Repository: airavata Updated Branches: refs/heads/master 732828710 -> 98c9a34ea
http://git-wip-us.apache.org/repos/asf/airavata/blob/98c9a34e/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/XBayaEngine.java ---------------------------------------------------------------------- diff --git a/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/XBayaEngine.java b/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/XBayaEngine.java index a6b0beb..0f548e3 100644 --- a/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/XBayaEngine.java +++ b/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/XBayaEngine.java @@ -146,10 +146,10 @@ public class XBayaEngine { } catch (RuntimeException e) { // This should not happen - e.printStackTrace(); + logger.error(e.getMessage(), e); getGUI().getErrorWindow().error(ErrorMessages.UNEXPECTED_ERROR, e); } catch (ComponentRegistryException e) { - e.printStackTrace(); + logger.error(e.getMessage(), e); getGUI().getErrorWindow().error(ErrorMessages.UNEXPECTED_ERROR, e); } http://git-wip-us.apache.org/repos/asf/airavata/blob/98c9a34e/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/concurrent/PredicatedTaskRunner.java ---------------------------------------------------------------------- diff --git a/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/concurrent/PredicatedTaskRunner.java b/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/concurrent/PredicatedTaskRunner.java index 1bed1f4..1c5f249 100644 --- a/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/concurrent/PredicatedTaskRunner.java +++ b/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/concurrent/PredicatedTaskRunner.java @@ -20,6 +20,9 @@ */ package org.apache.airavata.xbaya.concurrent; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + import java.util.concurrent.ConcurrentLinkedQueue; import java.util.concurrent.ExecutorService; import java.util.concurrent.Executors; @@ -36,6 +39,7 @@ public class PredicatedTaskRunner { protected ExecutorService threadPool; protected volatile boolean stop = false; + private static final Logger log = LoggerFactory.getLogger(PredicatedTaskRunner.class); public PredicatedTaskRunner(int numberOfThreads) { this.threadPool = Executors.newFixedThreadPool(numberOfThreads); @@ -117,7 +121,7 @@ public class PredicatedTaskRunner { } catch (Throwable e) { // we go on no matter what - e.printStackTrace(); + log.error(e.getMessage(), e); } } http://git-wip-us.apache.org/repos/asf/airavata/blob/98c9a34e/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/core/generators/ODEScriptFiler.java ---------------------------------------------------------------------- diff --git a/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/core/generators/ODEScriptFiler.java b/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/core/generators/ODEScriptFiler.java index a1573d4..7df94a7 100644 --- a/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/core/generators/ODEScriptFiler.java +++ b/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/core/generators/ODEScriptFiler.java @@ -42,6 +42,8 @@ import org.apache.airavata.xbaya.XBayaEngine; import org.apache.airavata.xbaya.file.XBayaPathConstants; import org.apache.airavata.xbaya.ui.utils.ErrorMessages; import org.gpel.model.GpelProcess; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; import org.xmlpull.infoset.XmlElement; import xsul5.XmlConstants; @@ -52,6 +54,7 @@ public class ODEScriptFiler { private XBayaEngine engine; private JFileChooser bpelFileChooser; + private static final Logger log = LoggerFactory.getLogger(XBayaEngine.class); private final FileFilter bpelFileFilter = new FileFilter() { @@ -117,7 +120,7 @@ public class ODEScriptFiler { try { temp = new URI("temp"); } catch (URISyntaxException e) { - e.printStackTrace(); // To change body of catch statement use File | Settings | File Templates. + log.error(e.getMessage(), e); } process = wf.getOdeProcess(WSDLUtil.appendWSDLQuary(temp), this.engine.getConfiguration().getODEURL()); String processString = process.xmlStringPretty(); http://git-wip-us.apache.org/repos/asf/airavata/blob/98c9a34e/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/interpretor/SystemComponentInvoker.java ---------------------------------------------------------------------- diff --git a/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/interpretor/SystemComponentInvoker.java b/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/interpretor/SystemComponentInvoker.java index d6a075a..a4706af 100644 --- a/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/interpretor/SystemComponentInvoker.java +++ b/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/interpretor/SystemComponentInvoker.java @@ -27,13 +27,15 @@ import