Examples with SBMLImportException org.vcell.sbml.vcell.SBMLImportException used on opensource projects

Example 1 with SBMLImportException

use of org.vcell.sbml.vcell.SBMLImportException in project vcell by virtualcell.

the class BiomodelsDB_TestSuite method write.

/**
 * write exception info, balancing informativeness with conciseness
 * @param sbmlWriter
 * @param me
 */
private static void write(PrintWriter sbmlWriter, ModelException me) {
    SBMLImportException e = me.importException;
    switch(me.importException.category) {
        case NON_INTEGER_STOICH:
        case RATE_RULE:
        case RESERVED_SPATIAL:
        case RESERVED_SPECIES:
        case INCONSISTENT_UNIT:
        case DELAY:
            sbmlWriter.println(me.entry + ":  " + e.category + " not supported by Virtual Cell");
            break;
        case UNSPECIFIED:
            sbmlWriter.println(me.entry + ":  " + e.category + " " + e.getAllCauses());
            e.printStackTrace(sbmlWriter);
            break;
        default:
            throw new UnsupportedOperationException("value " + me.importException.category + " missing from switch");
    }
}

Example 2 with SBMLImportException

use of org.vcell.sbml.vcell.SBMLImportException in project vcell by virtualcell.

the class BiomodelsDB_TestSuite method main.

