Managed multi-features coming from WFS
git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/EcologicalEngineGeoSpatialExtension@95491 82a268e6-3cf1-43bd-a215-b396298e98cf
This commit is contained in:
parent
6acbc54288
commit
1b595a2db9
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@ -4,6 +4,7 @@ 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 org.gcube.common.scope.api.ScopeProvider;
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import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
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@ -24,7 +25,9 @@ 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.ecoengine.utils.ResourceFactory;
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import org.gcube.dataanalysis.ecoengine.utils.Tuple;
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import org.gcube.dataanalysis.geo.connectors.wfs.WFS;
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import org.gcube.dataanalysis.geo.interfaces.GISDataConnector;
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import org.gcube.dataanalysis.geo.matrixmodel.RasterTable;
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import org.gcube.dataanalysis.geo.matrixmodel.XYExtractor;
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import org.gcube.dataanalysis.geo.utils.VectorOperations;
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import org.hibernate.SessionFactory;
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@ -192,7 +195,7 @@ public class OccurrenceEnrichment implements Transducerer {
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int elementsFromOccurrences = 4;
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int elementstoreport = elementsFromOccurrences + layers.length;
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// take all the observations
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for (Object row : rows) {
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Object[] elements = (Object[]) row;
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double x = elements[0] == null ? 0 : Double.parseDouble("" + elements[0]);
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@ -216,50 +219,89 @@ public class OccurrenceEnrichment implements Transducerer {
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// take the layers matrices
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int layeridx = 0;
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float statusSteps = 50f / (float) layers.length;
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// for each layer, enrich observations with layers info
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for (String layerID : layers) {
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if (layerID.length() == 0)
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continue;
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AnalysisLogger.getLogger().debug("OccurrenceEnrichment->Assigning layer " + layerID + " Layer enumerator: " + layeridx);
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// for each layer
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// extract xy information
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XYExtractor extractor = new XYExtractor(config);
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extractor.correctZ(0, layerID,resolution);
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extractor.correctZ(0, layerID, resolution);
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double zmin = extractor.zmin;
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double zmax = extractor.zmax;
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double bestZ = Math.min(Math.abs(zmin), Math.abs(zmax));
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outputParameters.put("Matching Z value in layer " + (layeridx + 1), "" + bestZ);
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outputParameters.put("Min Z value in layer "+ (layeridx + 1), "" + zmin);
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outputParameters.put("Max Z value in layer "+ (layeridx + 1), "" + zmax);
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outputParameters.put("Min Z value in layer " + (layeridx + 1), "" + zmin);
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outputParameters.put("Max Z value in layer " + (layeridx + 1), "" + zmax);
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AnalysisLogger.getLogger().debug("OccurrenceEnrichment->Best Z for this reference layer: " + bestZ);
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// perform the comparison closest to the surface
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// perform the closest extraction to the surface
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extractor.extractXYGrid(layerID, 0, BBxLL, BBxUR, BByLL, BByUR, bestZ, resolution, resolution);
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// retrieve the grid time values and tuples
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List<Double> gridValues = extractor.currentTimeValues;
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List<Tuple<Double>> grid3d = extractor.currentTuples;
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// use the layername as column name otherwise use a generic feature indication
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String layername = (layersnames.length > (layeridx) && layersnames[layeridx].trim().length() > 0) ? layersnames[layeridx].trim() : "feature" + (layeridx + 1);
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AnalysisLogger.getLogger().debug("OccurrenceEnrichment->Retrieved Layer Name: " + layername);
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columns += ",\"" + layername + "\"";
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columnsTypes += ",\"" + layername + "\" real";
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AnalysisLogger.getLogger().debug("OccurrenceEnrichment->Assigning grid points to the occurrences");
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// take the association
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// make the association
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List<Double> enriched = VectorOperations.assignGridValuesToPoints2D(grid3d, gridValues, coordinates4d, resolution);
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int k = 0;
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AnalysisLogger.getLogger().debug("OccurrenceEnrichment->Assigning values to the column " + (elementsFromOccurrences + layeridx));
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HashMap<Double, Map<String, String>> polygonsFeatures = null;
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if (extractor.currentconnector instanceof WFS)
