git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/EcologicalEngineSmartExecutor@131527 82a268e6-3cf1-43bd-a215-b396298e98cf
This commit is contained in:
parent
11c044a7bf
commit
4ac15d4fa1
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@ -3,6 +3,7 @@ package org.gcube.dataanalysis.executor.generators;
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import java.util.ArrayList;
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import java.util.List;
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import java.util.Properties;
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import java.util.UUID;
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import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
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import org.gcube.dataanalysis.ecoengine.configuration.ALG_PROPS;
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@ -15,6 +16,7 @@ import org.gcube.dataanalysis.ecoengine.interfaces.ActorNode;
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import org.gcube.dataanalysis.ecoengine.interfaces.Generator;
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import org.gcube.dataanalysis.ecoengine.interfaces.GenericAlgorithm;
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import org.gcube.dataanalysis.executor.job.management.DistributedProcessingAgent;
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import org.gcube.dataanalysis.executor.job.management.DistributedProcessingAgentWPS;
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public class D4ScienceDistributedProcessing implements Generator {
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@ -24,7 +26,7 @@ public class D4ScienceDistributedProcessing implements Generator {
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protected AlgorithmConfiguration config;
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protected ActorNode distributedModel;
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protected String mainclass;
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DistributedProcessingAgent agent;
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DistributedProcessingAgentWPS agent;
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public D4ScienceDistributedProcessing(){
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}
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@ -100,10 +102,13 @@ public class D4ScienceDistributedProcessing implements Generator {
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distributedModel.setup(config);
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String scope = config.getGcubeScope();
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AnalysisLogger.getLogger().info("Using the following scope for the computation:"+scope);
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String owner = config.getParam("ServiceUserName");
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String owner = config.getGcubeUserName();
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int leftNum = distributedModel.getNumberOfLeftElements();
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int rightNum = distributedModel.getNumberOfRightElements();
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agent = new DistributedProcessingAgent(config, scope, owner, mainclass, config.getPersistencePath(), algorithm, defaultContainerFolder, maxMessagesAllowedPerJob, forceUpload, leftNum, rightNum,config.getTaskID());
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if (config.getTaskID()==null || config.getTaskID().length()==0)
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config.setTaskID(""+UUID.randomUUID());
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agent = new DistributedProcessingAgentWPS(config, scope, owner, mainclass, config.getPersistencePath(), algorithm, defaultContainerFolder, maxMessagesAllowedPerJob, forceUpload, leftNum, rightNum,config.getTaskID());
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agent.setLogger(AnalysisLogger.getLogger());
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}
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@ -143,7 +148,7 @@ public class D4ScienceDistributedProcessing implements Generator {
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@Override
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public String getDescription() {
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return "A D4Science Cloud Processor for Species Distributions";
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return "A D4Science Cloud Processor";
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}
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}
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@ -0,0 +1,149 @@
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package org.gcube.dataanalysis.executor.generators;
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import java.util.ArrayList;
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import java.util.List;
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import java.util.Properties;
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import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
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import org.gcube.dataanalysis.ecoengine.configuration.ALG_PROPS;
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import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
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import org.gcube.dataanalysis.ecoengine.configuration.INFRASTRUCTURE;
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import org.gcube.dataanalysis.ecoengine.datatypes.ServiceType;
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import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType;
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import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.ServiceParameters;
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import org.gcube.dataanalysis.ecoengine.interfaces.ActorNode;
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import org.gcube.dataanalysis.ecoengine.interfaces.Generator;
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import org.gcube.dataanalysis.ecoengine.interfaces.GenericAlgorithm;
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import org.gcube.dataanalysis.executor.job.management.DistributedProcessingAgent;
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public class D4ScienceDistributedProcessingExecutor implements Generator {
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public static int maxMessagesAllowedPerJob = 20;
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public static boolean forceUpload = true;
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public static String defaultContainerFolder = "PARALLEL_PROCESSING";
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protected AlgorithmConfiguration config;
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protected ActorNode distributedModel;
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protected String mainclass;
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DistributedProcessingAgent agent;
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public D4ScienceDistributedProcessingExecutor(){
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}
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public D4ScienceDistributedProcessingExecutor(AlgorithmConfiguration config) {
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this.config = config;
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AnalysisLogger.setLogger(config.getConfigPath() + AlgorithmConfiguration.defaultLoggerFile);
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}
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public void compute() throws Exception {
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try {
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agent.compute();
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distributedModel.postProcess(agent.hasResentMessages(),false);
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} catch (Exception e) {
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distributedModel.postProcess(false,true);
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AnalysisLogger.getLogger().error("ERROR: An Error occurred ", e);
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throw e;
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} finally {
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shutdown();
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}
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}
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@Override
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public List<StatisticalType> getInputParameters() {
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List<StatisticalType> distributionModelParams = new ArrayList<StatisticalType>();
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distributionModelParams.add(new ServiceType(ServiceParameters.USERNAME,"ServiceUserName","The final user Name"));
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return distributionModelParams;
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}
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@Override
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public String getResources() {
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return agent.getResources();
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}
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@Override
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public float getStatus() {
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return agent.getStatus();
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}
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@Override
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public StatisticalType getOutput() {
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return distributedModel.getOutput();
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}
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@Override
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public ALG_PROPS[] getSupportedAlgorithms() {
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ALG_PROPS[] p = { ALG_PROPS.PHENOMENON_VS_PARALLEL_PHENOMENON};
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return p;
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}
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@Override
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public INFRASTRUCTURE getInfrastructure() {
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return INFRASTRUCTURE.D4SCIENCE;
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}
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@Override
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public void init() throws Exception {
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Properties p = AlgorithmConfiguration.getProperties(config.getConfigPath() + AlgorithmConfiguration.nodeAlgorithmsFile);
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String model = config.getModel();
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String algorithm = null;
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if ((model!=null) && (model.length()>0))
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algorithm = model;
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else
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algorithm=config.getAgent();
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mainclass = p.getProperty(algorithm);
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distributedModel = (ActorNode) Class.forName(mainclass).newInstance();
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distributedModel.setup(config);
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String scope = config.getGcubeScope();
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AnalysisLogger.getLogger().info("Using the following scope for the computation:"+scope);
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String owner = config.getParam("ServiceUserName");
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int leftNum = distributedModel.getNumberOfLeftElements();
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int rightNum = distributedModel.getNumberOfRightElements();
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agent = new DistributedProcessingAgent(config, scope, owner, mainclass, config.getPersistencePath(), algorithm, defaultContainerFolder, maxMessagesAllowedPerJob, forceUpload, leftNum, rightNum,config.getTaskID());
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agent.setLogger(AnalysisLogger.getLogger());
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}
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@Override
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public void setConfiguration(AlgorithmConfiguration config) {
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this.config = config;
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AnalysisLogger.setLogger(config.getConfigPath() + AlgorithmConfiguration.defaultLoggerFile);
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}
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@Override
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public void shutdown() {
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try {
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agent.shutdown();
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} catch (Exception e) {
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}
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try {
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distributedModel.stop();
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} catch (Exception e) {
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}
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}
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@Override
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public String getLoad() {
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return agent.getLoad();
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}
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@Override
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public String getResourceLoad() {
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return agent.getResourceLoad();
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}
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@Override
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public GenericAlgorithm getAlgorithm() {
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return distributedModel;
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}
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@Override
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public String getDescription() {
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return "A D4Science Cloud Processor for Species Distributions";
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}
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}
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@ -0,0 +1,229 @@
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package org.gcube.dataanalysis.executor.job.management;
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import java.io.File;
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import java.io.Serializable;
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import java.util.ArrayList;
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import java.util.List;
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import org.apache.log4j.Logger;
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import org.gcube.contentmanagement.graphtools.utils.HttpRequest;
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import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
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import org.gcube.contentmanagement.lexicalmatcher.utils.FileTools;
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import org.gcube.dataanalysis.ecoengine.configuration.ALG_PROPS;
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import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
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import org.gcube.dataanalysis.ecoengine.configuration.INFRASTRUCTURE;
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import org.gcube.dataanalysis.ecoengine.connectors.livemonitor.ResourceLoad;
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import org.gcube.dataanalysis.ecoengine.connectors.livemonitor.Resources;
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import org.gcube.dataanalysis.ecoengine.utils.Operations;
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import com.thoughtworks.xstream.XStream;
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public class DistributedProcessingAgentWPS {
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protected WPSJobManager jobManager;
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protected boolean deletefiles = true;
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protected String mainclass;
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public int maxElementsAllowedPerJob = 20;
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protected boolean forceUpload = true;
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protected boolean stop;
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protected String gscope;
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protected String userName;
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protected String pathToLib;
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protected String modelName;
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protected String containerFolder;
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protected AlgorithmConfiguration configuration;
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protected int rightSetNumberOfElements;
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protected int leftSetNumberOfElements;
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protected List<String> endpoints;
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protected int subdivisiondiv;
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protected String sessionID;
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protected static String defaultJobOutput = "execution.output";
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protected static String defaultScriptFile = "script";
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protected Logger logger;
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/**
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* A distributed processing agent. Performs a distributed computation doing the MAP of the product of two sets: A and B
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* Splits over B : A x B1 , A x B2, ... , A x Bn
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* Prepares a script to be executed on remote nodes
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* The computation is then sent to remote processors.
