private void removeIfPresent(Mutation m, byte[] family, byte[] qualifier) {
Map<byte[], List<KeyValue>> familyMap = m.getFamilyMap();
List<KeyValue> kvs = familyMap.get(family);
if (kvs != null) {
Iterator<KeyValue> iterator = kvs.iterator();
while (iterator.hasNext()) {
KeyValue kv = iterator.next();
if (Bytes.compareTo(kv.getQualifier(), qualifier) == 0) {
iterator.remove();
}
}
}
}
public HBaseStoreManager(org.apache.commons.configuration.Configuration config)
throws StorageException {
super(config, PORT_DEFAULT);
this.tableName = config.getString(TABLE_NAME_KEY, TABLE_NAME_DEFAULT);
this.hconf = HBaseConfiguration.create();
for (Map.Entry<String, String> confEntry : HBASE_CONFIGURATION.entrySet()) {
if (config.containsKey(confEntry.getKey())) {
hconf.set(confEntry.getValue(), config.getString(confEntry.getKey()));
}
}
// Copy a subset of our commons config into a Hadoop config
org.apache.commons.configuration.Configuration hbCommons =
config.subset(HBASE_CONFIGURATION_NAMESPACE);
@SuppressWarnings("unchecked") // I hope commons-config eventually fixes this
Iterator<String> keys = hbCommons.getKeys();
int keysLoaded = 0;
while (keys.hasNext()) {
String key = keys.next();
String value = hbCommons.getString(key);
logger.debug("HBase configuration: setting {}={}", key, value);
hconf.set(key, value);
keysLoaded++;
}
logger.debug("HBase configuration: set a total of {} configuration values", keysLoaded);
connectionPool = new HTablePool(hconf, connectionPoolSize);
openStores = new ConcurrentHashMap<String, HBaseKeyColumnValueStore>();
// TODO: allowing publicly mutate fields is bad, should be fixed
features = new StoreFeatures();
features.supportsScan = true;
features.supportsBatchMutation = true;
features.supportsTransactions = false;
features.supportsConsistentKeyOperations = true;
features.supportsLocking = false;
features.isKeyOrdered = false;
features.isDistributed = true;
features.hasLocalKeyPartition = false;
}
public List<Variant> getRecordSimpleStats(
String study, int missing_gt, float maf, String maf_allele) {
BasicDBObject compare =
new BasicDBObject("studies.stats.allele_maf", maf_allele)
.append("studies.stats.MAF", maf)
.append("studies.stats.missing", missing_gt);
List<Get> hbaseQuery = new ArrayList<>();
DBCollection collection = db.getCollection("variants");
Iterator<DBObject> result = collection.find(compare);
String chromosome = new String();
while (result.hasNext()) {
DBObject variant = result.next();
String position = variant.get("_id").toString();
// hbase query construction
Get get = new Get(position.getBytes());
hbaseQuery.add(get);
}
// Complete results, from HBase
tableName = study;
effectTableName = tableName + "effect";
Map<String, Variant> resultsMap = new HashMap<>();
try {
HTable table = new HTable(admin.getConfiguration(), tableName);
HTable effectTable = new HTable(admin.getConfiguration(), effectTableName);
Result[] hbaseResultEffect = effectTable.get(hbaseQuery);
Result[] hbaseResultStats = table.get(hbaseQuery);
// List<Variant> results = new LinkedList<>();
for (Result r : hbaseResultStats) {
String position = new String(r.getRow(), CHARSET_UTF_8);
String[] aux = position.split("_");
String inner_position = aux[1];
String chr = aux[0];
// position parsing
if (chr.startsWith("0")) {
chr = chr.substring(1);
}
while (inner_position.startsWith("0")) {
inner_position = inner_position.substring(1);
