Restrict

pom.xml

@@ -86,12 +86,12 @@
     <spring-cloud-sleuth.version>2.2.8.RELEASE</spring-cloud-sleuth.version>
 
     <!-- GBIF -->
-    <gbif-api.version>0.163</gbif-api.version>
+    <gbif-api.version>0.165</gbif-api.version>
     <gbif-common.version>0.52</gbif-common.version>
     <gbif-common-mybatis.version>1.1</gbif-common-mybatis.version>
     <gbif-common-ws.version>1.19</gbif-common-ws.version>
     <gbif-directory.version>1.12</gbif-directory.version>
-    <gbif-doi.version>2.16</gbif-doi.version>
+    <gbif-doi.version>2.17</gbif-doi.version>
     <gbif-download-query-tools.version>1.45</gbif-download-query-tools.version>
     <gbif-httputils.version>0.10</gbif-httputils.version>
     <gbif-metrics.version>1.2</gbif-metrics.version>

registry-cli/src/main/java/org/gbif/registry/cli/common/stubs/DatasetDoiDataCiteHandlingServiceStub.java

@@ -32,6 +32,9 @@ public class DatasetDoiDataCiteHandlingServiceStub implements DatasetDoiDataCite
   @Override
   public void datasetChanged(Dataset dataset, @Nullable DOI previousDoi) {}
 
+  @Override
+  public void datasetDeleted(DOI doi) {}
+
   @Override
   public void scheduleDatasetRegistration(DOI doi, DataCiteMetadata metadata, UUID datasetKey) {}
 

registry-cli/src/main/java/org/gbif/registry/cli/doiupdater/DoiUpdateListener.java

@@ -104,7 +104,7 @@ public void handleMessage(ChangeDoiMessage msg) {
         if (HttpStatus.SC_REQUEST_TOO_LONG == e.getStatus()) {
           LOG.warn(
               DOI_SMTP,
-              "Metadata of length {} is exceeding max datacite limit in attempt #{} "
+              "Metadata of length {} is exceeding max DataCite limit in attempt #{} "
                   + "while updating {} to {} with target {}. "
                   + "Trying again {}",
               msg.getMetadata().length(),
@@ -206,14 +206,19 @@ private void reserve(DOI doi, String xml, DoiData currState) throws DoiException
    * @param currState current state of the DOI in the database
    */
   private void delete(DOI doi, DoiData currState) throws DoiException {
+    // delete from DataCite
+    // findable DOIs will not be deleted
+    if (doiService.exists(doi)) {
+      doiService.delete(doi);
+    }
+
     if (currState.getStatus() == DoiStatus.REGISTERED) {
+      // if registered - mark as deleted
       DoiData newState = new DoiData(DoiStatus.DELETED, currState.getTarget());
       doiMapper.update(doi, newState, null);
       LOG.info("Marked registered doi {} as deleted", doi);
     } else {
-      if (doiService.exists(doi)) {
-        doiService.delete(doi);
-      }
+      // otherwise, erase it from database
       doiMapper.delete(doi);
       LOG.info("Deleted doi {}", doi);
     }
@@ -269,7 +274,7 @@ private void registerOrUpdate(DOI doi, URI target, String xml, DoiData currState
    * to fix a RESERVED DOI that should be updated (will be rejected). As opposed to
    * registerOrUpdate, this method will ask the doiService for the status of the DOI since when the
    * status is FAILED we loose the 'real' status before the failure. If the DOI doesn't exist on the
-   * DOI Service (e.g. Datacite) it will register it. If the DOI already exist it will try an
+   * DOI Service (e.g. DataCite) it will register it. If the DOI already exist it will try an
    * update. If any error occurs it will be logged and the will method with false.
    *
    * @param doi Digital Object Identifier
@@ -288,7 +293,7 @@ private boolean retryRegisterOrUpdate(DOI doi, URI target, String xml) throws Do
         LOG.info("Updated doi {} with target {}", doi, target);
       } else {
         LOG.info(
-            "Failed to update doi {} with target {}. Only doi with state REGISTERED can be retried. Datacite status: {}. ",
+            "Failed to update doi {} with target {}. Only doi with state REGISTERED can be retried. DataCite status: {}. ",
             doi,
             target,
             doiServiceData.getStatus());

registry-cli/src/test/java/org/gbif/registry/cli/doiupdater/DoiUpdaterListenerIT.java

