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

Example 1 with UnknownRepositoryException

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

the class AttributeRequestMapperImpl method processParentAndMappedby.

private void processParentAndMappedby(Map<String, Object> attributeRequest, Map<String, Attribute> attributes, EntityType entityType) {
    String attributeId = attributeRequest.get("id").toString();
    for (Entry<String, Object> entry : attributeRequest.entrySet()) {
        if (entry.getKey().equals("mappedByAttribute")) {
            String mappedByAttrId = getStringValue(entry.getValue());
            Attribute mappedByAttr = attributes.get(mappedByAttrId);
            if (mappedByAttr == null) {
                Repository<Attribute> repository = metaDataService.getRepository(AttributeMetadata.ATTRIBUTE_META_DATA, Attribute.class).orElseThrow(() -> new UnknownRepositoryException(AttributeMetadata.ATTRIBUTE_META_DATA));
                mappedByAttr = repository.findOneById(mappedByAttrId);
            }
            if (mappedByAttr == null) {
                throw new UnknownAttributeException(entityType, mappedByAttrId);
            }
            Attribute attribute = attributes.get(attributeId);
            attribute.setMappedBy(mappedByAttr);
        } else if (entry.getKey().equals("parent")) {
            String parentId = getStringValue(entry.getValue());
            Attribute parentAttr = attributes.get(parentId);
            if (parentAttr == null) {
                parentAttr = getAttributeFromParent(entityType.getExtends(), parentId);
            }
            Attribute attribute = attributes.get(attributeId);
            attribute.setParent(parentAttr);
        }
    }
}

Example 2 with UnknownRepositoryException

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

the class EmxDataProviderTest method testGetEntitiesAlternativeEntityTypeIdUnknownRepository.

@Test
void testGetEntitiesAlternativeEntityTypeIdUnknownRepository() {
    String entityTypeId = "base_EntityTypeId";
    EntityType entityType = when(mock(EntityType.class).getId()).thenReturn(entityTypeId).getMock();
    RepositoryCollection repositoryCollection = mock(RepositoryCollection.class);
    doThrow(new UnknownRepositoryException("EntityTypeId")).when(repositoryCollection).getRepository("EntityTypeId");
    when(emxImportJob.getSource()).thenReturn(repositoryCollection);
    assertThrows(UnknownRepositoryException.class, () -> emxDataProvider.getEntities(entityType).collect(toList()));
}

Example 3 with UnknownRepositoryException

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

the class EmxDataProviderTest method testGetEntitiesUnknownRepository.

@Test
void testGetEntitiesUnknownRepository() {
    String entityTypeId = "EntityTypeId";
    EntityType entityType = when(mock(EntityType.class).getId()).thenReturn(entityTypeId).getMock();
    RepositoryCollection repositoryCollection = mock(RepositoryCollection.class);
    doThrow(new UnknownRepositoryException(entityTypeId)).when(repositoryCollection).getRepository(entityType);
    when(emxImportJob.getSource()).thenReturn(repositoryCollection);
    assertThrows(UnknownRepositoryException.class, () -> emxDataProvider.getEntities(entityType).collect(toList()));
}

Example 4 with UnknownRepositoryException

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

the class AttributeResponseMapperImpl method getCategories.

private List<Category> getCategories(EntityType entityType) {
    Repository<Entity> repository = metaDataService.getRepository(entityType).orElseThrow(() -> new UnknownRepositoryException(entityType.getId()));
    Attribute idAttribute = entityType.getIdAttribute();
    Attribute labelAttribute = entityType.getLabelAttribute();
    return repository.query().findAll().map(entity -> Category.builder().setId(entity.get(idAttribute)).setLabel(entity.get(labelAttribute).toString()).build()).collect(toList());
}

Example 5 with UnknownRepositoryException

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

the class AttributeValidator method validateDefaultValue.

void validateDefaultValue(Attribute attr, boolean validateEntityReferences) {
    String value = attr.getDefaultValue();
    if (value != null) {
        if (attr.isUnique()) {
            throw new MolgenisDataException("Unique attribute " + attr.getName() + " cannot have default value");
        }
        if (attr.getExpression() != null) {
            throw new MolgenisDataException("Computed attribute " + attr.getName() + " cannot have default value");
        }
        AttributeType fieldType = attr.getDataType();
        if (attr.getMaxLength() != null && value.length() > attr.getMaxLength()) {
            throw new MolgenisDataException("Default value for attribute [" + attr.getName() + "] exceeds the maximum length [" + attr.getMaxLength() + "]");
        }
        if (fieldType == AttributeType.EMAIL) {
            checkEmail(value);
        }
        if (fieldType == AttributeType.HYPERLINK) {
            checkHyperlink(value);
        }
        if (fieldType == AttributeType.ENUM) {
            checkEnum(attr, value);
        }
        // Get typed value to check if the value is of the right type.
        Object typedValue;
        try {
            typedValue = EntityUtils.getTypedValue(value, attr, entityManager);
        } catch (NumberFormatException e) {
            throw new MolgenisValidationException(new ConstraintViolation(format("Invalid default value [%s] for data type [%s]", value, attr.getDataType())));
        }
        if (validateEntityReferences) {
            if (isSingleReferenceType(attr)) {
                Entity refEntity = (Entity) typedValue;
                EntityType refEntityType = attr.getRefEntity();
                if (dataService.getMeta().getRepository(refEntityType).orElseThrow(() -> new UnknownRepositoryException(refEntityType.getId())).query().eq(refEntityType.getIdAttribute().getName(), refEntity.getIdValue()).count() == 0) {
                    throw new MolgenisValidationException(new ConstraintViolation(format("Default value [%s] refers to an unknown entity", value)));
                }
            } else if (isMultipleReferenceType(attr)) {
                @SuppressWarnings("unchecked") Iterable<Entity> refEntitiesValue = (Iterable<Entity>) typedValue;
                EntityType refEntityType = attr.getRefEntity();
                if (dataService.query(refEntityType.getId()).in(refEntityType.getIdAttribute().getName(), stream(refEntitiesValue).map(Entity::getIdValue).collect(toList())).count() < Iterables.size(refEntitiesValue)) {
                    throw new MolgenisValidationException(new ConstraintViolation(format("Default value [%s] refers to one or more unknown entities", value)));
                }
            }
        }
    }
}