public static void main(String[] args) {
    try {
        Logging.init();
        /*sanity check -- we currently only have a copasi_java dll for 32-bit, so let's make sure 
			 * we're running on the right JVM. (Note we can run this on 64 bit machine, just have to install
			 * a 32 bit JVM...)
			 */
        OperatingSystemInfo osi = OperatingSystemInfo.getInstance();
        if (!osi.isWindows() || osi.is64bit()) {
            System.err.println("run on 32 bit JVM");
            System.exit(99);
        }
        // following are set in command line processing
        SortedSet<BiomodelsNetEntry> modelIDs = new TreeSet<BiomodelsNetEntry>();
        BioModelsWebServices service = null;
        File outDir = null;
        boolean isDetailed;
        {
            // scope for command line processing
            Options commandOptions = new Options();
            Option help = new Option("help", false, "show help");
            commandOptions.addOption(help);
            Option detailed = new Option("detailed", false, "record detailed information");
            commandOptions.addOption(detailed);
            Option output = new Option("output", true, "output directory");
            output.setRequired(true);
            commandOptions.addOption(output);
            OptionGroup primary = new OptionGroup();
            LOption min = new LOption("min", true, "minimum number of model to import", true);
            min.setType(Number.class);
            LOption only = new LOption("only", true, "run only this model", false);
            only.setType(Number.class);
            LOption include = new LOption("include", true, "run on models in specified file", false);
            include.setType(String.class);
            LOption exclude = new LOption("exclude", true, "exclude models in specified file", true);
            exclude.setType(String.class);
            primary.addOption(min).addOption(only).addOption(include).addOption(exclude);
            for (Object obj : primary.getOptions()) {
                // CLI old, non-generic API
                commandOptions.addOption((Option) obj);
            }
            CommandLine cmdLine = null;
            try {
                CommandLineParser parser = new DefaultParser();
                cmdLine = parser.parse(commandOptions, args);
            } catch (ParseException e1) {
                e1.printStackTrace();
                HelpFormatter hf = new HelpFormatter();
                hf.printHelp("BiomodelsDB_TestSuite", commandOptions);
                System.exit(2);
            }
            Option[] present = cmdLine.getOptions();
            Set<Option> optionSet = new HashSet<Option>(Arrays.asList(present));
            if (optionSet.contains(help)) {
                HelpFormatter hf = new HelpFormatter();
                hf.printHelp("BiomodelsDB_TestSuite", commandOptions);
                System.exit(0);
            }
            // placeholder, avoid messing with nulls
            LOption primaryOpt = new LOption("", false, "", true);
            @SuppressWarnings("unchecked") Collection<? extends Option> priOpts = primary.getOptions();
            priOpts.retainAll(optionSet);
            if (!priOpts.isEmpty()) {
                assert (priOpts.size() == 1);
                primaryOpt = (LOption) priOpts.iterator().next();
            }
            outDir = new File(cmdLine.getOptionValue(output.getOpt()));
            if (!outDir.exists()) {
                outDir.mkdirs();
            }
            isDetailed = optionSet.contains(detailed);
            BioModelsWebServicesServiceLocator locator = new BioModelsWebServicesServiceLocator();
            service = locator.getBioModelsWebServices();
            if (primaryOpt.downloads) {
                String[] modelStrings = service.getAllCuratedModelsId();
                for (String s : modelStrings) {
                    modelIDs.add(new BiomodelsNetEntry(s));
                }
            }
            if (primaryOpt == only) {
                Long only1 = (Long) cmdLine.getParsedOptionValue(only.getOpt());
                modelIDs.add(new BiomodelsNetEntry(only1.intValue()));
            } else if (primaryOpt == min) {
                Long lv = (Long) cmdLine.getParsedOptionValue(min.getOpt());
                int minimumModel = lv.intValue();
                for (int m = 0; m < minimumModel; m++) {
                    modelIDs.remove(new BiomodelsNetEntry(m));
                }
            } else if (primaryOpt == include) {
                FileBaseFilter fbf = new FileBaseFilter(cmdLine.getOptionValue(include.getOpt()));
                modelIDs.addAll(fbf.models);
            } else if (primaryOpt == exclude) {
                FileBaseFilter fbf = new FileBaseFilter(cmdLine.getOptionValue(exclude.getOpt()));
                modelIDs.removeAll(fbf.models);
            }
        }
        // end command line processing
        WriterFlusher flusher = new WriterFlusher(10);
        PrintWriter detailWriter;
        PrintWriter bngWriter;
        PrintWriter sbmlWriter;
        SBMLExceptionSorter sbmlExceptions;
        if (isDetailed) {
            detailWriter = new PrintWriter(new File(outDir, "compareDetail.txt"));
            bngWriter = new PrintWriter(new File(outDir, "bngErrors.txt"));
            sbmlWriter = new PrintWriter(new File(outDir, "sbmlErrors.txt"));
            sbmlExceptions = new LiveSorter();
            flusher.add(detailWriter);
            flusher.add(bngWriter);
            flusher.add(sbmlWriter);
        } else {
            detailWriter = new PrintWriter(new NullWriter());
            bngWriter = new PrintWriter(new NullWriter());
            sbmlWriter = new PrintWriter(new NullWriter());
            sbmlExceptions = new NullSorter();
        }
        PropertyLoader.loadProperties();
        /**
         * example properties
         *
         * vcell.COPASI.executable = "C:\\Program Files\\COPASI\\bin\\CopasiSE.exe"
         * vcell.mathSBML.directory = "c:\\developer\\eclipse\\workspace\\mathsbml\\"
         * vcell.mathematica.kernel.executable = "C:\\Program Files\\Wolfram Research\\Mathematica\\7.0\\MathKernel.exe"
         */
        ResourceUtil.setNativeLibraryDirectory();
        PrintWriter printWriter = new PrintWriter(new FileWriter(new File(outDir, "summary.log"), true));
        flusher.add(printWriter);
        listModels(printWriter, modelIDs);
        // SBMLSolver copasiSBMLSolver = new CopasiSBMLSolver();
        SBMLSolver copasiSBMLSolver = new SBMLSolver() {

            @Override
            public File solve(String filePrefix, File outDir, String sbmlText, SimSpec testSpec) throws IOException, SolverException, SbmlException {
                throw new RuntimeException("COPASI SOLVER REMOVED, REIMPLEMENT");
            }

