@Override
public List<Policy> findByResourceServer(
Map<String, String[]> attributes, String resourceServerId, int firstResult, int maxResult) {
QueryBuilder queryBuilder = new QueryBuilder().and("resourceServerId").is(resourceServerId);
attributes.forEach(
(name, value) -> {
if ("permission".equals(name)) {
if (Boolean.valueOf(value[0])) {
queryBuilder.and("type").in(new String[] {"resource", "scope"});
} else {
queryBuilder.and("type").notIn(new String[] {"resource", "scope"});
}
} else if ("id".equals(name)) {
queryBuilder.and("_id").in(value);
} else {
queryBuilder
.and(name)
.regex(Pattern.compile(".*" + value[0] + ".*", Pattern.CASE_INSENSITIVE));
}
});
DBObject sort = new BasicDBObject("name", 1);
return getMongoStore()
.loadEntities(
PolicyEntity.class, queryBuilder.get(), sort, firstResult, maxResult, invocationContext)
.stream()
.map(policy -> findById(policy.getId(), resourceServerId))
.collect(toList());
}
@Override
public QueryResponse getAllByPositionList(List<Position> positionList, QueryOptions options) {
// db.regulatory_region.find({"chunkIds": {$in:["1_200", "1_300"]}, "start": 601156})
String featureType = options.getString("featureType", null);
String featureClass = options.getString("featureClass", null);
List<DBObject> queries = new ArrayList<>();
for (Position position : positionList) {
String chunkId =
position.getChromosome() + "_" + getChunkId(position.getPosition(), CHUNKSIZE);
BasicDBList chunksId = new BasicDBList();
chunksId.add(chunkId);
QueryBuilder builder =
QueryBuilder.start("chunkIds").in(chunksId).and("start").is(position.getPosition());
if (featureType != null) {
builder.and("featureType").is(featureType);
}
if (featureClass != null) {
builder.and("featureClass").is(featureClass);
}
// System.out.println("Query: " + builder.get());
queries.add(builder.get());
}
System.out.println("Query: " + queries);
options = addExcludeReturnFields("chunkIds", options);
return executeQueryList(positionList, queries, options);
}
@Override
public QueryResult next(String chromosome, int position, QueryOptions options) {
String featureType = options.getString("featureType", null);
String featureClass = options.getString("featureClass", null);
BasicDBList chunksId = new BasicDBList();
String chunkId =
chromosome
+ "_"
+ getChunkId(position, regulatoryRegionChunkSize)
+ "_"
+ regulatoryRegionChunkSize / 1000
+ "k";
chunksId.add(chunkId);
// TODO: Add query to find next item considering next chunk
// db.regulatory_region.find({ "chromosome" : "19" , "start" : { "$gt" : 62005} , "featureType"
// : "TF_binding_site_motif"}).sort({start:1}).limit(1)
QueryBuilder builder;
if (options.getString("strand") == null
|| (options.getString("strand").equals("1") || options.getString("strand").equals("+"))) {
// db.core.find({chromosome: "1", start: {$gt: 1000000}}).sort({start: 1}).limit(1)
builder =
QueryBuilder.start("_chunkIds")
.in(chunksId)
.and("chromosome")
.is(chromosome)
.and("start")
.greaterThan(position);
options.put("sort", new BasicDBObject("start", 1));
options.put("limit", 1);
} else {
builder =
QueryBuilder.start("_chunkIds")
.in(chunksId)
.and("chromosome")
.is(chromosome)
.and("end")
.lessThan(position);
options.put("sort", new BasicDBObject("end", -1));
options.put("limit", 1);
}
if (featureType != null) {
builder.and("featureType").is(featureType);
}
if (featureClass != null) {
builder.and("featureClass").is(featureClass);
}
System.out.println(builder.get());
return executeQuery("result", builder.get(), options);
}
@Override
public List<QueryResult> getAllByRegionList(List<Region> regionList, QueryOptions options) {
// db.regulatory_region.find({"chunkIds": {$in:["1_200", "1_300"]}, "start": 601156})
QueryBuilder builder = new QueryBuilder();
List<Object> featureType = options.getList("featureType", null);
List<Object> featureClass = options.getList("featureClass", null);
// options = addExcludeReturnFields("chunkIds", options);
List<DBObject> queries = new ArrayList<>();
for (Region region : regionList) {
int firstChunkId = getChunkId(region.getStart(), regulatoryRegionChunkSize);
int lastChunkId = getChunkId(region.getEnd(), regulatoryRegionChunkSize);
BasicDBList chunksId = new BasicDBList();
for (int j = firstChunkId; j <= lastChunkId; j++) {
String chunkId =
region.getChromosome() + "_" + j + "_" + regulatoryRegionChunkSize / 1000 + "k";
chunksId.add(chunkId);
}
// logger.info(chunksId.toString());
builder =
builder
.start("_chunkIds")
.in(chunksId)
.and("start")
.lessThanEquals(region.getEnd())
.and("end")
.greaterThanEquals(region.getStart());
if (featureType != null && featureType.size() > 0) {
BasicDBList featureTypeDBList = new BasicDBList();
featureTypeDBList.addAll(featureType);
builder = builder.and("featureType").in(featureTypeDBList);
}
if (featureClass != null && featureClass.size() > 0) {
BasicDBList featureClassDBList = new BasicDBList();
featureClassDBList.addAll(featureClass);
builder = builder.and("featureClass").in(featureClassDBList);
}
queries.add(builder.get());
}
// System.out.println(">>"+regionList);
// System.out.println(">>"+builder.get().toString());
return executeQueryList2(regionList, queries, options);
}
@Override
public void addQuery(AdRequest request, QueryBuilder builder) {
if (request.date() != null) {
List<DBObject> condition_queries = new ArrayList<DBObject>();
/*
* Prefix der Indizieren beachten.