}
List<VariantFieldsProtos.VariantSample> samples = new LinkedList<>();
NavigableMap<byte[], byte[]> infoMap = r.getFamilyMap("i".getBytes());
byte[] byteStats = infoMap.get((study + "_stats").getBytes());
VariantFieldsProtos.VariantStats stats =
VariantFieldsProtos.VariantStats.parseFrom(byteStats);
byte[] byteInfo = infoMap.get((study + "_data").getBytes());
VariantFieldsProtos.VariantInfo info = VariantFieldsProtos.VariantInfo.parseFrom(byteInfo);
String alternate = StringUtils.join(info.getAlternateList(), ", ");
String reference = info.getReference();
Variant partialResult =
new Variant(
chr,
Integer.parseInt(inner_position),
Integer.parseInt(inner_position),
reference,
alternate);
String format = StringUtils.join(info.getFormatList(), ":");
NavigableMap<byte[], byte[]> sampleMap = r.getFamilyMap("d".getBytes());
Map<String, Map<String, String>> resultSampleMap = new HashMap<>();
// StringBuilder sampleRaw = new StringBuilder();
for (byte[] s : sampleMap.keySet()) {
String qual = (new String(s, CHARSET_UTF_8)).replaceAll(study + "_", "");
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]);
}
resultSampleMap.put(qual, singleSampleMap);
}
VariantStats variantStats =
new VariantStats(
chromosome,
Integer.parseInt(inner_position),
reference,
alternate,
stats.getMaf(),
stats.getMgf(),
stats.getMafAllele(),
stats.getMgfGenotype(),
stats.getMissingAlleles(),
stats.getMissingGenotypes(),
stats.getMendelianErrors(),
stats.getIsIndel(),
stats.getCasesPercentDominant(),
stats.getControlsPercentDominant(),
stats.getCasesPercentRecessive(),
stats.getControlsPercentRecessive());
partialResult.setStats(variantStats);
resultsMap.put(new String(r.getRow(), CHARSET_UTF_8), partialResult);
}
for (Result r : hbaseResultEffect) {
if (!r.isEmpty()) {
NavigableMap<byte[], byte[]> effectMap = r.getFamilyMap("e".getBytes());
Variant partialResult = resultsMap.get(new String(r.getRow(), CHARSET_UTF_8));
System.out.println("Recuperado " + partialResult.toString());
String s = partialResult.getReference() + "_" + partialResult.getAlternate();
VariantEffectProtos.EffectInfo effectInfo =
VariantEffectProtos.EffectInfo.parseFrom(effectMap.get(s.getBytes()));
VariantEffect variantEffect =
new VariantEffect(
partialResult.getChromosome(),
(int) partialResult.getStart(),
partialResult.getReference(),
partialResult.getAlternate(),
effectInfo.getFeatureId(),
effectInfo.getFeatureName(),
effectInfo.getFeatureType(),
effectInfo.getFeatureBiotype(),
effectInfo.getFeatureChromosome(),
effectInfo.getFeatureStart(),
effectInfo.getFeatureEnd(),
effectInfo.getFeatureStrand(),
effectInfo.getSnpId(),
effectInfo.getAncestral(),
effectInfo.getAlternative(),
effectInfo.getGeneId(),
effectInfo.getTranscriptId(),
effectInfo.getGeneName(),
effectInfo.getConsequenceType(),
effectInfo.getConsequenceTypeObo(),
effectInfo.getConsequenceTypeDesc(),
effectInfo.getConsequenceTypeType(),
effectInfo.getAaPosition(),
effectInfo.getAminoacidChange(),
effectInfo.getCodonChange());
resultsMap.put(new String(r.getRow(), CHARSET_UTF_8), partialResult);
}
}
} catch (InvalidProtocolBufferException e) {
System.err.println(e.getClass().getName() + ": " + e.getMessage());
} catch (IOException e) {
System.err.println(e.getClass().getName() + ": " + e.getMessage());
}
List<Variant> results = new ArrayList<>(resultsMap.values());
return results;
}