git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/SeaDataNetConnector@152839 82a268e6-3cf1-43bd-a215-b396298e98cf

src/log4j.properties

@@ -0,0 +1,15 @@
+log4j.rootLogger=DEBUG, stdout, rollingFile
+ 
+# Redirect log messages to console
+log4j.appender.stdout=org.apache.log4j.ConsoleAppender
+log4j.appender.stdout.Target=System.out
+log4j.appender.stdout.layout=org.apache.log4j.PatternLayout
+log4j.appender.stdout.layout.ConversionPattern=%d{yyyy-MM-dd HH:mm:ss} %-5p %c{1}:%L - %m%n
+ 
+ 
+log4j.appender.rollingFile=org.apache.log4j.RollingFileAppender
+log4j.appender.rollingFile.File=test.log
+log4j.appender.rollingFile.MaxFileSize=20MB
+log4j.appender.rollingFile.MaxBackupIndex=2
+log4j.appender.rollingFile.layout = org.apache.log4j.PatternLayout
+log4j.appender.rollingFile.layout.ConversionPattern=%d{yyyy-MM-dd HH:mm:ss} %-5p %c{1}:%L - %m%n

src/org/gcube/dataanalysis/seadatanet/DivaHTTPClient.java

@@ -141,10 +141,10 @@ public class DivaHTTPClient {
 	 * level depth level
 	 */
 	public static DivaAnalysisGetResponse getAnalysis(String id, double len, double stn, double x0, double x1, double dx, double y0, double y1, double dy, double level) throws Exception {
-			return getAnalysis(id, len, stn, x0, x1, dx, y0, y1, dy, level, false);
+			return getAnalysis(id, len, stn, x0, x1, dx, y0, y1, dy, level, false,0);
 		}
 	
-	public static DivaAnalysisGetResponse getAnalysis(String id, double len, double stn, double x0, double x1, double dx, double y0, double y1, double dy, double level, Boolean useCurrents) throws Exception {
+	public static DivaAnalysisGetResponse getAnalysis(String id, double len, double stn, double x0, double x1, double dx, double y0, double y1, double dy, double level, Boolean useCurrents, int currentsWeight) throws Exception {
 		HttpURLConnection httpUrlConnection = null;
 
 		try {
@@ -160,7 +160,7 @@ public class DivaHTTPClient {
 			get_url += "dy=" + dy + "&";
 			get_url += "level=" + level + "";
 			if (useCurrents)
-				get_url += "&adv=1";
+				get_url += "&adv="+currentsWeight;
 			// System.out.println("GET URL="+get_url);
 			AnalysisLogger.getLogger().debug("Get URL to sent: \n" + get_url);
 			URL url = new URL(get_url);

src/org/gcube/dataanalysis/seadatanet/SeaDataNetConnector_AutoCorrelation.java

@@ -9,6 +9,7 @@ import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.UUID;
 
+import org.gcube.contentmanagement.graphtools.utils.HttpRequest;
 import org.gcube.contentmanagement.graphtools.utils.MathFunctions;
 import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
 import org.gcube.dataanalysis.ecoengine.datatypes.ColumnType;
@@ -39,6 +40,10 @@ import com.vividsolutions.jts.io.WKTReader;
 
 public class SeaDataNetConnector_AutoCorrelation extends StandardLocalExternalAlgorithm {
 
+	//TODO 
+	//download file from thredds
+	//currents resolution at 1
+	
 	// Statistical result by DIVA
 	LinkedHashMap<String, String> statResultMap = new LinkedHashMap<String, String>();
 
@@ -73,6 +78,7 @@ public class SeaDataNetConnector_AutoCorrelation extends StandardLocalExternalAl
 	public static String ResolutionP = "ProjectionResolution";
 	public static String DepthHeightP = "DepthOrHeightLevel";
 	public static String UseCurrentsP = "UseCurrentsInformation";
+	public static String CurrentsWeightP = "CurrentsVelocityWeight";
 	
 	Double longMinVal = null;
 	Double longMaxVal = null;
@@ -134,6 +140,15 @@ public class SeaDataNetConnector_AutoCorrelation extends StandardLocalExternalAl
 			AnalysisLogger.getLogger().debug("Resolution: " + config.getParam(ResolutionP));
 			AnalysisLogger.getLogger().debug("Depth-Heigh Level: " + config.getParam(DepthHeightP));
 			AnalysisLogger.getLogger().debug("Use currents: " + config.getParam(UseCurrentsP));
+			AnalysisLogger.getLogger().debug("Currents weight: " + config.getParam(CurrentsWeightP));
+			
+			int currentsWeight = Integer.parseInt(config.getParam(CurrentsWeightP));
+			if (currentsWeight<0)
+				currentsWeight=0;
+			else
+				currentsWeight = currentsWeight*2000/100;
+				
+			AnalysisLogger.getLogger().debug("Recalculated currents weight: " + currentsWeight);
 			
