Examples with SBOLDocument org.sbolstandard.core.SBOLDocument used on opensource projects

Example 1 with SBOLDocument

use of org.sbolstandard.core.SBOLDocument in project ice by JBEI.

the class BulkFileSBOLUpload method processUpload.

public long processUpload() throws IOException {
    BulkUploadController controller = new BulkUploadController();
    long bulkUploadId = 0;
    SBOLDocument document = SBOLFactory.read(new FileInputStream(filePath.toFile()));
    try {
        // walk top level object
        for (SBOLRootObject rootObject : document.getContents()) {
            ICESBOLParserVisitor visitor = new ICESBOLParserVisitor(addType);
            rootObject.accept(visitor);
            BulkUploadAutoUpdate update = visitor.getUpdate();
            update.setBulkUploadId(bulkUploadId);
            Logger.info(userId + ": " + update.toString());
            update = controller.autoUpdateBulkUpload(userId, update, addType);
            if (bulkUploadId == 0)
                bulkUploadId = update.getBulkUploadId();
            // get "user sequence"
            String sequenceUser = getSequenceDocument(rootObject);
            long entryId = update.getEntryId();
            DNASequence dnaSequence = visitor.getFeaturedDNASequence();
            Sequence sequence = SequenceController.dnaSequenceToSequence(dnaSequence);
            Entry entry = DAOFactory.getEntryDAO().get(entryId);
            sequence.setEntry(entry);
            if (sequenceUser != null)
                sequence.setSequenceUser(sequenceUser);
            new SequenceController().save(userId, sequence);
        }
    } catch (Exception e) {
        Logger.error(e);
        throw new IOException(e);
    }
    return bulkUploadId;
}

Example 2 with SBOLDocument

use of org.sbolstandard.core.SBOLDocument in project ice by JBEI.

the class SBOLFormatter method createXmlDocument.

private SBOLDocument createXmlDocument(DnaComponent dnaComponent) {
    SBOLDocument document = SBOLFactory.createDocument();
    document.addContent(dnaComponent);
    return document;
}

Example 3 with SBOLDocument

use of org.sbolstandard.core.SBOLDocument in project ice by JBEI.

the class SBOLFormatter method format.

@Override
public void format(Sequence sequence, OutputStream outputStream) throws FormatterException, IOException {
    SBOLVisitor visitor = new SBOLVisitor();
    visitor.visit(sequence);
    SBOLDocument sbolDocument = createXmlDocument(visitor.getDnaComponent());
    SBOLFactory.write(sbolDocument, outputStream);
}

Example 4 with SBOLDocument

use of org.sbolstandard.core.SBOLDocument in project ice by JBEI.

the class BulkFileSBOLUpload method getSequenceDocument.

protected String getSequenceDocument(SBOLRootObject component) {
    SBOLDocument document = SBOLFactory.createDocument();
    document.addContent(component);
    ByteArrayOutputStream stream = new ByteArrayOutputStream();
    try {
        SBOLFactory.write(document, stream);
    } catch (IOException e) {
        Logger.error(e);
        return null;
    }
    try {
        return stream.toString(StandardCharsets.UTF_8.name());
    } catch (IOException e) {
        Logger.error(e);
        return null;
    }
}