@Test(groups = "dev")
public void autoWrapTest() throws EventDeliveryException {
ctx.put(MongoSink.AUTO_WRAP, Boolean.toString(true));
ctx.put(MongoSink.DB_NAME, "test_wrap");
MongoSink sink = new MongoSink();
Configurables.configure(sink, ctx);
sink.setChannel(channel);
sink.start();
Transaction tx = channel.getTransaction();
tx.begin();
String msg =
"2012/10/26 11:23:08 [error] 7289#0: *6430831 open() \"/usr/local/nginx/html/50x.html\" failed (2: No such file or directory), client: 10.160.105.161, server: sg15.redatoms.com, request: \"POST /mojo/ajax/embed HTTP/1.0\", upstream: \"fastcgi://unix:/tmp/php-fpm.sock:\", host: \"sg15.redatoms.com\", referrer: \"http://sg15.redatoms.com/mojo/mobile/package\"";
Event e = EventBuilder.withBody(msg.getBytes());
channel.put(e);
tx.commit();
tx.close();
sink.process();
sink.stop();
DB db = mongo.getDB("test_wrap");
DBCollection collection = db.getCollection("test_log");
DBCursor cursor = collection.find(new BasicDBObject(MongoSink.DEFAULT_WRAP_FIELD, msg));
assertTrue(cursor.hasNext());
DBObject dbObject = cursor.next();
assertNotNull(dbObject);
assertEquals(dbObject.get(MongoSink.DEFAULT_WRAP_FIELD), msg);
mongo.dropDatabase("test_wrap");
}
@Test(groups = "dev")
public void sinkSingleModelTest() throws EventDeliveryException {
ctx.put(MongoSink.MODEL, MongoSink.CollectionModel.single.name());
MongoSink sink = new MongoSink();
Configurables.configure(sink, ctx);
sink.setChannel(channel);
sink.start();
Transaction tx = channel.getTransaction();
tx.begin();
JSONObject msg = new JSONObject();
msg.put("name", "test");
msg.put("age", 11);
msg.put("birthday", new Date().getTime());
Event e = EventBuilder.withBody(msg.toJSONString().getBytes());
channel.put(e);
tx.commit();
tx.close();
sink.process();
sink.stop();
DB db = mongo.getDB("test_events");
DBCollection collection = db.getCollection("test_log");
DBCursor cursor = collection.find(new BasicDBObject(msg));
assertTrue(cursor.hasNext());
DBObject dbObject = cursor.next();
assertNotNull(dbObject);
assertEquals(dbObject.get("name"), msg.get("name"));
assertEquals(dbObject.get("age"), msg.get("age"));
assertEquals(dbObject.get("birthday"), msg.get("birthday"));
}
/**
* Returns an object containing basic information about the execution of the query that created
* this cursor This creates a <code>DBObject</code> with the key/value pairs: "cursor" : cursor
* type "nScanned" : number of records examined by the database for this query "n" : the number of
* records that the database returned "millis" : how long it took the database to execute the
* query
*
* @return a <code>DBObject</code>
* @dochub explain
*/
public DBObject explain() {
DBCursor c = copy();
c._explain = true;
if (c._limit > 0) {
// need to pass a negative batchSize as limit for explain
c._batchSize = c._limit * -1;
c._limit = 0;
}
return c.next();
}
@Test(groups = "dev")
public void timestampExistingFieldTest() throws EventDeliveryException, ParseException {
ctx.put(MongoSink.MODEL, MongoSink.CollectionModel.dynamic.name());
String tsField = "createdOn";
ctx.put(MongoSink.TIMESTAMP_FIELD, tsField);
