git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/EcologicalEngine@55569 82a268e6-3cf1-43bd-a215-b396298e98cf

ecologicalEngine.jardesc

@@ -11,6 +11,6 @@
         </sealing>
     </manifest>
     <selectedElements exportClassFiles="true" exportJavaFiles="false" exportOutputFolder="false">
-        <javaElement handleIdentifier="=EcologicalEngine/src"/>
+        <javaElement handleIdentifier="=EcologicalEngine1.2/src"/>
     </selectedElements>
 </jardesc>

src/org/gcube/dataanalysis/ecoengine/evaluation/bioclimate/BioClimateAnalysis.java

@@ -19,6 +19,8 @@ import org.gcube.dataanalysis.ecoengine.utils.Tuple;
 import org.hibernate.SessionFactory;
 import org.jfree.data.category.DefaultCategoryDataset;
 
+import com.mchange.v1.util.ArrayUtils;
+
 public class BioClimateAnalysis {
 
 	private static String countHighProbabilityCells = "select count(*) from %1$s where probability>%2$s";
@@ -182,9 +184,27 @@ public class BioClimateAnalysis {
 		globalEvolutionAnalysis(null, hspecTables, null, hspecTableNames, probabilityColumn, csquareColumn, threshold);
 	}
 
-
+	private  String[] checkTableNames(String [] tablesNames){
+		ArrayList<String> newtables = new ArrayList<String>();
+		for (String table:tablesNames){
+			int i=1;
+			String originalTable = table;
+			while (newtables.contains(table)){
+				table = originalTable+"_"+i;
+				i++;
+			}
+			newtables.add(table);
+		}
+		String [] tables = new String[tablesNames.length];
+		for (int j=0;j<tablesNames.length;j++){
+			tables[j] = newtables.get(j);
+		}
+		return tables;
+	}
+	
 	public void produceCharts(HashMap<String, HashMap<String, double[]>> GeoMap, String[] tablesNames) {
 		// produce a char for each feature
+		tablesNames = checkTableNames(tablesNames);
 		producedImages = new HashMap<String,Image> ();
 		for (String featurename : GeoMap.keySet()) {
 			DefaultCategoryDataset chart = new DefaultCategoryDataset();

src/org/gcube/dataanalysis/ecoengine/interfaces/Generator.java

@@ -10,14 +10,12 @@ public interface Generator extends ComputationalAgent{
 	
 	public INFRASTRUCTURE getInfrastructure();
 	
-	public void init();
+	public void init() throws Exception;
 	
 	public void setConfiguration(AlgorithmConfiguration config);
 	
 	public void shutdown();
 	
-	public void stopProcess();
-	
 	public String getLoad();
 	
 	public void generate() throws Exception;

src/org/gcube/dataanalysis/ecoengine/interfaces/SpatialProbabilityDistributionNode.java

@@ -1,7 +1,5 @@
 package org.gcube.dataanalysis.ecoengine.interfaces;
 
-import java.util.List;
-
 import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
 
 public interface SpatialProbabilityDistributionNode extends SpatialProbabilityDistribution {
@@ -22,4 +20,8 @@ public interface SpatialProbabilityDistributionNode extends SpatialProbabilityDi
 	public int getNumberOfSpecies();
 	
 	public int getNumberOfGeoInfo();
+	
+	public int getOverallProcessedInfo();
+	
+	public void stop();
 }

src/org/gcube/dataanalysis/ecoengine/processing/LocalSimpleSplitGenerator.java

@@ -140,11 +140,6 @@ public class LocalSimpleSplitGenerator implements Generator {
 		stopInterrupt = true;
 	}
 
-	@Override
-	public void stopProcess() {
-		stopInterrupt = true;
-	}
-
 	// waits for thread to be free
 	private void wait4Thread(int index) {
 		// wait until thread is free

src/org/gcube/dataanalysis/ecoengine/processing/LocalSplitGenerator.java

@@ -222,11 +222,6 @@ public class LocalSplitGenerator implements Generator {
 		
 	}
 
-	@Override
-	public void stopProcess() {
-		stopInterrupt = true;
-	}
-
 	// waits for thread to be free
 	private void wait4Thread(int index) {
 		// wait until thread is free

src/org/gcube/dataanalysis/ecoengine/processing/RainyCloudGenerator.java

@@ -37,7 +37,7 @@ public class RainyCloudGenerator implements Generator {
 
 		// if (oo.status.equals("DONE")||oo.status.equals("ERROR"))
 		if (oo.status.equals("DONE")) {
-			stopProcess();
+			shutdown();
 			return 100f;
 		} else {
 			float remoteStatus = (float) remoteGenerationManager.retrieveCompletion();
@@ -96,10 +96,6 @@ public class RainyCloudGenerator implements Generator {
 
