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Webservices Per Page Data: Add in memory caching of results
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For Peptide, Protein, and Coverage pages.
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@danjasuw
danjasuw committed Jun 17, 2019
1 parent 39e34f2 commit 1901552
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Showing 15 changed files with 539 additions and 10 deletions.
319 changes: 319 additions & 0 deletions ...vices/cache_results_in_memory/DataPagesMain_GetDataWebservices_CacheResults_InMemory.java
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package org.yeastrc.xlink.www.webservices_data_pages_main_get_data_webservices.cache_results_in_memory;

import java.util.Arrays;
import java.util.Calendar;
import java.util.concurrent.TimeUnit;
import java.util.concurrent.atomic.AtomicLong;

import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.yeastrc.xlink.www.cached_data_mgmt.CacheCurrentSizeMaxSizeResult;
import org.yeastrc.xlink.www.cached_data_mgmt.CachedDataCentralRegistry;
import org.yeastrc.xlink.www.cached_data_mgmt.CachedDataCommonIF;
import org.yeastrc.xlink.www.searcher_via_cached_data.config_size_etc_central_code.CachedDataCentralConfigStorageAndProcessing;
import org.yeastrc.xlink.www.searcher_via_cached_data.config_size_etc_central_code.CachedDataSizeOptions;

import com.google.common.cache.Cache;
import com.google.common.cache.CacheBuilder;


/**
*
*
*/
public class DataPagesMain_GetDataWebservices_CacheResults_InMemory implements CachedDataCommonIF {

private static final Logger log = LoggerFactory.getLogger( DataPagesMain_GetDataWebservices_CacheResults_InMemory.class );

/**
* Data Type of Cached Data
*
*/
public enum DataType {
PEPTIDE_SINGLE_SEARCH, PEPTIDE_MULTIPLE_SEARCHES,
PROTEINS_ALL_SINGLE_SEARCH, PROTEINS_ALL_MULTIPLE_SEARCHES,
PROTEINS_CROSSLINKS_SINGLE_SEARCH, PROTEINS_CROSSLINKS_MULTIPLE_SEARCHES,
PROTEINS_LOOPLINKS_SINGLE_SEARCH, PROTEINS_LOOPLINKS_MULTIPLE_SEARCHES,
PROTEIN_COVERAGE_SINGLE_SEARCH_MULTIPLE_SEARCHES
}

private static final int CACHE_MAX_SIZE_FULL_SIZE = 20;
private static final int CACHE_MAX_SIZE_SMALL = 2;

private static final int CACHE_TIMEOUT_FULL_SIZE = 100; // in days
private static final int CACHE_TIMEOUT_SMALL = 20; // in days


private static final AtomicLong cacheGetCount = new AtomicLong();
private static final AtomicLong cacheDBRetrievalCount = new AtomicLong();

private static volatile int prevDayOfYear = -1;

private static boolean debugLogLevelEnabled = false;

/**
* Static singleton instance
*/
private static DataPagesMain_GetDataWebservices_CacheResults_InMemory _instance = null; // Delay creating until first getInstance() call

/**
* Static get singleton instance
* @return
* @throws Exception
*/
public static synchronized DataPagesMain_GetDataWebservices_CacheResults_InMemory getInstance() throws Exception {

if ( _instance == null ) {
_instance = new DataPagesMain_GetDataWebservices_CacheResults_InMemory();
}
return _instance;
}

/**
* constructor
*/
private DataPagesMain_GetDataWebservices_CacheResults_InMemory() {
if ( log.isDebugEnabled() ) {
debugLogLevelEnabled = true;
log.debug( "debug log level enabled" );
}

cacheHolderInternal = new CacheHolderInternal( this );

// Register this class with the centralized Cached Data Registry, to support centralized cache clearing
CachedDataCentralRegistry.getInstance().register( this );
}

private CacheHolderInternal cacheHolderInternal;


@Override
public CacheCurrentSizeMaxSizeResult getCurrentCacheSizeAndMax() throws Exception {
return cacheHolderInternal.getCurrentCacheSizeAndMax();
}


@Override
public void clearCacheData() throws Exception {
clearCache();
}

/**
* Recreate the cache using current config values, if they exist, or else defaults
* @throws Exception
*/
public void clearCache() throws Exception {
printPrevCacheHitCounts( true /* forcePrintNow */ );
cacheHolderInternal.invalidate();
}

/**
* @param dataType
* @param requestJSONBytes
* @return - null if not in cache
* @throws Exception
*/
public byte[] getData( DataType dataType, byte[] requestJSONBytes ) throws Exception {

printPrevCacheHitCounts( false /* forcePrintNow */ );

if ( debugLogLevelEnabled ) {
cacheGetCount.incrementAndGet();
}

Cache<LocalCacheKey, LocalCacheValue> cache = cacheHolderInternal.getCache();

if ( cache != null ) {

LocalCacheKey localCacheKey = new LocalCacheKey();
localCacheKey.dataType = dataType;
localCacheKey.requestJSONBytes = requestJSONBytes;