            @Override
            public String getResultsFileColumnDelimiter() {
                throw new RuntimeException("COPASI SOLVER REMOVED, REIMPLEMENT");
            }
        };
        try {
            printWriter.println(" | *BIOMODEL ID* | *BioModel name* | *PASS* | *Rel Error (VC/COP)(VC/MSBML)(COP/MSBML)* | *Exception* | ");
            removeToxic(modelIDs, printWriter);
            for (BiomodelsNetEntry modelID : modelIDs) {
                String modelName = service.getModelNameById(modelID.toString());
                String modelSBML = service.getModelById(modelID.toString());
                Element bioModelInfo = new Element(BioModelsNetPanel.BIOMODELINFO_ELEMENT_NAME);
                bioModelInfo.setAttribute(BioModelsNetPanel.ID_ATTRIBUTE_NAME, modelID.toString());
                bioModelInfo.setAttribute(BioModelsNetPanel.SUPPORTED_ATTRIBUTE_NAME, "false");
                bioModelInfo.setAttribute("vcell_ran", "false");
                bioModelInfo.setAttribute("COPASI_ran", "false");
                bioModelInfo.setAttribute("mSBML_ran", "false");
                bioModelInfo.setAttribute(BioModelsNetPanel.MODELNAME_ATTRIBUTE_NAME, modelName);
                boolean bUseUTF8 = true;
                File sbmlFile = new File(outDir, modelID + ".sbml");
                XmlUtil.writeXMLStringToFile(modelSBML, sbmlFile.getAbsolutePath(), bUseUTF8);
                PrintStream saved_sysout = System.out;
                PrintStream saved_syserr = System.err;
                PrintStream new_sysout = null;
                PrintStream new_syserr = null;
                try {
                    String filePrefix = modelID.toString();
                    String sbmlText = modelSBML;
                    File logFile = new File(outDir, filePrefix + ".log");
                    new_sysout = new PrintStream(logFile);
                    new_syserr = new_sysout;
                    System.setOut(new_sysout);
                    System.setErr(new_syserr);
                    StringBuffer combinedErrorBuffer = new StringBuffer();
                    SimSpec simSpec = SimSpec.fromSBML(modelSBML);
                    String[] varsToTest = simSpec.getVarsList();
                    printWriter.print("ModelId: " + modelID + ": ");
                    // if a model crashes out the libSBML dll, we will terminate abruptly. Flush
                    // summary log before that happens
                    printWriter.flush();
                    try {
                        // 
                        // get VCell solution with an embedded "ROUND TRIP" (time and species concentrations)
                        // 
                        ODESolverResultSet vcellResults_RT = null;
                        try {
                            VCellSBMLSolver vcellSBMLSolver_RT = new VCellSBMLSolver();
                            vcellSBMLSolver_RT.setRoundTrip(false);
                            // TODO try with round-trip later.
                            String columnDelimiter = vcellSBMLSolver_RT.getResultsFileColumnDelimiter();
                            File resultFile = vcellSBMLSolver_RT.solve(filePrefix, outDir, sbmlFile.getAbsolutePath(), simSpec);
                            vcellResults_RT = readResultFile(resultFile, columnDelimiter);
                            bioModelInfo.setAttribute("vcell_ran", "true");
                        } catch (BNGException e) {
                            bngWriter.println(modelID + " " + e.getMessage());
                            throw e;
                        } catch (SBMLImportException e) {
                            ModelException me = new ModelException(modelID, e);
                            write(sbmlWriter, me);
                            sbmlExceptions.add(me);
                            throw e;
                        } catch (Exception e) {
                            printWriter.println("vcell solve(roundtrip=true) failed");
                            e.printStackTrace(printWriter);
                            System.out.println("vcell solve(roundtrip=true) failed");
                            e.printStackTrace(System.out);
                            combinedErrorBuffer.append(" *VCELL_RT* _" + e.getMessage() + "_ ");
                            Element vcellSolverReport = new Element("SolverReport");
                            vcellSolverReport.setAttribute("solverName", "vcell");
                            vcellSolverReport.setAttribute("errorMessage", e.getMessage());
                            bioModelInfo.addContent(vcellSolverReport);
                            bioModelInfo.setAttribute("vcell_ran", "false");
                        }
                        // 
                        // get COPASI solution (time and species concentrations)
                        // 
                        ODESolverResultSet copasiResults = null;
                        try {
                            String columnDelimiter = copasiSBMLSolver.getResultsFileColumnDelimiter();
                            File resultFile = copasiSBMLSolver.solve(filePrefix, outDir, sbmlText, simSpec);
                            copasiResults = readResultFile(resultFile, columnDelimiter);
                            bioModelInfo.setAttribute("COPASI_ran", "true");
                        } catch (Exception e) {
                            printWriter.println("Copasi solve() failed");
                            e.printStackTrace(printWriter);
                            System.out.println("Copasi solve() failed");
                            e.printStackTrace(System.out);
                            combinedErrorBuffer.append(" *COPASI* _" + e.getMessage() + "_ ");
                            Element copasiSolverReport = new Element("SolverReport");
                            copasiSolverReport.setAttribute("solverName", "COPASI");
                            copasiSolverReport.setAttribute("errorMessage", e.getMessage());
                            bioModelInfo.addContent(copasiSolverReport);
                            bioModelInfo.setAttribute("COPASI_ran", "false");
                        }
                        // 
                        // get mSBML solution (time and species concentrations)
                        // 
                        /*
							ODESolverResultSet mSBMLResults = null;
							if (idInt != 246 && idInt != 250 && idInt != 285 && idInt != 301) {
								try {
									MathSBMLSolver mSBMLSolver = new MathSBMLSolver();
									String columnDelimiter = mSBMLSolver.getResultsFileColumnDelimiter();
									org.sbml.libsbml.SBMLDocument sbmlDocument = new SBMLReader().readSBML(sbmlFile.getAbsolutePath());
									long level = sbmlDocument.getLevel();
									long version = sbmlDocument.getVersion();
									String mathsbmlFilePrefix = filePrefix;
									if (level!=2 || (level==2 && version>3)){
	//									sbmlDocument.setConsistencyChecksForConversion(libsbmlConstants.LIBSBML_CAT_MODELING_PRACTICE, false);
										long numErrors = sbmlDocument.checkL2v3Compatibility();

