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

Example 6 with DataService

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

the class DataServiceTokenServiceTest method beforeMethod.

@BeforeMethod
public void beforeMethod() {
    tokenGenerator = mock(TokenGenerator.class);
    dataService = mock(DataService.class);
    userDetailsService = mock(UserDetailsService.class);
    TokenFactory tokenFactory = mock(TokenFactory.class);
    when(tokenFactory.create()).thenAnswer(invocation -> mock(Token.class));
    tokenService = new DataServiceTokenService(tokenGenerator, dataService, userDetailsService, tokenFactory);
}

Example 7 with DataService

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

the class PluginInterceptorTest method createMolgenisPluginController.

private PluginController createMolgenisPluginController(String uri) {
    PluginController pluginController = new PluginController(uri) {
    };
    DataService dataService = mock(DataService.class);
    pluginController.setDataService(dataService);
    return pluginController;
}

Example 8 with DataService

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

the class PostgreSqlQueryUtils method isPersistedInPostgreSql.

/**
 * Returns whether the given entity is persisted in PostgreSQL
 *
 * @param entityType entity meta data
 * @return true is the entity is persisted in PostgreSQL
 */
static boolean isPersistedInPostgreSql(EntityType entityType) {
    String backend = entityType.getBackend();
    if (backend == null) {
        // TODO remove this check after getBackend always returns the backend
        if (null != getApplicationContext()) {
            DataService dataService = getApplicationContext().getBean(DataService.class);
            backend = dataService.getMeta().getDefaultBackend().getName();
        } else {
            // A workaround for the integration tests. getApplicationContext() should not be null
            return true;
        }
    }
    return backend.equals(PostgreSqlRepositoryCollection.POSTGRESQL);
}

Example 9 with DataService

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

the class DataPersisterImplTest method setUpBeforeMethod.

@SuppressWarnings("unchecked")
@BeforeMethod
public void setUpBeforeMethod() {
    dataService = mock(DataService.class, RETURNS_DEEP_STUBS);
    dataPersisterImpl = new DataPersisterImpl(metaDataService, dataService, entityTypeDependencyResolver);
    String entityTypeId0 = "entityTypeId0";
    entityType0 = mock(EntityType.class);
    when(entityType0.getId()).thenReturn(entityTypeId0).getMock();
    String entityTypeId1 = "entityTypeId1";
    entityType1 = mock(EntityType.class);
    when(entityType1.getId()).thenReturn(entityTypeId1).getMock();
    String entityTypeId2 = "entityTypeId2";
    entityType2 = mock(EntityType.class);
    when(entityType2.getId()).thenReturn(entityTypeId2).getMock();
    when(dataProvider.getEntityTypes()).thenReturn(Stream.of(entityType0, entityType1, entityType2));
    when(dataProvider.hasEntities(entityType0)).thenReturn(true);
    Entity entity0a = mock(Entity.class);
    Entity entity0b = mock(Entity.class);
    when(dataProvider.getEntities(entityType0)).thenReturn(Stream.of(entity0a, entity0b));
    when(dataProvider.hasEntities(entityType1)).thenReturn(true);
    Entity entity1a = mock(Entity.class);
    Entity entity1b = mock(Entity.class);
    Entity entity1c = mock(Entity.class);
    when(dataProvider.getEntities(entityType1)).thenReturn(Stream.of(entity1a, entity1b, entity1c));
    when(dataProvider.hasEntities(entityType2)).thenReturn(false);
    when(entityTypeDependencyResolver.resolve(asList(entityType0, entityType1, entityType2))).thenReturn(asList(entityType2, entityType1, entityType0));
    doAnswer(invocation -> {
        Stream<Entity> entityStream = (Stream<Entity>) invocation.getArguments()[1];
        try {
            // noinspection ResultOfMethodCallIgnored
            entityStream.collect(toList());
        } catch (IllegalStateException ignored) {
        }
        return null;
    }).when(dataService).add(anyString(), any(Stream.class));
    doAnswer(invocation -> {
        Stream<Entity> entityStream = (Stream<Entity>) invocation.getArguments()[1];
        try {
            // noinspection ResultOfMethodCallIgnored
            entityStream.collect(toList());
        } catch (IllegalStateException ignored) {
        }
        return null;
    }).when(dataService).update(anyString(), any(Stream.class));
}

Example 10 with DataService

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

the class OneToManyCategoryAlgorithmGeneratorTest method init.

