You are viewing a plain text version of this content. The canonical link for it is here.
Posted to commits@airavata.apache.org by sh...@apache.org on 2015/06/04 22:16:32 UTC
[79/81] [abbrv] airavata git commit: Merge moduleRefactor branch
http://git-wip-us.apache.org/repos/asf/airavata/blob/b4ede9cb/modules/gfac/gfac-impl/src/test/java/org/apache/airavata/core/gfac/services/impl/GSISSHProviderTestWithMyProxyAuth.java
----------------------------------------------------------------------
diff --cc modules/gfac/gfac-impl/src/test/java/org/apache/airavata/core/gfac/services/impl/GSISSHProviderTestWithMyProxyAuth.java
index 0000000,9e03173..61db417
mode 000000,100644..100644
--- a/modules/gfac/gfac-impl/src/test/java/org/apache/airavata/core/gfac/services/impl/GSISSHProviderTestWithMyProxyAuth.java
+++ b/modules/gfac/gfac-impl/src/test/java/org/apache/airavata/core/gfac/services/impl/GSISSHProviderTestWithMyProxyAuth.java
@@@ -1,0 -1,229 +1,229 @@@
+ ///*
+ // *
+ // * 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.core.gfac.services.impl;
+ //
+ //import java.io.File;
+ //import java.net.URL;
+ //import java.util.ArrayList;
+ //import java.util.Date;
+ //import java.util.List;
+ //import java.util.UUID;
+ //
+ //import org.apache.aiaravata.application.catalog.data.model.ApplicationInterface;
+ //import org.apache.airavata.commons.gfac.type.ActualParameter;
+ //import org.apache.airavata.commons.gfac.type.ApplicationDescription;
+ //import org.apache.airavata.commons.gfac.type.HostDescription;
+ //import org.apache.airavata.commons.gfac.type.ServiceDescription;
+ //import org.apache.airavata.gfac.GFacConfiguration;
+ //import org.apache.airavata.gfac.GFacException;
+ //import org.apache.airavata.gfac.SecurityContext;
+ //import org.apache.airavata.gfac.core.context.ApplicationContext;
+ //import org.apache.airavata.gfac.core.context.JobExecutionContext;
+ //import org.apache.airavata.gfac.core.context.MessageContext;
+ //import org.apache.airavata.gfac.impl.BetterGfacImpl;
+ //import org.apache.airavata.gfac.gsissh.security.GSISecurityContext;
+ //import org.apache.airavata.gfac.ssh.api.Cluster;
+ //import org.apache.airavata.gfac.ssh.api.SSHApiException;
+ //import org.apache.airavata.gfac.ssh.api.ServerInfo;
+ //import GSIAuthenticationInfo;
+ //import org.apache.airavata.gfac.ssh.impl.PBSCluster;
+ //import org.apache.airavata.gfac.ssh.impl.authentication.MyProxyAuthenticationInfo;
+ //import org.apache.airavata.gfac.ssh.util.CommonUtils;
+ //import org.apache.airavata.model.appcatalog.appdeployment.ApplicationDeploymentDescription;
+ //import org.apache.airavata.model.workspace.experiment.TaskDetails;
-//import org.apache.airavata.persistance.registry.jpa.impl.RegistryFactory;
++//import org.apache.airavata.experiment.registry.jpa.impl.RegistryFactory;
+ //import org.apache.airavata.schemas.gfac.ApplicationDeploymentDescriptionType;
+ //import org.apache.airavata.schemas.gfac.GsisshHostType;
+ //import org.apache.airavata.schemas.gfac.HpcApplicationDeploymentType;
+ //import org.apache.airavata.schemas.gfac.InputParameterType;
+ //import org.apache.airavata.schemas.gfac.JobTypeType;
+ //import org.apache.airavata.schemas.gfac.OutputParameterType;
+ //import org.apache.airavata.schemas.gfac.ProjectAccountType;
+ //import org.apache.airavata.schemas.gfac.QueueType;
+ //import org.apache.airavata.schemas.gfac.StringParameterType;
+ //import org.testng.annotations.BeforeClass;
+ //import org.testng.annotations.Test;
+ //
+ //public class GSISSHProviderTestWithMyProxyAuth {
+ // private JobExecutionContext jobExecutionContext;
+ //
+ // //FIXME: move job properties to configuration file
+ // private static final String hostAddress = "trestles.sdsc.edu";
+ // private static final String hostName = "trestles";
+ // private String myProxyUserName;
+ // private String myProxyPassword;
+ // private String workingDirectory;
+ // private String certificateLocation = "/Users/lahirugunathilake/Downloads/certificates";
+ //
+ // @BeforeClass
+ // public void setUp() throws Exception {
+ //// System.setProperty("myproxy.user", "ogce");
+ //// System.setProperty("myproxy.password", "");
+ //// System.setProperty("basedir", "/Users/lahirugunathilake/Downloads");
+ //// System.setProperty("gsi.working.directory", "/home/ogce");
+ //// System.setProperty("gsi.certificate.path", "/Users/lahirugunathilake/Downloads/certificates");
+ // certificateLocation = System.getProperty("trusted.cert.location");
+ // myProxyUserName = System.getProperty("myproxy.username");
+ // myProxyPassword = System.getProperty("myproxy.password");
+ // workingDirectory = System.getProperty("gsi.working.directory");
+ //
+ // if (myProxyUserName == null || myProxyPassword == null || certificateLocation == null) {
+ // System.out.println(">>>>>> Please run tests with my proxy user name and password. " +
+ // "E.g :- mvn clean install -Dmyproxy.username=xxx -Dmyproxy.password=xxx -Dgsi.working.directory=/path<<<<<<<");
+ // throw new Exception("Need my proxy user name password to run tests.");
+ // }
+ // URL resource = GSISSHProviderTestWithMyProxyAuth.class.getClassLoader().getResource(org.apache.airavata.common.utils.Constants.GFAC_CONFIG_XML);
+ // assert resource != null;
+ // System.out.println(resource.getFile());
+ // GFacConfiguration gFacConfiguration = GFacConfiguration.create(new File(resource.getPath()), null);
+ //
+ // /*
+ // * Host
+ // */
+ // HostDescription host = new HostDescription(GsisshHostType.type);
+ // host.getType().setHostAddress(hostAddress);
+ // host.getType().setHostName(hostName);
+ //
+ // /*
+ // * App
+ // */
+ // ApplicationDescription appDesc = new ApplicationDescription(HpcApplicationDeploymentType.type);
+ // HpcApplicationDeploymentType app = (HpcApplicationDeploymentType) appDesc.getType();
+ // ApplicationDeploymentDescriptionType.ApplicationName name = ApplicationDeploymentDescriptionType.ApplicationName.Factory.newInstance();
+ // name.setStringValue("EchoLocal");
+ // app.setApplicationName(name);
+ // ProjectAccountType projectAccountType = app.addNewProjectAccount();
+ // projectAccountType.setProjectAccountNumber("sds128");
+ //
+ // QueueType queueType = app.addNewQueue();
