// --------------------------------------------------------------------------------
private void verifyData() {
int typeIndex = typeCombo.getSelectionIndex();
if (typeIndex == -1) {
return;
}
String value = valueText.getText();
boolean verified = false;
switch (typeIndex) {
case 0: // Double
try {
Double.parseDouble(value);
verified = true;
} catch (Exception e) {
}
break;
case 1: // Integer
try {
Integer.parseInt(value);
verified = true;
} catch (Exception e) {
}
break;
case 2: // Long
try {
Long.parseLong(value);
verified = true;
} catch (Exception e) {
}
break;
case 3: // String
verified = true;
break;
case 4: // List
try {
Object o = dataManager.getDB().eval(value, null);
if (o instanceof BasicDBList) {
verified = true;
}
} catch (Exception e) {
}
break;
case 5: // Map
try {
Object o = dataManager.getDB().eval(value, null);
if (o instanceof BasicDBObject) {
verified = true;
}
} catch (Exception e) {
}
break;
case 6: // Date
try {
DateFormat df = new SimpleDateFormat("EEE MMM d HH:mm:ss z yyyy", Locale.ENGLISH);
df.parse(value);
verified = true;
} catch (Exception e) {
// e.printStackTrace();
}
break;
case 7: // ObjectId
try {
new ObjectId(value);
verified = true;
} catch (Exception e) {
}
break;
case 8: // Code
verified = true;
break;
case 9: // Binary always false
break;
case 10: // Boolean
if (value.equalsIgnoreCase("true") || value.equalsIgnoreCase("false")) {
verified = true;
}
break;
case 11: // null
if (value.equalsIgnoreCase("null")) {
verified = true;
}
break;
case 12: // Regex
try {
java.util.regex.Pattern.compile(value);
verified = true;
} catch (Exception e) {
}
break;
case 13: // Symbol not supported yet
break;
case 14: // Code with scope not supported yet
break;
case 15: // Timestamp not supported yet
break;
case 16: // Minkey not supported yet
break;
case 17: // Maxkey not supported yet
break;
}
updateButton.setEnabled(verified);
}
public Object objectDone() {
String name = curName();
Object o = super.objectDone();
BSONObject b = (BSONObject) o;
// override the object if it's a special type
if (!_lastArray) {
if (b.containsField("$oid")) {
o = new ObjectId((String) b.get("$oid"));
if (!isStackEmpty()) {
gotObjectId(name, (ObjectId) o);
} else {
setRoot(o);
}
} else if (b.containsField("$date")) {
SimpleDateFormat format = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss.SSS'Z'");
GregorianCalendar calendar = new GregorianCalendar(new SimpleTimeZone(0, "GMT"));
format.setCalendar(calendar);
String txtdate = (String) b.get("$date");
o = format.parse(txtdate, new ParsePosition(0));
if (o == null) {
// try older format with no ms
format = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss'Z'");
format.setCalendar(calendar);
o = format.parse(txtdate, new ParsePosition(0));
}
if (!isStackEmpty()) {
cur().put(name, o);
} else {
setRoot(o);
}
} else if (b.containsField("$regex")) {
o = Pattern.compile((String) b.get("$regex"), BSON.regexFlags((String) b.get("$options")));
if (!isStackEmpty()) {
cur().put(name, o);
} else {
setRoot(o);
}
} else if (b.containsField("$ts")) {
Long ts = ((Number) b.get("$ts")).longValue();
Long inc = ((Number) b.get("$inc")).longValue();
o = new BSONTimestamp(ts.intValue(), inc.intValue());
if (!isStackEmpty()) {
cur().put(name, o);
} else {
setRoot(o);
}
} else if (b.containsField("$code")) {
if (b.containsField("$scope")) {
o = new CodeWScope((String) b.get("$code"), (DBObject) b.get("$scope"));
} else {
o = new Code((String) b.get("$code"));
}
if (!isStackEmpty()) {
cur().put(name, o);
} else {
setRoot(o);
}
} else if (b.containsField("$ref")) {
o = new DBRef(null, (String) b.get("$ref"), b.get("$id"));
if (!isStackEmpty()) {
cur().put(name, o);
} else {
setRoot(o);
}
} else if (b.containsField("$minKey")) {
o = new MinKey();
