diff --git a/pom.xml b/pom.xml index a449560d1d..c03dbb0f75 100644 --- a/pom.xml +++ b/pom.xml @@ -67,6 +67,7 @@ vcell-cli vcell-rest vcell-restclient + vcell-nativelib diff --git a/vcell-nativelib/pom.xml b/vcell-nativelib/pom.xml new file mode 100644 index 0000000000..c548fec056 --- /dev/null +++ b/vcell-nativelib/pom.xml @@ -0,0 +1,167 @@ + + + 4.0.0 + + org.vcell + vcell-pom + 0.0.1-SNAPSHOT + + + vcell-nativelib + + + 23 + 23 + UTF-8 + 0.10.4 + ${java.specification.version} + ${java.specification.version} + sbml_to_fvsolver + org.vcell.pyvcell.SBMLSpatialTest + + + + + org.vcell + vcell-core + 0.0.1-SNAPSHOT + compile + + + + + + + + + + + + + + + + + + + + + + + + + org.junit.jupiter + junit-jupiter + test + + + + + + + org.codehaus.mojo + exec-maven-plugin + 3.1.1 + + + java + + java + + + ${mainClass} + + + + + + + org.apache.maven.plugins + maven-compiler-plugin + 3.11.0 + + ${maven.compiler.source} + ${maven.compiler.source} + + + + + org.apache.maven.plugins + maven-jar-plugin + 3.3.0 + + + + true + ${mainClass} + + + + + + + org.apache.maven.plugins + maven-assembly-plugin + 3.6.0 + + + package + + single + + + + + + + true + ${mainClass} + + + + jar-with-dependencies + + + + + + + + + + + native + + + + org.graalvm.buildtools + native-maven-plugin + ${native.maven.plugin.version} + true + + + build-native + + compile-no-fork + + package + + + test-native + + test + + test + + + + + + + + + + + \ No newline at end of file diff --git a/vcell-nativelib/src/main/java/org/vcell/Main.java b/vcell-nativelib/src/main/java/org/vcell/Main.java new file mode 100644 index 0000000000..dcecd9c406 --- /dev/null +++ b/vcell-nativelib/src/main/java/org/vcell/Main.java @@ -0,0 +1,58 @@ +package org.vcell; + +import cbit.util.xml.VCLoggerException; +import cbit.vcell.biomodel.BioModel; +import cbit.vcell.mapping.MappingException; +import cbit.vcell.mapping.SimulationContext; +import cbit.vcell.parser.ExpressionException; +import cbit.vcell.solver.Simulation; +import cbit.vcell.solver.SolverException; +import cbit.vcell.solver.TimeBounds; +import cbit.vcell.solver.UniformOutputTimeSpec; +import org.apache.logging.log4j.Logger; +import org.vcell.sbml.SBMLFakeSpatialBioModel; +import org.vcell.sbml.vcell.SBMLExporter; +import org.vcell.sbml.vcell.SBMLImporter; + +import java.beans.PropertyVetoException; +import java.io.File; +import java.io.FileInputStream; +import java.io.FileNotFoundException; +import java.io.InputStream; + +public class Main { + + private static Logger logger = org.apache.logging.log4j.LogManager.getLogger(Main.class); + + public static void sbmlToFiniteVolumeInput(File sbmlFile, File outputDir) throws FileNotFoundException, MappingException, VCLoggerException, PropertyVetoException, SolverException, ExpressionException { + SBMLExporter.MemoryVCLogger vcl = new SBMLExporter.MemoryVCLogger(); + boolean bValidateSBML = true; + InputStream is = new FileInputStream(sbmlFile); + SBMLImporter importer = new SBMLImporter(is, vcl, bValidateSBML); + BioModel bioModel = importer.getBioModel(); + bioModel.updateAll(false); + + final double duration = 5.0; // endpoint arg + final double time_step = 0.1; // endpoint arg + //final ISize meshSize = new ISize(10, 10, 10); // future endpoint arg + SimulationContext simContext = bioModel.getSimulationContext(0); + Simulation sim = new Simulation(simContext.getMathDescription(), simContext); + sim.getSolverTaskDescription().setTimeBounds(new TimeBounds(0.0, duration)); + sim.getSolverTaskDescription().setOutputTimeSpec(new UniformOutputTimeSpec(time_step)); + + SBMLFakeSpatialBioModel.writeInputFilesOnly(outputDir, sim); + } + + + + + public static void