refactor(core): simplify naming in bigraph/signature builders --- shorter method names & class renames --- docu updated

Author: PioBeat

README.md

@@ -1,6 +1,8 @@
 <img src="etc/assets/bigraph-framework-logo.png" style="zoom:67%;" />
 
-> Latest Version: **2.1.2**
+> Latest Version: **2.2.0**
+
+[![HiRSE Code Promo Badge](https://img.shields.io/badge/Promo-8db427?style=plastic&label=HiRSE&labelColor=005aa0&link=https%3A%2F%2Fgo.fzj.de%2FCodePromo)](https://rg-rse.pages.jsc.fz-juelich.de/hirse-code-promotion/public/HiRSE_Code_Promo_Slideshow.pdf)
 
 - User Manual: https://bigraphs.org/products/bigraph-framework/docs/
 
@@ -65,10 +67,10 @@ To following usage assumes the import statement `import static org.bigraphs.fram
 
 ```java
 // Create the signature
-DefaultDynamicSignature signature = pureSignatureBuilder()
+DynamicSignature signature = pureSignatureBuilder()
                 // Straightforward:
-                .addControl("A", 0)
-                .addControl("C", 1)
+                .add("A", 0)
+                .add("C", 1)
                 // More verbose:
                 .newControl()
                   .identifier(StringTypedName.of("User"))
@@ -78,14 +80,14 @@ DefaultDynamicSignature signature = pureSignatureBuilder()
 
 // Create two bigraphs
 PureBigraph bigraph1 = pureBuilder(signature)
-        .createRoot()
-        .addChild("A").addChild("C")
-        .createBigraph();
+        .root()
+        .child("A").child("C")
+        .create();
 
 PureBigraph bigraph2 = pureBuilder(signature)
         // "User" is the control, "alice" is an outer name     
-        .createRoot().addChild("User", "alice").addSite()
-        .createBigraph();
+        .root().child("User", "alice").site()
+        .create();
 
 // compose two bigraphs
 BigraphComposite composite = ops(bigraph2).compose(bigraph1);
@@ -101,8 +103,8 @@ complex structures easily.
 The following one shows, how to create nodes, and at the same time connecting them all with an edge:
 
 ```java
-PureBigraphBuilder<DefaultDynamicSignature> builder = pureBuilder(signature);
-builder.createRoot().connectByEdge(
+PureBigraphBuilder<DynamicSignature> builder = pureBuilder(signature);
+builder.root().connectByEdge(
     "Job",
             "Job",
     signature.getControlByName("Job")
@@ -117,8 +119,8 @@ after, close the link to automatically transform it to an edge:
 BigraphEntity.InnerName tmp_link = builder.createInnerName("link");
 
 // Create two nodes within different hierarchies
-builder.createRoot().addChild("Printer").linkToInner(tmp_link);
-builder.createRoot().addChild("Computer").linkToInner(tmp_link);
+builder.root().child("Printer").linkInner(tmp_link);
+builder.root().child("Computer").linkInner(tmp_link);
 
 // Finally, close the inner name. This will leave the edge intact.
 builder.closeInnerName(tmp_link);
@@ -144,9 +146,9 @@ To get the composition and tensor product of two bigraphs:
 PureBigraph G = ...;
 PureBigraph F = ...;
 PureBigraph H = ...;
-BigraphComposite<DefaultDynamicSignature> composite = ops(G);
+BigraphComposite<DynamicSignature> composite = ops(G);
 
-BigraphComposite<DefaultDynamicSignature> result = composite.compose(F);
+BigraphComposite<DynamicSignature> result = composite.compose(F);
 composite.juxtapose(F);
 composite.juxtapose(F).parallelProduct(H);
 ```
@@ -163,36 +165,36 @@ composite.juxtapose(F).parallelProduct(H);
   <dependency>
     <groupId>org.bigraphs.framework</groupId>
     <artifactId>bigraph-core</artifactId>
-    <version>2.1.2</version>
+    <version>2.2.0</version>
   </dependency>
   <!-- the rewriting module -->
   <dependency>
     <groupId>org.bigraphs.framework</groupId>
     <artifactId>bigraph-simulation</artifactId>
-    <version>2.1.2</version>
+    <version>2.2.0</version>
   </dependency>
   <!-- the visualization module -->
   <dependency>
     <groupId>org.bigraphs.framework</groupId>
     <artifactId>bigraph-visualization</artifactId>
-    <version>2.1.2</version>
+    <version>2.2.0</version>
   </dependency>
   <!-- the converter module -->
   <dependency>
     <groupId>org.bigraphs.framework</groupId>
     <artifactId>bigraph-converter</artifactId>
-    <version>2.1.2</version>
+    <version>2.2.0</version>
   </dependency>
 </dependencies>
 ```
 
