Recursive dependency linking

.github/workflows/ci_cd.yml

@@ -15,7 +15,7 @@ env:
 jobs:
   CI-Build:
     name: CI-build
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     if: ${{ github.event_name == 'push' }}
     steps:
       - uses: actions/checkout@v3
@@ -84,7 +84,7 @@ jobs:
         if: ${{ failure() }}
 
   CI-Test:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     strategy:
       matrix:
         test-group: [Fast, MathGen_IT, SBML_IT, SEDML_SBML_IT, SEDML_VCML_IT, BSTS_IT]
@@ -156,7 +156,7 @@ jobs:
 
   CD:
     name: CD
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     if: ${{ github.event_name == 'release' }}
 
     steps:

Dockerfile

@@ -1,4 +1,4 @@
-FROM eclipse-temurin:17 as jre-build
+FROM eclipse-temurin:17-jammy as jre-build
 
 # Create a custom Java runtime
 RUN $JAVA_HOME/bin/jlink \
@@ -10,13 +10,12 @@ RUN $JAVA_HOME/bin/jlink \
          --output /javaruntime
 
 # Define base image and copy in jlink created minimal Java 17 environment
-FROM python:3.9.7-slim
+FROM ubuntu:jammy
 ENV JAVA_HOME=/opt/java/openjdk
 ENV PATH "${JAVA_HOME}/bin:${PATH}"
 COPY --from=jre-build /javaruntime $JAVA_HOME
 
 # now we have Java 17 and Python 3.9
-
 ARG SIMULATOR_VERSION="7.5.0.11"
 ARG MAX_JAVA_MEM=0
 # Make sure you don't sap all of docker's memory when you set this.
@@ -47,8 +46,11 @@ LABEL \
     about.tags="rule-based modeling,kinetic modeling,dynamical simulation,systems biology,BNGL,SED-ML,COMBINE,OMEX" \
     maintainer="BioSimulators Team <[email protected]>"
 
-RUN apt-get -y update
-RUN apt-get install -y --no-install-recommends curl dnsutils apt-utils libfreetype6 fontconfig fonts-dejavu
+ENV DEBIAN_FRONTEND noninteractive
+RUN apt -y update && apt install -y software-properties-common
+RUN add-apt-repository ppa:deadsnakes/ppa -y
+RUN apt install -y --no-install-recommends curl python3.9-full python3-pip build-essential dnsutils \
+    apt-utils libfreetype6 fontconfig fonts-dejavu
 
 RUN mkdir -p /usr/local/app/vcell/lib && \
     mkdir -p /usr/local/app/vcell/simulation && \

vcell-admin/src/main/java/org/vcell/admin/VCComprehensiveStatistics.java

@@ -10,7 +10,7 @@
 import cbit.vcell.server.SimulationJobStatusPersistent;
 import cbit.vcell.server.SimulationJobStatusPersistent.SchedulerStatus;
 import cbit.vcell.server.SimulationStatusPersistent;
-import cbit.vcell.solver.Simulation;
+import cbit.vcell.solver.simulation.Simulation;
 import cbit.vcell.xml.XMLSource;
 import cbit.vcell.xml.XmlHelper;
 import org.vcell.db.ConnectionFactory;

vcell-admin/src/main/java/org/vcell/admin/cli/sim/ResultSetCrawler.java

@@ -27,15 +27,14 @@
 import cbit.vcell.modeldb.DatabaseServerImpl;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
-import org.vcell.db.ConnectionFactory;
 import org.vcell.util.DataAccessException;
 import org.vcell.util.document.ExternalDataIdentifier;
 import org.vcell.util.document.KeyValue;
 import org.vcell.util.document.User;
 import org.vcell.util.document.UserInfo;
 
 import cbit.vcell.resource.PropertyLoader;
-import cbit.vcell.solver.SimulationInfo;
+import cbit.vcell.solver.simulation.SimulationInfo;
 import cbit.vcell.util.AmplistorUtils;
 