+ // queueType.setQueueName("normal");
+ //
+ // app.setCpuCount(1);
+ // app.setJobType(JobTypeType.SERIAL);
+ // app.setNodeCount(1);
+ // app.setProcessorsPerNode(1);
+ //
+ // /*
+ // * Use bat file if it is compiled on Windows
+ // */
+ // app.setExecutableLocation("/bin/echo");
+ //
+ // /*
+ // * Default tmp location
+ // */
+ // String tempDir = "/home/ogce/scratch/";
+ // String date = (new Date()).toString();
+ // date = date.replaceAll(" ", "_");
+ // date = date.replaceAll(":", "_");
+ //
+ // tempDir = workingDirectory + File.separator
+ // + "SimpleEcho" + "_" + date + "_" + UUID.randomUUID();
+ //
+ // System.out.println(tempDir);
+ // app.setScratchWorkingDirectory(tempDir);
+ // app.setStaticWorkingDirectory(tempDir);
+ // app.setInputDataDirectory(tempDir + File.separator + "inputData");
+ // app.setOutputDataDirectory(tempDir + File.separator + "outputData");
+ // app.setStandardOutput(tempDir + File.separator + app.getApplicationName().getStringValue() + ".stdout");
+ // app.setStandardError(tempDir + File.separator + app.getApplicationName().getStringValue() + ".stderr");
+ // app.setMaxWallTime(5);
+ // app.setInstalledParentPath("/opt/torque/bin/");
+ //
+ // /*
+ // * Service
+ // */
+ // ServiceDescription serv = new ServiceDescription();
+ // serv.getType().setName("SimpleEcho");
+ //
+ // List<InputParameterType> inputList = new ArrayList<InputParameterType>();
+ //
+ // InputParameterType input = InputParameterType.Factory.newInstance();
+ // input.setParameterName("echo_input");
+ // input.setParameterType(StringParameterType.Factory.newInstance());
+ // inputList.add(input);
+ //
+ // InputParameterType[] inputParamList = inputList.toArray(new InputParameterType[inputList
+ //
+ // .size()]);
+ // List<OutputParameterType> outputList = new ArrayList<OutputParameterType>();
+ // OutputParameterType output = OutputParameterType.Factory.newInstance();
+ // output.setParameterName("echo_output");
+ // output.setParameterType(StringParameterType.Factory.newInstance());
+ // outputList.add(output);
+ //
+ // OutputParameterType[] outputParamList = outputList
+ // .toArray(new OutputParameterType[outputList.size()]);
+ //
+ // serv.getType().setInputParametersArray(inputParamList);
+ // serv.getType().setOutputParametersArray(outputParamList);
+ //
+ // jobExecutionContext = new JobExecutionContext(gFacConfiguration, serv.getType().getName());
+ // // Adding security context
+ // jobExecutionContext.addSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT, getSecurityContext(app));
+ // ApplicationContext applicationContext = new ApplicationContext();
+ // jobExecutionContext.setApplicationContext(applicationContext);
+ // applicationContext.setServiceDescription(serv);
+ // applicationContext.setApplicationDeploymentDescription(appDesc);
+ // applicationContext.setHostDescription(host);
+ //
+ // MessageContext inMessage = new MessageContext();
+ // ActualParameter echo_input = new ActualParameter();
+ // ((StringParameterType) echo_input.getType()).setValue("echo_output=hello");
+ // inMessage.addParameter("echo_input", echo_input);
+ //
+ //
+ // jobExecutionContext.setInMessageContext(inMessage);
+ //
+ // MessageContext outMessage = new MessageContext();
+ // ActualParameter echo_out = new ActualParameter();
+ //// ((StringParameterType)echo_input.getType()).setValue("echo_output=hello");
+ // outMessage.addParameter("echo_output", echo_out);
+ // jobExecutionContext.setRegistry(RegistryFactory.getLoggingRegistry());
+ // jobExecutionContext.setTaskData(new TaskDetails("11323"));
+ // jobExecutionContext.setOutMessageContext(outMessage);
+ //
+ // }
+ //
+ // private SecurityContext getSecurityContext(HpcApplicationDeploymentType app) {
+ // GSIAuthenticationInfo authenticationInfo
+ // = new MyProxyAuthenticationInfo(myProxyUserName, myProxyPassword, "myproxy.teragrid.org",
+ // 7512, 17280000, certificateLocation);
+ //
+ // // Server info
+ // ServerInfo serverInfo = new ServerInfo("ogce", "trestles.sdsc.edu");
+ // Cluster pbsCluster = null;
+ // try {
+ // pbsCluster = new PBSCluster(serverInfo, authenticationInfo, CommonUtils.getPBSJobManager(app.getInstalledParentPath()));
+ // } catch (SSHApiException e) {
+ // e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.
+ // }
+ // GSISecurityContext sshSecurityContext = new GSISecurityContext(pbsCluster);
+ // return sshSecurityContext;
+ // }
+ // @Test
+ // public void testGSISSHProvider() throws GFacException {
+ // BetterGfacImpl gFacAPI = new BetterGfacImpl();
+ // gFacAPI.submitJob(jobExecutionContext.getExperimentID(), jobExecutionContext.getTaskData().getTaskID(), jobExecutionContext.getGatewayID());
+ // System.out.println(jobExecutionContext.getJobDetails().getJobDescription());
+ // System.out.println(jobExecutionContext.getJobDetails().getJobID());
+ // }
+ //
+ //}
http://git-wip-us.apache.org/repos/asf/airavata/blob/b4ede9cb/modules/gfac/gfac-impl/src/test/java/org/apache/airavata/core/gfac/services/impl/LocalProviderTest.java
----------------------------------------------------------------------
diff --cc modules/gfac/gfac-impl/src/test/java/org/apache/airavata/core/gfac/services/impl/LocalProviderTest.java
index 0000000,aeb8158..b3974d2
mode 000000,100644..100644
--- a/modules/gfac/gfac-impl/src/test/java/org/apache/airavata/core/gfac/services/impl/LocalProviderTest.java
+++ b/modules/gfac/gfac-impl/src/test/java/org/apache/airavata/core/gfac/services/impl/LocalProviderTest.java
@@@ -1,0 -1,184 +1,184 @@@
+ ///*
+ // *
+ // * 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.core.gfac.services.impl;
+ //
+ //import java.io.File;
+ //import java.net.URL;
+ //import java.util.ArrayList;
+ //import java.util.List;
+ //
+ //import org.apache.airavata.common.utils.MonitorPublisher;
+ //import org.apache.airavata.commons.gfac.type.ActualParameter;
+ //import org.apache.airavata.commons.gfac.type.ApplicationDescription;
+ //import org.apache.airavata.commons.gfac.type.HostDescription;
+ //import org.apache.airavata.commons.gfac.type.ServiceDescription;
+ //import org.apache.airavata.gfac.GFacConfiguration;
+ //import org.apache.airavata.gfac.GFacException;
+ //import org.apache.airavata.gfac.core.context.ApplicationContext;