										if (numErrors==0){
											boolean bConversionWorked = sbmlDocument.setLevelAndVersion(2, 3, false);
											SBMLDocument doc = new SBMLDocument(sbmlDocument);
											doc.setLevelAndVersion(2,3,false);
											if (bConversionWorked){
												mathsbmlFilePrefix = filePrefix+"_L2V3";
												long newVersion = doc.getVersion();
												SBMLWriter sbmlWriter = new SBMLWriter();
												sbmlText = sbmlWriter.writeToString(doc);
												try {
													XmlUtil.writeXMLStringToFile(sbmlText, mathsbmlFilePrefix+".sbml", true);
												} catch (IOException e1) {
													e1.printStackTrace(System.out);
												} 
											}else{
												throw new RuntimeException("couldn't convert SBML from L"+level+"V"+version+" to L2V3");
											}
										}else{
											throw new RuntimeException("couldn't convert SBML from L"+level+"V"+version+" to L2V3, not compatible: "+sbmlDocument.getError(0));
										}
									}
									File resultFile = mSBMLSolver.solve(mathsbmlFilePrefix, outDir, sbmlText, simSpec);
									mSBMLResults = readResultFile(resultFile, columnDelimiter); 
									bioModelInfo.setAttribute("mSBML_ran","true");
								}catch (Exception e){
									printWriter.println("mSBML solve() failed");
									e.printStackTrace(printWriter);
									System.out.println("mSBML solve() failed");
									e.printStackTrace(System.out);
									combinedErrorBuffer.append(" *mSBML* _"+e.getMessage()+"_ ");