java.util.Map; import org.apache.airavata.workflow.model.exceptions.WorkflowException; import org.apache.airavata.xbaya.invoker.Invoker; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; import xsul.wsif.WSIFMessage; import xsul.xwsif_runtime.WSIFClient; public class SystemComponentInvoker implements Invoker { private Map<String, Object> outputs = new Hashtable<String, Object>(); - + private static final Logger log = LoggerFactory.getLogger(SystemComponentInvoker.class); /** * * @param key @@ -54,7 +56,7 @@ public class SystemComponentInvoker implements Invoker { out = this.outputs.get(name); Thread.sleep(200); } catch (InterruptedException e) { - e.printStackTrace(); + log.error(e.getMessage(), e); } } return out; http://git-wip-us.apache.org/repos/asf/airavata/blob/98c9a34e/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/invoker/DynamicInvoker.java ---------------------------------------------------------------------- diff --git a/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/invoker/DynamicInvoker.java b/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/invoker/DynamicInvoker.java index 5020ef4..d293fe4 100644 --- a/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/invoker/DynamicInvoker.java +++ b/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/invoker/DynamicInvoker.java @@ -27,6 +27,8 @@ import java.net.URLClassLoader; import org.apache.airavata.workflow.model.exceptions.WorkflowException; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; import xsul.wsif.WSIFMessage; import xsul.xwsif_runtime.WSIFClient; @@ -42,6 +44,7 @@ public class DynamicInvoker implements Invoker { private Object result; + private static final Logger log = LoggerFactory.getLogger(DynamicInvoker.class); /** * Constructs a DynamicInvoker. * @@ -120,8 +123,7 @@ public class DynamicInvoker implements Invoker { method.setAccessible(true); method.invoke(sysloader, new Object[] { this.jarUrl }); } catch (Throwable t) { - t.printStackTrace(); - throw new WorkflowException("Error, could not add URL to system classloader"); + throw new WorkflowException("Error, could not add URL to system classloader", t); } } @@ -133,8 +135,7 @@ public class DynamicInvoker implements Invoker { try { Thread.sleep(200); } catch (InterruptedException e) { - // TODO Auto-generated catch block - e.printStackTrace(); + log.error(e.getMessage(), e); } } http://git-wip-us.apache.org/repos/asf/airavata/blob/98c9a34e/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/invoker/SimpleInvoker.java ---------------------------------------------------------------------- diff --git a/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/invoker/SimpleInvoker.java b/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/invoker/SimpleInvoker.java index 54cb7f4..e615dc5 100644 --- a/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/invoker/SimpleInvoker.java +++ b/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/invoker/SimpleInvoker.java @@ -168,7 +168,7 @@ public class SimpleInvoker implements Invoker { try { wait(); } catch (InterruptedException e) { - e.printStackTrace(); + log.error(e.getMessage(), e); } } return this.outputMessage; http://git-wip-us.apache.org/repos/asf/airavata/blob/98c9a34e/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/messaging/EventDataRepository.java ---------------------------------------------------------------------- diff --git a/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/messaging/EventDataRepository.java b/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/messaging/EventDataRepository.java index 1168925..9b2d9f7 100644 --- a/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/messaging/EventDataRepository.java +++ b/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/messaging/EventDataRepository.java @@ -138,8 +138,7 @@ public class EventDataRepository implements TableModel, BoundedRangeModel { try { listener.monitoringPreStart(); } catch (Exception e) { - //just in case - e.printStackTrace(); + logger.error(e.getMessage(), e); } } } @@ -149,9 +148,8 @@ public class EventDataRepository implements TableModel, BoundedRangeModel { try { listener.monitoringPostStart(); } catch (Exception e) { - //just in case - e.printStackTrace(); - } + logger.error(e.getMessage(), e); + } } } @@ -160,8 +158,7 @@ public class EventDataRepository implements TableModel, BoundedRangeModel { try { listener.monitoringPreStop(); } catch (Exception e) { - //just in case - e.printStackTrace(); + logger.error(e.getMessage(), e); } } } @@ -171,8 +168,7 @@ public class EventDataRepository implements TableModel, BoundedRangeModel { try { listener.monitoringPostStop(); } catch (Exception e) { - //just in case - e.printStackTrace(); + logger.error(e.getMessage(), e); } } } http://git-wip-us.apache.org/repos/asf/airavata/blob/98c9a34e/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/messaging/Monitor.java ---------------------------------------------------------------------- diff --git a/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/messaging/Monitor.java b/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/messaging/Monitor.java index 57fd217..896b248 100644 --- a/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/messaging/Monitor.java +++ b/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/messaging/Monitor.java @@ -140,7 +140,7 @@ public class Monitor extends EventProducer { try { Monitor.this.start(); } catch (MonitorException e) { - e.printStackTrace(); + logger.error(e.getMessage(), e); } } }.start(); @@ -256,7 +256,7 @@ public class Monitor extends EventProducer { try { Thread.sleep(100); } catch (InterruptedException e) { - e.printStackTrace(); + logger.error(e.getMessage(), e); } } } http://git-wip-us.apache.org/repos/asf/airavata/blob/98c9a34e/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/ui/XBayaGUI.java ---------------------------------------------------------------------- diff --git a/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/ui/XBayaGUI.java b/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/ui/XBayaGUI.java index 1e44243..fb1a0b0 100644 --- a/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/ui/XBayaGUI.java +++ b/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/ui/XBayaGUI.java @@ -352,7 +352,7 @@ public class XBayaGUI implements EventListener, XBayaExecutionModeListener { try { listener.stateChanged(null); } catch (Exception e) { - e.printStackTrace(); + logger.error(e.getMessage(), e); } } } @@ -455,7 +455,7 @@ public class XBayaGUI implements EventListener, XBayaExecutionModeListener { } } catch (Exception e) { - e.printStackTrace(); + logger.error(e.getMessage(), e); } } if (actionSuccess) { http://git-wip-us.apache.org/repos/asf/airavata/blob/98c9a34e/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/ui/dialogs/graph/dynamic/DynamicNodeWindow.java ---------------------------------------------------------------------- diff --git a/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/ui/dialogs/graph/dynamic/DynamicNodeWindow.java b/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/ui/dialogs/graph/dynamic/DynamicNodeWindow.java index 50d3a76..3f0a97f 100644 --- a/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/ui/dialogs/graph/dynamic/DynamicNodeWindow.java +++ b/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/ui/dialogs/graph/dynamic/DynamicNodeWindow.java @@ -58,6 +58,8 @@ import org.apache.airavata.xbaya.ui.widgets.XBayaLabel; import org.apache.airavata.xbaya.ui.widgets.XBayaTextArea; import org.apache.airavata.xbaya.ui.widgets.component.ComponentTreeNode; import org.apache.airavata.xbaya.util.RegistryConstants; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; import org.xmlpull.infoset.XmlElement; import org.xmlpull.infoset.XmlNamespace; import org.xmlpull.v1.builder.XmlBuilderException; @@ -66,6 +68,8 @@ import xsul5.wsdl.WsdlDefinitions; public class DynamicNodeWindow { + private static final Logger log = LoggerFactory.getLogger(DynamicNodeWindow.class); + /** * CLASSES_DIR */ @@ -354,8 +358,7 @@ public class DynamicNodeWindow { .serializeToOutputStream(schema, new FileOutputStream(rootDir.getCanonicalPath() + File.separatorChar + "types.xsd")); } catch (Exception e) { - // TODO Auto-generated catch block - e.printStackTrace(); + log.error(e.getMessage(), e); } typesPath = rootDir.getCanonicalPath() + File.separatorChar + "mytype.jar"; @@ -369,8 +372,7 @@ public class DynamicNodeWindow { } catch (CloneNotSupportedException e) { this.engine.getGUI().getErrorWindow().error(e); } catch (IOException e) { - // TODO Auto-generated catch block - e.printStackTrace(); + log.error(e.getMessage(), e); } } else { http://git-wip-us.apache.org/repos/asf/airavata/blob/98c9a34e/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/ui/dialogs/registry/NewRegistryUserDialog.java ---------------------------------------------------------------------- diff --git a/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/ui/dialogs/registry/NewRegistryUserDialog.java b/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/ui/dialogs/registry/NewRegistryUserDialog.java index d677ffa..df9db51 100644 --- a/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/ui/dialogs/registry/NewRegistryUserDialog.java +++ b/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/ui/dialogs/registry/NewRegistryUserDialog.java @@ -122,7 +122,6 @@ public class NewRegistryUserDialog { setUserCreated(true); // JCRComponentRegistry registry = new