Merge branch 'develop' into fdias-2509-notification-ui

dataverse-webapp/src/main/java/edu/harvard/iq/dataverse/EjbDataverseEngine.java

@@ -24,6 +24,7 @@
 import edu.harvard.iq.dataverse.globalid.DOIDataCiteServiceBean;
 import edu.harvard.iq.dataverse.globalid.DOIEZIdServiceBean;
 import edu.harvard.iq.dataverse.globalid.FakePidProviderServiceBean;
+import edu.harvard.iq.dataverse.globalid.GlobalIdServiceBeanResolver;
 import edu.harvard.iq.dataverse.globalid.HandlenetServiceBean;
 import edu.harvard.iq.dataverse.guestbook.GuestbookResponseServiceBean;
 import edu.harvard.iq.dataverse.guestbook.GuestbookServiceBean;
@@ -210,6 +211,8 @@ public class EjbDataverseEngine {
     @Inject
     DatasetFieldValidationService fieldValidationService;
 
+    @Inject
+    GlobalIdServiceBeanResolver globalIdServiceBeanResolver;
 
     @Resource
     EJBContext ejbCtxt;
@@ -552,6 +555,11 @@ public DownloadDatasetLogDao downloadDatasetDao() {
                 public DatasetFieldValidationService fieldValidationService() {
                     return fieldValidationService;
                 }
+
+                @Override
+                public GlobalIdServiceBeanResolver globalIdServiceBeanResolver() {
+                    return globalIdServiceBeanResolver;
+                }
             };
         }
 

dataverse-webapp/src/main/java/edu/harvard/iq/dataverse/api/imports/ImportServiceBean.java

@@ -7,6 +7,7 @@
 import edu.harvard.iq.dataverse.api.dto.DatasetDTO;
 import edu.harvard.iq.dataverse.engine.command.DataverseRequest;
 import edu.harvard.iq.dataverse.engine.command.impl.CreateHarvestedDatasetCommand;
+import edu.harvard.iq.dataverse.engine.command.impl.DeleteDatasetCommand;
 import edu.harvard.iq.dataverse.engine.command.impl.DestroyDatasetCommand;
 import edu.harvard.iq.dataverse.persistence.datafile.DataFile;
 import edu.harvard.iq.dataverse.persistence.dataset.Dataset;
@@ -112,6 +113,30 @@ public Dataset doImportHarvestedDataset(DataverseRequest dataverseRequest, Harve
         }
     }
 
+    @TransactionAttribute(REQUIRES_NEW)
+    public void doDeleteHarvestedDataset(DataverseRequest request, HarvestingClient harvestingClient, String identifier) throws ImportException {
+        Dataset dataset = datasetDao.getDatasetByHarvestInfo(harvestingClient.getDataverse(), identifier);
+        if (dataset != null) {
+            // Purge all the SOLR documents associated with this client from the
+            // index server:
+            indexService.deleteHarvestedDocuments(dataset);
+
+            // files from harvested datasets are removed unceremoniously,
+            // directly in the database. no need to bother calling the
+            // DeleteFileCommand on them.
+            for (DataFile harvestedFile : dataset.getFiles()) {
+                DataFile merged = em.merge(harvestedFile);
+                em.remove(merged);
+            }
+
+            dataset.setFiles(null);
+            Dataset merged = em.merge(dataset);
+            engineSvc.submit(new DeleteDatasetCommand(request, merged));
+        } else {
+            throw new ImportException("No dataset found for " + identifier + ", skipping delete. ");
+        }
+    }
+
     private Dataset importDatasetDTOJson(DataverseRequest dataverseRequest, HarvestingClient harvestingClient, String harvestIdentifier, String json) throws ImportException {
         try {
             Dataset ds = harvestedJsonParser.parseDataset(json);

dataverse-webapp/src/main/java/edu/harvard/iq/dataverse/dataset/deaccession/DatasetDeaccessionService.java

@@ -1,13 +1,20 @@
 package edu.harvard.iq.dataverse.dataset.deaccession;
 