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*/
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public DistributedProcessingAgentWPS(AlgorithmConfiguration configuration,
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String gCubeScope,
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String computationOwner,
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String mainClass,
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String pathToLibFolder,
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String modelName,
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String containerFolder,
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int maxElementsPerJob,
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boolean forceReUploadofLibs,
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int leftSetNumberOfElements,
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int rightSetNumberOfElements,
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String sessionID
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) {
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this.stop = false;
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this.deletefiles = true;
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this.gscope=gCubeScope;
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this.mainclass=mainClass;
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this.maxElementsAllowedPerJob=maxElementsPerJob;
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this.forceUpload=forceReUploadofLibs;
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this.configuration=configuration;
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this.rightSetNumberOfElements=rightSetNumberOfElements;
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this.leftSetNumberOfElements=leftSetNumberOfElements;
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this.userName=computationOwner;
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this.pathToLib=pathToLibFolder;
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this.modelName=modelName;
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this.containerFolder=containerFolder;
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this.sessionID = sessionID;
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}
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public void setLogger(Logger logger){
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this.logger=logger;
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}
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public boolean hasResentMessages(){
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return jobManager.hasResentMessages();
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}
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public void compute() throws Exception {
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try {
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if (logger == null){
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logger = AnalysisLogger.getLogger();
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}
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if (gscope == null)
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throw new Exception("Null Scope");
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AnalysisLogger.getLogger().debug("SCOPE: "+gscope);
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jobManager = new WPSJobManager();
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// we split along right dimension so if elements are less than nodes, we should reduce the number of nodes
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// chunkize the number of species in order to lower the computational effort of the workers
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subdivisiondiv = rightSetNumberOfElements / (maxElementsAllowedPerJob);
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int rest = rightSetNumberOfElements % (maxElementsAllowedPerJob);
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if (rest > 0)
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subdivisiondiv++;
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if (subdivisiondiv == 0)
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subdivisiondiv = 1;
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executeWork(leftSetNumberOfElements, rightSetNumberOfElements, 0, subdivisiondiv, deletefiles, forceUpload);
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if (jobManager.wasAborted()) {
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logger.debug("Warning: Job was aborted");
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// distributionModel.postProcess(false,true);
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throw new Exception("Job System Error");
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}
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else{
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//postprocess
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// distributionModel.postProcess(jobManager.hasResentMessages(),false);
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}
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} catch (Exception e) {
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logger.error("ERROR: An Error occurred ", e);
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e.printStackTrace();
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throw e;
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} finally {
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shutdown();
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}
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}
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private void executeWork(int leftNum, int rightNum, int offset, int numberOfResources, boolean deletefiles, boolean forceUpload) throws Exception {
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int[] chunkSizes = Operations.takeChunks(rightNum, numberOfResources);
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List<String> arguments = new ArrayList<String>();
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// chunkize respect to the cells: take a chunk of cells vs all species at each node!
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for (int i = 0; i < chunkSizes.length; i++) {
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String argumentString = "0 " + leftNum + " " + offset + " " + chunkSizes[i];
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arguments.add(argumentString);
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offset += chunkSizes[i];
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logger.debug("Generator-> Argument " + i + ": " + argumentString);
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}
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jobManager.uploadAndExecuteChunkized(configuration,mainclass,arguments,sessionID);
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}
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public String getResources() {
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Resources res = new Resources();
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try {
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int activeNodes = jobManager.getActiveNodes();
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for (int i = 0; i < activeNodes; i++) {
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try {
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res.addResource("Worker_" + (i + 1), 100);
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} catch (Exception e1) {
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}
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}
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} catch (Exception e) {
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AnalysisLogger.getLogger().debug("D4ScienceGenerator->active nodes not ready");
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}
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if ((res != null) && (res.list != null))
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return HttpRequest.toJSon(res.list).replace("resId", "resID");
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else
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return "";
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}
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public float getStatus() {
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try {
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if (stop)
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return 100f;
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else
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if (jobManager!=null)
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return Math.max(0.5f, jobManager.getStatus() * 100f);
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else
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return 0;
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} catch (Exception e) {
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return 0f;
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}
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}
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public ALG_PROPS[] getSupportedAlgorithms() {
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ALG_PROPS[] p = { ALG_PROPS.PHENOMENON_VS_PARALLEL_PHENOMENON};
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return p;
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}
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public INFRASTRUCTURE getInfrastructure() {
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return INFRASTRUCTURE.D4SCIENCE;
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}
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public void shutdown() {
