Examples with MetaDataService org.molgenis.data.meta.MetaDataService used on opensource projects

Example 1 with MetaDataService

use of org.molgenis.data.meta.MetaDataService in project molgenis by molgenis.

the class DataExplorerControllerTest method initTrackingIdNotPresent.

@Test
public void initTrackingIdNotPresent() {
    String selectedEntityname = "selectedEntityname";
    String selectedEntityId = "selectedEntityId";
    MetaDataService metaDataService = mock(MetaDataService.class);
    when(dataService.getMeta()).thenReturn(metaDataService);
    when(metaDataService.getEntityTypes()).thenReturn(Stream.empty());
    controller.init(selectedEntityname, selectedEntityId, model);
    verify(model).addAttribute("hasTrackingId", false);
    verify(model).addAttribute("hasMolgenisTrackingId", false);
}

Example 2 with MetaDataService

use of org.molgenis.data.meta.MetaDataService in project molgenis by molgenis.

the class DataExplorerControllerTest method initSetNavigatorMenuPathNoNavigator.

@Test
public void initSetNavigatorMenuPathNoNavigator() {
    String selectedEntityname = "selectedEntityname";
    String selectedEntityId = "selectedEntityId";
    String navigatorPath = "path/to-navigator";
    MetaDataService metaDataService = mock(MetaDataService.class);
    when(dataService.getMeta()).thenReturn(metaDataService);
    when(metaDataService.getEntityTypes()).thenReturn(Stream.empty());
    controller.init(selectedEntityname, selectedEntityId, model);
    verify(model, never()).addAttribute("navigatorBaseUrl", navigatorPath);
}

Example 3 with MetaDataService

use of org.molgenis.data.meta.MetaDataService in project molgenis by molgenis.

the class EntityTypeValidatorTest method setUpBeforeMethod.

@SuppressWarnings("unchecked")
@BeforeMethod
public void setUpBeforeMethod() {
    dataService = mock(DataService.class);
    MetaDataService metaDataService = mock(MetaDataService.class);
    when(dataService.getMeta()).thenReturn(metaDataService);
    systemEntityTypeRegistry = mock(SystemEntityTypeRegistry.class);
    entityTypeValidator = new EntityTypeValidator(dataService, systemEntityTypeRegistry);
    String backendName = "backend";
    RepositoryCollection repoCollection = mock(RepositoryCollection.class);
    when(metaDataService.getBackend(backendName)).thenReturn(repoCollection);
    // valid entity meta
    entityType = when(mock(EntityType.class).getId()).thenReturn("entity").getMock();
    idAttr = when(mock(Attribute.class).getName()).thenReturn("idAttr").getMock();
    when(idAttr.getIdentifier()).thenReturn("#idAttr");
    when(idAttr.getDataType()).thenReturn(STRING);
    when(idAttr.isUnique()).thenReturn(true);
    when(idAttr.isNillable()).thenReturn(false);
    labelAttr = when(mock(Attribute.class).getName()).thenReturn("labelAttr").getMock();
    when(labelAttr.getIdentifier()).thenReturn("#labelAttr");
    when(labelAttr.getDataType()).thenReturn(STRING);
    entityQ = mock(Query.class);
    when(dataService.query(ENTITY_TYPE_META_DATA, EntityType.class)).thenReturn(entityQ);
    Query<EntityType> entityQ0 = mock(Query.class);
    Query<EntityType> entityQ1 = mock(Query.class);
    when(entityQ.eq(ATTRIBUTES, idAttr)).thenReturn(entityQ0);
    when(entityQ.eq(ATTRIBUTES, labelAttr)).thenReturn(entityQ1);
    when(entityQ0.findOne()).thenReturn(null);
    when(entityQ1.findOne()).thenReturn(null);
    attrQ = mock(Query.class);
    Query<Attribute> attrQ0 = mock(Query.class);
    Query<Attribute> attrQ1 = mock(Query.class);
    when(dataService.query(ATTRIBUTE_META_DATA, Attribute.class)).thenReturn(attrQ);
    when(attrQ.eq(CHILDREN, idAttr)).thenReturn(attrQ0);
    when(attrQ.eq(CHILDREN, labelAttr)).thenReturn(attrQ1);
    when(attrQ0.findOne()).thenReturn(null);
    when(attrQ1.findOne()).thenReturn(null);
    String packageName = "package";
    Package package_ = when(mock(Package.class).getId()).thenReturn(packageName).getMock();
    when(entityType.getPackage()).thenReturn(package_);
    String name = "name";
    String label = "label";
    when(entityType.getId()).thenReturn(packageName + PACKAGE_SEPARATOR + name);
    when(entityType.getLabel()).thenReturn(label);
    when(entityType.getOwnAllAttributes()).thenReturn(newArrayList(idAttr, labelAttr));
    when(entityType.getAllAttributes()).thenReturn(newArrayList(idAttr, labelAttr));
    when(entityType.getOwnIdAttribute()).thenReturn(idAttr);
    when(entityType.getOwnLabelAttribute()).thenReturn(labelAttr);
    when(entityType.getOwnLookupAttributes()).thenReturn(singletonList(labelAttr));
    when(entityType.isAbstract()).thenReturn(false);
    when(entityType.getExtends()).thenReturn(null);
    when(entityType.getBackend()).thenReturn(backendName);
}

Example 4 with MetaDataService

use of org.molgenis.data.meta.MetaDataService in project molgenis by molgenis.

the class GenomeBrowserServiceTest method testGetReferenceTracksAll.

