Merge branch 'main' into CST-5997-LiveImportFrom-Pubmed-NotWorking

dspace-api/src/main/java/org/dspace/core/Context.java

@@ -657,6 +657,15 @@ public class Context implements AutoCloseable {
         return myGroups;
     }
 
+    /**
+     * Get a set of all of the special groups uuids that current user is a member of.
+     *
+     * @return list of special groups uuids
+     */
+    public Set<UUID> getSpecialGroupUuids() {
+        return CollectionUtils.isEmpty(specialGroups) ? Set.of() : specialGroups;
+    }
+
     /**
      * Temporary change the user bound to the context, empty the special groups that
      * are retained to allow subsequent restore

dspace-api/src/main/java/org/dspace/discovery/indexobject/IndexFactoryImpl.java

@@ -113,9 +113,11 @@ public abstract class IndexFactoryImpl<T extends IndexableObject, S> implements
                         log.info("Full text is larger than the configured limit (discovery.solr.fulltext.charLimit)."
                                      + " Only the first {} characters were indexed.", charLimit);
                     } else {
+                        log.error("Tika parsing error. Could not index full text.", saxe);
                         throw new IOException("Tika parsing error. Could not index full text.", saxe);
                     }
                 } catch (TikaException ex) {
+                    log.error("Tika parsing error. Could not index full text.", ex);
                     throw new IOException("Tika parsing error. Could not index full text.", ex);
                 }
 

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

@@ -569,4 +569,9 @@ public class EPersonServiceImpl extends DSpaceObjectServiceImpl<EPerson> impleme
     public int countTotal(Context context) throws SQLException {
         return ePersonDAO.countRows(context);
     }
+
+    @Override
+    public String getName(EPerson dso) {
+        return dso.getName();
+    }
 }

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

@@ -829,4 +829,9 @@ public class GroupServiceImpl extends DSpaceObjectServiceImpl<Group> implements
                                            final MetadataField metadataField) throws SQLException {
         return groupDAO.findByMetadataField(context, searchValue, metadataField);
     }
+
+    @Override
+    public String getName(Group dso) {
+        return dso.getName();
+    }
 }

dspace-oai/src/main/java/org/dspace/xoai/controller/DSpaceOAIDataProvider.java

@@ -72,7 +72,12 @@ public class DSpaceOAIDataProvider {
 
     private DSpaceResumptionTokenFormatter resumptionTokenFormat = new DSpaceResumptionTokenFormatter();
 
-    @RequestMapping({"", "/"})
+    @RequestMapping("")
+    public void index(HttpServletResponse response, HttpServletRequest request) throws IOException {
+        response.sendRedirect(request.getRequestURI() + "/");
+    }
+
+    @RequestMapping({"/"})
     public String indexAction(HttpServletResponse response, Model model) throws ServletException {
         try {
             XOAIManager manager = xoaiManagerResolver.getManager();

dspace-server-webapp/src/main/java/org/dspace/app/rest/BitstreamRestController.java

@@ -153,8 +153,9 @@ public class BitstreamRestController {
             }
 
             org.dspace.app.rest.utils.BitstreamResource bitstreamResource =
-                new org.dspace.app.rest.utils.BitstreamResource(
+                new org.dspace.app.rest.utils.BitstreamResource(name, uuid,
-                    name, uuid, currentUser != null ? currentUser.getID() : null, citationEnabledForBitstream);
+                    currentUser != null ? currentUser.getID() : null,
+                    context.getSpecialGroupUuids(), citationEnabledForBitstream);
 
             //We have all the data we need, close the connection to the database so that it doesn't stay open during
             //download/streaming

dspace-server-webapp/src/main/java/org/dspace/app/rest/model/RelationshipRest.java

@@ -18,10 +18,18 @@ import org.dspace.app.rest.RestResourceController;
  * This class acts as a data holder for the RelationshipResource
  * Refer to {@link org.dspace.content.Relationship} for explanation about the properties
  */
+@LinksRest(links = {
+    @LinkRest(
+        name = RelationshipRest.RELATIONSHIP_TYPE,
+        method = "getRelationshipType"
+    )
+})
 public class RelationshipRest extends BaseObjectRest<Integer> {
     public static final String NAME = "relationship";
     public static final String CATEGORY = "core";
 
+    public static final String RELATIONSHIP_TYPE = "relationshipType";
+
     @JsonIgnore
     private UUID leftId;
     @JsonIgnore

dspace-server-webapp/src/main/java/org/dspace/app/rest/repository/RelationshipTypeRelationshipLinkRepository.java

