git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/EcologicalEngineSmartExecutor@132046 82a268e6-3cf1-43bd-a215-b396298e98cf

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

@@ -1,26 +1,40 @@
 package org.gcube.dataanalysis.ecoengine.interfaces;
 
-import java.io.File;
+import java.net.URLEncoder;
-import java.util.ArrayList;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
 
+import org.gcube.contentmanagement.graphtools.utils.HttpRequest;
 import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
-import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
+import org.gcube.dataanalysis.executor.util.InfraRetrieval;
-import org.gcube.dataanalysis.ecoengine.configuration.INFRASTRUCTURE;
-import org.gcube.dataanalysis.ecoengine.datatypes.DatabaseType;
-import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveType;
-import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType;
-import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.DatabaseParameters;
-import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.PrimitiveTypes;
-import org.gcube.dataanalysis.ecoengine.interfaces.Transducerer;
-import org.gcube.dataanalysis.ecoengine.utils.ResourceFactory;
 
+public abstract class StandardLocalInfraAlgorithm extends StandardLocalExternalAlgorithm {
 
-public abstract class StandardLocalInfraAlgorithm extends StandardLocalExternalAlgorithm{
 	
-	public boolean sendNotificationEmail(){
+		
-		return true;
+	public void sendNotificationEmail(String subject, String body) throws Exception {
+		
+		AnalysisLogger.getLogger().debug("Emailing System->Starting request of email in scope "+config.getGcubeScope());
+		
+		String serviceAddress = InfraRetrieval.findEmailingSystemAddress(config.getGcubeScope());
+		
+		String requestForMessage = serviceAddress  + "/messages/writeMessageToUsers" + "?gcube-token=" + config.getGcubeToken();
+		requestForMessage = requestForMessage.replace("http", "https").replace("80", ""); // remove the port (or set it to 443) otherwise you get an SSL error
+
+		AnalysisLogger.getLogger().debug("Emailing System->Request url is going to be " + requestForMessage);
+
+		// put the sender, the recipients, subject and body of the mail here
+		subject=URLEncoder.encode(subject,"UTF-8");
+		body=URLEncoder.encode(body,"UTF-8");
+		String requestParameters = "sender=dataminer&recipients="+config.getGcubeUserName()+"&subject="+subject+"&body="+body;
+
+		String response = HttpRequest.sendPostRequest(requestForMessage, requestParameters);
+		AnalysisLogger.getLogger().debug("Emailing System->Emailing response OK ");
+		
+		if (response==null){
+			Exception e = new Exception("Error in email sending response");
+			throw e;
+		}
+		
 	}
+	
+
 }

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

@@ -77,10 +77,15 @@ public class GenericWorker extends StandardLocalInfraAlgorithm{
 				logger.debug("GenericWorker-> isduplicate:" +isduplicate);
 				logger.debug("GenericWorker-> execution directory:" +config.getConfigPath());
 				logger.debug("GenericWorker-> nodeConfigurationFileObject.getName():" +nodeConfigurationFileObject.getName());
+				logger.debug("GenericWorker-> nodeConfigurationFileObject.getPath():" +nodeConfigurationFileObject.getAbsolutePath());
+				
+				logger.debug("GenericWorker-> session :" +session);
+				logger.debug("GenericWorker-> delete files :" +deleteFiles);
 				
 				File sandboxfile = new File(config.getConfigPath(),nodeConfigurationFileObject.getName());
 				
 				Files.copy(nodeConfigurationFileObject.toPath(), sandboxfile.toPath(), REPLACE_EXISTING);
+				
 				logger.debug("GenericWorker-> copied configuration file as " +sandboxfile.getAbsolutePath());
 				
 				ByteArrayOutputStream baos = new ByteArrayOutputStream();
@@ -88,11 +93,14 @@ public class GenericWorker extends StandardLocalInfraAlgorithm{
 				
 				System.setOut(ps);
 				System.setErr(ps);
-				node.executeNode(leftStartIndex, numberOfLeftElementsToProcess, rightStartIndex, numberOfRightElementsToProcess, isduplicate, 
+				int result = node.executeNode(leftStartIndex, numberOfLeftElementsToProcess, rightStartIndex, numberOfRightElementsToProcess, isduplicate, 
 						config.getConfigPath(), nodeConfigurationFileObject.getName(), "log.txt");
+				System.setOut(origOut);
+				System.setErr(origErr);
 				