LocalCacheValue localCacheValue =
cache.getIfPresent( localCacheKey );
if ( localCacheValue == null ) {
return null;
}
return localCacheValue.responseJSONBytes; // EARLY return
}

return null;
}

/**
* @param dataType
* @param requestJSONBytes
* @throws Exception
*/
public void putData( DataType dataType, byte[] requestJSONBytes, byte[] responseJSONBytes ) throws Exception {

Cache<LocalCacheKey, LocalCacheValue> cache = cacheHolderInternal.getCache();

if ( cache != null ) {

LocalCacheKey localCacheKey = new LocalCacheKey();
localCacheKey.dataType = dataType;
localCacheKey.requestJSONBytes = requestJSONBytes;

LocalCacheValue localCacheValue = new LocalCacheValue();
localCacheValue.responseJSONBytes = responseJSONBytes;

cache.put( localCacheKey, localCacheValue );
}
}


/**
* classes for holding data in the cache
*
* key to the cache
*
*/
private static class LocalCacheKey {

DataType dataType;
byte[] requestJSONBytes;

@Override
public int hashCode() {
final int prime = 31;
int result = 1;
result = prime * result + ((dataType == null) ? 0 : dataType.hashCode());
result = prime * result + Arrays.hashCode(requestJSONBytes);
return result;
}
@Override
public boolean equals(Object obj) {
if (this == obj)
return true;
if (obj == null)
return false;
if (getClass() != obj.getClass())
return false;
LocalCacheKey other = (LocalCacheKey) obj;
if (dataType != other.dataType)
return false;
if (!Arrays.equals(requestJSONBytes, other.requestJSONBytes))
return false;
return true;
}

}

/**
* RESPONSE Object
*
*/
private static class LocalCacheValue {

byte[] responseJSONBytes;
}

/**
* Class to hold and create the cache object
*
*/
private static class CacheHolderInternal {

private DataPagesMain_GetDataWebservices_CacheResults_InMemory parentObject;

private CacheHolderInternal( DataPagesMain_GetDataWebservices_CacheResults_InMemory parentObject ) {
this.parentObject = parentObject;
}

private boolean cacheDataInitialized;

/**
* cached data, left null if no caching
*/
private Cache<LocalCacheKey, LocalCacheValue> dbRecordsDataCache = null;

private int cacheMaxSize;

/**
* @return
* @throws Exception
*/
public synchronized CacheCurrentSizeMaxSizeResult getCurrentCacheSizeAndMax() throws Exception {
CacheCurrentSizeMaxSizeResult result = new CacheCurrentSizeMaxSizeResult();
if ( dbRecordsDataCache != null ) {
result.setCurrentSize( dbRecordsDataCache.size() );
result.setMaxSize( cacheMaxSize );
}
return result;
}

/**
* @throws Exception
*/
private synchronized Cache<LocalCacheKey, LocalCacheValue> getCache( ) throws Exception {
if ( ! cacheDataInitialized ) {
CachedDataSizeOptions cachedDataSizeOptions =
CachedDataCentralConfigStorageAndProcessing.getInstance().getCurrentSizeConfigValue();

if ( cachedDataSizeOptions == CachedDataSizeOptions.FEW ) {
// No Cache, just mark initialized, dbRecordsDataCache already set to null;
cacheDataInitialized = true;
return dbRecordsDataCache; // EARLY RETURN
}

int cacheTimeout = CACHE_TIMEOUT_FULL_SIZE;
cacheMaxSize = DataPagesMain_GetDataWebservices_CacheResults_InMemory.CACHE_MAX_SIZE_FULL_SIZE;
if ( cachedDataSizeOptions == CachedDataSizeOptions.HALF ) {
cacheMaxSize = cacheMaxSize / 2;
} else if ( cachedDataSizeOptions == CachedDataSizeOptions.SMALL ) {
cacheMaxSize = DataPagesMain_GetDataWebservices_CacheResults_InMemory.CACHE_MAX_SIZE_SMALL;
cacheTimeout = CACHE_TIMEOUT_SMALL;
}

dbRecordsDataCache = CacheBuilder.newBuilder()
.expireAfterAccess( cacheTimeout, TimeUnit.DAYS )
.maximumSize( cacheMaxSize )
.build();
// .build(); // no CacheLoader
cacheDataInitialized = true;
}
return dbRecordsDataCache;
}

private synchronized void invalidate() {
dbRecordsDataCache = null;
cacheDataInitialized = false;
}

