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feature(API.PID.reconcile): Added command and API to reconcile the PI…
…D of an unpublished dataset.
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src/main/java/edu/harvard/iq/dataverse/engine/command/impl/ReconcileDatasetPidCommand.java
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| package edu.harvard.iq.dataverse.engine.command.impl; | ||
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| import edu.harvard.iq.dataverse.*; | ||
| import edu.harvard.iq.dataverse.authorization.Permission; | ||
| import edu.harvard.iq.dataverse.authorization.users.AuthenticatedUser; | ||
| import edu.harvard.iq.dataverse.dataaccess.DataAccess; | ||
| import edu.harvard.iq.dataverse.engine.command.CommandContext; | ||
| import edu.harvard.iq.dataverse.engine.command.DataverseRequest; | ||
| import edu.harvard.iq.dataverse.engine.command.RequiredPermissions; | ||
| import edu.harvard.iq.dataverse.engine.command.exception.CommandException; | ||
| import edu.harvard.iq.dataverse.engine.command.exception.IllegalCommandException; | ||
| import edu.harvard.iq.dataverse.engine.command.exception.PermissionException; | ||
| import edu.harvard.iq.dataverse.export.ExportService; | ||
| import edu.harvard.iq.dataverse.pidproviders.PidProvider; | ||
| import edu.harvard.iq.dataverse.util.BundleUtil; | ||
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| import java.io.IOException; | ||
| import java.sql.Timestamp; | ||
| import java.util.Collections; | ||
| import java.util.Date; | ||
| import java.util.List; | ||
| import java.util.Set; | ||
| import java.util.logging.Level; | ||
| import java.util.logging.Logger; | ||
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| /** | ||
| * Given a draft datasetVersion (which has no published predecessors), and PID provider that is different to the current | ||
| * configured one this command reconfigures the PID provider, and updates the PID to the new provider (Removed the | ||
| * existing PID, registers a new one and notifies the user about the change). | ||
| * | ||
| * @author jdarms | ||
| */ | ||
| // No required permissions because we check for superuser status. | ||
| @RequiredPermissions({}) | ||
| public class ReconcileDatasetPidCommand extends AbstractDatasetCommand<Dataset> { | ||
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| private static final Logger logger = Logger.getLogger(ReconcileDatasetPidCommand.class.getName()); | ||
| PidProvider newPidProvider; | ||
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| public ReconcileDatasetPidCommand(DataverseRequest aRequest, Dataset theDataset, PidProvider newPidProvider) { | ||
| super(aRequest, theDataset); | ||
| this.newPidProvider = newPidProvider; | ||
| } | ||
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| @Override | ||
| public Dataset execute(CommandContext ctxt) throws CommandException { | ||
| // ensure that only superuser can execute the command. | ||
| if (!(getUser() instanceof AuthenticatedUser) || !getUser().isSuperuser()) { | ||
| throw new PermissionException(BundleUtil.getStringFromBundle("admin.api.auth.mustBeSuperUser"), this, | ||
| Collections.singleton(Permission.EditDataset), getDataset()); | ||
| } | ||
| // Datast must be unreleased! This means there is only one version! | ||
| if (getDataset().isReleased()) { //@TODO: Clarify whether this is the best check... | ||
| throw new IllegalCommandException("Dataset already published, cannot alter PID Provider", this); | ||
| } | ||
| // Dataset must not be harvested! | ||
| if (getDataset().isHarvested()) { | ||
| throw new IllegalCommandException("Dataset is harvested, cannot alter PID Provider", this); | ||
| } | ||
| PidProvider currentPidProvider = getDataset().getEffectivePidGenerator(); | ||
| // new PID Provider must be different to requested one! | ||
| if (this.newPidProvider.equals(currentPidProvider)) { | ||
| throw new IllegalCommandException("PID Provider " + currentPidProvider.getId() + " is same as configured. This Operation has no effect!", this); | ||
| } | ||
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| GlobalId oldId = getDataset().getGlobalId(); | ||
| if (oldId == null) { | ||
| throw new IllegalStateException("Dataset without a global identifier, cannot alter!"); | ||
| } | ||
| logger.fine("Reconciling dataset( id =`" + getDataset().getId() + ")` - removing globalId `" + getDataset().getGlobalId() + '`'); | ||
| // remove dataset PID | ||
| try { | ||
| if (currentPidProvider.alreadyRegistered(getDataset())) { //if not registered with PIDProvider than there is no need to delete it... | ||
| currentPidProvider.deleteIdentifier(getDataset()); // delete it externally | ||
| } | ||
| getDataset().setGlobalId(null); // remove it internally | ||
| getDataset().setGlobalIdCreateTime(null); | ||
| getDataset().setIdentifierRegistered(false); | ||
| } catch (Exception e) { | ||
| logger.log(Level.WARNING, "Identifier deletion was not successful:", e.getMessage()); | ||
| } | ||
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| if(ctxt.systemConfig().isFilePIDsEnabledForCollection(getDataset().getOwner())) { | ||
| reconcileFilePids(ctxt, currentPidProvider); | ||
| } | ||
| getDataset().setPidGenerator(this.newPidProvider); | ||
| newPidProvider.generatePid(getDataset()); // this updates Protocol, Authority, and Identifier and thus a new GlobalID | ||
| logger.fine("Reconciling dataset( id =`" + getDataset().getId() + ")` - creating new globalId `" + getDataset().getGlobalId() + '`'); | ||
