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

Example 6 with InvalidFormatParserException

use of org.jbei.ice.lib.parsers.InvalidFormatParserException 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 7 with InvalidFormatParserException

use of org.jbei.ice.lib.parsers.InvalidFormatParserException 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);
    }
}

Example 8 with InvalidFormatParserException

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

the class TraceSequences method parseTraceSequence.

private boolean parseTraceSequence(String fileName, byte[] bytes) {
    DNASequence dnaSequence = null;
    // First try parsing as ABI
    ABIParser abiParser = new ABIParser();
    try {
        dnaSequence = abiParser.parse(bytes);
    } catch (InvalidFormatParserException e) {
    //
    }
    if (dnaSequence == null) {
        // try parsing as fasta, genbank, etc
        dnaSequence = GeneralParser.getInstance().parse(bytes);
        if (dnaSequence == null || dnaSequence.getSequence() == null) {
            String errMsg = ("Could not parse \"" + fileName + "\". Only Fasta, GenBank & ABI files are supported.");
            Logger.error(errMsg);
            return false;
        }
    }
    TraceSequence traceSequence = importTraceSequence(fileName, dnaSequence.getSequence().toLowerCase(), new ByteArrayInputStream(bytes));
    if (traceSequence == null)
        return false;
    Sequence sequence = DAOFactory.getSequenceDAO().getByEntry(entry);
    if (sequence == null)
        return true;
    buildOrRebuildAlignment(traceSequence, sequence);
    return true;
}

Example 9 with InvalidFormatParserException

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

the class FileResource method createSequenceModel.

/**
 * Create a model of the uploaded sequence file. Note that this does not associate the sequence
 * with any existing entry. It just parses the uploaded file
 */
@POST
@Path("sequence/model")
@Consumes(MediaType.MULTIPART_FORM_DATA)
@Produces(MediaType.APPLICATION_JSON)
public Response createSequenceModel(@FormDataParam("file") InputStream fileInputStream, @FormDataParam("file") FormDataContentDisposition contentDispositionHeader) {
    final String fileName = contentDispositionHeader.getFileName();
    Sequences sequences = new Sequences(requireUserId());
    try {
        return super.respond(sequences.parseSequence(fileInputStream, fileName));
    } catch (InvalidFormatParserException e) {
        throw new WebApplicationException(e.getMessage());
    }
}

Example 10 with InvalidFormatParserException

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

the class FastaParser method parse.

@Override
public FeaturedDNASequence parse(Iterator<String> iterator, String... entryType) throws InvalidFormatParserException {
    try {
        String textSequence = getSequence(iterator);
        textSequence = cleanSequence(textSequence);
        textSequence = textSequence.replaceAll("\t", "\n");
        try (BufferedReader br = new BufferedReader(new StringReader(textSequence))) {
            FeaturedDNASequence sequence;
            RichSequenceIterator richSequences;
            if (entryType.length > 0 && entryType[0].equals("protein")) {
                richSequences = IOTools.readFastaProtein(br, null);
            } else {
                richSequences = IOTools.readFastaDNA(br, null);
            }
            if (richSequences.hasNext()) {
                RichSequence richSequence = richSequences.nextRichSequence();
                sequence = new FeaturedDNASequence(richSequence.seqString(), new LinkedList<>());
            } else {
                throw new InvalidFormatParserException("No sequence found in sequence file!");
            }
            return sequence;
        }
    } catch (BioException | IOException e) {
        throw new InvalidFormatParserException("Couldn't parse FASTA sequence!", e);
    }
}