http://git-wip-us.apache.org/repos/asf/airavata/blob/98c9a34e/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/gfac/monitor/util/AMQPConnectionUtil.java ---------------------------------------------------------------------- diff --git a/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/gfac/monitor/util/AMQPConnectionUtil.java b/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/gfac/monitor/util/AMQPConnectionUtil.java index b69cf52..6a4ed3b 100644 --- a/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/gfac/monitor/util/AMQPConnectionUtil.java +++ b/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/gfac/monitor/util/AMQPConnectionUtil.java @@ -23,6 +23,8 @@ package org.apache.airavata.gfac.monitor.util; import com.rabbitmq.client.Connection; import com.rabbitmq.client.ConnectionFactory; import com.rabbitmq.client.DefaultSaslConfig; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; import javax.net.ssl.KeyManagerFactory; import javax.net.ssl.SSLContext; @@ -32,6 +34,7 @@ import java.util.Collections; import java.util.List; public class AMQPConnectionUtil { + private final static Logger logger = LoggerFactory.getLogger(AMQPConnectionUtil.class); public static Connection connect(List<String>hosts,String vhost, String proxyFile) { Collections.shuffle(hosts); for (String host : hosts) { @@ -68,7 +71,7 @@ public class AMQPConnectionUtil { connection = factory.newConnection(); } catch (Exception e) { - e.printStackTrace(); + logger.error(e.getMessage(), e); return null; } return connection;
http://git-wip-us.apache.org/repos/asf/airavata/blob/98c9a34e/modules/gfac/gfac-monitor/src/test/java/org/apache/airavata/job/AMQPMonitorTest.java ---------------------------------------------------------------------- diff --git a/modules/gfac/gfac-monitor/src/test/java/org/apache/airavata/job/AMQPMonitorTest.java b/modules/gfac/gfac-monitor/src/test/java/org/apache/airavata/job/AMQPMonitorTest.java index a979890..daa2e91 100644 --- a/modules/gfac/gfac-monitor/src/test/java/org/apache/airavata/job/AMQPMonitorTest.java +++ b/modules/gfac/gfac-monitor/src/test/java/org/apache/airavata/job/AMQPMonitorTest.java @@ -48,6 +48,8 @@ import org.apache.airavata.model.messaging.event.JobStatusChangeEvent; import org.junit.Assert; import org.junit.Before; import org.junit.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; import java.io.File; import java.util.ArrayList; @@ -71,6 +73,7 @@ public class AMQPMonitorTest { private Thread pushThread; private String proxyFilePath; private ComputeResourceDescription computeResourceDescription; + private final static Logger logger = LoggerFactory.getLogger(AMQPMonitorTest.class); @Before public void setUp() throws Exception { @@ -108,7 +111,7 @@ public class AMQPMonitorTest { } }).start(); } catch (Exception e) { - e.printStackTrace(); + logger.error(e.getMessage(), e); } computeResourceDescription = new ComputeResourceDescription("TestComputerResoruceId", "TestHostName"); computeResourceDescription.setHostName("stampede-host"); http://git-wip-us.apache.org/repos/asf/airavata/blob/98c9a34e/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/security/TokenizedSSHAuthInfo.java ---------------------------------------------------------------------- diff --git a/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/security/TokenizedSSHAuthInfo.java b/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/security/TokenizedSSHAuthInfo.java index 5536e17..683985f 100644 --- a/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/security/TokenizedSSHAuthInfo.java +++ b/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/security/TokenizedSSHAuthInfo.java @@ -176,7 +176,7 @@ public class TokenizedSSHAuthInfo implements SSHPublicKeyFileAuthentication { bw.write(data); bw.close(); } catch (IOException e) { - e.printStackTrace(); + log.error(e.getMessage(), e); } return temp.getAbsolutePath(); } http://git-wip-us.apache.org/repos/asf/airavata/blob/98c9a34e/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/util/GFACSSHUtils.java ---------------------------------------------------------------------- diff --git a/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/util/GFACSSHUtils.java b/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/util/GFACSSHUtils.java index bbc258d..ab698ff 100644 --- a/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/util/GFACSSHUtils.java +++ b/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/util/GFACSSHUtils.java @@ -206,7 +206,8 @@ public class GFACSSHUtils { sshSecurityContext.setPbsCluster(pbsCluster); jobExecutionContext.addSecurityContext(key, sshSecurityContext); } catch (Exception e) { - e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates. + logger.error(e.getMessage(), e); + throw new GFacException("Error adding security Context", e); } } http://git-wip-us.apache.org/repos/asf/airavata/blob/98c9a34e/modules/messaging/core/src/main/java/org/apache/airavata/messaging/core/TestClient.java ---------------------------------------------------------------------- diff --git a/modules/messaging/core/src/main/java/org/apache/airavata/messaging/core/TestClient.java b/modules/messaging/core/src/main/java/org/apache/airavata/messaging/core/TestClient.java index 0f31f49..362f3f2 100644 --- a/modules/messaging/core/src/main/java/org/apache/airavata/messaging/core/TestClient.java +++ b/modules/messaging/core/src/main/java/org/apache/airavata/messaging/core/TestClient.java @@ -74,7 +74,7 @@ public class TestClient { System.out.println(" Message Received with message id '" + message.getMessageId() + "' and with message type '" + message.getType() + "' and with state : '" + event.getState().toString()); } catch (TException e) { - e.printStackTrace(); + logger.error(e.getMessage(), e); } } } @@ -82,7 +82,7 @@ public class TestClient { } catch (ApplicationSettingsException e) { logger.error("Error reading airavata server properties", e); }catch (Exception e) { - e.printStackTrace(); + logger.error(e.getMessage(), e); } } http://git-wip-us.apache.org/repos/asf/airavata/blob/98c9a34e/modules/orchestrator/airavata-orchestrator-service/src/main/java/org/apache/airavata/orchestrator/server/OrchestratorServer.java ---------------------------------------------------------------------- diff --git a/modules/orchestrator/airavata-orchestrator-service/src/main/java/org/apache/airavata/orchestrator/server/OrchestratorServer.java b/modules/orchestrator/airavata-orchestrator-service/src/main/java/org/apache/airavata/orchestrator/server/OrchestratorServer.java index d86960c..78957ac 100644 --- a/modules/orchestrator/airavata-orchestrator-service/src/main/java/org/apache/airavata/orchestrator/server/OrchestratorServer.java +++ b/modules/orchestrator/airavata-orchestrator-service/src/main/java/org/apache/airavata/orchestrator/server/OrchestratorServer.java @@ -104,7 +104,7 @@ public class OrchestratorServer implements IServer{ try { new OrchestratorServer().start(); } catch (Exception e) { - e.printStackTrace(); + logger.error(e.getMessage(), e); } } http://git-wip-us.apache.org/repos/asf/airavata/blob/98c9a34e/modules/orchestrator/airavata-orchestrator-service/src/main/java/org/apache/airavata/orchestrator/server/OrchestratorServerHandler.java ---------------------------------------------------------------------- diff --git a/modules/orchestrator/airavata-orchestrator-service/src/main/java/org/apache/airavata/orchestrator/server/OrchestratorServerHandler.java b/modules/orchestrator/airavata-orchestrator-service/src/main/java/org/apache/airavata/orchestrator/server/OrchestratorServerHandler.java index de293e4..e0548f4 100644 --- a/modules/orchestrator/airavata-orchestrator-service/src/main/java/org/apache/airavata/orchestrator/server/OrchestratorServerHandler.java +++ b/modules/orchestrator/airavata-orchestrator-service/src/main/java/org/apache/airavata/orchestrator/server/OrchestratorServerHandler.java @@ -97,7 +97,7 @@ public class OrchestratorServerHandler implements OrchestratorService.Iface, return orchestrator_cpi_serviceConstants.ORCHESTRATOR_CPI_VERSION; } - public OrchestratorServerHandler() { + public OrchestratorServerHandler() throws OrchestratorException{ // registering with zk try { if (ServerSettings.isRabbitMqPublishEnabled()) { @@ -129,16 +129,21 @@ public class OrchestratorServerHandler implements OrchestratorService.Iface, this); log.info("Finished starting ZK: " + zk); } catch (IOException e) { - e.printStackTrace(); + log.error(e.getMessage(), e); + throw new OrchestratorException("Error while initializing orchestrator service", e); } catch (InterruptedException e) { - e.printStackTrace(); + log.error(e.getMessage(), e); + throw new OrchestratorException("Error while initializing orchestrator service", e); } catch (KeeperException e) { - e.printStackTrace(); + log.error(e.getMessage(), e); + throw new OrchestratorException("Error while initializing orchestrator service", e); } } catch (ApplicationSettingsException e) { - e.printStackTrace(); + log.error(e.getMessage(), e); + throw new OrchestratorException("Error while initializing orchestrator service", e); }catch (AiravataException e) { - e.printStackTrace(); + log.error(e.getMessage(), e); + throw new OrchestratorException("Error while initializing orchestrator service", e); } // orchestrator init try { @@ -149,9 +154,11 @@ public class OrchestratorServerHandler implements OrchestratorService.Iface, orchestrator.initialize(); orchestrator.getOrchestratorContext().setZk(this.zk); } catch (OrchestratorException e) { - e.printStackTrace(); + log.error(e.getMessage(), e); + throw new OrchestratorException("Error while initializing orchestrator service", e); } catch (RegistryException