@Test
public void testGetReferenceTracksAll() {
    EntityType entity = mock(EntityType.class);
    when(entity.getLabel()).thenReturn("label");
    GenomeBrowserAttributes genomeBrowserAttributes = getGenomeBrowserAttributes("postion", "chrom", "normal", "mutant");
    GenomeBrowserTrack reference = GenomeBrowserTrack.create("ref_id", "label", "ref_label", entity, GenomeBrowserSettings.TrackType.VARIANT, null, GenomeBrowserSettings.MolgenisReferenceMode.NONE, genomeBrowserAttributes, null, null, null, null);
    EntityType molgenisEntity = mock(EntityType.class);
    when(molgenisEntity.getLabel()).thenReturn("label");
    GenomeBrowserTrack track = GenomeBrowserTrack.create("id", "label", "entityLabel", molgenisEntity, GenomeBrowserSettings.TrackType.VARIANT, Collections.singletonList(reference), GenomeBrowserSettings.MolgenisReferenceMode.ALL, genomeBrowserAttributes, "alert(\"test\")", "attr 1:attr1,reference attribute:REF,position on genome:POS", null, null);
    GenomeBrowserAttributes attrs1 = getGenomeBrowserAttributes("pos", "chr", "ref", "alt");
    GenomeBrowserAttributes attrs2 = getGenomeBrowserAttributes("POS", "CHROM", null, null);
    when(dataService.findAll(GenomeBrowserAttributesMetadata.GENOMEBROWSERATTRIBUTES, new QueryImpl<GenomeBrowserAttributes>().eq(GenomeBrowserAttributesMetadata.DEFAULT, true), GenomeBrowserAttributes.class)).thenReturn(Stream.of(attrs1, attrs2));
    EntityType type1 = mock(EntityType.class);
    EntityType type2 = mock(EntityType.class);
    EntityType type3 = mock(EntityType.class);
    Attribute labelAttr = mock(Attribute.class);
    when(labelAttr.getName()).thenReturn("refLabel");
    List<EntityType> types = new ArrayList<>();
    types.add(type1);
    when(type1.getIdValue()).thenReturn("type1");
    when(type1.getLabel()).thenReturn("label1");
    when(type1.getAttributeNames()).thenReturn(Arrays.asList("POS", "CHROM", "AAP", "NOOT", "MIES"));
    when(type1.getLabelAttribute()).thenReturn(labelAttr);
    types.add(type2);
    when(type2.getIdValue()).thenReturn("type2");
    when(type2.getLabel()).thenReturn("label2");
    when(type2.getAttributeNames()).thenReturn(Arrays.asList("pos", "chr", "ref", "alt", "aap"));
    when(type2.getLabelAttribute()).thenReturn(labelAttr);
    types.add(type3);
    when(type3.getIdValue()).thenReturn("type3");
    when(type3.getLabel()).thenReturn("label3");
    when(type3.getAttributeNames()).thenReturn(Arrays.asList("pos", "chr", "ref", "alternative", "monkey"));
    when(type3.getLabelAttribute()).thenReturn(labelAttr);
    MetaDataService metaDataService = mock(MetaDataService.class);
    when(dataService.getMeta()).thenReturn(metaDataService);
    when(metaDataService.getEntityTypes()).thenReturn(types.stream());
    Map<String, GenomeBrowserTrack> result = genomeBrowserService.getReferenceTracks(track);
    assertEquals(result.size(), 2);
    assertEquals(result.get("type2"), GenomeBrowserTrack.create("type2", "label2", "refLabel", type2, GenomeBrowserSettings.TrackType.VARIANT, Collections.emptyList(), GenomeBrowserSettings.MolgenisReferenceMode.ALL, attrs1, null, null, null, null));
    assertEquals(result.get("type1"), GenomeBrowserTrack.create("type1", "label1", "refLabel", type1, GenomeBrowserSettings.TrackType.VARIANT, Collections.emptyList(), GenomeBrowserSettings.MolgenisReferenceMode.ALL, attrs2, null, null, null, null));
}

Example 5 with MetaDataService

use of org.molgenis.data.meta.MetaDataService in project molgenis by molgenis.

the class PlatformIT method testDeletePackage.

@WithMockUser(username = USERNAME)
@Test(singleThreaded = true)
public void testDeletePackage() {
    populateUserPermissions();
    runAsSystem(() -> {
        MetaDataService metadataService = dataService.getMeta();
        Package parentPackage = packageFactory.create("parent").setLabel("parent");
        Package subPackage = packageFactory.create("parent_sub").setLabel("sub").setParent(parentPackage);
        metadataService.upsertPackages(Stream.of(parentPackage, subPackage));
        EntityType entityTypeInSubPackage = testHarness.createDynamicRefEntityType("entityInSub", subPackage);
        EntityType entityTypeInParentPackage = testHarness.createDynamicTestEntityType("entityInParent", parentPackage, entityTypeInSubPackage);
        metadataService.upsertEntityTypes(asList(entityTypeInSubPackage, entityTypeInParentPackage));
        List<Entity> entities = createAndAdd(entityTypeInParentPackage, entityTypeInSubPackage, 5);
        Set<Entity> refEntities = entities.stream().map(e -> e.getEntity(ATTR_XREF)).collect(toSet());
        assertPresent(entityTypeInParentPackage, entities);
        assertPresent(entityTypeInSubPackage, newArrayList(refEntities));
        dataService.deleteById(PACKAGE, "parent");
        assertNull(metadataService.getPackage("parent"));
        assertNull(metadataService.getPackage("parent_sub"));
        entities.forEach(this::assertNotPresent);
        refEntities.forEach(this::assertNotPresent);
    });
}