@BeforeMethod
public void init() {
    DataService dataService = Mockito.mock(DataService.class);
    categoryAlgorithmGenerator = new OneToManyCategoryAlgorithmGenerator(dataService);
    EntityType targetRefEntityType = entityTypeFactory.create("POTATO_REF");
    Attribute targetCodeAttribute = attrMetaFactory.create().setName("code").setDataType(INT);
    Attribute targetLabelAttribute = attrMetaFactory.create().setName("label");
    targetRefEntityType.addAttribute(targetCodeAttribute, ROLE_ID);
    targetRefEntityType.addAttribute(targetLabelAttribute, ROLE_LABEL);
    targetAttribute = attrMetaFactory.create().setName("Current Consumption Frequency of Potatoes").setDataType(CATEGORICAL);
    targetAttribute.setRefEntity(targetRefEntityType);
    Entity targetEntity1 = new DynamicEntity(targetRefEntityType, of("code", 1, "label", "Almost daily + daily"));
    Entity targetEntity2 = new DynamicEntity(targetRefEntityType, of("code", 2, "label", "Several times a week"));
    Entity targetEntity3 = new DynamicEntity(targetRefEntityType, of("code", 3, "label", "About once a week"));
    Entity targetEntity4 = new DynamicEntity(targetRefEntityType, of("code", 4, "label", "Never + fewer than once a week"));
    Entity targetEntity5 = new DynamicEntity(targetRefEntityType, of("code", 9, "label", "missing"));
    Mockito.when(dataService.findAll(targetRefEntityType.getId())).thenAnswer(invocation -> Stream.of(targetEntity1, targetEntity2, targetEntity3, targetEntity4, targetEntity5));
    targetEntityType = entityTypeFactory.create("target");
    targetEntityType.addAttribute(targetAttribute);
    EntityType sourceRefEntityType = createEntityType("LifeLines_POTATO_REF");
    sourceAttribute = attrMetaFactory.create().setName("MESHED_POTATO").setDataType(CATEGORICAL);
    sourceAttribute.setLabel("How often did you eat boiled or mashed potatoes (also in stew) in the past month? Baked potatoes are asked later");
    sourceAttribute.setRefEntity(sourceRefEntityType);
    Entity sourceEntity1 = new DynamicEntity(targetRefEntityType, of("code", 1, "label", "Not this month"));
    Entity sourceEntity2 = new DynamicEntity(targetRefEntityType, of("code", 2, "label", "1 day per month"));
    Entity sourceEntity3 = new DynamicEntity(targetRefEntityType, of("code", 3, "label", "2-3 days per month"));
    Entity sourceEntity4 = new DynamicEntity(targetRefEntityType, of("code", 4, "label", "1 day per week"));
    Entity sourceEntity5 = new DynamicEntity(targetRefEntityType, of("code", 5, "label", "2-3 days per week"));
    Entity sourceEntity6 = new DynamicEntity(targetRefEntityType, of("code", 6, "label", "4-5 days per week"));
    Entity sourceEntity7 = new DynamicEntity(targetRefEntityType, of("code", 7, "label", "6-7 days per week"));
    Mockito.when(dataService.findAll(sourceRefEntityType.getId())).thenAnswer(invocation -> Stream.of(sourceEntity1, sourceEntity2, sourceEntity3, sourceEntity4, sourceEntity5, sourceEntity6, sourceEntity7));
    EntityType sourceRefEntityType1 = createEntityType("Mitchelstown_POTATO_REF");
    sourceAttribute1 = attrMetaFactory.create().setName("MESHED_POTATO_1").setDataType(CATEGORICAL);
    sourceAttribute1.setLabel("How often did you eat boiled or mashed potatoes (also in stew) in the past month? Baked potatoes are asked later");
    sourceAttribute1.setRefEntity(sourceRefEntityType1);
    Entity sourceEntity8 = new DynamicEntity(targetRefEntityType, of("code", 1, "label", "never/less than 1 per month"));
    Entity sourceEntity9 = new DynamicEntity(targetRefEntityType, of("code", 2, "label", "1-3 per month"));
    Entity sourceEntity10 = new DynamicEntity(targetRefEntityType, of("code", 3, "label", "once a week"));
    Entity sourceEntity11 = new DynamicEntity(targetRefEntityType, of("code", 4, "label", "2-4 per week"));
    Entity sourceEntity12 = new DynamicEntity(targetRefEntityType, of("code", 5, "label", "5-6 per week"));
    Entity sourceEntity13 = new DynamicEntity(targetRefEntityType, of("code", 6, "label", "once a day"));
    Entity sourceEntity14 = new DynamicEntity(targetRefEntityType, of("code", 7, "label", "2-3 per day"));
    Entity sourceEntity15 = new DynamicEntity(targetRefEntityType, of("code", 8, "label", "4-5 per day"));
    Entity sourceEntity16 = new DynamicEntity(targetRefEntityType, of("code", 9, "label", "6+ per day"));
    Mockito.when(dataService.findAll(sourceRefEntityType1.getId())).thenAnswer(invocation -> Stream.of(sourceEntity8, sourceEntity9, sourceEntity10, sourceEntity11, sourceEntity12, sourceEntity13, sourceEntity14, sourceEntity15, sourceEntity16));
    EntityType sourceRefEntityType2 = createEntityType("Mitchelstown_Stroke_REF");
    sourceAttribute2 = attrMetaFactory.create().setName("Stroke").setDataType(CATEGORICAL);
    sourceAttribute2.setLabel("History of stroke");
    sourceAttribute2.setRefEntity(sourceRefEntityType2);
    Entity sourceEntity17 = new DynamicEntity(targetRefEntityType, of("code", 1, "label", "yes"));
    Entity sourceEntity18 = new DynamicEntity(targetRefEntityType, of("code", 2, "label", "no"));
    Entity sourceEntity19 = new DynamicEntity(targetRefEntityType, of("code", 9, "label", "missing"));
    Mockito.when(dataService.findAll(sourceRefEntityType2.getId())).thenAnswer(invocation -> Stream.of(sourceEntity17, sourceEntity18, sourceEntity19));
    sourceEntityType = entityTypeFactory.create("source");
    sourceEntityType.addAttributes(Lists.newArrayList(sourceAttribute, sourceAttribute1, sourceAttribute2));
}