e) { - e.printStackTrace(); + log.error(e.getMessage(), e); + throw new OrchestratorException("Error while initializing orchestrator service", e); } } http://git-wip-us.apache.org/repos/asf/airavata/blob/98c9a34e/modules/orchestrator/airavata-orchestrator-service/src/main/java/org/apache/airavata/orchestrator/util/DataModelUtils.java ---------------------------------------------------------------------- diff --git a/modules/orchestrator/airavata-orchestrator-service/src/main/java/org/apache/airavata/orchestrator/util/DataModelUtils.java b/modules/orchestrator/airavata-orchestrator-service/src/main/java/org/apache/airavata/orchestrator/util/DataModelUtils.java index ce71f2a..f2ccbff 100644 --- a/modules/orchestrator/airavata-orchestrator-service/src/main/java/org/apache/airavata/orchestrator/util/DataModelUtils.java +++ b/modules/orchestrator/airavata-orchestrator-service/src/main/java/org/apache/airavata/orchestrator/util/DataModelUtils.java @@ -29,9 +29,12 @@ import org.apache.aiaravata.application.catalog.data.impl.AppCatalogFactory; import org.apache.airavata.model.util.ExecutionType; import org.apache.airavata.model.workspace.experiment.Experiment; import org.apache.airavata.workflow.catalog.WorkflowCatalogFactory; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; public class DataModelUtils { + private final static Logger logger = LoggerFactory.getLogger(DataModelUtils.class); public static ExecutionType getExecutionType(Experiment experiment){ try { ApplicationInterface applicationInterface = AppCatalogFactory.getAppCatalog().getApplicationInterface(); @@ -46,7 +49,7 @@ public class DataModelUtils { } } } catch (AppCatalogException e) { - e.printStackTrace(); + logger.error(e.getMessage(), e); } return ExecutionType.UNKNOWN; } http://git-wip-us.apache.org/repos/asf/airavata/blob/98c9a34e/modules/orchestrator/airavata-orchestrator-service/src/main/java/org/apache/airavata/orchestrator/util/OrchestratorRecoveryHandler.java ---------------------------------------------------------------------- diff --git a/modules/orchestrator/airavata-orchestrator-service/src/main/java/org/apache/airavata/orchestrator/util/OrchestratorRecoveryHandler.java b/modules/orchestrator/airavata-orchestrator-service/src/main/java/org/apache/airavata/orchestrator/util/OrchestratorRecoveryHandler.java index ff16848..fb3bd51 100644 --- a/modules/orchestrator/airavata-orchestrator-service/src/main/java/org/apache/airavata/orchestrator/util/OrchestratorRecoveryHandler.java +++ b/modules/orchestrator/airavata-orchestrator-service/src/main/java/org/apache/airavata/orchestrator/util/OrchestratorRecoveryHandler.java @@ -88,7 +88,7 @@ public class OrchestratorRecoveryHandler implements Watcher { } // we do not move the old experiment in to new gfac node, gfac will do it } catch (Exception e) { // we attempt all the experiments - e.printStackTrace(); + log.error(e.getMessage(), e); } log.info("------------------------------------------------------------------------------------"); } http://git-wip-us.apache.org/repos/asf/airavata/blob/98c9a34e/modules/orchestrator/airavata-orchestrator-service/src/test/java/org/apache/airavata/orchestrator/client/util/Initialize.java ---------------------------------------------------------------------- diff --git a/modules/orchestrator/airavata-orchestrator-service/src/test/java/org/apache/airavata/orchestrator/client/util/Initialize.java b/modules/orchestrator/airavata-orchestrator-service/src/test/java/org/apache/airavata/orchestrator/client/util/Initialize.java index 6f61543..afe0617 100644 --- a/modules/orchestrator/airavata-orchestrator-service/src/test/java/org/apache/airavata/orchestrator/client/util/Initialize.java +++ b/modules/orchestrator/airavata-orchestrator-service/src/test/java/org/apache/airavata/orchestrator/client/util/Initialize.java @@ -134,7 +134,6 @@ public class Initialize { } } catch (SQLException e) { logger.error(e.getMessage(), e); - e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates. } } @@ -317,9 +316,9 @@ public class Initialize { Class.forName("org.apache.derby.jdbc.EmbeddedDriver"); DriverManager.getConnection("jdbc:derby:memory:unit-testing-jpa;create=true").close(); } catch (ClassNotFoundException e) { - e.printStackTrace(); + logger.error(e.getMessage(), e); } catch (SQLException e) { - e.printStackTrace(); + logger.error(e.getMessage(), e); } } @@ -327,7 +326,7 @@ public class Initialize { try { server.shutdown(); } catch (Exception e) { - e.printStackTrace(); + logger.error(e.getMessage(), e); } } } http://git-wip-us.apache.org/repos/asf/airavata/blob/98c9a34e/modules/orchestrator/orchestrator-core/src/main/java/org/apache/airavata/orchestrator/core/impl/GFACServiceJobSubmitter.java ---------------------------------------------------------------------- diff --git a/modules/orchestrator/orchestrator-core/src/main/java/org/apache/airavata/orchestrator/core/impl/GFACServiceJobSubmitter.java b/modules/orchestrator/orchestrator-core/src/main/java/org/apache/airavata/orchestrator/core/impl/GFACServiceJobSubmitter.java index c5578d8..fccbb44 100644 --- a/modules/orchestrator/orchestrator-core/src/main/java/org/apache/airavata/orchestrator/core/impl/GFACServiceJobSubmitter.java +++ b/modules/orchestrator/orchestrator-core/src/main/java/org/apache/airavata/orchestrator/core/impl/GFACServiceJobSubmitter.java @@ -105,17 +105,23 @@ public class GFACServiceJobSubmitter implements JobSubmitter, Watcher { } } } catch (TException e) { + logger.error(e.getMessage(), e); throw new OrchestratorException(e); } catch (InterruptedException e) { - e.printStackTrace(); + logger.error(e.getMessage(), e); + throw new OrchestratorException(e); } catch (KeeperException e) { - e.printStackTrace(); + logger.error(e.getMessage(), e); + throw new OrchestratorException(e); } catch (ApplicationSettingsException e) { - e.printStackTrace(); + logger.error(e.getMessage(), e); + throw new OrchestratorException(e); } catch (IOException e) { - e.printStackTrace(); + logger.error(e.getMessage(), e); + throw new OrchestratorException(e); } catch (Exception e) { - e.printStackTrace(); + logger.error(e.getMessage(), e); + throw new OrchestratorException(e); }finally { gfacClient.getOutputProtocol().getTransport().close(); } @@ -155,17 +161,23 @@ public class GFACServiceJobSubmitter implements JobSubmitter, Watcher { } } } catch (TException e) { + logger.error(e.getMessage(), e); throw new OrchestratorException(e); } catch (InterruptedException e) { - e.printStackTrace(); + logger.error(e.getMessage(), e); + throw new OrchestratorException(e); } catch (KeeperException e) { - e.printStackTrace(); + logger.error(e.getMessage(), e); + throw new OrchestratorException(e); } catch (ApplicationSettingsException e) { - e.printStackTrace(); + logger.error(e.getMessage(), e); + throw new OrchestratorException(e); } catch (IOException e) { - e.printStackTrace(); + logger.error(e.getMessage(), e); + throw new OrchestratorException(e); } catch (Exception e) { - e.printStackTrace(); + logger.error(e.getMessage(), e); + throw new OrchestratorException(e); }finally { } http://git-wip-us.apache.org/repos/asf/airavata/blob/98c9a34e/modules/orchestrator/orchestrator-core/src/main/java/org/apache/airavata/orchestrator/cpi/impl/AbstractOrchestrator.java ---------------------------------------------------------------------- diff --git a/modules/orchestrator/orchestrator-core/src/main/java/org/apache/airavata/orchestrator/cpi/impl/AbstractOrchestrator.java b/modules/orchestrator/orchestrator-core/src/main/java/org/apache/airavata/orchestrator/cpi/impl/AbstractOrchestrator.java index 1fc1ad2..dd3647a 100644 --- a/modules/orchestrator/orchestrator-core/src/main/java/org/apache/airavata/orchestrator/cpi/impl/AbstractOrchestrator.java +++ b/modules/orchestrator/orchestrator-core/src/main/java/org/apache/airavata/orchestrator/cpi/impl/AbstractOrchestrator.java @@ -119,7 +119,7 @@ public abstract class AbstractOrchestrator implements Orchestrator { setAiravataUserName(ServerSettings.getDefaultUser()); setGatewayName(ServerSettings.getDefaultUserGateway()); } catch (ApplicationSettingsException e) { - e.printStackTrace(); + logger.error(e.getMessage(), e); } } http://git-wip-us.apache.org/repos/asf/airavata/blob/98c9a34e/modules/orchestrator/orchestrator-core/src/test/java/org/apache/airavata/orchestrator/core/util/Initialize.java ---------------------------------------------------------------------- diff --git a/modules/orchestrator/orchestrator-core/src/test/java/org/apache/airavata/orchestrator/core/util/Initialize.java b/modules/orchestrator/orchestrator-core/src/test/java/org/apache/airavata/orchestrator/core/util/Initialize.java index 2823cdf..b590d79 100644 --- a/modules/orchestrator/orchestrator-core/src/test/java/org/apache/airavata/orchestrator/core/util/Initialize.java +++ b/modules/orchestrator/orchestrator-core/src/test/java/org/apache/airavata/orchestrator/core/util/Initialize.java @@ -134,7 +134,6 @@ public class Initialize { } } catch (SQLException e) { logger.error(e.getMessage(), e); - e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates. } } @@ -312,22 +311,12 @@ public class Initialize { } - private void startDerbyInEmbeddedMode(){ - try { - Class.forName("org.apache.derby.jdbc.EmbeddedDriver"); - DriverManager.getConnection("jdbc:derby:memory:unit-testing-jpa;create=true").close(); - } catch (ClassNotFoundException e) { - e.printStackTrace(); - } catch (SQLException e) { - e.printStackTrace(); - } - } - - public void stopDerbyServer() { + public void stopDerbyServer() throws SQLException{ try { server.shutdown(); } catch (Exception e) { - e.printStackTrace(); + logger.error(e.getMessage(), e); + throw new