Examples with BioModel cbit.vcell.biomodel.BioModel used on opensource projects

Example 6 with BioModel

use of cbit.vcell.biomodel.BioModel in project vcell by virtualcell.

the class SBMLImporter method getBioModel.

// /**
// * @ TODO: This method doesn't take care of adjusting species in nested
// parameter rules with the species_concetration_factor.
// * @param kinetics
// * @param paramExpr
// * @throws ExpressionException
// */
// private void substituteOtherGlobalParams(Kinetics kinetics, Expression
// paramExpr) throws ExpressionException, PropertyVetoException {
// String[] exprSymbols = paramExpr.getSymbols();
// if (exprSymbols == null || exprSymbols.length == 0) {
// return;
// }
// Model vcModel = vcBioModel.getSimulationContext(0).getModel();
// for (int kk = 0; kk < exprSymbols.length; kk++) {
// ModelParameter mp = vcModel.getModelParameter(exprSymbols[kk]);
// if (mp != null) {
// Expression expr = mp.getExpression();
// if (expr != null) {
// Expression newExpr = new Expression(expr);
// substituteGlobalParamRulesInPlace(newExpr, false);
// // param has constant value, add it as a kinetic parameter if it is not
// already in the kinetics
// kinetics.setParameterValue(exprSymbols[kk], newExpr.infix());
// kinetics.getKineticsParameter(exprSymbols[kk]).setUnitDefinition(getSBMLUnit(sbmlModel.getParameter(exprSymbols[kk]).getUnits(),
// null));
// if (newExpr.getSymbols() != null) {
// substituteOtherGlobalParams(kinetics, newExpr);
// }
// }
// }
// }
// }
/**
 * parse SBML file into biomodel logs errors to log4j if present in source
 * document
 *
 * @return new Biomodel
 * @throws IOException
 * @throws XMLStreamException
 */
public BioModel getBioModel() throws XMLStreamException, IOException {
    SBMLDocument document;
    String output = "didn't check";
    try {
        if (sbmlFileName != null) {
            // Read SBML model into libSBML SBMLDocument and create an SBML model
            SBMLReader reader = new SBMLReader();
            document = reader.readSBML(sbmlFileName);
            // document.checkConsistencyOffline();
            // long numProblems = document.getNumErrors();
            // 
            // System.out.println("\n\nSBML Import Error Report");
            // ByteArrayOutputStream os = new ByteArrayOutputStream();
            // PrintStream ps = new PrintStream(os);
            // document.printErrors(ps);
            // String output = os.toString();
            // if (numProblems > 0 && lg.isEnabledFor(Level.WARN)) {
            // lg.warn("Num problems in original SBML document : " + numProblems);
            // lg.warn(output);
            // }
            sbmlModel = document.getModel();
            if (sbmlModel == null) {
                throw new SBMLImportException("Unable to read SBML file : \n" + output);
            }
        } else {
            if (sbmlModel == null) {
                throw new IllegalStateException("Expected non-null SBML model");
            }
            document = sbmlModel.getSBMLDocument();
        }
        // Convert SBML Model to VCell model
        // An SBML model will correspond to a simcontext - which needs a
        // Model and a Geometry
        // SBML handles only nonspatial geometries at this time, hence
        // creating a non-spatial default geometry
        String modelName = sbmlModel.getId();
        if (modelName == null || modelName.trim().equals("")) {
            modelName = sbmlModel.getName();
        }
        // name, say 'newModel'
        if (modelName == null || modelName.trim().equals("")) {
            modelName = "newModel";
        }
        // get namespace based on SBML model level and version to use in
        // SBMLAnnotationUtil
        this.level = sbmlModel.getLevel();
        // this.version = sbmlModel.getVersion();
