Examples with VCLogger cbit.util.xml.VCLogger used on opensource projects

Example 1 with VCLogger

use of cbit.util.xml.VCLogger 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 2 with VCLogger

use of cbit.util.xml.VCLogger in project vcell by virtualcell.

the class VCellClientTest method startupWithOpen.

private static VCDocument startupWithOpen(String fileName) {
    VCDocument initialDocument = null;
    try {
        Document xmlDoc = XmlUtil.readXML(new File(fileName));
        String vcmlString = XmlUtil.xmlToString(xmlDoc, false);
        java.awt.Component parent = null;
        VCLogger vcLogger = new TranslationLogger(parent);
        initialDocument = XmlHelper.XMLToDocument(vcLogger, vcmlString);
    } catch (Exception e) {
        e.printStackTrace(System.out);
        JOptionPane.showMessageDialog(null, e.getMessage(), "vcell startup error", JOptionPane.ERROR_MESSAGE);
    }
    return initialDocument;
}

Example 3 with VCLogger

use of cbit.util.xml.VCLogger in project vcell by virtualcell.

the class BNGWindowManager method importSbml.

/**
 * Comment
 */
public void importSbml(String bngSbmlStr) {
    if (bngSbmlStr == null || bngSbmlStr.length() == 0) {
        throw new RuntimeException("SBMl string is empty, cannot import into VCell.");
    }
    // 
    // 1. Convert SBML string from BNG to SBML model, add unitDefintions to SBML model using VCell sbml compatible unit system
    // 2. Import unit modified SBML model into VCell as biomodel
    // 3. Enforce "cleaner" (looking) units on this imported biomodel (can use the units added to the sbml model above)
    // 4. Convert all LumpedKinetics reactions into DistributedKinetics.
    // 4. Convert this biomodel into vcml string and pass it into XMLInfo and then to RequestManager to open document.
    // 
    ModelUnitSystem mus = ModelUnitSystem.createDefaultVCModelUnitSystem();
    ModelUnitSystem sbmlCompatibleVCModelUnitSystem = ModelUnitSystem.createSBMLUnitSystem(mus.getVolumeSubstanceUnit(), mus.getVolumeUnit(), mus.getAreaUnit(), mus.getLengthUnit(), mus.getTimeUnit());
    // display to user to change units if desired.
    UnitSystemSelectionPanel unitSystemSelectionPanel = new UnitSystemSelectionPanel(true);
    unitSystemSelectionPanel.initialize(sbmlCompatibleVCModelUnitSystem);
    int retcode = DialogUtils.showComponentOKCancelDialog(getBngOutputPanel(), unitSystemSelectionPanel, "Select new unit system to import into VCell");
    ModelUnitSystem forcedModelUnitSystem = null;
    while (retcode == JOptionPane.OK_OPTION) {
        try {
            forcedModelUnitSystem = unitSystemSelectionPanel.createModelUnitSystem();
            break;
        } catch (Exception e) {
            e.printStackTrace(System.out);
            DialogUtils.showErrorDialog(getBngOutputPanel(), e.getMessage(), e);
            retcode = DialogUtils.showComponentOKCancelDialog(getBngOutputPanel(), unitSystemSelectionPanel, "Select new unit system to import into VCell");
        }
    }
    if (forcedModelUnitSystem == null) {
        DialogUtils.showErrorDialog(getBngOutputPanel(), "Units are required for import into Virtual Cell.");
    }
    try {
        // SBMLUnitTranslator.addUnitDefinitionsToSbmlModel(bngSbmlStr, forcedModelUnitSystem);
        String modifiedSbmlStr = bngSbmlStr;
        // Create a default VCLogger - SBMLImporter needs it
        cbit.util.xml.VCLogger logger = new cbit.util.xml.VCLogger() {

