git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/EcologicalEngine@61634 82a268e6-3cf1-43bd-a215-b396298e98cf

src/main/java/org/gcube/dataanalysis/ecoengine/configuration/ALG_PROPS.java

@@ -8,5 +8,6 @@ public enum ALG_PROPS {
 		SPECIES_VS_CSQUARE,
 		PHENOMENON_VS_GEOINFO,
 		SPECIES_ENVELOPES,
-		SPECIES_MODEL
+		SPECIES_MODEL,
+		PHENOMENON_VS_PARALLEL_PHENOMENON
 }

src/main/java/org/gcube/dataanalysis/ecoengine/datatypes/PrimitiveType.java

@@ -1,5 +1,7 @@
 package org.gcube.dataanalysis.ecoengine.datatypes;
 
+import java.util.HashMap;
+
 import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.PrimitiveTypes;
 
 
@@ -47,4 +49,14 @@ public class PrimitiveType extends StatisticalType{
 		this.type = type;
 	}
 	
+	public static HashMap<String,StatisticalType> stringMap2StatisticalMap(HashMap<String,String> stringmap){
+		HashMap<String,StatisticalType> map = new HashMap<String, StatisticalType>();
+		for (String key:stringmap.keySet()){
+			String value = stringmap.get(key);
+			PrimitiveType string = new PrimitiveType(String.class.getName(), value, PrimitiveTypes.STRING, key,key);
+			map.put(key,string);
+		}
+		
+		return map;
+	}
 }

src/main/java/org/gcube/dataanalysis/ecoengine/evaluation/DistributionQualityAnalysis.java

@@ -327,7 +327,7 @@ public class DistributionQualityAnalysis extends DataAnalysis {
 	
 	@Override
 	public StatisticalType getOutput() {
-		PrimitiveType p = new PrimitiveType(Map.class.getName(), output, PrimitiveTypes.MAP, "AnalysisResult","Analysis of the probability distribution quality");
+		PrimitiveType p = new PrimitiveType(Map.class.getName(), PrimitiveType.stringMap2StatisticalMap(output), PrimitiveTypes.MAP, "AnalysisResult","Analysis of the probability distribution quality");
 		return p;
 	}
 

src/main/java/org/gcube/dataanalysis/ecoengine/evaluation/HabitatRepresentativeness.java

@@ -316,7 +316,7 @@ public class HabitatRepresentativeness extends DataAnalysis {
 
 	@Override
 	public StatisticalType getOutput() {
-		PrimitiveType p = new PrimitiveType(Map.class.getName(), output, PrimitiveTypes.MAP, "AnalysisResult","Habitat Representativeness Score");
+		PrimitiveType p = new PrimitiveType(Map.class.getName(), PrimitiveType.stringMap2StatisticalMap(output), PrimitiveTypes.MAP, "AnalysisResult","Habitat Representativeness Score");
 		return p;
 	}
 	