 

vcell-admin/src/main/java/org/vcell/stochtest/StochtestRunService.java

@@ -12,7 +12,7 @@
 import cbit.vcell.mapping.SimulationContext.MathMappingCallback;
 import cbit.vcell.mapping.SimulationContext.NetworkGenerationRequirements;
 import cbit.vcell.mapping.SpeciesContextSpec;
-import cbit.vcell.messaging.server.SimulationTask;
+import cbit.vcell.messaging.server.StandardSimulationTask;
 import cbit.vcell.modeldb.DatabasePolicySQL;
 import cbit.vcell.modeldb.DatabaseServerImpl;
 import cbit.vcell.modeldb.ServerDocumentManager;
@@ -24,6 +24,8 @@
 import cbit.vcell.solver.ode.ODESimData;
 import cbit.vcell.solver.server.Solver;
 import cbit.vcell.solver.server.SolverStatus;
+import cbit.vcell.solver.simulation.Simulation;
+import cbit.vcell.solver.simulation.SimulationJob;
 import cbit.vcell.xml.XMLSource;
 import cbit.vcell.xml.XmlHelper;
 import cbit.vcell.xml.XmlParseException;
@@ -266,7 +268,7 @@ private static void runsolver(Simulation newSimulation, File baseDirectory, int
 				versSimulation = new TempSimulation(newSimulation, false);
 //				printout(ruleBasedTestDir.getAbsolutePath());
 				destDir = new File(baseDirectory,timeSeriesMultitrialData.datasetName);
-				SimulationTask simTask = new SimulationTask(new SimulationJob(versSimulation, 0, null),0);
+				StandardSimulationTask simTask = new StandardSimulationTask(new SimulationJob(versSimulation, 0, null),0);
 				Solver solver = ClientSimManager.createQuickRunSolver(destDir, simTask);
 				solver.startSolver();
 

vcell-admin/src/test/java/cbit/vcell/client/RuleBasedTest.java

@@ -9,7 +9,7 @@
 import cbit.vcell.mapping.SimulationContext.NetworkGenerationRequirements;
 import cbit.vcell.mapping.SpeciesContextSpec;
 import cbit.vcell.mathmodel.MathModel;
-import cbit.vcell.messaging.server.SimulationTask;
+import cbit.vcell.messaging.server.StandardSimulationTask;
 import cbit.vcell.modeldb.VCDatabaseScanner;
 import cbit.vcell.modeldb.VCDatabaseVisitor;
 import cbit.vcell.simdata.ODEDataBlock;
@@ -18,6 +18,8 @@
 import cbit.vcell.solver.ode.ODESimData;
 import cbit.vcell.solver.server.Solver;
 import cbit.vcell.solver.server.SolverStatus;
+import cbit.vcell.solver.simulation.Simulation;
+import cbit.vcell.solver.simulation.SimulationJob;
 import cbit.vcell.xml.XMLSource;
 import cbit.vcell.xml.XmlHelper;
 import com.google.gson.Gson;
@@ -128,7 +130,7 @@ private static void checkNonspatialStochasticSimContext(SimulationContext srcSim
 		srcSimContext.refreshMathDescription(new MathMappingCallbackTaskAdapter(null),networkGenerationRequirements);
 
 		//Create non-spatialStoch, ODE and RuleBased sims
-		Simulation nonspatialStochAppNewSim = 
+		Simulation nonspatialStochAppNewSim =
 				srcSimContext.addNewSimulation(STOCH_SIM_NAME/*SimulationOwner.DEFAULT_SIM_NAME_PREFIX*/,new MathMappingCallbackTaskAdapter(null),networkGenerationRequirements);
 
 		Simulation newODEAppNewSim = 
@@ -284,7 +286,7 @@ private static void runsolver(Simulation newSimulation, File baseDirectory, int
 				versSimulation = new TempSimulation(newSimulation, false);
 //				printout(ruleBasedTestDir.getAbsolutePath());
 				destDir = new File(baseDirectory,timeSeriesMultitrialData.datasetName);
-				SimulationTask simTask = new SimulationTask(new SimulationJob(versSimulation, 0, null),0);
+				StandardSimulationTask simTask = new StandardSimulationTask(new SimulationJob(versSimulation, 0, null),0);
 				Solver solver = ClientSimManager.createQuickRunSolver(destDir, simTask);
 				solver.startSolver();
 

