242 lines
10 KiB
Java
242 lines
10 KiB
Java
package org.gcube.dataanalysis.geo.algorithms;
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import java.util.ArrayList;
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import java.util.List;
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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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import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
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import org.gcube.dataanalysis.ecoengine.configuration.INFRASTRUCTURE;
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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.OutputTable;
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import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveTypesList;
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import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType;
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import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.PrimitiveTypes;
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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.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.ecoengine.utils.ResourceFactory;
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import org.gcube.dataanalysis.ecoengine.utils.Tuple;
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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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public class OccurrenceEnrichment implements Transducerer {
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static String OccurrencesTableNameParameter = "OccurrenceTable";
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static String LongitudeColumn= "LongitudeColumn";
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static String LatitudeColumn = "LatitudeColumn";
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static String ScientificNameColumn = "ScientificNameColumn";
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static String OutputTableLabelParameter = "OutputTableName";
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static String OutputTableDBNameParameter = "OutputTableDBName";
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static String FilterParameter = "OptionalFilter";
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static String Resolution = "Resolution";
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static String Layers = "Layers";
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static String yLL = "BBox_LowerLeftLat";
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static String xLL = "BBox_LowerLeftLong";
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static String yUR = "BBox_UpperRightLat";
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static String xUR = "BBox_UpperRightLong";
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AlgorithmConfiguration config;
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float status;
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private String [] layers;
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private String occurrencesTableName;
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private String longitudeColumn;
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private String latitudeColumn;
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private String scientificnameColumn;
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private String filter;
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private float resolution;
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private String outputTableLabel;
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private String outputTableDBName;
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private double BBxLL;
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private double BByLL;
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private double BBxUR;
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private double BByUR;
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@Override
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public List<StatisticalType> getInputParameters() {
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List<StatisticalType> inputs = new ArrayList<StatisticalType>();
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List<TableTemplates> template= new ArrayList<TableTemplates>();
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template.add(TableTemplates.OCCURRENCE_SPECIES);
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InputTable table = new InputTable(template,OccurrencesTableNameParameter ,"A geospatial table containing at least x,y information","");
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inputs.add(table);
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ColumnType p1 = new ColumnType(OccurrencesTableNameParameter , LongitudeColumn, "column with longitude values", "decimallongitude", false);
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inputs.add(p1);
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ColumnType p2 = new ColumnType(OccurrencesTableNameParameter , LatitudeColumn, "column with latitude values", "decimallatitude", false);
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inputs.add(p2);
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ColumnType p3 = new ColumnType(OccurrencesTableNameParameter , ScientificNameColumn, "column with Scientific Names", "scientificname", false);
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inputs.add(p3);
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IOHelper.addStringInput(inputs, FilterParameter, "A filter on one of the columns (e.g. basisofrecord='HumanObservation')", " ");
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IOHelper.addDoubleInput(inputs, Resolution, "The spatial resolution of the association between observations and environmental features.", "0.5");
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IOHelper.addRandomStringInput(inputs, OutputTableDBNameParameter, "The db name of the table to produce", "enrich_");
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IOHelper.addStringInput(inputs, OutputTableLabelParameter, "The name of the output table", "enrich_");
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PrimitiveTypesList listEnvLayers = new PrimitiveTypesList(String.class.getName(), PrimitiveTypes.STRING, Layers, "The list of environmental layers to use for enriching the points. Each entry is a Layer Title or UUID (preferred) of a layer indexed in the e-Infrastructure on GeoNetwork - You can retrieve it from GeoExplorer. Supports several standards (NETCDF, WFS, WCS ASC, GeoTiff )", false);
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inputs.add(listEnvLayers);
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IOHelper.addDoubleInput(inputs, xLL, "Lower Left Longitude of the Bounding Box", "-180");
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IOHelper.addDoubleInput(inputs, yLL, "Lower Left Latitute of the Bounding Box", "-90");
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IOHelper.addDoubleInput(inputs, xUR, "Upper Right Longitude of the Bounding Box", "180");
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IOHelper.addDoubleInput(inputs, yUR, "Upper Right Latitute of the Bounding Box", "90");
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DatabaseType.addDefaultDBPars(inputs);
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return inputs;
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}
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protected void getParameters() {
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layers = IOHelper.getInputParameter(config, Layers).split(AlgorithmConfiguration.getListSeparator());
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AnalysisLogger.getLogger().debug("Layers to take " + layers.length);
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occurrencesTableName=IOHelper.getInputParameter(config, OccurrencesTableNameParameter);
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longitudeColumn=IOHelper.getInputParameter(config, LongitudeColumn);
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latitudeColumn=IOHelper.getInputParameter(config, LatitudeColumn);
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scientificnameColumn=IOHelper.getInputParameter(config, ScientificNameColumn);
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filter=IOHelper.getInputParameter(config, FilterParameter);
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if (filter==null)
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filter="";
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filter=filter.trim();
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resolution=IOHelper.getInputParameter(config, Resolution)==null?0.5f:Float.parseFloat(IOHelper.getInputParameter(config, Resolution));
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outputTableLabel=IOHelper.getInputParameter(config, OutputTableLabelParameter);
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outputTableDBName=IOHelper.getInputParameter(config, OutputTableDBNameParameter);
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BBxLL=Double.parseDouble(IOHelper.getInputParameter(config, xLL));
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BByLL=Double.parseDouble(IOHelper.getInputParameter(config, yLL));
