Fix experiment running environment including upgrading gradle

Author: adamburkegh

build.gradle

@@ -15,7 +15,8 @@ apply plugin: 'eclipse'
 repositories {
     mavenLocal() 
     ivy {
-        layout 'pattern' , {
+        name 'ivyPromReleases'
+        patternLayout{
             artifact '[organisation]/Releases/Packages/[module]/[revision]/[artifact]-[revision].[ext]'
             ivy '[organisation]/Releases/Packages/[module]/[revision]/ivy.xml'
         }
@@ -25,7 +26,8 @@ repositories {
         }
     }
     ivy {
-        layout 'pattern' , {
+        name 'ivyPromLibraries'
+        patternLayout{
             artifact '[module]/[revision]/[artifact]-[revision].[ext]'
             ivy '[module]/[revision]/ivy.xml'
         }

gradle/wrapper/gradle-wrapper.properties

@@ -1,5 +1,5 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-6.6.1-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-7.3.2-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists

scripts/tpminer.bat

@@ -1,5 +1,5 @@
 
-echo off
+echo on
 
 set lg1=%1
 set md=%2
@@ -12,8 +12,14 @@ for %%a in ("%~dp0.") do @set TPHOME=%%~dpa
 
 echo "Preparing event log ..."
 
-REM echo "TPHOME" %TPHOME%
-REM echo "OUTD"   %OUTD%
+echo "TPHOME" %TPHOME%
+echo "OUTD"   %OUTD%
+
+set VDIR=%TPHOME%tpvenv\scripts
+set PYTHON_HOME=%VDIR%
+
+echo %VDIR%\activate.bat
+REM %VDIR%\activate.bat
 
 %PYTHON_HOME%\python %TPHOME%scripts\xesdcdt.py --outfile %OUTD%\%lg%.dcdt %lg1%
 

src/main/java/qut/pm/spm/PetrinetSource.java

@@ -1,14 +1,13 @@
 package qut.pm.spm;
 
-import org.processmining.acceptingpetrinet.models.AcceptingPetriNet;
 import org.processmining.models.graphbased.directed.petrinet.Petrinet;
 
 public class PetrinetSource {
 
-	private AcceptingPetriNet net;
+	private AcceptingStochasticNet net;
 	private String sourceId; // eg a filename
 
-	public PetrinetSource(AcceptingPetriNet source, String sourceId) {
+	public PetrinetSource(AcceptingStochasticNet source, String sourceId) {
 		super();
 		this.net = source;
 		this.sourceId = sourceId;
@@ -22,7 +21,7 @@ public String getSourceId() {
 		return sourceId;
 	}
 
-	public AcceptingPetriNet getAcceptingPetriNet() {
+	public AcceptingStochasticNet getAcceptingPetriNet() {
 		return net;
 	}
 

src/main/java/qut/pm/spm/RunStats.java

@@ -48,7 +48,7 @@ public class RunStats {
 	protected String outputModelFileName;
 
 	@Attribute
-	protected String miner;
+	protected String artifactCreator;
 
 	@Attribute
 	protected String machineName;
@@ -71,24 +71,24 @@ public class RunStats {
 	@Element
 	private RunState runState = RunState.INITIALIZING;
 
-	public RunStats(String inputLogFileName, String outputModelFileName, String miner) 
+	public RunStats(String inputLogFileName, String outputModelFileName, String artifactCreator) 
 	{
 		this.inputLogFileName = inputLogFileName;
 		this.outputModelFileName = outputModelFileName;
-		this.miner = miner;
+		this.artifactCreator = artifactCreator;
 		this.runDate = ClockUtil.currentTime();
 		try {
 			this.machineName = InetAddress.getLocalHost().getHostName();
 		}catch (Exception e){
-			this.machineName = "Unkown (" + e.getMessage() + ")";
+			this.machineName = "Unknown (" + e.getMessage() + ")";
 		}
 		runnerVersion = BUILD_VERSION;
 	}
 
 	protected RunStats(RunStats other) {
 		this.inputLogFileName = other.inputLogFileName;
 		this.outputModelFileName = other.outputModelFileName;
-		this.miner = other.miner;
+		this.artifactCreator = other.artifactCreator;
 		this.runDate = other.runDate;
 		this.runState = other.runState;
 		this.machineName = other.machineName;
@@ -144,7 +144,7 @@ public Map<Measure,Number> getAllMeasures(){
 	}
 
 	public String getArtifactCreator() {
-		return miner;
+		return artifactCreator;
 	}
 
 	public String formatStats() {

src/main/java/qut/pm/spm/conformance/EarthMoversTunedCalculator.java

@@ -35,7 +35,7 @@ public void calculate(PluginContext context, AcceptingStochasticNet net, XLog lo
 		LOGGER.info("Computing earth-movers' distance (SL) with mass coverage: " + MASS_COVERAGE);
 		EMSCParametersLogModelDefault parameters = new EMSCParametersLogModelDefault();
 		parameters.setComputeStochasticTraceAlignments(false);
-		parameters.setDebug(false);
+		parameters.setDebug(true);
 		parameters.setLogClassifier(classifier);
 		LanguageGenerationStrategyFromModelAbstract terminationStrategy = new LanguageGenerationStrategyFromModelDefault();
 		terminationStrategy.setMaxMassCovered(MASS_COVERAGE);

