Examples with PartData org.jbei.ice.lib.dto.entry.PartData used on opensource projects

Example 11 with PartData

use of org.jbei.ice.lib.dto.entry.PartData in project ice by JBEI.

the class CollectionEntries method getAvailableEntries.

/**
     * Retrieves entries available to user. "Availability" is determined by any permissions set on the entries
     *
     * @param field  sort field
     * @param asc    sort order
     * @param offset paging start
     * @param limit  maximum number of entries to retrieve
     * @param filter optional text to filter entries by
     * @return wrapper around list of parts that conform to the parameters and the maximum number
     * of such entries that are available
     */
protected Results<PartData> getAvailableEntries(ColumnField field, boolean asc, int offset, int limit, String filter) {
    VisibleEntries visibleEntries = new VisibleEntries(userId);
    List<PartData> entries = visibleEntries.getEntries(field, asc, offset, limit, filter);
    long count = visibleEntries.getEntryCount(filter);
    Results<PartData> results = new Results<>();
    results.setResultCount(count);
    results.setData(entries);
    return results;
}

Example 12 with PartData

use of org.jbei.ice.lib.dto.entry.PartData in project ice by JBEI.

the class Collection method getBulkUploadFolder.

/**
     * Retrieves bulk import and entries associated with it that are referenced by the
     * id in the parameter. Only owners or administrators are allowed to retrieve bulk imports
     *
     * @param id     unique identifier for bulk import
     * @param offset offset for upload entries (start)
     * @param limit  maximum number of entries to return with the upload
     * @return data transfer object with the retrieved bulk import data and associated entries
     * @throws PermissionException
     */
protected AbstractFolder getBulkUploadFolder(long id, int offset, int limit) {
    BulkUploadDAO uploadDAO = DAOFactory.getBulkUploadDAO();
    BulkUploadAuthorization authorization = new BulkUploadAuthorization();
    BulkUpload draft = uploadDAO.get(id);
    if (draft == null)
        return null;
    Account account = DAOFactory.getAccountDAO().getByEmail(userId);
    authorization.expectRead(account.getEmail(), draft);
    // retrieve the entries associated with the bulk import
    BulkUploadInfo info = draft.toDataTransferObject();
    List<Entry> list = uploadDAO.retrieveDraftEntries(id, offset, limit);
    for (Entry entry : list) {
        PartData partData = setFileData(userId, entry, ModelToInfoFactory.getInfo(entry));
        // check if any links and convert
        if (!entry.getLinkedEntries().isEmpty()) {
            Entry linked = (Entry) entry.getLinkedEntries().toArray()[0];
            PartData linkedData = partData.getLinkedParts().remove(0);
            linkedData = setFileData(userId, linked, linkedData);
            partData.getLinkedParts().add(linkedData);
        }
        info.getEntryList().add(partData);
    }
    info.setCount(uploadDAO.retrieveSavedDraftCount(id));
    return info;
}

Example 13 with PartData

use of org.jbei.ice.lib.dto.entry.PartData in project ice by JBEI.

the class BulkZipUpload method processUpload.

