException ioe) {
- // ignore
- }
- }
- }
- }
-
- // Second, try getting public key out of CA cert, if that's configured.
- if (caCertPath != null) {
- InputStream is = null;
- FileInputStream fis = null;
- try {
- fis = new FileInputStream(caCertPath);
- is = new BufferedInputStream(fis);
- X509Certificate cert = (X509Certificate) CertificateFactory
- .getInstance("X.509").generateCertificate(is);
- if (cert != null) {
- caPublicKey = cert.getPublicKey();
- }
- } catch (IOException e) {
- log.error("X509Authentication: Failed to load CA cert, file="
- + caCertPath + ", error=" + e.toString());
- } catch (CertificateException e) {
- log
- .error("X509Authentication: Failed to extract CA cert, file="
- + caCertPath + ", error=" + e.toString());
- } finally {
- if (is != null) {
- try {
- is.close();
- } catch (IOException ioe) {
- // ignore
- }
- }
-
- if (fis != null) {
- try {
- fis.close();
- } catch (IOException ioe) {
- // ignore
- }
- }
- }
- }
- }
-
- /**
- * Return the email address from certificate, or null if an
- * email address cannot be found in the certificate.
- *
- * Note that the certificate parsing has only been tested with certificates
- * granted by the MIT Certification Authority, and may not work elsewhere.
- *
- * @param certificate -
- * An X509 certificate object
- * @return - The email address found in certificate, or null if an email
- * address cannot be found in the certificate.
- */
- private static String getEmail(X509Certificate certificate)
- throws SQLException {
- Principal principal = certificate.getSubjectDN();
-
- if (principal == null) {
- return null;
- }
-
- String dn = principal.getName();
- if (dn == null) {
- return null;
- }
-
- StringTokenizer tokenizer = new StringTokenizer(dn, ",");
- String token = null;
- while (tokenizer.hasMoreTokens()) {
- int len = "emailaddress=".length();
-
- token = (String) tokenizer.nextToken();
-
- if (token.toLowerCase().startsWith("emailaddress=")) {
- // Make sure the token actually contains something
- if (token.length() <= len) {
- return null;
- }
-
- return token.substring(len).toLowerCase();
- }
- }
-
- return null;
- }
-
- /**
- * Verify CERTIFICATE against KEY. Return true if and only if CERTIFICATE is
- * valid and can be verified against KEY.
- *
- * @param context The current DSpace context
- * @param certificate -
- * An X509 certificate object
- * @return - True if CERTIFICATE is valid and can be verified against KEY,
- * false otherwise.
- */
- private static boolean isValid(Context context, X509Certificate certificate) {
- if (certificate == null) {
- return false;
- }
-
- // This checks that current time is within cert's validity window:
- try {
- certificate.checkValidity();
- } catch (CertificateException e) {
- log.info(LogHelper.getHeader(context, "authentication",
- "X.509 Certificate is EXPIRED or PREMATURE: "
- + e.toString()));
- return false;
- }
-
- // Try CA public key, if available.
- if (caPublicKey != null) {
- try {
- certificate.verify(caPublicKey);
- return true;
- } catch (GeneralSecurityException e) {
- log.info(LogHelper.getHeader(context, "authentication",
- "X.509 Certificate FAILED SIGNATURE check: "
- + e.toString()));
- }
- }
-
- // Try it with keystore, if available.
- if (caCertKeyStore != null) {
- try {
- Enumeration ke = caCertKeyStore.aliases();
-
- while (ke.hasMoreElements()) {
- String alias = (String) ke.nextElement();
- if (caCertKeyStore.isCertificateEntry(alias)) {
- Certificate ca = caCertKeyStore.getCertificate(alias);
- try {
- certificate.verify(ca.getPublicKey());
- return true;
- } catch (CertificateException ce) {
- // ignore
- }
- }
- }
- log
- .info(LogHelper
- .getHeader(context, "authentication",
- "Keystore method FAILED SIGNATURE check on client cert."));
- } catch (GeneralSecurityException e) {
- log.info(LogHelper.getHeader(context, "authentication",
- "X.509 Certificate FAILED SIGNATURE check: "
- + e.toString()));
- }
-
- }
- return false;
- }
-
- /**
- * Predicate, can new user automatically create EPerson. Checks
- * configuration value. You'll probably want this to be true to take
- * advantage of a Web certificate infrastructure with many more users than
- * are already known by DSpace.
- *
- * @throws SQLException if database error
- */
- @Override
- public boolean canSelfRegister(Context context, HttpServletRequest request,
- String username) throws SQLException {
- return configurationService
- .getBooleanProperty("authentication-x509.autoregister");
- }
-
- /**
- * Nothing extra to initialize.
- *
- * @throws SQLException if database error
- */
- @Override
- public void initEPerson(Context context, HttpServletRequest request,
- EPerson eperson) throws SQLException {
- }
-
- /**
- * We don't use EPerson password so there is no reason to change it.
- *
- * @throws SQLException if database error
- */
- @Override
- public boolean allowSetPassword(Context context,
- HttpServletRequest request, String username) throws SQLException {
- return false;
- }
-
- /**
- * Returns true, this is an implicit method.
- */
- @Override
- public boolean isImplicit() {
- return true;
- }
-
- /**
- * Returns a list of group names that the user should be added to upon
- * successful authentication, configured in dspace.cfg.
- *
- * @return List of special groups configured for this authenticator
- */
- private List getX509Groups() {
- List groupNames = new ArrayList();
-
- String[] groups = configurationService
- .getArrayProperty("authentication-x509.groups");
-
- if (ArrayUtils.isNotEmpty(groups)) {
- for (String group : groups) {
- groupNames.add(group.trim());
- }
- }
-
- return groupNames;
- }
-
- /**
- * Checks for configured email domain required to grant special groups
- * membership. If no email domain is configured to verify, special group
- * membership is simply granted.
- *
- * @param request -
- * The current request object
- * @param email -
- * The email address from the x509 certificate
- */
- private void setSpecialGroupsFlag(HttpServletRequest request, String email) {
- String emailDomain = null;
- emailDomain = (String) request
- .getAttribute("authentication.x509.emaildomain");
-
- HttpSession session = request.getSession(true);
-
- if (null != emailDomain && !"".equals(emailDomain)) {
- if (email.substring(email.length() - emailDomain.length()).equals(
- emailDomain)) {
- session.setAttribute("x509Auth", Boolean.TRUE);
- }
- } else {
- // No configured email domain to verify. Just flag
- // as authenticated so special groups are granted.
- session.setAttribute("x509Auth", Boolean.TRUE);
- }
- }
-
- /**
- * Return special groups configured in dspace.cfg for X509 certificate
- * authentication.
- *
- * @param context context
- * @param request object potentially containing the cert
- * @return An int array of group IDs
- * @throws SQLException if database error
- */
- @Override
- public List getSpecialGroups(Context context, HttpServletRequest request)
- throws SQLException {
- if (request == null) {
- return Collections.EMPTY_LIST;
- }
-
- Boolean authenticated = false;
- HttpSession session = request.getSession(false);
- authenticated = (Boolean) session.getAttribute("x509Auth");
- authenticated = (null == authenticated) ? false : authenticated;
-
- if (authenticated) {
- List groupNames = getX509Groups();
- List groups = new ArrayList<>();
-
- if (groupNames != null) {
- for (String groupName : groupNames) {
- if (groupName != null) {
- Group group = groupService.findByName(context, groupName);
- if (group != null) {
- groups.add(group);
- } else {
- log.warn(LogHelper.getHeader(context,
- "configuration_error", "unknown_group="
- + groupName));
- }
- }
- }
- }
-
- return groups;
- }
-
- return Collections.EMPTY_LIST;
- }
-
- /**
- * X509 certificate authentication. The client certificate is obtained from
- * the ServletRequest object.
- *
- * - If the certificate is valid, and corresponds to an existing EPerson,
- * and the user is allowed to login, return success.
- * - If the user is matched but is not allowed to login, it fails.
- * - If the certificate is valid, but there is no corresponding EPerson,
- * the
"authentication.x509.autoregister" configuration
- * parameter is checked (via canSelfRegister())
- *
- * - If it's true, a new EPerson record is created for the certificate,
- * and the result is success.
- * - If it's false, return that the user was unknown.
- *
- *
- *
- *
- * @return One of: SUCCESS, BAD_CREDENTIALS, NO_SUCH_USER, BAD_ARGS
- * @throws SQLException if database error
- */
- @Override
- public int authenticate(Context context, String username, String password,
- String realm, HttpServletRequest request) throws SQLException {
- // Obtain the certificate from the request, if any
- X509Certificate[] certs = null;
- if (request != null) {
- certs = (X509Certificate[]) request
- .getAttribute("jakarta.servlet.request.X509Certificate");
- }
-
- if ((certs == null) || (certs.length == 0)) {
- return BAD_ARGS;
- } else {
- // We have a cert -- check it and get username from it.
- try {
- if (!isValid(context, certs[0])) {
- log
- .warn(LogHelper
- .getHeader(context, "authenticate",
- "type=x509certificate, status=BAD_CREDENTIALS (not valid)"));
- return BAD_CREDENTIALS;
- }
-
- // And it's valid - try and get an e-person
- String email = getEmail(certs[0]);
- EPerson eperson = null;
- if (email != null) {
- eperson = ePersonService.findByEmail(context, email);
- }
- if (eperson == null) {
- // Cert is valid, but no record.
- if (email != null
- && canSelfRegister(context, request, null)) {
- // Register the new user automatically
- log.info(LogHelper.getHeader(context, "autoregister",
- "from=x.509, email=" + email));
-
- // TEMPORARILY turn off authorisation
- context.turnOffAuthorisationSystem();
- eperson = ePersonService.create(context);
- eperson.setEmail(email);
- eperson.setCanLogIn(true);
- authenticationService.initEPerson(context, request,
- eperson);
- ePersonService.update(context, eperson);
- context.dispatchEvents();
- context.restoreAuthSystemState();
- context.setCurrentUser(eperson);
- request.setAttribute(X509_AUTHENTICATED, true);
- setSpecialGroupsFlag(request, email);
- return SUCCESS;
- } else {
- // No auto-registration for valid certs
- log
- .warn(LogHelper
- .getHeader(context, "authenticate",
- "type=cert_but_no_record, cannot auto-register"));
- return NO_SUCH_USER;
- }
- } else if (!eperson.canLogIn()) { // make sure this is a login account
- log.warn(LogHelper.getHeader(context, "authenticate",
- "type=x509certificate, email=" + email
- + ", canLogIn=false, rejecting."));
- return BAD_ARGS;
- } else {
- log.info(LogHelper.getHeader(context, "login",
- "type=x509certificate"));
- context.setCurrentUser(eperson);
- request.setAttribute(X509_AUTHENTICATED, true);
- setSpecialGroupsFlag(request, email);
- return SUCCESS;
- }
- } catch (AuthorizeException ce) {
- log.warn(LogHelper.getHeader(context, "authorize_exception",
- ""), ce);
- }
-
- return BAD_ARGS;
- }
- }
-
- /**
- * Returns URL of password-login servlet.
- *
- * @param context DSpace context, will be modified (EPerson set) upon success.
- * @param request The HTTP request that started this operation, or null if not
- * applicable.
- * @param response The HTTP response from the servlet method.
- * @return fully-qualified URL
- */
- @Override
- public String loginPageURL(Context context, HttpServletRequest request,
- HttpServletResponse response) {
- return loginPageURL;
- }
-
- @Override
- public String getName() {
- return "x509";
- }
-
- @Override
- public boolean isUsed(final Context context, final HttpServletRequest request) {
- if (request != null &&
- context.getCurrentUser() != null &&
- request.getAttribute(X509_AUTHENTICATED) != null) {
- return true;
- }
- return false;
- }
-
- @Override
- public boolean canChangePassword(Context context, EPerson ePerson, String currentPassword) {
- return false;
- }
-}
diff --git a/dspace-api/src/main/java/org/dspace/authenticate/service/AuthenticationService.java b/dspace-api/src/main/java/org/dspace/authenticate/service/AuthenticationService.java
index 45ad8932daec..8409f1e27d05 100644
--- a/dspace-api/src/main/java/org/dspace/authenticate/service/AuthenticationService.java
+++ b/dspace-api/src/main/java/org/dspace/authenticate/service/AuthenticationService.java
@@ -29,11 +29,11 @@
* Configuration
* The stack of authentication methods is defined by one property in the DSpace configuration:
*
- * plugin.sequence.org.dspace.eperson.AuthenticationMethod = a list of method class names
+ * plugin.sequence.org.dspace.authenticate.AuthenticationMethod = a list of method class names
* e.g.
- * plugin.sequence.org.dspace.eperson.AuthenticationMethod = \
- * org.dspace.eperson.X509Authentication, \
- * org.dspace.eperson.PasswordAuthentication
+ * plugin.sequence.org.dspace.authenticate.AuthenticationMethod = \
+ * org.dspace.authenticate.IPAuthentication, \
+ * org.dspace.authenticate.PasswordAuthentication
*
*
* The "stack" is always traversed in order, with the methods
@@ -64,7 +64,7 @@ public interface AuthenticationService {
*
Meaning:
*
SUCCESS - authenticated OK.
*
BAD_CREDENTIALS - user exists, but credentials (e.g. password) don't match
- *
CERT_REQUIRED - not allowed to login this way without X.509 cert.
+ *
CERT_REQUIRED - not allowed to login this way without a cert.
*
NO_SUCH_USER - user not found using this method.
*
BAD_ARGS - user/password not appropriate for this method
*/
@@ -91,7 +91,7 @@ public int authenticate(Context context,
*
Meaning:
*
SUCCESS - authenticated OK.
*
BAD_CREDENTIALS - user exists, but credentials (e.g. password) don't match
- *
CERT_REQUIRED - not allowed to login this way without X.509 cert.
+ *
CERT_REQUIRED - not allowed to login this way without a cert.
*
NO_SUCH_USER - user not found using this method.
*
BAD_ARGS - user/password not appropriate for this method
*/
diff --git a/dspace-api/src/main/java/org/dspace/authority/orcid/Orcidv3SolrAuthorityImpl.java b/dspace-api/src/main/java/org/dspace/authority/orcid/Orcidv3SolrAuthorityImpl.java
index 494daa97734a..312a00c146af 100644
--- a/dspace-api/src/main/java/org/dspace/authority/orcid/Orcidv3SolrAuthorityImpl.java
+++ b/dspace-api/src/main/java/org/dspace/authority/orcid/Orcidv3SolrAuthorityImpl.java
@@ -10,6 +10,7 @@
import java.io.IOException;
import java.io.InputStream;
import java.net.URLEncoder;
+import java.nio.charset.StandardCharsets;
import java.util.ArrayList;
import java.util.Collections;
import java.util.LinkedList;
@@ -20,6 +21,7 @@
import org.apache.logging.log4j.Logger;
import org.dspace.authority.AuthorityValue;
import org.dspace.authority.SolrAuthorityInterface;
+import org.dspace.external.OrcidConnectionException;
import org.dspace.external.OrcidRestConnector;
import org.dspace.external.provider.orcid.xml.XMLtoBio;
import org.dspace.orcid.model.factory.OrcidFactoryUtils;
@@ -142,9 +144,15 @@ public Person getBio(String id) {
return null;
}
initializeAccessToken();
- InputStream bioDocument = orcidRestConnector.get(id + ((id.endsWith("/person")) ? "" : "/person"), accessToken);
- XMLtoBio converter = new XMLtoBio();
- return converter.convertSinglePerson(bioDocument);
+ try {
+ InputStream bioDocument = orcidRestConnector.get(id + ((id.endsWith("/person")) ? "" : "/person"),
+ accessToken);
+ XMLtoBio converter = new XMLtoBio();
+ return converter.convertSinglePerson(bioDocument);
+ } catch (OrcidConnectionException e) {
+ log.error("Error retrieving ORCID bio for ID=" + id, e);
+ return null;
+ }
}
@@ -167,29 +175,35 @@ public List queryBio(String text, int start, int rows) {
// Check / init access token
initializeAccessToken();
- String searchPath = "search?q=" + URLEncoder.encode(text) + "&start=" + start + "&rows=" + rows;
+ String searchPath = "search?q=" + URLEncoder.encode(text, StandardCharsets.UTF_8) + "&start=" + start +
+ "&rows=" + rows;
log.debug("queryBio searchPath=" + searchPath + " accessToken=" + accessToken);
- InputStream bioDocument = orcidRestConnector.get(searchPath, accessToken);
- XMLtoBio converter = new XMLtoBio();
- List results = converter.convert(bioDocument);
- List bios = new LinkedList<>();
- for (Result result : results) {
- OrcidIdentifier orcidIdentifier = result.getOrcidIdentifier();
- if (orcidIdentifier != null) {
- log.debug("Found OrcidId=" + orcidIdentifier.toString());
- String orcid = orcidIdentifier.getPath();
- Person bio = getBio(orcid);
- if (bio != null) {
- bios.add(bio);
+ try {
+ InputStream bioDocument = orcidRestConnector.get(searchPath, accessToken);
+ XMLtoBio converter = new XMLtoBio();
+ List results = converter.convert(bioDocument);
+ List bios = new LinkedList<>();
+ for (Result result : results) {
+ OrcidIdentifier orcidIdentifier = result.getOrcidIdentifier();
+ if (orcidIdentifier != null) {
+ log.debug("Found OrcidId=" + orcidIdentifier);
+ String orcid = orcidIdentifier.getPath();
+ Person bio = getBio(orcid);
+ if (bio != null) {
+ bios.add(bio);
+ }
}
}
+ try {
+ bioDocument.close();
+ } catch (IOException e) {
+ log.error(e.getMessage(), e);
+ }
+ return bios;
+ } catch (OrcidConnectionException e) {
+ log.error("Error searching ORCID for query=" + text, e);
+ return Collections.emptyList();
}
- try {
- bioDocument.close();
- } catch (IOException e) {
- log.error(e.getMessage(), e);
- }
- return bios;
}
/**
diff --git a/dspace-api/src/main/java/org/dspace/authorize/AuthorizeServiceImpl.java b/dspace-api/src/main/java/org/dspace/authorize/AuthorizeServiceImpl.java
index f2692cf394fc..60004bda9538 100644
--- a/dspace-api/src/main/java/org/dspace/authorize/AuthorizeServiceImpl.java
+++ b/dspace-api/src/main/java/org/dspace/authorize/AuthorizeServiceImpl.java
@@ -16,6 +16,7 @@
import java.util.Arrays;
import java.util.Date;
import java.util.List;
+import java.util.Objects;
import java.util.UUID;
import org.apache.commons.collections4.CollectionUtils;
@@ -48,6 +49,7 @@
import org.dspace.eperson.EPerson;
import org.dspace.eperson.Group;
import org.dspace.eperson.service.GroupService;
+import org.dspace.services.ConfigurationService;
import org.dspace.workflow.WorkflowItemService;
import org.springframework.beans.factory.annotation.Autowired;
@@ -84,6 +86,8 @@ public class AuthorizeServiceImpl implements AuthorizeService {
protected WorkflowItemService workflowItemService;
@Autowired(required = true)
private SearchService searchService;
+ @Autowired(required = true)
+ private ConfigurationService configurationService;
protected AuthorizeServiceImpl() {
@@ -508,17 +512,26 @@ public List getPoliciesActionFilter(Context c, DSpaceObject o,
return resourcePolicyService.find(c, o, actionID);
}
+ @Override
+ public void inheritPolicies(Context c, DSpaceObject src, DSpaceObject dest)
+ throws SQLException, AuthorizeException {
+ inheritPolicies(c, src, dest, false);
+ }
+
@Override
public void inheritPolicies(Context c, DSpaceObject src,
- DSpaceObject dest) throws SQLException, AuthorizeException {
+ DSpaceObject dest, boolean includeCustom) throws SQLException, AuthorizeException {
// find all policies for the source object
List policies = getPolicies(c, src);
- //Only inherit non-ADMIN policies (since ADMIN policies are automatically inherited)
- //and non-custom policies as these are manually applied when appropriate
+ // Only inherit non-ADMIN policies (since ADMIN policies are automatically inherited)
+ // and non-custom policies (usually applied manually?) UNLESS specified otherwise with includCustom
+ // (for example, item.addBundle() will inherit custom policies to enforce access conditions)
List nonAdminPolicies = new ArrayList<>();
for (ResourcePolicy rp : policies) {
- if (rp.getAction() != Constants.ADMIN && !StringUtils.equals(rp.getRpType(), ResourcePolicy.TYPE_CUSTOM)) {
+ if (rp.getAction() != Constants.ADMIN && (!StringUtils.equals(rp.getRpType(), ResourcePolicy.TYPE_CUSTOM)
+ || (includeCustom && StringUtils.equals(rp.getRpType(), ResourcePolicy.TYPE_CUSTOM)
+ && isNotAlreadyACustomRPOfThisTypeOnDSO(c, dest)))) {
nonAdminPolicies.add(rp);
}
}
@@ -943,4 +956,100 @@ private String formatCustomQuery(String query) {
return query + " AND ";
}
}
+
+ /**
+ * Add the default policies, which have not been already added to the given DSpace object
+ *
+ * @param context The relevant DSpace Context.
+ * @param dso The DSpace Object to add policies to
+ * @param defaultCollectionPolicies list of policies
+ * @throws SQLException An exception that provides information on a database access error or other errors.
+ * @throws AuthorizeException Exception indicating the current user of the context does not have permission
+ * to perform a particular action.
+ */
+ @Override
+ public void addDefaultPoliciesNotInPlace(Context context, DSpaceObject dso,
+ List defaultCollectionPolicies) throws SQLException, AuthorizeException {
+ boolean appendMode = configurationService
+ .getBooleanProperty("core.authorization.installitem.inheritance-read.append-mode", false);
+ for (ResourcePolicy defaultPolicy : defaultCollectionPolicies) {
+ if (!isAnIdenticalPolicyAlreadyInPlace(context, dso, defaultPolicy.getGroup(), Constants.READ,
+ defaultPolicy.getID()) &&
+ (!appendMode && isNotAlreadyACustomRPOfThisTypeOnDSO(context, dso) ||
+ appendMode && shouldBeAppended(context, dso, defaultPolicy))) {
+ ResourcePolicy newPolicy = resourcePolicyService.clone(context, defaultPolicy);
+ newPolicy.setdSpaceObject(dso);
+ newPolicy.setAction(Constants.READ);
+ newPolicy.setRpType(ResourcePolicy.TYPE_INHERITED);
+ resourcePolicyService.update(context, newPolicy);
+ }
+ }
+ }
+
+ /**
+ * Add a list of custom policies if there are already NO custom policies in place
+ *
+ */
+ @Override
+ public void addCustomPoliciesNotInPlace(Context context, DSpaceObject dso, List customPolicies)
+ throws SQLException, AuthorizeException {
+ boolean customPoliciesAlreadyInPlace =
+ findPoliciesByDSOAndType(context, dso, ResourcePolicy.TYPE_CUSTOM).size() > 0;
+ if (!customPoliciesAlreadyInPlace) {
+ addPolicies(context, customPolicies, dso);
+ }
+ }
+
+ /**
+ * Check whether or not there is already an RP on the given dso, which has actionId={@link Constants.READ} and
+ * resourceTypeId={@link ResourcePolicy.TYPE_CUSTOM}
+ *
+ * @param context DSpace context
+ * @param dso DSpace object to check for custom read RP
+ * @return True if there is no RP on the item with custom read RP, otherwise false
+ * @throws SQLException If something goes wrong retrieving the RP on the DSO
+ */
+ private boolean isNotAlreadyACustomRPOfThisTypeOnDSO(Context context, DSpaceObject dso) throws SQLException {
+ return isNotAlreadyACustomRPOfThisTypeOnDSO(context, dso, Constants.READ);
+ }
+
+ private boolean isNotAlreadyACustomRPOfThisTypeOnDSO(Context context, DSpaceObject dso, int action)
+ throws SQLException {
+ List rps = resourcePolicyService.find(context, dso, action);
+ for (ResourcePolicy rp : rps) {
+ if (rp.getRpType() != null && rp.getRpType().equals(ResourcePolicy.TYPE_CUSTOM)) {
+ return false;
+ }
+ }
+ return true;
+ }
+
+ /**
+ * Check if the provided default policy should be appended or not to the final
+ * item. If an item has at least one custom READ policy any anonymous READ
+ * policy with empty start/end date should be skipped
+ *
+ * @param context DSpace context
+ * @param dso DSpace object to check for custom read RP
+ * @param defaultPolicy The policy to check
+ * @return
+ * @throws SQLException If something goes wrong retrieving the RP on the DSO
+ */
+ private boolean shouldBeAppended(Context context, DSpaceObject dso, ResourcePolicy defaultPolicy)
+ throws SQLException {
+ boolean hasCustomPolicy = resourcePolicyService.find(context, dso, Constants.READ)
+ .stream()
+ .filter(rp -> (Objects.nonNull(rp.getRpType()) &&
+ Objects.equals(rp.getRpType(), ResourcePolicy.TYPE_CUSTOM)))
+ .findFirst()
+ .isPresent();
+
+ boolean isAnonymousGroup = Objects.nonNull(defaultPolicy.getGroup())
+ && StringUtils.equals(defaultPolicy.getGroup().getName(), Group.ANONYMOUS);
+
+ boolean datesAreNull = Objects.isNull(defaultPolicy.getStartDate())
+ && Objects.isNull(defaultPolicy.getEndDate());
+
+ return !(hasCustomPolicy && isAnonymousGroup && datesAreNull);
+ }
}
diff --git a/dspace-api/src/main/java/org/dspace/authorize/dao/impl/ResourcePolicyDAOImpl.java b/dspace-api/src/main/java/org/dspace/authorize/dao/impl/ResourcePolicyDAOImpl.java
index 3b09f9cf300b..1f9e5ea26677 100644
--- a/dspace-api/src/main/java/org/dspace/authorize/dao/impl/ResourcePolicyDAOImpl.java
+++ b/dspace-api/src/main/java/org/dspace/authorize/dao/impl/ResourcePolicyDAOImpl.java
@@ -182,7 +182,7 @@ public List findByEPersonGroupTypeIdAction(Context context, EPer
compareEpersonOrGroups
)
);
- return list(context, criteriaQuery, false, ResourcePolicy.class, 1, -1);
+ return list(context, criteriaQuery, false, ResourcePolicy.class, -1, -1);
}
@Override
diff --git a/dspace-api/src/main/java/org/dspace/authorize/service/AuthorizeService.java b/dspace-api/src/main/java/org/dspace/authorize/service/AuthorizeService.java
index e0a94833d76c..0e542d98f6d4 100644
--- a/dspace-api/src/main/java/org/dspace/authorize/service/AuthorizeService.java
+++ b/dspace-api/src/main/java/org/dspace/authorize/service/AuthorizeService.java
@@ -322,6 +322,19 @@ public void addPolicy(Context c, DSpaceObject o, int actionID, Group g, String t
*/
public List getPoliciesActionFilterExceptRpType(Context c, DSpaceObject o, int actionID,
String rpType) throws SQLException;
+ /**
+ * Add policies to an object to match those from a previous object
+ *
+ * @param c context
+ * @param src source of policies
+ * @param dest destination of inherited policies
+ * @param includeCustom whether TYPE_CUSTOM policies should be inherited
+ * @throws SQLException if there's a database problem
+ * @throws AuthorizeException if the current user is not authorized to add these policies
+ */
+ public void inheritPolicies(Context c, DSpaceObject src, DSpaceObject dest, boolean includeCustom)
+ throws SQLException, AuthorizeException;
+
/**
* Add policies to an object to match those from a previous object
*
@@ -604,4 +617,10 @@ long countAdminAuthorizedCollection(Context context, String query)
public void replaceAllPolicies(Context context, DSpaceObject source, DSpaceObject dest)
throws SQLException, AuthorizeException;
+ public void addDefaultPoliciesNotInPlace(Context context, DSpaceObject dso,
+ List defaultCollectionPolicies) throws SQLException, AuthorizeException;
+
+ public void addCustomPoliciesNotInPlace(Context context, DSpaceObject dso,
+ List defaultCollectionPolicies) throws SQLException, AuthorizeException;
+
}
diff --git a/dspace-api/src/main/java/org/dspace/checker/CheckerCommand.java b/dspace-api/src/main/java/org/dspace/checker/CheckerCommand.java
index a12ac3b98a2e..9ad9f553b445 100644
--- a/dspace-api/src/main/java/org/dspace/checker/CheckerCommand.java
+++ b/dspace-api/src/main/java/org/dspace/checker/CheckerCommand.java
@@ -131,7 +131,7 @@ public void process() throws SQLException {
collector.collect(context, info);
}
- context.uncacheEntity(bitstream);
+ context.commit();
bitstream = dispatcher.next();
}
}
diff --git a/dspace-api/src/main/java/org/dspace/checker/DailyReportEmailer.java b/dspace-api/src/main/java/org/dspace/checker/DailyReportEmailer.java
index 50ef4baa98e3..481b055fbb7d 100644
--- a/dspace-api/src/main/java/org/dspace/checker/DailyReportEmailer.java
+++ b/dspace-api/src/main/java/org/dspace/checker/DailyReportEmailer.java
@@ -75,6 +75,7 @@ public void sendReport(File attachment, int numberOfBitstreams)
email.setContent("Checker Report", "report is attached ...");
email.addAttachment(attachment, "checksum_checker_report.txt");
email.addRecipient(configurationService.getProperty("mail.admin"));
+ log.info("Sending checker report email to " + configurationService.getProperty("mail.admin"));
email.send();
}
}
@@ -109,18 +110,19 @@ public static void main(String[] args) {
Options options = new Options();
options.addOption("h", "help", false, "Help");
- options.addOption("d", "Deleted", false,
- "Send E-mail report for all bitstreams set as deleted for today");
- options.addOption("m", "Missing", false,
- "Send E-mail report for all bitstreams not found in assetstore for today");
- options.addOption("c", "Changed", false,
- "Send E-mail report for all bitstreams where checksum has been changed for today");
- options.addOption("a", "All", false,
- "Send all E-mail reports");
- options.addOption("u", "Unchecked", false,
- "Send the Unchecked bitstream report");
- options.addOption("n", "Not Processed", false,
- "Send E-mail report for all bitstreams set to longer be processed for today");
+ options.addOption("d", "deleted", false,
+ "Send email report for all bitstreams set as deleted for today");
+ options.addOption("m", "missing", false,
+ "Send email report for all bitstreams not found in assetstore for today");
+ options.addOption("c", "changed", false,
+ "Send email report for all bitstreams where checksum has been changed for today");
+ options.addOption("a", "all", false,
+ "Send all email reports (used by default)");
+ options.addOption("u", "unchecked", false,
+ "Send the unchecked (i.e. recently added) bitstream email report");
+ options.addOption("n", "not-processed", false,
+ "Send email report for all bitstreams set to no longer be processed for today (includes"
+ + " bitstreams marked as deleted or not found)");
try {
line = parser.parse(options, args);
@@ -133,13 +135,15 @@ public static void main(String[] args) {
if (line.hasOption('h')) {
HelpFormatter myhelp = new HelpFormatter();
- myhelp.printHelp("Checksum Reporter\n", options);
- System.out.println("\nSend Deleted bitstream email report: DailyReportEmailer -d");
- System.out.println("\nSend Missing bitstreams email report: DailyReportEmailer -m");
- System.out.println("\nSend Checksum Changed email report: DailyReportEmailer -c");
- System.out.println("\nSend bitstream not to be processed email report: DailyReportEmailer -n");
- System.out.println("\nSend Un-checked bitstream report: DailyReportEmailer -u");
- System.out.println("\nSend All email reports: DailyReportEmailer");
+ myhelp.printHelp("checker-emailer\n", options);
+ System.out.println("\nChecksum Checker Reporter usage examples:\n");
+ System.out.println(" - Send all email reports: checker-emailer -a");
+ System.out.println(" - Send deleted bitstream email report: checker-emailer -d");
+ System.out.println(" - Send missing bitstreams email report: checker-emailer -m");
+ System.out.println(" - Send checksum changed email report: checker-emailer -c");
+ System.out.println(" - Send bitstream not to be processed email report: checker-emailer -n");
+ System.out.println(" - Send unchecked bitstream email report: checker-emailer -u");
+ System.out.println("\nDefault (no arguments) is equivalent to 'checker-emailer -a'\n");
System.exit(0);
}
@@ -191,7 +195,9 @@ public static void main(String[] args) {
writer.write("\n--------------------------------- Report Spacer ---------------------------\n\n");
numBitstreams += reporter.getBitstreamNotFoundReport(context, yesterday, tomorrow, writer);
writer.write("\n--------------------------------- Report Spacer ---------------------------\n\n");
- numBitstreams += reporter.getNotToBeProcessedReport(context, yesterday, tomorrow, writer);
+ // not to be processed report includes deleted and not found bitstreams so it is not necessary to
+ // include the sum in the counter
+ reporter.getNotToBeProcessedReport(context, yesterday, tomorrow, writer);
writer.write("\n--------------------------------- Report Spacer ---------------------------\n\n");
numBitstreams += reporter.getUncheckedBitstreamsReport(context, writer);
writer.write("\n--------------------------------- End Report ---------------------------\n\n");
diff --git a/dspace-api/src/main/java/org/dspace/checker/SimpleReporterServiceImpl.java b/dspace-api/src/main/java/org/dspace/checker/SimpleReporterServiceImpl.java
index ddefb28e1b57..6c69764fdc79 100644
--- a/dspace-api/src/main/java/org/dspace/checker/SimpleReporterServiceImpl.java
+++ b/dspace-api/src/main/java/org/dspace/checker/SimpleReporterServiceImpl.java
@@ -70,6 +70,7 @@ public int getDeletedBitstreamReport(Context context, Date startDate, Date endDa
osw.write("\n");
osw.write(msg("deleted-bitstream-intro"));
+ osw.write(" ");
osw.write(applyDateFormatShort(startDate));
osw.write(" ");
osw.write(msg("date-range-to"));
@@ -111,7 +112,6 @@ public int getChangedChecksumReport(Context context, Date startDate, Date endDat
osw.write("\n");
osw.write(msg("checksum-did-not-match"));
osw.write(" ");
- osw.write("\n");
osw.write(applyDateFormatShort(startDate));
osw.write(" ");
osw.write(msg("date-range-to"));
diff --git a/dspace-api/src/main/java/org/dspace/checker/dao/impl/MostRecentChecksumDAOImpl.java b/dspace-api/src/main/java/org/dspace/checker/dao/impl/MostRecentChecksumDAOImpl.java
index 669621aeeb58..e37f0135dc59 100644
--- a/dspace-api/src/main/java/org/dspace/checker/dao/impl/MostRecentChecksumDAOImpl.java
+++ b/dspace-api/src/main/java/org/dspace/checker/dao/impl/MostRecentChecksumDAOImpl.java
@@ -56,8 +56,8 @@ public List findByNotProcessedInDateRange(Context context, D
criteriaQuery.where(criteriaBuilder.and(
criteriaBuilder.equal(mostRecentChecksumRoot.get(MostRecentChecksum_.toBeProcessed), false),
criteriaBuilder
- .lessThanOrEqualTo(mostRecentChecksumRoot.get(MostRecentChecksum_.processStartDate), startDate),
- criteriaBuilder.greaterThan(mostRecentChecksumRoot.get(MostRecentChecksum_.processStartDate), endDate)
+ .lessThanOrEqualTo(mostRecentChecksumRoot.get(MostRecentChecksum_.processStartDate), endDate),
+ criteriaBuilder.greaterThan(mostRecentChecksumRoot.get(MostRecentChecksum_.processStartDate), startDate)
)
);
List orderList = new LinkedList<>();
diff --git a/dspace-api/src/main/java/org/dspace/checker/service/SimpleReporterService.java b/dspace-api/src/main/java/org/dspace/checker/service/SimpleReporterService.java
index 1dc56c20a3de..f3e0b43d8899 100644
--- a/dspace-api/src/main/java/org/dspace/checker/service/SimpleReporterService.java
+++ b/dspace-api/src/main/java/org/dspace/checker/service/SimpleReporterService.java
@@ -72,7 +72,8 @@ public int getBitstreamNotFoundReport(Context context, Date startDate, Date endD
/**
* The bitstreams that were set to not be processed report for the specified
- * date range.
+ * date range. This includes bitstreams that are marked as deleted and bitstreams
+ * that are not found from the assetstore.