SQLException(e.getMessage(), e); } } } http://git-wip-us.apache.org/repos/asf/airavata/blob/98c9a34e/modules/registry/airavata-jpa-registry/src/main/java/org/apache/airavata/persistance/registry/jpa/impl/RegistryImpl.java ---------------------------------------------------------------------- diff --git a/modules/registry/airavata-jpa-registry/src/main/java/org/apache/airavata/persistance/registry/jpa/impl/RegistryImpl.java b/modules/registry/airavata-jpa-registry/src/main/java/org/apache/airavata/persistance/registry/jpa/impl/RegistryImpl.java index a76bb5d..ec60bd4 100644 --- a/modules/registry/airavata-jpa-registry/src/main/java/org/apache/airavata/persistance/registry/jpa/impl/RegistryImpl.java +++ b/modules/registry/airavata-jpa-registry/src/main/java/org/apache/airavata/persistance/registry/jpa/impl/RegistryImpl.java @@ -63,6 +63,7 @@ public class RegistryImpl implements Registry { projectRegistry = new ProjectRegistry(gatewayResource, user); } catch (ApplicationSettingsException e) { logger.error("Unable to read airavata server properties..", e); + throw new RegistryException("Unable to read airavata server properties..", e); } } http://git-wip-us.apache.org/repos/asf/airavata/blob/98c9a34e/modules/registry/airavata-jpa-registry/src/test/java/org/apache/airavata/persistance/registry/jpa/util/Initialize.java ---------------------------------------------------------------------- diff --git a/modules/registry/airavata-jpa-registry/src/test/java/org/apache/airavata/persistance/registry/jpa/util/Initialize.java b/modules/registry/airavata-jpa-registry/src/test/java/org/apache/airavata/persistance/registry/jpa/util/Initialize.java index d795f4a..84eae9d 100644 --- a/modules/registry/airavata-jpa-registry/src/test/java/org/apache/airavata/persistance/registry/jpa/util/Initialize.java +++ b/modules/registry/airavata-jpa-registry/src/test/java/org/apache/airavata/persistance/registry/jpa/util/Initialize.java @@ -93,7 +93,7 @@ public class Initialize { return false; } - public void initializeDB() { + public void initializeDB() throws SQLException{ String jdbcUrl = null; String jdbcDriver = null; String jdbcUser = null; @@ -138,7 +138,6 @@ public class Initialize { } } catch (SQLException e) { logger.error(e.getMessage(), e); - e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates. } } @@ -167,6 +166,7 @@ public class Initialize { } catch (RegistryException e) { logger.error("Unable to read properties", e); + throw new SQLException(e.getMessage(), e); } } @@ -321,22 +321,12 @@ public class Initialize { } - private void startDerbyInEmbeddedMode(){ - try { - Class.forName("org.apache.derby.jdbc.EmbeddedDriver"); - DriverManager.getConnection("jdbc:derby:memory:unit-testing-jpa;create=true").close(); - } catch (ClassNotFoundException e) { - e.printStackTrace(); - } catch (SQLException e) { - e.printStackTrace(); - } - } - - public void stopDerbyServer() { + public void stopDerbyServer() throws SQLException{ try { server.shutdown(); } catch (Exception e) { - e.printStackTrace(); + logger.error(e.getMessage(), e); + throw new SQLException("Error while stopping derby server", e); } } } http://git-wip-us.apache.org/repos/asf/airavata/blob/98c9a34e/modules/server/src/main/java/org/apache/airavata/server/ServerMain.java ---------------------------------------------------------------------- diff --git a/modules/server/src/main/java/org/apache/airavata/server/ServerMain.java b/modules/server/src/main/java/org/apache/airavata/server/ServerMain.java index c6e36e8..1b1a41b 100644 --- a/modules/server/src/main/java/org/apache/airavata/server/ServerMain.java +++ b/modules/server/src/main/java/org/apache/airavata/server/ServerMain.java @@ -189,7 +189,7 @@ public class ServerMain { try { Thread.sleep(5000); } catch (InterruptedException e) { - e.printStackTrace(); + logger.error(e.getMessage(), e); } } logger.info("Server"+(serverPID==-1? "(s)":" instance "+serverPID)+" stopped!!!"); @@ -265,9 +265,9 @@ public class ServerMain { serverStartedFile.deleteOnExit(); new RandomAccessFile(serverStartedFile,"rw").getChannel().lock(); } catch (FileNotFoundException e) { - e.printStackTrace(); + logger.error(e.getMessage(), e); } catch (IOException e) { - e.printStackTrace(); + logger.error(e.getMessage(), e); } } http://git-wip-us.apache.org/repos/asf/airavata/blob/98c9a34e/modules/workflow-model/workflow-engine/src/main/java/org/apache/airavata/workflow/engine/WorkflowEngineImpl.java ---------------------------------------------------------------------- diff --git a/modules/workflow-model/workflow-engine/src/main/java/org/apache/airavata/workflow/engine/WorkflowEngineImpl.java b/modules/workflow-model/workflow-engine/src/main/java/org/apache/airavata/workflow/engine/WorkflowEngineImpl.java index d53eb75..a8ee98b 100644 --- a/modules/workflow-model/workflow-engine/src/main/java/org/apache/airavata/workflow/engine/WorkflowEngineImpl.java +++ b/modules/workflow-model/workflow-engine/src/main/java/org/apache/airavata/workflow/engine/WorkflowEngineImpl.java @@ -67,11 +67,11 @@ public class WorkflowEngineImpl implements WorkflowEngine { try { workflowInterpreter.scheduleDynamically(); } catch (WorkflowException e) { - e.printStackTrace(); + logger.error(e.getMessage(), e); } catch (RegistryException e) { - e.printStackTrace(); + logger.error(e.getMessage(), e); } catch (AiravataException e) { - e.printStackTrace(); + logger.error(e.getMessage(), e); } }; }.start(); http://git-wip-us.apache.org/repos/asf/airavata/blob/98c9a34e/modules/workflow-model/workflow-engine/src/main/java/org/apache/airavata/workflow/engine/WorkflowUtils.java ---------------------------------------------------------------------- diff --git a/modules/workflow-model/workflow-engine/src/main/java/org/apache/airavata/workflow/engine/WorkflowUtils.java b/modules/workflow-model/workflow-engine/src/main/java/org/apache/airavata/workflow/engine/WorkflowUtils.java index b1d6073..fb2a6fa 100644 --- a/modules/workflow-model/workflow-engine/src/main/java/org/apache/airavata/workflow/engine/WorkflowUtils.java +++ b/modules/workflow-model/workflow-engine/src/main/java/org/apache/airavata/workflow/engine/WorkflowUtils.java @@ -29,9 +29,11 @@ import org.apache.aiaravata.application.catalog.data.impl.AppCatalogFactory; import org.apache.airavata.model.util.ExecutionType; import org.apache.airavata.model.workspace.experiment.Experiment; import org.apache.airavata.workflow.catalog.WorkflowCatalogFactory; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; public class WorkflowUtils { - + private static final Logger logger = LoggerFactory.getLogger(WorkflowUtils.class); public static ExecutionType getExecutionType(Experiment experiment){ try { ApplicationInterface applicationInterface = AppCatalogFactory.getAppCatalog().getApplicationInterface(); @@ -46,7 +48,7 @@ public class WorkflowUtils { } } } catch (AppCatalogException e) { - e.printStackTrace(); + logger.error(e.getMessage(), e); } return ExecutionType.UNKNOWN; } http://git-wip-us.apache.org/repos/asf/airavata/blob/98c9a34e/modules/workflow-model/workflow-engine/src/main/java/org/apache/airavata/workflow/engine/concurrent/PredicatedTaskRunner.java ---------------------------------------------------------------------- diff --git a/modules/workflow-model/workflow-engine/src/main/java/org/apache/airavata/workflow/engine/concurrent/PredicatedTaskRunner.java b/modules/workflow-model/workflow-engine/src/main/java/org/apache/airavata/workflow/engine/concurrent/PredicatedTaskRunner.java index 89557ab..6912113 100644 --- a/modules/workflow-model/workflow-engine/src/main/java/org/apache/airavata/workflow/engine/concurrent/PredicatedTaskRunner.java +++ b/modules/workflow-model/workflow-engine/src/main/java/org/apache/airavata/workflow/engine/concurrent/PredicatedTaskRunner.java @@ -20,6 +20,9 @@ */ package org.apache.airavata.workflow.engine.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 logger = 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(); + logger.error(e.getMessage(), e); } } http://git-wip-us.apache.org/repos/asf/airavata/blob/98c9a34e/modules/workflow-model/workflow-engine/src/main/java/org/apache/airavata/workflow/engine/interpretor/SystemComponentInvoker.java ---------------------------------------------------------------------- diff --git a/modules/workflow-model/workflow-engine/src/main/java/org/apache/airavata/workflow/engine/interpretor/SystemComponentInvoker.java b/modules/workflow-model/workflow-engine/src/main/java/org/apache/airavata/workflow/engine/interpretor/SystemComponentInvoker.java index 44d285d..4b9ef7e 100644 --- a/modules/workflow-model/workflow-engine/src/main/java/org/apache/airavata/workflow/engine/interpretor/SystemComponentInvoker.java +++ b/modules/workflow-model/workflow-engine/src/main/java/org/apache/airavata/workflow/engine/interpretor/SystemComponentInvoker.java @@ -27,11 +27,14 @@ import java.util.Map; import org.apache.airavata.workflow.engine.invoker.Invoker; 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; public class SystemComponentInvoker implements Invoker { + private static final Logger logger = LoggerFactory.getLogger(SystemComponentInvoker.class); private Map<String, Object> outputs = new Hashtable<String, Object>(); /** @@ -54,7 +57,7 @@ public class SystemComponentInvoker implements Invoker { out = this.outputs.get(name); Thread.sleep(200); } catch (InterruptedException e) { - e.printStackTrace(); + logger.error(e.getMessage(), e); } } return out; http://git-wip-us.apache.org/repos/asf/airavata/blob/98c9a34e/modules/workflow-model/workflow-engine/src/main/java/org/apache/airavata/workflow/engine/interpretor/WorkflowInterpreter.java ---------------------------------------------------------------------- diff --git a/modules/workflow-model/workflow-engine/src/main/java/org/apache/airavata/workflow/engine/interpretor/WorkflowInterpreter.java b/modules/workflow-model/workflow-engine/src/main/java/org/apache/airavata/workflow/engine/interpretor/WorkflowInterpreter.java index c236e7d..9b56b73 100644 --- a/modules/workflow-model/workflow-engine/src/main/java/org/apache/airavata/workflow/engine/interpretor/WorkflowInterpreter.java +++ b/modules/workflow-model/workflow-engine/src/main/java/org/apache/airavata/workflow/engine/interpretor/WorkflowInterpreter.java @@ -282,7 +282,7 @@ public class WorkflowInterpreter implements AbstractActivityListener{ try { Thread.sleep(400); } catch (InterruptedException e) { - e.printStackTrace(); + log.error(e.getMessage(), e); } } if (this.getWorkflow().getExecutionState() == WorkflowExecutionState.STOPPED) { @@ -311,13 +311,11 @@ public class WorkflowInterpreter implements AbstractActivityListener{ log.error("Error execution workflow Node : " + node.getID()); return; } catch (TException e) { - // TODO Auto-generated catch block - e.printStackTrace(); + log.error(e.getMessage(), e); } catch (RegistryException e) { - // TODO Auto-generated catch block - e.printStackTrace(); + log.error(e.getMessage(), e); } catch (AiravataException e) { - e.printStackTrace(); + log.error(e.getMessage(), e); } } }; @@ -395,7 +393,7 @@ public class WorkflowInterpreter implements AbstractActivityListener{ try { Thread.sleep(1000); } catch (InterruptedException e) { - e.printStackTrace(); + log.error(e.getMessage(), e); } notifyViaInteractor(WorkflowExecutionMessage.EXECUTION_TASK_END, new WorkflowInterpreterInteractor.TaskNotification("Stop Workflow", "Cleaning up resources for Workflow", uuid.toString())); @@ -579,7 +577,7 @@ public class WorkflowInterpreter implements AbstractActivityListener{ try { getRegistry().update(RegistryModelType.WORKFLOW_NODE_DETAIL, workflowNodeDetails, workflowNodeDetails.getNodeInstanceId()); } catch (RegistryException e) { - e.printStackTrace(); + log.error(e.getMessage(), e); } updateWorkflowNodeStatus(workflowNodeDetails, WorkflowNodeState.COMPLETED); } @@ -850,11 +848,9 @@ public class WorkflowInterpreter implements AbstractActivityListener{ } catch (WorkflowException e) { log.error(e.getLocalizedMessage(), e); } catch (RegistryException e) { - // TODO Auto-generated catch block - e.printStackTrace(); + log.error(e.getMessage(), e); } catch (TException e) { - // TODO Auto-generated catch block - e.printStackTrace(); + log.error(e.getMessage(), e); } } @@ -1078,7 +1074,7 @@ public class WorkflowInterpreter implements AbstractActivityListener{ try { getRegistry().update(RegistryModelType.WORKFLOW_NODE_DETAIL, nodeDetails, nodeDetails.getNodeInstanceId()); } catch (RegistryException e) { - e.printStackTrace(); + log.error(e.getMessage(), e); } } @@ -1096,7 +1092,7 @@ public class WorkflowInterpreter implements AbstractActivityListener{ try { getRegistry().update(RegistryModelType.WORKFLOW_NODE_DETAIL, nodeDetails, nodeDetails.getNodeInstanceId()); } catch (RegistryException e) { - e.printStackTrace(); + log.error(e.getMessage(), e); } } @@ -1492,9 +1488,9 @@ public class WorkflowInterpreter implements AbstractActivityListener{ publishNodeStatusChange(WorkflowNodeState.COMPLETED, node.getID(), experiment.getExperimentID()); updateWorkflowNodeStatus(nodeInstanceList.get(node), state); } catch (RegistryException e) { - e.printStackTrace(); + log.error(e.getMessage(), e); } catch (AiravataException e) { - e.printStackTrace(); + log.error(e.getMessage(), e); } } } @@ -1535,7 +1531,7 @@ public class WorkflowInterpreter implements AbstractActivityListener{ updateWorkflowNodeStatus(nodeInstanceList.get(node), state); } } catch (RegistryException e) { - e.printStackTrace(); + log.error(e.getMessage(), e); } } http://git-wip-us.apache.org/repos/asf/airavata/blob/98c9a34e/modules/workflow-model/workflow-engine/src/main/java/org/apache/airavata/workflow/engine/invoker/DynamicInvoker.java ---------------------------------------------------------------------- diff --git a/modules/workflow-model/workflow-engine/src/main/java/org/apache/airavata/workflow/engine/invoker/DynamicInvoker.java b/modules/workflow-model/workflow-engine/src/main/java/org/apache/airavata/workflow/engine/invoker/DynamicInvoker.java index b9466c4..dac8965 100644 --- a/modules/workflow-model/workflow-engine/src/main/java/org/apache/airavata/workflow/engine/invoker/DynamicInvoker.java +++ b/modules/workflow-model/workflow-engine/src/main/java/org/apache/airavata/workflow/engine/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; @@ -41,6 +43,7 @@ public class DynamicInvoker implements Invoker { private Object[] inputs; private Object result; + private static final Logger log = LoggerFactory.getLogger(DynamicInvoker.class); /** * Constructs a DynamicInvoker. @@ -133,8 +136,7 @@ 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/workflow-model/workflow-engine/src/main/java/org/apache/airavata/workflow/engine/invoker/SimpleInvoker.java ---------------------------------------------------------------------- diff --git a/modules/workflow-model/workflow-engine/src/main/java/org/apache/airavata/workflow/engine/invoker/SimpleInvoker.java b/modules/workflow-model/workflow-engine/src/main/java/org/apache/airavata/workflow/engine/invoker/SimpleInvoker.java index 70be0e9..5c9fd03 100644 --- a/modules/workflow-model/workflow-engine/src/main/java/org/apache/airavata/workflow/engine/invoker/SimpleInvoker.java +++ b/modules/workflow-model/workflow-engine/src/main/java/org/apache/airavata/workflow/engine/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/workflow-model/workflow-engine/src/main/java/org/apache/airavata/workflow/engine/util/XBayaUtil.java ---------------------------------------------------------------------- diff --git a/modules/workflow-model/workflow-engine/src/main/java/org/apache/airavata/workflow/engine/util/XBayaUtil.java b/modules/workflow-model/workflow-engine/src/main/java/org/apache/airavata/workflow/engine/util/XBayaUtil.java index ddee1ec..5921166 100644 --- a/modules/workflow-model/workflow-engine/src/main/java/org/apache/airavata/workflow/engine/util/XBayaUtil.java +++ b/modules/workflow-model/workflow-engine/src/main/java/org/apache/airavata/workflow/engine/util/XBayaUtil.java @@ -76,7 +76,7 @@ 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/modules/workflow-model/workflow-model-core/src/main/java/org/apache/airavata/workflow/model/component/ws/WSComponentApplication.java ---------------------------------------------------------------------- diff --git a/modules/workflow-model/workflow-model-core/src/main/java/org/apache/airavata/workflow/model/component/ws/WSComponentApplication.java b/modules/workflow-model/workflow-model-core/src/main/java/org/apache/airavata/workflow/model/component/ws/WSComponentApplication.java index 0447906..98c9486 100644 --- a/modules/workflow-model/workflow-model-core/src/main/java/org/apache/airavata/workflow/model/component/ws/WSComponentApplication.java +++ b/modules/workflow-model/workflow-model-core/src/main/java/org/apache/airavata/workflow/model/component/ws/WSComponentApplication.java @@ -46,67 +46,69 @@ import org.apache.airavata.model.appcatalog.appinterface.DataType; import org.apache.airavata.model.appcatalog.appinterface.InputDataObjectType; import org.apache.airavata.model.appcatalog.appinterface.OutputDataObjectType; import org.apache.airavata.workflow.model.utils.WorkflowConstants; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; import org.xmlpull.infoset.XmlNamespace; import xsul5.XmlConstants; -@XmlRootElement(name="Application") +@XmlRootElement(name = "Application") @XmlType(propOrder = {"applicationId", "name", "description", "inputParameters", "outputParameters"}) public class WSComponentApplication { - - private String applicationId; - private String name; - private String description; - private List<WSComponentApplicationParameter> inputParameters; - private List<WSComponentApplicationParameter> outputParameters; - - public WSComponentApplication() { - } - - public static void main(String[] args) { - WSComponentApplication app = new WSComponentApplication(); - app.setApplicationId("dsfds"); - app.setName("dfd"); - app.setDescription("sdfdsfds"); - app.addInputParameter(new WSComponentApplicationParameter("asas", DataType.STRING, null, "sdfds", 1)); - app.addOutputParameter(new WSComponentApplicationParameter("9842", DataType.STRING, null, null)); - app.addOutputParameter(new WSComponentApplicationParameter("AAAAA", DataType.STRING, "sdfsdf", "243bs sd fsd fs f dfd")); - ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream(); - try { - JAXBContext context = JAXBContext.newInstance(WSComponentApplication.class); - Marshaller marshaller = context.createMarshaller(); - marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true); // pretty - marshaller.setProperty(Marshaller.JAXB_ENCODING, "ISO-8859-1"); // specify encoding - // output xml to outputstream. - marshaller.marshal(app, byteArrayOutputStream); - org.xmlpull.infoset.XmlElement s = XMLUtil.stringToXmlElement(byteArrayOutputStream.toString()); - System.out.println(s.toString()); - } catch (JAXBException e) { - e.printStackTrace(); - } - try { - JAXBContext context = JAXBContext.newInstance(WSComponentApplication.class); - Unmarshaller unmarshaller = context.createUnmarshaller(); - // parse xml. - WSComponentApplication d = (WSComponentApplication)unmarshaller.unmarshal(new ByteArrayInputStream(byteArrayOutputStream.toByteArray())); - System.out.println(d.getApplicationId()); - } catch (JAXBException e) { - e.printStackTrace(); - } - } - - public static WSComponentApplication