fixed configuration reader, fixed flattening of topics

gradle/wrapper/gradle-wrapper.properties

 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-6.3-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists
+distributionUrl=https\://services.gradle.org/distributions/gradle-6.7.1-bin.zip

src/main/config/config.json

+{
+  "tina" : "-R -s 1 -c 0 -t 0 -b 0 -m 0 -v -PNML -bcg",
+  "pathto" : "",
+  "sift" : "",
+  "struct" : ""
+}
\ No newline at end of file

src/main/java/de/tudresden/inf/st/pnml/flatter/Main.java

@@ -3,6 +3,7 @@ package de.tudresden.inf.st.pnml.flatter;
 import de.tudresden.inf.st.pnml.flatter.config.ConfigReader;
 import de.tudresden.inf.st.pnml.flatter.transform.ChannelFlatter;
 import de.tudresden.inf.st.pnml.flatter.transform.ReferenceFlatter;
+import de.tudresden.inf.st.pnml.jastadd.model.*;
 import de.tudresden.inf.st.pnml.jastadd.model.PnmlParser;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -28,7 +29,8 @@ public class Main {
         }*/
 
         // parse the global not flatted petri net
-        pnmlPath = "pnml-relast-flatter/src/main/resources/minimal.pnml";
+        pnmlPath = "../pnml-relast-nets/src/main/resources/topicTestNets/structureTestNets/topic-structure-correct-3.pnml";
+        configPath = "src/main/config/config.json";
         PetriNet petriNet = PnmlParser.parsePnml(pnmlPath).get(0);
 
         // read config for analyzer from file
@@ -46,10 +48,12 @@ public class Main {
         // flat topic publishers / subscribers to instance based semantics
         logger.info("[FLATTER] Breaking down topic channels.");
         PetriNet topicFlattedPetriNet = ChannelFlatter.flatTopicChannels(petriNet);
+        printNet(topicFlattedPetriNet);
+
 
         // flat service clients / servers to instance based semantics
         logger.info("[FLATTER] Breaking down service channels.");
-        PetriNet serviceFlattedPetriNet = ChannelFlatter.flatTopicChannels(topicFlattedPetriNet);
+       // PetriNet serviceFlattedPetriNet = ChannelFlatter.flatServiceChannels(topicFlattedPetriNet);
 
         // flat input signals
 
@@ -60,8 +64,8 @@ public class Main {
         // TODO
 
         //  convert and add inhibitor arcs
-        NdrioProxy ndrioProxy = new NdrioProxy();
-        ndrioProxy.pnml2net(pnmlPath, "pnml-relast-flatter/src/main/resources/minimal.net");
+      //  NdrioProxy ndrioProxy = new NdrioProxy();
+    //    ndrioProxy.pnml2net(pnmlPath, "pnml-relast-flatter/src/main/resources/minimal.net");
 
