Latest version with correction by G.Coro
git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/SeaDataNetConnector@120149 82a268e6-3cf1-43bd-a215-b396298e98cf
This commit is contained in:
parent
874dee3b71
commit
61f3df67e4
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@ -91,7 +91,7 @@ public class DivaHTTPClient {
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responseStream.close();
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httpUrlConnection.disconnect();
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AnalysisLogger.getLogger().debug("Response "+response);
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return response;
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} catch (IOException e) {
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@ -159,7 +159,7 @@ public class DivaHTTPClient {
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String response = stringBuilder.toString();
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//System.out.println("RESPONSE STRING: "+response);
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AnalysisLogger.getLogger().debug("Response from Diva: "+response);
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AnalysisLogger.getLogger().debug("Response from DIVA Analysis: \n"+response);
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Document doc = loadXMLFromString(response);
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Node idNode = doc.getElementsByTagName("result").item(0);
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@ -171,8 +171,6 @@ public class DivaHTTPClient {
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responseStream.close();
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httpUrlConnection.disconnect();
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AnalysisLogger.getLogger().debug("Response "+response);
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//return response;
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return new DivaAnalysisGetResponse(identifier, vmin, vmax, stat_obs_count_used, stat_posteriori_stn);
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@ -204,14 +202,17 @@ public class DivaHTTPClient {
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//Create Document object by XMLResponse
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Document doc = loadXMLFromString(result_xml);
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//Print XML Response
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AnalysisLogger.getLogger().debug(result_xml);
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AnalysisLogger.getLogger().debug("DIVA XML Response: \n"+result_xml);
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Node root = doc.getDocumentElement();
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if(root== null) throw new SAXException("Error in HTTP response no root element found!");
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Integer obs_count=Integer.parseInt(root.getChildNodes().item(1).getTextContent());
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Integer obs_count= null;
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try{
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obs_count=Integer.parseInt(root.getChildNodes().item(1).getTextContent());
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}catch(NullPointerException pe ){
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throw new Exception("Error in uploading file to DIVA!");
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}
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Double obs_x0=Double.parseDouble(root.getChildNodes().item(3).getTextContent());
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Double obs_x1=Double.parseDouble(root.getChildNodes().item(5).getTextContent());
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Double obs_y0=Double.parseDouble(root.getChildNodes().item(7).getTextContent());
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@ -225,12 +226,13 @@ public class DivaHTTPClient {
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}
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public static void downloadFileDiva(String fileurl, String destinationFile) throws Exception{
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public static void downloadFileDiva(String fileid, String destinationFile) throws Exception{
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try {
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String fileurl = DivaHTTPClient.WEB_HTTP + DivaHTTPClient.DOWN_FILE_NC + fileid;
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URL smpFile = new URL(fileurl);
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URLConnection uc = (URLConnection) smpFile.openConnection();
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InputStream is = uc.getInputStream();
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AnalysisLogger.getLogger().debug("Retrieving file from " + fileurl + " to :" + destinationFile);
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AnalysisLogger.getLogger().debug("Retrieving DIVA file from " + fileurl + " to :" + destinationFile);
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inputStreamToFile(is, destinationFile);
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is.close();
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} catch (Exception e) {
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@ -7,7 +7,6 @@ import java.util.ArrayList;
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import java.util.HashMap;
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import java.util.LinkedHashMap;
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import java.util.List;
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import java.util.Map;
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import java.util.UUID;
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import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
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@ -23,208 +22,195 @@ import org.gcube.dataanalysis.ecoengine.utils.DatabaseFactory;
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import org.gcube.dataanalysis.ecoengine.utils.DatabaseUtils;
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import org.hibernate.SessionFactory;
