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Posted to commits@airavata.apache.org by la...@apache.org on 2015/03/23 20:38:37 UTC
[10/15] airavata git commit: merging wth master
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/master
Commit: 93ed077e87c3e29cd58301ead917fcf7e2025853
Parents: 1231c01 9a6eaaa
Author: Lahiru Gunathilake <gl...@gmail.com>
Authored: Wed Feb 25 01:09:40 2015 -0500
Committer: Lahiru Gunathilake <gl...@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);
+ }
+ }
+}