Examples with Dataverse edu.harvard.iq.dataverse.Dataverse used on opensource projects

Example 41 with Dataverse

use of edu.harvard.iq.dataverse.Dataverse in project dataverse by IQSS.

the class ConfirmEmailServiceBean method sendLinkOnEmailChange.

/**
 * @todo: We expect to send two messages. One at signup and another at email
 * change.
 */
private void sendLinkOnEmailChange(AuthenticatedUser aUser, String confirmationUrl) throws ConfirmEmailException {
    String messageBody = BundleUtil.getStringFromBundle("notification.email.changeEmail", Arrays.asList(aUser.getFirstName(), confirmationUrl, ConfirmEmailUtil.friendlyExpirationTime(systemConfig.getMinutesUntilConfirmEmailTokenExpires())));
    logger.log(Level.FINE, "messageBody:{0}", messageBody);
    try {
        String toAddress = aUser.getEmail();
        try {
            Dataverse rootDataverse = dataverseService.findRootDataverse();
            if (rootDataverse != null) {
                String rootDataverseName = rootDataverse.getName();
                // FIXME: consider refactoring this into MailServiceBean.sendNotificationEmail. CONFIRMEMAIL may be the only type where we don't want an in-app notification.
                UserNotification userNotification = new UserNotification();
                userNotification.setType(UserNotification.Type.CONFIRMEMAIL);
                String subject = MailUtil.getSubjectTextBasedOnNotification(userNotification, rootDataverseName, null);
                logger.fine("sending email to " + toAddress + " with this subject: " + subject);
                mailService.sendSystemEmail(toAddress, subject, messageBody);
            }
        } catch (Exception e) {
            logger.info("The root dataverse is not present. Don't send a notification to dataverseAdmin.");
        }
    } catch (Exception ex) {
        /**
         * @todo get more specific about the exception that's thrown when
         * `asadmin create-javamail-resource` (or equivalent) hasn't been
         * run.
         */
        throw new ConfirmEmailException("Problem sending email confirmation link possibily due to mail server not being configured.");
    }
    logger.log(Level.FINE, "attempted to send mail to {0}", aUser.getEmail());
}

Example 42 with Dataverse

use of edu.harvard.iq.dataverse.Dataverse in project dataverse by IQSS.

the class DeleteDataverseCommand method executeImpl.

@Override
protected void executeImpl(CommandContext ctxt) throws CommandException {
    // Make sure we don't delete root
    if (doomed.getOwner() == null) {
        throw new IllegalCommandException("Cannot delete the root dataverse", this);
    }
    // make sure the dataverse is emptyw
    if (ctxt.dvObjects().hasData(doomed)) {
        throw new IllegalCommandException("Cannot delete non-empty dataverses", this);
    }
    // ASSIGNMENTS
    for (RoleAssignment ra : ctxt.roles().directRoleAssignments(doomed)) {
        ctxt.em().remove(ra);
    }
    // ROLES
    for (DataverseRole ra : ctxt.roles().findByOwnerId(doomed.getId())) {
        ctxt.em().remove(ra);
    }
    // EXPLICIT GROUPS
    for (ExplicitGroup eg : ctxt.em().createNamedQuery("ExplicitGroup.findByOwnerId", ExplicitGroup.class).setParameter("ownerId", doomed.getId()).getResultList()) {
        ctxt.explicitGroups().removeGroup(eg);
    }
    // Input Level
    for (DataverseFieldTypeInputLevel inputLevel : doomed.getDataverseFieldTypeInputLevels()) {
        DataverseFieldTypeInputLevel merged = ctxt.em().merge(inputLevel);
        ctxt.em().remove(merged);
    }
    doomed.setDataverseFieldTypeInputLevels(new ArrayList<>());
    // DATAVERSE
    Dataverse doomedAndMerged = ctxt.em().merge(doomed);
    ctxt.em().remove(doomedAndMerged);
    // Remove from index
    ctxt.index().delete(doomed);
}

Example 43 with Dataverse

use of edu.harvard.iq.dataverse.Dataverse in project dataverse by IQSS.

the class DeleteGuestbookCommand method execute.

@Override
public Dataverse execute(CommandContext ctxt) throws CommandException {
    Dataverse merged = ctxt.em().merge(editedDv);
    Guestbook doomedAndMerged = ctxt.em().merge(doomed);
    ctxt.em().remove(doomedAndMerged);
    return merged;
}

Example 44 with Dataverse

use of edu.harvard.iq.dataverse.Dataverse in project dataverse by IQSS.

the class DestroyDatasetCommand method executeImpl.

