Making it clear that the soft memory cache is a singleton

josemduarte · josemduarte · commit 2b1860b8b5ac · 2017-09-07T22:03:20.000-07:00
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/FlatFileCache.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/FlatFileCache.java
@@ -29,27 +29,23 @@
 
 import java.io.*;
 
-/** Provides a cache for storing multiple small files in memory. Can be used to e.g cache gzip compressed PDB files for avoiding disk IO bottlenecks.
- *
+/** 
+ * Provides a cache for storing multiple small files in memory. Can be used to e.g cache gzip compressed PDB files 
+ * for avoiding disk IO bottlenecks.
+ * Note this is just a wrapper for the singleton cache.
+ * 
  * @author Andreas Prlic.
  *
  */
 public class FlatFileCache {
 
 	private final static Logger logger = LoggerFactory.getLogger(FlatFileCache.class);
 
-	private static FlatFileCache me ;
-
+	/**
+	 * The cache singleton.
+	 */
 	private static SoftHashMap<String, byte[]> cache = new SoftHashMap<String, byte[]>(0);
 
-	public static FlatFileCache getInstance() {
-
-	   if ( me == null){
-	      me = new FlatFileCache();
-	   }
-
-		return me;
-	}
 
 	// no public constructor;
 	private FlatFileCache(){
@@ -109,20 +105,17 @@ public  static InputStream getInputStream(String key){
 
 	}
 
-	public int size() {
+	public static int size() {
 		if ( cache != null)
 			return cache.size();
 		else
 			return -1;
 	}
 
-	public void clear(){
+	public static void clear(){
 	   cache.clear();
 	}
 
-	public static void destroy(){
-	   me.clear();
-	   me = null;
-	}
+	
 
 }
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/InputStreamProvider.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/InputStreamProvider.java
@@ -72,8 +72,7 @@ public InputStreamProvider() {
 		String prop = System.getProperty(CACHE_PROPERTY);
 		if ( prop != null && prop.equals("true")) {
 			cacheRawFiles = true;
-			// init the singleton
-			FlatFileCache.getInstance();
+
 		}
 
 	}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/FarmJobRunnable.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/FarmJobRunnable.java
@@ -611,7 +611,7 @@ protected void sendResultsToServer(List<String> results) {
 		if ( progressListeners != null)
 			notifySubmittingAlignments(results.size(), msg);
 		logger.info("{}: Sent {} results to server. job status: {}", userName, results.size(), counter);
-		logger.info("{}: fileCache size: {}", userName, FlatFileCache.getInstance().size());
+		logger.info("{}: fileCache size: {}", userName, FlatFileCache.size());
 	}
 
 
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestDownloadChemCompProvider.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestDownloadChemCompProvider.java
@@ -69,8 +69,7 @@ public void testRedirectWorks() {
 		file.delete();
 		
 		// very important: we have a memory cache of files, we need to reset it not to pollute the cache for later tests
-		FlatFileCache ffc = FlatFileCache.getInstance();
-		ffc.clear();
+		FlatFileCache.clear();
 		
 		assertNotNull(cc);
 		
@@ -101,8 +100,7 @@ public void testWeDontCacheGarbage() {
 		file.delete();
 		
 		// very important: we have a memory cache of files, we need to reset it not to pollute the cache for later tests
-		FlatFileCache ffc = FlatFileCache.getInstance();
-		ffc.clear();
+		FlatFileCache.clear();
 		
 		// we couldn't parse, thus there should be no content
 		assertNull(cc.getName());
@@ -116,6 +114,7 @@ public void testWeDontCacheGarbage() {
 	@Test
 	public void testIfWeCachedGarbageWeCanDetectIt() throws IOException {
 		// see #703
+		// TODO this test for the moment only asserts that we get an empty chemcomp, since we can't detect bad cached files yet
 		
 		File file = new File(DownloadChemCompProvider.getLocalFileName("HEM"));
 		
@@ -132,8 +131,7 @@ public void testIfWeCachedGarbageWeCanDetectIt() throws IOException {
 		file.delete();
 		
 		// very important: we have a memory cache of files, we need to reset it not to pollute the cache for later tests
-		FlatFileCache ffc = FlatFileCache.getInstance();
-		ffc.clear();
+		FlatFileCache.clear();
 		
 		assertNull(cc.getName());
 		

Original file line number	Diff line number	Diff line change
`@@ -72,8 +72,7 @@ public InputStreamProvider() {`
`72`	`72`	`String prop = System.getProperty(CACHE_PROPERTY);`
`73`	`73`	`if ( prop != null && prop.equals("true")) {`
`74`	`74`	`cacheRawFiles = true;`
`75`		`- // init the singleton`
`76`		`- FlatFileCache.getInstance();`
	`75`	`+`
`77`	`76`	`}`
`78`	`77`
`79`	`78`	`}`
Original file line number	Diff line number	Diff line change
`@@ -611,7 +611,7 @@ protected void sendResultsToServer(List<String> results) {`
`611`	`611`	`if ( progressListeners != null)`
`612`	`612`	`notifySubmittingAlignments(results.size(), msg);`
`613`	`613`	`logger.info("{}: Sent {} results to server. job status: {}", userName, results.size(), counter);`
`614`		`- logger.info("{}: fileCache size: {}", userName, FlatFileCache.getInstance().size());`
	`614`	`+ logger.info("{}: fileCache size: {}", userName, FlatFileCache.size());`
`615`	`615`	`}`
`616`	`616`
`617`	`617`