src/main/java/qut/pm/spm/miner/ToothpasteMinerHP.java

@@ -48,7 +48,7 @@ public void run(PluginContext uipc, XLog log, XEventClassifier classifier, File
 			throws Exception
 	{
 		File logFileObj = new File(logFile);
-		LOGGER.info("Invoking Toothpaste miner prototype out of process on {}", logFile);
+		LOGGER.info("Invoking Toothpaste miner out of process on {}", logFile);
 		callToothpasteMinerHP( logFileObj, outputModelFile );
 		Serializer serializer = new Persister();
 		PNMLRoot pnml = serializer.read(PNMLRoot.class, outputModelFile);

src/main/java/qut/pm/spm/reports/SPNDiscoverReporter.java

@@ -45,7 +45,7 @@ public int compare(ReportStats o1, ReportStats other) {
 				result = o1.artifactCreatorId.compareTo(other.artifactCreatorId);
 				if (result != 0)
 					return result;
-				result = o1.miner.compareTo(other.miner);
+				result = o1.artifactCreator.compareTo(other.artifactCreator);
 				return result;
 			}
 
@@ -93,7 +93,7 @@ public int compareTo(ReportStats other) {
 			result = artifactCreatorId.compareTo(other.artifactCreatorId);
 			if (result != 0)
 				return result;
-			result = this.miner.compareTo(other.miner);
+			result = this.artifactCreator.compareTo(other.artifactCreator);
 			return result;
 		}
 

src/main/java/qut/pm/toothpaste/ModelRunner.java

@@ -7,6 +7,7 @@
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.Collections;
 import java.util.List;
 import java.util.Properties;
 
@@ -16,8 +17,6 @@
 import org.deckfour.xes.classification.XEventNameClassifier;
 import org.deckfour.xes.info.XLogInfoFactory;
 import org.deckfour.xes.model.XLog;
-import org.processmining.acceptingpetrinet.models.AcceptingPetriNet;
-import org.processmining.acceptingpetrinet.models.impl.AcceptingPetriNetImpl;
 import org.processmining.contexts.uitopia.UIPluginContext;
 import org.processmining.framework.plugin.PluginContext;
 import org.processmining.models.connections.GraphLayoutConnection;
@@ -37,6 +36,7 @@
 import qut.pm.prom.helpers.HeadlessUIPluginContext;
 import qut.pm.prom.helpers.PetrinetExportUtils;
 import qut.pm.spm.AcceptingStochasticNet;
+import qut.pm.spm.AcceptingStochasticNetImpl;
 import qut.pm.spm.Measure;
 import qut.pm.spm.PetrinetSource;
 import qut.pm.spm.RunState;
@@ -89,6 +89,7 @@ private static enum Classifier{
 	private boolean exportDOT = false;
 	private int kfoldLogs = 1;
 	private int kfoldLogsStart = 1;
+	// private String modelInputFileName = "";
 	private List<StochasticNetLogMiner> miners;
 	private List<PetrinetSource> models;
 	private List<SPNQualityCalculator> calculators;
@@ -140,26 +141,26 @@ private void configureModels(Properties cfg) throws Exception{
 		for (String modelFile: modelFiles) {
 			String fname = modelPath + File.separator + modelFile.trim(); 
 			LOGGER.info("Loading model from {}",fname);
-			AcceptingPetriNet net = loadNet(new File(fname)); 
-			String shortName = modelFile.replace("omodel_", "");
-			shortName = shortName.substring(0, shortName.indexOf("_") );
-			LOGGER.info("Short name {}",shortName);
-			models.add( new PetrinetSource(net,shortName) );
+			AcceptingStochasticNet net = loadNet(new File(fname)); 
+			models.add( new PetrinetSource(net,net.getId()) );
 		}
 	}
 
-	private static AcceptingPetriNet loadNet(File file) throws Exception {
-		PluginContext context = 
-				new HeadlessDefinitelyNotUIPluginContext(new ConsoleUIPluginContext(), "modelrunner_loadnet");
+	private AcceptingStochasticNet loadNet(File file) throws Exception {
+		PluginContext context = new HeadlessDefinitelyNotUIPluginContext(new ConsoleUIPluginContext(),
+				"modelrunner_loadnet");
+		String shortName = file.getName().replace("osmodel_", "");
+		shortName = shortName.substring(0, shortName.indexOf("_") );
+		LOGGER.info("Short name {}",shortName);
 		Serializer serializer = new Persister();
 		PNMLRoot pnml = serializer.read(PNMLRoot.class, file);
 		StochasticNetDeserializer converter = new StochasticNetDeserializer();
 		Object[] objs = converter.convertToNet(context, pnml, file.getName(), true);
-		AcceptingPetriNet apn = new AcceptingPetriNetImpl((StochasticNet) objs[0],
-														  (Marking)objs[1],(Marking)objs[2]);
+		AcceptingStochasticNet apn = new AcceptingStochasticNetImpl(shortName, (StochasticNet) objs[0],
+				(Marking) objs[1], Collections.singleton((Marking) objs[2]));
 		return apn;
 	}
-
+	
 