if (!isStackEmpty()) {
cur().put(name, o);
} else {
setRoot(o);
}
} else if (b.containsField("$maxKey")) {
o = new MaxKey();
if (!isStackEmpty()) {
cur().put(name, o);
} else {
setRoot(o);
}
} else if (b.containsField("$uuid")) {
o = UUID.fromString((String) b.get("$uuid"));
if (!isStackEmpty()) {
cur().put(name, o);
} else {
setRoot(o);
}
}
}
return o;
}
public QueryResult getSimpleVariantsByRegion(
Region region, String sourceId, QueryOptions options) {
Long start, end, dbstart, dbend;
start = System.currentTimeMillis();
boolean includeStats;
boolean includeEffects;
if (!options.containsKey("stats") && !options.containsKey("effects")) {
includeStats = true;
includeEffects = true;
} else {
includeStats = options.containsKey("stats") && options.getBoolean("stats");
includeEffects = options.containsKey("effects") && options.getBoolean("effects");
}
QueryResult<Variant> queryResult =
new QueryResult<>(
String.format("%s:%d-%d", region.getChromosome(), region.getStart(), region.getEnd()));
List<Variant> results = new ArrayList<>();
String startRow = buildRowkey(region.getChromosome(), Long.toString(region.getStart()));
String stopRow = buildRowkey(region.getChromosome(), Long.toString(region.getEnd()));
BasicDBObject query =
new BasicDBObject("position", new BasicDBObject("$gte", startRow).append("$lte", stopRow))
.append("sources.sourceId", sourceId);
DBCollection collection = db.getCollection("variants");
dbstart = System.currentTimeMillis();
DBCursor variantInStudies = collection.find(query);
dbend = System.currentTimeMillis();
queryResult.setDbTime(dbend - dbstart);
for (DBObject result : variantInStudies) {
String[] rowkeyParts = result.get("position").toString().split("_");
String chromosome = rowkeyParts[0].replaceFirst("^0+(?!$)", "");
int position = Integer.parseInt(rowkeyParts[1]);
BasicDBList studies = (BasicDBList) result.get("sources");
BasicDBObject st = (BasicDBObject) studies.get(0);
String ref = (String) st.get("ref");
String alt = StringUtils.join((ArrayList<String>) st.get("alt"), ",");
// TODO Needs rework
Variant variant = new Variant(chromosome, position, position, ref, alt);
// Set stats informations
if (includeStats) {
VariantStats stats = new VariantStats();
BasicDBObject mongoStats = (BasicDBObject) st.get("stats");
stats.setMaf((float) (double) mongoStats.get("maf"));
stats.setMafAllele((String) mongoStats.get("alleleMaf"));
stats.setMissingGenotypes((int) mongoStats.get("missing"));
List<Genotype> genotypeCount = new ArrayList<>();
for (BasicDBObject s : (List<BasicDBObject>) mongoStats.get("genotypeCount")) {
for (Map.Entry<String, Object> entry : s.entrySet()) {
Genotype genotype = new Genotype(entry.getKey());
genotype.setCount((Integer) entry.getValue());
genotypeCount.add(genotype);
}
}
stats.setGenotypes(genotypeCount);
variant.setStats(stats);
}
// TODO Set consequence type names
if (includeEffects) {
BasicDBList mongoEffects = (BasicDBList) st.get("effects");
if (mongoEffects != null) {
for (Object e : mongoEffects) {
String effectObo = e.toString();
VariantEffect effect = new VariantEffect();
effect.setConsequenceTypeObo(effectObo);
variant.addEffect(effect);
}
}
}
results.add(variant);
}
queryResult.setResult(results);
queryResult.setNumResults(results.size());
end = System.currentTimeMillis();
queryResult.setTime(end - start);
return queryResult;
}
@Override
public QueryResult<Variant> getAllVariantsByRegionAndStudy(
Region region, String sourceId, QueryOptions options) {
Long start, end, dbstart, dbend;
start = System.currentTimeMillis();
QueryResult<Variant> queryResult =
new QueryResult<>(
String.format("%s:%d-%d", region.getChromosome(), region.getStart(), region.getEnd()));
List<Variant> results = new LinkedList<>();
boolean includeSamples;