+ //import org.apache.airavata.gfac.core.context.JobExecutionContext;
+ //import org.apache.airavata.gfac.core.context.MessageContext;
+ //import org.apache.airavata.gfac.core.provider.GFacProviderException;
+ //import org.apache.airavata.gfac.local.handler.LocalDirectorySetupHandler;
+ //import org.apache.airavata.gfac.local.provider.impl.LocalProvider;
+ //import org.apache.airavata.model.workspace.experiment.ExecutionUnit;
+ //import org.apache.airavata.model.workspace.experiment.Experiment;
+ //import org.apache.airavata.model.workspace.experiment.TaskDetails;
+ //import org.apache.airavata.model.workspace.experiment.WorkflowNodeDetails;
-//import org.apache.airavata.persistance.registry.jpa.impl.LoggingRegistryImpl;
++//import org.apache.airavata.experiment.registry.jpa.impl.LoggingRegistryImpl;
+ //import org.apache.airavata.schemas.gfac.ApplicationDeploymentDescriptionType;
+ //import org.apache.airavata.schemas.gfac.InputParameterType;
+ //import org.apache.airavata.schemas.gfac.OutputParameterType;
+ //import org.apache.airavata.schemas.gfac.StringParameterType;
+ //import org.apache.commons.lang.SystemUtils;
+ //import org.testng.annotations.BeforeTest;
+ //import org.testng.annotations.Test;
+ //
+ //import com.google.common.eventbus.EventBus;
+ //
+ //public class LocalProviderTest {
+ // private JobExecutionContext jobExecutionContext;
+ // @BeforeTest
+ // public void setUp() throws Exception {
+ //
+ // URL resource = this.getClass().getClassLoader().getResource(org.apache.airavata.common.utils.Constants.GFAC_CONFIG_XML);
+ // File configFile = new File(resource.getPath());
+ // GFacConfiguration gFacConfiguration = GFacConfiguration.create(configFile, null);
+ // //have to set InFlwo Handlers and outFlowHandlers
+ // ApplicationContext applicationContext = new ApplicationContext();
+ // HostDescription host = new HostDescription();
+ // host.getType().setHostName("localhost");
+ // host.getType().setHostAddress("localhost");
+ // applicationContext.setHostDescription(host);
+ // /*
+ // * App
+ // */
+ // ApplicationDescription appDesc = new ApplicationDescription();
+ // ApplicationDeploymentDescriptionType app = appDesc.getType();
+ // ApplicationDeploymentDescriptionType.ApplicationName name = ApplicationDeploymentDescriptionType.ApplicationName.Factory.newInstance();
+ // name.setStringValue("EchoLocal");
+ // app.setApplicationName(name);
+ //
+ // /*
+ // * Use bat file if it is compiled on Windows
+ // */
+ // if (SystemUtils.IS_OS_WINDOWS) {
+ // URL url = this.getClass().getClassLoader().getResource("echo.bat");
+ // app.setExecutableLocation(url.getFile());
+ // } else {
+ // //for unix and Mac
+ // app.setExecutableLocation("/bin/echo");
+ // }
+ //
+ // /*
+ // * Default tmp location
+ // */
+ // String tempDir = System.getProperty("java.io.tmpdir");
+ // if (tempDir == null) {
+ // tempDir = "/tmp";
+ // }
+ //
+ // app.setScratchWorkingDirectory(tempDir);
+ // app.setStaticWorkingDirectory(tempDir);
+ // app.setInputDataDirectory(tempDir + File.separator + "input");
+ // app.setOutputDataDirectory(tempDir + File.separator + "output");
+ // app.setStandardOutput(tempDir + File.separator + "echo.stdout");
+ // app.setStandardError(tempDir + File.separator + "echo.stderr");
+ //
+ // applicationContext.setApplicationDeploymentDescription(appDesc);
+ //
+ // /*
+ // * Service
+ // */
+ // ServiceDescription serv = new ServiceDescription();
+ // serv.getType().setName("SimpleEcho");
+ //
+ // List<InputParameterType> inputList = new ArrayList<InputParameterType>();
+ // InputParameterType input = InputParameterType.Factory.newInstance();
+ // input.setParameterName("echo_input");
+ // input.setParameterType(StringParameterType.Factory.newInstance());
+ // inputList.add(input);
+ // InputParameterType[] inputParamList = inputList.toArray(new InputParameterType[inputList
+ // .size()]);
+ //
+ // List<OutputParameterType> outputList = new ArrayList<OutputParameterType>();
+ // OutputParameterType output = OutputParameterType.Factory.newInstance();
+ // output.setParameterName("echo_output");
+ // output.setParameterType(StringParameterType.Factory.newInstance());
+ // outputList.add(output);
+ // OutputParameterType[] outputParamList = outputList
+ // .toArray(new OutputParameterType[outputList.size()]);
+ //
+ // serv.getType().setInputParametersArray(inputParamList);
+ // serv.getType().setOutputParametersArray(outputParamList);
+ //
+ // jobExecutionContext = new JobExecutionContext(gFacConfiguration, serv.getType().getName());
+ // jobExecutionContext.setApplicationContext(applicationContext);
+ // /*
+ // * Host
+ // */
+ // applicationContext.setServiceDescription(serv);
+ //
+ // MessageContext inMessage = new MessageContext();
+ // ActualParameter echo_input = new ActualParameter();
+ // ((StringParameterType) echo_input.getType()).setValue("echo_output=hello");
+ // inMessage.addParameter("echo_input", echo_input);
+ //
+ // jobExecutionContext.setInMessageContext(inMessage);
+ //
+ // MessageContext outMessage = new MessageContext();
+ // ActualParameter echo_out = new ActualParameter();
+ // outMessage.addParameter("echo_output", echo_out);
+ //
+ // jobExecutionContext.setOutMessageContext(outMessage);
+ //
+ // jobExecutionContext.setExperimentID("test123");
+ // jobExecutionContext.setExperiment(new Experiment("test123","project1","admin","testExp"));
+ // jobExecutionContext.setTaskData(new TaskDetails(jobExecutionContext.getExperimentID()));
+ // jobExecutionContext.setRegistry(new LoggingRegistryImpl());
+ // jobExecutionContext.setWorkflowNodeDetails(new WorkflowNodeDetails(jobExecutionContext.getExperimentID(),"none", ExecutionUnit.APPLICATION));
+ //
+ //
+ // }
+ //
+ // @Test
+ // public void testLocalDirectorySetupHandler() throws GFacException {
+ // LocalDirectorySetupHandler localDirectorySetupHandler = new LocalDirectorySetupHandler();
+ // localDirectorySetupHandler.invoke(jobExecutionContext);
+ //
+ // ApplicationDescription applicationDeploymentDescription = jobExecutionContext.getApplicationContext().getApplicationDeploymentDescription();
+ // ApplicationDeploymentDescriptionType app = applicationDeploymentDescription.getType();