*
* @param context context
* @param startDate the start date range.
diff --git a/dspace-api/src/main/java/org/dspace/content/BitstreamServiceImpl.java b/dspace-api/src/main/java/org/dspace/content/BitstreamServiceImpl.java
index bd56ad465163..3a2670395dbe 100644
--- a/dspace-api/src/main/java/org/dspace/content/BitstreamServiceImpl.java
+++ b/dspace-api/src/main/java/org/dspace/content/BitstreamServiceImpl.java
@@ -19,6 +19,8 @@
import org.apache.commons.collections4.CollectionUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.Logger;
+import org.dspace.app.requestitem.RequestItem;
+import org.dspace.app.requestitem.service.RequestItemService;
import org.dspace.authorize.AuthorizeException;
import org.dspace.authorize.service.AuthorizeService;
import org.dspace.content.dao.BitstreamDAO;
@@ -63,6 +65,8 @@ public class BitstreamServiceImpl extends DSpaceObjectServiceImpl imp
protected BundleService bundleService;
@Autowired(required = true)
protected BitstreamStorageService bitstreamStorageService;
+ @Autowired(required = true)
+ protected RequestItemService requestItemService;
protected BitstreamServiceImpl() {
super();
@@ -287,6 +291,15 @@ public void delete(Context context, Bitstream bitstream) throws SQLException, Au
//Remove all bundles from the bitstream object, clearing the connection in 2 ways
bundles.clear();
+ // Remove any RequestItem entities associated with this bitstream ensuring there are no requests referencing
+ // a deleted bitstream
+ List requestItems = requestItemService.findAll(context);
+ for (RequestItem requestItem : requestItems) {
+ if (bitstream.equals(requestItem.getBitstream())) {
+ requestItemService.delete(context, requestItem);
+ }
+ }
+
// Remove policies only after the bitstream has been updated (otherwise the current user has not WRITE rights)
authorizeService.removeAllPolicies(context, bitstream);
}
diff --git a/dspace-api/src/main/java/org/dspace/content/CollectionServiceImpl.java b/dspace-api/src/main/java/org/dspace/content/CollectionServiceImpl.java
index f5ef4f4b14a4..10f458b81975 100644
--- a/dspace-api/src/main/java/org/dspace/content/CollectionServiceImpl.java
+++ b/dspace-api/src/main/java/org/dspace/content/CollectionServiceImpl.java
@@ -13,13 +13,17 @@
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
+import java.util.HashSet;
import java.util.Iterator;
+import java.util.LinkedList;
import java.util.List;
import java.util.Map;
import java.util.MissingResourceException;
import java.util.Objects;
+import java.util.Queue;
import java.util.Set;
import java.util.UUID;
+import java.util.stream.Collectors;
import org.apache.commons.collections4.CollectionUtils;
import org.apache.commons.lang3.StringUtils;
@@ -838,6 +842,86 @@ public List findAuthorized(Context context, Community community, int
return myResults;
}
+ @Override
+ public List findAuthorized(Context context, Community community, List actions)
+ throws SQLException {
+
+ List myCollections = new ArrayList<>();
+ EPerson eperson = context.getCurrentUser();
+
+ //If eperson is Administrator return all colls or if a community is not null only the community's collections
+ if (authorizeService.isAdmin(context, eperson)) {
+ if (community != null) {
+ return community.getCollections();
+ }
+ myCollections = this.findAll(context);
+ return myCollections;
+ }
+
+ //Get the collections of the eperson where is is admin of a community
+ List directGroups = new ArrayList<>(eperson.getGroups()); // direct membership
+ Queue queue = new LinkedList<>(directGroups);
+ while (!queue.isEmpty()) {
+ Group current = queue.poll();
+ List parents = current.getParentGroups();
+
+ for (Group parent : parents) {
+ if (directGroups.add(parent)) {
+ queue.add(parent);
+ }
+ }
+ }
+
+ List resourcePolicies = resourcePolicyService
+ .find(context, eperson, directGroups, Constants.ADMIN, Constants.COMMUNITY);
+ List uuids = resourcePolicies.stream()
+ .map(policy -> policy.getdSpaceObject().getID())
+ .toList();
+
+ List communities = uuids.stream()
+ .map(uuid -> {
+ try {
+ return communityService.find(context, uuid);
+ } catch (SQLException e) {
+ return null; //ignore that uuid
+ }
+ })
+ .filter(Objects::nonNull)
+ .toList();
+
+ Set allCommunities = new HashSet<>(communities);
+ Set allCommAdminCollections = communities.stream()
+ .flatMap(cm -> cm.getCollections().stream())
+ .collect(Collectors.toSet());
+ Queue queueComm = new LinkedList<>(communities);
+
+ while (!queueComm.isEmpty()) {
+ Community com = queueComm.poll();
+ List childrenComms = com.getSubcommunities();
+ for (Community childComm : childrenComms) {
+ if (allCommunities.add(childComm)) {
+ queueComm.add(childComm);
+ allCommAdminCollections.addAll(childComm.getCollections());
+ }
+ }
+ }
+
+ //Now get the collection when the eperson can deposit or is admin or is in a group with those privileges
+ myCollections = collectionDAO.findAuthorizedByEPerson(context, eperson, actions);
+ Set allCollections = new HashSet<>(myCollections);
+ //Join EPerson Community Admin Collections with Collection Admins
+ allCollections.addAll(allCommAdminCollections);
+
+ List collsAllowed = new ArrayList<>(allCollections);
+
+ //A community is passed, only the community's collections will be used and existing in eperson Authorizations
+ if (community != null) {
+ collsAllowed.retainAll(community.getCollections());
+ }
+
+ return collsAllowed;
+ }
+
@Override
public Collection findByGroup(Context context, Group group) throws SQLException {
return collectionDAO.findByGroup(context, group);
diff --git a/dspace-api/src/main/java/org/dspace/content/ItemServiceImpl.java b/dspace-api/src/main/java/org/dspace/content/ItemServiceImpl.java
index 157b891486f0..99dc9459d84f 100644
--- a/dspace-api/src/main/java/org/dspace/content/ItemServiceImpl.java
+++ b/dspace-api/src/main/java/org/dspace/content/ItemServiceImpl.java
@@ -480,7 +480,7 @@ public void addBundle(Context context, Item item, Bundle bundle) throws SQLExcep
// now add authorization policies from owning item
// hmm, not very "multiple-inclusion" friendly
- authorizeService.inheritPolicies(context, item, bundle);
+ authorizeService.inheritPolicies(context, item, bundle, true);
// Add the bundle to in-memory list
item.addBundle(bundle);
@@ -1046,8 +1046,8 @@ public void adjustBundleBitstreamPolicies(Context context, Item item, Collection
// if come from InstallItem: remove all submission/workflow policies
authorizeService.removeAllPoliciesByDSOAndType(context, mybundle, ResourcePolicy.TYPE_SUBMISSION);
authorizeService.removeAllPoliciesByDSOAndType(context, mybundle, ResourcePolicy.TYPE_WORKFLOW);
- addCustomPoliciesNotInPlace(context, mybundle, defaultItemPolicies);
- addDefaultPoliciesNotInPlace(context, mybundle, defaultCollectionBundlePolicies);
+ authorizeService.addCustomPoliciesNotInPlace(context, mybundle, defaultItemPolicies);
+ authorizeService.addDefaultPoliciesNotInPlace(context, mybundle, defaultCollectionBundlePolicies);
for (Bitstream bitstream : mybundle.getBitstreams()) {
// If collection has default READ policies, remove the bundle's READ policies.
@@ -1093,8 +1093,8 @@ private void removeAllPoliciesAndAddDefault(Context context, Bitstream bitstream
throws SQLException, AuthorizeException {
authorizeService.removeAllPoliciesByDSOAndType(context, bitstream, ResourcePolicy.TYPE_SUBMISSION);
authorizeService.removeAllPoliciesByDSOAndType(context, bitstream, ResourcePolicy.TYPE_WORKFLOW);
- addCustomPoliciesNotInPlace(context, bitstream, defaultItemPolicies);
- addDefaultPoliciesNotInPlace(context, bitstream, defaultCollectionPolicies);
+ authorizeService.addCustomPoliciesNotInPlace(context, bitstream, defaultItemPolicies);
+ authorizeService.addDefaultPoliciesNotInPlace(context, bitstream, defaultCollectionPolicies);
}
@Override
@@ -1132,7 +1132,7 @@ public void adjustItemPolicies(Context context, Item item, Collection collection
authorizeService.removeAllPoliciesByDSOAndType(context, item, ResourcePolicy.TYPE_WORKFLOW);
// add default policies only if not already in place
- addDefaultPoliciesNotInPlace(context, item, defaultCollectionPolicies);
+ authorizeService.addDefaultPoliciesNotInPlace(context, item, defaultCollectionPolicies);
} finally {
context.restoreAuthSystemState();
}
@@ -1322,91 +1322,7 @@ public boolean isInProgressSubmission(Context context, Item item) throws SQLExce
*/
- /**
- * Add the default policies, which have not been already added to the given DSpace object
- *
- * @param context The relevant DSpace Context.
- * @param dso The DSpace Object to add policies to
- * @param defaultCollectionPolicies list of policies
- * @throws SQLException An exception that provides information on a database access error or other errors.
- * @throws AuthorizeException Exception indicating the current user of the context does not have permission
- * to perform a particular action.
- */
- protected void addDefaultPoliciesNotInPlace(Context context, DSpaceObject dso,
- List defaultCollectionPolicies) throws SQLException, AuthorizeException {
- boolean appendMode = configurationService
- .getBooleanProperty("core.authorization.installitem.inheritance-read.append-mode", false);
- for (ResourcePolicy defaultPolicy : defaultCollectionPolicies) {
- if (!authorizeService
- .isAnIdenticalPolicyAlreadyInPlace(context, dso, defaultPolicy.getGroup(), Constants.READ,
- defaultPolicy.getID()) &&
- (!appendMode && isNotAlreadyACustomRPOfThisTypeOnDSO(context, dso) ||
- appendMode && shouldBeAppended(context, dso, defaultPolicy))) {
- ResourcePolicy newPolicy = resourcePolicyService.clone(context, defaultPolicy);
- newPolicy.setdSpaceObject(dso);
- newPolicy.setAction(Constants.READ);
- newPolicy.setRpType(ResourcePolicy.TYPE_INHERITED);
- resourcePolicyService.update(context, newPolicy);
- }
- }
- }
- private void addCustomPoliciesNotInPlace(Context context, DSpaceObject dso, List customPolicies)
- throws SQLException, AuthorizeException {
- boolean customPoliciesAlreadyInPlace = authorizeService
- .findPoliciesByDSOAndType(context, dso, ResourcePolicy.TYPE_CUSTOM).size() > 0;
- if (!customPoliciesAlreadyInPlace) {
- authorizeService.addPolicies(context, customPolicies, dso);
- }
- }
-
- /**
- * Check whether or not there is already an RP on the given dso, which has actionId={@link Constants.READ} and
- * resourceTypeId={@link ResourcePolicy.TYPE_CUSTOM}
- *
- * @param context DSpace context
- * @param dso DSpace object to check for custom read RP
- * @return True if there is no RP on the item with custom read RP, otherwise false
- * @throws SQLException If something goes wrong retrieving the RP on the DSO
- */
- private boolean isNotAlreadyACustomRPOfThisTypeOnDSO(Context context, DSpaceObject dso) throws SQLException {
- List readRPs = resourcePolicyService.find(context, dso, Constants.READ);
- for (ResourcePolicy readRP : readRPs) {
- if (readRP.getRpType() != null && readRP.getRpType().equals(ResourcePolicy.TYPE_CUSTOM)) {
- return false;
- }
- }
- return true;
- }
-
- /**
- * Check if the provided default policy should be appended or not to the final
- * item. If an item has at least one custom READ policy any anonymous READ
- * policy with empty start/end date should be skipped
- *
- * @param context DSpace context
- * @param dso DSpace object to check for custom read RP
- * @param defaultPolicy The policy to check
- * @return
- * @throws SQLException If something goes wrong retrieving the RP on the DSO
- */
- private boolean shouldBeAppended(Context context, DSpaceObject dso, ResourcePolicy defaultPolicy)
- throws SQLException {
- boolean hasCustomPolicy = resourcePolicyService.find(context, dso, Constants.READ)
- .stream()
- .filter(rp -> (Objects.nonNull(rp.getRpType()) &&
- Objects.equals(rp.getRpType(), ResourcePolicy.TYPE_CUSTOM)))
- .findFirst()
- .isPresent();
-
- boolean isAnonimousGroup = Objects.nonNull(defaultPolicy.getGroup())
- && StringUtils.equals(defaultPolicy.getGroup().getName(), Group.ANONYMOUS);
-
- boolean datesAreNull = Objects.isNull(defaultPolicy.getStartDate())
- && Objects.isNull(defaultPolicy.getEndDate());
-
- return !(hasCustomPolicy && isAnonimousGroup && datesAreNull);
- }
/**
* Returns an iterator of Items possessing the passed metadata field, or only
diff --git a/dspace-api/src/main/java/org/dspace/content/authority/DSpaceControlledVocabulary.java b/dspace-api/src/main/java/org/dspace/content/authority/DSpaceControlledVocabulary.java
index 444332df97d2..1bef8b389898 100644
--- a/dspace-api/src/main/java/org/dspace/content/authority/DSpaceControlledVocabulary.java
+++ b/dspace-api/src/main/java/org/dspace/content/authority/DSpaceControlledVocabulary.java
@@ -34,23 +34,25 @@
* from {@code ${dspace.dir}/config/controlled-vocabularies/*.xml} and turns
* them into autocompleting authorities.
*
- * Configuration: This MUST be configured as a self-named plugin, e.g.: {@code
- * plugin.selfnamed.org.dspace.content.authority.ChoiceAuthority = \
+ * Configuration: This MUST be configured as a self-named plugin, e.g.: {@code
+ * plugin.selfnamed.org.dspace.content.authority.ChoiceAuthority =
* org.dspace.content.authority.DSpaceControlledVocabulary
* }
*
- * It AUTOMATICALLY configures a plugin instance for each XML file in the
+ *
It AUTOMATICALLY configures a plugin instance for each XML file in the
* controlled vocabularies directory. The name of the plugin is the basename of
* the file; e.g., {@code ${dspace.dir}/config/controlled-vocabularies/nsi.xml}
* would generate a plugin called "nsi".
*
- * Each configured plugin comes with three configuration options: {@code
- * vocabulary.plugin._plugin_.hierarchy.store =
- * # Store entire hierarchy along with selected value. Default: TRUE
- * vocabulary.plugin._plugin_.hierarchy.suggest =
- * # Display entire hierarchy in the suggestion list. Default: TRUE
- * vocabulary.plugin._plugin_.delimiter = ""
- * # Delimiter to use when building hierarchy strings. Default: "::"
+ * Each configured plugin comes with three configuration options:
+ *
+ * - {@code vocabulary.plugin._plugin_.hierarchy.store =
+ * # Store entire hierarchy along with selected value. Default: TRUE}
+ * - {@code vocabulary.plugin._plugin_.hierarchy.suggest =
+ * # Display entire hierarchy in the suggestion list. Default: TRUE}
+ * - {@code vocabulary.plugin._plugin_.delimiter = ""
+ * # Delimiter to use when building hierarchy strings. Default: "::"}
+ *
* }
*
* @author Michael B. Klein
@@ -58,11 +60,12 @@
public class DSpaceControlledVocabulary extends SelfNamedPlugin implements HierarchicalAuthority {
- private static Logger log = org.apache.logging.log4j.LogManager.getLogger(DSpaceControlledVocabulary.class);
+ private static final Logger log = org.apache.logging.log4j.LogManager.getLogger();
protected static String xpathTemplate = "//node[contains(translate(@label,'ABCDEFGHIJKLMNOPQRSTUVWXYZ'," +
- "'abcdefghijklmnopqrstuvwxyz'),'%s')]";
- protected static String idTemplate = "//node[@id = '%s']";
- protected static String labelTemplate = "//node[@label = '%s']";
+ "'abcdefghijklmnopqrstuvwxyz'),%s)]";
+ protected static String idTemplate = "//node[@id = %s]";
+ protected static String idTemplateQuoted = "//node[@id = '%s']";
+ protected static String labelTemplate = "//node[@label = %s]";
protected static String idParentTemplate = "//node[@id = '%s']/parent::isComposedBy/parent::node";
protected static String rootTemplate = "/node";
protected static String pluginNames[] = null;
@@ -106,7 +109,7 @@ public boolean accept(File dir, String name) {
File.separator + "config" +
File.separator + "controlled-vocabularies";
String[] xmlFiles = (new File(vocabulariesPath)).list(new xmlFilter());
- List names = new ArrayList();
+ List names = new ArrayList<>();
for (String filename : xmlFiles) {
names.add((new File(filename)).getName().replace(".xml", ""));
}
@@ -162,14 +165,23 @@ protected String buildString(Node node) {
public Choices getMatches(String text, int start, int limit, String locale) {
init();
log.debug("Getting matches for '" + text + "'");
- String xpathExpression = "";
String[] textHierarchy = text.split(hierarchyDelimiter, -1);
+ StringBuilder xpathExpressionBuilder = new StringBuilder();
for (int i = 0; i < textHierarchy.length; i++) {
- xpathExpression += String.format(xpathTemplate, textHierarchy[i].replaceAll("'", "'").toLowerCase());
+ xpathExpressionBuilder.append(String.format(xpathTemplate, "$var" + i));
}
+ String xpathExpression = xpathExpressionBuilder.toString();
XPath xpath = XPathFactory.newInstance().newXPath();
- int total = 0;
- List choices = new ArrayList();
+ xpath.setXPathVariableResolver(variableName -> {
+ String varName = variableName.getLocalPart();
+ if (varName.startsWith("var")) {
+ int index = Integer.parseInt(varName.substring(3));
+ return textHierarchy[index].toLowerCase();
+ }
+ throw new IllegalArgumentException("Unexpected variable: " + varName);
+ });
+ int total;
+ List choices;
try {
NodeList results = (NodeList) xpath.evaluate(xpathExpression, vocabulary, XPathConstants.NODESET);
total = results.getLength();
@@ -185,14 +197,23 @@ public Choices getMatches(String text, int start, int limit, String locale) {
@Override
public Choices getBestMatch(String text, String locale) {
init();
- log.debug("Getting best matches for '" + text + "'");
- String xpathExpression = "";
+ log.debug("Getting best matches for {}'", text);
String[] textHierarchy = text.split(hierarchyDelimiter, -1);
+ StringBuilder xpathExpressionBuilder = new StringBuilder();
for (int i = 0; i < textHierarchy.length; i++) {
- xpathExpression += String.format(labelTemplate, textHierarchy[i].replaceAll("'", "'"));
+ xpathExpressionBuilder.append(String.format(labelTemplate, "$var" + i));
}
+ String xpathExpression = xpathExpressionBuilder.toString();
XPath xpath = XPathFactory.newInstance().newXPath();
- List choices = new ArrayList();
+ xpath.setXPathVariableResolver(variableName -> {
+ String varName = variableName.getLocalPart();
+ if (varName.startsWith("var")) {
+ int index = Integer.parseInt(varName.substring(3));
+ return textHierarchy[index];
+ }
+ throw new IllegalArgumentException("Unexpected variable: " + varName);
+ });
+ List choices;
try {
NodeList results = (NodeList) xpath.evaluate(xpathExpression, vocabulary, XPathConstants.NODESET);
choices = getChoicesFromNodeList(results, 0, 1);
@@ -240,7 +261,7 @@ public Choices getTopChoices(String authorityName, int start, int limit, String
@Override
public Choices getChoicesByParent(String authorityName, String parentId, int start, int limit, String locale) {
init();
- String xpathExpression = String.format(idTemplate, parentId);
+ String xpathExpression = String.format(idTemplateQuoted, parentId);
return getChoicesByXpath(xpathExpression, start, limit);
}
@@ -264,15 +285,12 @@ public Integer getPreloadLevel() {
}
private boolean isRootElement(Node node) {
- if (node != null && node.getOwnerDocument().getDocumentElement().equals(node)) {
- return true;
- }
- return false;
+ return node != null && node.getOwnerDocument().getDocumentElement().equals(node);
}
private Node getNode(String key) throws XPathExpressionException {
init();
- String xpathExpression = String.format(idTemplate, key);
+ String xpathExpression = String.format(idTemplateQuoted, key);
Node node = getNodeFromXPath(xpathExpression);
return node;
}
@@ -284,7 +302,7 @@ private Node getNodeFromXPath(String xpathExpression) throws XPathExpressionExce
}
private List getChoicesFromNodeList(NodeList results, int start, int limit) {
- List choices = new ArrayList();
+ List choices = new ArrayList<>();
for (int i = 0; i < results.getLength(); i++) {
if (i < start) {
continue;
@@ -303,17 +321,17 @@ private List getChoicesFromNodeList(NodeList results, int start, int lim
private Map addOtherInformation(String parentCurr, String noteCurr,
List childrenCurr, String authorityCurr) {
- Map extras = new HashMap();
+ Map extras = new HashMap<>();
if (StringUtils.isNotBlank(parentCurr)) {
extras.put("parent", parentCurr);
}
if (StringUtils.isNotBlank(noteCurr)) {
extras.put("note", noteCurr);
}
- if (childrenCurr.size() > 0) {
- extras.put("hasChildren", "true");
- } else {
+ if (childrenCurr.isEmpty()) {
extras.put("hasChildren", "false");
+ } else {
+ extras.put("hasChildren", "true");
}
extras.put("id", authorityCurr);
return extras;
@@ -368,7 +386,7 @@ private String getNote(Node node) {
}
private List getChildren(Node node) {
- List children = new ArrayList();
+ List children = new ArrayList<>();
NodeList childNodes = node.getChildNodes();
for (int ci = 0; ci < childNodes.getLength(); ci++) {
Node firstChild = childNodes.item(ci);
@@ -391,7 +409,7 @@ private List getChildren(Node node) {
private boolean isSelectable(Node node) {
Node selectableAttr = node.getAttributes().getNamedItem("selectable");
if (null != selectableAttr) {
- return Boolean.valueOf(selectableAttr.getNodeValue());
+ return Boolean.parseBoolean(selectableAttr.getNodeValue());
} else { // Default is true
return true;
}
@@ -418,7 +436,7 @@ private String getAuthority(Node node) {
}
private Choices getChoicesByXpath(String xpathExpression, int start, int limit) {
- List choices = new ArrayList();
+ List choices = new ArrayList<>();
XPath xpath = XPathFactory.newInstance().newXPath();
try {
Node parentNode = (Node) xpath.evaluate(xpathExpression, vocabulary, XPathConstants.NODE);
diff --git a/dspace-api/src/main/java/org/dspace/content/crosswalk/PREMISCrosswalk.java b/dspace-api/src/main/java/org/dspace/content/crosswalk/PREMISCrosswalk.java
index 39b6c8f29c80..6b6c0fd7c5a4 100644
--- a/dspace-api/src/main/java/org/dspace/content/crosswalk/PREMISCrosswalk.java
+++ b/dspace-api/src/main/java/org/dspace/content/crosswalk/PREMISCrosswalk.java
@@ -20,9 +20,7 @@
import org.dspace.authorize.AuthorizeException;
import org.dspace.content.Bitstream;
import org.dspace.content.BitstreamFormat;
-import org.dspace.content.Bundle;
import org.dspace.content.DSpaceObject;
-import org.dspace.content.Item;
import org.dspace.content.factory.ContentServiceFactory;
import org.dspace.content.service.BitstreamFormatService;
import org.dspace.content.service.BitstreamService;
@@ -224,29 +222,17 @@ public Element disseminateElement(Context context, DSpaceObject dso)
// c. made-up name based on sequence ID and extension.
String sid = String.valueOf(bitstream.getSequenceID());
String baseUrl = configurationService.getProperty("dspace.ui.url");
- String handle = null;
- // get handle of parent Item of this bitstream, if there is one:
- List bn = bitstream.getBundles();
- if (bn.size() > 0) {
- List- bi = bn.get(0).getItems();
- if (bi.size() > 0) {
- handle = bi.get(0).getHandle();
- }
- }
// get or make up name for bitstream:
String bsName = bitstream.getName();
if (bsName == null) {
List ext = bitstream.getFormat(context).getExtensions();
bsName = "bitstream_" + sid + (ext.size() > 0 ? ext.get(0) : "");
}
- if (handle != null && baseUrl != null) {
+ if (baseUrl != null) {
oiv.setText(baseUrl
- + "/bitstream/"
- + URLEncoder.encode(handle, "UTF-8")
- + "/"
- + sid
- + "/"
- + URLEncoder.encode(bsName, "UTF-8"));
+ + "/bitstreams/"
+ + bitstream.getID()
+ + "/download");
} else {
oiv.setText(URLEncoder.encode(bsName, "UTF-8"));
}
diff --git a/dspace-api/src/main/java/org/dspace/content/dao/CollectionDAO.java b/dspace-api/src/main/java/org/dspace/content/dao/CollectionDAO.java
index 6bb65bbb46d8..13bcf5f52c02 100644
--- a/dspace-api/src/main/java/org/dspace/content/dao/CollectionDAO.java
+++ b/dspace-api/src/main/java/org/dspace/content/dao/CollectionDAO.java
@@ -48,6 +48,18 @@ public List findAll(Context context, MetadataField order, Integer li
List findAuthorizedByGroup(Context context, EPerson ePerson, List actions) throws SQLException;
+ /**
+ * Get all authorized collections of the current EPerson
+ *
+ * @param context DSpace context object
+ * @param ePerson the current EPerson
+ * @param actions list of actionsID ADD, READ, etc.
+ * @return the collections the eperson is defined
+ * @throws SQLException if database error
+ */
+ List findAuthorizedByEPerson(Context context, EPerson ePerson, List actions)
+ throws SQLException;
+
List findCollectionsWithSubscribers(Context context) throws SQLException;
int countRows(Context context) throws SQLException;
diff --git a/dspace-api/src/main/java/org/dspace/content/dao/impl/BitstreamDAOImpl.java b/dspace-api/src/main/java/org/dspace/content/dao/impl/BitstreamDAOImpl.java
index 25f102f6def4..66a775e39d80 100644
--- a/dspace-api/src/main/java/org/dspace/content/dao/impl/BitstreamDAOImpl.java
+++ b/dspace-api/src/main/java/org/dspace/content/dao/impl/BitstreamDAOImpl.java
@@ -178,7 +178,7 @@ public int countDeleted(Context context) throws SQLException {
@Override
public int countWithNoPolicy(Context context) throws SQLException {
Query query = createQuery(context,
- "SELECT count(bit.id) from Bitstream bit where bit.deleted<>true and bit.id not in" +
+ "SELECT count(bit.id) from Bitstream bit where bit.deleted<>true and bit not in" +
" (select res.dSpaceObject from ResourcePolicy res where res.resourceTypeId = " +
":typeId )");
query.setParameter("typeId", Constants.BITSTREAM);
diff --git a/dspace-api/src/main/java/org/dspace/content/dao/impl/CollectionDAOImpl.java b/dspace-api/src/main/java/org/dspace/content/dao/impl/CollectionDAOImpl.java
index 841da319f0b2..e47b1ed4a02b 100644
--- a/dspace-api/src/main/java/org/dspace/content/dao/impl/CollectionDAOImpl.java
+++ b/dspace-api/src/main/java/org/dspace/content/dao/impl/CollectionDAOImpl.java
@@ -10,8 +10,13 @@
import java.sql.SQLException;
import java.util.AbstractMap;
import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.LinkedList;
import java.util.List;
import java.util.Map;
+import java.util.Queue;
+import java.util.Set;
+import java.util.UUID;
import jakarta.persistence.Query;
import jakarta.persistence.criteria.CriteriaBuilder;
@@ -19,6 +24,7 @@
import jakarta.persistence.criteria.Join;
import jakarta.persistence.criteria.Predicate;
import jakarta.persistence.criteria.Root;
+import org.apache.logging.log4j.Logger;
import org.dspace.authorize.ResourcePolicy;
import org.dspace.authorize.ResourcePolicy_;
import org.dspace.content.Collection;
@@ -40,6 +46,11 @@
* @author kevinvandevelde at atmire.com
*/
public class CollectionDAOImpl extends AbstractHibernateDSODAO implements CollectionDAO {
+ /**
+ * log4j logger
+ */
+ private static Logger log = org.apache.logging.log4j.LogManager.getLogger(CollectionDAOImpl.class);
+
protected CollectionDAOImpl() {
super();
}
@@ -157,9 +168,103 @@ public List findAuthorizedByGroup(Context context, EPerson ePerson,
}
+ /**
+ * Get all authorized collections of the current EPerson
+ *
+ * @param context DSpace context object
+ * @param ePerson the current EPerson
+ * @param actions list of actionsID ADD, READ, etc.
+ * @return the collections the eperson is defined
+ * @throws SQLException if database error
+ */
+ @Override
+ public List findAuthorizedByEPerson(Context context, EPerson ePerson, List actions)
+ throws SQLException {
+
+ //NOTE steps 1) and 2) removes the need of WITH RECURSIVE and a NativeQuery
+
+ // 1) Get all groups a eperson belongs
+ /*ArrayList<>(ePerson.getGroups()) - This ensures you have a concrete copy and can modify it safely.
+ instead if List directGroups = ePerson.getGroups();
+ Also - Can be done using this query:
+ List directGroups = createQuery(context, """
+ SELECT g
+ FROM Group g
+ JOIN g.epeople e
+ WHERE e.id = :epersonId
+ """)
+ .setParameter("epersonId", ePerson.getID())
+ .getResultList();
+ */
+ List directGroups = new ArrayList<>(ePerson.getGroups()); // direct membership
+
+ // 2) Expand hierarquy of groups in memory (recursively)
+ Set allGroups = new HashSet<>(directGroups);
+ Queue queue = new LinkedList<>(directGroups);
+
+ /*
+ * Using the query avoids the change of the getParentGroups visibility in Group
+ * The List parents = current.getParentGroups() could be achieved using:
+ * List parents = createQuery(context,"""
+ SELECT g
+ FROM Group g
+ JOIN g.groups child
+ WHERE child = :child
+ """)
+ */
+ // //current.getMemberGroups()- Making public getParentGroups in Group Class (why it isn't already public?)
+ while (!queue.isEmpty()) {
+ Group current = queue.poll();
+ List parents = current.getParentGroups();
+
+ for (Group parent : parents) {
+ if (allGroups.add(parent)) {
+ queue.add(parent);
+ }
+ }
+ }
+
+ CriteriaBuilder cb = getCriteriaBuilder(context);
+ CriteriaQuery cq = getCriteriaQuery(cb, Collection.class);
+ Root collectionRoot = cq.from(Collection.class);
+
+ // Join to ResourcePolicy using metamodel
+ Join rpJoin = collectionRoot.join("resourcePolicies");
+ // Use metamodel for typesafe access
+ cq.select(collectionRoot).distinct(true);
+
+ List predicates = new ArrayList<>(actions.size());
+ // WHERE rp.resourceTypeId = :resourceType
+ predicates.add(cb.equal(rpJoin.get(ResourcePolicy_.resourceTypeId), Constants.COLLECTION));
+ // AND (:hasActions = false OR rp.actionId IN :actionIds)
+ if (actions != null && !actions.isEmpty()) {
+ predicates.add(rpJoin.get(ResourcePolicy_.actionId).in(actions));
+ }
+
+ // AND (rp.eperson.id = :epersonId OR (:hasGroups = true AND rp.epersonGroup.id IN :groupIds))
+ Predicate epersonPredicate = cb.equal(
+ rpJoin.get(ResourcePolicy_.eperson), ePerson
+ );
+ // Using only groups instead of groupsIDs
+ Predicate groupPredicate = cb.disjunction(); // false by default
+ if (allGroups != null && !allGroups.isEmpty()) {
+ groupPredicate = rpJoin.get(ResourcePolicy_.epersonGroup).in(allGroups);
+ }
+
+ // Combine access condition
+ Predicate accessPredicate = cb.or(epersonPredicate, groupPredicate);
+ predicates.add(accessPredicate);
+
+ // Apply WHERE clause
+ cq.where(cb.and(predicates.toArray(new Predicate[0])));
+
+ // Execute
+ return list(context, cq, true, Collection.class, -1, -1);
+ }
+
@Override
public List findCollectionsWithSubscribers(Context context) throws SQLException {
- return list(createQuery(context, "SELECT DISTINCT c FROM Collection c JOIN Subscription s ON c.id = " +
+ return list(createQuery(context, "SELECT DISTINCT c FROM Collection c JOIN Subscription s ON c = " +
"s.dSpaceObject"));
}
@@ -172,15 +277,26 @@ public int countRows(Context context) throws SQLException {
@SuppressWarnings("unchecked")
public List> getCollectionsWithBitstreamSizesTotal(Context context)
throws SQLException {
- String q = "select col as collection, sum(bit.sizeBytes) as totalBytes from Item i join i.collections col " +
- "join i.bundles bun join bun.bitstreams bit group by col";
+ String q = "select col.id, sum(bit.sizeBytes) as totalBytes from Item i join i.collections col " +
+ "join i.bundles bun join bun.bitstreams bit group by col.id";
Query query = createQuery(context, q);
+ CriteriaBuilder criteriaBuilder = getCriteriaBuilder(context);
+
List list = query.getResultList();
List> returnList = new ArrayList<>(list.size());
for (Object[] o : list) {
- returnList.add(new AbstractMap.SimpleEntry<>((Collection) o[0], (Long) o[1]));
+ CriteriaQuery criteriaQuery = criteriaBuilder.createQuery(Collection.class);
+ Root collectionRoot = criteriaQuery.from(Collection.class);
+ criteriaQuery.select(collectionRoot).where(criteriaBuilder.equal(collectionRoot.get("id"), (UUID) o[0]));
+ Query collectionQuery = createQuery(context, criteriaQuery);
+ Collection collection = (Collection) collectionQuery.getSingleResult();
+ if (collection != null) {
+ returnList.add(new AbstractMap.SimpleEntry<>(collection, (Long) o[1]));
+ } else {
+ log.warn("Unable to find Collection with UUID: {}", o[0]);
+ }
}
return returnList;
}
-}
\ No newline at end of file
+}
diff --git a/dspace-api/src/main/java/org/dspace/content/packager/AbstractMETSIngester.java b/dspace-api/src/main/java/org/dspace/content/packager/AbstractMETSIngester.java
index 77236be9d525..0ab5ac71cda5 100644
--- a/dspace-api/src/main/java/org/dspace/content/packager/AbstractMETSIngester.java
+++ b/dspace-api/src/main/java/org/dspace/content/packager/AbstractMETSIngester.java
@@ -498,8 +498,11 @@ protected DSpaceObject ingestObject(Context context, DSpaceObject parent,
// Finish creating the item. This actually assigns the handle,
// and will either install item immediately or start a workflow, based on params
PackageUtils.finishCreateItem(context, wsi, handle, params);
+ } else {
+ // We should have a workspace item during ingest, so this code is only here for safety.
+ // Update the object to make sure all changes are committed
+ PackageUtils.updateDSpaceObject(context, dso);
}
-
} else if (type == Constants.COLLECTION || type == Constants.COMMUNITY) {
// Add logo if one is referenced from manifest
addContainerLogo(context, dso, manifest, pkgFile, params);
@@ -513,6 +516,9 @@ protected DSpaceObject ingestObject(Context context, DSpaceObject parent,
// (this allows subclasses to do some final validation / changes as
// necessary)
finishObject(context, dso, params);
+
+ // Update the object to make sure all changes are committed
+ PackageUtils.updateDSpaceObject(context, dso);
} else if (type == Constants.SITE) {
// Do nothing by default -- Crosswalks will handle anything necessary to ingest at Site-level
@@ -520,18 +526,15 @@ protected DSpaceObject ingestObject(Context context, DSpaceObject parent,
// (this allows subclasses to do some final validation / changes as
// necessary)
finishObject(context, dso, params);
+
+ // Update the object to make sure all changes are committed
+ PackageUtils.updateDSpaceObject(context, dso);
} else {
throw new PackageValidationException(
"Unknown DSpace Object type in package, type="
+ String.valueOf(type));
}
- // -- Step 6 --
- // Finish things up!