            @Override
            public void sendMessage(Priority p, ErrorType et, String message) throws Exception {
                System.err.println("LOGGER: msgLevel=" + p + ", msgType=" + et + ", " + message);
                if (p == VCLogger.Priority.HighPriority) {
                    throw new RuntimeException("Import failed : " + message);
                }
            }

            public void sendAllMessages() {
            }

            public boolean hasMessages() {
                return false;
            }
        };
        // import sbml String into VCell biomodel
        File sbmlFile = File.createTempFile("temp", ".xml");
        sbmlFile.deleteOnExit();
        XmlUtil.writeXMLStringToFile(modifiedSbmlStr, sbmlFile.getAbsolutePath(), true);
        org.vcell.sbml.vcell.SBMLImporter sbmlImporter = new SBMLImporter(sbmlFile.getAbsolutePath(), logger, false);
        BioModel bioModel = sbmlImporter.getBioModel();
        // enforce 'cleaner looking' units on vc biomodel (the process of adding unit defintion to sbml model messes up the units, though they are correct units (eg., 1e-6m for um).
        BioModel modifiedBiomodel = ModelUnitConverter.createBioModelWithNewUnitSystem(bioModel, forcedModelUnitSystem);
        // convert any reaction that has GeneralLumpedKinetics to GeneralKinetics
        for (ReactionStep rs : modifiedBiomodel.getModel().getReactionSteps()) {
            Kinetics kinetics = rs.getKinetics();
            if (kinetics instanceof LumpedKinetics) {
                rs.setKinetics(DistributedKinetics.toDistributedKinetics((LumpedKinetics) kinetics));
            }
        }
        // convert biomodel to vcml string
        String vcmlString = XmlHelper.bioModelToXML(modifiedBiomodel);
        ExternalDocInfo externalDocInfo = new ExternalDocInfo(vcmlString);
        if (externalDocInfo != null) {
            getRequestManager().openDocument(externalDocInfo, this, true);
        }
    } catch (Exception e) {
        e.printStackTrace(System.out);
        throw new RuntimeException("Cound not convert BNG sbml string to VCell biomodel : ", e);
    }
}

Example 4 with VCLogger

use of cbit.util.xml.VCLogger in project vcell by virtualcell.

the class SbmlVcmlConverter method main.

/**
 * @param args -import or -export
 */
public static void main(String[] args) {
    Logging.init();
    ResourceUtil.setNativeLibraryDirectory();
    if (args.length < 2 || args.length > 3) {
        System.out.println("Usage:\n\t -export path_of_input_file\n\tOR\n\t -import path_of_input_file [-simulate]");
        System.exit(1);
    }
    if (args.length > 2 && args[0].equals("-export")) {
        System.out.println("Export cannot have arguments other than input file.");
        System.out.println("Usage:\n\t -export path_of_input_file\n\tOR\n\t-import path_of_input_file [-simulate]");
        System.exit(1);
    }
    try {
        String pathName = args[1];
        // Read xml file (Sbml or Vcml) into stringbuffer, pass the string into VCell's importer/exporter
        String xmlString = getXMLString(pathName);
        if (args[0].equals("-import")) {
            if (args.length > 3 || (args.length == 3 && !args[2].equals("-simulate"))) {
                System.out.println(args[2] + " : Unknown arguments for import; please check and re-run import command");
                System.out.println("Usage:\n\t -import path_of_input_file [-simulate]");
                System.exit(1);
            }
            boolean bSimulate = false;
            if (args.length == 3 && args[2].equals("-simulate")) {
                bSimulate = true;
            }
            // Create a default VCLogger - SBMLImporter needs it
            cbit.util.xml.VCLogger logger = new cbit.util.xml.VCLogger() {

                @Override
                public void sendMessage(Priority p, ErrorType et, String message) {
                    System.err.println("LOGGER: msgLevel=" + p + ", msgType=" + et + ", " + message);
                    if (p == VCLogger.Priority.HighPriority) {
                        throw new RuntimeException("Import failed : " + message);
                    }
                }

