201 lines
9.3 KiB
Java
201 lines
9.3 KiB
Java
package org.gcube.dataanalysis.executor.nodes.algorithms;
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import java.io.BufferedWriter;
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import java.io.File;
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import java.io.FileInputStream;
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import java.io.ObjectInputStream;
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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 java.util.concurrent.ConcurrentHashMap;
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import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
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import org.gcube.dataanalysis.ecoengine.spatialdistributions.AquamapsAlgorithmCore;
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import org.gcube.dataanalysis.ecoengine.utils.DatabaseFactory;
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import org.gcube.dataanalysis.ecoengine.utils.Transformations;
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import org.hibernate.SessionFactory;
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import com.thoughtworks.xstream.XStream;
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public class AquamapsSuitableFunctions {
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public static String countAllSpeciesQuery = "select count(*) from %1$s;";
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// public static String countAll = "select count(*) from %1$s;";
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public static String countAll = "EXPLAIN SELECT * FROM %1$s;";
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public static String countCsquareCodeQuery = "select count (*) from %1$s d where oceanarea>0";
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public static String selectAllSpeciesQuery = "select depthmin,meandepth,depthprefmin,pelagic,depthprefmax,depthmax,tempmin,layer,tempprefmin,tempprefmax,tempmax,salinitymin,salinityprefmin,salinityprefmax,salinitymax,primprodmin,primprodprefmin,primprodprefmax,primprodmax,iceconmin,iceconprefmin,iceconprefmax,iceconmax,landdistyn,landdistmin,landdistprefmin,landdistprefmax,landdistmax,nmostlat,smostlat,wmostlong,emostlong,faoareas,speciesid from %1$s order by speciesid limit %2$s offset %3$s;";
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public static String csquareCodeQuery = "select csquarecode,depthmean,depthmax,depthmin, sstanmean,sbtanmean,salinitymean,salinitybmean, primprodmean,iceconann,landdist,oceanarea,centerlat,centerlong,faoaream,eezall,lme from %1$s d where oceanarea>0 order by csquarecode limit %2$s offset %3$s";
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public static String createTableStatement = "CREATE TABLE %1$s ( speciesid character varying, csquarecode character varying, probability real, boundboxyn smallint, faoareayn smallint, faoaream integer, eezall character varying, lme integer) WITH (OIDS=FALSE ) #TABLESPACE#; CREATE INDEX CONCURRENTLY %1$s_idx ON %1$s USING btree (speciesid, csquarecode, faoaream, eezall, lme);";
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public static String metainfo = "boundboxyn, faoareayn, faoaream, eezall, lme";
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public static String selectAllSpeciesObservationQuery = "SELECT speciesid,maxclat,minclat from %1$s;";
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public static String probabilityInsertionStatement = "insert into %1$s (speciesid,csquarecode,probability %ADDEDINFORMATION%) VALUES %2$s";
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public static String deleteDuplicates = "delete from %1$s where speciesid='%2$s'";
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// Default Files
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private static String speciesFile = "species.dat";
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private static String csquaresFile = "csquares.dat";
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private static String maxminlatFile = "maxminlat.dat";
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private static String configFile = "config.dat";
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// file1
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public HashMap<String, List<Object>> allSpeciesObservations;
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// file2
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public List<Object> speciesVectors;
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// file3
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public List<Object> environmentVectors;
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public int numberOfSpecies;
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public int numberOfCells;
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//processing variables
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public AlgorithmConfiguration currentconfig;
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public HashMap<String, String> currentSpeciesBoundingBoxInfo;
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public String currentFAOAreas;
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public AquamapsAlgorithmCore core;
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public String type;
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public HashMap<String, Object> processedAreas;
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public ConcurrentHashMap<String, Map<String, Float>> completeDistribution;
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public AquamapsSuitableFunctions(AquamapsAlgorithmCore core, String type, AlgorithmConfiguration config) {
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this.core = core;
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this.type = type;
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this.currentconfig = config;
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}
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//PROBABILITY CALCULATION
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// calculates probability and takes into account the processes areas by this node
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public float calcProb(Object species, Object area) {
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float prob = (float) core.getSpeciesProb((Object[]) species, (Object[]) area);
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String speciesID = getMainInfoID(species);
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String csquareCode = getGeographicalID(area);
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if (completeDistribution == null)
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completeDistribution = new ConcurrentHashMap<String, Map<String, Float>>();
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Map<String, Float> geoDistrib = completeDistribution.get(speciesID);
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// if the map is null then generate a new map, otherwise update it
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if (geoDistrib == null) {
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geoDistrib = new ConcurrentHashMap<String, Float>();
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completeDistribution.put(speciesID, geoDistrib);
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}
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if (prob > 0.1) {
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// record the overall probability distribution
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geoDistrib.put(csquareCode, prob);
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if (processedAreas == null)
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processedAreas = new HashMap<String, Object>();
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processedAreas.put(csquareCode, area);
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}
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return prob;
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}
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//BOUNDING BOX CALCULATION
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// calculates the bounding box information
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public HashMap<String, Integer> calculateBoundingBox(Object[] csquarecode) {