-
- // Update the object to make sure all changes are committed
- PackageUtils.updateDSpaceObject(context, dso);
-
return dso;
}
diff --git a/dspace-api/src/main/java/org/dspace/content/packager/PDFPackager.java b/dspace-api/src/main/java/org/dspace/content/packager/PDFPackager.java
index 6c7baad45497..f63585f3c498 100644
--- a/dspace-api/src/main/java/org/dspace/content/packager/PDFPackager.java
+++ b/dspace-api/src/main/java/org/dspace/content/packager/PDFPackager.java
@@ -18,11 +18,11 @@
import org.apache.commons.lang3.ArrayUtils;
import org.apache.logging.log4j.Logger;
+import org.apache.pdfbox.Loader;
import org.apache.pdfbox.cos.COSDocument;
import org.apache.pdfbox.io.MemoryUsageSetting;
-import org.apache.pdfbox.io.RandomAccessBufferedFileInputStream;
+import org.apache.pdfbox.io.RandomAccessReadBuffer;
import org.apache.pdfbox.io.ScratchFile;
-import org.apache.pdfbox.pdfparser.PDFParser;
import org.apache.pdfbox.pdmodel.PDDocument;
import org.apache.pdfbox.pdmodel.PDDocumentInformation;
import org.dspace.authorize.AuthorizeException;
@@ -330,19 +330,24 @@ private void crosswalkPDF(Context context, Item item, InputStream metadata)
COSDocument cos = null;
try {
- ScratchFile scratchFile = null;
+ PDDocument document = null;
+
try {
- long useRAM = Runtime.getRuntime().freeMemory() * 80 / 100; // use up to 80% of JVM free memory
- scratchFile = new ScratchFile(
- MemoryUsageSetting.setupMixed(useRAM)); // then fallback to temp file (unlimited size)
+ // Use up to 80% of JVM free memory and fall back to a temp file (unlimited size)
+ long useRAM = Runtime.getRuntime().freeMemory() * 80 / 100;
+ document = Loader.loadPDF(
+ new RandomAccessReadBuffer(metadata),
+ () -> new ScratchFile(MemoryUsageSetting.setupMixed(useRAM)));
} catch (IOException ioe) {
log.warn("Error initializing scratch file: " + ioe.getMessage());
}
- PDFParser parser = new PDFParser(new RandomAccessBufferedFileInputStream(metadata), scratchFile);
- parser.parse();
- cos = parser.getDocument();
+ // sanity check: loaded PDF document must not be null.
+ if (document == null) {
+ throw new MetadataValidationException("The provided stream could not be parsed into a PDF document.");
+ }
+ cos = document.getDocument();
// sanity check: PDFBox breaks on encrypted documents, so give up.
if (cos.getEncryptionDictionary() != null) {
throw new MetadataValidationException("This packager cannot accept an encrypted PDF document.");
diff --git a/dspace-api/src/main/java/org/dspace/content/service/CollectionService.java b/dspace-api/src/main/java/org/dspace/content/service/CollectionService.java
index 3a865d9d63fd..c2b633821376 100644
--- a/dspace-api/src/main/java/org/dspace/content/service/CollectionService.java
+++ b/dspace-api/src/main/java/org/dspace/content/service/CollectionService.java
@@ -327,6 +327,18 @@ public void canEdit(Context context, Collection collection, boolean useInheritan
public List findAuthorized(Context context, Community community, int actionID)
throws java.sql.SQLException;
+ /**
+ * return an array of collections that user has a given permission on
+ *
+ * @param context DSpace Context
+ * @param community (optional) restrict search to a community, else null
+ * @param actions Listo of the of the action ADD, READ, ADMIN, etc.
+ * @return Collection [] of collections with matching permissions
+ * @throws SQLException if database error
+ */
+ public List findAuthorized(Context context, Community community, List actions)
+ throws java.sql.SQLException;
+
/**
*
* @param context DSpace Context
diff --git a/dspace-api/src/main/java/org/dspace/core/AbstractHibernateDAO.java b/dspace-api/src/main/java/org/dspace/core/AbstractHibernateDAO.java
index 3658a3c92305..e5e5c5c44a7a 100644
--- a/dspace-api/src/main/java/org/dspace/core/AbstractHibernateDAO.java
+++ b/dspace-api/src/main/java/org/dspace/core/AbstractHibernateDAO.java
@@ -468,6 +468,9 @@ public List findByX(Context context, Class clazz, Map equals,
for (Map.Entry entry : equals.entrySet()) {
criteria.where(criteriaBuilder.equal(root.get(entry.getKey()), entry.getValue()));
}
+
+ criteria.orderBy(criteriaBuilder.asc(root.get("id")));
+
return executeCriteriaQuery(context, criteria, cacheable, maxResults, offset);
}
diff --git a/dspace-api/src/main/java/org/dspace/discovery/SolrServiceImpl.java b/dspace-api/src/main/java/org/dspace/discovery/SolrServiceImpl.java
index a5fa04b3dc04..0c5c29cba3a3 100644
--- a/dspace-api/src/main/java/org/dspace/discovery/SolrServiceImpl.java
+++ b/dspace-api/src/main/java/org/dspace/discovery/SolrServiceImpl.java
@@ -18,6 +18,7 @@
import java.text.ParseException;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.Calendar;
import java.util.Collections;
import java.util.Date;
@@ -969,8 +970,20 @@ protected SolrQuery resolveToSolrQuery(Context context, DiscoverQuery discoveryQ
if (0 < discoveryQuery.getHitHighlightingFields().size()) {
solrQuery.setHighlight(true);
solrQuery.add(HighlightParams.USE_PHRASE_HIGHLIGHTER, Boolean.TRUE.toString());
+ boolean escapeHTML = configurationService.getBooleanProperty("discovery.highlights.escape-html", true);
+ String[] renderHTMLForFields =
+ configurationService.getArrayProperty("discovery.highlights.html-allowed-fields");
for (DiscoverHitHighlightingField highlightingField : discoveryQuery.getHitHighlightingFields()) {
solrQuery.addHighlightField(highlightingField.getField() + "_hl");
+ boolean allowHTMLInField = Arrays.stream(renderHTMLForFields)
+ .anyMatch(field -> highlightingField.getField().matches(field));
+ if (!escapeHTML || allowHTMLInField) {
+ solrQuery.add("f." + highlightingField.getField() + "_hl." + HighlightParams.METHOD, "original");
+ } else {
+ solrQuery.add("f." + highlightingField.getField() + "_hl." + HighlightParams.METHOD, "unified");
+ solrQuery.add("f." + highlightingField.getField() + "_hl." + HighlightParams.ENCODER, "html");
+ }
+
solrQuery.add("f." + highlightingField.getField() + "_hl." + HighlightParams.FRAGSIZE,
String.valueOf(highlightingField.getMaxChars()));
solrQuery.add("f." + highlightingField.getField() + "_hl." + HighlightParams.SNIPPETS,
diff --git a/dspace-api/src/main/java/org/dspace/disseminate/CitationDocumentServiceImpl.java b/dspace-api/src/main/java/org/dspace/disseminate/CitationDocumentServiceImpl.java
index c20961db7544..bf9f7b9d6a01 100644
--- a/dspace-api/src/main/java/org/dspace/disseminate/CitationDocumentServiceImpl.java
+++ b/dspace-api/src/main/java/org/dspace/disseminate/CitationDocumentServiceImpl.java
@@ -23,6 +23,8 @@
import org.apache.commons.lang3.tuple.Pair;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
+import org.apache.pdfbox.Loader;
+import org.apache.pdfbox.io.RandomAccessReadBuffer;
import org.apache.pdfbox.pdmodel.PDDocument;
import org.apache.pdfbox.pdmodel.PDPage;
import org.apache.pdfbox.pdmodel.PDPageContentStream;
@@ -30,6 +32,7 @@
import org.apache.pdfbox.pdmodel.common.PDRectangle;
import org.apache.pdfbox.pdmodel.font.PDFont;
import org.apache.pdfbox.pdmodel.font.PDType1Font;
+import org.apache.pdfbox.pdmodel.font.Standard14Fonts;
import org.dspace.authorize.AuthorizeException;
import org.dspace.authorize.service.AuthorizeService;
import org.dspace.content.Bitstream;
@@ -139,8 +142,8 @@ public void afterPropertiesSet() throws Exception {
//Load enabled collections
String[] citationEnabledCollections = configurationService
- .getArrayProperty("citation-page.enabled_collections");
- citationEnabledCollectionsList = Arrays.asList(citationEnabledCollections);
+ .getArrayProperty("citation-page.enabled_collections");
+ citationEnabledCollectionsList = new ArrayList(Arrays.asList(citationEnabledCollections));
//Load enabled communities, and add to collection-list
String[] citationEnabledCommunities = configurationService
@@ -304,7 +307,7 @@ public Pair makeCitedDocument(Context context, Bitstream bitstream
Item item = (Item) bitstreamService.getParentObject(context, bitstream);
final InputStream inputStream = bitstreamService.retrieve(context, bitstream);
try {
- sourceDocument = sourceDocument.load(inputStream);
+ sourceDocument = Loader.loadPDF(new RandomAccessReadBuffer(inputStream));
} finally {
inputStream.close();
}
@@ -335,9 +338,10 @@ protected void generateCoverPage(Context context, PDDocument document, PDPage co
int xwidth = 550;
int ygap = 20;
- PDFont fontHelvetica = PDType1Font.HELVETICA;
- PDFont fontHelveticaBold = PDType1Font.HELVETICA_BOLD;
- PDFont fontHelveticaOblique = PDType1Font.HELVETICA_OBLIQUE;
+ PDFont fontHelvetica = new PDType1Font(Standard14Fonts.FontName.HELVETICA);
+ PDFont fontHelveticaBold = new PDType1Font(Standard14Fonts.FontName.HELVETICA_BOLD);
+ PDFont fontHelveticaOblique = new PDType1Font(Standard14Fonts.FontName.HELVETICA_OBLIQUE);
+
contentStream.setNonStrokingColor(Color.BLACK);
String[][] content = {header1};
diff --git a/dspace-api/src/main/java/org/dspace/embargo/DefaultEmbargoSetter.java b/dspace-api/src/main/java/org/dspace/embargo/DefaultEmbargoSetter.java
index 7857a45eb8d5..265ec213da60 100644
--- a/dspace-api/src/main/java/org/dspace/embargo/DefaultEmbargoSetter.java
+++ b/dspace-api/src/main/java/org/dspace/embargo/DefaultEmbargoSetter.java
@@ -94,7 +94,6 @@ public void setEmbargo(Context context, Item item)
if (!(bnn.equals(Constants.LICENSE_BUNDLE_NAME) || bnn.equals(Constants.METADATA_BUNDLE_NAME) || bnn
.equals(CreativeCommonsServiceImpl.CC_BUNDLE_NAME))) {
//AuthorizeManager.removePoliciesActionFilter(context, bn, Constants.READ);
- generatePolicies(context, liftDate.toDate(), null, bn, item.getOwningCollection());
for (Bitstream bs : bn.getBitstreams()) {
//AuthorizeManager.removePoliciesActionFilter(context, bs, Constants.READ);
generatePolicies(context, liftDate.toDate(), null, bs, item.getOwningCollection());
diff --git a/dspace-api/src/main/java/org/dspace/eperson/EPerson.java b/dspace-api/src/main/java/org/dspace/eperson/EPerson.java
index 996fc96e3aa8..6f8e1043f9ec 100644
--- a/dspace-api/src/main/java/org/dspace/eperson/EPerson.java
+++ b/dspace-api/src/main/java/org/dspace/eperson/EPerson.java
@@ -369,7 +369,7 @@ public int getType() {
@Override
public String getName() {
- return getEmail();
+ return this.getFullName();
}
String getDigestAlgorithm() {
diff --git a/dspace-api/src/main/java/org/dspace/eperson/EPersonCLITool.java b/dspace-api/src/main/java/org/dspace/eperson/EPersonCLITool.java
index 343ddcccfa39..53451e07a9ec 100644
--- a/dspace-api/src/main/java/org/dspace/eperson/EPersonCLITool.java
+++ b/dspace-api/src/main/java/org/dspace/eperson/EPersonCLITool.java
@@ -50,7 +50,7 @@ public class EPersonCLITool {
private static final Option OPT_PHONE = new Option("t", "telephone", true, "telephone number, empty for none");
private static final Option OPT_LANGUAGE = new Option("l", "language", true, "the person's preferred language");
private static final Option OPT_REQUIRE_CERTIFICATE = new Option("c", "requireCertificate", true,
- "if 'true', an X.509 certificate will be " +
+ "if 'true', a certificate will be " +
"required for login");
private static final Option OPT_CAN_LOGIN = new Option("C", "canLogIn", true, "'true' if the user can log in");
diff --git a/dspace-api/src/main/java/org/dspace/eperson/Group.java b/dspace-api/src/main/java/org/dspace/eperson/Group.java
index 24b44b8149a4..8146bf702d0a 100644
--- a/dspace-api/src/main/java/org/dspace/eperson/Group.java
+++ b/dspace-api/src/main/java/org/dspace/eperson/Group.java
@@ -138,7 +138,7 @@ boolean contains(EPerson e) {
return getMembers().contains(e);
}
- List getParentGroups() {
+ public List getParentGroups() {
return parentGroups;
}
diff --git a/dspace-api/src/main/java/org/dspace/eperson/GroupServiceImpl.java b/dspace-api/src/main/java/org/dspace/eperson/GroupServiceImpl.java
index 4cec4c9c0d93..44727d3e5fb9 100644
--- a/dspace-api/src/main/java/org/dspace/eperson/GroupServiceImpl.java
+++ b/dspace-api/src/main/java/org/dspace/eperson/GroupServiceImpl.java
@@ -142,6 +142,8 @@ public void addMember(Context context, Group group, EPerson e) {
context.addEvent(
new Event(Event.ADD, Constants.GROUP, group.getID(), Constants.EPERSON, e.getID(), e.getEmail(),
getIdentifiers(context, group)));
+ log.info(LogHelper.getHeader(context, "add_group_eperson",
+ "group_id=" + group.getID() + ", eperson_id=" + e.getID()));
}
@Override
@@ -157,6 +159,8 @@ public void addMember(Context context, Group groupParent, Group groupChild) thro
context.addEvent(new Event(Event.ADD, Constants.GROUP, groupParent.getID(), Constants.GROUP, groupChild.getID(),
groupChild.getName(), getIdentifiers(context, groupParent)));
+ log.info(LogHelper.getHeader(context, "add_group_subgroup",
+ "group_id=" + groupParent.getID() + ", subgroup_id=" + groupChild.getID()));
}
/**
@@ -214,6 +218,8 @@ public void removeMember(Context context, Group group, EPerson ePerson) throws S
if (group.remove(ePerson)) {
context.addEvent(new Event(Event.REMOVE, Constants.GROUP, group.getID(), Constants.EPERSON, ePerson.getID(),
ePerson.getEmail(), getIdentifiers(context, group)));
+ log.info(LogHelper.getHeader(context, "remove_group_eperson",
+ "group_id=" + group.getID() + ", eperson_id=" + ePerson.getID()));
}
}
@@ -242,6 +248,8 @@ public void removeMember(Context context, Group groupParent, Group childGroup) t
context.addEvent(
new Event(Event.REMOVE, Constants.GROUP, groupParent.getID(), Constants.GROUP, childGroup.getID(),
childGroup.getName(), getIdentifiers(context, groupParent)));
+ log.info(LogHelper.getHeader(context, "remove_group_subgroup",
+ "group_id=" + groupParent.getID() + ", subgroup_id=" + childGroup.getID()));
}
}
diff --git a/dspace-api/src/main/java/org/dspace/external/OrcidConnectionException.java b/dspace-api/src/main/java/org/dspace/external/OrcidConnectionException.java
new file mode 100644
index 000000000000..3574045aab2b
--- /dev/null
+++ b/dspace-api/src/main/java/org/dspace/external/OrcidConnectionException.java
@@ -0,0 +1,33 @@
+/**
+ * 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.external;
+
+/**
+ * Exception thrown when there are issues with ORCID service connections.
+ *
+ * @author Boychuk Mykhaylo (mykhaylo.boychuk@4science.com)
+ */
+public class OrcidConnectionException extends Exception {
+
+ private final int statusCode;
+
+ public OrcidConnectionException(String message, int statusCode) {
+ super(message);
+ this.statusCode = statusCode;
+ }
+
+ public OrcidConnectionException(String message, int statusCode, Throwable cause) {
+ super(message, cause);
+ this.statusCode = statusCode;
+ }
+
+ public int getStatusCode() {
+ return statusCode;
+ }
+
+}
diff --git a/dspace-api/src/main/java/org/dspace/external/OrcidRestConnector.java b/dspace-api/src/main/java/org/dspace/external/OrcidRestConnector.java
index aa16af7a524d..3d61462cc354 100644
--- a/dspace-api/src/main/java/org/dspace/external/OrcidRestConnector.java
+++ b/dspace-api/src/main/java/org/dspace/external/OrcidRestConnector.java
@@ -9,10 +9,9 @@
import java.io.ByteArrayInputStream;
import java.io.InputStream;
-import java.nio.charset.StandardCharsets;
-import java.util.Scanner;
import org.apache.commons.lang3.StringUtils;
+import org.apache.http.HttpResponse;
import org.apache.http.client.methods.CloseableHttpResponse;
import org.apache.http.client.methods.HttpGet;
import org.apache.http.impl.client.CloseableHttpClient;
@@ -28,9 +27,6 @@
*/
public class OrcidRestConnector {
- /**
- * log4j logger
- */
private static final Logger log = LogManager.getLogger(OrcidRestConnector.class);
private final String url;
@@ -39,33 +35,33 @@ public OrcidRestConnector(String url) {
this.url = url;
}
- public InputStream get(String path, String accessToken) {
- CloseableHttpResponse getResponse = null;
- InputStream result = null;
- path = trimSlashes(path);
-
- String fullPath = url + '/' + path;
+ public InputStream get(String path, String accessToken) throws OrcidConnectionException {
+ String fullPath = url + '/' + trimSlashes(path);
HttpGet httpGet = new HttpGet(fullPath);
if (StringUtils.isNotBlank(accessToken)) {
httpGet.addHeader("Content-Type", "application/vnd.orcid+xml");
httpGet.addHeader("Authorization","Bearer " + accessToken);
}
try (CloseableHttpClient httpClient = DSpaceHttpClientFactory.getInstance().build()) {
- getResponse = httpClient.execute(httpGet);
- try (InputStream responseStream = getResponse.getEntity().getContent()) {
- // Read all the content of the response stream into a byte array to prevent TruncatedChunkException
- byte[] content = responseStream.readAllBytes();
- result = new ByteArrayInputStream(content);
+ try (CloseableHttpResponse httpResponse = httpClient.execute(httpGet)) {
+ if (!isSuccessful(httpResponse)) {
+ var statusCode = getStatusCode(httpResponse);
+ var reason = httpResponse.getStatusLine().getReasonPhrase();
+ var error = String.format("The request failed with:%d code, reason:%s ", statusCode, reason);
+ throw new OrcidConnectionException(error, statusCode);
+ }
+ try (InputStream responseStream = httpResponse.getEntity().getContent()) {
+ // Read all the content of the response stream into a byte array to prevent TruncatedChunkException
+ byte[] content = responseStream.readAllBytes();
+ return new ByteArrayInputStream(content);
+ }
}
+ } catch (OrcidConnectionException e) {
+ throw e;
} catch (Exception e) {
- getGotError(e, fullPath);
+ log.error("Error in rest connector for path: " + fullPath, e);
+ throw new OrcidConnectionException("Failed to execute ORCID request: " + fullPath, 0, e);
}
-
- return result;
- }
-
- protected void getGotError(Exception e, String fullPath) {
- log.error("Error in rest connector for path: " + fullPath, e);
}
public static String trimSlashes(String path) {
@@ -78,8 +74,13 @@ public static String trimSlashes(String path) {
return path;
}
- public static String convertStreamToString(InputStream is) {
- Scanner s = new Scanner(is, StandardCharsets.UTF_8).useDelimiter("\\A");
- return s.hasNext() ? s.next() : "";
+ private boolean isSuccessful(HttpResponse response) {
+ int statusCode = getStatusCode(response);
+ return statusCode >= 200 || statusCode <= 299;
}
-}
+
+ private int getStatusCode(HttpResponse response) {
+ return response.getStatusLine().getStatusCode();
+ }
+
+}
\ No newline at end of file
diff --git a/dspace-api/src/main/java/org/dspace/external/provider/impl/OrcidV3AuthorDataProvider.java b/dspace-api/src/main/java/org/dspace/external/provider/impl/OrcidV3AuthorDataProvider.java
index a9e10f92948d..fe2fdfa95381 100644
--- a/dspace-api/src/main/java/org/dspace/external/provider/impl/OrcidV3AuthorDataProvider.java
+++ b/dspace-api/src/main/java/org/dspace/external/provider/impl/OrcidV3AuthorDataProvider.java
@@ -21,6 +21,7 @@
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.content.dto.MetadataValueDTO;
+import org.dspace.external.OrcidConnectionException;
import org.dspace.external.OrcidRestConnector;
import org.dspace.external.model.ExternalDataObject;
import org.dspace.external.provider.AbstractExternalDataProvider;
@@ -89,6 +90,9 @@ public void init() throws IOException {
public void initializeAccessToken() {
// If we have reaches max retries or the access token is already set, return immediately
if (maxClientRetries <= 0 || StringUtils.isNotBlank(accessToken)) {
+ if (maxClientRetries <= 0) {
+ log.warn("Maximum retry attempts reached for ORCID token retrieval");
+ }
return;
}
try {
@@ -168,8 +172,14 @@ public Person getBio(String id) {
return null;
}
initializeAccessToken();
- InputStream bioDocument = orcidRestConnector.get(id + ((id.endsWith("/person")) ? "" : "/person"), accessToken);
- return converter.convertSinglePerson(bioDocument);
+ try {
+ InputStream bioDocument = orcidRestConnector.get(id + ((id.endsWith("/person")) ? "" : "/person"),
+ accessToken);
+ return converter.convertSinglePerson(bioDocument);
+ } catch (OrcidConnectionException e) {
+ log.error("Error retrieving ORCID bio for ID=" + id, e);
+ return null;
+ }
}
/**
@@ -200,21 +210,26 @@ public List searchExternalDataObjects(String query, int star
+ "&start=" + start
+ "&rows=" + limit;
log.debug("queryBio searchPath=" + searchPath + " accessToken=" + accessToken);
- InputStream bioDocument = orcidRestConnector.get(searchPath, accessToken);
- List results = converter.convert(bioDocument);
- List bios = new LinkedList<>();
- for (Result result : results) {
- OrcidIdentifier orcidIdentifier = result.getOrcidIdentifier();
- if (orcidIdentifier != null) {
- log.debug("Found OrcidId=" + orcidIdentifier.getPath());
- String orcid = orcidIdentifier.getPath();
- Person bio = getBio(orcid);
- if (bio != null) {
- bios.add(bio);
+ try {
+ InputStream bioDocument = orcidRestConnector.get(searchPath, accessToken);
+ List results = converter.convert(bioDocument);
+ List bios = new LinkedList<>();
+ for (Result result : results) {
+ OrcidIdentifier orcidIdentifier = result.getOrcidIdentifier();
+ if (orcidIdentifier != null) {
+ log.debug("Found OrcidId=" + orcidIdentifier.getPath());
+ String orcid = orcidIdentifier.getPath();
+ Person bio = getBio(orcid);
+ if (bio != null) {
+ bios.add(bio);
+ }
}
}
+ return bios.stream().map(bio -> convertToExternalDataObject(bio)).collect(Collectors.toList());
+ } catch (OrcidConnectionException e) {
+ log.error("Error searching ORCID for query=" + query, e);
+ return Collections.emptyList();
}
- return bios.stream().map(bio -> convertToExternalDataObject(bio)).collect(Collectors.toList());
}
@Override
@@ -233,8 +248,13 @@ public int getNumberOfResults(String query) {
+ "&start=" + 0
+ "&rows=" + 0;
log.debug("queryBio searchPath=" + searchPath + " accessToken=" + accessToken);
- InputStream bioDocument = orcidRestConnector.get(searchPath, accessToken);
- return Math.min(converter.getNumberOfResultsFromXml(bioDocument), MAX_INDEX);
+ try {
+ InputStream bioDocument = orcidRestConnector.get(searchPath, accessToken);
+ return Math.min(converter.getNumberOfResultsFromXml(bioDocument), MAX_INDEX);
+ } catch (OrcidConnectionException e) {
+ log.error("Error getting number of results from ORCID for query=" + query, e);
+ return 0;
+ }
}
@@ -296,4 +316,4 @@ public void setOrcidRestConnector(OrcidRestConnector orcidRestConnector) {
this.orcidRestConnector = orcidRestConnector;
}
-}
+}
\ No newline at end of file
diff --git a/dspace-api/src/main/java/org/dspace/health/UserCheck.java b/dspace-api/src/main/java/org/dspace/health/UserCheck.java
index 19a2a9ced355..875bb1bb0b60 100644
--- a/dspace-api/src/main/java/org/dspace/health/UserCheck.java
+++ b/dspace-api/src/main/java/org/dspace/health/UserCheck.java
@@ -50,26 +50,26 @@ public String run(ReportInfo ri) {
info.put("Self registered", 0);
for (EPerson e : epersons) {
- if (e.getEmail() != null && e.getEmail().length() > 0) {
+ if (e.getEmail() != null && !e.getEmail().isEmpty()) {
info.put("Have email", info.get("Have email") + 1);
}
if (e.canLogIn()) {
info.put("Can log in (password)",
info.get("Can log in (password)") + 1);
}
- if (e.getFirstName() != null && e.getFirstName().length() > 0) {
+ if (e.getFirstName() != null && !e.getFirstName().isEmpty()) {
info.put("Have 1st name", info.get("Have 1st name") + 1);
}
- if (e.getLastName() != null && e.getLastName().length() > 0) {
+ if (e.getLastName() != null && !e.getLastName().isEmpty()) {
info.put("Have 2nd name", info.get("Have 2nd name") + 1);
}
- if (e.getLanguage() != null && e.getLanguage().length() > 0) {
+ if (e.getLanguage() != null && !e.getLanguage().isEmpty()) {
info.put("Have lang", info.get("Have lang") + 1);
}
- if (e.getNetid() != null && e.getNetid().length() > 0) {
+ if (e.getNetid() != null && !e.getNetid().isEmpty()) {
info.put("Have netid", info.get("Have netid") + 1);
}
- if (e.getNetid() != null && e.getNetid().length() > 0) {
+ if (e.getNetid() != null && !e.getNetid().isEmpty()) {
info.put("Self registered", info.get("Self registered") + 1);
}
}
diff --git a/dspace-api/src/main/java/org/dspace/importer/external/epo/service/EpoImportMetadataSourceServiceImpl.java b/dspace-api/src/main/java/org/dspace/importer/external/epo/service/EpoImportMetadataSourceServiceImpl.java
index 552f607827a8..4ec1f4db39e7 100644
--- a/dspace-api/src/main/java/org/dspace/importer/external/epo/service/EpoImportMetadataSourceServiceImpl.java
+++ b/dspace-api/src/main/java/org/dspace/importer/external/epo/service/EpoImportMetadataSourceServiceImpl.java
@@ -29,9 +29,9 @@
import org.apache.commons.lang3.StringUtils;
import org.apache.http.HttpException;
import org.apache.http.client.utils.URIBuilder;
+import org.apache.jena.ext.xerces.impl.dv.util.Base64;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
-import org.apache.xerces.impl.dv.util.Base64;
import org.dspace.app.util.XMLUtils;
import org.dspace.content.Item;
import org.dspace.importer.external.datamodel.ImportRecord;
diff --git a/dspace-api/src/main/java/org/dspace/importer/external/metadatamapping/MetadatumDTO.java b/dspace-api/src/main/java/org/dspace/importer/external/metadatamapping/MetadatumDTO.java
index 265dd55eb933..b8a7507eaa61 100644
--- a/dspace-api/src/main/java/org/dspace/importer/external/metadatamapping/MetadatumDTO.java
+++ b/dspace-api/src/main/java/org/dspace/importer/external/metadatamapping/MetadatumDTO.java
@@ -105,4 +105,13 @@ public String getValue() {
public void setValue(String value) {
this.value = value;
}
+
+ /**
+ * Return string representation of MetadatumDTO
+ * @return string representation of format "[schema].[element].[qualifier]=[value]"
+ */
+ @Override
+ public String toString() {
+ return schema + "." + element + "." + qualifier + "=" + value;
+ }
}
diff --git a/dspace-api/src/main/java/org/dspace/importer/external/metadatamapping/contributor/ConditionalArrayElementAttributeProcessor.java b/dspace-api/src/main/java/org/dspace/importer/external/metadatamapping/contributor/ConditionalArrayElementAttributeProcessor.java
new file mode 100644
index 000000000000..f813a34c89b5
--- /dev/null
+++ b/dspace-api/src/main/java/org/dspace/importer/external/metadatamapping/contributor/ConditionalArrayElementAttributeProcessor.java
@@ -0,0 +1,127 @@
+/**
+ * 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.importer.external.metadatamapping.contributor;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Iterator;
+
+import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import org.apache.commons.lang3.StringUtils;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+
+/**
+ * This Processor extracts values from a JSON array, but only when a condition
+ * on another attribute is met. For example, to extract all values of
+ * /names/value where /names/types contains "ror_display".
+ *
+ * Configurable via:
+ * pathToArray: e.g., /names
+ * elementAttribute: e.g., /value
+ * filterAttribute: e.g., /types
+ * requiredValueInFilter: e.g., ror_display
+ *
+ * Supports filtering when the filter attribute is either a JSON array or a single string.
+ *
+ * Example JSON:
+ * {
+ * "items": [{
+ * "names": [
+ * { "types": ["label", "ror_display"], "value": "Instituto Federal do Piauí" },
+ * { "types": ["acronym"], "value": "IFPI" }
+ * ]
+ * }]
+ * }
+ * This processor can extract "Instituto Federal do Piauí" using proper configuration.
+ *
+ * Author: Jesiel (based on Mykhaylo Boychuk’s original processor)
+ */
+public class ConditionalArrayElementAttributeProcessor implements JsonPathMetadataProcessor {
+
+ private static final Logger log = LogManager.getLogger();
+
+ private String pathToArray;
+ private String elementAttribute;
+ private String filterAttribute;
+ private String requiredValueInFilter;
+
+ @Override
+ public Collection processMetadata(String json) {
+ JsonNode rootNode = convertStringJsonToJsonNode(json);
+ Collection results = new ArrayList<>();
+
+ if (rootNode == null) {
+ return results;
+ }
+
+ Iterator array = rootNode.at(pathToArray).iterator();
+ while (array.hasNext()) {
+ JsonNode element = array.next();
+ JsonNode filterNode = element.at(filterAttribute);
+
+ boolean match = false;
+
+ if (filterNode.isArray()) {
+ for (JsonNode filterValue : filterNode) {
+ if (requiredValueInFilter.equalsIgnoreCase(filterValue.textValue())) {
+ match = true;
+ break;
+ }
+ }
+ } else if (filterNode.isTextual()) {
+ if (requiredValueInFilter.equalsIgnoreCase(filterNode.textValue())) {
+ match = true;
+ }
+ }
+
+ if (match) {
+ JsonNode valueNode = element.at(elementAttribute);
+ if (valueNode.isTextual()) {
+ results.add(valueNode.textValue());
+ } else if (valueNode.isArray()) {
+ for (JsonNode item : valueNode) {
+ if (item.isTextual() && StringUtils.isNotBlank(item.textValue())) {
+ results.add(item.textValue());
+ }
+ }
+ }
+ }
+ }
+
+ return results;
+ }
+
+ private JsonNode convertStringJsonToJsonNode(String json) {
+ ObjectMapper mapper = new ObjectMapper();
+ try {
+ return mapper.readTree(json);
+ } catch (JsonProcessingException e) {
+ log.error("Unable to process JSON response.", e);
+ return null;
+ }
+ }
+
+ public void setPathToArray(String pathToArray) {
+ this.pathToArray = pathToArray;
+ }
+
+ public void setElementAttribute(String elementAttribute) {
+ this.elementAttribute = elementAttribute;
+ }
+
+ public void setFilterAttribute(String filterAttribute) {
+ this.filterAttribute = filterAttribute;
+ }
+
+ public void setRequiredValueInFilter(String requiredValueInFilter) {
+ this.requiredValueInFilter = requiredValueInFilter;
+ }
+}
\ No newline at end of file
diff --git a/dspace-api/src/main/java/org/dspace/importer/external/pubmed/service/PubmedImportMetadataSourceServiceImpl.java b/dspace-api/src/main/java/org/dspace/importer/external/pubmed/service/PubmedImportMetadataSourceServiceImpl.java
index c870161bf9bd..dc9954969394 100644
--- a/dspace-api/src/main/java/org/dspace/importer/external/pubmed/service/PubmedImportMetadataSourceServiceImpl.java
+++ b/dspace-api/src/main/java/org/dspace/importer/external/pubmed/service/PubmedImportMetadataSourceServiceImpl.java
@@ -55,6 +55,7 @@ public class PubmedImportMetadataSourceServiceImpl extends AbstractImportMetadat
private String urlFetch;
private String urlSearch;
+ private String apiKey;
private int attempt = 3;
@@ -210,6 +211,9 @@ public GetNbRecords(Query query) {
@Override
public Integer call() throws Exception {
URIBuilder uriBuilder = new URIBuilder(urlSearch);
+ if (StringUtils.isNotBlank(apiKey)) {
+ uriBuilder.addParameter("api_key", apiKey);
+ }
uriBuilder.addParameter("db", "pubmed");
uriBuilder.addParameter("term", query.getParameterAsClass("query", String.class));
Map> params = new HashMap>();
@@ -286,6 +290,9 @@ public Collection call() throws Exception {
List records = new LinkedList();
URIBuilder uriBuilder = new URIBuilder(urlSearch);
+ if (StringUtils.isNotBlank(apiKey)) {
+ uriBuilder.addParameter("api_key", apiKey);
+ }
uriBuilder.addParameter("db", "pubmed");
uriBuilder.addParameter("retstart", start.toString());
uriBuilder.addParameter("retmax", count.toString());
@@ -316,6 +323,9 @@ public Collection call() throws Exception {
String webEnv = getSingleElementValue(response, "WebEnv");
URIBuilder uriBuilder2 = new URIBuilder(urlFetch);
+ if (StringUtils.isNotBlank(apiKey)) {
+ uriBuilder2.addParameter("api_key", apiKey);
+ }
uriBuilder2.addParameter("db", "pubmed");
uriBuilder2.addParameter("retstart", start.toString());
uriBuilder2.addParameter("retmax", count.toString());
@@ -388,6 +398,9 @@ public GetRecord(Query q) {
public ImportRecord call() throws Exception {
URIBuilder uriBuilder = new URIBuilder(urlFetch);
+ if (StringUtils.isNotBlank(apiKey)) {
+ uriBuilder.addParameter("api_key", apiKey);
+ }
uriBuilder.addParameter("db", "pubmed");
uriBuilder.addParameter("retmode", "xml");
uriBuilder.addParameter("id", query.getParameterAsClass("id", String.class));
@@ -428,6 +441,9 @@ public FindMatchingRecords(Query q) {
public Collection call() throws Exception {
URIBuilder uriBuilder = new URIBuilder(urlSearch);
+ if (StringUtils.isNotBlank(apiKey)) {
+ uriBuilder.addParameter("api_key", apiKey);
+ }
uriBuilder.addParameter("db", "pubmed");
uriBuilder.addParameter("usehistory", "y");
uriBuilder.addParameter("term", query.getParameterAsClass("term", String.class));
@@ -457,6 +473,9 @@ public Collection call() throws Exception {
String queryKey = getSingleElementValue(response, "QueryKey");
URIBuilder uriBuilder2 = new URIBuilder(urlFetch);
+ if (StringUtils.isNotBlank(apiKey)) {
+ uriBuilder.addParameter("api_key", apiKey);
+ }
uriBuilder2.addParameter("db", "pubmed");
uriBuilder2.addParameter("retmode", "xml");
uriBuilder2.addParameter("WebEnv", webEnv);
@@ -532,4 +551,8 @@ public void setUrlSearch(String urlSearch) {
this.urlSearch = urlSearch;
}
+ public void setApiKey(String apiKey) {
+ this.apiKey = apiKey;
+ }
+
}
diff --git a/dspace-api/src/main/java/org/dspace/importer/external/ror/service/RorImportMetadataSourceServiceImpl.java b/dspace-api/src/main/java/org/dspace/importer/external/ror/service/RorImportMetadataSourceServiceImpl.java
index 8298b6d6f011..2cc6c66c7ab3 100644
--- a/dspace-api/src/main/java/org/dspace/importer/external/ror/service/RorImportMetadataSourceServiceImpl.java
+++ b/dspace-api/src/main/java/org/dspace/importer/external/ror/service/RorImportMetadataSourceServiceImpl.java
@@ -46,7 +46,7 @@ public class RorImportMetadataSourceServiceImpl extends AbstractImportMetadataSo
private String url;
- private int timeout = 1000;
+ private int timeout = 5000;
@Autowired
private LiveImportClient liveImportClient;
diff --git a/dspace-api/src/main/java/org/dspace/orcid/model/OrcidWorkFieldMapping.java b/dspace-api/src/main/java/org/dspace/orcid/model/OrcidWorkFieldMapping.java
index 781a9dcbd904..faefe798e92b 100644
--- a/dspace-api/src/main/java/org/dspace/orcid/model/OrcidWorkFieldMapping.java
+++ b/dspace-api/src/main/java/org/dspace/orcid/model/OrcidWorkFieldMapping.java
@@ -39,6 +39,7 @@ public class OrcidWorkFieldMapping {
* The metadata fields related to the work external identifiers.
