List of usage examples for org.apache.commons.lang3.exception ExceptionUtils printRootCauseStackTrace
public static void printRootCauseStackTrace(final Throwable throwable)
Prints a compact stack trace for the root cause of a throwable to System.err.
The compact stack trace starts with the root cause and prints stack frames up to the place where it was caught and wrapped.
From source file:io.stallion.plugins.javascript.JsTestSuite.java
public void run() { results = new TestResults(getName()).setFile(getFile()); tearDownSuite(this); for (Map.Entry<String, Function> entry : tests) { Log.info("Run test {0}", entry.getKey()); setUp(this); try {//w w w.j a v a 2 s . c o m entry.getValue().apply(this); results.addResult(entry.getKey(), true, false, null); } catch (AssertionError e) { ExceptionUtils.printRootCauseStackTrace(e); results.addResult(entry.getKey(), false, false, e); } catch (Exception e) { ExceptionUtils.printRootCauseStackTrace(e); results.addResult(entry.getKey(), false, true, e); } tearDown(this); } }
From source file:io.stallion.boot.MainRunner.java
/** * Runs the main Stallion service in auto-reload mode, which means that if a configuration file, * or a server-side javascript file, or a plugin file is touched, the entire application context * will reload and all server-side javascript will be re-processed. Use this when developing * to avoid having to manually restart every time you change a file. * * * @param args//w w w. j a v a2 s. com * @param plugins * @throws Exception */ public static void runWithAutoReload(String[] args, StallionJavaPlugin[] plugins) throws Exception { isDebugRunner = true; Console console = System.console(); while (true) { Log.info("(re)start in debug reloading mode."); try { reboot(args, plugins); if (doReload) { doReload = false; continue; } System.out.println("Interrupted. Type q to quit, any other key to reboot."); String input = console.readLine(); if (input.startsWith("q")) { break; } } catch (Exception e) { ExceptionUtils.printRootCauseStackTrace(e); System.out.println("Other exception. Type q to quit, any other key to reboot."); String input = console.readLine(); if (input.startsWith("q")) { break; } } } Log.info("Shutting down javascript and conf file watcher."); if (watcher != null) { watcher.setShouldRun(false); } watcherThread.interrupt(); watcherThread.join(); System.out.println("Exiting."); System.exit(0); }
From source file:io.stallion.tools.ScriptExecBase.java
public void executeJavascript(String source, URL url, String scriptPath, String folder, List<String> args, String plugin) throws Exception { ScriptEngine scriptEngine = null; if (plugin.equals("js") || plugin.equals("stallion")) { JsPluginEngine pluginEngine = PluginRegistry.instance().getEngine("main.js"); if (pluginEngine != null) { scriptEngine = pluginEngine.getScriptEngine(); }/* w ww. ja va 2 s .c om*/ } else if (!empty(plugin)) { JsPluginEngine pluginEngine = PluginRegistry.instance().getEngine(plugin); if (pluginEngine != null) { scriptEngine = pluginEngine.getScriptEngine(); } } if (scriptEngine == null) { ScriptEngineManager scriptEngineManager = new ScriptEngineManager(); scriptEngine = scriptEngineManager.getEngineByName("nashorn"); scriptEngine.eval(IOUtils.toString(getClass().getResource("/jslib/jvm-npm.js"), UTF8)); scriptEngine.eval(IOUtils.toString(getClass().getResource("/jslib/stallion_shared.js"), UTF8)); String nodePath = folder + "/node_modules"; scriptEngine.eval("require.NODE_PATH = \"" + nodePath + "\""); scriptEngine.put("myContext", new SandboxedContext(plugin, Sandbox.allPermissions(), new JsPluginSettings())); } if (true || newCommandOptions().isDevMode()) { Scanner in = new Scanner(System.in); while (true) { source = IOUtils.toString(url, UTF8); try { scriptEngine.eval("load(" + JSON.stringify(map(val("script", source), val("name", url.toString()))) + ");"); //scriptEngine.eval(IOUtils.) } catch (Exception e) { ExceptionUtils.printRootCauseStackTrace(e); } finally { } System.out.println("Hit enter to re-run the script. Type quit and hit enter to stop."); String line = in.nextLine().trim(); if (empty(line)) { continue; } else { break; } } } else { scriptEngine.eval(source); } }
From source file:org.kie.workbench.common.services.datamodel.backend.server.ModuleDataModelConcurrencyTest.java