vcell-admin/src/test/java/cbit/vcell/util/TestMissingSimData.java

@@ -39,8 +39,8 @@
 import cbit.vcell.simdata.ODEDataBlock;
 import cbit.vcell.simdata.SimulationData;
 import cbit.vcell.simdata.SimulationData.SimDataAmplistorInfo;
-import cbit.vcell.solver.Simulation;
-import cbit.vcell.solver.SimulationInfo;
+import cbit.vcell.solver.simulation.Simulation;
+import cbit.vcell.solver.simulation.SimulationInfo;
 import cbit.vcell.solver.SolverDescription;
 import cbit.vcell.solver.VCSimulationDataIdentifier;
 import cbit.vcell.solver.VCSimulationIdentifier;

vcell-api/src/main/java/org/vcell/rest/health/HealthService.java

@@ -25,7 +25,7 @@
 import cbit.vcell.server.SimulationJobStatus;
 import cbit.vcell.server.SimulationStatus;
 import cbit.vcell.server.VCellConnection;
-import cbit.vcell.solver.Simulation;
+import cbit.vcell.solver.simulation.Simulation;
 import cbit.vcell.solver.VCSimulationIdentifier;
 import cbit.vcell.xml.XMLSource;
 import cbit.vcell.xml.XmlHelper;

vcell-api/src/main/java/org/vcell/rest/server/RestDatabaseService.java

@@ -21,7 +21,7 @@
 import cbit.vcell.simdata.DataSetMetadata;
 import cbit.vcell.simdata.DataSetTimeSeries;
 import cbit.vcell.solver.MathOverrides;
-import cbit.vcell.solver.Simulation;
+import cbit.vcell.solver.simulation.Simulation;
 import cbit.vcell.solver.VCSimulationDataIdentifier;
 import cbit.vcell.solver.VCSimulationIdentifier;
 import cbit.vcell.xml.XMLSource;
@@ -30,7 +30,6 @@
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.restlet.representation.ByteArrayRepresentation;
-import org.restlet.representation.FileRepresentation;
 import org.vcell.rest.VCellApiApplication;
 import org.vcell.rest.common.BiomodelOMEXResource;
 import org.vcell.rest.common.OverrideRepresentation;

vcell-api/src/main/java/org/vcell/rest/server/TestRestServerBlinov.java

@@ -37,7 +37,7 @@
 import cbit.vcell.modeldb.SimContextRep;
 import cbit.vcell.modeldb.SimulationRep;
 import cbit.vcell.solver.MathOverrides;
-import cbit.vcell.solver.Simulation;
+import cbit.vcell.solver.simulation.Simulation;
 import cbit.vcell.xml.XMLSource;
 import cbit.vcell.xml.XmlHelper;
 import freemarker.template.Configuration;

vcell-cli/src/main/java/org/vcell/cli/run/ExecutionJob.java

@@ -88,8 +88,8 @@ public void preprocessArchive() throws PythonStreamException, IOException {
 
         // Unpack the Omex Archive
         try { // It's unlikely, but if we get errors here they're fatal.
-            this.sedmlPath2d3d = Paths.get(outputDir, "temp");
             this.omexHandler = new OmexHandler(inputFilePath, outputDir);
+            this.sedmlPath2d3d = Paths.get(outputDir, "temp");
             this.omexHandler.extractOmex();
             this.sedmlLocations = omexHandler.getSedmlLocationsAbsolute();
         } catch (IOException e){
@@ -99,7 +99,7 @@ public void preprocessArchive() throws PythonStreamException, IOException {
             logger.error(error);
             throw new RuntimeException(error, e);
         } catch (Exception e) { 
-            omexHandler.deleteExtractedOmex();
+            if (omexHandler != null) omexHandler.deleteExtractedOmex();
             String error = e.getMessage() + ", error for archive " + inputFilePath;
             this.cliRecorder.writeErrorList(bioModelBaseName);
             this.cliRecorder.writeDetailedResultList(bioModelBaseName + ", " + "unknown error with the archive file");

vcell-cli/src/main/java/org/vcell/cli/run/RunUtils.java

@@ -9,7 +9,7 @@
 import cbit.vcell.parser.SymbolTable;
 import cbit.vcell.simdata.*;
 import cbit.vcell.solver.AnnotatedFunction;
-import cbit.vcell.solver.SimulationJob;
+import cbit.vcell.solver.simulation.SimulationJob;
 import cbit.vcell.solver.VCSimulationDataIdentifier;
 import cbit.vcell.solver.VCSimulationIdentifier;
 import cbit.vcell.solver.ode.ODESolverResultSet;
@@ -166,7 +166,7 @@ public static void exportPDE2HDF5(SimulationJob vcellSimJob, File userDir, File
         // A ton of initialization
         int jobIndex = vcellSimJob.getJobIndex();
         User user = new User(userDir.getName(), null);
-        cbit.vcell.solver.Simulation vcellSim = vcellSimJob.getSimulation();
+        cbit.vcell.solver.simulation.Simulation vcellSim = vcellSimJob.getSimulation();
         ExportServiceImpl exportServiceImpl = new ExportServiceImpl();
 
