Merge pull request #53 from CST-Group/concepts

Concepts

.github/workflows/java-ci.yml

@@ -15,20 +15,20 @@ jobs:
     runs-on: ubuntu-22.04
     strategy:
       matrix:
-        java: [ '8', '11']
+        java: [ '8', '11', '17']
     name: JDK ${{ matrix.Java }} build
     steps:
-      - uses: actions/checkout@v3.5.0
+      - uses: actions/checkout@v4.1.1
       - name: Set up Java
-        uses: actions/setup-java@v3.11.0
+        uses: actions/setup-java@v4.2.1
         with:
           java-version: ${{ matrix.java }}
           distribution: 'adopt'
           cache: gradle
       - name: Before Script
         run: curl -L https://codeclimate.com/downloads/test-reporter/test-reporter-latest-linux-amd64 > ./cc-test-reporter && chmod +x ./cc-test-reporter && ./cc-test-reporter before-build
       - name: Validate Gradle wrapper
-        uses: gradle/wrapper-validation-action@v1.0.6
+        uses: gradle/wrapper-validation-action@v3.3.0
       - name:  Build with Gradle headless
         uses: coactions/[email protected]
         with:
@@ -40,7 +40,7 @@ jobs:
           rm -f ~/.gradle/caches/modules-2/modules-2.lock
           rm -f ~/.gradle/caches/modules-2/gc.properties
       - name: Test & publish code coverage
-        uses: paambaati/codeclimate-action@v3.2.0
+        uses: paambaati/codeclimate-action@v5.0.0
         env:
           CC_TEST_REPORTER_ID: 430594ee361ff2e93ebf0a942f639b8092c6f17b7c5098f9c75abc404311dfc7
           JACOCO_SOURCE_PATH: "${{github.workspace}}/src/main/java"

build.gradle

@@ -2,15 +2,21 @@ plugins {
 	id 'java-library-distribution'
   	id 'jacoco'
   	id 'maven-publish'
-        id 'com.adarshr.test-logger' version "3.2.0"
+        id 'com.adarshr.test-logger' version "4.0.0"
 }
 
 group = 'com.github.CST-Group'
 
 description = "CST"
 
-sourceCompatibility = 1.8
-targetCompatibility = 1.8
+java {
+   //sourceCompatibility = JavaVersion.VERSION_11
+   //targetCompatibility = JavaVersion.VERSION_11
+   sourceCompatibility = JavaVersion.VERSION_1_8
+   targetCompatibility = JavaVersion.VERSION_1_8
+}
+
+
 version = '1.4.0'
 
 repositories {
@@ -25,22 +31,26 @@ configurations {
 dependencies {
    configurations.implementation.extendsFrom(configurations.extraLibs)
 
-   api 'com.google.code.gson:gson:2.8.9'
+   api 'com.google.code.gson:gson:2.10.1'
    api 'net.openhft:compiler:2.3.0'  // Used by representation/owrl/CodeBuilder.java
    api group: 'org.json', name: 'json', version: '20230227'
-   api group: 'org.opt4j', name: 'opt4j-core', version: '3.1'  // Used in GLAS
-   api group: 'org.opt4j', name: 'opt4j-optimizers', version: '3.1'
-   api group: 'org.opt4j', name: 'opt4j-viewer', version: '3.1' 
-   api group: 'org.opt4j', name: 'opt4j-benchmarks', version: '3.1'
-   api group: 'org.opt4j', name: 'opt4j-operators', version: '3.1'
-   api group: 'org.opt4j', name: 'opt4j-satdecoding', version: '3.1'
-   api group: 'org.opt4j', name: 'opt4j-tutorial', version: '3.1'
+   api 'com.google.inject:guice:7.0.0'
+   //api 'com.github.sdarg:opt4j:3.3.0'  // Used in GLAS
+   //api 'com.github.sdarg:opt4j:4780f4e'  // Used in GLAS
+   api group: 'org.opt4j', name: 'opt4j-core', version: '3.1.4'  // Used in GLAS
+   api group: 'org.opt4j', name: 'opt4j-optimizers', version: '3.1.4'
+   api group: 'org.opt4j', name: 'opt4j-viewer', version: '3.1.4' 
+   api group: 'org.opt4j', name: 'opt4j-benchmarks', version: '3.1.4'
+   api group: 'org.opt4j', name: 'opt4j-operators', version: '3.1.4'
+   api group: 'org.opt4j', name: 'opt4j-satdecoding', version: '3.1.4'
+   api group: 'org.opt4j', name: 'opt4j-tutorial', version: '3.1.4'
    api 'org.antlr:antlr4-runtime:4.5.3' // Used in OwrlBaseListener
    api 'com.github.masecla22:java-express:0.2.2'
+   //api 'io.vacco.murmux:murmux:2.2.2'
    implementation 'ch.qos.logback:logback-classic:1.3.6' 
-   //testImplementation group: 'junit', name: 'junit', version: '4.13.2'
-    testImplementation 'org.junit.jupiter:junit-jupiter-api:5.7.0'
-    testRuntimeOnly 'org.junit.jupiter:junit-jupiter-engine:5.7.0'
+   testImplementation 'org.junit.jupiter:junit-jupiter-api:5.10.1'
+   testRuntimeOnly 'org.junit.jupiter:junit-jupiter-engine:5.10.1'
+   testRuntimeOnly("org.junit.platform:junit-platform-launcher")
 
