git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/EcologicalEngine@61775 82a268e6-3cf1-43bd-a215-b396298e98cf
This commit is contained in:
parent
ad3ce33d46
commit
8441ebc381
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@ -12,6 +12,7 @@ import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
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import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
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import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveType;
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import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType;
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import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent;
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import org.gcube.dataanalysis.ecoengine.interfaces.Evaluator;
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import org.gcube.dataanalysis.ecoengine.models.cores.aquamaps.Hspen;
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import org.gcube.dataanalysis.ecoengine.processing.factories.EvaluatorsFactory;
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@ -71,7 +72,7 @@ public class BioClimateAnalysis {
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private double[] avgSST;
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private double[] avgSalinity;
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private Evaluator eval;
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private ComputationalAgent eval;
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private float status;
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private boolean liveRender;
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@ -6,6 +6,8 @@ import java.util.List;
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import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
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import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType;
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import org.gcube.dataanalysis.ecoengine.interfaces.Clusterer;
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import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent;
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import org.gcube.dataanalysis.ecoengine.interfaces.Generator;
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public class ClusterersFactory {
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@ -29,9 +31,10 @@ public class ClusterersFactory {
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return input;
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}
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public static List<Clusterer> getClusterers(AlgorithmConfiguration config) throws Exception {
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List<Clusterer> clusterers = new ArrayList<Clusterer>();
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public static List<ComputationalAgent> getClusterers(AlgorithmConfiguration config) throws Exception {
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List<ComputationalAgent> clusterers = new ArrayList<ComputationalAgent>();
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clusterers.add(getClusterer(config));
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ProcessorsFactory.addAgent2List(clusterers,GeneratorsFactory.getGenerator(config));
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return clusterers;
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}
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@ -5,7 +5,9 @@ import java.util.List;
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import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
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import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType;
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import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent;
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import org.gcube.dataanalysis.ecoengine.interfaces.Evaluator;
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import org.gcube.dataanalysis.ecoengine.interfaces.Generator;
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public class EvaluatorsFactory {
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@ -30,9 +32,10 @@ public class EvaluatorsFactory {
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return input;
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}
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public static List<Evaluator> getEvaluators(AlgorithmConfiguration config) throws Exception {
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List<Evaluator> evaluators = new ArrayList<Evaluator>();
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public static List<ComputationalAgent> getEvaluators(AlgorithmConfiguration config) throws Exception {
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List<ComputationalAgent> evaluators = new ArrayList<ComputationalAgent>();
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evaluators.add(getEvaluator(config));
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ProcessorsFactory.addAgent2List(evaluators,GeneratorsFactory.getGenerator(config));
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return evaluators;
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}
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@ -9,6 +9,7 @@ import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
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import org.gcube.dataanalysis.ecoengine.configuration.ALG_PROPS;
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import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
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import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType;
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import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent;
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import org.gcube.dataanalysis.ecoengine.interfaces.Generator;
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import org.gcube.dataanalysis.ecoengine.interfaces.GenericAlgorithm;
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import org.gcube.dataanalysis.ecoengine.interfaces.SpatialProbabilityDistributionGeneric;
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@ -81,10 +82,10 @@ public class GeneratorsFactory {
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}
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public static List<Generator> getGenerators(AlgorithmConfiguration config) throws Exception {
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public static List<ComputationalAgent> getGenerators(AlgorithmConfiguration config) throws Exception {
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//modify this class in order to manage generators weight and match algorithm vs generators
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List<Generator> generators = new ArrayList<Generator>();
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List<ComputationalAgent> generators = new ArrayList<ComputationalAgent>();
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try {
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//initialize the logger
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AnalysisLogger.setLogger(config.getConfigPath() + AlgorithmConfiguration.defaultLoggerFile);
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@ -140,10 +141,12 @@ public class GeneratorsFactory {
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}
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//adds a generator to a sorted generators list
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public static void addGenerator2List(List<Generator> generators, Generator generator){
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public static void addGenerator2List(List<ComputationalAgent> generators, Generator generator){
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if (generator == null)
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return;
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int i=0;
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boolean inserted = false;
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for (Generator g: generators){
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for (ComputationalAgent g: generators){
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if (g.getInfrastructure().compareTo(generator.getInfrastructure())>0){
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generators.add(i, generator);
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inserted = true;
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@ -8,6 +8,7 @@ import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
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import org.gcube.dataanalysis.ecoengine.configuration.ALG_PROPS;
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import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
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import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType;
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import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent;
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import org.gcube.dataanalysis.ecoengine.interfaces.Model;
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import org.gcube.dataanalysis.ecoengine.interfaces.Modeler;
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@ -40,10 +41,10 @@ public class ModelersFactory {
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return input;
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}
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public static List<Modeler> getModelers(AlgorithmConfiguration config) throws Exception {
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public static List<ComputationalAgent> getModelers(AlgorithmConfiguration config) throws Exception {
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//modify this class in order to manage generators weight and match algorithm vs generators
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List<Modeler> modelers = new ArrayList<Modeler>();
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List<ComputationalAgent> modelers = new ArrayList<ComputationalAgent>();
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try {
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//initialize the logger
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AnalysisLogger.setLogger(config.getConfigPath() + AlgorithmConfiguration.defaultLoggerFile);
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@ -99,10 +100,10 @@ public static List<Modeler> getModelers(AlgorithmConfiguration config) throws Ex
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}
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//adds a generator to a sorted generators list
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public static void addModeler2List(List<Modeler> modelers, Modeler mod){
