Examples with QueryImpl org.molgenis.data.support.QueryImpl used on opensource projects

Example 76 with QueryImpl

use of org.molgenis.data.support.QueryImpl in project molgenis by molgenis.

the class RepositoryValidationDecoratorTest method beforeMethod.

@SuppressWarnings("unchecked")
@BeforeMethod
public void beforeMethod() {
    // ref entity meta
    refEntityName = "refEntity";
    refAttrIdName = "refId";
    Attribute refIdAttr = when(mock(Attribute.class).getName()).thenReturn(refAttrIdName).getMock();
    when(refIdAttr.getDataType()).thenReturn(STRING);
    refEntityType = mock(EntityType.class);
    when(refEntityType.getId()).thenReturn(refEntityName);
    when(refEntityType.getLabel()).thenReturn(refEntityName);
    when(refEntityType.getIdAttribute()).thenReturn(refIdAttr);
    when(refEntityType.getAtomicAttributes()).thenReturn(Arrays.asList(refIdAttr));
    // entity meta
    entityTypeId = "entity";
    attrIdName = "id";
    attrXrefName = "xrefAttr";
    attrNillableXrefName = "nillableXrefAttr";
    attrMrefName = "mrefAttr";
    attrNillableMrefName = "nillableMrefAttr";
    attrUniqueStringName = "uniqueStringAttr";
    attrUniqueXrefName = "uniqueXrefAttr";
    idAttr = when(mock(Attribute.class).getName()).thenReturn(attrIdName).getMock();
    when(idAttr.getDataType()).thenReturn(STRING);
    xrefAttr = when(mock(Attribute.class).getName()).thenReturn(attrXrefName).getMock();
    when(xrefAttr.getRefEntity()).thenReturn(refEntityType);
    when(xrefAttr.getDataType()).thenReturn(XREF);
    when(xrefAttr.isNillable()).thenReturn(false);
    nillableXrefAttr = when(mock(Attribute.class).getName()).thenReturn(attrNillableXrefName).getMock();
    when(nillableXrefAttr.getRefEntity()).thenReturn(refEntityType);
    when(nillableXrefAttr.getDataType()).thenReturn(XREF);
    when(nillableXrefAttr.isNillable()).thenReturn(true);
    mrefAttr = when(mock(Attribute.class).getName()).thenReturn(attrMrefName).getMock();
    when(mrefAttr.getRefEntity()).thenReturn(refEntityType);
    when(mrefAttr.getDataType()).thenReturn(MREF);
    when(mrefAttr.isNillable()).thenReturn(false);
    nillableMrefAttr = when(mock(Attribute.class).getName()).thenReturn(attrNillableMrefName).getMock();
    when(nillableMrefAttr.getRefEntity()).thenReturn(refEntityType);
    when(nillableMrefAttr.getDataType()).thenReturn(MREF);
    when(nillableMrefAttr.isNillable()).thenReturn(true);
    uniqueStringAttr = when(mock(Attribute.class).getName()).thenReturn(attrUniqueStringName).getMock();
    when(uniqueStringAttr.getDataType()).thenReturn(STRING);
    when(uniqueStringAttr.isUnique()).thenReturn(true);
    uniqueXrefAttr = when(mock(Attribute.class).getName()).thenReturn(attrUniqueXrefName).getMock();
    when(uniqueXrefAttr.getRefEntity()).thenReturn(refEntityType);
    when(uniqueXrefAttr.getDataType()).thenReturn(XREF);
    when(uniqueXrefAttr.isUnique()).thenReturn(true);
    entityType = mock(EntityType.class);
    when(entityType.getId()).thenReturn(entityTypeId);
    when(entityType.getLabel()).thenReturn(entityTypeId);
    when(entityType.getIdAttribute()).thenReturn(idAttr);
    when(entityType.getAttribute(attrIdName)).thenReturn(idAttr);
    when(entityType.getAttribute(attrXrefName)).thenReturn(xrefAttr);
