@BeforeTest
public void beforeTest() {
initMocks(this);
DefaultEntityMetaData emd = new DefaultEntityMetaData("MyEntity");
emd.addAttributeMetaData(new DefaultAttributeMetaData("ID").setAuto(true).setIdAttribute(true));
emd.addAllAttributeMetaData(asList(CHROM_META, POS_META));
emd.addAttributeMetaData(new DefaultAttributeMetaData("Description").setNillable(false));
entityMetaData = emd;
tabixRepository = new TabixRepository(tabixReader, entityMetaData, CHROM, POS);
}
@Override
public EntityMetaData getInputMetaData() {
DefaultEntityMetaData metadata =
new DefaultEntityMetaData(this.getClass().getName(), MapEntity.class);
metadata.addAttributeMetaData(new DefaultAttributeMetaData(UNIPROT_ID, FieldTypeEnum.STRING));
return metadata;
}
@Test
public void testAddAndGetEntity() {
readPackageTree();
PackageImpl defaultPackage = (PackageImpl) PackageImpl.defaultPackage;
DefaultEntityMetaData coderMetaData = new DefaultEntityMetaData("Coder");
coderMetaData.setDescription("A coder");
coderMetaData.setExtends(metaDataServiceImpl.getEntityMetaData("org_molgenis_Person"));
coderMetaData.setPackage(defaultPackage);
coderMetaData.addAttribute("ID", ROLE_ID);
coderMetaData.addAttribute("simple");
DefaultAttributeMetaData compoundAttribute = new DefaultAttributeMetaData("compound", COMPOUND);
coderMetaData.addAttributeMetaData(compoundAttribute);
compoundAttribute.addAttributePart(new DefaultAttributeMetaData("c1"));
compoundAttribute.addAttributePart(new DefaultAttributeMetaData("c2"));
assertEquals(coderMetaData.getIdAttribute().getName(), "ID");
metaDataServiceImpl.addEntityMeta(coderMetaData);
DefaultEntityMetaData retrieved = metaDataServiceImpl.getEntityMetaData("Coder");
assertEquals(retrieved, coderMetaData);
assertEquals(retrieved.getIdAttribute().getName(), "ID");
// reboot
DataServiceImpl dataService = new DataServiceImpl();
metaDataServiceImpl = new MetaDataServiceImpl(dataService);
AppSettings appSettings = Mockito.mock(AppSettings.class);
metaDataServiceImpl.setLanguageService(new LanguageService(dataService, appSettings));
metaDataServiceImpl.setDefaultBackend(manageableCrudRepositoryCollection);
retrieved = metaDataServiceImpl.getEntityMetaData("Coder");
assertEquals(retrieved.getIdAttribute().getName(), "ID");
assertTrue(
Iterables.elementsEqual(
retrieved.getAtomicAttributes(), coderMetaData.getAtomicAttributes()));
}
@Override
public EntityMetaData getOutputMetaData() {
DefaultEntityMetaData metadata =
new DefaultEntityMetaData(this.getClass().getName(), MapEntity.class);
metadata.addAttributeMetaData(new DefaultAttributeMetaData("targetType", FieldTypeEnum.STRING));
metadata.addAttributeMetaData(new DefaultAttributeMetaData("chemblId", FieldTypeEnum.STRING));
metadata.addAttributeMetaData(new DefaultAttributeMetaData("geneNames", FieldTypeEnum.STRING));
metadata.addAttributeMetaData(
new DefaultAttributeMetaData("description", FieldTypeEnum.STRING));
metadata.addAttributeMetaData(
new DefaultAttributeMetaData("compoundCount", FieldTypeEnum.DECIMAL));
metadata.addAttributeMetaData(
new DefaultAttributeMetaData("bioactivityCount", FieldTypeEnum.DECIMAL));
metadata.addAttributeMetaData(
new DefaultAttributeMetaData("proteinAccession", FieldTypeEnum.STRING));
metadata.addAttributeMetaData(new DefaultAttributeMetaData("synonyms", FieldTypeEnum.STRING));
metadata.addAttributeMetaData(new DefaultAttributeMetaData("organism", FieldTypeEnum.STRING));
metadata.addAttributeMetaData(
new DefaultAttributeMetaData("preferredName", FieldTypeEnum.STRING));