@@ -45,6 +45,7 @@
 import io.zonky.test.db.postgres.junit5.EmbeddedPostgresExtension;
 import io.zonky.test.db.postgres.junit5.PreparedDbExtension;
 
+import static org.gbif.api.model.common.DoiStatus.DELETED;
 import static org.gbif.api.model.common.DoiStatus.FAILED;
 import static org.gbif.api.model.common.DoiStatus.NEW;
 import static org.gbif.api.model.common.DoiStatus.REGISTERED;
@@ -183,7 +184,7 @@ public void handleMessageRegisteredDoiAndMessageStatusDeletedShouldMarkDoiAsDele
 
     // then
     assertEquals(new DoiData(DoiStatus.DELETED, TEST_TARGET), getActualInDb(doi));
-    assertEquals(new DoiData(REGISTERED, TEST_TARGET), getActualInDataCite(doi));
+    assertEquals(new DoiData(DELETED, TEST_TARGET), getActualInDataCite(doi));
   }
 
   @Test

registry-doi/src/main/java/org/gbif/registry/doi/DatasetDoiDataCiteHandlingService.java

@@ -36,6 +36,11 @@ public interface DatasetDoiDataCiteHandlingService {
    */
   void datasetChanged(Dataset dataset, @Nullable final DOI previousDoi);
 
+  /**
+   * Called when dataset to be deleted, tries to deactivate DOI.
+   */
+  void datasetDeleted(DOI doi);
+
   /**
    * Directly schedule the registration of a Dataset DOI.
    */

registry-doi/src/main/java/org/gbif/registry/doi/DatasetDoiDataCiteHandlingServiceImpl.java

@@ -105,6 +105,11 @@ public void datasetChanged(Dataset dataset, @Nullable DOI previousDoi) {
     }
   }
 
+  @Override
+  public void datasetDeleted(DOI doi) {
+    doiMessageManagingService.delete(doi);
+  }
+
   @Override
   public void scheduleDatasetRegistration(DOI doi, DataCiteMetadata metadata, UUID datasetKey) {
     try {

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

@@ -113,12 +113,15 @@ public class BaseNetworkEntityResource<T extends NetworkEntity> implements Netwo
   private final WithMyBatis withMyBatis;
   private final Class<T> objectClass;
 
+  private final RestrictionsHandler restrictionsHandler;
+
   protected BaseNetworkEntityResource(
-      BaseNetworkEntityMapper<T> mapper,
-      MapperServiceLocator mapperServiceLocator,
-      Class<T> objectClass,
-      EventManager eventManager,
-      WithMyBatis withMyBatis) {
+    BaseNetworkEntityMapper<T> mapper,
+    MapperServiceLocator mapperServiceLocator,
+    Class<T> objectClass,
+    EventManager eventManager,
+    WithMyBatis withMyBatis,
+    RestrictionsHandler restrictionsHandler) {
     this.mapper = mapper;
     this.commentMapper = mapperServiceLocator.getCommentMapper();
     this.machineTagMapper = mapperServiceLocator.getMachineTagMapper();
@@ -129,6 +132,7 @@ protected BaseNetworkEntityResource(
     this.objectClass = objectClass;
     this.eventManager = eventManager;
     this.withMyBatis = withMyBatis;
+    this.restrictionsHandler = restrictionsHandler;
   }
 
   /**
@@ -643,4 +647,8 @@ protected <D> PagingResponse<D> pagingResponse(Pageable page, Long count, List<D
     }
     return new PagingResponse<>(page, count, result);
   }
+
+  public RestrictionsHandler getRestrictionsHandler() {
+    return restrictionsHandler;
+  }
 }