*/
private Map externalIdentifierFields = new HashMap<>();
+ private Map> externalIdentifierPartOfMap = new HashMap<>();
/**
* The metadata field related to the work publication date.
@@ -129,6 +130,15 @@ public void setExternalIdentifierFields(String externalIdentifierFields) {
this.externalIdentifierFields = parseConfigurations(externalIdentifierFields);
}
+ public Map> getExternalIdentifierPartOfMap() {
+ return this.externalIdentifierPartOfMap;
+ }
+
+ public void setExternalIdentifierPartOfMap(
+ HashMap> externalIdentifierPartOfMap) {
+ this.externalIdentifierPartOfMap = externalIdentifierPartOfMap;
+ }
+
public String getPublicationDateField() {
return publicationDateField;
}
diff --git a/dspace-api/src/main/java/org/dspace/orcid/model/factory/OrcidFactoryUtils.java b/dspace-api/src/main/java/org/dspace/orcid/model/factory/OrcidFactoryUtils.java
index ce68ab47c26e..f08aff740580 100644
--- a/dspace-api/src/main/java/org/dspace/orcid/model/factory/OrcidFactoryUtils.java
+++ b/dspace-api/src/main/java/org/dspace/orcid/model/factory/OrcidFactoryUtils.java
@@ -7,21 +7,29 @@
*/
package org.dspace.orcid.model.factory;
-import java.io.BufferedReader;
+import static java.nio.charset.StandardCharsets.UTF_8;
+
import java.io.IOException;
import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.nio.charset.StandardCharsets;
+import java.util.ArrayList;
+import java.util.Base64;
import java.util.HashMap;
+import java.util.List;
import java.util.Map;
import java.util.Optional;
import org.apache.commons.lang3.StringUtils;
import org.apache.http.HttpResponse;
+import org.apache.http.NameValuePair;
+import org.apache.http.client.entity.UrlEncodedFormEntity;
import org.apache.http.client.methods.HttpPost;
import org.apache.http.impl.client.CloseableHttpClient;
+import org.apache.http.message.BasicNameValuePair;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.dspace.app.client.DSpaceHttpClientFactory;
import org.json.JSONObject;
+import org.json.JSONTokener;
/**
* Utility class for Orcid factory classes. This is used to parse the
@@ -29,13 +37,12 @@
* contributors and external ids configuration).
*
* @author Luca Giamminonni (luca.giamminonni at 4science.it)
- *
*/
public final class OrcidFactoryUtils {
- private OrcidFactoryUtils() {
+ private static final Logger log = LogManager.getLogger(OrcidFactoryUtils.class);
- }
+ private OrcidFactoryUtils() { }
/**
* Parse the given configurations value and returns a map with metadata fields
@@ -46,7 +53,7 @@ private OrcidFactoryUtils() {
* @return the configurations parsing result as map
*/
public static Map parseConfigurations(String configurations) {
- Map configurationMap = new HashMap();
+ Map configurationMap = new HashMap<>();
if (StringUtils.isBlank(configurations)) {
return configurationMap;
}
@@ -55,7 +62,6 @@ public static Map parseConfigurations(String configurations) {
String[] configurationSections = parseConfiguration(configuration);
configurationMap.put(configurationSections[0], configurationSections[1]);
}
-
return configurationMap;
}
@@ -87,37 +93,65 @@ private static String[] parseConfiguration(String configuration) {
*/
public static Optional retrieveAccessToken(String clientId, String clientSecret, String oauthUrl)
throws IOException {
- if (StringUtils.isNotBlank(clientSecret) && StringUtils.isNotBlank(clientId)
- && StringUtils.isNotBlank(oauthUrl)) {
- String authenticationParameters = "?client_id=" + clientId +
- "&client_secret=" + clientSecret +
- "&scope=/read-public&grant_type=client_credentials";
- HttpPost httpPost = new HttpPost(oauthUrl + authenticationParameters);
- httpPost.addHeader("Accept", "application/json");
- httpPost.addHeader("Content-Type", "application/x-www-form-urlencoded");
-
- HttpResponse response;
- try (CloseableHttpClient httpClient = DSpaceHttpClientFactory.getInstance().build()) {
- response = httpClient.execute(httpPost);
+ if (StringUtils.isBlank(clientSecret) || StringUtils.isBlank(clientId) || StringUtils.isBlank(oauthUrl)) {
+ String missingParams = (StringUtils.isBlank(clientId) ? "clientId " : "") +
+ (StringUtils.isBlank(clientSecret) ? "clientSecret " : "") +
+ (StringUtils.isBlank(oauthUrl) ? "oauthUrl" : "");
+ log.error("Cannot retrieve ORCID access token: missing required parameters:{} ", missingParams.trim());
+ return Optional.empty();
+ }
+
+ HttpPost httpPost = new HttpPost(oauthUrl);
+
+ String auth = clientId + ":" + clientSecret;
+ String encodedAuth = Base64.getEncoder().encodeToString(auth.getBytes(UTF_8));
+ addHeaders(httpPost, encodedAuth);
+
+ List params = new ArrayList<>();
+ params.add(new BasicNameValuePair("grant_type", "client_credentials"));
+ params.add(new BasicNameValuePair("scope", "/read-public"));
+ httpPost.setEntity(new UrlEncodedFormEntity(params, UTF_8));
+
+ try (CloseableHttpClient httpClient = DSpaceHttpClientFactory.getInstance().build()) {
+ log.debug("Sending ORCID token request to {}", oauthUrl);
+ HttpResponse response = httpClient.execute(httpPost);
+ if (!isSuccessful(response)) {
+ log.error("Failed to retrieve ORCID access token");
+ return Optional.empty();
}
- JSONObject responseObject = null;
- if (response != null && response.getStatusLine().getStatusCode() == 200) {
- try (InputStream is = response.getEntity().getContent();
- BufferedReader streamReader = new BufferedReader(new InputStreamReader(is,
- StandardCharsets.UTF_8))) {
- String inputStr;
- while ((inputStr = streamReader.readLine()) != null && responseObject == null) {
- if (inputStr.startsWith("{") && inputStr.endsWith("}") && inputStr.contains("access_token")) {
- responseObject = new JSONObject(inputStr);
- }
- }
+ // Parsing JSON response
+ try (InputStream is = response.getEntity().getContent()) {
+ JSONObject responseObject = new JSONObject(new JSONTokener(is));
+ if (responseObject.has("access_token")) {
+ String token = responseObject.getString("access_token");
+ log.debug("Successfully retrieved ORCID access token");
+ return Optional.of(token);
+ } else {
+ log.error("ORCID response missing access_token field:{} ", responseObject);
+ return Optional.empty();
}
}
- if (responseObject != null && responseObject.has("access_token")) {
- return Optional.of((String) responseObject.get("access_token"));
- }
}
- // Return empty by default
- return Optional.empty();
}
+
+ private static void addHeaders(HttpPost httpPost, String encodedAuth) {
+ httpPost.addHeader("Authorization", "Basic " + encodedAuth);
+ httpPost.addHeader("Accept", "application/json");
+ httpPost.addHeader("Content-Type", "application/x-www-form-urlencoded");
+ }
+
+ private static boolean isSuccessful(HttpResponse response) {
+ if (response == null) {
+ log.error("ORCID API request failed: null response received");
+ return false;
+ }
+ int statusCode = response.getStatusLine().getStatusCode();
+ if (statusCode != 200) {
+ var errorMsg = "ORCID API request failed with status code {}: {}";
+ log.error(errorMsg, statusCode, response.getStatusLine().getReasonPhrase());
+ return false;
+ }
+ return true;
+ }
+
}
diff --git a/dspace-api/src/main/java/org/dspace/orcid/model/factory/impl/OrcidWorkFactory.java b/dspace-api/src/main/java/org/dspace/orcid/model/factory/impl/OrcidWorkFactory.java
index 47619b3c1d63..280a5ac2155f 100644
--- a/dspace-api/src/main/java/org/dspace/orcid/model/factory/impl/OrcidWorkFactory.java
+++ b/dspace-api/src/main/java/org/dspace/orcid/model/factory/impl/OrcidWorkFactory.java
@@ -9,6 +9,7 @@
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
+import static org.orcid.jaxb.model.common.Relationship.PART_OF;
import static org.orcid.jaxb.model.common.Relationship.SELF;
import java.util.ArrayList;
@@ -73,12 +74,12 @@ public OrcidEntityType getEntityType() {
@Override
public Activity createOrcidObject(Context context, Item item) {
Work work = new Work();
+ work.setWorkType(getWorkType(context, item));
work.setJournalTitle(getJournalTitle(context, item));
work.setWorkContributors(getWorkContributors(context, item));
work.setWorkTitle(getWorkTitle(context, item));
work.setPublicationDate(getPublicationDate(context, item));
- work.setWorkExternalIdentifiers(getWorkExternalIds(context, item));
- work.setWorkType(getWorkType(context, item));
+ work.setWorkExternalIdentifiers(getWorkExternalIds(context, item, work));
work.setShortDescription(getShortDescription(context, item));
work.setLanguageCode(getLanguageCode(context, item));
work.setUrl(getUrl(context, item));
@@ -149,57 +150,65 @@ private PublicationDate getPublicationDate(Context context, Item item) {
}
/**
- * Creates an instance of ExternalIDs from the metadata values of the given
- * item, using the orcid.mapping.funding.external-ids configuration.
+ * Returns a list of external work IDs constructed in the org.orcid.jaxb
+ * ExternalIDs object
*/
- private ExternalIDs getWorkExternalIds(Context context, Item item) {
- ExternalIDs externalIdentifiers = new ExternalIDs();
- externalIdentifiers.getExternalIdentifier().addAll(getWorkSelfExternalIds(context, item));
- return externalIdentifiers;
+ private ExternalIDs getWorkExternalIds(Context context, Item item, Work work) {
+ ExternalIDs externalIDs = new ExternalIDs();
+ externalIDs.getExternalIdentifier().addAll(getWorkExternalIdList(context, item, work));
+ return externalIDs;
}
/**
* Creates a list of ExternalID, one for orcid.mapping.funding.external-ids
- * value, taking the values from the given item.
+ * value, taking the values from the given item and work type.
*/
- private List getWorkSelfExternalIds(Context context, Item item) {
+ private List getWorkExternalIdList(Context context, Item item, Work work) {
- List selfExternalIds = new ArrayList<>();
+ List externalIds = new ArrayList<>();
Map externalIdentifierFields = fieldMapping.getExternalIdentifierFields();
if (externalIdentifierFields.containsKey(SIMPLE_HANDLE_PLACEHOLDER)) {
String handleType = externalIdentifierFields.get(SIMPLE_HANDLE_PLACEHOLDER);
- selfExternalIds.add(getExternalId(handleType, item.getHandle(), SELF));
+ ExternalID handle = new ExternalID();
+ handle.setType(handleType);
+ handle.setValue(item.getHandle());
+ handle.setRelationship(SELF);
+ externalIds.add(handle);
}
+ // Resolve work type, used to determine identifier relationship type
+ // For version / funding relationships, we might want to use more complex
+ // business rules than just "work and id type"
+ final String workType = (work != null && work.getWorkType() != null) ?
+ work.getWorkType().value() : WorkType.OTHER.value();
getMetadataValues(context, item, externalIdentifierFields.keySet()).stream()
- .map(this::getSelfExternalId)
- .forEach(selfExternalIds::add);
+ .map(metadataValue -> this.getExternalId(metadataValue, workType))
+ .forEach(externalIds::add);
- return selfExternalIds;
- }
-
- /**
- * Creates an instance of ExternalID taking the value from the given
- * metadataValue. The type of the ExternalID is calculated using the
- * orcid.mapping.funding.external-ids configuration. The relationship of the
- * ExternalID is SELF.
- */
- private ExternalID getSelfExternalId(MetadataValue metadataValue) {
- Map externalIdentifierFields = fieldMapping.getExternalIdentifierFields();
- String metadataField = metadataValue.getMetadataField().toString('.');
- return getExternalId(externalIdentifierFields.get(metadataField), metadataValue.getValue(), SELF);
+ return externalIds;
}
/**
* Creates an instance of ExternalID with the given type, value and
* relationship.
*/
- private ExternalID getExternalId(String type, String value, Relationship relationship) {
+ private ExternalID getExternalId(MetadataValue metadataValue, String workType) {
+ Map externalIdentifierFields = fieldMapping.getExternalIdentifierFields();
+ Map> externalIdentifierPartOfMap = fieldMapping.getExternalIdentifierPartOfMap();
+ String metadataField = metadataValue.getMetadataField().toString('.');
+ String identifierType = externalIdentifierFields.get(metadataField);
+ // Default relationship type is SELF, configuration can
+ // override to PART_OF based on identifier and work type
+ Relationship relationship = SELF;
+ if (externalIdentifierPartOfMap.containsKey(identifierType)
+ && externalIdentifierPartOfMap.get(identifierType).contains(workType)) {
+ relationship = PART_OF;
+ }
ExternalID externalID = new ExternalID();
- externalID.setType(type);
- externalID.setValue(value);
+ externalID.setType(identifierType);
+ externalID.setValue(metadataValue.getValue());
externalID.setRelationship(relationship);
return externalID;
}
diff --git a/dspace-api/src/main/java/org/dspace/orcid/service/impl/OrcidQueueServiceImpl.java b/dspace-api/src/main/java/org/dspace/orcid/service/impl/OrcidQueueServiceImpl.java
index 261f8ef9a9f7..d69e8842f5a9 100644
--- a/dspace-api/src/main/java/org/dspace/orcid/service/impl/OrcidQueueServiceImpl.java
+++ b/dspace-api/src/main/java/org/dspace/orcid/service/impl/OrcidQueueServiceImpl.java
@@ -224,7 +224,7 @@ private List
- findAllEntitiesLinkableWith(Context context, Item profile, St
return findRelationshipsByItem(context, profile).stream()
.map(relationship -> getRelatedItem(relationship, profile))
- .filter(item -> entityType.equals(itemService.getEntityTypeLabel(item)))
+ .filter(item -> item.isArchived() && entityType.equals(itemService.getEntityTypeLabel(item)))
.collect(Collectors.toList());
}
diff --git a/dspace-api/src/main/java/org/dspace/profile/ResearcherProfileServiceImpl.java b/dspace-api/src/main/java/org/dspace/profile/ResearcherProfileServiceImpl.java
index 5de1ffa4ac93..b2466b33b56e 100644
--- a/dspace-api/src/main/java/org/dspace/profile/ResearcherProfileServiceImpl.java
+++ b/dspace-api/src/main/java/org/dspace/profile/ResearcherProfileServiceImpl.java
@@ -283,6 +283,8 @@ private Item createProfileItem(Context context, EPerson ePerson, Collection coll
itemService.addMetadata(context, item, "dc", "title", null, null, fullName);
itemService.addMetadata(context, item, "person", "email", null, null, ePerson.getEmail());
itemService.addMetadata(context, item, "dspace", "object", "owner", null, fullName, id, CF_ACCEPTED);
+ itemService.addMetadata(context, item, "person", "familyName", null, null, ePerson.getLastName());
+ itemService.addMetadata(context, item, "person", "givenName", null, null, ePerson.getFirstName());
item = installItemService.installItem(context, workspaceItem);
diff --git a/dspace-api/src/main/java/org/dspace/qaevent/service/impl/QAEventServiceImpl.java b/dspace-api/src/main/java/org/dspace/qaevent/service/impl/QAEventServiceImpl.java
index 98077a1c0c76..171cc4c31159 100644
--- a/dspace-api/src/main/java/org/dspace/qaevent/service/impl/QAEventServiceImpl.java
+++ b/dspace-api/src/main/java/org/dspace/qaevent/service/impl/QAEventServiceImpl.java
@@ -131,7 +131,7 @@ protected SolrClient getSolr() {
if (solr == null) {
String solrService = DSpaceServicesFactory.getInstance().getConfigurationService()
.getProperty("qaevents.solr.server", "http://localhost:8983/solr/qaevent");
- return new HttpSolrClient.Builder(solrService).build();
+ solr = new HttpSolrClient.Builder(solrService).build();
}
return solr;
}
diff --git a/dspace-api/src/main/java/org/dspace/scripts/DSpaceRunnable.java b/dspace-api/src/main/java/org/dspace/scripts/DSpaceRunnable.java
index 2ea0a52d6e34..8f905e01511e 100644
--- a/dspace-api/src/main/java/org/dspace/scripts/DSpaceRunnable.java
+++ b/dspace-api/src/main/java/org/dspace/scripts/DSpaceRunnable.java
@@ -117,7 +117,7 @@ private void handleHelpCommandLine() {
* @param args The primitive array of Strings representing the parameters
* @throws ParseException If something goes wrong
*/
- private StepResult parse(String[] args) throws ParseException {
+ protected StepResult parse(String[] args) throws ParseException {
commandLine = new DefaultParser().parse(getScriptConfiguration().getOptions(), args);
setup();
return StepResult.Continue;
diff --git a/dspace-api/src/main/java/org/dspace/sort/OrderFormatTitle.java b/dspace-api/src/main/java/org/dspace/sort/OrderFormatTitle.java
index b745f0719cb7..f6f9aaa38e50 100644
--- a/dspace-api/src/main/java/org/dspace/sort/OrderFormatTitle.java
+++ b/dspace-api/src/main/java/org/dspace/sort/OrderFormatTitle.java
@@ -9,7 +9,6 @@
import org.dspace.text.filter.DecomposeDiactritics;
import org.dspace.text.filter.LowerCaseAndTrim;
-import org.dspace.text.filter.StandardInitialArticleWord;
import org.dspace.text.filter.StripDiacritics;
import org.dspace.text.filter.TextFilter;
@@ -20,7 +19,7 @@
*/
public class OrderFormatTitle extends AbstractTextFilterOFD {
{
- filters = new TextFilter[] {new StandardInitialArticleWord(),
+ filters = new TextFilter[] {
new DecomposeDiactritics(),
new StripDiacritics(),
new LowerCaseAndTrim()};
diff --git a/dspace-api/src/main/java/org/dspace/sort/OrderFormatTitleMarc21.java b/dspace-api/src/main/java/org/dspace/sort/OrderFormatTitleMarc21.java
index fa9ba297258a..9148ca2a988a 100644
--- a/dspace-api/src/main/java/org/dspace/sort/OrderFormatTitleMarc21.java
+++ b/dspace-api/src/main/java/org/dspace/sort/OrderFormatTitleMarc21.java
@@ -9,7 +9,6 @@
import org.dspace.text.filter.DecomposeDiactritics;
import org.dspace.text.filter.LowerCaseAndTrim;
-import org.dspace.text.filter.MARC21InitialArticleWord;
import org.dspace.text.filter.StripDiacritics;
import org.dspace.text.filter.StripLeadingNonAlphaNum;
import org.dspace.text.filter.TextFilter;
@@ -21,7 +20,7 @@
*/
public class OrderFormatTitleMarc21 extends AbstractTextFilterOFD {
{
- filters = new TextFilter[] {new MARC21InitialArticleWord(),
+ filters = new TextFilter[] {
new DecomposeDiactritics(),
new StripDiacritics(),
new StripLeadingNonAlphaNum(),
diff --git a/dspace-api/src/main/java/org/dspace/statistics/SolrLoggerServiceImpl.java b/dspace-api/src/main/java/org/dspace/statistics/SolrLoggerServiceImpl.java
index 32de86744d13..5c3048085069 100644
--- a/dspace-api/src/main/java/org/dspace/statistics/SolrLoggerServiceImpl.java
+++ b/dspace-api/src/main/java/org/dspace/statistics/SolrLoggerServiceImpl.java
@@ -28,6 +28,7 @@
import java.text.ParseException;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.Calendar;
import java.util.Date;
import java.util.EnumSet;
@@ -228,6 +229,10 @@ public void postView(DSpaceObject dspaceObject, HttpServletRequest request,
throw new RuntimeException(e);
}
+ if (dspaceObject instanceof Bitstream && !isBitstreamLoggable((Bitstream) dspaceObject)) {
+ return;
+ }
+
if (solr == null) {
return;
}
@@ -275,6 +280,10 @@ public void postView(DSpaceObject dspaceObject,
@Override
public void postView(DSpaceObject dspaceObject,
String ip, String userAgent, String xforwardedfor, EPerson currentUser, String referrer) {
+ if (dspaceObject instanceof Bitstream && !isBitstreamLoggable((Bitstream) dspaceObject)) {
+ return;
+ }
+
if (solr == null) {
return;
}
@@ -1634,4 +1643,35 @@ public Object anonymizeIp(String ip) throws UnknownHostException {
throw new UnknownHostException("unknown ip format");
}
+
+ /**
+ * Checks if a given Bitstream's bundles are configured to be logged in Solr statistics.
+ *
+ * @param bitstream The bitstream to check.
+ * @return {@code true} if the bitstream event should be logged, {@code false} otherwise.
+ */
+ private boolean isBitstreamLoggable(Bitstream bitstream) {
+ String[] allowedBundles = configurationService
+ .getArrayProperty("solr-statistics.query.filter.bundles");
+ if (allowedBundles == null || allowedBundles.length == 0) {
+ return true;
+ }
+ List allowedBundlesList = Arrays.asList(allowedBundles);
+ try {
+ List actualBundles = bitstream.getBundles();
+ if (actualBundles.isEmpty()) {
+ return true;
+ }
+ for (Bundle bundle : actualBundles) {
+ if (allowedBundlesList.contains(bundle.getName())) {
+ return true;
+ }
+ }
+ } catch (SQLException e) {
+ log.error("Error checking bitstream bundles for logging statistics for bitstream {}",
+ bitstream.getID(), e);
+ return true;
+ }
+ return false;
+ }
}
diff --git a/dspace-api/src/main/java/org/dspace/statistics/export/processor/ExportEventProcessor.java b/dspace-api/src/main/java/org/dspace/statistics/export/processor/ExportEventProcessor.java
index 434de459bad9..44fc5f3dc9c5 100644
--- a/dspace-api/src/main/java/org/dspace/statistics/export/processor/ExportEventProcessor.java
+++ b/dspace-api/src/main/java/org/dspace/statistics/export/processor/ExportEventProcessor.java
@@ -136,9 +136,10 @@ protected String getBaseParameters(Item item)
.append(URLEncoder.encode(clientUA, UTF_8));
String hostName = Utils.getHostName(configurationService.getProperty("dspace.ui.url"));
+ String oaiPrefix = configurationService.getProperty("oai.identifier.prefix");
data.append("&").append(URLEncoder.encode("rft.artnum", UTF_8)).append("=").
- append(URLEncoder.encode("oai:" + hostName + ":" + item
+ append(URLEncoder.encode("oai:" + oaiPrefix + ":" + item
.getHandle(), UTF_8));
data.append("&").append(URLEncoder.encode("rfr_dat", UTF_8)).append("=")
.append(URLEncoder.encode(referer, UTF_8));
diff --git a/dspace-api/src/main/java/org/dspace/storage/bitstore/BitstreamStorageServiceImpl.java b/dspace-api/src/main/java/org/dspace/storage/bitstore/BitstreamStorageServiceImpl.java
index c89e5d7a54d1..9ebf3b29849c 100644
--- a/dspace-api/src/main/java/org/dspace/storage/bitstore/BitstreamStorageServiceImpl.java
+++ b/dspace-api/src/main/java/org/dspace/storage/bitstore/BitstreamStorageServiceImpl.java
@@ -423,7 +423,7 @@ public void migrate(Context context, Integer assetstoreSource, Integer assetstor
//modulo
if ((processedCounter % batchCommitSize) == 0) {
log.info("Migration Commit Checkpoint: " + processedCounter);
- context.dispatchEvents();
+ context.commit();
}
}
diff --git a/dspace-api/src/main/java/org/dspace/storage/bitstore/DSBitStoreService.java b/dspace-api/src/main/java/org/dspace/storage/bitstore/DSBitStoreService.java
index 7743b93ca4ba..a08af8104ccd 100644
--- a/dspace-api/src/main/java/org/dspace/storage/bitstore/DSBitStoreService.java
+++ b/dspace-api/src/main/java/org/dspace/storage/bitstore/DSBitStoreService.java
@@ -19,9 +19,11 @@
import java.util.List;
import java.util.Map;
+import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.Logger;
import org.dspace.content.Bitstream;
import org.dspace.core.Utils;
+import org.dspace.services.factory.DSpaceServicesFactory;
/**
* Native DSpace (or "Directory Scatter" if you prefer) asset store.
@@ -252,10 +254,13 @@ protected File getFile(Bitstream bitstream) throws IOException {
}
File bitstreamFile = new File(bufFilename.toString());
Path normalizedPath = bitstreamFile.toPath().normalize();
- if (!normalizedPath.startsWith(baseDir.getAbsolutePath())) {
+ String[] allowedAssetstoreRoots = DSpaceServicesFactory.getInstance().getConfigurationService()
+ .getArrayProperty("assetstore.allowed.roots", new String[]{});
+ if (!normalizedPath.startsWith(baseDir.getCanonicalPath())
+ && !StringUtils.startsWithAny(normalizedPath.toString(), allowedAssetstoreRoots)) {
log.error("Bitstream path outside of assetstore root requested:" +
"bitstream={}, path={}, assetstore={}",
- bitstream.getID(), normalizedPath, baseDir.getAbsolutePath());
+ bitstream.getID(), normalizedPath, baseDir.getCanonicalPath());
throw new IOException("Illegal bitstream path constructed");
}
return bitstreamFile;
diff --git a/dspace-api/src/main/java/org/dspace/storage/bitstore/S3BitStoreService.java b/dspace-api/src/main/java/org/dspace/storage/bitstore/S3BitStoreService.java
index 36456a8945ec..4ef6915f3c27 100644
--- a/dspace-api/src/main/java/org/dspace/storage/bitstore/S3BitStoreService.java
+++ b/dspace-api/src/main/java/org/dspace/storage/bitstore/S3BitStoreService.java
@@ -9,36 +9,20 @@
import static java.lang.String.valueOf;
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
+import java.net.URI;
import java.security.DigestInputStream;
import java.security.MessageDigest;
import java.security.NoSuchAlgorithmException;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
-import java.util.UUID;
+import java.util.concurrent.CompletionException;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
import java.util.function.Supplier;
-import com.amazonaws.AmazonClientException;
-import com.amazonaws.auth.AWSCredentials;
-import com.amazonaws.auth.AWSStaticCredentialsProvider;
-import com.amazonaws.auth.BasicAWSCredentials;
-import com.amazonaws.regions.Region;
-import com.amazonaws.regions.Regions;
-import com.amazonaws.services.s3.AmazonS3;
-import com.amazonaws.services.s3.AmazonS3ClientBuilder;
-import com.amazonaws.services.s3.model.AmazonS3Exception;
-import com.amazonaws.services.s3.model.GetObjectRequest;
-import com.amazonaws.services.s3.model.ObjectMetadata;
-import com.amazonaws.services.s3.transfer.Download;
-import com.amazonaws.services.s3.transfer.TransferManager;
-import com.amazonaws.services.s3.transfer.TransferManagerBuilder;
-import com.amazonaws.services.s3.transfer.Upload;
-import jakarta.validation.constraints.NotNull;
import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.DefaultParser;
import org.apache.commons.cli.HelpFormatter;
@@ -47,7 +31,6 @@
import org.apache.commons.cli.ParseException;
import org.apache.commons.io.output.NullOutputStream;
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.Bitstream;
@@ -58,6 +41,19 @@
import org.dspace.storage.bitstore.service.BitstreamStorageService;
import org.dspace.util.FunctionalUtils;
import org.springframework.beans.factory.annotation.Autowired;
+import software.amazon.awssdk.auth.credentials.AwsBasicCredentials;
+import software.amazon.awssdk.auth.credentials.AwsCredentialsProvider;
+import software.amazon.awssdk.auth.credentials.StaticCredentialsProvider;
+import software.amazon.awssdk.awscore.exception.AwsServiceException;
+import software.amazon.awssdk.core.async.AsyncRequestBody;
+import software.amazon.awssdk.core.async.AsyncResponseTransformer;
+import software.amazon.awssdk.http.HttpStatusCode;
+import software.amazon.awssdk.regions.Region;
+import software.amazon.awssdk.services.s3.S3AsyncClient;
+import software.amazon.awssdk.services.s3.S3CrtAsyncClientBuilder;
+import software.amazon.awssdk.services.s3.model.ChecksumAlgorithm;
+import software.amazon.awssdk.services.s3.model.HeadObjectResponse;
+import software.amazon.awssdk.services.s3.model.NoSuchBucketException;
/**
* Asset store using Amazon's Simple Storage Service (S3).
@@ -66,7 +62,7 @@
*
* @author Richard Rodgers, Peter Dietz
* @author Vincenzo Mecca (vins01-4science - vincenzo.mecca at 4science.com)
- *
+ * @author Mark Patton
*/
public class S3BitStoreService extends BaseBitStoreService {
@@ -83,30 +79,21 @@ public class S3BitStoreService extends BaseBitStoreService {
*/
static final String CSA = "MD5";
- // These settings control the way an identifier is hashed into
- // directory and file names
- //
- // With digitsPerLevel 2 and directoryLevels 3, an identifier
- // like 12345678901234567890 turns into the relative name
- // /12/34/56/12345678901234567890.
- //
- // You should not change these settings if you have data in the
- // asset store, as the BitstreamStorageManager will be unable
- // to find your existing data.
- protected static final int digitsPerLevel = 2;
- protected static final int directoryLevels = 3;
-
private boolean enabled = false;
+ /**
+ * Override AWS endpoint if not null
+ */
+ private String endpoint = null;
+
private String awsAccessKey;
private String awsSecretKey;
private String awsRegionName;
private boolean useRelativePath;
-
- /**
- * The maximum size of individual chunk to download from S3 when a file is accessed. Default 5Mb
- */
- private long bufferSize = 5 * 1024 * 1024;
+ private double targetThroughputGbps = 10.0;
+ private long minPartSizeBytes = 8 * 1024 * 1024L;
+ private ChecksumAlgorithm s3ChecksumAlgorithm = ChecksumAlgorithm.CRC32;
+ private Integer maxConcurrency = null;
/**
* container for all the assets
@@ -121,13 +108,7 @@ public class S3BitStoreService extends BaseBitStoreService {
/**
* S3 service
*/
- private AmazonS3 s3Service = null;
-
- /**
- * S3 transfer manager
- * this is reused between put calls to use less resources for multiple uploads
- */
- private TransferManager tm = null;
+ private S3AsyncClient s3AsyncClient = null;
private static final ConfigurationService configurationService
= DSpaceServicesFactory.getInstance().getConfigurationService();
@@ -137,16 +118,42 @@ public class S3BitStoreService extends BaseBitStoreService {
*
* @param regions wanted regions in client
* @param awsCredentials credentials of the client
+ * @param endpoint custom AWS endpoint
+ * @param targetThroughput target throughput in Gbps
+ * @param minPartSize minimum part size in bytes
+ * @param maxConcurrency maximum number of concurrent requests
* @return builder with the specified parameters
*/
- protected static Supplier amazonClientBuilderBy(
- @NotNull Regions regions,
- @NotNull AWSCredentials awsCredentials
+ protected static Supplier amazonClientBuilderBy(
+ Region region,
+ AwsCredentialsProvider credentialsProvider,
+ String endpoint,
+ double targetThroughput,
+ long minPartSize,
+ Integer maxConcurrency
) {
- return () -> AmazonS3ClientBuilder.standard()
- .withCredentials(new AWSStaticCredentialsProvider(awsCredentials))
- .withRegion(regions)
- .build();
+ return () -> {
+ S3CrtAsyncClientBuilder crtBuilder = S3AsyncClient.crtBuilder();
+
+ if (credentialsProvider != null) {
+ crtBuilder.credentialsProvider(credentialsProvider);
+ }
+
+ if (region != null) {
+ crtBuilder.region(region);
+ }
+
+ if (maxConcurrency != null) {
+ crtBuilder.maxConcurrency(maxConcurrency);
+ }
+
+ if (StringUtils.isNotBlank(endpoint)) {
+ crtBuilder.endpointOverride(URI.create(endpoint));
+ crtBuilder.forcePathStyle(true);
+ }
+
+ return crtBuilder.targetThroughputInGbps(targetThroughput).minimumPartSizeInBytes(minPartSize).build();
+ };
}
public S3BitStoreService() {}
@@ -154,10 +161,10 @@ public S3BitStoreService() {}
/**
* This constructor is used for test purpose.
*
- * @param s3Service AmazonS3 service
+ * @param s3AsyncClient AmazonS3 service
*/
- protected S3BitStoreService(AmazonS3 s3Service) {
- this.s3Service = s3Service;
+ protected S3BitStoreService(S3AsyncClient s3AsyncClient) {
+ this.s3AsyncClient = s3AsyncClient;
}
@Override
@@ -174,7 +181,6 @@ public boolean isEnabled() {
*/
@Override
public void init() throws IOException {
-
if (this.isInitialized() || !this.isEnabled()) {
return;
}
@@ -183,29 +189,31 @@ public void init() throws IOException {
if (StringUtils.isNotBlank(getAwsAccessKey()) && StringUtils.isNotBlank(getAwsSecretKey())) {
log.warn("Use local defined S3 credentials");
// region
- Regions regions = Regions.DEFAULT_REGION;
+ Region region = Region.US_EAST_1;
if (StringUtils.isNotBlank(awsRegionName)) {
try {
- regions = Regions.fromName(awsRegionName);
+ region = Region.of(awsRegionName);
} catch (IllegalArgumentException e) {
log.warn("Invalid aws_region: " + awsRegionName);
}
}
+
// init client
- s3Service = FunctionalUtils.getDefaultOrBuild(
- this.s3Service,
+ s3AsyncClient = FunctionalUtils.getDefaultOrBuild(
+ this.s3AsyncClient,
amazonClientBuilderBy(
- regions,
- new BasicAWSCredentials(getAwsAccessKey(), getAwsSecretKey())
- )
+ region,
+ StaticCredentialsProvider.create(AwsBasicCredentials.create(getAwsAccessKey(),
+ getAwsSecretKey())), endpoint, targetThroughputGbps,
+ minPartSizeBytes, maxConcurrency)
);
- log.warn("S3 Region set to: " + regions.getName());
+ log.warn("S3 Region set to: " + region.id());
} else {
log.info("Using a IAM role or aws environment credentials");
- s3Service = FunctionalUtils.getDefaultOrBuild(
- this.s3Service,
- AmazonS3ClientBuilder::defaultClient
- );
+ s3AsyncClient = FunctionalUtils.getDefaultOrBuild(
+ this.s3AsyncClient,
+ amazonClientBuilderBy(null, null , endpoint, targetThroughputGbps,
+ minPartSizeBytes, maxConcurrency));
}
// bucket name
@@ -216,13 +224,10 @@ public void init() throws IOException {
log.warn("S3 BucketName is not configured, setting default: " + bucketName);
}
- try {
- if (!s3Service.doesBucketExistV2(bucketName)) {
- s3Service.createBucket(bucketName);
- log.info("Creating new S3 Bucket: " + bucketName);
- }
- } catch (AmazonClientException e) {
- throw new IOException(e);
+
+ if (!doesBucketExist(bucketName)) {
+ s3AsyncClient.createBucket(r -> r.bucket(bucketName)).join();
+ log.info("Creating new S3 Bucket: " + bucketName);
}
this.initialized = true;
log.info("AWS S3 Assetstore ready to go! bucket:" + bucketName);
@@ -230,13 +235,23 @@ public void init() throws IOException {
this.initialized = false;
log.error("Can't initialize this store!", e);
}
+ }
- log.info("AWS S3 Assetstore ready to go! bucket:" + bucketName);
+ /**
+ * @param bucketName
+ * @return whether or not the specified bucket exists
+ */
+ public boolean doesBucketExist(String bucketName ) {
+ try {
+ s3AsyncClient.headBucket(r -> r.bucket(bucketName)).join();
+ return true;
+ } catch (CompletionException ce) {
+ if (!(ce.getCause() instanceof NoSuchBucketException)) {
+ log.error("headBucket(" + bucketName + ")", ce.getCause());
+ }
- tm = FunctionalUtils.getDefaultOrBuild(tm, () -> TransferManagerBuilder.standard()
- .withAlwaysCalculateMultipartMd5(true)
- .withS3Client(s3Service)
- .build());
+ return false;
+ }
}
/**
@@ -264,7 +279,15 @@ public InputStream get(Bitstream bitstream) throws IOException {
if (isRegisteredBitstream(key)) {
key = key.substring(REGISTERED_FLAG.length());
}
- return new S3LazyInputStream(key, bufferSize, bitstream.getSizeBytes());
+
+ final String objectKey = key;
+
+ try {
+ return s3AsyncClient.getObject(r -> r.bucket(bucketName).key(objectKey),
+ AsyncResponseTransformer.toBlockingInputStream()).join();
+ } catch (CompletionException e) {
+ throw new IOException(e.getCause());
+ }
}
/**
@@ -281,44 +304,40 @@ public InputStream get(Bitstream bitstream) throws IOException {
@Override
public void put(Bitstream bitstream, InputStream in) throws IOException {
String key = getFullKey(bitstream.getInternalId());
- //Copy istream to temp file, and send the file, with some metadata
- File scratchFile = File.createTempFile(bitstream.getInternalId(), "s3bs");
- try (
- FileOutputStream fos = new FileOutputStream(scratchFile);
- // Read through a digest input stream that will work out the MD5
- DigestInputStream dis = new DigestInputStream(in, MessageDigest.getInstance(CSA));
- ) {
- Utils.bufferedCopy(dis, fos);
- in.close();
+ ExecutorService executor = Executors.newSingleThreadExecutor();
- Upload upload = tm.upload(bucketName, key, scratchFile);
+ try (DigestInputStream dis = new DigestInputStream(in, MessageDigest.getInstance(CSA))) {
+ AsyncRequestBody body = AsyncRequestBody.fromInputStream(dis, null, executor);
- upload.waitForUploadResult();
+ s3AsyncClient.putObject(b -> b.bucket(bucketName).key(key).checksumAlgorithm(s3ChecksumAlgorithm),
+ body).join();
+
+ bitstream.setSizeBytes(s3AsyncClient.headObject(r -> r.bucket(bucketName).key(key))
+ .join().contentLength());
- bitstream.setSizeBytes(scratchFile.length());
// we cannot use the S3 ETAG here as it could be not a MD5 in case of multipart upload (large files) or if
// the bucket is encrypted
bitstream.setChecksum(Utils.toHex(dis.getMessageDigest().digest()));
bitstream.setChecksumAlgorithm(CSA);
-
- } catch (AmazonClientException | IOException | InterruptedException e) {
+ } catch (CompletionException e) {
+ log.error("put(" + bitstream.getInternalId() + ", is)", e.getCause());
+ throw new IOException(e.getCause());
+ } catch (IOException e) {
log.error("put(" + bitstream.getInternalId() + ", is)", e);
throw new IOException(e);
} catch (NoSuchAlgorithmException nsae) {
// Should never happen
log.warn("Caught NoSuchAlgorithmException", nsae);
} finally {
- if (!scratchFile.delete()) {
- scratchFile.deleteOnExit();
- }
+ executor.shutdown();
+ in.close();
}
}
/**
* Obtain technical metadata about an asset in the asset store.
