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From lah...@apache.org
Subject [13/13] airavata git commit: merging wth master
Date Wed, 25 Feb 2015 06:09:54 GMT
merging wth master


Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/93ed077e
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/93ed077e
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/93ed077e

Branch: refs/heads/queue-gfac-rabbitmq
Commit: 93ed077e87c3e29cd58301ead917fcf7e2025853
Parents: 1231c01 9a6eaaa
Author: Lahiru Gunathilake <glahiru@gmail.com>
Authored: Wed Feb 25 01:09:40 2015 -0500
Committer: Lahiru Gunathilake <glahiru@gmail.com>
Committed: Wed Feb 25 01:09:40 2015 -0500

----------------------------------------------------------------------
 .../client/samples/CreateLaunchExperiment.java  |  192 +-
 .../tools/RegisterSampleApplications.java       |   31 +-
 .../catalog/data/impl/ComputeResourceImpl.java  |   15 +-
 .../data/util/AppCatalogThriftConversion.java   |    9 +-
 modules/commons/utils/pom.xml                   |    4 +-
 .../airavata/common/utils/WSConstants.java      |   10 +-
 .../apache/airavata/common/utils/WSDLUtil.java  |  764 ++---
 .../apache/airavata/common/utils/XMLUtil.java   |   34 +-
 .../credential-store/pom.xml                    |    5 +
 modules/distribution/server/pom.xml             |   64 +-
 modules/gfac/gfac-bes/pom.xml                   |    5 +
 modules/gfac/gfac-gsissh/pom.xml                |   10 -
 .../handler/GSISSHDirectorySetupHandler.java    |    7 +-
 modules/gfac/gfac-ssh/pom.xml                   |   10 -
 .../ssh/handler/SSHDirectorySetupHandler.java   |    7 +-
 .../airavata/gfac/ssh/util/GFACSSHUtils.java    |   45 +-
 .../core/impl/RabbitMQStatusPublisher.java      |    5 +-
 modules/workflow-model/workflow-engine/pom.xml  |    5 +-
 .../engine/gfac/GFacRegistryClient.java         |  186 +-
 .../workflow/engine/gfac/SimpleWSClient.java    |  166 +-
 .../interpretor/SystemComponentInvoker.java     |   86 +-
 .../engine/interpretor/WorkflowInterpreter.java |   24 +-
 .../engine/invoker/AsynchronousInvoker.java     |   98 +-
 .../workflow/engine/invoker/DynamicInvoker.java |   48 +-
 .../workflow/engine/invoker/Invoker.java        |   84 +-
 .../workflow/engine/invoker/SimpleInvoker.java  |  411 +--
 .../workflow/engine/util/InterpreterUtil.java   |  112 +-
 .../workflow/engine/util/XBayaUtil.java         |   94 +-
 .../engine/workflow/proxy/WorkflowContext.java  |    4 +-
 .../workflow-model-component/pom.xml            |    7 +-
 .../workflow-model/workflow-model-core/pom.xml  |    8 +-
 .../component/system/SubWorkflowComponent.java  |    4 +-
 .../component/url/URLComponentRegistry.java     |   12 +-
 .../component/ws/WSComponentApplication.java    |    2 +-
 .../model/component/ws/WSComponentFactory.java  |    8 +-
 .../model/component/ws/WSComponentRegistry.java |   32 +-
 .../model/component/ws/WorkflowComponent.java   |  108 +-
 .../airavata/workflow/model/gpel/DSCUtil.java   |  140 +-
 .../workflow/model/gpel/script/BPELScript.java  | 1276 ++++----
 .../model/gpel/script/WorkflowWSDL.java         |  528 ++--
 .../model/graph/system/StreamSourceNode.java    |    7 +-
 .../workflow/model/ode/ODEBPELTransformer.java  | 1260 ++++----
 .../airavata/workflow/model/ode/ODEClient.java  |  200 +-
 .../model/ode/ODEDeploymentDescriptor.java      |  368 +--
 .../workflow/model/ode/ODEWSDLTransformer.java  |  872 +++---
 .../workflow/model/ode/WSDLCleaner.java         |  196 +-
 .../workflow/model/wf/TridentTransformer.java   |   50 +-
 .../airavata/workflow/model/wf/Workflow.java    |  542 ++--
 modules/xbaya-gui/pom.xml                       |    5 +
 .../xbaya/core/generators/BPELFiler.java        |   38 +-
 .../xbaya/core/generators/ODEScriptFiler.java   |   68 +-
 .../xbaya/invoker/factory/InvokerFactory.java   |   16 +-
 .../graph/dynamic/DynamicNodeWindow.java        |   72 +-
 tools/gsissh/pom.xml                            |    8 +-
 .../java/com/jcraft/jsch/ExtendedSession.java   |    2 -
 .../illinois/ncsa/BCGSS/BCGSSContextImpl.java   | 2894 +++++++++---------
 .../illinois/ncsa/BCGSS/CircularByteBuffer.java | 1648 +++++-----
 .../ncsa/BCGSS/GlobusTlsCipherFactory.java      |  126 +-
 .../illinois/ncsa/BCGSS/GlobusTlsClient.java    |  494 +--
 .../edu/illinois/ncsa/BCGSS/TlsHandlerUtil.java |  564 ++--
 .../apache/airavata/gsi/ssh/GSSContextX509.java |   32 +-
 .../gsi/ssh/impl/GSISSHAbstractCluster.java     |  163 +-
 .../apache/airavata/gsi/ssh/util/SSHUtils.java  |    4 +-
 .../impl/DefaultSSHApiTestWithMyProxyAuth.java  |   15 +-
 .../gsi/ssh/impl/VanilaTestWithSSHAuth.java     |   46 +-
 65 files changed, 7232 insertions(+), 7118 deletions(-)
----------------------------------------------------------------------


