git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/EcologicalEngine@55451 82a268e6-3cf1-43bd-a215-b396298e98cf

cfg/nodealgorithms.properties

@@ -0,0 +1 @@
+AQUAMAPS_SUITABLE=org.gcube.dataanalysis.peeng.models.AquamapsSuitableNode

src/org/gcube/dataanalysis/ecoengine/configuration/AlgorithmConfiguration.java

@@ -38,11 +38,15 @@ public class AlgorithmConfiguration extends LexicalEngineConfiguration implement
 	public static String defaultConnectionFile = "DestinationDBHibernate.cfg.xml";
 	public static String defaultLoggerFile = "ALog.properties";
 	public static String algorithmsFile = "algorithms.properties";
+	public static String nodeAlgorithmsFile = "nodealgorithms.properties";
 	public static String generatorsFile = "generators.properties";
 	public static String modelsFile = "models.properties";
 	public static String modelersFile = "modelers.properties";
 	public static String evaluatorsFile = "evaluators.properties";
 	public static String RapidMinerOperatorsFile = "operators.xml";
+	public static String StatisticalManagerService = "StatisticalManager";
+	public static String StatisticalManagerClass = "Services";
+	
 	
 	public static int chunkSize = 100000;
 	public static int refreshResourcesTime = 10;
@@ -69,6 +73,7 @@ public class AlgorithmConfiguration extends LexicalEngineConfiguration implement
 	private String occurrenceCellsTable;
 	private List<String> featuresTable;
 	private List<String> preprocessedTables;
+	private List<String> endpoints;
 	
 	//service and remote
 	private String remoteCalculatorEndpoint;
@@ -79,6 +84,7 @@ public class AlgorithmConfiguration extends LexicalEngineConfiguration implement
 	//modeling
 	private String model;
 	private String generator;
+	private String gcubeScope;
 	
 	//other properties
 	private HashMap<String, String> generalProperties;
@@ -181,4 +187,22 @@ public class AlgorithmConfiguration extends LexicalEngineConfiguration implement
 		AnalysisLogger.getLogger().info("Rapid Miner initialized");
 	}
 
+	public String getGcubeScope() {
+		return gcubeScope;
+	}
+
+	public void setGcubeScope(String gcubeScope) {
+		this.gcubeScope = gcubeScope;
+	}
+
+	public List<String> getEndpoints() {
+		return endpoints;
+	}
+
+	public void setEndpoints(List<String> endpoints) {
+		this.endpoints = endpoints;
+	}
+	
+	
+
 }

src/org/gcube/dataanalysis/ecoengine/configuration/INFRASTRUCTURE.java

@@ -0,0 +1,9 @@
+package org.gcube.dataanalysis.ecoengine.configuration;
+
+public enum INFRASTRUCTURE {
+
+	 RAINY_CLOUD,
+	 D4SCIENCE,
+	 LOCAL
+	 
+}

src/org/gcube/dataanalysis/ecoengine/configuration/WEIGHT.java

@@ -1,13 +0,0 @@
-package org.gcube.dataanalysis.ecoengine.configuration;
-
-public enum WEIGHT {
-
-	 VERY_HIGH,
-	 HIGH,
-	 MEDIUM_HIGH,
-	 MEDIUM,
-	 MEDIUM_LOW,
-	 LOW,
-	 LOWEST
-	 
-}

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

@@ -2,7 +2,7 @@ package org.gcube.dataanalysis.ecoengine.interfaces;
 
 import java.util.HashMap;
 
-import org.gcube.dataanalysis.ecoengine.configuration.WEIGHT;
+import org.gcube.dataanalysis.ecoengine.configuration.INFRASTRUCTURE;
 import org.gcube.dataanalysis.ecoengine.utils.VARTYPE;
 import org.gcube.dataanalysis.ecoengine.utils.VarCouple;
 
@@ -18,7 +18,7 @@ public interface ComputationalAgent {
 	public float getStatus();
 	
 	//gets the weight of the generator: according to this the generator will be placed in the execution order
-	public WEIGHT getWeight();
+	public INFRASTRUCTURE getInfrastructure();
 	
 	// gets the type of the content inside the generator: String, File, HashMap. 
 	public VARTYPE getContentType();

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

@@ -4,7 +4,7 @@ import java.util.HashMap;
 import java.util.List;
 
 import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
-import org.gcube.dataanalysis.ecoengine.configuration.WEIGHT;
+import org.gcube.dataanalysis.ecoengine.configuration.INFRASTRUCTURE;
 import org.gcube.dataanalysis.ecoengine.utils.ResourceFactory;
 import org.gcube.dataanalysis.ecoengine.utils.VarCouple;
 