*
- * Checksum used is (ETag) hex encoded 128-bit MD5 digest of an object's content as calculated by Amazon S3
- * (Does not use getContentMD5, as that is 128-bit MD5 digest calculated on caller's side)
+ * The MD5 checksum is calculated locally because it is not supported by AWS.
*
* @param bitstream The asset to describe
* @param attrs A List of desired metadata fields
@@ -329,7 +348,6 @@ public void put(Bitstream bitstream, InputStream in) throws IOException {
*/
@Override
public Map about(Bitstream bitstream, List attrs) throws IOException {
-
String key = getFullKey(bitstream.getInternalId());
// If this is a registered bitstream, strip the -R prefix before retrieving
if (isRegisteredBitstream(key)) {
@@ -339,20 +357,18 @@ public Map about(Bitstream bitstream, List attrs) throws
Map metadata = new HashMap<>();
try {
+ final String objectKey = key;
+ HeadObjectResponse response = s3AsyncClient.headObject(r -> r.bucket(bucketName).key(objectKey)).join();
- ObjectMetadata objectMetadata = s3Service.getObjectMetadata(bucketName, key);
- if (objectMetadata != null) {
- putValueIfExistsKey(attrs, metadata, "size_bytes", objectMetadata.getContentLength());
- putValueIfExistsKey(attrs, metadata, "modified", valueOf(objectMetadata.getLastModified().getTime()));
- }
-
+ putValueIfExistsKey(attrs, metadata, "size_bytes", response.contentLength());
+ putValueIfExistsKey(attrs, metadata, "modified", valueOf(response.lastModified().toEpochMilli()));
putValueIfExistsKey(attrs, metadata, "checksum_algorithm", CSA);
if (attrs.contains("checksum")) {
try (InputStream in = get(bitstream);
DigestInputStream dis = new DigestInputStream(in, MessageDigest.getInstance(CSA))
) {
- Utils.copy(dis, NullOutputStream.NULL_OUTPUT_STREAM);
+ Utils.copy(dis, NullOutputStream.INSTANCE);
byte[] md5Digest = dis.getMessageDigest().digest();
metadata.put("checksum", Utils.toHex(md5Digest));
} catch (NoSuchAlgorithmException nsae) {
@@ -362,15 +378,15 @@ public Map about(Bitstream bitstream, List attrs) throws
}
return metadata;
- } catch (AmazonS3Exception e) {
- if (e.getStatusCode() == HttpStatus.SC_NOT_FOUND) {
+ } catch (CompletionException e) {
+ if (e.getCause() instanceof AwsServiceException awsEx &&
+ awsEx.statusCode() == HttpStatusCode.NOT_FOUND) {
return metadata;
}
- } catch (AmazonClientException e) {
+
log.error("about(" + key + ", attrs)", e);
throw new IOException(e);
}
- return metadata;
}
/**
@@ -383,10 +399,10 @@ public Map about(Bitstream bitstream, List attrs) throws
public void remove(Bitstream bitstream) throws IOException {
String key = getFullKey(bitstream.getInternalId());
try {
- s3Service.deleteObject(bucketName, key);
- } catch (AmazonClientException e) {
- log.error("remove(" + key + ")", e);
- throw new IOException(e);
+ s3AsyncClient.deleteObject(r -> r.bucket(bucketName).key(key)).join();
+ } catch (CompletionException e) {
+ log.error("remove(" + key + ")", e.getCause());
+ throw new IOException(e.getCause());
}
}
@@ -497,6 +513,46 @@ public void setUseRelativePath(boolean useRelativePath) {
this.useRelativePath = useRelativePath;
}
+ public double getTargetThroughputGbps() {
+ return targetThroughputGbps;
+ }
+
+ public void setTargetThroughputGbps(double targetThroughputGbps) {
+ this.targetThroughputGbps = targetThroughputGbps;
+ }
+
+ public long getMinPartSizeBytes() {
+ return minPartSizeBytes;
+ }
+
+ public void setMinPartSizeBytes(long minPartSizeBytes) {
+ this.minPartSizeBytes = minPartSizeBytes;
+ }
+
+ public ChecksumAlgorithm getS3ChecksumAlgorithm() {
+ return s3ChecksumAlgorithm;
+ }
+
+ public void setS3ChecksumAlgorithm(ChecksumAlgorithm s3ChecksumAlgorithm) {
+ this.s3ChecksumAlgorithm = s3ChecksumAlgorithm;
+ }
+
+ public Integer getMaxConcurrency() {
+ return maxConcurrency;
+ }
+
+ public void setMaxConcurrency(Integer maxConcurrency) {
+ this.maxConcurrency = maxConcurrency;
+ }
+
+ public String getEndpoint() {
+ return endpoint;
+ }
+
+ public void setEndpoint(String endpoint) {
+ this.endpoint = endpoint;
+ }
+
/**
* Contains a command-line testing tool. Expects arguments:
* -a accessKey -s secretKey -f assetFileName
@@ -537,73 +593,18 @@ public static void main(String[] args) throws Exception {
S3BitStoreService store = new S3BitStoreService();
- AWSCredentials awsCredentials = new BasicAWSCredentials(accessKey, secretKey);
-
- store.s3Service = AmazonS3ClientBuilder.standard()
- .withCredentials(new AWSStaticCredentialsProvider(awsCredentials))
- .build();
+ StaticCredentialsProvider credentialsProvider = StaticCredentialsProvider.create(
+ AwsBasicCredentials.create(accessKey, secretKey));
- //Todo configurable region
- Region usEast1 = Region.getRegion(Regions.US_EAST_1);
- store.s3Service.setRegion(usEast1);
+ // Todo configurable region
+ store.s3AsyncClient = S3AsyncClient.builder().credentialsProvider(credentialsProvider).
+ region(Region.US_EAST_1).build();
// get hostname of DSpace UI to use to name bucket
String hostname = Utils.getHostName(configurationService.getProperty("dspace.ui.url"));
//Bucketname should be lowercase
store.bucketName = DEFAULT_BUCKET_PREFIX + hostname + ".s3test";
- store.s3Service.createBucket(store.bucketName);
- /* Broken in DSpace 6 TODO Refactor
- // time everything, todo, swtich to caliper
- long start = System.currentTimeMillis();
- // Case 1: store a file
- String id = store.generateId();
- System.out.print("put() file " + assetFile + " under ID " + id + ": ");
- FileInputStream fis = new FileInputStream(assetFile);
- //TODO create bitstream for assetfile...
- Map attrs = store.put(fis, id);
- long now = System.currentTimeMillis();
- System.out.println((now - start) + " msecs");
- start = now;
- // examine the metadata returned
- Iterator iter = attrs.keySet().iterator();
- System.out.println("Metadata after put():");
- while (iter.hasNext())
- {
- String key = (String)iter.next();
- System.out.println( key + ": " + (String)attrs.get(key) );
- }
- // Case 2: get metadata and compare
- System.out.print("about() file with ID " + id + ": ");
- Map attrs2 = store.about(id, attrs);
- now = System.currentTimeMillis();
- System.out.println((now - start) + " msecs");
- start = now;
- iter = attrs2.keySet().iterator();
- System.out.println("Metadata after about():");
- while (iter.hasNext())
- {
- String key = (String)iter.next();
- System.out.println( key + ": " + (String)attrs.get(key) );
- }
- // Case 3: retrieve asset and compare bits
- System.out.print("get() file with ID " + id + ": ");
- java.io.FileOutputStream fos = new java.io.FileOutputStream(assetFile+".echo");
- InputStream in = store.get(id);
- Utils.bufferedCopy(in, fos);
- fos.close();
- in.close();
- now = System.currentTimeMillis();
- System.out.println((now - start) + " msecs");
- start = now;
- // Case 4: remove asset
- System.out.print("remove() file with ID: " + id + ": ");
- store.remove(id);
- now = System.currentTimeMillis();
- System.out.println((now - start) + " msecs");
- System.out.flush();
- // should get nothing back now - will throw exception
- store.get(id);
-*/
+ store.s3AsyncClient.createBucket(r -> r.bucket(store.bucketName)).join();
}
/**
@@ -614,85 +615,4 @@ public static void main(String[] args) throws Exception {
public boolean isRegisteredBitstream(String internalId) {
return internalId.startsWith(REGISTERED_FLAG);
}
-
- public void setBufferSize(long bufferSize) {
- this.bufferSize = bufferSize;
- }
-
- /**
- * This inner class represent an InputStream that uses temporary files to
- * represent chunk of the object downloaded from S3. When the input stream is
- * read the class look first to the current chunk and download a new one once if
- * the current one as been fully read. The class is responsible to close a chunk
- * as soon as a new one is retrieved, the last chunk is closed when the input
- * stream itself is closed or the last byte is read (the first of the two)
- */
- public class S3LazyInputStream extends InputStream {
- private InputStream currentChunkStream;
- private String objectKey;
- private long endOfChunk = -1;
- private long chunkMaxSize;
- private long currPos = 0;
- private long fileSize;
-
- public S3LazyInputStream(String objectKey, long chunkMaxSize, long fileSize) throws IOException {
- this.objectKey = objectKey;
- this.chunkMaxSize = chunkMaxSize;
- this.endOfChunk = 0;
- this.fileSize = fileSize;
- downloadChunk();
- }
-
- @Override
- public int read() throws IOException {
- // is the current chunk completely read and other are available?
- if (currPos == endOfChunk && currPos < fileSize) {
- currentChunkStream.close();
- downloadChunk();
- }
-
- int byteRead = currPos < endOfChunk ? currentChunkStream.read() : -1;
- // do we get any data or are we at the end of the file?
- if (byteRead != -1) {
- currPos++;
- } else {
- currentChunkStream.close();
- }
- return byteRead;
- }
-
- /**
- * This method download the next chunk from S3
- *
- * @throws IOException
- * @throws FileNotFoundException
- */
- private void downloadChunk() throws IOException, FileNotFoundException {
- // Create a DownloadFileRequest with the desired byte range
- long startByte = currPos; // Start byte (inclusive)
- long endByte = Long.min(startByte + chunkMaxSize - 1, fileSize - 1); // End byte (inclusive)
- GetObjectRequest getRequest = new GetObjectRequest(bucketName, objectKey)
- .withRange(startByte, endByte);
-
- File currentChunkFile = File.createTempFile("s3-disk-copy-" + UUID.randomUUID(), "temp");
- currentChunkFile.deleteOnExit();
- try {
- Download download = tm.download(getRequest, currentChunkFile);
- download.waitForCompletion();
- currentChunkStream = new DeleteOnCloseFileInputStream(currentChunkFile);
- endOfChunk = endOfChunk + download.getProgress().getBytesTransferred();
- } catch (AmazonClientException | InterruptedException e) {
- currentChunkFile.delete();
- throw new IOException(e);
- }
- }
-
- @Override
- public void close() throws IOException {
- if (currentChunkStream != null) {
- currentChunkStream.close();
- }
- }
-
- }
}
diff --git a/dspace-api/src/main/java/org/dspace/subscriptions/SubscriptionEmailNotificationServiceImpl.java b/dspace-api/src/main/java/org/dspace/subscriptions/SubscriptionEmailNotificationServiceImpl.java
index 8fb01cd36e92..c803f1407e05 100644
--- a/dspace-api/src/main/java/org/dspace/subscriptions/SubscriptionEmailNotificationServiceImpl.java
+++ b/dspace-api/src/main/java/org/dspace/subscriptions/SubscriptionEmailNotificationServiceImpl.java
@@ -67,6 +67,7 @@ public SubscriptionEmailNotificationServiceImpl(Map
public void perform(Context context, DSpaceRunnableHandler handler, String subscriptionType, String frequency) {
List communityItems = new ArrayList<>();
List collectionsItems = new ArrayList<>();
+ EPerson currentEperson = context.getCurrentUser();
try {
List subscriptions =
findAllSubscriptionsBySubscriptionTypeAndFrequency(context, subscriptionType, frequency);
@@ -77,7 +78,10 @@ public void perform(Context context, DSpaceRunnableHandler handler, String subsc
for (Subscription subscription : subscriptions) {
DSpaceObject dSpaceObject = subscription.getDSpaceObject();
EPerson ePerson = subscription.getEPerson();
-
+ // Set the current user to the subscribed eperson because the Solr query checks
+ // the permissions of the current user in the ANONYMOUS group.
+ // If there is no user (i.e., `current user = null`), it will send an email with no new items.
+ context.setCurrentUser(ePerson);
if (!authorizeService.authorizeActionBoolean(context, ePerson, dSpaceObject, READ, true)) {
iterator++;
continue;
@@ -126,6 +130,8 @@ public void perform(Context context, DSpaceRunnableHandler handler, String subsc
handler.handleException(e);
context.abort();
}
+ // Reset the current user because it was changed to subscriber eperson
+ context.setCurrentUser(currentEperson);
}
@SuppressWarnings("rawtypes")
diff --git a/dspace-api/src/main/java/org/dspace/text/filter/InitialArticleWord.java b/dspace-api/src/main/java/org/dspace/text/filter/InitialArticleWord.java
deleted file mode 100644
index 167b201e0f7a..000000000000
--- a/dspace-api/src/main/java/org/dspace/text/filter/InitialArticleWord.java
+++ /dev/null
@@ -1,172 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.text.filter;
-
-/**
- * Abstract class for implementing initial article word filters
- * Allows you to create new classes with their own rules for mapping
- * languages to article word lists.
- *
- * @author Graham Triggs
- */
-public abstract class InitialArticleWord implements TextFilter {
- /**
- * When no language is passed, use null and let implementation decide what to do
- */
- @Override
- public String filter(String str) {
- return filter(str, null);
- }
-
- /**
- * Do an initial definite/indefinite article filter on the passed string.
- * On matching an initial word, can strip or move to the end, depending on the
- * configuration of the implementing class.
- *
- * @param str The string to parse
- * @param lang The language of the passed string
- * @return String The filtered string
- */
- @Override
- public String filter(String str, String lang) {
- // Get the list of article words for this language
- String[] articleWordArr = getArticleWords(lang);
-
- // If we have an article word array, process the string
- if (articleWordArr != null && articleWordArr.length > 0) {
- String initialArticleWord = null;
- int curPos = 0;
- int initialStart = -1;
- int initialEnd = -1;
-
- // Iterate through the characters until we find something significant, or hit the end
- while (initialEnd < 0 && curPos < str.length()) {
- // Have we found a significant character
- if (Character.isLetterOrDigit(str.charAt(curPos))) {
- // Mark this as the cut point for the initial word
- initialStart = curPos;
-
- // Loop through the article words looking for a match
- for (int idx = 0; initialEnd < 0 && idx < articleWordArr.length; idx++) {
- // Extract a fragment from the string to test
- // Must be same length as the article word
- if (idx > 1 && initialArticleWord != null) {
- // Only need to do so if we haven't already got one
- // of the right length
- if (initialArticleWord.length() != articleWordArr[idx].length()) {
- initialArticleWord = extractText(str, curPos, articleWordArr[idx].length());
- }
- } else {
- initialArticleWord = extractText(str, curPos, articleWordArr[idx].length());
- }
-
- // Does the fragment match an article word?
- if (initialArticleWord != null && initialArticleWord.equalsIgnoreCase(articleWordArr[idx])) {
- // Check to see if the next character in the source
- // is a whitespace
- boolean isNextWhitespace = Character.isWhitespace(
- str.charAt(curPos + articleWordArr[idx].length())
- );
-
- // Check to see if the last character of the article word is a letter or digit
- boolean endsLetterOrDigit = Character
- .isLetterOrDigit(initialArticleWord.charAt(initialArticleWord.length() - 1));
-
- // If the last character of the article word is a letter or digit,
- // then it must be followed by whitespace, if not, it can be anything
- // Setting endPos signifies that we have found an article word
- if (endsLetterOrDigit && isNextWhitespace) {
- initialEnd = curPos + initialArticleWord.length();
- } else if (!endsLetterOrDigit) {
- initialEnd = curPos + initialArticleWord.length();
- }
- }
- }
-
- // Quit the loop, as we have a significant character
- break;
- }
-
- // Keep going
- curPos++;
- }
-
- // If endPos is positive, then we've found an article word
- if (initialEnd > 0) {
- // Find a cut point in the source string, removing any whitespace after the article word
- int cutPos = initialEnd;
- while (cutPos < str.length() && Character.isWhitespace(str.charAt(cutPos))) {
- cutPos++;
- }
-
- // Are we stripping the article word?
- if (stripInitialArticle) {
- // Yes, simply return everything after the cut
- return str.substring(cutPos);
- } else {
- // No - move the initial article word to the end
- return new StringBuilder(str.substring(cutPos))
- .append(wordSeparator)
- .append(str.substring(initialStart, initialEnd))
- .toString();
- }
- }
- }
-
- // Didn't do any processing, or didn't find an initial article word
- // Return the original string
- return str;
- }
-
- protected InitialArticleWord(boolean stripWord) {
- this.wordSeparator = ", ";
- stripInitialArticle = stripWord;
- }
-
- protected InitialArticleWord() {
- this.wordSeparator = ", ";
- stripInitialArticle = false;
- }
-
- /**
- * Abstract method to get the list of words to use in the initial word filter
- *
- * @param lang The language to retrieve article words for
- * @return An array of definite/indefinite article words
- */
- protected abstract String[] getArticleWords(String lang);
- // Separator to use when appending article to end
- private final String wordSeparator;
-
- // Flag to signify initial article word should be removed
- // If false, then the initial article word is appended to the end
- private boolean stripInitialArticle = false;
-
- /**
- * Helper method to extract text from a string.
- * Ensures that there is significant data (ie. non-whitespace)
- * after the segment requested.
- *
- * @param str
- * @param pos
- * @param len
- * @return
- */
- private String extractText(String str, int pos, int len) {
- int testPos = pos + len;
- while (testPos < str.length() && Character.isWhitespace(str.charAt(testPos))) {
- testPos++;
- }
-
- if (testPos < str.length()) {
- return str.substring(pos, pos + len);
- }
-
- return null;
- }
-}
diff --git a/dspace-api/src/main/java/org/dspace/text/filter/Language.java b/dspace-api/src/main/java/org/dspace/text/filter/Language.java
deleted file mode 100644
index 9be68d2ddfb9..000000000000
--- a/dspace-api/src/main/java/org/dspace/text/filter/Language.java
+++ /dev/null
@@ -1,142 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.text.filter;
-
-import java.util.HashMap;
-import java.util.Map;
-
-/**
- * Define languages - both as IANA and ISO639-2 codes
- *
- * @author Graham Triggs
- */
-public class Language {
- public final String IANA;
- public final String ISO639_1;
- public final String ISO639_2;
-
- public static final Language AFRIKAANS = Language.create("af", "af", "afr");
- public static final Language ALBANIAN = Language.create("sq", "sq", "alb");
- public static final Language ARABIC = Language.create("ar", "ar", "ara");
- public static final Language BALUCHI = Language.create("bal", "", "bal");
- public static final Language BASQUE = Language.create("eu", "", "baq");
- public static final Language BRAHUI = Language.create("", "", "");
- public static final Language CATALAN = Language.create("ca", "ca", "cat");
- public static final Language CLASSICAL_GREEK = Language.create("grc", "", "grc");
- public static final Language DANISH = Language.create("da", "da", "dan");
- public static final Language DUTCH = Language.create("nl", "ni", "dut");
- public static final Language ENGLISH = Language.create("en", "en", "eng");
- public static final Language ESPERANTO = Language.create("eo", "eo", "epo");
- public static final Language FRENCH = Language.create("fr", "fr", "fre");
- public static final Language FRISIAN = Language.create("fy", "fy", "fri");
- public static final Language GALICIAN = Language.create("gl", "gl", "glg");
- public static final Language GERMAN = Language.create("de", "de", "ger");
- public static final Language GREEK = Language.create("el", "el", "gre");
- public static final Language HAWAIIAN = Language.create("haw", "", "haw");
- public static final Language HEBREW = Language.create("he", "he", "heb");
- public static final Language HUNGARIAN = Language.create("hu", "hu", "hun");
- public static final Language ICELANDIC = Language.create("is", "is", "ice");
- public static final Language IRISH = Language.create("ga", "ga", "gle");
- public static final Language ITALIAN = Language.create("it", "it", "ita");
- public static final Language MALAGASY = Language.create("mg", "mg", "mlg");
- public static final Language MALTESE = Language.create("mt", "mt", "mlt");
- public static final Language NEAPOLITAN_ITALIAN = Language.create("nap", "", "nap");
- public static final Language NORWEGIAN = Language.create("no", "no", "nor");
- public static final Language PORTUGUESE = Language.create("pt", "pt", "por");
- public static final Language PANJABI = Language.create("pa", "pa", "pan");
- public static final Language PERSIAN = Language.create("fa", "fa", "per");
- public static final Language PROVENCAL = Language.create("pro", "", "pro");
- public static final Language PROVENCAL_OCCITAN = Language.create("oc", "oc", "oci");
- public static final Language ROMANIAN = Language.create("ro", "ro", "rum");
- public static final Language SCOTS = Language.create("sco", "", "sco");
- public static final Language SCOTTISH_GAELIC = Language.create("gd", "gd", "gae");
- public static final Language SHETLAND_ENGLISH = Language.create("", "", "");
- public static final Language SPANISH = Language.create("es", "es", "spa");
- public static final Language SWEDISH = Language.create("sv", "sv", "swe");
- public static final Language TAGALOG = Language.create("tl", "tl", "tgl");
- public static final Language TURKISH = Language.create("tr", "tr", "tur");
- public static final Language URDU = Language.create("ur", "ur", "urd");
- public static final Language WALLOON = Language.create("wa", "wa", "wln");
- public static final Language WELSH = Language.create("cy", "cy", "wel");
- public static final Language YIDDISH = Language.create("yi", "yi", "yid");
-
- public static Language getLanguage(String lang) {
- return LanguageMaps.getLanguage(lang);
- }
-
- public static Language getLanguageForIANA(String iana) {
- return LanguageMaps.getLanguageForIANA(iana);
- }
-
- public static Language getLanguageForISO639_2(String iso) {
- return LanguageMaps.getLanguageForISO639_2(iso);
- }
-
- private static synchronized Language create(String iana, String iso639_1, String iso639_2) {
- Language lang = LanguageMaps.getLanguageForIANA(iana);
-
- lang = (lang != null ? lang : LanguageMaps.getLanguageForISO639_1(iso639_1));
- lang = (lang != null ? lang : LanguageMaps.getLanguageForISO639_2(iso639_2));
-
- return (lang != null ? lang : new Language(iana, iso639_1, iso639_2));
- }
-
- private static class LanguageMaps {
- private static final Map langMapIANA = new HashMap();
- private static final Map langMapISO639_1 = new HashMap();
- private static final Map langMapISO639_2 = new HashMap();
-
- static void add(Language l) {
- if (l.IANA != null && l.IANA.length() > 0 && !langMapIANA.containsKey(l.IANA)) {
- langMapIANA.put(l.IANA, l);
- }
-
- if (l.ISO639_1 != null && l.ISO639_1.length() > 0 && !langMapISO639_1.containsKey(l.ISO639_1)) {
- langMapISO639_1.put(l.ISO639_1, l);
- }
-
- if (l.ISO639_2 != null && l.ISO639_2.length() > 0 && !langMapISO639_2.containsKey(l.ISO639_2)) {
- langMapISO639_2.put(l.ISO639_2, l);
- }
- }
-
- public static Language getLanguage(String lang) {
- if (langMapIANA.containsKey(lang)) {
- return langMapIANA.get(lang);
- }
-
- return langMapISO639_2.get(lang);
- }
-
- public static Language getLanguageForIANA(String iana) {
- return langMapIANA.get(iana);
- }
-
- public static Language getLanguageForISO639_1(String iso) {
- return langMapISO639_1.get(iso);
- }
-
- public static Language getLanguageForISO639_2(String iso) {
- return langMapISO639_2.get(iso);
- }
- }
-
- private Language(String iana, String iso639_1, String iso639_2) {
- IANA = iana;
- ISO639_1 = iso639_1;
- ISO639_2 = iso639_2;
-
- LanguageMaps.add(this);
- }
-
- private Language() {
- IANA = null;
- ISO639_1 = null;
- ISO639_2 = null;
- }
-}
diff --git a/dspace-api/src/main/java/org/dspace/text/filter/MARC21InitialArticleWord.java b/dspace-api/src/main/java/org/dspace/text/filter/MARC21InitialArticleWord.java
deleted file mode 100644
index c82b9ccfcf83..000000000000
--- a/dspace-api/src/main/java/org/dspace/text/filter/MARC21InitialArticleWord.java
+++ /dev/null
@@ -1,329 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.text.filter;
-
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Comparator;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import org.apache.commons.lang3.ArrayUtils;
-import org.apache.commons.lang3.StringUtils;
-import org.dspace.services.factory.DSpaceServicesFactory;
-
-/**
- * Implements MARC 21 standards to disregard initial
- * definite or indefinite article in sorting.
- *
- * Note: This only works for languages defined with IANA code entries.
- *
- * @author Graham Triggs
- */
-public class MARC21InitialArticleWord extends InitialArticleWord {
- public MARC21InitialArticleWord() {
- // Default behaviour is to strip the initial word completely
- super(true);
- }
-
- public MARC21InitialArticleWord(boolean stripWord) {
- super(stripWord);
- }
-
- /**
- * Return the list of definite and indefinite article codes
- * for this language.
- */
- @Override
- protected String[] getArticleWords(String lang) {
- // No language - no words
- if (StringUtils.isEmpty(lang)) {
- return defaultWords;
- }
-
- Language l = Language.getLanguage(lang);
-
- // Is the language in our map?
- if (l != null && ianaArticleMap.containsKey(l.IANA)) {
- // Get the list of words for this language
- ArticlesForLang articles = ianaArticleMap.get(l.IANA);
-
- if (articles != null) {
- return articles.words;
- }
- }
-
- return null;
- }
-
- // Mapping of IANA codes to article word lists
- private static Map ianaArticleMap = new HashMap();
-
- private static String[] defaultWords = null;
-
- // Static initialisation - convert word -> languages map
- // into language -> words map
- static {
- /* Define a mapping for article words to the languages that have them.
- * Take from: http://www.loc.gov/marc/bibliographic/bdapp-e.html
- */
- Object[][] articleWordArray = {
- {"a", Language.ENGLISH, Language.GALICIAN, Language.HUNGARIAN, Language.PORTUGUESE, Language.ROMANIAN,
- Language.SCOTS, Language.YIDDISH},
- {"a'", Language.SCOTTISH_GAELIC},
- {"al", Language.ROMANIAN},
- {"al-", Language.ARABIC, Language.BALUCHI, Language.BRAHUI, Language.PANJABI, Language.PERSIAN,
- Language.TURKISH, Language.URDU},
- {"am", Language.SCOTTISH_GAELIC},
- {"an", Language.ENGLISH, Language.IRISH, Language.SCOTS, Language.SCOTTISH_GAELIC, Language.YIDDISH},
- {"an t-", Language.IRISH, Language.SCOTTISH_GAELIC},
- {"ane", Language.SCOTS},
- {"ang", Language.TAGALOG},
- {"ang mga", Language.TAGALOG},
- {"as", Language.GALICIAN, Language.PORTUGUESE},
- {"az", Language.HUNGARIAN},
- {"bat", Language.BASQUE},
- {"bir", Language.TURKISH},
- {"d'", Language.ENGLISH},
- {"da", Language.SHETLAND_ENGLISH},
- {"das", Language.GERMAN},
- {"de", Language.DANISH, Language.DUTCH, Language.ENGLISH, Language.FRISIAN, Language.NORWEGIAN,
- Language.SWEDISH},
- {"dei", Language.NORWEGIAN},
- {"dem", Language.GERMAN},
- {"den", Language.DANISH, Language.GERMAN, Language.NORWEGIAN, Language.SWEDISH},
- {"der", Language.GERMAN, Language.YIDDISH},
- {"des", Language.GERMAN, Language.WALLOON},
- {"det", Language.DANISH, Language.NORWEGIAN, Language.SWEDISH},
- {"di", Language.YIDDISH},
- {"die", Language.AFRIKAANS, Language.GERMAN, Language.YIDDISH},
- {"dos", Language.YIDDISH},
- {"e", Language.NORWEGIAN},
- {"e", Language.FRISIAN}, // should be 'e - leading apostrophes are ignored
- {"een", Language.DUTCH},
- {"eene", Language.DUTCH},
- {"egy", Language.HUNGARIAN},
- {"ei", Language.NORWEGIAN},
- {"ein", Language.GERMAN, Language.NORWEGIAN, Language.WALLOON},
- {"eine", Language.GERMAN},
- {"einem", Language.GERMAN},
- {"einen", Language.GERMAN},
- {"einer", Language.GERMAN},
- {"eines", Language.GERMAN},
- {"eit", Language.NORWEGIAN},
- {"el", Language.CATALAN, Language.SPANISH},
- {"el-", Language.ARABIC},
- {"els", Language.CATALAN},
- {"en", Language.CATALAN, Language.DANISH, Language.NORWEGIAN, Language.SWEDISH},
- {"enne", Language.WALLOON},
- {"et", Language.DANISH, Language.NORWEGIAN},
- {"ett", Language.SWEDISH},
- {"eyn", Language.YIDDISH},
- {"eyne", Language.YIDDISH},
- {"gl'", Language.ITALIAN},
- {"gli", Language.PROVENCAL},
- {"ha-", Language.HEBREW},
- {"hai", Language.CLASSICAL_GREEK, Language.GREEK},
- {"he", Language.HAWAIIAN},
- {"h\u0113", Language.CLASSICAL_GREEK, Language.GREEK}, // e macron
- {"he-", Language.HEBREW},
- {"heis", Language.GREEK},
- {"hen", Language.GREEK},
- {"hena", Language.GREEK},
- {"henas", Language.GREEK},
- {"het", Language.DUTCH},
- {"hin", Language.ICELANDIC},
- {"hina", Language.ICELANDIC},
- {"hinar", Language.ICELANDIC},
- {"hinir", Language.ICELANDIC},
- {"hinn", Language.ICELANDIC},
- {"hinna", Language.ICELANDIC},
- {"hinnar", Language.ICELANDIC},
- {"hinni", Language.ICELANDIC},
- {"hins", Language.ICELANDIC},
- {"hinu", Language.ICELANDIC},
- {"hinum", Language.ICELANDIC},
- {"hi\u01d2", Language.ICELANDIC},
- {"ho", Language.CLASSICAL_GREEK, Language.GREEK},
- {"hoi", Language.CLASSICAL_GREEK, Language.GREEK},
- {"i", Language.ITALIAN},
- {"ih'", Language.PROVENCAL},
- {"il", Language.ITALIAN, Language.PROVENCAL_OCCITAN},
- {"il-", Language.MALTESE},
- {"in", Language.FRISIAN},
- {"it", Language.FRISIAN},
- {"ka", Language.HAWAIIAN},
- {"ke", Language.HAWAIIAN},
- {"l'", Language.CATALAN, Language.FRENCH, Language.ITALIAN, Language.PROVENCAL_OCCITAN, Language.WALLOON},
- {"l-", Language.MALTESE},
- {"la", Language.CATALAN, Language.ESPERANTO, Language.FRENCH, Language.ITALIAN, Language.PROVENCAL_OCCITAN,
- Language.SPANISH},
- {"las", Language.PROVENCAL_OCCITAN, Language.SPANISH},
- {"le", Language.FRENCH, Language.ITALIAN, Language.PROVENCAL_OCCITAN},
- {"les", Language.CATALAN, Language.FRENCH, Language.PROVENCAL_OCCITAN, Language.WALLOON},
- {"lh", Language.PROVENCAL_OCCITAN},
- {"lhi", Language.PROVENCAL_OCCITAN},
- {"li", Language.PROVENCAL_OCCITAN},
- {"lis", Language.PROVENCAL_OCCITAN},
- {"lo", Language.ITALIAN, Language.PROVENCAL_OCCITAN, Language.SPANISH},
- {"los", Language.PROVENCAL_OCCITAN, Language.SPANISH},
- {"lou", Language.PROVENCAL_OCCITAN},
- {"lu", Language.PROVENCAL_OCCITAN},
- {"mga", Language.TAGALOG},
- {"m\u0303ga", Language.TAGALOG},
- {"mia", Language.GREEK},
- {"n", Language.AFRIKAANS, Language.DUTCH, Language.FRISIAN}, // should be 'n - leading
- // apostrophes are ignored
- {"na", Language.HAWAIIAN, Language.IRISH, Language.SCOTTISH_GAELIC},
- {"na h-", Language.IRISH, Language.SCOTTISH_GAELIC},
- {"nje", Language.ALBANIAN},
- {"ny", Language.MALAGASY},
- {"o", Language.NEAPOLITAN_ITALIAN}, // should be 'o - leading apostrophes are ignored
- {"o", Language.GALICIAN, Language.HAWAIIAN, Language.PORTUGUESE, Language.ROMANIAN},
- {"os", Language.PORTUGUESE},
- {"r", Language.ICELANDIC}, // should be 'r - leading apostrophes are ignored
- {"s", Language.GERMAN}, // should be 's - leading apostrophes are ignored
- {"sa", Language.TAGALOG},
- {"sa mga", Language.TAGALOG},
- {"si", Language.TAGALOG},
- {"sin\u00e1", Language.TAGALOG},
- {"t", Language.DUTCH, Language.FRISIAN}, // should be 't - leading apostrophes are ignored
- {"ta", Language.CLASSICAL_GREEK, Language.GREEK},
- {"tais", Language.CLASSICAL_GREEK},
- {"tas", Language.CLASSICAL_GREEK},
- {"t\u0113", Language.CLASSICAL_GREEK}, // e macron
- {"t\u0113n", Language.CLASSICAL_GREEK, Language.GREEK}, // e macron
- {"t\u0113s", Language.CLASSICAL_GREEK, Language.GREEK}, // e macron
- {"the", Language.ENGLISH},
- {"t\u014d", Language.CLASSICAL_GREEK, Language.GREEK}, // o macron
- {"tois", Language.CLASSICAL_GREEK},
- {"t\u014dn", Language.CLASSICAL_GREEK, Language.GREEK}, // o macron
- {"tou", Language.CLASSICAL_GREEK, Language.GREEK},
- {"um", Language.PORTUGUESE},
- {"uma", Language.PORTUGUESE},
- {"un", Language.CATALAN, Language.FRENCH, Language.ITALIAN, Language.PROVENCAL_OCCITAN, Language.ROMANIAN,
- Language.SPANISH},
- {"un'", Language.ITALIAN},
- {"una", Language.CATALAN, Language.ITALIAN, Language.PROVENCAL_OCCITAN, Language.SPANISH},
- {"une", Language.FRENCH},
- {"unei", Language.ROMANIAN},
- {"unha", Language.GALICIAN},
- {"uno", Language.ITALIAN, Language.PROVENCAL_OCCITAN},
- {"uns", Language.PROVENCAL_OCCITAN},
- {"unui", Language.ROMANIAN},
- {"us", Language.PROVENCAL_OCCITAN},
- {"y", Language.WELSH},
- {"ye", Language.ENGLISH},
- {"yr", Language.WELSH}
- };
-
- // Initialize the lang -> article map
- ianaArticleMap = new HashMap();
-
- int wordIdx = 0;
- int langIdx = 0;
-
- // Iterate through word/language array
- // Generate temporary language map
- Map> langWordMap = new HashMap>();
- for (wordIdx = 0; wordIdx < articleWordArray.length; wordIdx++) {
- for (langIdx = 1; langIdx < articleWordArray[wordIdx].length; langIdx++) {
- Language lang = (Language) articleWordArray[wordIdx][langIdx];
-
- if (lang != null && lang.IANA.length() > 0) {
- List words = langWordMap.get(lang);
-
- if (words == null) {
- words = new ArrayList();
- langWordMap.put(lang, words);
- }
-
- // Add language to list if we haven't done so already
- if (!words.contains(articleWordArray[wordIdx][0])) {
- words.add((String) articleWordArray[wordIdx][0]);
- }
- }
- }
- }
-
- // Iterate through languages
- for (Map.Entry> langToWord : langWordMap.entrySet()) {
- Language lang = langToWord.getKey();
- List wordList = langToWord.getValue();
-
- // Convert the list into an array of strings
- String[] words = new String[wordList.size()];
-
- for (int idx = 0; idx < wordList.size(); idx++) {
- words[idx] = wordList.get(idx);
- }
-
- // Sort the array into length order - longest to shortest
- // This ensures maximal matching on the article words
- Arrays.sort(words, new MARC21InitialArticleWord.InverseLengthComparator());
-
- // Add language/article entry to map
- ianaArticleMap.put(lang.IANA, new MARC21InitialArticleWord.ArticlesForLang(lang, words));
- }
-
- // Setup default stop words for null languages
- String[] defaultLangs = DSpaceServicesFactory.getInstance().getConfigurationService()
- .getArrayProperty("marc21wordfilter.defaultlang");
- if (ArrayUtils.isNotEmpty(defaultLangs)) {
- int wordCount = 0;
- ArticlesForLang[] afl = new ArticlesForLang[defaultLangs.length];
-
- for (int idx = 0; idx < afl.length; idx++) {
- Language l = Language.getLanguage(defaultLangs[idx]);
- if (l != null && ianaArticleMap.containsKey(l.IANA)) {
- afl[idx] = ianaArticleMap.get(l.IANA);
- if (afl[idx] != null) {
- wordCount += afl[idx].words.length;
- }
- }
- }
-
- if (wordCount > 0) {
- int destPos = 0;
- defaultWords = new String[wordCount];
- for (int idx = 0; idx < afl.length; idx++) {
- if (afl[idx] != null) {
- System.arraycopy(afl[idx].words, 0, defaultWords, destPos, afl[idx].words.length);
- destPos += afl[idx].words.length;
- }
- }
- }
- }
- }
-
- // Wrapper class for inserting word arrays into a map
- private static class ArticlesForLang {
- final Language lang;
- final String[] words;
-
- ArticlesForLang(Language lang, String[] words) {
- this.lang = lang;
- this.words = (String[]) ArrayUtils.clone(words);
- }
- }
-
- // Compare strings according to their length - longest to shortest
- private static class InverseLengthComparator implements Comparator, Serializable {
- @Override
- public int compare(Object arg0, Object arg1) {
- return ((String) arg1).length() - ((String) arg0).length();
- }
-
- ;
-
- }
-
- ;
-}
diff --git a/dspace-api/src/main/java/org/dspace/text/filter/StandardInitialArticleWord.java b/dspace-api/src/main/java/org/dspace/text/filter/StandardInitialArticleWord.java
deleted file mode 100644
index ade72b150f5c..000000000000
--- a/dspace-api/src/main/java/org/dspace/text/filter/StandardInitialArticleWord.java
+++ /dev/null
@@ -1,30 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.text.filter;
-
-/**
- * Implements existing DSpace initial article word behaviour
- *
- * Note: This only works for languages defined with ISO code entries.
