Examples with GenBankParser org.jbei.ice.lib.parsers.genbank.GenBankParser used on opensource projects

Example 1 with GenBankParser

use of org.jbei.ice.lib.parsers.genbank.GenBankParser in project ice by JBEI.

the class GeneralParser method registerParsers.

private void registerParsers() {
    parsers.add(new GenBankParser());
    parsers.add(new FastaParser());
    parsers.add(new PlainParser());
}

Example 2 with GenBankParser

use of org.jbei.ice.lib.parsers.genbank.GenBankParser in project ice by JBEI.

the class PartSequence method parseSequenceFile.

/**
 * Parses a sequence in a file and associates it with the current entry
 *
 * @param inputStream      input stream of bytes representing the file
 * @param fileName         name of file being parsed
 * @param extractHierarchy for SBOL2 sequences only. If set to <code>true</code>, creates a hierarchy of ICE entries
 *                         as needed
 * @return wrapper around the internal model used to represent sequence information
 * @throws IOException on Exception parsing the contents of the file
 */
public SequenceInfo parseSequenceFile(InputStream inputStream, String fileName, boolean extractHierarchy) throws IOException {
    AbstractParser parser;
    // write sequence file to disk (tmp)
    String tmpDir = new ConfigurationSettings().getPropertyValue(ConfigurationKey.TEMPORARY_DIRECTORY);
    if (StringUtils.isEmpty(tmpDir))
        throw new IllegalArgumentException("Cannot parse sequence without valid tmp directory");
    Path tmpPath = Paths.get(tmpDir);
    if (!Files.isDirectory(tmpPath) || !Files.isWritable(tmpPath))
        throw new IllegalArgumentException("Cannot write to tmp directory: " + tmpPath.toString());
    Path sequencePath = Paths.get(tmpPath.toString(), UUID.randomUUID().toString() + "-" + fileName);
    Files.copy(inputStream, sequencePath, StandardCopyOption.REPLACE_EXISTING);
    // detect sequence
    SequenceFormat format;
    try (InputStream fileInputStream = Files.newInputStream(sequencePath);
        LineIterator iterator = IOUtils.lineIterator(fileInputStream, StandardCharsets.UTF_8)) {
        if (!iterator.hasNext())
            throw new IOException("Cannot read stream for " + fileName);
        String firstLine = iterator.next();
        format = SequenceUtil.detectFormat(firstLine);
    }
    // special handling for sbol format
    try {
        if (format == SBOL2) {
            SBOLParser sbolParser = new SBOLParser(this.userId, Long.toString(this.entry.getId()), extractHierarchy);
            return sbolParser.parseToEntry(Files.newInputStream(sequencePath), fileName);
        }
        switch(format) {
            case GENBANK:
                parser = new GenBankParser();
                break;
            case FASTA:
                parser = new FastaParser();
                break;
            default:
            case PLAIN:
                parser = new PlainParser();
                break;
        }
        LineIterator iterator = IOUtils.lineIterator(Files.newInputStream(sequencePath), StandardCharsets.UTF_8);
        SequenceFile sequenceFile = new SequenceFile();
        String entryType = this.entry.getRecordType();
        // special handling for SBOL (todo: clean this up in future release)
        FeaturedDNASequence dnaSequence = parser.parse(iterator, entryType);
        Sequence sequence = SequenceUtil.dnaSequenceToSequence(dnaSequence);
        if (sequence == null)
            throw new IOException("Could not create sequence object");
        // copy original sequence file to file system
        try {
            Files.copy(sequencePath, sequenceFile.getFilePath(), StandardCopyOption.REPLACE_EXISTING);
            sequence.setSequenceUser(sequenceFile.getFileName());
        } catch (Exception e) {
            // ok to ignore. Can get back sequence as long as sequence object is saved. cannot download original
            Logger.warn("Exception writing sequence to file: " + e.getMessage());
        }
        sequence.setFileName(fileName);
        sequence.setFormat(format);
        sequence = saveSequenceObject(sequence);
        SequenceInfo info = sequence.toDataTransferObject();
        info.setSequence(dnaSequence);
        return info;
    } catch (InvalidFormatParserException ifpe) {
        Logger.error(ifpe);
        return null;
    } finally {
        Files.deleteIfExists(sequencePath);
    }
}

Example 3 with GenBankParser

use of org.jbei.ice.lib.parsers.genbank.GenBankParser in project ice by JBEI.

the class SBOLParser method parseToGenBank.

