diff --git a/src/main/java/org/gcube/dataanalysis/geo/algorithms/MapsCreator.java b/src/main/java/org/gcube/dataanalysis/geo/algorithms/MapsCreator.java new file mode 100644 index 0000000..0ced728 --- /dev/null +++ b/src/main/java/org/gcube/dataanalysis/geo/algorithms/MapsCreator.java @@ -0,0 +1,335 @@ +package org.gcube.dataanalysis.geo.algorithms; + +import it.cnr.aquamaps.CSquare; +import it.geosolutions.geonetwork.util.GNInsertConfiguration; +import it.geosolutions.geoserver.rest.encoder.GSLayerEncoder; +import it.geosolutions.geoserver.rest.encoder.feature.GSFeatureTypeEncoder; + +import java.util.ArrayList; +import java.util.Date; +import java.util.List; +import java.util.UUID; + +import org.gcube.common.scope.api.ScopeProvider; +import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; +import org.gcube.dataanalysis.ecoengine.datatypes.ColumnType; +import org.gcube.dataanalysis.ecoengine.datatypes.DatabaseType; +import org.gcube.dataanalysis.ecoengine.datatypes.InputTable; +import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType; +import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.TableTemplates; +import org.gcube.dataanalysis.ecoengine.interfaces.StandardLocalExternalAlgorithm; +import org.gcube.dataanalysis.ecoengine.utils.DatabaseFactory; +import org.gcube.dataanalysis.ecoengine.utils.DatabaseUtils; +import org.gcube.spatial.data.geonetwork.LoginLevel; +import org.gcube.spatial.data.geonetwork.configuration.Configuration; +import org.gcube.spatial.data.geonetwork.iso.GcubeISOMetadata; +import org.gcube.spatial.data.geonetwork.iso.Thesaurus; +import org.gcube.spatial.data.gis.GISInterface; +import org.gcube.spatial.data.gis.model.report.PublishResponse; +import org.geotoolkit.metadata.iso.extent.DefaultExtent; +import org.hibernate.SessionFactory; +import org.opengis.metadata.citation.PresentationForm; +import org.opengis.metadata.identification.TopicCategory; +import org.opengis.metadata.spatial.GeometricObjectType; +import org.opengis.metadata.spatial.TopologyLevel; + +import scala.collection.Iterator; + +public class MapsCreator extends StandardLocalExternalAlgorithm { + + private static final String crs = "GEOGCS[\"WGS 84\", DATUM[\"World Geodetic System 1984\", SPHEROID[\"WGS 84\", 6378137.0, 298.257223563, AUTHORITY[\"EPSG\",\"7030\"]]," + "AUTHORITY[\"EPSG\",\"6326\"]], PRIMEM[\"Greenwich\", 0.0, AUTHORITY[\"EPSG\",\"8901\"]], UNIT[\"degree\", 0.017453292519943295]," + "AXIS[\"Geodetic longitude\", EAST], AXIS[\"Geodetic latitude\", NORTH], AUTHORITY[\"EPSG\",\"4326\"]]"; + + static String databaseParameterName = "FishBase"; + static String dbuserParameterName = "user"; + static String dbpasswordParameterName = "password"; + static String dburlParameterName = "FishBase"; + + static String inputTableParameter = "InputTable"; + static String outputTableParameter = "OutputTable"; + static String xParameter = "xDimension"; + static String yParameter = "yDimension"; + static String csquareParameter = "csquaresDimension"; + + static String probabilityParameter = "Probability"; + static String resolutionParameter = "Resolution"; + static String layerNameParameter = "MapName"; + static int maxNPoints = 19000; + SessionFactory gisdbconnection = null; + SessionFactory smdbconnection = null; + private static String createTable = "create table %1$s (geomid serial, x real, y real, probability real);"; + private static String columnsNames = " geomid, x , y, probability"; + private static String addGeometryColumn = "Select AddGeometryColumn('%1$s','the_geom',4326,'POLYGON',2);"; + + static String makeSquare = "ST_SetSRID(ST_MakePolygon(ST_GeomFromText('LINESTRING(%1$s ,%2$s, %3$s, %4$s, %1$s)')),4326)"; + + @Override + public String getDescription() { + return "A transducer