 				String log = new String(baos.toByteArray(), StandardCharsets.UTF_8);
 				//manage known issues
+				/*
 				log=log.replace(".XMLStreamException: Unbound namespace URI", "Known Except");
 				log=log.replace("java.io.IOException: Error copying XML", "Known Except");
 				log=log.replace("java.io.FileNotFoundException: /home/gcube/tomcat/tmp/ConfigurationFile", "Known Except");
@@ -101,23 +109,24 @@ public class GenericWorker extends StandardLocalInfraAlgorithm{
 				logger.debug("GenericWorker-> Execution Fulllog" );
 				logger.debug("GenericWorker-> " + log);
 				logger.debug("GenericWorker-> Script executed! " );
+				*/
 				
 				boolean del = sandboxfile.delete();
 				logger.debug("GenericWorker-> deleted sandbox file: "+del );
 				logger.debug("GenericWorker-> all done");
 				
 				
-				
+				//if (log.contains("Exception:")){
-				
+				if (result!= 0){
-				if (log.contains("Exception:")){
 					outputParameters.put(OutputParameter, TASK_FAILURE);
 					String cutLog = URLEncoder.encode(log, "UTF-8");
+					/*
 					int maxlen = 20240;
-					int startidx = log.indexOf("Exception:");
+					
-					log = log.substring(startidx);
 					if (log.length()>maxlen)
 						cutLog = cutLog.substring(0,maxlen)+"...";
-					
+					*/
+					cutLog = log;
 					outputParameters.put("Log", cutLog);
 					logger.debug("GenericWorker-> Failure!");
 				}

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

@@ -3,6 +3,7 @@ package org.gcube.dataanalysis.executor.job.management;
 import java.io.BufferedReader;
 import java.io.InputStream;
 import java.io.InputStreamReader;
+import java.net.URLDecoder;
 import java.util.ArrayList;
 import java.util.LinkedHashMap;
 import java.util.List;
@@ -164,7 +165,7 @@ public class WPSJobManager {
 				if (failure)
 				{
 					exitstatus = GenericWorker.TASK_FAILURE;
-					AnalysisLogger.getLogger().debug("WPSJobManager->Task Number "+taskNumber+" - Failure cause: " + result);
+					AnalysisLogger.getLogger().debug("WPSJobManager->Task Number "+taskNumber+" - Failure cause: " + URLDecoder.decode(result,"UTF-8"));
 				}
 //				AnalysisLogger.getLogger().debug("Process execution finished: " + exitstatus);
 				

src/main/java/org/gcube/dataanalysis/executor/nodes/algorithms/AquamapsSuitableNode.java

@@ -228,6 +228,7 @@ public class AquamapsSuitableNode extends ActorNode {
 		} catch (Exception e) {
 			System.err.println("ERROR " + e);
 			e.printStackTrace();
+			return -1;
 		}
 		finally{
 			

src/main/java/org/gcube/dataanalysis/executor/nodes/algorithms/CMSY.java

@@ -16,6 +16,7 @@ import org.gcube.dataanalysis.ecoengine.interfaces.ActorNode;
 import org.gcube.dataanalysis.ecoengine.utils.IOHelper;
 import org.gcube.dataanalysis.ecoengine.utils.Transformations;
 import org.gcube.dataanalysis.executor.scripts.OSCommand;
+import org.gcube.dataanalysis.executor.util.LocalRScriptsManager;
 import org.gcube.dataanalysis.executor.util.RScriptsManager;
 import org.gcube.dataanalysis.executor.util.StorageUtils;
 
@@ -83,7 +84,7 @@ public class CMSY extends ActorNode {
 	public int executeNode(int leftStartIndex, int numberOfLeftElementsToProcess, int rightStartIndex, int numberOfRightElementsToProcess,  boolean duplicate, String sandboxFolder, String nodeConfigurationFileObject, String logfileNameToProduce) {
 		try {
 			status = 0;
-			config = Transformations.restoreConfig(nodeConfigurationFileObject);
+			config = Transformations.restoreConfig(new File (sandboxFolder,nodeConfigurationFileObject).getAbsolutePath());
 			String outputFile = config.getParam(processOutput);
 			AnalysisLogger.getLogger().info("CMSY expected output "+outputFile);
 			