+ // junit.framework.Assert.assertTrue(new File(app.getStaticWorkingDirectory()).exists());
+ // junit.framework.Assert.assertTrue(new File(app.getScratchWorkingDirectory()).exists());
+ // junit.framework.Assert.assertTrue(new File(app.getInputDataDirectory()).exists());
+ // junit.framework.Assert.assertTrue(new File(app.getOutputDataDirectory()).exists());
+ // }
+ //
+ // @Test
+ // public void testLocalProvider() throws GFacException,GFacProviderException {
+ // LocalDirectorySetupHandler localDirectorySetupHandler = new LocalDirectorySetupHandler();
+ // localDirectorySetupHandler.invoke(jobExecutionContext);
+ // LocalProvider localProvider = new LocalProvider();
+ // localProvider.setMonitorPublisher(new MonitorPublisher(new EventBus()));
+ // localProvider.initialize(jobExecutionContext);
+ // localProvider.execute(jobExecutionContext);
+ // localProvider.dispose(jobExecutionContext);
+ // }
+ //}
http://git-wip-us.apache.org/repos/asf/airavata/blob/b4ede9cb/modules/gfac/gfac-service/pom.xml
----------------------------------------------------------------------
diff --cc modules/gfac/gfac-service/pom.xml
index 0000000,99497a3..83999e3
mode 000000,100644..100644
--- a/modules/gfac/gfac-service/pom.xml
+++ b/modules/gfac/gfac-service/pom.xml
@@@ -1,0 -1,100 +1,100 @@@
+ <?xml version="1.0" encoding="UTF-8"?>
+
+ <!--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 (theÏ "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. -->
+
+ <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+
+ <modelVersion>4.0.0</modelVersion>
+
+ <parent>
+ <artifactId>airavata-gfac</artifactId>
+ <groupId>org.apache.airavata</groupId>
+ <version>0.16-SNAPSHOT</version>
+ <relativePath>../pom.xml</relativePath>
+ </parent>
+
+ <name>Airavata Gfac Service</name>
+ <artifactId>airavata-gfac-service</artifactId>
+ <packaging>jar</packaging>
+ <url>http://airavata.apache.org/</url>
+
+ <dependencies>
+ <dependency>
+ <groupId>org.apache.thrift</groupId>
+ <artifactId>libthrift</artifactId>
+ <version>${thrift.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.slf4j</groupId>
+ <artifactId>slf4j-log4j12</artifactId>
+ <version>${org.slf4j.version}</version>
+ </dependency>
+ <!--<dependency>-->
+ <!--<groupId>org.apache.airavata</groupId>-->
+ <!--<artifactId>airavata-client-api</artifactId>-->
+ <!--<version>${project.version}</version>-->
+ <!--</dependency>-->
+ <dependency>
+ <groupId>org.apache.airavata</groupId>
+ <artifactId>airavata-common-utils</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.airavata</groupId>
+ <artifactId>airavata-registry-cpi</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.airavata</groupId>
- <artifactId>airavata-jpa-registry</artifactId>
++ <artifactId>airavata-experiment-catalog</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.airavata</groupId>
+ <artifactId>airavata-gfac-client</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.airavata</groupId>
+ <artifactId>airavata-gfac-core</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.airavata</groupId>
+ <artifactId>airavata-gfac-impl</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.airavata</groupId>
+ <artifactId>airavata-model-utils</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.airavata</groupId>
+ <artifactId>airavata-api-stubs</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.airavata</groupId>
+ <artifactId>airavata-server-configuration</artifactId>
+ <scope>test</scope>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.curator</groupId>
+ <artifactId>curator-framework</artifactId>
+ <version>${curator.version}</version>
+ </dependency>
+ </dependencies>
+
+ <properties>
+ <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+ <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
+ </properties>
+
+ </project>
http://git-wip-us.apache.org/repos/asf/airavata/blob/b4ede9cb/modules/gfac/gfac-service/src/main/java/org/apache/airavata/gfac/server/GfacServerHandler.java
----------------------------------------------------------------------
diff --cc modules/gfac/gfac-service/src/main/java/org/apache/airavata/gfac/server/GfacServerHandler.java
index 0000000,64c06e4..f6338a8
mode 000000,100644..100644
--- a/modules/gfac/gfac-service/src/main/java/org/apache/airavata/gfac/server/GfacServerHandler.java
+++ b/modules/gfac/gfac-service/src/main/java/org/apache/airavata/gfac/server/GfacServerHandler.java
@@@ -1,0 -1,421 +1,421 @@@
+ /*
+ *
+ * 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.gfac.server;
+
+ import com.google.common.eventbus.EventBus;
+ import org.airavata.appcatalog.cpi.AppCatalog;
+ import org.apache.aiaravata.application.catalog.data.impl.AppCatalogFactory;
+ import org.apache.airavata.common.exception.AiravataException;
+ import org.apache.airavata.common.exception.ApplicationSettingsException;
+ import org.apache.airavata.common.logger.AiravataLogger;
+ import org.apache.airavata.common.logger.AiravataLoggerFactory;
+ import org.apache.airavata.common.utils.AiravataZKUtils;
+ import org.apache.airavata.common.utils.Constants;
+ import org.apache.airavata.common.utils.MonitorPublisher;
+ import org.apache.airavata.common.utils.ServerSettings;
+ import org.apache.airavata.common.utils.ThriftUtils;
+ import org.apache.airavata.common.utils.listener.AbstractActivityListener;
+ import org.apache.airavata.gfac.GFacConfiguration;
+ import org.apache.airavata.gfac.GFacException;
+ import org.apache.airavata.gfac.core.GFac;
+ import org.apache.airavata.gfac.core.handler.GFacHandlerConfig;
+ import org.apache.airavata.gfac.core.handler.GFacHandlerException;
+ import org.apache.airavata.gfac.core.handler.ThreadedHandler;
+ import org.apache.airavata.gfac.core.GFacThreadPoolExecutor;
+ import org.apache.airavata.gfac.core.GFacUtils;
+ import org.apache.airavata.gfac.cpi.GfacService;
+ import org.apache.airavata.gfac.cpi.gfac_cpi_serviceConstants;
+ import org.apache.airavata.gfac.impl.BetterGfacImpl;
+ import org.apache.airavata.gfac.impl.InputHandlerWorker;
+ import org.apache.airavata.messaging.core.MessageContext;
+ import org.apache.airavata.messaging.core.MessageHandler;
+ import org.apache.airavata.messaging.core.MessagingConstants;