algorithm to produce a GIS map either from a probability distribution or from a set of points. A maximum of " + maxNPoints + " is allowed"; + } + + @Override + public void init() throws Exception { + log("MAPS_CREATOR"); + + } + + @Override + protected void process() throws Exception { + + try { + log("Beginning process"); + String databaseJdbc = getInputParameter(dburlParameterName); + + String databaseUser = getInputParameter(dbuserParameterName); + String databasePwd = getInputParameter(dbpasswordParameterName); + + log("GIS Database Parameters to use: " + databaseJdbc + " , " + databaseUser); + + double resolution = Double.parseDouble(config.getParam(resolutionParameter)); + log("Resolution:" + resolution); + log("Connecting to gisDB..."); + AlgorithmConfiguration gisconfig = new AlgorithmConfiguration(); + gisconfig.setParam("DatabaseDriver", "org.postgresql.Driver"); + gisconfig.setParam("DatabaseURL", "jdbc:postgresql://geoserver-test.d4science-ii.research-infrastructures.eu/timeseriesgisdb"); + gisconfig.setParam("DatabaseUserName", databaseUser); + gisconfig.setParam("DatabasePassword", databasePwd); + gisconfig.setConfigPath(config.getConfigPath()); + + gisdbconnection = DatabaseUtils.initDBSession(gisconfig); + // connect to the GIS DB + log("Initialized gisDBConnection!"); + + // connect to the SM DB + smdbconnection = DatabaseUtils.initDBSession(config); + log("Initialized SMDBConnection!"); + // points retrieval + List points = null; + log("Retrieving points.."); + if (config.getParam(xParameter) != null && config.getParam(yParameter) != null) { + log("..from coordinates"); + // select the points from the SM DB up to a maximum of 190000 points + points = DatabaseFactory.executeSQLQuery("select " + config.getParam(xParameter) + "," + config.getParam(yParameter) + "," + config.getParam(probabilityParameter) + " from " + config.getParam(inputTableParameter) + " limit " + maxNPoints, smdbconnection); + } + else if (config.getParam(csquareParameter)!=null){ + log("..from csquares"); + List csquares= DatabaseFactory.executeSQLQuery("select " + config.getParam(csquareParameter) +" from " + config.getParam(inputTableParameter) + " limit " + maxNPoints, smdbconnection); + points = new ArrayList(); + //build points from csquares + for (Object csquare:csquares){ + CSquare c = it.cnr.aquamaps.CSquare.apply(""+csquare); + // x,y + Iterator iterator = c.center().valuesIterator(); + double x = Double.parseDouble(""+iterator.next()); + double y = Double.parseDouble(""+iterator.next()); + Object[] pair = {x,y}; + points.add(pair); + } + log("Points built from csquares!"); + } + + log("Creating GIS table"); + String gisTableName = "stat" + UUID.randomUUID().toString().replace("-", ""); + // create a table on the gis db + String createTable$ = String.format(createTable, gisTableName); + log(createTable$); + try { + DatabaseFactory.executeSQLUpdate(DatabaseUtils.dropTableStatement(gisTableName), gisdbconnection); + } catch (Exception e) { + log("Impossible to drop table:" + e.getLocalizedMessage()); + } + DatabaseFactory.executeSQLUpdate(String.format(createTable, gisTableName), gisdbconnection); + DatabaseFactory.executeSQLQuery(String.format(addGeometryColumn, gisTableName), gisdbconnection); + log("Fulfilling elements"); + List values = new ArrayList(); + int i = 0; + List squares = new ArrayList(); + for (Object point : points) { + Object[] elements = (Object[]) point; + double x = Double.parseDouble("" + elements[0]); + double y = Double.parseDouble("" + elements[1]); + String probS = "" + elements[2]; + double x1 = Math.max(-180, x - resolution); + double x2 = Math.min(180, x + resolution); + double y1 = Math.max(-90, y - resolution); + double y2 = Math.max(180, y + resolution); + String square = String.format(makeSquare, "" + x1 + " " + y1, x1 + " " + y2, x2 + " " + y2, x2 + " " + y1); + Object[] pair = new Object[2]; + pair[0] = "" + i; + pair[1] = square; + squares.add(pair); + // insert into stat34cbc4ce921a410fbf4bac0d9c21fcf5 ( x , y, probability, the_geom) values ('0.25','0.25','34.0', ST_SetSRID(ST_MakePolygon(ST_GeomFromText('LINESTRING(-0.25 -0.25 ,-0.25 180.0, 0.75 180.0, 0.75 -0.25, -0.25 -0.25)')),4326)) + String[] selements = { "" + i, "" + x, "" + y, probS }; + values.add(selements); + i++; + } + + log("Writing chunks"); + // write chunks into the DB + DatabaseUtils.insertChunksIntoTable(gisTableName, columnsNames, values, 5000, gisdbconnection); + log("Writing Geometries"); + DatabaseFactory.executeSQLUpdate(DatabaseUtils.insertIntoColumn(gisTableName, "geomid", "the_geom", squares), gisdbconnection); + log("Publishing Table"); + String username = config.getParam("ServiceUserName"); + if (username == null) + username = "statistical.manager"; + + String layerName = config.getParam(layerNameParameter); + PublishResponse response = publishTable(config.getGcubeScope(), gisTableName, resolution, username, layerName); + if (response == null) { + log("Error in generating map - dropping gis table"); + try { + DatabaseFactory.executeSQLUpdate(DatabaseUtils.dropTableStatement(gisTableName), gisdbconnection); + log("gis table dropped"); + } catch (Exception e) { + log("Impossible to drop table:" + e.getLocalizedMessage()); + } + throw new Exception("Impossible to publish on GeoNetwork or GeoServer: " + gisTableName); + } else { + addOutputString("GIS map title", layerName); + addOutputString("GIS map UUID", "" + response.getPublishedMetadata().getFileIdentifier()); + addOutputString("Associated Geospatial Table", gisTableName); + addOutputString("Generated by ", username); + addOutputString("Resolution", "" + resolution); + } + log("All Done!"); + } catch (Exception e) { + e.printStackTrace(); + throw e; + } finally { + if (smdbconnection != null) + DatabaseUtils.closeDBConnection(smdbconnection); + if (gisdbconnection != null) + DatabaseUtils.closeDBConnection(gisdbconnection); + } + + } + + public PublishResponse publishTable(String scope, String tableName, double resolution, String username, String layerName) throws Exception { + String datastore = "timeseriesws"; + String defaultStyle = "Species_prob"; + String workspace = "aquamaps"; + + GSFeatureTypeEncoder fte = new GSFeatureTypeEncoder(); + fte.setEnabled(true); + fte.setLatLonBoundingBox(-180.0, -90.0, 180.0, 90.0, crs); + fte.setName(tableName); + fte.setNativeCRS(crs); + GSLayerEncoder le = new GSLayerEncoder(); + le.setDefaultStyle(defaultStyle); + le.setEnabled(true); + GcubeISOMetadata meta = fillMeta(resolution, username, layerName, scope); + GISInterface gis = GISInterface.get(); + Configuration gnConfig = gis.getGeoNetworkReader().getConfiguration(); + log("Using the following GNetwork:" + gnConfig.getGeoNetworkEndpoint()); + PublishResponse resp = gis.publishDBTable(workspace, datastore, fte, le, meta.getMetadata(), new GNInsertConfiguration(gnConfig.getScopeGroup() + "", "datasets", "_none_", true), LoginLevel.DEFAULT); + log(resp); + log("ID:" + resp.getReturnedMetaId()); + log("Result:" + resp.getMetaOperationResult()); + if (resp.getReturnedMetaId()==0) + return null; + else + return resp; + } + + private GcubeISOMetadata fillMeta(double resolution, String username, String title, String scope) throws Exception { + + if (scope == null) + scope = ScopeProvider.instance.get(); + + ScopeProvider.instance.set(scope); + + GcubeISOMetadata meta = new GcubeISOMetadata(); + meta.setAbstractField("This metadata is just a test"); + meta.setCreationDate(new