- *
- * @author Graham Triggs
- */
-public class StandardInitialArticleWord extends InitialArticleWord {
- private static final String[] articleWords = {"the", "an", "a"};
-
- @Override
- protected String[] getArticleWords(String lang) {
- if (lang != null && lang.startsWith("en")) {
- return articleWords;
- }
-
- return null;
- }
-
-}
-
diff --git a/dspace-api/src/main/java/org/dspace/util/DateMathParser.java b/dspace-api/src/main/java/org/dspace/util/DateMathParser.java
index 9ff252e8ce3f..13f9216c9bdb 100644
--- a/dspace-api/src/main/java/org/dspace/util/DateMathParser.java
+++ b/dspace-api/src/main/java/org/dspace/util/DateMathParser.java
@@ -13,6 +13,7 @@
import java.time.LocalDateTime;
import java.time.LocalTime;
import java.time.ZoneId;
+import java.time.ZoneOffset;
import java.time.ZonedDateTime;
import java.time.format.DateTimeFormatter;
import java.time.format.DateTimeFormatterBuilder;
@@ -107,7 +108,7 @@ public class DateMathParser {
private static final Logger LOG = LogManager.getLogger();
- public static final TimeZone UTC = TimeZone.getTimeZone("UTC");
+ public static final TimeZone UTC = TimeZone.getTimeZone(ZoneOffset.UTC);
/**
* Default TimeZone for DateMath rounding (UTC)
diff --git a/dspace-api/src/main/resources/Messages.properties b/dspace-api/src/main/resources/Messages.properties
index efbbeedde053..9d15bd0621a8 100644
--- a/dspace-api/src/main/resources/Messages.properties
+++ b/dspace-api/src/main/resources/Messages.properties
@@ -72,20 +72,20 @@ org.dspace.checker.ResultsLogger.store-number
org.dspace.checker.ResultsLogger.to-be-processed = To be processed
org.dspace.checker.ResultsLogger.user-format-description = User format description
org.dspace.checker.SimpleReporterImpl.bitstream-id = Bitstream Id
-org.dspace.checker.SimpleReporterImpl.bitstream-not-found-report = The following is a BITSTREAM NOT FOUND report for
-org.dspace.checker.SimpleReporterImpl.bitstream-will-no-longer-be-processed = The following is a BITSTREAM WILL NO LONGER BE PROCESSED report for
+org.dspace.checker.SimpleReporterImpl.bitstream-not-found-report = The following is a BITSTREAM NOT FOUND report from
+org.dspace.checker.SimpleReporterImpl.bitstream-will-no-longer-be-processed = The following is a BITSTREAM WILL NO LONGER BE PROCESSED report from
org.dspace.checker.SimpleReporterImpl.check-id = Check Id
org.dspace.checker.SimpleReporterImpl.checksum = Checksum
org.dspace.checker.SimpleReporterImpl.checksum-algorithm = Checksum Algorithm
org.dspace.checker.SimpleReporterImpl.checksum-calculated = Checksum Calculated
-org.dspace.checker.SimpleReporterImpl.checksum-did-not-match = The following is a CHECKSUM DID NOT MATCH report for
+org.dspace.checker.SimpleReporterImpl.checksum-did-not-match = The following is a CHECKSUM DID NOT MATCH report from
org.dspace.checker.SimpleReporterImpl.checksum-expected = Checksum Expected
org.dspace.checker.SimpleReporterImpl.date-range-to = to
org.dspace.checker.SimpleReporterImpl.deleted = Deleted
-org.dspace.checker.SimpleReporterImpl.deleted-bitstream-intro = The following is a BITSTREAM SET DELETED report for
+org.dspace.checker.SimpleReporterImpl.deleted-bitstream-intro = The following is a BITSTREAM SET DELETED report from
org.dspace.checker.SimpleReporterImpl.description = Description
org.dspace.checker.SimpleReporterImpl.format-id = Format Id
-org.dspace.checker.SimpleReporterImpl.howto-add-unchecked-bitstreams = To add these bitstreams to be checked run the checksum checker with the -u option
+org.dspace.checker.SimpleReporterImpl.howto-add-unchecked-bitstreams = To add these bitstreams to be checked run the checksum checker again
org.dspace.checker.SimpleReporterImpl.internal-id = Internal Id
org.dspace.checker.SimpleReporterImpl.name = Name
org.dspace.checker.SimpleReporterImpl.no-bitstreams-changed = There were no bitstreams found with changed checksums
diff --git a/dspace-api/src/main/resources/org/dspace/storage/rdbms/sqlmigration/postgres/V7.6_2025.10.29__Fix-request-items-with-deleted-bitstreams.sql b/dspace-api/src/main/resources/org/dspace/storage/rdbms/sqlmigration/postgres/V7.6_2025.10.29__Fix-request-items-with-deleted-bitstreams.sql
new file mode 100644
index 000000000000..4f0c54c975c6
--- /dev/null
+++ b/dspace-api/src/main/resources/org/dspace/storage/rdbms/sqlmigration/postgres/V7.6_2025.10.29__Fix-request-items-with-deleted-bitstreams.sql
@@ -0,0 +1,14 @@
+--
+-- 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/
+--
+
+DELETE
+FROM requestitem
+WHERE bitstream_id IN
+ (SELECT bs.uuid
+ FROM bitstream AS bs
+ WHERE bs.deleted IS TRUE)
diff --git a/dspace-api/src/main/resources/spring/spring-dspace-addon-import-services.xml b/dspace-api/src/main/resources/spring/spring-dspace-addon-import-services.xml
index e693d26e538e..5cfef3bd22fb 100644
--- a/dspace-api/src/main/resources/spring/spring-dspace-addon-import-services.xml
+++ b/dspace-api/src/main/resources/spring/spring-dspace-addon-import-services.xml
@@ -70,6 +70,7 @@
+
diff --git a/dspace-api/src/test/data/dspaceFolder/config/spring/api/workflow-actions.xml b/dspace-api/src/test/data/dspaceFolder/config/spring/api/workflow-actions.xml
index 0d074362279e..a7c725c524fe 100644
--- a/dspace-api/src/test/data/dspaceFolder/config/spring/api/workflow-actions.xml
+++ b/dspace-api/src/test/data/dspaceFolder/config/spring/api/workflow-actions.xml
@@ -23,7 +23,6 @@
-
@@ -46,7 +45,6 @@
-
@@ -66,21 +64,14 @@
-
-
-
-
-
-
-
+
-
-
+
diff --git a/dspace-api/src/test/java/org/dspace/AbstractDSpaceIntegrationTest.java b/dspace-api/src/test/java/org/dspace/AbstractDSpaceIntegrationTest.java
index 791fdbc66abc..2822cdcf6018 100644
--- a/dspace-api/src/test/java/org/dspace/AbstractDSpaceIntegrationTest.java
+++ b/dspace-api/src/test/java/org/dspace/AbstractDSpaceIntegrationTest.java
@@ -12,6 +12,7 @@
import java.io.IOException;
import java.net.URL;
import java.sql.SQLException;
+import java.time.ZoneOffset;
import java.util.Properties;
import java.util.TimeZone;
@@ -73,8 +74,10 @@ public static void initTestEnvironment() {
//Stops System.exit(0) throws exception instead of exitting
System.setSecurityManager(new NoExitSecurityManager());
- //set a standard time zone for the tests
- TimeZone.setDefault(TimeZone.getTimeZone("Europe/Dublin"));
+ // All tests should assume UTC timezone by default (unless overridden in the test itself)
+ // This ensures that Spring doesn't attempt to change the timezone of dates that are read from the
+ // database (via Hibernate). We store all dates in the database as UTC.
+ TimeZone.setDefault(TimeZone.getTimeZone(ZoneOffset.UTC));
//load the properties of the tests
testProps = new Properties();
diff --git a/dspace-api/src/test/java/org/dspace/AbstractDSpaceTest.java b/dspace-api/src/test/java/org/dspace/AbstractDSpaceTest.java
index 136af83f076f..4452955a3b64 100644
--- a/dspace-api/src/test/java/org/dspace/AbstractDSpaceTest.java
+++ b/dspace-api/src/test/java/org/dspace/AbstractDSpaceTest.java
@@ -12,6 +12,7 @@
import java.io.IOException;
import java.net.URL;
import java.sql.SQLException;
+import java.time.ZoneOffset;
import java.util.Properties;
import java.util.TimeZone;
@@ -82,8 +83,10 @@ protected AbstractDSpaceTest() { }
@BeforeClass
public static void initKernel() {
try {
- //set a standard time zone for the tests
- TimeZone.setDefault(TimeZone.getTimeZone("Europe/Dublin"));
+ // All tests should assume UTC timezone by default (unless overridden in the test itself)
+ // This ensures that Spring doesn't attempt to change the timezone of dates that are read from the
+ // database (via Hibernate). We store all dates in the database as UTC.
+ TimeZone.setDefault(TimeZone.getTimeZone(ZoneOffset.UTC));
//load the properties of the tests
testProps = new Properties();
diff --git a/dspace-api/src/test/java/org/dspace/app/bulkedit/MetadataExportSearchIT.java b/dspace-api/src/test/java/org/dspace/app/bulkedit/MetadataExportSearchIT.java
index 63a87a48f554..15a6371e920b 100644
--- a/dspace-api/src/test/java/org/dspace/app/bulkedit/MetadataExportSearchIT.java
+++ b/dspace-api/src/test/java/org/dspace/app/bulkedit/MetadataExportSearchIT.java
@@ -251,4 +251,35 @@ public void exportMetadataSearchNonExistinFacetsTest() throws Exception {
assertNotNull(exception);
assertEquals("nonExisting is not a valid search filter", exception.getMessage());
}
+
+ @Test
+ public void exportMetadataSearchDoubleQuotedArgumentTest() throws Exception {
+ context.turnOffAuthorisationSystem();
+ Item quotedItem1 = ItemBuilder.createItem(context, collection)
+ .withTitle("The Special Runnable Item")
+ .withSubject("quoted-subject")
+ .build();
+ Item quotedItem2 = ItemBuilder.createItem(context, collection)
+ .withTitle("The Special Item")
+ .withSubject("quoted-subject")
+ .build();
+ context.restoreAuthSystemState();
+
+ int result = runDSpaceScript(
+ "metadata-export-search",
+ "-q", "title:\"Special Runnable\"",
+ "-n", filename);
+
+ assertEquals(0, result);
+
+ Item[] expectedResult = new Item[] {quotedItem1};
+ checkItemsPresentInFile(filename, expectedResult);
+
+ File file = new File(filename);
+ try (Reader reader = Files.newReader(file, Charset.defaultCharset());
+ CSVReader csvReader = new CSVReader(reader)) {
+ List lines = csvReader.readAll();
+ assertEquals("Unexpected extra items in export", 2, lines.size());
+ }
+ }
}
diff --git a/dspace-api/src/test/java/org/dspace/app/client/DSpaceHttpClientFactoryTest.java b/dspace-api/src/test/java/org/dspace/app/client/DSpaceHttpClientFactoryTest.java
index b518f19ff4d3..ca91bb5dc9ce 100644
--- a/dspace-api/src/test/java/org/dspace/app/client/DSpaceHttpClientFactoryTest.java
+++ b/dspace-api/src/test/java/org/dspace/app/client/DSpaceHttpClientFactoryTest.java
@@ -17,6 +17,7 @@
import static org.mockito.Mockito.verifyNoMoreInteractions;
import static org.mockito.Mockito.when;
+import java.net.InetAddress;
import java.util.List;
import java.util.concurrent.TimeUnit;
import java.util.concurrent.atomic.AtomicReference;
@@ -107,7 +108,14 @@ public void testBuildWithProxyConfiguredAndHostToIgnoreSet() throws Exception {
@Test
public void testBuildWithProxyConfiguredAndHostPrefixToIgnoreSet() throws Exception {
- setHttpProxyOnConfigurationService("local*", "www.test.com");
+ // Get hostname assigned to 127.0.0.1 (usually is "localhost", but not always)
+ InetAddress address = InetAddress.getByAddress(new byte[]{127, 0, 0, 1});
+ String hostname = address.getHostName();
+ // Take first 4 characters hostname as the prefix (e.g. "loca" in "localhost")
+ String hostnamePrefix = hostname.substring(0, 4);
+ // Save hostname prefix to our list of hosts to ignore, followed by an asterisk.
+ // (This should result in our Proxy ignoring our localhost)
+ setHttpProxyOnConfigurationService(hostnamePrefix + "*", "www.test.com");
CloseableHttpClient httpClient = httpClientFactory.build();
assertThat(mockProxy.getRequestCount(), is(0));
assertThat(mockServer.getRequestCount(), is(0));
@@ -122,7 +130,14 @@ public void testBuildWithProxyConfiguredAndHostPrefixToIgnoreSet() throws Except
@Test
public void testBuildWithProxyConfiguredAndHostSuffixToIgnoreSet() throws Exception {
- setHttpProxyOnConfigurationService("www.test.com", "*host");
+ // Get hostname assigned to 127.0.0.1 (usually is "localhost", but not always)
+ InetAddress address = InetAddress.getByAddress(new byte[]{127, 0, 0, 1});
+ String hostname = address.getHostName();
+ // Take last 4 characters hostname as the suffix (e.g. "host" in "localhost")
+ String hostnameSuffix = hostname.substring(hostname.length() - 4);
+ // Save hostname suffix to our list of hosts to ignore, preceded by an asterisk.
+ // (This should result in our Proxy ignoring our localhost)
+ setHttpProxyOnConfigurationService("www.test.com", "*" + hostnameSuffix);
CloseableHttpClient httpClient = httpClientFactory.build();
assertThat(mockProxy.getRequestCount(), is(0));
assertThat(mockServer.getRequestCount(), is(0));
diff --git a/dspace-api/src/test/java/org/dspace/app/mediafilter/JPEGFilterTest.java b/dspace-api/src/test/java/org/dspace/app/mediafilter/JPEGFilterTest.java
new file mode 100644
index 000000000000..1181dc7a60f0
--- /dev/null
+++ b/dspace-api/src/test/java/org/dspace/app/mediafilter/JPEGFilterTest.java
@@ -0,0 +1,270 @@
+/**
+ * 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.assertEquals;
+import static org.junit.Assert.assertNotEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertSame;
+
+import java.awt.RenderingHints;
+import java.awt.image.BufferedImage;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.net.URL;
+
+import org.dspace.AbstractUnitTest;
+import org.dspace.content.Item;
+import org.dspace.services.ConfigurationService;
+import org.dspace.services.factory.DSpaceServicesFactory;
+import org.junit.Test;
+import org.mockito.Mock;
+
+public class JPEGFilterTest extends AbstractUnitTest {
+
+ @Mock
+ private ConfigurationService mockConfigurationService;
+
+ @Mock
+ private DSpaceServicesFactory mockDSpaceServicesFactory;
+
+ @Mock
+ private InputStream mockInputStream;
+
+ @Mock
+ private Item mockItem;
+
+ /**
+ * Tests that the convertRotationToDegrees method returns 0 for an input value
+ * that doesn't match any of the defined rotation cases.
+ */
+ @Test
+ public void testConvertRotationToDegrees_UnknownValue_ReturnsZero() {
+ int result = JPEGFilter.convertRotationToDegrees(5);
+ assertEquals(0, result);
+ }
+
+ /**
+ * Test getNormalizedInstance method with a null input.
+ * This tests the edge case of passing a null BufferedImage to the method.
+ * The method should throw a NullPointerException when given a null input.
+ */
+ @Test(expected = NullPointerException.class)
+ public void testGetNormalizedInstanceWithNullInput() {
+ JPEGFilter filter = new JPEGFilter();
+ filter.getNormalizedInstance(null);
+ }
+
+ /**
+ * Test getThumbDim method with a null BufferedImage input.
+ * This tests the edge case where the input image is null, which should result in an exception.
+ */
+ @Test(expected = NullPointerException.class)
+ public void testGetThumbDimWithNullBufferedImage() throws Exception {
+ JPEGFilter filter = new JPEGFilter();
+ Item currentItem = null;
+ BufferedImage buf = null;
+ boolean verbose = false;
+ int xmax = 100;
+ int ymax = 100;
+ boolean blurring = false;
+ boolean hqscaling = false;
+ int brandHeight = 0;
+ int brandFontPoint = 0;
+ int rotation = 0;
+ String brandFont = null;
+
+ filter.getThumbDim(
+ currentItem, buf, verbose, xmax, ymax, blurring, hqscaling,
+ brandHeight, brandFontPoint, rotation, brandFont
+ );
+ }
+
+ /**
+ * Tests that the rotateImage method returns the original image when the rotation angle is 0.
+ * This is an edge case explicitly handled in the method implementation.
+ */
+ @Test
+ public void testRotateImageWithZeroAngle() {
+ BufferedImage originalImage = new BufferedImage(100, 100, BufferedImage.TYPE_INT_RGB);
+ BufferedImage rotatedImage = JPEGFilter.rotateImage(originalImage, 0);
+ assertSame(
+ "When rotation angle is 0, the original image should be returned",
+ originalImage, rotatedImage
+ );
+ }
+
+ /**
+ * Test case for convertRotationToDegrees method when input is 6.
+ * Expected to return 90 degrees for the rotation value of 6.
+ */
+ @Test
+ public void test_convertRotationToDegrees_whenInputIs6_returns90() {
+ int input = 6;
+ int expected = 90;
+ int result = JPEGFilter.convertRotationToDegrees(input);
+ assertEquals(expected, result);
+ }
+
+ /**
+ * Tests that getBlurredInstance method applies a blur effect to the input image.
+ * It verifies that the returned image is not null, has the same dimensions as the input,
+ * and is different from the original image (indicating that blurring has occurred).
+ */
+ @Test
+ public void test_getBlurredInstance_appliesBlurEffect() {
+ JPEGFilter filter = new JPEGFilter();
+ BufferedImage original = new BufferedImage(100, 100, BufferedImage.TYPE_INT_RGB);
+
+ BufferedImage blurred = filter.getBlurredInstance(original);
+
+ assertNotNull("Blurred image should not be null", blurred);
+ assertEquals("Width should be the same", original.getWidth(), blurred.getWidth());
+ assertEquals("Height should be the same", original.getHeight(), blurred.getHeight());
+ assertNotEquals("Blurred image should be different from original", original, blurred);
+ }
+
+ /**
+ * Test case for getBundleName method of JPEGFilter class.
+ * This test verifies that the getBundleName method returns the expected string "THUMBNAIL".
+ */
+ @Test
+ public void test_getBundleName_returnsExpectedString() {
+ JPEGFilter filter = new JPEGFilter();
+ String result = filter.getBundleName();
+ assertEquals("THUMBNAIL", result);
+ }
+
+ /**
+ * Tests that the getDescription method returns the expected string "Generated Thumbnail".
+ * This verifies that the method correctly provides the description for the JPEG filter.
+ */
+ @Test
+ public void test_getDescription_1() {
+ JPEGFilter filter = new JPEGFilter();
+ String description = filter.getDescription();
+ assertEquals("Generated Thumbnail", description);
+ }
+
+ /**
+ * Tests that getFilteredName method appends ".jpg" to the input filename.
+ */
+ @Test
+ public void test_getFilteredName_appendsJpgExtension() {
+ JPEGFilter filter = new JPEGFilter();
+ String oldFilename = "testimage";
+ String expectedResult = "testimage.jpg";
+ String actualResult = filter.getFilteredName(oldFilename);
+ assertEquals(expectedResult, actualResult);
+ }
+
+ /**
+ * Test case for getFormatString method of JPEGFilter class.
+ * Verifies that the method returns the expected string "JPEG".
+ */
+ @Test
+ public void test_getFormatString_returnsJPEG() {
+ JPEGFilter filter = new JPEGFilter();
+ String result = filter.getFormatString();
+ assertEquals("JPEG", result);
+ }
+
+ /**
+ * Tests the behavior of getImageRotationUsingImageReader when an ImageProcessingException occurs.
+ * This test verifies that the method handles an ImageProcessingException by logging the error
+ * and returning 0 degrees rotation.
+ */
+ @Test
+ public void test_getImageRotationUsingImageReader_imageProcessingException() {
+ InputStream errorStream = new InputStream() {
+ @Override
+ public int read() throws IOException {
+ throw new IOException("Simulated image processing error");
+ }
+ };
+ int result = JPEGFilter.getImageRotationUsingImageReader(errorStream);
+ assertEquals(0, result);
+ }
+
+ /**
+ * Testcase for getImageRotationUsingImageReader when the image doesn't contain orientation metadata.
+ * This test verifies that the method returns 0 when there's no ExifIFD0Directory
+ * or when it doesn't contain the TAG_ORIENTATION.
+ */
+ @Test
+ public void test_getImageRotationUsingImageReader_noOrientationMetadata() throws IOException {
+ URL resource = this.getClass().getResource("cat.jpg");
+ int rotationAngle = -1;
+ try (InputStream inputStream = new FileInputStream(resource.getFile())) {
+ // Call the method under test
+ rotationAngle = JPEGFilter.getImageRotationUsingImageReader(inputStream);
+ }
+ assertEquals(0, rotationAngle);
+ }
+
+ /**
+ * Tests the getImageRotationUsingImageReader method when the image contains
+ * valid EXIF orientation metadata.
+ *
+ * This test verifies that the method correctly reads the orientation tag
+ * from the EXIF metadata and returns the appropriate rotation angle in degrees.
+ */
+ @Test
+ public void test_getImageRotationUsingImageReader_withValidExifOrientation() throws Exception {
+ // Create a mock InputStream with EXIF metadata containing orientation information
+ URL resource = this.getClass().getResource("cat-rotated-90.jpg");
+ int rotationAngle = -1;
+ try (InputStream inputStream = new FileInputStream(resource.getFile())) {
+ // Call the method under test
+ rotationAngle = JPEGFilter.getImageRotationUsingImageReader(inputStream);
+ }
+
+ // Assert the expected rotation angle
+ // Note: The expected value should be adjusted based on the mock data
+ assertEquals(90, rotationAngle);
+ }
+
+ /**
+ * Tests the getScaledInstance method of JPEGFilter class with higher quality scaling.
+ * This test verifies that the method correctly scales down an image in multiple passes
+ * when higherQuality is true and the image dimensions are larger than the target dimensions.
+ */
+ @Test
+ public void test_getScaledInstance() {
+ JPEGFilter filter = new JPEGFilter();
+ BufferedImage originalImage = new BufferedImage(400, 300, BufferedImage.TYPE_INT_RGB);
+ int targetWidth = 100;
+ int targetHeight = 75;
+ Object hint = RenderingHints.VALUE_INTERPOLATION_BILINEAR;
+ boolean higherQuality = true;
+
+ BufferedImage result = filter.getScaledInstance(originalImage, targetWidth, targetHeight, hint, higherQuality);
+
+ assertNotNull(result);
+ assertEquals(targetWidth, result.getWidth());
+ assertEquals(targetHeight, result.getHeight());
+ }
+
+ /**
+ * Tests the rotateImage method with a non-zero angle.
+ * This test verifies that the image is rotated correctly when given a non-zero angle.
+ */
+ @Test
+ public void test_rotateImage_nonZeroAngle() {
+ BufferedImage originalImage = new BufferedImage(100, 50, BufferedImage.TYPE_INT_RGB);
+ int angle = 90;
+
+ BufferedImage rotatedImage = JPEGFilter.rotateImage(originalImage, angle);
+
+ assertNotNull(rotatedImage);
+ assertEquals(50, rotatedImage.getWidth());
+ assertEquals(100, rotatedImage.getHeight());
+ }
+
+}
diff --git a/dspace-api/src/test/java/org/dspace/authenticate/ShibAuthenticationTest.java b/dspace-api/src/test/java/org/dspace/authenticate/ShibAuthenticationTest.java
new file mode 100644
index 000000000000..e0f0fc57a9ea
--- /dev/null
+++ b/dspace-api/src/test/java/org/dspace/authenticate/ShibAuthenticationTest.java
@@ -0,0 +1,136 @@
+/**
+ * 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.authenticate;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+import static org.mockito.ArgumentMatchers.any;
+import static org.mockito.ArgumentMatchers.anyString;
+import static org.mockito.ArgumentMatchers.eq;
+import static org.mockito.ArgumentMatchers.isNull;
+import static org.mockito.Mockito.mock;
+import static org.mockito.Mockito.times;
+import static org.mockito.Mockito.verify;
+import static org.mockito.Mockito.when;
+
+import jakarta.servlet.http.HttpServletRequest;
+import org.dspace.AbstractUnitTest;
+import org.dspace.content.MetadataField;
+import org.dspace.content.service.MetadataFieldService;
+import org.dspace.core.Context;
+import org.dspace.eperson.EPerson;
+import org.dspace.eperson.service.EPersonService;
+import org.dspace.services.ConfigurationService;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.ArgumentCaptor;
+
+/**
+ * Unit tests for ShibAuthentication
+ */
+public class ShibAuthenticationTest extends AbstractUnitTest {
+
+ private ShibAuthentication shibAuthentication;
+ private EPersonService ePersonService;
+ private ConfigurationService configurationService;
+
+ @Before
+ public void setup() {
+ shibAuthentication = new ShibAuthentication();
+ ePersonService = mock(EPersonService.class);
+ shibAuthentication.ePersonService = ePersonService;
+ configurationService = mock(ConfigurationService.class);
+ shibAuthentication.configurationService = configurationService;
+ when(configurationService.getProperty("authentication-shibboleth.netid-header")).thenReturn("SHIB-NETID");
+ when(configurationService.getProperty("authentication-shibboleth.email-header")).thenReturn("SHIB-MAIL");
+ when(configurationService.getArrayProperty("authentication-shibboleth.eperson.metadata"))
+ .thenReturn(new String[]{"SHIB-telephone => eperson.phone"});
+ when(configurationService.getBooleanProperty("authentication-shibboleth.eperson.metadata.autocreate", true))
+ .thenReturn(true);
+ MetadataFieldService metadataFieldService = mock(MetadataFieldService.class);
+ shibAuthentication.metadataFieldService = metadataFieldService;
+
+ try {
+ when(metadataFieldService.findByElement(any(Context.class), any(String.class), any(String.class), any()))
+ .thenReturn(mock(MetadataField.class));
+ } catch (Exception e) {
+ // ignore checked exceptions from mock
+ }
+ }
+
+ @Test
+ public void testPhoneMetadataUpdateOrder() throws Exception {
+ Context context = mock(Context.class);
+ HttpServletRequest request = mock(HttpServletRequest.class);
+ EPerson eperson = mock(EPerson.class);
+ when(request.getAttribute("SHIB-NETID")).thenReturn("test-user");
+ when(request.getAttribute("SHIB-MAIL")).thenReturn("test@example.com");
+ String phoneValue = "555-1234";
+ when(request.getAttribute("SHIB-telephone")).thenReturn(phoneValue);
+ shibAuthentication.initialize(context);
+ assertNotNull("metadataHeaderMap should be initialized", shibAuthentication.metadataHeaderMap);
+ assertTrue("metadataHeaderMap should contain SHIB-telephone", shibAuthentication.metadataHeaderMap
+ .containsKey("SHIB-telephone"));
+ shibAuthentication.updateEPerson(context, request, eperson);
+ ArgumentCaptor languageCaptor = ArgumentCaptor.forClass(String.class);
+ ArgumentCaptor valueCaptor = ArgumentCaptor.forClass(String.class);
+
+ verify(ePersonService, times(1)).setMetadataSingleValue(
+ any(Context.class),
+ eq(eperson),
+ eq("eperson"),
+ eq("phone"),
+ isNull(),
+ languageCaptor.capture(),
+ valueCaptor.capture()
+ );
+
+ assertNull("The language argument should be NULL.", languageCaptor.getValue());
+ assertEquals("The value argument should be the phone number.", phoneValue, valueCaptor.getValue());
+ }
+
+ @Test
+ public void testInitializeLoadsMultipleMappings() throws Exception {
+ Context context = mock(Context.class);
+ when(configurationService.getArrayProperty("authentication-shibboleth.eperson.metadata"))
+ .thenReturn(new String[]{
+ "SHIB-telephone => eperson.phone",
+ "SHIB-dept => eperson.department"
+ });
+ shibAuthentication.initialize(context);
+
+ assertNotNull("metadataHeaderMap should be initialized", shibAuthentication.metadataHeaderMap);
+ assertTrue("metadataHeaderMap should contain SHIB-telephone", shibAuthentication.metadataHeaderMap
+ .containsKey("SHIB-telephone"));
+ assertTrue("metadataHeaderMap should contain SHIB-dept", shibAuthentication.metadataHeaderMap
+ .containsKey("SHIB-dept"));
+ }
+
+ @Test
+ public void testNoMetadataMappingNoUpdate() throws Exception {
+ Context context = mock(Context.class);
+ HttpServletRequest request = mock(HttpServletRequest.class);
+ EPerson eperson = mock(EPerson.class);
+ when(configurationService.getArrayProperty("authentication-shibboleth.eperson.metadata"))
+ .thenReturn(new String[0]);
+ shibAuthentication.initialize(context);
+ shibAuthentication.updateEPerson(context, request, eperson);
+
+ verify(ePersonService, times(0)).setMetadataSingleValue(
+ any(Context.class),
+ any(EPerson.class),
+ anyString(),
+ anyString(),
+ any(),
+ any(),
+ any()
+ );
+ }
+}
diff --git a/dspace-api/src/test/java/org/dspace/authority/orcid/MockOrcid.java b/dspace-api/src/test/java/org/dspace/authority/orcid/MockOrcid.java
index 511df79f1e50..b6be6d1f3ac2 100644
--- a/dspace-api/src/test/java/org/dspace/authority/orcid/MockOrcid.java
+++ b/dspace-api/src/test/java/org/dspace/authority/orcid/MockOrcid.java
@@ -11,6 +11,7 @@
import java.io.InputStream;
+import org.dspace.external.OrcidConnectionException;
import org.dspace.external.OrcidRestConnector;
import org.mockito.ArgumentMatchers;
import org.mockito.Mockito;
@@ -38,7 +39,7 @@ public void init() {
* Call this to set up mocking for any test classes that need it. We don't set it in init()
* or other AbstractIntegrationTest implementations will complain of unnecessary Mockito stubbing
*/
- public void setupNoResultsSearch() {
+ public void setupNoResultsSearch() throws OrcidConnectionException {
when(orcidRestConnector.get(ArgumentMatchers.startsWith("search?"), ArgumentMatchers.any()))
.thenAnswer(new Answer() {
@Override
@@ -51,7 +52,7 @@ public InputStream answer(InvocationOnMock invocation) {
* Call this to set up mocking for any test classes that need it. We don't set it in init()
* or other AbstractIntegrationTest implementations will complain of unnecessary Mockito stubbing
*/
- public void setupSingleSearch() {
+ public void setupSingleSearch() throws OrcidConnectionException {
when(orcidRestConnector.get(ArgumentMatchers.startsWith("search?q=Bollini"), ArgumentMatchers.any()))
.thenAnswer(new Answer() {
@Override
@@ -64,7 +65,7 @@ public InputStream answer(InvocationOnMock invocation) {
* Call this to set up mocking for any test classes that need it. We don't set it in init()
* or other AbstractIntegrationTest implementations will complain of unnecessary Mockito stubbing
*/
- public void setupSearchWithResults() {
+ public void setupSearchWithResults() throws OrcidConnectionException {
when(orcidRestConnector.get(ArgumentMatchers.endsWith("/person"), ArgumentMatchers.any()))
.thenAnswer(new Answer() {
@Override
diff --git a/dspace-api/src/test/java/org/dspace/authorize/AuthorizeServiceTest.java b/dspace-api/src/test/java/org/dspace/authorize/AuthorizeServiceTest.java
index 70eaa2a0b909..e8bb428db53a 100644
--- a/dspace-api/src/test/java/org/dspace/authorize/AuthorizeServiceTest.java
+++ b/dspace-api/src/test/java/org/dspace/authorize/AuthorizeServiceTest.java
@@ -9,14 +9,24 @@
package org.dspace.authorize;
import java.sql.SQLException;
+import java.util.ArrayList;
+import java.util.List;
import org.dspace.AbstractUnitTest;
import org.dspace.authorize.factory.AuthorizeServiceFactory;
import org.dspace.authorize.service.ResourcePolicyService;
+import org.dspace.content.Bundle;
+import org.dspace.content.Collection;
import org.dspace.content.Community;
+import org.dspace.content.Item;
+import org.dspace.content.WorkspaceItem;
import org.dspace.content.factory.ContentServiceFactory;
+import org.dspace.content.service.BundleService;
import org.dspace.content.service.CollectionService;
import org.dspace.content.service.CommunityService;
+import org.dspace.content.service.InstallItemService;
+import org.dspace.content.service.ItemService;
+import org.dspace.content.service.WorkspaceItemService;
import org.dspace.core.Constants;
import org.dspace.eperson.EPerson;
import org.dspace.eperson.Group;
@@ -38,6 +48,10 @@ public class AuthorizeServiceTest extends AbstractUnitTest {
.getResourcePolicyService();
protected CommunityService communityService = ContentServiceFactory.getInstance().getCommunityService();
protected CollectionService collectionService = ContentServiceFactory.getInstance().getCollectionService();
+ protected ItemService itemService = ContentServiceFactory.getInstance().getItemService();
+ protected BundleService bundleService = ContentServiceFactory.getInstance().getBundleService();
+ protected WorkspaceItemService workspaceItemService = ContentServiceFactory.getInstance().getWorkspaceItemService();
+ protected InstallItemService installItemService = ContentServiceFactory.getInstance().getInstallItemService();
public AuthorizeServiceTest() {
}
@@ -127,6 +141,89 @@ public void testauthorizeMethodRespectSpecialGroups() {
throw new AssertionError(ex);
}
}
+
+ /**
+ * When a bundle is created it should inherit custom policies (deduped)
+ * from the item, as otherwise bitstream bundles created via filter-media etc.
