Examples with DefaultParser org.apache.commons.cli.DefaultParser used on opensource projects

Example 51 with DefaultParser

use of org.apache.commons.cli.DefaultParser in project tika by apache.

the class ResultsReporter method main.

public static void main(String[] args) throws Exception {
    DefaultParser defaultCLIParser = new DefaultParser();
    CommandLine commandLine = null;
    try {
        commandLine = defaultCLIParser.parse(OPTIONS, args);
    } catch (ParseException e) {
        System.out.println(e.getMessage());
        USAGE();
        return;
    }
    JDBCUtil dbUtil = null;
    if (commandLine.hasOption("db")) {
        Path db = Paths.get(commandLine.getOptionValue("db"));
        if (!H2Util.databaseExists(db)) {
            throw new RuntimeException("I'm sorry, but I couldn't find this h2 database: " + db + "\nMake sure not to include the .mv.db at the end.");
        }
        dbUtil = new H2Util(db);
    } else if (commandLine.hasOption("jdbc")) {
        String driverClass = null;
        if (commandLine.hasOption("jdbcdriver")) {
            driverClass = commandLine.getOptionValue("jdbcdriver");
        }
        dbUtil = new JDBCUtil(commandLine.getOptionValue("jdbc"), driverClass);
    } else {
        System.err.println("Must specify either -db for the default in-memory h2 database\n" + "or -jdbc for a full jdbc connection string");
        USAGE();
        return;
    }
    try (Connection c = dbUtil.getConnection()) {
        Path tmpReportsFile = null;
        try {
            ResultsReporter resultsReporter = null;
            String reportsFile = commandLine.getOptionValue("rf");
            if (reportsFile == null) {
                tmpReportsFile = getDefaultReportsConfig(c);
                resultsReporter = ResultsReporter.build(tmpReportsFile);
            } else {
                resultsReporter = ResultsReporter.build(Paths.get(reportsFile));
            }
            Path reportsRootDirectory = Paths.get(commandLine.getOptionValue("rd", "reports"));
            if (Files.isDirectory(reportsRootDirectory)) {
                LOG.warn("'Reports' directory exists.  Will overwrite existing reports.");
            }
            resultsReporter.execute(c, reportsRootDirectory);
        } finally {
            if (tmpReportsFile != null) {
                Files.delete(tmpReportsFile);
            }
        }
    }
}

Example 52 with DefaultParser

use of org.apache.commons.cli.DefaultParser in project tika by apache.

the class FSBatchProcessCLI method execute.

private void execute(String[] args) throws Exception {
    CommandLineParser cliParser = new DefaultParser();
    CommandLine line = cliParser.parse(options, args);
    if (line.hasOption("help")) {
        usage();
        System.exit(BatchProcessDriverCLI.PROCESS_NO_RESTART_EXIT_CODE);
    }
    Map<String, String> mapArgs = new HashMap<String, String>();
    for (Option option : line.getOptions()) {
        String v = option.getValue();
        if (v == null || v.equals("")) {
            v = "true";
        }
        mapArgs.put(option.getOpt(), v);
    }
    BatchProcessBuilder b = new BatchProcessBuilder();
    TikaInputStream is = null;
    BatchProcess process = null;
    try {
        is = getConfigInputStream(args, false);
        process = b.build(is, mapArgs);
    } finally {
        IOUtils.closeQuietly(is);
    }
    final Thread mainThread = Thread.currentThread();
    ExecutorService executor = Executors.newSingleThreadExecutor();
    Future<ParallelFileProcessingResult> futureResult = executor.submit(process);
    ParallelFileProcessingResult result = futureResult.get();
    System.out.println(FINISHED_STRING);
    System.out.println("\n");
    System.out.println(result.toString());
    System.exit(result.getExitStatus());
}

Example 53 with DefaultParser

use of org.apache.commons.cli.DefaultParser in project tika by apache.

the class TikaEvalCLI method handleCompare.