        String ns = document.getNamespace();
        try {
            // create SBML unit system for the model and create the bioModel.
            ModelUnitSystem modelUnitSystem;
            try {
                modelUnitSystem = createSBMLUnitSystemForVCModel();
            } catch (Exception e) {
                e.printStackTrace(System.out);
                throw new SBMLImportException("Inconsistent unit system. Cannot import SBML model into VCell", Category.INCONSISTENT_UNIT, e);
            }
            Geometry geometry = new Geometry(BioModelChildSummary.COMPARTMENTAL_GEO_STR, 0);
            vcBioModel = new BioModel(null, modelUnitSystem);
            SimulationContext simulationContext = new SimulationContext(vcBioModel.getModel(), geometry, null, null, Application.NETWORK_DETERMINISTIC);
            vcBioModel.addSimulationContext(simulationContext);
            simulationContext.setName(vcBioModel.getSimulationContext(0).getModel().getName());
        // vcBioModel.getSimulationContext(0).setName(vcBioModel.getSimulationContext(0).getModel().getName()+"_"+vcBioModel.getSimulationContext(0).getGeometry().getName());
        } catch (PropertyVetoException e) {
            e.printStackTrace(System.out);
            throw new SBMLImportException("Could not create simulation context corresponding to the input SBML model", e);
        }
        // SBML annotation
        sbmlAnnotationUtil = new SBMLAnnotationUtil(vcBioModel.getVCMetaData(), vcBioModel, ns);
        translateSBMLModel();
        try {
            // **** TEMPORARY BLOCK - to name the biomodel with proper name,
            // rather than model id
            String biomodelName = sbmlModel.getName();
            // if name is not set, use id
            if ((biomodelName == null) || biomodelName.trim().equals("")) {
                biomodelName = sbmlModel.getId();
            }
            // if id is not set, use a default, say, 'newModel'
            if ((biomodelName == null) || biomodelName.trim().equals("")) {
                biomodelName = "newBioModel";
            }
            vcBioModel.setName(biomodelName);
        // **** end - TEMPORARY BLOCK
        } catch (Exception e) {
            e.printStackTrace(System.out);
            throw new SBMLImportException("Could not create Biomodel", e);
        }
        sbmlAnnotationUtil.readAnnotation(vcBioModel, sbmlModel);
        sbmlAnnotationUtil.readNotes(vcBioModel, sbmlModel);
        vcBioModel.refreshDependencies();
        Issue[] warningIssues = localIssueList.toArray(new Issue[localIssueList.size()]);
        if (warningIssues != null && warningIssues.length > 0) {
            StringBuffer messageBuffer = new StringBuffer("Issues encountered during SBML Import:\n");
            int issueCount = 0;
            for (int i = 0; i < warningIssues.length; i++) {
                if (warningIssues[i].getSeverity() == Issue.SEVERITY_WARNING || warningIssues[i].getSeverity() == Issue.SEVERITY_INFO) {
                    messageBuffer.append(warningIssues[i].getCategory() + " " + warningIssues[i].getSeverityName() + " : " + warningIssues[i].getMessage() + "\n");
                    issueCount++;
                }
            }
            if (issueCount > 0) {
                try {
                    logger.sendMessage(VCLogger.Priority.MediumPriority, VCLogger.ErrorType.OverallWarning, messageBuffer.toString());
                } catch (Exception e) {
                    e.printStackTrace(System.out);
                }
            // PopupGenerator.showWarningDialog(requester,messageBuffer.toString(),new
            // String[] { "OK" }, "OK");
            }
        }
    } catch (Exception e) {
        throw new SBMLImportException("Unable to read SBML file : \n" + output, e);
    }
    return vcBioModel;
}