MongoSink sink = new MongoSink();
Configurables.configure(sink, ctx);
sink.setChannel(channel);
sink.start();
JSONObject msg = new JSONObject();
msg.put("age", 11);
msg.put("birthday", new Date().getTime());
String dateText = "2013-02-19T14:20:53+08:00";
msg.put(tsField, dateText);
Transaction tx;
for (int i = 0; i < 10; i++) {
tx = channel.getTransaction();
tx.begin();
msg.put("name", "test" + i);
JSONObject header = new JSONObject();
header.put(MongoSink.COLLECTION, "my_events");
header.put(MongoSink.DB_NAME, "dynamic_db");
Event e = EventBuilder.withBody(msg.toJSONString().getBytes(), header);
channel.put(e);
tx.commit();
tx.close();
}
sink.process();
sink.stop();
msg.put(tsField, MongoSink.dateTimeFormatter.parseDateTime(dateText).toDate());
for (int i = 0; i < 10; i++) {
msg.put("name", "test" + i);
System.out.println("i = " + i);
DB db = mongo.getDB("dynamic_db");
DBCollection collection = db.getCollection("my_events");
DBCursor cursor = collection.find(new BasicDBObject(msg));
assertTrue(cursor.hasNext());
DBObject dbObject = cursor.next();
assertNotNull(dbObject);
assertEquals(dbObject.get("name"), msg.get("name"));
assertEquals(dbObject.get("age"), msg.get("age"));
assertEquals(dbObject.get("birthday"), msg.get("birthday"));
assertTrue(dbObject.get(tsField) instanceof Date);
System.out.println("ts = " + dbObject.get(tsField));
}
}
public Collection<SpaceTypeDescriptor> loadMetadata() {
DBCollection metadata = getCollection(METADATA_COLLECTION_NAME);
DBCursor cursor = metadata.find(new BasicDBObject());
while (cursor.hasNext()) {
DBObject type = cursor.next();
Object b = type.get(TYPE_DESCRIPTOR_FIELD_NAME);
readMetadata(b);
}
return getSortedTypes();
}
@Test(groups = "dev")
public void sinkDynamicDbTest() throws EventDeliveryException {
ctx.put(MongoSink.MODEL, MongoSink.CollectionModel.dynamic.name());
MongoSink sink = new MongoSink();
Configurables.configure(sink, ctx);
sink.setChannel(channel);
sink.start();
JSONObject msg = new JSONObject();
msg.put("age", 11);
msg.put("birthday", new Date().getTime());
Transaction tx;
for (int i = 0; i < 10; i++) {
tx = channel.getTransaction();
tx.begin();
msg.put("name", "test" + i);
JSONObject header = new JSONObject();
header.put(MongoSink.COLLECTION, "my_events");
header.put(MongoSink.DB_NAME, "dynamic_db");
Event e = EventBuilder.withBody(msg.toJSONString().getBytes(), header);
channel.put(e);
tx.commit();
tx.close();
}
sink.process();
sink.stop();
for (int i = 0; i < 10; i++) {
msg.put("name", "test" + i);
System.out.println("i = " + i);
DB db = mongo.getDB("dynamic_db");
DBCollection collection = db.getCollection("my_events");
DBCursor cursor = collection.find(new BasicDBObject(msg));
assertTrue(cursor.hasNext());
DBObject dbObject = cursor.next();
assertNotNull(dbObject);
assertEquals(dbObject.get("name"), msg.get("name"));
assertEquals(dbObject.get("age"), msg.get("age"));
assertEquals(dbObject.get("birthday"), msg.get("birthday"));
}
}
/**
* Creates a copy of an existing database cursor. The new cursor is an iterator, even if the
* original was an array.