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try {
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jobManager.stop();
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} catch (Exception e) {
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}
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stop = true;
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}
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public String getLoad() {
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long tk = System.currentTimeMillis();
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ResourceLoad rs = null;
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if (jobManager!=null)
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rs = new ResourceLoad(tk, 1*subdivisiondiv);
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else
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rs = new ResourceLoad(tk, 0);
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return rs.toString();
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}
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private long lastTime;
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private int lastProcessed;
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public String getResourceLoad() {
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long thisTime = System.currentTimeMillis();
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int processedRecords = 0;
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if ((jobManager!=null) && (subdivisiondiv>0))
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processedRecords = 1*subdivisiondiv;
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int estimatedProcessedRecords = 0;
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if (processedRecords == lastProcessed) {
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estimatedProcessedRecords = Math.round(((float) thisTime * (float) lastProcessed) / (float) lastTime);
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} else {
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lastProcessed = processedRecords;
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estimatedProcessedRecords = lastProcessed;
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}
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lastTime = thisTime;
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ResourceLoad rs = new ResourceLoad(thisTime, estimatedProcessedRecords);
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return rs.toString();
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}
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}
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@ -9,6 +9,7 @@ import java.io.FileOutputStream;
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import java.io.IOException;
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import java.io.InputStream;
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import java.io.PrintStream;
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import java.net.URLEncoder;
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import java.nio.charset.StandardCharsets;
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import java.nio.file.Files;
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import java.util.UUID;
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@ -37,6 +38,7 @@ public class GenericWorker extends StandardLocalExternalAlgorithm{
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public static String OutputParameter = "Process_Outcome";
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public static String TASK_SUCCESS = "TASK_SUCCESS";
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public static String TASK_FAILURE = "TASK_FAILURE";
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public static String TASK_UNDEFINED = "TASK_UNDEFINED";
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private static void inputStreamToFile(InputStream is, String path) throws FileNotFoundException, IOException {
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FileOutputStream out = new FileOutputStream(new File(path));
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@ -65,9 +67,9 @@ public class GenericWorker extends StandardLocalExternalAlgorithm{
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File tempDir = null ;
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try {
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Handler.activateProtocol();
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String locDir = session;
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if (session == null)
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locDir = ("" + UUID.randomUUID()).replace("-", "");
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// invoke the algorithm
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logger.debug("GenericWorker-> Creating algorithm " + algorithmClass);
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@ -91,7 +93,7 @@ public class GenericWorker extends StandardLocalExternalAlgorithm{
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System.setOut(ps);
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System.setErr(ps);
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node.executeNode(rightStartIndex, numberOfRightElementsToProcess, leftStartIndex, numberOfLeftElementsToProcess, isduplicate,
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node.executeNode(leftStartIndex, numberOfLeftElementsToProcess, rightStartIndex, numberOfRightElementsToProcess, isduplicate,
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config.getConfigPath(), nodeConfigurationFileObject.getName(), "log.txt");
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String log = new String(baos.toByteArray(), StandardCharsets.UTF_8);
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@ -103,8 +105,14 @@ public class GenericWorker extends StandardLocalExternalAlgorithm{
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logger.debug("GenericWorker-> deleted sandbox file: "+del );
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logger.debug("GenericWorker-> all done");
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if (log.contains("Exception:") && log.contains("Caused by:")){
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if (log.contains("Exception:")){
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outputParameters.put(OutputParameter, TASK_FAILURE);
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String cutLog = URLEncoder.encode(log, "UTF-8");
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int maxlen = 20240;
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if (log.length()>maxlen)
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cutLog = cutLog.substring(0,maxlen)+"...";
|
||||
|
||||
outputParameters.put("Log", cutLog);
|
||||
logger.debug("GenericWorker-> Failure!");
|
||||
}
|
||||
else
|
||||
|
|
@ -112,6 +120,7 @@ public class GenericWorker extends StandardLocalExternalAlgorithm{
|
|||
logger.debug("GenericWorker-> Success!");
|
||||
} catch (Throwable e) {
|
||||
outputParameters.put(OutputParameter, TASK_FAILURE);
|
||||
outputParameters.put("Log", e.getLocalizedMessage());
|
||||
e.printStackTrace();
|
||||
logger.debug("GenericWorker-> ERROR: " + e.getLocalizedMessage());
|
||||
status = 100f;
|
||||
|
|
@ -134,6 +143,9 @@ public class GenericWorker extends StandardLocalExternalAlgorithm{
|
|||
logger.debug("GenericWorker-> deleting temporary directory");
|
||||
tempDir.delete();
|
||||
}
|
||||
if (nodeConfigurationFileObject!=null && nodeConfigurationFileObject.exists())
|
||||
nodeConfigurationFileObject.delete();
|
||||
|
||||
}catch(Exception e3){
|
||||
e3.printStackTrace();
|
||||
logger.debug("GenericWorker-> Error deleting files");
|
||||
|
|
@ -157,16 +169,16 @@ public class GenericWorker extends StandardLocalExternalAlgorithm{
|
|||
protected void process() throws Exception {
|
||||
AnalysisLogger.getLogger().debug("Parameters: "+config.getGeneralProperties());
|
||||
|
||||
String algorithmClass = config.getParam("AlgorithmClass");
|
||||
String algorithmClass = config.getParam(AlgorithmClassParameter);
|
||||
|
||||
int rightStartIndex = Integer.parseInt(config.getParam("RightSetStartIndex"));
|
||||
int numberOfRightElementsToProcess =Integer.parseInt(config.getParam("NumberOfRightElementsToProcess"));
|
||||
int leftStartIndex =Integer.parseInt(config.getParam("LeftSetStartIndex"));
|
||||
int numberOfLeftElementsToProcess =Integer.parseInt(config.getParam("NumberOfLeftElementsToProcess"));
|
||||
boolean isduplicate=Boolean.parseBoolean(config.getParam("IsDuplicate"));
|
||||
String session=config.getParam("Session");
|
||||
File nodeConfigurationFileObject=new File (config.getParam("ConfigurationFile"));
|
||||
boolean deleteFiles= Boolean.parseBoolean(config.getParam("DeleteTemporaryFiles"));
|
||||
int rightStartIndex = Integer.parseInt(config.getParam(RightSetStartIndexParameter));
|
||||
int numberOfRightElementsToProcess =Integer.parseInt(config.getParam(NumberOfRightElementsToProcessParameter));
|
||||
int leftStartIndex =Integer.parseInt(config.getParam(LeftSetStartIndexParameter));
|
||||
int numberOfLeftElementsToProcess =Integer.parseInt(config.getParam(NumberOfLeftElementsToProcessParameter));
|
||||
boolean isduplicate=Boolean.parseBoolean(config.getParam(IsDuplicateParameter));
|
||||
String session=config.getParam(SessionParameter);
|
||||
File nodeConfigurationFileObject=new File (config.getParam(ConfigurationFileParameter));
|
||||
boolean deleteFiles= Boolean.parseBoolean(config.getParam(DeleteTemporaryFilesParameter));
|
||||
|
||||
AnalysisLogger.getLogger().debug("Executing the algorithm");
|
||||
executeAlgorithm(algorithmClass, rightStartIndex, numberOfRightElementsToProcess, leftStartIndex, numberOfLeftElementsToProcess, isduplicate, session, nodeConfigurationFileObject, deleteFiles);
|
||||
|
|
