@Test
public void shouldSearchForExistingGroupBeforeUpdating() throws Exception {
FlwGroup toBeUpdatedGroup =
new FlwGroupBuilder()
.groupId("5ba9a0928dde95d187544babf6c0ad24")
.name("afrisis team 1")
.domain("care-bihar")
.awcCode("001")
.caseSharing(true)
.reporting(true)
.build();
FlwGroup notToBeUpdatedGroup =
flwGroupWithNameAndId("5ba9a0928dde95d187544babf6c0af36", "ashok team 1");
template.saveOrUpdateAll(Arrays.asList(toBeUpdatedGroup, notToBeUpdatedGroup));
FlwGroup updatedGroup = updatedGroup();
careService.saveOrUpdateAllByExternalPrimaryKey(FlwGroup.class, Arrays.asList(updatedGroup));
FlwGroup loadedFlwGroup = template.load(FlwGroup.class, toBeUpdatedGroup.getId());
FlwGroup unchangedFlwGroup = template.load(FlwGroup.class, notToBeUpdatedGroup.getId());
assertReflectionEqualsWithIgnore(
updatedGroup(), loadedFlwGroup, new String[] {"id", "creationTime", "lastModifiedTime"});
assertDateIgnoringSeconds(new Date(), loadedFlwGroup.getCreationTime());
assertDateIgnoringSeconds(new Date(), loadedFlwGroup.getLastModifiedTime());
assertEquals("ashok team 1", unchangedFlwGroup.getName());
}
@Test
public void testLoadSIF() throws Exception {
String filepath = TestUtils.DATA_DIR + "sample/BRCA_sif.txt";
List<String> expectedAttributeNames =
Arrays.asList(
"TCGA_EXPERIMENT",
"TCGA_BATCH",
"TUMOR_NORMAL",
"BIRDSEED_GENDER",
"LEVEL2_NOISE",
"LEVEL3_SEGMENT_COUNT",
"PURITY PLOIDY",
"DELTA",
"CANCER_DNA_FRACTION",
"SUBCLONAL_GENOME_FRACTION");
tstLoadFi(filepath, 0, false); // Sample information file, shouldn't have tracks.
Set<String> attrNames = new HashSet<String>(AttributeManager.getInstance().getAttributeNames());
assertTrue(
attrNames.size()
>= expectedAttributeNames.size()); // Can be larger because of default attributes
for (String name : expectedAttributeNames) {
assertTrue(expectedAttributeNames.contains(name));
}
}
@Test
public void shouldSearchExistingFlwsAndUpdateFlw() {
Flw toBeUpdatedFlw =
flw(
"5ba9a0928dde95d187544babf6c0ad24",
"FirstName1",
flwGroupWithNameAndId("64a9a0928dde95d187544babf6c0ad38", "oldGroupName"));
Flw notToBeUpdateFlw = flw("5ba9a0928dde95d187544babf6c0ad25", "FirstName2", new FlwGroup());
template.saveOrUpdateAll(Arrays.asList(toBeUpdatedFlw, notToBeUpdateFlw));
Flw newFlw =
flw(
"5ba9a0928dde95d187544babf6c0ad24",
"FirstName3",
flwGroupWithNameAndId("38a9a0928dde95d187544babf6c0ad64", "newGroupName"));
ArrayList<Flw> flwsToUpdate = new ArrayList<>();
flwsToUpdate.add(newFlw);
careService.saveOrUpdateAllByExternalPrimaryKey(Flw.class, flwsToUpdate);
Flw updatedFlw = template.load(Flw.class, toBeUpdatedFlw.getId());
assertReflectionEqualsWithIgnore(
newFlw, updatedFlw, new String[] {"id", "creationTime", "lastModifiedTime"});
assertDateIgnoringSeconds(new Date(), updatedFlw.getCreationTime());
assertDateIgnoringSeconds(new Date(), updatedFlw.getLastModifiedTime());
Flw unchangedFlw = template.load(Flw.class, notToBeUpdateFlw.getId());
assertEquals("FirstName2", unchangedFlw.getFirstName());
}
@BeforeClass
public static void prepare() throws Exception // NOPMD
{
Registry.activateStandaloneMode();
Utilities.setJUnitTenant();
LOG.debug("Preparing...");
final ApplicationContext appCtx = Registry.getGlobalApplicationContext();
assertTrue(
"Application context of type "
+ appCtx.getClass()
+ " is not a subclass of "
+ ConfigurableApplicationContext.class,
appCtx instanceof ConfigurableApplicationContext);
final ConfigurableApplicationContext applicationContext =
(ConfigurableApplicationContext) appCtx;
final ConfigurableListableBeanFactory beanFactory = applicationContext.getBeanFactory();
assertTrue(
"Bean Factory of type "
+ beanFactory.getClass()
+ " is not of type "
+ BeanDefinitionRegistry.class,
beanFactory instanceof BeanDefinitionRegistry);