 }
 
@@ -57,15 +67,15 @@ jar {
 }
 
 task javadocJar(type: Jar) {
-    classifier = 'javadoc'
+    archiveClassifier = 'javadoc'
     from javadoc
     from {
     	configurations.extraLibs.collect { it.isDirectory() ? it : zipTree(it) }
     }
     javadoc.options.addStringOption('Xdoclint:none', '-quiet') // this is to avoid complaints about documentation missing parameter description
 }
 task sourcesJar(type: Jar) {
-    classifier = 'sources'
+    archiveClassifier = 'sources'
     from sourceSets.main.allSource
     from {
     	configurations.extraLibs.collect { it.isDirectory() ? it : zipTree(it) }

gradle/wrapper/gradle-wrapper.properties

@@ -1,5 +1,5 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-7.6.1-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.4-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists

src/main/java/br/unicamp/cst/attention/CFM.java

@@ -34,8 +34,8 @@
  * (i) the sum of the values​generated by the bottom-up feature maps and 
  * (ii) the sum of the values ​​generated by the top-down feature maps. 
  * 
- * If (i) > (ii), the winner of the attentional cycle is classified as bottom-up. 
- * If (ii) > (i), the winner of the attentional cycle is classified as top-down.
+ * If (i) {@code >} (ii), the winner of the attentional cycle is classified as bottom-up. 
+ * If (ii) {@code >} (i), the winner of the attentional cycle is classified as top-down.
  * 
  * @author leolellisr
  * 

src/main/java/br/unicamp/cst/behavior/asbac/AffordanceExtractorCodelet.java

@@ -275,7 +275,7 @@ public List<Percept> searchRelevantPercepts(AffordanceType aff, List<Percept> pe
      * Preprocess and init the computation of the cartesian product.
      * @param aff
      * @param relevantPercepts
-     * @return a list of map<String,Percept>
+     * @return a list of {@code Map<String,Percept>}
      */
     public List<Map<String, Percept>> getPerceptsCombinations(AffordanceType aff, Map<String, List<Percept>> relevantPercepts){
 

src/main/java/br/unicamp/cst/core/entities/Codelet.java

@@ -58,32 +58,32 @@ public abstract class Codelet implements Runnable, MemoryObserver {
 	/**
 	 * Activation level of the Codelet. Ranges from 0.0 to 1.0d.
 	 */
-	protected double activation = 0.0d;
+	protected volatile double activation = 0.0d;
 
 	/**
 	 * Threshold of the codelet, which is used to decide if it runs or not. If
 	 * activation is equal or greater than activation, codelet runs
 	 * proc().Ranges from 0.0 to 1.0d.
 	 */
-	protected double threshold = 0.0d;
+	protected volatile double threshold = 0.0d;
 	/**
 	 * Input memories, the ones that are read.
 	 */
-	protected List<Memory> inputs = new ArrayList<Memory>();
+	protected volatile List<Memory> inputs = new ArrayList<Memory>();
 	/**
 	 * Output memories, the ones that are written.
 	 */
-	protected List<Memory> outputs = new ArrayList<Memory>();
+	protected volatile List<Memory> outputs = new ArrayList<Memory>();
 	/**
 	 * Input memories, the ones that were broadcasted.
 	 */
-	protected List<Memory> broadcast = new ArrayList<Memory>();
+	protected volatile List<Memory> broadcast = new ArrayList<Memory>();
 
 	/** defines if proc() should be automatically called in a loop */
-	protected boolean loop = true; //
+	protected volatile boolean loop = true; //
 
 	/** defines if codelet is a memory observer (runs when memory input changes) */
-	protected boolean isMemoryObserver = false; //
+	protected volatile boolean isMemoryObserver = false; //
 
 	/**
 	 * If the proc() method is set to be called automatically in a loop, this
@@ -97,7 +97,7 @@ public abstract class Codelet implements Runnable, MemoryObserver {
 	 * A codelet is a priori enabled to run its proc(). However, if it tries to
 	 * read from a given output and fails, it becomes not able to do so.
 	 */
-	private boolean enabled = true;
+	private volatile boolean enabled = true;
 
 	/** Must be zero for this codelet to be enabled */
 	private int enable_count = 0;
@@ -106,10 +106,10 @@ public abstract class Codelet implements Runnable, MemoryObserver {
 	protected String name = Thread.currentThread().getName();
 
