@Test
  public void testAffinitymatrixInputReducer() throws Exception {
    AffinityMatrixInputMapper mapper = new AffinityMatrixInputMapper();
    Configuration conf = getConfiguration();
    conf.setInt(Keys.AFFINITY_DIMENSIONS, RAW_DIMENSIONS);

    // set up the dummy writer and the M/R context
    DummyRecordWriter<IntWritable, MatrixEntryWritable> mapWriter = new DummyRecordWriter<>();
    Mapper<LongWritable, Text, IntWritable, MatrixEntryWritable>.Context mapContext =
        DummyRecordWriter.build(mapper, conf, mapWriter);

    // loop through all the points and test each one is converted
    // successfully to a DistributedRowMatrix.MatrixEntry
    for (String s : RAW) {
      mapper.map(new LongWritable(), new Text(s), mapContext);
    }
    // store the data for checking later
    Map<IntWritable, List<MatrixEntryWritable>> map = mapWriter.getData();

    // now reduce the data
    AffinityMatrixInputReducer reducer = new AffinityMatrixInputReducer();
    DummyRecordWriter<IntWritable, VectorWritable> redWriter = new DummyRecordWriter<>();
    Reducer<IntWritable, MatrixEntryWritable, IntWritable, VectorWritable>.Context redContext =
        DummyRecordWriter.build(
            reducer, conf, redWriter, IntWritable.class, MatrixEntryWritable.class);
    for (IntWritable key : mapWriter.getKeys()) {
      reducer.reduce(key, mapWriter.getValue(key), redContext);
    }

    // check that all the elements are correctly ordered
    assertEquals("Number of reduce results", RAW_DIMENSIONS, redWriter.getData().size());
    for (IntWritable row : redWriter.getKeys()) {
      List<VectorWritable> list = redWriter.getValue(row);
      assertEquals("Should only be one vector", 1, list.size());
      // check that the elements in the array are correctly ordered
      Vector v = list.get(0).get();
      for (Vector.Element e : v.all()) {
        // find this value in the original map
        MatrixEntryWritable toCompare = new MatrixEntryWritable();
        toCompare.setRow(-1);
        toCompare.setCol(e.index());
        toCompare.setVal(e.get());
        assertTrue("This entry was correctly placed in its row", map.get(row).contains(toCompare));
      }
    }
  }
  /**
   * Testing the mapper is fairly straightforward: there are two matrices to be processed
   * simultaneously (cut matrix of sensitivities, and the affinity matrix), and since both are
   * symmetric, two entries from each will be grouped together with the same key (or, in the case of
   * an entry along the diagonal, only two entries).
   *
   * <p>The correct grouping of these quad or pair vertices is the only output of the mapper.
   *
   * @throws Exception
   */
  @Test
  public void testEigencutsAffinityCutsMapper() throws Exception {
    EigencutsAffinityCutsMapper mapper = new EigencutsAffinityCutsMapper();
    Configuration conf = new Configuration();
    conf.setInt(EigencutsKeys.AFFINITY_DIMENSIONS, this.affinity.length);

    // set up the writer
    DummyRecordWriter<Text, VertexWritable> writer = new DummyRecordWriter<Text, VertexWritable>();
    Mapper<IntWritable, VectorWritable, Text, VertexWritable>.Context context =
        DummyRecordWriter.build(mapper, conf, writer);

    // perform the maps
    for (int i = 0; i < this.affinity.length; i++) {
      VectorWritable aff = new VectorWritable(new DenseVector(this.affinity[i]));
      VectorWritable sens = new VectorWritable(new DenseVector(this.sensitivity[i]));
      IntWritable key = new IntWritable(i);
      mapper.map(key, aff, context);
      mapper.map(key, sens, context);
    }

    // were the vertices constructed correctly? if so, then for two 4x4
    // matrices, there should be 10 unique keys with 56 total entries
    assertEquals("Number of keys", 10, writer.getKeys().size());
    for (int i = 0; i < this.affinity.length; i++) {
      for (int j = 0; j < this.affinity.length; j++) {
        Text key = new Text(Math.max(i, j) + "_" + Math.min(i, j));
        List<VertexWritable> values = writer.getValue(key);

