Examples of Shard

Examples of com.volantis.mcs.dissection.impl.Shard

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            int shardIndex = requestedShards.getShard(area.getIndex());

            // Retrieve the appropriate shard from the area. If the shard index
            // is invalid for some reason then we may not get back exactly the
            // one that we asked for but we will get one back.
            Shard shard
                = area.retrieveShard(dissectionContext, shardIndex,
                                     (AvailableShardsImpl) availableShards);
            if (shard == null) {
                throw new DissectionException(
                        exceptionLocalizer.format("shard-not-found"));
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Examples of net.sf.katta.protocol.metadata.IndexMetaData.Shard

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        }
      });
      for (final FileStatus fileStatus : listStatus) {
        String shardPath = fileStatus.getPath().toString();
        if (fileStatus.isDir() || shardPath.endsWith(".zip")) {
          shards.add(new Shard(createShardName(indexName, shardPath), shardPath));
        }
      }
    } catch (final IOException e) {
      throw new IndexDeployException(ErrorType.INDEX_NOT_ACCESSIBLE, "could not access index path: " + indexPathString,
              e);
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Examples of net.sf.katta.protocol.metadata.IndexMetaData.Shard

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  }

  @Test(timeout = 70000)
  public void testIndexManagement() throws Exception {
    IndexMetaData indexMD = new IndexMetaData("index1", "indexPath", 2);
    indexMD.getShards().add(new Shard(AbstractIndexOperation.createShardName(indexMD.getName(), "path1"), "path1"));
    Node node = Mocks.mockNode();

    assertNull(_protocol.getIndexMD("index1"));
    assertEquals(0, _protocol.getIndices().size());
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Examples of net.sf.katta.protocol.metadata.IndexMetaData.Shard

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  public void testAddRemoveIndexForSearching() throws Exception {
    InteractionProtocol protocol = mock(InteractionProtocol.class);
    Client client = new Client(ISleepServer.class, new DefaultNodeSelectionPolicy(), protocol,
            new ClientConfiguration());
    IndexMetaData indexMD = new IndexMetaData("index1", "path", 1);
    indexMD.getShards().add(new Shard("shard1", "path"));
    indexMD.getShards().add(new Shard("shard2", "path"));
    client.addIndexForSearching(indexMD);
    verify(protocol, times(2)).registerChildListener(eq(client), eq(PathDef.SHARD_TO_NODES), anyString(),
            any(IAddRemoveListener.class));

    client.removeIndex(indexMD.getName());
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Examples of net.sf.katta.protocol.metadata.IndexMetaData.Shard

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  public void testAddRemoveIndexForWatching() throws Exception {
    InteractionProtocol protocol = mock(InteractionProtocol.class);
    Client client = new Client(ISleepServer.class, new DefaultNodeSelectionPolicy(), protocol,
            new ClientConfiguration());
    IndexMetaData indexMD = new IndexMetaData("index1", "path", 1);
    indexMD.getShards().add(new Shard("shard1", "path"));
    indexMD.getShards().add(new Shard("shard2", "path"));
    client.addIndexForWatching(indexMD.getName());
    verify(protocol, times(1)).registerDataListener(eq(client), eq(PathDef.INDICES_METADATA), anyString(),
            any(IZkDataListener.class));

    client.removeIndex(indexMD.getName());
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Examples of org.apache.hadoop.contrib.index.mapred.Shard

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      Arrays.sort(shardNames, 0, count);

      Shard[] shards = new Shard[count >= numShards ? count : numShards];
      for (int i = 0; i < count; i++) {
        shards[i] =
            new Shard(versionNumber, parent + shardNames[i], generation);
      }

      int number = count;
      for (int i = count; i < numShards; i++) {
        String shardPath;
        while (true) {
          shardPath = parent + NUMBER_FORMAT.format(number++);
          if (!fs.exists(new Path(shardPath))) {
            break;
          }
        }
        shards[i] = new Shard(versionNumber, shardPath, generation);
      }
      return shards;
    } else {
      Shard[] shards = new Shard[numShards];
      for (int i = 0; i < shards.length; i++) {
        shards[i] =
            new Shard(versionNumber, parent + NUMBER_FORMAT.format(i),
                generation);
      }
      return shards;
    }
  }
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Examples of org.apache.hadoop.contrib.index.mapred.Shard