    when(entityType.getAttribute(attrNillableXrefName)).thenReturn(nillableXrefAttr);
    when(entityType.getAttribute(attrMrefName)).thenReturn(mrefAttr);
    when(entityType.getAttribute(attrNillableMrefName)).thenReturn(nillableMrefAttr);
    when(entityType.getAttribute(attrUniqueStringName)).thenReturn(uniqueStringAttr);
    when(entityType.getAttribute(attrUniqueXrefName)).thenReturn(uniqueXrefAttr);
    when(entityType.getAtomicAttributes()).thenReturn(Arrays.asList(idAttr, xrefAttr, nillableXrefAttr, mrefAttr, nillableMrefAttr, uniqueStringAttr, uniqueXrefAttr));
    // ref entities
    String refEntity0Id = "idref0";
    refEntity0 = mock(Entity.class);
    when(refEntity0.getEntityType()).thenReturn(refEntityType);
    when(refEntity0.getIdValue()).thenReturn(refEntity0Id);
    when(refEntity0.get(refAttrIdName)).thenReturn(refEntity0Id);
    when(refEntity0.getString(refAttrIdName)).thenReturn(refEntity0Id);
    refEntity0Clone = mock(Entity.class);
    when(refEntity0Clone.getEntityType()).thenReturn(refEntityType);
    when(refEntity0Clone.getIdValue()).thenReturn(refEntity0Id);
    when(refEntity0Clone.get(refAttrIdName)).thenReturn(refEntity0Id);
    when(refEntity0Clone.getString(refAttrIdName)).thenReturn(refEntity0Id);
    String refEntity1Id = "idref1";
    refEntity1 = mock(Entity.class);
    when(refEntity1.getEntityType()).thenReturn(refEntityType);
    when(refEntity1.getIdValue()).thenReturn(refEntity1Id);
    when(refEntity1.get(refAttrIdName)).thenReturn(refEntity1Id);
    when(refEntity1.getString(refAttrIdName)).thenReturn(refEntity1Id);
    refEntity1Clone = mock(Entity.class);
    when(refEntity1Clone.getEntityType()).thenReturn(refEntityType);
    when(refEntity1Clone.getIdValue()).thenReturn(refEntity1Id);
    when(refEntity1Clone.get(refAttrIdName)).thenReturn(refEntity1Id);
    when(refEntity1Clone.getString(refAttrIdName)).thenReturn(refEntity1Id);
    // beans
    delegateRepository = mock(Repository.class);
    when(delegateRepository.getEntityType()).thenReturn(entityType);
    when(delegateRepository.getName()).thenReturn(entityTypeId);
    when(delegateRepository.findAll(new QueryImpl<>().fetch(new Fetch().field(attrUniqueStringName).field(attrUniqueXrefName)))).thenReturn(Stream.empty());
    refRepo = mock(Repository.class);
    when(refRepo.getEntityType()).thenReturn(refEntityType);
    dataService = mock(DataService.class);
    when(dataService.getRepository(entityTypeId)).thenReturn(delegateRepository);
    when(dataService.getRepository(refEntityName)).thenReturn(refRepo);
    when(dataService.findAll(refEntityName, new QueryImpl<>().fetch(new Fetch().field(refAttrIdName)))).thenReturn(Stream.of(refEntity0, refEntity1));
    metaDataService = mock(MetaDataService.class);
    when(dataService.getMeta()).thenReturn(metaDataService);
    expressionValidator = mock(ExpressionValidator.class);
    entityAttributesValidator = mock(EntityAttributesValidator.class);
    defaultValueReferenceValidator = mock(DefaultValueReferenceValidator.class);
    repositoryValidationDecorator = new RepositoryValidationDecorator(dataService, delegateRepository, entityAttributesValidator, defaultValueReferenceValidator);
}