Example 7 with BioModel

use of cbit.vcell.biomodel.BioModel in project vcell by virtualcell.

the class SBMLImporterTest method testImport.

@Test
public void testImport() throws XMLStreamException, IOException {
    HashMap<Integer, FAULT> faults = new HashMap();
    faults.put(6, FAULT.RESERVED_WORD);
    faults.put(15, FAULT.RESERVED_WORD);
    faults.put(92, FAULT.RESERVED_WORD);
    faults.put(114, FAULT.RESERVED_WORD);
    faults.put(115, FAULT.RESERVED_WORD);
    faults.put(117, FAULT.RESERVED_WORD);
    faults.put(148, FAULT.RESERVED_WORD);
    faults.put(154, FAULT.RESERVED_WORD);
    faults.put(155, FAULT.RESERVED_WORD);
    faults.put(154, FAULT.RESERVED_WORD);
    faults.put(155, FAULT.RESERVED_WORD);
    faults.put(156, FAULT.RESERVED_WORD);
    faults.put(157, FAULT.RESERVED_WORD);
    faults.put(158, FAULT.RESERVED_WORD);
    faults.put(159, FAULT.RESERVED_WORD);
    faults.put(274, FAULT.RESERVED_WORD);
    faults.put(279, FAULT.RESERVED_WORD);
    faults.put(282, FAULT.RESERVED_WORD);
    faults.put(288, FAULT.RESERVED_WORD);
    faults.put(346, FAULT.RESERVED_WORD);
    faults.put(24, FAULT.DELAY);
    faults.put(25, FAULT.DELAY);
    faults.put(34, FAULT.DELAY);
    faults.put(196, FAULT.DELAY);
    faults.put(39, FAULT.NONINTEGER_STOICH);
    faults.put(59, FAULT.NONINTEGER_STOICH);
    faults.put(63, FAULT.NONINTEGER_STOICH);
    faults.put(81, FAULT.NONINTEGER_STOICH);
    faults.put(145, FAULT.NONINTEGER_STOICH);
    faults.put(151, FAULT.NONINTEGER_STOICH);
    faults.put(199, FAULT.NONINTEGER_STOICH);
    faults.put(206, FAULT.NONINTEGER_STOICH);
    faults.put(232, FAULT.NONINTEGER_STOICH);
    faults.put(244, FAULT.NONINTEGER_STOICH);
    faults.put(246, FAULT.NONINTEGER_STOICH);
    faults.put(110, FAULT.INCONSISTENT_UNIT_SYSTEM);
    faults.put(178, FAULT.INCONSISTENT_UNIT_SYSTEM);
    faults.put(228, FAULT.INCONSISTENT_UNIT_SYSTEM);
    faults.put(245, FAULT.INCONSISTENT_UNIT_SYSTEM);
    faults.put(252, FAULT.INCONSISTENT_UNIT_SYSTEM);
    faults.put(262, FAULT.INCONSISTENT_UNIT_SYSTEM);
    faults.put(263, FAULT.INCONSISTENT_UNIT_SYSTEM);
    faults.put(264, FAULT.INCONSISTENT_UNIT_SYSTEM);
    faults.put(267, FAULT.INCONSISTENT_UNIT_SYSTEM);
    faults.put(283, FAULT.INCONSISTENT_UNIT_SYSTEM);
    faults.put(300, FAULT.INCONSISTENT_UNIT_SYSTEM);
    faults.put(316, FAULT.INCONSISTENT_UNIT_SYSTEM);
    faults.put(317, FAULT.INCONSISTENT_UNIT_SYSTEM);
    faults.put(319, FAULT.INCONSISTENT_UNIT_SYSTEM);
    faults.put(322, FAULT.INCONSISTENT_UNIT_SYSTEM);
    faults.put(323, FAULT.INCONSISTENT_UNIT_SYSTEM);
    faults.put(337, FAULT.INCONSISTENT_UNIT_SYSTEM);
    faults.put(327, FAULT.EXPRESSION_BINDING_EXCEPTION);
    faults.put(340, FAULT.XOR_MISSING);
    faults.put(248, FAULT.EXPRESSION_BINDING_EXCEPTION);
    faults.put(305, FAULT.EXPRESSION_BINDING_EXCEPTION);
    faults.put(353, FAULT.NONINTEGER_STOICH);
    faults.put(367, FAULT.RESERVED_WORD);
    faults.put(382, FAULT.RESERVED_WORD);
    faults.put(383, FAULT.NONINTEGER_STOICH);
    faults.put(384, FAULT.NONINTEGER_STOICH);
    faults.put(385, FAULT.NONINTEGER_STOICH);
    faults.put(386, FAULT.NONINTEGER_STOICH);
    faults.put(387, FAULT.NONINTEGER_STOICH);
    faults.put(388, FAULT.NONINTEGER_STOICH);
    faults.put(392, FAULT.NONINTEGER_STOICH);
    faults.put(401, FAULT.NONINTEGER_STOICH);
    faults.put(402, FAULT.RESERVED_WORD);
    faults.put(403, FAULT.RESERVED_WORD);
    faults.put(405, FAULT.INCONSISTENT_UNIT_SYSTEM);
    faults.put(539, FAULT.JSBML_ERROR);
    File[] sbmlFiles = SBMLUnitTranslatorTest.getBiomodelsCuratedSBMLFiles();
    // File[] sbmlFiles = new File[] {
    // new File("/Users/schaff/Documents/workspace-maven/BioModels_Database-r30_pub-sbml_files/curated/BIOMD0000000001.xml"),
    // new File("/Users/schaff/Documents/workspace-maven/BioModels_Database-r30_pub-sbml_files/curated/BIOMD0000000101.xml"),
    // new File("/Users/schaff/Documents/workspace-maven/sbml-test-suite/cases/semantic/00001/00001-sbml-l3v1.xml")
    // };
    VCLogger vcl = new TLogger();
    int start = 401;
    for (int index = start; index < sbmlFiles.length; index++) {
        File sbmlFile = sbmlFiles[index];
        int sbmlNumber = Integer.parseInt(sbmlFile.getName().substring(6).replace(".xml", ""));
        if (faults.containsKey(sbmlNumber)) {
            System.err.println("skipping this model, " + faults.get(sbmlNumber).name());
            continue;
        }
        System.out.println("testing " + sbmlFile);
        SBMLImporter importer = new SBMLImporter(sbmlFile.getAbsolutePath(), vcl, false);
        BioModel bioModel = importer.getBioModel();
    }
}