                public void sendAllMessages() {
                }

                public boolean hasMessages() {
                    return false;
                }
            };
            // invoke SBMLImporter, which returns a Biomodel, convert that to VCML using XMLHelper
            try {
                // import SBML model into VCML, store VCML string in 'fileName.vcml'
                // Instantiate an SBMLImporter to get the speciesUnitsHash - to compute the conversion factor from VC->SB species units.
                // and import SBML  (sbml->bioModel)
                org.vcell.sbml.vcell.SBMLImporter sbmlImporter = new org.vcell.sbml.vcell.SBMLImporter(pathName, logger, false);
                BioModel bioModel = sbmlImporter.getBioModel();
                // Hashtable<String, SBMLImporter.SBVCConcentrationUnits> speciesUnitsHash = sbmlImporter.getSpeciesUnitsHash();
                // double timeFactor = sbmlImporter.getSBMLTimeUnitsFactor();
                // convert biomodel to vcml and save to file.
                String vcmlString = XmlHelper.bioModelToXML(bioModel);
                String fileExtensionStr;
                if (pathName.endsWith(".xml")) {
                    fileExtensionStr = ".xml";
                } else if (pathName.endsWith(".sbml")) {
                    fileExtensionStr = ".sbml";
                } else {
                    throw new RuntimeException("Unknown file extension for SBML file name; Exiting SbmlConverter.");
                }
                String vcmlFileName = pathName.replace(fileExtensionStr, ".vcml");
                File vcmlFile = new File(vcmlFileName);
                XmlUtil.writeXMLStringToFile(vcmlString, vcmlFile.getAbsolutePath(), true);
                // If user doesn't choose to simulate, you are done.
                if (!bSimulate) {
                    return;
                }
                // Generate math for lone simContext
                SimulationContext simContext = (SimulationContext) bioModel.getSimulationContext(0);
                MathDescription mathDesc = simContext.createNewMathMapping().getMathDescription();
                simContext.setMathDescription(mathDesc);
                // Create basic simulation, with IDA solver (set in solve method) and other defaults, and end time 'Te'
                org.vcell.util.document.SimulationVersion simVersion = new org.vcell.util.document.SimulationVersion(new KeyValue("12345"), "name", new org.vcell.util.document.User("user", new KeyValue("123")), new org.vcell.util.document.GroupAccessNone(), // versionBranchPointRef
                null, // branchID
                new java.math.BigDecimal(1.0), new java.util.Date(), org.vcell.util.document.VersionFlag.Archived, "", null);
                Simulation sim1 = new Simulation(simVersion, simContext.getMathDescription());
                simContext.addSimulation(sim1);
                sim1.setName("sim1");
                // using a default end time of 10.0 secs, and a forcing default output time step of 0.01.
                // If user wants anything different, user can modify the .idaInput file and re-run simulation separately.
                // double newEndTime = endTime * timeFactor;
                double newEndTime = endTime;
                sim1.getSolverTaskDescription().setTimeBounds(new cbit.vcell.solver.TimeBounds(0, newEndTime));
                TimeStep timeStep_1 = new TimeStep();
                sim1.getSolverTaskDescription().setTimeStep(new TimeStep(timeStep_1.getMinimumTimeStep(), timeStep_1.getDefaultTimeStep(), newEndTime / 10000));
                sim1.getSolverTaskDescription().setOutputTimeSpec(new UniformOutputTimeSpec((newEndTime - 0) / numTimeSteps));
                sim1.getSolverTaskDescription().setErrorTolerance(new ErrorTolerance(1e-10, 1e-12));
                // save the new vcml with generated math and new sim in file named : fileName_IDA_simulation.vcml
                String newVcmlString = XmlHelper.bioModelToXML(bioModel);
                String newVcmlFileName = vcmlFile.getPath().replace(".vcml", "_IDA_simulation.vcml");
                File newVcmlFile = new File(newVcmlFileName);
                XmlUtil.writeXMLStringToFile(newVcmlString, newVcmlFile.getAbsolutePath(), true);
                // Solve simulation, which also generates and saves the .idainput file and .csv
                // SimSpec to get vars to solve and output in .csv
                SimSpec simSpec = SimSpec.fromSBML(xmlString);
                solveSimulation(new SimulationJob(sim1, 0, null), vcmlFile.getPath(), simSpec);
            } catch (Exception e) {
                e.printStackTrace(System.err);
                // and an annotation saying why it failed.
                try {
                    String fileExtensionStr;