Example 77 with QueryImpl

use of org.molgenis.data.support.QueryImpl in project molgenis by molgenis.

the class UserServiceImplTest method getUser.

@Test
public void getUser() {
    String username = "username";
    User existingUser = mock(User.class);
    when(existingUser.getId()).thenReturn("1");
    when(existingUser.getUsername()).thenReturn(username);
    when(existingUser.getPassword()).thenReturn("encrypted-password");
    when(dataService.findOne(USER, new QueryImpl<User>().eq(UserMetaData.USERNAME, username), User.class)).thenReturn(existingUser);
    assertEquals(molgenisUserServiceImpl.getUser(username), existingUser);
}

Example 78 with QueryImpl

use of org.molgenis.data.support.QueryImpl in project molgenis by molgenis.

the class DefaultEntityValidator method checkUniques.

private Set<ConstraintViolation> checkUniques(Iterable<? extends Entity> entities, EntityType meta, DatabaseAction dbAction) {
    Set<ConstraintViolation> violations = Sets.newLinkedHashSet();
    for (Attribute attr : meta.getAtomicAttributes()) {
        if (attr.isUnique() && !attr.equals(meta.getIdAttribute()) && !(attr.equals(meta.getLabelAttribute()) && (dbAction == DatabaseAction.ADD_UPDATE_EXISTING))) {
            // Gather all attribute values
            // FIXME: keeping everything in memory is not scaleable
            List<Object> values = Lists.newArrayList();
            for (Entity entity : entities) {
                Object value = entity.get(attr.getName());
                values.add(value);
            }
            // Create 'in' query, should find only find itself or nothing
            if (!values.isEmpty()) {
                String entityTypeId = meta.getId();
                long count = dataService.count(entityTypeId, new QueryImpl<>().in(attr.getName(), values));
                if (count > 0) {
                    // Go through the list to find the violators
                    long found = 0;
                    Iterator<? extends Entity> it = entities.iterator();
                    while (it.hasNext() && (found < count)) {
                        Entity entity = it.next();
                        Object value = entity.get(attr.getName());
                        Entity existing = dataService.findOne(entityTypeId, new QueryImpl<>().eq(attr.getName(), value));
                        if (existing != null) {
                            // if dbAction is ADD
                            if (((dbAction == null) && !idEquals(entity, existing, meta)) || ((dbAction != null) && (dbAction == DatabaseAction.ADD))) {
                                String message = String.format("The attribute '%s' of entity '%s' with key '%s' must be unique, but the value '%s' already exists.", attr.getName(), meta.getId(), entity.getString(meta.getLabelAttribute().getName()), value);
                                violations.add(new ConstraintViolation(message));
                            }
                            found++;
                        }
                    }
                }
            }
        }
    }
    return violations;
}

Example 79 with QueryImpl

use of org.molgenis.data.support.QueryImpl in project molgenis by molgenis.

the class QueryValidatorTest method validateValidProvider.

