@Test
public void testFindAll() {
Query q = new QueryImpl();
q.eq(OWNER, "flup");
when(dataService.findAll(ENTITY_NAME)).thenReturn(Stream.of(mappingProjectEntity));
when(userService.getUser("flup")).thenReturn(owner);
when(mappingTargetRepository.toMappingTargets(mappingTargetEntities))
.thenReturn(asList(mappingTarget1, mappingTarget2));
List<MappingProject> result = mappingProjectRepositoryImpl.getAllMappingProjects();
mappingProject.setIdentifier("mappingProjectID");
assertEquals(result, asList(mappingProject));
}
@Override
public Stream<Entity> findAll(Query q) {
if (q.getRules().isEmpty()) {
return getEntities().stream();
}
if ((q.getRules().size() != 1) || (q.getRules().get(0).getOperator() != Operator.EQUALS)) {
throw new MolgenisDataException("The only query allowed on this Repository is gene EQUALS");
}
String geneSymbol = (String) q.getRules().get(0).getValue();
List<Entity> entities = getEntitiesByGeneSymbol().get(geneSymbol);
return entities != null ? entities.stream() : Stream.empty();
}
@Override
protected List<Entity> getBatch(Query<Entity> q) {
Consumer<SearchRequestBuilder> searchRequestBuilderConsumer =
searchRequestBuilder ->
searchRequestGenerator.buildSearchRequest(
searchRequestBuilder,
type,
SearchType.QUERY_AND_FETCH,
q,
null,
null,
null,
entityType);
return elasticsearchFacade
.searchForIds(searchRequestBuilderConsumer, q.toString(), type, indexName)
.map(idString -> convert(idString, entityType.getIdAttribute()))
.map(idObject -> elasticsearchEntityFactory.getReference(entityType, idObject))
.collect(toList());
}
/**
* Validates query based on the given entity type, converts query values to the expected type if
* necessary.
*
* @param query query
* @param entityType entity type
* @throws MolgenisValidationException if query is invalid
*/
public void validate(Query<? extends Entity> query, EntityType entityType) {
query.getRules().forEach(queryRule -> validateQueryRule(queryRule, entityType));
}
private EntityCollectionResponseV2 createEntityCollectionResponse(
String entityName, EntityCollectionRequestV2 request, HttpServletRequest httpRequest) {
EntityMetaData meta = dataService.getEntityMetaData(entityName);
Query q = request.getQ() != null ? request.getQ().createQuery(meta) : new QueryImpl();
q.pageSize(request.getNum()).offset(request.getStart()).sort(request.getSort());
Fetch fetch =
AttributeFilterToFetchConverter.convert(
request.getAttrs(), meta, languageService.getCurrentUserLanguageCode());
if (fetch != null) {
q.fetch(fetch);
}
if (request.getAggs() != null) {
// return aggregates for aggregate query
AggregateQuery aggsQ = request.getAggs().createAggregateQuery(meta, q);
AttributeMetaData xAttr = aggsQ.getAttributeX();
AttributeMetaData yAttr = aggsQ.getAttributeY();
if (xAttr == null && yAttr == null) {
throw new MolgenisQueryException("Aggregate query is missing 'x' or 'y' attribute");
}
AggregateResult aggs = dataService.aggregate(entityName, aggsQ);
AttributeMetaDataResponseV2 xAttrResponse =
xAttr != null
? new AttributeMetaDataResponseV2(
entityName, meta, xAttr, fetch, permissionService, dataService, languageService)
: null;
AttributeMetaDataResponseV2 yAttrResponse =
yAttr != null
? new AttributeMetaDataResponseV2(
entityName, meta, yAttr, fetch, permissionService, dataService, languageService)
: null;
return new EntityAggregatesResponse(
aggs, xAttrResponse, yAttrResponse, BASE_URI + '/' + entityName);
} else {
Long count = dataService.count(entityName, q);
Iterable<Entity> it;
if (count > 0) {
it =
new Iterable<Entity>() {
@Override
public Iterator<Entity> iterator() {
return dataService.findAll(entityName, q).iterator();
}
};
} else {
it = Collections.emptyList();
}
EntityPager pager = new EntityPager(request.getStart(), request.getNum(), count, it);
List<Map<String, Object>> entities = new ArrayList<>();
for (Entity entity : it) {
Map<String, Object> responseData = new LinkedHashMap<String, Object>();
createEntityValuesResponse(entity, fetch, responseData);
entities.add(responseData);
}
UriComponentsBuilder builder = UriComponentsBuilder.fromUriString(getFullURL(httpRequest));
String prevHref = null;
if (pager.getPrevStart() != null) {
builder.replaceQueryParam("start", pager.getPrevStart());
prevHref = builder.build(false).toUriString();
}
String nextHref = null;
if (pager.getNextStart() != null) {
builder.replaceQueryParam("start", pager.getNextStart());
nextHref = builder.build(false).toUriString();
}
return new EntityCollectionResponseV2(
pager,
entities,
fetch,
BASE_URI + '/' + entityName,
meta,
permissionService,
dataService,
languageService,
prevHref,
nextHref);
}
}