@Test
public void testConditioning() {
XTandemMain main =
new XTandemMain(
XTandemUtilities.getResourceStream("smallSample/tandem.params"),
"smallSample/tandem.params");
main.loadScoringTest();
main.loadSpectra();
Scorer sa = main.getScoreRunner();
IScoredScan[] conditionedScans = sa.getScans();
final IScoredScan conditionedScan = conditionedScans[0];
SpectrumCondition sc = sa.getSpectrumCondition();
final IScoringAlgorithm alg = sa.getAlgorithm();
IMeasuredSpectrum scan = alg.conditionSpectrum(conditionedScan, sc);
Set<Integer> goodMasses = buildMassSet();
final ISpectrumPeak[] sps = scan.getPeaks();
for (int i = 0; i < sps.length; i++) {
ISpectrumPeak sp = sps[i];
validateMass(sp, peaks[2 * i], goodMasses);
// validatePeak(sp,peaks[2 * i],peaks[2 * i + 1]);
}
Assert.assertEquals(goodMasses.size(), 0);
XTandemUtilities.breakHere();
}
@Test
public void scanTest() {
Map<String, Map<String, ByteIterator>> keyMap = new HashMap<>();
for (int i = 0; i < 5; i++) {
String insertKey = KEY_PREFIX + i;
keyMap.put(insertKey, insertRow(insertKey));
}
Set<String> fieldSet = new HashSet<>();
fieldSet.add("FIELD0");
fieldSet.add("FIELD1");
int startIndex = 1;
int resultRows = 3;
Vector<HashMap<String, ByteIterator>> resultVector = new Vector<>();
orientDBClient.scan(CLASS, KEY_PREFIX + startIndex, resultRows, fieldSet, resultVector);
// Check the resultVector is the correct size
assertEquals(
"Assert the correct number of results rows were returned", resultRows, resultVector.size());
// Check each vector row to make sure we have the correct fields
int testIndex = startIndex;
for (HashMap<String, ByteIterator> result : resultVector) {
assertEquals(
"Assert that this row has the correct number of fields", fieldSet.size(), result.size());
for (String field : fieldSet) {
assertEquals(
"Assert this field is correct in this row",
keyMap.get(KEY_PREFIX + testIndex).get(field).toString(),
result.get(field).toString());
}
testIndex++;
}
}
protected ArrayList<HRegionInfo> getRegionInfoList(String tableName) throws IOException {
Set<HRegionInfo> hRegionInfoSet = new TreeSet<>();
try (HTable table = new HTable(conf, tableName)) {
hRegionInfoSet.addAll(table.getRegionLocations().keySet());
}
return new ArrayList<>(hRegionInfoSet);
}
// FIXME: fails! needs MarcCombiningReader for mhld or at least a diff version of RawRecordReader
@Test
public void testMultMHLDsWithSameID() throws IOException {
// bib134, multMhlds1
String bibFilePath = testDataParentPath + File.separator + "mhldMergeBibs134.mrc";
String mhldFilePath = testDataParentPath + File.separator + "mhldMergeMhlds1Mult.mrc";
Map<String, Record> mergedRecs =
MergeSummaryHoldings.mergeMhldsIntoBibRecordsAsMap(bibFilePath, mhldFilePath);
Record mergedRec = mergedRecs.get("a1");
assertEquals("Expected three 852", 3, mergedRec.getVariableFields("852").size());
Set<String> expectedVals = new HashSet<String>();
expectedVals.add("Location1");
expectedVals.add("Location2");
RecordTestingUtils.assertSubfieldHasExpectedValues(mergedRec, "852", 'b', expectedVals);
expectedVals.clear();
expectedVals.add("(month)");
expectedVals.add("(season)");
RecordTestingUtils.assertSubfieldHasExpectedValues(mergedRec, "853", 'b', expectedVals);