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

@@ -0,0 +1,77 @@
+package org.gcube.dataanalysis.ecoengine.interfaces;
+
+import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
+
+public abstract class ActorNode implements GenericAlgorithm{
+
+	// initialization of ta single node
+	public abstract void initSingleNode(AlgorithmConfiguration config);
+
+	// get the internal processing status for the single step calculation
+	public abstract float getInternalStatus();
+
+	// execute a single node
+	public abstract int executeNode(int cellStarIndex, int numberOfRightElementsToProcess, int leftStartIndex, int numberOfLeftElementsToProcess, boolean duplicate, String sandboxFolder, String nodeConfigurationFileObject, String logfileNameToProduce);
+
+	// An initialization phase in which the inputs are initialized
+	public abstract void setup(AlgorithmConfiguration config) throws Exception;
+
+	// get overall number of species to process
+	public abstract int getNumberOfRightElements();
+
+	// get overall number of geographical information to process
+	public abstract int getNumberOfLeftElements();
+
+	// get overall number of processed species
+	public abstract int getNumberOfProcessedElements();
+
+	// stop the sexecution of the node
+	public abstract void stop();
+
+	// prostprocess after the whole calculation : reduce operation
+	public abstract void postProcess(boolean manageDuplicates, boolean manageFault);
+
+	public static void main(String[] args) throws Exception {
+		try {
+			System.out.println("Generic Node: Process Started ");
+			try {
+				for (int i = 0; i < args.length; i++) {
+					System.out.println("Generic Node: RECEIVED INPUT " + args[i]);
+				}
+			} catch (Exception e) {
+			}
+
+			System.out.println("Generic Node: checking arguments from " + args[0]);
+			String[] rargs = args[0].split("_");
+
+			int order = Integer.parseInt(rargs[0]);
+			System.out.println("Generic Node: order: " + order);
+			int chunksize = Integer.parseInt(rargs[1]);
+			System.out.println("Generic Node: chunk: " + chunksize);
+			int speciesOrder = Integer.parseInt(rargs[2]);
+			System.out.println("Generic Node: species: " + speciesOrder);
+			int speciesChunksize = Integer.parseInt(rargs[3]);
+			System.out.println("Generic Node: species chunk size: " + speciesChunksize);
+			String path = rargs[4];
+			System.out.println("Generic Node: path: " + path);
+			String algorithmClass = rargs[5];
+			System.out.println("Generic Node: algorithmClass: " + algorithmClass);
+			Boolean duplicate = Boolean.parseBoolean(rargs[6]);
+			System.out.println("Generic Node: duplicate message: " + duplicate);
+			String nodeConfiguration = rargs[7];
+			System.out.println("Generic Node: config: " + nodeConfiguration);
+			String logfile = args[1];
+			System.out.println("Generic Node: logfile: " + logfile);
+
+			System.out.println("Generic Node: executing class");
+
+			SpatialProbabilityDistributionNode node = (SpatialProbabilityDistributionNode) Class.forName(algorithmClass).newInstance();
+
+			node.executeNode(order, chunksize, speciesOrder, speciesChunksize, duplicate, path, nodeConfiguration, logfile);
+		} catch (Exception e) {
+			System.out.println("ERROR " + e.getMessage());
+			System.out.println(e);
+		}
+	}
+
+}

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

@@ -54,7 +54,7 @@ public abstract class DataAnalysis implements Evaluator{
 	
 	@Override
 	public StatisticalType getOutput() {
-		PrimitiveType p = new PrimitiveType(Map.class.getName(), out, PrimitiveTypes.MAP, "AnalysisResult","Analysis Values");
+		PrimitiveType p = new PrimitiveType(Map.class.getName(), PrimitiveType.stringMap2StatisticalMap(out), PrimitiveTypes.MAP, "AnalysisResult","Analysis Values");
 		return p;
 	}
 	

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

@@ -8,7 +8,7 @@ public interface Generator extends ComputationalAgent{
 
 	public ALG_PROPS[] getSupportedAlgorithms();
 	
-	public SpatialProbabilityDistribution getAlgorithm();
+	public GenericAlgorithm getAlgorithm();
 
 	public String getLoad();
 	

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

@@ -5,7 +5,7 @@ import java.util.List;
 import org.gcube.dataanalysis.ecoengine.configuration.ALG_PROPS;
 import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType;
 
-public interface SpatialProbabilityDistribution {
+public interface GenericAlgorithm {
 			
 			//defines the properties of this algorithm
 			public ALG_PROPS[] getProperties();

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

@@ -6,7 +6,7 @@ import java.util.Map;
 import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
 
 //implements a SpatialProbabilityDistribution where data are taken from a Database
-public interface SpatialProbabilityDistributionGeneric extends SpatialProbabilityDistribution{
+public interface SpatialProbabilityDistributionGeneric extends GenericAlgorithm{
 			
 		//initialization of the distribution model
 		public void init(AlgorithmConfiguration config) throws Exception;

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

@@ -5,9 +5,9 @@ import java.io.FileWriter;
 
 import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
 
-public abstract class SpatialProbabilityDistributionNode implements SpatialProbabilityDistribution {
+public abstract class SpatialProbabilityDistributionNode implements GenericAlgorithm {
 			
-	//initialization of ta single node
+	//initialization of the  single node
 	public abstract void initSingleNode(AlgorithmConfiguration config);
 