 	/** The time for the last proc() execution for profiling purposes */
-	long laststarttime = 0l;
+	volatile long laststarttime = 0l;
 
 	/** This variable is a safe lock for multithread access */
-	public Lock lock = new ReentrantLock();
+	public volatile Lock lock = new ReentrantLock();
 
 	/**
 	 * This method is used in every Codelet to capture input, broadcast and
@@ -131,7 +131,7 @@ public abstract class Codelet implements Runnable, MemoryObserver {
 	 */
 	public abstract void proc();
 
-	private Timer timer = new Timer();
+	private volatile Timer timer = new Timer();
 
 	/**
 	 * Option for profiling execution times
@@ -172,8 +172,10 @@ public synchronized void run() {
 	 * Starts this codelet execution.
 	 */
 	public synchronized void start() {
+            if (isMemoryObserver == false) {
 		Thread t = new Thread(this);
 		t.start();
+            }    
 	}
 
 	/**
@@ -801,17 +803,22 @@ public synchronized void setIsMemoryObserver(boolean isMemoryObserver) {
 		this.isMemoryObserver = isMemoryObserver;
 	}
 
+        @SuppressWarnings("empty-statement")
         public synchronized void setPublishSubscribe(boolean enable) {
             if (enable) {
                 setIsMemoryObserver(true);
                 for (Memory m : inputs) {
                     m.addMemoryObserver(this);
                 }
             } else {
-                setIsMemoryObserver(false);
                 for (Memory m : inputs) {
                     m.removeMemoryObserver(this);
                 }
+                setIsMemoryObserver(false);
+                try { this.wait(300L); } 
+                catch(InterruptedException e) {
+                    // just ignore exception
+                };
                 run();
             }
         }    

src/main/java/br/unicamp/cst/core/entities/CodeletContainer.java

@@ -7,35 +7,40 @@
 
 public class CodeletContainer implements Memory {
 
-	private HashMap<String, List<Memory>> mapInputs = new HashMap<String, List<Memory>>();
+	private volatile HashMap<String, List<Memory>> mapInputs = new HashMap<String, List<Memory>>();
 
 
-	private HashMap<String, List<Memory>> mapOutputs = new HashMap<String, List<Memory>>();
+	private volatile HashMap<String, List<Memory>> mapOutputs = new HashMap<String, List<Memory>>();
 
 
-	private HashMap<String, List<Memory>> mapBroadcast = new HashMap<String, List<Memory>>();
+	private volatile HashMap<String, List<Memory>> mapBroadcast = new HashMap<String, List<Memory>>();
 
 	/**
 	 * Output memories, the ones that are written.
 	 */
-	protected List<Memory> outputs = new ArrayList<Memory>();
+	protected volatile List<Memory> outputs = new ArrayList<Memory>();
 
 	/**
 	 * Input memories, the ones that were broadcasted.
 	 */
-	private List<Memory> broadcast = new ArrayList<Memory>();
+	private volatile List<Memory> broadcast = new ArrayList<Memory>();
 
 	/**
 	 * Input memories, the ones that are read.
 	 */
-	protected List<Memory> inputs = new ArrayList<Memory>();
+	protected volatile List<Memory> inputs = new ArrayList<Memory>();
 
-	private ArrayList<Codelet> codelets;
+	private volatile ArrayList<Codelet> codelets;
 
 	/**
-	 * Type of the codelet container
+	 * Name of the codelet container
 	 */
 	private String name;
+
+        /**
+         * Id for the CodeletContainer
+         */
+        private Long id;
 
 
 	public CodeletContainer() {
@@ -51,6 +56,27 @@ public CodeletContainer(ArrayList<Codelet> codelets, boolean isToStartCodelets)
 			this.addCodelet(codelet, isToStartCodelets);
 		});
 	}
+
+        /**
+	 * Gets the id of the CodeletContainer.
+	 * 
+	 * @return the id of the CodeletContainer.
+	 */
+        @Override
+	public synchronized Long getId() {
+		return this.id;
+	}
+
+	/**
+	 * Sets the id of the CodeletContainer.
+	 * 
+	 * @param id
+	 *            the id of the CodeletContainer to set.
+	 */
+        @Override
+	public synchronized void setId(Long id) {
+		this.id = id;
+	}
 
 	/**
 	 * Gets this Codelet activation.

src/main/java/br/unicamp/cst/core/entities/Memory.java

@@ -98,5 +98,19 @@ public interface Memory {
 	 */
 	public void removeMemoryObserver(MemoryObserver memoryObserver);
 
+        /**
+	 * Gets the id of the Memory.
+	 * 
+	 * @return the id of the Memory.
+	 */
+	public Long getId();
+
+	/**
+	 * Sets the id of the Memory.
+	 * 
+	 * @param id
+	 *            the id of the Memory to set.
+	 */
+	public void setId(Long id);
 
 }