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

Example 6 with MolgenisDataException

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

the class GavinJob method call.

@Override
public Void call(Progress progress) throws Exception {
    progress.setProgressMax(5);
    progress.progress(0, "Preprocessing input file...");
    Multiset<LineType> lineTypes = parser.tryTransform(inputFile, processedInputFile, errorFile);
    progress.status(format("Parsed input file. Found {0} lines ({1} comments, {2} valid VCF, {3} valid CADD, " + "{4} errors, {5} indels without CADD score, {6} skipped)", lineTypes.size(), lineTypes.count(COMMENT), lineTypes.count(VCF), lineTypes.count(CADD), lineTypes.count(ERROR), lineTypes.count(INDEL_NOCADD), lineTypes.count(SKIPPED)));
    gavinJobExecution.setLineTypes(lineTypes);
    if (lineTypes.contains(SKIPPED)) {
        throw new MolgenisDataException(format("Input file contains too many lines. Maximum is {0}.", Parser.MAX_LINES));
    }
    if (lineTypes.containsAll(Arrays.asList(CADD, VCF))) {
        throw new MolgenisDataException("Input file contains mixed line types. Please use one type only, either VCF or CADD.");
    }
    if (!lineTypes.contains(CADD) && !lineTypes.contains(VCF)) {
        throw new MolgenisDataException("Not a single valid variant line found.");
    }
    File exacInputFile = processedInputFile;
    if (!lineTypes.contains(CADD)) {
        progress.progress(1, "Annotating with cadd...");
        annotatorRunner.runAnnotator(cadd, processedInputFile, caddOutputFile, true);
        exacInputFile = caddOutputFile;
    } else {
        progress.progress(1, "File already annotated by cadd, skipping cadd annotation.");
    }
    progress.progress(2, "Annotating with exac...");
    annotatorRunner.runAnnotator(exac, exacInputFile, exacOutputFile, true);
    progress.progress(3, "Annotating with snpEff...");
    annotatorRunner.runAnnotator(snpeff, exacOutputFile, snpeffOutputFile, false);
    progress.progress(4, "Annotating with gavin...");
    annotatorRunner.runAnnotator(gavin, snpeffOutputFile, gavinOutputFile, false);
    progress.progress(5, "Result is ready for download.");
    String path = menuReaderService.getMenu().findMenuItemPath(GAVIN_APP);
    // TODO Filter
    // TODO write to database
    // TODO result -> GeneNetwork
    // TODO VCF pipe aware import
    progress.setResultUrl(format("{0}/result/{1}", path, jobIdentifier));
    return null;
}

Example 7 with MolgenisDataException

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

the class ExcelSheetWriter method add.

/**
 * Add a new row to the sheet
 */
@Override
public void add(Entity entity) {
    if (entity == null)
        throw new IllegalArgumentException("Entity cannot be null");
    if (cachedAttributes == null)
        throw new MolgenisDataException("The attribute names are not defined, call writeAttributeNames first");
    int i = 0;
    Row poiRow = sheet.createRow(row++);
    for (Attribute attribute : cachedAttributes) {
        Cell cell = poiRow.createCell(i++, CellType.STRING);
        cell.setCellValue(toValue(entity.get(attribute.getName())));
    }
    entity.getIdValue();
}

Example 8 with MolgenisDataException

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

the class ConnectionRetryConfigTest method testRetryPolicyMolgenisDataException.

@Test
public void testRetryPolicyMolgenisDataException() {
    RetryContext context = retryPolicy.open(null);
    retryPolicy.registerThrowable(context, new MolgenisDataException("Failed to connect"));
    assertTrue(retryPolicy.canRetry(context));
}

Example 9 with MolgenisDataException

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

the class CsvIterator method get.

private Entity get() {
    if (getNext) {
        try {
            String[] values = csvReader.readNext();
            if (values != null && values.length == colNamesMap.size()) {
                List<String> valueList = Arrays.asList(values);
                for (int i = 0; i < values.length; ++i) {
                    // subsequent separators indicate
                    // null
                    // values instead of empty strings
                    String value = values[i].isEmpty() ? null : values[i];
                    values[i] = processCell(value, false);
                }
                next = new DynamicEntity(entityType);
                for (String name : colNamesMap.keySet()) {
                    next.set(name, valueList.get(colNamesMap.get(name)));
                }
            } else if (values != null && (values.length > 1 || (values.length == 1 && values[0].length() > 0)) && values.length < colNamesMap.size()) {
                throw new MolgenisDataException(format("Number of values (%d) doesn't match the number of headers (%d): [%s]", values.length, colNamesMap.size(), stream(values).collect(joining(","))));
            } else {
                next = null;
            }
            getNext = false;
        } catch (IOException e) {
            throw new MolgenisDataException(format("Exception reading line of csv file [%s]", repositoryName), e);
        }
    }
    return next;
}

Example 10 with MolgenisDataException

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

the class CsvRepositoryCollection method loadEntityNames.

private void loadEntityNames() {
    String extension = StringUtils.getFilenameExtension(file.getName());
    entityTypeIds = Lists.newArrayList();
    entityTypeIdsLowerCase = Lists.newArrayList();
    if (extension.equalsIgnoreCase("zip")) {
        ZipFile zipFile = null;
        try {
            zipFile = new ZipFile(file);
            for (Enumeration<? extends ZipEntry> e = zipFile.entries(); e.hasMoreElements(); ) {
                ZipEntry entry = e.nextElement();
                if (!entry.getName().contains(MAC_ZIP) && !entry.isDirectory()) {
                    String name = getRepositoryName(entry.getName());
                    entityTypeIds.add(name);
                    entityTypeIdsLowerCase.add(name.toLowerCase());
                }
            }
        } catch (Exception e) {
            throw new MolgenisDataException(e);
        } finally {
            IOUtils.closeQuietly(zipFile);
        }
    } else {
        String name = getRepositoryName(file.getName());
        entityTypeIds.add(name);
        entityTypeIdsLowerCase.add(name.toLowerCase());
    }
}