return metadata;
}
/** Test that a new entity has at least all attributes as of the existing entity. */
@Test
public void canIntegrateEntityMetadataCheckFalse() {
String entityName = "testEntity";
DataServiceImpl dataServiceImpl = Mockito.mock(DataServiceImpl.class);
when(dataServiceImpl.hasRepository(entityName)).thenReturn(Boolean.TRUE);
DefaultEntityMetaData existingEntityMetaData = new DefaultEntityMetaData(entityName);
existingEntityMetaData.addAttribute("ID", ROLE_ID);
existingEntityMetaData.addAttributeMetaData(new DefaultAttributeMetaData("existingAttribute"));
DefaultEntityMetaData newEntityMetaData = new DefaultEntityMetaData(entityName);
newEntityMetaData.addAttribute("ID", ROLE_ID);
when(dataServiceImpl.getEntityMetaData(entityName)).thenReturn(existingEntityMetaData);
MetaDataServiceImpl metaDataService = new MetaDataServiceImpl(dataServiceImpl);
assertFalse(metaDataService.canIntegrateEntityMetadataCheck(newEntityMetaData));
}
@Test
public void testFindAttributes() {
DefaultEntityMetaData sourceEntityMetaData = new DefaultEntityMetaData("sourceEntityMetaData");
EntityMetaData targetEntityMetaData = new DefaultEntityMetaData("targetEntityMetaData");
DefaultAttributeMetaData targetAttribute = new DefaultAttributeMetaData("targetAttribute");
// Mock the id's of the attribute entities that should be searched
List<String> attributeIdentifiers = Arrays.asList("1", "2");
when(semanticSearchServiceHelper.getAttributeIdentifiers(sourceEntityMetaData))
.thenReturn(attributeIdentifiers);
// Mock the createDisMaxQueryRule method
List<QueryRule> rules = new ArrayList<QueryRule>();
QueryRule targetQueryRuleLabel =
new QueryRule(AttributeMetaDataMetaData.LABEL, Operator.FUZZY_MATCH, "height");
rules.add(targetQueryRuleLabel);
QueryRule targetQueryRuleOntologyTermTag =
new QueryRule(AttributeMetaDataMetaData.LABEL, Operator.FUZZY_MATCH, "standing height");
rules.add(targetQueryRuleOntologyTermTag);
QueryRule targetQueryRuleOntologyTermTagSyn =
new QueryRule(AttributeMetaDataMetaData.LABEL, Operator.FUZZY_MATCH, "length");
rules.add(targetQueryRuleOntologyTermTagSyn);
QueryRule disMaxQueryRule = new QueryRule(rules);
disMaxQueryRule.setOperator(Operator.DIS_MAX);
when(semanticSearchServiceHelper.createDisMaxQueryRuleForAttribute(
targetEntityMetaData, targetAttribute))
.thenReturn(disMaxQueryRule);
MapEntity entity1 =
new MapEntity(
ImmutableMap.of(
AttributeMetaDataMetaData.NAME,
"height_0",
AttributeMetaDataMetaData.LABEL,
"height",
AttributeMetaDataMetaData.DESCRIPTION,
"this is a height measurement in m!"));
List<Entity> attributeMetaDataEntities = Arrays.<Entity>asList(entity1);
List<QueryRule> disMaxQueryRules =
Lists.newArrayList(
new QueryRule(AttributeMetaDataMetaData.IDENTIFIER, Operator.IN, attributeIdentifiers),
new QueryRule(Operator.AND),
disMaxQueryRule);
AttributeMetaData attributeHeight = new DefaultAttributeMetaData("height_0");
AttributeMetaData attributeWeight = new DefaultAttributeMetaData("weight_0");
sourceEntityMetaData.addAttributeMetaData(attributeHeight);
sourceEntityMetaData.addAttributeMetaData(attributeWeight);
// Case 1
when(dataService.findAll(
AttributeMetaDataMetaData.ENTITY_NAME, new QueryImpl(disMaxQueryRules)))
.thenReturn(attributeMetaDataEntities);
Iterable<AttributeMetaData> termsActual1 =
semanticSearchService.findAttributes(
sourceEntityMetaData, targetEntityMetaData, targetAttribute);
Iterable<AttributeMetaData> termsExpected1 = Arrays.<AttributeMetaData>asList(attributeHeight);
assertEquals(termsActual1, termsExpected1);
