private PoolSummary compilePoolSummary(Pool pool) {
PoolSummary.Builder poolSummaryBuilder = aPoolSummary().withPoolName(pool.getName());
for (Device device : pool.getDevices()) {
compileResultsForDevice(pool, poolSummaryBuilder, device);
}
Device watchdog = getPoolWatchdog(pool.getName());
compileResultsForDevice(pool, poolSummaryBuilder, watchdog);
return poolSummaryBuilder.build();
}
/**
* get all worksite
*
* @return
*/
public WorkSite[] batch() {
WorkSite[] sites = null;
super.lockMulti();
try {
int size = mapSite.size();
if (size > 0) {
sites = new WorkSite[size];
mapSite.values().toArray(sites);
}
} catch (Throwable exp) {
Logger.fatal(exp);
} finally {
super.unlockMulti();
}
return sites;
}
@Test
public void testPools() {
try {
int expected = getDataSet().getTable("Pool").getRowCount();
int actual = getPoolDAO().count();
TestCase.assertEquals("Wrong number of Pools", expected, actual);
System.out.println("Expected number of Pools: " + expected + ", actual: " + actual);
for (Pool d : random(getPoolDAO(), actual, 1)) {
TestCase.assertNotNull(d);
TestCase.assertNotNull(d.getId());
}
} catch (Exception e) {
e.printStackTrace();
TestCase.fail();
}
}
/** check timeout site */
private void check() {
int size = mapTime.size();
if (size == 0) return;
ArrayList<SiteHost> dels = new ArrayList<SiteHost>(size);
ArrayList<SiteHost> notifys = new ArrayList<SiteHost>(size);
super.lockSingle();
try {
long nowTime = System.currentTimeMillis();
for (SiteHost host : mapTime.keySet()) {
Long value = mapTime.get(host);
if (value == null) {
dels.add(host);
continue;
}
long time = value.longValue();
if (nowTime - time >= deleteTime) {
dels.add(host);
} else if (nowTime - time >= refreshTimeout) {
notifys.add(host);
}
}
} catch (Throwable exp) {
exp.printStackTrace();
} finally {
super.unlockSingle();
}
// remove timeout site
for (SiteHost host : dels) {
Logger.error("WorkPool.check, delete timeout site:%s", host);
remove(host);
}
// notify site
SiteHost listen = Launcher.getInstance().getLocalHost();
for (SiteHost host : notifys) {
Logger.warning("WorkPool.check, notify timeout site:%s", host);
this.sendTimeout(host, listen, 2);
}
}
public void start() {
inputs = new AtomicReferenceArray<>(0);
outputs = inputs;
freeReceptors = new CopyOnWriteArrayList<>();
sequence = 0;
finalSequence = 0;
finalProduct = null;
reuseReceptors = new ArrayList<>(0);
executor = Executors.newSingleThreadExecutor();
started = true;
if (poolSize > 0) {
group = new ThreadGroup("FatPipe");
group.setMaxPriority(Thread.MAX_PRIORITY);
}
signals = new SignalImpl[ARBITARY_THREADS + poolSize];
threads = new Thread[ARBITARY_THREADS + poolSize];
startTime = System.currentTimeMillis();
sleptTime = 0;
toSleepTime = 0;
for (int i = 0; i < poolSize; i++) {
Thread t = new Thread(group, this, name + "-" + i);
t.setDaemon(true);
threads[i] = t;
t.start();
if (sleep == 0) t.setPriority(Thread.MAX_PRIORITY);
else if (sleep < 0) t.setPriority(Thread.NORM_PRIORITY);
else t.setPriority(Thread.MIN_PRIORITY);
}
for (int i = 0; i < signals.length; i++) {
signals[i] = new SignalImpl(lock);
}
if (pool != null) pool.add(this);
lock.release();
}
public JSONObject saveImportedElements(HttpSession session, JSONObject json) {
if (json.has("elements")) {
Plate currentPlate = null;
Pool currentPool = null;
try {
String description = json.getString("description");
String creationDate = json.getString("creationDate");
String plateMaterialType = null;
if (json.has("plateMaterialType") && !json.getString("plateMaterialType").equals("")) {
plateMaterialType = json.getString("plateMaterialType");
}
JSONObject elements = json.getJSONObject("elements");
JSONArray pools = JSONArray.fromObject(elements.get("pools"));
JSONArray savedPlates = new JSONArray();
ObjectMapper mapper = new ObjectMapper();
for (JSONArray innerPoolList : (Iterable<JSONArray>) pools) {
for (JSONObject pool : (Iterable<JSONObject>) innerPoolList) {
log.info(pool.toString());
PlatePool platePool =
mapper.readValue(pool.toString(), new TypeReference<PlatePool>() {});
currentPool = platePool;
for (Plate<LinkedList<Library>, Library> plate : platePool.getPoolableElements()) {
JSONObject j = new JSONObject();
// if (json.has("tagBarcode")) {
// String tagBarcode = json.getString("tagBarcode");
//
// plate.setTagBarcode(requestManager.listAllTagBarcodesByStrategyName());
// }
if (plate.getDescription() == null) {
plate.setDescription(description);
}
if (plate.getCreationDate() == null) {
// plate.setCreationDate(DateFormat.getInstance().parse(creationDate));
}
if (plate.getPlateMaterialType() == null && plateMaterialType != null) {
plate.setPlateMaterialType(PlateMaterialType.valueOf(plateMaterialType));
}
log.info("Saving plate: " + plate.toString());
currentPlate = plate;
long plateId = requestManager.savePlate(plate);
j.put("plateId", plateId);
savedPlates.add(j);
currentPlate = null;
}
log.info("Saving pool: " + pool.toString());
requestManager.savePool(platePool);
currentPool = null;
}
}
JSONObject resp = new JSONObject();
resp.put("plates", savedPlates);
return resp;
} catch (IOException e) {
if (currentPool != null) {
log.error(
"Error saving pool elements on new plate save. Deleting pool "
+ currentPool.toString());
// clear out child elements to make sure plate meets delete requirements
currentPool.getPoolableElements().clear();
try {
requestManager.deletePool(currentPool);
} catch (IOException e1) {
log.error("Cannot delete pool. Nothing left to do.");
e1.printStackTrace();
}
}
if (currentPlate != null) {
log.error(
"Error saving plate elements on new plate save. Deleting plate "
+ currentPlate.toString());
// clear out child elements to make sure plate meets delete requirements
currentPlate.getElements().clear();
try {
requestManager.deletePlate(currentPlate);
} catch (IOException e1) {
log.error("Cannot delete plate. Nothing left to do.");
e1.printStackTrace();
}
}
log.error("Caused by...");
e.printStackTrace();
return JSONUtils.SimpleJSONError("Cannot save imported plate: " + e.getMessage());
}
} else {
return JSONUtils.SimpleJSONError("No valid plates available to save");
}
}