Example #1
0
  private HTableDescriptor ensureTableExists(String tableName) throws StorageException {
    HBaseAdmin adm = getAdminInterface();

    HTableDescriptor desc;

    try { // Create our table, if necessary
      if (adm.tableExists(tableName)) {
        desc = adm.getTableDescriptor(tableName.getBytes());
      } else {
        desc = new HTableDescriptor(tableName);
        adm.createTable(desc);
      }
    } catch (IOException e) {
      throw new TemporaryStorageException(e);
    }

    return desc;
  }
Example #2
0
  @Override
  public void setConfigurationProperty(final String key, final String value)
      throws StorageException {
    byte[] name = tableName.getBytes();

    HTableDescriptor desc = ensureTableExists(tableName);

    try {
      HBaseAdmin adm = getAdminInterface();

      adm.disableTable(tableName);

      desc.setValue(key, value);

      adm.modifyTable(name, desc);
      adm.enableTable(tableName);
    } catch (IOException e) {
      throw new PermanentStorageException(e);
    }
  }
Example #3
0
  /**
   * Deletes the specified table with all its columns. ATTENTION: Invoking this method will delete
   * the table if it exists and therefore causes data loss.
   */
  @Override
  public void clearStorage() throws StorageException {
    HBaseAdmin adm = getAdminInterface();

    try { // first of all, check if table exists, if not - we are done
      if (!adm.tableExists(tableName)) {
        logger.debug("clearStorage() called before table {} was created, skipping.", tableName);
        return;
      }
    } catch (IOException e) {
      throw new TemporaryStorageException(e);
    }

    HTable table = null;

    try {
      table = new HTable(hconf, tableName);

      Scan scan = new Scan();
      scan.setBatch(100);
      scan.setCacheBlocks(false);
      scan.setCaching(2000);

      ResultScanner scanner = null;

      try {
        scanner = table.getScanner(scan);

        for (Result res : scanner) {
          table.delete(new Delete(res.getRow()));
        }
      } finally {
        IOUtils.closeQuietly(scanner);
      }
    } catch (IOException e) {
      throw new TemporaryStorageException(e);
    } finally {
      IOUtils.closeQuietly(table);
    }
  }
Example #4
0
  private void ensureColumnFamilyExists(String tableName, String columnFamily)
      throws StorageException {
    HBaseAdmin adm = getAdminInterface();
    HTableDescriptor desc = ensureTableExists(tableName);

    Preconditions.checkNotNull(desc);

    HColumnDescriptor cf = desc.getFamily(columnFamily.getBytes());

    // Create our column family, if necessary
    if (cf == null) {
      try {
        adm.disableTable(tableName);
        desc.addFamily(
            new HColumnDescriptor(columnFamily).setCompressionType(Compression.Algorithm.GZ));
        adm.modifyTable(tableName.getBytes(), desc);

        try {
          logger.debug(
              "Added HBase ColumnFamily {}, waiting for 1 sec. to propogate.", columnFamily);
          Thread.sleep(1000L);
        } catch (InterruptedException ie) {
          throw new TemporaryStorageException(ie);
        }

        adm.enableTable(tableName);
      } catch (TableNotFoundException ee) {
        logger.error("TableNotFoundException", ee);
        throw new PermanentStorageException(ee);
      } catch (org.apache.hadoop.hbase.TableExistsException ee) {
        logger.debug("Swallowing exception {}", ee);
      } catch (IOException ee) {
        throw new TemporaryStorageException(ee);
      }
    } else { // check if compression was enabled, if not - enable it
      if (cf.getCompressionType() == null
          || cf.getCompressionType() == Compression.Algorithm.NONE) {
        try {
          adm.disableTable(tableName);

          adm.modifyColumn(tableName, cf.setCompressionType(Compression.Algorithm.GZ));

          adm.enableTable(tableName);
        } catch (IOException e) {
          throw new TemporaryStorageException(e);
        }
      }
    }
  }
  @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;
  }