Examples with Assert org.testng.Assert used on opensource projects

Example 1 with Assert

use of org.testng.Assert in project gatk by broadinstitute.

the class CreatePanelOfNormalsIntegrationTest method assertRamPoNDuplicate.

/**
     * Assert that we can create a valid ram pon duplicate.
     *
     * @param pon never {@code null}
     */
private void assertRamPoNDuplicate(final PCACoveragePoN pon) {
    final PCACoveragePoN ramPoN = new RamPCACoveragePoN(pon);
    PoNTestUtils.assertEqualsMatrix(pon.getLogNormalizedCounts(), ramPoN.getLogNormalizedCounts(), false);
    PoNTestUtils.assertEqualsMatrix(pon.getLogNormalizedPInverseCounts(), ramPoN.getLogNormalizedPInverseCounts(), false);
    PoNTestUtils.assertEqualsMatrix(pon.getNormalizedCounts(), ramPoN.getNormalizedCounts(), false);
    PoNTestUtils.assertEqualsMatrix(pon.getReducedPanelCounts(), ramPoN.getReducedPanelCounts(), false);
    PoNTestUtils.assertEqualsMatrix(pon.getReducedPanelPInverseCounts(), ramPoN.getReducedPanelPInverseCounts(), false);
    PoNTestUtils.assertEqualsDoubleArrays(pon.getTargetFactors(), ramPoN.getTargetFactors());
    final List<Target> ponPanelTargets = pon.getPanelTargets();
    final List<Target> ponTargets = pon.getTargets();
    final List<Target> ponRawTargets = pon.getRawTargets();
    final List<Target> ramPoNPanelTargets = ramPoN.getPanelTargets();
    final List<Target> ramPoNTargets = ramPoN.getTargets();
    final List<Target> ramPoNRawTargets = ramPoN.getRawTargets();
    Assert.assertEquals(ponPanelTargets.size(), ramPoNPanelTargets.size());
    Assert.assertEquals(ponTargets.size(), ramPoNTargets.size());
    // Make sure every target is the same
    Assert.assertTrue(IntStream.range(0, ponRawTargets.size()).boxed().allMatch(i -> ponRawTargets.get(i).equals(ramPoNRawTargets.get(i))));
    Assert.assertTrue(IntStream.range(0, ponTargets.size()).boxed().allMatch(i -> ponTargets.get(i).equals(ramPoNTargets.get(i))));
    Assert.assertTrue(IntStream.range(0, ponPanelTargets.size()).boxed().allMatch(i -> ponPanelTargets.get(i).equals(ramPoNPanelTargets.get(i))));
    // Make sure every sample name is the same
    Assert.assertTrue(IntStream.range(0, pon.getSampleNames().size()).boxed().allMatch(i -> pon.getSampleNames().get(i).equals(ramPoN.getSampleNames().get(i))));
    Assert.assertTrue(IntStream.range(0, pon.getPanelSampleNames().size()).boxed().allMatch(i -> pon.getPanelSampleNames().get(i).equals(ramPoN.getPanelSampleNames().get(i))));
    // Make sure every target name is the same
    Assert.assertTrue(IntStream.range(0, pon.getTargetNames().size()).boxed().allMatch(i -> pon.getTargetNames().get(i).equals(ramPoN.getTargetNames().get(i))));
    Assert.assertTrue(IntStream.range(0, pon.getPanelTargetNames().size()).boxed().allMatch(i -> pon.getPanelTargetNames().get(i).equals(ramPoN.getPanelTargetNames().get(i))));
}

Example 2 with Assert

use of org.testng.Assert in project gatk-protected by broadinstitute.

the class IntegerCopyNumberTransitionProbabilityCacheUnitTest method testBasicSoundness.