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BBxUR=Double.parseDouble(IOHelper.getInputParameter(config, xUR));
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BByUR=Double.parseDouble(IOHelper.getInputParameter(config, yUR));
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String scope = config.getGcubeScope();
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AnalysisLogger.getLogger().debug("Extraction: Externally set scope " + scope);
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if (scope == null) {
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scope = ScopeProvider.instance.get();
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AnalysisLogger.getLogger().debug("Extraction: Internally set scope " + scope);
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config.setGcubeScope(scope);
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}
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}
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@Override
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public void init() throws Exception {
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AnalysisLogger.getLogger().debug("Occurrence Enrichment Initialization");
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}
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@Override
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public void shutdown() {
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AnalysisLogger.getLogger().debug("Occurrence Enrichment Shutdown");
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}
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@Override
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public String getDescription() {
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return "An algorithm performing occurrences enrichment. Takes as input one table containing occurrence points for a set of species and a list of environmental layers from the e-infrastructure GeoNetwork (through the GeoExplorer application). Produces one table reporting the set of environmental values associated to the occurrence points.";
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}
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@Override
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public void compute() throws Exception {
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//TODO: report times
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SessionFactory dbconnection=null;
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try{
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dbconnection=DatabaseUtils.initDBSession(config);
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String columns = longitudeColumn+","+latitudeColumn+","+scientificnameColumn;
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String columnsToProduce = longitudeColumn+","+latitudeColumn+","+scientificnameColumn;
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//take the occurrence points
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List<Object> rows = (List<Object>)DatabaseFactory.executeSQLQuery(DatabaseUtils.getDinstictElements(occurrencesTableName, columns, filter),dbconnection);
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if (rows==null || rows.size()==0)
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throw new Exception("Could not find occurrence data");
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int rowsize = rows.size();
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List<Tuple<Double>> coordinates4d = new ArrayList<Tuple<Double>>();
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List<String[]> enrichment = new ArrayList<String[]>();
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int elementstoreport = 4;
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int elementsfromoccurrences = 3;
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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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double y =elements[1]==null?0:Double.parseDouble(""+elements[1]);
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String species=elements[2]==null?"":""+elements[2];
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Tuple<Double> el = new Tuple<Double>(x,y);
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coordinates4d.add(el);
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String[] singlerow = new String[elementstoreport];
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singlerow [0]=""+x;
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singlerow[1]=""+y;
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singlerow[2]=""+species;
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}
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//take the layers matrices
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int layeridx = 0;
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for (String layerID:layers){
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//for each layer
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XYExtractor extractor = new XYExtractor(config);
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extractor.extractXYGrid(layerID, 0, BBxLL, BBxUR, BByLL, BByUR, 0, resolution,resolution);
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List<Double> gridValues = extractor.currentTimeValues;
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List<Tuple<Double>> grid3d =extractor.currentTuples;
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int time = 0;
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//take the association
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List<Double> enriched = VectorOperations.assignGridValuesToPoints(grid3d, time , gridValues, coordinates4d, resolution);
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int k=0;
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for (Double value:enriched){
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String[] singlerow =enrichment.get(k);
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singlerow[layeridx+elementsfromoccurrences] = ""+value;
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k++;
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}
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layeridx++;
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}
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//write the complete association into the db
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DatabaseFactory.executeSQLQuery(DatabaseUtils.dropTableStatement(outputTableDBName),dbconnection);
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//TODO: create table
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DatabaseUtils.insertChunksIntoTable(outputTableDBName, columnsToProduce, enrichment, 5000, dbconnection);
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}catch(Exception e){
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if (dbconnection!=null)
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dbconnection.close();
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}
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}
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@Override
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public StatisticalType getOutput() {
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List<TableTemplates> templateHspec = new ArrayList<TableTemplates>();
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templateHspec.add(TableTemplates.GENERIC);
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OutputTable p = new OutputTable(templateHspec, OutputTableLabelParameter, OutputTableDBNameParameter, "Output table");
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return p;
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}
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@Override
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public float getStatus() {
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return status;
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}
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@Override
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public INFRASTRUCTURE getInfrastructure() {
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return INFRASTRUCTURE.LOCAL;
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}
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@Override
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public void setConfiguration(AlgorithmConfiguration config) {
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this.config = config;
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}
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protected ResourceFactory resourceManager;
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public String getResourceLoad() {
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if (resourceManager == null)
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resourceManager = new ResourceFactory();
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return resourceManager.getResourceLoad(1);
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}
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public String getResources() {
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return ResourceFactory.getResources(100f);
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}
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}
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