Examples with RunAsSystem org.molgenis.security.core.runas.RunAsSystem used on opensource projects

Example 11 with RunAsSystem

use of org.molgenis.security.core.runas.RunAsSystem in project molgenis by molgenis.

the class AccountServiceImpl method resetPassword.

@Override
@RunAsSystem
public void resetPassword(String userEmail) {
    User user = dataService.query(USER, User.class).eq(EMAIL, userEmail).findOne();
    if (user != null) {
        String newPassword = idGenerator.generateId(SHORT_SECURE_RANDOM);
        user.setPassword(newPassword);
        user.setChangePassword(true);
        dataService.update(USER, user);
        // send password reseted email to user
        SimpleMailMessage mailMessage = new SimpleMailMessage();
        mailMessage.setTo(user.getEmail());
        mailMessage.setSubject("Your new password request");
        mailMessage.setText(createPasswordResettedEmailText(newPassword));
        mailSender.send(mailMessage);
    } else {
        throw new MolgenisUserException("Invalid email address.");
    }
}

Example 12 with RunAsSystem

use of org.molgenis.security.core.runas.RunAsSystem in project molgenis by molgenis.

the class UsersGroupsPopulatorImpl method populate.

@Override
@Transactional
@RunAsSystem
public void populate() {
    if (adminPassword == null) {
        throw new RuntimeException("please configure the admin.password property in your molgenis-server.properties");
    }
    // create admin user
    User userAdmin = userFactory.create();
    userAdmin.setUsername(USERNAME_ADMIN);
    userAdmin.setPassword(adminPassword);
    userAdmin.setEmail(adminEmail);
    userAdmin.setActive(true);
    userAdmin.setSuperuser(true);
    userAdmin.setChangePassword(false);
    // create anonymous user
    User anonymousUser = userFactory.create();
    anonymousUser.setUsername(ANONYMOUS_USERNAME);
    anonymousUser.setPassword(ANONYMOUS_USERNAME);
    anonymousUser.setEmail(anonymousEmail);
    anonymousUser.setActive(true);
    anonymousUser.setSuperuser(false);
    anonymousUser.setChangePassword(false);
    // create all users group
    Group allUsersGroup = groupFactory.create();
    allUsersGroup.setName(AccountService.ALL_USER_GROUP);
    // persist entities
    dataService.add(USER, Stream.of(userAdmin, anonymousUser));
    dataService.add(GROUP, allUsersGroup);
}

Example 13 with RunAsSystem

use of org.molgenis.security.core.runas.RunAsSystem in project molgenis by molgenis.

the class IndexJobSchedulerImpl method scheduleIndexJob.

@Override
@RunAsSystem
public void scheduleIndexJob(String transactionId) {
    LOG.trace("Index transaction with id {}...", transactionId);
    IndexActionGroup indexActionGroup = dataService.findOneById(INDEX_ACTION_GROUP, transactionId, IndexActionGroup.class);
    if (indexActionGroup != null) {
        Stream<Entity> indexActions = dataService.findAll(INDEX_ACTION, new QueryImpl<>().eq(INDEX_ACTION_GROUP_ATTR, indexActionGroup));
        Map<String, Long> numberOfActionsPerEntity = indexActions.collect(groupingBy(indexAction -> indexAction.getString(ENTITY_TYPE_ID), counting()));
        indexStatus.addActionCounts(numberOfActionsPerEntity);
        IndexJobExecution indexJobExecution = indexJobExecutionFactory.create();
        indexJobExecution.setUser("admin");
        indexJobExecution.setIndexActionJobID(transactionId);
        jobExecutor.submit(indexJobExecution, executorService).whenComplete((a, b) -> indexStatus.removeActionCounts(numberOfActionsPerEntity));
    } else {
        LOG.debug("No index job found for id [{}].", transactionId);
    }
}

Example 14 with RunAsSystem

use of org.molgenis.security.core.runas.RunAsSystem in project molgenis by molgenis.

the class UntypedTagService method getTagsForPackage.

@Override
@RunAsSystem
public Iterable<SemanticTag<Package, LabeledResource, LabeledResource>> getTagsForPackage(Package p) {
    Entity packageEntity = dataService.findOne(PACKAGE, new QueryImpl<>().eq(PackageMetadata.ID, p.getId()));
    if (packageEntity == null) {
        throw new UnknownEntityException("Unknown package [" + p.getId() + "]");
    }
    List<SemanticTag<Package, LabeledResource, LabeledResource>> tags = Lists.newArrayList();
    for (Entity tagEntity : packageEntity.getEntities(PackageMetadata.TAGS)) {
        tags.add(SemanticTag.asTag(p, tagEntity));
    }
    return tags;
}

Example 15 with RunAsSystem

use of org.molgenis.security.core.runas.RunAsSystem in project molgenis by molgenis.

the class UntypedTagService method getTagsForAttribute.

@Override
@RunAsSystem
public Multimap<Relation, LabeledResource> getTagsForAttribute(EntityType entityType, Attribute attribute) {
    Entity entity = findAttributeEntity(entityType, attribute.getName());
    if (entity == null)
        return ArrayListMultimap.create();
    Multimap<Relation, LabeledResource> tags = ArrayListMultimap.create();
    for (Entity tagEntity : entity.getEntities(AttributeMetadata.TAGS)) {
        SemanticTag<Attribute, LabeledResource, LabeledResource> tag = SemanticTag.asTag(attribute, tagEntity);
        tags.put(tag.getRelation(), tag.getObject());
    }
    return tags;
}