@Test
public void testBasicSoundness() {
    for (final RealMatrix transitionMatrix : TRANSITION_MATRICES) {
        final IntegerCopyNumberTransitionProbabilityCache cache = new IntegerCopyNumberTransitionProbabilityCache(new IntegerCopyNumberTransitionMatrix(transitionMatrix, 0));
        for (final int dist : DISTANCES) {
            final RealMatrix transitionMatrixExponentiated = cache.getTransitionProbabilityMatrix(dist);
            /* assert positivity */
            Assert.assertTrue(Arrays.stream(transitionMatrixExponentiated.getData()).flatMapToDouble(Arrays::stream).allMatch(d -> d >= 0));
            /* assert conservation of probability */
            for (int c = 0; c < transitionMatrix.getColumnDimension(); c++) {
                Assert.assertEquals(Arrays.stream(transitionMatrixExponentiated.getColumn(c)).sum(), 1.0, EPSILON);
            }
            /* assert correctness, T(2*d) = T(d)*T(d) */
            assertEqualMatrices(cache.getTransitionProbabilityMatrix(2 * dist), transitionMatrixExponentiated.multiply(transitionMatrixExponentiated));
        }
        /* assert loss of initial state over long distances, i.e. all columns must be equal */
        final RealMatrix longRangeTransitionMatrix = cache.getTransitionProbabilityMatrix(Integer.MAX_VALUE);
        final double[] firstColumn = longRangeTransitionMatrix.getColumn(0);
        final RealMatrix syntheticLongRangeTransitionMatrix = new Array2DRowRealMatrix(firstColumn.length, firstColumn.length);
        for (int i = 0; i < firstColumn.length; i++) {
            syntheticLongRangeTransitionMatrix.setColumn(i, firstColumn);
        }
        assertEqualMatrices(longRangeTransitionMatrix, syntheticLongRangeTransitionMatrix);
        final double[] stationary = cache.getStationaryProbabilityVector().toArray();
        ArrayAsserts.assertArrayEquals(stationary, firstColumn, EPSILON);
    }
}

Example 3 with Assert

use of org.testng.Assert in project gatk-protected by broadinstitute.

the class CreatePanelOfNormalsIntegrationTest method assertRamPoNDuplicate.

/**
     * Assert that we can create a valid ram pon duplicate.
     *
     * @param pon never {@code null}
     */
private void assertRamPoNDuplicate(final PCACoveragePoN pon) {
    final PCACoveragePoN ramPoN = new RamPCACoveragePoN(pon);
    PoNTestUtils.assertEqualsMatrix(pon.getLogNormalizedCounts(), ramPoN.getLogNormalizedCounts(), false);
    PoNTestUtils.assertEqualsMatrix(pon.getLogNormalizedPInverseCounts(), ramPoN.getLogNormalizedPInverseCounts(), false);
    PoNTestUtils.assertEqualsMatrix(pon.getNormalizedCounts(), ramPoN.getNormalizedCounts(), false);
    PoNTestUtils.assertEqualsMatrix(pon.getReducedPanelCounts(), ramPoN.getReducedPanelCounts(), false);
    PoNTestUtils.assertEqualsMatrix(pon.getReducedPanelPInverseCounts(), ramPoN.getReducedPanelPInverseCounts(), false);
    PoNTestUtils.assertEqualsDoubleArrays(pon.getTargetFactors(), ramPoN.getTargetFactors());
    final List<Target> ponPanelTargets = pon.getPanelTargets();
    final List<Target> ponTargets = pon.getTargets();
    final List<Target> ponRawTargets = pon.getRawTargets();
    final List<Target> ramPoNPanelTargets = ramPoN.getPanelTargets();
    final List<Target> ramPoNTargets = ramPoN.getTargets();
    final List<Target> ramPoNRawTargets = ramPoN.getRawTargets();
    Assert.assertEquals(ponPanelTargets.size(), ramPoNPanelTargets.size());
    Assert.assertEquals(ponTargets.size(), ramPoNTargets.size());
    // Make sure every target is the same
    Assert.assertTrue(IntStream.range(0, ponRawTargets.size()).boxed().allMatch(i -> ponRawTargets.get(i).equals(ramPoNRawTargets.get(i))));
    Assert.assertTrue(IntStream.range(0, ponTargets.size()).boxed().allMatch(i -> ponTargets.get(i).equals(ramPoNTargets.get(i))));
    Assert.assertTrue(IntStream.range(0, ponPanelTargets.size()).boxed().allMatch(i -> ponPanelTargets.get(i).equals(ramPoNPanelTargets.get(i))));
    // Make sure every sample name is the same
    Assert.assertTrue(IntStream.range(0, pon.getSampleNames().size()).boxed().allMatch(i -> pon.getSampleNames().get(i).equals(ramPoN.getSampleNames().get(i))));
    Assert.assertTrue(IntStream.range(0, pon.getPanelSampleNames().size()).boxed().allMatch(i -> pon.getPanelSampleNames().get(i).equals(ramPoN.getPanelSampleNames().get(i))));
    // Make sure every target name is the same
    Assert.assertTrue(IntStream.range(0, pon.getTargetNames().size()).boxed().allMatch(i -> pon.getTargetNames().get(i).equals(ramPoN.getTargetNames().get(i))));
    Assert.assertTrue(IntStream.range(0, pon.getPanelTargetNames().size()).boxed().allMatch(i -> pon.getPanelTargetNames().get(i).equals(ramPoN.getPanelTargetNames().get(i))));
}