assertEquals("Expected one 863", 2, mergedRec.getVariableFields("863").size());
assertEquals("Expected one 866", 1, mergedRec.getVariableFields("866").size());
// fail("Implement me");
System.out.println("Test testMultMHLDsWithSameID() successful");
}
@Test
public void testJedisClusterRunsWithMultithreaded()
throws InterruptedException, ExecutionException, IOException {
Set<HostAndPort> jedisClusterNode = new HashSet<HostAndPort>();
jedisClusterNode.add(new HostAndPort("127.0.0.1", 7379));
final JedisCluster jc = new JedisCluster(jedisClusterNode);
jc.set("foo", "bar");
ThreadPoolExecutor executor =
new ThreadPoolExecutor(10, 100, 0, TimeUnit.SECONDS, new ArrayBlockingQueue<Runnable>(10));
List<Future<String>> futures = new ArrayList<Future<String>>();
for (int i = 0; i < 50; i++) {
executor.submit(
new Callable<String>() {
@Override
public String call() throws Exception {
// FIXME : invalidate slot cache from JedisCluster to test
// random connection also does work
return jc.get("foo");
}
});
}
for (Future<String> future : futures) {
String value = future.get();
assertEquals("bar", value);
}
jc.close();
}
/** Test of isEmpty method, of class Set. */
@Test
public void testIsEmpty() {
Set<Integer> set = new Set<Integer>();
assertTrue(set.isEmpty());
set.addElement(0);
assertFalse(set.isEmpty());
}
/** Test of elementExists method, of class Set. */
@Test
public void testElementExists() {
Set<Integer> set = new Set<Integer>();
assertFalse(set.elementExists(1));
set.addElement(1);
assertTrue(set.elementExists(1));
}
@Test
public void testCloseable() throws IOException {
Set<HostAndPort> jedisClusterNode = new HashSet<HostAndPort>();
jedisClusterNode.add(new HostAndPort(nodeInfo1.getHost(), nodeInfo1.getPort()));
JedisCluster jc = null;
try {
jc = new JedisCluster(jedisClusterNode);
jc.set("51", "foo");
} finally {
if (jc != null) {
jc.close();
}
}
Iterator<JedisPool> poolIterator = jc.getClusterNodes().values().iterator();
while (poolIterator.hasNext()) {
JedisPool pool = poolIterator.next();
try {
pool.getResource();
fail("JedisCluster's internal pools should be already destroyed");
} catch (JedisConnectionException e) {
// ok to go...
}
}
}
@Test
public void tableNameCaseDoesNotMatter() {
JdbcContentPersistenceService.ConcurrentUpperCaseHashMap map =
new JdbcContentPersistenceService.ConcurrentUpperCaseHashMap(10);
map.put("lower", true);
Assert.assertTrue(map.containsKey("lower"));
Assert.assertTrue(map.containsKey("Lower"));
Assert.assertTrue(map.containsKey("LOWER"));
Assert.assertTrue(map.get("lower"));
Assert.assertTrue(map.get("Lower"));
Assert.assertTrue(map.get("LOWER"));
map.putIfAbsent("UPPER", true);
Assert.assertTrue(map.containsKey("upper"));
Assert.assertTrue(map.containsKey("Upper"));
Assert.assertTrue(map.containsKey("UPPER"));
Assert.assertTrue(map.get("upper"));
Assert.assertTrue(map.get("Upper"));
Assert.assertTrue(map.get("UPPER"));
Set<String> keys = map.keySet();
Assert.assertEquals(2, keys.size());
Assert.assertTrue(keys.contains("LOWER"));
Assert.assertTrue(keys.contains("UPPER"));
}
@Test
public void testFlatMapMaxConcurrent() {
final int m = 4;
final AtomicInteger subscriptionCount = new AtomicInteger();
Observable<Integer> source =
Observable.range(1, 10)
.flatMap(
