diff --git a/.classpath b/.classpath index 8fe0193..9d2171e 100644 --- a/.classpath +++ b/.classpath @@ -1,8 +1,10 @@ - - - - - - - - + + + + + + + + + + diff --git a/pom.xml b/pom.xml index c3f8cb3..0bc8a42 100644 --- a/pom.xml +++ b/pom.xml @@ -130,6 +130,18 @@ maxent-princeton 3.3.3 + + ch.qos.logback + logback-classic + 1.0.13 + test + + + junit + junit + 4.11 + test + @@ -161,15 +173,6 @@ - - - maven-compiler-plugin - 3.1 - - 1.6 - 1.6 - - org.apache.maven.plugins maven-surefire-plugin @@ -184,7 +187,6 @@ org.apache.maven.plugins maven-assembly-plugin - 2.2 ${distroDirectory}/descriptor.xml diff --git a/src/main/java/org/gcube/dataanalysis/geo/algorithms/PointsMapsCreator.java b/src/main/java/org/gcube/dataanalysis/geo/algorithms/PointsMapsCreator.java index 0abe039..0b72a23 100644 --- a/src/main/java/org/gcube/dataanalysis/geo/algorithms/PointsMapsCreator.java +++ b/src/main/java/org/gcube/dataanalysis/geo/algorithms/PointsMapsCreator.java @@ -3,7 +3,6 @@ package org.gcube.dataanalysis.geo.algorithms; import java.util.ArrayList; import java.util.List; -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; @@ -58,30 +57,4 @@ public class PointsMapsCreator extends MapsCreator { } - public static void main(String[] args) throws Exception { - AlgorithmConfiguration config = new AlgorithmConfiguration(); - config.setConfigPath("./cfg/"); - config.setPersistencePath("./cfg/"); - config.setGcubeScope("/gcube/devsec"); - 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"); - config.setParam(dbuserParameterName, "postgres"); - config.setParam(dbpasswordParameterName, "d4science2"); - - config.setParam(inputTableParameter, "occurrence_species_id_fb60ce42_1704_43f9_91a3_2df7d82b1b96"); - config.setParam(xParameter, "decimallongitude"); - config.setParam(yParameter, "decimallatitude"); - config.setParam(infoParameter, "scientificname"); - config.setParam("ServiceUserName", "gianpaolo.coro"); - config.setParam(layerNameParameter, "Generic Species"); - - MapsCreator maps = new PointsMapsCreator(); - maps.setConfiguration(config); - maps.init(); - maps.compute(); - - } } diff --git a/src/main/java/org/gcube/dataanalysis/geo/algorithms/RasterDataPublisher.java b/src/main/java/org/gcube/dataanalysis/geo/algorithms/RasterDataPublisher.java index ed59141..9c40271 100644 --- a/src/main/java/org/gcube/dataanalysis/geo/algorithms/RasterDataPublisher.java +++ b/src/main/java/org/gcube/dataanalysis/geo/algorithms/RasterDataPublisher.java @@ -12,7 +12,6 @@ import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveTypesList; import org.gcube.dataanalysis.ecoengine.datatypes.ServiceType; import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.PrimitiveTypes; import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.ServiceParameters; -import org.gcube.dataanalysis.ecoengine.evaluation.bioclimate.InterpolateTables; import org.gcube.dataanalysis.ecoengine.interfaces.StandardLocalInfraAlgorithm; import org.gcube.dataanalysis.executor.scripts.OSCommand; import org.gcube.dataanalysis.geo.utils.GeospatialDataPublicationLevel; @@ -103,7 +102,7 @@ public class RasterDataPublisher extends StandardLocalInfraAlgorithm{ String [] topicsListArr = new String[listTopics.size()]; topics = listTopics.toArray(topicsListArr); - boolean result = ThreddsPublisher.publishOnThredds(scope, username, newf.getAbsolutePath(), layerTitle, layerName, abstractField, topics, resolution,isprivate); + boolean result = ThreddsPublisher.publishOnThredds(username, newf.getAbsolutePath(), layerTitle, layerName, abstractField, topics, resolution,isprivate); if (result) { addOutputString("Created map name", layerTitle); diff --git a/src/main/java/org/gcube/dataanalysis/geo/connectors/netcdf/NetCDFDataExplorer.java b/src/main/java/org/gcube/dataanalysis/geo/connectors/netcdf/NetCDFDataExplorer.java index c9a2fe7..ef21deb 100644 --- a/src/main/java/org/gcube/dataanalysis/geo/connectors/netcdf/NetCDFDataExplorer.java +++ b/src/main/java/org/gcube/dataanalysis/geo/connectors/netcdf/NetCDFDataExplorer.java @@ -6,9 +6,10 @@ import java.util.LinkedHashMap; import java.util.List; import org.gcube.contentmanagement.graphtools.utils.MathFunctions; -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; import org.gcube.dataanalysis.ecoengine.utils.Tuple; import org.gcube.dataanalysis.geo.utils.VectorOperations; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; import ucar.ma2.Array; import ucar.ma2.ArrayByte; @@ -40,7 +41,9 @@ public class NetCDFDataExplorer { // http://thredds.research-infrastructures.eu:8080/thredds/catalog/public/netcdf/catalog.xml public static String timePrefix = "time:"; - + + private static final Logger LOGGER = LoggerFactory.getLogger(NetCDFDataExplorer.class); + public NetCDFDataExplorer(String openDapLink, String layer) { calcZRange(openDapLink, layer); } @@ -49,19 +52,17 @@ public class NetCDFDataExplorer { try { List values = new ArrayList(); if (isGridDataset(openDapLink)) { - AnalysisLogger.getLogger().debug("Managing Grid File"); + LOGGER.debug("Managing Grid File"); return manageGridDataset(layer, openDapLink, time, triplets); } /* - * else if (isPointDataset(openDapLink)) { AnalysisLogger.getLogger().debug("Managing Points File"); } + * else if (isPointDataset(openDapLink)) { LOGGER.debug("Managing Points File"); } */ else - AnalysisLogger.getLogger().debug("Warning: the NETCDF file is of an unknown type"); + LOGGER.debug("Warning: the NETCDF file is of an unknown type"); return values; } catch (Exception e) { - AnalysisLogger.getLogger().debug("ERROR: " + e.getMessage()); - AnalysisLogger.getLogger().debug(e); - // e.printStackTrace(); + LOGGER.error("ERROR",e); return null; } } @@ -76,8 +77,8 @@ public class NetCDFDataExplorer { List gridTypes = gds.getGrids(); for (GridDatatype gdt : gridTypes) { - // AnalysisLogger.getLogger().debug("Inside File - layer name: " + gdt.getFullName()); - AnalysisLogger.getLogger().debug("Inside File - layer name: " + gdt.getName()); + // LOGGER.debug("Inside File - layer name: " + gdt.getFullName()); + LOGGER.debug("Inside File - layer name: " + gdt.getName()); if (layer.equalsIgnoreCase(gdt.getName())) { CoordinateAxis zAxis = gdt.getCoordinateSystem().getVerticalAxis(); minZ = zAxis.getMinValue(); @@ -87,9 +88,8 @@ public class NetCDFDataExplorer { } } } catch (Exception e) { - e.printStackTrace(); - AnalysisLogger.getLogger().debug("NetCDF Explorer Error:" + e.getLocalizedMessage()); - AnalysisLogger.getLogger().debug(e); + LOGGER.error("NetCDF