 ### Gradle
 
 ```groovy
-compile "org.bigraphs.framework:bigraph-core:2.1.2"
-compile "org.bigraphs.framework:bigraph-simulation:2.1.2"
-compile "org.bigraphs.framework:bigraph-visualization:2.1.2"
-compile "org.bigraphs.framework:bigraph-converter:2.1.2"
+compile "org.bigraphs.framework:bigraph-core:2.2.0"
+compile "org.bigraphs.framework:bigraph-simulation:2.2.0"
+compile "org.bigraphs.framework:bigraph-visualization:2.2.0"
+compile "org.bigraphs.framework:bigraph-converter:2.2.0"
 ```
 
 ### Logging

converter/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>org.bigraphs.framework</groupId>
         <artifactId>framework-parent</artifactId>
-        <version>3.0.0-SNAPSHOT</version>
+        <version>2.2.0</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
     <modelVersion>4.0.0</modelVersion>

converter/src/main/java/org/bigraph/model/SignatureAdapter.java

@@ -6,7 +6,7 @@
 import org.bigraphs.framework.core.Signature;
 import org.bigraphs.framework.core.datatypes.FiniteOrdinal;
 import org.bigraphs.framework.core.datatypes.StringTypedName;
-import org.bigraphs.framework.core.impl.signature.DefaultDynamicSignature;
+import org.bigraphs.framework.core.impl.signature.DynamicSignature;
 import org.bigraph.model.assistants.IObjectIdentifier;
 import org.bigraph.model.interfaces.ISignature;
 
@@ -17,7 +17,7 @@
 /**
  * Adapter for our {@link Signature} class to be used with {@link org.bigraph.model.savers.SignatureXMLSaver}.
  * <p>
- * This is an adapter for the signature of type {@link DefaultDynamicSignature}.
+ * This is an adapter for the signature of type {@link DynamicSignature}.
  *
  * @author Dominik Grzelak
  */

converter/src/main/java/org/bigraphs/framework/converter/bigred/DefaultBigraphXMLLoader.java

@@ -3,8 +3,8 @@
 import org.bigraphs.framework.core.BigraphEntityType;
 import org.bigraphs.framework.core.Control;
 import org.bigraphs.framework.core.impl.BigraphEntity;
-import org.bigraphs.framework.core.impl.signature.DefaultDynamicControl;
-import org.bigraphs.framework.core.impl.signature.DefaultDynamicSignature;
+import org.bigraphs.framework.core.impl.signature.DynamicControl;
+import org.bigraphs.framework.core.impl.signature.DynamicSignature;
 import org.bigraphs.framework.core.impl.pure.MutableBuilder;
 import org.bigraphs.framework.core.impl.pure.PureBigraph;
 import org.apache.commons.lang3.tuple.Pair;
@@ -26,8 +26,8 @@ public class DefaultBigraphXMLLoader extends BigraphXmlLoaderSupport implements
     private DefaultSignatureXMLLoader sxl = new DefaultSignatureXMLLoader();
     private Path pathToSignature;
     protected int portIndexCounter = 0;
-    protected DefaultDynamicSignature signature = null;
-    protected MutableBuilder<DefaultDynamicSignature> builder;
+    protected DynamicSignature signature = null;
+    protected MutableBuilder<DynamicSignature> builder;
 
     public DefaultBigraphXMLLoader() {
         super();
@@ -38,7 +38,7 @@ public DefaultBigraphXMLLoader() {
      *
      * @param signature the signature
      */
-    public DefaultBigraphXMLLoader(DefaultDynamicSignature signature) {
+    public DefaultBigraphXMLLoader(DynamicSignature signature) {
         super();
         this.signature = signature;
     }
@@ -77,7 +77,7 @@ private void reset() {
             parentStack.clear();
     }
 
-    public DefaultDynamicSignature getSignature() {
+    public DynamicSignature getSignature() {
         return signature;
     }
 
@@ -190,7 +190,7 @@ protected void processEndRoot(EndElement endElement) {
     protected void processStartNode(StartElement startElement) {
         portIndexCounter = 0;
         Iterator<Attribute> attributes = startElement.getAttributes();
-        DefaultDynamicControl controlByName = null;
+        DynamicControl controlByName = null;
         String label = "";
         while (attributes.hasNext()) {
             Attribute attribute = attributes.next();

converter/src/main/java/org/bigraphs/framework/converter/bigred/DefaultReactionRuleXMLLoader.java

