Merge branch 'dev' into #343_suggest_change_and_log

# Conflicts:
#	registry-service/src/main/java/org/gbif/registry/service/collections/PrimaryCollectionEntityService.java
#	registry-ws/src/main/java/org/gbif/registry/ws/resources/collections/PersonResource.java

registry-events/src/main/java/org/gbif/registry/search/DatasetIndexUpdateListener.java

@@ -19,7 +19,6 @@
 import org.gbif.api.model.registry.Installation;
 import org.gbif.api.model.registry.Network;
 import org.gbif.api.model.registry.Organization;
-import org.gbif.api.model.registry.Tag;
 import org.gbif.api.service.registry.DatasetService;
 import org.gbif.registry.events.ChangedComponentEvent;
 import org.gbif.registry.events.CreateEvent;
@@ -100,14 +99,17 @@ public final <T> void updated(UpdateEvent<T> event) {
   public final <T> void deleted(DeleteEvent<T> event) {
     if (event.getObjectClass().equals(Dataset.class)) {
       indexService.delete((Dataset) event.getOldObject());
+    } else if (event.getObjectClass().equals(Organization.class)) {
+      indexService.index((Organization) event.getOldObject());
+    } else if (event.getObjectClass().equals(Network.class)) {
+      indexService.index((Network) event.getOldObject());
     }
   }
 
   @Subscribe
   public final void updatedComponent(ChangedComponentEvent event) {
     // only fire in case of tagged datasets
-    if (event.getTargetClass().equals(Dataset.class)
-        && event.getComponentClass().equals(Tag.class)) {
+    if (event.getTargetClass().equals(Dataset.class)) {
       // we only put tagged datasets onto the queue for this event type!
       UUID key = event.getTargetEntityKey();
       try {

registry-integration-tests/src/test/java/org/gbif/registry/ws/it/NetworkEntityIT.java

@@ -33,6 +33,7 @@
 import org.gbif.registry.database.TestCaseDatabaseInitializer;
 import org.gbif.registry.search.test.EsManageServer;
 import org.gbif.registry.test.TestDataFactory;
+import org.gbif.registry.ws.client.NetworkEntityClient;
 import org.gbif.registry.ws.it.fixtures.TestConstants;
 import org.gbif.ws.client.filter.SimplePrincipalProvider;
 import org.gbif.ws.security.KeyStore;
@@ -62,11 +63,11 @@
 import org.springframework.security.core.authority.SimpleGrantedAuthority;
 import org.springframework.security.core.context.SecurityContext;
 import org.springframework.security.core.context.SecurityContextHolder;
+import org.springframework.test.context.ContextConfiguration;
 
 import com.google.common.base.Preconditions;
 import com.google.common.base.Throwables;
 import com.google.common.collect.Lists;
-import org.springframework.test.context.ContextConfiguration;
 
 import static org.gbif.registry.ws.it.LenientAssert.assertLenientEquals;
 import static org.junit.jupiter.api.Assertions.assertEquals;
@@ -79,7 +80,11 @@
  * A generic test for all network entities that implement all interfaces required by the
  * BaseNetworkEntityResource.
  */
-@ContextConfiguration(initializers = {BaseItTest.ContextInitializer.class, BaseItTest.EsContainerContextInitializer.class})
+@ContextConfiguration(
+    initializers = {
+      BaseItTest.ContextInitializer.class,
+      BaseItTest.EsContainerContextInitializer.class
+    })
 public abstract class NetworkEntityIT<
         T extends
             NetworkEntity & Contactable & Taggable & MachineTaggable & Commentable & Endpointable
@@ -91,8 +96,7 @@ public abstract class NetworkEntityIT<
 
   private final TestDataFactory testDataFactory;
 
-  @Autowired
-  private DataSource dataSource;
+  @Autowired private DataSource dataSource;
 