+ import org.apache.airavata.messaging.core.Publisher;
+ import org.apache.airavata.messaging.core.PublisherFactory;
+ import org.apache.airavata.messaging.core.impl.RabbitMQTaskLaunchConsumer;
+ import org.apache.airavata.model.messaging.event.MessageType;
+ import org.apache.airavata.model.messaging.event.TaskSubmitEvent;
+ import org.apache.airavata.model.messaging.event.TaskTerminateEvent;
+ import org.apache.airavata.model.workspace.experiment.ExperimentState;
+ import org.apache.airavata.model.workspace.experiment.ExperimentStatus;
-import org.apache.airavata.persistance.registry.jpa.impl.RegistryFactory;
++import org.apache.airavata.experiment.catalog.impl.RegistryFactory;
+ import org.apache.airavata.registry.cpi.Registry;
+ import org.apache.airavata.registry.cpi.RegistryException;
+ import org.apache.airavata.registry.cpi.RegistryModelType;
+ import org.apache.curator.RetryPolicy;
+ import org.apache.curator.framework.CuratorFramework;
+ import org.apache.curator.framework.CuratorFrameworkFactory;
+ import org.apache.curator.retry.ExponentialBackoffRetry;
+ import org.apache.thrift.TBase;
+ import org.apache.thrift.TException;
+ import org.apache.zookeeper.CreateMode;
+ import org.apache.zookeeper.ZooDefs;
+ import org.apache.zookeeper.data.Stat;
+ import org.xml.sax.SAXException;
+
+ import javax.xml.parsers.ParserConfigurationException;
+ import javax.xml.xpath.XPathExpressionException;
+ import java.io.File;
+ import java.io.IOException;
+ import java.net.URL;
+ import java.util.ArrayList;
+ import java.util.Calendar;
+ import java.util.HashMap;
+ import java.util.List;
+ import java.util.Map;
+ import java.util.concurrent.BlockingQueue;
+
+ public class GfacServerHandler implements GfacService.Iface {
+ private final static AiravataLogger logger = AiravataLoggerFactory.getLogger(GfacServerHandler.class);
+ private static RabbitMQTaskLaunchConsumer rabbitMQTaskLaunchConsumer;
+ private static int requestCount=0;
+ private Registry registry;
+ private AppCatalog appCatalog;
+ private String gatewayName;
+ private String airavataUserName;
+ private CuratorFramework curatorClient;
+ private MonitorPublisher publisher;
+ private String gfacServer;
+ private String gfacExperiments;
+ private String airavataServerHostPort;
+ private BlockingQueue<TaskSubmitEvent> taskSubmitEvents;
+ private static File gfacConfigFile;
+ private static List<ThreadedHandler> daemonHandlers = new ArrayList<ThreadedHandler>();
+ private static List<AbstractActivityListener> activityListeners = new ArrayList<AbstractActivityListener>();
+
+ public GfacServerHandler() throws Exception {
+ try {
+ // start curator client
+ String zkhostPort = AiravataZKUtils.getZKhostPort();
+ RetryPolicy retryPolicy = new ExponentialBackoffRetry(1000, 5);
+ curatorClient = CuratorFrameworkFactory.newClient(zkhostPort, retryPolicy);
+ curatorClient.start();
+ gfacServer = ServerSettings.getSetting(Constants.ZOOKEEPER_GFAC_SERVER_NODE, "/gfac-server");
+ gfacExperiments = ServerSettings.getSetting(Constants.ZOOKEEPER_GFAC_EXPERIMENT_NODE, "/gfac-experiments");
+ airavataServerHostPort = ServerSettings.getSetting(Constants.GFAC_SERVER_HOST)
+ + ":" + ServerSettings.getSetting(Constants.GFAC_SERVER_PORT);
+ storeServerConfig();
+ publisher = new MonitorPublisher(new EventBus());
+ registry = RegistryFactory.getDefaultRegistry();
+ appCatalog = AppCatalogFactory.getAppCatalog();
+ setGatewayProperties();
+ startDaemonHandlers();
+ // initializing Better Gfac Instance
+ BetterGfacImpl.getInstance().init(registry, appCatalog, curatorClient, publisher);
+ if (ServerSettings.isGFacPassiveMode()) {
+ rabbitMQTaskLaunchConsumer = new RabbitMQTaskLaunchConsumer();
+ rabbitMQTaskLaunchConsumer.listen(new TaskLaunchMessageHandler());
+ }
+ startStatusUpdators(registry, curatorClient, publisher, rabbitMQTaskLaunchConsumer);
+
+ } catch (Exception e) {
+ throw new Exception("Error initialising GFAC", e);
+ }
+ }
+
+ public static void main(String[] args) {
+ RabbitMQTaskLaunchConsumer rabbitMQTaskLaunchConsumer = null;
+ try {
+ rabbitMQTaskLaunchConsumer = new RabbitMQTaskLaunchConsumer();
+ rabbitMQTaskLaunchConsumer.listen(new TestHandler());
+ } catch (AiravataException e) {
+ logger.error(e.getMessage(), e);
+ }
+ }
+ private void storeServerConfig() throws Exception {
+ Stat stat = curatorClient.checkExists().forPath(gfacServer);
+ if (stat == null) {
+ curatorClient.create().withMode(CreateMode.PERSISTENT).withACL(ZooDefs.Ids.OPEN_ACL_UNSAFE)
+ .forPath(gfacServer, new byte[0]);
+ }
+ String instanceId = ServerSettings.getSetting(Constants.ZOOKEEPER_GFAC_SERVER_NAME);
+ String instanceNode = gfacServer + File.separator + instanceId;
+ stat = curatorClient.checkExists().forPath(instanceNode);
+ if (stat == null) {
+ curatorClient.create().withMode(CreateMode.EPHEMERAL).withACL(ZooDefs.Ids.OPEN_ACL_UNSAFE).forPath(instanceNode, airavataServerHostPort.getBytes());
+ curatorClient.getChildren().watched().forPath(instanceNode);
+ }
+ stat = curatorClient.checkExists().forPath(gfacExperiments);
+ if (stat == null) {
+ curatorClient.create().withMode(CreateMode.PERSISTENT).withACL(ZooDefs.Ids.OPEN_ACL_UNSAFE).forPath(gfacExperiments, airavataServerHostPort.getBytes());
+ }
+ stat = curatorClient.checkExists().forPath(gfacExperiments + File.separator + instanceId);
+ if (stat == null) {
+ curatorClient.create().withMode(CreateMode.PERSISTENT).withACL(ZooDefs.Ids.OPEN_ACL_UNSAFE)
+ .forPath(gfacExperiments + File.separator + instanceId, airavataServerHostPort.getBytes());
+ }
+ }
+
+ private long ByateArrayToLong(byte[] data) {
+ long value = 0;
+ for (int i = 0; i < data.length; i++)
+ {
+ value += ((long) data[i] & 0xffL) << (8 * i);
+ }
+ return value;
+ }
+
+ public String getGFACServiceVersion() throws TException {
+ return gfac_cpi_serviceConstants.GFAC_CPI_VERSION;
+ }
+
+ /**
+ * * After creating the experiment Data and Task Data in the orchestrator
+ * * Orchestrator has to invoke this operation for each Task per experiment to run
+ * * the actual Job related actions.
+ * *
+ * * @param experimentID
+ * * @param taskID
+ * * @param gatewayId:
+ * * The GatewayId is inferred from security context and passed onto gfac.