main(String[] args) { + try { + File sbml_file = new File("/Users/jimschaff/Documents/workspace/vcell/vcell-rest/src/test/resources/TinySpacialProject_Application0.xml"); + sbmlToFiniteVolumeInput(sbml_file, new File("/Users/jimschaff/Documents/workspace/vcell/vcell-rest/src/test/resources/")); + System.out.println("Hello, World!"); + } catch (Exception e) { + logger.error("Error processing spatial model", e); + } + } +} \ No newline at end of file diff --git a/vcell-nativelib/src/main/java/org/vcell/pyvcell/FiniteVolumeUtils.java b/vcell-nativelib/src/main/java/org/vcell/pyvcell/FiniteVolumeUtils.java new file mode 100644 index 0000000000..e6b3d7f2fe --- /dev/null +++ b/vcell-nativelib/src/main/java/org/vcell/pyvcell/FiniteVolumeUtils.java @@ -0,0 +1,4 @@ +package org.vcell.pyvcell; + +public class FiniteVolumeUtils { +} diff --git a/vcell-nativelib/src/test/java/org/vcell/pyvcell/SBMLSpatialTest.java b/vcell-nativelib/src/test/java/org/vcell/pyvcell/SBMLSpatialTest.java new file mode 100644 index 0000000000..3cb37d26a7 --- /dev/null +++ b/vcell-nativelib/src/test/java/org/vcell/pyvcell/SBMLSpatialTest.java @@ -0,0 +1,143 @@ +package org.vcell.pyvcell; + + +import cbit.vcell.biomodel.BioModel; +import cbit.vcell.field.FieldDataIdentifierSpec; +import cbit.vcell.mapping.SimulationContext; +import cbit.vcell.messaging.server.SimulationTask; +import cbit.vcell.parser.ExpressionException; +import cbit.vcell.resource.PropertyLoader; +import cbit.vcell.solver.*; +import cbit.vcell.solvers.FVSolverStandalone; +import org.apache.log4j.ConsoleAppender; +import org.apache.log4j.Logger; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Tag; +import org.junit.jupiter.api.Test; +import org.vcell.sbml.vcell.SBMLExporter; +import org.vcell.sbml.vcell.SBMLImporter; + +import java.io.File; +import java.io.IOException; +import java.io.InputStream; +import java.nio.file.Files; + +@Tag("SBML_IT") +public class SBMLSpatialTest { + + private static File workingDir; + + public static class MyFiniteVolumeSolver extends FVSolverStandalone { + public MyFiniteVolumeSolver(SimulationTask simulationTask, File dataDir) throws SolverException { + super(simulationTask, dataDir, false); + } + @Override + public void initialize() throws SolverException { + super.initialize(); + } + } + + public static class SBMLSpatialSolver { + + private static class TempSimulationJob extends SimulationJob { + public TempSimulationJob(TempSimulation argSim, int jobIndex, FieldDataIdentifierSpec[] argFDIS) { + super(argSim, jobIndex, argFDIS); + } + @Override + public TempSimulation getSimulation() { + return (TempSimulation)super.getSimulation(); + } + } + + public static void simulate(File workingDir, Simulation simulation) throws SolverException, ExpressionException { + + TempSimulation tempSimulation = new TempSimulation(simulation,false); + tempSimulation.setSimulationOwner(simulation.getSimulationOwner()); + TempSimulationJob tempSimulationJob = new TempSimulationJob(tempSimulation, 0, null); + + SimulationTask simTask = new SimulationTask(tempSimulationJob, 0); + MyFiniteVolumeSolver solver = new MyFiniteVolumeSolver(simTask, workingDir); + solver.runSolver(); + } + + public static void writeInputFilesOnly(File workingDir, Simulation simulation) throws SolverException, ExpressionException { + + TempSimulation tempSimulation = new TempSimulation(simulation,false); + tempSimulation.setSimulationOwner(simulation.getSimulationOwner()); + TempSimulationJob tempSimulationJob = new TempSimulationJob(tempSimulation, 0, null); + + SimulationTask simTask = new SimulationTask(tempSimulationJob, 0); + MyFiniteVolumeSolver solver = new