   @RegisterExtension
   public TestCaseDatabaseInitializer databaseRule = new TestCaseDatabaseInitializer();
@@ -673,6 +677,16 @@ public void testIdentifierSearch(ServiceType serviceType) {
     assertEquals(0, res.getResults().size());
   }
 
+  @Test
+  public void updateEntityKeyMismatchTest() {
+    ServiceType serviceType = ServiceType.CLIENT;
+    NetworkEntityClient<T> crudClient = (NetworkEntityClient<T>) client;
+    T entity = create(newEntity(serviceType), serviceType, 1);
+
+    assertThrows(
+        IllegalArgumentException.class, () -> crudClient.updateResource(UUID.randomUUID(), entity));
+  }
+
   /** @return a new example instance */
   protected abstract T newEntity(ServiceType serviceType);
 

registry-integration-tests/src/test/java/org/gbif/registry/ws/it/OrganizationCreationIT.java

@@ -142,9 +142,7 @@ private void setupPrincipal(String name, Enum... roles) {
     }
   }
 
-  /**
-   * It is not in the scope of this test to test the email bits.
-   */
+  /** It is not in the scope of this test to test the email bits. */
   @ParameterizedTest
   @EnumSource(ServiceType.class)
   public void testEndorsements(ServiceType serviceType) {
@@ -345,14 +343,28 @@ public void testSetEndorsementsByNonAdmin(ServiceType serviceType) {
 
     // reset principal - use USER role
     setupPrincipal(TEST_USER, USER);
+
     OrganizationService userService =
         getService(serviceType, organizationResource, userOrganizationClient);
 
     Organization createdOrganization = userService.get(organization.getKey());
     createdOrganization.setEndorsementApproved(true);
 
-    // make sure an app can not change the endorsementApproved directly
-    assertThrows(AccessDeniedException.class, () -> userService.update(createdOrganization));
+    if (serviceType == ServiceType.RESOURCE) {
+      // we use the resource class directly to use the update method of the API, which is the one that is secured
+      OrganizationResource userServiceResource =
+          (OrganizationResource)
+              getService(serviceType, organizationResource, userOrganizationClient);
+
+      // make sure an app can not change the endorsementApproved directly
+      assertThrows(
+          AccessDeniedException.class,
+          () -> userServiceResource.update(createdOrganization.getKey(), createdOrganization));
+    } else if (serviceType == ServiceType.CLIENT) {
+      // the client always uses the secured method
+      // make sure an app can not change the endorsementApproved directly
+      assertThrows(AccessDeniedException.class, () -> userService.update(createdOrganization));
+    }
   }
 
   @Test

registry-integration-tests/src/test/java/org/gbif/registry/ws/it/collections/BaseCollectionEntityIT.java

@@ -35,6 +35,7 @@
 import org.gbif.registry.database.TestCaseDatabaseInitializer;
 import org.gbif.registry.identity.service.IdentityService;
 import org.gbif.registry.search.test.EsManageServer;
+import org.gbif.registry.ws.client.collections.CrudClient;
 import org.gbif.registry.ws.it.BaseItTest;
 import org.gbif.ws.NotFoundException;
 import org.gbif.ws.client.filter.SimplePrincipalProvider;
@@ -46,6 +47,7 @@
 
 import javax.validation.ValidationException;
 
+import org.junit.jupiter.api.Test;
 import org.junit.jupiter.api.extension.RegisterExtension;
 import org.junit.jupiter.params.ParameterizedTest;
 import org.junit.jupiter.params.provider.EnumSource;
@@ -187,6 +189,19 @@ public void updateInvalidEntityTest(ServiceType serviceType) {
     assertThrows(ValidationException.class, () -> service.update(newEntity));
   }
 
