git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/EcologicalEngine@53921 82a268e6-3cf1-43bd-a215-b396298e98cf

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

@@ -1,6 +1,7 @@
 package org.gcube.dataanalysis.ecoengine.configuration;
 
 import java.io.FileInputStream;
+import java.io.Serializable;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Properties;
@@ -12,7 +13,9 @@ import org.hibernate.SessionFactory;
 
 import com.rapidminer.RapidMiner;
 
-public class AlgorithmConfiguration extends LexicalEngineConfiguration{
+public class AlgorithmConfiguration extends LexicalEngineConfiguration implements Serializable{
+
+	private static final long serialVersionUID = 1L;
 
 	public static Properties getProperties(String absoluteFilePath) {
 		Properties props = new Properties();

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

@@ -148,7 +148,12 @@ public class InterpolateTables {
 					DatabaseFactory.executeSQLUpdate(copyFileQuery, referencedbConnection);
 					status = Math.min(status + statusstep, 99);
 				}
-
+				
+				AnalysisLogger.getLogger().debug("DELETING ALL TEMPORARY FILES");
+				for (int i = 0; i < producedfiles.length; i++) {
+					producedfiles[i].delete();
+				}
+				
 				interpolatedTables[interpolatedTables.length - 1] = table2;
 
 				AnalysisLogger.getLogger().debug("ALL TABLES HAVE BEEN PRODUCED");

src/org/gcube/dataanalysis/ecoengine/spatialdistributions/AquamapsSuitable.java

@@ -41,7 +41,7 @@ public class AquamapsSuitable implements SpatialProbabilityDistributionTable{
 		if ((config.getParam("PreprocessedTable")!=null)&&(config.getParam("PreprocessedTable").length()>0))
 			hspenMinMaxLat = config.getParam("PreprocessedTable");
 		
-		AnalysisLogger.getLogger().trace("Aquamaps Algorithm Init(->getting min max latitudes from "+hspenMinMaxLat);
+		AnalysisLogger.getLogger().trace("Aquamaps Algorithm Init ->getting min max latitudes from "+hspenMinMaxLat);
 		
 		allSpeciesObservations = new HashMap<String, List<Object>>();
 		List<Object> SpeciesObservations = DatabaseFactory.executeSQLQuery(String.format(selectAllSpeciesObservationQuery, hspenMinMaxLat), dbHibConnection);
@@ -54,7 +54,7 @@ public class AquamapsSuitable implements SpatialProbabilityDistributionTable{
 			allSpeciesObservations.put((String)speciesid, maxminInfo);
 		}
 		
-		AnalysisLogger.getLogger().trace("Aquamaps Algorithm Init(->init finished");
+		AnalysisLogger.getLogger().trace("Aquamaps Algorithm Init ->init finished");
 	}
 
 	@Override

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

@@ -2,6 +2,8 @@ package org.gcube.dataanalysis.ecoengine.utils;
 
 import java.util.List;
 
+import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
+import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
 import org.hibernate.SessionFactory;
 
 public class DatabaseUtils {
@@ -175,4 +177,46 @@ public class DatabaseUtils {
 
 		return creationStatement;
 	}
+	
+	public static void createBigTable(boolean createTable, String table, String dbdriver, String dbuser, String dbpassword, String dburl, String creationStatement, SessionFactory dbHibConnection) throws Exception {
+		if (createTable) {
+			try {
+				DatabaseFactory.executeSQLUpdate("drop table " + table, dbHibConnection);
+			} catch (Exception e) {
+//				e.printStackTrace();
+			}
+			
+			DatabaseFactory.executeUpdateNoTransaction(creationStatement, dbdriver, dbuser, dbpassword, dburl, true);
+		}
+	}
+	
+	public static SessionFactory initDBSession(AlgorithmConfiguration config) {
+		SessionFactory dbHibConnection = null;
+		try {
+			if ((config != null) && (config.getConfigPath() != null)) {
+				String defaultDatabaseFile = config.getConfigPath() + AlgorithmConfiguration.defaultConnectionFile;
+				
+				config.setDatabaseDriver(config.getParam("DatabaseDriver"));
+				config.setDatabaseUserName(config.getParam("DatabaseUserName"));
+				config.setDatabasePassword(config.getParam("DatabasePassword"));
+				config.setDatabaseURL(config.getParam("DatabaseURL"));
+				
+				dbHibConnection = DatabaseFactory.initDBConnection(defaultDatabaseFile, config);
+			}
+		} catch (Exception e) {
+			e.printStackTrace();
+//			AnalysisLogger.getLogger().trace(e);
+		}
+		return dbHibConnection;
+	}
+	
+	public static void closeDBConnection(SessionFactory dbHibConnection){
+		try{
+			dbHibConnection.close();
+		}catch(Exception e){
+			
+		}	
+	}
+	
+	
 }

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

@@ -362,4 +362,16 @@ public class Operations {
 				double [] parabinterp = parabolicInterpolation(1,10,9);
 				System.out.println("");
 		}
+		
+		public static int chunkize(int numberOfElements,int partitionFactor){
+			int chunksize = numberOfElements/ partitionFactor;
+			if (chunksize == 0)
+				chunksize = 1;
+			int numOfChunks = numberOfElements / chunksize;
+			if ((numberOfElements % chunksize) != 0)
+				numOfChunks += 1;
+			
+			return chunksize;
+		}
+		
 }

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

@@ -1,10 +1,16 @@
 package org.gcube.dataanalysis.ecoengine.utils;
 
+import java.io.BufferedWriter;
+import java.io.FileInputStream;
+import java.io.FileWriter;
+
 import org.gcube.contentmanagement.graphtools.data.BigSamplesTable;
+import org.gcube.contentmanagement.lexicalmatcher.utils.FileTools;
 
 import com.rapidminer.example.ExampleSet;
 import com.rapidminer.example.table.DataRow;
 import com.rapidminer.example.table.ExampleTable;
+import com.thoughtworks.xstream.XStream;
 
 public class Transformations {
 
@@ -115,4 +121,31 @@ public class Transformations {
 		return out;
 	}
 	
+	
+	public static Object getObjectFromFile(String file) throws Exception{
+		
+		/*
+		FileInputStream fis = new FileInputStream(file);
+		ObjectInputStream ois = new ObjectInputStream(fis);
+		return ois.readObject();
+		*/
+		XStream xstream = new XStream();
+		return xstream.fromXML(new FileInputStream(file));
+//		return xstream.fromXML(FileTools.loadString(file, "UTF-8"));
+	}
+	
+	public static void dumpObjectToFile(String file, Object toWrite) throws Exception {
+		
+		XStream xstream = new XStream();
+		BufferedWriter bw = new BufferedWriter(new FileWriter(file));
+		bw.write(xstream.toXML(toWrite));
+		bw.close();
+		/*
+		FileOutputStream fos = new FileOutputStream(file);
+		ObjectOutputStream ois = new ObjectOutputStream(fos);
+		ois.writeObject(toWrite);
+		*/
+	}
+
+	
 }