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polygonsFeatures = ((WFS) extractor.currentconnector).getPolygonsFeatures();
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boolean enrichWithEnvironmentalFeatures = true;
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Map<String, String> features=null;
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String emptyRow = "";
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if (polygonsFeatures != null && polygonsFeatures.size() > 0){
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AnalysisLogger.getLogger().debug("OccurrenceEnrichment->Managing Web Features");
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enrichWithEnvironmentalFeatures = false;
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int ncolumns = polygonsFeatures.keySet().size();
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emptyRow = RasterTable.generateEmptyValues(ncolumns);
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features = polygonsFeatures.values().iterator().next();
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columnsTypes += ","+RasterTable.propertiesMapToColumnString(features, true);
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columns += ","+RasterTable.propertiesMapToColumnString(features, false);
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}
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else{
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columns += ",\"" + layername + "\"";
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columnsTypes += ",\"" + layername + "\" real";
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}
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for (Double value : enriched) {
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String[] singlerow = enrichment.get(k);
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if (value == null || Double.isNaN(value) || Double.isInfinite(value))
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singlerow[elementsFromOccurrences + layeridx] = "-9999";
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else
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singlerow[elementsFromOccurrences + layeridx] = "" + value;
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if (enrichWithEnvironmentalFeatures) {
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if (value == null || Double.isNaN(value) || Double.isInfinite(value))
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singlerow[elementsFromOccurrences + layeridx] = "-9999";
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else {
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singlerow[elementsFromOccurrences + layeridx] = "" + value;
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}
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}
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else{
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if (value == null || Double.isNaN(value) || Double.isInfinite(value))
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singlerow[elementsFromOccurrences + layeridx] = emptyRow;
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else {
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singlerow[elementsFromOccurrences + layeridx] = RasterTable.propertiesMapToDatabaseString(features);
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}
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}
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k++;
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}
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AnalysisLogger.getLogger().debug("OccurrenceEnrichment->Added values to the row");
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layeridx++;
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status = status + statusSteps;
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}
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}//end for on the layer, switch to the next layer
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// write the complete association into the db
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AnalysisLogger.getLogger().debug("OccurrenceEnrichment->Dropping table " + outputTableDBName);
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@ -272,7 +314,7 @@ public class OccurrenceEnrichment implements Transducerer {
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AnalysisLogger.getLogger().debug("OccurrenceEnrichment->Creating table " + outputTableDBName + " query:" + createquery);
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DatabaseFactory.executeSQLUpdate(createquery, dbconnection);
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AnalysisLogger.getLogger().debug("OccurrenceEnrichment->Inserting chunks");
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DatabaseUtils.insertChunksIntoTable(outputTableDBName, columns, enrichment, 5000, dbconnection);
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DatabaseUtils.insertChunksIntoTable(outputTableDBName, columns, enrichment, 5000, dbconnection,false);
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AnalysisLogger.getLogger().debug("OccurrenceEnrichment->Whole process complete in " + ((double) (System.currentTimeMillis() - t0) / 1000f) + " s");
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} catch (Exception e) {
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e.printStackTrace();
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@ -5,6 +5,7 @@ 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 org.gcube.common.scope.api.ScopeProvider;
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import org.gcube.contentmanagement.graphtools.utils.MathFunctions;
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@ -21,6 +22,7 @@ import org.gcube.dataanalysis.ecoengine.signals.SignalConverter;
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import org.gcube.dataanalysis.ecoengine.signals.SignalProcessing;
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import org.gcube.dataanalysis.ecoengine.utils.IOHelper;
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import org.gcube.dataanalysis.ecoengine.utils.Tuple;
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import org.gcube.dataanalysis.geo.connectors.wfs.WFS;
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import org.gcube.dataanalysis.geo.interfaces.GISDataConnector;
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import org.gcube.dataanalysis.geo.matrixmodel.RasterTable;
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import org.gcube.dataanalysis.geo.matrixmodel.TimeSeriesExtractor;
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@ -180,7 +182,11 @@ public class TimeExtraction extends XYExtraction{
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AnalysisLogger.getLogger().debug("Extractor: ****Rasterizing grid into table****");