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public static void addModeler2List(List<ComputationalAgent> modelers, Modeler mod){
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int i=0;
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boolean inserted = false;
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for (Modeler g: modelers){
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for (ComputationalAgent g: modelers){
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if (g.getInfrastructure().compareTo(mod.getInfrastructure())>0){
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modelers.add(i, mod);
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inserted = true;
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@ -1,5 +1,6 @@
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package org.gcube.dataanalysis.ecoengine.processing.factories;
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import java.io.File;
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import java.util.ArrayList;
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import java.util.HashMap;
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import java.util.List;
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@ -9,11 +10,12 @@ import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
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import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
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import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType;
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import org.gcube.dataanalysis.ecoengine.interfaces.Clusterer;
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import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent;
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import org.gcube.dataanalysis.ecoengine.interfaces.Evaluator;
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import org.gcube.dataanalysis.ecoengine.interfaces.Generator;
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import org.gcube.dataanalysis.ecoengine.interfaces.GenericAlgorithm;
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import org.gcube.dataanalysis.ecoengine.interfaces.Model;
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import org.gcube.dataanalysis.ecoengine.interfaces.Modeler;
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import org.gcube.dataanalysis.ecoengine.interfaces.GenericAlgorithm;
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import org.gcube.dataanalysis.ecoengine.interfaces.Transducerer;
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import org.gcube.dataanalysis.ecoengine.utils.DatabaseFactory;
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@ -94,18 +96,25 @@ public class ProcessorsFactory {
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}
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public static Object getProcessor(AlgorithmConfiguration config, String file) throws Exception {
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public static ComputationalAgent getProcessor(AlgorithmConfiguration config, String file) throws Exception {
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return getProcessor(config, file,null);
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}
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public static ComputationalAgent getProcessor(AlgorithmConfiguration config, String file,String explicitAlgorithm) throws Exception {
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// modify this class in order to take the right generator algorithm
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try {
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// initialize the logger
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AnalysisLogger.setLogger(config.getConfigPath() + AlgorithmConfiguration.defaultLoggerFile);
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// take the algorithm
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String algorithm = config.getAgent();
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String algorithm = explicitAlgorithm;
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if (explicitAlgorithm==null)
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algorithm = config.getAgent();
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if (algorithm == null)
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throw new Exception("PROCESSOR NOT SPECIFIED");
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// take the algorithms list
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Properties p = AlgorithmConfiguration.getProperties(file);
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String algorithmclass = p.getProperty(algorithm);
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if (algorithmclass==null)
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return null;
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Object algclass = Class.forName(algorithmclass).newInstance();
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if (algclass instanceof Generator) {
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Generator g = (Generator) algclass;
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@ -153,4 +162,21 @@ public class ProcessorsFactory {
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return map;
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}
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//adds a generator to a sorted generators list
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public static void addAgent2List(List<ComputationalAgent> agents, ComputationalAgent agent){
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if (agent == null)
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return;
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int i=0;
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boolean inserted = false;
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for (ComputationalAgent g: agents){
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if (g.getInfrastructure().compareTo(agent.getInfrastructure())>0){
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agents.add(i, agent);
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inserted = true;
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break;
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}
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i++;
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}
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if (!inserted)
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agents.add(agent);
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}
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}
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@ -5,7 +5,7 @@ import java.util.List;
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import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
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import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType;
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import org.gcube.dataanalysis.ecoengine.interfaces.Clusterer;
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import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent;
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import org.gcube.dataanalysis.ecoengine.interfaces.Transducerer;
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public class TransducerersFactory {
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@ -30,10 +30,12 @@ public class TransducerersFactory {
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return input;
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}
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public static List<Transducerer> getTransducerers(AlgorithmConfiguration config) throws Exception {
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List<Transducerer> clusterers = new ArrayList<Transducerer>();
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clusterers.add(getTransducerer(config));
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return clusterers;
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public static List<ComputationalAgent> getTransducerers(AlgorithmConfiguration config) throws Exception {
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List<ComputationalAgent> trans = new ArrayList<ComputationalAgent>();
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trans.add(getTransducerer(config));
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ProcessorsFactory.addAgent2List(trans,GeneratorsFactory.getGenerator(config));
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return trans;
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}
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}
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@ -6,6 +6,7 @@ import java.util.List;
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import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
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import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType;
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import org.gcube.dataanalysis.ecoengine.interfaces.Clusterer;
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import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent;
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import org.gcube.dataanalysis.ecoengine.interfaces.Evaluator;
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import org.gcube.dataanalysis.ecoengine.interfaces.Generator;
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import org.gcube.dataanalysis.ecoengine.interfaces.Transducerer;
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@ -64,7 +65,7 @@ public static void main(String[] args) throws Exception {
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System.out.println("Database Default Values: "+map);
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System.out.println("\n***TEST 11- Get Evaluators with a config***");
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List<Evaluator> eval = EvaluatorsFactory.getEvaluators(testConfigEvaluator());
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List<ComputationalAgent> eval = EvaluatorsFactory.getEvaluators(testConfigEvaluator());
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System.out.println("Database Default Values: "+eval);
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System.out.println("\n***TEST 12- Get All Supported features***");
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@ -5,6 +5,7 @@ import java.util.List;
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import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
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import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
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import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent;