Example 8 with BioModel

use of cbit.vcell.biomodel.BioModel in project vcell by virtualcell.

the class SBMLStandaloneImporterTest method main.

public static void main(String[] args) {
    Logging.init();
    try {
        SBMLStandaloneImporter sa = new SBMLStandaloneImporter();
        for (; ; ) {
            /*
			JFileChooser jfc = new JFileChooser( new File(System.getProperty("user.dir")));
			int returnVal = jfc.showOpenDialog(null);
			if(returnVal == JFileChooser.APPROVE_OPTION) {
				File f= jfc.getSelectedFile();
				BioModel bm = sa.importSBML(f);
				System.out.println(bm.getName());
			}
			*/
            BioModel bm = sa.importSBML(new File("samp.sbml"));
            System.out.println(bm.getName());
        }
    } catch (Exception e) {
        System.err.println(e.getMessage());
        e.printStackTrace();
    }
}

Example 9 with BioModel

use of cbit.vcell.biomodel.BioModel in project vcell by virtualcell.

the class StandaloneSEDMLTest method doit.

public static void doit(File archiveFile) throws Exception {
    ArchiveComponents ac = null;
    ac = Libsedml.readSEDMLArchive(new FileInputStream(archiveFile));
    SEDMLDocument sedmlDoc = ac.getSedmlDocument();
    SedML sedml = sedmlDoc.getSedMLModel();
    if (sedml == null || sedml.getModels().isEmpty()) {
        throw new RuntimeException("sedml null or empty");
    }
    ModelResolver resolver = new ModelResolver(sedml);
    // resolver.add(new FileModelResolver());
    resolver.add(new ArchiveModelResolver(ac));
    resolver.add(new BioModelsModelsRetriever());
    resolver.add(new URLResourceRetriever());
    // resolver.add(new RelativeFileModelResolver(FileUtils.getFullPath(archiveFile.getAbsolutePath())));
    // 
    // iterate through all the elements and show them at the console
    // 
    List<org.jlibsedml.Model> mmm = sedml.getModels();
    for (Model mm : mmm) {
        System.out.println(mm.toString());
    }
    List<org.jlibsedml.Simulation> sss = sedml.getSimulations();
    for (org.jlibsedml.Simulation ss : sss) {
        System.out.println(ss.toString());
    }
    List<AbstractTask> ttt = sedml.getTasks();
    for (AbstractTask tt : ttt) {
        System.out.println(tt.toString());
    }
    List<DataGenerator> ddd = sedml.getDataGenerators();
    for (DataGenerator dd : ddd) {
        System.out.println(dd.toString());
    }
    List<Output> ooo = sedml.getOutputs();
    for (Output oo : ooo) {
        System.out.println(oo.toString());
    }
    // 
    // extract models referenced in tasks.
    // 
    KisaoOntology kisaoInstance = KisaoOntology.getInstance();
    // HashMap<String,Model> flattenedModels = new HashMap<String, Model>();
    List<AbstractTask> taskList = sedml.getTasks();
    for (AbstractTask task : taskList) {
        String modelReference = task.getModelReference();
        org.jlibsedml.Model sedmlOriginalModel = sedml.getModelWithId(modelReference);
        String sbmlModelString = resolver.getModelString(sedmlOriginalModel);
        // sbmlSource with all the changes applied
        XMLSource sbmlSource = new XMLSource(sbmlModelString);
        org.jlibsedml.Simulation sedmlSimulation = sedml.getSimulation(task.getSimulationReference());
        Algorithm algorithm = sedmlSimulation.getAlgorithm();
        KisaoTerm sedmlKisao = kisaoInstance.getTermById(algorithm.getKisaoID());
        // 
        // try to find a VCell solverDescription to match the Kisao term
        // 
        // UniformTimeCourse [initialTime=0.0, numberOfPoints=1000, outputEndTime=1.0, outputStartTime=0.0,
        // Algorithm [kisaoID=KISAO:0000019], getId()=SimSlow]
        // identify the vCell solvers that would match best the sedml solver kisao id
        List<SolverDescription> solverDescriptions = new ArrayList<>();
        for (SolverDescription sd : SolverDescription.values()) {
            KisaoTerm solverKisaoTerm = kisaoInstance.getTermById(sd.getKisao());
            if (solverKisaoTerm == null) {
                break;
            }
            boolean isExactlySame = solverKisaoTerm.equals(sedmlKisao);