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double matrix[][] = new double[1][];
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matrix[0] = signal;
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RasterTable raster = new RasterTable(xValue, xValue, yValue, yValue, zValue, resolutionValue, resolutionValue, matrix, config);
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HashMap<Double,Map<String, String>> polygonsFeatures = null;
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if (intersector.currentconnector instanceof WFS)
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polygonsFeatures = ((WFS) intersector.currentconnector).getPolygonsFeatures();
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RasterTable raster = new RasterTable(xValue, xValue, yValue, yValue, zValue, resolutionValue, resolutionValue, matrix, polygonsFeatures, config);
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int signalRate = 1;
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if (samplingFrequencyValue>0)
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@ -4,6 +4,7 @@ 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 org.gcube.common.scope.api.ScopeProvider;
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import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
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@ -18,6 +19,7 @@ import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.TableTemplates;
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import org.gcube.dataanalysis.ecoengine.interfaces.Transducerer;
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import org.gcube.dataanalysis.ecoengine.utils.IOHelper;
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import org.gcube.dataanalysis.ecoengine.utils.ResourceFactory;
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import org.gcube.dataanalysis.geo.connectors.wfs.WFS;
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import org.gcube.dataanalysis.geo.interfaces.GISDataConnector;
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import org.gcube.dataanalysis.geo.matrixmodel.RasterTable;
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import org.gcube.dataanalysis.geo.matrixmodel.XYExtractor;
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@ -157,11 +159,15 @@ public class XYExtraction implements Transducerer {
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outputParameters.put("Max Z value in the Layer", ""+extractor.zmax);
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double[][] matrix = extractor.extractXYGrid(layerNameValue, time, BBxLL, BBxUR, BByLL, BByUR, zValue, xResValue, yResValue);
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System.out.println("ELAPSED TIME: " + (System.currentTimeMillis() - t0));
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HashMap<Double,Map<String, String>> polygonsFeatures = null;
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if (extractor.currentconnector instanceof WFS)
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polygonsFeatures = ((WFS) extractor.currentconnector).getPolygonsFeatures();
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AnalysisLogger.getLogger().debug("ELAPSED TIME: " + (System.currentTimeMillis() - t0));
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AnalysisLogger.getLogger().debug("Extractor: Matrix Extracted");
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AnalysisLogger.getLogger().debug("Extractor: ****Rasterizing grid into table****");
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status = 30;
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RasterTable raster = new RasterTable(BBxLL, BBxUR, BByLL, BByUR, zValue, time, xResValue, yResValue, matrix, config);
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RasterTable raster = new RasterTable(BBxLL, BBxUR, BByLL, BByUR, zValue, time, xResValue, yResValue, matrix, polygonsFeatures,config);
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raster.setTablename(tableNameValue);
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raster.deleteTable();
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raster.dumpGeoTable();
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@ -5,6 +5,7 @@ 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 org.gcube.common.scope.api.ScopeProvider;
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import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
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@ -18,6 +19,7 @@ import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.TableTemplates;
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import org.gcube.dataanalysis.ecoengine.signals.SignalProcessing;
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import org.gcube.dataanalysis.ecoengine.utils.IOHelper;
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import org.gcube.dataanalysis.ecoengine.utils.Tuple;
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import org.gcube.dataanalysis.geo.connectors.wfs.WFS;
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import org.gcube.dataanalysis.geo.matrixmodel.RasterTable;
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import org.gcube.dataanalysis.geo.matrixmodel.ZExtractor;
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@ -119,7 +121,12 @@ public class ZExtraction extends XYExtraction{
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double matrix[][] = new double[1][];
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matrix[0] = signal;
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RasterTable raster = new RasterTable(xValue, xValue, yValue, yValue, zValue, time,resolutionValue, resolutionValue, matrix, config);
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HashMap<Double,Map<String, String>> polygonsFeatures = null;
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if (extractor.currentconnector instanceof WFS)
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polygonsFeatures = ((WFS) extractor.currentconnector).getPolygonsFeatures();
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RasterTable raster = new RasterTable(xValue, xValue, yValue, yValue, zValue, time,resolutionValue, resolutionValue, matrix, polygonsFeatures,config);
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int signalRate = 1;
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@ -2,11 +2,14 @@ package org.gcube.dataanalysis.geo.connectors.wfs;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.HashMap;
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import java.util.List;
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import java.util.Map;
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import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