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import weka.classifiers.trees.m5.Impurity;
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public class SeaDataNetConnector extends StandardLocalExternalAlgorithm {
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//Statistical result by DIVA
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// Statistical result by DIVA
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LinkedHashMap<String, String> statResultMap = new LinkedHashMap<String, String>();
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//HashMap for
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// HashMap for
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LinkedHashMap<String, StatisticalType> outputDivaMap = new LinkedHashMap<String, StatisticalType>();
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SessionFactory dbconnection;
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@Override
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public void init() throws Exception {
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// TODO Auto-generated method stub
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}
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@Override
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public String getDescription() {
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// TODO Auto-generated method stub
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return "Connector for the SeaDataNet infrastructure";
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return "A connector for the SeaDataNet infrastructure. This algorithms invokes the Data-Interpolating Variational Analysis (DIVA) SeaDataNet service to interpolate spatial data. " +
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"The model uses GEBCO bathymetry data and requires an estimate of the maximum spatial span of the correlation between points and the signal-to-noise ratio, among the other parameters. " +
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"It can interpolate up to 100,000 points randomly taken from the input table. " +
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"As output, it produces a NetCDF file with a uniform grid of values. " +
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"This powerful interpolation model is described in Troupin et al. 2012, 'Generation of analysis and consistent error fields using the Data Interpolating Variational Analysis (Diva)', Ocean Modelling, 52-53, 90-101.";
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}
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File outputfile;
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@Override
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protected void process() throws Exception {
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String outpath = config.getPersistencePath();
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File neofile = new File(outpath,"seadn_diva_"+UUID.randomUUID()+".nc");
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/*
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BufferedWriter fileWriter = new BufferedWriter(new FileWriter(neofile));
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fileWriter.write("test test");
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fileWriter.close();
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*/
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//outputfile=neofile;
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AnalysisLogger.getLogger().debug("Input Table: "+config.getParam("InputTable"));
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AnalysisLogger.getLogger().debug("Input Long: "+config.getParam("Longitude"));
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AnalysisLogger.getLogger().debug("Input Lat: "+config.getParam("Latitude"));
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AnalysisLogger.getLogger().debug("Input Qt: "+config.getParam("Quantity"));
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AnalysisLogger.getLogger().debug("Longitude min X: "+config.getParam("LongitudeMinValue"));
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AnalysisLogger.getLogger().debug("Longitude max X: "+config.getParam("LongitudeMaxValue"));
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AnalysisLogger.getLogger().debug("Longitude resolution: "+config.getParam("LongitudeResolution"));
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AnalysisLogger.getLogger().debug("Latitude min Y: "+config.getParam("LatitudeMinValue"));
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AnalysisLogger.getLogger().debug("Latitude max Y: "+config.getParam("LatitudeMaxValue"));
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AnalysisLogger.getLogger().debug("Latitude resolution: "+config.getParam("LatitudeResolution"));
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AnalysisLogger.getLogger().debug("Correlation length: "+config.getParam("CorrelationLength"));
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AnalysisLogger.getLogger().debug("Signal noise value: "+config.getParam("SignalNoise"));
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AnalysisLogger.getLogger().debug("Depth Level: "+config.getParam("DepthLevel"));
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File neofile = null;
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File fileForDiva = null;
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try {
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String outpath = config.getPersistencePath();
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neofile = new File(outpath, "seadn_diva_" + UUID.randomUUID() + ".nc");
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AnalysisLogger.getLogger().debug("Input Parameters");
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AnalysisLogger.getLogger().debug("Input Table: " + config.getParam("InputTable"));
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AnalysisLogger.getLogger().debug("Input Long: " + config.getParam("Longitude"));
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AnalysisLogger.getLogger().debug("Input Lat: " + config.getParam("Latitude"));
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AnalysisLogger.getLogger().debug("Input Qt: " + config.getParam("Quantity"));