parse(org.xmlpull.infoset.XmlElement element) { - String xmlString = XMLUtil.xmlElementToString(element); - try { - JAXBContext context = JAXBContext.newInstance(WSComponentApplication.class); - Unmarshaller unmarshaller = context.createUnmarshaller(); - return (WSComponentApplication) unmarshaller.unmarshal(new ByteArrayInputStream(xmlString.getBytes())); - } catch (JAXBException e) { - e.printStackTrace(); - return null; - } - - } + private static final Logger log = LoggerFactory.getLogger(WSComponentApplication.class); + private String applicationId; + private String name; + private String description; + private List<WSComponentApplicationParameter> inputParameters; + private List<WSComponentApplicationParameter> outputParameters; + + public WSComponentApplication() { + } + + public static void main(String[] args) { + WSComponentApplication app = new WSComponentApplication(); + app.setApplicationId("dsfds"); + app.setName("dfd"); + app.setDescription("sdfdsfds"); + app.addInputParameter(new WSComponentApplicationParameter("asas", DataType.STRING, null, "sdfds", 1)); + app.addOutputParameter(new WSComponentApplicationParameter("9842", DataType.STRING, null, null)); + app.addOutputParameter(new WSComponentApplicationParameter("AAAAA", DataType.STRING, "sdfsdf", "243bs sd fsd fs f dfd")); + ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream(); + try { + JAXBContext context = JAXBContext.newInstance(WSComponentApplication.class); + Marshaller marshaller = context.createMarshaller(); + marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true); // pretty + marshaller.setProperty(Marshaller.JAXB_ENCODING, "ISO-8859-1"); // specify encoding + // output xml to outputstream. + marshaller.marshal(app, byteArrayOutputStream); + org.xmlpull.infoset.XmlElement s = XMLUtil.stringToXmlElement(byteArrayOutputStream.toString()); + System.out.println(s.toString()); + } catch (JAXBException e) { + log.error(e.getMessage(), e); + } + try { + JAXBContext context = JAXBContext.newInstance(WSComponentApplication.class); + Unmarshaller unmarshaller = context.createUnmarshaller(); + // parse xml. + WSComponentApplication d = (WSComponentApplication) unmarshaller.unmarshal(new ByteArrayInputStream(byteArrayOutputStream.toByteArray())); + System.out.println(d.getApplicationId()); + } catch (JAXBException e) { + log.error(e.getMessage(), e); + } + } + + public static WSComponentApplication parse(org.xmlpull.infoset.XmlElement element) { + String xmlString = XMLUtil.xmlElementToString(element); + try { + JAXBContext context = JAXBContext.newInstance(WSComponentApplication.class); + Unmarshaller unmarshaller = context.createUnmarshaller(); + return (WSComponentApplication) unmarshaller.unmarshal(new ByteArrayInputStream(xmlString.getBytes())); + } catch (JAXBException e) { + log.error(e.getMessage(), e); + return null; + } + + } public static WSComponentApplication parse(JsonObject applicationObject) { WSComponentApplication wsComponentApplication = new WSComponentApplication(); @@ -115,25 +117,25 @@ public class WSComponentApplication { wsComponentApplication.applicationId = applicationObject.getAsJsonPrimitive(WorkflowConstants.APPLICATION_COMPONENT_APPLICATION).getAsString(); if (applicationObject.get(WorkflowConstants.APPLICATION_INPUT) != null) { - JsonArray inputArray = applicationObject.getAsJsonArray(WorkflowConstants.APPLICATION_INPUT); - WSComponentApplicationParameter inputParameter; - JsonObject inputObject; - for (JsonElement jsonElement : inputArray) { - if (jsonElement instanceof JsonObject) { - inputObject = (JsonObject) jsonElement; - inputParameter = new WSComponentApplicationParameter(); - inputParameter.setDefaultValue(inputObject.getAsJsonPrimitive(WorkflowConstants.APPLICATION_DATA_DEFAULT_VALUE).getAsString()); - inputParameter.setDescription(inputObject.getAsJsonPrimitive(WorkflowConstants.APPLICATION_DATA_DESCRIPTION).getAsString()); - inputParameter.setName(inputObject.getAsJsonPrimitive(WorkflowConstants.APPLICATION_DATA_NAME).getAsString()); - inputParameter.setType(DataType.valueOf(inputObject.getAsJsonPrimitive(WorkflowConstants.APPLICATION_DATA_DATA_TYPE).getAsString())); - inputParameter.setInputOrder(inputObject.getAsJsonPrimitive(WorkflowConstants.APPLICATION_DATA_INPUT_ORDER).getAsInt()); - if (inputObject.getAsJsonPrimitive(WorkflowConstants.APPLICATION_DATA_APP_ARGUMENT) != null) { - inputParameter.setApplicationArgument(inputObject.getAsJsonPrimitive(WorkflowConstants.APPLICATION_DATA_APP_ARGUMENT).getAsString()); - } - wsComponentApplication.addInputParameter(inputParameter); - } - } - } + JsonArray inputArray = applicationObject.getAsJsonArray(WorkflowConstants.APPLICATION_INPUT); + WSComponentApplicationParameter inputParameter; + JsonObject inputObject; + for (JsonElement jsonElement : inputArray) { + if (jsonElement instanceof JsonObject) { + inputObject = (JsonObject) jsonElement; + inputParameter = new WSComponentApplicationParameter(); + inputParameter.setDefaultValue(inputObject.getAsJsonPrimitive(WorkflowConstants.APPLICATION_DATA_DEFAULT_VALUE).getAsString()); + inputParameter.setDescription(inputObject.getAsJsonPrimitive(WorkflowConstants.APPLICATION_DATA_DESCRIPTION).getAsString()); + inputParameter.setName(inputObject.getAsJsonPrimitive(WorkflowConstants.APPLICATION_DATA_NAME).getAsString()); + inputParameter.setType(DataType.valueOf(inputObject.getAsJsonPrimitive(WorkflowConstants.APPLICATION_DATA_DATA_TYPE).getAsString())); + inputParameter.setInputOrder(inputObject.getAsJsonPrimitive(WorkflowConstants.APPLICATION_DATA_INPUT_ORDER).getAsInt()); + if (inputObject.getAsJsonPrimitive(WorkflowConstants.APPLICATION_DATA_APP_ARGUMENT) != null) { + inputParameter.setApplicationArgument(inputObject.getAsJsonPrimitive(WorkflowConstants.APPLICATION_DATA_APP_ARGUMENT).getAsString()); + } + wsComponentApplication.addInputParameter(inputParameter); + } + } + } if (applicationObject.get(WorkflowConstants.APPLICATION_OUTPUT) != null) { JsonArray outputArray = applicationObject.getAsJsonArray(WorkflowConstants.APPLICATION_OUTPUT); @@ -154,27 +156,27 @@ public class WSComponentApplication { return wsComponentApplication; } - public org.xmlpull.infoset.XmlElement toXml(){ - try { - JAXBContext context = JAXBContext.newInstance(WSComponentApplication.class); - Marshaller marshaller = context.createMarshaller(); - marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true); // pretty - marshaller.setProperty(Marshaller.JAXB_ENCODING, "ISO-8859-1"); // specify encoding - // output xml to outputstream. - ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream(); - marshaller.marshal(this, byteArrayOutputStream); - return XMLUtil.stringToXmlElement(byteArrayOutputStream.toString()); - } catch (Exception e) { - e.printStackTrace(); - return null; - } - } + public org.xmlpull.infoset.XmlElement toXml() { + try { + JAXBContext context = JAXBContext.newInstance(WSComponentApplication.class); + Marshaller marshaller = context.createMarshaller(); + marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true); // pretty + marshaller.setProperty(Marshaller.JAXB_ENCODING, "ISO-8859-1"); // specify encoding + // output xml to outputstream. + ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream(); + marshaller.marshal(this, byteArrayOutputStream); + return XMLUtil.stringToXmlElement(byteArrayOutputStream.toString()); + } catch (Exception e) { + log.error(e.getMessage(), e); + return null; + } + } public JsonObject toJSON() { JsonObject componentObject = new JsonObject(); componentObject.addProperty(WorkflowConstants.APPLICATION_COMPONENT_DESCRIPTION, this.description); - componentObject.addProperty(WorkflowConstants.APPLICATION_COMPONENT_NAME, this.name); - componentObject.addProperty(WorkflowConstants.APPLICATION_COMPONENT_APPLICATION, this.applicationId); + componentObject.addProperty(WorkflowConstants.APPLICATION_COMPONENT_NAME, this.name); + componentObject.addProperty(WorkflowConstants.APPLICATION_COMPONENT_APPLICATION, this.applicationId); JsonArray inputArray = new JsonArray(); JsonObject inputObject; for (WSComponentApplicationParameter inputParameter : this.inputParameters) { @@ -182,12 +184,12 @@ public class WSComponentApplication { inputObject.addProperty(WorkflowConstants.APPLICATION_DATA_DESCRIPTION, inputParameter.getDescription()); inputObject.addProperty(WorkflowConstants.APPLICATION_DATA_NAME, inputParameter.getName()); inputObject.addProperty(WorkflowConstants.APPLICATION_DATA_DEFAULT_VALUE, inputParameter.getDefaultValue()); - inputObject.addProperty(WorkflowConstants.APPLICATION_DATA_DATA_TYPE, inputParameter.getType().toString()); - inputObject.addProperty(WorkflowConstants.APPLICATION_DATA_INPUT_ORDER, inputParameter.getInputOrder()); - if (inputParameter.getApplicationArgument() != null) { - inputObject.addProperty(WorkflowConstants.APPLICATION_DATA_APP_ARGUMENT, inputParameter.getApplicationArgument()); - } - inputArray.add(inputObject); + inputObject.addProperty(WorkflowConstants.APPLICATION_DATA_DATA_TYPE, inputParameter.getType().toString()); + inputObject.addProperty(WorkflowConstants.APPLICATION_DATA_INPUT_ORDER, inputParameter.getInputOrder()); + if (inputParameter.getApplicationArgument() != null) { + inputObject.addProperty(WorkflowConstants.APPLICATION_DATA_APP_ARGUMENT, inputParameter.getApplicationArgument()); + } + inputArray.add(inputObject); } componentObject.add(WorkflowConstants.APPLICATION_INPUT, inputArray); @@ -195,90 +197,94 @@ public class WSComponentApplication { JsonObject outputObject; for (WSComponentApplicationParameter outputParameter : this.outputParameters) { outputObject = new