@@ -97,8 +97,8 @@ public abstract class DataAnalysis implements Evaluator{
 	 * The weight of this procedure is the lowest as it runs on local machine
 	 */
 	@Override
-	public WEIGHT getWeight() {
+	public INFRASTRUCTURE getInfrastructure() {
-		return WEIGHT.LOWEST;
+		return INFRASTRUCTURE.LOCAL;
 	}
 
 	/**

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

@@ -2,14 +2,13 @@ package org.gcube.dataanalysis.ecoengine.interfaces;
 
 import org.gcube.dataanalysis.ecoengine.configuration.ALG_PROPS;
 import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
-import org.gcube.dataanalysis.ecoengine.configuration.WEIGHT;
+import org.gcube.dataanalysis.ecoengine.configuration.INFRASTRUCTURE;
 
 public interface Generator extends ComputationalAgent{
 
 	public ALG_PROPS[] getSupportedAlgorithms();
 	
-	//gets the weight of the generator: according to this the generator will be placed in the execution order
+	public INFRASTRUCTURE getInfrastructure();
-	public WEIGHT getWeight();
 	
 	public void init();
 	

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

@@ -2,14 +2,14 @@ package org.gcube.dataanalysis.ecoengine.interfaces;
 
 import org.gcube.dataanalysis.ecoengine.configuration.ALG_PROPS;
 import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
-import org.gcube.dataanalysis.ecoengine.configuration.WEIGHT;
+import org.gcube.dataanalysis.ecoengine.configuration.INFRASTRUCTURE;
 
 public interface Modeler extends ComputationalAgent{
 
 	public ALG_PROPS[] getSupportedModels();
 	
 	//gets the weight of the generator: according to this the generator will be placed in the execution order
-	public WEIGHT getWeight();
+	public INFRASTRUCTURE getInfrastructure();
 	
 	public void setmodel(Model model);
 	

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

@@ -0,0 +1,25 @@
+package org.gcube.dataanalysis.ecoengine.interfaces;
+
+import java.util.List;
+
+import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
+
+public interface SpatialProbabilityDistributionNode extends SpatialProbabilityDistribution {
+			
+	//initialization of the distribution model
+	public void initSingleNode(AlgorithmConfiguration config);
+	
+	//preprocessing after the whole calculation
+	public void postProcess();
+
+	//get the internal processing status for the single step calculation
+	public float getInternalStatus();
+	
+	public int executeNode(int cellOrdinal, int chunksize, int speciesOrdinal, int speciesChunkSize, String pathToFiles, String logfile);
+	
+	public void setup(AlgorithmConfiguration config) throws Exception;
+	
+	public int getNumberOfSpecies();
+	
+	public int getNumberOfGeoInfo();
+}

src/org/gcube/dataanalysis/ecoengine/modeling/SimpleModeler.java

@@ -4,7 +4,7 @@ import java.util.HashMap;
 
 import org.gcube.dataanalysis.ecoengine.configuration.ALG_PROPS;
 import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
-import org.gcube.dataanalysis.ecoengine.configuration.WEIGHT;
+import org.gcube.dataanalysis.ecoengine.configuration.INFRASTRUCTURE;
 import org.gcube.dataanalysis.ecoengine.interfaces.Model;
 import org.gcube.dataanalysis.ecoengine.interfaces.Modeler;
 import org.gcube.dataanalysis.ecoengine.utils.VARTYPE;
@@ -69,8 +69,8 @@ public class SimpleModeler implements Modeler{
 	}
 
 	@Override
-	public WEIGHT getWeight() {
+	public INFRASTRUCTURE getInfrastructure() {
-		return WEIGHT.LOWEST;
+		return INFRASTRUCTURE.LOCAL;
 	}
 
 	public VARTYPE getContentType() {

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

@@ -14,7 +14,7 @@ import org.gcube.contentmanagement.graphtools.utils.HttpRequest;
 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.configuration.WEIGHT;
+import org.gcube.dataanalysis.ecoengine.configuration.INFRASTRUCTURE;
 import org.gcube.dataanalysis.ecoengine.connectors.livemonitor.ResourceLoad;
 import org.gcube.dataanalysis.ecoengine.connectors.livemonitor.Resources;
 import org.gcube.dataanalysis.ecoengine.interfaces.Generator;
@@ -328,8 +328,8 @@ public class LocalSimpleSplitGenerator implements Generator {
 	}
 
 	@Override
-	public WEIGHT getWeight() {
+	public INFRASTRUCTURE getInfrastructure() {
-		return WEIGHT.LOWEST;
+		return INFRASTRUCTURE.LOCAL;
 	}
 