*
* @return the new cursor
*/
public DBCursor copy() {
DBCursor c = new DBCursor(_collection, _query, _keysWanted, _readPref);
c._orderBy = _orderBy;
c._hint = _hint;
c._hintDBObj = _hintDBObj;
c._limit = _limit;
c._skip = _skip;
c._options = _options;
c._batchSize = _batchSize;
c._snapshot = _snapshot;
c._explain = _explain;
if (_specialFields != null) c._specialFields = new BasicDBObject(_specialFields.toMap());
return c;
}
public TaskWrite(Map map1, Map m_max, Map m_min, DBCollection coll, ModbusSlaveSet slave) {
try {
synchronized (slave) {
Calendar calener = Calendar.getInstance();
Date d1 = calener.getTime();
Date d2 = new Date(calener.getTime().getTime() - 5000);
BasicDBObject b2 = new BasicDBObject();
b2.put("$gte", d2);
b2.put("$lte", d1);
DBCursor cursor =
coll.find(new BasicDBObject("_id", b2)).sort(new BasicDBObject("_id", -1)).limit(1);
while (cursor.hasNext()) {
DBObject dbo = cursor.next();
Set set1 = map1.entrySet();
Iterator it1 = set1.iterator();
while (it1.hasNext()) {
Map.Entry<String, Map<String, String>> entry =
(Map.Entry<String, Map<String, String>>) it1.next();
Map<String, String> map2 = entry.getValue();
for (Iterator it2 = map2.entrySet().iterator(); it2.hasNext(); ) {
Map.Entry<String, String> entry2 = (Map.Entry<String, String>) it2.next();
String name = entry2.getKey().toString();
String paramAddr = entry2.getValue().toString();
int fun = (int) (Double.parseDouble(paramAddr));
if (paramAddr.substring(0, 1).equals("4")) {
double value = Double.parseDouble(dbo.get(name).toString());
double dmax = (Double) m_max.get(name);
double dmin = (Double) m_min.get(name);
double dValue = 0;
if (value > dmax || value < dmin) {
if (value >= 0) {
dValue = 32000 * (int) (value / dmax);
}
if (value < 0) {
dValue = -32000 * (int) (value / dmin);
}
// slave.getProcessImage(3).setInputRegister(fun % 10000, (short) dValue);
} else { /// 参数超限报警
JOptionPane.showMessageDialog(null, "参数超限");
slave.stop();
}
}
if (paramAddr.substring(0, 1).equals("3")) {
double value = Double.parseDouble(dbo.get(name).toString());
double dmax = (Double) m_max.get(name);
double dmin = (Double) m_min.get(name);
double dValue = 0;
if (value > dmax || value < dmin) {
if (value >= 0) {
dValue = 32000 * (int) (value / dmax);
}
if (value < 0) {
dValue = -32000 * (int) (value / dmin);
}
// slave.getProcessImage(3).setHoldingRegister(fun % 10000, (short) dValue);
} else { /// 参数超限报警
JOptionPane.showMessageDialog(null, "参数超限");
slave.stop();
}
;
}
if (paramAddr.substring(0, 1).equals("2")) {
String value = dbo.get(name).toString();
/// slave.getProcessImage(4).setInput(fun % 10000, Boolean.valueOf(value));
}
if (paramAddr.substring(0, 1).equals("1")) {
String value = dbo.get(name).toString();
// slave.getProcessImage(4).setCoil(fun % 10000, Boolean.valueOf(value));
}
}
}
}
}
} catch (Exception ex) {
}
}
public void receiveData(
String ip,
String paramName,
String paramNo,
int paramBote,
int paramLength,
int parmParity,
int parmStopBit,
int parmDelay) {
try {
try {
m = new Mongo(ip, 27017);
db = m.getDB(paramName);
// db.authenticate("test", "123".toCharArray());
} catch (UnknownHostException ex) {
ex.printStackTrace();
} catch (MongoException e) {
e.printStackTrace();
}
final DBCollection coll = db.getCollection("DATAIN");
final DBCollection collout = db.getCollection("DATAOUT");
DBCollection meta = db.getCollection("META");
// 记录数据字段
final Map map1 = new HashMap();
final Map map2 = new HashMap();
Map map00 = new HashMap();
Map map01 = new HashMap();
Map map02 = new HashMap();
Map map03 = new HashMap();
final Map m_ai_max = new HashMap();
final Map m_ai_min = new HashMap();
final Map m_ao_max = new HashMap();
final Map m_ao_min = new HashMap();
DBCursor cursor = meta.find();
while (cursor.hasNext()) {