        // if we're on a diagonal, there should only be 2 entries
        // otherwise, there should be 4
        if (i == j) {
          assertEquals("Diagonal entry", 2, values.size());
          for (VertexWritable v : values) {
            assertFalse("Diagonal values are zero", v.getValue() > 0);
          }
        } else {
          assertEquals("Off-diagonal entry", 4, values.size());
          if (i + j == 3) { // all have values greater than 0
            for (VertexWritable v : values) {
              assertTrue("Off-diagonal non-zero entries", v.getValue() > 0);
            }
          }
        }
      }
    }
  }
  /**
   * Fairly straightforward: the task here is to reassemble the rows of the affinity matrix. The
   * tricky part is that any specific element in the list of elements which does NOT lay on the
   * diagonal will be so because it did not drop below the sensitivity threshold, hence it was not
   * "cut".
   *
   * <p>On the flip side, there will be many entries whose coordinate is now set to the diagonal,
   * indicating they were previously affinity entries whose sensitivities were below the threshold,
   * and hence were "cut" - set to 0 at their original coordinates, and had their values added to
   * the diagonal entry (hence the numerous entries with the coordinate of the diagonal).
   *
   * @throws Exception
   */
  @Test
  public void testEigencutsAffinityCutsReducer() throws Exception {
    Configuration conf = new Configuration();
    Path affinity = new Path("affinity");
    Path sensitivity = new Path("sensitivity");
    conf.set(EigencutsKeys.AFFINITY_PATH, affinity.getName());
    conf.setInt(EigencutsKeys.AFFINITY_DIMENSIONS, this.affinity.length);

    // since we need the working paths to distinguish the vertex types,
    // we can't use the mapper (since we have no way of manually setting
    // the Context.workingPath() )
    Map<Text, List<VertexWritable>> data = buildMapData(affinity, sensitivity, this.sensitivity);

    // now, set up the combiner
    EigencutsAffinityCutsCombiner combiner = new EigencutsAffinityCutsCombiner();
    DummyRecordWriter<Text, VertexWritable> comWriter =
        new DummyRecordWriter<Text, VertexWritable>();
    Reducer<Text, VertexWritable, Text, VertexWritable>.Context comContext =
        DummyRecordWriter.build(combiner, conf, comWriter, Text.class, VertexWritable.class);

    // perform the combining
    for (Map.Entry<Text, List<VertexWritable>> entry : data.entrySet()) {
      combiner.reduce(entry.getKey(), entry.getValue(), comContext);
    }

    // finally, set up the reduction writers
    EigencutsAffinityCutsReducer reducer = new EigencutsAffinityCutsReducer();
    DummyRecordWriter<IntWritable, VectorWritable> redWriter =
        new DummyRecordWriter<IntWritable, VectorWritable>();
    Reducer<Text, VertexWritable, IntWritable, VectorWritable>.Context redContext =
        DummyRecordWriter.build(reducer, conf, redWriter, Text.class, VertexWritable.class);

    // perform the reduction
    for (Text key : comWriter.getKeys()) {
      reducer.reduce(key, comWriter.getValue(key), redContext);
    }

    // now, check that the affinity matrix is correctly formed
    for (IntWritable row : redWriter.getKeys()) {
      List<VectorWritable> results = redWriter.getValue(row);
      // there should only be 1 vector
      assertEquals("Only one vector with a given row number", 1, results.size());
      Vector therow = results.get(0).get();
      for (Vector.Element e : therow.all()) {
        // check the diagonal
        if (row.get() == e.index()) {
          assertEquals(
              "Correct diagonal sum of cuts",
              sumOfRowCuts(row.get(), this.sensitivity),
              e.get(),
              EPSILON);
        } else {
          // not on the diagonal...if it was an element labeled to be cut,
          // it should have a value of 0. Otherwise, it should have kept its
          // previous value
          if (this.sensitivity[row.get()][e.index()] == 0.0) {
            // should be what it was originally
            assertEquals(
                "Preserved element", this.affinity[row.get()][e.index()], e.get(), EPSILON);
          } else {
            // should be 0
            assertEquals("Cut element", 0.0, e.get(), EPSILON);
          }
        }
      }
    }
  }