final XmlBeanDefinitionReader xmlReader =
new XmlBeanDefinitionReader((BeanDefinitionRegistry) beanFactory);
xmlReader.setDocumentReaderClass(ScopeTenantIgnoreDocReader.class);
xmlReader.loadBeanDefinitions(
new ClassPathResource(
"/merchandisefulfilmentprocess/test/merchandisefulfilmentprocess-spring-test.xml"));
xmlReader.loadBeanDefinitions(
new ClassPathResource(
"/merchandisefulfilmentprocess/test/merchandisefulfilmentprocess-spring-test-fraudcheck.xml"));
xmlReader.loadBeanDefinitions(
new ClassPathResource(
"/merchandisefulfilmentprocess/test/process/order-process-spring.xml"));
modelService = (ModelService) getBean("modelService");
processService = (DefaultBusinessProcessService) getBean("businessProcessService");
definitonFactory = processService.getProcessDefinitionFactory();
LOG.warn("Prepare Process Definition factory...");
definitonFactory.add(
"classpath:/merchandisefulfilmentprocess/test/process/payment-process.xml");
// setup command factory to mock
final DefaultCommandFactoryRegistryImpl commandFactoryReg =
appCtx.getBean(DefaultCommandFactoryRegistryImpl.class);
commandFactoryReg.setCommandFactoryList(
Arrays.asList((CommandFactory) appCtx.getBean("mockupCommandFactory")));
taskServiceStub = appCtx.getBean(TaskServiceStub.class);
productService = appCtx.getBean("defaultProductService", DefaultProductService.class);
cartService = appCtx.getBean("defaultCartService", DefaultCartService.class);
userService = appCtx.getBean("defaultUserService", DefaultUserService.class);
}
@Test
public void shouldCreateNewFlw() {
Flw newFlw =
flw(
"5ba9a0928dde95d187544babf6c0ad24",
"FirstName1",
flwGroupWithNameAndId("64a9a0928dde95d187544babf6c0ad38", "oldGroupName"));
careService.saveOrUpdateAllByExternalPrimaryKey(Flw.class, Arrays.asList(newFlw));
List<Flw> flwsFromDb = template.loadAll(Flw.class);
assertEquals(1, flwsFromDb.size());
assertReflectionContains(newFlw, flwsFromDb, new String[] {"id"});
}
public static void assertColumns(ColumnFamily cf, String... columnNames) {
Collection<IColumn> columns = cf == null ? new TreeSet<IColumn>() : cf.getSortedColumns();
List<String> L = new ArrayList<String>();
for (IColumn column : columns) {
L.add(new String(column.name()));
}
assert Arrays.equals(L.toArray(new String[columns.size()]), columnNames)
: "Columns ["
+ ((cf == null) ? "" : cf.getComparator().getColumnsString(columns))
+ "]"
+ " is not expected ["
+ StringUtils.join(columnNames, ",")
+ "]";
}
/**
* Test loading segmented data file from a sql database, using a profile
*
* @throws Exception
*/
@Test
public void testLoadSegProfile() throws Exception {
String path = TestUtils.DATA_DIR + "sql/seg_canFam2_profile.dbxml";
int expectedTracks = 6;
List<Track> tracks = trackLoader.load(new ResourceLocator(path), genome);
assertEquals(expectedTracks, tracks.size());
Set<String> expSampleIds =
new HashSet<String>(
Arrays.asList("0123-A", "0123-B-1", "0123-C-1", "0123-C-2", "0123-C-3"));
Set<String> actSampleIds = new HashSet<String>(5);
for (Track track : tracks) {
if (track instanceof DataSourceTrack) {
actSampleIds.add(track.getName());
}
}
assertEquals(expSampleIds, actSampleIds);
}
@Test
public void shouldSaveNewGroup() throws Exception {
FlwGroup newGroup =
new FlwGroupBuilder()
.groupId("5ba9a0928dde95d187544babf6c0ad24")
.name("amir team 1")
.domain("care-mp")
.awcCode("007")
.caseSharing(true)
.reporting(true)
.build();
careService.saveOrUpdateAllByExternalPrimaryKey(FlwGroup.class, Arrays.asList(newGroup));
List<FlwGroup> flwGroupsFromDb = template.loadAll(FlwGroup.class);
assertEquals(1, flwGroupsFromDb.size());
assertReflectionContains(newGroup, flwGroupsFromDb, new String[] {"id"});
}
/**
* Test loading sample information file from a sql database, using a profile
*
* @throws Exception