new Func1<Integer, Observable<Integer>>() {
@Override
public Observable<Integer> call(Integer t1) {
return compose(Observable.range(t1 * 10, 2), subscriptionCount, m)
.subscribeOn(Schedulers.computation());
}
},
m);
TestSubscriber<Integer> ts = new TestSubscriber<Integer>();
source.subscribe(ts);
ts.awaitTerminalEvent();
ts.assertNoErrors();
Set<Integer> expected =
new HashSet<Integer>(
Arrays.asList(
10, 11, 20, 21, 30, 31, 40, 41, 50, 51, 60, 61, 70, 71, 80, 81, 90, 91, 100, 101));
Assert.assertEquals(expected.size(), ts.getOnNextEvents().size());
Assert.assertTrue(expected.containsAll(ts.getOnNextEvents()));
}
private List<String> executeDDL(
String ddlFileName,
@Nullable String dataFileName,
boolean isLocalTable,
@Nullable String[] args)
throws Exception {
Path ddlFilePath = new Path(currentQueryPath, ddlFileName);
FileSystem fs = ddlFilePath.getFileSystem(conf);
assertTrue(ddlFilePath + " existence check", fs.exists(ddlFilePath));
String template = FileUtil.readTextFile(new File(ddlFilePath.toUri()));
String dataFilePath = null;
if (dataFileName != null) {
dataFilePath = getDataSetFile(dataFileName).toString();
}
String compiled = compileTemplate(template, dataFilePath, args);
List<ParsedResult> parsedResults = SimpleParser.parseScript(compiled);
List<String> createdTableNames = new ArrayList<String>();
for (ParsedResult parsedResult : parsedResults) {
// parse a statement
Expr expr = sqlParser.parse(parsedResult.getStatement());
assertNotNull(ddlFilePath + " cannot be parsed", expr);
if (expr.getType() == OpType.CreateTable) {
CreateTable createTable = (CreateTable) expr;
String tableName = createTable.getTableName();
assertTrue("Table creation is failed.", client.updateQuery(parsedResult.getStatement()));
TableDesc createdTable = client.getTableDesc(tableName);
String createdTableName = createdTable.getName();
assertTrue(
"table '" + createdTableName + "' creation check", client.existTable(createdTableName));
if (isLocalTable) {
createdTableGlobalSet.add(createdTableName);
createdTableNames.add(tableName);
}
} else if (expr.getType() == OpType.DropTable) {
DropTable dropTable = (DropTable) expr;
String tableName = dropTable.getTableName();
assertTrue(
"table '" + tableName + "' existence check",
client.existTable(CatalogUtil.buildFQName(currentDatabase, tableName)));
assertTrue("table drop is failed.", client.updateQuery(parsedResult.getStatement()));
assertFalse(
"table '" + tableName + "' dropped check",
client.existTable(CatalogUtil.buildFQName(currentDatabase, tableName)));
if (isLocalTable) {
createdTableGlobalSet.remove(tableName);
}
} else {
assertTrue(ddlFilePath + " is not a Create or Drop Table statement", false);
}
}
return createdTableNames;
}
/**
* these are the masses XTandem has
*
* @return
*/
public static Set<Integer> buildMassSet() {
Set<Integer> holder = new HashSet<Integer>();
for (int i = 0; i < peaks.length; i += 2) {
holder.add(asInt(peaks[i]));
}
return holder;
}
@Test
public void testHash() {
Set<Integer> set = new HashSet<Integer>();
for (WordNgram w : myNgrams) {
set.add(w.hashCode());
}
assertTrue("hash code test", set.size() > 8);
}
/** Test of addElement method, of class Set. */
@Test
public void testAddElement() {
Set<String> set = new Set<String>();