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try{
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double longitudeMinValue = Double.parseDouble(config.getParam("LongitudeMinValue"));
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}catch(Exception e){
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new Exception ("Bad value for LongitudeMinValue");
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}
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dbconnection = DatabaseUtils.initDBSession(config);
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AnalysisLogger.getLogger().debug("Longitude min X: " + config.getParam("LongitudeMinValue"));
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AnalysisLogger.getLogger().debug("Longitude max X: " + config.getParam("LongitudeMaxValue"));
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AnalysisLogger.getLogger().debug("Longitude resolution: " + config.getParam("LongitudeResolution"));
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String query = "select "+config.getParam("Longitude")+","+
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config.getParam("Latitude")+","+config.getParam("Quantity")
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+ " From " + getInputParameter("InputTable")+" ORDER BY RANDOM() limit 1000";
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AnalysisLogger.getLogger().debug("Query: "+query);
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List<Object> dataList = DatabaseFactory.executeSQLQuery(query , dbconnection);
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File fileForDiva= new File(outpath,"file_for_diva_"+UUID.randomUUID()+".txt");
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BufferedWriter fileWriterDiva = new BufferedWriter(new FileWriter(fileForDiva));
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AnalysisLogger.getLogger().debug("writing input file in: "+fileForDiva.getAbsolutePath() );
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for(Object o : dataList){
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Object[] oarray = (Object[]) o;
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fileWriterDiva.write(" "+oarray[0]+" "+oarray[1]+" "+oarray[2]+"\n");
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}
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fileWriterDiva.close();
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//integration DivaHttpClient
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//UPLOADFILE for DIVA
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DivaHTTPClient neo= new DivaHTTPClient();
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DivaFilePostResponse response=neo.uploadFile(fileForDiva);
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AnalysisLogger.getLogger().debug("Server Response: "+response.getSessionid());
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try{
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//ANALYSIS
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Double correlationVal = Double.parseDouble(config.getParam("CorrelationLength"));
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Double signalNoiseVal = Double.parseDouble(config.getParam("SignalNoise"));
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Double longMinVal = Double.parseDouble(config.getParam("LongitudeMinValue"));
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if(longMinVal<-180)
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throw new Exception("Longitudine minumum value is less than -180.");
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Double longMaxVal = Double.parseDouble(config.getParam("LongitudeMaxValue"));
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if(longMaxVal>180)
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throw new Exception("Longitudine maximum value is more than 180.");
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Double longResolutionVal = Double.parseDouble(config.getParam("LongitudeResolution"));
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Double latMinVal = Double.parseDouble(config.getParam("LatitudeMinValue"));
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if(latMinVal<-90)
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throw new Exception("Latitude minumum value is less than -90.");
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Double latMaxVal = Double.parseDouble(config.getParam("LatitudeMaxValue"));
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if(latMaxVal>90)
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throw new Exception("Latitude maximum value is more than 90.");
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AnalysisLogger.getLogger().debug("Latitude min Y: " + config.getParam("LatitudeMinValue"));
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AnalysisLogger.getLogger().debug("Latitude max Y: " + config.getParam("LatitudeMaxValue"));
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AnalysisLogger.getLogger().debug("Latitude resolution: " + config.getParam("LatitudeResolution"));
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Double latResolutionVal = Double.parseDouble(config.getParam("LatitudeResolution"));
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Double depthLevelVal = Double.parseDouble(config.getParam("DepthLevel"));
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if((depthLevelVal<-10)||(depthLevelVal>10))
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throw new Exception("Depth Level is out of range [-10,10]");
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AnalysisLogger.getLogger().debug("Correlation length: " + config.getParam("CorrelationLength"));
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AnalysisLogger.getLogger().debug("Signal noise value: " + config.getParam("SignalNoise"));
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AnalysisLogger.getLogger().debug("Depth Level: " + config.getParam("DepthLevel"));
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DivaAnalysisGetResponse respAnalysis = neo.getAnalysis(response.getSessionid(),
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correlationVal, signalNoiseVal, longMinVal, longMaxVal, longResolutionVal,