 			AnalysisLogger.getLogger().debug("Checking parameters consistency");
 			//->try - catch to manage case of NULL values
@@ -191,9 +206,18 @@ public class SeaDataNetConnector_AutoCorrelation extends StandardLocalExternalAl
 			status = 30;
 			
 			int velocityuploadingOK = 200;
-			if (useCurrents)
+			if (useCurrents && currentsWeight>0){
-				velocityuploadingOK = DivaHTTPClient.postVelocityFiles(response.getSessionid(), "u", "v", new File ("./example.nc"));
+				String currentsFile = "http://data.d4science.org/QW43dXd0RDRIYUJUOENpNXF1ekoxNnFLeUdSTjZQWGZHbWJQNStIS0N6Yz0"; //under VRE Folders->BiodiversityLab
-			
+				String tempFile = "currents"+UUID.randomUUID()+".nc";
+				AnalysisLogger.getLogger().debug("Downloading oceans currents file from "+currentsFile);
+				HttpRequest.downloadFile(currentsFile, tempFile);
+				File tempcurrentsfile = new File(tempFile);
+				AnalysisLogger.getLogger().debug("Sending ocean currents to DIVA - local File exists "+tempcurrentsfile.exists());
+				velocityuploadingOK = DivaHTTPClient.postVelocityFiles(response.getSessionid(), "u", "v", tempcurrentsfile);
+				AnalysisLogger.getLogger().debug("Done - Sending ocean currents to DIVA");
+				tempcurrentsfile.delete();
+			}
+				//velocityuploadingOK = DivaHTTPClient.postVelocityFiles(response.getSessionid(), "u", "v", new File ("./example.nc"));
 			if (velocityuploadingOK!=200)
 				throw new Exception("Could not upload currents files. Response "+velocityuploadingOK);
 			
@@ -205,7 +229,7 @@ public class SeaDataNetConnector_AutoCorrelation extends StandardLocalExternalAl
 			
 			AnalysisLogger.getLogger().debug("Requesting analysis to DIVA...");
 			long t0 = System.currentTimeMillis();
-			DivaAnalysisGetResponse respAnalysis = DivaHTTPClient.getAnalysis(response.getSessionid(), fitResponse.getLength_scale(), fitResponse.getSignal_to_noise(), longMinVal, longMaxVal, resolutionVal, latMinVal, latMaxVal, resolutionVal, depthLevelVal, useCurrents);
+			DivaAnalysisGetResponse respAnalysis = DivaHTTPClient.getAnalysis(response.getSessionid(), fitResponse.getLength_scale(), fitResponse.getSignal_to_noise(), longMinVal, longMaxVal, resolutionVal, latMinVal, latMaxVal, resolutionVal, depthLevelVal, useCurrents, currentsWeight);
 			AnalysisLogger.getLogger().debug("Response from DIVA analysis: "+respAnalysis);
 			long t1 = System.currentTimeMillis();
 			//->Record the time of the analysis
@@ -217,7 +241,7 @@ public class SeaDataNetConnector_AutoCorrelation extends StandardLocalExternalAl
 			statResultMap.put("Number of observations used", "" + respAnalysis.getStat_obs_count_used());
 			statResultMap.put("Signal-to-noise ratio", "" + fitResponse.getSignal_to_noise());
 			statResultMap.put("Geographical length of the correlation (deg)", "" + fitResponse.getLength_scale());
-			statResultMap.put("Fit quality", "" + fitResponse.getFit_quality());
+			statResultMap.put("Quality of the automatic signal-to-noise ratio estimate", "" + fitResponse.getFit_quality());
 			//statResultMap.put("A posteriori estimate of signal-to-noise ratio", "" + respAnalysis.getStat_posteriori_stn());
 			
 			AnalysisLogger.getLogger().debug("Map of results to be returned: "+statResultMap);
@@ -264,6 +288,7 @@ public class SeaDataNetConnector_AutoCorrelation extends StandardLocalExternalAl
 		PrimitiveType p5 = new PrimitiveType(Double.class.getName(), null, PrimitiveTypes.NUMBER, ResolutionP, "Resolution of the projection (minimum 0.1deg. - maximum 10deg.)", "1");
 		PrimitiveType p6 = new PrimitiveType(Double.class.getName(), null, PrimitiveTypes.NUMBER, DepthHeightP, "Depth (a negative value) or height (a positive value) of the observations (in meters).", "0");
 		PrimitiveType p7 = new PrimitiveType(Boolean.class.getName(), null, PrimitiveTypes.BOOLEAN, UseCurrentsP, "Involve information about average annual global currents velocity.", "true");
+		PrimitiveType p8 = new PrimitiveType(Double.class.getName(), null, PrimitiveTypes.NUMBER, CurrentsWeightP, "The weight of the currents velocity in the analysis in percentace (0-100)", "50");
 		
 		inputs.add(p1);
 		inputs.add(p2);
@@ -272,6 +297,7 @@ public class SeaDataNetConnector_AutoCorrelation extends StandardLocalExternalAl
 		inputs.add(p5);
 		inputs.add(p6);
 		inputs.add(p7);
+		inputs.add(p8);
 		
 		DatabaseType.addDefaultDBPars(inputs);
 

src/org/gcube/dataanalysis/seadatanet/test/TestSeaDataNetConnectorAutoCorr.java

@@ -84,6 +84,8 @@ public class TestSeaDataNetConnectorAutoCorr {
 	 
 	 config.setParam("UseCurrentsInformation", "true");
 	 
+	 config.setParam("CurrentsVelocityWeight", "1");
+	 
 	 
 	 config.setParam("DatabaseUserName","dmalgorithms_u");
 	 config.setParam("DatabasePassword","cdec755ed6633ba");