 	private void configureMiners(Properties cfg) {
 		miners = new ArrayList<>();
@@ -241,17 +242,17 @@ private void runSingleMinerRun(StochasticNetLogMiner miner, String inputLogName,
 										   throws Exception 
 	{
 		UIPluginContext uipc = 
-				new HeadlessUIPluginContext(new ConsoleUIPluginContext(), "spmrunner_logparser");	
+				new HeadlessUIPluginContext(new ConsoleUIPluginContext(), "tp_runnerlogparser");	
 		final String SEP = " -- ";
 		noteRunStart(miner, inputLogName, SEP);
 		String inputLogPrefix = logPrefix(inputLogName);
-		String outputModelName = nameFile(inputLogPrefix,miner.getShortID(),"omodel",PNML);
+		String outputModelName = nameFile(inputLogPrefix,miner.getShortID(),"osmodel",PNML);
 		RunStats runStats = new RunStats(inputLogName,outputModelName, miner.getReadableID());
 		TaskStats stats = new TaskStats("spmlogparser");
 		stats.markRunning();
 		try {
 			XLog log = loadLog(uipc, inputLogName, stats);
-			uipc = new HeadlessUIPluginContext(new ConsoleUIPluginContext(), "spmrunner_mining");
+			uipc = new HeadlessUIPluginContext(new ConsoleUIPluginContext(), "tp_runnermining");
 			stats = closeTaskAndMakeNew(runStats, stats, "miner");
 			LOGGER.debug(stats.formatStats()); 
 			File modelFile = new File(outputModelName);
@@ -265,7 +266,7 @@ private void runSingleMinerRun(StochasticNetLogMiner miner, String inputLogName,
 			stats = makeNewTask("visualize");
 			exportVisualization(miner,inputLogPrefix);
 			stats.markEnd();
-			uipc = new HeadlessUIPluginContext(new ConsoleUIPluginContext(), "spmrunner_postrun");	
+			uipc = new HeadlessUIPluginContext(new ConsoleUIPluginContext(), "tp_runnerpostrun");	
 			if (miner.isStochasticNetProducer()) {
 				TaskStats compStats = new TaskStats("complog"); 
 				// note these log count stats in compStats currently unused
@@ -407,14 +408,66 @@ private void noteRunEnd(StochasticNetLogMiner artifactRun, String inputLogPrefix
 		}
 	}
 
+	private TaskStats makeNewTask(RunStats runStats, String newTaskName) {
+		TaskStats newTaskStats = new TaskStats(newTaskName);
+		newTaskStats.markRunning();
+		runStats.addTask(newTaskStats);
+		return newTaskStats;
+	}
+
+	
+	private void calculatePostStats(PluginContext context, String inputLogPrefix, 
+			PetrinetSource model, XLog log, RunStats runStats) 
+				throws Exception
+	{		
+		TaskStats stats = null;
+		for (SPNQualityCalculator calc: calculators) {
+			stats = makeNewTask("calculate " + calc.getReadableId());
+			calc.calculate(context, model.getAcceptingPetriNet(), log, 
+					classifierFor(log), stats);
+			closeTask(runStats,stats);
+			// Conservatively export stats after every run
+			LOGGER.info(runStats.formatStats());
+			exportRun(model.getSourceId(), inputLogPrefix, runStats);
+		}
+	}
+
+	
+	public void runPredefinedModelVsLog(PetrinetSource model, String inputLogName ) throws Exception{
+		UIPluginContext uipc = 
+				new HeadlessUIPluginContext(new ConsoleUIPluginContext(), "tp_runnermvl");	
+		RunStats runStats = new RunStats(inputLogName,model.getNet().getLabel(), model.getSourceId());
+		String df = logPrefix(inputLogName);
+		// RunStats runStats = initPredefRunStats(model, "predef");
+		TaskStats stats = makeNewTask(runStats, "tpmlogparser");
+		try {
+			XLog log = loadLog(uipc, inputLogName, stats);
+			calculatePostStats(uipc, df, model, log, runStats);
+		} catch (Exception e) {
+			exportRun(model.getSourceId(), df, runStats);
+			throw new RuntimeException(e);
+		}
+	}
+	
 
+	
+	public void runPredefinedModelCollectionVsLog() throws Exception{
+		for (String df: dataFiles) {
+			for (PetrinetSource model : models) {
+				runPredefinedModelVsLog(model,df);
+			}
+		}
+	}	
 
 	public void runAll() throws Exception{
 		for (String df: dataFiles) {
 			// Basic sanity checks happen already at config load time
 			if (!miners.isEmpty()) {
 				runAllMiners(df);
 			}
+			if (miners.isEmpty() && !models.isEmpty()) {
+				runPredefinedModelCollectionVsLog();
+			}
 		}
 	}