Merge actual 7.5. version into TUL

.github/workflows/build.yml

@@ -39,7 +39,7 @@ jobs:
           #  - failsafe.rerunFailingTestsCount => try again for flakey tests, and keep track of/report on number of retries
           - type: "Integration Tests"
             java: 11
-            mvnflags: "-DskipIntegrationTests=false -Denforcer.skip=true -Dcheckstyle.skip=true -Dlicense.skip=true -Dxml.skip=true -Dfailsafe.rerunFailingTestsCount=2"
+            mvnflags: "-DskipIntegrationTests=false -Denforcer.skip=true -Dcheckstyle.skip=true -Dlicense.skip=true -Dxml.skip=true -Dfailsafe.rerunFailingTestsCount=2 -fae"
             resultsdir: "**/target/failsafe-reports/**"
       # Do NOT exit immediately if one matrix job fails
       # This ensures ITs continue running even if Unit Tests fail, or visa versa

.github/workflows/docker.yml

@@ -7,7 +7,6 @@ on:
   push:
     branches:
       - dtq-dev
-      - dtq-dev-present
   pull_request:
   workflow_dispatch:
 
@@ -178,4 +177,4 @@ jobs:
           --request POST \
           https://api.github.com/repos/dataquest-dev/\
           dspace-angular/actions/workflows/deploy.yml/dispatches \
-          --data "{\"ref\":\"refs/heads/customer/TUL\"}"
+          --data "{\"ref\":\"refs/heads/dtq-dev-7.5\"}"

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

@@ -103,6 +103,17 @@ public static void main(String[] argv)
     protected CreateAdministrator()
         throws Exception {
         context = new Context();
+        try {
+            context.getDBConfig();
+        } catch (NullPointerException npr) {
+            // if database is null, there is no point in continuing. Prior to this exception and catch,
+            // NullPointerException was thrown, that wasn't very helpful.
+            throw new IllegalStateException("Problem connecting to database. This" +
+                    " indicates issue with either network or version (or possibly some other). " +
+                    "If you are running this in docker-compose, please make sure dspace-cli was " +
+                    "built from the same sources as running dspace container AND that they are in " +
+                    "the same project/network.");
+        }
         groupService = EPersonServiceFactory.getInstance().getGroupService();
         ePersonService = EPersonServiceFactory.getInstance().getEPersonService();
         clarinUserRegistrationService = ClarinServiceFactory.getInstance().getClarinUserRegistration();

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

@@ -522,4 +522,12 @@ public static List<String> differenceInSubmissionFields(Collection fromCollectio
 
         return ListUtils.removeAll(fromFieldName, toFieldName);
     }
+
+
+    public static String formatNetId(String netId, String organization) {
+        if (StringUtils.isBlank(netId)) {
+            return null;
+        }
+        return netId + "[" + organization + "]";
+    }
 }

dspace-api/src/main/java/org/dspace/authenticate/clarin/ClarinShibAuthentication.java

@@ -24,6 +24,7 @@
 import org.apache.commons.lang3.StringUtils;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
+import org.dspace.app.util.Util;
 import org.dspace.authenticate.AuthenticationMethod;
 import org.dspace.authenticate.factory.AuthenticateServiceFactory;
 import org.dspace.authorize.AuthorizeException;
@@ -82,6 +83,9 @@ public class ClarinShibAuthentication implements AuthenticationMethod {
      */
     private static final Logger log = LogManager.getLogger(ClarinShibAuthentication.class);
 
+    // If the user which are in the login process has email already associated with a different users email.
+    private boolean isDuplicateUser = false;
+
     /**
      * Additional metadata mappings
      **/
@@ -249,7 +253,7 @@ public int authenticate(Context context, String username, String password,
             EPerson eperson = findEPerson(context, request);
 
             // Step 2: Register New User, if necessary
-            if (eperson == null && autoRegister) {
+            if (eperson == null && autoRegister && !isDuplicateUser) {
                 eperson = registerNewEPerson(context, request);
             }
 
@@ -550,7 +554,8 @@ protected EPerson findEPerson(Context context, HttpServletRequest request) throw
 
         // 1) First, look for a netid header.
         if (netidHeader != null) {
-            String netid = findSingleAttribute(request, netidHeader);
+            String org = shibheaders.get_idp();
+            String netid = Util.formatNetId(findSingleAttribute(request, netidHeader), org);
             if (StringUtils.isEmpty(netid)) {
                 netid = shibheaders.get_single(netidHeader);
             }
@@ -605,6 +610,7 @@ protected EPerson findEPerson(Context context, HttpServletRequest request) throw
                                     "'. This might be a possible hacking attempt to steal another users " +
                                     "credentials. If the user's netid has changed you will need to manually " +
                                     "change it to the correct value or unset it in the database.");
+                    this.isDuplicateUser = true;
                     eperson = null;
                 }
             }
@@ -687,7 +693,7 @@ protected EPerson registerNewEPerson(Context context, HttpServletRequest request
         // CLARIN
 