+import edu.harvard.iq.dataverse.DataverseRequestServiceBean;
+import edu.harvard.iq.dataverse.EjbDataverseEngine;
 import edu.harvard.iq.dataverse.annotations.PermissionNeeded;
 import edu.harvard.iq.dataverse.annotations.processors.permissions.extractors.DatasetFromVersion;
+import edu.harvard.iq.dataverse.globalid.GlobalIdServiceBeanResolver;
 import edu.harvard.iq.dataverse.interceptors.LoggedCall;
 import edu.harvard.iq.dataverse.interceptors.Restricted;
+import edu.harvard.iq.dataverse.persistence.DvObject;
 import edu.harvard.iq.dataverse.persistence.dataset.Dataset;
 import edu.harvard.iq.dataverse.persistence.dataset.DatasetVersion;
 import edu.harvard.iq.dataverse.persistence.user.Permission;
 import edu.harvard.iq.dataverse.search.index.IndexServiceBean;
+import io.vavr.control.Option;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 import javax.ejb.Stateless;
 import javax.inject.Inject;
@@ -20,12 +27,23 @@
 @Stateless
 public class DatasetDeaccessionService {
 
+    private static final Logger log = LoggerFactory.getLogger(DatasetDeaccessionService.class);
+
     @PersistenceContext
     private EntityManager em;
 
     @Inject
     private IndexServiceBean indexService;
 
+    @Inject
+    private EjbDataverseEngine commandEngine;
+
+    @Inject
+    private DataverseRequestServiceBean dvRequestService;
+
+    @Inject
+    private GlobalIdServiceBeanResolver globalIdServiceBeanResolver;
+
     // -------------------- LOGIC --------------------
 
     @LoggedCall
@@ -51,17 +69,34 @@ public List<DatasetVersion> deaccessReleasedVersions(
 
     // -------------------- PRIVATE --------------------
 
-    private DatasetVersion deaccessDatasetVersion(DatasetVersion deaccessionVersion,
-                                                 String deaccessionReason, String deaccessionForwardURLFor)  {
-        deaccessionVersion.setVersionNote(deaccessionReason);
-        deaccessionVersion.setArchiveNote(deaccessionForwardURLFor);
-        deaccessionVersion.setVersionState(DatasetVersion.VersionState.DEACCESSIONED);
-        deaccessionVersion.setLastUpdateTime(new Date());
-        DatasetVersion merged = em.merge(deaccessionVersion);
+    private DatasetVersion deaccessDatasetVersion(DatasetVersion version, String deaccessionReason, String deaccessionForwardURLFor) {
+        version.setVersionNote(deaccessionReason);
+        version.setArchiveNote(deaccessionForwardURLFor);
+        version.setVersionState(DatasetVersion.VersionState.DEACCESSIONED);
+        version.setLastUpdateTime(new Date());
+        DatasetVersion merged = em.merge(version);
 
         Dataset dataset = merged.getDataset();
         indexService.indexDataset(dataset, true);
         em.merge(dataset);
+
+        dataset.getFiles().stream()
+                .filter(df -> df.getFileMetadatas().stream()
+                        .allMatch(fm -> fm.getDatasetVersion().isDeaccessioned()))
+                .forEach(this::unregisterGlobalId);
+
+        if (dataset.isDeaccessioned()) {
+            unregisterGlobalId(dataset);
+        }
+
         return merged;
     }
+
+    private void unregisterGlobalId(DvObject object) {
+        if (object.isIdentifierRegistered()) {
+            Option.of(globalIdServiceBeanResolver.resolve(object.getProtocol())).toTry()
+                    .andThenTry(service -> service.deleteIdentifier(object))
+                    .onFailure(e -> log.warn("Failed to unregister identifier {}", object.getGlobalId(), e));
+        }
+    }
 }

dataverse-webapp/src/main/java/edu/harvard/iq/dataverse/engine/command/CommandContext.java

@@ -29,6 +29,7 @@
 import edu.harvard.iq.dataverse.globalid.DOIDataCiteServiceBean;
 import edu.harvard.iq.dataverse.globalid.DOIEZIdServiceBean;
 import edu.harvard.iq.dataverse.globalid.FakePidProviderServiceBean;
+import edu.harvard.iq.dataverse.globalid.GlobalIdServiceBeanResolver;
 import edu.harvard.iq.dataverse.globalid.HandlenetServiceBean;
 import edu.harvard.iq.dataverse.guestbook.GuestbookResponseServiceBean;
 import edu.harvard.iq.dataverse.guestbook.GuestbookServiceBean;
@@ -154,4 +155,6 @@ public interface CommandContext {
     DownloadDatasetLogDao downloadDatasetDao();
 
     DatasetFieldValidationService fieldValidationService();
+
+    GlobalIdServiceBeanResolver globalIdServiceBeanResolver();
 }

dataverse-webapp/src/main/java/edu/harvard/iq/dataverse/globalid/DOIDataCiteRegisterService.java