JCRComponentRegistry(getUsername(),getPassword()); } catch (Exception e) { - e.printStackTrace(); engine.getGUI().getErrorWindow().error(e.getMessage()); } } else { http://git-wip-us.apache.org/repos/asf/airavata/blob/98c9a34e/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/ui/dialogs/registry/browser/JCRBrowserDialog.java ---------------------------------------------------------------------- diff --git a/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/ui/dialogs/registry/browser/JCRBrowserDialog.java b/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/ui/dialogs/registry/browser/JCRBrowserDialog.java index 6400a98..bdc10e3 100644 --- a/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/ui/dialogs/registry/browser/JCRBrowserDialog.java +++ b/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/ui/dialogs/registry/browser/JCRBrowserDialog.java @@ -31,12 +31,15 @@ import javax.swing.JDialog; import javax.swing.JPanel; import org.apache.airavata.xbaya.XBayaEngine; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; public class JCRBrowserDialog extends JDialog { /** * */ + private static final Logger log = LoggerFactory.getLogger(JCRBrowserDialog.class); private static final long serialVersionUID = 2866874255829295553L; private JPanel contentPanel = new JPanel(); private XBayaEngine engine; @@ -50,7 +53,7 @@ public class JCRBrowserDialog extends JDialog { dialog.setDefaultCloseOperation(JDialog.DISPOSE_ON_CLOSE); dialog.setVisible(true); } catch (Exception e) { - e.printStackTrace(); + log.error(e.getMessage(), e); } } http://git-wip-us.apache.org/repos/asf/airavata/blob/98c9a34e/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/ui/dialogs/workflow/WorkflowImportWindow.java ---------------------------------------------------------------------- diff --git a/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/ui/dialogs/workflow/WorkflowImportWindow.java b/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/ui/dialogs/workflow/WorkflowImportWindow.java index 529d057..a5f366f 100644 --- a/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/ui/dialogs/workflow/WorkflowImportWindow.java +++ b/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/ui/dialogs/workflow/WorkflowImportWindow.java @@ -54,6 +54,8 @@ import org.apache.airavata.xbaya.ui.utils.ErrorMessages; import org.apache.airavata.xbaya.ui.widgets.GridPanel; import org.apache.airavata.xbaya.ui.widgets.XbayaEnhancedList; import org.apache.thrift.TException; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; import org.xmlpull.infoset.XmlElement; public class WorkflowImportWindow { @@ -69,6 +71,8 @@ public class WorkflowImportWindow { private XbayaEnhancedList<RegistrySearchResult> list; private Client client; + + private static final Logger log = LoggerFactory.getLogger(WorkflowImportWindow.class); /** * Constructs a RegistryLoaderWindow. * @@ -122,13 +126,13 @@ public class WorkflowImportWindow { WorkflowImportWindow.this.list.setEnabled(true); } } catch (InvalidRequestException e) { - e.printStackTrace(); + log.error(e.getMessage(), e); } catch (AiravataClientException e) { - e.printStackTrace(); + log.error(e.getMessage(), e); } catch (AiravataSystemException e) { - e.printStackTrace(); + log.error(e.getMessage(), e); } catch (TException e) { - e.printStackTrace(); + log.error(e.getMessage(), e); } } }); @@ -167,7 +171,6 @@ public class WorkflowImportWindow { } hide(); } catch (Exception e) { - e.printStackTrace(); engine.getGUI().getErrorWindow().error(e); } } @@ -177,7 +180,6 @@ public class WorkflowImportWindow { try { getClient().deleteWorkflow(i.getResourceName()); } catch (Exception e) { - e.printStackTrace(); engine.getGUI().getErrorWindow().error(e); } } http://git-wip-us.apache.org/repos/asf/airavata/blob/98c9a34e/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/ui/experiment/LaunchApplicationWindow.java ---------------------------------------------------------------------- diff --git a/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/ui/experiment/LaunchApplicationWindow.java b/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/ui/experiment/LaunchApplicationWindow.java index 9637352..26d2c6f 100644 --- a/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/ui/experiment/LaunchApplicationWindow.java +++ b/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/ui/experiment/LaunchApplicationWindow.java @@ -101,9 +101,9 @@ public class LaunchApplicationWindow { thriftClientData = engine.getConfiguration().getThriftClientData(ThriftServiceType.API_SERVICE); try { airavataClient = XBayaUtil.getAiravataClient(thriftClientData); - } catch (AiravataClientConnectException e) { - e.printStackTrace(); - } + } catch (AiravataClientConnectException