Date(System.currentTimeMillis())); + meta.setExtent((DefaultExtent) DefaultExtent.WORLD); + meta.setGeometricObjectType(GeometricObjectType.SURFACE); + meta.setPresentationForm(PresentationForm.MAP_DIGITAL); + meta.setPurpose("Publish Geometric Layer"); + meta.setResolution(resolution); + if (title == null || title.length() == 0) + meta.setTitle("Probability Distribution"); + else + meta.setTitle(title); + + meta.setTopologyLevel(TopologyLevel.GEOMETRY_ONLY); + meta.setUser(username); + + meta.addCredits("Generated via the Statistical Manager Service"); + meta.addGraphicOverview("http://www.d4science.org/D4ScienceOrg-Social-theme/images/custom/D4ScienceInfrastructure.png"); + + Thesaurus generalThesaurus = meta.getConfig().getThesauri().get("General"); + meta.addKeyword(title, generalThesaurus); + meta.addKeyword(username, generalThesaurus); + meta.addKeyword("StatisticalManager", generalThesaurus); + meta.addKeyword("Probability Distribution", generalThesaurus); + + meta.addTopicCategory(TopicCategory.BIOTA); + return meta; + } + + public static void main(String[] args) throws Exception { + AlgorithmConfiguration config = new AlgorithmConfiguration(); + config.setConfigPath("./cfg/"); + config.setPersistencePath("./cfg/"); + config.setGcubeScope("/gcube"); + config.setParam("DatabaseUserName", "utente"); + config.setParam("DatabasePassword", "d4science"); + config.setParam("DatabaseURL", "jdbc:postgresql://statistical-manager.d.d4science.research-infrastructures.eu/testdb"); + + config.setParam(dburlParameterName, "jdbc:postgresql://geoserver-test.d4science-ii.research-infrastructures.eu/timeseriesgisdb"); + // jdbc:postgresql://statistical-manager.d.d4science.research-infrastructures.eu/testdb, DatabasePassword=d4science, DatabaseUserName=utente, password=d4science2 + // config.setParam(dburlParameterName,"jdbc:postgresql://146.48.122.125/timeseriesgisdb"); + config.setParam(dbuserParameterName, "postgres"); + config.setParam(dbpasswordParameterName, "d4science2"); + + config.setParam(inputTableParameter, "occcluster_id_59005678_4863_49ba_9c66_ebac80829da3"); + config.setParam(xParameter, "centerlong"); + config.setParam(yParameter, "centerlat"); + config.setParam(probabilityParameter, "faoaream"); + config.setParam(resolutionParameter, "0.5"); + config.setParam("ServiceUserName", "gianpaolo.coro"); + config.setParam(layerNameParameter, "Generic Species"); + + MapsCreator maps = new MapsCreator(); + maps.setConfiguration(config); + maps.compute(); + + } + + @Override + public void shutdown() { + + } + + @Override + protected void setInputParameters() { + try { + List templates = new ArrayList(); + addRemoteDatabaseInput(databaseParameterName, dburlParameterName, dbuserParameterName, dbpasswordParameterName, "driver", "dialect"); + templates.add(TableTemplates.GENERIC); + addStringInput(layerNameParameter, "The name of the layer to produce", "Statistical Prob. Distribution"); + InputTable tinput = new InputTable(templates, inputTableParameter, "The table information to geo-spatialize"); + ColumnType xColumn = new ColumnType(inputTableParameter, xParameter, "The column containing longitude information", "", false); + ColumnType yColumn = new ColumnType(inputTableParameter, yParameter, "The column containing latitude information", "", false); + ColumnType probabilityDimension = new ColumnType(inputTableParameter, probabilityParameter, "The column containing probability information", "", false); + + inputs.add(tinput); + inputs.add(xColumn); + inputs.add(yColumn); + inputs.add(probabilityDimension); + addDoubleInput(resolutionParameter, "The map resolution in degrees", "0.5"); + DatabaseType.addDefaultDBPars(inputs); + + } catch (Throwable e) { + e.printStackTrace(); + } + + } + + @Override + public StatisticalType getOutput() { + + return null; + } + +}