 	//get the internal processing status for the single step calculation

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

@@ -7,7 +7,7 @@ import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
 import org.hibernate.SessionFactory;
 
 //implements a SpatialProbabilityDistribution where data are taken from a Database
-public interface SpatialProbabilityDistributionTable extends SpatialProbabilityDistribution{
+public interface SpatialProbabilityDistributionTable extends GenericAlgorithm{
 		
 		//define the properties of this algorithm
 		public ALG_PROPS[] getProperties();

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

@@ -19,7 +19,7 @@ import org.gcube.dataanalysis.ecoengine.connectors.livemonitor.ResourceLoad;
 import org.gcube.dataanalysis.ecoengine.connectors.livemonitor.Resources;
 import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType;
 import org.gcube.dataanalysis.ecoengine.interfaces.Generator;
-import org.gcube.dataanalysis.ecoengine.interfaces.SpatialProbabilityDistribution;
+import org.gcube.dataanalysis.ecoengine.interfaces.GenericAlgorithm;
 import org.gcube.dataanalysis.ecoengine.interfaces.SpatialProbabilityDistributionGeneric;
 
 public class LocalSimpleSplitGenerator implements Generator {
@@ -352,7 +352,7 @@ public class LocalSimpleSplitGenerator implements Generator {
 	}
 
 	@Override
-	public SpatialProbabilityDistribution getAlgorithm() {
+	public GenericAlgorithm getAlgorithm() {
 		return distributionModel;
 	}
 

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

@@ -21,7 +21,7 @@ import org.gcube.dataanalysis.ecoengine.connectors.livemonitor.ResourceLoad;
 import org.gcube.dataanalysis.ecoengine.connectors.livemonitor.Resources;
 import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType;
 import org.gcube.dataanalysis.ecoengine.interfaces.Generator;
-import org.gcube.dataanalysis.ecoengine.interfaces.SpatialProbabilityDistribution;
+import org.gcube.dataanalysis.ecoengine.interfaces.GenericAlgorithm;
 import org.gcube.dataanalysis.ecoengine.interfaces.SpatialProbabilityDistributionTable;
 import org.gcube.dataanalysis.ecoengine.utils.DatabaseFactory;
 import org.hibernate.SessionFactory;
@@ -512,7 +512,7 @@ public class LocalSplitGenerator implements Generator {
 	}
 
 	@Override
-	public SpatialProbabilityDistribution getAlgorithm() {
+	public GenericAlgorithm getAlgorithm() {
 		return distributionModel;
 	}
 

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

@@ -14,7 +14,7 @@ import org.gcube.dataanalysis.ecoengine.connectors.RemoteHspecOutputObject;
 import org.gcube.dataanalysis.ecoengine.connectors.livemonitor.ResourceLoad;
 import org.gcube.dataanalysis.ecoengine.connectors.livemonitor.Resources;
 import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType;
-import org.gcube.dataanalysis.ecoengine.interfaces.SpatialProbabilityDistribution;
+import org.gcube.dataanalysis.ecoengine.interfaces.GenericAlgorithm;
 
 //deprecated
 public class RainyCloudGenerator {

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

@@ -10,7 +10,7 @@ import org.gcube.dataanalysis.ecoengine.configuration.ALG_PROPS;
 import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
 import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType;
 import org.gcube.dataanalysis.ecoengine.interfaces.Generator;
-import org.gcube.dataanalysis.ecoengine.interfaces.SpatialProbabilityDistribution;
+import org.gcube.dataanalysis.ecoengine.interfaces.GenericAlgorithm;
 import org.gcube.dataanalysis.ecoengine.interfaces.SpatialProbabilityDistributionGeneric;
 
 public class GeneratorsFactory {
@@ -102,7 +102,7 @@ public class GeneratorsFactory {
 			}
 			else	
 			{
-				SpatialProbabilityDistribution sp = (SpatialProbabilityDistribution) algclass;
+				GenericAlgorithm sp = (GenericAlgorithm) algclass;
 				//take alg's properties
 				ALG_PROPS[] algp = sp.getProperties();
 				//take all generators

src/main/java/org/gcube/dataanalysis/ecoengine/processing/factories/ProcessorsFactory.java

