예제 #1
0
  @Override
  public void setOwner(ORecord owner) {
    if (owner != null && this.owner != null && !this.owner.equals(owner)) {
      throw new IllegalStateException(
          "This data structure is owned by document "
              + owner
              + " if you want to use it in other document create new rid bag instance and copy content of current one.");
    }
    if (this.owner != null) {
      for (OIdentifiable entry : newEntries.keySet()) {
        ORecordInternal.unTrack(this.owner, entry);
      }
      for (OIdentifiable entry : changes.keySet()) {
        ORecordInternal.unTrack(this.owner, entry);
      }
    }

    this.owner = owner;
    if (this.owner != null) {
      for (OIdentifiable entry : newEntries.keySet()) {
        ORecordInternal.track(this.owner, entry);
      }
      for (OIdentifiable entry : changes.keySet()) {
        ORecordInternal.track(this.owner, entry);
      }
    }
  }
  public void testForwardIteration() throws IOException {
    final int records = 10000;

    long seed = System.currentTimeMillis();
    MersenneTwisterFast mersenneTwisterFast = new MersenneTwisterFast(seed);
    System.out.println("testForwardIteration seed : " + seed);

    NavigableMap<OClusterPosition, byte[]> positionRecordMap = new TreeMap<OClusterPosition, byte[]>();

    ORecordVersion recordVersion = OVersionFactory.instance().createVersion();
    recordVersion.increment();
    recordVersion.increment();

    for (int i = 0; i < records; i++) {
      int recordSize = mersenneTwisterFast.nextInt(2 * OClusterPage.MAX_RECORD_SIZE) + 1;
      byte[] record = new byte[recordSize];
      mersenneTwisterFast.nextBytes(record);

      final OPhysicalPosition physicalPosition = paginatedCluster.createRecord(record, recordVersion, (byte) 2);
      positionRecordMap.put(physicalPosition.clusterPosition, record);
    }

    Iterator<OClusterPosition> positionIterator = positionRecordMap.keySet().iterator();
    while (positionIterator.hasNext()) {
      OClusterPosition clusterPosition = positionIterator.next();
      if (mersenneTwisterFast.nextBoolean()) {
        Assert.assertTrue(paginatedCluster.deleteRecord(clusterPosition));
        positionIterator.remove();
      }
    }

    OPhysicalPosition physicalPosition = new OPhysicalPosition();
    physicalPosition.clusterPosition = OClusterPositionFactory.INSTANCE.valueOf(0);

    OPhysicalPosition[] positions = paginatedCluster.ceilingPositions(physicalPosition);
    Assert.assertTrue(positions.length > 0);

    int counter = 0;
    for (OClusterPosition testedPosition : positionRecordMap.keySet()) {
      Assert.assertTrue(positions.length > 0);
      Assert.assertEquals(positions[0].clusterPosition, testedPosition);

      OPhysicalPosition positionToFind = positions[0];
      positions = paginatedCluster.higherPositions(positionToFind);

      counter++;
    }

    Assert.assertEquals(paginatedCluster.getEntries(), counter);

    Assert.assertEquals(paginatedCluster.getFirstPosition(), positionRecordMap.firstKey());
    Assert.assertEquals(paginatedCluster.getLastPosition(), positionRecordMap.lastKey());
  }
예제 #3
0
  @Override
  public Set<Element> get(Object key) {
    Get get = new Get(ByteArraySerializer.fromObject(key));
    Result result;
    try {
      result = backingTable.get(get);
    } catch (IOException e) {
      LOG.severe("Cannot get from backing table");
      e.printStackTrace();
      return null;
    }

    NavigableMap<byte[], byte[]> map = result.getFamilyMap(Bytes.toBytes(VALUES));
    if (null == map) return null;

    HashSet<Element> elementHashSet = new HashSet<Element>();

    for (byte[] byteArray : map.keySet()) {

      if (indexClass.equals(HVertex.class) || indexClass.equals(Vertex.class)) {
        HVertex hVertex = new HVertex(hGraph);
        hVertex.setId(byteArray);
        elementHashSet.add(hVertex);
      } else {
        final HEdge hEdge = new HEdge(hGraph);
        hEdge.setId(byteArray);
        elementHashSet.add(hEdge);
      }
    }

    return elementHashSet;
  }
예제 #4
0
  /**
   * Save the state of the {@code TreeSet} instance to a stream (that is, serialize it).
   *
   * @serialData Emits the comparator used to order this set, or {@code null} if it obeys its
   *     elements' natural ordering (Object), followed by the size of the set (the number of
   *     elements it contains) (int), followed by all of its elements (each an Object) in order (as
   *     determined by the set's Comparator, or by the elements' natural ordering if the set has no
   *     Comparator).
   */
  private void writeObject(java.io.ObjectOutputStream s) throws java.io.IOException {
    // Write out any hidden stuff
    s.defaultWriteObject();

    // Write out Comparator
    s.writeObject(m.comparator());

    // Write out size
    s.writeInt(m.size());

    // Write out all elements in the proper order.
    for (Iterator i = m.keySet().iterator(); i.hasNext(); ) s.writeObject(i.next());
  }
예제 #5
0
 @Override
 public Set<String> keySet() {
   return configMap.keySet();
 }
예제 #6
0
 private int getChangesSerializedSize() {
   Set<OIdentifiable> changedIds = new HashSet<OIdentifiable>(changes.keySet());
   changedIds.addAll(newEntries.keySet());
   return ChangeSerializationHelper.INSTANCE.getChangesSerializedSize(changedIds.size());
 }
  @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;
  }
  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;
  }
예제 #9
0
 /**
  * Returns an Iterator on the elements of this {@code TreeSet}.
  *
  * @return an Iterator on the elements of this {@code TreeSet}.
  * @see Iterator
  */
 @Override
 public Iterator<E> iterator() {
   return backingMap.keySet().iterator();
 }