set.addElement("m");
set.addElement("h");
set.addElement("m");
assertTrue(set.elementExists("m"));
assertFalse(set.elementExists("n"));
}
/** Test of deleteElement method, of class Set. */
@Test(expected = ElementNotFoundException.class)
public void testDeleteElement() throws Exception {
Set<Integer> set = new Set<Integer>();
set.deleteElement(3);
set.addElement(1);
set.addElement(4);
set.deleteElement(1);
assertFalse(set.elementExists(1));
}
@Test(expected = JedisClusterMaxRedirectionsException.class)
public void testRedisClusterMaxRedirections() {
Set<HostAndPort> jedisClusterNode = new HashSet<HostAndPort>();
jedisClusterNode.add(new HostAndPort("127.0.0.1", 7379));
JedisCluster jc = new JedisCluster(jedisClusterNode);
int slot51 = JedisClusterCRC16.getSlot("51");
// This will cause an infinite redirection loop
node2.clusterSetSlotMigrating(slot51, JedisClusterTestUtil.getNodeId(node3.clusterNodes()));
jc.set("51", "foo");
}
@Test(expected = JedisConnectionException.class)
public void testIfPoolConfigAppliesToClusterPools() {
GenericObjectPoolConfig config = new GenericObjectPoolConfig();
config.setMaxTotal(0);
config.setMaxWaitMillis(2000);
Set<HostAndPort> jedisClusterNode = new HashSet<HostAndPort>();
jedisClusterNode.add(new HostAndPort("127.0.0.1", 7379));
JedisCluster jc = new JedisCluster(jedisClusterNode, config);
jc.set("52", "poolTestValue");
}
@Test
public void testDiscoverNodesAutomatically() {
Set<HostAndPort> jedisClusterNode = new HashSet<HostAndPort>();
jedisClusterNode.add(new HostAndPort("127.0.0.1", 7379));
JedisCluster jc = new JedisCluster(jedisClusterNode);
assertEquals(3, jc.getClusterNodes().size());
JedisCluster jc2 = new JedisCluster(new HostAndPort("127.0.0.1", 7379));
assertEquals(3, jc2.getClusterNodes().size());
}
@Test
public void testAskResponse() throws InterruptedException {
Set<HostAndPort> jedisClusterNode = new HashSet<HostAndPort>();
jedisClusterNode.add(new HostAndPort("127.0.0.1", 7379));
JedisCluster jc = new JedisCluster(jedisClusterNode);
int slot51 = JedisClusterCRC16.getSlot("51");
node3.clusterSetSlotImporting(slot51, JedisClusterTestUtil.getNodeId(node2.clusterNodes()));
node2.clusterSetSlotMigrating(slot51, JedisClusterTestUtil.getNodeId(node3.clusterNodes()));
jc.set("51", "foo");
assertEquals("foo", jc.get("51"));
}
@Test
public void userServiceReturnsExpectedData() throws Exception {
setContext(
"<ldap-user-service id='ldapUDS' user-search-filter='(uid={0})' group-search-filter='member={0}' /><ldap-server ldif='classpath:test-server.ldif'/>");
UserDetailsService uds = (UserDetailsService) appCtx.getBean("ldapUDS");
UserDetails ben = uds.loadUserByUsername("ben");
Set<String> authorities = AuthorityUtils.authorityListToSet(ben.getAuthorities());
assertEquals(3, authorities.size());
assertTrue(authorities.contains("ROLE_DEVELOPERS"));
}
@Test(expected = JedisClusterMaxRedirectionsException.class, timeout = 2000)
public void testReturnConnectionOnRedirection() {
Set<HostAndPort> jedisClusterNode = new HashSet<HostAndPort>();
jedisClusterNode.add(new HostAndPort("127.0.0.1", 7379));
JedisPoolConfig config = new JedisPoolConfig();
config.setMaxTotal(1);
JedisCluster jc = new JedisCluster(jedisClusterNode, 0, 2, config);