Explorer Error",e); + } } @@ -103,10 +103,10 @@ public class NetCDFDataExplorer { List gridTypes = gds.getGrids(); for (GridDatatype gdt : gridTypes) { - AnalysisLogger.getLogger().debug("Inside File - layer name: " + gdt.getName() + " layer to find " + layer); + LOGGER.debug("Inside File - layer name: " + gdt.getName() + " layer to find " + layer); // if the layer is an HTTP link then take the first innser layer if (layer.equalsIgnoreCase(gdt.getName()) || layer.toLowerCase().startsWith("http:")) { - AnalysisLogger.getLogger().debug("Found layer " + layer + " inside file"); + LOGGER.debug("Found layer " + layer + " inside file"); GridDatatype grid = gds.findGridDatatype(gdt.getName()); CoordinateAxis zAxis = gdt.getCoordinateSystem().getVerticalAxis(); CoordinateAxis xAxis = gdt.getCoordinateSystem().getXHorizAxis(); @@ -114,7 +114,7 @@ public class NetCDFDataExplorer { double resolutionZ = 0; try { resolutionZ = Math.abs((double) (zAxis.getMaxValue() - zAxis.getMinValue()) / (double) zAxis.getShape()[0]); - AnalysisLogger.getLogger().debug("Zmin:" + zAxis.getMinValue() + " Zmax:" + zAxis.getMaxValue()); + LOGGER.debug("Zmin:" + zAxis.getMinValue() + " Zmax:" + zAxis.getMaxValue()); } catch (Exception e) { } @@ -122,7 +122,7 @@ public class NetCDFDataExplorer { int tsize = triplets.size(); long t01 = System.currentTimeMillis(); LatLonRect llr = null; - AnalysisLogger.getLogger().debug("Extracting subset..."); + LOGGER.debug("Extracting subset..."); GridDatatype gdtsub = grid.makeSubset(new Range(time, time), null, llr, 1, 1, 1); Array data = gdtsub.readVolumeData(time); // note order is t, z, y, x int[] shapeD = data.getShape(); @@ -145,11 +145,11 @@ public class NetCDFDataExplorer { double resolutionX = Math.abs((double) (xAxis.getMaxValue() - xAxis.getMinValue()) / (double) xD); double resolutionY = Math.abs((double) (yAxis.getMaxValue() - yAxis.getMinValue()) / (double) yD); - AnalysisLogger.getLogger().debug("Shape: Z:" + zD + " X:" + xD + " Y:" + yD); + LOGGER.debug("Shape: Z:" + zD + " X:" + xD + " Y:" + yD); - AnalysisLogger.getLogger().debug("Layer Information Retrieval ELAPSED Time: " + (System.currentTimeMillis() - t01)); + LOGGER.debug("Layer Information Retrieval ELAPSED Time: " + (System.currentTimeMillis() - t01)); int rank = data.getRank(); - AnalysisLogger.getLogger().debug("Rank of the layer: " + rank); + LOGGER.debug("Rank of the layer: " + rank); ArrayFloat.D3 data3Float = null; ArrayDouble.D3 data3Double = null; @@ -201,15 +201,15 @@ public class NetCDFDataExplorer { // if (((xmax == 360) && (xmin == 0)) || ((xmax == 359.5) && (xmin == 0.5))) { // if ((xmin>=0) || (ymin == -77.0104751586914 && ymax==89.94786834716797)) { - AnalysisLogger.getLogger().debug("X dimension: " + xD + " Xmin:" + xmin + " Xmax:" + xmax + " Xmaxidx:" + xmaxidx+" XRes: "+resolutionX); - AnalysisLogger.getLogger().debug("Y dimension: " + yD + " Ymin:" + ymin + " Ymax:" + ymax + " Ymaxidx:" + ymaxidx+" YRes: "+resolutionY); + LOGGER.debug("X dimension: " + xD + " Xmin:" + xmin + " Xmax:" + xmax + " Xmaxidx:" + xmaxidx+" XRes: "+resolutionX); + LOGGER.debug("Y dimension: " + yD + " Ymin:" + ymin + " Ymax:" + ymax + " Ymaxidx:" + ymaxidx+" YRes: "+resolutionY); if ((xmin >= 0)) { xmax = 180; xmin = -180; is0_360 = true; } - AnalysisLogger.getLogger().debug("Assigning "+tsize+" grid elements to the NetCDF values"); + LOGGER.debug("Assigning "+tsize+" grid elements to the NetCDF values"); for (int i = 0; i < tsize; i++) { int zint = 0; int xint = 0; @@ -250,9 +250,9 @@ public class NetCDFDataExplorer { x = x - inverseOrigin.getLongitude(); y = y - inverseOrigin.getLatitude(); if (i==0) - AnalysisLogger.getLogger().debug("bb: " + idxbb[0] +","+idxbb[1]+" origin: "+idxo[0]+","+idxo[1]+" middle "+xD/2+","+yD/2+" shift "+(idxo[0]-(xD/2))+" inverse shift on origin "+inverseOrigin); + LOGGER.debug("bb: " + idxbb[0] +","+idxbb[1]+" origin: "+idxo[0]+","+idxo[1]+" middle "+xD/2+","+yD/2+" shift "+(idxo[0]-(xD/2))+" inverse shift on origin "+inverseOrigin); }catch(Exception e){ - AnalysisLogger.getLogger().debug("Error getting x,y corrections "+e.getLocalizedMessage()); + LOGGER.debug("Error getting x,y corrections "+e.getLocalizedMessage()); e.printStackTrace(); } @@ -304,7 +304,7 @@ public class NetCDFDataExplorer { else if (data2Long != null) val = Double.valueOf(data2Long.get(yint, xint)); - /*AnalysisLogger.getLogger().debug("Choice "+ (data3Float!=null)+","+ + /*LOGGER.debug("Choice "+ (data3Float!=null)+","+ (data3Int!=null)+","+ (data3Double!=null)+","+ (data3Long!=null)+","+ @@ -313,9 +313,9 @@ public class NetCDFDataExplorer { (data2Double!=null)+","+ (data2Long!=null)); */ -// AnalysisLogger.getLogger().debug("Assigning "+val+" to "+x+","+y+" ["+xint+","+yint+"]"); -// AnalysisLogger.getLogger().debug("checking "+data2Float.get(yint, xint)+" vs "); -// try{AnalysisLogger.getLogger().debug("checking2 "+data2Float.get(xint,yint));}catch(Exception e){} +// LOGGER.debug("Assigning "+val+" to "+x+","+y+" ["+xint+","+yint+"]"); +// LOGGER.debug("checking "+data2Float.get(yint, xint)+" vs "); +// try{LOGGER.debug("checking2 "+data2Float.get(xint,yint));}catch(Exception e){} values.add(val); @@ -334,16 +334,16 @@ public class NetCDFDataExplorer { } public static GridDatatype getGrid(String layer, String netcdffile) throws Exception{ - AnalysisLogger.getLogger().debug("Opening File : " + netcdffile); - AnalysisLogger.getLogger().debug("Searching for layer: " + layer); + LOGGER.debug("Opening File : " + netcdffile); + LOGGER.debug("Searching for layer: " + layer); GridDataset gds = ucar.nc2.dt.grid.GridDataset.open(netcdffile); List gridTypes = gds.getGrids(); StringBuffer sb = new StringBuffer(); for (GridDatatype gdt : gridTypes) { - AnalysisLogger.getLogger().debug("Inside File - layer name: " + gdt.getName()); + LOGGER.debug("Inside File - layer name: " + gdt.getName()); sb.append(gdt.getName()+" "); if (layer.equals(gdt.getName())) { - AnalysisLogger.getLogger().debug("Found layer " + layer + " inside file"); + LOGGER.debug("Found layer " + layer + " inside file"); GridDatatype grid = gds.findGridDatatype(gdt.getName()); return grid; } @@ -358,9 +358,9 @@ public class NetCDFDataExplorer { GridDataset gds = ucar.nc2.dt.grid.GridDataset.open(filename); List gridTypes = gds.getGrids(); for (GridDatatype gdt : gridTypes) { - AnalysisLogger.getLogger().debug("Inside File - layer name: " + gdt.getName()); + LOGGER.debug("Inside