*/
for (int i = 0; i < DateConditionDefinition.MAX_PERIOD_COUNT; i++) {
QueryBuilder condition = QueryBuilder.start();
// from part of the query
BasicDBObject query_from_1 =
new BasicDBObject(
AdDBConstants.ADDB_AD_DATE_FROM + i, new BasicDBObject("$lte", request.date()));
BasicDBObject query_from_2 =
new BasicDBObject(AdDBConstants.ADDB_AD_DATE_FROM + i, AdDBConstants.ADDB_AD_DATE_ALL);
List<BasicDBObject> queries = new ArrayList<BasicDBObject>();
queries.add(query_from_1);
queries.add(query_from_2);
BasicDBObject query_from = new BasicDBObject("$or", queries);
condition.and(query_from);
// to part of the query
BasicDBObject query_to_1 =
new BasicDBObject(
AdDBConstants.ADDB_AD_DATE_TO + i, new BasicDBObject("$gte", request.date()));
BasicDBObject query_to_2 =
new BasicDBObject(AdDBConstants.ADDB_AD_DATE_TO + i, AdDBConstants.ADDB_AD_DATE_ALL);
queries = new ArrayList<BasicDBObject>();
queries.add(query_to_1);
queries.add(query_to_2);
BasicDBObject query_to = new BasicDBObject("$or", queries);
condition.and(query_to);
condition_queries.add(condition.get());
}
builder.and(new BasicDBObject("$or", condition_queries));
}
}
public List<T> findByAttributes(Map<String, String> attributes) {
QueryBuilder qb = QueryBuilder.start();
for (String k : attributes.keySet()) {
qb.and("attributes." + k).is(attributes.get(k));
}
return makeList(null, getDbCollection().find(qb.get()));
}
@Override
public QueryResponse getAllByRegionList(List<Region> regionList, QueryOptions options) {
// db.regulatory_region.find({"chunkIds": {$in:["1_200", "1_300"]}, "start": 601156})
String featureType = options.getString("featureType", null);
String featureClass = options.getString("featureClass", null);
List<DBObject> queries = new ArrayList<>();
List<String> ids = new ArrayList<>(regionList.size());
for (Region region : regionList) {
int firstChunkId = getChunkId(region.getStart(), CHUNKSIZE);
int lastChunkId = getChunkId(region.getEnd(), CHUNKSIZE);
BasicDBList chunksId = new BasicDBList();
for (int j = firstChunkId; j <= lastChunkId; j++) {
String chunkId = region.getChromosome() + "_" + j;
chunksId.add(chunkId);
}
QueryBuilder builder =
QueryBuilder.start("chunkIds")
.in(chunksId)
.and("start")
.lessThanEquals(region.getEnd())
.and("end")
.greaterThanEquals(region.getStart());
if (featureType != null) {
builder.and("featureType").is(featureType);
}
if (featureClass != null) {
builder.and("featureClass").is(featureClass);
}
System.out.println("Query: " + builder.get());
queries.add(builder.get());
ids.add(region.toString());
}
options = addExcludeReturnFields("chunkIds", options);
return executeQueryList(ids, queries, options);
}
@Override
public void addQuery(AdRequest request, QueryBuilder builder) {
if (request.day() == null) {
return;
}
int day = request.day().getDay();
if (day == Day.ALL.getDay()) {
return;
}
List<String> days = new ArrayList<String>();
days.add(String.valueOf(day));
days.add(String.valueOf(Day.ALL.getDay()));
BasicDBObject dq = new BasicDBObject(AdDBConstants.ADDB_AD_DAY, new BasicDBObject("$in", days));
builder.and(dq);
}