         // insert into tina
 
@@ -84,4 +88,91 @@ public class Main {
         // TODO
 
     }
+
+    public static void printNet(PetriNet petriNet) {
+
+        logger.error("--------------- STRUCTURE ---------------");
+        logger.error("----------------- PLACES ----------------");
+
+        for (Place p : petriNet.allPlaces()) {
+            //logger.error("id: " + p.getId());
+            logger.error("Place " + p.asOutputSignalPlace().getId() + " -- " + p.asOutputSignalPlace().getStaticPlaceInformation().getSubNet());
+        }
+
+        logger.error("-------------- TRANSITIONS --------------");
+
+        for (Transition t : petriNet.allTransitions()) {
+
+            if (t.asInputSignalTransition().getStaticTransitionInformation().isServiceTransitionInformation()) {
+                logger.error("--- Transition: " + t.getId() + " subnet: " + t.asInputSignalTransition().getStaticTransitionInformation().getSubNet()
+                        + " service: " + t.asInputSignalTransition().getStaticTransitionInformation().asServiceTransitionInformation().getServiceName() + " ---------");
+            } else if(t.asInputSignalTransition().getStaticTransitionInformation().isTopicTransitionInformation()){
+                logger.error("--- Transition: " + t.getId() + " subnet: " + t.asInputSignalTransition().getStaticTransitionInformation().getSubNet()
+                        + " topic: " + t.asInputSignalTransition().getStaticTransitionInformation().asTopicTransitionInformation().getTopic() + " ---------");
+            }else{
+                logger.error("--- Transition: " + t.getId());
+            }
+
+            if(t.asInputSignalTransition().getInputSignalClause() != null && t.asInputSignalTransition().getInputSignalClause().getNumChild() > 0){
+      //          logger.error("------ Clause: " + t.asInputSignalTransition().getInputSignalClause().printExp());
+            }
+
+            for (Place p : t.asInputSignalTransition().incomingPlaces()) {
+
+                logger.error("------ Inputplace:  " + p.getId() + " subnet: " + p.asOutputSignalPlace().getStaticPlaceInformation().getSubNet() + " ---------");
+            }
+
+            for (Place p : t.asInputSignalTransition().outgoingPlaces()) {
+
+                logger.error("------ Outputplace: " + p.getId() + " subnet: " + p.asOutputSignalPlace().getStaticPlaceInformation().getSubNet() + " ---------");
+            }
+        }
+
+        logger.error("----------------- REF PLACES -----------------");
+
+        for (RefPlace rp : petriNet.allRefPlaces()){
+            logger.error("--- RefPlace: " + rp.getId());
+        }
+
+        logger.error("----------------- REF TRANSITIONS -----------------");
+
+        for (RefTransition rt : petriNet.allRefTransitions()){
+            logger.error("--- RefTransition: " + rt.getId());
+        }
+
+        logger.error("----------------- ARCS -----------------");
+
+        for (Arc a : petriNet.allArcs()) {
+            logger.error("Arc: " + a.getId() + " -- source: " + a.getSource().getId() + " -- target: " + a.getTarget().getId());
+        }
+
+        logger.error("--------------- T SIGNALS (STATIC)---------------");
+
+        for (Transition t : petriNet.allTransitions()) {
+            InputSignalTransition ist = t.asInputSignalTransition();
+
+            if (ist != null && ist.getStaticInputSignalBindingList() != null) {
+                ist.getStaticInputSignalBindingList().forEach(inputSignalBinding -> logger.error(" (" + t.getName().getText() + ") Signal: " + inputSignalBinding.getInputSignalID()));
+            }
+        }
+
+        logger.error("--------------- T SIGNALS (MUTUAL)---------------");
+
+        for (Transition t : petriNet.allTransitions()) {
+            InputSignalTransition ist = t.asInputSignalTransition();
+
+            if (ist != null && ist.getMutualInputSignalBindingList() != null) {
+                ist.getMutualInputSignalBindingList().forEach(inputSignalBinding -> logger.error(" (" + t.getName().getText() + ") Signal: " + inputSignalBinding.getInputSignalID()));
+            }
+        }
+
+   //     logger.error("--------------- TOOL SPECIFIC ---------------");
+
+        for (Transition t : petriNet.allTransitions()) {
+            InputSignalTransition ist = t.asInputSignalTransition();
+            if(ist != null && ist.getNumToolspecific() > 0) {
+       //         logger.error("ToolSpecific: (" + ist.getName().getText() + ") " + ist.getToolspecific(0).getFormattedXMLBuffer().toString());
+            }
+        }
+    }
 }

src/main/java/de/tudresden/inf/st/pnml/flatter/config/ConfigReader.java

@@ -49,6 +49,7 @@ public class ConfigReader {
     public String[] getTinaConfigParams(){
 