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

@@ -152,6 +152,7 @@ public class DatasetResource extends BaseNetworkEntityResource<Dataset>
   private final TagMapper tagMapper;
   private final NetworkMapper networkMapper;
   private final DatasetProcessStatusMapper datasetProcessStatusMapper;
+  private final RestrictionsHandler restrictionsHandler;
   private final DatasetDoiDataCiteHandlingService doiDataCiteHandlingService;
   private final DataCiteMetadataBuilderService metadataBuilderService;
   private final DoiIssuingService doiIssuingService;
@@ -169,13 +170,15 @@ public DatasetResource(
       DataCiteMetadataBuilderService metadataBuilderService,
       DoiIssuingService doiIssuingService,
       WithMyBatis withMyBatis,
-      @Autowired(required = false) MessagePublisher messagePublisher) {
+      @Autowired(required = false) MessagePublisher messagePublisher,
+      RestrictionsHandler restrictionsHandler) {
     super(
         mapperServiceLocator.getDatasetMapper(),
         mapperServiceLocator,
         Dataset.class,
         eventManager,
-        withMyBatis);
+        withMyBatis,
+        restrictionsHandler);
     this.registryDatasetService = registryDatasetService;
     this.searchService = searchService;
     this.metadataMapper = mapperServiceLocator.getMetadataMapper();
@@ -190,6 +193,7 @@ public DatasetResource(
     this.doiIssuingService = doiIssuingService;
     this.messagePublisher = messagePublisher;
     this.withMyBatis = withMyBatis;
+    this.restrictionsHandler = restrictionsHandler;
   }
 
   @GetMapping("search")
@@ -310,6 +314,19 @@ public byte[] getMetadataDocumentAsBytes(@PathVariable("key") UUID datasetKey) {
     return null;
   }
 
+  @DeleteMapping("{key}")
+  @Secured({ADMIN_ROLE, EDITOR_ROLE, IPT_ROLE})
+  @Transactional
+  @Override
+  public void delete(@PathVariable UUID key) {
+    Dataset dataset = get(key);
+    super.delete(key);
+
+    if (dataset != null && dataset.getDoi() != null) {
+      doiDataCiteHandlingService.datasetDeleted(dataset.getDoi());
+    }
+  }
+
   @PostMapping(value = "{key}/document", consumes = MediaType.APPLICATION_XML_VALUE)
   @Secured({ADMIN_ROLE, EDITOR_ROLE})
   public Metadata insertMetadata(
@@ -444,6 +461,9 @@ private Dataset preserveGBIFDatasetProperties(Dataset updatedDataset, Dataset ex
    */
   public void updateFromPreferredMetadata(UUID uuid, String user) {
     Dataset dataset = super.get(uuid);
+
+    restrictionsHandler.checkDenyPublisher(dataset.getPublishingOrganizationKey());
+
     if (dataset == null) {
       throw new NotFoundException(
           "Dataset " + uuid + " not existing", URI.create("/dataset/{key}/document"));
@@ -572,6 +592,8 @@ public UUID create(@RequestBody @Trim Dataset dataset) {
       dataset.setLicense(License.CC_BY_4_0);
     }
 
+    restrictionsHandler.checkDenyPublisher(dataset.getPublishingOrganizationKey());
+
     final UUID key = super.create(dataset);
     // now that we have a UUID schedule to scheduleRegistration the DOI
     // to get the latest timestamps we need to read a new copy of the dataset
@@ -586,6 +608,9 @@ public void update(Dataset dataset) {
     if (old == null) {
       throw new IllegalArgumentException("Dataset " + dataset.getKey() + " not existing");
     }
+
+    restrictionsHandler.checkDenyPublisher(dataset.getPublishingOrganizationKey());
+
     // replace current license? Only if dataset being updated has a supported license
     if (!replaceLicense(dataset.getLicense())) {
       LOG.warn(

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

@@ -20,6 +20,7 @@
 import org.gbif.api.model.registry.Dataset;
 import org.gbif.api.model.registry.Installation;
 import org.gbif.api.model.registry.Organization;
+import org.gbif.api.model.registry.PrePersist;
 import org.gbif.api.model.registry.metasync.MetasyncHistory;
 import org.gbif.api.model.registry.search.KeyTitleResult;
 import org.gbif.api.service.registry.InstallationService;
@@ -45,6 +46,7 @@
 
 import javax.validation.Valid;
 import javax.validation.constraints.NotNull;
+import javax.validation.groups.Default;
 
 import org.codehaus.jettison.json.JSONException;
 import org.codehaus.jettison.json.JSONObject;
@@ -72,6 +74,8 @@
 
 import static com.google.common.base.Preconditions.checkArgument;
 import static org.gbif.registry.security.UserRoles.ADMIN_ROLE;
+import static org.gbif.registry.security.UserRoles.EDITOR_ROLE;
+import static org.gbif.registry.security.UserRoles.IPT_ROLE;
 