@@ -2,8 +2,8 @@
 
 import org.bigraphs.framework.core.exceptions.InvalidReactionRuleException;
 import org.bigraphs.framework.core.impl.BigraphEntity;
-import org.bigraphs.framework.core.impl.signature.DefaultDynamicControl;
-import org.bigraphs.framework.core.impl.signature.DefaultDynamicSignature;
+import org.bigraphs.framework.core.impl.signature.DynamicControl;
+import org.bigraphs.framework.core.impl.signature.DynamicSignature;
 import org.bigraphs.framework.core.EcoreBigraph;
 import org.bigraphs.framework.core.impl.pure.MutableBuilder;
 import org.bigraphs.framework.core.impl.pure.PureBigraph;
@@ -22,12 +22,12 @@
  */
 public class DefaultReactionRuleXMLLoader implements BigraphXmlLoaderSupport.XmlProcessorCallback, BigRedXmlLoader {
     protected Queue<ChangeAction> actionStack = new ArrayDeque<>();
-    protected MutableBuilder<DefaultDynamicSignature> builder;
+    protected MutableBuilder<DynamicSignature> builder;
     protected final DefaultBigraphXMLLoader bxl;
     protected boolean bigraphParsed = false;
     protected PureBigraph redex;
     protected PureBigraph reactum;
-    protected DefaultDynamicSignature signature = null;
+    protected DynamicSignature signature = null;
 
     private enum ChangeEvent {
         DISCONNECT("disconnect"), CONNECT("connect"),
@@ -80,7 +80,7 @@ public DefaultReactionRuleXMLLoader() {
      *
      * @param signature the signature
      */
-    public DefaultReactionRuleXMLLoader(DefaultDynamicSignature signature) {
+    public DefaultReactionRuleXMLLoader(DynamicSignature signature) {
 //        this();
         this.signature = signature;
         this.bxl = new DefaultBigraphXMLLoader(this.signature);
@@ -198,7 +198,7 @@ private void executeAddEvent(ChangeAction changeAction) {
             parent = builder.availableNodes().get(parentName);
         }
         if (type.equalsIgnoreCase("node")) {
-            DefaultDynamicControl control = redex.getSignature().getControlByName(changeAction.params.get("control"));
+            DynamicControl control = redex.getSignature().getControlByName(changeAction.params.get("control"));
             BigraphEntity newNode = builder.createNewNode(control, elementName);
             builder.availableNodes().put(elementName, (BigraphEntity.NodeEntity) newNode);
             if (Objects.nonNull(parent)) {
@@ -336,7 +336,7 @@ private boolean canParseInteger(String value) {
         }
     }
 
-    public DefaultDynamicSignature getSignature() {
+    public DynamicSignature getSignature() {
         return signature;
     }
 }

converter/src/main/java/org/bigraphs/framework/converter/bigred/DefaultSignatureXMLLoader.java

@@ -2,7 +2,7 @@
 
 import org.bigraphs.framework.core.ControlStatus;
 import org.bigraphs.framework.core.datatypes.StringTypedName;
-import org.bigraphs.framework.core.impl.signature.DefaultDynamicSignature;
+import org.bigraphs.framework.core.impl.signature.DynamicSignature;
 import org.bigraphs.framework.core.impl.signature.DynamicSignatureBuilder;
 import org.apache.commons.lang3.tuple.MutablePair;
 import org.apache.commons.lang3.tuple.Pair;
@@ -39,7 +39,7 @@ public DefaultSignatureXMLLoader() {
         super();
     }
 
-    public DefaultDynamicSignature importObject() {
+    public DynamicSignature importObject() {
         return b.create();
     }
 

converter/src/main/java/org/bigraphs/framework/converter/bigred/DefaultSimulationSpecXMLLoader.java

@@ -1,7 +1,7 @@
 package org.bigraphs.framework.converter.bigred;
 
 import org.bigraphs.framework.core.exceptions.InvalidReactionRuleException;
-import org.bigraphs.framework.core.impl.signature.DefaultDynamicSignature;
+import org.bigraphs.framework.core.impl.signature.DynamicSignature;
 import org.bigraphs.framework.core.impl.pure.PureBigraph;
 import org.bigraphs.framework.core.reactivesystem.AbstractSimpleReactiveSystem;
 import org.bigraphs.framework.core.reactivesystem.ReactiveSystem;
@@ -31,7 +31,7 @@ public class DefaultSimulationSpecXMLLoader implements BigRedXmlLoader {
     private DefaultReactionRuleXMLLoader rxl;
     private DefaultBigraphXMLLoader bxl;
     protected String xmlFile;
-    protected DefaultDynamicSignature signature = null;
+    protected DynamicSignature signature = null;
     private AbstractSimpleReactiveSystem<PureBigraph> reactiveSystem;
 
     public DefaultSimulationSpecXMLLoader(AbstractSimpleReactiveSystem<PureBigraph> reactiveSystem) {

converter/src/main/java/org/bigraphs/framework/converter/jlibbig/JLibBigBigraphDecoder.java

