git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/EcologicalEngineGeoSpatialExtension@120156 82a268e6-3cf1-43bd-a215-b396298e98cf
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package org.gcube.dataanalysis.geo.vti;
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import java.util.ArrayList;
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import java.util.Date;
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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.graphtools.utils.DateGuesser;
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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.datatypes.ColumnType;
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import org.gcube.dataanalysis.ecoengine.datatypes.DatabaseType;
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import org.gcube.dataanalysis.ecoengine.datatypes.InputTable;
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import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.TableTemplates;
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import org.gcube.dataanalysis.ecoengine.utils.DatabaseFactory;
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import org.gcube.dataanalysis.ecoengine.utils.DatabaseUtils;
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import org.gcube.dataanalysis.ecoengine.utils.IOHelper;
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import org.gcube.dataanalysis.geo.utils.CSquareCodesConverter;
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import org.gcube.dataanalysis.geo.vti.vesselsprocessing.MonthlyFishingEffortCalculator;
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public class EstimateMonthlyFishingEffort extends GridCWP2Coordinates{
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static String VesselsLatitudesColumn = "VesselsLatitudesColumn";
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static String VesselsLongitudesColumn = "VesselsLongitudesColumn";
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static String VesselsTimestampsColumn = "VesselsTimestampsColumn";
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static String VesselsHoursColumn = "VesselsActivityHoursColumn";
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static String VesselsActivityClassificationColumn = "VesselsActivityClassificationColumn";
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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, inputTableParameter, "The table to which the algorithm will add information");
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inputs.add(tinput);
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ColumnType Dimension1 = new ColumnType(inputTableParameter, VesselsLatitudesColumn, "The column containing vessels latitudes", "y", false);
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ColumnType Dimension2 = new ColumnType(inputTableParameter, VesselsLongitudesColumn, "The column containing vessels longitudes", "x", false);
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ColumnType Dimension3 = new ColumnType(inputTableParameter, VesselsTimestampsColumn, "The column containing the time stamp of the vessels transmitted information", "datetime", false);
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ColumnType Dimension4 = new ColumnType(inputTableParameter, VesselsHoursColumn, "The column containing the activity hours spent by the vessels in steaming, howling or fishing", "activity_hours", false);
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ColumnType Dimension5 = new ColumnType(inputTableParameter, VesselsActivityClassificationColumn, "The column containing the a simple point-by-point activity classification as Fishing, Steaming, Howling etc.", "activity_class_speed", false);
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inputs.add(Dimension1);
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inputs.add(Dimension2);
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inputs.add(Dimension3);
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inputs.add(Dimension4);
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inputs.add(Dimension5);
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IOHelper.addStringInput(inputs, outputTableParameter, "The name of the output table", "monthfish_");
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DatabaseType.addDefaultDBPars(inputs);
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}
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@Override
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public String getDescription() {
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return "An algorithm that estimates fishing exploitation at 0.5 degrees resolution from activity-classified vessels trajectories. " +
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"Produces a table with csquare codes, latitudes, longitudes and resolution and associated overall fishing hours in the time frame of the vessels activity. " +
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"Requires each activity point to be classified as Fishing or other. " +
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"This algorithm is based on the paper 'Deriving Fishing Monthly Effort and Caught Species' (Coro et al. 2013, in proc. of OCEANS - Bergen, 2013 MTS/IEEE). " +
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"Example of input table (NAFO anonymised data): http://goo.gl/3auJkM";
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}
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@Override
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protected void process() throws Exception {
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status = 0;
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AnalysisLogger.setLogger(config.getConfigPath() + AlgorithmConfiguration.defaultLoggerFile);
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long t0 = System.currentTimeMillis();
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String table = IOHelper.getInputParameter(config, inputTableParameter);
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outTable = ("mfe_" + UUID.randomUUID()).replace("-", "");
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outTableLabel = IOHelper.getInputParameter(config, outputTableParameter);
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AnalysisLogger.getLogger().debug("EstimateMonthlyFishingEffort: received parameters: " + config.getGeneralProperties());
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AnalysisLogger.getLogger().debug("EstimateMonthlyFishingEffort: input table: "+ table +" outputTable: " + outTable + " outLabel: " + outTableLabel);
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status = 10;
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try{
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addInformationColumsToTable(table);
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AnalysisLogger.getLogger().debug("EstimateMonthlyFishingEffort: finished in "+(System.currentTimeMillis()-t0)+" ms");
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} catch (Throwable e) {
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throw new Exception(e.getMessage());
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} finally {
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status = 100;
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}
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}
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public void addInformationColumsToTable(String table) throws Exception{
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AnalysisLogger.getLogger().debug("EstimateMonthlyFishingEffort: initializing connection");
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long t0 = System.currentTimeMillis();
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try {
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//error check
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if (config.getParam(VesselsLatitudesColumn)==null || config.getParam(VesselsLongitudesColumn)==null || config.getParam(VesselsTimestampsColumn)==null || config.getParam(VesselsHoursColumn)==null || config.getParam(VesselsActivityClassificationColumn)==null)
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throw new Exception ("Error with input parameters, please check that all the required inputs have been provided.");
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connection = DatabaseUtils.initDBSession(config);
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AnalysisLogger.getLogger().debug("EstimateMonthlyFishingEffort: database: " + config.getDatabaseURL());
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// create a new output table
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AnalysisLogger.getLogger().debug("EstimateMonthlyFishingEffort: dropping table " + outTable + " if exists");
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try {
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DatabaseFactory.executeSQLUpdate(DatabaseUtils.dropTableStatement(outTable), connection);
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} catch (Exception e) {