// 记录数据类型
DBObject dbo = cursor.next();
String name = dbo.get("_id").toString();
String type = dbo.get("type").toString();
String addr = dbo.get("addr").toString();
Double max = (Double) dbo.get("max");
Double min = (Double) dbo.get("min");
if (type.equals("AI")) {
map00.put(name, addr);
m_ai_max.put(name, max);
m_ai_min.put(name, min);
}
if (type.equals("DI")) {
map01.put(name, addr);
}
if (type.equals("AO")) {
map02.put(name, addr);
}
if (type.equals("DO")) {
map03.put(name, addr);
}
}
map1.put("AI", map00);
map1.put("DI", map01);
map2.put("AO", map02);
map2.put("DO", map03);
SerialParameters params = new SerialParameters();
params.setCommPortId(paramNo);
params.setBaudRate(paramBote);
params.setDataBits(paramLength);
params.setParity(parmParity);
params.setStopBits(parmStopBit);
ModbusFactory modbusFactory = new ModbusFactory();
slave = modbusFactory.createRtuSlave(params);
slave.addProcessImage(getModscanProcessImage(1, map00, coll));
slave.addProcessImage(getModscanProcessImage(2, map01, coll));
slave.addProcessImage(getModscanProcessImage(3, map02, collout));
slave.addProcessImage(getModscanProcessImage(4, map03, collout));
new Thread(
new Runnable() {
public void run() {
try {
slave.start();
// JOptionPane.showMessageDialog(f, "通讯连接成功！");
} catch (ModbusInitException e) {
e.printStackTrace();
}
}
})
.start();
ScheduledExecutorService timerRead = Executors.newScheduledThreadPool(1);
timerRead.scheduleAtFixedRate(
new Runnable() {
public void run() {
new TaskRead(map1, m_ai_max, m_ai_min, coll, slave);
}
},
500,
parmDelay,
TimeUnit.MILLISECONDS);
ScheduledExecutorService timerWrite = Executors.newScheduledThreadPool(2);
timerWrite.scheduleAtFixedRate(
new Runnable() {
public void run() {
new TaskWrite(map2, m_ao_max, m_ao_min, collout, slave);
}
},
500,
parmDelay,
TimeUnit.MILLISECONDS);
} catch (Exception ex) {
}
}
public QueryResult<VariantInfo> getRecordsMongo(
int page, int start, int limit, MutableInt count, Map<String, String> options) {
long startTime = System.currentTimeMillis();
QueryResult<VariantInfo> queryResult = new QueryResult<>();
List<VariantInfo> res = new ArrayList<>();
String sourceId = options.get("studyId");
DBCollection coll = db.getCollection("variants");
BasicDBObject elemMatch = new BasicDBObject("sourceId", sourceId);
DBObject query = new BasicDBObject();
BasicDBList orList = new BasicDBList();
Map<String, List<String>> sampleGenotypes = processSamplesGT(options);
System.out.println("map = " + options);
if (options.containsKey("region") && !options.get("region").equals("")) {
String[] regions = options.get("region").split(",");
Pattern pattern = Pattern.compile("(\\w+):(\\d+)-(\\d+)");
Matcher matcher, matcherChr;
for (int i = 0; i < regions.length; i++) {
String region = regions[i];
matcher = pattern.matcher(region);
if (matcher.find()) {
String chr = matcher.group(1);
int s = Integer.valueOf(matcher.group(2));
int e = Integer.valueOf(matcher.group(3));
DBObject regionClause = new BasicDBObject("chr", chr);
regionClause.put("pos", new BasicDBObject("$gte", s).append("$lte", e));
orList.add(regionClause);
} else {
Pattern patternChr = Pattern.compile("(\\w+)");
matcherChr = patternChr.matcher(region);
if (matcherChr.find()) {
String chr = matcherChr.group();
DBObject regionClause = new BasicDBObject("chr", chr);
orList.add(regionClause);
}
}
}
query.put("$or", orList);
} else if (options.containsKey("genes") && !options.get("genes").equals("")) {
orList = processGeneList(options.get("genes"));
if (orList.size() > 0) {
query.put("$or", orList);
} else {
queryResult.setWarningMsg("Wrong gene name");
queryResult.setResult(res);
queryResult.setNumResults(res.size());
return queryResult;
}
}