@Test public void testConcurrentResourceUpdates() throws URISyntaxException { final URL pomUrl = this.getClass().getResource("/DataModelBackendTest1/pom.xml"); final org.uberfire.java.nio.file.Path nioPomPath = ioService.get(pomUrl.toURI()); final Path pomPath = paths.convert(nioPomPath); final URL resourceUrl = this.getClass().getResource("/DataModelBackendTest1/src/main/resources/empty.rdrl"); final org.uberfire.java.nio.file.Path nioResourcePath = ioService.get(resourceUrl.toURI()); final Path resourcePath = paths.convert(nioResourcePath); //Force full build before attempting incremental changes final KieModule module = moduleService.resolveModule(resourcePath); final BuildResults buildResults = buildService.build(module); assertNotNull(buildResults);// w w w . j ava 2s . c o m assertEquals(0, buildResults.getErrorMessages().size()); assertEquals(1, buildResults.getInformationMessages().size()); //Perform incremental build final int THREADS = 200; final Result result = new Result(); ExecutorService es = Executors.newCachedThreadPool(); for (int i = 0; i < THREADS; i++) { final int operation = (i % 3); switch (operation) { case 0: es.execute(new Runnable() { @Override public void run() { try { logger.debug("[Thread: " + Thread.currentThread().getName() + "] Request to update POM received"); invalidateCaches(module, pomPath); buildChangeListener.updateResource(pomPath); logger.debug("[Thread: " + Thread.currentThread().getName() + "] POM update completed"); } catch (Throwable e) { result.setFailed(true); result.setMessage(e.getMessage()); ExceptionUtils.printRootCauseStackTrace(e); } } }); break; case 1: es.execute(new Runnable() { @Override public void run() { try { logger.debug("[Thread: " + Thread.currentThread().getName() + "] Request to update Resource received"); invalidateCaches(module, resourcePath); buildChangeListener.addResource(resourcePath); logger.debug( "[Thread: " + Thread.currentThread().getName() + "] Resource update completed"); } catch (Throwable e) { result.setFailed(true); result.setMessage(e.getMessage()); ExceptionUtils.printRootCauseStackTrace(e); } } }); break; case 2: es.execute(new Runnable() { @Override public void run() { try { logger.debug("[Thread: " + Thread.currentThread().getName() + "] Request for DataModel received"); dataModelService.getDataModel(resourcePath); logger.debug("[Thread: " + Thread.currentThread().getName() + "] DataModel request completed"); } catch (Throwable e) { result.setFailed(true); result.setMessage(e.getMessage()); ExceptionUtils.printRootCauseStackTrace(e); } } }); } } es.shutdown(); try { es.awaitTermination(5, TimeUnit.MINUTES); } catch (InterruptedException e) { } if (result.isFailed()) { fail(result.getMessage()); } }
From source file:org.kie.workbench.common.services.datamodel.backend.server.ProjectDataModelConcurrencyTest.java
@Test public void testConcurrentResourceUpdates() throws URISyntaxException { final URL pomUrl = this.getClass().getResource("/DataModelBackendTest1/pom.xml"); final org.uberfire.java.nio.file.Path nioPomPath = ioService.get(pomUrl.toURI()); final Path pomPath = paths.convert(nioPomPath); final URL resourceUrl = this.getClass().getResource("/DataModelBackendTest1/src/main/resources/empty.rdrl"); final org.uberfire.java.nio.file.Path nioResourcePath = ioService.get(resourceUrl.toURI()); final Path resourcePath = paths.convert(nioResourcePath); //Force full build before attempting incremental changes final KieProject project = projectService.resolveProject(resourcePath); final BuildResults buildResults = buildService.build(project); assertNotNull(buildResults);/* www . j a v a2 s . com*/ assertEquals(0, buildResults.getErrorMessages().size()); assertEquals(1, buildResults.getInformationMessages().size()); //Perform incremental build final int THREADS = 200; final Result result = new Result(); ExecutorService es = Executors.newCachedThreadPool(); for (int i = 0; i < THREADS; i++) { final int operation = (i % 3); switch (operation) { case 0: es.execute(new Runnable() { @Override public void run() { try { logger.debug("[Thread: " + Thread.currentThread().getName() + "] Request to update POM received"); invalidateCaches(project, pomPath); buildChangeListener.updateResource(pomPath); logger.debug("[Thread: " + Thread.currentThread().getName() + "] POM update completed"); } catch (Throwable e) { result.setFailed(true); result.setMessage(e.getMessage()); ExceptionUtils.printRootCauseStackTrace(e); } } }); break; case 1: es.execute(new Runnable() { @Override public void run() { try { logger.debug("[Thread: " + Thread.currentThread().getName() + "] Request to update Resource received"); invalidateCaches(project, resourcePath); buildChangeListener.addResource(resourcePath); logger.debug( "[Thread: " + Thread.currentThread().getName() + "] Resource update completed"); } catch (Throwable