+ * will be created without READ policies
+ */
+ @Test
+ public void testInheritanceOfCustomPolicies() {
+ try {
+ context.turnOffAuthorisationSystem();
+ Community community = communityService.create(null, context);
+ Collection collection = collectionService.create(context, community);
+ WorkspaceItem wsItem = workspaceItemService.create(context, collection, false);
+ Item item = installItemService.installItem(context, wsItem);
+ // Simulate access conditions adding READ policy to the item
+ ResourcePolicy itemCustomRead = resourcePolicyService.create(context, eperson, null);
+ itemCustomRead.setAction(Constants.READ);
+ itemCustomRead.setRpType(ResourcePolicy.TYPE_CUSTOM);
+ // Simulate a random ADMIN action policy that might have been added manually
+ ResourcePolicy itemCustomAdmin = resourcePolicyService.create(context, eperson, null);
+ itemCustomAdmin.setAction(Constants.ADMIN);
+ itemCustomAdmin.setRpType(ResourcePolicy.TYPE_CUSTOM);
+ List customPolicies = new ArrayList<>();
+ customPolicies.add(itemCustomRead);
+ customPolicies.add(itemCustomAdmin);
+ authorizeService.addPolicies(context, customPolicies, item);
+ // Create a bundle, this should call inheritPolicies via itemService.addBundle
+ Bundle bundle = bundleService.create(context, item, "THUMBNAIL");
+ List newPolicies = authorizeService
+ .findPoliciesByDSOAndType(context, bundle, ResourcePolicy.TYPE_CUSTOM);
+ Assert.assertEquals("Bundle should inherit custom policy from item", 1, newPolicies.size());
+ Assert.assertNotEquals("Bundle should ONLY inherit non-admin custom policy from item",
+ Constants.ADMIN, newPolicies.get(0).getAction());
+ } catch (Exception e) {
+ throw new RuntimeException(e);
+ } finally {
+ context.restoreAuthSystemState();
+ }
+ }
+
+ /**
+ * For other DSOs (which pass false) and for a bundle explicitly calling
+ * inheritPolicies(..., false), the TYPE_CUSTOM policies should not be inherited
+ * but other non-admin policies should be inherited as usual
+ */
+ @Test
+ public void testNonInheritanceOfCustomPolicies() {
+ try {
+ context.turnOffAuthorisationSystem();
+ Community community = communityService.create(null, context);
+ Collection collection = collectionService.create(context, community);
+ WorkspaceItem wsItem = workspaceItemService.create(context, collection, false);
+ Item item = installItemService.installItem(context, wsItem);
+ Bundle bundle = bundleService.create(context, item, "THUMBNAIL");
+ // Simulate a custom READ policy added by access conditions step
+ ResourcePolicy itemCustomRead = resourcePolicyService.create(context, eperson, null);
+ itemCustomRead.setAction(Constants.READ);
+ itemCustomRead.setRpType(ResourcePolicy.TYPE_CUSTOM);
+ // Simulate an ordinary default read item policy inherited from collection
+ ResourcePolicy itemDefaultRead = resourcePolicyService.create(context, eperson, null);
+ itemDefaultRead.setAction(Constants.READ);
+ itemDefaultRead.setRpType(ResourcePolicy.TYPE_INHERITED);
+ List customPolicies = new ArrayList<>();
+ customPolicies.add(itemCustomRead);
+ customPolicies.add(itemDefaultRead);
+ authorizeService.addPolicies(context, customPolicies, item);
+ // Now, inherit policies for bundle with includeCustom=false (which is how other DSOs behave)
+ authorizeService.inheritPolicies(context, item, bundle, false);
+ List newCustomPolicies = authorizeService
+ .findPoliciesByDSOAndType(context, bundle, ResourcePolicy.TYPE_CUSTOM);
+ List newInheritedPolicies = authorizeService
+ .findPoliciesByDSOAndType(context, bundle, ResourcePolicy.TYPE_INHERITED);
+ Assert.assertEquals("Bundle should not inherit custom policy from item, if false passed",
+ 0, newCustomPolicies.size());
+ Assert.assertEquals("Bundle should inherit non-custom, non-admin policies as usual",
+ ResourcePolicy.TYPE_INHERITED, newInheritedPolicies.get(0).getRpType());
+ } catch (Exception e) {
+ throw new RuntimeException(e);
+ } finally {
+ context.restoreAuthSystemState();
+ }
+ }
+
//
// @Test
// public void testIsCollectionAdmin() throws SQLException, AuthorizeException, IOException {
diff --git a/dspace-api/src/test/java/org/dspace/builder/ItemBuilder.java b/dspace-api/src/test/java/org/dspace/builder/ItemBuilder.java
index 5e9545fcafbd..d3e4d0ff8f78 100644
--- a/dspace-api/src/test/java/org/dspace/builder/ItemBuilder.java
+++ b/dspace-api/src/test/java/org/dspace/builder/ItemBuilder.java
@@ -113,6 +113,14 @@ public ItemBuilder withScopusIdentifier(String scopus) {
return addMetadataValue(item, "dc", "identifier", "scopus", scopus);
}
+ public ItemBuilder withISSN(String issn) {
+ return addMetadataValue(item, "dc", "identifier", "issn", issn);
+ }
+
+ public ItemBuilder withISBN(String isbn) {
+ return addMetadataValue(item, "dc", "identifier", "isbn", isbn);
+ }
+
public ItemBuilder withRelationFunding(String funding) {
return addMetadataValue(item, "dc", "relation", "funding", funding);
}
diff --git a/dspace-api/src/test/java/org/dspace/checker/ChecksumCheckerIT.java b/dspace-api/src/test/java/org/dspace/checker/ChecksumCheckerIT.java
new file mode 100644
index 000000000000..34198ff1ebfe
--- /dev/null
+++ b/dspace-api/src/test/java/org/dspace/checker/ChecksumCheckerIT.java
@@ -0,0 +1,193 @@
+/**
+ * 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.checker;
+
+import static java.nio.charset.StandardCharsets.UTF_8;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.sql.SQLException;
+import java.time.Instant;
+import java.util.ArrayList;
+import java.util.Date;
+import java.util.List;
+
+import org.apache.commons.io.IOUtils;
+import org.dspace.AbstractIntegrationTestWithDatabase;
+import org.dspace.builder.BitstreamBuilder;
+import org.dspace.builder.CollectionBuilder;
+import org.dspace.builder.CommunityBuilder;
+import org.dspace.builder.ItemBuilder;
+import org.dspace.checker.factory.CheckerServiceFactory;
+import org.dspace.checker.service.ChecksumHistoryService;
+import org.dspace.checker.service.MostRecentChecksumService;
+import org.dspace.content.Bitstream;
+import org.dspace.content.Collection;
+import org.dspace.content.Community;
+import org.dspace.content.Item;
+import org.dspace.core.Context;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class ChecksumCheckerIT extends AbstractIntegrationTestWithDatabase {
+ protected List bitstreams;
+ protected MostRecentChecksumService checksumService =
+ CheckerServiceFactory.getInstance().getMostRecentChecksumService();
+
+ @Before
+ public void setup() throws Exception {
+ context.turnOffAuthorisationSystem();
+
+ Community parentCommunity = CommunityBuilder.createCommunity(context).build();
+ Collection collection = CollectionBuilder.createCollection(context, parentCommunity)
+ .build();
+ Item item = ItemBuilder.createItem(context, collection).withTitle("Test item")
+ .build();
+
+ int numBitstreams = 3;
+ bitstreams = new ArrayList<>();
+ for (int i = 0; i < numBitstreams; i++) {
+ String content = "Test bitstream " + i;
+ bitstreams.add(
+ BitstreamBuilder.createBitstream(
+ context, item, IOUtils.toInputStream(content, UTF_8)
+ ).build()
+ );
+ }
+
+ context.restoreAuthSystemState();
+
+ // Call the "updateMissingBitstreams" method so that the test bitstreams
+ // already have checksums in the past when CheckerCommand runs.
+ // Otherwise, the CheckerCommand will simply update the test
+ // bitstreams without going through the BitstreamDispatcher.
+ checksumService = CheckerServiceFactory.getInstance().getMostRecentChecksumService();
+ checksumService.updateMissingBitstreams(context);
+
+ // The "updateMissingBitstreams" method updates the test bitstreams in
+ // a random order. To verify that the expected bitstreams were
+ // processed, reset the timestamps so that the bitstreams are
+ // checked in a specific order (oldest first).
+ Instant checksumInstant = Instant.ofEpochMilli(0);
+ for (Bitstream bitstream: bitstreams) {
+ MostRecentChecksum mrc = checksumService.findByBitstream(context, bitstream);
+ mrc.setProcessStartDate(Date.from(checksumInstant));
+ mrc.setProcessEndDate(Date.from(checksumInstant));
+ checksumInstant = checksumInstant.plusSeconds(10);
+ }
+ context.commit();
+ }
+
+ @After
+ public void cleanUp() throws SQLException {
+ // Need to clean up ChecksumHistory because of a referential integrity
+ // constraint violation between the most_recent_checksum table and
+ // bitstream tables
+ ChecksumHistoryService checksumHistoryService = CheckerServiceFactory.getInstance().getChecksumHistoryService();
+
+ for (Bitstream bitstream: bitstreams) {
+ checksumHistoryService.deleteByBitstream(context, bitstream);
+ }
+ }
+
+ @Test
+ public void testChecksumsRecordedWhenProcesingIsInterrupted() throws SQLException {
+ CheckerCommand checker = new CheckerCommand(context);
+
+ // The start date to use for the checker process
+ Date checkerStartDate = Date.from(Instant.now());
+
+ // Verify that all checksums are before the checker start date
+ for (Bitstream bitstream: bitstreams) {
+ MostRecentChecksum checksum = checksumService.findByBitstream(context, bitstream);
+ Date lastChecksumDate = checksum.getProcessStartDate();
+ assertTrue("lastChecksumDate (" + lastChecksumDate + ") <= checkerStartDate (" + checkerStartDate + ")",
+ lastChecksumDate.before(checkerStartDate));
+ }
+
+ // Dispatcher that throws an exception when a third bitstream is
+ // retrieved.
+ BitstreamDispatcher dispatcher = new ExpectionThrowingDispatcher(
+ context, checkerStartDate, false, 2);
+ checker.setDispatcher(dispatcher);
+
+
+ // Run the checksum checker
+ checker.setProcessStartDate(checkerStartDate);
+ try {
+ checker.process();
+ fail("SQLException should have been thrown");
+ } catch (SQLException sqle) {
+ // Rollback any pending transaction
+ context.rollback();
+ }
+
+ // Verify that the checksums of the first two bitstreams (that were
+ // processed before the exception) have been successfully recorded in
+ // the database, while the third bitstream was not updated.
+ int bitstreamCount = 0;
+ for (Bitstream bitstream: bitstreams) {
+ MostRecentChecksum checksum = checksumService.findByBitstream(context, bitstream);
+ Date lastChecksumDate = checksum.getProcessStartDate();
+
+ bitstreamCount = bitstreamCount + 1;
+ if (bitstreamCount <= 2) {
+ assertTrue("lastChecksumDate (" + lastChecksumDate + ") <= checkerStartDate (" + checkerStartDate + ")",
+ lastChecksumDate.after(checkerStartDate));
+ } else {
+ assertTrue("lastChecksumDate (" + lastChecksumDate + ") >= checkerStartDate (" + checkerStartDate + ")",
+ lastChecksumDate.before(checkerStartDate));
+ }
+ }
+ }
+
+ /**
+ * Subclass of SimpleDispatcher that only allows a limited number of "next"
+ * class before throwing a SQLException.
+ */
+ class ExpectionThrowingDispatcher extends SimpleDispatcher {
+ // The number of "next" calls to allow before throwing a SQLException
+ protected int maxNextCalls;
+
+ // The number of "next" method calls seen so far.
+ protected int numNextCalls = 0;
+
+ /**
+ * Constructor.
+ *
+ * @param context Context
+ * @param startTime timestamp for beginning of checker process
+ * @param looping indicates whether checker should loop infinitely
+ * through most_recent_checksum table
+ * @param maxNextCalls the number of "next" method calls to allow before
+ * throwing a SQLException.
+ */
+ public ExpectionThrowingDispatcher(Context context, Date startTime, boolean looping, int maxNextCalls) {
+ super(context, startTime, looping);
+ this.maxNextCalls = maxNextCalls;
+ }
+
+ /**
+ * Selects the next candidate bitstream.
+ *
+ * After "maxNextClass" number of calls, this method throws a
+ * SQLException.
+ *
+ * @throws SQLException if database error
+ */
+ @Override
+ public synchronized Bitstream next() throws SQLException {
+ numNextCalls = numNextCalls + 1;
+ if (numNextCalls > maxNextCalls) {
+ throw new SQLException("Max 'next' method calls exceeded");
+ }
+ return super.next();
+ }
+ }
+}
diff --git a/dspace-api/src/test/java/org/dspace/content/BitstreamTest.java b/dspace-api/src/test/java/org/dspace/content/BitstreamTest.java
index e85a0fc7b78d..abf19f328210 100644
--- a/dspace-api/src/test/java/org/dspace/content/BitstreamTest.java
+++ b/dspace-api/src/test/java/org/dspace/content/BitstreamTest.java
@@ -12,6 +12,7 @@
import static org.hamcrest.CoreMatchers.notNullValue;
import static org.hamcrest.CoreMatchers.nullValue;
import static org.hamcrest.MatcherAssert.assertThat;
+import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
@@ -25,6 +26,9 @@
import java.io.FileInputStream;
import java.io.IOException;
import java.sql.SQLException;
+import java.util.ArrayList;
+import java.util.Comparator;
+import java.util.Iterator;
import java.util.List;
import java.util.UUID;
@@ -148,6 +152,44 @@ public void testFindAll() throws SQLException {
assertTrue("testFindAll 2", added);
}
+ @Test
+ public void testFindAllBatches() throws Exception {
+ //Adding some data for processing and cleaning this up at the end
+ context.turnOffAuthorisationSystem();
+ File f = new File(testProps.get("test.bitstream").toString());
+ List inserted = new ArrayList<>();
+ for (int i = 0; i < 5; i++) {
+ Bitstream bs = bitstreamService.create(context, new FileInputStream(f));
+ inserted.add(bs);
+ }
+ context.restoreAuthSystemState();
+
+ // sorted list of all bitstreams
+ List all = bitstreamService.findAll(context);
+ List expected = new ArrayList<>(all);
+ expected.sort(Comparator.comparing(bs -> bs.getID().toString()));
+
+ int total = bitstreamService.countTotal(context);
+ int batchSize = 2;
+ int numberOfBatches = (int) Math.ceil((double) total / batchSize);
+
+ //collect in batches
+ List collected = new ArrayList<>();
+ for (int i = 0; i < numberOfBatches; i++) {
+ Iterator it = bitstreamService.findAll(context, batchSize, i * batchSize);
+ it.forEachRemaining(collected::add);
+ }
+
+ assertEquals("Batched results should match sorted findAll", expected, collected);
+
+ // Cleanup
+ context.turnOffAuthorisationSystem();
+ for (Bitstream b : inserted) {
+ bitstreamService.delete(context, b);
+ }
+ context.restoreAuthSystemState();
+ }
+
/**
* Test of create method, of class Bitstream.
*/
diff --git a/dspace-api/src/test/java/org/dspace/content/CollectionTest.java b/dspace-api/src/test/java/org/dspace/content/CollectionTest.java
index a177571ffa46..d943a4a31613 100644
--- a/dspace-api/src/test/java/org/dspace/content/CollectionTest.java
+++ b/dspace-api/src/test/java/org/dspace/content/CollectionTest.java
@@ -1159,6 +1159,184 @@ public void testFindAuthorizedOptimized() throws Exception {
assertFalse("testFindAuthorizeOptimized D.C", personDCollections.contains(collectionC));
}
+ /**
+ * Test of findAuthorizedEpersonAndGroups method, of class Collection.
+ * We create some collections and a user and groups and subgroups and add the user to one subgroup
+ * and one collection
+ * The parent group will be added to the other collection.
+ */
+ @Test
+ public void testFindAuthorizedByEPerson() throws Exception {
+ context.turnOffAuthorisationSystem();
+ Community com = communityService.create(null, context);
+ Collection collectionA = collectionService.create(context, com);
+ Collection collectionB = collectionService.create(context, com);
+ Collection collectionC = collectionService.create(context, com);
+
+ com.addCollection(collectionA);
+ com.addCollection(collectionB);
+ com.addCollection(collectionC);
+
+ Group groupParent = groupService.create(context);
+ Group groupChild = groupService.create(context);
+
+ groupService.addMember(context, groupParent, groupChild);
+
+ EPerson epersonA = ePersonService.create(context);
+
+ //Add epersonA to the child group
+ groupService.addMember(context, groupChild, epersonA);
+
+ //personA can submit to collectionA and collectionC
+ authorizeService.addPolicy(context, collectionA, Constants.ADD, epersonA);
+ authorizeService.addPolicy(context, collectionB, Constants.ADD, groupParent);
+
+ context.restoreAuthSystemState();
+
+ context.setCurrentUser(epersonA);
+ List personACollections =
+ collectionService.findAuthorized(context, null, List.of(Constants.ADD, Constants.ADMIN));
+ assertTrue("testFindAuthorizedByEPerson A", personACollections.size() == 2);
+ assertTrue("testFindAuthorizedByEPerson A.A", personACollections.contains(collectionA));
+ assertTrue("testFindAuthorizedByEPerson A.B", personACollections.contains(collectionB));
+ assertFalse("testFindAuthorizedByEPerson A.C", personACollections.contains(collectionC));
+ }
+
+ /**
+ * Test of testFindAuthorizedEPersonCommunityAdmin method, of class Collection.
+ * This will test what collections care retrieved if a user is a Com Administrator
+ * eperson A is Top of B (and by the caso of B,C and D) but not of E
+ * eperson E is Top of E nad of D so it can get THE E and D Collections
+ *
+ */
+ @Test
+ public void testFindAuthorizedEPersonCommunityAdmin() throws Exception {
+ context.turnOffAuthorisationSystem();
+ Community comA = communityService.create(null, context);
+ Community comB = communityService.create(null, context);
+ Community comC = communityService.create(null, context);
+ Community comD = communityService.create(null, context);
+ Community comE = communityService.create(null, context);
+
+ Collection collectionA1 = collectionService.create(context, comA);
+ Collection collectionC1 = collectionService.create(context, comC);
+ Collection collectionC2 = collectionService.create(context, comC);
+ Collection collectionD1 = collectionService.create(context, comD);
+ Collection collectionE1 = collectionService.create(context, comE);
+ Collection collectionE2 = collectionService.create(context, comE);
+
+ //Create Com hierarchies
+ comA.addSubCommunity(comB);
+ comA.addSubCommunity(comC);
+ comB.addSubCommunity(comD);
+
+ comA.addCollection(collectionA1);
+ comC.addCollection(collectionC1);
+ comC.addCollection(collectionC2);
+ comD.addCollection(collectionD1);
+ comE.addCollection(collectionE1);
+ comE.addCollection(collectionE2);
+
+
+ Group groupA = groupService.create(context);
+ Group groupB = groupService.create(context);
+ Group groupC = groupService.create(context);
+ Group groupD = groupService.create(context);
+ Group groupE = groupService.create(context);
+
+ EPerson epersonA = ePersonService.create(context);
+ EPerson epersonB = ePersonService.create(context);
+
+ //Add epersonA to the child group
+ groupService.addMember(context, groupA, epersonA);
+ //Add epersonB to the child group
+ groupService.addMember(context, groupE, epersonB);
+ groupService.addMember(context, groupD, epersonB);
+
+ //personA can submit to collectionA and collectionB
+ authorizeService.addPolicy(context, comA, Constants.ADMIN, groupA);
+ authorizeService.addPolicy(context, comD, Constants.ADMIN, groupD);
+ authorizeService.addPolicy(context, comE, Constants.ADMIN, groupE);
+
+ context.restoreAuthSystemState();
+
+ //PersonA Can get AllCollection From Top to Bottom com ComA, but not from ComE
+ context.setCurrentUser(epersonA);
+ List personACollectionsAdminCommA =
+ collectionService.findAuthorized(context, null, List.of(Constants.ADD, Constants.ADMIN));
+ assertTrue("testFindAuthorizedEPersonCommunityAdmin A", personACollectionsAdminCommA.size() == 4);
+ assertTrue("testFindAuthorizedEPersonCommunityAdmin A.A", personACollectionsAdminCommA
+ .containsAll(List.of(collectionA1, collectionD1, collectionC1, collectionC2)));
+ assertFalse("testFindAuthorizedEPersonCommunityAdmin A.B", personACollectionsAdminCommA
+ .containsAll(List.of(collectionE1, collectionE2)));
+
+ //PersonB Can get AllCollection From Top to Bottom com ComE, but not from ComA
+ context.setCurrentUser(epersonB);
+ List personACollectionsAdminCommE =
+ collectionService.findAuthorized(context, null, List.of(Constants.ADD, Constants.ADMIN));
+ assertTrue("testFindAuthorizedEPersonCommunityAdmin B", personACollectionsAdminCommE.size() == 3);
+ assertFalse("testFindAuthorizedEPersonCommunityAdmin B.A", personACollectionsAdminCommE
+ .containsAll(List.of(collectionA1, collectionC1, collectionC2)));
+ assertTrue("testFindAuthorizedEPersonCommunityAdmin B.B", personACollectionsAdminCommE
+ .containsAll(List.of(collectionD1, collectionE1, collectionE2)));
+ }
+
+ /**
+ * Test of testFindNotAuthorizedEPersonDifferentActions method, of class Collection.
+ * We create some collections and a user and a group add the user as ADMIN by adding ti
+ * toa group and that group to a Collection and add the user as submitter to another
+ * we pass actions that shouldn't return collections if only those actions are passed
+ * And we test if only on collection is retrieved if we pass the Corresponding action
+ */
+ @Test
+ public void testFindAuthorizedEPersonDifferentActions() throws Exception {
+ context.turnOffAuthorisationSystem();
+ Community com = communityService.create(null, context);
+ Collection collectionA = collectionService.create(context, com);
+ Collection collectionB = collectionService.create(context, com);
+
+ com.addCollection(collectionA);
+ com.addCollection(collectionB);
+
+ Group group = groupService.create(context);
+
+ EPerson epersonA = ePersonService.create(context);
+
+ //Add epersonA to the child group
+ groupService.addMember(context, group, epersonA);
+
+ //personA can submit to collectionA and collectionB
+ authorizeService.addPolicy(context, collectionA, Constants.ADD, epersonA);
+ authorizeService.addPolicy(context, collectionB, Constants.ADMIN, group);
+
+ context.restoreAuthSystemState();
+
+ //Person does not Have other permission than ADD - So should not return a Colelction if we pass other
+ //Actions. In this case WRITE OR DELETE
+ context.setCurrentUser(epersonA);
+ List personACollectionsRD =
+ collectionService.findAuthorized(context, null, List.of(Constants.WRITE, Constants.DELETE));
+ assertTrue("testFindAuthorizedEPersonDifferentActions A", personACollectionsRD.isEmpty());
+ assertFalse("testFindAuthorizedEPersonDifferentActions A.A", personACollectionsRD.contains(collectionA));
+ assertFalse("testFindAuthorizedEPersonDifferentActions A.B", personACollectionsRD.contains(collectionB));
+
+ //But It Should get Collection B if we pass the ADMIN Action too
+ List personACollectionsADD =
+ collectionService.findAuthorized(context, null,
+ List.of(Constants.WRITE, Constants.DELETE, Constants.ADD));
+ assertTrue("testFindAuthorizedEPersonDifferentActions B", personACollectionsADD.size() == 1);
+ assertTrue("testFindAuthorizedEPersonDifferentActions B.A", personACollectionsADD.contains(collectionA));
+ assertFalse("testFindAuthorizedEPersonDifferentActions B.B", personACollectionsADD.contains(collectionB));
+
+ //But It Should get Collection A if we pass the ADD Action too
+ List personACollections =
+ collectionService.findAuthorized(context, null,
+ List.of(Constants.WRITE, Constants.DELETE, Constants.ADMIN));
+ assertTrue("testFindAuthorizedEPersonDifferentActions C", personACollections.size() == 1);
+ assertFalse("testFindAuthorizedEPersonDifferentActions C.A", personACollections.contains(collectionA));
+ assertTrue("testFindAuthorizedEPersonDifferentActions C.B", personACollections.contains(collectionB));
+ }
+
/**
* Test of countItems method, of class Collection.
*/
diff --git a/dspace-api/src/test/java/org/dspace/content/DuplicateDetectionTest.java b/dspace-api/src/test/java/org/dspace/content/DuplicateDetectionIT.java
similarity index 97%
rename from dspace-api/src/test/java/org/dspace/content/DuplicateDetectionTest.java
rename to dspace-api/src/test/java/org/dspace/content/DuplicateDetectionIT.java
index 0b6c909f03e8..424233b47898 100644
--- a/dspace-api/src/test/java/org/dspace/content/DuplicateDetectionTest.java
+++ b/dspace-api/src/test/java/org/dspace/content/DuplicateDetectionIT.java
@@ -17,8 +17,6 @@
import java.util.List;
import java.util.Optional;
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
import org.dspace.AbstractIntegrationTestWithDatabase;
import org.dspace.builder.CollectionBuilder;
import org.dspace.builder.CommunityBuilder;
@@ -31,7 +29,6 @@
import org.dspace.services.ConfigurationService;
import org.dspace.services.factory.DSpaceServicesFactory;
import org.dspace.xmlworkflow.storedcomponents.XmlWorkflowItem;
-import org.junit.Before;
import org.junit.Test;
/**
@@ -40,7 +37,7 @@
*
* @author Kim Shepherd
*/
-public class DuplicateDetectionTest extends AbstractIntegrationTestWithDatabase {
+public class DuplicateDetectionIT extends AbstractIntegrationTestWithDatabase {
private DuplicateDetectionService duplicateDetectionService = ContentServiceFactory.getInstance()
.getDuplicateDetectionService();
private ConfigurationService configurationService = DSpaceServicesFactory.getInstance().getConfigurationService();
@@ -54,9 +51,7 @@ public class DuplicateDetectionTest extends AbstractIntegrationTestWithDatabase
private final String item1Title = "Public item I";
private final String item1Author = "Smith, Donald";
- private static final Logger log = LogManager.getLogger();
-
- @Before
+ @Override
public void setUp() throws Exception {
super.setUp();
// Temporarily enable duplicate detection and set comparison distance to 1
@@ -100,7 +95,7 @@ public void setUp() throws Exception {
.withAuthor("Smith, Donald Y.")
.withSubject("ExtraEntry 3")
.build();
-
+ context.restoreAuthSystemState();
}
@@ -210,7 +205,7 @@ public void testSearchDuplicates() throws Exception {
public void testSearchDuplicatesWithReservedSolrCharacters() throws Exception {
-
+ context.turnOffAuthorisationSystem();
Item item4 = ItemBuilder.createItem(context, col)
.withTitle("Testing: An Important Development Step")
.withIssueDate(item1IssueDate)
@@ -223,6 +218,7 @@ public void testSearchDuplicatesWithReservedSolrCharacters() throws Exception {
.withAuthor("Smith, Donald X.")
.withSubject("ExtraEntry 2")
.build();
+ context.restoreAuthSystemState();
// Get potential duplicates of item 4 and make sure no exceptions are thrown
List potentialDuplicates = new ArrayList<>();
@@ -254,6 +250,7 @@ public void testSearchDuplicatesWithReservedSolrCharacters() throws Exception {
@Test
public void testSearchDuplicatesWithVeryLongTitle() throws Exception {
+ context.turnOffAuthorisationSystem();
Item item6 = ItemBuilder.createItem(context, col)
.withTitle("Testing: This title is over 200 characters long and should behave just the same as a " +
"shorter title, with or without reserved characters. This integration test will prove that " +
@@ -272,6 +269,8 @@ public void testSearchDuplicatesWithVeryLongTitle() throws Exception {
.withSubject("ExtraEntry 2")
.build();
+ context.restoreAuthSystemState();
+
// Get potential duplicates of item 4 and make sure no exceptions are thrown
List potentialDuplicates = new ArrayList<>();
try {
@@ -303,6 +302,8 @@ public void testSearchDuplicatesExactMatch() throws Exception {
// Set distance to 0 manually
configurationService.setProperty("duplicate.comparison.distance", 0);
+ context.turnOffAuthorisationSystem();
+
Item item8 = ItemBuilder.createItem(context, col)
.withTitle("This integration test will prove that the edit distance of 0 results in an exact match")
.withIssueDate(item1IssueDate)
@@ -323,7 +324,7 @@ public void testSearchDuplicatesExactMatch() throws Exception {
.withAuthor("Smith, Donald X.")