if (options.containsKey("conseq_type") && !options.get("conseq_type").equals("")) {
String[] cts = options.get("conseq_type").split(",");
BasicDBList ctList = new BasicDBList();
for (String ct : cts) {
ctList.add(ct);
}
elemMatch.put("effects", new BasicDBObject("$in", ctList));
}
if (sampleGenotypes.size() > 0) {
for (Map.Entry<String, List<String>> entry : sampleGenotypes.entrySet()) {
BasicDBList gtList = new BasicDBList();
for (String gt : entry.getValue()) {
gtList.add(gt);
}
elemMatch.put("samples." + entry.getKey() + ".GT", new BasicDBObject("$in", gtList));
}
}
if (options.containsKey("miss_gt") && !options.get("miss_gt").equalsIgnoreCase("")) {
Integer val = Integer.valueOf(options.get("miss_gt"));
Object missGt = getMongoOption(options.get("option_miss_gt"), val);
elemMatch.put("stats.missGenotypes", missGt);
}
BasicDBList andControls = new BasicDBList();
if (options.containsKey("maf_1000g_controls")
&& !options.get("maf_1000g_controls").equalsIgnoreCase("")) {
BasicDBList or = new BasicDBList();
or.add(new BasicDBObject("attributes.1000G_maf", new BasicDBObject("$exists", false)));
or.add(
new BasicDBObject(
"attributes.1000G_maf",
new BasicDBObject("$lte", options.get("maf_1000g_controls"))));
andControls.add(new BasicDBObject("$or", or));
}
if (options.containsKey("maf_1000g_afr_controls")
&& !options.get("maf_1000g_afr_controls").equalsIgnoreCase("")) {
BasicDBList or = new BasicDBList();
or.add(new BasicDBObject("attributes.1000G_AFR_maf", new BasicDBObject("$exists", false)));
or.add(
new BasicDBObject(
"attributes.1000G_AFR_maf",
new BasicDBObject("$lte", options.get("maf_1000g_afr_controls"))));
andControls.add(new BasicDBObject("$or", or));
}
if (options.containsKey("maf_1000g_asi_controls")
&& !options.get("maf_1000g_asi_controls").equalsIgnoreCase("")) {
BasicDBList or = new BasicDBList();
or.add(new BasicDBObject("attributes.1000G_ASI_maf", new BasicDBObject("$exists", false)));
or.add(
new BasicDBObject(
"attributes.1000G_ASI_maf",
new BasicDBObject("$lte", options.get("maf_1000g_asi_controls"))));
andControls.add(new BasicDBObject("$or", or));
}
if (options.containsKey("maf_1000g_eur_controls")
&& !options.get("maf_1000g_eur_controls").equalsIgnoreCase("")) {
System.out.print("EUR");
BasicDBList or = new BasicDBList();
or.add(new BasicDBObject("attributes.1000G_EUR_maf", new BasicDBObject("$exists", false)));
or.add(
new BasicDBObject(
"attributes.1000G_EUR_maf",
new BasicDBObject("$lte", options.get("maf_1000g_eur_controls"))));
andControls.add(new BasicDBObject("$or", or));
}
if (options.containsKey("maf_1000g_ame_controls")
&& !options.get("maf_1000g_ame_controls").equalsIgnoreCase("")) {
System.out.print("AME");
BasicDBList or = new BasicDBList();
or.add(new BasicDBObject("attributes.1000G_AME_maf", new BasicDBObject("$exists", false)));
or.add(
new BasicDBObject(
"attributes.1000G_AME_maf",
new BasicDBObject("$lte", options.get("maf_1000g_ame_controls"))));
andControls.add(new BasicDBObject("$or", or));
}
if (options.containsKey("maf_evs_controls")
&& !options.get("maf_evs_controls").equalsIgnoreCase("")) {
BasicDBList or = new BasicDBList();
or.add(new BasicDBObject("attributes.EVS_maf", new BasicDBObject("$exists", false)));
or.add(
new BasicDBObject(
"attributes.EVS_maf", new BasicDBObject("$lte", options.get("maf_evs_controls"))));
andControls.add(new BasicDBObject("$or", or));
}
if (options.containsKey("maf_bier_controls")
&& !options.get("maf_bier_controls").equalsIgnoreCase("")) {
BasicDBList or = new BasicDBList();
or.add(new BasicDBObject("attributes.BIER_maf", new BasicDBObject("$exists", false)));
or.add(
new BasicDBObject(
"attributes.BIER_maf", new BasicDBObject("$lte", options.get("maf_bier_controls"))));
andControls.add(new BasicDBObject("$or", or));
}