@ -177,15 +189,15 @@ public class GenericWorker extends StandardLocalExternalAlgorithm{
|
|||
@Override
|
||||
protected void setInputParameters() {
|
||||
|
||||
addStringInput("AlgorithmClass", "The full class path of the algorithm", "org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymFlexibleWorkflowTransducer");
|
||||
addIntegerInput("RightSetStartIndex", "The start index of the right set in a cartesian product of the input", "1");
|
||||
addIntegerInput("NumberOfRightElementsToProcess", "The number of elements to process in the right set", "1");
|
||||
addIntegerInput("LeftSetStartIndex", "The start index of the left set in a cartesian product of the input", "1");
|
||||
addIntegerInput("NumberOfLeftElementsToProcess", "The number of elements to process in the left set", "1");
|
||||
addBooleanInput("IsDuplicate", "Indicate if this sub computation is a duplicate of another sub-computation", "false");
|
||||
addStringInput("Session", "The session this sub-computation belongs to", "123456");
|
||||
addFileInput("ConfigurationFile", "A configuration file for the algorithm in an XML serialisation format for the AlgorithmConfiguration Object", "config.dat");
|
||||
addBooleanInput("DeleteTemporaryFiles","Delete local temporary files after the computation","true");
|
||||
addStringInput(AlgorithmClassParameter, "The full class path of the algorithm", "org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymFlexibleWorkflowTransducer");
|
||||
addIntegerInput(RightSetStartIndexParameter, "The start index of the right set in a cartesian product of the input", "1");
|
||||
addIntegerInput(NumberOfRightElementsToProcessParameter, "The number of elements to process in the right set", "1");
|
||||
addIntegerInput(LeftSetStartIndexParameter, "The start index of the left set in a cartesian product of the input", "1");
|
||||
addIntegerInput(NumberOfLeftElementsToProcessParameter, "The number of elements to process in the left set", "1");
|
||||
addBooleanInput(IsDuplicateParameter, "Indicate if this sub computation is a duplicate of another sub-computation", "false");
|
||||
addStringInput(SessionParameter, "The session this sub-computation belongs to", "123456");
|
||||
addFileInput(ConfigurationFileParameter, "A configuration file for the algorithm in an XML serialisation format for the AlgorithmConfiguration Object", "config.dat");
|
||||
addBooleanInput(DeleteTemporaryFilesParameter,"Delete local temporary files after the computation","true");
|
||||
}
|
||||
|
||||
@Override
|
||||
|
|
|
|||
|
|
@ -0,0 +1,46 @@
|
|||
package org.gcube.dataanalysis.executor.job.management;
|
||||
|
||||
import java.io.File;
|
||||
|
||||
import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
|
||||
import org.gcube.contentmanagement.lexicalmatcher.utils.FileTools;
|
||||
import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
|
||||
|
||||
import com.thoughtworks.xstream.XStream;
|
||||
|
||||
public class GenericWorkerCaller {
|
||||
|
||||
|
||||
public static String getGenericWorkerCall(String algorithm, String session, AlgorithmConfiguration configuration,int leftSetIndex,int rightSetIndex,int leftElements,int rightElements, boolean isduplicate,boolean deleteTemporaryFiles) throws Exception{
|
||||
ClassLoader classLoader = Thread.currentThread().getContextClassLoader();
|
||||
String xmlconfig = new XStream().toXML(configuration);
|
||||
xmlconfig = xmlconfig.replace("\n", "").replace("\t", "");
|
||||
xmlconfig = xmlconfig.replaceAll(">[ ]+<", "> <");
|
||||
|
||||
AnalysisLogger.getLogger().debug("CONFIG of Task:");
|
||||
AnalysisLogger.getLogger().debug("algorithm: "+algorithm);
|
||||
AnalysisLogger.getLogger().debug("leftSetIndex: "+leftSetIndex);
|
||||
AnalysisLogger.getLogger().debug("leftElements: "+leftElements);
|
||||
AnalysisLogger.getLogger().debug("rightSetIndex: "+rightSetIndex);
|
||||
AnalysisLogger.getLogger().debug("rightElements: "+rightElements);
|
||||
AnalysisLogger.getLogger().debug("session: "+session);
|
||||
AnalysisLogger.getLogger().debug("isduplicate: "+isduplicate);
|
||||
AnalysisLogger.getLogger().debug("deleteTemporaryFiles: "+deleteTemporaryFiles);
|
||||
|
||||
File is = new File(classLoader.getResource("WPSGWTemplate.xml").getFile());
|
||||
String call=FileTools.loadString(is.getAbsolutePath(), "UTF-8");
|
||||
AnalysisLogger.getLogger().debug("call template : "+call);
|
||||
call = call.replace("#"+GenericWorker.AlgorithmClassParameter+"#", algorithm);
|
||||
call = call.replace("#"+GenericWorker.LeftSetStartIndexParameter+"#", ""+leftSetIndex);
|
||||
call = call.replace("#"+GenericWorker.NumberOfLeftElementsToProcessParameter+"#", ""+leftElements);
|
||||
call = call.replace("#"+GenericWorker.RightSetStartIndexParameter+"#", ""+rightSetIndex);
|
||||
call = call.replace("#"+GenericWorker.NumberOfRightElementsToProcessParameter+"#", ""+rightElements);
|
||||
call = call.replace("#"+GenericWorker.SessionParameter+"#", session);
|
||||
call = call.replace("#"+GenericWorker.IsDuplicateParameter+"#", ""+isduplicate);
|
||||
call = call.replace("#"+GenericWorker.DeleteTemporaryFilesParameter+"#", ""+deleteTemporaryFiles);
|
||||
call = call.replace("#"+GenericWorker.ConfigurationFileParameter+"#", ""+xmlconfig);
|
||||
|
||||
return call;
|
||||
|
||||
}
|
||||
}
|
||||
|
|
@ -444,7 +444,7 @@ public class QueueJobManager {
|
|||
// AnalysisLogger.getLogger().info("Contacting node " + (order + 1) + " OK on " + selectedEPR);
|
||||
*/
|
||||
|
||||
ScopeProvider.instance.set(scope);
|
||||
// ScopeProvider.instance.set(scope);
|
||||
|
||||
ExecutorPlugin runExecutorPlugin = new ExecutorPlugin();
|
||||
SmartExecutorPluginQuery runQuery = new SmartExecutorPluginQuery(runExecutorPlugin);
|
||||
|
|
@ -458,7 +458,9 @@ public class QueueJobManager {
|
|||
SpecificEndpointDiscoveryFilter sedf = new SpecificEndpointDiscoveryFilter(selectedEPR);
|
||||
runQuery.setEndpointDiscoveryFilter(sedf);
|
||||
SmartExecutorProxy proxy = new ProxyBuilderImpl<SmartExecutor, SmartExecutorProxy>(runExecutorPlugin, runQuery).build();
|
||||
AnalysisLogger.getLogger().debug("Launching Smart Executor in namely Scope: "+scope+" real scope "+ScopeProvider.instance.get());
|
||||
|
||||
//AnalysisLogger.getLogger().debug("Launching Smart Executor in namely Scope: "+scope+" real scope "+ScopeProvider.instance.get());
|
||||
AnalysisLogger.getLogger().debug("Launching Smart Executor in namely Scope: "+scope);
|
||||
LaunchParameter launchParameter = new LaunchParameter(pluginName, inputs);
|
||||
String excecutionIdentifier = proxy.launch(launchParameter);
|
||||
tasksProxies.add(new WorkerWatcher(proxy, excecutionIdentifier, AnalysisLogger.getLogger()));
|
||||
|
|
|
|||
|
|
@ -1,311 +0,0 @@
|
|||
package org.gcube.dataanalysis.executor.job.management;
|
||||
|
||||
import java.io.File;
|
||||
import java.util.ArrayList;
|
||||
import java.util.HashMap;
|
||||
import java.util.List;
|
||||
import java.util.Map;
|
||||
import java.util.UUID;
|
||||
|
||||
import javax.xml.ws.EndpointReference;
|
||||
|
||||
import org.gcube.common.clients.ProxyBuilderImpl;
|
||||
import org.gcube.common.scope.api.ScopeProvider;
|
||||
import org.gcube.contentmanagement.blobstorage.service.IClient;
|
||||
import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
|
||||
import org.gcube.contentmanager.storageclient.wrapper.AccessType;
|
||||
import org.gcube.contentmanager.storageclient.wrapper.StorageClient;
|
||||
import org.gcube.dataanalysis.executor.scripts.ScriptIOWorker;
|
||||
import org.gcube.vremanagement.executor.api.SmartExecutor;
|
||||
import org.gcube.vremanagement.executor.api.types.LaunchParameter;
|
||||
import org.gcube.vremanagement.executor.client.plugins.ExecutorPlugin;
|
||||
import org.gcube.vremanagement.executor.client.plugins.query.SmartExecutorPluginQuery;
|
||||
import org.gcube.vremanagement.executor.client.plugins.query.filter.SpecificEndpointDiscoveryFilter;
|
||||
import org.gcube.vremanagement.executor.client.proxies.SmartExecutorProxy;
|
||||
import org.gcube.vremanagement.executor.plugin.PluginState;
|
||||
|
||||
public class RemoteJobManager {
|
||||
|
||||
// TODO Chek here:
|
||||
//private static String pluginName = "ExecutorScript";
|
||||
private static String pluginName = "SmartGenericWorker";
|
||||
|
||||
private int actualNumberOfNodes;
|
||||
private List<String> eprs;
|
||||
float status;
|
||||
boolean abort;
|
||||
boolean shutdown;
|
||||
protected int activeNodes;
|
||||
String scope;
|
||||
|
||||
public int getActiveNodes() {
|
||||
return activeNodes;
|
||||
}
|
||||
|
||||
public float getStatus() {
|
||||
return status;
|
||||
}
|
||||
|
||||
public int getNumberOfNodes() {
|
||||
return actualNumberOfNodes;
|
||||
}
|
||||
|
||||
public void setNumberOfNodes(int newNumberOfNodes) {
|
||||
actualNumberOfNodes = newNumberOfNodes;
|
||||
}
|
||||
|
||||
public void init(String scope, int numberOfNodes) throws Exception {
|
||||
this.scope = scope;
|
||||
AnalysisLogger.getLogger().debug("Using the following scope for this computation: "+ scope);
|
||||
shutdown = false;
|
||||
yetuploaded = false;
|
||||
if (eprs == null)
|
||||
actualNumberOfNodes = findNodes(scope);
|
||||
else
|
||||
actualNumberOfNodes = eprs.size();
|
||||
|
||||
if (numberOfNodes < actualNumberOfNodes)
|
||||
actualNumberOfNodes = numberOfNodes;
|
||||
|
||||
}
|
||||
|
||||
public RemoteJobManager(String scope, int numberOfNodes) throws Exception {
|
||||
init(scope, numberOfNodes);
|
||||
}
|
||||
|
||||
public RemoteJobManager(String scope, int numberOfNodes, List<String> eprs) throws Exception {
|
||||
this.eprs = eprs;
|
||||
init(scope, numberOfNodes);
|
||||
}
|
||||
|
||||
List<String> filenames;
|
||||
List<String> fileurls;
|
||||
boolean yetuploaded;
|
||||
String session;
|
||||
|
||||
@SuppressWarnings("unchecked")
|
||||
public boolean uploadAndExecute(String serviceClass, String serviceName, String owner, String localDir, String remoteDir, String outputDir, String script, List<String> arguments, boolean deletefiles) throws Exception {
|
||||
boolean executeAll = false;
|
||||
long t0 = System.currentTimeMillis();