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import org.gcube.dataanalysis.ecoengine.interfaces.Generator;
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import org.gcube.dataanalysis.ecoengine.processing.factories.GeneratorsFactory;
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@ -25,7 +26,7 @@ public static void main(String[] args) throws Exception {
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*/
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System.out.println("TEST 2");
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List<Generator> generators = GeneratorsFactory.getGenerators(testConfigLocal());
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List<ComputationalAgent> generators = GeneratorsFactory.getGenerators(testConfigLocal());
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generators.get(0).init();
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generate(generators.get(0));
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generators = null;
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@ -33,7 +34,7 @@ public static void main(String[] args) throws Exception {
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}
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private static void generate(Generator generator) throws Exception {
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private static void generate(ComputationalAgent generator) throws Exception {
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if (generator != null) {
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RegressionComplexGeneration tgs = new RegressionComplexGeneration();
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@ -44,10 +45,10 @@ public static void main(String[] args) throws Exception {
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String resLoad = generator.getResourceLoad();
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String ress = generator.getResources();
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String species = generator.getLoad();
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// String species = generator.getLoad();
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System.out.println("LOAD: " + resLoad);
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System.out.println("RESOURCES: " + ress);
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System.out.println("SPECIES: " + species);
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// System.out.println("SPECIES: " + species);
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System.out.println("STATUS: " + generator.getStatus());
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Thread.sleep(1000);
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}
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@ -57,9 +58,9 @@ public static void main(String[] args) throws Exception {
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}
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public class ThreadCalculator implements Runnable {
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Generator dg;
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ComputationalAgent dg;
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public ThreadCalculator(Generator dg) {
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public ThreadCalculator(ComputationalAgent dg) {
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this.dg = dg;
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}
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@ -4,6 +4,7 @@ import java.util.List;
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import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
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import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
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import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent;
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import org.gcube.dataanalysis.ecoengine.interfaces.Generator;
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import org.gcube.dataanalysis.ecoengine.processing.factories.GeneratorsFactory;
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@ -16,7 +17,7 @@ public class RegressionSimpleGeneration {
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public static void main(String[] args) throws Exception {
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System.out.println("TEST 1");
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List<Generator> generators = GeneratorsFactory.getGenerators(testConfig1());
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List<ComputationalAgent> generators = GeneratorsFactory.getGenerators(testConfig1());
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generators.get(0).init();
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generate(generators.get(0));
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generators = null;
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@ -30,7 +31,7 @@ public static void main(String[] args) throws Exception {
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}
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private static void generate(Generator generator) throws Exception {
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private static void generate(ComputationalAgent generator) throws Exception {
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if (generator != null) {
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RegressionSimpleGeneration tgs = new RegressionSimpleGeneration();
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@ -41,10 +42,10 @@ public static void main(String[] args) throws Exception {
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String resLoad = generator.getResourceLoad();
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String ress = generator.getResources();
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String species = generator.getLoad();
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// String species = generator.getLoad();
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System.out.println("LOAD: " + resLoad);
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System.out.println("RESOURCES: " + ress);
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System.out.println("SPECIES: " + species);
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// System.out.println("SPECIES: " + species);
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System.out.println("STATUS: " + generator.getStatus());
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Thread.sleep(1000);
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}
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@ -54,9 +55,9 @@ public static void main(String[] args) throws Exception {
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}
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public class ThreadCalculator implements Runnable {
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Generator dg;
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ComputationalAgent dg;
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public ThreadCalculator(Generator dg) {
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public ThreadCalculator(ComputationalAgent dg) {
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this.dg = dg;
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}
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@ -9,6 +9,7 @@ import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveType;
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import org.gcube.dataanalysis.ecoengine.datatypes.ServiceType;
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import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.PrimitiveTypes;
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import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.ServiceParameters;
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import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent;
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import org.gcube.dataanalysis.ecoengine.interfaces.Generator;
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import org.gcube.dataanalysis.ecoengine.interfaces.Modeler;
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import org.gcube.dataanalysis.ecoengine.processing.factories.GeneratorsFactory;
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@ -21,14 +22,14 @@ public class TestBayesianModels {
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*
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*/
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public static void main1(String[] args) throws Exception {
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public static void main(String[] args) throws Exception {
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/*
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List<Generator> generators = GeneratorsFactory.getGenerators(testConfigLocal1());
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generators.get(0).init();
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Regressor.process(generators.get(0));
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generators = null;
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*/
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List<Modeler> generators = ModelersFactory.getModelers(testConfigLocal1());
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List<ComputationalAgent> generators = ModelersFactory.getModelers(testConfigLocal1());
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generators.get(0).init();
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Regressor.process(generators.get(0));
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generators = null;
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@ -36,9 +37,9 @@ public static void main1(String[] args) throws Exception {
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}
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public static void main(String[] args) throws Exception {
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public static void main1(String[] args) throws Exception {
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List<Generator> generators = GeneratorsFactory.getGenerators(testConfigLocal2());
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List<ComputationalAgent> generators = GeneratorsFactory.getGenerators(testConfigLocal2());
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generators.get(0).init();
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Regressor.process(generators.get(0));
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generators = null;
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@ -9,6 +9,7 @@ import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveType;
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import org.gcube.dataanalysis.ecoengine.datatypes.ServiceType;
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import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.PrimitiveTypes;
|
||||
