Examples with PermissionException org.jbei.ice.lib.access.PermissionException used on opensource projects

Example 16 with PermissionException

use of org.jbei.ice.lib.access.PermissionException in project ice by JBEI.

the class AnnotationResource method rebuildAnnotations.

@PUT
@Path("/indexes")
public Response rebuildAnnotations() {
    String userId = requireUserId();
    Annotations annotations = new Annotations(userId);
    try {
        annotations.rebuild();
    } catch (PermissionException pe) {
        Logger.error(pe);
        throw new WebApplicationException(Response.Status.FORBIDDEN);
    }
    return super.respond(true);
}

Example 17 with PermissionException

use of org.jbei.ice.lib.access.PermissionException in project ice by JBEI.

the class AnnotationResource method curate.

/**
 * Curate available annotations to include or exclude them from auto-annotation feature
 *
 * @param list list of annotations each with specified curate
 */
@PUT
@Produces(MediaType.APPLICATION_JSON)
public Response curate(List<DNAFeature> list) {
    String userId = requireUserId();
    Annotations annotations = new Annotations(userId);
    try {
        final Type fooType = new TypeToken<ArrayList<DNAFeature>>() {
        }.getType();
        final Gson gson = new GsonBuilder().create();
        final ArrayList<DNAFeature> features = gson.fromJson(gson.toJsonTree(list), fooType);
        annotations.curate(features);
        return super.respond(true);
    } catch (PermissionException e) {
        Logger.error(e);
        throw new WebApplicationException(Response.Status.FORBIDDEN);
    }
}

Example 18 with PermissionException

use of org.jbei.ice.lib.access.PermissionException in project ice by JBEI.

the class ApiKeyResource method getApiKeys.

/**
 * retrieves list of api keys created by user
 */
@GET
@Produces(MediaType.APPLICATION_JSON)
public Response getApiKeys(@DefaultValue("0") @QueryParam("offset") int offset, @DefaultValue("15") @QueryParam("limit") int limit, @DefaultValue("true") @QueryParam("asc") boolean asc, @DefaultValue("creationTime") @QueryParam("sort") String sort, @DefaultValue("false") @QueryParam("getAll") boolean getAll) {
    String userId = requireUserId();
    UserApiKeys apiKeys = new UserApiKeys(userId);
    try {
        return super.respond(apiKeys.getKeys(limit, offset, sort, asc, getAll));
    } catch (PermissionException pe) {
        throw new WebApplicationException(Response.Status.FORBIDDEN);
    }
}

Example 19 with PermissionException

use of org.jbei.ice.lib.access.PermissionException in project ice by JBEI.

the class GroupController method deleteGroup.

public boolean deleteGroup(String userIdStr, long groupId) {
    Account account = DAOFactory.getAccountDAO().getByEmail(userIdStr);
    Group group = dao.get(groupId);
    if (group == null)
        return false;
    if (group.getType() == GroupType.PUBLIC && account.getType() != AccountType.ADMIN) {
        String errMsg = "Non admin " + account.getEmail() + " attempting to delete public group";
        Logger.error(errMsg);
        throw new PermissionException(errMsg);
    }
    if (group.getMembers() != null) {
        for (Account member : group.getMembers()) {
            accountController.removeMemberFromGroup(group.getId(), member.getEmail());
        }
    }
    DAOFactory.getPermissionDAO().clearPermissions(group);
    dao.delete(group);
    return true;
}

Example 20 with PermissionException

use of org.jbei.ice.lib.access.PermissionException in project ice by JBEI.

the class Groups method addGroup.

/**
 * Adds group to the list of groups for current user
 *
 * @param userGroup information about group to be added, including members (local and remote)
 * @return added group
 */
public UserGroup addGroup(UserGroup userGroup) {
    if (userGroup.getType() == null)
        userGroup.setType(GroupType.PRIVATE);
    if (userGroup.getType() == GroupType.PUBLIC && !accountController.isAdministrator(userId)) {
        String errMsg = "Non admin '" + userId + "' attempting to create public group";
        Logger.error(errMsg);
        throw new PermissionException(errMsg);
    }
    Account account = accountDAO.getByEmail(userId);
    Group group = new Group();
    group.setUuid(Utils.generateUUID());
    group.setLabel(userGroup.getLabel());
    group.setDescription(userGroup.getDescription() == null ? "" : userGroup.getDescription());
    group.setType(userGroup.getType());
    group.setOwner(account);
    group.setAutoJoin(userGroup.isAutoJoin());
    group.setCreationTime(new Date());
    group = dao.create(group);
    // add local members
    if (userGroup.getMembers() != null && !userGroup.getMembers().isEmpty()) {
        for (AccountTransfer accountTransfer : userGroup.getMembers()) {
            Account memberAccount = accountDAO.getByEmail(accountTransfer.getEmail());
            if (memberAccount == null)
                continue;
            group.getMembers().add(memberAccount);
            memberAccount.getGroups().add(group);
            accountDAO.update(memberAccount);
        }
    }
    // add remote members
    for (RemoteUser remoteUser : userGroup.getRemoteMembers()) {
        RegistryPartner partner = remoteUser.getPartner();
        if (partner == null)
            continue;
        RemotePartner remotePartner = remotePartnerDAO.get(partner.getId());
        if (remotePartner == null)
            continue;
        AccountTransfer accountTransfer = remoteUser.getUser();
        if (accountTransfer == null || StringUtils.isEmpty(accountTransfer.getEmail()))
            continue;
        String email = accountTransfer.getEmail();
        RemoteClientModel remoteClientModel = remoteClientModelDAO.getModel(email, remotePartner);
        if (remoteClientModel == null) {
            remoteClientModel = new RemoteClientModel();
            remoteClientModel.setEmail(email);
            remoteClientModel.setRemotePartner(remotePartner);
            remoteClientModel = remoteClientModelDAO.create(remoteClientModel);
        }
        remoteClientModel.getGroups().add(group);
        remoteClientModelDAO.update(remoteClientModel);
    }
    return group.toDataTransferObject();
}