Merge pull request #412 from cogmission/java_serialize

Introduces new PersistenceAPI

Author: cogmission

.classpath

@@ -17,5 +17,8 @@
 	<classpathentry kind="lib" path="libs/rxjava-1.0.10.jar" sourcepath="/Users/cogmission/Resources/RxJava/rxjava-1.0.10-sources.jar"/>
 	<classpathentry kind="lib" path="libs/slf4j-api-1.7.10.jar"/>
 	<classpathentry kind="lib" path="libs/trove-3.1a1.jar" sourcepath="/Users/cogmission/Resources/trove/3.1a1/trove-3.1a1-src.jar"/>
+	<classpathentry kind="lib" path="libs/java-util-1.19.3.jar" sourcepath="/Users/cogmission/.m2/repository/com/cedarsoftware/java-util/1.19.3/java-util-1.19.3-sources.jar"/>
+	<classpathentry kind="lib" path="libs/objenesis-2.1.jar"/>
+	<classpathentry combineaccessrules="false" kind="src" path="/fast-serialization"/>
 	<classpathentry kind="output" path="bin"/>
 </classpath>

Changelog.txt

@@ -0,0 +1,21 @@
+Changes for Serialization branch (notes for CHANGELOG.md)
+
+1. Renamed class ClassifierResult to Classification
+2. Renamed class EncoderResult to Encoding
+3. Removed extraneous constructor from FastRandom
+4. Added functionality to gradle build script: 
+   a.) Ability to see standard out/err
+   b.) Changed ability to skip tests when code hasn't changed to "always run tests"
+   c.) Added ability to toggle (b) so that it will skip again.
+5. Changed return type of assemble method of MultiEncoderAssembler from void to MultiEncoder
+6. Added getEncoderOfType(FieldMetaType type) method to MultiEncoder for convenient returning.
+7. Fixed erroneous creation of Sensors in every Layer of a multi-layer network (except the layer
+   representing the entry point or input - where it belongs)
+8. Added Persistable interface which extends Serializable and all HTM object which are serializable
+   implement.
+9. Added CheckPointer rx.Observable operator which executes check point operation and notification 
+   containing byte[] of serialized Network (can be ignored if not needed because it's save to disk)
+10. Added PersistenceAPI interface now implemented by Network.
+11. Added NetworkSerializer interface (and NetworkSerializerImpl) which executes FST serialization
+    and simultaneously implements the Kryo interface also.
+12. Added the SerialConfig class which contains config information for the NetworkSerializer.

[ htm.java Integration Test ] BasicTemporalMemoryTest.launch

@@ -1,10 +1,10 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <launchConfiguration type="org.eclipse.jdt.junit.launchconfig">
 <listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_PATHS">
-<listEntry value="/htm.java/src/test/java/org/numenta/nupic/integration/BasicTemporalMemoryTest.java"/>
+<listEntry value="/htm.java"/>
 </listAttribute>
 <listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_TYPES">
-<listEntry value="1"/>
+<listEntry value="4"/>
 </listAttribute>
 <mapAttribute key="org.eclipse.debug.core.preferred_launchers">
 <mapEntry key="[run]" value="org.eclipse.jdt.junit.launchconfig"/>

build.gradle

@@ -23,6 +23,16 @@ repositories {
     mavenCentral()
 }
 
+// COMMENT OUT TO SKIP TESTS WHEN CODE HASN'T CHANGED
+test {
+   outputs.upToDateWhen { false }
+}
+
+/* UNCOMMENT TO SEE STANDARD_OUT & STANDARD_ERR DURING BUILD
+test {
+    testLogging.showStandardStreams = true
+}*/
+
 dependencies {
     compile group: 'joda-time', name: 'joda-time', version: '2.5'
     compile(group: 'com.chaschev', name: 'chutils', version:'1.4') {
@@ -37,8 +47,10 @@ dependencies {
     compile group: 'com.fasterxml.jackson.core', name: 'jackson-core', version:'2.4.4'
     compile group: 'com.fasterxml.jackson.core', name: 'jackson-databind', version:'2.4.4'
     compile group: 'org.slf4j', name: 'slf4j-api', version:'1.7.10'
-    compile group: 'io.reactivex', name: 'rxjava', version: '1.0.10'
-    testCompile group: 'junit', name: 'junit', version:'4.11'
+	compile group: 'io.reactivex', name: 'rxjava', version: '1.0.10'
+	compile group: 'de.ruedigermoeller', name: 'fst', version: '2.45'
+	compile group: 'com.cedarsoftware', name: 'java-util', version: '1.19.3'
+	testCompile group: 'junit', name: 'junit', version:'4.11'
     testCompile group: 'ch.qos.logback', name: 'logback-classic', version:'1.1.2'
 }
 