import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.ServiceParameters;
|
||||
import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent;
|
||||
import org.gcube.dataanalysis.ecoengine.interfaces.Generator;
|
||||
import org.gcube.dataanalysis.ecoengine.interfaces.Modeler;
|
||||
import org.gcube.dataanalysis.ecoengine.processing.factories.GeneratorsFactory;
|
||||
|
|
@ -21,14 +22,14 @@ public class TestBayesianModelsDBTest {
|
|||
*
|
||||
*/
|
||||
|
||||
public static void main1(String[] args) throws Exception {
|
||||
public static void main(String[] args) throws Exception {
|
||||
/*
|
||||
List<Generator> generators = GeneratorsFactory.getGenerators(testConfigLocal1());
|
||||
generators.get(0).init();
|
||||
Regressor.process(generators.get(0));
|
||||
generators = null;
|
||||
*/
|
||||
List<Modeler> generators = ModelersFactory.getModelers(testConfigLocal1());
|
||||
List<ComputationalAgent> generators = ModelersFactory.getModelers(testConfigLocal1());
|
||||
generators.get(0).init();
|
||||
Regressor.process(generators.get(0));
|
||||
generators = null;
|
||||
|
|
@ -36,9 +37,9 @@ public static void main1(String[] args) throws Exception {
|
|||
|
||||
}
|
||||
|
||||
public static void main(String[] args) throws Exception {
|
||||
public static void main1(String[] args) throws Exception {
|
||||
|
||||
List<Generator> generators = GeneratorsFactory.getGenerators(testConfigLocal2());
|
||||
List<ComputationalAgent> generators = GeneratorsFactory.getGenerators(testConfigLocal2());
|
||||
generators.get(0).init();
|
||||
Regressor.process(generators.get(0));
|
||||
generators = null;
|
||||
|
|
|
|||
|
|
@ -6,6 +6,7 @@ import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
|
|||
import org.gcube.dataanalysis.ecoengine.clustering.DBScan;
|
||||
import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
|
||||
import org.gcube.dataanalysis.ecoengine.interfaces.Clusterer;
|
||||
import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent;
|
||||
import org.gcube.dataanalysis.ecoengine.interfaces.Transducerer;
|
||||
import org.gcube.dataanalysis.ecoengine.processing.factories.ClusterersFactory;
|
||||
|
||||
|
|
@ -18,14 +19,14 @@ public class TestClusterer {
|
|||
public static void main(String[] args) throws Exception {
|
||||
|
||||
System.out.println("TEST 1");
|
||||
List<Clusterer> clus = ClusterersFactory.getClusterers(testConfigLocal2());
|
||||
List<ComputationalAgent> clus = ClusterersFactory.getClusterers(testConfigLocal2());
|
||||
clus .get(0).init();
|
||||
cluster(clus .get(0));
|
||||
clus = null;
|
||||
|
||||
}
|
||||
|
||||
private static void cluster(Clusterer clus) throws Exception {
|
||||
private static void cluster(ComputationalAgent clus) throws Exception {
|
||||
|
||||
if (clus != null) {
|
||||
TestClusterer tgs = new TestClusterer();
|
||||
|
|
@ -43,9 +44,9 @@ public class TestClusterer {
|
|||
}
|
||||
|
||||
public class ThreadCalculator implements Runnable {
|
||||
Clusterer dg;
|
||||
ComputationalAgent dg;
|
||||
|
||||
public ThreadCalculator(Clusterer dg) {
|
||||
public ThreadCalculator(ComputationalAgent dg) {
|
||||
this.dg = dg;
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -10,6 +10,7 @@ import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType;
|
|||
import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.PrimitiveTypes;
|
||||
import org.gcube.dataanalysis.ecoengine.evaluation.DiscrepancyAnalysis;
|
||||
import org.gcube.dataanalysis.ecoengine.evaluation.bioclimate.InterpolateTables.INTERPOLATIONFUNCTIONS;
|
||||
import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent;
|
||||
import org.gcube.dataanalysis.ecoengine.interfaces.Evaluator;
|
||||
import org.gcube.dataanalysis.ecoengine.interfaces.Transducerer;
|
||||
import org.gcube.dataanalysis.ecoengine.processing.factories.EvaluatorsFactory;
|
||||
|
|
@ -57,7 +58,7 @@ public static void main(String[] args) throws Exception {
|
|||
*/
|
||||
// List<Evaluator> trans = null;
|
||||
// trans = EvaluatorsFactory.getEvaluators(testConfigLocal12());
|
||||
List<Transducerer> trans = TransducerersFactory.getTransducerers(testConfigLocal5b());
|
||||
List<ComputationalAgent> trans = TransducerersFactory.getTransducerers(testConfigLocal5b());
|
||||
trans.get(0).init();
|
||||
Regressor.process(trans.get(0));
|
||||
|
||||
|
|
@ -166,10 +167,10 @@ public static void main(String[] args) throws Exception {
|
|||
config.setParam("scientificNameColumn", "scientificname");
|
||||
config.setParam("eventDateColumn", "eventdate");
|
||||
config.setParam("lastModificationColumn", "modified");
|
||||
/*
|
||||
|
||||
config.setParam("rightTableName", "occurrence_species2");
|
||||
config.setParam("leftTableName", "occurrence_species1");
|
||||
*/
|
||||
|
||||
/*
|
||||
config.setParam("rightTableName", "occurrence_species_id1e8f7b48_b99a_48a3_8b52_89976fd79cd4");
|
||||
config.setParam("leftTableName", "occurrence_species_id0045886b_2a7c_4ede_afc4_3157c694b893");
|
||||
|
|
@ -177,8 +178,8 @@ public static void main(String[] args) throws Exception {
|
|||
//"processedoccurrences_id_e7b77fc2_f1cf_4a46_b7b7_898b663b65dd" OBIS
|
||||
//"processedoccurrences_id_bd3fdae3_a64e_4215_8eb3_c1bd95981dd2" GBIF
|
||||
|
||||
config.setParam("leftTableName", "processedoccurrences_id_e7b77fc2_f1cf_4a46_b7b7_898b663b65dd");
|
||||
config.setParam("rightTableName", "processedoccurrences_id_bd3fdae3_a64e_4215_8eb3_c1bd95981dd2");
|
||||
// config.setParam("leftTableName", "processedoccurrences_id_e7b77fc2_f1cf_4a46_b7b7_898b663b65dd");
|
||||
// config.setParam("rightTableName", "processedoccurrences_id_bd3fdae3_a64e_4215_8eb3_c1bd95981dd2");
|
||||
|
||||
|
||||
config.setParam("finalTableName", "occurrencessubtractedarticle3");
|
||||
|
|
|
|||
|
|
@ -7,6 +7,7 @@ import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
|
|||
import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
|
||||
import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveType;
|
||||
import org.gcube.dataanalysis.ecoengine.evaluation.DiscrepancyAnalysis;
|
||||
import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent;
|
||||
import org.gcube.dataanalysis.ecoengine.interfaces.Evaluator;
|
||||
import org.gcube.dataanalysis.ecoengine.processing.factories.EvaluatorsFactory;
|
||||
|
||||
|
|
@ -19,7 +20,7 @@ public class TestEvaluation {
|
|||
public static void main(String[] args) throws Exception {
|
||||
|
||||
//test Quality
|
||||
List<Evaluator> evaluators = EvaluatorsFactory.getEvaluators(testQuality());
|
||||
List<ComputationalAgent> evaluators = EvaluatorsFactory.getEvaluators(testQuality());
|
||||
evaluate(evaluators.get(0),testQuality());
|
||||
evaluators = null;
|
||||
|
||||
|
|
@ -33,7 +34,7 @@ public static void main(String[] args) throws Exception {
|
|||
}
|
||||
|
||||
|
||||
private static void evaluate(Evaluator evaluator, AlgorithmConfiguration config) throws Exception {
|
||||
private static void evaluate(ComputationalAgent evaluator, AlgorithmConfiguration config) throws Exception {
|
||||
|
||||
if (evaluator != null) {
|
||||
TestEvaluation tgs = new TestEvaluation();
|
||||
|
|
@ -64,10 +65,10 @@ public static void main(String[] args) throws Exception {
|
|||
}
|
||||
|
||||
public class ThreadCalculator implements Runnable {
|
||||
Evaluator dg;
|
||||
ComputationalAgent dg;
|
||||
AlgorithmConfiguration config;
|
||||
|
||||
public ThreadCalculator(Evaluator dg, AlgorithmConfiguration config) {
|
||||
public ThreadCalculator(ComputationalAgent dg, AlgorithmConfiguration config) {
|
||||
this.dg = dg;
|
||||
this.config = config;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -11,6 +11,7 @@ import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.PrimitiveTypes;
|
|||
import org.gcube.dataanalysis.ecoengine.evaluation.DiscrepancyAnalysis;
|
||||
import org.gcube.dataanalysis.ecoengine.evaluation.bioclimate.InterpolateTables.INTERPOLATIONFUNCTIONS;
|
||||
import org.gcube.dataanalysis.ecoengine.interfaces.Clusterer;
|
||||
import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent;
|
||||
import org.gcube.dataanalysis.ecoengine.interfaces.Evaluator;
|
||||
import org.gcube.dataanalysis.ecoengine.interfaces.Transducerer;
|
||||
import org.gcube.dataanalysis.ecoengine.processing.factories.ClusterersFactory;
|
||||
|
|
@ -59,7 +60,7 @@ public static void main(String[] args) throws Exception {
|
|||
*/
|
||||
// List<Evaluator> trans = null;
|
||||
// trans = EvaluatorsFactory.getEvaluators(testConfigLocal12());
|
||||
List<Clusterer> trans = ClusterersFactory.getClusterers(testConfigLocal2());
|
||||
List<ComputationalAgent> trans = ClusterersFactory.getClusterers(testConfigLocal2());
|
||||
trans.get(0).init();
|
||||
Regressor.process(trans.get(0));
|
||||
|
||||
|
|
|
|||
|
|
@ -1,91 +0,0 @@
|
|||
package org.gcube.dataanalysis.ecoengine.test.checks;
|
||||
|
||||
import java.util.HashMap;
|
||||
import java.util.List;
|
||||
|
||||
import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
|
||||
import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
|
||||
import org.gcube.dataanalysis.ecoengine.interfaces.Generator;
|
||||
import org.gcube.dataanalysis.ecoengine.processing.factories.GeneratorsFactory;
|
||||
|
||||
public class TestSingleHSPECGeneration {
|
||||
/**
|
||||
* example of parallel processing on a single machine the procedure will generate a new table for a distribution on suitable species
|
||||
*
|
||||
*/
|
||||
|
||||
public static void main(String[] args) throws Exception {
|
||||
|
||||
List<Generator> generators = GeneratorsFactory.getGenerators(testConfigLocal());
|
||||
generators.get(0).init();
|
||||
generate(generators.get(0));
|
||||
generators = null;
|
||||
|
||||
}
|
||||
|
||||
|
||||
private static void generate(Generator generator) throws Exception {
|
||||
|
||||
if (generator != null) {
|
||||
TestSingleHSPECGeneration tgs = new TestSingleHSPECGeneration();
|
||||
ThreadCalculator tc = tgs.new ThreadCalculator(generator);
|
||||
Thread t = new Thread(tc);
|
||||
t.start();
|
||||
while (generator.getStatus() < 100) {
|
||||
|
||||
String resLoad = generator.getResourceLoad();
|
||||
String ress = generator.getResources();
|
||||
String species = generator.getLoad();
|
||||
System.out.println("LOAD: " + resLoad);
|
||||
System.out.println("RESOURCES: " + ress);
|
||||
System.out.println("SPECIES: " + species);
|
||||
System.out.println("STATUS: " + generator.getStatus());
|
||||
Thread.sleep(1000);
|
||||
}
|
||||
} else
|
||||
AnalysisLogger.getLogger().trace("Generator Algorithm Not Supported");
|
||||
|
||||
}
|
||||
|
||||
public class ThreadCalculator implements Runnable {
|
||||
Generator dg;
|
||||
|
||||
public ThreadCalculator(Generator dg) {
|
||||
this.dg = dg;
|
||||
}
|
||||
|
||||
public void run() {
|
||||
try {
|
||||
|
||||
dg.compute();
|
||||
|
||||
} catch (Exception e) {
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
|
||||
private static AlgorithmConfiguration testConfigLocal() {
|
||||
|
||||
AlgorithmConfiguration config = new AlgorithmConfiguration();
|
||||
config.setConfigPath("./cfg/");
|
||||
config.setPersistencePath("./");
|
||||
config.setNumberOfResources(5);
|
||||
config.setModel("AQUAMAPS_SUITABLE");
|
||||
|
||||