*/
@Test
public void testLoadSampleInfoProfile() throws Exception {
AttributeManager.getInstance().clearAllAttributes();
String path = TestUtils.DATA_DIR + "sql/sampleinfo_brca_sif_profile.dbxml";
int expectedTracks = 0;
List<Track> tracks = trackLoader.load(new ResourceLocator(path), genome);
assertEquals(expectedTracks, tracks.size());
String[] attrNames =
"TCGA_EXPERIMENT TCGA_BATCH TUMOR_NORMAL BIRDSEED_GENDER LEVEL2_NOISE LEVEL3_SEGMENT_COUNT PURITY PLOIDY DELTA CANCER_DNA_FRACTION SUBCLONAL_GENOME_FRACTION"
.split("\\s+");
Set<String> expAttrNames = new HashSet<String>(Arrays.asList(attrNames));
List<String> actAttrNames = AttributeManager.getInstance().getAttributeNames();
actAttrNames.remove("NAME");
actAttrNames.remove("DATA TYPE");
actAttrNames.remove("DATA FILE");
assertEquals(actAttrNames.size(), expAttrNames.size());
for (String attrName : actAttrNames) {
assertTrue(expAttrNames.contains(attrName));
}
}
@Test
public void downloadAsInputStream() throws IOException {
InputStream byteStream = object.downloadObjectAsInputStream();
assertTrue(Arrays.equals(bytes, IOUtils.toByteArray(byteStream)));
}
@Test
public void downloadAsByteArray() {
byte[] result = object.downloadObject();
assertTrue(Arrays.equals(bytes, result));
}
/** Read a contiguous set of registers. */
@Override
public TimestampedData readTimeStamped(int ireg, int creg) {
try {
synchronized (this.concurrentClientLock) {
synchronized (this.callbackLock) {
// Wait until the write cache isn't busy. This honors the visibility semantic
// we intend to portray, namely that issuing a read after a write has been
// issued will see the state AFTER the write has had a chance to take effect.
while (this.writeCacheStatus != WRITE_CACHE_STATUS.IDLE) {
this.callbackLock.wait();
}
// If there's no read window given or what's there either can't service any
// more reads or it doesn't contain the required registers, auto-make a new window.
if (this.readWindow == null
|| !this.readWindow.isOkToRead()
|| !this.readWindow.contains(ireg, creg)) {
// If we can re-use the window that was there before that will help increase
// the chance that we don't need to take the time to switch the controller to
// read mode (with a different window) and thus can respond faster.
if (this.readWindow != null && this.readWindow.contains(ireg, creg)) {
setReadWindow(this.readWindow);
} else {
// Make a one-shot that just covers the data we need right now
setReadWindow(new ReadWindow(ireg, creg, READ_MODE.ONLY_ONCE));
}
}
// We can only fetch registers that lie within the current register window.
// This actually should never trigger now, as the above should ALWAYS auto-adjust
// the window if necessary, but we have it here still as a check.
if (!this.readWindow.contains(ireg, creg)) {
throw new IllegalArgumentException(
String.format(
"read request (%d,%d) outside of read window (%d, %d)",
ireg, creg, this.readWindow.getIregFirst(), this.readWindow.getCreg()));
}
// Wait until the read cache is valid
while (this.readWindowChanged || !this.readCacheStatus.isValid()) {
this.callbackLock.wait();
}
// Extract the data and return!
this.readCacheLock.lockInterruptibly();
try {
assertTrue(!BuildConfig.DEBUG || this.readWindowActuallyRead.contains(this.readWindow));
// The data of interest is somewhere in the read window, but not necessarily at the
// start.
int ibFirst = ireg - this.readWindowActuallyRead.getIregFirst() + dibCacheOverhead;
TimestampedData result = new TimestampedData();
result.data = Arrays.copyOfRange(this.readCache, ibFirst, ibFirst + creg);
result.nanoTime = this.nanoTimeReadCacheValid;
return result;
} finally {
this.readCacheLock.unlock();
// If that was a one-time read, invalidate the data so we won't read it again a second
// time.
