Examples with MolgenisDataException org.molgenis.data.MolgenisDataException used on opensource projects

Example 31 with MolgenisDataException

use of org.molgenis.data.MolgenisDataException in project molgenis by molgenis.

the class ExcelUtils method toValue.

// Gets a cell value as String and process the value with the given cellProcessors
static String toValue(Cell cell, List<CellProcessor> cellProcessors) {
    String value;
    switch(cell.getCellTypeEnum()) {
        case BLANK:
            value = null;
            break;
        case STRING:
            value = cell.getStringCellValue();
            break;
        case NUMERIC:
            if (DateUtil.isCellDateFormatted(cell)) {
                try {
                    // Excel dates are LocalDateTime, stored without timezone.
                    // Interpret them as UTC to prevent ambiguous DST overlaps which happen in other timezones.
                    LocaleUtil.setUserTimeZone(LocaleUtil.TIMEZONE_UTC);
                    Date dateCellValue = cell.getDateCellValue();
                    value = formatUTCDateAsLocalDateTime(dateCellValue);
                } finally {
                    LocaleUtil.resetUserTimeZone();
                }
            } else {
                // excel stores integer values as double values
                // read an integer if the double value equals the
                // integer value
                double x = cell.getNumericCellValue();
                if (x == Math.rint(x) && !Double.isNaN(x) && !Double.isInfinite(x))
                    value = String.valueOf((long) x);
                else
                    value = String.valueOf(x);
            }
            break;
        case BOOLEAN:
            value = String.valueOf(cell.getBooleanCellValue());
            break;
        case FORMULA:
            // evaluate formula
            FormulaEvaluator evaluator = cell.getSheet().getWorkbook().getCreationHelper().createFormulaEvaluator();
            CellValue cellValue = evaluator.evaluate(cell);
            switch(cellValue.getCellTypeEnum()) {
                case BOOLEAN:
                    value = String.valueOf(cellValue.getBooleanValue());
                    break;
                case NUMERIC:
                    if (DateUtil.isCellDateFormatted(cell)) {
                        try {
                            // Excel dates are LocalDateTime, stored without timezone.
                            // Interpret them as UTC to prevent ambiguous DST overlaps which happen in other timezones.
                            LocaleUtil.setUserTimeZone(LocaleUtil.TIMEZONE_UTC);
                            Date javaDate = DateUtil.getJavaDate(cellValue.getNumberValue(), false);
                            value = formatUTCDateAsLocalDateTime(javaDate);
                        } finally {
                            LocaleUtil.resetUserTimeZone();
                        }
                    } else {
                        // excel stores integer values as double values
                        // read an integer if the double value equals the
                        // integer value
                        double x = cellValue.getNumberValue();
                        if (x == Math.rint(x) && !Double.isNaN(x) && !Double.isInfinite(x))
                            value = String.valueOf((long) x);
                        else
                            value = String.valueOf(x);
                    }
                    break;
                case STRING:
                    value = cellValue.getStringValue();
                    break;
                case BLANK:
                    value = null;
                    break;
                default:
                    throw new MolgenisDataException("unsupported cell type: " + cellValue.getCellTypeEnum());
            }
            break;
        default:
            throw new MolgenisDataException("unsupported cell type: " + cell.getCellTypeEnum());
    }
    return AbstractCellProcessor.processCell(value, false, cellProcessors);
}

Example 32 with MolgenisDataException

use of org.molgenis.data.MolgenisDataException in project molgenis by molgenis.

the class VcfToEntity method createSampleEntities.

private List<Entity> createSampleEntities(VcfRecord vcfRecord, String entityPosAlt, String entityId) {
    List<Entity> samples = new ArrayList<>();
    Iterator<VcfSample> sampleIterator = vcfRecord.getSamples().iterator();
    if (vcfRecord.getNrSamples() > 0) {
        Iterator<String> sampleNameIterator = vcfMeta.getSampleNames().iterator();
        for (int j = 0; sampleIterator.hasNext(); ++j) {
            String[] format = vcfRecord.getFormat();
            VcfSample sample = sampleIterator.next();
            Entity sampleEntity = new DynamicEntity(sampleEntityType);
            for (int i = 0; i < format.length; i = i + 1) {
                String strValue = sample.getData(i);
                Object value = null;
                EntityType sampleEntityType = sampleEntity.getEntityType();
                Attribute attr = sampleEntityType.getAttribute(format[i]);
                if (attr != null) {
                    if (strValue != null) {
                        value = getTypedValue(strValue, attr);
                    }
                } else {
                    if (Arrays.equals(EMPTY_FORMAT, format)) {
                        LOG.debug("Found a dot as format, assuming no samples present");
                    } else {
                        throw new MolgenisDataException("Sample entity contains an attribute [" + format[i] + "] which is not specified in vcf headers");
                    }
                }
                sampleEntity.set(format[i], value);
            }
            sampleEntity.set(ID, entityId + j);
            // FIXME remove entity ID from Sample label after #1400 is fixed, see also:
            // jquery.molgenis.table.js line 152
            String original_name = sampleNameIterator.next();
            sampleEntity.set(NAME, entityPosAlt + "_" + original_name);
            sampleEntity.set(ORIGINAL_NAME, original_name);
            samples.add(sampleEntity);
        }
    }
    return samples;
}

