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ecological-engine-smart-executor
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git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/EcologicalEngineSmartExecutor@154440 82a268e6-3cf1-43bd-a215-b396298e98cf

This commit is contained in:
Lucio Lelii 2017-09-22 14:37:28 +00:00
parent c5e12d5439
commit df9a34cff0
4 changed files with 131 additions and 107 deletions
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9
pom.xml
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@ -75,6 +75,15 @@
<groupId>org.gcube.core</groupId>
<artifactId>common-scope</artifactId>
</dependency>
<!-- https://mvnrepository.com/artifact/com.googlecode.json-simple/json-simple -->
<dependency>
<groupId>com.googlecode.json-simple</groupId>
<artifactId>json-simple</artifactId>
<version>1.1.1</version>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>

19
src/main/java/org/gcube/dataanalysis/ecoengine/interfaces/StandardLocalInfraAlgorithm.java
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@ -12,6 +12,8 @@ import org.gcube.common.resources.gcore.GCoreEndpoint;
import org.gcube.common.scope.api.ScopeProvider;
import org.gcube.resources.discovery.client.api.DiscoveryClient;
import org.gcube.resources.discovery.client.queries.impl.XQuery;
import org.json.simple.JSONArray;
import org.json.simple.JSONObject;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@ -32,16 +34,27 @@ public abstract class StandardLocalInfraAlgorithm extends StandardLocalExternalA
}
@SuppressWarnings("unchecked")
private boolean sendMessage(String token, String email, String subject, String body) throws Exception {
String socialServiceEnpoint = retrieveSocialServiceEnpoint();
LOGGER.debug("contacting social service endpoint {}",socialServiceEnpoint+SEND_MESSAGE_METHOD+"?gcube-token="+token);
PostMethod putMessage = new PostMethod(socialServiceEnpoint+SEND_MESSAGE_METHOD+"?gcube-token="+token);
String jsonRequest = String.format("{\"subject\":\"%s\", \"body\":\"%s\", \"recipients\":[\"%s\"]}",subject,body, email);
putMessage.setRequestEntity(new StringRequestEntity(jsonRequest, "application/json" , "UTF-8"));
JSONObject obj = new JSONObject();
obj.put("subject", subject);
obj.put("body", body);
JSONArray list = new JSONArray();
list.add(email);
obj.put("recipients", list);
LOGGER.debug("json request is {}", jsonRequest);
//String jsonRequest = String.format("{\"subject\":\"%s\", \"body\":\"%s\", \"recipients\":[{\"id\":\"%s\"}]}",subject,body, email);
putMessage.setRequestEntity(new StringRequestEntity(obj.toJSONString(), "application/json" , "UTF-8"));
LOGGER.debug("json request is {}", obj.toJSONString());
HttpClient httpClient = new HttpClient();