// Note that this is the only place outside of the callback that we ever update
// readCacheStatus or writeCacheStatus
if (this.readCacheStatus == READ_CACHE_STATUS.VALID_ONLYONCE)
this.readCacheStatus = READ_CACHE_STATUS.IDLE;
}
}
}
} catch (InterruptedException e) {
Util.handleCapturedInterrupt(e);
// Can't return (no data to return!) so we must throw
throw SwerveRuntimeException.wrap(e);
}
}
private void validateSliceLarge(ColumnFamilyStore cfStore) throws IOException {
String key = "row3";
ColumnFamily cf;
cf =
cfStore.getColumnFamily(
key,
new QueryPath("Standard1"),
"col1000".getBytes(),
ArrayUtils.EMPTY_BYTE_ARRAY,
false,
3);
assertColumns(cf, "col1000", "col1001", "col1002");
assertEquals(new String(cf.getColumn("col1000".getBytes()).value()), "v1000");
assertEquals(new String(cf.getColumn("col1001".getBytes()).value()), "v1001");
assertEquals(new String(cf.getColumn("col1002".getBytes()).value()), "v1002");
cf =
cfStore.getColumnFamily(
key,
new QueryPath("Standard1"),
"col1195".getBytes(),
ArrayUtils.EMPTY_BYTE_ARRAY,
false,
3);
assertColumns(cf, "col1195", "col1196", "col1197");
assertEquals(new String(cf.getColumn("col1195".getBytes()).value()), "v1195");
assertEquals(new String(cf.getColumn("col1196".getBytes()).value()), "v1196");
assertEquals(new String(cf.getColumn("col1197".getBytes()).value()), "v1197");
cf =
cfStore.getColumnFamily(
key,
new QueryPath("Standard1"),
"col1996".getBytes(),
ArrayUtils.EMPTY_BYTE_ARRAY,
true,
1000);
IColumn[] columns = cf.getSortedColumns().toArray(new IColumn[0]);
for (int i = 1000; i < 1996; i++) {
String expectedName = "col" + i;
IColumn column = columns[i - 1000];
assert Arrays.equals(column.name(), expectedName.getBytes())
: cfStore.getComparator().getString(column.name()) + " is not " + expectedName;
assert Arrays.equals(column.value(), ("v" + i).getBytes());
}
cf =
cfStore.getColumnFamily(
key,
new QueryPath("Standard1"),
"col1990".getBytes(),
ArrayUtils.EMPTY_BYTE_ARRAY,
false,
3);
assertColumns(cf, "col1990", "col1991", "col1992");
assertEquals(new String(cf.getColumn("col1990".getBytes()).value()), "v1990");
assertEquals(new String(cf.getColumn("col1991".getBytes()).value()), "v1991");
assertEquals(new String(cf.getColumn("col1992".getBytes()).value()), "v1992");
cf =
cfStore.getColumnFamily(
key,
new QueryPath("Standard1"),
ArrayUtils.EMPTY_BYTE_ARRAY,
ArrayUtils.EMPTY_BYTE_ARRAY,
true,
3);
assertColumns(cf, "col1997", "col1998", "col1999");
assertEquals(new String(cf.getColumn("col1999".getBytes()).value()), "v1999");
assertEquals(new String(cf.getColumn("col1998".getBytes()).value()), "v1998");
assertEquals(new String(cf.getColumn("col1997".getBytes()).value()), "v1997");
cf =
cfStore.getColumnFamily(
key,
new QueryPath("Standard1"),
"col9000".getBytes(),
ArrayUtils.EMPTY_BYTE_ARRAY,
true,
3);
assertColumns(cf, "col1997", "col1998", "col1999");
cf =
cfStore.getColumnFamily(
key,
new QueryPath("Standard1"),
"col9000".getBytes(),
ArrayUtils.EMPTY_BYTE_ARRAY,
false,
3);
assertColumns(cf);
}