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      Arrays.sort(shardNames, 0, count);

      Shard[] shards = new Shard[count >= numShards ? count : numShards];
      for (int i = 0; i < count; i++) {
        shards[i] =
            new Shard(versionNumber, parent + shardNames[i], generation);
      }

      int number = count;
      for (int i = count; i < numShards; i++) {
        String shardPath;
        while (true) {
          shardPath = parent + NUMBER_FORMAT.format(number++);
          if (!fs.exists(new Path(shardPath))) {
            break;
          }
        }
        shards[i] = new Shard(versionNumber, shardPath, generation);
      }
      return shards;
    } else {
      Shard[] shards = new Shard[numShards];
      for (int i = 0; i < shards.length; i++) {
        shards[i] =
            new Shard(versionNumber, parent + NUMBER_FORMAT.format(i),
                generation);
      }
      return shards;
    }
  }
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Examples of org.broadinstitute.gatk.engine.datasources.reads.Shard

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//        view.getReferenceContext(shard.getGenomeLoc()).getBase();
//    }

    @Test
    public void testOverlappingReferenceBases() {
        Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(genomeLocParser.createGenomeLoc(sequenceFile.getSequenceDictionary().getSequence(0).getSequenceName(),
                                                                                                                   sequenceFile.getSequence("chrM").length() - 10,
                                                                                                                   sequenceFile.getSequence("chrM").length())));
        LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, null, genomeLocParser, shard.getGenomeLocs().get(0), null, sequenceFile, null);
        LocusReferenceView view = new LocusReferenceView(dataProvider);

        byte[] results = view.getReferenceBases(genomeLocParser.createGenomeLoc(sequenceFile.getSequenceDictionary().getSequence(0).getSequenceName(),
                                                                                sequenceFile.getSequence("chrM").length() - 10,
                                                                                sequenceFile.getSequence("chrM").length() + 9));
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Examples of org.broadinstitute.gatk.engine.datasources.reads.Shard

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    /** Queries outside the bounds of the shard should result in reference context window trimmed at the shard boundary. */
    @Test
    public void testBoundsFailure() {
        Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(genomeLocParser.createGenomeLoc(sequenceFile.getSequenceDictionary().getSequence(0).getSequenceName(), 1, 50)));

        LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, null, genomeLocParser, shard.getGenomeLocs().get(0), null, sequenceFile, null);
        LocusReferenceView view = new LocusReferenceView(dataProvider);

        GenomeLoc locus = genomeLocParser.createGenomeLoc(sequenceFile.getSequenceDictionary().getSequence(0).getSequenceName(), 50, 51);

        ReferenceContext rc = view.getReferenceContext(locus);
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Examples of org.broadinstitute.gatk.engine.datasources.reads.Shard

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     * Compares the contents of the fasta and view at a specified location.
     *
     * @param loc
     */
    protected void validateLocation( GenomeLoc loc ) {
        Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(loc));
        GenomeLocusIterator shardIterator = new GenomeLocusIterator(genomeLocParser,loc);

        LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, null, genomeLocParser, loc, null, sequenceFile, null);
        LocusReferenceView view = new LocusReferenceView(dataProvider);

        while (shardIterator.hasNext()) {
            GenomeLoc locus = shardIterator.next();

            ReferenceSequence expectedAsSeq = sequenceFile.getSubsequenceAt(locus.getContig(), locus.getStart(), locus.getStop());
            char expected = Character.toUpperCase(StringUtil.bytesToString(expectedAsSeq.getBases()).charAt(0));
            char actual = view.getReferenceContext(locus).getBaseAsChar();

            Assert.assertEquals(actual, expected, String.format("Value of base at position %s in shard %s does not match expected", locus.toString(), shard.getGenomeLocs())
            );
        }
    }
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