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HashMap<String, Integer> boundingInfo = core.calculateBoundingBox("" + csquarecode[0], currentSpeciesBoundingBoxInfo.get("$pass_NS"), currentSpeciesBoundingBoxInfo.get("$pass_N"), currentSpeciesBoundingBoxInfo.get("$pass_S"), AquamapsAlgorithmCore.getElement(csquarecode, 12),// centerlat
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AquamapsAlgorithmCore.getElement(csquarecode, 13),// centerlong
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AquamapsAlgorithmCore.getElement(csquarecode, 14),// faoaream
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currentSpeciesBoundingBoxInfo.get("$paramData_NMostLat"), currentSpeciesBoundingBoxInfo.get("$paramData_SMostLat"), currentSpeciesBoundingBoxInfo.get("$paramData_WMostLong"), currentSpeciesBoundingBoxInfo.get("$paramData_EMostLong"), currentFAOAreas, currentSpeciesBoundingBoxInfo.get("$northern_hemisphere_adjusted"), currentSpeciesBoundingBoxInfo.get("$southern_hemisphere_adjusted"));
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return boundingInfo;
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}
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// initializes currentFAOAreas and currentSpeciesBoundingBoxInfo
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public void getBoundingBoxInformation(Object[] speciesInfoRow, Object[] speciesObservations) {
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Object[] row = speciesInfoRow;
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String $paramData_NMostLat = AquamapsAlgorithmCore.getElement(row, 28);
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String $paramData_SMostLat = AquamapsAlgorithmCore.getElement(row, 29);
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String $paramData_WMostLong = AquamapsAlgorithmCore.getElement(row, 30);
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String $paramData_EMostLong = AquamapsAlgorithmCore.getElement(row, 31);
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currentFAOAreas = AquamapsAlgorithmCore.getElement(row, 32);
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// adjust FAO areas
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currentFAOAreas = core.procFAO_2050(currentFAOAreas);
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// get Bounding Box Information
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// System.out.println("TYPE:"+type);
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currentSpeciesBoundingBoxInfo = core.getBoundingBoxInfo($paramData_NMostLat, $paramData_SMostLat, $paramData_WMostLong, $paramData_EMostLong, speciesObservations, type);
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// end of get BoundingBoxInformation
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}
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// DATABASE INTERACTION
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public static void writeOnDB(List<String> buffer, String destinationTable, SessionFactory dbHibConnection) {
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int endIndex = buffer.size();
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if (endIndex > 0) {
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System.out.println("\tWriting Buffer is not empty: "+endIndex);
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String $probabilityInsertionStatement = AquamapsSuitableFunctions.probabilityInsertionStatement.replace("%ADDEDINFORMATION%", ","+metainfo);
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StringBuffer sb = new StringBuffer();
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// System.out.println("writeOnDB()->PROBABILITIES BUFFER SIZE DELETION");
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for (int i = 0; i < endIndex; i++) {
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sb.append("(" + buffer.get(i) + ")");
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if (i < endIndex - 1) {
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sb.append(",");
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}
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}
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String insertionString = String.format($probabilityInsertionStatement, destinationTable, sb.toString());
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try {
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// System.out.println(insertionString);
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DatabaseFactory.executeSQLUpdate(insertionString, dbHibConnection);
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} catch (Exception e) {
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e.printStackTrace();
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}
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}
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else
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System.out.println("\tWarning : writing buffer is empty!");
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System.out.println("\tWriting on DB FINISHED");
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}
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//FILES MANAGEMENT
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public void dumpAll(String path) throws Exception {
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Transformations.dumpObjectToFile(path + configFile, currentconfig);
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// Transformations.dumpObjectToFile(path + csquaresFile, environmentVectors);
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}
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public void rebuildConfig(String configFile) throws Exception{
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FileInputStream fis = new FileInputStream(new File(configFile));
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currentconfig = (AlgorithmConfiguration) new XStream().fromXML(fis);
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fis.close();
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}
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// when uploaded the files will be local
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public void rebuildAll(int cellOrdinal, int chunksize, int speciesOrdinal, int speciesChunkSize, String pathToFiles) throws Exception {
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// currentconfig = (AlgorithmConfiguration) Transformations.getObjectFromFile(pathToFiles+configFile);
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/*
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try{
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environmentVectors = (List<Object>) Transformations.getObjectFromFile(pathToFiles+csquaresFile);
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}catch(Exception e){
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System.out.println("\tError in retrieving environmental vectors");
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}
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*/
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}
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public String getAdditionalInformation(Object species, Object area) {
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Object[] arearray = (Object[]) area;
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HashMap<String, Integer> boundingInfo = calculateBoundingBox(arearray);
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String addedInformation = "'" + boundingInfo.get("$InBox") + "','" + boundingInfo.get("$InFAO") + "','" + arearray[14] + "','" + arearray[15] + "','" + arearray[16] + "'";
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return addedInformation;
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}
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//AUXILIARY FUNCTIONS
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public static String getMainInfoID(Object speciesInfo) {
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String s = "" + ((Object[]) speciesInfo)[33];
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return s;
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}
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public static String getGeographicalID(Object geoInfo) {
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String s = "" + ((Object[]) geoInfo)[0];
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return s;
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}
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}
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