e) { result.setFailed(true); result.setMessage(e.getMessage()); ExceptionUtils.printRootCauseStackTrace(e); } } }); break; case 2: es.execute(new Runnable() { @Override public void run() { try { logger.debug("[Thread: " + Thread.currentThread().getName() + "] Request for DataModel received"); dataModelService.getDataModel(resourcePath); logger.debug("[Thread: " + Thread.currentThread().getName() + "] DataModel request completed"); } catch (Throwable e) { result.setFailed(true); result.setMessage(e.getMessage()); ExceptionUtils.printRootCauseStackTrace(e); } } }); } } es.shutdown(); try { es.awaitTermination(5, TimeUnit.MINUTES); } catch (InterruptedException e) { } if (result.isFailed()) { fail(result.getMessage()); } }
From source file:ubic.gemma.core.apps.DifferentialExpressionAnalysisCli.java
private void processExperiment(ExpressionExperiment ee) { Collection<DifferentialExpressionAnalysis> results; DifferentialExpressionAnalysisConfig config = new DifferentialExpressionAnalysisConfig(); try {// w w w.j a v a 2s .c o m ee = this.eeService.thawLite(ee); if (delete) { AbstractCLI.log.info("Deleting any analyses for experiment=" + ee); differentialExpressionAnalyzerService.deleteAnalyses(ee); successObjects.add("Deleted analysis for: " + ee.toString()); return; } Collection<ExperimentalFactor> experimentalFactors = ee.getExperimentalDesign() .getExperimentalFactors(); if (experimentalFactors.size() == 0) { if (this.expressionExperiments.size() == 1) { /* * Only need to be noisy if this is the only ee. Batch processing should be less so. */ throw new RuntimeException( "Experiment does not have an experimental design populated: " + ee.getShortName()); } AbstractCLI.log .warn("Experiment does not have an experimental design populated: " + ee.getShortName()); return; } Collection<ExperimentalFactor> factors = this.guessFactors(ee); if (factors.size() > 0) { /* * Manual selection of factors */ ExperimentalFactor subsetFactor = this.getSubsetFactor(ee); AbstractCLI.log.info("Using " + factors.size() + " factors provided as arguments"); if (subsetFactor != null) { if (factors.contains(subsetFactor)) { throw new IllegalArgumentException( "Subset factor cannot also be included as factor to analyze"); } AbstractCLI.log.info("Subsetting by " + subsetFactor); } config.setAnalysisType(this.type); config.setFactorsToInclude(factors); config.setSubsetFactor(subsetFactor); config.setModerateStatistics(this.ebayes); config.setPersist(this.persist); boolean rnaSeq = super.eeService.isRNASeq(ee); config.setUseWeights(rnaSeq); /* * Interactions included by default. It's actually only complicated if there is a subset factor. */ if (type == null && factors.size() == 2) { config.getInteractionsToInclude().add(factors); } results = this.differentialExpressionAnalyzerService.runDifferentialExpressionAnalyses(ee, config); } else { /* * Automatically */ if (tryToCopyOld) { this.tryToRedoBasedOnOldAnalysis(ee); } Collection<ExperimentalFactor> factorsToUse = new HashSet<>(); if (this.ignoreBatch) { for (ExperimentalFactor ef : experimentalFactors) { if (!ExperimentalDesignUtils.isBatch(ef)) { factorsToUse.add(ef); } } } else { factorsToUse.addAll(experimentalFactors); } if (factorsToUse.isEmpty()) { throw new RuntimeException("No factors available for " + ee.getShortName()); } if (factorsToUse.size() > 3) { if (!tryToCopyOld) { throw new RuntimeException("Experiment has too many factors to run automatically: " + ee.getShortName() + "; try using the -redo flag to base it on an old analysis, or select factors manually"); } results = this.tryToRedoBasedOnOldAnalysis(ee); } else { config.setFactorsToInclude(factorsToUse); config.setPersist(this.persist); config.setModerateStatistics(this.ebayes); if (factorsToUse.size() == 2) { // include interactions by default config.addInteractionToInclude(factorsToUse); } boolean rnaSeq = super.eeService.isRNASeq(ee); config.setUseWeights(rnaSeq); results = this.differentialExpressionAnalyzerService.runDifferentialExpressionAnalyses(ee, config); } } if (results == null) { throw new Exception( "Failed to process differential expression for experiment " + ee.getShortName()); } if (!this.persist) { AbstractCLI.log.info("Writing results to disk"); for (DifferentialExpressionAnalysis r : results) { expressionDataFileService.writeDiffExArchiveFile(ee, r, config); } } successObjects.add(ee.toString()); } catch (Exception e) { AbstractCLI.log.error("Error while processing " + ee + ": " + e.getMessage()); ExceptionUtils.printRootCauseStackTrace(e); errorObjects.add(ee + ": " + e.getMessage()); } }