e) { + logger.error(e.getMessage(), e); + } initGUI(); } @@ -164,18 +164,14 @@ public class LaunchApplicationWindow { try { hosts = airavataClient.getAllComputeResourceNames(); - } catch (InvalidRequestException e2) { - // TODO Auto-generated catch block - e2.printStackTrace(); - } catch (AiravataClientException e2) { - // TODO Auto-generated catch block - e2.printStackTrace(); - } catch (AiravataSystemException e2) { - // TODO Auto-generated catch block - e2.printStackTrace(); - } catch (TException e2) { - // TODO Auto-generated catch block - e2.printStackTrace(); + } catch (InvalidRequestException e) { + logger.error(e.getMessage(), e); + } catch (AiravataClientException e) { + logger.error(e.getMessage(), e); + } catch (AiravataSystemException e) { + logger.error(e.getMessage(), e); + } catch (TException e) { + logger.error(e.getMessage(), e); } @@ -234,23 +230,19 @@ public class LaunchApplicationWindow { JButton okButton = new JButton("Run"); okButton.addActionListener(new AbstractAction() { - public void actionPerformed(ActionEvent e) { + public void actionPerformed(ActionEvent event) { try { execute(); - } catch (AiravataClientConnectException e1) { - e1.printStackTrace(); - } catch (InvalidRequestException e1) { - // TODO Auto-generated catch block - e1.printStackTrace(); - } catch (AiravataClientException e1) { - // TODO Auto-generated catch block - e1.printStackTrace(); - } catch (AiravataSystemException e1) { - // TODO Auto-generated catch block - e1.printStackTrace(); - } catch (TException e1) { - // TODO Auto-generated catch block - e1.printStackTrace(); + } catch (AiravataClientConnectException e) { + logger.error(e.getMessage(), e); + } catch (InvalidRequestException e) { + logger.error(e.getMessage(), e); + } catch (AiravataClientException e) { + logger.error(e.getMessage(), e); + } catch (AiravataSystemException e) { + logger.error(e.getMessage(), e); + } catch (TException e) { + logger.error(e.getMessage(), e); } } }); @@ -386,15 +378,13 @@ public class LaunchApplicationWindow { Thread.sleep(1000); status = airavataClient.getExperimentStatus(experiment.getExperimentID()).getExperimentState().toString().trim(); } catch (InterruptedException e) { - // TODO Auto-generated catch block - e.printStackTrace(); + logger.error(e.getMessage(), e); } } try { Thread.sleep(1000); } catch (InterruptedException e) { - // TODO Auto-generated catch block - e.printStackTrace(); + logger.error(e.getMessage(), e); } if(status.equals("COMPLETED")){ http://git-wip-us.apache.org/repos/asf/airavata/blob/98c9a34e/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/ui/experiment/RegistryWorkflowPublisherWindow.java ---------------------------------------------------------------------- diff --git a/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/ui/experiment/RegistryWorkflowPublisherWindow.java b/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/ui/experiment/RegistryWorkflowPublisherWindow.java index 3ea33cd..c2eef03 100644 --- a/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/ui/experiment/RegistryWorkflowPublisherWindow.java +++ b/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/ui/experiment/RegistryWorkflowPublisherWindow.java @@ -106,7 +106,6 @@ public class RegistryWorkflowPublisherWindow { hide(); } } catch (Exception e) { - e.printStackTrace(); this.engine.getGUI().getErrorWindow().error(e.getMessage()); } } http://git-wip-us.apache.org/repos/asf/airavata/blob/98c9a34e/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/ui/experiment/WorkflowInterpreterLaunchWindow.java ---------------------------------------------------------------------- diff --git a/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/ui/experiment/WorkflowInterpreterLaunchWindow.java b/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/ui/experiment/WorkflowInterpreterLaunchWindow.java index 3e9d1a6..c542aa7 100644 --- a/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/ui/experiment/WorkflowInterpreterLaunchWindow.java +++ b/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/ui/experiment/WorkflowInterpreterLaunchWindow.java @@ -373,7 +373,7 @@ public class WorkflowInterpreterLaunchWindow { try { return OrchestratorClientFactory.createOrchestratorClient(serverHost, serverPort); } catch (AiravataClientConnectException e) { - e.printStackTrace(); + logger.error(e.getMessage(), e); } return null; } http://git-wip-us.apache.org/repos/asf/airavata/blob/98c9a34e/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/ui/graph/GraphCanvas.java ---------------------------------------------------------------------- diff --git a/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/ui/graph/GraphCanvas.java b/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/ui/graph/GraphCanvas.java