File - layer name: " + gdt.getName()); if (layer.equalsIgnoreCase(gdt.getName())) { - AnalysisLogger.getLogger().debug("Found layer " + layer + " inside file"); + LOGGER.debug("Found layer " + layer + " inside file"); GridDatatype grid = gds.findGridDatatype(gdt.getName()); GridCoordSystem gcs = grid.getCoordinateSystem(); long timeSteps = 0; @@ -382,7 +382,7 @@ public class NetCDFDataExplorer { zint = Math.abs((int) Math.round((z - zAxis.getMinValue()) / resolutionZ)); } - AnalysisLogger.getLogger().debug("Z index to take: " + zint); + LOGGER.debug("Z index to take: " + zint); int[] xy = gcs.findXYindexFromLatLon(x, y, null); for (int j = 0; j < timeSteps; j++) { @@ -396,7 +396,7 @@ public class NetCDFDataExplorer { valuesMap.put(timePrefix + date, Double.parseDouble("" + val)); } } catch (Exception e) { - AnalysisLogger.getLogger().debug("Error in getting grid values in (" + x + "," + y + "," + z + "= with zint: " + zint + " resolution: " + resolutionZ + " and shape: " + zAxis.getShape()[0]); + LOGGER.debug("Error in getting grid values in (" + x + "," + y + "," + z + "= with zint: " + zint + " resolution: " + resolutionZ + " and shape: " + zAxis.getShape()[0]); } } break; @@ -417,7 +417,7 @@ public class NetCDFDataExplorer { } } } catch (Exception ee) { - AnalysisLogger.getLogger().debug("NetCDFDataExplorer-> WARNING: Error in getting value: " + ee.getLocalizedMessage()); + LOGGER.debug("NetCDFDataExplorer-> WARNING: Error in getting value: " + ee.getLocalizedMessage()); } return val; } @@ -444,33 +444,33 @@ public class NetCDFDataExplorer { else break; tolerance = tolerance + 0.25f; - AnalysisLogger.getLogger().debug("NetCDFDataExplorer-> -> tolerance = " + tolerance); + LOGGER.debug("NetCDFDataExplorer-> -> tolerance = " + tolerance); } if (iter != null) { try { while (iter.hasNext()) { ucar.nc2.ft.PointFeature pf = iter.next(); - AnalysisLogger.getLogger().debug("NetCDFDataExplorer-> -> EarthLoc: " + pf.getLocation()); - AnalysisLogger.getLogger().debug("NetCDFDataExplorer-> -> EarthTime: " + pf.getObservationTime()); + LOGGER.debug("NetCDFDataExplorer-> -> EarthLoc: " + pf.getLocation()); + LOGGER.debug("NetCDFDataExplorer-> -> EarthTime: " + pf.getObservationTime()); StructureData sd = pf.getData(); List mems = sd.getMembers(); for (Member m : mems) { String unit = m.getUnitsString(); if ((unit != null) && (unit.length() > 0)) { - AnalysisLogger.getLogger().debug("NetCDFDataExplorer-> -> description: " + m.getDescription()); - AnalysisLogger.getLogger().debug("NetCDFDataExplorer-> -> data param: " + m.getDataParam()); - AnalysisLogger.getLogger().debug("NetCDFDataExplorer-> -> name: " + m.getName()); - AnalysisLogger.getLogger().debug("NetCDFDataExplorer-> -> unit: " + m.getUnitsString()); - AnalysisLogger.getLogger().debug("NetCDFDataExplorer-> -> type: " + m.getDataType()); + LOGGER.debug("NetCDFDataExplorer-> -> description: " + m.getDescription()); + LOGGER.debug("NetCDFDataExplorer-> -> data param: " + m.getDataParam()); + LOGGER.debug("NetCDFDataExplorer-> -> name: " + m.getName()); + LOGGER.debug("NetCDFDataExplorer-> -> unit: " + m.getUnitsString()); + LOGGER.debug("NetCDFDataExplorer-> -> type: " + m.getDataType()); Array arr = sd.getArray(m.getName()); - AnalysisLogger.getLogger().debug("NetCDFDataExplorer-> -> is Time: " + m.getDataType()); + LOGGER.debug("NetCDFDataExplorer-> -> is Time: " + m.getDataType()); Double val = takeFirstDouble(arr); - AnalysisLogger.getLogger().debug("NetCDFDataExplorer-> -> extracted value: " + val); + LOGGER.debug("NetCDFDataExplorer-> -> extracted value: " + val); } } - AnalysisLogger.getLogger().debug("NetCDFDataExplorer-> -> EarthTime: "); + LOGGER.debug("NetCDFDataExplorer-> -> EarthTime: "); } } finally { iter.finish(); @@ -484,12 +484,12 @@ public class NetCDFDataExplorer { // A GridDatatype is like a specialized Variable that explicitly handles X,Y,Z,T dimensions public static boolean isGridDataset(String filename) { try { - AnalysisLogger.getLogger().debug("Analyzing file " + filename); + LOGGER.debug("Analyzing file " + filename); Formatter errlog = new Formatter(); FeatureDataset fdataset = FeatureDatasetFactoryManager.open(FeatureType.GRID, filename, null, errlog); if (fdataset == null) { // System.out.printf("GRID Parse failed --> %s\n", errlog); - AnalysisLogger.getLogger().debug("NetCDFDataExplorer-> NOT GRID"); + LOGGER.debug("NetCDFDataExplorer-> NOT GRID"); return false; } else return true; @@ -505,7 +505,7 @@ public class NetCDFDataExplorer { Formatter errlog = new Formatter(); FeatureDataset fdataset = FeatureDatasetFactoryManager.open(FeatureType.POINT, filename, null, errlog); if (fdataset == null) { - AnalysisLogger.getLogger().debug("NetCDFDataExplorer-> NOT POINT"); + LOGGER.debug("NetCDFDataExplorer-> NOT POINT"); return false; } else return true; @@ -524,7 +524,7 @@ public class NetCDFDataExplorer { if (fdataset == null) { // System.out.printf(fts[i]+": Parse failed --> %s\n",errlog); } else { - AnalysisLogger.getLogger().debug("NetCDFDataExplorer-> " + fts[i] + " OK!"); + LOGGER.debug("NetCDFDataExplorer-> " + fts[i] + " OK!"); isdataset = true; } } diff --git a/src/main/java/org/gcube/dataanalysis/geo/meta/GenericLayerMetadata.java b/src/main/java/org/gcube/dataanalysis/geo/meta/GenericLayerMetadata.java index 123047f..df3badd 100644 --- a/src/main/java/org/gcube/dataanalysis/geo/meta/GenericLayerMetadata.java +++ b/src/main/java/org/gcube/dataanalysis/geo/meta/GenericLayerMetadata.java @@ -1,6 +1,5 @@ package org.gcube.dataanalysis.geo.meta; -import it.geosolutions.geonetwork.GNClient; import it.geosolutions.geonetwork.util.GNInsertConfiguration; import java.io.File; @@ -20,7 +19,6 @@ import java.util.UUID; import javax.xml.bind.JAXBException; -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; import org.gcube.spatial.data.geonetwork.GeoNetwork; import org.gcube.spatial.data.geonetwork.GeoNetworkAdministration; import org.gcube.spatial.data.geonetwork.LoginLevel; @@ -68,9 +66,13 @@ import org.opengis.metadata.spatial.GeometricObjectType; import org.opengis.metadata.spatial.SpatialRepresentationType; import org.opengis.metadata.spatial.TopologyLevel; import org.opengis.util.InternationalString; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; public class GenericLayerMetadata { + private static final Logger LOGGER = LoggerFactory.getLogger(GenericLayerMetadata.class); + private String geonetworkUrl = "http://geoserver-dev2.d4science-ii.research-infrastructures.eu/geonetwork/"; private String geoserverUrl = "http://geoserver-dev.d4science-ii.research-infrastructures.eu/geonetwork/"; private String geonetworkUser = "admin"; @@ -368,7 +370,7 @@ public class GenericLayerMetadata { ArrayList usages = new ArrayList(Arrays.asList(usage)); //build categories by guessing on the filename List categories = guessTopicCategory(categoryTypes); - AnalysisLogger.getLogger().debug("Guessed Topics: "+categories); + LOGGER.debug("Guessed Topics: "+categories); // Spatial Rapresentation Info DefaultGeometricObjects geoObjs = new DefaultGeometricObjects(); geoObjs.setGeometricObjectType(GeometricObjectType.COMPLEX); @@ -562,7 +564,7 @@ public class GenericLayerMetadata { ArrayList usages = new ArrayList(Arrays.asList(usage)); //build categories by guessing on the filename List categories = guessTopicCategory(categoryTypes); - AnalysisLogger.getLogger().debug("Guessed Topics: "+categories); + LOGGER.debug("Guessed Topics: "+categories); // Spatial Rapresentation Info DefaultGeometricObjects geoObjs = new DefaultGeometricObjects(); geoObjs.setGeometricObjectType(GeometricObjectType.COMPLEX); @@ -599,7 +601,7 @@ public class GenericLayerMetadata { String estdescription = getDescription(url); String estProtocol = getProtocol(url); String estName = getName(title, abstractField, estProtocol, url); - AnalysisLogger.getLogger().debug("URL:" + url + "\nDescription:" + estdescription + "\nName:" + estName + "\nProtocol:" + estProtocol); + LOGGER.debug("URL:" + url + "\nDescription:" + estdescription + "\nName:" + estName + "\nProtocol:" + estProtocol); onlineres.setDescription(new DefaultInternationalString(estdescription)); onlineres.setName(estName); onlineres.setProtocol(estProtocol); @@ -668,14 +670,15 @@ public class GenericLayerMetadata { // Metadata Obj: DefaultMetadata meta = new DefaultMetadata(party, sourceGenerationDate, ident); - meta.setFileIdentifier(UUID.randomUUID().toString()); + String id = UUID.randomUUID().toString(); + meta.setFileIdentifier(id); meta.getSpatialRepresentationInfo().add(spatial); meta.setDistributionInfo(distribution); meta.getMetadataConstraints().add(constraints); meta.getDataQualityInfo().add(processQuality); meta.setLanguage(Locale.ENGLISH); -// AnalysisLogger.getLogger().debug(meta); + LOGGER.debug("id of generated metadata is {}",id); GeoNetworkAdministration readerScope = GeoNetwork.get(); @@ -686,11 +689,15 @@ public class GenericLayerMetadata { GNInsertConfiguration configuration = readerScope.getCurrentUserConfiguration("datasets", "_none_"); + + if (isprivate) readerScope.insertMetadata(configuration, meta); else readerScope.insertAndPromoteMetadata(configuration, meta); + + //old command /* GNClient client = new GNClient(geonetworkUrl); @@ -783,7 +790,7 @@ public class GenericLayerMetadata { ArrayList usages = new ArrayList(Arrays.asList(usage)); //build categories by guessing on the filename List categories = guessTopicCategory(categoryTypes); - AnalysisLogger.getLogger().debug("Guessed Topics: "+categories); + LOGGER.debug("Guessed Topics: "+categories); // Spatial Rapresentation Info DefaultGeometricObjects geoObjs = new DefaultGeometricObjects(); geoObjs.setGeometricObjectType(GeometricObjectType.COMPLEX); @@ -930,7 +937,7 @@ public class GenericLayerMetadata { if (abstractTitle.matches(".