@@ -93,11 +94,12 @@ public class CMSY extends ActorNode {
 			StorageUtils.downloadInputFile(config.getParam(stocksFile), filestock);
 			AnalysisLogger.getLogger().debug("Check fileID: "+fileid+" "+new File(fileid).exists());
 			AnalysisLogger.getLogger().debug("Check fileStocks: "+filestock+" "+new File(filestock).exists());
-			RScriptsManager scriptmanager = new RScriptsManager();
+			//RScriptsManager scriptmanager = new RScriptsManager();
+			LocalRScriptsManager scriptmanager = new LocalRScriptsManager();
 			
 			HashMap<String,String> codeinj = new HashMap<String,String>();
 			codeinj.put("HLH_M07",config.getParam(stock));
-			config.setConfigPath("./");
+			//config.setConfigPath("./");
 			scriptmanager.executeRScript(config, scriptName, "", new HashMap<String,String>(), "", "outputfile.txt", codeinj, true,false,false,sandboxFolder);
 			
 			outputFileName = scriptmanager.getCurrentOutputFileName();
@@ -109,6 +111,7 @@ public class CMSY extends ActorNode {
 			AnalysisLogger.getLogger().info("CMSY Finished");
 		}catch(Exception e){
 			e.printStackTrace();
+			return -1;
 		}	
 			
 		return 0;

src/main/java/org/gcube/dataanalysis/executor/nodes/algorithms/FAOMSY.java

@@ -102,7 +102,7 @@ public class FAOMSY extends ActorNode {
 	public int executeNode(int leftStartIndex, int numberOfLeftElementsToProcess, int rightStartIndex, int numberOfRightElementsToProcess,  boolean duplicate, String sandboxFolder, String nodeConfigurationFileObject, String logfileNameToProduce) {
 		try {
 			status = 0;
-			config = Transformations.restoreConfig(nodeConfigurationFileObject);
+			config = config = Transformations.restoreConfig(new File (sandboxFolder,nodeConfigurationFileObject).getAbsolutePath());
 			String outputFile = config.getParam(processOutput)+"_part"+rightStartIndex;
 			String nonprocessedoutputFile = config.getParam(nonProcessedOutput)+"_part"+rightStartIndex;
 			AnalysisLogger.getLogger().info("FAOMSY ranges: "+" Li:"+leftStartIndex+" NLi:"+leftStartIndex+" Ri:"+rightStartIndex+" NRi:"+numberOfRightElementsToProcess);
@@ -152,6 +152,7 @@ public class FAOMSY extends ActorNode {
 			AnalysisLogger.getLogger().info("FAOMSY Finished");
 		}catch(Exception e){
 			e.printStackTrace();
+			return -1;
 		}	
 			
 		return 0;

src/main/java/org/gcube/dataanalysis/executor/nodes/algorithms/ICCATVPA.java

@@ -158,7 +158,7 @@ public class ICCATVPA extends ActorNode {
 	public int executeNode(int leftStartIndex, int numberOfLeftElementsToProcess, int rightStartIndex, int numberOfRightElementsToProcess,  boolean duplicate, String sandboxFolder, String nodeConfigurationFileObject, String logfileNameToProduce) {
 		try {
 			status = 0;
-			config = Transformations.restoreConfig(nodeConfigurationFileObject);
+			config = config = Transformations.restoreConfig(new File (sandboxFolder,nodeConfigurationFileObject).getAbsolutePath());
 			
 			String outputFile = config.getParam(processOutputParam);
 			String localzipFile = "iccat_zip.zip"; 
@@ -239,6 +239,7 @@ public class ICCATVPA extends ActorNode {
 			AnalysisLogger.getLogger().info("ICCAT-VPA : Finished");
 		}catch(Exception e){
 			e.printStackTrace();
+			return -1;
 		}	
 			
 		return 0;

src/main/java/org/gcube/dataanalysis/executor/nodes/algorithms/LWR.java

@@ -111,7 +111,7 @@ public class LWR extends ActorNode {
 		String insertQuery = null;
 		try {
 			status = 0;
-			AlgorithmConfiguration config = Transformations.restoreConfig(nodeConfigurationFileObject);
+			AlgorithmConfiguration config = config = Transformations.restoreConfig(new File (sandboxFolder,nodeConfigurationFileObject).getAbsolutePath());
 			config.setConfigPath(sandboxFolder);
 			System.out.println("Initializing DB");
 			dbconnection = DatabaseUtils.initDBSession(config);

