Examples with GroupController org.jbei.ice.lib.group.GroupController used on opensource projects

Example 21 with GroupController

use of org.jbei.ice.lib.group.GroupController in project ice by JBEI.

the class Entries method createEntry.

/**
 * Create an entry in the database.
 * <p/>
 * Generates a new Part Number, the record id (UUID), version id, and timestamps.
 * Optionally set the record globally visible or schedule an index rebuild.
 *
 * @param account           account of user creating entry
 * @param entry             entry record being created
 * @param accessPermissions list of permissions to associate with created entry
 * @return entry that was saved in the database.
 */
private Entry createEntry(Account account, Entry entry, ArrayList<AccessPermission> accessPermissions) {
    if (entry.getRecordId() == null) {
        entry.setRecordId(Utils.generateUUID());
        entry.setVersionId(entry.getRecordId());
    }
    entry.setCreationTime(Calendar.getInstance().getTime());
    entry.setModificationTime(entry.getCreationTime());
    if (StringUtils.isEmpty(entry.getOwner()))
        entry.setOwner(account.getFullName());
    if (StringUtils.isEmpty(entry.getOwnerEmail()))
        entry.setOwnerEmail(account.getEmail());
    if (entry.getSelectionMarkers() != null) {
        for (SelectionMarker selectionMarker : entry.getSelectionMarkers()) {
            selectionMarker.setEntry(entry);
        }
    }
    if (entry.getLinks() != null) {
        for (Link link : entry.getLinks()) {
            link.setEntry(entry);
        }
    }
    if (entry.getStatus() == null)
        entry.setStatus("");
    if (entry.getBioSafetyLevel() == null)
        entry.setBioSafetyLevel(0);
    entry = dao.create(entry);
    EntryPermissions permissions = new EntryPermissions(entry.getRecordId(), userId);
    // check for pi
    String piEmail = entry.getPrincipalInvestigatorEmail();
    if (StringUtils.isNotEmpty(piEmail)) {
        permissions.addAccount(piEmail, true);
    }
    // add write permissions for owner
    permissions.addAccount(account.getEmail(), true);
    // add read permission for all public groups
    ArrayList<Group> groups = new GroupController().getAllPublicGroupsForAccount(account);
    for (Group group : groups) {
        permissions.addGroup(group.getId(), false);
    }
    if (accessPermissions != null) {
        for (AccessPermission accessPermission : accessPermissions) {
            permissions.addAccount(accessPermission);
        }
    }
    // rebuild blast database
    if (sequenceDAO.hasSequence(entry.getId())) {
        RebuildBlastIndexTask task = new RebuildBlastIndexTask(Action.CREATE, entry.getPartNumber());
        IceExecutorService.getInstance().runTask(task);
    }
    return entry;
}

Example 22 with GroupController

use of org.jbei.ice.lib.group.GroupController in project ice by JBEI.

the class ApplicationInitialize method startUp.

/**
 * Responsible for initializing the system and checking for the existence of needed
 * data (such as settings) and creating as needed
 */
public static void startUp() {
    IceExecutorService.getInstance().startService();
    // check for and create public group
    GroupController groupController = new GroupController();
    groupController.createOrRetrievePublicGroup();
    // check for and create admin account
    AccountController accountController = new AccountController();
    accountController.createAdminAccount();
    // check for and create default settings
    ConfigurationSettings settings = new ConfigurationSettings();
    settings.initPropertyValues();
    try {
        // check blast database exists and build if it doesn't
        RebuildBlastIndexTask task = new RebuildBlastIndexTask();
        IceExecutorService.getInstance().runTask(task);
        AutoAnnotationBlastDbBuildTask autoAnnotationBlastDbBuildTask = new AutoAnnotationBlastDbBuildTask();
        IceExecutorService.getInstance().runTask(autoAnnotationBlastDbBuildTask);
    } catch (Exception e) {
        Logger.error(e);
    }
}

Example 23 with GroupController

use of org.jbei.ice.lib.group.GroupController in project ice by JBEI.

the class HibernateSearch method checkEnableSecurityFilter.

/**
 * Enables the security filter if the account does not have administrative privileges
 *
 * @param userId        identifier for account which is checked for administrative privs
 * @param fullTextQuery search fulltextquery for which filter is enabled
 */
private void checkEnableSecurityFilter(String userId, FullTextQuery fullTextQuery) {
    Set<String> groupUUIDs = new HashSet<>();
    Set<String> folderIds = new HashSet<>();
    if (StringUtils.isEmpty(userId)) {
        groupUUIDs.add(GroupController.PUBLIC_GROUP_UUID);
    } else {
        AccountController accountController = new AccountController();
        if (accountController.isAdministrator(userId)) {
            return;
        }
        groupUUIDs = new GroupController().retrieveAccountGroupUUIDs(userId);
        folderIds = new Folders(userId).getCanReadFolderIds();
    }
    fullTextQuery.enableFullTextFilter("security").setParameter("account", userId).setParameter("folderIds", folderIds).setParameter("groupUUids", groupUUIDs);
}