// This will cause an infinite redirection between node 2 and 3
node3.clusterSetSlotMigrating(15363, JedisClusterTestUtil.getNodeId(node2.clusterNodes()));
jc.get("e");
}
@Test
public void testMigrateToNewNode() throws InterruptedException {
log.info("test migrate slot to new node");
Set<HostAndPort> jedisClusterNode = new HashSet<HostAndPort>();
jedisClusterNode.add(nodeInfo1);
JedisCluster jc = new JedisCluster(jedisClusterNode);
node4.clusterMeet(localHost, nodeInfo1.getPort());
String node3Id = JedisClusterTestUtil.getNodeId(node3.clusterNodes());
String node4Id = JedisClusterTestUtil.getNodeId(node4.clusterNodes());
JedisClusterTestUtil.waitForClusterReady(node4);
node3.clusterSetSlotMigrating(15363, node4Id);
node4.clusterSetSlotImporting(15363, node3Id);
try {
node4.set("e", "e");
} catch (JedisMovedDataException jme) {
assertEquals(15363, jme.getSlot());
assertEquals(new HostAndPort(localHost, nodeInfo3.getPort()), jme.getTargetNode());
}
try {
node3.set("e", "e");
} catch (JedisAskDataException jae) {
assertEquals(15363, jae.getSlot());
assertEquals(new HostAndPort(localHost, nodeInfo4.getPort()), jae.getTargetNode());
}
jc.set("e", "e");
try {
node4.get("e");
} catch (JedisMovedDataException jme) {
assertEquals(15363, jme.getSlot());
assertEquals(new HostAndPort(localHost, nodeInfo3.getPort()), jme.getTargetNode());
}
try {
node3.get("e");
} catch (JedisAskDataException jae) {
assertEquals(15363, jae.getSlot());
assertEquals(new HostAndPort(localHost, nodeInfo4.getPort()), jae.getTargetNode());
}
assertEquals("e", jc.get("e"));
node4.clusterSetSlotNode(15363, node4Id);
node3.clusterSetSlotNode(15363, node4Id);
// assertEquals("e", jc.get("e"));
assertEquals("e", node4.get("e"));
// assertEquals("e", node3.get("e"));
}
@Test
public void testRemoveService() {
ServiceHolder tested = new ServiceHolder();
Object service = new Object();
// Get the hash set.
Set<Object> servicesSet = getField(tested, Set.class);
servicesSet.add(service);
tested.removeService(service);
assertTrue("Set should be empty after removeal.", servicesSet.isEmpty());
}
public static Set<BigInteger> createPrimesSet(int max) {
Set<BigInteger> primes = new HashSet<BigInteger>();
BigInteger n = new BigInteger("2");
BigInteger maxValue = new BigInteger(String.valueOf(max));
while (n.compareTo(maxValue) < 0) {
primes.add(n);
n = n.nextProbablePrime();
}
System.out.println("Primes under " + max + " generated.");
return primes;
}
@Test
public void testClusterCountKeysInSlot() {
Set<HostAndPort> jedisClusterNode = new HashSet<HostAndPort>();
jedisClusterNode.add(new HostAndPort(nodeInfo1.getHost(), nodeInfo1.getPort()));
JedisCluster jc = new JedisCluster(jedisClusterNode);
for (int index = 0; index < 5; index++) {
jc.set("foo{bar}" + index, "hello");
}
int slot = JedisClusterCRC16.getSlot("foo{bar}");
assertEquals(5, node1.clusterCountKeysInSlot(slot).intValue());
}
@Test
public void testJedisClusterTimeout() {
Set<HostAndPort> jedisClusterNode = new HashSet<HostAndPort>();
jedisClusterNode.add(new HostAndPort(nodeInfo1.getHost(), nodeInfo1.getPort()));
JedisCluster jc = new JedisCluster(jedisClusterNode, 4000);
for (JedisPool pool : jc.getClusterNodes().values()) {
Jedis jedis = pool.getResource();