config.setParam("DistributionTable","hspec_suitable_baskingshark_aquamaps");
|
||||
config.setParam("CsquarecodesTable","hcaf_d");
|
||||
config.setParam("EnvelopeTable","hspen_baskingshark");
|
||||
config.setParam("PreprocessedTable", "maxminlat_hspen");
|
||||
config.setParam("CreateTable","true");
|
||||
/*
|
||||
config.setParam("DatabaseUserName","gcube");
|
||||
config.setParam("DatabasePassword","d4science2");
|
||||
config.setParam("DatabaseURL","jdbc:postgresql://localhost/testdb");
|
||||
config.setParam("DatabaseDriver","org.postgresql.Driver");
|
||||
*/
|
||||
|
||||
return config;
|
||||
}
|
||||
}
|
||||
|
|
@ -1,84 +0,0 @@
|
|||
package org.gcube.dataanalysis.ecoengine.test.checks;
|
||||
|
||||
import java.util.List;
|
||||
|
||||
import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
|
||||
import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
|
||||
import org.gcube.dataanalysis.ecoengine.interfaces.Transducerer;
|
||||
import org.gcube.dataanalysis.ecoengine.processing.factories.TransducerersFactory;
|
||||
|
||||
public class TestTransducer {
|
||||
/**
|
||||
* example of parallel processing on a single machine the procedure will generate a new table for a distribution on suitable species
|
||||
*
|
||||
*/
|
||||
|
||||
public static void main(String[] args) throws Exception {
|
||||
|
||||
System.out.println("TEST 1");
|
||||
List<Transducerer> trans = TransducerersFactory.getTransducerers(testConfigLocal());
|
||||
trans.get(0).init();
|
||||
transduce(trans.get(0));
|
||||
trans = null;
|
||||
|
||||
}
|
||||
|
||||
private static void transduce(Transducerer trans) throws Exception {
|
||||
|
||||
if (trans != null) {
|
||||
TestTransducer tgs = new TestTransducer();
|
||||
ThreadCalculator tc = tgs.new ThreadCalculator(trans);
|
||||
Thread t = new Thread(tc);
|
||||
t.start();
|
||||
while (trans.getStatus() < 100) {
|
||||
|
||||
System.out.println("STATUS: " + trans.getStatus());
|
||||
Thread.sleep(1000);
|
||||
}
|
||||
} else
|
||||
AnalysisLogger.getLogger().trace("Generator Algorithm Not Supported");
|
||||
|
||||
}
|
||||
|
||||
public class ThreadCalculator implements Runnable {
|
||||
Transducerer dg;
|
||||
|
||||
public ThreadCalculator(Transducerer dg) {
|
||||
this.dg = dg;
|
||||
}
|
||||
|
||||
public void run() {
|
||||
try {
|
||||
|
||||
dg.compute();
|
||||
|
||||
} catch (Exception e) {
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
private static AlgorithmConfiguration testConfigLocal() {
|
||||
|
||||
AlgorithmConfiguration config = new AlgorithmConfiguration();
|
||||
config.setConfigPath("./cfg/");
|
||||
config.setPersistencePath("./");
|
||||
config.setNumberOfResources(1);
|
||||
config.setAgent("BIOCLIMATE_HSPEC");
|
||||
|
||||
//config.setParam("HSPEC_TABLE_LIST", "hcaf_d, hcaf_d_2015_LINEAR_01338580273835,hcaf_d_2018_LINEAR_11338580276548,hcaf_d_2021_LINEAR_21338580279237,hcaf_d_2024_LINEAR_31338580282780,hcaf_d_2027_LINEAR_41338580283400,hcaf_d_2030_LINEAR_51338580284030,hcaf_d_2033_LINEAR_61338580284663,hcaf_d_2036_LINEAR_71338580285205,hcaf_d_2039_LINEAR_81338580285958,hcaf_d_2042_LINEAR_91338580286545,hcaf_d_2050");
|
||||
//config.setParam("HSPEC_TABLE_NAMES", "test,test,test,test,test,test,test,test,test,test,test,test");
|
||||
config.setParam("HSPEC_TABLE_LIST", "hspec_validation"+AlgorithmConfiguration.getListSeparator()+"hspec_validation2");
|
||||
config.setParam("HSPEC_TABLE_NAMES", "test"+AlgorithmConfiguration.getListSeparator()+"test");
|
||||
|
||||
config.setParam("Threshold", "0.5");
|
||||
|
||||
config.setParam("DatabaseUserName", "gcube");
|
||||
config.setParam("DatabasePassword", "d4science2");
|
||||
config.setParam("DatabaseURL", "jdbc:postgresql://localhost/testdb");
|
||||
config.setParam("DatabaseDriver", "org.postgresql.Driver");
|
||||
|
||||
return config;
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -1,187 +0,0 @@
|
|||
package org.gcube.dataanalysis.ecoengine.test.checks;
|
||||
|
||||
import java.util.List;
|
||||
|
||||
import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
|
||||
import org.gcube.dataanalysis.ecoengine.evaluation.bioclimate.InterpolateTables.INTERPOLATIONFUNCTIONS;
|
||||
import org.gcube.dataanalysis.ecoengine.interfaces.Transducerer;
|
||||
import org.gcube.dataanalysis.ecoengine.processing.factories.TransducerersFactory;
|
||||
import org.gcube.dataanalysis.ecoengine.test.regression.Regressor;
|
||||
|
||||
public class TestTransducers {
|
||||
|
||||
public static void main(String[] args) throws Exception {
|
||||
|
||||
System.out.println("TEST 1");
|
||||
List<Transducerer> trans = null;
|
||||
/*
|
||||
trans = TransducerersFactory.getTransducerers(testConfigLocal());
|
||||
trans.get(0).init();
|
||||
Regressor.process(trans.get(0));
|
||||
trans = null;
|
||||
|
||||
trans = TransducerersFactory.getTransducerers(testConfigLocal2());
|
||||
trans.get(0).init();
|
||||
Regressor.process(trans.get(0));
|
||||
trans = null;
|
||||
|
||||
trans = TransducerersFactory.getTransducerers(testConfigLocal3());
|
||||
trans.get(0).init();
|
||||
Regressor.process(trans.get(0));
|
||||
trans = null;
|
||||
|
||||
trans = TransducerersFactory.getTransducerers(testConfigLocal4());
|
||||
trans.get(0).init();
|
||||
Regressor.process(trans.get(0));
|
||||
trans = null;
|
||||
*/
|
||||
|
||||
/*
|
||||
trans = TransducerersFactory.getTransducerers(testConfigLocal8());
|
||||
trans.get(0).init();
|
||||
Regressor.process(trans.get(0));
|
||||
trans = null;
|
||||
|
||||
trans = TransducerersFactory.getTransducerers(testConfigLocal6());
|
||||
trans.get(0).init();
|
||||
Regressor.process(trans.get(0));
|
||||
trans = null;
|
||||
*/
|
||||
|
||||
trans = TransducerersFactory.getTransducerers(testConfigLocal7());
|
||||
trans.get(0).init();
|
||||
Regressor.process(trans.get(0));
|
||||
trans = null;
|
||||
|
||||
}
|
||||
|
||||
|
||||
private static AlgorithmConfiguration testConfigLocal() {
|
||||
|
||||
AlgorithmConfiguration config = Regressor.getConfig();
|
||||
config.setAgent("BIOCLIMATE_HSPEC");
|
||||
config.setParam("HSPEC_TABLE_LIST", "hspec_validation"+AlgorithmConfiguration.getListSeparator()+"hspec_validation2");
|
||||
config.setParam("HSPEC_TABLE_NAMES", "test"+AlgorithmConfiguration.getListSeparator()+"test");
|
||||
config.setParam("Threshold", "0.5");
|
||||
|
||||
return config;
|
||||
}
|
||||
|
||||
private static AlgorithmConfiguration testConfigLocal2() {
|
||||
|
||||
AlgorithmConfiguration config = Regressor.getConfig();
|
||||
config.setAgent("BIOCLIMATE_HCAF");
|
||||
config.setParam("HCAF_TABLE_LIST","hcaf_d"+AlgorithmConfiguration.getListSeparator()+"hcaf_d_2016_linear_01332632269756"+AlgorithmConfiguration.getListSeparator()+"hcaf_d_2016_linear_01336062995861"+AlgorithmConfiguration.getListSeparator()+"hcaf_d_2050");
|
||||
config.setParam("HCAF_TABLE_NAMES", "test"+AlgorithmConfiguration.getListSeparator()+"test"+AlgorithmConfiguration.getListSeparator()+"test"+AlgorithmConfiguration.getListSeparator()+"test");
|
||||
|
||||
return config;
|
||||
}
|
||||
|
||||
private static AlgorithmConfiguration testConfigLocal3() {
|
||||
|
||||
AlgorithmConfiguration config = Regressor.getConfig();
|
||||
config.setAgent("BIOCLIMATE_HSPEN");
|
||||
config.setParam("HSPEN_TABLE_LIST","hspen"+AlgorithmConfiguration.getListSeparator()+"hspen_2016"+AlgorithmConfiguration.getListSeparator()+"hspen_2020"+AlgorithmConfiguration.getListSeparator()+"hspen_2050");
|
||||
config.setParam("HSPEN_TABLE_NAMES", "test"+AlgorithmConfiguration.getListSeparator()+"test"+AlgorithmConfiguration.getListSeparator()+"test"+AlgorithmConfiguration.getListSeparator()+"test");
|
||||
|
||||
return config;
|
||||
}
|
||||
|
||||
|
||||
private static AlgorithmConfiguration testConfigLocal4() {
|
||||
|
||||
AlgorithmConfiguration config = Regressor.getConfig();
|
||||
config.setAgent("HCAF_INTERPOLATION");
|
||||
|
||||
config.setParam("FirstHCAF","hcaf_d");
|
||||
config.setParam("SecondHCAF","hcaf_d_2050");
|
||||
config.setParam("YearStart","2012");
|
||||
config.setParam("YearEnd","2050");
|
||||
config.setParam("NumberOfInterpolations","2");
|
||||
config.setParam("InterpolationFunction",INTERPOLATIONFUNCTIONS.LINEAR.name());
|
||||
|
||||
return config;
|
||||
}
|
||||
|
||||
private static AlgorithmConfiguration testConfigLocal5() {
|
||||
|
||||
AlgorithmConfiguration config = Regressor.getConfig();
|
||||
config.setAgent("OCCURRENCES_MERGER");
|
||||
|
||||
config.setParam("longitudeColumn", "decimallongitude");
|
||||
config.setParam("latitudeColumn", "decimallatitude");
|
||||
config.setParam("recordedByColumn", "recordedby");
|
||||
config.setParam("scientificNameColumn", "scientificname");
|
||||
config.setParam("eventDateColumn", "eventdate");
|
||||
config.setParam("lastModificationColumn", "modified");
|
||||
config.setParam("rightTableName", "occurrencetestduplicates2");
|
||||
config.setParam("leftTableName", "occurrencetestduplicates");
|
||||
config.setParam("finalTableName", "occurrencesmerged");
|
||||
config.setParam("spatialTolerance", "0.5");
|
||||
config.setParam("confidence", "90");
|
||||
|
||||
|
||||
return config;
|
||||
}
|
||||
|
||||
private static AlgorithmConfiguration testConfigLocal6() {
|
||||
|
||||
AlgorithmConfiguration config = Regressor.getConfig();
|
||||
config.setAgent("OCCURRENCES_INSEAS_ONEARTH");
|
||||
|
||||
config.setParam("longitudeColumn", "decimallongitude");
|
||||
config.setParam("latitudeColumn", "decimallatitude");
|
||||
config.setParam("OccurrencePointsTableName", "whitesharkoccurrences2");
|
||||
config.setParam("finalTableName", "whitesharkoccurrencesfilteredseas");
|
||||
config.setParam("FilterType", "IN_THE_WATER");
|
||||
// config.setParam("FilterType", "ON_EARTH");
|
||||
|
||||
return config;
|
||||
}
|
||||
|
||||
private static AlgorithmConfiguration testConfigLocal7() {
|
||||
|
||||
AlgorithmConfiguration config = Regressor.getConfig();
|
||||
config.setAgent("OCCURRENCES_DUPLICATE_DELETER");
|
||||
|
||||
config.setParam("longitudeColumn", "decimallongitude");
|
||||
config.setParam("latitudeColumn", "decimallatitude");
|
||||
config.setParam("recordedByColumn", "recordedby");
|
||||
config.setParam("scientificNameColumn", "scientificname");
|
||||
config.setParam("eventDateColumn", "eventdate");
|
||||
config.setParam("lastModificationColumn", "modified");
|
||||
config.setParam("OccurrencePointsTableName", "occurrence_species_id5397d3c4_a7eb_4227_adb4_d9d7d36e8b21");
|
||||
config.setParam("finalTableName", "occurrencesnoduplicates");
|
||||
config.setParam("spatialTolerance", "0.5");
|
||||
config.setParam("confidence", "80");
|
||||
config.setParam("DatabaseUserName","utente");
|
||||
config.setParam("DatabasePassword","d4science");
|
||||
config.setParam("DatabaseURL","jdbc:postgresql://dbtest.next.research-infrastructures.eu/testdb");
|
||||
config.setParam("DatabaseDriver","org.postgresql.Driver");
|
||||
|
||||
return config;
|
||||
}
|
||||
|
||||
|
||||
private static AlgorithmConfiguration testConfigLocal8() {
|
||||
|
||||
AlgorithmConfiguration config = Regressor.getConfig();
|
||||
config.setAgent("OCCURRENCES_INTERSECTOR");
|
||||
|
||||
config.setParam("longitudeColumn", "decimallongitude");
|
||||