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

@@ -1,5 +1,6 @@
 package org.gcube.dataanalysis.executor.nodes.transducers;
 
+import java.io.File;
 import java.util.List;
 
 import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
@@ -69,7 +70,7 @@ public class OccurrenceMergingNode extends ActorNode {
 		
 		try{
 			status = 0;
-			AlgorithmConfiguration config = Transformations.restoreConfig(nodeConfigurationFileObject);
+			AlgorithmConfiguration config = Transformations.restoreConfig(new File(sandboxFolder,nodeConfigurationFileObject).getAbsolutePath());
 			config.setConfigPath(sandboxFolder);
 			processor.setConfiguration(config);
 			AnalysisLogger.getLogger().info("Initializing variables");

src/main/java/org/gcube/dataanalysis/executor/tests/TestEmailingSystem.java

@@ -0,0 +1,69 @@
+package org.gcube.dataanalysis.executor.tests;
+
+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.ecoengine.interfaces.StandardLocalInfraAlgorithm;
+import org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymFlexibleWorkflowTransducer;
+import org.gcube.dataanalysis.executor.nodes.transducers.bionym.utils.YasmeenGlobalParameters;
+
+public class TestEmailingSystem {
+
+	public static void main (String args[]) throws Exception{
+		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.setPersistencePath("./");
+		//config.setGcubeScope("/gcube/devNext/NextNext");
+		config.setGcubeScope("/gcube/devNext/NextNext");
+		config.setParam("ServiceUserName", "gianpaolo.coro");
+		config.setParam("DatabaseDriver", "org.postgresql.Driver");
+		config.setGcubeUserName("gianpaolo.coro");
+		config.setGcubeToken("f9d49d76-cd60-48ed-9f8e-036bcc1fc045-98187548");
+		
+		ScopeProvider.instance.set(config.getGcubeScope());
+		StandardLocalInfraAlgorithm infraAlg = new StandardLocalInfraAlgorithm() {
+			
+			@Override
+			public void shutdown() {
+				// TODO Auto-generated method stub
+				
+			}
+			
+			@Override
+			protected void setInputParameters() {
+				// TODO Auto-generated method stub
+				
+			}
+			
+			@Override
+			protected void process() throws Exception {
+				// TODO Auto-generated method stub
+				
+			}
+			
+			@Override
+			public void init() throws Exception {
+				// TODO Auto-generated method stub
+				
+			}
+			
+			@Override
+			public String getDescription() {
+				// TODO Auto-generated method stub
+				return null;
+			}
+		};
+		infraAlg.setConfiguration(config);
+		infraAlg.sendNotificationEmail("hello&ernrinndnknd","test++èèééé222");
+		
+		
+	}
+	
+
+
+}

src/main/java/org/gcube/dataanalysis/executor/util/InfraRetrieval.java

@@ -55,4 +55,31 @@ public class InfraRetrieval {
 		return addresses;
 	}
 	
+	
+	public static String findEmailingSystemAddress(String scope) throws Exception {
+
+			String resource = "jersey-servlet";
+			String serviceName = "SocialNetworking";
+			String serviceClass = "Portal";
+			SimpleQuery query = ICFactory.queryFor(GCoreEndpoint.class);
+			query.addCondition(String.format("$resource/Profile/ServiceClass/text() eq '%s'",serviceClass));
+			query.addCondition("$resource/Profile/DeploymentData/Status/text() eq 'ready'");
+			query.addCondition(String.format("$resource/Profile/ServiceName/text() eq '%s'",serviceName));
+			query.setResult("$resource/Profile/AccessPoint/RunningInstanceInterfaces//Endpoint[@EntryName/string() eq \""+resource+"\"]/text()");
+
+			DiscoveryClient<String> client = ICFactory.client();
+			List<String> endpoints = client.submit(query);
+			if (endpoints == null || endpoints.isEmpty()) throw new Exception("Cannot retrieve the GCoreEndpoint serviceName: "+serviceName +", serviceClass: " +serviceClass +", in scope: "+scope);
+			
+			String resourceEntyName = endpoints.get(0);
+			
+			if(resourceEntyName==null)
+				throw new Exception("Endpoint:"+resource+", is null for serviceName: "+serviceName +", serviceClass: " +serviceClass +", in scope: "+scope);
+			
+			return resourceEntyName;
+			
+	}
+
+	
+	
 }