@Before
public void start() {
helper.createServer();
helper.server.start();
helper.createClient();
helper.client.start();
helper.waitForRegistration(1);
}
/**
* Delete a random ME. Revert delete.
*
* @throws ESException ESException
* @throws SerializationException SerializationException
*/
@Test
public void deleteAndRevertDeleteTest() throws SerializationException, ESException {
System.out.println("DeleteAndRevertDeleteTest");
final IntegrationTestHelper testHelper =
new IntegrationTestHelper(randomSeed, getTestProject());
testHelper.doDeleteAndRevert();
commitChanges();
assertTrue(ModelUtil.areEqual(getTestProject(), getCompareProject()));
}
@Test
public void testStreamingCloud() throws IOException, GeneralSecurityException {
String[] ARGS = {
"--apiKey=" + helper.getApiKey(),
"--references=" + helper.PLATINUM_GENOMES_BRCA1_REFERENCES,
"--datasetId=" + helper.PLATINUM_GENOMES_DATASET,
"--output=" + outputPrefix,
"--project=" + helper.getTestProject(),
"--runner=BlockingDataflowPipelineRunner",
"--stagingLocation=" + helper.getTestStagingGcsFolder(),
"--useGrpc=true"
};
testBase(ARGS);
}
@Test
public void can_write_replace_resource_in_json() {
// write device timezone
final String timeZone = "Europe/Paris";
WriteResponse response =
helper.server.send(helper.getClient(), new WriteRequest(Mode.REPLACE, 3, 0, 15, timeZone));
// verify result
assertEquals(ResponseCode.CHANGED, response.getCode());
// read the timezone to check the value changed
ReadResponse readResponse = helper.server.send(helper.getClient(), new ReadRequest(3, 0, 15));
LwM2mResource resource = (LwM2mResource) readResponse.getContent();
assertEquals(timeZone, resource.getValue());
}
@Test
public void can_write_object_instance() {
// write device timezone and offset
LwM2mResource utcOffset = LwM2mSingleResource.newStringResource(14, "+02");
LwM2mResource timeZone = LwM2mSingleResource.newStringResource(15, "Europe/Paris");
WriteResponse response =
helper.server.send(
helper.getClient(), new WriteRequest(Mode.REPLACE, 3, 0, utcOffset, timeZone));
// verify result
assertEquals(ResponseCode.CHANGED, response.getCode());
// read the timezone to check the value changed
ReadResponse readResponse = helper.server.send(helper.getClient(), new ReadRequest(3, 0));
LwM2mObjectInstance instance = (LwM2mObjectInstance) readResponse.getContent();
assertEquals(utcOffset, instance.getResource(14));
assertEquals(timeZone, instance.getResource(15));
}
@Test
public void testPaginatedLocal() throws IOException, GeneralSecurityException {
String[] ARGS = {
"--apiKey=" + helper.getApiKey(),
"--references=" + helper.PLATINUM_GENOMES_BRCA1_REFERENCES,
"--datasetId=" + helper.PLATINUM_GENOMES_DATASET,
"--output=" + outputPrefix,
"--useGrpc=false"
};
testBase(ARGS);
}
@Test
public void cannot_write_non_writable_resource() {
// try to write unwritable resource like manufacturer on device
final String manufacturer = "new manufacturer";
WriteResponse response =
helper.server.send(
helper.getClient(), new WriteRequest(Mode.REPLACE, 3, 0, 0, manufacturer));
// verify result
assertEquals(ResponseCode.METHOD_NOT_ALLOWED, response.getCode());
}
@Ignore
// TODO enable this test. For it to work, we'll need to add alpn to the classpath
// and figure out https://github.com/googlegenomics/dataflow-java/issues/119
@Test
public void testStreamingLocal() throws IOException, GeneralSecurityException {
String[] ARGS = {
"--apiKey=" + helper.getApiKey(),
"--references=" + helper.PLATINUM_GENOMES_BRCA1_REFERENCES,
"--datasetId=" + helper.PLATINUM_GENOMES_DATASET,
"--output=" + outputPrefix,
"--useGrpc=true"
};
testBase(ARGS);
}
/**
* This move an element in a many reference list to another position.
*
* @throws EmfStoreException EmfStoreException
* @throws SerializationException SerializationException
*/
@Test
public void multiReferenceMoveTest() throws SerializationException, EmfStoreException {
System.out.println("MultiReferenceMoveTest");
final IntegrationTestHelper testHelper =
new IntegrationTestHelper(randomSeed, getTestProject());
new EMFStoreCommand() {
@Override
protected void doRun() {
testHelper.doMultiReferenceMove();
}
}.run(false);
commitChanges();
assertTrue(
IntegrationTestHelper.areEqual(
getTestProject(), getCompareProject(), "MultiReferenceMoveTest"));
}
private void testBase(String[] ARGS) throws IOException, GeneralSecurityException {
// Run the pipeline.
VariantSimilarity.main(ARGS);
// Download the pipeline results.
List<GraphResult> results = Lists.newArrayList();
for (GcsPath path : helper.gcsUtil.expand(GcsPath.fromUri(outputPrefix + "*"))) {
BufferedReader reader = helper.openOutput(path.toString());
for (String line = reader.readLine(); line != null; line = reader.readLine()) {
results.add(GraphResult.fromString(line));
}
}
// Check the pipeline results.
assertEquals(helper.PLATINUM_GENOMES_NUMBER_OF_SAMPLES, results.size());
assertThat(results, CoreMatchers.allOf(CoreMatchers.hasItems(EXPECTED_RESULT)));
}
@After
public void tearDown() throws Exception {
for (GcsPath path : helper.gcsUtil.expand(GcsPath.fromUri(outputPrefix + "*"))) {
helper.deleteOutput(path.toString());
}
}
@BeforeClass
public static void setUpBeforeClass() throws Exception {
helper = new IntegrationTestHelper();
outputPrefix = helper.getTestOutputGcsFolder() + "variantSimilarity";
}
