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

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Mykhaylo
2022-06-08 13:16:16 +02:00
parent 99875b307d 0e461d546a
commit 1de78d5e66
12 changed files with 185 additions and 12 deletions
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9
dspace-api/src/main/java/org/dspace/core/Context.java
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@@ -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

2
dspace-api/src/main/java/org/dspace/discovery/indexobject/IndexFactoryImpl.java
View File

@@ -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);
}

5
dspace-api/src/main/java/org/dspace/eperson/EPersonServiceImpl.java
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@@ -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();
}
}

5
dspace-api/src/main/java/org/dspace/eperson/GroupServiceImpl.java
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@@ -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();
}
}

7
dspace-oai/src/main/java/org/dspace/xoai/controller/DSpaceOAIDataProvider.java
View File

@@ -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();

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

@@ -153,8 +153,9 @@ public class BitstreamRestController {
}
org.dspace.app.rest.utils.BitstreamResource bitstreamResource =
new org.dspace.app.rest.utils.BitstreamResource(
name, uuid, currentUser != null ? currentUser.getID() : null, citationEnabledForBitstream);
new org.dspace.app.rest.utils.BitstreamResource(name, uuid,
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

8
dspace-server-webapp/src/main/java/org/dspace/app/rest/model/RelationshipRest.java
View File

@@ -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

56
dspace-server-webapp/src/main/java/org/dspace/app/rest/repository/RelationshipTypeRelationshipLinkRepository.java Normal file
View File

@@ -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);
}
}
}

22
dspace-server-webapp/src/main/java/org/dspace/app/rest/utils/BitstreamResource.java
View File

@@ -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()) {
EPerson currentUser = ePersonService.find(context, currentUserUUID);
context.setCurrentUser(currentUser);
try (Context context = initializeContext()) {
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()) {
EPerson currentUser = ePersonService.find(context, currentUserUUID);
context.setCurrentUser(currentUser);
try (Context context = initializeContext()) {
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;
}
}

4
dspace-server-webapp/src/test/java/org/dspace/app/oai/OAIpmhIT.java
View File

@@ -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

50
dspace-server-webapp/src/test/java/org/dspace/app/rest/BitstreamRestControllerIT.java
View File

@@ -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();

24
dspace-server-webapp/src/test/java/org/dspace/app/rest/RelationshipRestRepositoryIT.java
View File

@@ -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());
}
}