/**
 * Parse the SBOL document to genbank format, save and associate with entry
 *
 * @param sbolDocument SBOL document to parse
 * @param fileName     name of file that was parsed to extract the SBOL information
 * @param entry        ICE entry to associate sequence document with
 * @param uri          optional uri to associate with sequence
 * @return Sequence info data transfer object for saved sequence
 */
private SequenceInfo parseToGenBank(SBOLDocument sbolDocument, String fileName, Entry entry, String uri) {
    ByteArrayOutputStream out = new ByteArrayOutputStream();
    String rdf;
    // convert to rdf string to save raw document
    try {
        sbolDocument.write(out);
        rdf = out.toString();
    } catch (SBOLConversionException e) {
        rdf = null;
    }
    // convert to genbank
    Sequence sequence = null;
    FeaturedDNASequence dnaSequence = null;
    try {
        out.reset();
        SBOLWriter.write(sbolDocument, out, "GENBANK");
        if (out.size() > 0) {
            GenBankParser parser = new GenBankParser();
            dnaSequence = parser.parse(IOUtils.lineIterator(new ByteArrayInputStream(out.toByteArray()), Charset.defaultCharset()));
            sequence = SequenceUtil.dnaSequenceToSequence(dnaSequence);
        }
    } catch (SBOLConversionException | IOException e) {
        Logger.error("Error converting SBOL to genBank: " + e.getMessage());
    }
    // convert to ice data model (sequence)
    if (sequence == null) {
        sequence = new Sequence();
    }
    if (!StringUtils.isEmpty(rdf))
        sequence.setSequenceUser(rdf);
    sequence.setFormat(SequenceFormat.SBOL2);
    sequence.setEntry(entry);
    if (fileName != null)
        sequence.setFileName(fileName);
    if (!StringUtils.isEmpty(uri))
        sequence.setUri(uri);
    sequence = DAOFactory.getSequenceDAO().create(sequence);
    SequenceInfo sequenceInfo = new SequenceInfo();
    sequenceInfo.setEntryId(entry.getId());
    sequenceInfo.setSequence(dnaSequence);
    sequenceInfo.setFormat(sequence.getFormat());
    if (fileName != null)
        sequenceInfo.setFilename(fileName);
    return sequenceInfo;
}

Example 4 with GenBankParser

use of org.jbei.ice.lib.parsers.genbank.GenBankParser in project ice by JBEI.

the class PartSequence method parseSequenceFile.

/**
     * Parses a sequence in a file and associates it with the current entry
     *
     * @param inputStream input stream of bytes representing the file
     * @param fileName    name of file being parsed
     * @return wrapper around the internal model used to represent sequence information
     * @throws IOException on Exception parsing the contents of the file
     */
public SequenceInfo parseSequenceFile(InputStream inputStream, String fileName) throws IOException {
    try {
        AbstractParser parser;
        String sequenceString = Utils.getString(inputStream);
        switch(detectFormat(sequenceString)) {
            case GENBANK:
                parser = new GenBankParser();
                break;
            case SBOL2:
                SBOLParser sbolParser = new SBOLParser(this.userId, Long.toString(this.entry.getId()));
                return sbolParser.parseToEntry(sequenceString, fileName);
            case FASTA:
                parser = new FastaParser();
                break;
            default:
            case PLAIN:
                parser = new PlainParser();
                break;
        }
        // parse actual sequence
        DNASequence sequence = parser.parse(sequenceString);
        return save(sequence, sequenceString, fileName);
    } catch (InvalidFormatParserException e) {
        Logger.error(e);
        throw new IOException(e);
    }
}