+  @Test
+  public void updateEntityKeyMismatchTest() {
+    CrudClient<T> crudClient = (CrudClient<T>) client;
+
+    T entity = newEntity();
+    UUID key = crudClient.create(entity);
+    T entityCreated = crudClient.get(key);
+
+    assertThrows(
+        IllegalArgumentException.class,
+        () -> crudClient.updateResource(UUID.randomUUID(), entityCreated));
+  }
+
   @ParameterizedTest
   @EnumSource(ServiceType.class)
   public void getMissingEntity(ServiceType serviceType) {

registry-persistence/src/main/resources/org/gbif/registry/persistence/mapper/DatasetMapper.xml

@@ -443,9 +443,10 @@
   </select>
 
   <select id="listNetworks" resultType="java.util.UUID">
-    SELECT network_key
-    FROM dataset_network
-    WHERE dataset_key = #{targetEntityKey,jdbcType=OTHER}
+    SELECT nk.network_key
+    FROM dataset_network AS nk
+    JOIN network n ON n.key = nk.network_key AND n.deleted IS NULL
+    WHERE nk.dataset_key = #{targetEntityKey,jdbcType=OTHER}
   </select>
 
   <!-- Joined delete of comment to trigger cascade delete of the join table -->

registry-ws/src/main/java/org/gbif/registry/ws/resources/BaseNetworkEntityResource.java

@@ -232,15 +232,16 @@ public PagingResponse<T> listByIdentifier(String identifier, Pageable page) {
    * @param entity entity that extends NetworkEntity
    */
   @PutMapping(value = "{key}", consumes = MediaType.APPLICATION_JSON_VALUE)
+  @Secured({ADMIN_ROLE, EDITOR_ROLE, IPT_ROLE})
   @Validated({PostPersist.class, Default.class})
   @Trim
   @Transactional
-  @Secured({ADMIN_ROLE, EDITOR_ROLE, IPT_ROLE})
   public void update(@PathVariable("key") UUID key, @Valid @RequestBody @Trim T entity) {
     checkArgument(key.equals(entity.getKey()));
     update(entity);
   }
 
+  @Transactional
   @Override
   public void update(T entity) {
     Authentication authentication = SecurityContextHolder.getContext().getAuthentication();

registry-ws/src/main/java/org/gbif/registry/ws/resources/NetworkResource.java

@@ -63,6 +63,7 @@ public class NetworkResource extends BaseNetworkEntityResource<Network> implemen
   private final DatasetMapper datasetMapper;
   private final NetworkMapper networkMapper;
   private final OrganizationMapper organizationMapper;
+  private final EventManager eventManager;
 
   public NetworkResource(
       MapperServiceLocator mapperServiceLocator,
@@ -74,6 +75,7 @@ public NetworkResource(
         Network.class,
         eventManager,
         withMyBatis);
+    this.eventManager = eventManager;
     this.datasetMapper = mapperServiceLocator.getDatasetMapper();
     this.networkMapper = mapperServiceLocator.getNetworkMapper();
     this.organizationMapper = mapperServiceLocator.getOrganizationMapper();
@@ -125,7 +127,7 @@ public PagingResponse<Dataset> listConstituents(
   @Override
   public void addConstituent(@PathVariable("key") UUID networkKey, @PathVariable UUID datasetKey) {
     networkMapper.addDatasetConstituent(networkKey, datasetKey);
-    ChangedComponentEvent.newInstance(datasetKey, Dataset.class, Network.class);
+    eventManager.post(ChangedComponentEvent.newInstance(datasetKey, Dataset.class, Network.class));
   }
 
   @DeleteMapping("{key}/constituents/{datasetKey}")
@@ -134,7 +136,7 @@ public void addConstituent(@PathVariable("key") UUID networkKey, @PathVariable U
   public void removeConstituent(
       @PathVariable("key") UUID networkKey, @PathVariable UUID datasetKey) {
     networkMapper.deleteDatasetConstituent(networkKey, datasetKey);
-    ChangedComponentEvent.newInstance(datasetKey, Dataset.class, Network.class);
+    eventManager.post(ChangedComponentEvent.newInstance(datasetKey, Dataset.class, Network.class));
   }
 
   @GetMapping("suggest")