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

Example 1 with EntityManager

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

the class EntityUtilsTest method getTypedValueStringAttributeEntityManagerXref.

@Test
public void getTypedValueStringAttributeEntityManagerXref() {
    String valueStr = "0";
    Attribute attr = mock(Attribute.class);
    EntityType refEntityType = mock(EntityType.class);
    Attribute refIdAttr = mock(Attribute.class);
    when(refIdAttr.getDataType()).thenReturn(STRING);
    when(refEntityType.getIdAttribute()).thenReturn(refIdAttr);
    when(attr.getRefEntity()).thenReturn(refEntityType);
    when(attr.getDataType()).thenReturn(XREF);
    Entity entity = mock(Entity.class);
    EntityManager entityManager = mock(EntityManager.class);
    when(entityManager.getReference(refEntityType, valueStr)).thenReturn(entity);
    assertEquals(EntityUtils.getTypedValue(valueStr, attr, entityManager), entity);
}

Example 2 with EntityManager

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

the class RestServiceTest method setUpBeforeMethod.

@BeforeMethod
public void setUpBeforeMethod() {
    dataService = mock(DataService.class);
    idGenerator = mock(IdGenerator.class);
    FileStore fileStore = mock(FileStore.class);
    fileMetaFactory = mock(FileMetaFactory.class);
    entityManager = mock(EntityManager.class);
    servletUriComponentsBuilderFactory = mock(ServletUriComponentsBuilderFactory.class);
    this.restService = new RestService(dataService, idGenerator, fileStore, fileMetaFactory, entityManager, servletUriComponentsBuilderFactory);
}

Example 3 with EntityManager

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

the class QueryValidatorTest method setUpBeforeMethod.

@BeforeMethod
public void setUpBeforeMethod() {
    EntityManager entityManager = mock(EntityManager.class);
    this.queryValidator = new QueryValidator(entityManager);
}

Example 4 with EntityManager

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

the class EntityUtils method getTypedValue.

/**
 * Convert a string value to a typed value based on the attribute data type.
 *
 * @param valueStr      string value
 * @param attr          attribute
 * @param entityManager entity manager used to convert referenced entity values
 * @return typed value
 */
public static Object getTypedValue(String valueStr, Attribute attr, EntityManager entityManager) {
    if (valueStr == null)
        return null;
    switch(attr.getDataType()) {
        case BOOL:
            return Boolean.valueOf(valueStr);
        case CATEGORICAL:
        case FILE:
        case XREF:
            EntityType xrefEntity = attr.getRefEntity();
            Object xrefIdValue = getTypedValue(valueStr, xrefEntity.getIdAttribute(), entityManager);
            return entityManager.getReference(xrefEntity, xrefIdValue);
        case CATEGORICAL_MREF:
        case MREF:
        case ONE_TO_MANY:
            EntityType mrefEntity = attr.getRefEntity();
            List<String> mrefIdStrValues = ListEscapeUtils.toList(valueStr);
            return mrefIdStrValues.stream().map(mrefIdStrValue -> getTypedValue(mrefIdStrValue, mrefEntity.getIdAttribute(), entityManager)).map(mrefIdValue -> entityManager.getReference(mrefEntity, mrefIdValue)).collect(toList());
        case COMPOUND:
            throw new IllegalArgumentException("Compound attribute has no value");
        case DATE:
            try {
                return parseLocalDate(valueStr);
            } catch (DateTimeParseException e) {
                throw new MolgenisDataException(format(FAILED_TO_PARSE_ATTRIBUTE_AS_DATE_MESSAGE, attr.getName(), valueStr), e);
            }
        case DATE_TIME:
            try {
                return parseInstant(valueStr);
            } catch (DateTimeParseException e) {
                throw new MolgenisDataException(format(FAILED_TO_PARSE_ATTRIBUTE_AS_DATETIME_MESSAGE, attr.getName(), valueStr), e);
            }
        case DECIMAL:
            return Double.valueOf(valueStr);
        case EMAIL:
        case ENUM:
        case HTML:
        case HYPERLINK:
        case SCRIPT:
        case STRING:
        case TEXT:
            return valueStr;
        case INT:
            return Integer.valueOf(valueStr);
        case LONG:
            return Long.valueOf(valueStr);
        default:
            throw new UnexpectedEnumException(attr.getDataType());
    }
}

Example 5 with EntityManager

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

the class PartialEntityTest method setUpBeforeMethod.

@BeforeMethod
public void setUpBeforeMethod() {
    Attribute idAttr = when(mock(Attribute.class).getName()).thenReturn("id").getMock();
    meta = when(mock(EntityType.class).getId()).thenReturn("entity").getMock();
    when(meta.getIdAttribute()).thenReturn(idAttr);
    originalEntity = mock(Entity.class);
    decoratedEntity = mock(Entity.class);
    when(decoratedEntity.getEntityType()).thenReturn(meta);
    when(decoratedEntity.getIdValue()).thenReturn("id");
    fetch = new Fetch().field("id");
    entityManager = mock(EntityManager.class);
    when(entityManager.getReference(meta, "id")).thenReturn(originalEntity);
    partialEntity = new PartialEntity(decoratedEntity, fetch, entityManager);
}