         // Header values
-        String netid = findSingleAttribute(request, netidHeader);
+        String netid = Util.formatNetId(findSingleAttribute(request, netidHeader), org);
         String email = findSingleAttribute(request, emailHeader);
         String fname = findSingleAttribute(request, fnameHeader);
         String lname = findSingleAttribute(request, lnameHeader);
@@ -706,7 +712,7 @@ protected EPerson registerNewEPerson(Context context, HttpServletRequest request
             lname = shibheaders.get_single(lnameHeader);
         }
 
-        if ( email == null && netid == null) {
+        if ( email == null ) {
             // We require that there be an email, first name, and last name. If we
             // don't have at least these three pieces of information then we fail.
             String message = "Unable to register new eperson because we are unable to find an email address along " +
@@ -809,7 +815,7 @@ protected void updateEPerson(Context context, HttpServletRequest request, EPerso
         String fnameHeader = configurationService.getProperty("authentication-shibboleth.firstname-header");
         String lnameHeader = configurationService.getProperty("authentication-shibboleth.lastname-header");
 
-        String netid = findSingleAttribute(request, netidHeader);
+        String netid = Util.formatNetId(findSingleAttribute(request, netidHeader), shibheaders.get_idp());
         String email = findSingleAttribute(request, emailHeader);
         String fname = findSingleAttribute(request, fnameHeader);
         String lname = findSingleAttribute(request, lnameHeader);

dspace-api/src/main/java/org/dspace/authenticate/clarin/ShibHeaders.java

@@ -17,6 +17,9 @@
 import org.apache.commons.lang.StringUtils;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
+import org.dspace.app.util.Util;
+import org.dspace.services.ConfigurationService;
+import org.dspace.services.factory.DSpaceServicesFactory;
 
 /**
  * Shibboleth authentication header abstraction for DSpace
@@ -29,6 +32,8 @@ public class ShibHeaders {
     // constants
     //
     private static final String header_separator_ = ";";
+    private String netIdHeader = "";
+    ConfigurationService configurationService = DSpaceServicesFactory.getInstance().getConfigurationService();
 
     // variables
     //
@@ -58,10 +63,12 @@ public ShibHeaders(String shibHeaders) {
 
     public void initialise(HttpServletRequest request, List<String> interesting) {
         headers_ = new Headers(request, header_separator_, interesting);
+        this.initializeNetIdHeader();
     }
 
     public void initialise(String shibHeaders) {
         headers_ = new Headers(shibHeaders, header_separator_);
+        this.initializeNetIdHeader();
     }
 
     //
@@ -97,6 +104,10 @@ public List<String> get(String key) {
     public String get_single(String name) {
         List<String> values = get(name);
         if (values != null && !values.isEmpty()) {
+            // Format netId
+            if (StringUtils.equals(name, this.netIdHeader)) {
+                return Util.formatNetId(values.get(0), this.get_idp());
+            }
             return values.get(0);
         }
         return null;
@@ -137,4 +148,8 @@ public void log_headers() {
                     i.getKey(), StringUtils.join(i.getValue().toArray(), ",") ));
         }
     }
+
+    private void initializeNetIdHeader() {
+        this.netIdHeader = configurationService.getProperty("authentication-shibboleth.netid-header");
+    }
 }

dspace-api/src/main/java/org/dspace/content/dao/impl/clarin/ClarinVerificationTokenDAOImpl.java

@@ -9,8 +9,12 @@
 
 import java.sql.SQLException;
 import javax.persistence.Query;
+import javax.persistence.criteria.CriteriaBuilder;
+import javax.persistence.criteria.CriteriaQuery;
+import javax.persistence.criteria.Root;
 
 import org.dspace.content.clarin.ClarinVerificationToken;
+import org.dspace.content.clarin.ClarinVerificationToken_;
 import org.dspace.content.dao.clarin.ClarinVerificationTokenDAO;
 import org.dspace.core.AbstractHibernateDAO;
 import org.dspace.core.Context;
@@ -39,13 +43,14 @@ public ClarinVerificationToken findByToken(Context context, String token) throws
 
     @Override
     public ClarinVerificationToken findByNetID(Context context, String netID) throws SQLException {
-        Query query = createQuery(context, "SELECT cvt " +
-                "FROM ClarinVerificationToken cvt " +
-                "WHERE cvt.ePersonNetID = :netID");
-
-        query.setParameter("netID", netID);
-        query.setHint("org.hibernate.cacheable", Boolean.TRUE);
-
-        return singleResult(query);
+        CriteriaBuilder criteriaBuilder = getCriteriaBuilder(context);
+        CriteriaQuery criteriaQuery = getCriteriaQuery(criteriaBuilder, ClarinVerificationToken.class);
+        Root<ClarinVerificationToken> clarinVerificationTokenRoot = criteriaQuery.from(ClarinVerificationToken.class);
+        criteriaQuery.select(clarinVerificationTokenRoot);
+        criteriaQuery.where(criteriaBuilder.like(clarinVerificationTokenRoot.get(ClarinVerificationToken_.ePersonNetID),
+                "%" + netID + "%"));
+        criteriaQuery.orderBy(criteriaBuilder.asc(clarinVerificationTokenRoot.
+                get(ClarinVerificationToken_.ePersonNetID)));
+        return singleResult(context, criteriaQuery);
     }
 }