}

/**
*
*/
private void printPrevCacheHitCounts( boolean forcePrintNow ) {

Calendar now = Calendar.getInstance();

int nowDayOfYear = now.get( Calendar.DAY_OF_YEAR );

if ( prevDayOfYear != nowDayOfYear || forcePrintNow ) {

if ( prevDayOfYear != -1 ) {
if ( debugLogLevelEnabled ) {
log.debug( "Cache total gets and db loads(misses) for previous day (or since last cache recreate): 'total gets': " + cacheGetCount.intValue()
+ ", misses: " + cacheDBRetrievalCount.intValue() );
}
}
if ( forcePrintNow ) {
if ( debugLogLevelEnabled ) {
log.debug( "Cache total gets and db loads(misses) since last print: 'total gets': " + cacheGetCount.intValue()
+ ", misses: " + cacheDBRetrievalCount.intValue() );
}
}

prevDayOfYear = nowDayOfYear;
// Reset cache hit and miss counters
cacheGetCount.set(0);
cacheDBRetrievalCount.set(0);
}

}


}
23 changes: 22 additions & 1 deletion ...in_get_data_webservices/peptide_page/PeptidePage_MultipleSearches_MainDisplayService.java
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Expand Up @@ -45,6 +45,8 @@
import org.yeastrc.xlink.www.searcher.ProjectIdsForProjectSearchIdsSearcher;
import org.yeastrc.xlink.www.web_utils.GenerateVennDiagramDataToJSON;
import org.yeastrc.xlink.www.web_utils.MarshalObjectToJSON;
import org.yeastrc.xlink.www.webservices_data_pages_main_get_data_webservices.cache_results_in_memory.DataPagesMain_GetDataWebservices_CacheResults_InMemory;
import org.yeastrc.xlink.www.webservices_data_pages_main_get_data_webservices.cache_results_in_memory.DataPagesMain_GetDataWebservices_CacheResults_InMemory.DataType;
import org.yeastrc.xlink.www.webservices_data_pages_main_get_data_webservices.peptide_page.PeptidePage_MultipleSearches_MainDisplayService_CachedResultManager.PeptidePage_MultipleSearches_MainDisplayService_CachedResultManager_Result;
import org.yeastrc.xlink.www.webservices_utils.Unmarshal_RestRequest_JSON_ToObject;

Expand Down Expand Up @@ -164,15 +166,30 @@ public class PeptidePage_MultipleSearches_MainDisplayService {
//////// Auth complete
//////////////////////////////////////////

{ // Check Cached response in RAM
byte[] cachedWebserviceResponseJSONAsBytes =
DataPagesMain_GetDataWebservices_CacheResults_InMemory.getInstance()
.getData( DataType.PEPTIDE_MULTIPLE_SEARCHES, requestJSONBytes );
if ( cachedWebserviceResponseJSONAsBytes != null ) {
// Have Cached response so just return it
return cachedWebserviceResponseJSONAsBytes; // EARLY RETURN !!!!!!!!!!!!!!
}
}
{
// First check Cached response on disk
// Next check Cached response on disk
PeptidePage_MultipleSearches_MainDisplayService_CachedResultManager_Result result =
PeptidePage_MultipleSearches_MainDisplayService_CachedResultManager.getSingletonInstance()
.retrieveDataFromCache( projectSearchIdsList, requestJSONBytes );

byte[] cachedWebserviceResponseJSONAsBytes = result.getWebserviceResponseJSONAsBytes();
if ( cachedWebserviceResponseJSONAsBytes != null ) {
// Have Cached response so just return it

{ // Cache response to RAM
DataPagesMain_GetDataWebservices_CacheResults_InMemory.getInstance()
.putData( DataType.PEPTIDE_MULTIPLE_SEARCHES, requestJSONBytes, cachedWebserviceResponseJSONAsBytes );
}

return cachedWebserviceResponseJSONAsBytes; // EARLY RETURN !!!!!!!!!!!!!!
}
}
Expand Down Expand Up @@ -376,6 +393,10 @@ public class PeptidePage_MultipleSearches_MainDisplayService {

byte[] webserviceResultByteArray = MarshalObjectToJSON.getInstance().getJSONByteArray( webserviceResult );

{ // Cache response to RAM
DataPagesMain_GetDataWebservices_CacheResults_InMemory.getInstance()
.putData( DataType.PEPTIDE_MULTIPLE_SEARCHES, requestJSONBytes, webserviceResultByteArray );
}
{
// Cache response to disk
PeptidePage_MultipleSearches_MainDisplayService_CachedResultManager.getSingletonInstance()
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2 changes: 2 additions & 0 deletions ...ces/peptide_page/PeptidePage_MultipleSearches_MainDisplayService_CachedResultManager.java
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Expand Up @@ -14,6 +14,8 @@
*
* Manage Cached results for PeptidePage_MultipleSearches_MainDisplayService
*
* Cache bytes to Disk File using CachedDataInFileMgmt
*
* Interfaces with the CachedDataInFileMgmt for saving and retrieving the result JSON for caching
*
* Added to CachedDataInFileMgmtRegistration to register it
Expand Down

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