@@ -0,0 +1,56 @@
+/**
+ * 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.rest.repository;
+
+import java.sql.SQLException;
+import javax.annotation.Nullable;
+import javax.servlet.http.HttpServletRequest;
+
+import org.dspace.app.rest.model.RelationshipRest;
+import org.dspace.app.rest.model.RelationshipTypeRest;
+import org.dspace.app.rest.projection.Projection;
+import org.dspace.content.Relationship;
+import org.dspace.content.RelationshipType;
+import org.dspace.content.service.RelationshipService;
+import org.dspace.core.Context;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.data.domain.Pageable;
+import org.springframework.data.rest.webmvc.ResourceNotFoundException;
+import org.springframework.security.access.prepost.PreAuthorize;
+import org.springframework.stereotype.Component;
+
+/**
+ * Link repository for "relationshipType" subresource of an individual Relationship.
+ */
+@Component(RelationshipRest.CATEGORY + "." + RelationshipRest.NAME + "." + RelationshipRest.RELATIONSHIP_TYPE)
+public class RelationshipTypeRelationshipLinkRepository extends AbstractDSpaceRestRepository
+        implements LinkRestRepository {
+
+    @Autowired
+    RelationshipService relationshipService;
+
+    @PreAuthorize("permitAll()")
+    public RelationshipTypeRest getRelationshipType(@Nullable HttpServletRequest request,
+                                                            Integer relationshipId,
+                                                            @Nullable Pageable optionalPageable,
+                                                            Projection projection) {
+        try {
+            Context context = obtainContext();
+            Relationship relationship = relationshipService.find(context, relationshipId);
+            if (relationship == null) {
+                throw new ResourceNotFoundException("No such relationship: " + relationshipId);
+            }
+            int total = relationshipService.countByRelationshipType(context, relationship.getRelationshipType());
+            Pageable pageable = utils.getPageable(optionalPageable);
+            RelationshipType relationshipType = relationship.getRelationshipType();
+            return converter.toRest(relationshipType, projection);
+        } catch (SQLException e) {
+            throw new RuntimeException(e);
+        }
+    }
+}

dspace-server-webapp/src/main/java/org/dspace/app/rest/utils/BitstreamResource.java

@@ -11,6 +11,7 @@ import java.io.ByteArrayInputStream;
 import java.io.IOException;
 import java.io.InputStream;
 import java.sql.SQLException;
+import java.util.Set;
 import java.util.UUID;
 
 import org.apache.commons.io.IOUtils;
@@ -40,6 +41,7 @@ public class BitstreamResource extends AbstractResource {
     private UUID currentUserUUID;
     private boolean shouldGenerateCoverPage;
     private byte[] file;
+    private Set<UUID> currentSpecialGroups;
 
     private BitstreamService bitstreamService = ContentServiceFactory.getInstance().getBitstreamService();
     private EPersonService ePersonService = EPersonServiceFactory.getInstance().getEPersonService();
@@ -47,11 +49,12 @@ public class BitstreamResource extends AbstractResource {
         new DSpace().getServiceManager()
                     .getServicesByType(CitationDocumentService.class).get(0);
 
-    public BitstreamResource(String name, UUID uuid, UUID currentUserUUID,
+    public BitstreamResource(String name, UUID uuid, UUID currentUserUUID, Set<UUID> currentSpecialGroups,
         boolean shouldGenerateCoverPage) {
         this.name = name;
         this.uuid = uuid;
         this.currentUserUUID = currentUserUUID;
+        this.currentSpecialGroups = currentSpecialGroups;
         this.shouldGenerateCoverPage = shouldGenerateCoverPage;
     }
 
@@ -84,9 +87,8 @@ public class BitstreamResource extends AbstractResource {
 
     @Override
     public InputStream getInputStream() throws IOException {
-        try (Context context = new Context()) {
+        try (Context context = initializeContext()) {
-            EPerson currentUser = ePersonService.find(context, currentUserUUID);
+
-            context.setCurrentUser(currentUser);
             Bitstream bitstream = bitstreamService.find(context, uuid);
             InputStream out;
 
@@ -110,9 +112,7 @@ public class BitstreamResource extends AbstractResource {
 
     @Override
     public long contentLength() throws IOException {
-        try (Context context = new Context()) {
+        try (Context context = initializeContext()) {
-            EPerson currentUser = ePersonService.find(context, currentUserUUID);
-            context.setCurrentUser(currentUser);
             Bitstream bitstream = bitstreamService.find(context, uuid);
             if (shouldGenerateCoverPage) {
                 return getCoverpageByteArray(context, bitstream).length;
@@ -123,4 +123,12 @@ public class BitstreamResource extends AbstractResource {
             throw new IOException(e);
         }
     }
+
+    private Context initializeContext() throws SQLException {
+        Context context = new Context();
+        EPerson currentUser = ePersonService.find(context, currentUserUUID);
+        context.setCurrentUser(currentUser);
+        currentSpecialGroups.forEach(context::setSpecialGroup);
+        return context;
+    }
 }

dspace-server-webapp/src/test/java/org/dspace/app/oai/OAIpmhIT.java

@@ -63,9 +63,9 @@ public class OAIpmhIT extends AbstractControllerIntegrationTest {
     private ConfigurationService configurationService;
 