index 517e0f7..6e89cbe 100644 --- a/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/ui/graph/GraphCanvas.java +++ b/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/ui/graph/GraphCanvas.java @@ -1365,7 +1365,7 @@ public class GraphCanvas implements XBayaExecutionModeListener{ // return !XMLUtil.isEqual(originalWorkflowElement, getWorkflow().toXML()); return !JSONUtil.isEqual(originalWorkflowElementJson, getWorkflow().toJSON()); } catch (Exception e) { - e.printStackTrace(); + logger.error(e.getMessage(), e); return true; } } http://git-wip-us.apache.org/repos/asf/airavata/blob/98c9a34e/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/util/XBayaUtil.java ---------------------------------------------------------------------- diff --git a/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/util/XBayaUtil.java b/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/util/XBayaUtil.java index ad827b7..db25a1a 100644 --- a/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/util/XBayaUtil.java +++ b/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/util/XBayaUtil.java @@ -132,7 +132,7 @@ public class XBayaUtil { } catch (SocketTimeoutException e) { return false; } catch (Exception e) { - e.printStackTrace(); + logger.error(e.getMessage(), e); return false; } } http://git-wip-us.apache.org/repos/asf/airavata/blob/98c9a34e/tools/gsissh/src/main/java/SSHDemo.java ---------------------------------------------------------------------- diff --git a/tools/gsissh/src/main/java/SSHDemo.java b/tools/gsissh/src/main/java/SSHDemo.java index 8ef7b63..c5e410c 100644 --- a/tools/gsissh/src/main/java/SSHDemo.java +++ b/tools/gsissh/src/main/java/SSHDemo.java @@ -40,6 +40,8 @@ import com.jcraft.jsch.*; import org.apache.airavata.gsi.ssh.jsch.ExtendedJSch; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; import javax.swing.*; import java.awt.*; @@ -50,6 +52,7 @@ import java.io.InputStream; */ public class SSHDemo { + private static final Logger logger = LoggerFactory.getLogger(SSHDemo.class); static { JSch.setConfig("gssapi-with-mic.x509", "org.apache.airavata.gsi.ssh.GSSContextX509"); JSch.setConfig("userauth.gssapi-with-mic", "com.jcraft.jsch.UserAuthGSSAPIWithMICGSSCredentials"); @@ -123,13 +126,13 @@ public class SSHDemo { try { Thread.sleep(1000); } catch (Exception ignored) { + logger.debug(ignored.getMessage(), ignored); } } channel.disconnect(); session.disconnect(); } catch (Exception e) { - e.printStackTrace(); - System.out.println(e); + logger.error(e.getMessage(), e); } } http://git-wip-us.apache.org/repos/asf/airavata/blob/98c9a34e/tools/gsissh/src/main/java/edu/illinois/ncsa/BCGSS/GlobusTlsClient.java ---------------------------------------------------------------------- diff --git a/tools/gsissh/src/main/java/edu/illinois/ncsa/BCGSS/GlobusTlsClient.java b/tools/gsissh/src/main/java/edu/illinois/ncsa/BCGSS/GlobusTlsClient.java index 780de5d..0da3bca 100644 --- a/tools/gsissh/src/main/java/edu/illinois/ncsa/BCGSS/GlobusTlsClient.java +++ b/tools/gsissh/src/main/java/edu/illinois/ncsa/BCGSS/GlobusTlsClient.java @@ -35,6 +35,8 @@ import org.globus.gsi.stores.ResourceSigningPolicyStore; import org.globus.gsi.stores.ResourceSigningPolicyStoreParameters; import org.globus.gsi.trustmanager.X509ProxyCertPathValidator; import org.globus.gsi.util.CertificateUtil; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; import javax.crypto.Cipher; import java.io.ByteArrayInputStream; @@ -52,6 +54,7 @@ public class GlobusTlsClient extends DefaultTlsClient private Certificate clientCert = new Certificate(new X509CertificateStructure[0]); private PrivateKey clientPrivateKey = null; private X509Certificate[] peerCerts = null; + private static final Logger logger = LoggerFactory.getLogger(GlobusTlsClient.class); public X509Certificate[] getPeerCerts() { return peerCerts; @@ -129,7 +132,7 @@ public class GlobusTlsClient extends DefaultTlsClient throw new Exception("X509ProxyCertPathValidator did not return a result"); } } catch (Exception e) { - e.printStackTrace(); + logger.error(e.getMessage(), e); throw new TlsFatalAlert(AlertDescription.user_canceled); } } @@ -161,7 +164,7 @@ public class GlobusTlsClient extends DefaultTlsClient cipher.init(Cipher.ENCRYPT_MODE, clientPrivateKey); return cipher.doFinal(md5andsha1); } catch (Exception e) { - e.printStackTrace(); + logger.error(e.getMessage(), e); throw new IOException(e); } } http://git-wip-us.apache.org/repos/asf/airavata/blob/98c9a34e/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/GSSContextX509.java ---------------------------------------------------------------------- diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/GSSContextX509.java b/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/GSSContextX509.java index 522acf2..e0fc007 100644 --- a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/GSSContextX509.java +++ b/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/GSSContextX509.java @@ -42,6 +42,8 @@ import org.gridforum.jgss.ExtendedGSSManager; import org.ietf.jgss.