 	@Override
 	public void shutdown() {
-	}
-
-	@Override
-	public void stopProcess() {
 		interruptProcessing = true;
 	}
 

src/org/gcube/dataanalysis/ecoengine/test/PerformanceTests.java

@@ -0,0 +1,37 @@
+package org.gcube.dataanalysis.ecoengine.test;
+
+import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
+import org.gcube.dataanalysis.ecoengine.user.GeneratorT;
+import org.gcube.dataanalysis.ecoengine.user.ModelerT;
+
+public class PerformanceTests {
+
+	public static void main(String[] args) throws Exception {
+		String configPath = "./cfg/";
+		String csquareTable = "hcaf_d";
+		String preprocessedTable = "maxminlat_hspen";
+		String envelopeTable = "hspen";
+		int numberOfResources = 4;
+		String speciesCode = "Fis-22747";
+		String userName = "gianpaolo.coro";
+		String generatorName = "AQUAMAPS_SUITABLE";
+
+		String finalDistributionTable = "hspec_suitable_local";
+
+		// Generate
+		long t0 = System.currentTimeMillis();
+		// Generate
+		AlgorithmConfiguration config = GeneratorT.getGenerationConfig(numberOfResources, generatorName, envelopeTable, preprocessedTable, "", userName, csquareTable, finalDistributionTable, configPath);
+		config.setPersistencePath("./");
+		config.setParam("ServiceUserName", "gianpaolo.coro");
+		config.setParam("DatabaseUserName","utente");
+		config.setParam("DatabasePassword","d4science");
+		config.setParam("DatabaseURL","jdbc:postgresql://dbtest.research-infrastructures.eu/aquamapsorgupdated");
+		config.setParam("DatabaseDriver","org.hibernate.dialect.PostgreSQLDialect");
+				
+		GeneratorT.generate(config);
+		
+		System.out.println("OVERALL ELAPSED: "+(System.currentTimeMillis()-t0));
+	}
+
+}

src/org/gcube/dataanalysis/ecoengine/test/regressions/TestBioClimateAnalysis.java

@@ -27,7 +27,7 @@ public class TestBioClimateAnalysis {
 		"hspen2012_06_02_08_54_48_004",
 		"hspen2012_06_02_08_55_53_415"
 		};
-		
+		/*
 		final String [] envelopeTablesNames = {
 				"hspen2012_06_01_21_52_47_460",
 				"hspen2012_06_01_21_52_47_485",
@@ -40,6 +40,20 @@ public class TestBioClimateAnalysis {
 				"hspen2012_06_02_08_54_48_004",
 				"hspen2012_06_02_08_55_53_415"
 				};
+		*/
+		
+		final String [] envelopeTablesNames = {
+				"test",
+				"test",
+				"test",
+				"test",
+				"test",
+				"test",
+				"test",
+				"test",
+				"test",
+				"test"
+				};
 		
 		
 		bioClimate.speciesEvolutionAnalysis(envelopeTables,envelopeTablesNames, BioClimateAnalysis.salinityMinFeature, BioClimateAnalysis.salinityDefaultRange);

src/org/gcube/dataanalysis/ecoengine/utils/DatabaseFactory.java

@@ -134,10 +134,10 @@ public class DatabaseFactory{
 		Configuration cfg = new Configuration();
 		cfg = cfg.configure(DocumentBuilderFactory.newInstance().newDocumentBuilder().parse(new ByteArrayInputStream(document.asXML().getBytes())));
 		cfg.setProperty("hibernate.hbm2ddl.auto", "create");
-		
+
 		SessionFactory DBSessionFactory = null;
 		DBSessionFactory = cfg.buildSessionFactory();
-
+		
 		// close stream
 		stream.close();
 		return DBSessionFactory;

src/org/gcube/dataanalysis/ecoengine/utils/DatabaseUtils.java

@@ -204,6 +204,7 @@ public class DatabaseUtils {
 				dbHibConnection = DatabaseFactory.initDBConnection(defaultDatabaseFile, config);
 			}
 		} catch (Exception e) {
+			System.out.println("ERROR IN DB INITIALIZATION : "+e.getLocalizedMessage());
 			e.printStackTrace();
 //			AnalysisLogger.getLogger().trace(e);
 		}