// Case 2
when(dataService.findAll(
AttributeMetaDataMetaData.ENTITY_NAME, new QueryImpl(disMaxQueryRules)))
.thenReturn(Arrays.<Entity>asList());
Iterable<AttributeMetaData> termsActual2 =
semanticSearchService.findAttributes(
sourceEntityMetaData, targetEntityMetaData, targetAttribute);
Iterable<AttributeMetaData> termsExpected2 = Arrays.<AttributeMetaData>asList();
assertEquals(termsActual2, termsExpected2);
Mockito.reset(ontologyService);
attribute.setDescription("Standing height (Ångstrøm)");
when(ontologyService.findOntologyTerms(
ontologies, ImmutableSet.of("standing", "height", "ångstrøm"), 100))
.thenReturn(ontologyTerms);
Hit<OntologyTerm> result = semanticSearchService.findTags(attribute, ontologies);
assertEquals(result, Hit.<OntologyTerm>create(standingHeight, 0.76471f));
}
@Override
public Map<String, DefaultEntityMetaData> getEntityMetaData(RepositoryCollection source) {
// TODO: this task is actually a 'merge' instead of 'import'
// so we need to consider both new metadata as existing ...
Map<String, DefaultEntityMetaData> entities =
new LinkedHashMap<String, DefaultEntityMetaData>();
// load attributes first (because entities are optional).
for (Entity a : source.getRepositoryByEntityName("attributes")) {
int i = 1;
String entityName = a.getString("entity");
// required
if (entityName == null) throw new IllegalArgumentException("attributes.entity is missing");
if (a.get("name") == null) throw new IllegalArgumentException("attributes.name is missing");
// create entity if not yet defined
if (entities.get(entityName) == null)
entities.put(entityName, new DefaultEntityMetaData(entityName));
DefaultEntityMetaData md = entities.get(entityName);
DefaultAttributeMetaData am = new DefaultAttributeMetaData(a.getString("name"));
if (a.get("dataType") != null) {
FieldType t = MolgenisFieldTypes.getType(a.getString("dataType"));
if (t == null)
throw new IllegalArgumentException(
"attributes.type error on line " + i + ": " + a.getString("dataType") + " unknown");
am.setDataType(t);
}
if (a.get("nillable") != null) am.setNillable(a.getBoolean("nillable"));
if (a.get("auto") != null) am.setAuto(a.getBoolean("auto"));
if (a.get("idAttribute") != null) am.setIdAttribute(a.getBoolean("idAttribute"));
md.addAttributeMetaData(am);
}
// load all entities (optional)
if (source.getRepositoryByEntityName("entities") != null) {
int i = 1;
for (Entity e : source.getRepositoryByEntityName("entities")) {
i++;
String entityName = e.getString("name");
// required
if (entityName == null)
throw new IllegalArgumentException("entity.name is missing on line " + i);
if (entities.get(entityName) == null)
entities.put(entityName, new DefaultEntityMetaData(entityName));
DefaultEntityMetaData md = entities.get(entityName);
if (e.get("description") != null) md.setDescription(e.getString("description"));
}
}
// re-iterate to map the mrefs/xref refEntity (or give error if not found)
// TODO: consider also those in existing db
int i = 1;
for (Entity a : source.getRepositoryByEntityName("attributes")) {
i++;
if (a.get("refEntity") != null) {
DefaultEntityMetaData em = entities.get(a.getString("entity"));
DefaultAttributeMetaData am =
(DefaultAttributeMetaData) em.getAttribute(a.getString("name"));
if (entities.get(a.getString("refEntity")) == null) {
throw new IllegalArgumentException(
"attributes.refEntity error on line "
+ i
+ ": "
+ a.getString("refEntity")
+ " unknown");
}
am.setRefEntity(entities.get(a.getString("refEntity")));
}
}
return entities;
}
