Examples with MappingProject org.molgenis.semanticmapper.mapping.model.MappingProject used on opensource projects

Example 21 with MappingProject

use of org.molgenis.semanticmapper.mapping.model.MappingProject in project molgenis by molgenis.

the class AlgorithmServiceImplIT method testWhenSourceHasMultipleMatchesThenFirstMappingGetsCreated.

@Test
public void testWhenSourceHasMultipleMatchesThenFirstMappingGetsCreated() {
    EntityType targetEntityType = entityTypeFactory.create("target");
    Attribute targetAttribute = attrMetaFactory.create().setName("targetHeight");
    targetAttribute.setDescription("height");
    targetEntityType.addAttribute(targetAttribute);
    EntityType sourceEntityType = entityTypeFactory.create("source");
    Attribute sourceAttribute1 = attrMetaFactory.create().setName("sourceHeight1");
    sourceAttribute1.setDescription("height");
    Attribute sourceAttribute2 = attrMetaFactory.create().setName("sourceHeight2");
    sourceAttribute2.setDescription("height");
    sourceEntityType.addAttributes(Arrays.asList(sourceAttribute1, sourceAttribute2));
    User owner = userFactory.create();
    owner.setUsername("flup");
    owner.setPassword("geheim");
    owner.setId("12345");
    owner.setActive(true);
    owner.setEmail("flup@blah.com");
    owner.setFirstName("Flup");
    owner.setLastName("de Flap");
    MappingProject project = new MappingProject("project", owner);
    project.addTarget(targetEntityType);
    EntityMapping mapping = project.getMappingTarget("target").addSource(sourceEntityType);
    Map<Attribute, ExplainedAttribute> mappings = ImmutableMap.of(sourceAttribute1, ExplainedAttribute.create(sourceAttribute1), sourceAttribute2, ExplainedAttribute.create(sourceAttribute2));
    LinkedHashMultimap<Relation, OntologyTerm> ontologyTermTags = LinkedHashMultimap.create();
    when(semanticSearchService.decisionTreeToFindRelevantAttributes(sourceEntityType, targetAttribute, ontologyTermTags.values(), null)).thenReturn(mappings);
    when(ontologyTagService.getTagsForAttribute(targetEntityType, targetAttribute)).thenReturn(ontologyTermTags);
    algorithmService.autoGenerateAlgorithm(sourceEntityType, targetEntityType, mapping, targetAttribute);
    assertEquals(mapping.getAttributeMapping("targetHeight").getSourceAttributes().get(0), sourceAttribute1);
}

Example 22 with MappingProject

use of org.molgenis.semanticmapper.mapping.model.MappingProject in project molgenis by molgenis.

the class MappingServiceImplTest method createMappingProjectWithMappings.

private MappingProject createMappingProjectWithMappings() {
    MappingProject mappingProject = mappingService.addMappingProject("TestRun", user, hopMetaData.getId());
    MappingTarget target = mappingProject.getMappingTarget(hopMetaData.getId());
    when(mappingProjectRepo.getMappingProject("TestRun")).thenReturn(mappingProject);
    EntityMapping mapping = target.addSource(geneMetaData);
    AttributeMapping idMapping = mapping.addAttributeMapping("identifier");
    idMapping.setAlgorithm("$('id').value()");
    AttributeMapping attrMapping = mapping.addAttributeMapping("height");
    attrMapping.setAlgorithm("$('length').value()");
    return mappingProject;
}

Example 23 with MappingProject

use of org.molgenis.semanticmapper.mapping.model.MappingProject in project molgenis by molgenis.

the class MappingServiceImplTest method testUpdateMappingProject.

@Test
public void testUpdateMappingProject() {
    MappingProject mappingProject = Mockito.mock(MappingProject.class);
    mappingService.updateMappingProject(mappingProject);
    Mockito.verifyZeroInteractions(mappingProject);
    Mockito.verify(mappingProjectRepo).update(mappingProject);
}

Example 24 with MappingProject

use of org.molgenis.semanticmapper.mapping.model.MappingProject in project molgenis by molgenis.

the class MappingServiceImplTest method testApplyMappingsUpdate.