JsonObject(); - outputObject.addProperty(WorkflowConstants.APPLICATION_DATA_DESCRIPTION, outputParameter.getDescription()); - outputObject.addProperty(WorkflowConstants.APPLICATION_DATA_NAME, outputParameter.getName()); - outputObject.addProperty(WorkflowConstants.APPLICATION_DATA_DATA_TYPE, outputParameter.getType().toString()); - outputArray.add(outputObject); + outputObject.addProperty(WorkflowConstants.APPLICATION_DATA_DESCRIPTION, outputParameter.getDescription()); + outputObject.addProperty(WorkflowConstants.APPLICATION_DATA_NAME, outputParameter.getName()); + outputObject.addProperty(WorkflowConstants.APPLICATION_DATA_DATA_TYPE, outputParameter.getType().toString()); + outputArray.add(outputObject); } - componentObject.add(WorkflowConstants.APPLICATION_OUTPUT, outputArray); + componentObject.add(WorkflowConstants.APPLICATION_OUTPUT, outputArray); return componentObject; } public WSComponentApplication(ApplicationInterfaceDescription application) { - setApplicationId(application.getApplicationInterfaceId()); - setName(application.getApplicationName()); - setDescription(application.getApplicationDescription()); - + setApplicationId(application.getApplicationInterfaceId()); + setName(application.getApplicationName()); + setDescription(application.getApplicationDescription()); + List<InputDataObjectType> applicationInputs = application.getApplicationInputs(); for (InputDataObjectType inputDataObjectType : applicationInputs) { - addInputParameter(new WSComponentApplicationParameter(inputDataObjectType.getName(), inputDataObjectType.getType(), - inputDataObjectType.getUserFriendlyDescription(), inputDataObjectType.getValue(), - inputDataObjectType.getApplicationArgument(), inputDataObjectType.getInputOrder())); - } + addInputParameter(new WSComponentApplicationParameter(inputDataObjectType.getName(), inputDataObjectType.getType(), + inputDataObjectType.getUserFriendlyDescription(), inputDataObjectType.getValue(), + inputDataObjectType.getApplicationArgument(), inputDataObjectType.getInputOrder())); + } List<OutputDataObjectType> applicationOutputs = application.getApplicationOutputs(); for (OutputDataObjectType outputDataObjectType : applicationOutputs) { - addOutputParameter(new WSComponentApplicationParameter(outputDataObjectType.getName(), - outputDataObjectType.getType() ,outputDataObjectType.getName(), outputDataObjectType.getValue())); - } - } - - @XmlAttribute (required = true, name = "application") - public String getApplicationId() { - return applicationId; - } - public void setApplicationId(String applicationId) { - this.applicationId = applicationId; - } - @XmlAttribute (required = true) - public String getName() { - return name; - } - public void setName(String name) { - this.name = name; - } - -// @XmlElementWrapper(name = "Input") - @XmlElement(name = "Input") - public List<WSComponentApplicationParameter> getInputParameters() { - return inputParameters; - } - - public void setInputParameters( - List<WSComponentApplicationParameter> inputParameters) { - this.inputParameters = inputParameters; - } - - @XmlElement(name = "Output") - public List<WSComponentApplicationParameter> getOutputParameters() { - return outputParameters; - } - public void setOutputParameters( - List<WSComponentApplicationParameter> outputParameters) { - this.outputParameters = outputParameters; - } - - public void addInputParameter(WSComponentApplicationParameter inputParameter){ - if (inputParameters==null){ - inputParameters = new ArrayList<WSComponentApplicationParameter>(); - } - inputParameters.add(inputParameter); - } - - public void addOutputParameter(WSComponentApplicationParameter outputParameter){ - if (outputParameters==null){ - outputParameters = new ArrayList<WSComponentApplicationParameter>(); - } - outputParameters.add(outputParameter); - } - - @XmlAttribute (required = false) - public String getDescription() { - return description; - } - - public void setDescription(String description) { - this.description = description; - } + addOutputParameter(new WSComponentApplicationParameter(outputDataObjectType.getName(), + outputDataObjectType.getType(), outputDataObjectType.getName(), outputDataObjectType.getValue())); + } + } + + @XmlAttribute(required = true, name = "application") + public String getApplicationId() { + return applicationId; + } + + public void setApplicationId(String applicationId) { + this.applicationId = applicationId; + } + + @XmlAttribute(required = true) + public String getName() { + return name; + } + + public void setName(String name) { + this.name = name; + } + + // @XmlElementWrapper(name = "Input") + @XmlElement(name = "Input") + public List<WSComponentApplicationParameter> getInputParameters() { + return inputParameters; + } + + public void setInputParameters( + List<WSComponentApplicationParameter> inputParameters) { + this.inputParameters = inputParameters; + } + + @XmlElement(name = "Output") + public List<WSComponentApplicationParameter> getOutputParameters() { + return outputParameters; + } + + public void setOutputParameters( + List<WSComponentApplicationParameter> outputParameters) { + this.outputParameters = outputParameters; + } + + public void addInputParameter(WSComponentApplicationParameter inputParameter) { + if (inputParameters == null) { + inputParameters = new ArrayList<WSComponentApplicationParameter>(); + } + inputParameters.add(inputParameter); + } + + public void addOutputParameter(WSComponentApplicationParameter outputParameter) { + if (outputParameters == null) { + outputParameters = new ArrayList<WSComponentApplicationParameter>(); + } + outputParameters.add(outputParameter); + } + + @XmlAttribute(required = false) + public String getDescription() { + return description; + } + + public void setDescription(String description) { + this.description = description; + } } http://git-wip-us.apache.org/repos/asf/airavata/blob/98c9a34e/modules/workflow-model/workflow-model-core/src/main/java/org/apache/airavata/workflow/model/component/ws/WSComponentRegistry.java ---------------------------------------------------------------------- diff --git a/modules/workflow-model/workflow-model-core/src/main/java/org/apache/airavata/workflow/model/component/ws/WSComponentRegistry.java b/modules/workflow-model/workflow-model-core/src/main/java/org/apache/airavata/workflow/model/component/ws/WSComponentRegistry.java index e9d4efd..976a777 100644 --- a/modules/workflow-model/workflow-model-core/src/main/java/org/apache/airavata/workflow/model/component/ws/WSComponentRegistry.java +++ b/modules/workflow-model/workflow-model-core/src/main/java/org/apache/airavata/workflow/model/component/ws/WSComponentRegistry.java @@ -36,6 +36,8 @@ import org.apache.airavata.workflow.model.component.ComponentRegistryException; import org.apache.airavata.workflow.model.component.system.SubWorkflowComponent; import org.apache.airavata.workflow.model.component.url.URLComponentReference; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; import xsul.wsdl.WsdlDefinitions; import xsul.wsdl.WsdlException; import xsul.wsdl.WsdlResolver; @@ -47,6 +49,7 @@ public class WSComponentRegistry extends ComponentRegistry { private Map<String, Component> componentMap; private ComponentReference treeLeaf; + private static final Logger log = LoggerFactory.getLogger(WSComponentRegistry.class); /** * Create a WSComponentRegistry @@ -73,9 +76,9 @@ public class WSComponentRegistry extends ComponentRegistry { // } catch (ComponentException e) { // e.printStackTrace(); } catch (WsdlException e) { - e.printStackTrace(); + log.error(e.getMessage(), e); } catch (URISyntaxException e) { - e.printStackTrace(); + log.error(e.getMessage(), e); } } http://git-wip-us.apache.org/repos/asf/airavata/blob/98c9a34e/modules/workflow-model/workflow-model-core/src/main/java/org/apache/airavata/workflow/model/gpel/script/WorkflowWSDL.java ---------------------------------------------------------------------- diff --git a/modules/workflow-model/workflow-model-core/src/main/java/org/apache/airavata/workflow/model/gpel/script/WorkflowWSDL.java b/modules/workflow-model/workflow-model-core/src/main/java/org/apache/airavata/workflow/model/gpel/script/WorkflowWSDL.java index d4dcac8..42ba184 100644 --- a/modules/workflow-model/workflow-model-core/src/main/java/org/apache/airavata/workflow/model/gpel/script/WorkflowWSDL.java +++ b/modules/workflow-model/workflow-model-core/src/main/java/org/apache/airavata/workflow/model/gpel/script/WorkflowWSDL.java @@ -45,6 +45,8 @@ import org.apache.airavata.workflow.model.graph.ws.WSGraph; import org.apache.airavata.workflow.model.utils.WorkflowConstants; import org.apache.airavata.workflow.model.utils.ApplicationVersion; import org.apache.airavata.workflow.model.wf.Workflow; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; import org.xmlpull.infoset.XmlComment; import org.xmlpull.infoset.XmlElement; import org.xmlpull.infoset.XmlNamespace; @@ -120,6 +122,7 @@ public class WorkflowWSDL { private QName portTypeQName; private Map<QName, PartnerLinkRole> partnerLinkRoleMap; + private static final Logger log = LoggerFactory.getLogger(WorkflowWSDL.class); /** * Constructs a WorkflowWsdl. @@ -332,7 +335,7 @@ public class WorkflowWSDL { try { annotation.addElement(XMLUtil.deepClone(appinfo)); } catch (UtilsException e) { - e.printStackTrace(); + log.error(e.getMessage(), e); } } @@ -375,7 +378,7 @@ public class WorkflowWSDL { try { annotation.addElement(XMLUtil.deepClone(appinfo)); } catch (UtilsException e) { - e.printStackTrace(); + log.error(e.getMessage(), e); } } @@ -394,7 +397,7 @@ public class WorkflowWSDL { try { valueElement = XMLUtil.deepClone((XmlElement) value); } catch (UtilsException e) { - e.printStackTrace(); + log.error(e.getMessage(), e); } XmlElement annotation = element.element(null, WSConstants.ANNOTATION_TAG, true); XmlElement defaultElement = annotation.addElement(WSComponentPort.DEFAULT); @@ -519,7 +522,7 @@ public class WorkflowWSDL { return new QName(paramType.getNamespaceURI(), paramType.getLocalPart(), namespace.getPrefix()); } } catch (UtilsException e) { - e.printStackTrace(); + log.error(e.getMessage(), e); } return null; } http://git-wip-us.apache.org/repos/asf/airavata/blob/98c9a34e/modules/workflow-model/workflow-model-core/src/main/java/org/apache/airavata/workflow/model/graph/impl/NodeImpl.java ---------------------------------------------------------------------- diff --git a/modules/workflow-model/workflow-model-core/src/main/java/org/apache/airavata/workflow/model/graph/impl/NodeImpl.java b/modules/workflow-model/workflow-model-core/src/main/java/org/apache/airavata/workflow/model/graph/impl/NodeImpl.java index 6c5fd75..f709fc7 100644 --- a/modules/workflow-model/workflow-model-core/src/main/java/org/apache/airavata/workflow/model/graph/impl/NodeImpl.java +++ b/modules/workflow-model/workflow-model-core/src/main/java/org/apache/airavata/workflow/model/graph/impl/NodeImpl.java @@ -815,7 +815,7 @@ public abstract class NodeImpl implements Node { try { o.nodeUpdated(type); } catch (Exception e) { - e.printStackTrace(); + logger.error(e.getMessage(), e); } } } http://git-wip-us.apache.org/repos/asf/airavata/blob/98c9a34e/modules/workflow-model/workflow-model-core/src/main/java/org/apache/airavata/workflow/model/graph/system/ParameterNode.java ---------------------------------------------------------------------- diff --git a/modules/workflow-model/workflow-model-core/src/main/java/org/apache/airavata/workflow/model/graph/system/ParameterNode.java b/modules/workflow-model/workflow-model-core/src/main/java/org/apache/airavata/workflow/model/graph/system/ParameterNode.java index 42aaabb..b819e4f 100644 --- a/modules/workflow-model/workflow-model-core/src/main/java/org/apache/airavata/workflow/model/graph/system/ParameterNode.java +++ b/modules/workflow-model/workflow-model-core/src/main/java/org/apache/airavata/workflow/model/graph/system/ParameterNode.java @@ -37,6 +37,8 @@ import org.apache.airavata.workflow.model.graph.Graph; import org.apache.airavata.workflow.model.graph.GraphException; import org.apache.airavata.workflow.model.graph.GraphSchema; import org.apache.airavata.workflow.model.graph.Port; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; import org.xmlpull.infoset.XmlElement; import org.xmlpull.infoset.XmlNamespace; @@ -52,6 +54,8 @@ abstract public class ParameterNode extends SystemNode { private boolean configured; + private static final Logger log = LoggerFactory.getLogger(ParameterNode.class); + /** * Type of the parameter (e.g. xsd:string, xsd:int) */ @@ -166,7 +170,7 @@ abstract public class ParameterNode extends SystemNode { try { this.metadata = XMLUtil.deepClone(metadata); } catch (UtilsException e) { - e.printStackTrace(); + log.error(e.getMessage(), e); } // Reformat @@ -328,7 +332,7 @@ abstract public class ParameterNode extends SystemNode { try { metadataElement.addChild(XMLUtil.deepClone(this.metadata)); } catch (UtilsException e) { - e.printStackTrace(); + log.error(e.getMessage(), e); } } http://git-wip-us.apache.org/repos/asf/airavata/blob/98c9a34e/modules/workflow-model/workflow-model-core/src/main/java/org/apache/airavata/workflow/model/graph/ws/WSNode.java ---------------------------------------------------------------------- diff --git a/modules/workflow-model/workflow-model-core/src/main/java/org/apache/airavata/workflow/model/graph/ws/WSNode.java b/modules/workflow-model/workflow-model-core/src/main/java/org/apache/airavata/workflow/model/graph/ws/WSNode.java index 3894a0e..372ac4f 100644 --- a/modules/workflow-model/workflow-model-core/src/main/java/org/apache/airavata/workflow/model/graph/ws/WSNode.java +++ b/modules/workflow-model/workflow-model-core/src/main/java/org/apache/airavata/workflow/model/graph/ws/WSNode.java @@ -34,6 +34,8 @@ import org.apache.airavata.workflow.model.graph.GraphException; import org.apache.airavata.workflow.model.graph.GraphSchema; import org.apache.airavata.workflow.model.graph.impl.NodeImpl; import org.apache.airavata.workflow.model.graph.util.GraphUtil; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; import org.xmlpull.infoset.XmlElement; public class WSNode extends NodeImpl implements ForEachExecutableNode{ @@ -44,6 +46,7 @@ public class WSNode extends NodeImpl implements ForEachExecutableNode{ protected String operationName; + private static final Logger log = LoggerFactory.getLogger(WSNode.class); /** * Constructs a WsdlNode. * @@ -159,7 +162,7 @@ public class WSNode extends NodeImpl implements ForEachExecutableNode{ try { setComponent(new WSComponent(application)); } catch (ComponentException e) { - e.printStackTrace(); + log.error(e.getMessage(), e); } // XmlElement wsdlElement = nodeElement.element(null, GraphSchema.NODE_WSDL_QNAME_TAG); // if (wsdlElement != null) { @@ -187,7 +190,7 @@ public class WSNode extends NodeImpl implements ForEachExecutableNode{ try { setComponent(new WSComponent(application)); } catch (ComponentException e) { - e.printStackTrace(); + log.error(e.getMessage(), e); } } http://git-wip-us.apache.org/repos/asf/airavata/blob/98c9a34e/modules/workflow-model/workflow-model-core/src/main/java/org/apache/airavata/workflow/model/ode/ODEWSDLTransformer.java ---------------------------------------------------------------------- diff --git a/modules/workflow-model/workflow-model-core/src/main/java/org/apache/airavata/workflow/model/ode/ODEWSDLTransformer.java b/modules/workflow-model/workflow-model-core/src/main/java/org/apache/airavata/workflow/model/ode/ODEWSDLTransformer.java index 6daf51d..5998950 100644 --- a/modules/workflow-model/workflow-model-core/src/main/java/org/apache/airavata/workflow/model/ode/ODEWSDLTransformer.java +++ b/modules/workflow-model/workflow-model-core/src/main/java/org/apache/airavata/workflow/model/ode/ODEWSDLTransformer.java @@ -35,6 +35,8 @@ import org.apache.airavata.common.utils.WSDLUtil; import org.apache.airavata.workflow.model.exceptions.WorkflowRuntimeException; import org.apache.airavata.workflow.model.gpel.DSCUtil; import org.apache.airavata.workflow.model.utils.WorkflowConstants; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; import org.xmlpull.infoset.XmlBuilderException; import org.xmlpull.infoset.XmlInfosetBuilder; import org.xmlpull.infoset.XmlNamespace; @@ -51,6 +53,7 @@ import xsul5.wsdl.WsdlService; public class ODEWSDLTransformer { + private static final Logger log = LoggerFactory.getLogger(ODEWSDLTransformer.class); /** * SCHEMA_LOCATION_URI */ @@ -332,8 +335,7 @@ public class ODEWSDLTransformer { } } } catch (XmlBuilderException 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/ws-messenger/commons/src/main/java/org/apache/airavata/wsmg/commons/config/ConfigurationManager.java ---------------------------------------------------------------------- diff --git a/modules/ws-messenger/commons/src/main/java/org/apache/airavata/wsmg/commons/config/ConfigurationManager.java b/modules/ws-messenger/commons/src/main/java/org/apache/airavata/wsmg/commons/config/ConfigurationManager.java index 0df388d..004a98c 100644 --- a/modules/ws-messenger/commons/src/main/java/org/apache/airavata/wsmg/commons/config/ConfigurationManager.java +++ b/modules/ws-messenger/commons/src/main/java/org/apache/airavata/wsmg/commons/config/ConfigurationManager.java @@ -24,9 +24,11 @@ package org.apache.airavata.wsmg.commons.config; import org.apache.airavata.common.exception.ApplicationSettingsException; import org.apache.airavata.common.utils.ServerSettings; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; public class ConfigurationManager { - + protected static final Logger logger = LoggerFactory.getLogger(ConfigurationManager.class); // protected Properties configurations = new Properties(); // public ConfigurationManager(String configFileName) { @@ -37,12 +39,12 @@ public class ConfigurationManager { // } // } - public String getConfig(String configName) { + public String getConfig(String configName) throws Exception { try { return ServerSettings.getSetting(configName); } catch (ApplicationSettingsException e) { - e.printStackTrace(); - return null; + logger.error(e.getMessage(), e); + throw new Exception(e.getMessage(), e); } } http://git-wip-us.apache.org/repos/asf/airavata/blob/98c9a34e/modules/ws-messenger/commons/src/main/java/org/apache/airavata/wsmg/commons/storage/JdbcStorage.java ---------------------------------------------------------------------- diff --git a/modules/ws-messenger/commons/src/main/java/org/apache/airavata/wsmg/commons/storage/JdbcStorage.java b/modules/ws-messenger/commons/src/main/java/org/apache/airavata/wsmg/commons/storage/JdbcStorage.java index c24ed19..03c4a0a 100644 --- a/modules/ws-messenger/commons/src/main/java/org/apache/airavata/wsmg/commons/storage/JdbcStorage.java +++ b/modules/ws-messenger/commons/src/main/java/org/apache/airavata/wsmg/commons/storage/JdbcStorage.java @@ -92,14 +92,14 @@ public class JdbcStorage { closeConnection(conn); } - public Connection connect() { + public Connection connect() throws SQLException{ Connection conn = null; try { conn = connectionPool.getConnection(); } catch (SQLException e) { - e.printStackTrace(); log.error(e.getMessage(), e); + throw new SQLException(e); } return conn; } http://git-wip-us.apache.org/repos/asf/airavata/blob/98c9a34e/modules/ws-messenger/message-monitor/src/main/java/org/apache/airavata/ws/monitor/EventDataRepository.java ---------------------------------------------------------------------- diff --git