 @Validated
 @Primary
@@ -91,16 +95,18 @@ public class InstallationResource extends BaseNetworkEntityResource<Installation
   private final MessagePublisher messagePublisher;
 
   public InstallationResource(
-      MapperServiceLocator mapperServiceLocator,
-      EventManager eventManager,
-      WithMyBatis withMyBatis,
-      @Autowired(required = false) MessagePublisher messagePublisher) {
+    MapperServiceLocator mapperServiceLocator,
+    EventManager eventManager,
+    WithMyBatis withMyBatis,
+    @Autowired(required = false) MessagePublisher messagePublisher,
+    RestrictionsHandler restrictionsHandler) {
     super(
         mapperServiceLocator.getInstallationMapper(),
         mapperServiceLocator,
         Installation.class,
         eventManager,
-        withMyBatis);
+        withMyBatis,
+        restrictionsHandler);
     this.datasetMapper = mapperServiceLocator.getDatasetMapper();
     this.installationMapper = mapperServiceLocator.getInstallationMapper();
     this.organizationMapper = mapperServiceLocator.getOrganizationMapper();
@@ -287,4 +293,21 @@ public PagingResponse<Installation> listByType(InstallationType type, Pageable p
     long total = installationMapper.countWithFilter(type);
     return pagingResponse(page, total, installationMapper.listWithFilter(type, page));
   }
+
+  @PostMapping(consumes = MediaType.APPLICATION_JSON_VALUE)
+  @Validated({PrePersist.class, Default.class})
+  @Trim
+  @Transactional
+  @Secured({ADMIN_ROLE, EDITOR_ROLE, IPT_ROLE})
+  @Override
+  public UUID create(Installation entity) {
+    getRestrictionsHandler().checkDenyPublisher(entity.getOrganizationKey());
+    return super.create(entity);
+  }
+
+  @Override
+  public void update(Installation entity) {
+    getRestrictionsHandler().checkDenyPublisher(entity.getOrganizationKey());
+    super.update(entity);
+  }
 }

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

@@ -67,15 +67,17 @@ public class NetworkResource extends BaseNetworkEntityResource<Network> implemen
   private final EventManager eventManager;
 
   public NetworkResource(
-      MapperServiceLocator mapperServiceLocator,
-      EventManager eventManager,
-      WithMyBatis withMyBatis) {
+    MapperServiceLocator mapperServiceLocator,
+    EventManager eventManager,
+    WithMyBatis withMyBatis,
+    RestrictionsHandler restrictionsHandler) {
     super(
         mapperServiceLocator.getNetworkMapper(),
         mapperServiceLocator,
         Network.class,
         eventManager,
-        withMyBatis);
+        withMyBatis,
+        restrictionsHandler);
     this.eventManager = eventManager;
     this.datasetMapper = mapperServiceLocator.getDatasetMapper();
     this.networkMapper = mapperServiceLocator.getNetworkMapper();

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

@@ -75,13 +75,15 @@ public NodeResource(
       MapperServiceLocator mapperServiceLocator,
       EventManager eventManager,
       Augmenter nodeAugmenter,
-      WithMyBatis withMyBatis) {
+      WithMyBatis withMyBatis,
+      RestrictionsHandler restrictionsHandler) {
     super(
         mapperServiceLocator.getNodeMapper(),
         mapperServiceLocator,
         Node.class,
         eventManager,
-        withMyBatis);
+        withMyBatis,
+        restrictionsHandler);
     this.nodeMapper = mapperServiceLocator.getNodeMapper();
     this.organizationMapper = mapperServiceLocator.getOrganizationMapper();
     this.nodeAugmenter = nodeAugmenter;

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

@@ -383,7 +383,7 @@ public Map<Integer, Map<Integer, Long>> getDownloadedRecordsByDataset(
       @RequestParam(value = "datasetKey", required = false) UUID datasetKey,
       @RequestParam(value = "publishingOrgKey", required = false) UUID publishingOrgKey) {
     return groupByYear(
-        occurrenceDownloadMapper.getDownloadsByDataset(
+        occurrenceDownloadMapper.getDownloadedRecordsByDataset(
             fromDate,
             toDate,
             Optional.ofNullable(publishingCountry).map(Country::getIso2LetterCode).orElse(null),