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

Example 21 with FeaturedDNASequence

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

the class PartSequence method save.

// creates a new sequence and associates it with entry
public void save(FeaturedDNASequence dnaSequence) {
    entryAuthorization.expectWrite(userId, entry);
    // check if there is already an existing sequence
    if (sequenceDAO.getByEntry(this.entry) != null)
        throw new IllegalArgumentException("Entry already has a sequence associated with it. Please delete first");
    // update raw sequence if no sequence is passed
    // if ((dnaSequence.getFeatures() == null || dnaSequence.getFeatures().isEmpty())) {
    // // sometimes the whole sequence is sent in the string portion (when there are no features)
    // // no features to add
    // dnaSequence = GeneralParser.parse(dnaSequence.getSequence());
    // }
    // convert sequence wrapper to sequence storage model
    Sequence sequence = SequenceUtil.dnaSequenceToSequence(dnaSequence);
    if (sequence == null)
        return;
    saveSequenceObject(sequence);
}

Example 22 with FeaturedDNASequence

use of org.jbei.ice.lib.dto.FeaturedDNASequence 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 23 with FeaturedDNASequence

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

the class PartSequence method getFeaturedSequence.

private FeaturedDNASequence getFeaturedSequence(Entry entry, boolean canEdit, boolean includeAllFeatures) {
    Sequence sequence = sequenceDAO.getByEntry(entry);
    if (sequence == null) {
        return null;
    }
    List<SequenceFeature> sequenceFeatures;
    if (includeAllFeatures) {
        sequenceFeatures = sequenceFeatureDAO.getEntrySequenceFeatures(entry);
    } else {
        sequenceFeatures = sequenceFeatureDAO.pageSequenceFeatures(entry, 0, 20);
    }
    FeaturedDNASequence featuredDNASequence = SequenceUtil.sequenceToDNASequence(sequence, sequenceFeatures);
    featuredDNASequence.setCanEdit(canEdit);
    featuredDNASequence.setIdentifier(entry.getPartNumber());
    Configuration configuration = DAOFactory.getConfigurationDAO().get(ConfigurationKey.URI_PREFIX);
    if (configuration != null) {
        String uriPrefix = configuration.getValue();
        featuredDNASequence.setUri(uriPrefix + "/entry/" + entry.getId());
    }
    return featuredDNASequence;
}

Example 24 with FeaturedDNASequence

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

the class Sequences method parseSequence.

// public FeaturedDNASequence retrievePartSequence(String userId, String recordId) {
// Entry entry = hasEntry.getEntry(recordId);
// if (entry == null)
// throw new IllegalArgumentException("The part " + recordId + " could not be located");
// 
// if (entry.getVisibility() == Visibility.REMOTE.getValue()) {
// WebEntries webEntries = new WebEntries();
// return webEntries.getSequence(recordId);
// }
// 
// if (!new PermissionsController().isPubliclyVisible(entry))
// authorization.expectRead(userId, entry);
// 
// boolean canEdit = authorization.canWrite(userId, entry);
// return getFeaturedSequence(entry, canEdit);
// }
public SequenceInfo parseSequence(InputStream inputStream, String fileName) throws InvalidFormatParserException {
    int dotIndex = fileName.lastIndexOf('.');
    if (dotIndex != -1) {
        String ext = fileName.substring(dotIndex + 1);
        // unique case for sbol since it can result in multiple entries created
        if ("rdf".equalsIgnoreCase(ext) || "xml".equalsIgnoreCase(ext) || "sbol".equalsIgnoreCase(ext)) {
            // todo : cannot parse sbol yet
            return null;
        }
    }
    // parse actual sequence
    try {
        String sequenceString = IOUtils.toString(inputStream, Charset.defaultCharset());
        FeaturedDNASequence dnaSequence = GeneralParser.parse(sequenceString);
        if (dnaSequence == null)
            throw new InvalidFormatParserException("Could not parse sequence string");
        Sequence sequence = SequenceUtil.dnaSequenceToSequence(dnaSequence);
        sequence.setSequenceUser(sequenceString);
        if (!StringUtils.isBlank(fileName))
            sequence.setFileName(fileName);
        SequenceInfo info = sequence.toDataTransferObject();
        info.setSequence(dnaSequence);
        return info;
    } catch (IOException e) {
        throw new InvalidFormatParserException(e);
    }
}

Example 25 with FeaturedDNASequence

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

the class Sequences method bulkUpdate.

/**
 * Bulk update sequences based on uploaded zip file
 * containing sequences, where the sequence name is the (unique) part number of the entry.
 * If there is an existing sequence associated with the entry, it is deleted.
 *
 * @param userId          userId of user making request
 * @param fileInputStream input stream of zip file
 */
public List<String> bulkUpdate(String userId, InputStream fileInputStream) throws IOException {
    if (!new AccountController().isAdministrator(userId))
        throw new PermissionException("Must have admin privileges to use this feature");
    List<String> errors = new ArrayList<>();
    Logger.info("Starting bulk update of sequences");
    try (ZipInputStream stream = new ZipInputStream(fileInputStream)) {
        ZipEntry zipEntry;
        while ((zipEntry = stream.getNextEntry()) != null) {
            if (zipEntry.isDirectory())
                continue;
            String name = zipEntry.getName();
            if (name.contains("/"))
                name = name.substring(name.lastIndexOf("/") + 1);
            if (name.startsWith(".") || name.startsWith("_"))
                continue;
            ByteArrayOutputStream out = new ByteArrayOutputStream();
            int len;
            byte[] data = new byte[1024];
            while ((len = stream.read(data)) > 0) {
                out.write(data, 0, len);
            }
            stream.closeEntry();
            String entryName = name.substring(0, name.indexOf('.'));
            Entry entry = DAOFactory.getEntryDAO().getByPartNumber(entryName);
            if (entry == null) {
                errors.add(name);
                continue;
            }
            String sequenceString = new String(out.toByteArray());
            FeaturedDNASequence dnaSequence = GeneralParser.parse(sequenceString);
            if (dnaSequence == null) {
                Logger.error("Could not parse sequence for " + name);
                errors.add(name);
                continue;
            }
            Logger.info("Updating sequence for entry " + entry.getPartNumber() + " as part of bulk update");
            PartSequence partSequence = new PartSequence(userId, entry.getPartNumber());
            partSequence.delete();
            partSequence.save(dnaSequence);
        }
    }
    Logger.info("Completed bulk upload of sequences with " + errors.size() + " errors");
    return errors;
}