18
src/main/java/org/gcube/dataanalysis/executor/job/management/GenericWorker.java
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@ -13,16 +13,17 @@ import java.net.URLEncoder;
import java.nio.charset.StandardCharsets;
import java.nio.file.Files;
import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
import org.gcube.contentmanager.storageclient.model.protocol.smp.Handler;
import org.gcube.dataanalysis.ecoengine.interfaces.ActorNode;
import org.gcube.dataanalysis.ecoengine.interfaces.StandardLocalInfraAlgorithm;
import org.apache.log4j.Logger;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
public class GenericWorker extends StandardLocalInfraAlgorithm{
private static String genericWorkerDir = "/genericworker/";
private static Logger logger = LoggerFactory.getLogger(GenericWorker.class);
public static String AlgorithmClassParameter = "AlgorithmClass";
public static String RightSetStartIndexParameter = "RightSetStartIndex";
@ -61,7 +62,6 @@ public class GenericWorker extends StandardLocalInfraAlgorithm{
PrintStream origOut = System.out;
PrintStream origErr = System.err;
status = 0f;
Logger logger = AnalysisLogger.getLogger();
StringBuffer sb = new StringBuffer();
File tempDir = null ;
try {
@ -137,8 +137,7 @@ public class GenericWorker extends StandardLocalInfraAlgorithm{
} catch (Throwable e) {
outputParameters.put(OutputParameter, TASK_FAILURE);
outputParameters.put("Log", e.getLocalizedMessage());
e.printStackTrace();
logger.debug("GenericWorker-> ERROR: " + e.getLocalizedMessage());
logger.error("GenericWorker-> ERROR: " ,e);
status = 100f;
throw new Exception(e.getLocalizedMessage());
}
@ -163,8 +162,7 @@ public class GenericWorker extends StandardLocalInfraAlgorithm{
nodeConfigurationFileObject.delete();
}catch(Exception e3){
e3.printStackTrace();
logger.debug("GenericWorker-> Error deleting files");
logger.warn("GenericWorker-> Error deleting files",e3);
}
status = 100f;
}
@ -183,7 +181,7 @@ public class GenericWorker extends StandardLocalInfraAlgorithm{
@Override
protected void process() throws Exception {
AnalysisLogger.getLogger().debug("Parameters: "+config.getGeneralProperties());
logger.debug("Parameters: "+config.getGeneralProperties());
String algorithmClass = config.getParam(AlgorithmClassParameter);
@ -196,9 +194,9 @@ public class GenericWorker extends StandardLocalInfraAlgorithm{
File nodeConfigurationFileObject=new File (config.getParam(ConfigurationFileParameter));
boolean deleteFiles= Boolean.parseBoolean(config.getParam(DeleteTemporaryFilesParameter));
AnalysisLogger.getLogger().debug("Executing the algorithm");
logger.debug("Executing the algorithm");
executeAlgorithm(algorithmClass, rightStartIndex, numberOfRightElementsToProcess, leftStartIndex, numberOfLeftElementsToProcess, isduplicate, session, nodeConfigurationFileObject, deleteFiles);
AnalysisLogger.getLogger().debug("Algorithm executed!");
logger.debug("Algorithm executed!");
}

16
src/main/java/org/gcube/dataanalysis/executor/nodes/transducers/OccurrenceMergingNode.java
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@ -2,8 +2,6 @@ package org.gcube.dataanalysis.executor.nodes.transducers;
import java.io.File;
import java.util.List;
import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
import org.gcube.dataanalysis.ecoengine.configuration.ALG_PROPS;
import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType;
@ -12,9 +10,13 @@ import org.gcube.dataanalysis.ecoengine.transducers.OccurrencePointsMerger;
import org.gcube.dataanalysis.ecoengine.utils.Transformations;
import org.gcube.dataanalysis.executor.generators.D4ScienceDistributedProcessing;
import org.hibernate.SessionFactory;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
public class OccurrenceMergingNode extends ActorNode {
private static Logger logger = LoggerFactory.getLogger(OccurrenceMergingNode.class);
// variables
protected AlgorithmConfiguration currentconfig;
protected SessionFactory dbHibConnection;
@ -69,12 +71,14 @@ public class OccurrenceMergingNode extends ActorNode {
try{
status = 0;
AlgorithmConfiguration config = Transformations.restoreConfig(new File(sandboxFolder,nodeConfigurationFileObject).getAbsolutePath());
String configFileAbsolutePath = new File(sandboxFolder,nodeConfigurationFileObject).getAbsolutePath();
logger.debug("config file absolute path is {}", configFileAbsolutePath);
AlgorithmConfiguration config = Transformations.restoreConfig(configFileAbsolutePath);
config.setConfigPath(sandboxFolder);
processor.setConfiguration(config);
AnalysisLogger.getLogger().info("Initializing variables");
logger.info("Initializing variables");
processor.init();
AnalysisLogger.getLogger().info("Initializing DB");
logger.info("Initializing DB");
processor.initDB(false);
status = 0.5f;
processor.takeRange(leftStartIndex, numberOfLeftElementsToProcess, rightStarIndex, numberOfRightElementsToProcess);
@ -123,7 +127,7 @@ public class OccurrenceMergingNode extends ActorNode {
try {
processor.postProcess();
} catch (Exception e) {
AnalysisLogger.getLogger().info("Postprocessing Inapplicable");
logger.info("Postprocessing Inapplicable");
}
}