boolean includeStats;
boolean includeEffects;
if (!options.containsKey("samples")
&& !options.containsKey("stats")
&& !options.containsKey("effects")) {
includeSamples = true;
includeStats = true;
includeEffects = true;
} else {
includeSamples = options.containsKey("samples") && options.getBoolean("samples");
includeStats = options.containsKey("stats") && options.getBoolean("stats");
includeEffects = options.containsKey("effects") && options.getBoolean("effects");
}
try {
String startRow = buildRowkey(region.getChromosome(), Long.toString(region.getStart()));
String stopRow = buildRowkey(region.getChromosome(), Long.toString(region.getEnd()));
HTable table = new HTable(admin.getConfiguration(), tableName);
dbstart = System.currentTimeMillis();
Scan regionScan = new Scan(startRow.getBytes(), stopRow.getBytes());
ResultScanner scanres = table.getScanner(regionScan);
dbend = System.currentTimeMillis();
queryResult.setDbTime(dbend - dbstart);
// Iterate over results and, optionally, their samples and statistics
for (Result result : scanres) {
String[] rowkeyParts = new String(result.getRow(), CHARSET_UTF_8).split("_");
String chromosome = rowkeyParts[0].replaceFirst("^0+(?!$)", "");
int position = Integer.parseInt(rowkeyParts[1]);
// Get basic result fields from Protocol Buffers message
NavigableMap<byte[], byte[]> infoMap = result.getFamilyMap("i".getBytes());
byte[] byteInfo = infoMap.get((sourceId + "_data").getBytes());
VariantFieldsProtos.VariantInfo protoInfo =
VariantFieldsProtos.VariantInfo.parseFrom(byteInfo);
String reference = protoInfo.getReference();
String alternate = StringUtils.join(protoInfo.getAlternateList(), ",");
String format = StringUtils.join(protoInfo.getFormatList(), ":");
Variant variant = new Variant(chromosome, position, position, reference, alternate);
// Set samples if requested
if (includeSamples) {
NavigableMap<byte[], byte[]> sampleMap = result.getFamilyMap("d".getBytes());
Map<String, Map<String, String>> resultSampleMap = new HashMap<>();
// Set samples
for (byte[] s : sampleMap.keySet()) {
String sampleName = (new String(s, CHARSET_UTF_8)).replaceAll(sourceId + "_", "");
VariantFieldsProtos.VariantSample sample =
VariantFieldsProtos.VariantSample.parseFrom(sampleMap.get(s));
String sample1 = sample.getSample();
String[] values = sample1.split(":");
String[] fields = format.split(":");
Map<String, String> singleSampleMap = new HashMap<>();
for (int i = 0; i < fields.length; i++) {
singleSampleMap.put(fields[i], values[i]);
}
// TODO
// variant.addSampleData(sampleName, singleSampleMap);
}
}
// Set stats if requested
if (includeStats) {
byte[] byteStats = infoMap.get((sourceId + "_stats").getBytes());
VariantFieldsProtos.VariantStats protoStats =
VariantFieldsProtos.VariantStats.parseFrom(byteStats);
VariantStats variantStats =
new VariantStats(
chromosome,
position,
reference,
alternate,
protoStats.getMaf(),
protoStats.getMgf(),
protoStats.getMafAllele(),
protoStats.getMgfGenotype(),
protoStats.getMissingAlleles(),
protoStats.getMissingGenotypes(),
protoStats.getMendelianErrors(),
protoStats.getIsIndel(),
protoStats.getCasesPercentDominant(),
protoStats.getControlsPercentDominant(),
protoStats.getCasesPercentRecessive(),
protoStats.getControlsPercentRecessive());
variant.setStats(variantStats);
}
if (includeEffects) {
QueryResult<VariantEffect> queryEffects = getEffectsByVariant(variant, options);
variant.setEffect(queryEffects.getResult());
}
results.add(variant);
}
} catch (IOException e) {
System.err.println(e.getClass().getName() + ": " + e.getMessage());
}
queryResult.setResult(results);
queryResult.setNumResults(results.size());
end = System.currentTimeMillis();
queryResult.setTime(end - start);
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;
}