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latMinVal, latMaxVal, latResolutionVal, depthLevelVal);
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statResultMap.put("Minimum value of the analysis",""+respAnalysis.getVmin());
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statResultMap.put("Maximum value of the analysis", ""+respAnalysis.getVmax());
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statResultMap.put("Number of observations used", ""+respAnalysis.getStat_obs_count_used());
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statResultMap.put("Posterior probability of the model", ""+respAnalysis.getStat_posteriori_stn());
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//DOWNLOAD FILE
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neo.downloadFileDiva(neo.WEB_HTTP+neo.DOWN_FILE_NC+respAnalysis.getIdentifier(),
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neofile.getAbsolutePath());
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}
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catch(Exception e){
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throw e;
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}
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finally{
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neofile.delete();
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AnalysisLogger.getLogger().debug("file deleted");;
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Double correlationVal = null;
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Double signalNoiseVal = null;
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Double longMinVal = null;
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Double longMaxVal = null;
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Double longResolutionVal = null;
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Double latMinVal = null;
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Double latMaxVal = null;
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Double latResolutionVal = null;
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Double depthLevelVal = null;
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AnalysisLogger.getLogger().debug("Checking parameters");
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try {
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// ANALYSIS
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correlationVal = Double.parseDouble(config.getParam("CorrelationLength"));
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if (correlationVal <0 )
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throw new Exception("Correlation span cannot be negative.");
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signalNoiseVal = Double.parseDouble(config.getParam("SignalNoise"));
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if (signalNoiseVal <0 )
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throw new Exception("Signal-to-noise ratio cannot be negative.");
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longMinVal = Double.parseDouble(config.getParam("LongitudeMinValue"));
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if (longMinVal < -180)
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throw new Exception("Longitudine minumum value is less than -180.");
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longMaxVal = Double.parseDouble(config.getParam("LongitudeMaxValue"));
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if (longMaxVal > 180)
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throw new Exception("Longitudine maximum value is more than 180.");
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longResolutionVal = Double.parseDouble(config.getParam("LongitudeResolution"));
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latMinVal = Double.parseDouble(config.getParam("LatitudeMinValue"));
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if (latMinVal < -85)
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throw new Exception("Latitude minumum value is less than -85.");
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latMaxVal = Double.parseDouble(config.getParam("LatitudeMaxValue"));
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if (latMaxVal > 85)
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throw new Exception("Latitude maximum value is more than 85.");
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latResolutionVal = Double.parseDouble(config.getParam("LatitudeResolution"));
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depthLevelVal = Double.parseDouble(config.getParam("DepthLevel"));
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if (depthLevelVal < 0)
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throw new Exception("Depth Level cannot be negative");
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} catch (NumberFormatException e) {
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throw new Exception("Parameter values are incomplete");
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}
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AnalysisLogger.getLogger().debug("Parameters are OK");
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AnalysisLogger.getLogger().debug("Initializing DB connection");
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dbconnection = DatabaseUtils.initDBSession(config);
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String query = "select "
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+ config.getParam("Longitude") + "," + config.getParam("Latitude") + "," + config.getParam("Quantity") + " From " + getInputParameter("InputTable") +
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" ORDER BY RANDOM() limit 100000";
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AnalysisLogger.getLogger().debug("Query for extracting data from the DB: " + query);
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List<Object> dataList = DatabaseFactory.executeSQLQuery(query, dbconnection);
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int ndata = dataList.size();
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fileForDiva = new File(outpath, "file_for_diva_" + UUID.randomUUID() + ".txt");
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BufferedWriter fileWriterDiva = new BufferedWriter(new FileWriter(fileForDiva));