     	SimulationContext simContext = (SimulationContext)vcellSim.getSimulationOwner();
@@ -623,8 +623,8 @@ private static void exportDocument(ExportServiceImpl exportServiceImpl, DataServ
     }
 
     private static ExportSpecs getExportSpecs(OutputContext outputContext, User user, DataServerImpl dataServerImpl, VCSimulationDataIdentifier vcId,
-                                       DataSetControllerImpl dsControllerImpl, cbit.vcell.solver.Simulation vcellSim, int jobIndex,
-                                       VCSimulationIdentifier vcSimID, SimulationContext simContext) throws DataAccessException {
+                                              DataSetControllerImpl dsControllerImpl, cbit.vcell.solver.simulation.Simulation vcellSim, int jobIndex,
+                                              VCSimulationIdentifier vcSimID, SimulationContext simContext) throws DataAccessException {
 
         PDEDataContext pdeDataContext = new ServerPDEDataContext(outputContext, user, dataServerImpl, vcId);
         List<String> variableNames = RunUtils.getListOfVariableNames(pdeDataContext.getDataIdentifiers());

vcell-cli/src/main/java/org/vcell/cli/run/SolverHandler.java

@@ -6,7 +6,7 @@
 import cbit.vcell.field.FieldDataIdentifierSpec;
 import cbit.vcell.mapping.MathSymbolMapping;
 import cbit.vcell.math.FunctionColumnDescription;
-import cbit.vcell.messaging.server.SimulationTask;
+import cbit.vcell.messaging.server.StandardSimulationTask;
 import cbit.vcell.parser.Expression;
 import cbit.vcell.parser.ExpressionException;
 import cbit.vcell.parser.ExpressionMathMLParser;
@@ -17,6 +17,9 @@
 import cbit.vcell.solver.server.Solver;
 import cbit.vcell.solver.server.SolverFactory;
 import cbit.vcell.solver.server.SolverStatus;
+import cbit.vcell.solver.simulation.Simulation;
+import cbit.vcell.solver.simulation.SimulationJob;
+import cbit.vcell.solver.simulation.SimulationOwner;
 import cbit.vcell.solver.stoch.GibsonSolver;
 import cbit.vcell.solver.stoch.HybridSolver;
 import cbit.vcell.solvers.AbstractCompiledSolver;
@@ -396,15 +399,15 @@ public void simulateAllTasks(ExternalDocInfo externalDocInfo, SedML sedml, CLIRe
 
 					AbstractTask task = tempSimulationToTaskMap.get(tempSimulationJob.getTempSimulation());
 
-					SimulationTask simTask;
-					String kisao = "null";
-					ODESolverResultSet odeSolverResultSet = null;
-					SolverTaskDescription std = null;
-					SolverDescription sd = null;
-					int solverStatus = SolverStatus.SOLVER_READY;
+                StandardSimulationTask simTask;
+                String kisao = "null";
+				ODESolverResultSet odeSolverResultSet = null;
+				SolverTaskDescription std = null;
+				SolverDescription sd = null;
+				int solverStatus = SolverStatus.SOLVER_READY;
 
-					Simulation sim = tempSimulationJob.getSimulation();
-					simTask = new SimulationTask(tempSimulationJob, 0);
+				Simulation sim = tempSimulationJob.getSimulation();
+				simTask = new StandardSimulationTask(tempSimulationJob, 0);
 					Span sim_span = null;
 					try {
 						sim_span = Tracer.startSpan(Span.ContextType.SIMULATION_RUN, sim.getName(), Map.of("simName", sim.getName()));

vcell-cli/src/main/java/org/vcell/cli/run/hdf5/NonspatialResultsConverter.java

@@ -1,6 +1,6 @@
 package org.vcell.cli.run.hdf5;
 