private void handleCompare(String[] subsetArgs) throws Exception {
    List<String> argList = new ArrayList(Arrays.asList(subsetArgs));
    boolean containsBC = false;
    String inputDir = null;
    String extractsA = null;
    String alterExtract = null;
    //confirm there's a batch-config file
    for (int i = 0; i < argList.size(); i++) {
        String arg = argList.get(i);
        if (arg.equals("-bc")) {
            containsBC = true;
        } else if (arg.equals("-inputDir")) {
            if (i + 1 >= argList.size()) {
                System.err.println("Must specify directory after -inputDir");
                ExtractComparer.USAGE();
                return;
            }
            inputDir = argList.get(i + 1);
            i++;
        } else if (arg.equals("-extractsA")) {
            if (i + 1 >= argList.size()) {
                System.err.println("Must specify directory after -extractsA");
                ExtractComparer.USAGE();
                return;
            }
            extractsA = argList.get(i + 1);
            i++;
        } else if (arg.equals("-alterExtract")) {
            if (i + 1 >= argList.size()) {
                System.err.println("Must specify type 'as_is', 'first_only' or " + "'concatenate_content' after -alterExtract");
                ExtractComparer.USAGE();
                return;
            }
            alterExtract = argList.get(i + 1);
            i++;
        }
    }
    if (alterExtract != null && !alterExtract.equals("as_is") && !alterExtract.equals("concatenate_content") && !alterExtract.equals("first_only")) {
        System.out.println("Sorry, I don't understand:" + alterExtract + ". The values must be one of: as_is, first_only, concatenate_content");
        ExtractComparer.USAGE();
        return;
    }
    //if the user doesn't specify inputDir, crawl extractsA
    if (inputDir == null && extractsA != null) {
        argList.add("-inputDir");
        argList.add(extractsA);
    }
    Path tmpBCConfig = null;
    try {
        tmpBCConfig = Files.createTempFile("tika-eval", ".xml");
        if (!containsBC) {
            Files.copy(this.getClass().getResourceAsStream("/tika-eval-comparison-config.xml"), tmpBCConfig, StandardCopyOption.REPLACE_EXISTING);
            argList.add("-bc");
            argList.add(tmpBCConfig.toAbsolutePath().toString());
        }
        String[] updatedArgs = argList.toArray(new String[argList.size()]);
        DefaultParser defaultCLIParser = new DefaultParser();
        try {
            CommandLine commandLine = defaultCLIParser.parse(ExtractComparer.OPTIONS, updatedArgs);
            if (commandLine.hasOption("db") && commandLine.hasOption("jdbc")) {
                System.out.println("Please specify either the default -db or the full -jdbc, not both");
                ExtractComparer.USAGE();
                return;
            }
        } catch (ParseException e) {
            System.out.println(e.getMessage() + "\n");
            ExtractComparer.USAGE();
            return;
        }
        FSBatchProcessCLI.main(updatedArgs);
    } finally {
        if (tmpBCConfig != null && Files.isRegularFile(tmpBCConfig)) {
            Files.delete(tmpBCConfig);
        }
    }
}

Example 54 with DefaultParser

use of org.apache.commons.cli.DefaultParser 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);
}

Example 55 with DefaultParser

use of org.apache.commons.cli.DefaultParser in project toolkit by googleapis.

the class ConfigGeneratorTool method main.

public static void main(String[] args) throws Exception {
    Options options = new Options();
    options.addOption("h", "help", false, "show usage");
    options.addOption(Option.builder().longOpt("descriptor_set").desc("The descriptor set representing the compiled input protos.").hasArg().argName("DESCRIPTOR-SET").required(true).build());
    options.addOption(Option.builder().longOpt("service_yaml").desc("The service YAML configuration file or files.").hasArg().argName("SERVICE-YAML").required(true).build());
    options.addOption(Option.builder("o").longOpt("output").desc("The directory in which to output the generated config.").hasArg().argName("OUTPUT-FILE").required(true).build());
    CommandLine cl = (new DefaultParser()).parse(options, args);
    if (cl.hasOption("help")) {
        HelpFormatter formater = new HelpFormatter();
        formater.printHelp("ConfigGeneratorTool", options);
    }
    int exitCode = generate(cl.getOptionValue("descriptor_set"), cl.getOptionValues("service_yaml"), cl.getOptionValue("output"));
    System.exit(exitCode);
}