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import org.gcube.dataanalysis.ecoengine.utils.Tuple;
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import org.gcube.dataanalysis.geo.interfaces.GISDataConnector;
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import org.gcube.dataanalysis.geo.utils.CSquareCodesConverter;
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import com.vividsolutions.jts.geom.Coordinate;
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import com.vividsolutions.jts.geom.GeometryFactory;
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@ -16,6 +19,9 @@ import com.vividsolutions.jts.geom.impl.CoordinateArraySequence;
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public class WFS implements GISDataConnector {
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List<FeaturedPolygon> featuresInTime;
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HashMap<Double,Map<String, String>> polygonsFeatures;
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@Override
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public List<Double> getFeaturesInTimeInstantAndArea(String layerURL, String layerName, int time, List<Tuple<Double>> coordinates3d, double BBxL, double BBxR, double BByL, double BByR) throws Exception {
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@ -24,9 +30,10 @@ public class WFS implements GISDataConnector {
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if (layerURL == null)
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return null;
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List<FeaturedPolygon> featuresInTime = new ArrayList<FeaturedPolygon>();
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featuresInTime = new ArrayList<FeaturedPolygon>();
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AnalysisLogger.getLogger().debug("taking WFS features");
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featuresInTime = WFSDataExplorer.getFeatures(layerURL, layerName, BBxL, BByL, BBxR, BByR);
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polygonsFeatures=new HashMap<Double, Map<String,String>>();
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int tsize = coordinates3d.size();
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AnalysisLogger.getLogger().debug("Intersecting " + tsize + " vs " + featuresInTime.size() + " elements");
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int ttc = 0;
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@ -40,8 +47,34 @@ public class WFS implements GISDataConnector {
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boolean found = false;
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for (FeaturedPolygon poly : featuresInTime) {
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if (poly != null && poly.p != null && poly.p.covers(po)) {
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/*
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AnalysisLogger.getLogger().debug(poly.p.getCentroid()+
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"["+CSquareCodesConverter.convertAtResolution(poly.p.getCentroid().getY(), poly.p.getCentroid().getX(), 0.5)+"] "+
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"("+(poly.p.getCentroid().getX()-0.25)+" -- "+(poly.p.getCentroid().getX()+0.25) +" ; "+
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(poly.p.getCentroid().getY()-0.25)+" -- "+(poly.p.getCentroid().getY()+0.25) +") "+
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" ["+poly.features+"]"+
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" covers "+po+ "["+CSquareCodesConverter.convertAtResolution(po.getY(), po.getX(), 0.5)+"]");
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AnalysisLogger.getLogger().debug("{"+poly.p.contains(po)+
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";"+po.isWithinDistance(poly.p.getCentroid(), 0.24)+
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";"+po.isWithinDistance(poly.p.getCentroid(), 0.25)+
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";"+poly.p.getCentroid().distance(po)+
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";"+poly.p.distance(po)+
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";"+poly.p.convexHull().contains(po)+
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";"+poly.p.convexHull().touches(po)+
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";"+poly.p.touches(po)+
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";"+poly.p.crosses(po)+
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";"+po.crosses(poly.p)+
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";"+po.coveredBy(poly.p)+
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";"+po.intersection(poly.p)+
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";"+poly.p.contains(po)+
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";"+poly.p.covers(po)+
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"}");
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*/
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featuresarray[k] = poly.value;
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polygonsFeatures.put(poly.value, poly.features);
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found = true;
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break;
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}
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@ -64,6 +97,7 @@ public class WFS implements GISDataConnector {
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return features;
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}
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@Override
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public double getMinZ(String layerURL, String layerName) {
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return 0;
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@ -74,4 +108,7 @@ public class WFS implements GISDataConnector {
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return 0;
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}
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public HashMap<Double, Map<String, String>> getPolygonsFeatures() {
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return polygonsFeatures;
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}
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}
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@ -87,18 +87,21 @@ public class WFSDataExplorer {
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String jsonString = callWFS(geoserver, layer, xL, yL, xR, yR);
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// System.out.println("JSON:"+jsonString);
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LinkedHashMap<String, Object> map = JsonMapper.parse(jsonString);