if (andControls.size() > 0) {
elemMatch.append("$and", andControls);
}
query.put("sources", new BasicDBObject("$elemMatch", elemMatch));
System.out.println("#############################");
System.out.println(query);
System.out.println("#############################");
long dbStart = System.currentTimeMillis();
DBObject sort = null;
DBCursor cursor;
if (options.containsKey("sort")) {
sort = getQuerySort(options.get("sort"));
cursor = coll.find(query).sort(sort).skip(start).limit(limit);
} else {
cursor = coll.find(query).skip(start).limit(limit);
}
count.setValue(cursor.count());
queryResult.setDbTime(dbStart - System.currentTimeMillis());
for (DBObject obj : cursor) {
BasicDBObject elem = (BasicDBObject) obj;
VariantInfo vi = new VariantInfo();
VariantStats vs = new VariantStats();
String chr = elem.getString("chr");
int pos = elem.getInt("pos");
vi.setChromosome(chr);
vi.setPosition(pos);
BasicDBList studies = (BasicDBList) elem.get("sources");
Iterator<Object> it = studies.iterator();
while (it.hasNext()) {
BasicDBObject study = (BasicDBObject) it.next();
if (study.getString("sourceId").equalsIgnoreCase(sourceId)) {
BasicDBObject stats = (BasicDBObject) study.get("stats");
String ref = study.getString("ref");
BasicDBList alt = (BasicDBList) study.get("alt");
vi.setRef(ref);
vi.setAlt(Joiner.on(",").join(alt.toArray()));
vs.setMaf((float) stats.getDouble("maf"));
vs.setMgf((float) stats.getDouble("mgf"));
vs.setMafAllele(stats.getString("alleleMaf"));
vs.setMgfAllele(stats.getString("genotypeMaf"));
vs.setMissingAlleles(stats.getInt("missAllele"));
vs.setMissingGenotypes(stats.getInt("missGenotypes"));
vs.setMendelinanErrors(stats.getInt("mendelErr"));
vs.setCasesPercentDominant((float) stats.getDouble("casesPercentDominant"));
vs.setControlsPercentDominant((float) stats.getDouble("controlsPercentDominant"));
vs.setCasesPercentRecessive((float) stats.getDouble("casesPercentRecessive"));
vs.setControlsPercentRecessive((float) stats.getDouble("controlsPercentRecessive"));
BasicDBObject samples = (BasicDBObject) study.get("samples");
for (String sampleName : samples.keySet()) {
DBObject sample = (DBObject) samples.get(sampleName);
if (sample.containsField("GT")) {
String sampleGT = (String) sample.get("GT");
vi.addSammpleGenotype(sampleName, sampleGT);
}
}
vi.setSnpid((String) study.get("snpId"));
if (study.containsField("effects")) {
BasicDBList conseqTypes = (BasicDBList) study.get("effects");
conseqTypes.remove("");
String cts = Joiner.on(",").join(conseqTypes.iterator());
vi.addConsequenceTypes(cts);
}
if (study.containsField("genes")) {
BasicDBList genesList = (BasicDBList) study.get("genes");
String genes = Joiner.on(",").join(genesList.iterator());
vi.addGenes(genes);
}
if (study.containsField("attributes")) {
BasicDBObject attr = (BasicDBObject) study.get("attributes");
if (attr.containsField("1000G_maf")) {
vi.addControl("1000G_maf", (String) attr.get("1000G_maf"));
vi.addControl("1000G_amaf", (String) attr.get("1000G_amaf"));
vi.addControl("1000G_gt", (String) attr.get("1000G_gt"));
}
if (attr.containsField("1000G_ASI_maf")) {
vi.addControl("1000G-ASI_maf", (String) attr.get("1000G_ASI_maf"));
vi.addControl("1000G-ASI_amaf", (String) attr.get("1000G_ASI_amaf"));
vi.addControl("1000G-ASI_gt", (String) attr.get("1000G_ASI_gt"));
}
if (attr.containsField("1000G_AFR_maf")) {
vi.addControl("1000G-AFR_maf", (String) attr.get("1000G_AFR_maf"));
vi.addControl("1000G-AFR_amaf", (String) attr.get("1000G_AFR_amaf"));
vi.addControl("1000G-AFR_gt", (String) attr.get("1000G_AFR_gt"));
}
if (attr.containsField("1000G_AME_maf")) {
vi.addControl("1000G-AME_maf", (String) attr.get("1000G_AME_maf"));
vi.addControl("1000G-AME_amaf", (String) attr.get("1000G_AME_amaf"));