@@ -87,18 +87,18 @@ public String reserveIdentifier(String identifier, Map<String, String> metadata,
 
     public void registerIdentifier(String identifier, Map<String, String> metadata, DvObject dvObject) throws IOException {
         String xmlMetadata = getMetadataFromDvObject(identifier, metadata, dvObject);
-        DOIDataCiteRegisterCache rc = findByDOI(identifier);
+        DOIDataCiteRegisterCache rc = Optional.ofNullable(findByDOI(identifier))
+                .orElseGet(DOIDataCiteRegisterCache::new);
         String target = metadata.get("_target");
-        if (rc != null) {
-            rc.setDoi(identifier);
-            rc.setXml(xmlMetadata);
-            rc.setStatus("public");
-            if (target == null || target.trim().length() == 0) {
-                target = rc.getUrl();
-            } else {
-                rc.setUrl(target);
-            }
+        rc.setDoi(identifier);
+        rc.setXml(xmlMetadata);
+        rc.setStatus("public");
+        if (target == null || target.trim().length() == 0) {
+            target = rc.getUrl();
+        } else {
+            rc.setUrl(target);
         }
+        em.merge(rc);
         registerDOI(identifier.split(":")[1], target, xmlMetadata);
     }
 
@@ -121,6 +121,7 @@ public String getMetadataForDeactivateId(String identifier) {
         resource.setTitles(Collections.singletonList("This item has been removed from publication"));
         resource.setPublisher(":unav");
         resource.setPublicationYear("9999");
+        resource.setCreators(Collections.singletonList(new DataCiteResource.Creator(":unav")));
         return convertToXml(resource);
     }
 

dataverse-webapp/src/main/java/edu/harvard/iq/dataverse/globalid/GlobalIdServiceBean.java

@@ -5,15 +5,10 @@
 import edu.harvard.iq.dataverse.persistence.GlobalId;
 import edu.harvard.iq.dataverse.settings.SettingsServiceBean.Key;
 
-import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
-import java.util.function.Function;
-import java.util.logging.Level;
 import java.util.logging.Logger;
 
-import static edu.harvard.iq.dataverse.globalid.GlobalIdServiceBean.logger;
-
 public interface GlobalIdServiceBean {
 
     Logger logger = Logger.getLogger(GlobalIdServiceBean.class.getCanonicalName());
@@ -56,45 +51,19 @@ public interface GlobalIdServiceBean {
 
     boolean publicizeIdentifier(DvObject studyIn);
 
+    /**
+     * @deprecated use {@link GlobalIdServiceBeanResolver} instead
+     */
+    @Deprecated
     static GlobalIdServiceBean getBean(String protocol, CommandContext ctxt) {
-        final Function<CommandContext, GlobalIdServiceBean> protocolHandler = BeanDispatcher.DISPATCHER.get(protocol);
-        if (protocolHandler != null) {
-            return protocolHandler.apply(ctxt);
-        } else {
-            logger.log(Level.SEVERE, "Unknown protocol: {0}", protocol);
-            return null;
-        }
+        return ctxt.globalIdServiceBeanResolver().resolve(protocol);
     }
 
+    /**
+     * @deprecated use {@link GlobalIdServiceBeanResolver} instead
+     */
     static GlobalIdServiceBean getBean(CommandContext ctxt) {
         return getBean(ctxt.settings().getValueForKey(Key.Protocol), ctxt);
     }
 
 }
-
-/**
- * Static utility class for dispatching implementing beans, based on protocol and providers.
- *
- * @author michael
- */
-class BeanDispatcher {
-    static final Map<String, Function<CommandContext, GlobalIdServiceBean>> DISPATCHER = new HashMap<>();
-
-    static {
-        DISPATCHER.put("hdl", ctxt -> ctxt.handleNet());
-        DISPATCHER.put("doi", ctxt -> {
-            String doiProvider = ctxt.settings().getValueForKey(Key.DoiProvider);
-            switch (doiProvider) {
-                case "EZID":
-                    return ctxt.doiEZId();
-                case "DataCite":
-                    return ctxt.doiDataCite();
-                case "FAKE":
-                    return ctxt.fakePidProvider();
-                default:
-                    logger.log(Level.SEVERE, "Unknown doiProvider: {0}", doiProvider);
-                    return null;
-            }
-        });
-    }
-}