 	@Override

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

@@ -16,7 +16,7 @@ import org.gcube.contentmanagement.graphtools.utils.MathFunctions;
 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.configuration.WEIGHT;
+import org.gcube.dataanalysis.ecoengine.configuration.INFRASTRUCTURE;
 import org.gcube.dataanalysis.ecoengine.connectors.livemonitor.ResourceLoad;
 import org.gcube.dataanalysis.ecoengine.connectors.livemonitor.Resources;
 import org.gcube.dataanalysis.ecoengine.interfaces.Generator;
@@ -487,8 +487,8 @@ public class LocalSplitGenerator implements Generator {
 	}
 
 	@Override
-	public WEIGHT getWeight() {
+	public INFRASTRUCTURE getInfrastructure() {
-		return WEIGHT.LOWEST;
+		return INFRASTRUCTURE.LOCAL;
 	}
 
 	@Override

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

@@ -6,7 +6,7 @@ import org.gcube.contentmanagement.graphtools.utils.HttpRequest;
 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.configuration.WEIGHT;
+import org.gcube.dataanalysis.ecoengine.configuration.INFRASTRUCTURE;
 import org.gcube.dataanalysis.ecoengine.connectors.RemoteGenerationManager;
 import org.gcube.dataanalysis.ecoengine.connectors.RemoteHspecInputObject;
 import org.gcube.dataanalysis.ecoengine.connectors.RemoteHspecOutputObject;
@@ -174,8 +174,8 @@ public class RainyCloudGenerator implements Generator {
 	}
 
 	@Override
-	public WEIGHT getWeight() {
+	public INFRASTRUCTURE getInfrastructure() {
-		return WEIGHT.HIGH;
+		return INFRASTRUCTURE.D4SCIENCE;
 	}
 
 	@Override

src/org/gcube/dataanalysis/ecoengine/processing/factories/GeneratorsFactory.java

@@ -141,7 +141,7 @@ public class GeneratorsFactory {
 		int i=0;
 		boolean inserted = false;
 		for (Generator g: generators){
-			if (g.getWeight().compareTo(generator.getWeight())>0){
+			if (g.getInfrastructure().compareTo(generator.getInfrastructure())>0){
 				generators.add(i, generator);
 				inserted = true;
 				break;

src/org/gcube/dataanalysis/ecoengine/processing/factories/ModelersFactory.java

@@ -98,7 +98,7 @@ public static List<Modeler> getModelers(AlgorithmConfiguration config) throws Ex
 		int i=0;
 		boolean inserted = false;
 		for (Modeler g: modelers){
-			if (g.getWeight().compareTo(mod.getWeight())>0){
+			if (g.getInfrastructure().compareTo(mod.getInfrastructure())>0){
 				modelers.add(i, mod);
 				inserted = true;
 				break;

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

@@ -0,0 +1,48 @@
+package org.gcube.dataanalysis.ecoengine.test.regressions;
+
+import org.gcube.dataanalysis.ecoengine.evaluation.bioclimate.BioClimateAnalysis;
+
+public class TestBioClimateAnalysis {
+	
+	
+	public static void main(String args[]) throws Exception{
+		
+		String dburl = "jdbc:postgresql://node49.p.d4science.research-infrastructures.eu/aquamaps";
+		String dbUser = "gcube";
+		String dbPassword = "bilico1980";
+		
+		BioClimateAnalysis bioClimate=new BioClimateAnalysis("./cfg/","./",dburl, dbUser, dbPassword, true);
+		
+		
+		
+		final String [] envelopeTables = {
+		"hspen2012_06_01_21_52_47_460",
+		"hspen2012_06_01_21_52_47_485",
+		"hspen2012_06_01_21_52_47_615",
+		"hspen2012_06_01_21_52_46_795",
+		"hspen2012_06_02_03_26_13_154",
+		"hspen2012_06_02_03_26_16_534",
+		"hspen2012_06_02_03_26_43_412",
+		"hspen2012_06_02_03_27_26_762",
+		"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",
+				"hspen2012_06_01_21_52_47_615",
+				"hspen2012_06_01_21_52_46_795",
+				"hspen2012_06_02_03_26_13_154",
+				"hspen2012_06_02_03_26_16_534",
+				"hspen2012_06_02_03_26_43_412",
+				"hspen2012_06_02_03_27_26_762",
+				"hspen2012_06_02_08_54_48_004",
+				"hspen2012_06_02_08_55_53_415"
+				};
+		
+		
+		bioClimate.speciesEvolutionAnalysis(envelopeTables,envelopeTablesNames, BioClimateAnalysis.salinityMinFeature, BioClimateAnalysis.salinityDefaultRange);
+		
+	}
+}

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

@@ -2,6 +2,7 @@ package org.gcube.dataanalysis.ecoengine.utils;
 
 public enum VARTYPE {
 	STRING,
+	EPR_LIST,
 	INFRA,
 	SERVICE,
 	DATABASEUSERNAME,