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AnalysisLogger.getLogger().debug("Writing input file in: " + fileForDiva.getAbsolutePath());
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for (Object o : dataList) {
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Object[] oarray = (Object[]) o;
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fileWriterDiva.write(" " + oarray[0] + " " + oarray[1] + " " + oarray[2] + "\n");
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}
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fileWriterDiva.close();
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AnalysisLogger.getLogger().debug("Sending data to DIVA: Uploading "+ndata+" records");
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// integration DivaHttpClient
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// UPLOADFILE for DIVA
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DivaFilePostResponse response = DivaHTTPClient.uploadFile(fileForDiva);
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AnalysisLogger.getLogger().debug("DIVA Server Response for the Upload:\n" + response.getSessionid());
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AnalysisLogger.getLogger().debug("Requiring analysis to DIVA...");
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long t0 = System.currentTimeMillis();
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DivaAnalysisGetResponse respAnalysis = DivaHTTPClient.getAnalysis(response.getSessionid(), correlationVal, signalNoiseVal, longMinVal, longMaxVal, longResolutionVal, latMinVal, latMaxVal, latResolutionVal, depthLevelVal);
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long t1 = System.currentTimeMillis();
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AnalysisLogger.getLogger().debug("Analysis finished in "+(t1-t0)+" ms");
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statResultMap.put("Minimum value of the analysis", "" + respAnalysis.getVmin());
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statResultMap.put("Maximum value of the analysis", "" + respAnalysis.getVmax());
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statResultMap.put("Number of observations used", "" + respAnalysis.getStat_obs_count_used());
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statResultMap.put("Posterior probability of the model", "" + respAnalysis.getStat_posteriori_stn());
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AnalysisLogger.getLogger().debug("Map of results to be returned: "+statResultMap);
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AnalysisLogger.getLogger().debug("Downloading result file in "+neofile.getAbsolutePath());
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// DOWNLOAD FILE
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DivaHTTPClient.downloadFileDiva(respAnalysis.getIdentifier(), neofile.getAbsolutePath());
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AnalysisLogger.getLogger().debug("Downloading finished");
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} catch (Exception e) {
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if (neofile.exists()){
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neofile.delete();
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AnalysisLogger.getLogger().debug("Output file "+neofile.getAbsolutePath()+" deleted!");
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}
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throw e;
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} finally {
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if (fileForDiva.exists()){
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fileForDiva.delete();
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AnalysisLogger.getLogger().debug("Input file "+fileForDiva.getAbsolutePath()+" deleted!");
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}
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}
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}
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@Override
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protected void setInputParameters() {
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List<TableTemplates> templates = new ArrayList<TableTemplates>();
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templates.add(TableTemplates.GENERIC);
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InputTable tinput = new InputTable(templates, "InputTable", "Input tabular resource");
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InputTable tinput = new InputTable(templates, "InputTable", "Input tabular resource. Up to 100,000 points will be randomly taken from this table.");
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inputs.add(tinput);
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ColumnType p1 = new ColumnType("InputTable", "Longitude", "The column containing longitude decimal values", "longitude", false);
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ColumnType p2 = new ColumnType("InputTable", "Latitude", "The column containing latitude decimal values", "latitude", false);
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ColumnType p3 = new ColumnType("InputTable", "Quantity", "The column containing quantity values", "quantity", false);
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inputs.add(p1);
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inputs.add(p2);
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inputs.add(p3);
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PrimitiveType p4 = new PrimitiveType(Double.class.getName(),
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null, PrimitiveTypes.NUMBER, "LongitudeMinValue",
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"Minimum value of Longitude Range","-180");
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PrimitiveType p5 = new PrimitiveType(Double.class.getName(),
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null, PrimitiveTypes.NUMBER, "LongitudeMaxValue",
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"Maximum value of Longitude Range","180");
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PrimitiveType p6 = new PrimitiveType(Double.class.getName(),
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null, PrimitiveTypes.NUMBER, "LongitudeResolution",