@DataProvider(name = "validateValidProvider")
public static Iterator<Object[]> validateValidProvider() {
    List<Object[]> queries = new ArrayList<>(256);
    EnumSet.of(EQUALS).forEach(operator -> {
        // BOOL
        Entity boolEntityType = createEntityType(BOOL);
        asList(Boolean.TRUE, Boolean.FALSE, null, "true", "false", "True", "False").forEach(value -> queries.add(new Object[] { boolEntityType, new QueryImpl<>().eq("attr", value) }));
        // CATEGORICAL, XREF, CATEGORICAL_MREF, MREF, ONE_TO_MANY
        EnumSet.of(STRING, INT, LONG, EMAIL, HYPERLINK).forEach(refIdAttrType -> EnumSet.of(CATEGORICAL, XREF, CATEGORICAL_MREF, MREF, ONE_TO_MANY).forEach(refAttrType -> {
            Entity refEntityType = createEntityType(refAttrType, refIdAttrType);
            asList("1", 1, 1L, null).forEach(idValue -> queries.add(new Object[] { refEntityType, new QueryImpl<>().eq("attr", idValue) }));
            Entity refEntity = when(mock(Entity.class).getIdValue()).thenReturn("1").getMock();
            queries.add(new Object[] { refEntityType, new QueryImpl<>().eq("attr", refEntity) });
        }));
        // DATE
        Entity dateEntityType = createEntityType(DATE);
        asList(LocalDate.now(), "2016-11-25", null).forEach(value -> queries.add(new Object[] { dateEntityType, new QueryImpl<>().eq("attr", value) }));
        // DATE_TIME
        Entity dateTimeEntityType = createEntityType(DATE_TIME);
        asList(Instant.now(), "1985-08-12T11:12:13+0500", null).forEach(value -> queries.add(new Object[] { dateTimeEntityType, new QueryImpl<>().eq("attr", value) }));
        // DECIMAL
        Entity decimalEntityType = createEntityType(DECIMAL);
        asList(1.23, "1.23", 1, 1L, null).forEach(value -> queries.add(new Object[] { decimalEntityType, new QueryImpl<>().eq("attr", value) }));
        // EMAIL, HTML, HYPERLINK, SCRIPT, STRING, TEXT
        EnumSet.of(EMAIL, HTML, HYPERLINK, SCRIPT, STRING, TEXT).forEach(attrType -> {
            Entity entityType = createEntityType(attrType);
            asList("abc", 1, 1L, 1.23, null).forEach(value -> queries.add(new Object[] { entityType, new QueryImpl<>().eq("attr", value) }));
        });
        // INT, LONG
        EnumSet.of(INT, LONG).forEach(attrType -> {
            Entity entityType = createEntityType(attrType);
            asList(1, 1L, "1", null).forEach(value -> queries.add(new Object[] { entityType, new QueryImpl<>().eq("attr", value) }));
        });
        // FILE
        Entity fileEntityType = createEntityType(FILE, STRING);
        asList("file0", mock(FileMeta.class), null).forEach(idValue -> queries.add(new Object[] { fileEntityType, new QueryImpl<>().eq("attr", idValue) }));
        // ENUM
        Entity enumEntityType = createEntityType(ENUM);
        asList(TestEnum.ENUM0, TestEnum.ENUM1, "ENUM0", "ENUM1", null).forEach(value -> queries.add(new Object[] { enumEntityType, new QueryImpl<>().eq("attr", value) }));
    });
    EnumSet.of(GREATER, GREATER_EQUAL, LESS, LESS_EQUAL).forEach(operator -> {
        Entity entityType = createEntityType(INT);
        QueryImpl<Entity> query = new QueryImpl<>();
        query.addRule(new QueryRule("attr", operator, 1));
        queries.add(new Object[] { entityType, query });
    });
    EnumSet.of(FUZZY_MATCH, FUZZY_MATCH_NGRAM, LIKE).forEach(operator -> {
        Entity entityType = createEntityType(STRING);
        QueryImpl<Entity> query = new QueryImpl<>();
        query.addRule(new QueryRule("attr", operator, "abc"));
        queries.add(new Object[] { entityType, query });
    });
    EnumSet.of(IN, RANGE).forEach(operator -> {
        Entity entityType = createEntityType(INT);
        QueryImpl<Entity> query = new QueryImpl<>();
        query.addRule(new QueryRule("attr", operator, asList(1, 2)));
        queries.add(new Object[] { entityType, query });
    });
    return queries.iterator();
}

Example 80 with QueryImpl

use of org.molgenis.data.support.QueryImpl in project molgenis by molgenis.

the class AttributeRepositorySecurityDecoratorTest method findOneQueryUserPermissionDenied.

@WithMockUser(username = USERNAME)
@Test
public void findOneQueryUserPermissionDenied() throws Exception {
    String entityType0Name = "entity0";
    EntityType entityType0 = when(mock(EntityType.class).getId()).thenReturn(entityType0Name).getMock();
    String attr0Name = "entity0attr0";
    Attribute attr0 = when(mock(Attribute.class).getName()).thenReturn(attr0Name).getMock();
    when(attr0.getEntity()).thenReturn(entityType0);
    Query<Attribute> q = new QueryImpl<>();
    when(delegateRepository.findOne(q)).thenReturn(attr0);
    when(permissionService.hasPermission(new EntityTypeIdentity(entityType0Name), EntityTypePermission.COUNT)).thenReturn(false);
    assertNull(repo.findOne(q));
}