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

Example 11 with GroupController

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

the class BulkUploads method create.

/**
 * Creates a new bulk upload. If upload type is not bulk edit, then the status is set to in progress.
 * Default permissions consisting of read permissions for the public groups that the requesting user is
 * a part of are added
 *
 * @param userId identifier for user making request
 * @param info   bulk upload data
 * @return created upload
 */
public BulkUploadInfo create(String userId, BulkUploadInfo info) {
    Account account = accountController.getByEmail(userId);
    BulkUpload upload = new BulkUpload();
    upload.setName(info.getName());
    upload.setAccount(account);
    upload.setCreationTime(new Date());
    upload.setLastUpdateTime(upload.getCreationTime());
    if (info.getStatus() == BulkUploadStatus.BULK_EDIT) {
        // only one instance of bulk edit is allowed to remain
        clearBulkEdits(userId);
        upload.setStatus(BulkUploadStatus.BULK_EDIT);
    } else
        upload.setStatus(BulkUploadStatus.IN_PROGRESS);
    upload.setImportType(info.getType());
    // set default permissions
    GroupController groupController = new GroupController();
    ArrayList<Group> publicGroups = groupController.getAllPublicGroupsForAccount(account);
    for (Group group : publicGroups) {
        Permission permission = new Permission();
        permission.setCanRead(true);
        permission.setUpload(upload);
        permission.setGroup(group);
        permission = DAOFactory.getPermissionDAO().create(permission);
        upload.getPermissions().add(permission);
    }
    upload = dao.create(upload);
    if (info.getEntryList() != null) {
        for (PartData data : info.getEntryList()) {
            Entry entry = entryDAO.get(data.getId());
            // todo if entry is in another bulk upload, then update will fail
            if (entry == null)
                continue;
            upload.getContents().add(entry);
        }
    }
    dao.update(upload);
    return upload.toDataTransferObject();
}

Example 12 with GroupController

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

the class EntriesAsCSV method writeList.

/**
 * Iterate through list of entries and extract values
 *
 * @throws IOException on Exception write values to file
 */
private void writeList(EntryFieldLabel... fields) throws IOException {
    // filter entries based on what the user is allowed to see if the user is not an admin
    Account account = this.accountDAO.getByEmail(userId);
    if (account.getType() != AccountType.ADMIN) {
        List<Group> accountGroups = new GroupController().getAllGroups(account);
        entries = permissionDAO.getCanReadEntries(account, accountGroups, entries);
    }
    if (entries == null) {
        Logger.warn("No entries to convert to csv format");
        return;
    }
    // write headers
    Path tmpPath = Paths.get(Utils.getConfigValue(ConfigurationKey.TEMPORARY_DIRECTORY));
    File tmpFile = File.createTempFile("ice-", ".csv", tmpPath.toFile());
    csvPath = tmpFile.toPath();
    FileWriter fileWriter = new FileWriter(tmpFile);
    if (fields == null || fields.length == 0)
        fields = getEntryFields();
    String[] headers = getCSVHeaders(fields);
    Set<Long> sequenceSet = new HashSet<>();
    try (CSVWriter writer = new CSVWriter(fileWriter)) {
        writer.writeNext(headers);
        // write entry fields
        for (long entryId : entries) {
            Entry entry = dao.get(entryId);
            // get contents and write data out
            String[] line = new String[fields.length + 4];
            line[0] = entry.getCreationTime().toString();
            line[1] = entry.getPartNumber();
            // write field values
            int i = 1;
            for (EntryFieldLabel field : fields) {
                line[i + 1] = EntryUtil.entryFieldToValue(entry, field);
                i += 1;
            }
            // write sequence information
            if (this.includeSequences && sequenceDAO.hasSequence(entryId)) {
                line[i + 1] = getSequenceName(entry);
                sequenceSet.add(entryId);
            } else {
                line[i + 1] = "";
            }
            // get parents for entry
            EntryLinks links = new EntryLinks(this.userId, entry.getPartNumber());
            StringBuilder parents = new StringBuilder();
            for (PartData data : links.getParents()) {
                parents.append(data.getPartId()).append(",");
            }
            if (!StringUtils.isEmpty(parents.toString()))
                parents = new StringBuilder(parents.substring(0, parents.length() - 1));
            line[i + 2] = ("\"" + parents + "\"");
            // write line
            writer.writeNext(line);
        }
    }
    if (!sequenceSet.isEmpty())
        writeZip(sequenceSet);
}

Example 13 with GroupController

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

the class EntryPermissions method getEntryPermissions.

/**
 * Retrieves permissions associated with a part. Requires that the requesting user has write permissions
 * on the specified part
 *
 * @return list of available permissions for the specified part
 * @throws PermissionException if the requesting user does not have write permissions for the part
 */
public List<AccessPermission> getEntryPermissions() {
    // viewing permissions requires write permissions
    authorization.expectWrite(userId, entry);
    ArrayList<AccessPermission> accessPermissions = new ArrayList<>();
    List<Permission> permissions = permissionDAO.getEntryPermissions(entry);
    GroupController groupController = new GroupController();
    Group publicGroup = groupController.createOrRetrievePublicGroup();
    for (Permission permission : permissions) {
        if (permission.getAccount() == null && permission.getGroup() == null)
            continue;
        if (permission.getGroup() != null && permission.getGroup() == publicGroup)
            continue;
        accessPermissions.add(permission.toDataTransferObject());
    }
    return accessPermissions;
}

Example 14 with GroupController

use of org.jbei.ice.lib.group.GroupController 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 15 with GroupController

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

the class EntriesAsCSV method writeList.

/**
     * Iterate through list of entries and extract values
     *
     * @param userId identifier of user making request
     * @throws IOException on Exception write values to file
     */
private void writeList(String userId, EntryField... fields) throws IOException {
    // filter entries based on what the user is allowed to see if the user is not an admin
    Account account = this.accountDAO.getByEmail(userId);
    if (account.getType() != AccountType.ADMIN) {
        List<Group> accountGroups = new GroupController().getAllGroups(account);
        entries = permissionDAO.getCanReadEntries(account, accountGroups, entries);
    }
    if (entries == null) {
        Logger.warn("No entries to convert to csv format");
        return;
    }
    // write headers
    Path tmpPath = Paths.get(Utils.getConfigValue(ConfigurationKey.TEMPORARY_DIRECTORY));
    File tmpFile = File.createTempFile("ice-", ".csv", tmpPath.toFile());
    csvPath = tmpFile.toPath();
    FileWriter fileWriter = new FileWriter(tmpFile);
    if (fields == null || fields.length == 0)
        fields = getEntryFields();
    String[] headers = getCSVHeaders(fields);
    Set<Long> sequenceSet = new HashSet<>();
    try (CSVWriter writer = new CSVWriter(fileWriter)) {
        writer.writeNext(headers);
        // write entry fields
        for (long entryId : entries) {
            Entry entry = dao.get(entryId);
            //  get contents and write data out
            String[] line = new String[fields.length + 3];
            line[0] = entry.getCreationTime().toString();
            line[1] = entry.getPartNumber();
            int i = 1;
            for (EntryField field : fields) {
                line[i + 1] = EntryUtil.entryFieldToValue(entry, field);
                i += 1;
            }
            if (this.includeSequences && sequenceDAO.hasSequence(entryId)) {
                line[i + 1] = getSequenceName(entry);
                sequenceSet.add(entryId);
            } else {
                line[i + 1] = "";
            }
            writer.writeNext(line);
        }
    }
    writeZip(userId, sequenceSet);
}