+ * * @return sucess/failure
+ * *
+ * *
+ *
+ * @param experimentId
+ * @param taskId
+ * @param gatewayId
+ */
+ public boolean submitJob(String experimentId, String taskId, String gatewayId, String tokenId) throws TException {
+ requestCount++;
+ logger.info("-----------------------------------------------------" + requestCount + "-----------------------------------------------------");
+ logger.infoId(experimentId, "GFac Received submit job request for the Experiment: {} TaskId: {}", experimentId, taskId);
+ InputHandlerWorker inputHandlerWorker = new InputHandlerWorker(BetterGfacImpl.getInstance(), experimentId,
+ taskId, gatewayId, tokenId);
+ // try {
+ // if( gfac.submitJob(experimentId, taskId, gatewayId)){
+ logger.debugId(experimentId, "Submitted job to the Gfac Implementation, experiment {}, task {}, gateway " +
+ "{}", experimentId, taskId, gatewayId);
+
+ GFacThreadPoolExecutor.getCachedThreadPool().execute(inputHandlerWorker);
+
+ // we immediately return when we have a threadpool
+ return true;
+ }
+
+ public boolean cancelJob(String experimentId, String taskId, String gatewayId, String tokenId) throws TException {
+ logger.infoId(experimentId, "GFac Received cancel job request for Experiment: {} TaskId: {} ", experimentId, taskId);
+ try {
+ if (BetterGfacImpl.getInstance().cancel(experimentId, taskId, gatewayId, tokenId)) {
+ logger.debugId(experimentId, "Successfully cancelled job, experiment {} , task {}", experimentId, taskId);
+ return true;
+ } else {
+ logger.errorId(experimentId, "Job cancellation failed, experiment {} , task {}", experimentId, taskId);
+ return false;
+ }
+ } catch (Exception e) {
+ logger.errorId(experimentId, "Error cancelling the experiment {}.", experimentId);
+ throw new TException("Error cancelling the experiment : " + e.getMessage(), e);
+ }
+ }
+
+ public Registry getRegistry() {
+ return registry;
+ }
+
+ public void setRegistry(Registry registry) {
+ this.registry = registry;
+ }
+
+ public String getGatewayName() {
+ return gatewayName;
+ }
+
+ public void setGatewayName(String gatewayName) {
+ this.gatewayName = gatewayName;
+ }
+
+ public String getAiravataUserName() {
+ return airavataUserName;
+ }
+
+ public void setAiravataUserName(String airavataUserName) {
+ this.airavataUserName = airavataUserName;
+ }
+
+ protected void setGatewayProperties() throws ApplicationSettingsException {
+ setAiravataUserName(ServerSettings.getDefaultUser());
+ setGatewayName(ServerSettings.getDefaultUserGateway());
+ }
+
+ private GFac getGfac() throws TException {
+ GFac gFac = BetterGfacImpl.getInstance();
+ gFac.init(registry, appCatalog, curatorClient, publisher);
+ return gFac;
+ }
+
+ public void startDaemonHandlers() {
+ List<GFacHandlerConfig> daemonHandlerConfig = null;
+ String className = null;
+ try {
+ URL resource = GfacServerHandler.class.getClassLoader().getResource(org.apache.airavata.common.utils.Constants.GFAC_CONFIG_XML);
+ if (resource != null) {
+ gfacConfigFile = new File(resource.getPath());
+ }
+ daemonHandlerConfig = GFacConfiguration.getDaemonHandlers(gfacConfigFile);
+ for (GFacHandlerConfig handlerConfig : daemonHandlerConfig) {
+ className = handlerConfig.getClassName();
+ Class<?> aClass = Class.forName(className).asSubclass(ThreadedHandler.class);
+ ThreadedHandler threadedHandler = (ThreadedHandler) aClass.newInstance();
+ threadedHandler.initProperties(handlerConfig.getProperties());
+ daemonHandlers.add(threadedHandler);
+ }
+ } catch (ParserConfigurationException | IOException | XPathExpressionException | ClassNotFoundException |
+ InstantiationException | IllegalAccessException | GFacHandlerException | SAXException e) {
+ logger.error("Error parsing gfac-config.xml, double check the xml configuration", e);
+ }
+ for (ThreadedHandler tHandler : daemonHandlers) {
+ (new Thread(tHandler)).start();
+ }
+ }
+
+
+ public static void startStatusUpdators(Registry registry, CuratorFramework curatorClient, MonitorPublisher publisher,
+
+ RabbitMQTaskLaunchConsumer rabbitMQTaskLaunchConsumer) {
+ try {
+ String[] listenerClassList = ServerSettings.getActivityListeners();
+ Publisher rabbitMQPublisher = PublisherFactory.createActivityPublisher();
+ for (String listenerClass : listenerClassList) {
+ Class<? extends AbstractActivityListener> aClass = Class.forName(listenerClass).asSubclass(AbstractActivityListener.class);
+ AbstractActivityListener abstractActivityListener = aClass.newInstance();
+ activityListeners.add(abstractActivityListener);
+ abstractActivityListener.setup(publisher, registry, curatorClient, rabbitMQPublisher, rabbitMQTaskLaunchConsumer);
+ logger.info("Registering listener: " + listenerClass);
+ publisher.registerListener(abstractActivityListener);
+ }
+ } catch (Exception e) {
+ logger.error("Error loading the listener classes configured in airavata-server.properties", e);
+ }
+ }
+ private static class TestHandler implements MessageHandler{
+ @Override
+ public Map<String, Object> getProperties() {
+ Map<String, Object> props = new HashMap<String, Object>();
+ ArrayList<String> keys = new ArrayList<String>();
+ keys.add(ServerSettings.getLaunchQueueName());
+ keys.add(ServerSettings.getCancelQueueName());
+ props.put(MessagingConstants.RABBIT_ROUTING_KEY, keys);
+ props.put(MessagingConstants.RABBIT_QUEUE, ServerSettings.getLaunchQueueName());
+ return props;
+ }
+
+ @Override
+ public void onMessage(MessageContext message) {
+ TaskSubmitEvent event = new TaskSubmitEvent();
+ TBase messageEvent = message.getEvent();
+ byte[] bytes = new byte[0];
+ try {
+ bytes = ThriftUtils.serializeThriftObject(messageEvent);
+ ThriftUtils.createThriftFromBytes(bytes, event);
+ System.out.println(event.getExperimentId());
+ } catch (TException e) {
+ logger.error(e.getMessage(), e);
+ }
+ }
+ }
+
+ private class TaskLaunchMessageHandler implements MessageHandler {
+ private String experimentNode;
+ private String nodeName;
+
+ public TaskLaunchMessageHandler() {
+ experimentNode = ServerSettings.getSetting(Constants.ZOOKEEPER_GFAC_EXPERIMENT_NODE, "/gfac-experiments");
+ nodeName = ServerSettings.getSetting(Constants.ZOOKEEPER_GFAC_SERVER_NAME,"gfac-node0");
+ }
+
+ public Map<String, Object> getProperties() {
+ Map<String, Object> props = new HashMap<String, Object>();
+ ArrayList<String> keys = new ArrayList<String>();
+ keys.add(ServerSettings.getLaunchQueueName());
+ keys.add(ServerSettings.getCancelQueueName());
+ props.put(MessagingConstants.RABBIT_ROUTING_KEY, keys);
+ props.put(MessagingConstants.RABBIT_QUEUE, ServerSettings.getLaunchQueueName());
+ return props;
+ }
+
+ public void onMessage(MessageContext message) {
+ System.out.println(" Message Received with message id '" + message.getMessageId()