         Gson gson = new Gson();
+        System.out.println("Content " + getConfigFileContent());
         FlatterConfig fc = gson.fromJson(getConfigFileContent(), FlatterConfig.class);
         return fc.tina.split(" ");
     }

src/main/java/de/tudresden/inf/st/pnml/flatter/template/TemplateConstants.java

@@ -7,11 +7,13 @@ public final class TemplateConstants {
     public static final String PUBLISHER_CONNECTOR_PLACE = "PublisherConnectorPlace";
     public static final String PUBLISHER_INPUT_TRANSITION = "PublisherInputTransition";
     public static final String PUBLISHER_OVERFLOW_TRANSITION = "PublisherOverflowTransition";
-    public static final String PUBLISHER_OUTPUT_TRANSITION = "PublisherOverflowTransition";
+    public static final String PUBLISHER_OUTPUT_TRANSITION = "PublisherOutputTransition";
 
     // topic dispatcher
     public static final String DISPATCHER_INPUT_TRANSITION = "DispatcherInputTransition";
     public static final String DISPATCHER_OUTPUT_TRANSITION = "DispatcherOutputTransition";
+    public static final String DISPATCHER_INPUT_PLACE = "DispatcherInputPlace";
+    public static final String DISPATCHER_OVERFLOW_TRANSITION = "DispatcherOverflowTransition";
 
     // topic callback
     public static final String CALLBACK_INPUT_PLACE = "CallbackInputPlace";
@@ -26,4 +28,5 @@ public final class TemplateConstants {
     // channel elements
     public static final String CHANNEL_CONNECTOR_PLACE = "ChannelConnectorPlace";
     public static final String CHANNEL_CONNECTOR_TRANSITION = "ChannelConnectorTransition";
+
 }

src/main/java/de/tudresden/inf/st/pnml/flatter/template/TopicTemplates.java

 package de.tudresden.inf.st.pnml.flatter.template;
 
+import de.tudresden.inf.st.pnml.jastadd.model.Name;
 import de.tudresden.inf.st.pnml.jastadd.model.PetriNet;
 import de.tudresden.inf.st.pnml.jastadd.model.PnObject;
 import de.tudresden.inf.st.pnml.jastadd.model.PnmlParser;
@@ -8,12 +9,14 @@ public class TopicTemplates extends PnmlTemplate {
 
     public static PetriNet getTopicPublisherPetriNet(String idSuffix){
 
-        PetriNet templateNet = PnmlParser.parsePnml(homeDirectory + "/src/main/resources/TopicPublisherTemplate.pnml").get(0);
+        PetriNet templateNet = PnmlParser.parsePnml(homeDirectory + "/src/main/resources/templates/TopicPublisherTemplate.pnml").get(0);
 
         for(PnObject po : templateNet.allObjects()){
             if(!po.getId().equals(TemplateConstants.PUBLISHER_TEMPLATE_PAGE)){
                 po.setId(po.getId() + "-" + idSuffix);
-                po.getName().setText(po.getName().getText() + "-" + idSuffix);
+                Name name = new Name();
+                name.setText(po.getId() + "-" + idSuffix);
+                po.setName(name);
             }
         }
 
@@ -22,12 +25,14 @@ public class TopicTemplates extends PnmlTemplate {
 
     public static PetriNet getTopicDispatcherPetriNet(String idSuffix){
 
-        PetriNet templateNet = PnmlParser.parsePnml(homeDirectory + "/src/main/resources/TopicSubDispatcherTemplate.pnml").get(0);
+        PetriNet templateNet = PnmlParser.parsePnml(homeDirectory + "/src/main/resources/templates/TopicSubDispatcherTemplate.pnml").get(0);
 
         for(PnObject po : templateNet.allObjects()){
             if(!po.getId().equals(TemplateConstants.DISPATCHER_TEMPLATE_PAGE)){
                 po.setId(po.getId() + "-" + idSuffix);
-                po.getName().setText(po.getName().getText() + "-" + idSuffix);
+                Name name = new Name();
+                name.setText(po.getId() + "-" + idSuffix);
+                po.setName(name);
             }
         }
 