@@ -6,8 +6,8 @@
 import org.bigraphs.framework.core.impl.pure.MutableBuilder;
 import org.bigraphs.framework.core.impl.pure.PureBigraph;
 import org.bigraphs.framework.core.impl.pure.PureBigraphBuilder;
-import org.bigraphs.framework.core.impl.signature.DefaultDynamicControl;
-import org.bigraphs.framework.core.impl.signature.DefaultDynamicSignature;
+import org.bigraphs.framework.core.impl.signature.DynamicControl;
+import org.bigraphs.framework.core.impl.signature.DynamicSignature;
 import org.bigraphs.framework.core.impl.signature.DynamicSignatureBuilder;
 import it.uniud.mads.jlibbig.core.attachedProperties.Property;
 import it.uniud.mads.jlibbig.core.attachedProperties.PropertyTarget;
@@ -26,8 +26,8 @@ public class JLibBigBigraphDecoder implements BigraphObjectDecoder<PureBigraph,
     private HashMap<String, BigraphEntity.Edge> newEdges = new LinkedHashMap<>();
     private HashMap<String, BigraphEntity.OuterName> newOuterNames = new LinkedHashMap<>();
     private HashMap<String, BigraphEntity.InnerName> newInnerNames = new LinkedHashMap<>();
-    private MutableBuilder<DefaultDynamicSignature> builder;
-    private DefaultDynamicSignature signature;
+    private MutableBuilder<DynamicSignature> builder;
+    private DynamicSignature signature;
     private it.uniud.mads.jlibbig.core.std.Bigraph jBigraph;
 
     private Map<String, it.uniud.mads.jlibbig.core.std.OuterName> jLibBigOuterNames = new LinkedHashMap<>();
@@ -37,7 +37,7 @@ public class JLibBigBigraphDecoder implements BigraphObjectDecoder<PureBigraph,
     private Map<String, it.uniud.mads.jlibbig.core.std.Node> jLibBigNodes = new LinkedHashMap<>(); // PlaceEntity
     private Map<Integer, it.uniud.mads.jlibbig.core.std.Site> jLibBigSites = new LinkedHashMap<>(); // PlaceEntity
 
-    public synchronized PureBigraph decode(it.uniud.mads.jlibbig.core.std.Bigraph bigraph, DefaultDynamicSignature signature) {
+    public synchronized PureBigraph decode(it.uniud.mads.jlibbig.core.std.Bigraph bigraph, DynamicSignature signature) {
         this.jBigraph = bigraph;
         this.signature = signature;
         EPackage ePackage = createOrGetBigraphMetaModel(this.signature);
@@ -59,7 +59,7 @@ public synchronized PureBigraph decode(it.uniud.mads.jlibbig.core.std.Bigraph bi
         performLinkage(bigraph);
 
         // Create bigraph
-        PureBigraphBuilder<DefaultDynamicSignature>.InstanceParameter meta = this.builder.new InstanceParameter(
+        PureBigraphBuilder<DynamicSignature>.InstanceParameter meta = this.builder.new InstanceParameter(
                 this.builder.getMetaModel(),
                 this.signature,
                 this.newRoots,
@@ -199,7 +199,7 @@ private BigraphEntity getParentOfNode(PlaceEntity node, Bigraph jBigraph) {
     private BigraphEntity.NodeEntity createNode(Node n, BigraphEntity parent) {
         String control = n.getControl().getName();
         String nodeId = n.getEditable().getName();
-        DefaultDynamicControl controlByName = signature.getControlByName(control);
+        DynamicControl controlByName = signature.getControlByName(control);
         // Check if node has an ID property - use that instead
         if(n.getProperty("_id") != null) {
             nodeId = String.valueOf(n.getProperty("_id").get());
@@ -228,11 +228,11 @@ private BigraphEntity.SiteEntity createSite(Site n, BigraphEntity currentParent)
         return newSite;
     }
 
-    private DefaultDynamicSignature parseSignature(it.uniud.mads.jlibbig.core.std.Signature sig) {
+    private DynamicSignature parseSignature(it.uniud.mads.jlibbig.core.std.Signature sig) {
         DynamicSignatureBuilder signatureBuilder = pureSignatureBuilder();
         for (Iterator<Control> it = sig.iterator(); it.hasNext(); ) {
             Control control = it.next();
-            signatureBuilder.addControl(control.getName(), control.getArity(), control.isActive() ? ControlStatus.ACTIVE : ControlStatus.PASSIVE);
+            signatureBuilder.add(control.getName(), control.getArity(), control.isActive() ? ControlStatus.ACTIVE : ControlStatus.PASSIVE);
         }
         return signatureBuilder.create();
     }