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// System.out.println(map);
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List<FeaturedPolygon> fpolygons = new ArrayList<FeaturedPolygon>();
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FeaturedPolygon poly = null;
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int polygonId = 0;
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for (String key : map.keySet()) {
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if (key.contains("features")) {
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HashMap<String, Object> propertiesMap = (HashMap<String, Object>) map.get(key);
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// cycle on all the properties
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for (String properties : propertiesMap.keySet()) {
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if (properties.contains("properties")) {
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polygonId++;
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if (poly == null)
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poly = new FeaturedPolygon();
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LinkedHashMap<String, String> props = (LinkedHashMap<String, String>) propertiesMap.get(properties);
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// fill the properties of the fpolygon
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for (String keyprop : props.keySet()) {
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@ -107,8 +110,12 @@ public class WFSDataExplorer {
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String value = props.get(keyprop);
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try {
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String lowcaseprop = keyprop.toLowerCase();
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if ((poly.value == null) && !lowcaseprop.startsWith("id") && !lowcaseprop.endsWith("id"))
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poly.setValue(Double.parseDouble(value));
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// System.out.println(poly.p.getCentroid()+" -> "+value);
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//add the first double value to the polygon
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if ((poly.value == null) && !lowcaseprop.startsWith("id") && !lowcaseprop.endsWith("id")){
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poly.setValue((double)polygonId);
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poly.addFeature(keyprop, value);
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}
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else
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poly.addFeature(keyprop, value);
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} catch (Exception e2) {
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@ -119,8 +119,9 @@ public class MatrixExtractor {
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/**
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* Extract raw values in a time instant according to a set of grid points and a bounding box
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*/
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public GISDataConnector connector;
|
||||
public List<Double> getRawValuesInTimeInstantAndBoundingBox(String layerTitle, int time, List<Tuple<Double>> coordinates3d, double xL, double xR, double yL, double yR, double resolution, boolean saveLayer) throws Exception {
|
||||
GISDataConnector connector = getConnector(layerTitle, resolution);
|
||||
connector = getConnector(layerTitle, resolution);
|
||||
// execute connector
|
||||
if (connector != null)
|
||||
return connector.getFeaturesInTimeInstantAndArea(layerURL, layerName, time, coordinates3d, xL, xR, yL, yR);
|
||||
|
|
@ -128,7 +129,10 @@ public class MatrixExtractor {
|
|||
throw new Exception("ERROR: Connector not found for layer " + layerTitle + " - Cannot Rasterize!");
|
||||
|
||||
}
|
||||
|
||||
public GISDataConnector getCurrentConnector(){
|
||||
return connector;
|
||||
}
|
||||
|
||||
public double zmin;
|
||||
public double zmax;
|
||||
|
||||
|
|
|
|||
|
|
@ -1,7 +1,9 @@
|
|||
package org.gcube.dataanalysis.geo.matrixmodel;
|
||||
|
||||
import java.util.ArrayList;
|
||||
import java.util.HashMap;
|
||||
import java.util.List;
|
||||
import java.util.Map;
|
||||
import java.util.UUID;
|
||||
|
||||
import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
|
||||
|
|
@ -22,6 +24,7 @@ import org.hibernate.SessionFactory;
|
|||
public class RasterTable {
|
||||
|
||||
private double valuesMatrix[][];
|
||||
private HashMap<Double, Map<String, String>> valuesPropertiesMap;
|
||||
double x1;
|
||||
double x2;
|
||||
double y1;
|
||||
|
|
@ -31,15 +34,20 @@ public class RasterTable {
|
|||
double xResolution;
|
||||
double yResolution;
|
||||
List<Tuple<Double>> coordinates;
|
||||
|
||||
|
||||
private AlgorithmConfiguration configuration;
|
||||
private String tablename = "rstr" + ("" + UUID.randomUUID()).replace("-", "");
|
||||
static String createTableStatement = "CREATE TABLE %1$s (id serial, csquarecode character varying, x real, y real, z real, t real, fvalue real)";
|
||||
static String columnsnames = "csquarecode, x , y , z , t, fvalue";
|
||||
// static String createTableStatement = "CREATE TABLE %1$s (id serial, csquarecode character varying, x real, y real, z real, t real, fvalue real)";
|
||||
static String createTableStatementStandard = "CREATE TABLE %1$s (id serial, csquarecode character varying, x real, y real, z real, t real, fvalue character varying)";
|
||||
static String createTableStatementWithFields = "CREATE TABLE %1$s (id serial, approx_x real, approx_y real, z real, t real, %2$s)";
|
||||
|
||||
static String columnsnamesStandard = "csquarecode, x , y , z , t, fvalue";
|
||||
static String columnsnamesWithFields = "approx_x , approx_y , z , t , %1$s";
|
||||
|
||||
public static String csquareColumn = "csquarecode";
|
||||
public static String valuesColumn = "fvalue";
|
||||
public static String idColumn = "id";
|
||||
|
||||
|
||||
public String getTablename() {
|
||||
return tablename;
|
||||
}
|
||||
|
|
@ -47,25 +55,35 @@ public class RasterTable {
|
|||
public void setTablename(String tablename) {
|
||||
this.tablename = tablename;
|
||||
}
|
||||
|
||||
public List<Tuple<Double>> getCoordinates(){
|
||||
|
||||
public List<Tuple<Double>> getCoordinates() {
|
||||
return coordinates;
|
||||
}
|
||||
|
||||
|
||||
public void setCoordinates(List<Tuple<Double>> coordinates) {
|
||||
this.coordinates=coordinates;
|
||||
}
|
||||
|
||||
public RasterTable(double x1, double x2, double y1, double y2, double z, double xResolution, double yResolution, double[][] values, AlgorithmConfiguration configuration) {
|