/**
 * Applying a mapping multiple times to the same target should update the existing entities.
 */
@SuppressWarnings("unchecked")
@Test
public void testApplyMappingsUpdate() {
    String entityTypeId = "updateEntity";
    @SuppressWarnings("unchecked") Repository<Entity> updateEntityRepo = Mockito.mock(Repository.class);
    when(updateEntityRepo.getName()).thenReturn(entityTypeId);
    EntityType targetMeta = entityTypeFactory.create(TARGET_HOP_ENTITY).setPackage(package_);
    targetMeta.addAttribute(attrMetaFactory.create().setName("identifier"), ROLE_ID);
    targetMeta.addAttribute(attrMetaFactory.create().setName("height").setDataType(DECIMAL).setNillable(false));
    targetMeta.addAttribute(attrMetaFactory.create().setName("source"));
    when(dataService.hasRepository(entityTypeId)).thenReturn(true);
    when(dataService.getRepository(entityTypeId)).thenReturn(updateEntityRepo);
    when(updateEntityRepo.getEntityType()).thenReturn(targetMeta);
    when(metaDataService.createRepository(argThat(obj -> obj.getLabel().equals(entityTypeId)))).thenReturn(updateEntityRepo);
    // add an entity to the source
    List<Entity> sourceGeneEntities = newArrayList();
    List<Entity> expectedEntities = newArrayList();
    createEntities(targetMeta, sourceGeneEntities, expectedEntities);
    when(updateEntityRepo.count()).thenReturn(4L);
    when(updateEntityRepo.findAll(ArgumentMatchers.any(), ArgumentMatchers.any())).thenReturn(expectedEntities.stream());
    Mockito.doAnswer(invocationOnMock -> {
        @SuppressWarnings("unchecked") Consumer<List<Entity>> consumer = (Consumer<List<Entity>>) invocationOnMock.<Consumer>getArgument(0);
        consumer.accept(sourceGeneEntities);
        return null;
    }).when(geneRepo).forEachBatched(ArgumentMatchers.any(Consumer.class), ArgumentMatchers.eq(MAPPING_BATCH_SIZE));
    // make project and apply mappings once
    MappingProject project = createMappingProjectWithMappings();
    when(entityManager.create(targetMeta, EntityManager.CreationMode.POPULATE)).thenAnswer(invocation -> new DynamicEntity(targetMeta));
    // apply mapping again
    assertEquals(mappingService.applyMappings("TestRun", entityTypeId, false, "packageId", "label", progress), 4);
    Mockito.verify(geneRepo).forEachBatched(ArgumentMatchers.any(Consumer.class), ArgumentMatchers.any(Integer.class));
    Mockito.verify(updateEntityRepo).upsertBatch(batchCaptor.capture());
    Assert.assertTrue(EntityUtils.equalsEntities(batchCaptor.getValue(), expectedEntities));
    Mockito.verify(progress).status("Applying mappings to repository [HopEntity]");
    Mockito.verify(progress).status("Mapping source [Genes]...");
    Mockito.verify(progress).increment(1);
    Mockito.verify(progress).status("Mapped 4 [Genes] entities.");
    Mockito.verify(progress).status("Done applying mappings to repository [HopEntity]");
    Mockito.verifyZeroInteractions(permissionSystemService);
}

Example 25 with MappingProject

use of org.molgenis.semanticmapper.mapping.model.MappingProject in project molgenis by molgenis.

the class MappingServiceImplTest method testCloneMappingProjectString.

@Test
public void testCloneMappingProjectString() {
    MappingProject mappingProject = Mockito.mock(MappingProject.class);
    when(mappingProjectRepo.getMappingProject("0")).thenReturn(mappingProject);
    mappingService.cloneMappingProject("0");
    Mockito.verify(mappingProject).removeIdentifiers();
    Mockito.verify(mappingProjectRepo).add(mappingProject);
}