vi.addControl("1000G-AME_gt", (String) attr.get("1000G_AME_gt"));
}
if (attr.containsField("1000G_EUR_maf")) {
vi.addControl("1000G-EUR_maf", (String) attr.get("1000G_EUR_maf"));
vi.addControl("1000G-EUR_amaf", (String) attr.get("1000G_EUR_amaf"));
vi.addControl("1000G-EUR_gt", (String) attr.get("1000G_EUR_gt"));
}
if (attr.containsField("EVS_maf")) {
vi.addControl("EVS_maf", (String) attr.get("EVS_maf"));
vi.addControl("EVS_amaf", (String) attr.get("EVS_amaf"));
vi.addControl("EVS_gt", (String) attr.get("EVS_gt"));
}
if (attr.containsField("BIER_maf")) {
vi.addControl("BIER_maf", (String) attr.get("BIER_maf"));
vi.addControl("BIER_amaf", (String) attr.get("BIER_amaf"));
vi.addControl("BIER_gt", (String) attr.get("BIER_gt"));
}
if (attr.containsField("PolyphenScore")) {
vi.setPolyphen_score(Double.parseDouble(attr.getString("PolyphenScore")));
vi.setPolyphen_effect(Integer.parseInt(attr.getString("PolyphenEffect")));
}
if (attr.containsField("SIFTScore")) {
vi.setSift_score(Double.parseDouble(attr.getString("SIFTScore")));
vi.setSift_effect(Integer.parseInt(attr.getString("SIFTEffect")));
}
}
continue;
}
}
vi.addStats(vs);
res.add(vi);
}
queryResult.setResult(res);
queryResult.setTime(startTime - System.currentTimeMillis());
return queryResult;
}
@Override
public QueryResult getVariantsHistogramByRegion(
Region region, String sourceId, boolean histogramLogarithm, int histogramMax) {
QueryResult<ObjectMap> queryResult =
new QueryResult<>(
String.format("%s:%d-%d", region.getChromosome(), region.getStart(), region.getEnd()));
List<ObjectMap> data = new ArrayList<>();
String startRow = buildRowkey(region.getChromosome(), Long.toString(region.getStart()));
String stopRow = buildRowkey(region.getChromosome(), Long.toString(region.getEnd()));
long startTime = System.currentTimeMillis();
long startDbTime = System.currentTimeMillis();
BasicDBObject query =
new BasicDBObject("position", new BasicDBObject("$gte", startRow).append("$lte", stopRow))
.append("studies.studyId", sourceId);
DBCollection collection = db.getCollection("variants");
DBCursor queryResults = collection.find(query);
queryResult.setDbTime(System.currentTimeMillis() - startDbTime);
int resultSize = queryResults.size();
if (resultSize > histogramMax) { // Need to group results to fit maximum size of the histogram
int sumChunkSize = resultSize / histogramMax;
int i = 0, j = 0;
int featuresCount = 0;
ObjectMap item = null;
for (DBObject result : queryResults) {
// featuresCount += result.getInt("features_count");
// if (i == 0) {
// item = new ObjectMap("chromosome", result.getString("chromosome"));
// item.put("chunkId", result.getInt("chunk_id"));
// item.put("start", result.getInt("start"));
// } else if (i == sumChunkSize - 1 || j == resultSize - 1) {
// if (histogramLogarithm) {
// item.put("featuresCount", (featuresCount > 0) ?
// Math.log(featuresCount) : 0);
// } else {
// item.put("featuresCount", featuresCount);
// }
// item.put("end", result.getInt("end"));
// data.add(item);
// i = -1;
// featuresCount = 0;
// }
// j++;
// i++;
}
} else {
for (DBObject result : queryResults) {
// ObjectMap item = new ObjectMap("chromosome",
// result.getString("chromosome"));
// item.put("chunkId", result.getInt("chunk_id"));
// item.put("start", result.getInt("start"));
// if (histogramLogarithm) {
// int features_count = result.getInt("features_count");
// result.put("featuresCount", (features_count > 0) ?
// Math.log(features_count) : 0);
// } else {
// item.put("featuresCount", result.getInt("features_count"));
// }
// item.put("end", result.getInt("end"));
// data.add(item);
}
}
queryResult.setResult(data);
queryResult.setNumResults(data.size());
queryResult.setTime(System.currentTimeMillis() - startTime);
return queryResult;
}