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

pom.xml

@@ -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>

src/main/java/org/gcube/dataanalysis/ecoengine/interfaces/StandardLocalInfraAlgorithm.java

@@ -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();
 

src/main/java/org/gcube/dataanalysis/executor/job/management/GenericWorker.java

@@ -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.error("GenericWorker-> ERROR: " ,e);
-			logger.debug("GenericWorker-> ERROR: " + e.getLocalizedMessage());
 			status = 100f;
 			throw new Exception(e.getLocalizedMessage());
 		}
@@ -163,8 +162,7 @@ public class GenericWorker extends StandardLocalInfraAlgorithm{
 					nodeConfigurationFileObject.delete();
 
 			}catch(Exception e3){
-				e3.printStackTrace();
+				logger.warn("GenericWorker-> Error deleting files",e3);
-				logger.debug("GenericWorker-> Error deleting files");
 			}
 			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!");
 
 	}
 

src/main/java/org/gcube/dataanalysis/executor/nodes/transducers/OccurrenceMergingNode.java

@@ -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");
 		}
 		
 	}