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

Example 21 with AccessPermission

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

the class EntryCreator 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.
     */
public 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);
    // check for pi
    String piEmail = entry.getPrincipalInvestigatorEmail();
    if (StringUtils.isNotEmpty(piEmail)) {
        Account pi = DAOFactory.getAccountDAO().getByEmail(piEmail);
        if (pi != null) {
            // add write permission for the PI
            addWritePermission(pi, entry);
        }
    }
    // add write permissions for owner
    addWritePermission(account, entry);
    // add read permission for all public groups
    ArrayList<Group> groups = new GroupController().getAllPublicGroupsForAccount(account);
    for (Group group : groups) {
        addReadPermission(null, group, entry);
    }
    if (accessPermissions != null) {
        for (AccessPermission accessPermission : accessPermissions) {
            if (accessPermission.getArticle() == AccessPermission.Article.ACCOUNT) {
                Account accessAccount = DAOFactory.getAccountDAO().get(accessPermission.getArticleId());
                // add account read permission
                addReadPermission(accessAccount, null, entry);
            } else {
                // add group read permission
                Group group = DAOFactory.getGroupDAO().get(accessPermission.getArticleId());
                addReadPermission(null, group, entry);
            }
        }
    }
    // rebuild blast database
    if (sequenceDAO.hasSequence(entry.getId())) {
        BlastPlus.scheduleBlastIndexRebuildTask(true);
    }
    return entry;
}

Example 22 with AccessPermission

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

the class EntryPermissionTask method addPermissions.

protected void addPermissions(Entry entry) {
    for (AccessPermission access : permissions) {
        // account or group
        Account account = null;
        Group group = null;
        switch(access.getArticle()) {
            case ACCOUNT:
            default:
                account = accountDAO.get(access.getArticleId());
                break;
            case GROUP:
                group = groupDAO.get(access.getArticleId());
                break;
        }
        // does the permissions already exists
        if (permissionDAO.hasPermission(entry, null, null, account, group, access.isCanRead(), access.isCanWrite()))
            return;
        // add the permission if not
        Permission permission = new Permission();
        permission.setEntry(entry);
        entry.getPermissions().add(permission);
        permission.setGroup(group);
        permission.setFolder(null);
        permission.setUpload(null);
        permission.setAccount(account);
        permission.setCanRead(access.isCanRead());
        permission.setCanWrite(access.isCanWrite());
        permissionDAO.create(permission);
    }
}

Example 23 with AccessPermission

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

the class EntryPermissions method add.

/**
     * Adds a new permission to the specified entry. If the entry does not exist, a new one is created
     *
     * @param access permissions to be added to the entry
     * @return created permission if successful, null otherwise
     * @throws PermissionException if the requesting user does not have write permissions on the entry
     */
public AccessPermission add(AccessPermission access) {
    if (access == null)
        return null;
    authorization.expectWrite(userId, entry);
    Permission permission = addPermission(access, entry, null, null);
    if (permission == null)
        return null;
    return permission.toDataTransferObject();
}

Example 24 with AccessPermission

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

the class FolderPermissionsTest method testCreateFolderPermission.

@Test
public void testCreateFolderPermission() throws Exception {
    Account account = AccountCreator.createTestAccount("FolderPermissionsTest.testCreateFolderPermission", false);
    String userId = account.getEmail();
    Folder folder = new Folder();
    folder.setOwnerEmail(userId);
    folder.setType(FolderType.PRIVATE);
    folder.setDescription("test folder");
    folder.setName("test");
    folder = DAOFactory.getFolderDAO().create(folder);
    Assert.assertNotNull(folder);
    FolderPermissions folderPermissions = new FolderPermissions(userId, folder.getId());
    AccessPermission accessPermission = new AccessPermission();
    // create a new account
    Account account2 = AccountCreator.createTestAccount("FolderPermissionsTest.testCreateFolderPermission2", false);
    // give read permission to folder for account
    accessPermission.setArticle(AccessPermission.Article.ACCOUNT);
    accessPermission.setType(AccessPermission.Type.READ_FOLDER);
    accessPermission.setArticleId(account2.getId());
    accessPermission.setTypeId(folder.getId());
    Assert.assertNotNull(folderPermissions.createPermission(accessPermission));
}

Example 25 with AccessPermission

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

the class PermissionsController method addPermission.

protected Permission addPermission(AccessPermission access, Entry entry, Folder folder, BulkUpload upload) {
    // account or group
    Account account = null;
    Group group = null;
    switch(access.getArticle()) {
        case ACCOUNT:
        default:
            account = accountDAO.get(access.getArticleId());
            break;
        case GROUP:
            group = groupDAO.get(access.getArticleId());
            break;
    }
    // does the permissions already exists
    if (dao.hasPermission(entry, folder, upload, account, group, access.isCanRead(), access.isCanWrite())) {
        return dao.retrievePermission(entry, folder, upload, account, group, access.isCanRead(), access.isCanWrite());
    }
    // add the permission if not
    Permission permission = new Permission();
    permission.setEntry(entry);
    if (entry != null)
        entry.getPermissions().add(permission);
    permission.setGroup(group);
    permission.setFolder(folder);
    permission.setUpload(upload);
    permission.setAccount(account);
    permission.setCanRead(access.isCanRead());
    permission.setCanWrite(access.isCanWrite());
    return dao.create(permission);
}