assertEquals(jedis.getClient().getConnectionTimeout(), 4000);
assertEquals(jedis.getClient().getSoTimeout(), 4000);
jedis.close();
}
}
@Test
public void testRecalculateSlotsWhenMoved() throws InterruptedException {
Set<HostAndPort> jedisClusterNode = new HashSet<HostAndPort>();
jedisClusterNode.add(new HostAndPort("127.0.0.1", 7379));
JedisCluster jc = new JedisCluster(jedisClusterNode);
int slot51 = JedisClusterCRC16.getSlot("51");
node2.clusterDelSlots(slot51);
node3.clusterDelSlots(slot51);
node3.clusterAddSlots(slot51);
JedisClusterTestUtil.waitForClusterReady(node1, node2, node3);
jc.set("51", "foo");
assertEquals("foo", jc.get("51"));
}
/** slot->nodes 15363 node3 e */
@Test
public void testMigrate() {
log.info("test migrate slot");
Set<HostAndPort> jedisClusterNode = new HashSet<HostAndPort>();
jedisClusterNode.add(nodeInfo1);
JedisCluster jc = new JedisCluster(jedisClusterNode);
String node3Id = JedisClusterTestUtil.getNodeId(node3.clusterNodes());
String node2Id = JedisClusterTestUtil.getNodeId(node2.clusterNodes());
node3.clusterSetSlotMigrating(15363, node2Id);
node2.clusterSetSlotImporting(15363, node3Id);
try {
node2.set("e", "e");
} catch (JedisMovedDataException jme) {
assertEquals(15363, jme.getSlot());
assertEquals(new HostAndPort(localHost, nodeInfo3.getPort()), jme.getTargetNode());
}
try {
node3.set("e", "e");
} catch (JedisAskDataException jae) {
assertEquals(15363, jae.getSlot());
assertEquals(new HostAndPort(localHost, nodeInfo2.getPort()), jae.getTargetNode());
}
jc.set("e", "e");
try {
node2.get("e");
} catch (JedisMovedDataException jme) {
assertEquals(15363, jme.getSlot());
assertEquals(new HostAndPort(localHost, nodeInfo3.getPort()), jme.getTargetNode());
}
try {
node3.get("e");
} catch (JedisAskDataException jae) {
assertEquals(15363, jae.getSlot());
assertEquals(new HostAndPort(localHost, nodeInfo2.getPort()), jae.getTargetNode());
}
assertEquals("e", jc.get("e"));
node2.clusterSetSlotNode(15363, node2Id);
node3.clusterSetSlotNode(15363, node2Id);
// assertEquals("e", jc.get("e"));
assertEquals("e", node2.get("e"));
// assertEquals("e", node3.get("e"));
}
@Test(timeout = 2000)
public void testReturnConnectionOnJedisConnectionException() throws InterruptedException {
Set<HostAndPort> jedisClusterNode = new HashSet<HostAndPort>();
jedisClusterNode.add(new HostAndPort("127.0.0.1", 7379));
JedisPoolConfig config = new JedisPoolConfig();
config.setMaxTotal(1);
JedisCluster jc = new JedisCluster(jedisClusterNode, config);
Jedis j = jc.getClusterNodes().get("127.0.0.1:7380").getResource();
ClientKillerUtil.tagClient(j, "DEAD");
ClientKillerUtil.killClient(j, "DEAD");
j.close();
jc.get("test");
}
private void checkValue(
List<BusinessObject.Value> boValues, boolean strict, String name, Object... values) {
Set<Object> expected = CollectionUtils.newSetFromIterator(Arrays.asList(values).iterator());
Set<Object> actual = CollectionUtils.newSet();
for (BusinessObject.Value boValue : boValues) {
Map<?, ?> data = (Map<?, ?>) boValue.getValue();
actual.add(data.get(name));
}
if (strict) {
Assert.assertEquals("Values: ", expected, actual);
} else {
expected.removeAll(actual);
Assert.assertTrue("Missing values: " + expected, expected.isEmpty());
}
}