*; import com.jcraft.jsch.JSchException; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; /** * This class is based on GSSContextKrb5; it substitutes the globus @@ -53,6 +55,7 @@ public class GSSContextX509 implements com.jcraft.jsch.GSSContext { private GSSContext context = null; private GSSCredential credential; + private static final Logger logger = LoggerFactory.getLogger(GSSContextX509.class); public void create(String user, String host) throws JSchException { try { @@ -181,7 +184,7 @@ public class GSSContextX509 implements com.jcraft.jsch.GSSContext { MessageProp prop = new MessageProp(0, false); return context.getMIC(message, s, l, prop); } catch (GSSException ex) { - ex.printStackTrace(); + logger.error(ex.getMessage(), ex); return null; } } http://git-wip-us.apache.org/repos/asf/airavata/blob/98c9a34e/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/GSISSHAbstractCluster.java ---------------------------------------------------------------------- diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/GSISSHAbstractCluster.java b/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/GSISSHAbstractCluster.java index a8faf53..5e966bc 100644 --- a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/GSISSHAbstractCluster.java +++ b/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/GSISSHAbstractCluster.java @@ -312,10 +312,9 @@ public class GSISSHAbstractCluster implements Cluster { try { Thread.sleep(5000); } catch (InterruptedException e1) { - e1.printStackTrace(); + log.error(e1.getMessage(), e1); } log.error("Error occured during job submission but doing a retry"); - e.printStackTrace(); } } } @@ -397,7 +396,7 @@ public class GSISSHAbstractCluster implements Cluster { try { Thread.sleep(5000); } catch (InterruptedException e1) { - e1.printStackTrace(); + log.error(e1.getMessage(), e1); } reconnect(serverInfo, authenticationInfo); if (retry == 0) { @@ -423,7 +422,7 @@ public class GSISSHAbstractCluster implements Cluster { try { Thread.sleep(5000); } catch (InterruptedException e1) { - e1.printStackTrace(); + log.error(e1.getMessage(), e1); } reconnect(serverInfo, authenticationInfo); if (retry == 0) { @@ -437,7 +436,7 @@ public class GSISSHAbstractCluster implements Cluster { try { Thread.sleep(5000); } catch (InterruptedException e1) { - e1.printStackTrace(); + log.error(e1.getMessage(), e1); } reconnect(serverInfo, authenticationInfo); if(retry==0) { @@ -484,7 +483,7 @@ public class GSISSHAbstractCluster implements Cluster { try { Thread.sleep(5000); } catch (InterruptedException e1) { - e1.printStackTrace(); + log.error(e1.getMessage(), e1); } reconnect(serverInfo, authenticationInfo); if (retry == 0) { @@ -496,7 +495,7 @@ public class GSISSHAbstractCluster implements Cluster { try { Thread.sleep(5000); } catch (InterruptedException e1) { - e1.printStackTrace(); + log.error(e1.getMessage(), e1); } reconnect(serverInfo, authenticationInfo); if (retry == 0) { @@ -519,12 +518,12 @@ public class GSISSHAbstractCluster implements Cluster { files = SSHUtils.listDirectory(directoryPath, session); retry=0; } catch (IOException e) { - e.printStackTrace(); + log.error(e.getMessage(), e); retry--; try { Thread.sleep(5000); } catch (InterruptedException e1) { - e1.printStackTrace(); + log.error(e1.getMessage(), e1); } reconnect(serverInfo, authenticationInfo); if (retry == 0) { @@ -541,7 +540,7 @@ public class GSISSHAbstractCluster implements Cluster { try { Thread.sleep(5000); } catch (InterruptedException e1) { - e1.printStackTrace(); + log.error(e1.getMessage(), e1); } reconnect(serverInfo, authenticationInfo); if (retry == 0) { @@ -566,7 +565,7 @@ public class GSISSHAbstractCluster implements Cluster { try { Thread.sleep(5000); } catch (InterruptedException e1) { - e1.printStackTrace(); + log.error(e1.getMessage(), e1); } reconnect(serverInfo, authenticationInfo); if (retry == 0) { http://git-wip-us.apache.org/repos/asf/airavata/blob/98c9a34e/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/StandardOutReader.java ---------------------------------------------------------------------- diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/StandardOutReader.java b/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/StandardOutReader.java index 4846da8..00cbe01 100644 --- a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/StandardOutReader.java +++ b/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/StandardOutReader.java @@ -24,6 +24,8 @@ import com.jcraft.jsch.Channel; import com.jcraft.jsch.ChannelExec; import org.apache.airavata.gsi.ssh.api.CommandOutput; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; import java.io.ByteArrayOutputStream; import java.io.IOException; @@ -32,6 +34,7 @@ import java.io.OutputStream; public class StandardOutReader implements CommandOutput { + private static final Logger logger = LoggerFactory.getLogger(StandardOutReader.class); String stdOutputString = null; ByteArrayOutputStream errorStream = new ByteArrayOutputStream(); public void onOutput(Channel channel) { @@ -57,7 +60,7 @@ public class StandardOutReader implements CommandOutput { String output = pbsOutput.toString(); this.setStdOutputString(output); } catch (IOException e) { - e.printStackTrace(); + logger.error(e.getMessage(), e); } } http://git-wip-us.apache.org/repos/asf/airavata/blob/98c9a34e/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/SystemCommandOutput.java ---------------------------------------------------------------------- diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/SystemCommandOutput.java b/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/SystemCommandOutput.java index 6e3b8e6..37e1d69 100644 --- a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/SystemCommandOutput.java +++ b/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/SystemCommandOutput.java @@ -23,6 +23,8 @@ package org.apache.airavata.gsi.ssh.impl; import com.jcraft.jsch.Channel; import org.apache.airavata.gsi.ssh.api.CommandOutput; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; import java.io.IOException; import java.io.InputStream; @@ -36,6 +38,7 @@ import java.io.OutputStream; public class SystemCommandOutput implements CommandOutput { + private static final Logger logger = LoggerFactory.getLogger(SystemCommandOutput.class); public void onOutput(Channel channel) { try { InputStream inputStream = channel.getInputStream(); @@ -58,7 +61,7 @@ public class SystemCommandOutput implements CommandOutput { } } catch (IOException e) { - e.printStackTrace(); + logger.error(e.getMessage(), e); } } http://git-wip-us.apache.org/repos/asf/airavata/blob/98c9a34e/tools/gsissh/src/test/java/org/apache/airavata/gsi/ssh/impl/DefaultSSHApiTestWithMyProxyAuth.java ---------------------------------------------------------------------- diff --git a/tools/gsissh/src/test/java/org/apache/airavata/gsi/ssh/impl/DefaultSSHApiTestWithMyProxyAuth.java b/tools/gsissh/src/test/java/org/apache/airavata/gsi/ssh/impl/DefaultSSHApiTestWithMyProxyAuth.java index 747b740..f53f29b 100644 --- a/tools/gsissh/src/test/java/org/apache/airavata/gsi/ssh/impl/DefaultSSHApiTestWithMyProxyAuth.java +++ b/tools/gsissh/src/test/java/org/apache/airavata/gsi/ssh/impl/DefaultSSHApiTestWithMyProxyAuth.java @@ -71,9 +71,9 @@ public class DefaultSSHApiTestWithMyProxyAuth { try { CommandExecutor.executeCommand(commandInfo, serverInfo, authenticationInfo, commandOutput, new ConfigReader()); } catch (SSHApiException e) { - e.printStackTrace(); + log.error(e.getMessage(), e); } catch (IOException e) { - e.printStackTrace(); + log.error(e.getMessage(), e); } } http://git-wip-us.apache.org/repos/asf/airavata/blob/98c9a34e/tools/registry-tool/src/main/java/org/apache/airavata/registry/tool/DBMigrator.java ---------------------------------------------------------------------- diff --git a/tools/registry-tool/src/main/java/org/apache/airavata/registry/tool/DBMigrator.java b/tools/registry-tool/src/main/java/org/apache/airavata/registry/tool/DBMigrator.java index 487d737..958ac23 100644 --- a/tools/registry-tool/src/main/java/org/apache/airavata/registry/tool/DBMigrator.java +++ b/tools/registry-tool/src/main/java/org/apache/airavata/registry/tool/DBMigrator.java @@ -101,19 +101,14 @@ public class DBMigrator { updateConfigTable(connection); } } catch (ClassNotFoundException e) { - e.printStackTrace(); logger.error("Unable to find SQL scripts..." , e); } catch (InstantiationException e) { - e.printStackTrace(); logger.error("Error while updating the database..." , e); } catch (IllegalAccessException e) { - e.printStackTrace(); logger.error("Error while updating the database..." , e); } catch (SQLException e) { - e.printStackTrace(); logger.error("Error while updating the database..." , e); } catch (Exception e) { - e.printStackTrace(); logger.error("Error while updating the database..." , e); } } @@ -170,7 +165,7 @@ public class DBMigrator { } } } catch (SQLException e) { - e.printStackTrace(); + logger.error(e.getMessage() , e); } return null; } @@ -180,7 +175,7 @@ public class DBMigrator { Statement statement = conn.createStatement(); statement.execute(query) ; } catch (SQLException e) { - e.printStackTrace(); + logger.error(e.getMessage() , e); } }