+ + "' and with message type '" + message.getType());
+ if (message.getType().equals(MessageType.LAUNCHTASK)) {
+ try {
+ TaskSubmitEvent event = new TaskSubmitEvent();
+ TBase messageEvent = message.getEvent();
+ byte[] bytes = ThriftUtils.serializeThriftObject(messageEvent);
+ ThriftUtils.createThriftFromBytes(bytes, event);
+ // update experiment status to executing
+ ExperimentStatus status = new ExperimentStatus();
+ status.setExperimentState(ExperimentState.EXECUTING);
+ status.setTimeOfStateChange(Calendar.getInstance().getTimeInMillis());
+ registry.update(RegistryModelType.EXPERIMENT_STATUS, status, event.getExperimentId());
+ experimentNode = ServerSettings.getSetting(Constants.ZOOKEEPER_GFAC_EXPERIMENT_NODE, "/gfac-experiments");
+ try {
+ GFacUtils.createExperimentEntryForPassive(event.getExperimentId(), event.getTaskId(), curatorClient,
+ experimentNode, nodeName, event.getTokenId(), message.getDeliveryTag());
+ AiravataZKUtils.getExpStatePath(event.getExperimentId());
+ submitJob(event.getExperimentId(), event.getTaskId(), event.getGatewayId(), event.getTokenId());
+ } catch (Exception e) {
+ logger.error(e.getMessage(), e);
+ rabbitMQTaskLaunchConsumer.sendAck(message.getDeliveryTag());
+ }
+ } catch (TException e) {
+ logger.error(e.getMessage(), e); //nobody is listening so nothing to throw
+ } catch (RegistryException e) {
+ logger.error("Error while updating experiment status", e);
+ }
+ } else if (message.getType().equals(MessageType.TERMINATETASK)) {
+ boolean cancelSuccess = false;
+ TaskTerminateEvent event = new TaskTerminateEvent();
+ TBase messageEvent = message.getEvent();
+ try {
+ byte[] bytes = ThriftUtils.serializeThriftObject(messageEvent);
+ ThriftUtils.createThriftFromBytes(bytes, event);
+ boolean saveDeliveryTagSuccess = GFacUtils.setExperimentCancel(event.getExperimentId(), curatorClient, message.getDeliveryTag());
+ if (saveDeliveryTagSuccess) {
+ cancelSuccess = cancelJob(event.getExperimentId(), event.getTaskId(), event.getGatewayId(), event.getTokenId());
+ System.out.println(" Message Received with message id '" + message.getMessageId()
+ + "' and with message type '" + message.getType());
+ } else {
+ throw new GFacException("Terminate Task fail to save delivery tag : " + String.valueOf(message.getDeliveryTag()) + " \n" +
+ "This happens when another cancel operation is being processed or experiment is in one of final states, complete|failed|cancelled.");
+ }
+ } catch (Exception e) {
+ logger.error(e.getMessage(), e);
+ }finally {
+ if (cancelSuccess) {
+ // if cancel success , AiravataExperimentStatusUpdator will send an ack to this message.
+ } else {
+ try {
+ if (GFacUtils.ackCancelRequest(event.getExperimentId(), curatorClient)) {
+ if (!rabbitMQTaskLaunchConsumer.isOpen()) {
+ rabbitMQTaskLaunchConsumer.reconnect();
+ }
+ rabbitMQTaskLaunchConsumer.sendAck(message.getDeliveryTag());
+ }
+ } catch (Exception e) {
+ logger.error("Error while ack to cancel request, experimentId: " + event.getExperimentId());
+ }
+ }
+ }
+ }
+ }
+ }
+ }
http://git-wip-us.apache.org/repos/asf/airavata/blob/b4ede9cb/modules/gfac/gfac-service/src/test/java/org/apache/airavata/gfac/client/util/Initialize.java
----------------------------------------------------------------------
diff --cc modules/gfac/gfac-service/src/test/java/org/apache/airavata/gfac/client/util/Initialize.java
index 0000000,651f414..15d384c
mode 000000,100644..100644
--- a/modules/gfac/gfac-service/src/test/java/org/apache/airavata/gfac/client/util/Initialize.java
+++ b/modules/gfac/gfac-service/src/test/java/org/apache/airavata/gfac/client/util/Initialize.java
@@@ -1,0 -1,330 +1,329 @@@
+ /*
+ *
+ * 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.gfac.client.util;
+
+ import org.apache.airavata.common.exception.ApplicationSettingsException;
-import org.apache.airavata.common.utils.AiravataUtils;
+ import org.apache.airavata.common.utils.ServerSettings;
-import org.apache.airavata.persistance.registry.jpa.ResourceType;
-import org.apache.airavata.persistance.registry.jpa.resources.*;
++import org.apache.airavata.experiment.catalog.ResourceType;
++import org.apache.airavata.experiment.catalog.resources.*;
+ import org.apache.airavata.registry.cpi.RegistryException;
+ import org.apache.derby.drda.NetworkServerControl;
+ import org.slf4j.Logger;
+ import org.slf4j.LoggerFactory;
+
+ import java.io.BufferedReader;
+ import java.io.IOException;
+ import java.io.InputStream;
+ import java.io.InputStreamReader;
+ import java.net.InetAddress;
+ import java.sql.*;
+ import java.util.StringTokenizer;
+
+ public class Initialize {
+ private static final Logger logger = LoggerFactory.getLogger(Initialize.class);
+ public static final String DERBY_SERVER_MODE_SYS_PROPERTY = "derby.drda.startNetworkServer";
+ public String scriptName = "registry-derby.sql";
+ private NetworkServerControl server;
+ private static final String delimiter = ";";
+ public static final String PERSISTANT_DATA = "Configuration";
+
+ public Initialize(String scriptName) {
+ this.scriptName = scriptName;
+ }
+
+ public static boolean checkStringBufferEndsWith(StringBuffer buffer, String suffix) {
+ if (suffix.length() > buffer.length()) {
+ return false;
+ }
+ // this loop is done on purpose to avoid memory allocation performance
+ // problems on various JDKs
+ // StringBuffer.lastIndexOf() was introduced in jdk 1.4 and
+ // implementation is ok though does allocation/copying
+ // StringBuffer.toString().endsWith() does massive memory
+ // allocation/copying on JDK 1.5
+ // See http://issues.apache.org/bugzilla/show_bug.cgi?id=37169
+ int endIndex = suffix.length() - 1;
+ int bufferIndex = buffer.length() - 1;
+ while (endIndex >= 0) {
+ if (buffer.charAt(bufferIndex) != suffix.charAt(endIndex)) {
+ return false;
+ }
+ bufferIndex--;
+ endIndex--;
+ }
+ return true;
+ }
+
+ private static boolean isServerStarted(NetworkServerControl server, int ntries)
+ {
+ for (int i = 1; i <= ntries; i ++)
+ {
+ try {
+ Thread.sleep(500);
+ server.ping();
+ return true;
+ }
+ catch (Exception e) {
+ if (i == ntries)
+ return false;
+ }
+ }
+ return false;
+ }
+
+ public void initializeDB() throws SQLException{
+ String jdbcUrl = null;
+ String jdbcUser = null;
+ String jdbcPassword = null;
+ try{
+ jdbcUrl = ServerSettings.getSetting("registry.jdbc.url");
+ jdbcUser = ServerSettings.getSetting("registry.jdbc.user");
+ jdbcPassword = ServerSettings.getSetting("registry.jdbc.password");
+ jdbcUrl = jdbcUrl + "?" + "user=" + jdbcUser + "&" + "password=" + jdbcPassword;
+ } catch (ApplicationSettingsException e) {
+ logger.error("Unable to read properties", e);
+ }