/**
     * Process the zip file. It expects that there is exactly one file with the .csv extension.
     * This means that a .csv cannot be used as an attachment
     * </p>
     * Also, all dot files are ignored
     */
public ProcessedBulkUpload processUpload() {
    ProcessedBulkUpload processedBulkUpload = new ProcessedBulkUpload();
    String csvFile = null;
    HashMap<String, InputStream> files = new HashMap<>();
    try {
        ZipFile zipFile = new ZipFile(zipFilePath.toFile());
        Enumeration<? extends ZipEntry> enumeration = zipFile.entries();
        // go through zip elements
        while (enumeration.hasMoreElements()) {
            ZipEntry zipEntry = enumeration.nextElement();
            // does not go into directories for now
            if (zipEntry.isDirectory())
                continue;
            String name = zipEntry.getName();
            if (name.contains("/"))
                name = name.substring(name.lastIndexOf("/") + 1);
            // ignore all dot files
            if (name.startsWith("."))
                continue;
            // get main csv
            if (name.endsWith(".csv")) {
                if (csvFile != null) {
                    processedBulkUpload.setSuccess(false);
                    processedBulkUpload.setUserMessage("Duplicate csv file in zip archive. It should only contain one.");
                    return processedBulkUpload;
                }
                csvFile = Utils.getString(zipFile.getInputStream(zipEntry));
            } else {
                InputStream inputStream = zipFile.getInputStream(zipEntry);
                files.put(name, inputStream);
            }
        }
    } catch (IOException e) {
        processedBulkUpload.setSuccess(false);
        processedBulkUpload.setUserMessage(e.getCause().getMessage());
        return processedBulkUpload;
    }
    if (csvFile == null) {
        processedBulkUpload.setSuccess(false);
        processedBulkUpload.setUserMessage("Could not find a csv file in the zip archive");
        return processedBulkUpload;
    }
    try {
        ByteArrayInputStream inputStream = new ByteArrayInputStream(csvFile.getBytes(StandardCharsets.UTF_8));
        // retrieve the partData and validates
        List<PartWithSample> updates = super.getBulkUploadDataFromFile(inputStream);
        if (updates == null) {
            processedBulkUpload.setSuccess(false);
            processedBulkUpload.setUserMessage("Validation failed");
            for (EntryField field : invalidFields) {
                processedBulkUpload.getHeaders().add(new EntryHeaderValue(false, field));
            }
            return processedBulkUpload;
        }
        // validate files to ensure that for each partData with a file, that the file is available
        for (PartWithSample partWithSample : updates) {
            // check sequences
            PartData data = partWithSample.getPartData();
            String sequenceFile = data.getSequenceFileName();
            if (StringUtils.isNotBlank(sequenceFile) && files.get(sequenceFile) == null) {
                processedBulkUpload.setSuccess(false);
                processedBulkUpload.setUserMessage("Sequence file \"" + sequenceFile + "\" not found in the zip archive");
                return processedBulkUpload;
            }
            // check attachments
            String attachmentFile;
            if (data.getAttachments() != null && !data.getAttachments().isEmpty()) {
                attachmentFile = data.getAttachments().get(0).getFilename();
                if (StringUtils.isNotBlank(attachmentFile) && files.get(attachmentFile) == null) {
                    processedBulkUpload.setSuccess(false);
                    processedBulkUpload.setUserMessage("Attachment file \"" + sequenceFile + "\" not found in the zip archive");
                    return processedBulkUpload;
                }
            }
        // todo : trace sequences
        }
        // create actual registry parts
        BulkEntryCreator creator = new BulkEntryCreator();
        long uploadId = creator.createBulkUpload(userId, addType);
        // create entries
        if (!creator.createEntries(userId, uploadId, updates, files)) {
            String errorMsg = "Error creating entries for upload";
            throw new IOException(errorMsg);
        //todo: delete upload id
        }
        processedBulkUpload.setUploadId(uploadId);
        return processedBulkUpload;
    } catch (IOException e) {
        Logger.error(e);
        processedBulkUpload.setSuccess(false);
        processedBulkUpload.setUserMessage(e.getCause() != null ? e.getCause().getMessage() : e.getMessage());
        return processedBulkUpload;
    }
}

Example 14 with PartData

use of org.jbei.ice.lib.dto.entry.PartData in project ice by JBEI.

the class TransferTask method execute.

public void execute() {
    RemoteTransfer transfer = new RemoteTransfer();
    Account account = DAOFactory.getAccountDAO().getByEmail(userId);
    if (account.getType() != AccountType.ADMIN)
        return;
    Entries retriever = new Entries(account.getEmail());
    List<Long> entries = retriever.getEntriesFromSelectionContext(entrySelection);
    Logger.info(userId + ": requesting transfer to " + remoteId);
    List<PartData> dataList = transfer.getPartsForTransfer(entries);
    List<Long> remoteIds = transfer.transferEntries(remoteId, dataList);
    // check folder
    if (StringUtils.isEmpty(this.entrySelection.getFolderId()))
        return;
    // create remoteFolder
    long folderId = Long.decode(this.entrySelection.getFolderId());
    Folder folder = DAOFactory.getFolderDAO().get(folderId);
    Logger.info("Adding " + remoteIds.size() + " transferred entries to remote folder");
    transfer.transferFolder(remoteId, folder.toDataTransferObject(), remoteIds);
}

Example 15 with PartData

use of org.jbei.ice.lib.dto.entry.PartData in project ice by JBEI.

the class RemoteTransfer method transferEntries.

/**
     * Performs the transfer of the entry objects to the remote partner specified.
     * It is the responsibility of the destination to ensure that the hierarchical reln is reconstructed
     *
     * @param remoteId unique identifier for remote partner the parts are to be transferred to
     * @param entries  list of entries to be transferred. Note that the entries contain the linked
     *                 entries as well and these may or may not already exist on the recipient
     * @return list of ids of the transferred entries. These are the ids on the remote recipient and not this ice instance
     */
public List<Long> transferEntries(long remoteId, List<PartData> entries) {
    RemotePartner partner = this.remotePartnerDAO.get(remoteId);
    if (partner == null)
        throw new IllegalArgumentException("Invalid remote host id: " + remoteId);
    int exceptionCount = 0;
    String url = partner.getUrl();
    List<Long> remoteIds = new LinkedList<>();
    for (PartData data : entries) {
        try {
            PartData object = remoteContact.transferPart(url, data);
            if (object == null) {
                exceptionCount += 1;
                continue;
            }
            remoteIds.add(object.getId());
            if (data.getLinkedParts() != null) {
                remoteIds.addAll(object.getLinkedParts().stream().map(PartData::getId).collect(Collectors.toList()));
            }
            // transfers attachments and sequences
            performTransfer(partner, data);
        } catch (Exception e) {
            exceptionCount += 1;
            if (exceptionCount >= 5) {
                Logger.error(e);
                Logger.error(exceptionCount + " exceptions encountered during transfer. Aborting");
                return null;
            }
            Logger.error(e);
        }
    }
    return remoteIds;
}