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"Longitude resolution (minimum 0.1 - maximum 10)", "1");
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PrimitiveType p7 = new PrimitiveType(Double.class.getName(),
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null, PrimitiveTypes.NUMBER, "LatitudeMinValue",
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"Minimum value of Latitude Range","-85");
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PrimitiveType p8 = new PrimitiveType(Double.class.getName(),
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null, PrimitiveTypes.NUMBER, "LatitudeMaxValue",
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"Maximum value of Latitude Range","85");
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PrimitiveType p9 = new PrimitiveType(Double.class.getName(),
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null, PrimitiveTypes.NUMBER, "LatitudeResolution",
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"Latitude resolution (minimum 0.1 - maximum 10)", "1");
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PrimitiveType p10 = new PrimitiveType(Double.class.getName(),
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null, PrimitiveTypes.NUMBER, "CorrelationLength",
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"Correlation length (arc degrees)", "10.35");
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PrimitiveType p11 = new PrimitiveType(Double.class.getName(),
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null, PrimitiveTypes.NUMBER, "SignalNoise",
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"Signal to noise ratio (non-dimensional)", "1.08");
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PrimitiveType p12 = new PrimitiveType(Double.class.getName(),
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null, PrimitiveTypes.NUMBER, "DepthLevel",
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"Depth level", "0");
|
||||
|
||||
PrimitiveType p4 = new PrimitiveType(Double.class.getName(), null, PrimitiveTypes.NUMBER, "LongitudeMinValue", "Minimum deg. value of the longitude range (min -180)", "-180");
|
||||
|
||||
PrimitiveType p5 = new PrimitiveType(Double.class.getName(), null, PrimitiveTypes.NUMBER, "LongitudeMaxValue", "Maximum deg. value of the longitude range (max 180)", "180");
|
||||
|
||||
PrimitiveType p6 = new PrimitiveType(Double.class.getName(), null, PrimitiveTypes.NUMBER, "LongitudeResolution", "Longitude resolution (minimum 0.1 - maximum 10)", "1");
|
||||
|
||||
PrimitiveType p7 = new PrimitiveType(Double.class.getName(), null, PrimitiveTypes.NUMBER, "LatitudeMinValue", "Minimum deg value of Latitude Range (min -85)", "-85");
|
||||
|
||||
PrimitiveType p8 = new PrimitiveType(Double.class.getName(), null, PrimitiveTypes.NUMBER, "LatitudeMaxValue", "Maximum value of Latitude Range (max 90)", "85");
|
||||
|
||||
PrimitiveType p9 = new PrimitiveType(Double.class.getName(), null, PrimitiveTypes.NUMBER, "LatitudeResolution", "Latitude resolution (minimum 0.1 - maximum 10)", "1");
|
||||
|
||||
PrimitiveType p10 = new PrimitiveType(Double.class.getName(), null, PrimitiveTypes.NUMBER, "CorrelationLength", "Correlation length (arc degrees)", "10.35");
|
||||
|
||||
PrimitiveType p11 = new PrimitiveType(Double.class.getName(), null, PrimitiveTypes.NUMBER, "SignalNoise", "Signal to noise ratio", "1.08");
|
||||
|
||||
PrimitiveType p12 = new PrimitiveType(Double.class.getName(), null, PrimitiveTypes.NUMBER, "DepthLevel", "Depth level (meters)", "0");
|
||||
|
||||
inputs.add(p4);
|
||||
inputs.add(p5);
|
||||
inputs.add(p6);
|
||||
|
|
@ -234,50 +220,34 @@ public class SeaDataNetConnector extends StandardLocalExternalAlgorithm {
|
|||
inputs.add(p10);
|
||||
inputs.add(p11);
|
||||
inputs.add(p12);
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
DatabaseType.addDefaultDBPars(inputs);
|
||||
|
||||
|
||||
|
||||
}
|
||||
|
||||
@Override
|
||||
public void shutdown() {
|
||||
|
||||
if (dbconnection!=null) dbconnection.close();
|
||||
|
||||
|
||||
if (dbconnection != null)
|
||||
dbconnection.close();
|
||||
|
||||
}
|
||||
|
||||
public StatisticalType getOutput(){
|
||||
|
||||
|
||||
|
||||
PrimitiveType file = new PrimitiveType(File.class.getName(),
|
||||
outputfile,
|
||||
PrimitiveTypes.FILE,
|
||||
"NetCDFOutputFile",
|
||||
"Output file in NetCDF format");
|
||||
|
||||
|
||||
for (String key:statResultMap.keySet()){
|
||||
String value = statResultMap.get(key);
|
||||
PrimitiveType val = new PrimitiveType(String.class.getName(),value,
|
||||
PrimitiveTypes.STRING, key, key);
|
||||
outputDivaMap.put(key, val);
|
||||
}
|
||||
|
||||
|
||||
public StatisticalType getOutput() {
|
||||
|
||||
PrimitiveType file = new PrimitiveType(File.class.getName(), outputfile, PrimitiveTypes.FILE, "NetCDFOutputFile", "Output file in NetCDF format");
|
||||
|
||||
for (String key : statResultMap.keySet()) {
|
||||
String value = statResultMap.get(key);
|
||||
PrimitiveType val = new PrimitiveType(String.class.getName(), value, PrimitiveTypes.STRING, key, key);
|
||||
outputDivaMap.put(key, val);
|
||||
}
|
||||
|
||||
outputDivaMap.put("Netcdf output file", file);
|
||||
|
||||
PrimitiveType hashma = new PrimitiveType(HashMap.class.getName(), outputDivaMap
|
||||
, PrimitiveTypes.MAP,
|
||||
"Diva results","Output of DIVA fit");
|
||||
|
||||
|
||||
|
||||
return hashma;
|
||||
}
|
||||
PrimitiveType hashma = new PrimitiveType(HashMap.class.getName(), outputDivaMap, PrimitiveTypes.MAP, "Diva results", "Output of DIVA fit");
|
||||
|
||||
return hashma;
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -48,12 +48,12 @@ public class TestSeaDataNetConnector {
|
|||
config.setParam("Latitude", "centerlat");
|
||||
config.setParam("Quantity", "landdist");
|
||||
|
||||
config.setParam("LongitudeMinValue", "-200");
|
||||
config.setParam("LongitudeMinValue", "-180");
|
||||
config.setParam("LongitudeMaxValue", "180");
|
||||
config.setParam("LongitudeResolution", "3");
|
||||
|
||||
config.setParam("LatitudeMinValue", "-90");
|
||||
config.setParam("LatitudeMaxValue", "90");
|
||||
config.setParam("LatitudeMinValue", "-80");
|
||||
config.setParam("LatitudeMaxValue", "80");
|
||||
config.setParam("LatitudeResolution", "3");
|
||||
|
||||
config.setParam("CorrelationLength", "10");
|
||||
|
|
|
|||
Loading…
Reference in New Issue