config.setParam("latitudeColumn", "decimallatitude");
|
||||
config.setParam("recordedByColumn", "recordedby");
|
||||
config.setParam("scientificNameColumn", "scientificname");
|
||||
config.setParam("eventDateColumn", "eventdate");
|
||||
config.setParam("lastModificationColumn", "modified");
|
||||
config.setParam("rightTableName", "occurrencetestduplicates2");
|
||||
config.setParam("leftTableName", "occurrencetestduplicates");
|
||||
config.setParam("finalTableName", "occurrencesintersected");
|
||||
config.setParam("spatialTolerance", "0.5");
|
||||
config.setParam("confidence", "80");
|
||||
|
||||
|
||||
return config;
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -1,77 +0,0 @@
|
|||
package org.gcube.dataanalysis.ecoengine.test.checks;
|
||||
|
||||
import java.util.List;
|
||||
|
||||
import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
|
||||
import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
|
||||
import org.gcube.dataanalysis.ecoengine.interfaces.Generator;
|
||||
import org.gcube.dataanalysis.ecoengine.processing.factories.GeneratorsFactory;
|
||||
|
||||
public class TestsDUMMYGeneration {
|
||||
/**
|
||||
* example of parallel processing on a single machine the procedure will generate a new table for a distribution on suitable species
|
||||
*
|
||||
*/
|
||||
|
||||
public static void main(String[] args) throws Exception {
|
||||
|
||||
System.out.println("TEST 1");
|
||||
List<Generator> generators = GeneratorsFactory.getGenerators(testConfig());
|
||||
generators.get(0).init();
|
||||
generate(generators.get(0));
|
||||
generators = null;
|
||||
}
|
||||
|
||||
|
||||
private static void generate(Generator generator) throws Exception {
|
||||
|
||||
if (generator != null) {
|
||||
TestsDUMMYGeneration tgs = new TestsDUMMYGeneration();
|
||||
ThreadCalculator tc = tgs.new ThreadCalculator(generator);
|
||||
Thread t = new Thread(tc);
|
||||
t.start();
|
||||
while (generator.getStatus() < 100) {
|
||||
|
||||
String resLoad = generator.getResourceLoad();
|
||||
String ress = generator.getResources();
|
||||
String species = generator.getLoad();
|
||||
System.out.println("LOAD: " + resLoad);
|
||||
System.out.println("RESOURCES: " + ress);
|
||||
System.out.println("SPECIES: " + species);
|
||||
System.out.println("STATUS: " + generator.getStatus());
|
||||
Thread.sleep(1000);
|
||||
}
|
||||
} else
|
||||
AnalysisLogger.getLogger().trace("Generator Algorithm Not Supported");
|
||||
|
||||
}
|
||||
|
||||
public class ThreadCalculator implements Runnable {
|
||||
Generator dg;
|
||||
|
||||
public ThreadCalculator(Generator dg) {
|
||||
this.dg = dg;
|
||||
}
|
||||
|
||||
public void run() {
|
||||
try {
|
||||
|
||||
dg.compute();
|
||||
|
||||
} catch (Exception e) {
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
|
||||
private static AlgorithmConfiguration testConfig() {
|
||||
AlgorithmConfiguration config = new AlgorithmConfiguration();
|
||||
config.setConfigPath("./cfg/");
|
||||
config.setPersistencePath("./");
|
||||
config.setNumberOfResources(10);
|
||||
config.setModel("DUMMY");
|
||||
return config;
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -4,6 +4,7 @@ import java.util.List;
|
|||
|
||||
import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
|
||||
import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
|
||||
import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent;
|
||||
import org.gcube.dataanalysis.ecoengine.interfaces.Modeler;
|
||||
import org.gcube.dataanalysis.ecoengine.processing.factories.ModelersFactory;
|
||||
|
||||
|
|
@ -16,13 +17,13 @@ public class TestsHSPENTraining {
|
|||
public static void main(String[] args) throws Exception {
|
||||
|
||||
System.out.println("TEST 1");
|
||||
List<Modeler> modelers=ModelersFactory.getModelers(testConfig());
|
||||
List<ComputationalAgent> modelers=ModelersFactory.getModelers(testConfig());
|
||||
train(modelers.get(0),testConfig());
|
||||
modelers = null;
|
||||
}
|
||||
|
||||
|
||||
private static void train(Modeler modeler,AlgorithmConfiguration config) throws Exception {
|
||||
private static void train(ComputationalAgent modeler,AlgorithmConfiguration config) throws Exception {
|
||||
|
||||
if (modeler != null) {
|
||||
TestsHSPENTraining tgs = new TestsHSPENTraining();
|
||||
|
|
@ -45,10 +46,10 @@ public static void main(String[] args) throws Exception {
|
|||
}
|
||||
|
||||
public class ThreadCalculator implements Runnable {
|
||||
Modeler dg;
|
||||
ComputationalAgent dg;
|
||||
AlgorithmConfiguration config;
|
||||
|
||||
public ThreadCalculator(Modeler dg,AlgorithmConfiguration config) {
|
||||
public ThreadCalculator(ComputationalAgent dg,AlgorithmConfiguration config) {
|
||||
this.dg = dg;
|
||||
this.config = config;
|
||||
}
|
||||
|
|
@ -56,7 +57,7 @@ public static void main(String[] args) throws Exception {
|
|||
public void run() {
|
||||
try {
|
||||
|
||||
dg.model(null);
|
||||
dg.compute();
|
||||
|
||||
} catch (Exception e) {
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,77 +0,0 @@
|
|||
package org.gcube.dataanalysis.ecoengine.test.checks;
|
||||
|
||||
import java.util.List;
|
||||
|
||||
import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
|
||||
import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
|
||||
import org.gcube.dataanalysis.ecoengine.interfaces.Generator;
|
||||
import org.gcube.dataanalysis.ecoengine.processing.factories.GeneratorsFactory;
|
||||
|
||||
public class TestsTESTGeneration {
|
||||
/**
|
||||
* example of parallel processing on a single machine the procedure will generate a new table for a distribution on suitable species
|
||||
*
|
||||
*/
|
||||
|
||||
public static void main(String[] args) throws Exception {
|
||||
|
||||
System.out.println("TEST 1");
|
||||
List<Generator> generators = GeneratorsFactory.getGenerators(testConfig());
|
||||
generators.get(0).init();
|
||||
generate(generators.get(0));
|
||||
generators = null;
|
||||
}
|
||||
|
||||
|
||||
private static void generate(Generator generator) throws Exception {
|
||||
|
||||
if (generator != null) {
|
||||
TestsTESTGeneration tgs = new TestsTESTGeneration();
|
||||
ThreadCalculator tc = tgs.new ThreadCalculator(generator);
|
||||
Thread t = new Thread(tc);
|
||||
t.start();
|
||||
while (generator.getStatus() < 100) {
|
||||
|
||||
String resLoad = generator.getResourceLoad();
|
||||
String ress = generator.getResources();
|
||||
String species = generator.getLoad();
|
||||
System.out.println("LOAD: " + resLoad);
|
||||
System.out.println("RESOURCES: " + ress);
|
||||
System.out.println("SPECIES: " + species);
|
||||
System.out.println("STATUS: " + generator.getStatus());
|
||||
Thread.sleep(1000);
|
||||
}
|
||||
} else
|
||||
AnalysisLogger.getLogger().trace("Generator Algorithm Not Supported");
|
||||
|
||||
}
|
||||
|
||||
public class ThreadCalculator implements Runnable {
|
||||
Generator dg;
|
||||
|
||||
public ThreadCalculator(Generator dg) {
|
||||
this.dg = dg;
|
||||
}
|
||||
|
||||
public void run() {
|
||||
try {
|
||||
|
||||
dg.compute();
|
||||
|
||||
} catch (Exception e) {
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
|
||||
private static AlgorithmConfiguration testConfig() {
|
||||
AlgorithmConfiguration config = new AlgorithmConfiguration();
|
||||
config.setConfigPath("./cfg/");
|
||||
config.setPersistencePath("./");
|
||||
config.setNumberOfResources(2);
|
||||
config.setModel("TEST");
|
||||
return config;
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -6,6 +6,7 @@ import java.util.List;
|
|||
import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
|
||||
import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveType;
|
||||
import org.gcube.dataanalysis.ecoengine.evaluation.DiscrepancyAnalysis;
|
||||
import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent;
|
||||
import org.gcube.dataanalysis.ecoengine.interfaces.Evaluator;
|
||||
import org.gcube.dataanalysis.ecoengine.interfaces.Generator;
|
||||
import org.gcube.dataanalysis.ecoengine.interfaces.Modeler;
|
||||
|
|
@ -50,7 +51,7 @@ public class ExperimentsForLatimeria {
|
|||
|
||||
public static void generateHSPENTable() throws Exception{
|
||||
System.out.println("*****************************HSPEN FILTER**********************************");
|
||||
List<Transducerer> trans = null;
|
||||
List<ComputationalAgent> trans = null;
|
||||
trans = TransducerersFactory.getTransducerers(PresetConfigGenerator.configHSPENfilter(envelopeTable, speciesID));
|
||||
trans.get(0).init();
|
||||
Regressor.process(trans.get(0));
|
||||
|
|
@ -58,7 +59,7 @@ public class ExperimentsForLatimeria {
|
|||
}
|
||||
|
||||
public static void generateAquamapsNativeSuitable() throws Exception{
|
||||
List<Generator> generators = null;
|
||||
List<ComputationalAgent> generators = null;
|
||||
System.out.println("*****************************AQUAMAPS SUITABLE**********************************");
|
||||
generators = GeneratorsFactory.getGenerators(PresetConfigGenerator.configAquamapsSuitable(aquamapsSuitableTable,envelopeTable));
|
||||
generators.get(0).init();
|
||||
|
|
@ -75,7 +76,7 @@ public class ExperimentsForLatimeria {
|
|||
|
||||
public static void generatePresenceTable() throws Exception{
|
||||
System.out.println("*****************************PRESENCE TABLE**********************************");
|
||||
List<Transducerer> trans = null;
|
||||
List<ComputationalAgent> trans = null;
|
||||
trans = TransducerersFactory.getTransducerers(PresetConfigGenerator.configPresenceTable(presenceTable, -1, speciesID));
|
||||
trans.get(0).init();
|
||||
Regressor.process(trans.get(0));
|
||||
|
|
@ -85,7 +86,7 @@ public class ExperimentsForLatimeria {
|
|||
|
||||
public static void generateRandomAbsenceTable() throws Exception{
|
||||
System.out.println("*****************************RANDOM ABSENCES**********************************");
|
||||
List<Transducerer> trans = null;
|
||||
List<ComputationalAgent> trans = null;
|
||||
trans = TransducerersFactory.getTransducerers(PresetConfigGenerator.configAbsenceTable(true, absenceRandomTable, aquamapsNativeTable, numberOfPoints, speciesID));
|
||||
trans.get(0).init();
|
||||
Regressor.process(trans.get(0));
|
||||
|
|
@ -94,7 +95,7 @@ public class ExperimentsForLatimeria {
|
|||
|
||||
public static void generateAbsenceTable() throws Exception{
|
||||
System.out.println("*****************************ABSENCES**********************************");
|
||||
List<Transducerer> trans = null;
|
||||
List<ComputationalAgent> trans = null;
|
||||
trans = TransducerersFactory.getTransducerers(PresetConfigGenerator.configAbsenceTable(false, absenceStaticTable, aquamapsNativeTable, numberOfPoints, speciesID));
|
||||
trans.get(0).init();
|
||||
Regressor.process(trans.get(0));
|
||||
|
|
@ -103,7 +104,7 @@ public class ExperimentsForLatimeria {
|
|||
|
||||
public static void trainNeuralNetworks() throws Exception{
|
||||
|
||||
List<Modeler> modelers = null;
|
||||
List<ComputationalAgent> modelers = null;
|
||||
System.out.println("*****************************TRAINING NN SUITABLE WITH STATIC ABSENCES**********************************");
|
||||
modelers = ModelersFactory.getModelers(PresetConfigGenerator.configSuitableNeuralNetworkTraining(presenceTable,absenceStaticTable,staticsuitable,speciesID,"100"+AlgorithmConfiguration.getListSeparator()+"2",nnname));