|
||||
//if not yet uploaded , upload required files
|
||||
if (!yetuploaded) {
|
||||
ScopeProvider.instance.set(scope);
|
||||
IClient client = new StorageClient(serviceClass, serviceName, owner, AccessType.SHARED).getClient();
|
||||
// IClient client = new StorageClient(serviceClass, serviceName, owner, AccessType.SHARED, gscope).getClient();
|
||||
File dir = new File(localDir);
|
||||
File[] files = dir.listFiles();
|
||||
AnalysisLogger.getLogger().debug("Start uploading");
|
||||
filenames = new ArrayList<String>();
|
||||
fileurls = new ArrayList<String>();
|
||||
for (File sfile : files) {
|
||||
String localf = sfile.getAbsolutePath();
|
||||
String filename = sfile.getName();
|
||||
String remotef = remoteDir + sfile.getName();
|
||||
client.put(true).LFile(localf).RFile(remotef);
|
||||
String url = client.getUrl().RFile(remotef);
|
||||
AnalysisLogger.getLogger().debug("URL created: " + url);
|
||||
filenames.add(filename);
|
||||
fileurls.add(url);
|
||||
}
|
||||
AnalysisLogger.getLogger().debug("Upload end");
|
||||
yetuploaded = true;
|
||||
session = (""+UUID.randomUUID()).replace("-", "");
|
||||
}
|
||||
|
||||
//if the number of available nodes is higher than zero launch the tasks
|
||||
if (actualNumberOfNodes > 0) {
|
||||
|
||||
AnalysisLogger.getLogger().debug("Executing script on " + actualNumberOfNodes + " nodes");
|
||||
int len = arguments.size();
|
||||
List<WorkerWatcher> tasksProxies = new ArrayList<WorkerWatcher>();
|
||||
activeNodes = 0;
|
||||
//launch the tasks
|
||||
for (int i = 0; i < actualNumberOfNodes; i++) {
|
||||
String argum = "";
|
||||
//supply the arguments if they are available
|
||||
if (i < len)
|
||||
argum = arguments.get(i);
|
||||
//generate the input map according to the arguments
|
||||
Map<String, Object> inputs = generateInput(filenames, fileurls, outputDir, script, argum, i, scope, serviceClass, serviceName, owner, remoteDir,session,deletefiles);
|
||||
AnalysisLogger.getLogger().debug("-> Owner: " + owner + " ServiceClass: " + serviceClass + " ServiceName:" + serviceName + " remoteDir:" + remoteDir);
|
||||
|
||||
|
||||
//take the i-th endpoint of the executor
|
||||
String selectedEPR = eprs.get(i);
|
||||
AnalysisLogger.getLogger().debug("Launching node " + (i + 1) + " on " + selectedEPR);
|
||||
//run the executor script
|
||||
|
||||
/*
|
||||
ExecutorCall call = new ExecutorCall(pluginName, gscope);
|
||||
call.setEndpointReference(selectedEPR);
|
||||
TaskCall task = null;
|
||||
task = call.launch(inputs);
|
||||
TaskProxy proxy = task.getProxy();
|
||||
*/
|
||||
|
||||
ExecutorPlugin runExecutorPlugin = new ExecutorPlugin();
|
||||
SmartExecutorPluginQuery runQuery = new SmartExecutorPluginQuery(runExecutorPlugin);
|
||||
|
||||
/* TODO Add key_value filter here
|
||||
* Tuple<String, String>[] tuples = new Tuple[n];
|
||||
*
|
||||
* runQuery.addConditions(pluginName, tuples);
|
||||
*/
|
||||
runQuery.addConditions(pluginName);
|
||||
SpecificEndpointDiscoveryFilter sedf = new SpecificEndpointDiscoveryFilter(selectedEPR);
|
||||
runQuery.setEndpointDiscoveryFilter(sedf);
|
||||
SmartExecutorProxy proxy = new ProxyBuilderImpl<SmartExecutor, SmartExecutorProxy>(runExecutorPlugin, runQuery).build();
|
||||
|
||||
|
||||
LaunchParameter launchParameter = new LaunchParameter(pluginName, inputs);
|
||||
String excecutionIdentifier = proxy.launch(launchParameter);
|
||||
|
||||
tasksProxies.add(new WorkerWatcher(proxy, excecutionIdentifier, AnalysisLogger.getLogger()));
|
||||
|
||||
AnalysisLogger.getLogger().debug("Launching node " + (i + 1) + " OK on " + selectedEPR);
|
||||
//add the task to the list in order to reuse it
|
||||
}
|
||||
|
||||
activeNodes = actualNumberOfNodes;
|
||||
AnalysisLogger.getLogger().debug("Launch Finished - Controlling Status");
|
||||
int allstatus = 0;
|
||||
abort = false;
|
||||
//control the execution: go until there are active nodes or the process must stop
|
||||
while ((activeNodes != 0) && (!abort) && (!shutdown)) {
|
||||
//for each node get the task state
|
||||
int nworkers = tasksProxies.size();
|
||||
int i=0;
|
||||
while (i < nworkers) {
|
||||
WorkerWatcher proxy = tasksProxies.get(i);
|
||||
|
||||
/* ---- */
|
||||
PluginState enumState = proxy.getState();
|
||||
String state = enumState.toString();
|
||||
/* ----- */
|
||||
|
||||
|
||||
AnalysisLogger.getLogger().debug("REMOTE JOB MANAGER-> STATE " + state );
|
||||
//control for aborted computation
|
||||
abort = ((state == null) || state.equals("FAILED") || (!state.equals("DONE") && !state.equals("RUNNING")));
|
||||
//control for finished computation
|
||||
boolean finished = false;
|
||||
if (state != null)
|
||||
finished = state.equals("DONE");
|
||||
//if finished update the active nodes
|
||||
if (finished) {
|
||||
tasksProxies.remove(i);
|
||||
allstatus++;
|
||||
activeNodes--;
|
||||
nworkers--;
|
||||
if (activeNodes == 0)
|
||||
break;
|
||||
}
|
||||
else
|
||||
i++;
|
||||
|
||||
status = Math.min(((float) allstatus / (float) actualNumberOfNodes) * 100f, 95f);
|
||||
if (abort)
|
||||
break;
|
||||
if (shutdown)
|
||||
break;
|
||||
// AnalysisLogger.getLogger().debug(String.format("Task " + i + "executed started at %Tc with %s state ", proxy.getStartTime(), state));
|
||||
//sleep before polling again
|
||||
Thread.sleep(2000);
|
||||
}
|
||||
}
|
||||
|
||||
activeNodes = 0;
|
||||
|
||||
AnalysisLogger.getLogger().debug("All Tasks have Finished");
|
||||
if (!abort) {
|
||||
AnalysisLogger.getLogger().debug("All Task were successful");
|
||||
/*
|
||||
* List<StorageObject> listElements = client.showDir().RDir(remoteDir); for (StorageObject obj : listElements) { AnalysisLogger.getLogger().debug("obj stored in directory " + remoteDir + ": " + obj.getName()); }
|
||||
*/
|
||||
} else
|
||||
AnalysisLogger.getLogger().debug("Tasks were NOT successful");
|
||||
} else
|
||||
AnalysisLogger.getLogger().debug("Warning: could not execute tasks: No Nodes Available!");
|
||||
AnalysisLogger.getLogger().debug("Whole procedure done in " + (System.currentTimeMillis() - t0) + " ms");
|
||||
status = 100f;
|
||||
return executeAll;
|
||||
}
|
||||
|
||||
public boolean wasAborted() {
|
||||
return abort;
|
||||
}
|
||||
|
||||
public void stop() {
|
||||
shutdown = true;
|
||||
}
|
||||
|
||||
@SuppressWarnings("unchecked")
|
||||
private List<EndpointReference> getFilteredEndpoints(String scopeString){
|
||||
ScopeProvider.instance.set(scopeString);
|
||||
|
||||
ExecutorPlugin executorPlugin = new ExecutorPlugin();
|
||||
SmartExecutorPluginQuery query = new SmartExecutorPluginQuery(executorPlugin);
|
||||
|
||||
/*
|
||||
Tuple<String, String>[] tuples = new Tuple[1];
|
||||
tuples[0] = new Tuple<String, String>("Version", "1.0.0-SNAPSHOT");
|
||||
query.addConditions("SmartGenericWorker", tuples);
|
||||
*/
|
||||
|
||||
query.addConditions(pluginName);
|
||||
|
||||
/* Used to add extra filter to ServiceEndpoint discovery */
|
||||
query.setServiceEndpointQueryFilter(null);
|
||||
|
||||
/* Used to add extra filter to GCore Endpoint discovery */
|
||||
query.setEndpointDiscoveryFilter(null);
|
||||
|
||||
|
||||
return query.fire();
|
||||
}
|
||||
|
||||
|
||||
private int findNodes(String scopeString) throws Exception {
|
||||
return getFilteredEndpoints(scopeString).size();
|
||||
}
|
||||
|
||||
/*
|
||||
private int findNodes(String scopeString) throws Exception {
|
||||
GCUBEScope scope = GCUBEScope.getScope(scopeString);
|
||||
ISClient client = GHNContext.getImplementation(ISClient.class);
|
||||
WSResourceQuery wsquery = client.getQuery(WSResourceQuery.class);
|
||||
wsquery.addAtomicConditions(new AtomicCondition("//gc:ServiceName", "Executor"));
|
||||
wsquery.addAtomicConditions(new AtomicCondition("/child::*[local-name()='Task']/name[text()='"+pluginName+"']", pluginName));
|
||||
List<RPDocument> listdoc = client.execute(wsquery, scope);
|
||||
EndpointReferenceType epr = null;
|
||||
eprs = new ArrayList<EndpointReferenceType>();
|
||||
int numberOfEP = 0;
|
||||
for (RPDocument resource : listdoc) {
|
||||
epr = resource.getEndpoint();
|
||||
numberOfEP++;
|
||||
eprs.add(epr);
|
||||
}
|
||||
AnalysisLogger.getLogger().debug("Found " + numberOfEP + " endpoints");
|
||||
|
||||
return numberOfEP;
|
||||
}
|
||||
*/
|
||||
|
||||
private Map<String, Object> generateInput(Object filenames, Object fileurls, String outputDir, String script, String argum, int i, String scope, String serviceClass, String serviceName, String owner, String remoteDir,String session,boolean deletefiles) {
|
||||
Map<String, Object> inputs = new HashMap<String, Object>();
|
||||
inputs.put("FILE_NAMES", filenames);
|
||||
inputs.put("FILE_URLS", fileurls);
|
||||
inputs.put("OUTPUTDIR", ScriptIOWorker.toInputString(outputDir));
|
||||
inputs.put("SCRIPT", ScriptIOWorker.toInputString(script));
|
||||
inputs.put("ARGUMENTS", ScriptIOWorker.toInputString(argum));
|
||||
inputs.put("NODE_IDENTIFIER", "" + i);
|
||||
inputs.put("SCOPE", ScriptIOWorker.toInputString(scope));
|
||||
inputs.put("SERVICE_CLASS", ScriptIOWorker.toInputString(serviceClass));
|
||||
inputs.put("SERVICE_NAME", ScriptIOWorker.toInputString(serviceName));
|
||||
inputs.put("OWNER", ScriptIOWorker.toInputString(owner));
|
||||
inputs.put("REMOTEDIR", ScriptIOWorker.toInputString(remoteDir));
|
||||
inputs.put("CLEAN_CACHE",""+deletefiles);
|
||||
// inputs.put("SESSION", ScriptIO.toInputString(session));
|
||||
return inputs;
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,326 @@
|
|||
package org.gcube.dataanalysis.executor.job.management;
|
||||
|
||||
import java.io.File;
|
||||
import java.util.ArrayList;
|
||||
import java.util.HashMap;
|
||||
import java.util.LinkedHashMap;
|
||||
import java.util.List;
|
||||
import java.util.Map;
|
||||
import java.util.Timer;
|
||||
import java.util.TimerTask;
|
||||
import java.util.UUID;
|
||||
import java.util.concurrent.ExecutorService;
|
||||
import java.util.concurrent.Executors;
|
||||
|
||||
import javax.jms.ExceptionListener;
|
||||
import javax.jms.JMSException;
|
||||
import javax.jms.Message;
|
||||