http://git-wip-us.apache.org/repos/asf/airavata/blob/93ed077e/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CreateLaunchExperiment.java
----------------------------------------------------------------------
diff --cc airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CreateLaunchExperiment.java
index 78c2d71,a5bc81c..90b8e6d
--- a/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CreateLaunchExperiment.java
+++ b/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CreateLaunchExperiment.java
@@@ -57,10 -57,10 +57,10 @@@ public class CreateLaunchExperiment 
      private static final String DEFAULT_GATEWAY = "default.registry.gateway";
      private static Airavata.Client airavataClient;
  
 -    private static String echoAppId = "Echo_2e539083-665d-40fd-aaa2-4a751028326b";
 +    private static String echoAppId = "Echo_1365a7fd-eae1-4575-b447-99afb4d79c82";
      private static String mpiAppId = "HelloMPI_720e159f-198f-4daa-96ca-9f5eafee92c9";
      private static String wrfAppId = "WRF_7ad5da38-c08b-417c-a9ea-da9298839762";
-     private static String amberAppId = "Amber_42124128-628b-484c-829d-aff8b584eb00";
+     private static String amberAppId = "Amber_9e4f28b6-7a5d-4fe1-b07f-2053f8f0deb3";
      private static String gromacsAppId = "GROMACS_05622038-9edd-4cb1-824e-0b7cb993364b";
      private static String espressoAppId = "ESPRESSO_10cc2820-5d0b-4c63-9546-8a8b595593c1";
      private static String lammpsAppId = "LAMMPS_10893eb5-3840-438c-8446-d26c7ecb001f";
@@@ -106,7 -104,7 +106,6 @@@
  //                final String expId = createExperimentForBR2Amber(airavataClient);
  //                final String expId = createExperimentWRFStampede(airavataClient);
  //                final String expId = createExperimentForStampedeAmber(airavataClient);
- //                final String expId = createExperimentForTrestlesAmber(airavataClient);
 -                final String expId = createExperimentForTrestlesAmber(airavataClient);
  //                final String expId = createExperimentGROMACSStampede(airavataClient);
  //                final String expId = createExperimentESPRESSOStampede(airavataClient);
  //                final String expId = createExperimentLAMMPSStampede(airavataClient);