libs/fst-2.45.jar

@@ -38,7 +38,7 @@
 	</scm>
 	<properties>
 		<argLine>-Xmx2048m -Xms1024m</argLine>
-    </properties>
+	</properties>
 	<dependencies>
 		<dependency>
 			<groupId>joda-time</groupId>
@@ -49,8 +49,8 @@
 			<groupId>com.chaschev</groupId>
 			<artifactId>chutils</artifactId>
 			<version>1.4</version>
-			<!--WE ONLY INTERESTED IN ASCIITable from this library, so exclude all 
-				transitive dependencies -->
+			<!--We're only interested in ASCIITable from this library, so exclude 
+				all transitive dependencies -->
 			<exclusions>
 				<exclusion>
 					<groupId>org.mockito</groupId>
@@ -117,6 +117,16 @@
 			<version>1.0.10</version>
 			<scope />
 		</dependency>
+		<dependency>
+			<groupId>com.cedarsoftware</groupId>
+			<artifactId>java-util</artifactId>
+			<version>1.19.3</version>
+		</dependency>
+		<dependency>
+			<groupId>de.ruedigermoeller</groupId>
+			<artifactId>fst</artifactId>
+			<version>2.45</version>
+		</dependency>
 		<dependency>
 			<groupId>org.openjdk.jmh</groupId>
 			<artifactId>jmh-core</artifactId>

libs/java-util-1.19.3.jar

@@ -40,7 +40,9 @@
  * 
  * @author David Ray
  */
-public class ComputeCycle {
+public class ComputeCycle implements Persistable {
+    private static final long serialVersionUID = 1L;
+    
     public Set<Cell> activeCells = new LinkedHashSet<>();
     public Set<Cell> winnerCells = new LinkedHashSet<>();
     public Set<Cell> predictiveCells = new LinkedHashSet<>();
@@ -149,4 +151,83 @@ public Set<DistalDendrite> matchingSegments() {
     public Set<Cell> matchingCells() {
         return matchingCells;
     }
+
+    /* (non-Javadoc)
+     * @see java.lang.Object#hashCode()
+     */
+    @Override
+    public int hashCode() {
+        final int prime = 31;
+        int result = 1;
+        result = prime * result + ((activeCells == null) ? 0 : activeCells.hashCode());
+        result = prime * result + ((activeSegments == null) ? 0 : activeSegments.hashCode());
+        result = prime * result + ((learningSegments == null) ? 0 : learningSegments.hashCode());
+        result = prime * result + ((matchingCells == null) ? 0 : matchingCells.hashCode());
+        result = prime * result + ((matchingSegments == null) ? 0 : matchingSegments.hashCode());
+        result = prime * result + ((predictedInactiveCells == null) ? 0 : predictedInactiveCells.hashCode());
+        result = prime * result + ((predictiveCells == null) ? 0 : predictiveCells.hashCode());
+        result = prime * result + ((successfullyPredictedColumns == null) ? 0 : successfullyPredictedColumns.hashCode());
+        result = prime * result + ((winnerCells == null) ? 0 : winnerCells.hashCode());
+        return result;
+    }
+
+    /* (non-Javadoc)
+     * @see java.lang.Object#equals(java.lang.Object)
+     */
+    @Override
+    public boolean equals(Object obj) {
+        if(this == obj)
+            return true;
+        if(obj == null)
+            return false;
+        if(getClass() != obj.getClass())
+            return false;
+        ComputeCycle other = (ComputeCycle)obj;
+        if(activeCells == null) {
+            if(other.activeCells != null)
+                return false;
+        } else if(!activeCells.equals(other.activeCells))
+            return false;
+        if(activeSegments == null) {
+            if(other.activeSegments != null)
+                return false;
+        } else if(!activeSegments.equals(other.activeSegments))
+            return false;
+        if(learningSegments == null) {
+            if(other.learningSegments != null)
+                return false;
+        } else if(!learningSegments.equals(other.learningSegments))
+            return false;
+        if(matchingCells == null) {
+            if(other.matchingCells != null)
+                return false;
+        } else if(!matchingCells.equals(other.matchingCells))
+            return false;
+        if(matchingSegments == null) {
+            if(other.matchingSegments != null)
+                return false;
+        } else if(!matchingSegments.equals(other.matchingSegments))
+            return false;
+        if(predictedInactiveCells == null) {
+            if(other.predictedInactiveCells != null)
+                return false;
+        } else if(!predictedInactiveCells.equals(other.predictedInactiveCells))
+            return false;
+        if(predictiveCells == null) {
+            if(other.predictiveCells != null)
+                return false;
+        } else if(!predictiveCells.equals(other.predictiveCells))
+            return false;
+        if(successfullyPredictedColumns == null) {
+            if(other.successfullyPredictedColumns != null)
+                return false;
+        } else if(!successfullyPredictedColumns.equals(other.successfullyPredictedColumns))
+            return false;
+        if(winnerCells == null) {
+            if(other.winnerCells != null)
+                return false;
+        } else if(!winnerCells.equals(other.winnerCells))
+            return false;
+        return true;
+    }
 }