MyFiniteVolumeSolver(simTask, workingDir); + solver.initialize(); + } + } + + @BeforeAll + public static void before() throws IOException { + PropertyLoader.setProperty(PropertyLoader.installationRoot, ".."); + Logger.getLogger(SBMLExporter.class).addAppender(new ConsoleAppender()); + // create temporary working directory + workingDir = Files.createTempDirectory("sbml-test-suite-working-dir-").toFile(); + } + + @AfterAll + public static void after() { + // delete temporary working directory + try { + Files.delete(workingDir.toPath()); + } catch (Exception e) { + e.printStackTrace(); + } + } + + private static InputStream getFileFromResourceAsStream(String path) { + InputStream inputStream = SBMLSpatialTest.class.getResourceAsStream(path); + if (inputStream == null) { + throw new RuntimeException("file not found! " + path); + } else { + return inputStream; + } + } + + @Test + public void testSbmlTestSuiteImport() throws Exception{ + TLogger vcl = new TLogger(); + InputStream testFileInputStream = getFileFromResourceAsStream("/TinySpacialProject_Application0.xml"); // endpoint arg + boolean bValidateSBML = true; + SBMLImporter importer = new SBMLImporter(testFileInputStream, vcl, bValidateSBML); + try { + BioModel bioModel = importer.getBioModel(); + bioModel.updateAll(false); + + final double duration = 5.0; // endpoint arg + final double time_step = 0.1; // endpoint arg + //final ISize meshSize = new ISize(10, 10, 10); // future endpoint arg + SimulationContext simContext = bioModel.getSimulationContext(0); + Simulation sim = new Simulation(simContext.getMathDescription(), simContext); + sim.getSolverTaskDescription().setTimeBounds(new TimeBounds(0.0, duration)); + sim.getSolverTaskDescription().setOutputTimeSpec(new UniformOutputTimeSpec(time_step)); + + System.out.println("INPUT FILES ONLY"); + SBMLSpatialSolver.writeInputFilesOnly(workingDir, sim); + printWorkingDir(); + + System.out.println("ALL FILES INCLUDING OUTPUT"); + SBMLSpatialSolver.simulate(workingDir, sim); + printWorkingDir(); + + }catch (Exception e){ + e.printStackTrace(); + } + } + + private static void printWorkingDir() { + // print contents of workingDir + File[] files = workingDir.listFiles(); + for (File file : files) { + System.out.println(file.getName()); + } + } + +} + diff --git a/vcell-nativelib/src/test/java/org/vcell/pyvcell/TLogger.java b/vcell-nativelib/src/test/java/org/vcell/pyvcell/TLogger.java new file mode 100644 index 0000000000..a86e8044b7 --- /dev/null +++ b/vcell-nativelib/src/test/java/org/vcell/pyvcell/TLogger.java @@ -0,0 +1,37 @@ +package org.vcell.pyvcell; + +import cbit.util.xml.VCLogger; +import cbit.util.xml.VCLoggerException; + +import java.util.ArrayList; +import java.util.List; + +public class TLogger extends VCLogger { + public final List highPriority = new ArrayList<>(); + public final List medPriority = new ArrayList<>(); + public final List lowPriority = new ArrayList<>(); + + @Override + public boolean hasMessages() { + return false; + } + + @Override + public void sendAllMessages() { + } + + @Override + public void sendMessage(Priority p, ErrorType et, String message) + throws VCLoggerException { + String msg = p + " " + et + ": " + message; + if (p == Priority.HighPriority) { + highPriority.add(msg); + } else if (p == Priority.MediumPriority) { + medPriority.add(msg); + } else if (p == Priority.LowPriority) { + lowPriority.add(msg); + } + System.err.println(p + " " + et + ": " + message); + } + +} \ No newline at end of file diff --git a/vcell-nativelib/src/test/resources/TinySpacialProject_Application0.xml b/vcell-nativelib/src/test/resources/TinySpacialProject_Application0.xml new file mode 100644 index 0000000000..51a2a9d86d --- /dev/null +++ b/vcell-nativelib/src/test/resources/TinySpacialProject_Application0.xml @@ -0,0 +1,239 @@ + + + + +