									Element mSBMLSolverReport = new Element("SolverReport");
									mSBMLSolverReport.setAttribute("solverName","mSBML");
									mSBMLSolverReport.setAttribute("errorMessage",e.getMessage());
									bioModelInfo.addContent(mSBMLSolverReport);

									bioModelInfo.setAttribute("mSBML_ran","false");
								}
							}
							 */
                        // 
                        // compare results from COPASI and VCELL_RT
                        // 
                        Boolean bCOPASI_VCELL_matched = null;
                        if (copasiResults != null && vcellResults_RT != null) {
                            try {
                                SimulationComparisonSummary summary = MathTestingUtilities.compareResultSets(copasiResults, vcellResults_RT, varsToTest, TestCaseNew.REGRESSION, 1e-5, 1e-5);
                                double maxRelError = summary.getMaxRelativeError();
                                bioModelInfo.setAttribute("COPASI_VCELL_maxRelErr", Double.toString(maxRelError));
                                if (maxRelError < 1) {
                                    bCOPASI_VCELL_matched = true;
                                } else {
                                    detailWriter.println(modelID + " " + modelName);
                                    bCOPASI_VCELL_matched = false;
                                    Element solverComparison = new Element("SolverComparison");
                                    solverComparison.setAttribute("solver1", "vcell");
                                    solverComparison.setAttribute("solver2", "COPASI");
                                    VariableComparisonSummary[] failedVCSummaries = summary.getFailingVariableComparisonSummaries(1e-5, 1e-5);
                                    for (VariableComparisonSummary vcSummary : failedVCSummaries) {
                                        Element failedVariableSummary = getVariableSummary(vcSummary);
                                        solverComparison.addContent(failedVariableSummary);
                                        String ss = vcSummary.toShortString();
                                        detailWriter.print('\t');
                                        detailWriter.println(ss);
                                        System.out.println(ss);
                                    }
                                    detailWriter.println();
                                    bioModelInfo.addContent(solverComparison);
                                }
                            } catch (Exception e) {
                                printWriter.println("COMPARE VC/COPASI failed");
                                e.printStackTrace(printWriter);
                                System.out.println("COMPARE VC/COPASI failed");
                                e.printStackTrace(System.out);
                                combinedErrorBuffer.append(" *COMPARE VC/COPASI* _" + e.getMessage() + "_ ");
                                Element solverComparison = new Element("SolverComparison");
                                solverComparison.setAttribute("solver1", "vcell");
                                solverComparison.setAttribute("solver2", "COPASI");
                                solverComparison.setAttribute("error", e.getMessage());
                                bioModelInfo.addContent(solverComparison);
                            }
                        }
                        /*						
							Boolean bmSBML_VCELL_matched = null;
							if (mSBMLResults!=null && vcellResults_RT!=null){
								try {
									SimulationComparisonSummary summary = MathTestingUtilities.compareUnEqualResultSets(mSBMLResults, vcellResults_RT, varsToTest, 1e-5, 1e-5, 1);
									double maxRelError = summary.getMaxRelativeError();
									bioModelInfo.setAttribute("mSBML_VCELL_maxRelErr", Double.toString(maxRelError));

									if (maxRelError<1){
										bmSBML_VCELL_matched = true;
									}else{
										bmSBML_VCELL_matched = false;
										Element solverComparison = new Element("SolverComparison");
										solverComparison.setAttribute("solver1","vcell");
										solverComparison.setAttribute("solver2","mSBML");
										VariableComparisonSummary[] failedVCSummaries = summary.getFailingVariableComparisonSummaries(1e-5, 1e-5);
										for (VariableComparisonSummary vcSummary : failedVCSummaries){
											Element failedVariableSummary = getVariableSummary(vcSummary);
											solverComparison.addContent(failedVariableSummary);
											System.out.println(vcSummary.toShortString());
										}
										bioModelInfo.addContent(solverComparison);
									}
								} catch (Exception e) {
									printWriter.println("COMPARE VCRT/mSBML failed");
									e.printStackTrace(printWriter);
									System.out.println("COMPARE VCRT/mSBML failed");
									e.printStackTrace(System.out);
									combinedErrorBuffer.append(" *COMPARE VCRT/mSBML* _"+e.getMessage()+"_ ");

									Element solverComparison = new Element("SolverComparison");
									solverComparison.setAttribute("solver1","vcell");
									solverComparison.setAttribute("solver2","mSBML");
									solverComparison.setAttribute("error",e.getMessage());
									bioModelInfo.addContent(solverComparison);
								}
							}