|
||||
modelers.get(0).init();
|
||||
|
|
@ -133,7 +134,7 @@ public class ExperimentsForLatimeria {
|
|||
|
||||
public static void trainSuitableNeuralNetworks() throws Exception{
|
||||
|
||||
List<Modeler> modelers = null;
|
||||
List<ComputationalAgent> modelers = null;
|
||||
System.out.println("*****************************TRAINING NN SUITABLE WITH STATIC ABSENCES**********************************");
|
||||
modelers = ModelersFactory.getModelers(PresetConfigGenerator.configSuitableNeuralNetworkTraining(presenceTable,absenceStaticTable,staticsuitable,speciesID,"100"+AlgorithmConfiguration.getListSeparator()+"2",nnname));
|
||||
modelers.get(0).init();
|
||||
|
|
@ -144,7 +145,7 @@ public class ExperimentsForLatimeria {
|
|||
public static void trainNativeNeuralNetworks() throws Exception{
|
||||
|
||||
System.out.println("*****************************TRAINING NN NATIVE WITH STATIC ABSENCES**********************************");
|
||||
List<Modeler> modelers = null;
|
||||
List<ComputationalAgent> modelers = null;
|
||||
modelers = ModelersFactory.getModelers(PresetConfigGenerator.configNativeNeuralNetworkTraining(presenceTable,absenceStaticTable,staticnative,speciesID,"100"+AlgorithmConfiguration.getListSeparator()+"2",nnname));
|
||||
modelers.get(0).init();
|
||||
Regressor.process(modelers.get(0));
|
||||
|
|
@ -154,7 +155,7 @@ public class ExperimentsForLatimeria {
|
|||
|
||||
|
||||
public static void generateAquamapsNativeSuitableNeuralNetwokrs() throws Exception{
|
||||
List<Generator> generators = null;
|
||||
List<ComputationalAgent> generators = null;
|
||||
System.out.println("*****************************GENERATING NN SUITABLE WITH STATIC ABSENCES**********************************");
|
||||
generators = GeneratorsFactory.getGenerators(PresetConfigGenerator.configAquamapsNNSuitable(nnsuitableTable,staticsuitable,envelopeTable,speciesID,nnname));
|
||||
generators.get(0).init();
|
||||
|
|
@ -185,7 +186,7 @@ public class ExperimentsForLatimeria {
|
|||
|
||||
public static void calcdiscrepancy(String table1,String table2) throws Exception{
|
||||
System.out.println("*****************************DISCREPANCY: "+table1+" vs "+table2+"************************************");
|
||||
List<Evaluator> evaluators = null;
|
||||
List<ComputationalAgent> evaluators = null;
|
||||
evaluators = EvaluatorsFactory.getEvaluators(PresetConfigGenerator.configDiscrepancyAnalysis(table1, table2));
|
||||
evaluators.get(0).init();
|
||||
Regressor.process(evaluators.get(0));
|
||||
|
|
@ -197,7 +198,7 @@ public class ExperimentsForLatimeria {
|
|||
|
||||
public static void calcquality(String table,String presenceTable, String absenceTable) throws Exception{
|
||||
System.out.println("*****************************QUALITY: "+table+" vs "+presenceTable+" and "+absenceTable+"************************************");
|
||||
List<Evaluator> evaluators = null;
|
||||
List<ComputationalAgent> evaluators = null;
|
||||
evaluators = EvaluatorsFactory.getEvaluators(PresetConfigGenerator.configQualityAnalysis(presenceTable,absenceTable,table));
|
||||
evaluators.get(0).init();
|
||||
Regressor.process(evaluators.get(0));
|
||||
|
|
@ -210,7 +211,7 @@ public class ExperimentsForLatimeria {
|
|||
|
||||
public static void generateHCAFFilter() throws Exception{
|
||||
System.out.println("*****************************HCAF FILTER ON : "+x1+","+y1+","+x2+","+y2+"************************************");
|
||||
List<Transducerer> trans = null;
|
||||
List<ComputationalAgent> trans = null;
|
||||
trans = TransducerersFactory.getTransducerers(PresetConfigGenerator.configHCAFfilter(filteredhcaf, x1, y1, x2, y2));
|
||||
trans.get(0).init();
|
||||
Regressor.process(trans.get(0));
|
||||
|
|
@ -219,7 +220,7 @@ public class ExperimentsForLatimeria {
|
|||
|
||||
public static void calcHRS(String hcaf,String absenceTable,String presenceTable) throws Exception{
|
||||
System.out.println("*****************************HRS: "+absenceTable+","+presenceTable+" vs "+hcaf+"************************************");
|
||||
List<Evaluator> evaluators = null;
|
||||
List<ComputationalAgent> evaluators = null;
|
||||
evaluators = EvaluatorsFactory.getEvaluators(PresetConfigGenerator.configHRSAnalysis(filteredhcaf, absenceTable, presenceTable));
|
||||
evaluators.get(0).init();
|
||||
Regressor.process(evaluators.get(0));
|
||||
|
|
|
|||
|
|
@ -6,6 +6,7 @@ import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
|
|||
import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveType;
|
||||
import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.PrimitiveTypes;
|
||||
import org.gcube.dataanalysis.ecoengine.interfaces.Clusterer;
|
||||
import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent;
|
||||
import org.gcube.dataanalysis.ecoengine.processing.factories.ClusterersFactory;
|
||||
|
||||
public class RegressionTestClusterers {
|
||||
|
|
@ -17,7 +18,7 @@ public class RegressionTestClusterers {
|
|||
public static void main(String[] args) throws Exception {
|
||||
|
||||
System.out.println("TEST 1");
|
||||
List<Clusterer> clus;
|
||||
List<ComputationalAgent> clus;
|
||||
|
||||
|
||||
clus = ClusterersFactory.getClusterers(testConfigLocal());
|
||||
|
|
|
|||
|
|
@ -3,6 +3,7 @@ package org.gcube.dataanalysis.ecoengine.test.regression;
|
|||
import java.util.List;
|
||||
|
||||
import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
|
||||
import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent;
|
||||
import org.gcube.dataanalysis.ecoengine.interfaces.Evaluator;
|
||||
import org.gcube.dataanalysis.ecoengine.processing.factories.EvaluatorsFactory;
|
||||
|
||||
|
|
@ -14,7 +15,7 @@ public class RegressionTestEvaluators {
|
|||
|
||||
public static void main(String[] args) throws Exception {
|
||||
|
||||
List<Evaluator> evaluators = EvaluatorsFactory.getEvaluators(testConfig1());
|
||||
List<ComputationalAgent> evaluators = EvaluatorsFactory.getEvaluators(testConfig1());
|
||||
evaluators.get(0).init();
|
||||
Regressor.process(evaluators.get(0));
|
||||
evaluators = null;
|
||||
|
|
|
|||
|
|
@ -3,6 +3,7 @@ package org.gcube.dataanalysis.ecoengine.test.regression;
|
|||
import java.util.List;
|
||||
|
||||
import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
|
||||
import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent;
|
||||
import org.gcube.dataanalysis.ecoengine.interfaces.Generator;
|
||||
import org.gcube.dataanalysis.ecoengine.processing.factories.GeneratorsFactory;
|
||||
|
||||
|
|
@ -16,7 +17,7 @@ public static void main(String[] args) throws Exception {
|
|||
|
||||
System.out.println("TEST 1");
|
||||
|
||||
List<Generator> generators = GeneratorsFactory.getGenerators(testConfigLocal());
|
||||
List<ComputationalAgent> generators = GeneratorsFactory.getGenerators(testConfigLocal());
|
||||
generators.get(0).init();
|
||||
Regressor.process(generators.get(0));
|
||||
generators = null;
|
||||
|
|
|
|||
|
|
@ -3,6 +3,7 @@ package org.gcube.dataanalysis.ecoengine.test.regression;
|
|||
import java.util.List;
|
||||
|
||||
import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
|
||||
import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent;
|
||||
import org.gcube.dataanalysis.ecoengine.interfaces.Generator;
|
||||
import org.gcube.dataanalysis.ecoengine.interfaces.Modeler;
|
||||
import org.gcube.dataanalysis.ecoengine.processing.factories.GeneratorsFactory;
|
||||
|
|
@ -18,7 +19,7 @@ public static void main(String[] args) throws Exception {
|
|||
|
||||
System.out.println("TEST 1");
|
||||
|
||||
List<Modeler> modelers = ModelersFactory.getModelers(testConfigLocal());
|
||||
List<ComputationalAgent> modelers = ModelersFactory.getModelers(testConfigLocal());
|
||||
modelers.get(0).init();
|
||||
Regressor.process(modelers.get(0));
|
||||
modelers = null;
|
||||
|
|
|
|||
|
|
@ -4,6 +4,7 @@ import java.util.List;
|
|||
|
||||
import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
|
||||
import org.gcube.dataanalysis.ecoengine.evaluation.bioclimate.InterpolateTables.INTERPOLATIONFUNCTIONS;
|
||||
import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent;
|
||||
import org.gcube.dataanalysis.ecoengine.interfaces.Transducerer;
|
||||
import org.gcube.dataanalysis.ecoengine.processing.factories.TransducerersFactory;
|
||||
|
||||
|
|
@ -12,7 +13,7 @@ public class RegressionTestTransducers {
|
|||
public static void main(String[] args) throws Exception {
|
||||
|
||||
System.out.println("TEST 1");
|
||||
List<Transducerer> trans = null;
|
||||
List<ComputationalAgent> trans = null;
|
||||
/*
|
||||
trans = TransducerersFactory.getTransducerers(testConfigLocal());
|
||||
trans.get(0).init();
|
||||
|
|
|
|||
|
|
@ -1,5 +1,6 @@
|
|||
package org.gcube.dataanalysis.ecoengine.test.regression;
|
||||
|
||||
import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
|
||||
import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
|
||||
import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent;
|
||||
|
||||
|
|
@ -51,13 +52,14 @@ public class Regressor {
|
|||
public static AlgorithmConfiguration getConfig() {
|
||||
|
||||
AlgorithmConfiguration config = new AlgorithmConfiguration();
|
||||
|
||||
config.setConfigPath("./cfg/");
|
||||
config.setPersistencePath("./");
|
||||
config.setParam("DatabaseUserName","gcube");
|
||||
config.setParam("DatabasePassword","d4science2");
|
||||
config.setParam("DatabaseURL","jdbc:postgresql://146.48.87.169/testdb");
|
||||
config.setParam("DatabaseDriver","org.postgresql.Driver");
|
||||
|
||||
AnalysisLogger.setLogger(config.getConfigPath()+AlgorithmConfiguration.defaultLoggerFile);
|
||||
return config;
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -281,7 +281,7 @@ public class OccurrencePointsMerger implements Transducerer {
|
|||
@Override
|
||||
public void init() throws Exception {
|
||||
|
||||
// AnalysisLogger.setLogger(config.getConfigPath() + AlgorithmConfiguration.defaultLoggerFile);
|
||||
// AnalysisLogger.setLogger(config.getConfigPath() + AlgorithmConfiguration.defaultLoggerFile);
|
||||
lonFld = config.getParam(longitudeColumn);
|
||||
latFld = config.getParam(latitudeColumn);
|
||||
recordedByFld = config.getParam(recordedByColumn);
|
||||
|
|
@ -479,16 +479,18 @@ public class OccurrencePointsMerger implements Transducerer {
|
|||
public List<Object> leftRows;
|
||||
public List<Object> rightRows;
|
||||
|
||||
public int getNumLeftObjects(){
|
||||
if (leftRows!=null)
|
||||
public int getNumLeftObjects() {
|
||||
if (leftRows != null)
|
||||
return leftRows.size();
|
||||
else return 0;
|
||||
else
|
||||
return 0;
|
||||
}
|
||||
|
||||
public int getNumRightObjects(){
|
||||
if (rightRows!=null)
|
||||
public int getNumRightObjects() {
|
||||
if (rightRows != null)
|
||||
return rightRows.size();
|
||||
else return 0;
|
||||
else
|
||||
return 0;
|
||||
}
|
||||
|
||||
public void takeFullRanges() {
|
||||
|
|
@ -512,13 +514,17 @@ public class OccurrencePointsMerger implements Transducerer {
|
|||
public void computeRange() throws Exception {
|
||||
try {
|
||||
AnalysisLogger.getLogger().info("Processing " + leftTableName + " vs " + rightTableName);