import javax.jms.MessageListener;
|
||||
|
||||
import org.apache.activemq.ActiveMQConnection;
|
||||
import org.gcube.common.clients.ProxyBuilderImpl;
|
||||
import org.gcube.common.resources.gcore.ServiceEndpoint;
|
||||
import org.gcube.common.resources.gcore.ServiceEndpoint.AccessPoint;
|
||||
import org.gcube.common.scope.api.ScopeProvider;
|
||||
import org.gcube.contentmanagement.blobstorage.resource.StorageObject;
|
||||
import org.gcube.contentmanagement.blobstorage.service.IClient;
|
||||
import org.gcube.contentmanagement.graphtools.utils.HttpRequest;
|
||||
import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
|
||||
import org.gcube.contentmanager.storageclient.wrapper.AccessType;
|
||||
import org.gcube.contentmanager.storageclient.wrapper.MemoryType;
|
||||
import org.gcube.contentmanager.storageclient.wrapper.StorageClient;
|
||||
import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
|
||||
import org.gcube.dataanalysis.ecoengine.utils.Operations;
|
||||
import org.gcube.dataanalysis.executor.messagequeue.ATTRIBUTE;
|
||||
import org.gcube.dataanalysis.executor.messagequeue.Consumer;
|
||||
import org.gcube.dataanalysis.executor.messagequeue.Producer;
|
||||
import org.gcube.dataanalysis.executor.messagequeue.QCONSTANTS;
|
||||
import org.gcube.dataanalysis.executor.messagequeue.QueueManager;
|
||||
import org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymFlexibleWorkflowTransducer;
|
||||
import org.gcube.dataanalysis.executor.nodes.transducers.bionym.utils.YasmeenGlobalParameters;
|
||||
import org.gcube.dataanalysis.executor.scripts.ScriptIOWorker;
|
||||
import org.gcube.dataanalysis.executor.util.InfraRetrieval;
|
||||
import org.gcube.resources.discovery.client.api.DiscoveryClient;
|
||||
import org.gcube.resources.discovery.client.queries.api.SimpleQuery;
|
||||
import org.gcube.vremanagement.executor.api.SmartExecutor;
|
||||
import org.gcube.vremanagement.executor.api.types.LaunchParameter;
|
||||
import org.gcube.vremanagement.executor.client.plugins.ExecutorPlugin;
|
||||
import org.gcube.vremanagement.executor.client.plugins.query.SmartExecutorPluginQuery;
|
||||
import org.gcube.vremanagement.executor.client.plugins.query.filter.ListEndpointDiscoveryFilter;
|
||||
import org.gcube.vremanagement.executor.client.plugins.query.filter.SpecificEndpointDiscoveryFilter;
|
||||
import org.gcube.vremanagement.executor.client.proxies.SmartExecutorProxy;
|
||||
|
||||
import com.thoughtworks.xstream.XStream;
|
||||
|
||||
import static org.gcube.resources.discovery.icclient.ICFactory.*;
|
||||
|
||||
public class WPSJobManager {
|
||||
|
||||
static final int pollingTime = 5000;
|
||||
static final int maxTrialsPerThread = 3;
|
||||
|
||||
|
||||
int overallFailures = 0;
|
||||
int overallSuccess = 0;
|
||||
int overallTasks = 0;
|
||||
|
||||
|
||||
boolean stopThreads = false;
|
||||
boolean hasResentMessages = false;
|
||||
|
||||
final public synchronized void incrementOverallFailures() {
|
||||
overallFailures++;
|
||||
}
|
||||
|
||||
final public synchronized void hasResentTrue() {
|
||||
if (!hasResentMessages)
|
||||
hasResentMessages=true;
|
||||
}
|
||||
|
||||
final public synchronized void incrementOverallSuccess() {
|
||||
overallSuccess++;
|
||||
}
|
||||
|
||||
final public synchronized void stop() {
|
||||
stopThreads=true;
|
||||
}
|
||||
|
||||
final public synchronized boolean isStopped() {
|
||||
return stopThreads;
|
||||
}
|
||||
|
||||
public class TasksWatcher implements Runnable {
|
||||
AlgorithmConfiguration configuration;
|
||||
String algorithm;
|
||||
String username;
|
||||
String token;
|
||||
String wpsHost;
|
||||
int wpsPort;
|
||||
int taskNumber;
|
||||
String session;
|
||||
public String exitstatus=GenericWorker.TASK_UNDEFINED;
|
||||
int leftSetIndex;
|
||||
int rightSetIndex;
|
||||
int leftElements;
|
||||
int rightElements;
|
||||
|
||||
|
||||
public TasksWatcher(String algorithm, String username, String token, String wpsHost, int wpsPort, String session, int taskNumber, AlgorithmConfiguration configuration, int leftSetIndex, int rightSetIndex, int leftElements, int rightElements) {
|
||||
this.algorithm = algorithm;
|
||||
this.token = token;
|
||||
this.wpsHost = wpsHost;
|
||||
this.wpsPort = wpsPort;
|
||||
this.taskNumber = taskNumber;
|
||||
this.session = session;
|
||||
this.username = username;
|
||||
this.configuration = configuration;
|
||||
this.leftSetIndex = leftSetIndex;
|
||||
this.leftElements = leftElements;
|
||||
this.rightSetIndex = rightSetIndex;
|
||||
this.rightElements = rightElements;
|
||||
}
|
||||
|
||||
|
||||
public void callTask(boolean isduplicate){
|
||||
String url = "http://" + wpsHost + ":" + wpsPort + "/wps/WebProcessingService";
|
||||
|
||||
boolean deleteTemporaryFiles = true;
|
||||
AnalysisLogger.getLogger().debug("Task Number : " + taskNumber+" GO!");
|
||||
try {
|
||||
String algorithmCall = GenericWorkerCaller.getGenericWorkerCall(algorithm, session, configuration, leftSetIndex, rightSetIndex, leftElements, rightElements, isduplicate, deleteTemporaryFiles);
|
||||
String result = HttpRequest.PostXmlString(url, wpsHost, wpsPort, new LinkedHashMap<String, String>(), username, token, algorithmCall);
|
||||
// AnalysisLogger.getLogger().debug("Result: " + result);
|
||||
|
||||
boolean success = false;
|
||||
boolean failure = false;
|
||||
|
||||
if (result.contains(GenericWorker.TASK_SUCCESS))
|
||||
success = true;
|
||||
else if (result.contains(GenericWorker.TASK_FAILURE))
|
||||
failure = true;
|
||||
|
||||
String statusLocation = "";
|
||||
|
||||
while (!success && !isStopped() && (!failure) ) { //while !success and failure
|
||||
if (result == null || result.contains(GenericWorker.TASK_FAILURE) || result.contains("Exception"))
|
||||
failure = true;
|
||||
|
||||
else if (result.contains(GenericWorker.TASK_SUCCESS))
|
||||
success = true;
|
||||
else if (result.contains("<wps:ProcessAccepted>Process Accepted</wps:ProcessAccepted>")) {
|
||||
statusLocation = result.substring(result.indexOf("statusLocation=") + "statusLocation=".length());
|
||||
statusLocation = statusLocation.substring(0, statusLocation.indexOf(">"));
|
||||
statusLocation = statusLocation.replace("\"", "");
|
||||
statusLocation = statusLocation + "&gcube-token=" + token;
|
||||
// AnalysisLogger.getLogger().debug("Status Location: " + statusLocation);
|
||||
result= "";
|
||||
} else {
|
||||
Thread.sleep(pollingTime);
|
||||
result = HttpRequest.sendGetRequest(statusLocation, "");
|
||||
// AnalysisLogger.getLogger().debug("Result in location: " + result);
|
||||
}
|
||||
// request = HttpRequest.sendGetRequest(url, ""); // AnalysisLogger.getLogger().debug("Answer for task "+taskNumber+": "+request); }catch(Exception e){ AnalysisLogger.getLogger().debug("Request failure for task "+taskNumber+": "+e.getLocalizedMessage()); } if (request.contains("<wps:ProcessSucceeded>")) success = true; if (request.contains("<ows:Exception>")){ failure = true; incrementOverallFailures(); } try { Thread.sleep(pollingTime); } catch (InterruptedException e) { e.printStackTrace(); } }
|
||||
}
|
||||
|
||||
if (isStopped() && statusLocation!=null && statusLocation.length()>0){
|
||||
String wpscancel = statusLocation.replace("RetrieveResultServlet", "CancelComputationServlet");
|
||||
result = HttpRequest.sendGetRequest(wpscancel, "");
|
||||
}
|
||||
|
||||
|
||||
exitstatus = GenericWorker.TASK_SUCCESS;
|
||||
if (failure)
|
||||
{
|
||||
exitstatus = GenericWorker.TASK_FAILURE;
|
||||
AnalysisLogger.getLogger().debug("Task Number "+taskNumber+" - Failure cause: " + result);
|
||||
}
|
||||
// AnalysisLogger.getLogger().debug("Process execution finished: " + exitstatus);
|
||||
|
||||
} catch (Exception e) {
|
||||
e.printStackTrace();
|
||||
AnalysisLogger.getLogger().debug(e);
|
||||
AnalysisLogger.getLogger().debug("Task Number "+taskNumber+" - Process exception: " + e.getLocalizedMessage());
|
||||
exitstatus = GenericWorker.TASK_FAILURE;
|
||||
|
||||
}finally{
|
||||
|
||||
}
|
||||
}
|
||||
@Override
|
||||
public void run() {
|
||||
int trials = 0;
|
||||
boolean duplicate = false;
|
||||
while (!exitstatus.equals(GenericWorker.TASK_SUCCESS) && trials<maxTrialsPerThread){
|
||||
callTask(duplicate);
|
||||
if (exitstatus.equals(GenericWorker.TASK_FAILURE)){
|
||||
trials++;
|
||||
hasResentTrue();
|
||||
duplicate = true;
|
||||
AnalysisLogger.getLogger().debug("Task Number "+taskNumber+" - Retrying n."+trials);
|
||||
}
|
||||
}
|
||||
|
||||
if (exitstatus.equals(GenericWorker.TASK_SUCCESS))
|
||||
incrementOverallSuccess();
|
||||
else
|
||||
incrementOverallFailures();
|
||||
|
||||
AnalysisLogger.getLogger().debug("Task Number "+taskNumber+" - Finished: " + exitstatus);
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
public int getNumberOfNodes() {
|
||||
return 1;
|
||||
}
|
||||
|
||||
public int getActiveNodes() {
|
||||
return 1;
|
||||
}
|
||||
|
||||
public float getStatus() {
|
||||
return (float)(overallFailures+overallSuccess)/(float)overallTasks;
|
||||
}
|
||||
|
||||
public boolean wasAborted() {
|
||||
return stopThreads;
|
||||
}
|
||||
|
||||
public boolean hasResentMessages() {
|
||||
return hasResentMessages;
|
||||
}
|
||||
|
||||
public void uploadAndExecuteChunkized(AlgorithmConfiguration configuration, String algorithmClass, List<String> arguments, String session) {
|
||||
ExecutorService executor = null;
|
||||
try{
|
||||
int numberofservices = 1;
|
||||
|
||||
AnalysisLogger.getLogger().debug("Estimating the number of services");
|
||||
|
||||
List<String> wpsservices = InfraRetrieval.retrieveService("DataMiner", configuration.getGcubeScope());
|
||||
|
||||
if (wpsservices==null || wpsservices.size()==0)
|
||||
throw new Exception ("No Dataminer GCore Endpoint found in the VRE "+configuration.getGcubeScope());
|
||||
|
||||
List<String> differentServices = new ArrayList<String>();
|
||||
for (String service:wpsservices){
|
||||
|
||||
service = service.substring(service.indexOf("/")+2);
|
||||
service = service.substring(0,service.indexOf(":"));
|
||||
if (!differentServices.contains(service))