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AnalysisLogger.getLogger().debug("EstimateMonthlyFishingEffort: table " + outTable + " does not exist yet");
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}
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AnalysisLogger.getLogger().debug("EstimateMonthlyFishingEffort: creating the new table " + outTable);
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String csquareCol = "csquares";
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String longitudeCol = "center_longitude";
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String latitudeCol = "center_latitude";
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String resolutionCol = "resolution";
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String fishingeffortCol = "fishing_effort";
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DatabaseFactory.executeSQLUpdate("create table "+outTable+" ("+csquareCol+" character varying, "+longitudeCol+" real, "+latitudeCol+" real, "+resolutionCol+" real, "+fishingeffortCol+" real)", connection);
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String selectVinfo = "select "+
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"\""+config.getParam(VesselsLongitudesColumn)+"\""+","+
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"\""+config.getParam(VesselsLatitudesColumn)+"\""+","+
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"\""+config.getParam(VesselsTimestampsColumn)+"\""+","+
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"\""+config.getParam(VesselsHoursColumn)+"\""+","+
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"\""+config.getParam(VesselsActivityClassificationColumn)+"\""+
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" from "+table;
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AnalysisLogger.getLogger().debug("EstimateMonthlyFishingEffort: select info: "+selectVinfo);
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//get all the information and calculate min and max date
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List<Object> vesselsInfo = DatabaseFactory.executeSQLQuery(selectVinfo, connection);
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int ncoords = vesselsInfo.size();
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AnalysisLogger.getLogger().debug("EstimateMonthlyFishingEffort: Rebuilding effort from n. coords: "+ncoords);
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//pass information to csquare aggregator
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Date minDate = null;
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Date maxDate = null;
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//x,y,date,hours,activity
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List<Object> infoRows= new ArrayList<Object>();
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for (Object vesselInfo:vesselsInfo){
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Object [] vesselrow = (Object[]) vesselInfo;
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Double x = Double.parseDouble(""+vesselrow[0]);
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Double y = Double.parseDouble(""+vesselrow[1]);
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Date d = DateGuesser.convertDate(""+vesselrow[2]).getTime();
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if (minDate==null)
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{
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String pattern = DateGuesser.getPattern(""+vesselrow[2]);
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AnalysisLogger.getLogger().debug("EstimateMonthlyFishingEffort: Time detected : "+d);
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AnalysisLogger.getLogger().debug("EstimateMonthlyFishingEffort: Time pattern : "+pattern+" estimated from "+vesselrow[2]);
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}
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if (minDate==null || minDate.after(d))
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minDate=d;
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if (maxDate==null || maxDate.before(d))
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maxDate=d;
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Double hours = Double.parseDouble(""+vesselrow[3]);
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String activity = ""+vesselrow[4];
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Object[] infoRow = new Object[5];
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infoRow [0] = x;infoRow [1] = y; infoRow [2] = d;infoRow [3] = hours;infoRow [4] = activity;
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infoRows.add(infoRow);
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}
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AnalysisLogger.getLogger().debug("EstimateMonthlyFishingEffort: Rebuilt effort: minDate"+minDate+" maxDate "+maxDate);
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//build information with center long lat and resolution
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MonthlyFishingEffortCalculator mfec = new MonthlyFishingEffortCalculator();
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AnalysisLogger.getLogger().debug("EstimateMonthlyFishingEffort: Estimating monthly effort");
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Map<String,Double> fme = mfec.calculateMonthlyFishingEffort(infoRows, minDate, maxDate);
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List<String[]> values = new ArrayList<String[]>();
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//go through the map and produce output
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for (String csquare:fme.keySet()){
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String[] valuesRow = new String[5];
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valuesRow[0]=csquare;
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valuesRow[4]= ""+fme.get(csquare);
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CSquareCodesConverter converter = new CSquareCodesConverter();
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converter.parse(csquare);
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valuesRow[1] = ""+converter.getCurrentLong();
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valuesRow[2]=""+converter.getCurrentLat();
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valuesRow[3]=""+converter.getCurrentResolution();
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values.add(valuesRow);
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}
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int fmenum = fme.size();
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AnalysisLogger.getLogger().debug("EstimateMonthlyFishingEffort: number of csquares found "+fmenum);
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String colnames = csquareCol+","+longitudeCol+","+latitudeCol+","+resolutionCol+","+fishingeffortCol;
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AnalysisLogger.getLogger().debug("EstimateMonthlyFishingEffort: inserting chunks into the table "+outTable);
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// write the vector into the table
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DatabaseUtils.insertChunksIntoTable(outTable, colnames.toString(), values, fme.size(), connection, true);
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AnalysisLogger.getLogger().debug("EstimateMonthlyFishingEffort: inserting chunks done!");
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AnalysisLogger.getLogger().debug("EstimateMonthlyFishingEffort: finished");
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} catch (Throwable e) {
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e.printStackTrace();
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AnalysisLogger.getLogger().debug("EstimateMonthlyFishingEffort : ERROR!: " + e.getLocalizedMessage());
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try {
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AnalysisLogger.getLogger().debug("EstimateMonthlyFishingEffort: dropping " + outTable);
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DatabaseFactory.executeSQLUpdate(DatabaseUtils.dropTableStatement(outTable), connection);
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} catch (Exception e1) {
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AnalysisLogger.getLogger().debug("EstimateMonthlyFishingEffort: could not drop " + outTable);
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}
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throw new Exception(e.getMessage());
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} finally {
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shutdown();
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AnalysisLogger.getLogger().debug("EstimateMonthlyFishingEffort finished in " + (System.currentTimeMillis() - t0) + " ms");
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}
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}
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}
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