git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/EcologicalEngine@59093 82a268e6-3cf1-43bd-a215-b396298e98cf

deployDesktop.jardesc

@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<jardesc>
+    <jar path="C:/Users/coro/Desktop/ecological-engine-1.3.0-SNAPSHOT.jar"/>
+    <options buildIfNeeded="true" compress="true" descriptionLocation="/EcologicalEngine/deployDesktop.jardesc" exportErrors="true" exportWarnings="true" includeDirectoryEntries="false" overwrite="true" saveDescription="true" storeRefactorings="false" useSourceFolders="false"/>
+    <storedRefactorings deprecationInfo="true" structuralOnly="false"/>
+    <selectedProjects/>
+    <manifest generateManifest="true" manifestLocation="" manifestVersion="1.0" reuseManifest="false" saveManifest="false" usesManifest="true">
+        <sealing sealJar="false">
+            <packagesToSeal/>
+            <packagesToUnSeal/>
+        </sealing>
+    </manifest>
+    <selectedElements exportClassFiles="true" exportJavaFiles="false" exportOutputFolder="false">
+        <javaElement handleIdentifier="=EcologicalEngine/src\/main\/java"/>
+    </selectedElements>
+</jardesc>

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

@@ -36,21 +36,23 @@ public static void main(String[] args) throws Exception {
 		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;
-		*/
+		
 }
 
 	
@@ -148,11 +150,15 @@ public static void main(String[] args) throws Exception {
 		config.setParam("scientificNameColumn", "scientificname");
 		config.setParam("eventDateColumn", "eventdate");
 		config.setParam("lastModificationColumn", "modified");
-		config.setParam("OccurrencePointsTableName", "occurrencetestduplicates");
+		config.setParam("OccurrencePointsTableName", "occurrence_species_id5397d3c4_a7eb_4227_adb4_d9d7d36e8b21");
 		config.setParam("finalTableName", "occurrencesnoduplicates");
-		config.setParam("spatialTolerance", "20");
-		config.setParam("confidence", "60");
-
+		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;
 	}
 

src/main/java/org/gcube/dataanalysis/ecoengine/test/experiments/latimeria/ExperimentsForLatimeria.java

@@ -23,6 +23,7 @@ public class ExperimentsForLatimeria {
 	static String absenceRandomTable = "absence_data_latimeria_random";
 	static String absenceStaticTable = "absence_data_latimeria";
 	static String presenceTable = "presence_data_latimeria";
+	static String presenceTableNoEarth = "presence_data_latimeria_sea";
 	static String envelopeTable = "hspen_latimeria";
 	
 	static String aquamapsSuitableTable = "hspec_suitable_latimeria_chalumnae";
@@ -215,7 +216,7 @@ public class ExperimentsForLatimeria {
 		trans = null;
 	}
 	
-	public static void calcHRS(String hcaf,String absenceTable) throws Exception{
+	public static void calcHRS(String hcaf,String absenceTable,String presenceTable) throws Exception{
 		System.out.println("*****************************HRS: "+absenceTable+","+presenceTable+" vs "+hcaf+"************************************");
 		List<Evaluator>  evaluators = null;
 		evaluators = EvaluatorsFactory.getEvaluators(PresetConfigGenerator.configHRSAnalysis(filteredhcaf, absenceTable, presenceTable));
@@ -263,7 +264,7 @@ public class ExperimentsForLatimeria {
 
 		//filter the hcaf on Indonesia
 		
-		calcHRS(filteredhcaf,absenceStaticTable);
+//		calcHRS(filteredhcaf,absenceStaticTable);
 //		calcHRS(filteredhcaf,absenceRandomTable);
 	}
 	
@@ -285,6 +286,10 @@ public class ExperimentsForLatimeria {
 //		generateAquamapsNativeSuitableNeuralNetwokrs();
 		//Analysis
 		
+		calcdiscrepancy(aquamapsSuitableTable, nnsuitableTable);
+		calcdiscrepancy(aquamapsNativeTable, nnnativeTable);
+		
+		
 		/*
 		calcdiscrepancy(aquamapsSuitableTable, nnsuitableTable);
 		calcdiscrepancy(aquamapsNativeTable, nnnativeTable);
@@ -292,12 +297,14 @@ public class ExperimentsForLatimeria {
 		calcquality(aquamapsSuitableTable, presenceTable, absenceStaticTable);
 		calcquality(nnsuitableTable, presenceTable, absenceStaticTable);
 		