@@ -36,12 +41,14 @@ public class TopicTemplates extends PnmlTemplate {
 
     public static PetriNet getTopicCallbackQueuePetriNet(String idSuffix){
 
-        PetriNet templateNet = PnmlParser.parsePnml(homeDirectory + "/src/main/resources/TopicSubCallbackQueueTemplate.pnml").get(0);
+        PetriNet templateNet = PnmlParser.parsePnml(homeDirectory + "/src/main/resources/templates/TopicSubCallbackQueueTemplate.pnml").get(0);
 
         for(PnObject po : templateNet.allObjects()){
             if(!po.getId().equals(TemplateConstants.CALLBACK_QUEUE_TEMPLATE_PAGE)){
                 po.setId(po.getId() + "-" + idSuffix);
-                po.getName().setText(po.getName().getText() + "-" + idSuffix);
+                Name name = new Name();
+                name.setText(po.getId() + "-" + idSuffix);
+                po.setName(name);
             }
         }
 

src/main/java/de/tudresden/inf/st/pnml/flatter/transform/ChannelFlatter.java

 package de.tudresden.inf.st.pnml.flatter.transform;
 
+import de.tudresden.inf.st.pnml.base.constants.PnmlConstants;
 import de.tudresden.inf.st.pnml.flatter.template.TemplateConstants;
 import de.tudresden.inf.st.pnml.flatter.template.TopicTemplates;
 import de.tudresden.inf.st.pnml.jastadd.model.*;
@@ -22,6 +23,8 @@ public class ChannelFlatter {
         int channelCount = 0;
 
         List<Transition> topicTransitions = new ArrayList<>();
+        List<Arc> arcsToRemove = new ArrayList<>();
+        List<Transition> transitionsToRemove = new ArrayList<>();
 
         // process topic transitions
         for(Transition t : petriNet.allTransitions()){
@@ -61,13 +64,17 @@ public class ChannelFlatter {
                 for (Map.Entry<String, Place> entry : inputMapping.entrySet()) {
 
                     // include the template publisher
-                    PetriNet publisherPetriNet = TopicTemplates.getTopicPublisherPetriNet("-" + publisherCount);
+                    PetriNet publisherPetriNet = TopicTemplates.getTopicPublisherPetriNet(String.valueOf(publisherCount));
                     includeTemplateInstance(petriNet, publisherPetriNet, entry.getKey(), entry.getValue().asOutputSignalPlace().getStaticPlaceInformation().getLocation());
 
                     // connect the publisher inputs
                     Arc inputArc = new Arc();
                     Arc overFlowArc = new Arc();
                     Arc outArc = new Arc();
+                    inputArc.setId("pub-inputArc-" + publisherCount);
+                    overFlowArc.setId("pub-overFlowArc-" + publisherCount);
+                    outArc.setId("pub-outArc-" + publisherCount);
+
 
                     inputArc.setSource(entry.getValue());
                     inputArc.setTarget((Node) getPnObjectByID(petriNet, TemplateConstants.PUBLISHER_INPUT_TRANSITION + "-" + publisherCount));
@@ -92,12 +99,13 @@ public class ChannelFlatter {
                 for (Map.Entry<String, List<Place>> entry : outputMapping.entrySet()) {
 
                     // include dispatcher queues
-                    PetriNet dispatcherNet = TopicTemplates.getTopicDispatcherPetriNet("-" + dispatcherCount);
+                    PetriNet dispatcherNet = TopicTemplates.getTopicDispatcherPetriNet(String.valueOf(dispatcherCount));
                     includeTemplateInstance(petriNet, dispatcherNet, entry.getKey(), entry.getValue().get(0).asOutputSignalPlace().getStaticPlaceInformation().getLocation());
 
