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

Example 6 with InputStreamWrapper

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

the class FileResource method getAttachment.

@GET
@Path("attachment/{fileId}")
public Response getAttachment(@PathParam("fileId") String fileId) {
    String userId = requireUserId();
    try {
        InputStreamWrapper wrapper = attachments.getAttachmentByFileId(userId, fileId);
        if (wrapper == null) {
            return respond(Response.Status.NOT_FOUND);
        }
        StreamingOutput stream = output -> IOUtils.copy(wrapper.getInputStream(), output);
        return addHeaders(Response.ok(stream), wrapper.getName());
    } catch (IOException e) {
        Logger.error(e);
        throw new WebApplicationException(e);
    }
}

Example 7 with InputStreamWrapper

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

the class RemoteEntriesAsCSV method writeDataEntries.

protected void writeDataEntries(RemotePartner partner, List<PartData> entries, List<EntryFieldLabel> fields, CSVWriter writer, ZipOutputStream zos) {
    if (entries == null)
        return;
    for (PartData partData : entries) {
        String[] line = new String[fields.size() + 4];
        line[0] = partner.getUrl();
        line[1] = new Date(partData.getCreationTime()).toString();
        line[2] = partData.getPartId();
        int i = 2;
        for (EntryFieldLabel field : fields) {
            line[i + 1] = PartDataUtil.entryFieldToValue(partData, field);
            i += 1;
        }
        // write sequence to zip file
        if (partData.isHasSequence()) {
            try {
                // get remote sequence
                FeaturedDNASequence featuredDNASequence = remoteEntries.getPublicEntrySequence(partner.getId(), Long.toString(partData.getId()));
                if (featuredDNASequence != null) {
                    String name = partData.getPartId() + ".gb";
                    // write sequence to zip
                    line[i + 1] = name;
                    Sequence sequence = SequenceUtil.dnaSequenceToSequence(featuredDNASequence);
                    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);
                } else {
                    line[i + 1] = "";
                }
            } catch (Exception e) {
                line[i + 1] = "";
            }
        } else {
            line[i + 1] = "";
        }
        writer.writeNext(line);
    }
}

Example 8 with InputStreamWrapper

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

the class RemoteEntriesAsCSV method writeZip.

private boolean writeZip(File tmpZip, ZipOutputStream zos) {
    try {
        // 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();
        return true;
    } catch (Exception e) {
        Logger.error(e);
        return false;
    }
}

Example 9 with InputStreamWrapper

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

the class RemoteSequence method get.

public InputStreamWrapper get(String type) {
    FeaturedDNASequence featuredDNASequence = remoteContact.getPublicEntrySequence(partner.getUrl(), Long.toString(remotePartId), partner.getApiKey());
    if (featuredDNASequence == null)
        return new InputStreamWrapper(new byte[] { '\0' }, "no_sequence");
    String name = featuredDNASequence.getName();
    try {
        Sequence sequence = SequenceUtil.dnaSequenceToSequence(featuredDNASequence);
        ByteArrayOutputStream byteStream = new ByteArrayOutputStream();
        AbstractFormatter formatter;
        switch(type.toLowerCase()) {
            case "genbank":
            default:
                name = name + ".gb";
                formatter = new GenbankFormatter(name);
                break;
            case "fasta":
                formatter = new FastaFormatter();
                break;
            case "sbol1":
                formatter = new SBOLFormatter();
                name = name + ".xml";
                break;
            case "sbol2":
                formatter = new SBOL2Formatter();
                name = name + ".xml";
                break;
            case "gff3":
                formatter = new GFF3Formatter();
                name = name + ".gff3";
                break;
        }
        formatter.format(sequence, byteStream);
        return new InputStreamWrapper(byteStream.toByteArray(), name);
    } catch (Exception e) {
        Logger.error(e);
        return new InputStreamWrapper(new byte[] { '\0' }, "no_sequence");
    }
}

Example 10 with InputStreamWrapper

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

the class RemoteTransfer method performTransfer.

/**
 * Transfers the sequence file for the part and any parts that are linked to it.
 * If the attached sequence was uploaded as a file or pasted, the system
 * transfers that. If not if attempts to convert the attached sequence to genbank format
 * and transfers that
 *
 * @param partner destination for the sequence transfer
 * @param data    data for part whose sequences are to be transferred
 */
protected void performTransfer(RemotePartner partner, PartData data) {
    String url = partner.getUrl();
    // check main entry for sequence
    if (sequenceDAO.hasSequence(data.getId())) {
        InputStreamWrapper wrapper = new SequenceAsString(SequenceFormat.GENBANK, data.getId(), true).get();
        if (wrapper != null && wrapper.getInputStream() != null) {
            try {
                String sequenceString = new String(wrapper.getInputStream().readAllBytes(), StandardCharsets.UTF_8);
                remoteContact.transferSequence(url, data.getRecordId(), data.getType(), sequenceString);
            } catch (IOException e) {
                Logger.error("Cannot transfer sequence", e);
            }
        }
    }
    // check child entries
    if (data.getLinkedParts() == null)
        return;
    for (PartData linked : data.getLinkedParts()) {
        performTransfer(partner, linked);
    }
}