|
||||
// AnalysisLogger.getLogger().info("ELEMENTS " + getNumLeftObjects() + " vs " + getNumRightObjects());
|
||||
status = 10;
|
||||
int rightCounter = 0;
|
||||
int similaritiesCounter = 0;
|
||||
int allrightrows = rightRows.size();
|
||||
if ((allrightrows > 0) && (getNumLeftObjects() > 0)) {
|
||||
for (Object rRow : rightRows) {
|
||||
// AnalysisLogger.getLogger().info("RR CONV");
|
||||
// transform into an occurrence object
|
||||
OccurrenceRecord rightOcc = row2OccurrenceRecord((Object[]) rRow);
|
||||
// AnalysisLogger.getLogger().info("RR CONV - OK");
|
||||
// for each element in sx
|
||||
int k = 0;
|
||||
boolean found = false;
|
||||
|
|
@ -526,9 +532,10 @@ public class OccurrencePointsMerger implements Transducerer {
|
|||
OccurrenceRecord bestleftOcc = null;
|
||||
for (Object lRow : leftRows) {
|
||||
OccurrenceRecord leftOcc = null;
|
||||
// AnalysisLogger.getLogger().info("LL CONV");
|
||||
leftOcc = row2OccurrenceRecord((Object[]) lRow);
|
||||
p = extProb(leftOcc, rightOcc);
|
||||
|
||||
// AnalysisLogger.getLogger().info("P");
|
||||
if (p >= confidenceValue) {
|
||||
bestleftOcc = leftOcc;
|
||||
found = true;
|
||||
|
|
@ -559,13 +566,15 @@ public class OccurrencePointsMerger implements Transducerer {
|
|||
persist();
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
AnalysisLogger.getLogger().info("Found " + similaritiesCounter + " similarities on " + rightCounter + " elements");
|
||||
status = 90;
|
||||
// transform the complete list into a table
|
||||
persist();
|
||||
// close DB connection
|
||||
} catch (Exception e) {
|
||||
System.err.println("Error in computation");
|
||||
AnalysisLogger.getLogger().info(e);
|
||||
throw e;
|
||||
} finally {
|
||||
shutdown();
|
||||
|
|
@ -577,101 +586,10 @@ public class OccurrencePointsMerger implements Transducerer {
|
|||
@Override
|
||||
public void compute() throws Exception {
|
||||
|
||||
try {
|
||||
// init DB connection
|
||||
AnalysisLogger.getLogger().info("Initializing DB Connection");
|
||||
dbconnection = DatabaseUtils.initDBSession(config);
|
||||
AnalysisLogger.getLogger().info("Taking Table Description");
|
||||
extractColumnNames();
|
||||
initDB(true);
|
||||
takeFullRanges();
|
||||
computeRange();
|
||||
|
||||
AnalysisLogger.getLogger().info("Taken Table Description: " + columns);
|
||||
AnalysisLogger.getLogger().info("Creating final table: " + finalTableName);
|
||||
// create new merged table
|
||||
try {
|
||||
DatabaseFactory.executeSQLUpdate(DatabaseUtils.dropTableStatement(finalTableName), dbconnection);
|
||||
} catch (Exception e1) {
|
||||
|
||||
}
|
||||
prepareFinalTable();
|
||||
// take the elements from sx table
|
||||
AnalysisLogger.getLogger().info("Taking elements from left table: " + leftTableName);
|
||||
List<Object> leftRows = DatabaseFactory.executeSQLQuery(DatabaseUtils.getColumnsElementsStatement(leftTableName, columns.toString(), ""), dbconnection);
|
||||
// take the elements from dx table
|
||||
AnalysisLogger.getLogger().info("Taking elements from right table: " + rightTableName);
|
||||
List<Object> rightRows = DatabaseFactory.executeSQLQuery(DatabaseUtils.getColumnsElementsStatement(rightTableName, columns.toString(), ""), dbconnection);
|
||||
// for each element in dx
|
||||
List<OccurrenceRecord> leftRecords = new ArrayList<OccurrencePointsMerger.OccurrenceRecord>();
|
||||
AnalysisLogger.getLogger().info("Processing " + leftTableName + " vs " + rightTableName);
|
||||
status = 10;
|
||||
int rightCounter = 0;
|
||||
int similaritiesCounter = 0;
|
||||
int allrightrows = rightRows.size();
|
||||
for (Object rRow : rightRows) {
|
||||
// transform into an occurrence object
|
||||
OccurrenceRecord rightOcc = row2OccurrenceRecord((Object[]) rRow);
|
||||
// for each element in sx
|
||||
int k = 0;
|
||||
int leftrecordsSize = 0;
|
||||
boolean found = false;
|
||||
float p = 0;
|
||||
OccurrenceRecord bestleftOcc = null;
|
||||
for (Object lRow : leftRows) {
|
||||
OccurrenceRecord leftOcc = null;
|
||||
// only for the first iteration on the left occurrences perform the transformation
|
||||
/*
|
||||
* if (leftrecordsSize <= k) { // transform into an occurrence object leftOcc = row2OccurrenceRecord((Object[]) lRow); leftRecords.add(leftOcc); leftrecordsSize++; // System.out.println("ADDED "+k+"-th elements size: "+leftRecords.size()); } else leftOcc = leftRecords.get(k);
|
||||
*/
|
||||
leftOcc = row2OccurrenceRecord((Object[]) lRow);
|
||||
// evaluate P(dx,sx)
|
||||
p = extProb(leftOcc, rightOcc);
|
||||
|
||||
if (p >= confidenceValue) {
|
||||
bestleftOcc = leftOcc;
|
||||
found = true;
|
||||
similaritiesCounter++;
|
||||
AnalysisLogger.getLogger().info("Found a similarity with P=" + p + " between (" + "\"" + leftOcc.scientificName + "\"" + ",\"" + leftOcc.x + "\"" + "," + "\"" + leftOcc.y + "\"" + "," + "\"" + leftOcc.recordedby + "\"" + "," + "\"" + convert2conventionalFormat(leftOcc.eventdate) + "\"" + ") VS " + "(" + "\"" + rightOcc.scientificName + "\"" + "," + "\"" + rightOcc.x + "\"" + "," + "\"" + rightOcc.y + "\"" + "," + "\"" + rightOcc.recordedby + "\"" + "," + "\"" + convert2conventionalFormat(rightOcc.eventdate) + "\"" + ")");
|
||||
// break;
|
||||
if (!firstbest)
|
||||
manageHighProbability(p, bestleftOcc, rightOcc);
|
||||
else
|
||||
break;
|
||||
} else if (!firstbest)
|
||||
manageLowProbability(p, bestleftOcc, rightOcc);
|
||||
k++;
|
||||
}
|
||||
rightCounter++;
|
||||
|
||||
if (firstbest) {
|
||||
if (found)
|
||||
manageHighProbability(p, bestleftOcc, rightOcc);
|
||||
else
|
||||
manageLowProbability(p, bestleftOcc, rightOcc);
|
||||
}
|
||||
|
||||
status = Math.min(90, 10f + (80 * ((float) rightCounter) / ((float) allrightrows)));
|
||||
|
||||
if (rightCounter % 500 == 0) {
|
||||
AnalysisLogger.getLogger().info("Persisting ... " + rightCounter + " over " + allrightrows);
|
||||
persist();
|
||||
}
|
||||
}
|
||||
|
||||
AnalysisLogger.getLogger().info("Found " + similaritiesCounter + " similarities on " + rightCounter + " elements");
|
||||
status = 90;
|
||||
// transform the complete list into a table
|
||||
persist();
|
||||
// close DB connection
|
||||
} catch (Exception e) {
|
||||
throw e;
|
||||
} finally {
|
||||
if (dbconnection != null)
|
||||
try {
|
||||
dbconnection.close();
|
||||
} catch (Exception e) {
|
||||
}
|
||||
status = 100;
|
||||
AnalysisLogger.getLogger().info("Occ Points Processing Finished and db closed");
|
||||
}
|
||||
}
|
||||
|
||||
public static void main(String[] args) throws Exception {
|
||||
|
|
|
|||
|
|
@ -6,12 +6,13 @@ import java.util.List;
|
|||
import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
|
||||
import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveType;
|
||||
import org.gcube.dataanalysis.ecoengine.evaluation.DiscrepancyAnalysis;
|
||||
import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent;
|
||||
import org.gcube.dataanalysis.ecoengine.interfaces.Evaluator;
|
||||
import org.gcube.dataanalysis.ecoengine.processing.factories.EvaluatorsFactory;
|
||||
|
||||
public class EvaluatorT implements Runnable{
|
||||
|
||||
Evaluator dg;
|
||||
ComputationalAgent dg;
|
||||
AlgorithmConfiguration config;
|
||||
|
||||
|
||||
|
|
@ -26,15 +27,15 @@ public class EvaluatorT implements Runnable{
|
|||
}
|
||||
}
|
||||
|
||||
public EvaluatorT(Evaluator dg, AlgorithmConfiguration config) {
|
||||
public EvaluatorT(ComputationalAgent dg, AlgorithmConfiguration config) {
|
||||
this.dg = dg;
|
||||
this.config = config;
|
||||
}
|
||||
|
||||
public static void evaluate(AlgorithmConfiguration config) throws Exception {
|
||||
|
||||
List<Evaluator> evaluators = EvaluatorsFactory.getEvaluators(config);
|
||||
Evaluator evaluator = evaluators.get(0);
|
||||
List<ComputationalAgent> evaluators = EvaluatorsFactory.getEvaluators(config);
|
||||
ComputationalAgent evaluator = evaluators.get(0);
|
||||
|
||||
if (evaluator != null) {
|
||||
EvaluatorT tc = new EvaluatorT(evaluator,config);
|
||||
|
|
|
|||
|
|
@ -3,13 +3,14 @@ package org.gcube.dataanalysis.ecoengine.user;
|
|||
import java.util.List;
|
||||
|
||||
import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
|
||||
import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent;
|
||||
import org.gcube.dataanalysis.ecoengine.interfaces.Generator;
|
||||
import org.gcube.dataanalysis.ecoengine.processing.factories.GeneratorsFactory;
|
||||
|
||||
public class GeneratorT implements Runnable{
|
||||
Generator dg;
|
||||
ComputationalAgent dg;
|
||||
|
||||
public GeneratorT(Generator dg) {
|
||||
public GeneratorT(ComputationalAgent dg) {
|
||||
this.dg = dg;
|
||||
}
|
||||
|
||||
|
|
@ -25,8 +26,8 @@ public class GeneratorT implements Runnable{
|
|||
|
||||
public static void generate(AlgorithmConfiguration config) throws Exception {
|
||||
|
||||
List<Generator> generators = GeneratorsFactory.getGenerators(config);
|
||||
Generator generator = generators.get(0);
|
||||
List<ComputationalAgent> generators = GeneratorsFactory.getGenerators(config);
|
||||
ComputationalAgent generator = generators.get(0);
|
||||
|
||||
if (generator != null) {
|
||||
generator.init();
|
||||
|
|
@ -37,10 +38,10 @@ public class GeneratorT implements Runnable{
|
|||
|
||||
String resLoad = generator.getResourceLoad();
|
||||
String ress = generator.getResources();
|
||||
String species = generator.getLoad();
|
||||
// String species = generator.getLoad();
|
||||
System.out.println("LOAD: " + resLoad);
|
||||
System.out.println("RESOURCES: " + ress);
|
||||
System.out.println("SPECIES: " + species);
|
||||
// System.out.println("SPECIES: " + species);
|
||||
System.out.println("STATUS: " + generator.getStatus());
|
||||
Thread.sleep(1000);
|
||||
}
|
||||
|
|
|
|||
|
|
@ -3,15 +3,16 @@ package org.gcube.dataanalysis.ecoengine.user;
|
|||
import java.util.List;
|
||||
|
||||
import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
|
||||
import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent;
|
||||
import org.gcube.dataanalysis.ecoengine.interfaces.Modeler;
|
||||
import org.gcube.dataanalysis.ecoengine.processing.factories.ModelersFactory;
|
||||
|
||||
public class ModelerT implements Runnable {
|
||||
|
||||
Modeler dg;
|
||||
ComputationalAgent dg;
|
||||
AlgorithmConfiguration config;
|
||||
|
||||
public ModelerT(Modeler dg, AlgorithmConfiguration config) {
|
||||
public ModelerT(ComputationalAgent dg, AlgorithmConfiguration config) {
|
||||
this.dg = dg;
|
||||
this.config = config;
|
||||
}
|
||||
|
|
@ -19,7 +20,7 @@ public class ModelerT implements Runnable {
|
|||
public void run() {
|
||||
try {
|
||||
|
||||
dg.model(null);
|
||||
dg.compute();
|
||||
|
||||
} catch (Exception e) {
|
||||
}
|
||||
|
|
@ -27,8 +28,8 @@ public class ModelerT implements Runnable {
|
|||
|
||||
public static void train(AlgorithmConfiguration config) throws Exception {
|
||||
|
||||
List<Modeler> modelers = ModelersFactory.getModelers(config);
|
||||
Modeler modeler = modelers.get(0);
|
||||
List<ComputationalAgent> modelers = ModelersFactory.getModelers(config);
|
||||
ComputationalAgent modeler = modelers.get(0);
|
||||
|
||||
if (modeler != null) {
|
||||
ModelerT tc = new ModelerT(modeler, config);
|
||||
|
|
|
|||
Loading…
Reference in New Issue