||||
init(x1, x2, y1, y2, z, 0, xResolution, yResolution, values, configuration);
|
||||
}
|
||||
|
||||
public RasterTable(double x1, double x2, double y1, double y2, double z, double time, double xResolution, double yResolution, double[][] values, AlgorithmConfiguration configuration) {
|
||||
init(x1, x2, y1, y2, z, time, xResolution, yResolution, values, configuration);
|
||||
this.coordinates = coordinates;
|
||||
}
|
||||
|
||||
public void init(double x1, double x2, double y1, double y2, double z, double time, double xResolution, double yResolution, double[][] values, AlgorithmConfiguration configuration){
|
||||
public RasterTable(double x1, double x2, double y1, double y2, double z, double xResolution, double yResolution, double[][] values, AlgorithmConfiguration configuration) {
|
||||
init(x1, x2, y1, y2, z, 0, xResolution, yResolution, values, null, configuration);
|
||||
}
|
||||
|
||||
public RasterTable(double x1, double x2, double y1, double y2, double z, double time, double xResolution, double yResolution, double[][] values, AlgorithmConfiguration configuration) {
|
||||
init(x1, x2, y1, y2, z, time, xResolution, yResolution, values, null, configuration);
|
||||
}
|
||||
|
||||
public RasterTable(double x1, double x2, double y1, double y2, double z, double xResolution, double yResolution, double[][] values, HashMap<Double, Map<String, String>> valuesPropertiesMap, AlgorithmConfiguration configuration) {
|
||||
init(x1, x2, y1, y2, z, 0, xResolution, yResolution, values, valuesPropertiesMap, configuration);
|
||||
}
|
||||
|
||||
public RasterTable(double x1, double x2, double y1, double y2, double z, double time, double xResolution, double yResolution, double[][] values, HashMap<Double, Map<String, String>> valuesPropertiesMap, AlgorithmConfiguration configuration) {
|
||||
init(x1, x2, y1, y2, z, time, xResolution, yResolution, values, valuesPropertiesMap, configuration);
|
||||
}
|
||||
|
||||
public void init(double x1, double x2, double y1, double y2, double z, double time, double xResolution, double yResolution, double[][] values, HashMap<Double, Map<String, String>> valuesPropertiesMap, AlgorithmConfiguration configuration) {
|
||||
this.valuesMatrix = values;
|
||||
if (valuesPropertiesMap!=null && valuesPropertiesMap.size()>0)
|
||||
this.valuesPropertiesMap = valuesPropertiesMap;
|
||||
this.configuration = configuration;
|
||||
this.x1 = x1;
|
||||
this.x2 = x2;
|
||||
|
|
@ -76,6 +94,7 @@ public class RasterTable {
|
|||
this.xResolution = xResolution;
|
||||
this.yResolution = yResolution;
|
||||
}
|
||||
|
||||
public void dumpGeoTable() {
|
||||
|
||||
// open the connection to the db
|
||||
|
|
@ -83,57 +102,92 @@ public class RasterTable {
|
|||
try {
|
||||
AnalysisLogger.getLogger().debug("Database Initialized");
|
||||
// create a table
|
||||
DatabaseFactory.executeSQLUpdate(String.format(createTableStatement, tablename), dbconnection);
|
||||
String columnNames = columnsnamesStandard;
|
||||
String emptycolumns = "";
|
||||
if (valuesPropertiesMap == null)
|
||||
DatabaseFactory.executeSQLUpdate(String.format(createTableStatementStandard, tablename), dbconnection);
|
||||
else {
|
||||
AnalysisLogger.getLogger().debug("Managing Table with Custom Fields");
|
||||
Map<String, String> valuesMap = valuesPropertiesMap.values().iterator().next();
|
||||
emptycolumns = generateEmptyValues(valuesMap.size());
|
||||
DatabaseFactory.executeSQLUpdate(String.format(createTableStatementWithFields, tablename, propertiesMapToColumnString(valuesMap, true)), dbconnection);
|
||||
columnNames = String.format(columnsnamesWithFields, propertiesMapToColumnString(valuesMap, false));
|
||||
AnalysisLogger.getLogger().debug("Column names: "+columnNames);
|
||||
}
|
||||
AnalysisLogger.getLogger().debug("Table " + tablename + " created");
|
||||
if (coordinates==null)
|
||||
if (coordinates == null)
|
||||
coordinates = VectorOperations.generateCoordinateTripletsInBoundingBox(x1, x2, y1, y2, z, xResolution, yResolution);
|
||||
|
||||
|
||||
int triplets = coordinates.size();
|
||||
AnalysisLogger.getLogger().debug("Generated " + triplets + " coordinates triples");
|
||||
List<Double> values = associateValueToCoordinates(coordinates, valuesMatrix);
|
||||
AnalysisLogger.getLogger().debug("Association to values completed - fulfilling buffer");
|
||||
// for each element in the matrix, build the corresponding csquare code
|
||||
StringBuffer sb = new StringBuffer();
|
||||
int rowcounter = 1;
|
||||
for (int i = 0; i < triplets; i++) {
|
||||
// save the string in a buffer
|
||||
Tuple<Double> cset = coordinates.get(i);
|
||||
double x = cset.getElements().get(0);
|
||||
double y = cset.getElements().get(1);
|
||||
String csquare = CSquareCodesConverter.convertAtResolution(y,x, xResolution);
|
||||
String csquare = CSquareCodesConverter.convertAtResolution(y, x, xResolution);
|
||||
String valueForTable = "";
|
||||
// if we have fields insert fields, otherwise insert double numbers
|
||||
Double value = values.get(i);
|
||||
//we do not use NaNs in this case every value will be filled
|
||||
if (value.isNaN())
|
||||
value = 0d;
|
||||
|
||||
double zVal = z;
|
||||
if (cset.getElements().size()>2)
|
||||
zVal = cset.getElements().get(2);
|
||||
|
||||
String tVal = ""+time;
|
||||
if (cset.getElements().size()>3){
|
||||
|
||||
tVal = ""+cset.getElements().get(3);
|
||||
if (Double.isNaN(cset.getElements().get(3)) || (Double.isInfinite(cset.getElements().get(3))))
|
||||
tVal="NULL";
|
||||
|
||||
if (valuesPropertiesMap == null) {
|
||||
// we do not use NaNs in this case every value will be filled
|
||||
if (value.isNaN())
|
||||
value = 0d;
|
||||
valueForTable = "" + value;
|
||||
} else {
|
||||
// we do not use NaNs in this case every value will be filled
|
||||
if (value.isNaN())
|
||||
valueForTable = null;
|
||||
else
|
||||
valueForTable = propertiesMapToDatabaseString(valuesPropertiesMap.get(values.get(i)));
|
||||
}
|
||||
|
||||
sb.append("('" + csquare + "'," + x + "," + y + "," + zVal + "," + tVal +",'" + value + "')");
|
||||
|
||||
if (i % 5000 == 0) {
|
||||
// AnalysisLogger.getLogger().debug("Partial Inserting Buffer of " + sb.length() + " Values");
|
||||
String insertStatement = DatabaseUtils.insertFromBuffer(tablename, columnsnames, sb);
|
||||
DatabaseFactory.executeSQLUpdate(insertStatement, dbconnection);
|
||||
// AnalysisLogger.getLogger().debug("Partial Insertion completed with Success!");
|
||||
|
||||
double zVal = z;
|
||||
if (cset.getElements().size() > 2)
|
||||
zVal = cset.getElements().get(2);
|
||||
|
||||
String tVal = "" + time;
|
||||
if (cset.getElements().size() > 3) {
|
||||
|
||||
tVal = "" + cset.getElements().get(3);
|
||||
if (Double.isNaN(cset.getElements().get(3)) || (Double.isInfinite(cset.getElements().get(3))))
|
||||
tVal = "NULL";
|
||||
}
|
||||
|
||||
if (valueForTable != null) {