                    if (pathName.endsWith(".xml")) {
                        fileExtensionStr = ".xml";
                    } else if (pathName.endsWith(".sbml")) {
                        fileExtensionStr = ".sbml";
                    } else {
                        throw new RuntimeException("Unknown file extension for SBML file name; Exiting SbmlConverter.");
                    }
                    String dummyVcmlFileName = pathName.replace(fileExtensionStr, ".vcml");
                    File dummyVcmlFile = new File(dummyVcmlFileName);
                    BioModel dummy_biomodel = new BioModel(null);
                    String dummyName = dummyVcmlFile.getName().substring(0, dummyVcmlFile.getName().indexOf(".vcml"));
                    dummy_biomodel.setName(dummyName);
                    dummy_biomodel.setDescription("SBML Model could not be automatically converted to VCML : " + e.getMessage());
                    String vcmlString = XmlHelper.bioModelToXML(dummy_biomodel);
                    XmlUtil.writeXMLStringToFile(vcmlString, dummyVcmlFile.getAbsolutePath(), true);
                } catch (Exception e1) {
                    e.printStackTrace(System.err);
                }
            }
        } else if (args[0].equals("-export")) {
            try {
                BioModel bioModel = XmlHelper.XMLToBioModel(new XMLSource(xmlString));
                for (int i = 0; i < bioModel.getSimulationContexts().length; i++) {
                    SimulationContext simContext = bioModel.getSimulationContext(i);
                    if (simContext.getGeometry().getDimension() == 0 && !simContext.isStoch()) {
                        if (!simContext.getGeometryContext().isAllSizeSpecifiedPositive()) {
                            Structure structure = simContext.getModel().getStructure(0);
                            double structureSize = 1.0;
                            StructureMapping structMapping = simContext.getGeometryContext().getStructureMapping(structure);
                            StructureSizeSolver.updateAbsoluteStructureSizes(simContext, structure, structureSize, structMapping.getSizeParameter().getUnitDefinition());
                        }
                        // Export the application itself, with default overrides
                        String sbmlString = XmlHelper.exportSBML(bioModel, 2, 4, 0, false, simContext, null);
                        String filePath = pathName.substring(0, pathName.lastIndexOf("\\") + 1);
                        String sbmlFileName = TokenMangler.mangleToSName(bioModel.getName() + "_" + i);
                        File sbmlFile = new File(filePath + sbmlFileName + ".xml");
                        XmlUtil.writeXMLStringToFile(sbmlString, sbmlFile.getAbsolutePath(), true);
                        // Now export each simulation in the application that has overrides
                        Simulation[] simulations = bioModel.getSimulations(simContext);
                        for (int j = 0; j < simulations.length; j++) {
                            if (simulations[j].getMathOverrides().hasOverrides()) {
                                // Check for parameter scan and create simJob to pass into exporter
                                for (int k = 0; k < simulations[j].getScanCount(); k++) {
                                    SimulationJob simJob = new SimulationJob(simulations[j], k, null);
                                    sbmlString = XmlHelper.exportSBML(bioModel, 2, 4, 0, false, simContext, simJob);
                                    String fileName = TokenMangler.mangleToSName(sbmlFileName + "_" + j + "_" + k);
                                    sbmlFile = new File(filePath + fileName + ".xml");
                                    XmlUtil.writeXMLStringToFile(sbmlString, sbmlFile.getAbsolutePath(), true);
                                }
                            }
                        }
                    }
                }
                System.out.println("Successfully translated model : " + pathName);
            } catch (Exception e) {
                e.printStackTrace(System.err);
            }
        }
        System.exit(0);
    } catch (IOException e) {
        e.printStackTrace(System.err);
        System.exit(1);
    }
}

Example 5 with VCLogger

use of cbit.util.xml.VCLogger in project vcell by virtualcell.

the class SBMLImporterTest method main.

public static void main(String[] args) {
    Logging.init();
    try {
        VCLogger vcl = new TLogger();
        SBMLImporter imp = new SBMLImporter("samp.sbml", vcl, false);
        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 = imp.getBioModel();
            System.out.println(bm.getName());
        }
    } catch (Exception e) {
        System.err.println(e.getMessage());
        e.printStackTrace();
    }
}