Example 4 with Assert

use of org.testng.Assert in project JGroups by belaban.

the class GroupRequestTest method testCancel.

public void testCancel() throws Exception {
    MyCorrelator corr = new MyCorrelator(true, null, 0);
    GroupRequest<Integer> req = new GroupRequest<>(corr, Arrays.asList(a, b, c), RequestOptions.SYNC());
    corr.setGroupRequest(req);
    req.cancel(true);
    RspList<Integer> rsps = req.execute(new Buffer(buf, 0, buf.length), true);
    System.out.println("rsps:\n" + rsps);
    assert rsps.size() == 3;
    long num_not_received = rsps.values().stream().filter(rsp -> !rsp.wasReceived()).count();
    assert num_not_received == 3;
    assert req.isCancelled();
    final GroupRequest<Integer> req2 = new GroupRequest<>(corr, Arrays.asList(a, b, c), RequestOptions.SYNC());
    corr.setGroupRequest(req2);
    new Thread(() -> {
        Util.sleep(1000);
        req2.cancel(true);
    }).start();
    rsps = req2.execute(new Buffer(buf, 0, buf.length), true);
    System.out.println("rsps:\n" + rsps);
    assert rsps.size() == 3;
    num_not_received = rsps.values().stream().filter(rsp -> !rsp.wasReceived()).count();
    assert num_not_received == 3;
    assert req2.isCancelled();
}

Example 5 with Assert

use of org.testng.Assert in project JGroups by belaban.

the class ExecutingServiceTest2 method testDisconnect.

@Test
public void testDisconnect() throws Exception {
    JChannel channel1 = new JChannel(Util.getTestStack(new CENTRAL_EXECUTOR()));
    JChannel channel2 = new JChannel(Util.getTestStack(new CENTRAL_EXECUTOR()));
    channels.add(channel1);
    channels.add(channel2);
    channel1.connect("test-cluster");
    channel2.connect("test-cluster");
    Util.waitUntilAllChannelsHaveSameView(20000, 1000, channel1, channel2);
    final ExecutionService executionService = new ExecutionService(channel1);
    ExecutionRunner executionRunner1 = new ExecutionRunner(channel1);
    ExecutionRunner executionRunner2 = new ExecutionRunner(channel2);
    Thread runner1 = new Thread(executionRunner1);
    threads.add(runner1);
    runner1.start();
    Thread runner2 = new Thread(executionRunner2);
    threads.add(runner2);
    runner2.start();
    final AtomicInteger submittedTasks = new AtomicInteger();
    final AtomicInteger finishedTasks = new AtomicInteger();
    final FutureListener<Void> listener = future -> {
        finishedTasks.incrementAndGet();
        synchronized (ExecutingServiceTest2.this) {
            ExecutingServiceTest2.this.notify();
        }
    };
    Thread submitter = new Thread(new Runnable() {

        @Override
        public void run() {
            // Two long running tasks that should be sent to each runner
            submit(true);
            submit(true);
            while (!Thread.interrupted()) {
                submit(false);
                // Throttle
                try {
                    Thread.sleep(50);
                } catch (InterruptedException e) {
                    Thread.currentThread().interrupt();
                }
            }
        }

        private void submit(boolean wait) {
            Callable<Void> task = new Wait(wait);
            NotifyingFuture<Void> future = executionService.submit(task);
            submittedTasks.incrementAndGet();
            future.setListener(listener);
        }
    });
    threads.add(submitter);
    submitter.start();
    // Run for 2 seconds
    Thread.sleep(500);
    // Close channel
    channel2.close();
    // Stop submitting
    submitter.interrupt();
    submitter.join();
    // Wait for running tasks to finish
    synchronized (this) {
        int lastFinished = finishedTasks.get();
        while (submittedTasks.get() > finishedTasks.get()) {
            wait(10000);
            if (lastFinished == finishedTasks.get()) {
                assert false : "Tasks still outstanding, none finished in the last 10s";
            }
            lastFinished = finishedTasks.get();
        }
    }
    Assert.assertEquals(submittedTasks.get(), finishedTasks.get(), "Tasks not finished");
}