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

Example 1 with InvalidFormatParserException

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

the class FastaParser method parse.

@Override
public FeaturedDNASequence parse(String textSequence) throws InvalidFormatParserException {
    try {
        textSequence = cleanSequence(textSequence);
        try (BufferedReader br = new BufferedReader(new StringReader(textSequence))) {
            FeaturedDNASequence sequence;
            RichSequenceIterator 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);
    }
}

Example 2 with InvalidFormatParserException

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

the class SBOLParser method parseToEntry.

public SequenceInfo parseToEntry(String textSequence, String fileName) throws InvalidFormatParserException {
    SBOLDocument document;
    try {
        document = SBOLReader.read(new ByteArrayInputStream(textSequence.getBytes(StandardCharsets.UTF_8)));
    } catch (SBOLValidationException e) {
        Logger.error(e);
        throw new InvalidFormatParserException("Invalid SBOL file: " + e.getMessage());
    } catch (IOException e) {
        Logger.error(e);
        throw new InvalidFormatParserException("Server error parsing file");
    } catch (SBOLConversionException e) {
        Logger.error(e);
        throw new InvalidFormatParserException("Error converting file to SBOL 2.0");
    }
    // parse raw document and return
    SequenceInfo sequenceInfo = parseToGenBank(document, fileName, entry, null);
    // document parsed successfully, go through module definitions
    for (ModuleDefinition moduleDefinition : document.getModuleDefinitions()) {
        try {
            createICEModuleDefinitionRecord(document, moduleDefinition);
        } catch (SBOLValidationException e) {
            Logger.error("Could not import module definition", e);
        }
    }
    // go through component definitions
    for (ComponentDefinition componentDefinition : document.getComponentDefinitions()) {
        try {
            createICEComponentDefinitionRecord(document, componentDefinition);
        } catch (SBOLValidationException e) {
            Logger.error("Could not import component definition", e);
        }
    }
    return sequenceInfo;
}

Example 3 with InvalidFormatParserException

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

the class SBOLParser method parseToEntry.

public SequenceInfo parseToEntry(InputStream stream, String fileName) throws InvalidFormatParserException {
    SBOLDocument document;
    try {
        document = SBOLReader.read(stream);
    } catch (SBOLValidationException e) {
        Logger.error(e);
        throw new InvalidFormatParserException("Invalid SBOL file: " + e.getMessage());
    } catch (IOException e) {
        Logger.error(e);
        throw new InvalidFormatParserException("Server error parsing file");
    } catch (SBOLConversionException e) {
        Logger.error(e);
        throw new InvalidFormatParserException("Error converting file to SBOL 2.0");
    }
    // parse raw document and return
    SequenceInfo sequenceInfo = parseToGenBank(document, fileName, entry, null);
    if (!this.extractHierarchy)
        return sequenceInfo;
    // document parsed successfully, go through module definitions
    for (ModuleDefinition moduleDefinition : document.getModuleDefinitions()) {
        try {
            createICEModuleDefinitionRecord(document, moduleDefinition);
        } catch (SBOLValidationException e) {
            Logger.error("Could not import module definition", e);
        }
    }
    // go through component definitions
    for (ComponentDefinition componentDefinition : document.getComponentDefinitions()) {
        try {
            createICEComponentDefinitionRecord(document, componentDefinition);
        } catch (SBOLValidationException e) {
            Logger.error("Could not import component definition", e);
        }
    }
    return sequenceInfo;
}

Example 4 with InvalidFormatParserException

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

the class PartTraceSequences 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.parse(new String(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 5 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
 * @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);
    }
}