|
||||
differentServices.add(service);
|
||||
|
||||
}
|
||||
numberofservices = differentServices.size();
|
||||
|
||||
AnalysisLogger.getLogger().debug("WPSJobManager->Number of dataminer services "+numberofservices);
|
||||
int parallelisation = numberofservices*2;
|
||||
AnalysisLogger.getLogger().debug("WPSJobManager->Number of parallel processes (parallelisation) : "+parallelisation);
|
||||
|
||||
List<String> wpshosts = InfraRetrieval.retrieveAddresses("DataAnalysis",configuration.getGcubeScope(),"-----");
|
||||
|
||||
if (wpshosts==null || wpshosts.size()==0)
|
||||
throw new Exception ("WPSJobManager->No Dataminer Service Endpoint found in the VRE "+configuration.getGcubeScope());
|
||||
|
||||
|
||||
String wpshost = wpshosts.get(0);
|
||||
wpshost = wpshost.substring(wpshost.indexOf("/")+2);
|
||||
//String wpshostAddress = wpshost.substring(0,wpshost.indexOf(":"));
|
||||
String wpshostAddress = wpshost.substring(0,wpshost.indexOf("/"));
|
||||
//String wpshostPort = wpshost.substring(wpshost.indexOf(":")+1,wpshost.indexOf("/"));
|
||||
//http://dataminer1-devnext.d4science.org:80/wps/gcube/resourc
|
||||
wpshost=wpshostAddress;
|
||||
int wpsport = 80;
|
||||
overallTasks=arguments.size();
|
||||
|
||||
executor = Executors.newFixedThreadPool(parallelisation);
|
||||
int taskNumber = 0;
|
||||
|
||||
AnalysisLogger.getLogger().debug("WPSJobManager->Executing algorithm class:"+algorithmClass);
|
||||
|
||||
|
||||
for (String argument:arguments) {
|
||||
String[] lfnlnr = argument.split(" ");
|
||||
int leftOff = Integer.parseInt(lfnlnr[0]);
|
||||
int leftNum = Integer.parseInt(lfnlnr[1]);
|
||||
int rightOff = Integer.parseInt(lfnlnr[2]);
|
||||
int rightNum = Integer.parseInt(lfnlnr[3]);
|
||||
|
||||
TasksWatcher watcher = new TasksWatcher(algorithmClass,
|
||||
configuration.getGcubeUserName(),
|
||||
configuration.getGcubeToken(),wpshost,wpsport,session,taskNumber,configuration, leftOff, rightOff,leftNum,rightNum);
|
||||
|
||||
executor.execute(watcher);
|
||||
AnalysisLogger.getLogger().debug("WPSJobManager->Task number "+taskNumber+" launched!");
|
||||
taskNumber++;
|
||||
}
|
||||
|
||||
int njobs = overallFailures+overallSuccess;
|
||||
int pnjobs =njobs;
|
||||
while (njobs<overallTasks){
|
||||
Thread.sleep(pollingTime);
|
||||
float percFailure = (float)(overallFailures)/(float)overallTasks;
|
||||
//if (percFailure>0.5)
|
||||
if (overallFailures>0)
|
||||
stop();
|
||||
njobs = overallFailures+overallSuccess;
|
||||
if (pnjobs<njobs){
|
||||
AnalysisLogger.getLogger().debug("WPSJobManager->Number of finished jobs "+njobs+" of "+overallTasks);
|
||||
AnalysisLogger.getLogger().debug("WPSJobManager->Number of errors "+overallFailures+" - perc failure "+percFailure);
|
||||
}
|
||||
}
|
||||
|
||||
AnalysisLogger.getLogger().debug("WPSJobManager->Overall computation finished");
|
||||
}catch(Exception e){
|
||||
e.printStackTrace();
|
||||
}
|
||||
finally{
|
||||
if (executor!=null){
|
||||
AnalysisLogger.getLogger().debug("WPSJobManager->Shutting down the executions");
|
||||
executor.shutdown();
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -70,6 +70,8 @@ public abstract class GenericRScript extends StandardLocalExternalAlgorithm {
|
|||
List<StatisticalType> inputs = getInputParameters();
|
||||
for (String input : inputvariables) {
|
||||
String value = config.getParam(input);
|
||||
if (value == null)
|
||||
value = "";
|
||||
String defaultValue = inputs.get(i).getDefaultValue();
|
||||
defaultValue = defaultValue.replace("(", "\\(").replace(")", "\\)").replace("[", "\\[").replace("]", "\\]").replace("|", "\\|").replace(".", "\\.").replace("?", "\\?").replace("*", "\\*").replace("+", "\\+").replace("{", "\\{").replace("}", "\\}");
|
||||
// inputParameters.put(defaultValue, value);
|
||||
|
|
|
|||
|
|
@ -1,5 +1,8 @@
|
|||
package org.gcube.dataanalysis.executor.tests;
|
||||
|
||||
import org.gcube.common.authorization.library.provider.AuthorizationProvider;
|
||||
import org.gcube.common.authorization.library.provider.SecurityTokenProvider;
|
||||
import org.gcube.common.scope.api.ScopeProvider;
|
||||
import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
|
||||
import org.gcube.dataanalysis.executor.generators.D4ScienceDistributedProcessing;
|
||||
import org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymFlexibleWorkflowTransducer;
|
||||
|
|
@ -11,7 +14,7 @@ public class RegressionTestBiOnym {
|
|||
// Generate
|
||||
AlgorithmConfiguration config = new AlgorithmConfiguration();
|
||||
config.setConfigPath("./cfg/");
|
||||
|
||||
|
||||
config.setParam("DatabaseUserName","utente");
|
||||
config.setParam("DatabasePassword","d4science");
|
||||
config.setParam("DatabaseURL","jdbc:postgresql://statistical-manager.d.d4science.research-infrastructures.eu/testdb");
|
||||
|
|
@ -43,14 +46,15 @@ public class RegressionTestBiOnym {
|
|||
config.setParam(BionymFlexibleWorkflowTransducer.destinationTableParam, "taxamatchoutputlocal");
|
||||
config.setParam(BionymFlexibleWorkflowTransducer.destinationTableLableParam, "taxamatchoutputlabel");
|
||||
//1000
|
||||
// config.setParam(BionymFlexibleWorkflowTransducer.originTableParam, "taxamatchinput1000");
|
||||
// config.setParam(BionymFlexibleWorkflowTransducer.rawnamesColumnParam, "rawstrings");
|
||||
config.setParam(BionymFlexibleWorkflowTransducer.originTableParam, "taxamatchinput1000");
|
||||
config.setParam(BionymFlexibleWorkflowTransducer.rawnamesColumnParam, "rawstrings");
|
||||
|
||||
// config.setParam(BionymFlexibleWorkflowTransducer.originTableParam, "taxamatchinput");
|
||||
// config.setParam(BionymFlexibleWorkflowTransducer.rawnamesColumnParam, "rawstrings");
|
||||
//4
|
||||
config.setParam(BionymFlexibleWorkflowTransducer.originTableParam, "generic_id1ecb405c_980f_47a4_926a_3043d065fc7d");
|
||||
config.setParam(BionymFlexibleWorkflowTransducer.rawnamesColumnParam, "field0");
|
||||
//config.setParam(BionymFlexibleWorkflowTransducer.originTableParam, "generic_id1ecb405c_980f_47a4_926a_3043d065fc7d");
|
||||
//config.setParam(BionymFlexibleWorkflowTransducer.rawnamesColumnParam, "field0");
|
||||
|
||||
//2
|
||||
// config.setParam(BionymFlexibleWorkflowTransducer.originTableParam, "generic_id471e6d50_d243_4112_bc07_e22152438e5c");
|
||||
// config.setParam(BionymFlexibleWorkflowTransducer.rawnamesColumnParam, "field0");
|
||||
|
|
@ -62,7 +66,13 @@ public class RegressionTestBiOnym {
|
|||
config.setAgent("BIONYM");
|
||||
|
||||
config.setPersistencePath("./");
|
||||
config.setGcubeScope( "/gcube");
|
||||
String scope = "/gcube/devNext/NextNext";
|
||||
config.setGcubeScope( scope );
|
||||
ScopeProvider.instance.set(scope);
|
||||
String authorizationToken = "cb289202-e7d6-45ee-8076-a80bc4d4be51-98187548";
|
||||
SecurityTokenProvider.instance.set(authorizationToken);
|
||||
config.setGcubeToken(authorizationToken);
|
||||
config.setGcubeUserName("gianpaolo.coro");
|
||||
// config.setGcubeScope( "/d4science.research-infrastructures.eu");
|
||||
config.setParam("ServiceUserName", "gianpaolo.coro");
|
||||
|
||||
|
|
|
|||
|
|
@ -1,29 +0,0 @@
|
|||
package org.gcube.dataanalysis.executor.tests;
|
||||
|
||||
import java.util.ArrayList;
|
||||
import java.util.List;
|
||||
|
||||
import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
|
||||
import org.gcube.dataanalysis.executor.job.management.RemoteJobManager;
|
||||
|
||||
public class TestRemoteJobLaunch {
|
||||
|
||||
|
||||
public static void main(String [] args) throws Exception{
|
||||
String scope = "/gcube";
|
||||
String serviceClass = "TestGP";
|
||||
String serviceName = "TestGPHome";
|
||||
String owner = "GP";
|
||||
String directory = "./shipping/";
|
||||
String remotedirectory = "/shipping/";
|
||||
String tempDir = "./";
|
||||
String scriptName = "execute.sh";
|
||||
int numberOfNodes = 1;
|
||||
List<String> argums = new ArrayList<String>();
|
||||
argums.add("0_178204_0_3_./");
|
||||
AnalysisLogger.setLogger("./cfg/ALog.properties");
|
||||
RemoteJobManager job = new RemoteJobManager(scope,numberOfNodes);
|
||||
// job.uploadAndExecute(serviceClass, serviceName, owner, directory, remotedirectory, tempDir, scriptName, argums);
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,105 @@
|
|||
package org.gcube.dataanalysis.executor.tests;
|
||||
|
||||
import java.util.ArrayList;
|
||||
import java.util.List;
|
||||
|
||||
import org.gcube.common.scope.api.ScopeProvider;
|
||||
import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
|
||||
import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
|
||||
import org.gcube.dataanalysis.executor.job.management.GenericWorker;
|
||||
import org.gcube.dataanalysis.executor.job.management.WPSJobManager;
|
||||
import org.gcube.dataanalysis.executor.job.management.WPSJobManager.TasksWatcher;
|
||||
import org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymFlexibleWorkflowTransducer;
|
||||
import org.gcube.dataanalysis.executor.nodes.transducers.bionym.utils.YasmeenGlobalParameters;
|
||||
|
||||
public class TestWPSJobs {
|
||||
|
||||
public static AlgorithmConfiguration buildTestConfiguration(){
|
||||
AlgorithmConfiguration config = new AlgorithmConfiguration();
|
||||
config.setConfigPath("./cfg/");
|
||||
AnalysisLogger.setLogger(config.getConfigPath() + AlgorithmConfiguration.defaultLoggerFile);
|
||||
config.setParam("DatabaseUserName", "utente");
|
||||
config.setParam("DatabasePassword", "d4science");
|
||||
config.setParam("DatabaseURL", "jdbc:postgresql://statistical-manager.d.d4science.research-infrastructures.eu/testdb");
|
||||
|
||||
config.setParam(YasmeenGlobalParameters.parserNameParam, YasmeenGlobalParameters.BuiltinParsers.SIMPLE.name());
|
||||
config.setParam(YasmeenGlobalParameters.taxaAuthorityFileParam, YasmeenGlobalParameters.BuiltinDataSources.WORMS_PISCES.name());
|
||||
config.setParam(YasmeenGlobalParameters.activatePreParsingProcessing, "true");
|
||||
config.setParam(YasmeenGlobalParameters.useStemmedGenusAndSpecies, "false");
|
||||
|
||||