|
||||
rowcounter++;
|
||||
if (valuesPropertiesMap == null)
|
||||
sb.append("('" + csquare + "'," + x + "," + y + "," + zVal + "," + tVal + ",'" + valueForTable + "')");
|
||||
else
|
||||
sb.append("(" + x + "," + y + "," + zVal + "," + tVal + "," + valueForTable + ")");
|
||||
}
|
||||
if (rowcounter % 5000 == 0) {
|
||||
// AnalysisLogger.getLogger().debug("Partial Inserting Buffer of " + sb.length() + " Values");
|
||||
|
||||
String insertStatement = DatabaseUtils.insertFromBuffer(tablename, columnNames, sb);
|
||||
// AnalysisLogger.getLogger().debug("Inserting Buffer " + insertStatement);
|
||||
DatabaseFactory.executeSQLUpdate(insertStatement, dbconnection);
|
||||
|
||||
// AnalysisLogger.getLogger().debug("Partial Insertion completed with Success!");
|
||||
sb = new StringBuffer();
|
||||
} else if (i < triplets - 1)
|
||||
}
|
||||
else if (valueForTable != null)
|
||||
sb.append(",");
|
||||
|
||||
}
|
||||
|
||||
AnalysisLogger.getLogger().debug("Inserting Final Buffer of " + sb.length() + " Values");
|
||||
// AnalysisLogger.getLogger().debug("Inserting Final Buffer " + sb);
|
||||
// AnalysisLogger.getLogger().debug("Inserting Final Buffer " + sb);
|
||||
// save all the strings on the table
|
||||
if (sb.length() > 0) {
|
||||
String insertStatement = DatabaseUtils.insertFromBuffer(tablename, columnsnames, sb);
|
||||
String insertStatement = DatabaseUtils.insertFromString(tablename, columnNames, sb.substring(0, sb.length()-1));
|
||||
// AnalysisLogger.getLogger().debug("Inserting Buffer " + insertStatement);
|
||||
DatabaseFactory.executeSQLUpdate(insertStatement, dbconnection);
|
||||
AnalysisLogger.getLogger().debug("Insertion completed with Success!");
|
||||
}
|
||||
|
|
@ -147,38 +201,78 @@ public class RasterTable {
|
|||
}
|
||||
}
|
||||
|
||||
|
||||
public static String propertiesMapToDatabaseString(Map<String, String> valuesMap) {
|
||||
StringBuffer sb = new StringBuffer();
|
||||
int m = valuesMap.size();
|
||||
int i = 0;
|
||||
for (String value : valuesMap.values()) {
|
||||
sb.append("'" + value .replace("'", ""+(char)96)+ "'");
|
||||
if (i < m - 1)
|
||||
sb.append(",");
|
||||
|
||||
i++;
|
||||
}
|
||||
|
||||
return sb.toString();
|
||||
}
|
||||
|
||||
public static String propertiesMapToColumnString(Map<String, String> valuesMap, boolean withtype) {
|
||||
StringBuffer sb = new StringBuffer();
|
||||
int m = valuesMap.size();
|
||||
int i = 0;
|
||||
for (String keys : valuesMap.keySet()) {
|
||||
sb.append(keys);
|
||||
if (withtype)
|
||||
sb.append(" character varying");
|
||||
if (i < m - 1)
|
||||
sb.append(",");
|
||||
|
||||
i++;
|
||||
}
|
||||
|
||||
return sb.toString();
|
||||
}
|
||||
|
||||
public static String generateEmptyValues(int nValues) {
|
||||
StringBuffer sb = new StringBuffer();
|
||||
for (int j = 0; j < nValues; j++) {
|
||||
sb.append("NULL");
|
||||
if (j < nValues - 1)
|
||||
sb.append(",");
|
||||
}
|
||||
return sb.toString();
|
||||
}
|
||||
|
||||
public void deleteTable() {
|
||||
SessionFactory dbconnection = null;
|
||||
try {
|
||||
dbconnection = DatabaseUtils.initDBSession(configuration);
|
||||
DatabaseFactory.executeSQLUpdate(DatabaseUtils.dropTableStatement(tablename), dbconnection);
|
||||
} catch (Exception e) {
|
||||
// e.printStackTrace();
|
||||
AnalysisLogger.getLogger().debug("Impossible to delete table "+tablename+" : "+e.getLocalizedMessage());
|
||||
// e.printStackTrace();
|
||||
AnalysisLogger.getLogger().debug("Impossible to delete table " + tablename + " : " + e.getLocalizedMessage());
|
||||
} finally {
|
||||
DatabaseUtils.closeDBConnection(dbconnection);
|
||||
}
|
||||
}
|
||||
|
||||
public static List<Double> associateValueToCoordinates(List<Tuple<Double>> coordinates, double[][] data){
|
||||
public static List<Double> associateValueToCoordinates(List<Tuple<Double>> coordinates, double[][] data) {
|
||||
List<Double> values = new ArrayList<Double>();
|
||||
|
||||
|
||||
int k = 0;
|
||||
int g = 0;
|
||||
int ntriplets = coordinates.size();
|
||||
int xsteps = data[0].length-1;
|
||||
int xsteps = data[0].length - 1;
|
||||
for (int t = 0; t < ntriplets; t++) {
|
||||
values.add(data[k][g]);
|
||||
if (g == xsteps) {
|
||||
g = 0;
|
||||
k++;
|
||||
}
|
||||
else
|
||||
} else
|
||||
g++;
|
||||
}
|
||||
|
||||
return values;
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -12,9 +12,10 @@ import org.gcube.dataanalysis.geo.connectors.table.TableMatrixRepresentation;
|
|||
|
||||
public class TestExtraction {
|
||||
|
||||
static AlgorithmConfiguration[] configs = { testXYExtractionNetCDF(),testXYExtractionAquaMaps(),testXYExtractionTable(),testXYExtractionTable2()};
|
||||
static AlgorithmConfiguration[] configs = { testXYExtractionNetCDF(),testXYExtractionAquaMaps(),testXYExtractionTable(),testXYExtractionTable2(),testDirectExtraction()};
|
||||
// static AlgorithmConfiguration[] configs = { testXYExtractionTable2()};
|
||||
// static AlgorithmConfiguration[] configs = { testDirectExtraction()};
|
||||
// static AlgorithmConfiguration[] configs = { testXYExtractionAquaMaps()};
|
||||
public static void main(String[] args) throws Exception {
|
||||
|
||||
System.out.println("TEST 1");
|
||||
|
|
@ -82,8 +83,8 @@ public class TestExtraction {
|
|||
config.setParam("BBox_UpperRightLong","50");
|
||||
config.setParam("XResolution","0.5");
|
||||
config.setParam("YResolution","0.5");
|
||||
config.setParam("OutputTableName","testextraction");
|
||||
config.setParam("OutputTableLabel","testextraction");
|
||||
config.setParam("OutputTableName","testextractiondirect");
|
||||
config.setParam("OutputTableLabel","testextractiondirect");
|
||||
|
||||
return config;
|
||||
}
|
||||
|
|
@ -133,7 +134,7 @@ public class TestExtraction {
|
|||
AlgorithmConfiguration config = testXYExtractionNetCDF();
|
||||
config.setAgent("XYEXTRACTOR_TABLE");
|
||||
|
||||
config.setParam("OutputTableName","testextractiontable");
|
||||
config.setParam("OutputTableName","testextractiontable2");
|
||||
config.setParam("DatabaseUserName", "utente");
|
||||
config.setParam("DatabasePassword", "d4science");
|
||||
config.setParam("DatabaseURL", "jdbc:postgresql://statistical-manager.d.d4science.research-infrastructures.eu/testdb");
|
||||
|
|
|
|||
|
|
@ -19,6 +19,7 @@ import org.gcube.dataanalysis.ecoengine.utils.IOHelper;
|
|||
public class TestOccurrenceEnrichment {
|
||||
|
||||
static AlgorithmConfiguration[] configs = { testOccEnrichment()};
|
||||
// static AlgorithmConfiguration[] configs = { testOccEnrichmentWPS()};
|
||||
public static void main(String[] args) throws Exception {
|
||||
|
||||
System.out.println("TEST 1");
|
||||
|
|
@ -81,4 +82,37 @@ public class TestOccurrenceEnrichment {
|
|||
return config;
|
||||
}
|
||||
|
||||
|
||||
private static AlgorithmConfiguration testOccEnrichmentWPS() {
|
||||
|
||||
AlgorithmConfiguration config = new AlgorithmConfiguration();
