Examples with InputStreamWrapper org.jbei.ice.lib.entry.sequence.InputStreamWrapper used on opensource projects

Example 1 with InputStreamWrapper

use of org.jbei.ice.lib.entry.sequence.InputStreamWrapper in project ice by JBEI.

the class RemoteEntriesAsCSV method writeLocalEntries.

protected void writeLocalEntries(List<Long> entries, List<EntryFieldLabel> fields, CSVWriter writer, ZipOutputStream zos) {
    if (entries == null)
        return;
    SequenceDAO sequenceDAO = DAOFactory.getSequenceDAO();
    Configuration configuration = DAOFactory.getConfigurationDAO().get(ConfigurationKey.URI_PREFIX);
    String thisUrl = configuration == null ? "" : configuration.getValue();
    for (Long id : entries) {
        Entry entry = DAOFactory.getEntryDAO().get(id);
        String[] line = new String[fields.size() + 4];
        line[0] = thisUrl;
        line[1] = entry.getCreationTime().toString();
        line[2] = entry.getPartNumber();
        int i = 2;
        for (EntryFieldLabel field : fields) {
            line[i + 1] = EntryUtil.entryFieldToValue(entry, field);
            i += 1;
        }
        // write sequence to zip file
        long entryId = entry.getId();
        if (sequenceDAO.hasSequence(entryId)) {
            String name = entry.getPartNumber() + ".gb";
            try {
                Sequence sequence = sequenceDAO.getByEntry(entry);
                line[i + 1] = name;
                GenbankFormatter genbankFormatter = new GenbankFormatter(name);
                ByteArrayOutputStream byteStream = new ByteArrayOutputStream();
                genbankFormatter.format(sequence, byteStream);
                ByteArrayInputStream inputStream = new ByteArrayInputStream(byteStream.toByteArray());
                InputStreamWrapper wrapper = new InputStreamWrapper(inputStream, name);
                putZipEntry(wrapper, zos);
            } catch (Exception e) {
                line[i + 1] = "";
            }
        } else {
            line[i + 1] = "";
        }
        writer.writeNext(line);
    }
}

Example 2 with InputStreamWrapper

use of org.jbei.ice.lib.entry.sequence.InputStreamWrapper in project ice by JBEI.

the class FileResource method downloadSequence.

@GET
@Path("{partId}/sequence/{type}")
public Response downloadSequence(@PathParam("partId") final String partId, @PathParam("type") final String downloadType, @DefaultValue("-1") @QueryParam("remoteId") long remoteId, @QueryParam("sid") String sid) {
    if (StringUtils.isEmpty(sessionId))
        sessionId = sid;
    final String userId = getUserId(sessionId);
    if (remoteId != -1) {
        RemoteSequence sequence = new RemoteSequence(remoteId, Long.decode(partId));
        final InputStreamWrapper wrapper = sequence.get(downloadType);
        StreamingOutput stream = output -> IOUtils.copy(wrapper.getInputStream(), output);
        return addHeaders(Response.ok(stream), wrapper.getName());
    } else {
        InputStreamWrapper wrapper = new PartSequence(userId, partId).toFile(SequenceFormat.fromString(downloadType), true);
        StreamingOutput stream = output -> IOUtils.copy(wrapper.getInputStream(), output);
        return addHeaders(Response.ok(stream), wrapper.getName());
    }
}

Example 3 with InputStreamWrapper

use of org.jbei.ice.lib.entry.sequence.InputStreamWrapper in project ice by JBEI.

the class EntriesAsCSV method customize.

public ByteArrayOutputStream customize(EntrySelection selection, SequenceFormat format, boolean onePerFolder) throws IOException {
    Entries retriever = new Entries(this.userId);
    this.entries = retriever.getEntriesFromSelectionContext(selection);
    ByteArrayOutputStream baos = new ByteArrayOutputStream();
    try (ZipOutputStream zos = new ZipOutputStream(baos)) {
        for (long entryId : this.entries) {
            // get the entry
            Entry entry = DAOFactory.getEntryDAO().get(entryId);
            if (entry == null) {
                // write to csv file
                Logger.error("ERROR : no entry " + entryId);
                continue;
            }
            if (!sequenceDAO.hasSequence(entry.getId())) {
                continue;
            }
            // get the sequence
            InputStreamWrapper wrapper = new PartSequence(userId, Long.toString(entryId)).toFile(format, onePerFolder);
            if (wrapper == null) {
                Logger.error("ERROR : no sequence " + entryId);
                continue;
            }
            if (onePerFolder)
                wrapper.setName(entry.getPartNumber() + File.separatorChar + wrapper.getName());
            else
                wrapper.setName(wrapper.getName());
            putZipEntry(wrapper, zos);
        }
        this.includeSequences = false;
        writeList(selection.getFields().toArray(new EntryFieldLabel[0]));
        // write the csv file to zip file
        FileInputStream fis = new FileInputStream(csvPath.toFile());
        InputStreamWrapper wrapper = new InputStreamWrapper(fis, "entries.csv");
        putZipEntry(wrapper, zos);
    }
    return baos;
}

Example 4 with InputStreamWrapper

use of org.jbei.ice.lib.entry.sequence.InputStreamWrapper in project ice by JBEI.

the class EntriesAsCSV method writeZip.

private void writeZip(Set<Long> sequenceSet) {
    Path tmpPath = Paths.get(Utils.getConfigValue(ConfigurationKey.TEMPORARY_DIRECTORY));
    try {
        File tmpZip = File.createTempFile("zip-", ".zip", tmpPath.toFile());
        // out
        FileOutputStream fos = new FileOutputStream(tmpZip);
        ZipOutputStream zos = new ZipOutputStream(fos);
        // get sequence formats
        for (long entryId : sequenceSet) {
            for (String format : formats) {
                InputStreamWrapper wrapper = new PartSequence(userId, Long.toString(entryId)).toFile(SequenceFormat.fromString(format), true);
                putZipEntry(wrapper, zos);
            }
        }
        // write the csv file
        FileInputStream fis = new FileInputStream(csvPath.toFile());
        InputStreamWrapper wrapper = new InputStreamWrapper(fis, "entries.csv");
        putZipEntry(wrapper, zos);
        zos.close();
        csvPath = tmpZip.toPath();
    } catch (Exception e) {
        Logger.error(e);
    }
}

Example 5 with InputStreamWrapper

use of org.jbei.ice.lib.entry.sequence.InputStreamWrapper in project ice by JBEI.

the class Attachments method getAttachmentByFileId.

/**
 * Retrieves a previously uploaded attachment to an entry by it's unique file identifier
 * This file identifier is assigned on upload
 *
 * @return wrapper around file byte array and name
 * @throws PermissionException if the attachment referenced by the fileId exists but
 *                             the user does not have read permissions on the entry associated with the attachment
 * @throws IOException         on exception retrieving file
 */
public InputStreamWrapper getAttachmentByFileId(String userId, String fileId) throws IOException {
    Attachment attachment = dao.getByFileId(fileId);
    if (attachment == null)
        return null;
    entryAuthorization.expectRead(userId, attachment.getEntry());
    String dataDir = Utils.getConfigValue(ConfigurationKey.DATA_DIRECTORY);
    byte[] bytes = Files.readAllBytes(Paths.get(dataDir, attachmentDirName, attachment.getFileId()));
    return new InputStreamWrapper(bytes, attachment.getFileName());
}