http://git-wip-us.apache.org/repos/asf/airavata/blob/93ed077e/modules/messaging/core/src/main/java/org/apache/airavata/messaging/core/impl/RabbitMQStatusPublisher.java
----------------------------------------------------------------------
diff --cc modules/messaging/core/src/main/java/org/apache/airavata/messaging/core/impl/RabbitMQStatusPublisher.java
index 70ed942,0000000..ae5e29e
mode 100644,000000..100644
--- a/modules/messaging/core/src/main/java/org/apache/airavata/messaging/core/impl/RabbitMQStatusPublisher.java
+++ b/modules/messaging/core/src/main/java/org/apache/airavata/messaging/core/impl/RabbitMQStatusPublisher.java
@@@ -1,103 -1,0 +1,102 @@@
 +/*
 + *
 + * Licensed to the Apache Software Foundation (ASF) under one
 + * or more contributor license agreements.  See the NOTICE file
 + * distributed with this work for additional information
 + * regarding copyright ownership.  The ASF licenses this file
 + * to you under the Apache License, Version 2.0 (the
 + * "License"); you may not use this file except in compliance
 + * with the License.  You may obtain a copy of the License at
 + *
 + *   http://www.apache.org/licenses/LICENSE-2.0
 + *
 + * Unless required by applicable law or agreed to in writing,
 + * software distributed under the License is distributed on an
 + * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
 + * KIND, either express or implied.  See the License for the
 + * specific language governing permissions and limitations
 + * under the License.
 + *
 + */
 +
 +package org.apache.airavata.messaging.core.impl;
 +
 +import org.apache.airavata.common.exception.AiravataException;
 +import org.apache.airavata.common.exception.ApplicationSettingsException;
 +import org.apache.airavata.common.utils.ServerSettings;
 +import org.apache.airavata.common.utils.ThriftUtils;
 +import org.apache.airavata.messaging.core.MessageContext;
 +import org.apache.airavata.messaging.core.MessagingConstants;
 +import org.apache.airavata.messaging.core.Publisher;
- import org.apache.airavata.messaging.core.stats.StatCounter;
 +import org.apache.airavata.model.messaging.event.*;
 +import org.apache.thrift.TException;
 +import org.slf4j.Logger;
 +import org.slf4j.LoggerFactory;
 +
 +public class RabbitMQStatusPublisher implements Publisher {
 +
 +    private static Logger log = LoggerFactory.getLogger(RabbitMQStatusPublisher.class);
 +
 +    private RabbitMQProducer rabbitMQProducer;
 +
-     StatCounter statCounter = StatCounter.getInstance();
++//    StatCounter statCounter = StatCounter.getInstance();
 +
 +    public RabbitMQStatusPublisher() throws Exception {
 +        String brokerUrl;
 +        String exchangeName;
 +        try {
 +            brokerUrl = ServerSettings.getSetting(MessagingConstants.RABBITMQ_BROKER_URL);
 +            exchangeName = ServerSettings.getSetting(MessagingConstants.RABBITMQ_STATUS_EXCHANGE_NAME);
 +        } catch (ApplicationSettingsException e) {
 +            String message = "Failed to get read the required properties from airavata to
initialize rabbitmq";
 +            log.error(message, e);
 +            throw new AiravataException(message, e);
 +        }
 +        rabbitMQProducer = new RabbitMQProducer(brokerUrl, exchangeName);
 +        rabbitMQProducer.open();
 +    }
 +
 +    public void publish(MessageContext msgCtx) throws AiravataException {
 +        try {
 +            log.info("Publishing status to rabbitmq...");
 +            byte[] body = ThriftUtils.serializeThriftObject(msgCtx.getEvent());
 +            Message message = new Message();
 +            message.setEvent(body);
 +            message.setMessageId(msgCtx.getMessageId());
 +            message.setMessageType(msgCtx.getType());
 +            message.setUpdatedTime(msgCtx.getUpdatedTime().getTime());
 +            String gatewayId = msgCtx.getGatewayId();
 +            String routingKey = null;
 +            if (msgCtx.getType().equals(MessageType.EXPERIMENT)){
 +                ExperimentStatusChangeEvent event = (ExperimentStatusChangeEvent) msgCtx.getEvent();
 +                routingKey = gatewayId + "." + event.getExperimentId();
 +            } else if (msgCtx.getType().equals(MessageType.TASK)) {
 +                TaskStatusChangeEvent event = (TaskStatusChangeEvent) msgCtx.getEvent();
 +                routingKey =  gatewayId + "." + event.getTaskIdentity().getExperimentId()
+ "." +
 +                        event.getTaskIdentity().getWorkflowNodeId() + "." + event.getTaskIdentity().getTaskId();
 +            }else if (msgCtx.getType().equals(MessageType.WORKFLOWNODE)){
 +                WorkflowNodeStatusChangeEvent event = (WorkflowNodeStatusChangeEvent) msgCtx.getEvent();
 +                WorkflowIdentifier workflowNodeIdentity = event.getWorkflowNodeIdentity();
 +                routingKey =  gatewayId + "." + workflowNodeIdentity.getExperimentId() +
"." + workflowNodeIdentity.getWorkflowNodeId();
 +            }else if (msgCtx.getType().equals(MessageType.JOB)){
 +                JobStatusChangeEvent event = (JobStatusChangeEvent)msgCtx.getEvent();
 +                JobIdentifier identity = event.getJobIdentity();
 +                routingKey =  gatewayId + "." + identity.getExperimentId() + "." +
 +                        identity.getWorkflowNodeId() + "." +
 +                        identity.getTaskId() + "." +
 +                        identity.getJobId();
 +            }
 +            byte[] messageBody = ThriftUtils.serializeThriftObject(message);
 +            rabbitMQProducer.send(messageBody, routingKey);
-             statCounter.add(message);
++//            statCounter.add(message);
 +        } catch (TException e) {
 +            String msg = "Error while deserializing the object";
 +            log.error(msg, e);
 +            throw new AiravataException(msg, e);
 +        } catch (Exception e) {
 +            String msg = "Error while sending to rabbitmq";
 +            log.error(msg, e);
 +            throw new AiravataException(msg, e);
 +        }
 +    }
 +}


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