     // All OAI-PMH paths that we test against
-    private final String ROOT_PATH = "/oai";
+    private final String ROOT_PATH = "/oai/";
     private final String DEFAULT_CONTEXT_PATH = "request";
-    private final String DEFAULT_CONTEXT = ROOT_PATH + "/" + DEFAULT_CONTEXT_PATH;
+    private final String DEFAULT_CONTEXT = ROOT_PATH + DEFAULT_CONTEXT_PATH;
 
     // Mock to ensure XOAI caching is disabled for all tests (see @Before method)
     @MockBean

dspace-server-webapp/src/test/java/org/dspace/app/rest/BitstreamRestControllerIT.java

@@ -684,6 +684,56 @@ public class BitstreamRestControllerIT extends AbstractControllerIntegrationTest
             checkNumberOfStatsRecords(bitstream, 1);
     }
 
+    @Test
+    public void restrictedSpecialGroupBitstreamTest() throws Exception {
+        context.turnOffAuthorisationSystem();
+
+        parentCommunity = CommunityBuilder.createCommunity(context)
+            .withName("Parent Community")
+            .build();
+
+        Collection col1 = CollectionBuilder.createCollection(context, parentCommunity)
+            .withName("Collection 1")
+            .build();
+
+        Group restrictedGroup = GroupBuilder.createGroup(context)
+            .withName("Restricted Group")
+            .build();
+
+        String bitstreamContent = "Private!";
+        try (InputStream is = IOUtils.toInputStream(bitstreamContent, CharEncoding.UTF_8)) {
+
+            Item item = ItemBuilder.createItem(context, col1)
+                .withTitle("item 1")
+                .withIssueDate("2013-01-17")
+                .withAuthor("Doe, John")
+                .build();
+
+            bitstream = BitstreamBuilder
+                .createBitstream(context, item, is)
+                .withName("Test Embargoed Bitstream")
+                .withDescription("This bitstream is embargoed")
+                .withMimeType("text/plain")
+                .withReaderGroup(restrictedGroup)
+                .build();
+        }
+
+        context.restoreAuthSystemState();
+
+        String authToken = getAuthToken(eperson.getEmail(), password);
+        getClient(authToken).perform(get("/api/core/bitstreams/" + bitstream.getID() + "/content"))
+            .andExpect(status().isForbidden());
+
+        configurationService.setProperty("authentication-password.login.specialgroup", "Restricted Group");
+
+        authToken = getAuthToken(eperson.getEmail(), password);
+        getClient(authToken).perform(get("/api/core/bitstreams/" + bitstream.getID() + "/content"))
+            .andExpect(status().isOk());
+
+        checkNumberOfStatsRecords(bitstream, 1);
+
+    }
+
     @Test
     public void restrictedGroupBitstreamAccessGrantByAdminsTest() throws Exception {
         context.turnOffAuthorisationSystem();

dspace-server-webapp/src/test/java/org/dspace/app/rest/RelationshipRestRepositoryIT.java

@@ -3164,4 +3164,28 @@ public class RelationshipRestRepositoryIT extends AbstractEntityIntegrationTest
                    .andExpect(jsonPath("$.page.totalElements", is(2)));
     }
 
+    @Test
+    public void findTheCreatedRelationshipTypeTest() throws Exception {
+
+        context.turnOffAuthorisationSystem();
+
+        Relationship relationship = RelationshipBuilder
+            .createRelationshipBuilder(context, author1, orgUnit1, isOrgUnitOfPersonRelationshipType).build();
+
+        context.restoreAuthSystemState();
+
+        Integer relationshipId = relationship.getID();
+        getClient().perform(get("/api/core/relationships/" + relationshipId))
+                   .andExpect(status().isOk())
+                   .andExpect(jsonPath("$.id", is(relationship.getID())))
+                   .andExpect(jsonPath("$._embedded.relationships").doesNotExist())
+                   .andExpect(jsonPath("$._links.relationshipType.href",
+                       containsString("/api/core/relationships/" + relationshipId + "/relationshipType"))
+                   );
+
+        String adminToken = getAuthToken(admin.getEmail(), password);
+        getClient(adminToken).perform(get("/api/core/relationships/" + relationshipId + "/relationshipType"))
+                             .andExpect(status().isOk());
+    }
+
 }