							//
							// compare results from COPASI and mSBML
							//
							Boolean bCOPASI_mSBML_matched = null;
							if (copasiResults!=null && mSBMLResults!=null){
								try {
									SimulationComparisonSummary summary = MathTestingUtilities.compareUnEqualResultSets(copasiResults, mSBMLResults, varsToTest, 1e-5, 1e-5, 1);
									double maxRelError = summary.getMaxRelativeError();
									bioModelInfo.setAttribute("COPASI_mSBML_maxRelErr", Double.toString(maxRelError));

									if (maxRelError<1){
										bCOPASI_mSBML_matched = true;
									}else{
										bCOPASI_mSBML_matched = false;
										Element solverComparison = new Element("SolverComparison");
										solverComparison.setAttribute("solver1","COPASI");
										solverComparison.setAttribute("solver2","mSBML");
										solverComparison.setAttribute("result","failed");
										VariableComparisonSummary[] vcSummaries = summary.getVariableComparisonSummaries();
										for (VariableComparisonSummary vcSummary : vcSummaries){
											Element failedVariableSummary = getVariableSummary(vcSummary);
											solverComparison.addContent(failedVariableSummary);
											System.out.println(vcSummary.toShortString());
										}
										bioModelInfo.addContent(solverComparison);
									}
								} catch (Exception e) {
									printWriter.println("COMPARE COPASI/mSBML failed");
									e.printStackTrace(printWriter);
									System.out.println("COMPARE COPASI/mSBML failed");
									e.printStackTrace(System.out);
									combinedErrorBuffer.append(" *COMPARE COPASI/mSBML* _"+e.getMessage()+"_ ");

									Element solverComparison = new Element("SolverComparison");
									solverComparison.setAttribute("solver1","COPASI");
									solverComparison.setAttribute("solver2","mSBML");
									solverComparison.setAttribute("error",e.getMessage());
								}
							}
							 */
                        if ((bCOPASI_VCELL_matched != null && bCOPASI_VCELL_matched.booleanValue())) {
                            // || /*(bmSBML_VCELL_matched!=null && bmSBML_VCELL_matched.booleanValue()) */ )
                            bioModelInfo.setAttribute(BioModelsNetPanel.SUPPORTED_ATTRIBUTE_NAME, "true");
                            printWriter.println("PASS");
                        } else {
                            bioModelInfo.setAttribute(BioModelsNetPanel.SUPPORTED_ATTRIBUTE_NAME, "false");
                            printWriter.println("FAIL");
                        }
                    } catch (Exception e) {
                        e.printStackTrace(printWriter);
                        combinedErrorBuffer.append(" *UNKNOWN* _" + e.getMessage() + "_ ");
                        bioModelInfo.setAttribute(BioModelsNetPanel.SUPPORTED_ATTRIBUTE_NAME, "false");
                        bioModelInfo.setAttribute("exception", e.getMessage());
                    }
                    printWriter.flush();
                    // write for each model just in case files get corrupted (it happened).
                    write(bioModelInfo, new File(outDir, modelID + "_report.xml"));
                } finally {
                    if (new_sysout != null) {
                        new_sysout.close();
                        new_sysout = null;
                    }
                    if (new_syserr != null) {
                        new_syserr.close();
                        new_syserr = null;
                    }
                    System.setOut(saved_sysout);
                    System.setOut(saved_syserr);
                }
            }
            // this writes out the SBML import exceptions grouped by type
            if (!sbmlExceptions.isEmpty()) {
                Map<Category, Collection<ModelException>> map = sbmlExceptions.getMap();
                try (PrintWriter pw = new PrintWriter(new File(outDir, "sbmlSorted.txt"))) {
                    // SBMLImportException.Category
                    for (Category c : Category.values()) {
                        Collection<ModelException> meCollection = map.get(c);
                        for (ModelException me : meCollection) {
                            write(pw, me);
                        }
                    }
                }
            }
        } finally {
            printWriter.close();
            detailWriter.close();
            bngWriter.close();
        }
    } catch (Throwable e) {
        e.printStackTrace(System.out);
        e.printStackTrace(System.err);
    }
    System.exit(0);
}