config.setParam(BionymFlexibleWorkflowTransducer.matcherParamPrefix + "_" + 1, YasmeenGlobalParameters.BuiltinMatchers.GSAy.name());
|
||||
config.setParam(BionymFlexibleWorkflowTransducer.thresholdParamPrefix + "_" + 1, "0.6");
|
||||
config.setParam(BionymFlexibleWorkflowTransducer.maxresultsParamPrefix + "_" + 1, "10");
|
||||
|
||||
config.setParam(BionymFlexibleWorkflowTransducer.matcherParamPrefix + "_" + 2, YasmeenGlobalParameters.BuiltinMatchers.FUZZYMATCH.name());
|
||||
config.setParam(BionymFlexibleWorkflowTransducer.thresholdParamPrefix + "_" + 2, "0.6");
|
||||
config.setParam(BionymFlexibleWorkflowTransducer.maxresultsParamPrefix + "_" + 2, "10");
|
||||
|
||||
config.setParam(BionymFlexibleWorkflowTransducer.matcherParamPrefix + "_" + 3, YasmeenGlobalParameters.BuiltinMatchers.LEVENSHTEIN.name());
|
||||
config.setParam(BionymFlexibleWorkflowTransducer.thresholdParamPrefix + "_" + 3, "0.4");
|
||||
config.setParam(BionymFlexibleWorkflowTransducer.maxresultsParamPrefix + "_" + 3, "10");
|
||||
|
||||
config.setParam(BionymFlexibleWorkflowTransducer.matcherParamPrefix + "_" + 4, YasmeenGlobalParameters.BuiltinMatchers.TRIGRAM.name());
|
||||
config.setParam(BionymFlexibleWorkflowTransducer.thresholdParamPrefix + "_" + 4, "0.4");
|
||||
config.setParam(BionymFlexibleWorkflowTransducer.maxresultsParamPrefix + "_" + 4, "10");
|
||||
|
||||
config.setParam(BionymFlexibleWorkflowTransducer.destinationTableParam, "taxamatchoutputlocal");
|
||||
config.setParam(BionymFlexibleWorkflowTransducer.destinationTableLableParam, "taxamatchoutputlabel");
|
||||
|
||||
// 4
|
||||
//config.setParam(BionymFlexibleWorkflowTransducer.originTableParam, "generic_id1ecb405c_980f_47a4_926a_3043d065fc7d");
|
||||
//config.setParam(BionymFlexibleWorkflowTransducer.rawnamesColumnParam, "field0");
|
||||
|
||||
config.setParam(BionymFlexibleWorkflowTransducer.originTableParam, "taxamatchinput1000");
|
||||
config.setParam(BionymFlexibleWorkflowTransducer.rawnamesColumnParam, "rawstrings");
|
||||
|
||||
config.setAgent("BIONYM");
|
||||
config.setPersistencePath("./");
|
||||
config.setGcubeScope("/gcube/devNext/NextNext");
|
||||
// config.setGcubeScope("/gcube/devsec/devVRE");
|
||||
config.setParam("ServiceUserName", "gianpaolo.coro");
|
||||
config.setParam("DatabaseDriver", "org.postgresql.Driver");
|
||||
config.setGcubeUserName("gianpaolo.coro");
|
||||
config.setGcubeToken("cb289202-e7d6-45ee-8076-a80bc4d4be51-98187548");
|
||||
|
||||
return config;
|
||||
}
|
||||
|
||||
public static void main1(String[] args) throws Exception {
|
||||
|
||||
String host = "dataminer1-devnext.d4science.org";
|
||||
String session = "12345";
|
||||
int port = 80;
|
||||
String algorithm = "org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymFlexibleWorkflowTransducer";
|
||||
AlgorithmConfiguration config = buildTestConfiguration();
|
||||
|
||||
WPSJobManager manager = new WPSJobManager();
|
||||
TasksWatcher taskWatcher = manager.new TasksWatcher(algorithm, config.getGcubeUserName(), config.getGcubeToken(), host, port, session, 1, config, 1, 1, 1, 1);
|
||||
Thread t = new Thread(taskWatcher);
|
||||
t.start();
|
||||
|
||||
while (taskWatcher.exitstatus.equals(GenericWorker.TASK_UNDEFINED)){
|
||||
Thread.sleep(1000);
|
||||
System.out.print(".");
|
||||
}
|
||||
|
||||
AnalysisLogger.getLogger().debug("Task 1 terminated with output "+taskWatcher.exitstatus );
|
||||
//taskWatcher.run();
|
||||
}
|
||||
|
||||
public static void main(String[] args) throws Exception {
|
||||
AlgorithmConfiguration config = buildTestConfiguration();
|
||||
String algorithm = "org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymFlexibleWorkflowTransducer";
|
||||
ScopeProvider.instance.set(config.getGcubeScope());
|
||||
WPSJobManager jobmanager = new WPSJobManager();
|
||||
int nArguments = 100;
|
||||
List<String> arguments = new ArrayList<String>();
|
||||
for (int i=1;i<=nArguments;i++){
|
||||
String argument = "1 1 "+i+" 1";
|
||||
arguments.add(argument);
|
||||
}
|
||||
String sessionID ="1234";
|
||||
jobmanager.uploadAndExecuteChunkized(config, algorithm, arguments,sessionID);
|
||||
|
||||
}
|
||||
}
|
||||
|
|
@ -29,7 +29,7 @@ public class DataTransferer {
|
|||
//String scope = "/d4science.research-infrastructures.eu/gCubeApps";
|
||||
|
||||
String scope = "/gcube/devsec/devVRE";
|
||||
ScopeProvider.instance.set(scope);
|
||||
//test only ScopeProvider.instance.set(scope);
|
||||
//String transferGHN = "dewn04.madgik.di.uoa.gr";
|
||||
String transferGHN = "access.d4science.org";
|
||||
int transferPort = 8080;
|
||||
|
|
@ -71,7 +71,7 @@ public class DataTransferer {
|
|||
// returns the number of transferred bytes
|
||||
public static boolean transferFileToService(String scope, String username, String service, int port, String fileAbsolutePath, String remoteFolder) throws Exception {
|
||||
AnalysisLogger.getLogger().debug("Transferring file " + fileAbsolutePath + " to " + service + ":" + port);
|
||||
ScopeProvider.instance.set(scope);
|
||||
// ScopeProvider.instance.set(scope);
|
||||
|
||||
AgentLibrary library = transferAgent().at(service, port).build();
|
||||
ArrayList<URI> input = new ArrayList<URI>();
|
||||
|
|
@ -82,7 +82,7 @@ public class DataTransferer {
|
|||
String localfolder = localFile.getParent();
|
||||
String file = localFile.getName();
|
||||
AnalysisLogger.getLogger().debug("Uploading file " + file + " onto storage");
|
||||
ScopeProvider.instance.set(scope);
|
||||
// ScopeProvider.instance.set(scope);
|
||||
AnalysisLogger.getLogger().info("Loading file on scope: " + scope);
|
||||
|
||||
String storagesmpurl = StorageUtils.uploadFilesOnStorage(scope, username, localfolder, "/",file,true);
|
||||
|
|
|
|||
|
|
@ -17,7 +17,7 @@ public class InfraRetrieval {
|
|||
return new ArrayList<String>();
|
||||
|
||||
// AnalysisLogger.getLogger().debug("RetrieveAddressesFromInfra->Setting Scope to " + scope+" and executing query");
|
||||
ScopeProvider.instance.set(scope);
|
||||
// ScopeProvider.instance.set(scope);
|
||||
|
||||
SimpleQuery query = ICFactory.queryFor(ServiceEndpoint.class);
|
||||
query.addCondition("$resource/Profile/Category/text() eq '" + Category + "'").addCondition("$resource/Profile[Name[not(contains(., '" + exclude + "'))]]").setResult("$resource/Profile/AccessPoint/Interface/Endpoint/text()");
|
||||
|
|
@ -31,7 +31,7 @@ public class InfraRetrieval {
|
|||
if (scope == null || scope.length() == 0)
|
||||
return new ArrayList<String>();
|
||||
|
||||
ScopeProvider.instance.set(scope);
|
||||
// ScopeProvider.instance.set(scope);
|
||||
|
||||
SimpleQuery query = ICFactory.queryFor(ServiceEndpoint.class);
|
||||
query.addCondition("$resource/Profile/Category/text() eq '" + Category + "'").addCondition("$resource/Profile/Name/text() eq '" + Name+ "'").addCondition("$resource/Profile[Name[not(contains(., '" + exclude + "'))]]").setResult("$resource/Profile/AccessPoint/Interface/Endpoint/text()");
|
||||
|
|
@ -45,7 +45,7 @@ public class InfraRetrieval {
|
|||
if (scope == null || scope.length() == 0)
|
||||
return new ArrayList<String>();
|
||||
|
||||
ScopeProvider.instance.set(scope);
|
||||
// ScopeProvider.instance.set(scope);
|
||||
|
||||
SimpleQuery query = ICFactory.queryFor(GCoreEndpoint.class);
|
||||
query.addCondition("$resource/Profile/ServiceName/text() eq '"+service+"'").setResult("$resource/Profile/AccessPoint/RunningInstanceInterfaces/Endpoint/text()");
|
||||
|
|
|
|||
|
|
@ -13,6 +13,7 @@ import java.util.LinkedHashMap;
|
|||
import java.util.List;
|
||||
import java.util.UUID;
|
||||
|
||||
import org.gcube.common.authorization.library.provider.SecurityTokenProvider;
|
||||
import org.gcube.common.scope.api.ScopeProvider;
|
||||
import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
|
||||
import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
|
||||
|
|
@ -114,6 +115,7 @@ public class RScriptsManager {
|
|||
String scope = config.getGcubeScope();
|
||||
if (scope == null)
|
||||
scope = ScopeProvider.instance.get();
|
||||
//SecurityTokenProvider.instance.set(authorizationToken);
|
||||
|
||||
AnalysisLogger.getLogger().debug("Current User: " + owner);
|
||||
AnalysisLogger.getLogger().debug("Current Scope: " + scope);
|
||||
|
|
|
|||
|
|
@ -55,7 +55,7 @@ public class StorageUtils {
|
|||
|
||||
public static String uploadFilesOnStorage(String scope, String user, String localFolder, String remoteFolder, String file, boolean httplink) throws Exception {
|
||||
try {
|
||||
ScopeProvider.instance.set(scope);
|
||||
// ScopeProvider.instance.set(scope);
|
||||
AnalysisLogger.getLogger().info("Loading file on scope: " + scope);
|
||||
IClient client = new StorageClient(AlgorithmConfiguration.StatisticalManagerClass, AlgorithmConfiguration.StatisticalManagerService, user, AccessType.SHARED, MemoryType.VOLATILE).getClient();
|
||||
String remotef = remoteFolder+file.replace(" ","%20");
|
||||
|
|
@ -77,7 +77,7 @@ public class StorageUtils {
|
|||
|
||||
public static String uploadFilesOnStorage(String scope, String user, String localFolder, String file) throws Exception {
|
||||
try {
|
||||
ScopeProvider.instance.set(scope);
|
||||
// ScopeProvider.instance.set(scope);
|
||||
AnalysisLogger.getLogger().info("Loading file on scope: " + scope);
|
||||
IClient client = new StorageClient(AlgorithmConfiguration.StatisticalManagerClass, AlgorithmConfiguration.StatisticalManagerService, user, AccessType.SHARED, MemoryType.VOLATILE).getClient();
|
||||
String remotef = "/"+file;
|
||||
|
|
@ -142,7 +142,7 @@ public class StorageUtils {
|
|||
|
||||
public static void downloadFilefromStorage(String scope, String user, String localFolder, String file) throws Exception {
|
||||
try {
|
||||
ScopeProvider.instance.set(scope);
|
||||
// ScopeProvider.instance.set(scope);
|
||||
AnalysisLogger.getLogger().info("Retrieving file on scope: " + scope);
|
||||
IClient client = new StorageClient(AlgorithmConfiguration.StatisticalManagerClass, AlgorithmConfiguration.StatisticalManagerService, user, AccessType.SHARED, MemoryType.VOLATILE).getClient();
|
||||
String remotef = "/"+file;
|
||||
|
|
|
|||
Loading…
Reference in New Issue