@@ -13,7 +13,7 @@ import org.gcube.dataanalysis.ecoengine.interfaces.Evaluator;
 import org.gcube.dataanalysis.ecoengine.interfaces.Generator;
 import org.gcube.dataanalysis.ecoengine.interfaces.Model;
 import org.gcube.dataanalysis.ecoengine.interfaces.Modeler;
-import org.gcube.dataanalysis.ecoengine.interfaces.SpatialProbabilityDistribution;
+import org.gcube.dataanalysis.ecoengine.interfaces.GenericAlgorithm;
 import org.gcube.dataanalysis.ecoengine.interfaces.Transducerer;
 import org.gcube.dataanalysis.ecoengine.utils.DatabaseFactory;
 
@@ -63,7 +63,7 @@ public class ProcessorsFactory {
 			return ((Transducerer) algclass).getDescription();
 		} 
 		else
-			return ((SpatialProbabilityDistribution) algclass).getDescription();
+			return ((GenericAlgorithm) algclass).getDescription();
 
 	}
 	
@@ -90,7 +90,7 @@ public class ProcessorsFactory {
 			return ((Transducerer) algclass).getInputParameters();
 		} 
 		else
-			return ((SpatialProbabilityDistribution) algclass).getInputParameters();
+			return ((GenericAlgorithm) algclass).getInputParameters();
 
 	}
 

src/main/java/org/gcube/dataanalysis/ecoengine/test/checks/TestDBNEXTEvaluators.java

@@ -57,7 +57,7 @@ public static void main(String[] args) throws Exception {
 	*/
 //		List<Evaluator> trans = null;
 //		trans = EvaluatorsFactory.getEvaluators(testConfigLocal12());
-		List<Transducerer> trans = TransducerersFactory.getTransducerers(testConfigLocal5c());
+		List<Transducerer> trans = TransducerersFactory.getTransducerers(testConfigLocal5b());
 		trans.get(0).init();
 		Regressor.process(trans.get(0));
 		
@@ -174,12 +174,16 @@ public static void main(String[] args) throws Exception {
 		config.setParam("rightTableName", "occurrence_species_id1e8f7b48_b99a_48a3_8b52_89976fd79cd4");
 		config.setParam("leftTableName", "occurrence_species_id0045886b_2a7c_4ede_afc4_3157c694b893");
 		*/
-		config.setParam("rightTableName", "occurrence_species_id7a77d613_c21d_495d_8a04_b9534cf5e159");
+		//"processedoccurrences_id_e7b77fc2_f1cf_4a46_b7b7_898b663b65dd" OBIS
-		config.setParam("leftTableName", "occurrence_species_idbb2931ef_af2c_495a_ad5f_4ef81ad16159");
+		//"processedoccurrences_id_bd3fdae3_a64e_4215_8eb3_c1bd95981dd2" GBIF
 		
-		config.setParam("finalTableName", "occurrencessubtracted2");
+		config.setParam("leftTableName", "processedoccurrences_id_e7b77fc2_f1cf_4a46_b7b7_898b663b65dd");
-		config.setParam("spatialTolerance", "0.000001");
+		config.setParam("rightTableName", "processedoccurrences_id_bd3fdae3_a64e_4215_8eb3_c1bd95981dd2");
-		config.setParam("confidence", "90");
+		
+		
+		config.setParam("finalTableName", "occurrencessubtractedarticle3");
+		config.setParam("spatialTolerance", "0.01");
+		config.setParam("confidence", "0");
 		
 		config.setParam("DatabaseUserName","utente");
 		config.setParam("DatabasePassword","d4science");

src/main/java/org/gcube/dataanalysis/ecoengine/transducers/OccurrencePointsMerger.java

@@ -336,7 +336,7 @@ public class OccurrencePointsMerger implements Transducerer {
 		float probability = 0;
 		float distance = (float) Math.sqrt(Math.abs(left.x - right.x) + Math.abs(left.y - right.y));
 		if (distance > spatialToleranceValue)
-			probability = 0;
+			probability = -1;
 		else {
 			float pSpecies = probabilityStrings(right.scientificName, left.scientificName);
 			float pRecordedBy = probabilityStrings(right.recordedby, left.recordedby);