@Override
protected void executeImpl(CommandContext ctxt) throws CommandException {
    // first check if dataset is released, and if so, if user is a superuser
    if (doomed.isReleased() && (!(getUser() instanceof AuthenticatedUser) || !getUser().isSuperuser())) {
        throw new PermissionException("Destroy can only be called by superusers.", this, Collections.singleton(Permission.DeleteDatasetDraft), doomed);
    }
    // If there is a dedicated thumbnail DataFile, it needs to be reset
    // explicitly, or we'll get a constraint violation when deleting:
    doomed.setThumbnailFile(null);
    final Dataset managedDoomed = ctxt.em().merge(doomed);
    List<String> datasetAndFileSolrIdsToDelete = new ArrayList<>();
    // files need to iterate through and remove 'by hand' to avoid
    // optimistic lock issues... (plus the physical files need to be
    // deleted too!)
    Iterator<DataFile> dfIt = doomed.getFiles().iterator();
    while (dfIt.hasNext()) {
        DataFile df = dfIt.next();
        // Gather potential Solr IDs of files. As of this writing deaccessioned files are never indexed.
        String solrIdOfPublishedFile = IndexServiceBean.solrDocIdentifierFile + df.getId();
        datasetAndFileSolrIdsToDelete.add(solrIdOfPublishedFile);
        String solrIdOfDraftFile = IndexServiceBean.solrDocIdentifierFile + df.getId() + IndexServiceBean.draftSuffix;
        datasetAndFileSolrIdsToDelete.add(solrIdOfDraftFile);
        ctxt.engine().submit(new DeleteDataFileCommand(df, getRequest(), true));
        dfIt.remove();
    }
    // also, lets delete the uploaded thumbnails!
    deleteDatasetLogo(doomed);
    // ASSIGNMENTS
    for (RoleAssignment ra : ctxt.roles().directRoleAssignments(doomed)) {
        ctxt.em().remove(ra);
    }
    // ROLES
    for (DataverseRole ra : ctxt.roles().findByOwnerId(doomed.getId())) {
        ctxt.em().remove(ra);
    }
    IdServiceBean idServiceBean = IdServiceBean.getBean(ctxt);
    try {
        if (idServiceBean.alreadyExists(doomed)) {
            idServiceBean.deleteIdentifier(doomed);
        }
    } catch (Exception e) {
        logger.log(Level.WARNING, "Identifier deletion was not successfull:", e.getMessage());
    }
    Dataverse toReIndex = managedDoomed.getOwner();
    // dataset
    ctxt.em().remove(managedDoomed);
    // add potential Solr IDs of datasets to list for deletion
    String solrIdOfPublishedDatasetVersion = IndexServiceBean.solrDocIdentifierDataset + doomed.getId();
    datasetAndFileSolrIdsToDelete.add(solrIdOfPublishedDatasetVersion);
    String solrIdOfDraftDatasetVersion = IndexServiceBean.solrDocIdentifierDataset + doomed.getId() + IndexServiceBean.draftSuffix;
    datasetAndFileSolrIdsToDelete.add(solrIdOfDraftDatasetVersion);
    String solrIdOfDeaccessionedDatasetVersion = IndexServiceBean.solrDocIdentifierDataset + doomed.getId() + IndexServiceBean.deaccessionedSuffix;
    datasetAndFileSolrIdsToDelete.add(solrIdOfDeaccessionedDatasetVersion);
    IndexResponse resultOfSolrDeletionAttempt = ctxt.solrIndex().deleteMultipleSolrIds(datasetAndFileSolrIdsToDelete);
    logger.log(Level.FINE, "Result of attempt to delete dataset and file IDs from the search index: {0}", resultOfSolrDeletionAttempt.getMessage());
    ctxt.index().indexDataverse(toReIndex);
}

Example 45 with Dataverse

use of edu.harvard.iq.dataverse.Dataverse in project dataverse by IQSS.

the class CreateDataverseCommand method execute.

@Override
public Dataverse execute(CommandContext ctxt) throws CommandException {
    if (created.getOwner() == null) {
        if (ctxt.dataverses().isRootDataverseExists()) {
            throw new IllegalCommandException("Root Dataverse already exists. Cannot create another one", this);
        }
    }
    if (created.getCreateDate() == null) {
        created.setCreateDate(new Timestamp(new Date().getTime()));
    }
    if (created.getCreator() == null) {
        final User user = getRequest().getUser();
        if (user.isAuthenticated()) {
            created.setCreator((AuthenticatedUser) user);
        } else {
            throw new IllegalCommandException("Guest users cannot create a Dataverse.", this);
        }
    }
    if (created.getDataverseType() == null) {
        created.setDataverseType(Dataverse.DataverseType.UNCATEGORIZED);
    }
    if (created.getDefaultContributorRole() == null) {
        created.setDefaultContributorRole(ctxt.roles().findBuiltinRoleByAlias(DataverseRole.EDITOR));
    }
    // @todo for now we are saying all dataverses are permission root
    created.setPermissionRoot(true);
    if (ctxt.dataverses().findByAlias(created.getAlias()) != null) {
        throw new IllegalCommandException("A dataverse with alias " + created.getAlias() + " already exists", this);
    }
    // Save the dataverse
    Dataverse managedDv = ctxt.dataverses().save(created);
    // Find the built in admin role (currently by alias)
    DataverseRole adminRole = ctxt.roles().findBuiltinRoleByAlias(DataverseRole.ADMIN);
    String privateUrlToken = null;
    ctxt.roles().save(new RoleAssignment(adminRole, getRequest().getUser(), managedDv, privateUrlToken));
    managedDv.setPermissionModificationTime(new Timestamp(new Date().getTime()));
    managedDv = ctxt.dataverses().save(managedDv);
    ctxt.index().indexDataverse(managedDv);
    if (facetList != null) {
        ctxt.facets().deleteFacetsFor(managedDv);
        int i = 0;
        for (DatasetFieldType df : facetList) {
            ctxt.facets().create(i++, df, managedDv);
        }
    }
    if (inputLevelList != null) {
        ctxt.fieldTypeInputLevels().deleteFacetsFor(managedDv);
        for (DataverseFieldTypeInputLevel obj : inputLevelList) {
            obj.setDataverse(managedDv);
            ctxt.fieldTypeInputLevels().create(obj);
        }
    }
    return managedDv;
}