                     Arc channelToDispatcherArc = new Arc();
+                    channelToDispatcherArc.setId("channelToDispatcherArc-" + dispatcherCount);
                     channelToDispatcherArc.setSource((Node) getPnObjectByID(petriNet, TemplateConstants.CHANNEL_CONNECTOR_TRANSITION + "-" + channelCount));
-                    channelToDispatcherArc.setTarget((Node) getPnObjectByID(petriNet, TemplateConstants.DISPATCHER_INPUT_TRANSITION + "-" + dispatcherCount));
+                    channelToDispatcherArc.setTarget((Node) getPnObjectByID(petriNet, TemplateConstants.DISPATCHER_INPUT_PLACE + "-" + dispatcherCount));
                     topPage.addObject(channelToDispatcherArc);
 
                     petriNet.flushTreeCache();
@@ -105,15 +113,19 @@ public class ChannelFlatter {
                     // include subscriber queues
                     for(Place p : entry.getValue()){
 
-                        PetriNet subscriberNet = TopicTemplates.getTopicCallbackQueuePetriNet("-" + callbackCount);
+                        PetriNet subscriberNet = TopicTemplates.getTopicCallbackQueuePetriNet(String.valueOf(callbackCount));
                         includeTemplateInstance(petriNet, subscriberNet, entry.getKey(), p.asOutputSignalPlace().getStaticPlaceInformation().getLocation());
 
                         Arc callbackInputArc = new Arc();
                         Arc callbackOverFlowArc = new Arc();
                         Arc callbackOutArc = new Arc();
 
+                        callbackInputArc.setId("callbackInputArc-" + dispatcherCount);
+                        callbackOverFlowArc.setId("callbackOverFlowArc-" + dispatcherCount);
+                        callbackOutArc.setId("callbackOutArc-" + dispatcherCount);
+
                         callbackInputArc.setSource((Node) getPnObjectByID(petriNet, TemplateConstants.DISPATCHER_OUTPUT_TRANSITION + "-" + dispatcherCount));
-                        callbackOverFlowArc.setSource((Node) getPnObjectByID(petriNet, TemplateConstants.DISPATCHER_OUTPUT_TRANSITION + "-" + dispatcherCount));
+                        callbackOverFlowArc.setSource((Node) getPnObjectByID(petriNet, TemplateConstants.CALLBACK_INPUT_PLACE + "-" + dispatcherCount));
 
                         callbackInputArc.setTarget((Node) getPnObjectByID(petriNet, TemplateConstants.CALLBACK_INPUT_PLACE + "-" + callbackCount));
                         callbackOverFlowArc.setTarget((Node) getPnObjectByID(petriNet, TemplateConstants.CALLBACK_OVERFLOW_TRANSITION + "-" + callbackCount));
@@ -129,22 +141,45 @@ public class ChannelFlatter {
 
                 petriNet.flushTreeCache();
 
-                // clean up old channel
-
-                // TODO
+                // objects to be cleaned up
+                arcsToRemove.addAll(t.getInArcs());
+                arcsToRemove.addAll(t.getOutArcs());
+                transitionsToRemove.add(t);
 
             }
 
             channelCount++;
         }
 
-        return null;
+        // clean up old channel data
+        for(Arc a : arcsToRemove){
+            a.removeSelf();
+        }
+
+        for(Transition t : transitionsToRemove){
+            t.removeSelf();
+        }
+
+        petriNet.flushTreeCache();
+
+        return petriNet;
     }
 