Example 33 with MolgenisDataException

use of org.molgenis.data.MolgenisDataException in project molgenis by molgenis.

the class VcfWriterUtils method writeFormatString.

private static void writeFormatString(BufferedWriter writer, Entity sample) throws IOException {
    StringBuilder formatColumn = new StringBuilder();
    // write GT first if available
    if (sample.getEntityType().getAttribute(FORMAT_GT) != null) {
        formatColumn.append(FORMAT_GT);
    }
    EntityType entityType = sample.getEntityType();
    for (Attribute sampleAttribute : entityType.getAttributes()) {
        String sampleAttributeName = sampleAttribute.getName();
        if (!sampleAttributeName.equals(FORMAT_GT) && !sampleAttributeName.equals(VcfRepository.ORIGINAL_NAME)) {
            // skip the field that were generated for the use of the entity within molgenis
            if (!sampleAttribute.equals(entityType.getIdAttribute()) && !sampleAttribute.equals(entityType.getLabelAttribute())) {
                if (formatColumn.length() != 0)
                    formatColumn.append(':');
                formatColumn.append(sampleAttributeName);
            }
        }
    }
    if (formatColumn.length() > 0) {
        formatColumn.append('\t');
        writer.write(formatColumn.toString());
    } else {
        throw new MolgenisDataException("Missing FORMAT information while trying to print first sample");
    }
}

Example 34 with MolgenisDataException

use of org.molgenis.data.MolgenisDataException in project molgenis by molgenis.

the class VcfUtils method getPedigree.

/**
 * Get pedigree data from VCF Now only support child, father, mother No fancy data structure either Output:
 * result.put(childID, Arrays.asList(new String[]{motherID, fatherID}));
 */
public static HashMap<String, Trio> getPedigree(Scanner inputVcfFileScanner) {
    HashMap<String, Trio> result = new HashMap<>();
    while (inputVcfFileScanner.hasNextLine()) {
        String line = inputVcfFileScanner.nextLine();
        // quit when we don't see header lines anymore
        if (!line.startsWith(VcfRepository.PREFIX)) {
            break;
        }
        // expecting e.g. ##PEDIGREE=<Child=100400,Mother=100402,Father=100401>
        if (line.startsWith("##PEDIGREE")) {
            System.out.println("Pedigree data line: " + line);
            String childID = null;
            String motherID = null;
            String fatherID = null;
            String lineStripped = line.replace("##PEDIGREE=<", "").replace(">", "");
            String[] lineSplit = lineStripped.split(",", -1);
            for (String element : lineSplit) {
                if (element.startsWith("Child")) {
                    childID = element.replace("Child=", "");
                } else if (element.startsWith("Mother")) {
                    motherID = element.replace("Mother=", "");
                } else if (element.startsWith("Father")) {
                    fatherID = element.replace("Father=", "");
                } else {
                    throw new MolgenisDataException("Expected Child, Mother or Father, but found: " + element + " in line " + line);
                }
            }
            if (childID != null && motherID != null && fatherID != null) {
                // good
                result.put(childID, new Trio(new Sample(childID), new Sample(motherID), new Sample(fatherID)));
            } else {
                throw new MolgenisDataException("Missing Child, Mother or Father ID in line " + line);
            }
        }
    }
    return result;
}

Example 35 with MolgenisDataException

use of org.molgenis.data.MolgenisDataException in project molgenis by molgenis.

the class VcfReaderFactoryImpl method get.

@Override
public VcfReader get() {
    try {
        InputStream inputStream = new FileInputStream(file);
        if (file.getName().endsWith(".gz")) {
            inputStream = new GZIPInputStream(inputStream);
        } else if (file.getName().endsWith(".zip")) {
            ZipFile zipFile = new ZipFile(file.getPath());
            Enumeration<? extends ZipEntry> e = zipFile.entries();
            // your only file
            ZipEntry entry = e.nextElement();
            inputStream = zipFile.getInputStream(entry);
        }
        VcfReader reader = new VcfReader(new InputStreamReader(inputStream, UTF_8));
        // bootstrap reader so close() can close all readers
        vcfReaderRegistry.add(reader);
        return reader;
    } catch (IOException e) {
        throw new MolgenisDataException("Failed to create VCF Reader for file" + file.getAbsolutePath(), e);
    }
}