-		calcHRS(filteredhcaf,absenceStaticTable);
-		calcHRS(filteredhcaf,null);
-		*/
 		calcquality(aquamapsNativeTable, presenceTable, absenceStaticTable);
 		calcquality(nnnativeTable, presenceTable, absenceStaticTable);
 		
+		calcHRS(filteredhcaf,absenceStaticTable,presenceTableNoEarth);
+		calcHRS(filteredhcaf,null,presenceTableNoEarth);
+		*/
+		
+		
 		
 	}
 }

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

@@ -176,6 +176,7 @@ public class OccurrencePointsDuplicatesDeleter extends OccurrencePointsMerger{
 			persist();
 			// close DB connection
 		} catch (Exception e) {
+			AnalysisLogger.getLogger().trace("An error occurred "+e.getLocalizedMessage());
 			throw e;
 		} finally {
 			if (dbconnection != null)

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

@@ -146,33 +146,44 @@ public class OccurrencePointsMerger implements Transducerer {
 		for (Object name : columnsNames) {
 
 			String name$ = "" + name;
-			String value$ = "''";
+			String value$ = "NULL";
 			if (name$.equalsIgnoreCase(lonFld)) {
 				value$ = "'" + record.x + "'";
 			} else if (name$.equalsIgnoreCase(latFld)) {
 				value$ = "'" + record.y + "'";
 			} else if (name$.equalsIgnoreCase(recordedByFld)) {
 				if (record.recordedby != null)
-					value$ = "'" + record.recordedby + "'";
+					value$ = "'" + record.recordedby.replace("'", "") + "'";
 			} else if (name$.equalsIgnoreCase(scientificNameFld)) {
 				if (record.scientificName != null)
-					value$ = "'" + record.scientificName + "'";
+					value$ = "'" + record.scientificName.replace("'", "") + "'";
 			} else if (name$.equalsIgnoreCase(eventDatFld)) {
 				if (record.eventdate != null) {
-					value$ = "'" + convert2conventionalFormat(record.eventdate) + "'";
+					String dat = convert2conventionalFormat(record.eventdate);
+					if ((dat!=null)&&(dat.length()>0))
+						value$ = "'" + convert2conventionalFormat(record.eventdate) + "'";
+					else
+						value$ = "NULL";
 					// value$="'"+record.eventdate.getTimeInMillis()+"'";
 				}
 			} else if (name$.equalsIgnoreCase(modifDatFld)) {
 				if (record.modifdate != null) {
-					value$ = "'" + convert2conventionalFormat(record.modifdate) + "'";
+					String dat = convert2conventionalFormat(record.modifdate) ;
+					if ((dat!=null)&&(dat.length()>0))
+						value$ = "'" + convert2conventionalFormat(record.modifdate) + "'";
+					else 
+						value$ = "NULL";
 					// value$="'"+record.modifdate.getTimeInMillis()+"'";
 				}
 			} else {
 				if (record.otherValues != null) {
-					value$ = "'" + record.otherValues.get(k) + "'";
+					value$ = "'" + record.otherValues.get(k).replace("'", "") + "'";
 					k++;
 				}
 			}
+			if (value$.equals("'null'"))
+				value$ = "NULL";
+			
 			buffer.append(value$);
 			if (index < nNames - 1) {
 				buffer.append(",");
@@ -404,7 +415,7 @@ public class OccurrencePointsMerger implements Transducerer {
 			}
 
 			String updateQ = DatabaseUtils.insertFromBuffer(finalTableName, columns.toString(), buffer);
-//			 System.out.println("Update:\n"+updateQ);
+			 System.out.println("Update:\n"+updateQ);
 			AnalysisLogger.getLogger().debug("Update:\n"+updateQ);
 			DatabaseFactory.executeSQLUpdate(updateQ, dbconnection);
 			AnalysisLogger.getLogger().debug("Objects inserted");