     private static void insertChannelElements(PetriNet petriNet, int channelCount) {
 
-        Place channelPlace = new Place();
-        Transition channelTransition = new Transition();
+        OutputSignalPlace channelPlace = new OutputSignalPlace();
+        PlaceInformation newPi = new PlaceInformation();
+        newPi.setLocation("channel");
+        newPi.setSubNet("channel");
+        newPi.setType(PnmlConstants.PLACE_TYPE_DISCRETE);
+        channelPlace.setMutualPlaceInformation(newPi);
+
+        InputSignalTransition channelTransition = new InputSignalTransition();
+        TransitionInformation newTi = new DefaultTransitionInformation();
+        newTi.setLocation("channel");
+        newTi.setSubNet("channel");
+        newTi.setType(PnmlConstants.TRANSITION_TYPE_DISCRETE);
+        channelTransition.setMutualTransitionInformation(newTi);
 
         channelPlace.setId(TemplateConstants.CHANNEL_CONNECTOR_PLACE + "-" + channelCount);
         channelTransition.setId(TemplateConstants.CHANNEL_CONNECTOR_TRANSITION + "-" + channelCount);
@@ -153,6 +188,12 @@ public class ChannelFlatter {
         topPage.addObject(channelPlace);
         topPage.addObject(channelTransition);
 
+        Arc channelArc = new Arc();
+        channelArc.setId("ChannelArc-" + channelCount);
+        channelArc.setTarget(channelTransition);
+        channelArc.setSource(channelPlace);
+        topPage.addObject(channelArc);
+
         petriNet.flushTreeCache();
     }
 
@@ -168,22 +209,47 @@ public class ChannelFlatter {
 
         // include places, transitions
         for(Transition t : templateInstance.allTransitions()){
-            t.asInputSignalTransition().getMutualTransitionInformation().setSubNet(subnet);
-            t.asInputSignalTransition().getMutualTransitionInformation().setLocation(location);
+
+            System.out.println("Adding: " + t.getId());
+
+            TransitionInformation newTi = new DefaultTransitionInformation();
+            newTi.setLocation(location);
+            newTi.setSubNet(subnet);
+            newTi.setType(t.asInputSignalTransition().getStaticTransitionInformation().getType());
+            t.asInputSignalTransition().setMutualTransitionInformation(newTi);
+
             topPage.addObject(t);
         }
 
         for(Place p : templateInstance.allPlaces()){
-            p.asOutputSignalPlace().getMutualPlaceInformation().setSubNet(subnet);
-            p.asOutputSignalPlace().getMutualPlaceInformation().setLocation(location);
+
+            PlaceInformation newPi = new PlaceInformation();
+            newPi.setLocation(location);
+            newPi.setSubNet(subnet);
+            newPi.setType(p.asOutputSignalPlace().getStaticPlaceInformation().getType());
+            p.asOutputSignalPlace().setMutualPlaceInformation(newPi);
+
             topPage.addObject(p);
         }
 
+        petriNet.flushTreeCache();
+
         // connect elements by arcs
         for(Arc a : templateInstance.allArcs()){
             Arc newArc = new Arc();
+            newArc.setId("arc-" + a.getSource().getId() + "-" + a.getTarget().getId());
+            System.out.println("Target: " + a.getTarget().getId());
             newArc.setTarget((Node) getPnObjectByID(petriNet, a.getTarget().getId()));
             newArc.setSource((Node) getPnObjectByID(petriNet, a.getSource().getId()));
+
+            if(a.getNumToolspecific() > 0) {
+                ToolInfo ti = new ToolInfo();
+                ti.setFormattedXMLBuffer(a.getToolspecific(0).getFormattedXMLBuffer());
+                ti.setTool(a.getToolspecific(0).getTool());
+                ti.setVersion(a.getToolspecific(0).getVersion());
+                newArc.addToolspecific(ti);
+            }
+
             topPage.addObject(newArc);
         }
 

src/main/resources/templates/TopicSubDispatcherTemplate.pnml

@@ -142,6 +142,8 @@
             </arc>
             <arc id="arc-6" source="DispatcherInputPlace" target="DispatcherInputTransition">
             </arc>
+            <arc id="arc-7" source="DispatcherInputPlace" target="DispatcherOverflowTransition">
+            </arc>
         </page>
     </net>
 </pnml>