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

Example 46 with MolgenisDataException

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

the class AmazonBucketClientImpl method getMostRecentMatchingKey.

// in case of an key expression all matching keys are collected and the most recent file is downloaded.
private String getMostRecentMatchingKey(AmazonS3 s3Client, String bucketName, String regex) {
    ObjectListing objectListing = s3Client.listObjects(bucketName);
    TreeMap<Date, String> keys = new TreeMap<>();
    for (S3ObjectSummary objectSummary : objectListing.getObjectSummaries()) {
        if (objectSummary.getKey().matches(regex)) {
            keys.put(objectSummary.getLastModified(), objectSummary.getKey());
        }
    }
    if (keys.size() == 0)
        throw new MolgenisDataException("No key matching regular expression: " + regex);
    return keys.lastEntry().getValue();
}

Example 47 with MolgenisDataException

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

the class CsvWriter method add.

@Override
public void add(Entity entity) {
    if (cachedAttributeNames == null)
        throw new MolgenisDataException("No attribute names defined call writeAttributeNames first");
    int i = 0;
    String[] values = new String[cachedAttributeNames.size()];
    for (String colName : cachedAttributeNames) {
        values[i++] = toValue(entity.get(colName));
    }
    csvWriter.writeNext(values);
    if (csvWriter.checkError())
        throw new MolgenisDataException("An exception occured writing the csv file");
}

Example 48 with MolgenisDataException

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

the class ConnectionRetryConfigTest method testInterruptFailingTries.

@Test
public void testInterruptFailingTries() throws Exception {
    Future<Client> result = executorService.submit(() -> {
        RetryCallback<Client, RuntimeException> fail = c -> {
            throw new MolgenisDataException();
        };
        return retryTemplate.execute(fail);
    });
    result.cancel(true);
    try {
        result.get(100, TimeUnit.MILLISECONDS);
        fail("Should throw cancellation exception!");
    } catch (CancellationException ignore) {
    }
    assertTrue(result.isDone());
    assertTrue(result.isCancelled());
}

Example 49 with MolgenisDataException

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

the class ClientFactory method tryCreateClient.

private Client tryCreateClient(RetryContext retryContext) throws InterruptedException {
    if (Thread.interrupted()) {
        throw new InterruptedException();
    }
    TransportClient result = preBuiltTransportClientFactory.build(clusterName, null).addTransportAddresses(createInetTransportAddresses());
    if (result.connectedNodes().isEmpty()) {
        result.close();
        LOG.error("Failed to connect to Elasticsearch cluster '{}' on {}. Retry count = {}", clusterName, inetAddresses, retryContext.getRetryCount());
        throw new MolgenisDataException(String.format("Failed to connect to Elasticsearch cluster '%s' on %s. Is Elasticsearch running?", clusterName, inetAddresses));
    }
    return result;
}

Example 50 with MolgenisDataException

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

the class RestService method updateMappedByEntitiesOneToMany.

/**
 * For entities with the given attribute that is part of a bidirectional one-to-many relationship update the other side of the relationship.
 *
 * @param entity         created or updated entity
 * @param existingEntity existing entity
 * @param attr           bidirectional one-to-many attribute
 */
private void updateMappedByEntitiesOneToMany(@Nonnull Entity entity, @Nullable Entity existingEntity, @Nonnull Attribute attr) {
    if (attr.getDataType() != ONE_TO_MANY || !attr.isMappedBy()) {
        throw new IllegalArgumentException(format("Attribute [%s] is not of type [%s] or not mapped by another attribute", attr.getName(), attr.getDataType().toString()));
    }
    // update ref entities of created/updated entity
    Attribute refAttr = attr.getMappedBy();
    Stream<Entity> stream = stream(entity.getEntities(attr.getName()).spliterator(), false);
    if (existingEntity != null) {
        // filter out unchanged ref entities
        Set<Object> refEntityIds = stream(existingEntity.getEntities(attr.getName()).spliterator(), false).map(Entity::getIdValue).collect(toSet());
        stream = stream.filter(refEntity -> !refEntityIds.contains(refEntity.getIdValue()));
    }
    List<Entity> updatedRefEntities = stream.map(refEntity -> {
        if (refEntity.getEntity(refAttr.getName()) != null) {
            throw new MolgenisDataException(format("Updating [%s] with id [%s] not allowed: [%s] is already referred to by another [%s]", attr.getRefEntity().getId(), refEntity.getIdValue().toString(), refAttr.getName(), entity.getEntityType().getId()));
        }
        refEntity.set(refAttr.getName(), entity);
        return refEntity;
    }).collect(toList());
    // update ref entities of existing entity
    if (existingEntity != null) {
        Set<Object> refEntityIds = stream(entity.getEntities(attr.getName()).spliterator(), false).map(Entity::getIdValue).collect(toSet());
        List<Entity> updatedRefEntitiesExistingEntity = stream(existingEntity.getEntities(attr.getName()).spliterator(), false).filter(refEntity -> !refEntityIds.contains(refEntity.getIdValue())).map(refEntity -> {
            refEntity.set(refAttr.getName(), null);
            return refEntity;
        }).collect(toList());
        updatedRefEntities = Stream.concat(updatedRefEntities.stream(), updatedRefEntitiesExistingEntity.stream()).collect(toList());
    }
    if (!updatedRefEntities.isEmpty()) {
        dataService.update(attr.getRefEntity().getId(), updatedRefEntities.stream());
    }
}