-import cbit.vcell.solver.Simulation;
+import cbit.vcell.solver.simulation.Simulation;
 import cbit.vcell.parser.ExpressionException;
 import cbit.vcell.solver.TempSimulation;
 import ncsa.hdf.hdf5lib.exceptions.HDF5Exception;

vcell-cli/src/main/java/org/vcell/cli/run/hdf5/SpatialResultsConverter.java

@@ -1,7 +1,5 @@
 package org.vcell.cli.run.hdf5;
 
-import cbit.vcell.modelopt.MathSystemHash;
-import cbit.vcell.solver.Simulation;
 import cbit.vcell.parser.ExpressionException;
 import cbit.vcell.solver.TempSimulation;
 import ncsa.hdf.hdf5lib.exceptions.HDF5Exception;

vcell-cli/src/main/java/org/vcell/cli/vcml/VcmlOmexConverter.java

@@ -4,7 +4,7 @@
 import cbit.util.xml.VCLoggerException;
 import cbit.util.xml.XmlUtil;
 import cbit.vcell.biomodel.BioModel;
-import cbit.vcell.solver.Simulation;
+import cbit.vcell.solver.simulation.Simulation;
 import cbit.vcell.xml.XmlHelper;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;

vcell-cli/src/main/java/org/vcell/cli/vcml/VcmlValidator.java

@@ -5,7 +5,7 @@
 import cbit.vcell.mapping.SimulationContext;
 import cbit.vcell.math.MathCompareResults;
 import cbit.vcell.math.MathDescription;
-import cbit.vcell.solver.SimulationSymbolTable;
+import cbit.vcell.solver.simulation.SimulationSymbolTable;
 import cbit.vcell.xml.XMLSource;
 import cbit.vcell.xml.XmlHelper;
 import org.apache.logging.log4j.LogManager;

vcell-cli/src/test/java/org/vcell/cli/run/BiosimulationsExecTest.java

@@ -173,8 +173,9 @@ public void testBiosimulationsProject(String testCaseProjectID) throws Exception
 					computedH5File.toAbsolutePath().toString()
 			});
 			command.start(new int[] { 0, 1 });
-			assertFalse(command.getStdoutString().contains("position"), "H5 files have significant differences: " +
-					command.getStdoutString().substring(0, 300));
+			String stdOutString = command.getStdoutString();
+			assertFalse(stdOutString.contains("position"), "H5 files have significant differences: " +
+					stdOutString.substring(0, Math.min(300, stdOutString.length())));
 
 		} catch (Exception | AssertionError e){
 			FAULT fault = this.determineFault(e);

vcell-client/src/main/java/cbit/plot/gui/Plot2DDataPanel.java

@@ -9,35 +9,27 @@
  */
 
 package cbit.plot.gui;
-import java.awt.Component;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.awt.event.MouseEvent;
 import java.io.File;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.ListIterator;
-import java.util.Vector;
 
-import javax.swing.ButtonGroup;
 import javax.swing.JFileChooser;
 import javax.swing.JFrame;
 import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
 import javax.swing.JPanel;
 import javax.swing.JPopupMenu;
-import javax.swing.JRadioButton;
 import javax.swing.KeyStroke;
-import javax.swing.table.DefaultTableModel;
 
-import org.apache.commons.lang3.StringUtils;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.vcell.util.UtilCancelException;
 import org.vcell.util.gui.DialogUtils;
 import org.vcell.util.gui.NonEditableDefaultTableModel;
 import org.vcell.util.gui.ScrollTable;
-import org.vcell.util.gui.SimpleUserMessage;
 import org.vcell.util.gui.SpecialtyTableRenderer;
 
 import com.google.common.io.Files;
@@ -47,11 +39,9 @@
 import cbit.vcell.desktop.VCellTransferable;
 import cbit.vcell.math.ReservedVariable;
 import cbit.vcell.parser.Expression;
-import cbit.vcell.parser.SimpleSymbolTable;
 import cbit.vcell.parser.SymbolTableEntry;
 import cbit.vcell.simdata.Hdf5Utils;
-import cbit.vcell.simdata.Hdf5Utils.HDF5WriteHelper;
-import cbit.vcell.solver.Simulation;
+import cbit.vcell.solver.simulation.Simulation;
 import ncsa.hdf.hdf5lib.H5;
 import ncsa.hdf.hdf5lib.HDF5Constants;
 import javax.swing.JLabel;