a/modules/ws-messenger/message-monitor/src/main/java/org/apache/airavata/ws/monitor/EventDataRepository.java b/modules/ws-messenger/message-monitor/src/main/java/org/apache/airavata/ws/monitor/EventDataRepository.java index 7390967..1c20cf8 100644 --- a/modules/ws-messenger/message-monitor/src/main/java/org/apache/airavata/ws/monitor/EventDataRepository.java +++ b/modules/ws-messenger/message-monitor/src/main/java/org/apache/airavata/ws/monitor/EventDataRepository.java @@ -111,13 +111,13 @@ public class EventDataRepository implements TableModel, BoundedRangeModel { this.tableModelChangeEvent = new ChangeEvent(this); // We only need one. this.events = new ArrayList<EventData>(); } - public void addEvent(XmlElement message) { + public void addEvent(XmlElement message) throws Exception { addEvent(new EventData(message)); } /** - * @param message + * @param event */ - public void addEvent(EventData event) { + public void addEvent(EventData event) throws Exception { // no need the check for not null because second clause is evaluated only if // not null if (this.filter == null || this.filter.isAcceptable(event)) { @@ -143,50 +143,50 @@ public class EventDataRepository implements TableModel, BoundedRangeModel { } } - public void triggerListenerForPreMonitorStart() { + public void triggerListenerForPreMonitorStart() throws Exception { for (EventDataListener listener : getMonitorEventListerners()) { try { listener.monitoringPreStart(); } catch (Exception e) { - //just in case - e.printStackTrace(); + logger.error(e.getMessage(), e); + throw new Exception(e.getMessage(), e); } } } - public void triggerListenerForPostMonitorStart() { + public void triggerListenerForPostMonitorStart() throws Exception{ for (EventDataListener listener : getMonitorEventListerners()) { try { listener.monitoringPostStart(); } catch (Exception e) { - //just in case - e.printStackTrace(); + logger.error(e.getMessage(), e); + throw new Exception(e.getMessage(), e); } } } - public void triggerListenerForPreMonitorStop() { + public void triggerListenerForPreMonitorStop() throws Exception { for (EventDataListener listener : getMonitorEventListerners()) { try { listener.monitoringPreStop(); } catch (Exception e) { - //just in case - e.printStackTrace(); + logger.error(e.getMessage(), e); + throw new Exception(e.getMessage(), e); } } } - public void triggerListenerForPostMonitorStop() { + public void triggerListenerForPostMonitorStop() throws Exception { for (EventDataListener listener : getMonitorEventListerners()) { try { listener.monitoringPostStop(); } catch (Exception e) { - //just in case - e.printStackTrace(); + logger.error(e.getMessage(), e); + throw new Exception(e.getMessage(), e); } } } - private void triggerListenerForMonitorEvent(EventData event) { + private void triggerListenerForMonitorEvent(EventData event) throws Exception{ for (EventDataListener listener : getMonitorEventListerners()) { try { listener.notify(this, event); @@ -196,8 +196,8 @@ public class EventDataRepository implements TableModel, BoundedRangeModel { listener.onFail(event); } } catch (Exception e) { - //just in case - e.printStackTrace(); + logger.error(e.getMessage(), e); + throw new Exception(e.getMessage(), e); } } } http://git-wip-us.apache.org/repos/asf/airavata/blob/98c9a34e/modules/ws-messenger/message-monitor/src/main/java/org/apache/airavata/ws/monitor/Monitor.java ---------------------------------------------------------------------- diff --git a/modules/ws-messenger/message-monitor/src/main/java/org/apache/airavata/ws/monitor/Monitor.java b/modules/ws-messenger/message-monitor/src/main/java/org/apache/airavata/ws/monitor/Monitor.java index 72fdc81..0666bd1 100644 --- a/modules/ws-messenger/message-monitor/src/main/java/org/apache/airavata/ws/monitor/Monitor.java +++ b/modules/ws-messenger/message-monitor/src/main/java/org/apache/airavata/ws/monitor/Monitor.java @@ -94,7 +94,7 @@ public class Monitor extends EventProducer { /** * @throws MonitorException */ - public synchronized void start() throws MonitorException { + public synchronized void start() throws Exception { //Make sure currently we are not doing any monitoring stop(); @@ -139,7 +139,10 @@ public class Monitor extends EventProducer { this.wsmgClient = null; getEventDataRepository().triggerListenerForPostMonitorStop(); } - } finally{ + } catch (Exception e) { + logger.error(e.getMessage(), e); + throw new MonitorException(e.getMessage(), e); + } finally{ monitoringCompleted=true; } } @@ -153,8 +156,8 @@ public class Monitor extends EventProducer { public void run() { try { Monitor.this.start(); - } catch (MonitorException e) { - e.printStackTrace(); + } catch (Exception e) { + logger.error(e.getMessage(), e); } } }.start(); @@ -212,7 +215,11 @@ public class Monitor extends EventProducer { System.out.println(XMLUtil.xmlElementToString(event)); } for (String key : keys) { - this.eventDataMap.get(key).addEvent(eventData); + try { + this.eventDataMap.get(key).addEvent(eventData); + } catch (Exception e) { + logger.error(e.getMessage(), e); + } } } @@ -246,12 +253,13 @@ public class Monitor extends EventProducer { /** * Wait until the monitoring is completed */ - public void waitForCompletion(){ + public void waitForCompletion() throws Exception { while(!monitoringCompleted && !monitoringFailed){ try { Thread.sleep(100); } catch (InterruptedException e) { - e.printStackTrace(); + logger.error(e.getMessage(), e); + throw new Exception(e.getMessage(), e); } } } http://git-wip-us.apache.org/repos/asf/airavata/blob/98c9a34e/modules/ws-messenger/messagebox/src/main/java/org/apache/airavata/wsmg/msgbox/MsgBoxServiceLifeCycle.java ---------------------------------------------------------------------- diff --git a/modules/ws-messenger/messagebox/src/main/java/org/apache/airavata/wsmg/msgbox/MsgBoxServiceLifeCycle.java b/modules/ws-messenger/messagebox/src/main/java/org/apache/airavata/wsmg/msgbox/MsgBoxServiceLifeCycle.java index f0a62b4..0876ae9 100644 --- a/modules/ws-messenger/messagebox/src/main/java/org/apache/airavata/wsmg/msgbox/MsgBoxServiceLifeCycle.java +++ b/modules/ws-messenger/messagebox/src/main/java/org/apache/airavata/wsmg/msgbox/MsgBoxServiceLifeCycle.java @@ -72,7 +72,7 @@ public class MsgBoxServiceLifeCycle implements ServiceLifeCycle { try { registry.getAiravataManager().unsetMessageBoxURI(); } catch (AiravataAPIInvocationException e) { - e.printStackTrace(); + logger.error(e.getMessage(), e); } thread.interrupt(); try { http://git-wip-us.apache.org/repos/asf/airavata/blob/98c9a34e/modules/ws-messenger/messagebox/src/test/java/org/apache/airavata/wsmg/msgbox/InMemoryMessageBoxServer.java ---------------------------------------------------------------------- diff --git a/modules/ws-messenger/messagebox/src/test/java/org/apache/airavata/wsmg/msgbox/InMemoryMessageBoxServer.java b/modules/ws-messenger/messagebox/src/test/java/org/apache/airavata/wsmg/msgbox/InMemoryMessageBoxServer.java index 0ba8d43..0eee964 100644 --- a/modules/ws-messenger/messagebox/src/test/java/org/apache/airavata/wsmg/msgbox/InMemoryMessageBoxServer.java +++ b/modules/ws-messenger/messagebox/src/test/java/org/apache/airavata/wsmg/msgbox/InMemoryMessageBoxServer.java @@ -40,6 +40,7 @@ public class InMemoryMessageBoxServer { private static SimpleHTTPServer receiver; public static int TESTING_PORT = 7630; + private static final Logger log = LoggerFactory.getLogger(InMemoryMessageBoxServer.class); public static final String FAILURE_MESSAGE = "Intentional Failure"; @@ -149,7 +150,7 @@ public class InMemoryMessageBoxServer { serverSocket = new ServerSocket(0); serverSocket.close(); } catch (IOException e) { - e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates. + log.error(e.getMessage(), e); } return serverSocket.getLocalPort(); } http://git-wip-us.apache.org/repos/asf/airavata/blob/98c9a34e/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/XBaya.java ---------------------------------------------------------------------- diff --git a/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/XBaya.java b/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/XBaya.java index 5192a93..0368a6a 100644 --- a/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/XBaya.java +++ b/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/XBaya.java @@ -55,8 +55,7 @@ public class XBaya { try { this.engine.getGUI().getErrorWindow().error(ErrorMessages.UNEXPECTED_ERROR, e); } catch (Throwable t) { - // Cannot do anything - e.printStackTrace(); + logger.error(e.getMessage(), e); } } catch (Error e) { logger.error(e.getMessage(), e); @@ -64,7 +63,7 @@ public class XBaya { this.engine.getGUI().getErrorWindow().error(ErrorMessages.UNEXPECTED_ERROR, e); } catch (Throwable t) { // Cannot do anything - System.out.println(e); + 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/XBayaConfiguration.java ---------------------------------------------------------------------- diff --git a/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/XBayaConfiguration.java b/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/XBayaConfiguration.java index 5e6d364..77a0aa0 100644 --- a/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/XBayaConfiguration.java +++ b/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/XBayaConfiguration.java @@ -773,7 +773,7 @@ public class XBayaConfiguration extends Observable implements Observer { } triggerObservers(getJcrComponentRegistry()); } catch (AiravataClientConnectException e) { - e.printStackTrace(); + logger.error(e.getMessage(), e); } } } @@ -831,7 +831,7 @@ public class XBayaConfiguration extends Observable implements Observer { try { listner.executionModeChanged(this); } catch (Exception e) { - e.printStackTrace(); + logger.error(e.getMessage(), e); } } }