dspace-api/src/main/java/org/dspace/content/packager/RoleDisseminator.java

@@ -17,6 +17,7 @@
 import java.sql.SQLException;
 import java.util.ArrayList;
 import java.util.List;
+import java.util.Objects;
 import javax.xml.stream.XMLOutputFactory;
 import javax.xml.stream.XMLStreamException;
 import javax.xml.stream.XMLStreamWriter;
@@ -78,6 +79,8 @@ public class RoleDisseminator implements PackageDisseminator {
     public static final String CAN_LOGIN = "CanLogin";
     public static final String REQUIRE_CERTIFICATE = "RequireCertificate";
     public static final String SELF_REGISTERED = "SelfRegistered";
+    public static final String WELCOME_INFO = "welcomeInfo";
+    public static final String CAN_EDIT_SUBMISSION_METADATA = "canEditSubmissionMetadata";
 
     // Valid type values for Groups (only used when Group is associated with a Community or Collection)
     public static final String GROUP_TYPE_ADMIN = "ADMIN";
@@ -461,6 +464,13 @@ protected void writeEPerson(EPerson eperson, XMLStreamWriter writer,
             writer.writeEmptyElement(SELF_REGISTERED);
         }
 
+        if (Objects.nonNull(eperson.getWelcomeInfo())) {
+            writer.writeEmptyElement(WELCOME_INFO);
+        }
+
+        if (Objects.nonNull(eperson.getCanEditSubmissionMetadata())) {
+            writer.writeEmptyElement(CAN_EDIT_SUBMISSION_METADATA);
+        }
         writer.writeEndElement();
     }
 

dspace-api/src/main/java/org/dspace/eperson/EPerson.java

@@ -80,6 +80,12 @@ public class EPerson extends DSpaceObject implements DSpaceObjectLegacySupport {
     @ManyToMany(fetch = FetchType.LAZY, mappedBy = "epeople")
     private final List<Group> groups = new ArrayList<>();
 
+    @Column(name = "welcome_info")
+    private String welcomeInfo;
+
+    @Column(name = "can_edit_submission_metadata")
+    private Boolean canEditSubmissionMetadata;
+
     /**
      * The e-mail field (for sorting)
      */
@@ -446,6 +452,18 @@ public Date getPreviousActive() {
         return previousActive;
     }
 
+    public String getWelcomeInfo() {
+        return welcomeInfo;
+    }
+    public void setWelcomeInfo(String welcomeInfo) {
+        this.welcomeInfo = welcomeInfo;
+    }
+    public Boolean getCanEditSubmissionMetadata() {
+        return canEditSubmissionMetadata;
+    }
+    public void setCanEditSubmissionMetadata(Boolean canEditSubmissionMetadata) {
+        this.canEditSubmissionMetadata = canEditSubmissionMetadata;
+    }
     public boolean hasPasswordSet() {
         return StringUtils.isNotBlank(getPassword());
     }

dspace-api/src/main/java/org/dspace/handle/HandleClarinServiceImpl.java

@@ -430,6 +430,32 @@ public String getDeadSince(Context context, String handle) throws SQLException {
                 format(timestamptz) : null;
     }
 
+    @Override
+    public Handle createHandle(Context context, String handleStr) throws SQLException, AuthorizeException {
+        // Check authorisation: Only admins may create DC types
+        if (!authorizeService.isAdmin(context)) {
+            throw new AuthorizeException(
+                    "Only administrators may modify the handle registry");
+        }
+
+        String handleId;
+        // Do we want to generate the new handleId or use entered handleStr?
+        if (StringUtils.isNotBlank(handleStr)) {
+            // We use handleStr entered by use
+            handleId = handleStr;
+        } else {
+            // We generate new handleId
+            handleId = createId(context);
+        }
+
+        Handle handle = handleDAO.create(context, new Handle());
+        // Set handleId
+        handle.setHandle(handleId);
+        this.save(context, handle);
+        log.debug("Created new Handle with handle " + handleId);
+        return handle;
+    }
+
     /**
      * Strips the part identifier from the handle
      *

dspace-api/src/main/java/org/dspace/handle/service/HandleClarinService.java

@@ -215,4 +215,15 @@ public void update(Context context, Handle handleObject, String newHandle,
      * @throws SQLException if database error
      */
     public String getDeadSince(Context context, String handle) throws SQLException;
+
+    /**
+     * Create handle without dspace object.
+     * This method is created for migration purposes.
+     * @param context  context
+     * @param handle   handle of Handle object
+     * @return created Handle
+     * @throws SQLException       if database error
+     * @throws AuthorizeException if authorization error
+     */
+    public Handle createHandle(Context context, String handle) throws SQLException, AuthorizeException;
 }