src/org/gcube/dataanalysis/ecoengine/utils/Operations.java

@@ -365,11 +365,16 @@ public class Operations {
 		
 		public static int chunkize(int numberOfElements,int partitionFactor){
 			int chunksize = numberOfElements/ partitionFactor;
+			int rest = numberOfElements % partitionFactor;
 			if (chunksize == 0)
 				chunksize = 1;
+			else if (rest !=0)
+				chunksize++;
+			/*
 			int numOfChunks = numberOfElements / chunksize;
 			if ((numberOfElements % chunksize) != 0)
 				numOfChunks += 1;
+			*/
 			
 			return chunksize;
 		}

src/org/gcube/dataanalysis/ecoengine/utils/ResourceFactory.java

@@ -1,8 +1,14 @@
 package org.gcube.dataanalysis.ecoengine.utils;
 
+import java.util.ArrayList;
+import java.util.List;
+
 import org.gcube.contentmanagement.graphtools.utils.HttpRequest;
 import org.gcube.dataanalysis.ecoengine.connectors.livemonitor.ResourceLoad;
 import org.gcube.dataanalysis.ecoengine.connectors.livemonitor.Resources;
+import org.gcube.dataanalysis.ecoengine.connectors.livemonitor.SingleResource;
+
+import com.google.gson.Gson;
 
 public class ResourceFactory {
 
@@ -42,4 +48,72 @@ public class ResourceFactory {
 		return rs.toString();
 	}
 	
+	public static String getOverallResourceLoad(List<String> resourceLoadJson){
+		long time = -1;
+		double val = 0d;
+		for (String json:resourceLoadJson){
+			String[] arrays = json.replace("[", "").replace("]", "").split(",");
+			Long timestamp = Long.parseLong(arrays[0]);
+			Double value = Double.parseDouble(arrays[1]) ;
+			if (time<0) time = timestamp;
+			val += value;
+		} 
+		
+		ResourceLoad rs = new ResourceLoad(time, val);
+		return rs.toString();
+	}
+	
+	public static String getOverallResources(List<String> resourcesJson){
+		List<SingleResource> generalList = new ArrayList<SingleResource>();
+		int size = resourcesJson.size();
+		if (size==0) return "[]";
+		if (size==1) return resourcesJson.get(0);
+		
+		int i=1;
+		for (String json:resourcesJson){
+			Gson gson = new Gson();
+			Resources rr = gson.fromJson("{\"list\":"+json.replace("resID", "resId")+"}", Resources.class);
+			List<SingleResource> l = rr.list;
+			for (SingleResource sr: l){
+				if (sr.value>0){
+					sr.resId=sr.resId+"."+i;
+					generalList.add(sr);
+				}
+			}
+			i++;
+		} 
+		
+		return HttpRequest.toJSon(generalList).replace("resId", "resID");
+	}
+	
+	public static void main(String[] args){
+		ArrayList<String> arrayL = new ArrayList<String>();
+		arrayL.add("[1339150993573, 1203.0]");
+		arrayL.add("[1339150993573, 2503.0]");
+		arrayL.add("[1339150993573, 503.0]");
+		String s =  getOverallResourceLoad(arrayL);
+		System.out.println("S1:"+s);
+		
+		ArrayList<String> arrayR = new ArrayList<String>();
+		arrayR.add("[" +
+				"{\"resID\":\"Thread_1\",\"value\":100.0}," +
+				"{\"resID\":\"Thread_2\",\"value\":100.0}," +
+				"{\"resID\":\"Thread_3\",\"value\":100.0}," +
+				"{\"resID\":\"Thread_4\",\"value\":100.0}" +
+				"]");
+
+		arrayR.add("[" +
+				"{\"resID\":\"Thread_1\",\"value\":100.0}," +
+				"{\"resID\":\"Thread_2\",\"value\":100.0}," +
+				"{\"resID\":\"Thread_3\",\"value\":100.0}," +
+				"{\"resID\":\"Thread_4\",\"value\":100.0}" +
+				"]");
+
+		
+		String s2 =  getOverallResources(arrayR);
+		System.out.println("S2:"+s2);
+		
+	}
+	
+	
 }