.withSubject("ExtraEntry")
.build();
-
+ context.restoreAuthSystemState();
// Get potential duplicates of item 4 and make sure no exceptions are thrown
List potentialDuplicates = new ArrayList<>();
try {
@@ -387,6 +388,8 @@ public void testSearchDuplicatesWithMultipleFields() throws Exception {
configurationService.setProperty("duplicate.comparison.metadata.field",
new String[]{"dc.title", "dc.contributor.author"});
+ context.turnOffAuthorisationSystem();
+
Item item10 = ItemBuilder.createItem(context, col)
.withTitle("Compare both title and author")
.withIssueDate(item1IssueDate)
@@ -407,6 +410,8 @@ public void testSearchDuplicatesWithMultipleFields() throws Exception {
.withSubject("ExtraEntry 2")
.build();
+ context.restoreAuthSystemState();
+
// Get potential duplicates of item 10 and make sure no exceptions are thrown
List potentialDuplicates = new ArrayList<>();
try {
diff --git a/dspace-api/src/test/java/org/dspace/content/authority/DSpaceControlledVocabularyTest.java b/dspace-api/src/test/java/org/dspace/content/authority/DSpaceControlledVocabularyTest.java
index 255b070e5eac..524c6407b7bd 100644
--- a/dspace-api/src/test/java/org/dspace/content/authority/DSpaceControlledVocabularyTest.java
+++ b/dspace-api/src/test/java/org/dspace/content/authority/DSpaceControlledVocabularyTest.java
@@ -8,6 +8,7 @@
package org.dspace.content.authority;
import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotEquals;
import static org.junit.Assert.assertNotNull;
import java.io.IOException;
@@ -86,6 +87,7 @@ public void testGetMatches() throws IOException, ClassNotFoundException {
CoreServiceFactory.getInstance().getPluginService().getNamedPlugin(Class.forName(PLUGIN_INTERFACE), "farm");
assertNotNull(instance);
Choices result = instance.getMatches(text, start, limit, locale);
+ assertNotEquals("At least one match expected", 0, result.values.length);
assertEquals("north 40", result.values[0].value);
}
diff --git a/dspace-api/src/test/java/org/dspace/orcid/service/OrcidEntityFactoryServiceIT.java b/dspace-api/src/test/java/org/dspace/orcid/service/OrcidEntityFactoryServiceIT.java
index 912efcfcf323..c73e7adecc41 100644
--- a/dspace-api/src/test/java/org/dspace/orcid/service/OrcidEntityFactoryServiceIT.java
+++ b/dspace-api/src/test/java/org/dspace/orcid/service/OrcidEntityFactoryServiceIT.java
@@ -73,6 +73,9 @@ public class OrcidEntityFactoryServiceIT extends AbstractIntegrationTestWithData
private Collection projects;
+ private static final String isbn = "978-0-439-02348-1";
+ private static final String issn = "1234-1234X";
+
@Before
public void setup() {
@@ -117,6 +120,7 @@ public void testWorkCreation() {
.withLanguage("en_US")
.withType("Book")
.withIsPartOf("Journal")
+ .withISBN(isbn)
.withDoiIdentifier("doi-id")
.withScopusIdentifier("scopus-id")
.build();
@@ -149,11 +153,100 @@ public void testWorkCreation() {
assertThat(work.getExternalIdentifiers(), notNullValue());
List externalIds = work.getExternalIdentifiers().getExternalIdentifier();
- assertThat(externalIds, hasSize(3));
+ assertThat(externalIds, hasSize(4));
+ assertThat(externalIds, has(selfExternalId("doi", "doi-id")));
+ assertThat(externalIds, has(selfExternalId("eid", "scopus-id")));
+ assertThat(externalIds, has(selfExternalId("handle", publication.getHandle())));
+ // Book type should have SELF rel for ISBN
+ assertThat(externalIds, has(selfExternalId("isbn", isbn)));
+
+ }
+
+ @Test
+ public void testJournalArticleAndISSN() {
+ context.turnOffAuthorisationSystem();
+
+ Item publication = ItemBuilder.createItem(context, publications)
+ .withTitle("Test publication")
+ .withAuthor("Walter White")
+ .withAuthor("Jesse Pinkman")
+ .withEditor("Editor")
+ .withIssueDate("2021-04-30")
+ .withDescriptionAbstract("Publication description")
+ .withLanguage("en_US")
+ .withType("Article")
+ .withIsPartOf("Journal")
+ .withISSN(issn)
+ .withDoiIdentifier("doi-id")
+ .withScopusIdentifier("scopus-id")
+ .build();
+
+ context.restoreAuthSystemState();
+
+ Activity activity = entityFactoryService.createOrcidObject(context, publication);
+ assertThat(activity, instanceOf(Work.class));
+
+ Work work = (Work) activity;
+ assertThat(work.getJournalTitle(), notNullValue());
+ assertThat(work.getJournalTitle().getContent(), is("Journal"));
+ assertThat(work.getLanguageCode(), is("en"));
+ assertThat(work.getPublicationDate(), matches(date("2021", "04", "30")));
+ assertThat(work.getShortDescription(), is("Publication description"));
+ assertThat(work.getPutCode(), nullValue());
+ assertThat(work.getWorkType(), is(WorkType.JOURNAL_ARTICLE));
+ assertThat(work.getWorkTitle(), notNullValue());
+ assertThat(work.getWorkTitle().getTitle(), notNullValue());
+ assertThat(work.getWorkTitle().getTitle().getContent(), is("Test publication"));
+ assertThat(work.getWorkContributors(), notNullValue());
+ assertThat(work.getUrl(), matches(urlEndsWith(publication.getHandle())));
+
+ List contributors = work.getWorkContributors().getContributor();
+ assertThat(contributors, hasSize(3));
+ assertThat(contributors, has(contributor("Walter White", AUTHOR, FIRST)));
+ assertThat(contributors, has(contributor("Editor", EDITOR, FIRST)));
+ assertThat(contributors, has(contributor("Jesse Pinkman", AUTHOR, ADDITIONAL)));
+
+ assertThat(work.getExternalIdentifiers(), notNullValue());
+
+ List externalIds = work.getExternalIdentifiers().getExternalIdentifier();
+ assertThat(externalIds, hasSize(4));
assertThat(externalIds, has(selfExternalId("doi", "doi-id")));
assertThat(externalIds, has(selfExternalId("eid", "scopus-id")));
assertThat(externalIds, has(selfExternalId("handle", publication.getHandle())));
+ // journal-article should have PART_OF rel for ISSN
+ assertThat(externalIds, has(externalId("issn", issn, Relationship.PART_OF)));
+ }
+ @Test
+ public void testJournalWithISSN() {
+ context.turnOffAuthorisationSystem();
+
+ Item publication = ItemBuilder.createItem(context, publications)
+ .withTitle("Test journal")
+ .withEditor("Editor")
+ .withType("Journal")
+ .withISSN(issn)
+ .build();
+
+ context.restoreAuthSystemState();
+
+ Activity activity = entityFactoryService.createOrcidObject(context, publication);
+ assertThat(activity, instanceOf(Work.class));
+
+ Work work = (Work) activity;
+ assertThat(work.getWorkType(), is(WorkType.JOURNAL_ISSUE));
+ assertThat(work.getWorkTitle(), notNullValue());
+ assertThat(work.getWorkTitle().getTitle(), notNullValue());
+ assertThat(work.getWorkTitle().getTitle().getContent(), is("Test journal"));
+ assertThat(work.getUrl(), matches(urlEndsWith(publication.getHandle())));
+
+ assertThat(work.getExternalIdentifiers(), notNullValue());
+
+ List externalIds = work.getExternalIdentifiers().getExternalIdentifier();
+ assertThat(externalIds, hasSize(2));
+ // journal-issue should have SELF rel for ISSN
+ assertThat(externalIds, has(selfExternalId("issn", issn)));
+ assertThat(externalIds, has(selfExternalId("handle", publication.getHandle())));
}
@Test
@@ -163,6 +256,7 @@ public void testEmptyWorkWithUnknownTypeCreation() {
Item publication = ItemBuilder.createItem(context, publications)
.withType("TYPE")
+ .withISSN(issn)
.build();
context.restoreAuthSystemState();
@@ -183,8 +277,9 @@ public void testEmptyWorkWithUnknownTypeCreation() {
assertThat(work.getExternalIdentifiers(), notNullValue());
List externalIds = work.getExternalIdentifiers().getExternalIdentifier();
- assertThat(externalIds, hasSize(1));
+ assertThat(externalIds, hasSize(2));
assertThat(externalIds, has(selfExternalId("handle", publication.getHandle())));
+ assertThat(externalIds, has(externalId("issn", issn, Relationship.PART_OF)));
}
@Test
diff --git a/dspace-api/src/test/java/org/dspace/statistics/SolrLoggerServiceImplIT.java b/dspace-api/src/test/java/org/dspace/statistics/SolrLoggerServiceImplIT.java
index 82f8680aea27..956ba81f4931 100644
--- a/dspace-api/src/test/java/org/dspace/statistics/SolrLoggerServiceImplIT.java
+++ b/dspace-api/src/test/java/org/dspace/statistics/SolrLoggerServiceImplIT.java
@@ -12,6 +12,7 @@
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertTrue;
+import java.io.ByteArrayInputStream;
import java.io.IOException;
import java.io.Writer;
import java.nio.charset.StandardCharsets;
@@ -29,8 +30,14 @@
import org.apache.solr.common.SolrDocument;
import org.apache.solr.common.SolrInputDocument;
import org.dspace.AbstractIntegrationTestWithDatabase;
+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.Collection;
import org.dspace.content.Community;
+import org.dspace.content.Item;
import org.dspace.content.factory.ContentServiceFactory;
import org.dspace.core.Constants;
import org.dspace.core.factory.CoreServiceFactory;
@@ -305,4 +312,56 @@ public void testDeleteRobots()
}
assertEquals("Wrong number of documents remaining --", 1, nDocs);
}
+
+ @Test
+ public void testPostViewShouldNotLogIgnoredBundles() throws Exception {
+ ContentServiceFactory csf = ContentServiceFactory.getInstance();
+ MockSolrLoggerServiceImpl solrLoggerService = DSpaceServicesFactory.getInstance()
+ .getServiceManager()
+ .getServiceByName("solrLoggerService", MockSolrLoggerServiceImpl.class);
+ solrLoggerService.bitstreamService = csf.getBitstreamService();
+ solrLoggerService.contentServiceFactory = csf;
+ solrLoggerService.configurationService = DSpaceServicesFactory.getInstance().getConfigurationService();
+ solrLoggerService.clientInfoService = CoreServiceFactory.getInstance().getClientInfoService();
+ solrLoggerService.afterPropertiesSet();
+ SolrStatisticsCore solrStatisticsCore = DSpaceServicesFactory.getInstance()
+ .getServiceManager()
+ .getServiceByName(SolrStatisticsCore.class.getName(), MockSolrStatisticsCore.class);
+
+ solrStatisticsCore.getSolr().deleteByQuery("*:*");
+ solrStatisticsCore.getSolr().commit();
+
+ context.turnOffAuthorisationSystem();
+ Community community = CommunityBuilder
+ .createCommunity(context)
+ .withName("Test Community").build();
+ Collection collection = CollectionBuilder
+ .createCollection(context, community)
+ .withName("Test Collection").build();
+ Item item = ItemBuilder
+ .createItem(context, collection)
+ .withTitle("Test Item for Logging").build();
+ Bitstream originalBitstream = BitstreamBuilder
+ .createBitstream(context, item, new ByteArrayInputStream("original content".getBytes()), "ORIGINAL")
+ .withName("original.txt")
+ .build();
+ Bitstream thumbnailBitstream = BitstreamBuilder
+ .createBitstream(context, item, new ByteArrayInputStream("thumbnail content".getBytes()), "THUMBNAIL")
+ .withName("thumbnail.jpg")
+ .build();
+
+ context.restoreAuthSystemState();
+ solrLoggerService.postView(originalBitstream, null, eperson);
+ solrLoggerService.postView(thumbnailBitstream, null, eperson);
+
+ solrStatisticsCore.getSolr().commit();
+
+ SolrQuery thumbnailQuery = new SolrQuery("id:" + thumbnailBitstream.getID().toString());
+ QueryResponse thumbnailResponse = solrStatisticsCore.getSolr().query(thumbnailQuery);
+ assertEquals("Thumbnail bundle should NOT be logged", 0, thumbnailResponse.getResults().getNumFound());
+
+ SolrQuery originalQuery = new SolrQuery("id:" + originalBitstream.getID().toString());
+ QueryResponse originalResponse = solrStatisticsCore.getSolr().query(originalQuery);
+ assertEquals("ORIGINAL bundle SHOULD be logged", 1, originalResponse.getResults().getNumFound());
+ }
}
diff --git a/dspace-api/src/test/java/org/dspace/statistics/export/ITIrusExportUsageEventListener.java b/dspace-api/src/test/java/org/dspace/statistics/export/ITIrusExportUsageEventListener.java
index 0c861a0d293d..48cf0b14b6bd 100644
--- a/dspace-api/src/test/java/org/dspace/statistics/export/ITIrusExportUsageEventListener.java
+++ b/dspace-api/src/test/java/org/dspace/statistics/export/ITIrusExportUsageEventListener.java
@@ -116,6 +116,7 @@ public void setUp() throws Exception {
configurationService.setProperty("irus.statistics.tracker.enabled", true);
configurationService.setProperty("irus.statistics.tracker.type-field", "dc.type");
configurationService.setProperty("irus.statistics.tracker.type-value", "Excluded type");
+ configurationService.setProperty("oai.identifier.prefix", "localhost");
context.turnOffAuthorisationSystem();
diff --git a/dspace-api/src/test/java/org/dspace/statistics/export/processor/ExportEventProcessorIT.java b/dspace-api/src/test/java/org/dspace/statistics/export/processor/ExportEventProcessorIT.java
index fb53d0c83c54..96909a9e3dbd 100644
--- a/dspace-api/src/test/java/org/dspace/statistics/export/processor/ExportEventProcessorIT.java
+++ b/dspace-api/src/test/java/org/dspace/statistics/export/processor/ExportEventProcessorIT.java
@@ -62,6 +62,7 @@ public void setUp() throws Exception {
configurationService.setProperty("irus.statistics.tracker.enabled", true);
configurationService.setProperty("irus.statistics.tracker.type-field", "dc.type");
configurationService.setProperty("irus.statistics.tracker.type-value", "Excluded type");
+ configurationService.setProperty("oai.identifier.prefix", "localhost");
context.turnOffAuthorisationSystem();
publication = EntityTypeBuilder.createEntityTypeBuilder(context, "Publication").build();
diff --git a/dspace-api/src/test/java/org/dspace/storage/bitstore/BitstreamStorageServiceImplIT.java b/dspace-api/src/test/java/org/dspace/storage/bitstore/BitstreamStorageServiceImplIT.java
new file mode 100644
index 000000000000..5b15cba1c4c1
--- /dev/null
+++ b/dspace-api/src/test/java/org/dspace/storage/bitstore/BitstreamStorageServiceImplIT.java
@@ -0,0 +1,262 @@
+/**
+ * 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.storage.bitstore;
+
+import static java.nio.charset.StandardCharsets.UTF_8;
+import static org.hamcrest.MatcherAssert.assertThat;
+import static org.hamcrest.Matchers.equalTo;
+import static org.junit.Assert.fail;
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.sql.SQLException;
+import java.util.HashMap;
+import java.util.Map;
+
+import org.apache.commons.io.IOUtils;
+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.Collection;
+import org.dspace.content.Item;
+import org.dspace.content.factory.ContentServiceFactory;
+import org.dspace.content.service.BitstreamService;
+import org.dspace.core.Context;
+import org.dspace.storage.bitstore.factory.StorageServiceFactory;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Rule;
+import org.junit.Test;
+import org.junit.rules.TemporaryFolder;
+
+public class BitstreamStorageServiceImplIT extends AbstractIntegrationTestWithDatabase {
+ private BitstreamService bitstreamService = ContentServiceFactory.getInstance().getBitstreamService();
+ private BitstreamStorageServiceImpl bitstreamStorageService =
+ (BitstreamStorageServiceImpl) StorageServiceFactory.getInstance().getBitstreamStorageService();
+ private Collection collection;
+
+ private Map originalBitstores;
+
+ private static final Integer SOURCE_STORE = 0;
+ private static final Integer DEST_STORE = 1;
+
+ @Rule
+ public final TemporaryFolder tempStoreDir = new TemporaryFolder();
+
+ @Before
+ public void setup() throws Exception {
+
+ context.turnOffAuthorisationSystem();
+
+ parentCommunity = CommunityBuilder.createCommunity(context)
+ .build();
+
+ collection = CollectionBuilder.createCollection(context, parentCommunity)
+ .build();
+
+ originalBitstores = bitstreamStorageService.getStores();
+ Map stores = new HashMap<>();
+ DSBitStoreService sourceStore = new DSBitStoreService();
+ sourceStore.setBaseDir(tempStoreDir.newFolder("src"));
+
+ stores.put(SOURCE_STORE, sourceStore);
+ bitstreamStorageService.setStores(stores);
+
+ context.restoreAuthSystemState();
+ }
+
+ @After
+ public void cleanUp() throws IOException {
+ // Restore the bitstore storage stores
+ bitstreamStorageService.setStores(originalBitstores);
+ }
+
+ /**
+ * Test batch commit checkpointing, using the default batch commit size of 1
+ *
+ * @throws Exception if an exception occurs.
+ */
+ @Test
+ public void testDefaultBatchCommitSize() throws Exception {
+ Context context = this.context;
+
+ // Destination assetstore fails after two bitstreams have been migrated
+ DSBitStoreService destinationStore = new LimitedTempDSBitStoreService(tempStoreDir, 2);
+ Map stores = bitstreamStorageService.getStores();
+ stores.put(DEST_STORE, destinationStore);
+
+ // Create three bitstreams in the source assetstore
+ createBitstreams(context, 3);
+
+ // Three bitstreams in source assetstore at the start
+ assertThat(bitstreamService.countByStoreNumber(context, SOURCE_STORE).intValue(), equalTo(3));
+
+ // No bitstreams in destination assetstore at the start
+ assertThat(bitstreamService.countByStoreNumber(context, DEST_STORE).intValue(), equalTo(0));
+
+ /// Commit any pending transaction to database
+ context.commit();
+
+ // Migrate bitstreams
+ context.turnOffAuthorisationSystem();
+
+ boolean deleteOld = false;
+ Integer batchCommitSize = 1;
+ try {
+ bitstreamStorageService.migrate(
+ context, SOURCE_STORE, DEST_STORE, deleteOld,
+ batchCommitSize
+ );
+ fail("IOException should have been thrown");
+ } catch (IOException ioe) {
+ // Rollback any pending transaction
+ context.rollback();
+ }
+
+ context.restoreAuthSystemState();
+
+ // One bitstream should still be in the source assetstore, due to the
+ // interrupted migration
+ assertThat(bitstreamService.countByStoreNumber(context, SOURCE_STORE).intValue(), equalTo(1));
+
+ // Two bitstreams should have migrated to the destination assetstore
+ assertThat(bitstreamService.countByStoreNumber(context, DEST_STORE).intValue(), equalTo(2));
+ }
+
+ /**
+ * Test batch commit checkpointing, using the default batch commit size of 3
+ *
+ * @throws Exception if an exception occurs.
+ */
+ @Test
+ public void testBatchCommitSizeThree() throws Exception {
+ Context context = this.context;
+
+ // Destination assetstore fails after four bitstreams have been migrated
+ DSBitStoreService destinationStore = new LimitedTempDSBitStoreService(tempStoreDir, 4);
+ Map stores = bitstreamStorageService.getStores();
+ stores.put(DEST_STORE, destinationStore);
+
+ // Create five bitstreams in the source assetstore
+ createBitstreams(context, 5);
+
+ // Five bitstreams in source assetstore at the start
+ assertThat(bitstreamService.countByStoreNumber(context, SOURCE_STORE).intValue(), equalTo(5));
+
+ // No bitstreams in destination assetstore at the start
+ assertThat(bitstreamService.countByStoreNumber(context, DEST_STORE).intValue(), equalTo(0));
+
+ // Commit any pending transaction to database
+ context.commit();
+
+ // Migrate bitstreams
+ context.turnOffAuthorisationSystem();
+
+ boolean deleteOld = false;
+ Integer batchCommitSize = 3;
+ try {
+ bitstreamStorageService.migrate(
+ context, SOURCE_STORE, DEST_STORE, deleteOld,
+ batchCommitSize
+ );
+ fail("IOException should have been thrown");
+ } catch (IOException ioe) {
+ // Rollback any pending transaction
+ context.rollback();
+ }
+
+ context.restoreAuthSystemState();
+
+ // Since the batch commit size is 3, only three bitstreams should be
+ // marked as migrated, so there should still be two bitstreams
+ // in the source assetstore, due to the interrupted migration
+ assertThat(bitstreamService.countByStoreNumber(context, SOURCE_STORE).intValue(), equalTo(2));
+
+ // Three bitstreams should have migrated to the destination assetstore
+ assertThat(bitstreamService.countByStoreNumber(context, DEST_STORE).intValue(), equalTo(3));
+ }
+
+ private void createBitstreams(Context context, int numBitstreams)
+ throws SQLException {
+ context.turnOffAuthorisationSystem();
+ for (int i = 0; i < numBitstreams; i++) {
+ String content = "Test bitstream " + i;
+ createBitstream(content);
+ }
+ context.restoreAuthSystemState();
+ context.commit();
+ }
+
+ private Bitstream createBitstream(String content) {
+ try {
+ return BitstreamBuilder
+ .createBitstream(context, createItem(), toInputStream(content))
+ .build();
+ } catch (SQLException | AuthorizeException | IOException e) {
+ throw new RuntimeException(e);
+ }
+ }
+
+ private Item createItem() {
+ return ItemBuilder.createItem(context, collection)
+ .withTitle("Test item")
+ .build();
+ }
+
+
+ private InputStream toInputStream(String content) {
+ return IOUtils.toInputStream(content, UTF_8);
+ }
+
+
+ /**
+ * DSBitStoreService variation that only allows a limited number of puts
+ * to the bit store before throwing an IOException, to test the
+ * error handling of the BitstreamStorageService.migrate() method.
+ */
+ class LimitedTempDSBitStoreService extends DSBitStoreService {
+ // The number of put calls allowed before throwing an IOException
+ protected int maxPuts = Integer.MAX_VALUE;
+
+ // The number of "put" method class seen so far.
+ protected int putCallCount = 0;
+
+ /**
+ * Constructor.
+ *
+ * @param maxPuts the number of put calls to allow before throwing an
+ * IOException
+ */
+ public LimitedTempDSBitStoreService(TemporaryFolder tempStoreDir, int maxPuts) throws IOException {
+ super();
+ setBaseDir(tempStoreDir.newFolder());
+ this.maxPuts = maxPuts;
+ }
+
+ /**
+ * Store a stream of bits.
+ *
+ * After "maxPut" number of calls, this method throws an IOException.
+ * @param in The stream of bits to store
+ * @throws java.io.IOException If a problem occurs while storing the bits
+ */
+ @Override
+ public void put(Bitstream bitstream, InputStream in) throws IOException {
+ putCallCount = putCallCount + 1;
+ if (putCallCount > maxPuts) {
+ throw new IOException("Max 'put' method calls exceeded");
+ } else {
+ super.put(bitstream, in);
+ }
+ }
+ }
+}
diff --git a/dspace-api/src/test/java/org/dspace/storage/bitstore/S3BitStoreServiceIT.java b/dspace-api/src/test/java/org/dspace/storage/bitstore/S3BitStoreServiceIT.java
index 6ea21eac8d6d..c1c1ed3ccc77 100644
--- a/dspace-api/src/test/java/org/dspace/storage/bitstore/S3BitStoreServiceIT.java
+++ b/dspace-api/src/test/java/org/dspace/storage/bitstore/S3BitStoreServiceIT.java
@@ -7,13 +7,12 @@
*/
package org.dspace.storage.bitstore;
-import static com.amazonaws.regions.Regions.DEFAULT_REGION;
import static java.nio.charset.StandardCharsets.UTF_8;
import static org.dspace.storage.bitstore.S3BitStoreService.CSA;
import static org.hamcrest.MatcherAssert.assertThat;
-import static org.hamcrest.Matchers.contains;
import static org.hamcrest.Matchers.equalTo;
import static org.hamcrest.Matchers.hasEntry;
+import static org.hamcrest.Matchers.hasItem;
import static org.hamcrest.Matchers.instanceOf;
import static org.hamcrest.Matchers.is;
import static org.hamcrest.Matchers.notNullValue;
@@ -26,22 +25,16 @@
import java.io.File;
import java.io.IOException;
import java.io.InputStream;
+import java.net.URI;
+import java.nio.file.Paths;
import java.security.MessageDigest;
import java.security.NoSuchAlgorithmException;
import java.sql.SQLException;
+import java.util.ArrayList;
import java.util.List;
import java.util.Map;
-import com.amazonaws.auth.AWSStaticCredentialsProvider;
-import com.amazonaws.auth.AnonymousAWSCredentials;
-import com.amazonaws.client.builder.AwsClientBuilder.EndpointConfiguration;
-import com.amazonaws.services.s3.AmazonS3;
-import com.amazonaws.services.s3.AmazonS3ClientBuilder;
-import com.amazonaws.services.s3.model.AmazonS3Exception;
-import com.amazonaws.services.s3.model.Bucket;
-import com.amazonaws.services.s3.model.ObjectMetadata;
-import io.findify.s3mock.S3Mock;
-import org.apache.commons.io.FileUtils;
+import com.adobe.testing.s3mock.testcontainers.S3MockContainer;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang.BooleanUtils;
import org.dspace.AbstractIntegrationTestWithDatabase;
@@ -59,47 +52,60 @@
import org.dspace.services.factory.DSpaceServicesFactory;
import org.hamcrest.Matcher;
import org.hamcrest.Matchers;
-import org.junit.After;
+import org.junit.AfterClass;
import org.junit.Before;
+import org.junit.BeforeClass;
import org.junit.Test;
-
-
+import software.amazon.awssdk.auth.credentials.AnonymousCredentialsProvider;
+import software.amazon.awssdk.awscore.exception.AwsServiceException;
+import software.amazon.awssdk.regions.Region;
+import software.amazon.awssdk.services.s3.S3AsyncClient;
+import software.amazon.awssdk.services.s3.model.Bucket;
+import software.amazon.awssdk.services.s3.model.ChecksumAlgorithm;
+import software.amazon.awssdk.services.s3.model.HeadObjectResponse;
/**
* @author Luca Giamminonni (luca.giamminonni at 4science.com)
*/
public class S3BitStoreServiceIT extends AbstractIntegrationTestWithDatabase {
+ private static S3MockContainer s3Mock = new S3MockContainer("4.8.0");
+
+ private static S3AsyncClient s3AsyncClient;
private static final String DEFAULT_BUCKET_NAME = "dspace-asset-localhost";
private S3BitStoreService s3BitStoreService;
- private AmazonS3 amazonS3Client;
-
- private S3Mock s3Mock;
-
private Collection collection;
- private File s3Directory;
-
private ConfigurationService configurationService = DSpaceServicesFactory.getInstance().getConfigurationService();
+ @BeforeClass
+ public static void setupS3() {
+ s3Mock.start();
+
+ s3AsyncClient = S3AsyncClient.crtBuilder()
+ .endpointOverride(URI.create("http://127.0.0.1:" + s3Mock.getHttpServerPort()))
+ .credentialsProvider(AnonymousCredentialsProvider.create())
+ .region(Region.US_EAST_1)
+ .build();
+ }
+
+ @AfterClass
+ public static void cleanupS3() {
+ s3Mock.close();
+ s3AsyncClient.close();
+ }
@Before
public void setup() throws Exception {
-
configurationService.setProperty("assetstore.s3.enabled", "true");
- s3Directory = new File(System.getProperty("java.io.tmpdir"), "s3");
-
- s3Mock = S3Mock.create(8001, s3Directory.getAbsolutePath());
- s3Mock.start();
- amazonS3Client = createAmazonS3Client();
-
- s3BitStoreService = new S3BitStoreService(amazonS3Client);
+ s3BitStoreService = new S3BitStoreService(s3AsyncClient);
s3BitStoreService.setEnabled(BooleanUtils.toBoolean(
configurationService.getProperty("assetstore.s3.enabled")));
- s3BitStoreService.setBufferSize(22);
+ s3BitStoreService.setS3ChecksumAlgorithm(ChecksumAlgorithm.SHA256);
+
context.turnOffAuthorisationSystem();
parentCommunity = CommunityBuilder.createCommunity(context)
@@ -111,23 +117,17 @@ public void setup() throws Exception {
context.restoreAuthSystemState();
}
- @After
- public void cleanUp() throws IOException {
- FileUtils.deleteDirectory(s3Directory);
- s3Mock.shutdown();
- }
-
@Test
public void testBitstreamPutAndGetWithAlreadyPresentBucket() throws IOException {
String bucketName = "testbucket";
- amazonS3Client.createBucket(bucketName);
+ s3AsyncClient.createBucket(r -> r.bucket(bucketName)).join();
s3BitStoreService.setBucketName(bucketName);
s3BitStoreService.init();
- assertThat(amazonS3Client.listBuckets(), contains(bucketNamed(bucketName)));
+ assertThat(s3AsyncClient.listBuckets().join().buckets(), hasItem(bucketNamed(bucketName)));
context.turnOffAuthorisationSystem();
String content = "Test bitstream content";
@@ -149,7 +149,7 @@ public void testBitstreamPutAndGetWithAlreadyPresentBucket() throws IOException
private void checkGetPut(String bucketName, String content, Bitstream bitstream) throws IOException {
s3BitStoreService.put(bitstream, toInputStream(content));
- String expectedChecksum = Utils.toHex(generateChecksum(content));
+ String expectedChecksum = Utils.toHex(generateChecksum("MD5", content));
assertThat(bitstream.getSizeBytes(), is((long) content.length()));
assertThat(bitstream.getChecksum(), is(expectedChecksum));
@@ -157,20 +157,16 @@ private void checkGetPut(String bucketName, String content, Bitstream bitstream)
InputStream inputStream = s3BitStoreService.get(bitstream);
assertThat(IOUtils.toString(inputStream, UTF_8), is(content));
-
- String key = s3BitStoreService.getFullKey(bitstream.getInternalId());
- ObjectMetadata objectMetadata = amazonS3Client.getObjectMetadata(bucketName, key);
- assertThat(objectMetadata.getContentMD5(), is(expectedChecksum));
}
@Test
- public void testBitstreamPutAndGetWithoutSpecifingBucket() throws IOException {
+ public void testBitstreamPutAndGetWithoutSpecifyingBucket() throws IOException {
s3BitStoreService.init();
assertThat(s3BitStoreService.getBucketName(), is(DEFAULT_BUCKET_NAME));
- assertThat(amazonS3Client.listBuckets(), contains(bucketNamed(DEFAULT_BUCKET_NAME)));
+ assertThat(s3AsyncClient.listBuckets().join().buckets(), hasItem(bucketNamed(DEFAULT_BUCKET_NAME)));
context.turnOffAuthorisationSystem();
String content = "Test bitstream content";
@@ -179,7 +175,7 @@ public void testBitstreamPutAndGetWithoutSpecifingBucket() throws IOException {
s3BitStoreService.put(bitstream, toInputStream(content));
- String expectedChecksum = Utils.toHex(generateChecksum(content));
+ String expectedChecksum = Utils.toHex(generateChecksum("MD5", content));
assertThat(bitstream.getSizeBytes(), is((long) content.length()));
assertThat(bitstream.getChecksum(), is(expectedChecksum));
@@ -187,11 +183,6 @@ public void testBitstreamPutAndGetWithoutSpecifingBucket() throws IOException {
InputStream inputStream = s3BitStoreService.get(bitstream);
assertThat(IOUtils.toString(inputStream, UTF_8), is(content));
-
- String key = s3BitStoreService.getFullKey(bitstream.getInternalId());
- ObjectMetadata objectMetadata = amazonS3Client.getObjectMetadata(DEFAULT_BUCKET_NAME, key);
- assertThat(objectMetadata.getContentMD5(), is(expectedChecksum));
-
}
@Test
@@ -213,9 +204,9 @@ public void testBitstreamPutAndGetWithSubFolder() throws IOException {
String key = s3BitStoreService.getFullKey(bitstream.getInternalId());
assertThat(key, startsWith("test/DSpace7/"));
- ObjectMetadata objectMetadata = amazonS3Client.getObjectMetadata(DEFAULT_BUCKET_NAME, key);
- assertThat(objectMetadata, notNullValue());
-
+ HeadObjectResponse response = s3AsyncClient.headObject(r ->
+ r.bucket(DEFAULT_BUCKET_NAME).key(key)).join();
+ assertThat(response, notNullValue());
}
@Test
@@ -235,8 +226,8 @@ public void testBitstreamDeletion() throws IOException {
s3BitStoreService.remove(bitstream);
IOException exception = assertThrows(IOException.class, () -> s3BitStoreService.get(bitstream));
- assertThat(exception.getCause(), instanceOf(AmazonS3Exception.class));
- assertThat(((AmazonS3Exception) exception.getCause()).getStatusCode(), is(404));
+ assertThat(exception.getCause(), instanceOf(AwsServiceException.class));
+ assertThat(((AwsServiceException) exception.getCause()).statusCode(), is(404));
}
@@ -264,7 +255,7 @@ public void testAbout() throws IOException {
assertThat(about, hasEntry(is("modified"), notNullValue()));
assertThat(about.size(), is(2));
- String expectedChecksum = Utils.toHex(generateChecksum(content));
+ String expectedChecksum = Utils.toHex(generateChecksum("MD5", content));
about = s3BitStoreService.about(bitstream, List.of("size_bytes", "modified", "checksum"));
assertThat(about, hasEntry("size_bytes", 22L));
@@ -337,7 +328,7 @@ public void givenBitStreamIdentifierWhenIntermediatePathIsComputedThenNotEndingD
String computedPath = this.s3BitStoreService.getIntermediatePath(path.toString());
int slashes = computeSlashes(path.toString());
assertThat(computedPath, Matchers.endsWith(File.separator));
- assertThat(computedPath.split(File.separator).length, Matchers.equalTo(slashes));
+ assertThat(countPathElements(computedPath), Matchers.equalTo(slashes));
path.append("2");
computedPath = this.s3BitStoreService.getIntermediatePath(path.toString());
@@ -362,31 +353,31 @@ public void givenBitStreamIdentidierWhenIntermediatePathIsComputedThenMustBeSpli
String computedPath = this.s3BitStoreService.getIntermediatePath(path.toString());
int slashes = computeSlashes(path.toString());
assertThat(computedPath, Matchers.endsWith(File.separator));
- assertThat(computedPath.split(File.separator).length, Matchers.equalTo(slashes));
+ assertThat(countPathElements(computedPath), Matchers.equalTo(slashes));
path.append("2");
computedPath = this.s3BitStoreService.getIntermediatePath(path.toString());
slashes = computeSlashes(path.toString());
assertThat(computedPath, Matchers.endsWith(File.separator));
- assertThat(computedPath.split(File.separator).length, Matchers.equalTo(slashes));
+ assertThat(countPathElements(computedPath), Matchers.equalTo(slashes));
path.append("3");
computedPath = this.s3BitStoreService.getIntermediatePath(path.toString());
slashes = computeSlashes(path.toString());
assertThat(computedPath, Matchers.endsWith(File.separator));
- assertThat(computedPath.split(File.separator).length, Matchers.equalTo(slashes));
+ assertThat(countPathElements(computedPath), Matchers.equalTo(slashes));
path.append("4");
computedPath = this.s3BitStoreService.getIntermediatePath(path.toString());
slashes = computeSlashes(path.toString());
assertThat(computedPath, Matchers.endsWith(File.separator));
- assertThat(computedPath.split(File.separator).length, Matchers.equalTo(slashes));
+ assertThat(countPathElements(computedPath), Matchers.equalTo(slashes));
path.append("56789");
computedPath = this.s3BitStoreService.getIntermediatePath(path.toString());
slashes = computeSlashes(path.toString());
assertThat(computedPath, Matchers.endsWith(File.separator));
- assertThat(computedPath.split(File.separator).length, Matchers.equalTo(slashes));
+ assertThat(countPathElements(computedPath), Matchers.equalTo(slashes));
}
@Test
@@ -409,16 +400,16 @@ public void givenBitStreamIdentifierWithSlashesWhenSanitizedThenSlashesMustBeRem
public void testDoNotInitializeConfigured() throws Exception {
String assetstores3enabledOldValue = configurationService.getProperty("assetstore.s3.enabled");
configurationService.setProperty("assetstore.s3.enabled", "false");
- s3BitStoreService = new S3BitStoreService(amazonS3Client);
+ s3BitStoreService = new S3BitStoreService(s3AsyncClient);
s3BitStoreService.init();
assertFalse(s3BitStoreService.isInitialized());
assertFalse(s3BitStoreService.isEnabled());
configurationService.setProperty("assetstore.s3.enabled", assetstores3enabledOldValue);
}
- private byte[] generateChecksum(String content) {
+ private byte[] generateChecksum(String algorithm, String content) {
try {
- MessageDigest m = MessageDigest.getInstance("MD5");
+ MessageDigest m = MessageDigest.getInstance(algorithm);
m.update(content.getBytes());
return m.digest();
} catch (NoSuchAlgorithmException e) {
@@ -426,13 +417,6 @@ private byte[] generateChecksum(String content) {
}
}
- private AmazonS3 createAmazonS3Client() {
- return AmazonS3ClientBuilder.standard()
- .withCredentials(new AWSStaticCredentialsProvider(new AnonymousAWSCredentials()))
- .withEndpointConfiguration(new EndpointConfiguration("http://127.0.0.1:8001", DEFAULT_REGION.getName()))
- .build();
- }
-
private Item createItem() {
return ItemBuilder.createItem(context, collection)
.withTitle("Test item")
@@ -450,7 +434,7 @@ private Bitstream createBitstream(String content) {
}
private Matcher bucketNamed(String name) {
- return LambdaMatcher.matches(bucket -> bucket.getName().equals(name));
+ return LambdaMatcher.matches(bucket -> bucket.name().equals(name));
}
private InputStream toInputStream(String content) {
@@ -465,4 +449,12 @@ private int computeSlashes(String internalId) {
return Math.min(slashes, S3BitStoreService.directoryLevels);
}
+ // Count the number of elements in a Unix or Windows path.
+ // We use 'Paths' instead of splitting on slashes because these OSes use different path separators.
+ private int countPathElements(String stringPath) {
+ List pathElements = new ArrayList<>();
+ Paths.get(stringPath).forEach(p -> pathElements.add(p.toString()));
+ return pathElements.size();
+ }
+
}
diff --git a/dspace-api/src/test/resources/org/dspace/app/mediafilter/cat-rotated-90.jpg b/dspace-api/src/test/resources/org/dspace/app/mediafilter/cat-rotated-90.jpg
new file mode 100644
index 000000000000..5c0f91c4eda7
Binary files /dev/null and b/dspace-api/src/test/resources/org/dspace/app/mediafilter/cat-rotated-90.jpg differ
diff --git a/dspace-api/src/test/resources/org/dspace/app/mediafilter/cat.jpg b/dspace-api/src/test/resources/org/dspace/app/mediafilter/cat.jpg
new file mode 100644
index 000000000000..b282aa970c88
Binary files /dev/null and b/dspace-api/src/test/resources/org/dspace/app/mediafilter/cat.jpg differ
diff --git a/dspace-iiif/pom.xml b/dspace-iiif/pom.xml
index 4a93ed41c006..968c2678b7bc 100644
--- a/dspace-iiif/pom.xml
+++ b/dspace-iiif/pom.xml
@@ -15,7 +15,7 @@
org.dspace
dspace-parent
- 8.2
+ 8.3
..
diff --git a/dspace-oai/pom.xml b/dspace-oai/pom.xml
index 8a9bd8aa4044..01bdb90c2285 100644
--- a/dspace-oai/pom.xml
+++ b/dspace-oai/pom.xml
@@ -8,7 +8,7 @@
dspace-parent
org.dspace
- 8.2
+ 8.3
..
diff --git a/dspace-oai/src/main/java/org/dspace/xoai/util/ItemUtils.java b/dspace-oai/src/main/java/org/dspace/xoai/util/ItemUtils.java
index 40a193ea2905..78c98533e0b4 100644
--- a/dspace-oai/src/main/java/org/dspace/xoai/util/ItemUtils.java
+++ b/dspace-oai/src/main/java/org/dspace/xoai/util/ItemUtils.java
@@ -18,6 +18,7 @@
import com.lyncode.xoai.dataprovider.xml.xoai.Element;
import com.lyncode.xoai.dataprovider.xml.xoai.Metadata;
import com.lyncode.xoai.util.Base64Utils;
+import org.apache.commons.text.StringEscapeUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.app.util.factory.UtilServiceFactory;
@@ -143,7 +144,7 @@ private static Element createBundlesElement(Context context, Item item) throws S
bitstream.getField().add(createValue("name", name));
}
if (oname != null) {
- bitstream.getField().add(createValue("originalName", name));
+ bitstream.getField().add(createValue("originalName", oname));
}
if (description != null) {
bitstream.getField().add(createValue("description", description));
@@ -165,6 +166,19 @@ private static Element createBundlesElement(Context context, Item item) throws S
return bundles;
}
+ /**
+ * Sanitizes a string to remove characters that are invalid
+ * in XML 1.0 using the Apache Commons Text library.
+ * @param value The string to sanitize.
+ * @return A sanitized string, or null if the input was null.
+ */
+ private static String sanitize(String value) {
+ if (value == null) {
+ return null;
+ }
+ return StringEscapeUtils.escapeXml10(value);
+ }
+
/**
* This method will add metadata information about associated resource policies for a give bitstream.
* It will parse of relevant policies and add metadata information
@@ -281,7 +295,7 @@ private static void fillSchemaElement(Element schema, MetadataValue val) throws
valueElem = language;
}
- valueElem.getField().add(createValue("value", val.getValue()));
+ valueElem.getField().add(createValue("value", sanitize(val.getValue())));
if (val.getAuthority() != null) {
valueElem.getField().add(createValue("authority", val.getAuthority()));
if (val.getConfidence() != Choices.CF_NOVALUE) {
diff --git a/dspace-rdf/pom.xml b/dspace-rdf/pom.xml
index f18177116b45..180b7844c210 100644
--- a/dspace-rdf/pom.xml
+++ b/dspace-rdf/pom.xml
@@ -9,7 +9,7 @@
org.dspace
dspace-parent
- 8.2
+ 8.3
..
diff --git a/dspace-server-webapp/pom.xml b/dspace-server-webapp/pom.xml
index e38e99a30cb2..adba3efc08d0 100644
--- a/dspace-server-webapp/pom.xml
+++ b/dspace-server-webapp/pom.xml
@@ -14,7 +14,7 @@
org.dspace
dspace-parent
- 8.2
+ 8.3
..
@@ -481,6 +481,13 @@