|
||||
|
||||
config.setAgent("OCCURRENCE_ENRICHMENT");
|
||||
config.setConfigPath("./cfg/");
|
||||
config.setPersistencePath("./");
|
||||
|
||||
config.setParam("DatabaseUserName", "utente");
|
||||
config.setParam("DatabasePassword", "d4science");
|
||||
config.setParam("DatabaseURL", "jdbc:postgresql://statistical-manager.d.d4science.research-infrastructures.eu/testdb");
|
||||
config.setParam("DatabaseDriver", "org.postgresql.Driver");
|
||||
config.setGcubeScope("/gcube/devsec/devVRE");
|
||||
|
||||
config.setParam("OccurrenceTable","occurrence_carch");
|
||||
config.setParam("LongitudeColumn","decimallongitude");
|
||||
config.setParam("LatitudeColumn","decimallatitude");
|
||||
config.setParam("ScientificNameColumn","scientificname");
|
||||
config.setParam("TimeColumn","eventdate");
|
||||
config.setParam("OptionalFilter","");
|
||||
config.setParam("Resolution","0.5");
|
||||
config.setParam("OutputTableDBName","testenrichmentwps");
|
||||
config.setParam("OutputTableName","testenrichmentwps");
|
||||
String sep=AlgorithmConfiguration.getListSeparator();
|
||||
|
||||
//WFS: carcharodon
|
||||
config.setParam("Layers","b8a17d86-c62f-4e73-b5c9-bdb3366015c9");
|
||||
|
||||
|
||||
return config;
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -13,8 +13,10 @@ import org.gcube.dataanalysis.geo.connectors.table.TableMatrixRepresentation;
|
|||
|
||||
public class TestTimeExtraction {
|
||||
|
||||
static AlgorithmConfiguration[] configs = { testTimeExtractionTable(), testTimeExtractionNetCDF(),testTimeExtractionTable2()};
|
||||
// static AlgorithmConfiguration[] configs = { testTimeExtractionTable(), testTimeExtractionNetCDF(),testTimeExtractionTable2()};
|
||||
// static AlgorithmConfiguration[] configs = { testTimeExtractionNetCDF()};
|
||||
static AlgorithmConfiguration[] configs = { testTExtractionAquamaps()};
|
||||
|
||||
public static void main(String[] args) throws Exception {
|
||||
|
||||
System.out.println("TEST 1");
|
||||
|
|
@ -32,6 +34,36 @@ public class TestTimeExtraction {
|
|||
}
|
||||
|
||||
|
||||
private static AlgorithmConfiguration testTExtractionAquamaps() {
|
||||
|
||||
AlgorithmConfiguration config = new AlgorithmConfiguration();
|
||||
|
||||
config.setAgent("TIMEEXTRACTION");
|
||||
config.setConfigPath("./cfg/");
|
||||
config.setPersistencePath("./");
|
||||
config.setParam("DatabaseUserName","gcube");
|
||||
config.setParam("DatabasePassword","d4science2");
|
||||
config.setParam("DatabaseURL","jdbc:postgresql://localhost/testdb");
|
||||
config.setParam("DatabaseDriver","org.postgresql.Driver");
|
||||
config.setGcubeScope("/gcube/devsec/devVRE");
|
||||
|
||||
config.setParam("Layer","40198411-9ceb-420f-8f39-a7e1b8128d6b");
|
||||
|
||||
config.setParam("OutputTableName","testtextractionaquamaps");
|
||||
config.setParam("OutputTableLabel","testtextractionaquamaps");
|
||||
|
||||
config.setParam("X","121");
|
||||
config.setParam("Y","-4");
|
||||
config.setParam("Resolution","0.5");
|
||||
config.setParam("Z","0");
|
||||
config.setParam("SamplingFreq","-1");
|
||||
config.setParam("MinFrequency","-1");
|
||||
config.setParam("MaxFrequency","-1");
|
||||
config.setParam("FrequencyError","-1");
|
||||
|
||||
return config;
|
||||
}
|
||||
|
||||
private static AlgorithmConfiguration testTimeExtractionNetCDF() {
|
||||
|
||||
AlgorithmConfiguration config = new AlgorithmConfiguration();
|
||||
|
|
|
|||
|
|
@ -13,8 +13,8 @@ import org.gcube.dataanalysis.geo.connectors.table.TableMatrixRepresentation;
|
|||
|
||||
public class TestZExtraction {
|
||||
|
||||
// static AlgorithmConfiguration[] configs = { testTimeExtractionTable(), testTimeExtractionNetCDF(),testTimeExtractionTable2()};
|
||||
static AlgorithmConfiguration[] configs = { testZExtractionNetCDF()};
|
||||
// static AlgorithmConfiguration[] configs = { testTimeExtractionTable(), testZExtractionLongNetCDF(),testZExtractionNetCDF(),testTimeExtractionTable2()};
|
||||
static AlgorithmConfiguration[] configs = { testZExtractionAquamaps()};
|
||||
|
||||
public static void main(String[] args) throws Exception {
|
||||
|
||||
|
|
@ -32,6 +32,31 @@ public class TestZExtraction {
|
|||
}
|
||||
}
|
||||
|
||||
private static AlgorithmConfiguration testZExtractionAquamaps() {
|
||||
|
||||
AlgorithmConfiguration config = new AlgorithmConfiguration();
|
||||
|
||||
config.setAgent("ZEXTRACTION");
|
||||
config.setConfigPath("./cfg/");
|
||||
config.setPersistencePath("./");
|
||||
config.setParam("DatabaseUserName","gcube");
|
||||
config.setParam("DatabasePassword","d4science2");
|
||||
config.setParam("DatabaseURL","jdbc:postgresql://localhost/testdb");
|
||||
config.setParam("DatabaseDriver","org.postgresql.Driver");
|
||||
config.setGcubeScope("/gcube/devsec/devVRE");
|
||||
|
||||
config.setParam("Layer","40198411-9ceb-420f-8f39-a7e1b8128d6b");
|
||||
|
||||
config.setParam("OutputTableName","testzextractionaquamaps");
|
||||
config.setParam("OutputTableLabel","testzextractionaquamaps");
|
||||
|
||||
config.setParam("TimeIndex","0");
|
||||
config.setParam("X","121");
|
||||
config.setParam("Y","-4");
|
||||
config.setParam("Resolution","0.5");
|
||||
|
||||
return config;
|
||||
}
|
||||
|
||||
private static AlgorithmConfiguration testZExtractionLongNetCDF() {
|
||||
|
||||
|
|
@ -49,8 +74,8 @@ public class TestZExtraction {
|
|||
config.setParam("Layer","6411b110-7572-457a-a662-a16e4ff09e4e");
|
||||
// config.setParam("Layer","dffa504b-dbc8-4553-896e-002549f8f5d3");
|
||||
|
||||
config.setParam("OutputTableName","testtimeextraction");
|
||||
config.setParam("OutputTableLabel","testtimeextraction");
|
||||
config.setParam("OutputTableName","testzextractionlong");
|
||||
config.setParam("OutputTableLabel","testzextractionlong");
|
||||
|
||||
config.setParam("TimeIndex","0");
|
||||
config.setParam("X","0");
|
||||
|
|
@ -75,8 +100,8 @@ public class TestZExtraction {
|
|||
|
||||
config.setParam("Layer","7f90e153-0c5c-4d45-a498-a6374593e68d");
|
||||
|
||||
config.setParam("OutputTableName","testtimeextraction");
|
||||
config.setParam("OutputTableLabel","testtimeextraction");
|
||||
config.setParam("OutputTableName","testzextractionstandard");
|
||||
config.setParam("OutputTableLabel","testzextractionstandard");
|
||||
|
||||
config.setParam("TimeIndex","0");
|
||||
config.setParam("X","0");
|
||||
|
|
@ -101,8 +126,8 @@ public class TestZExtraction {
|
|||
|
||||
config.setParam("Layer","c565e32c-c5b3-4964-b44f-06dc620563e9");
|
||||
|
||||
config.setParam("OutputTableName","testtimeextraction2");
|
||||
config.setParam("OutputTableLabel","testtimeextraction2");
|
||||
config.setParam("OutputTableName","testtimeextraction");
|
||||
config.setParam("OutputTableLabel","testtimeextraction");
|
||||
|
||||
config.setParam("Z","0");
|
||||
config.setParam("X","-47.97");
|
||||
|
|
|
|||
Loading…
Reference in New Issue