Example 24 with GroupController

use of org.jbei.ice.lib.group.GroupController in project ice by JBEI.

the class RemoteEntriesAsCSV method writeList.

private boolean writeList(List<RemotePartner> partners) throws IOException {
    Path tmpPath = Paths.get(Utils.getConfigValue(ConfigurationKey.TEMPORARY_DIRECTORY));
    File tmpFile = File.createTempFile("remote-ice-", ".csv", tmpPath.toFile());
    csvPath = tmpFile.toPath();
    FileWriter fileWriter = new FileWriter(tmpFile);
    List<EntryFieldLabel> fields = getEntryFields();
    String[] headers = getCSVHeaders(fields);
    // csv file headers
    File tmpZip = File.createTempFile("zip-", ".zip", tmpPath.toFile());
    FileOutputStream fos = new FileOutputStream(tmpZip);
    try (CSVWriter writer = new CSVWriter(fileWriter);
        ZipOutputStream zos = new ZipOutputStream(fos)) {
        writer.writeNext(headers);
        // go through partners
        for (RemotePartner partner : partners) {
            try {
                Logger.info("Retrieving from " + partner.getUrl());
                PartnerEntries partnerEntries = remoteEntries.getPublicEntries(partner.getId(), 0, Integer.MAX_VALUE, null, true);
                Results<PartData> webEntries = partnerEntries.getEntries();
                if (webEntries == null || webEntries.getData() == null) {
                    Logger.error("Could not retrieve entries for " + partner.getUrl());
                    continue;
                }
                Logger.info("Obtained " + webEntries.getResultCount() + " from " + partner.getUrl());
                // go through entries for each partner and write to the zip file
                writeDataEntries(partner, webEntries.getData(), fields, writer, zos);
            } catch (Exception e) {
                Logger.warn("Exception retrieving entries " + e.getMessage());
            }
        }
        // write local entries
        if (this.includeLocal) {
            Logger.info("Retrieving local public entries");
            Group publicGroup = new GroupController().createOrRetrievePublicGroup();
            Set<Group> groups = new HashSet<>();
            groups.add(publicGroup);
            EntryDAO entryDAO = DAOFactory.getEntryDAO();
            List<Long> results = entryDAO.retrieveVisibleEntries(null, groups, ColumnField.CREATED, true, 0, Integer.MAX_VALUE, null);
            writeLocalEntries(results, fields, writer, zos);
        }
        // write the csv file to the zip
        writeZip(tmpZip, zos);
    }
    return true;
}

Example 25 with GroupController

use of org.jbei.ice.lib.group.GroupController in project ice by JBEI.

the class FolderContents method addEntriesToFolders.

/**
 * Attempts to add the specified list of entries to the specified folder destinations.
 * The user making the request must have read privileges on the entries and write privileges on the destination
 * folders.
 * Any entries that the user is not permitted to read will not be be added and any destination folders that the user
 * does not have write privileges for will not have entries added to it
 *
 * @param userId  unique identifier for user making request
 * @param entries list of entry identifiers to be added. Specified user must have read privileges on any
 *                that are to be added
 * @param folders list of folders that that entries are to be added to
 * @return list of destination folders that were updated successfully
 */
List<FolderDetails> addEntriesToFolders(String userId, List<Long> entries, List<FolderDetails> folders) {
    Account account = DAOFactory.getAccountDAO().getByEmail(userId);
    List<Group> accountGroups = new GroupController().getAllGroups(account);
    if (!folderAuthorization.isAdmin(userId))
        entries = DAOFactory.getPermissionDAO().getCanReadEntries(account, accountGroups, entries);
    if (entries == null || entries.isEmpty())
        return new ArrayList<>();
    for (FolderDetails details : folders) {
        Folder folder = folderDAO.get(details.getId());
        if (folder == null) {
            Logger.warn("Could not add entries to folder " + details.getId() + " which doesn't exist");
            continue;
        }
        if (!folderAuthorization.canWrite(userId, folder)) {
            Logger.warn(userId + " lacks write privs on folder " + folder.getId());
            continue;
        }
        // check if the folder is remote or local
        if (folder.getType() == FolderType.REMOTE) {
            Logger.info("Adding entries to remote folder " + folder.getId());
            addToRemoteFolder(account, folder, entries);
        } else {
            List<Entry> entryModelList = DAOFactory.getEntryDAO().getEntriesByIdSet(entries);
            folderDAO.addFolderContents(folder, entryModelList);
            if (folder.isPropagatePermissions()) {
                List<Permission> folderPermissions = permissionDAO.getFolderPermissions(folder);
                addEntryPermission(userId, folderPermissions, entryModelList);
            }
            details.setCount(folderDAO.getFolderSize(folder.getId(), null, true));
        }
    }
    return folders;
}