+ startDerbyInServerMode();
+ if(!isServerStarted(server, 20)){
+ throw new RuntimeException("Derby server cound not started within five seconds...");
+ }
+
+ Connection conn = null;
+ try {
+ Class.forName(Utils.getJDBCDriver()).newInstance();
+ conn = DriverManager.getConnection(jdbcUrl, jdbcUser, jdbcPassword);
+ if (!isDatabaseStructureCreated(PERSISTANT_DATA, conn)) {
+ executeSQLScript(conn);
+ logger.info("New Database created for Registry");
+ } else {
+ logger.debug("Database already created for Registry!");
+ }
+ } catch (Exception e) {
+ logger.error(e.getMessage(), e);
+ throw new RuntimeException("Database failure", e);
+ } finally {
+ try {
+ if (conn != null){
+ if (!conn.getAutoCommit()) {
+ conn.commit();
+ }
+ conn.close();
+ }
+ } catch (SQLException e) {
+ logger.error(e.getMessage(), e);
+ }
+ }
+
+ try{
+ GatewayResource gatewayResource = new GatewayResource();
+ gatewayResource.setGatewayId(ServerSettings.getSetting("default.registry.gateway"));
+ gatewayResource.setGatewayName(ServerSettings.getSetting("default.registry.gateway"));
+ gatewayResource.setDomain("test-domain");
+ gatewayResource.setEmailAddress("test-email");
+ gatewayResource.save();
+
+ UserResource userResource = new UserResource();
+ userResource.setUserName(ServerSettings.getSetting("default.registry.user"));
+ userResource.setPassword(ServerSettings.getSetting("default.registry.password"));
+ userResource.save();
+
+ WorkerResource workerResource = (WorkerResource) gatewayResource.create(ResourceType.GATEWAY_WORKER);
+ workerResource.setUser(userResource.getUserName());
+ workerResource.save();
+
+ ProjectResource projectResource = (ProjectResource)workerResource.create(ResourceType.PROJECT);
+ projectResource.setGatewayId(gatewayResource.getGatewayId());
+ projectResource.setId("default");
+ projectResource.setName("default");
+ projectResource.setWorker(workerResource);
+ projectResource.save();
+
+
+ } catch (ApplicationSettingsException e) {
+ logger.error("Unable to read properties", e);
+ throw new SQLException(e.getMessage(), e);
+ } catch (RegistryException e) {
+ logger.error("Unable to save data to registry", e);
+ throw new SQLException(e.getMessage(), e);
+ }
+ }
+
+ public static boolean isDatabaseStructureCreated(String tableName, Connection conn) {
+ try {
+ System.out.println("Running a query to test the database tables existence.");
+ // check whether the tables are already created with a query
+ Statement statement = null;
+ try {
+ statement = conn.createStatement();
+ ResultSet rs = statement.executeQuery("select * from " + tableName);
+ if (rs != null) {
+ rs.close();
+ }
+ } finally {
+ try {
+ if (statement != null) {
+ statement.close();
+ }
+ } catch (SQLException e) {
+ return false;
+ }
+ }
+ } catch (SQLException e) {
+ return false;
+ }
+
+ return true;
+ }
+
+ private void executeSQLScript(Connection conn) throws Exception {
+ StringBuffer sql = new StringBuffer();
+ BufferedReader reader = null;
+ try{
+
+ InputStream inputStream = this.getClass().getClassLoader().getResourceAsStream(scriptName);
+ reader = new BufferedReader(new InputStreamReader(inputStream));
+ String line;
+ while ((line = reader.readLine()) != null) {
+ line = line.trim();
+ if (line.startsWith("//")) {
+ continue;
+ }
+ if (line.startsWith("--")) {
+ continue;
+ }
+ StringTokenizer st = new StringTokenizer(line);
+ if (st.hasMoreTokens()) {
+ String token = st.nextToken();
+ if ("REM".equalsIgnoreCase(token)) {
+ continue;
+ }
+ }
+ sql.append(" ").append(line);
+
+ // SQL defines "--" as a comment to EOL
+ // and in Oracle it may contain a hint
+ // so we cannot just remove it, instead we must end it
+ if (line.indexOf("--") >= 0) {
+ sql.append("\n");
+ }
+ if ((checkStringBufferEndsWith(sql, delimiter))) {
+ executeSQL(sql.substring(0, sql.length() - delimiter.length()), conn);
+ sql.replace(0, sql.length(), "");
+ }
+ }
+ // Catch any statements not followed by ;
+ if (sql.length() > 0) {
+ executeSQL(sql.toString(), conn);
+ }
+ }catch (IOException e){
+ logger.error("Error occurred while executing SQL script for creating Airavata database", e);
+ throw new Exception("Error occurred while executing SQL script for creating Airavata database", e);
+ }finally {
+ if (reader != null) {
+ reader.close();
+ }
+
+ }
+
+ }
+
+ private static void executeSQL(String sql, Connection conn) throws Exception {
+ // Check and ignore empty statements
+ if ("".equals(sql.trim())) {
+ return;
+ }
+
+ Statement statement = null;
+ try {
+ logger.debug("SQL : " + sql);
+
+ boolean ret;
+ int updateCount = 0, updateCountTotal = 0;
+ statement = conn.createStatement();
+ ret = statement.execute(sql);
+ updateCount = statement.getUpdateCount();
+ do {
+ if (!ret) {
+ if (updateCount != -1) {
+ updateCountTotal += updateCount;
+ }
+ }
+ ret = statement.getMoreResults();
+ if (ret) {
+ updateCount = statement.getUpdateCount();
+ }
+ } while (ret);
+
+ logger.debug(sql + " : " + updateCountTotal + " rows affected");
+
+ SQLWarning warning = conn.getWarnings();
+ while (warning != null) {
+ logger.warn(warning + " sql warning");
+ warning = warning.getNextWarning();
+ }
+ conn.clearWarnings();
+ } catch (SQLException e) {
+ if (e.getSQLState().equals("X0Y32")) {
+ // eliminating the table already exception for the derby
+ // database
+ logger.info("Table Already Exists", e);
+ } else {
+ throw new Exception("Error occurred while executing : " + sql, e);
+ }
+ } finally {
+ if (statement != null) {
+ try {
+ statement.close();
+ } catch (SQLException e) {
+ logger.error("Error occurred while closing result set.", e);
+ }
+ }
+ }
+ }
+
+ private void startDerbyInServerMode() {
+ try {
+ System.setProperty(DERBY_SERVER_MODE_SYS_PROPERTY, "true");
+ server = new NetworkServerControl(InetAddress.getByName(Utils.getHost()),
+ 20000,
+ Utils.getJDBCUser(), Utils.getJDBCPassword());
+ java.io.PrintWriter consoleWriter = new java.io.PrintWriter(System.out, true);
+ server.start(consoleWriter);
+ } catch (IOException e) {
+ logger.error("Unable to start Apache derby in the server mode! Check whether " +
+ "specified port is available");
+ } catch (Exception e) {
+ logger.error("Unable to start Apache derby in the server mode! Check whether " +
+ "specified port is available");
+ }
+
+ }
+
+ public void stopDerbyServer() throws SQLException{
+ try {
+ server.shutdown();
+ } catch (Exception e) {
+ logger.error(e.getMessage(), e);
+ throw new SQLException("Error while stopping derby server", e);
+ }
+ }
+ }
http://git-wip-us.apache.org/repos/asf/airavata/blob/b4ede9cb/modules/orchestrator/orchestrator-core/pom.xml
----------------------------------------------------------------------