            if (isExactlySame && !solverKisaoTerm.isObsolete()) {
                // we make a list with all the solvers that match the kisao
                solverDescriptions.add(sd);
            }
        }
        if (solverDescriptions.isEmpty()) {
            throw new RuntimeException("cannot find the solverDescription with exact match for Kisao term '" + sedmlKisao + "'");
        }
        // choose first one
        SolverDescription solverDescription = solverDescriptions.get(0);
        // find out everything else we need about the application we're going to use,
        // some of the info will be needed when we parse the sbml file
        boolean bSpatial = false;
        Application appType = Application.NETWORK_DETERMINISTIC;
        Set<SolverDescription.SolverFeature> sfList = solverDescription.getSupportedFeatures();
        for (SolverDescription.SolverFeature sf : sfList) {
            switch(sf) {
                case Feature_Rulebased:
                    appType = Application.RULE_BASED_STOCHASTIC;
                    break;
                case Feature_Stochastic:
                    appType = Application.NETWORK_STOCHASTIC;
                    break;
                case Feature_Deterministic:
                    appType = Application.NETWORK_DETERMINISTIC;
                    break;
                case Feature_Spatial:
                    bSpatial = true;
                    break;
                default:
                    break;
            }
        }
        BioModel bioModel = (BioModel) XmlHelper.importSBML(transLogger, sbmlSource, bSpatial);
        // 
        // we already have an application loaded from the sbml file, with initial conditions and stuff
        // which may be not be suitable because the sedml kisao may need a different app type
        // so we do a "copy as" to the right type and then delete the original we loaded from the sbml file
        // 
        // the new application we're making from the old one
        SimulationContext newSimulationContext = null;
        if (bioModel.getSimulationContexts().length == 1) {
            SimulationContext oldSimulationContext = bioModel.getSimulationContext(0);
            String newSCName = bioModel.getFreeSimulationContextName();
            newSimulationContext = SimulationContext.copySimulationContext(oldSimulationContext, newSCName, bSpatial, appType);
            bioModel.addSimulationContext(newSimulationContext);
            bioModel.removeSimulationContext(oldSimulationContext);
        } else {
            newSimulationContext = bioModel.addNewSimulationContext("App1", appType);
        }
        // 
        // making the new vCell simulation based on the sedml simulation
        // 
        newSimulationContext.refreshDependencies();
        MathMappingCallback callback = new MathMappingCallbackTaskAdapter(progressListener);
        newSimulationContext.refreshMathDescription(callback, NetworkGenerationRequirements.ComputeFullStandardTimeout);
        Simulation newSimulation = new Simulation(newSimulationContext.getMathDescription());
        newSimulation.setName(sedmlSimulation.getName());
        bioModel.addSimulation(newSimulation);
        // and set the vCell simulation parameters accordingly
        if (sedmlSimulation instanceof UniformTimeCourse) {
        } else if (sedmlSimulation instanceof OneStep) {
        } else if (sedmlSimulation instanceof SteadyState) {
        } else {
        }
        System.out.println(XmlHelper.bioModelToXML(bioModel));
    }
}

Example 10 with BioModel

use of cbit.vcell.biomodel.BioModel in project vcell by virtualcell.

the class SimulationServiceImpl method computeModel.

public SimulationInfo computeModel(SBMLModel model, SimulationSpec simSpec) throws ThriftDataAccessException, TException {
    try {
        SBMLImporter importer = new SBMLImporter(model.getFilepath(), vcLogger(), true);
        BioModel bioModel = importer.getBioModel();
        return computeModel(bioModel, simSpec, null);
    } catch (Exception exc) {
        exc.printStackTrace(System.out);
        return null;
    }
}