| if (!newPidProvider.registerWhenPublished()) { | ||
| registerExternalIdentifier(getDataset(), ctxt, true); // this updates GlobalIdCreateTime and IdentifierRegistered | ||
| } | ||
| // keep old Id als alternative identifier | ||
| AlternativePersistentIdentifier api; | ||
| api = new AlternativePersistentIdentifier(); | ||
| api.setProtocol(oldId.getProtocol()); | ||
| api.setAuthority(oldId.getAuthority()); | ||
| api.setIdentifier(oldId.getIdentifier()); | ||
| api.setDvObject(getDataset()); | ||
| api.setStorageLocationDesignator(true);// cf. Dataset#getIdentifierForFileStorage() | ||
| if(getDataset().getAlternativePersistentIndentifiers()!=null) { | ||
| getDataset().getAlternativePersistentIndentifiers().add(api); | ||
| }else{ | ||
| getDataset().setAlternativePersistentIndentifiers(Set.of(api)); | ||
| } | ||
| // We keep the old persistent identifier as AlternativePersistentIdentifier with storageLocationDesignator true. | ||
| // This keep the link the object store intact, without altering the files. | ||
| // IMHO: This command should also update the storage. First, maintenance of the storage becomes a mess if there is a counterintuitive layout. | ||
| // Second, it could occur that another object is minted with the old identifier and consequently we have a conflict in our storage system. | ||
| // We accept this risk for now since a super user can update the storage manually from old file path to the new one, and remove the AlternativeIdentifer form the database. | ||
| // This removed the old identifier totally from the system and avoids all side effects... | ||
| // @TODO: Move files on storage once the storage API support a move operation! | ||
| ctxt.em().merge(getDataset()); | ||
| ctxt.em().flush(); | ||
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| logger.fine("Reconciling dataset( id =`" + getDataset().getId() + ")` - Replaced old globalId `" + oldId + " with new globalId `" + getDataset().getGlobalId() + '`'); | ||
| // notify all users with direct role assignments about the changed persistent identifier | ||
| List<RoleAssignment> ras = ctxt.roles().directRoleAssignments(getDataset()); | ||
| for (RoleAssignment ra : ras) { | ||
| for (AuthenticatedUser au : ctxt.roleAssignees().getExplicitUsers(ctxt.roleAssignees().getRoleAssignee(ra.getAssigneeIdentifier()))) { | ||
| ctxt.notifications().sendNotification(au, new Timestamp(new Date().getTime()), UserNotification.Type.PIDRECONCILED,getDataset().getLatestVersion().getId(),"Persistent identifier changed!"); | ||
| } | ||
| } | ||
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| return getDataset(); | ||
| } | ||
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| private void reconcileFilePids(CommandContext ctxt, PidProvider currentPidProvider) { | ||
| // remove datafile PIDs | ||
| try { | ||
| for (DataFile df : getDataset().getFiles()) { | ||
| if (currentPidProvider.alreadyRegistered(df)) { | ||
| currentPidProvider.deleteIdentifier(df);// delete it external | ||
| } | ||
| GlobalId oldPid=df.getGlobalId(); | ||
| df.setGlobalId(null); // and remove it internally from data structure | ||
| df.setGlobalIdCreateTime(null); | ||
| df.setIdentifierRegistered(false); | ||
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| AlternativePersistentIdentifier api; | ||
| api = new AlternativePersistentIdentifier(); | ||
| api.setProtocol(oldPid.getProtocol()); | ||
| api.setAuthority(oldPid.getAuthority()); | ||
| api.setIdentifier(oldPid.getIdentifier()); | ||
| api.setDvObject(df); | ||
| api.setStorageLocationDesignator(true); // cf. Dataset#getIdentifierForFileStorage() | ||
| if(df.getAlternativePersistentIndentifiers()!=null) { | ||
| df.getAlternativePersistentIndentifiers().add(api); | ||
| }else{ | ||
| df.setAlternativePersistentIndentifiers(Set.of(api)); | ||
| } | ||
| // DataFiles are not a child of DvObjectContainer hence we cannot update the PIDProvider for them! cf. DvObjectContainer.setPidGenerator(this.newPidProvider); | ||
| // We don't need to update the PIDProvider since the configuration of the Dataset, which is already updated, is used. | ||
| // @TODO: Is this true? | ||
| newPidProvider.generatePid(df); // this updates Protocol, Authority, and Identifier and thus a new GlobalID | ||
| logger.fine("Reconciling datafile( id =`" + df.getId() + ")` - creating new globalId `" +df.getGlobalId() + '`'); | ||
| if (!newPidProvider.registerWhenPublished()) { | ||
| registerExternalIdentifier(df, ctxt, true); // this updates GlobalIdCreateTime and IdentifierRegistered | ||
| } | ||
| } | ||
| } catch (Exception e) { | ||
| logger.log(Level.WARNING, "Identifier deletion was not successful:", e.getMessage()); | ||
| } | ||
| } | ||
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| @Override | ||
| public boolean onSuccess(CommandContext ctxt, Object r) { | ||
| //update search index with the state | ||
| ctxt.index().asyncIndexDataset(getDataset(), true); | ||
| //invalidate all existing Export caches | ||
| // currently, Exports are only possible for published datasets... | ||
| // so there is no need to invalide caches... | ||
| // yet here is the needed snippet | ||
| // try { | ||
| // ExportService.getInstance().clearAllCachedFormats(getDataset()); | ||
| // } catch (IOException e) { | ||
| // throw new RuntimeException(e); | ||
| // } | ||
| return true; | ||
| } | ||
| } |
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