Exported by VCell 7.3

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 100000 + x + + + + + + + + 10 + + + + + 1 + 100000 + x + + + + + + + + + + + + + + + + + + + + + Kf_r0 + s0 + + + + + + Kr_r0 + s1 + + + + + + + + + \ No newline at end of file diff --git a/vcell-rest/src/test/resources/SimID_1784145872_0_.functions b/vcell-rest/src/test/resources/SimID_1784145872_0_.functions new file mode 100644 index 0000000000..badda39958 --- /dev/null +++ b/vcell-rest/src/test/resources/SimID_1784145872_0_.functions @@ -0,0 +1,10 @@ +##--------------------------------------------- +## /Users/jimschaff/Documents/workspace/vcell/vcell-rest/src/test/resources/SimID_1784145872_0_.functions +##--------------------------------------------- + +subdomain0::J_r0; (s0 - (0.5 * s1)); ; Volume_VariableType; false +subdomain0::s0_init_umol_l_1; (100000.0 * x); ; Volume_VariableType; false +subdomain0::s1_init_umol_l_1; (10.0 - (100000.0 * x)); ; Volume_VariableType; false +subdomain0::Size_c0; vcRegionVolume('subdomain0'); ; Volume_Region_VariableType; false +subdomain0::vobj_subdomain00_size; vcRegionVolume('subdomain0'); ; Volume_Region_VariableType; false + diff --git a/vcell-rest/src/test/resources/SimID_1784145872_0_.fvinput b/vcell-rest/src/test/resources/SimID_1784145872_0_.fvinput new file mode 100644 index 0000000000..407e4ef4bb --- /dev/null +++ b/vcell-rest/src/test/resources/SimID_1784145872_0_.fvinput @@ -0,0 +1,51 @@ +# Simulation Parameters +SIMULATION_PARAM_BEGIN +SOLVER SUNDIALS_PDE_SOLVER 1.0E-7 1.0E-9 0.1 +BASE_FILE_NAME /Users/jimschaff/Documents/workspace/vcell/vcell-rest/src/test/resources/SimID_1784145872_0_ +ENDING_TIME 5.0 +TIME_STEP 0.1 +KEEP_EVERY 1 +SIMULATION_PARAM_END + +# Model description: FEATURE name handle boundary_conditions +MODEL_BEGIN +FEATURE subdomain0 0 flux flux +MODEL_END + +# Mesh file +MESH_BEGIN +VCG_FILE /Users/jimschaff/Documents/workspace/vcell/vcell-rest/src/test/resources/SimID_1784145872_0_.vcg +MESH_END + +# Variables : type name domain time_dependent_flag advection_flag grad_flag solve_whole_mesh_flag solve_regions +VARIABLE_BEGIN +VOLUME_PDE s0 subdomain0 false false false false subdomain0 +VOLUME_PDE s1 subdomain0 false false false false subdomain0 +VARIABLE_END + +POST_PROCESSING_BLOCK_BEGIN +POST_PROCESSING_BLOCK_END + +COMPARTMENT_BEGIN subdomain0 + +EQUATION_BEGIN s0 +INITIAL (100000.0 * x); +RATE - (s0 - (0.5 * s1)); +DIFFUSION 1.0E-9; +VELOCITY_X 0.0; +BOUNDARY_XM 0.0; +BOUNDARY_XP 0.0; +EQUATION_END + +EQUATION_BEGIN s1 +INITIAL (10.0 - (100000.0 * x)); +RATE (s0 - (0.5 * s1)); +DIFFUSION 1.0E-9; +VELOCITY_X 0.0; +BOUNDARY_XM 0.0; +BOUNDARY_XP 0.0; +EQUATION_END + +COMPARTMENT_END + + diff --git a/vcell-rest/src/test/resources/SimID_1784145872_0_.subdomains b/vcell-rest/src/test/resources/SimID_1784145872_0_.subdomains new file mode 100644 index 0000000000..da35e333bd --- /dev/null +++ b/vcell-rest/src/test/resources/SimID_1784145872_0_.subdomains @@ -0,0 +1,3 @@ +# CompartmentSubDomain name, handle +# MembraneSubDomain name, inside compartment name, handle, outside compartment name, handle +CompartmentSubDomain, subdomain0, 0 diff --git a/vcell-rest/src/test/resources/SimID_1784145872_0_.vcg b/vcell-rest/src/test/resources/SimID_1784145872_0_.vcg new file mode 100644 index 0000000000..d8118ab316 --- /dev/null +++ b/vcell-rest/src/test/resources/SimID_1784145872_0_.vcg @@ -0,0 +1,10 @@ +name spatialGeom +dimension 1 +size 10.0 +origin 0.0 +volumeRegions 1 +subdomain00 10.0 0 +membraneRegions 0 +volumeSamples 200 +789C636018058309000001900001 +cells 0