+: ")) { String variablename = title.substring(title.indexOf(":")); - AnalysisLogger.getLogger().debug("detected variable " + variablename); + LOGGER.debug("detected variable " + variablename); return variablename; } else { if (url.contains("catalog.xml")) { @@ -967,7 +974,7 @@ public class GenericLayerMetadata { int column = -1; if ((column = layerName.indexOf(":")) > 0) layerName = layerName.substring(column + 1); - AnalysisLogger.getLogger().debug("Layer Name: " + layerName); + LOGGER.debug("Layer Name: " + layerName); return layerName; } else return title; diff --git a/src/main/java/org/gcube/dataanalysis/geo/test/infra/RetrieveOGCLinks.java b/src/main/java/org/gcube/dataanalysis/geo/test/infra/RetrieveOGCLinks.java deleted file mode 100644 index 21e9581..0000000 --- a/src/main/java/org/gcube/dataanalysis/geo/test/infra/RetrieveOGCLinks.java +++ /dev/null @@ -1,87 +0,0 @@ -package org.gcube.dataanalysis.geo.test.infra; - -import java.io.BufferedReader; -import java.io.BufferedWriter; -import java.io.File; -import java.io.FileReader; -import java.io.FileWriter; -import java.util.List; - -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; -import org.gcube.dataanalysis.geo.infrastructure.GeoNetworkInspector; -import org.gcube.dataanalysis.geo.matrixmodel.MatrixExtractor; -import org.opengis.metadata.Metadata; - -public class RetrieveOGCLinks { - - static String scope = "/d4science.research-infrastructures.eu/gCubeApps/BiodiversityLab"; - - public static void main(String[] args) throws Exception{ - AlgorithmConfiguration config = new AlgorithmConfiguration(); - AnalysisLogger.setLogger("./cfg/ALog.properties"); - 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"); - - MatrixExtractor extractor = new MatrixExtractor(config); - extractor.getConnector("http://geoserver.d4science-ii.research-infrastructures.eu/geoserver/ows?service=WFS&version=1.0.0&request=GetFeature&typeName=lluidiamaculata20121218223748535cet&format=json&maxfeatures=1", 0.5); - - } - - public static void main1(String[] args) throws Exception{ - AnalysisLogger.setLogger("./cfg/ALog.properties"); - GeoNetworkInspector gnInspector = new GeoNetworkInspector(); - gnInspector.setScope(scope); - BufferedReader br = new BufferedReader(new FileReader(new File("AquamapsSpecies.txt"))); - String line = br.readLine(); - BufferedWriter bw = new BufferedWriter(new FileWriter(new File("AquamapsSpeciesLinks.csv"))); - - System.out.println("speciesname,WMS,WFS,algorithm,abstract"); - bw.write("speciesname,WMS,WFS,algorithm,abstract\n"); - while (line!=null){ - String speciesname = line; - - List metadts = gnInspector.getAllGNInfobyTitle(speciesname, "1"); - - for (Metadata meta:metadts){ - String abstractS = ""+meta.getIdentificationInfo().iterator().next().getAbstract(); - String WFS = gnInspector.getWFSLink(meta); - String WMS = gnInspector.getWFSLink(meta); - String algoritm = "OTHER"; - - if (abstractS.contains("AquaMaps NativeRange2050 algorithm")){ - algoritm = "NATIVE 2050"; - } - else if (abstractS.contains("AquaMaps SuitableRange algorithm")){ - algoritm = "SUITABLE"; - } - else if (abstractS.contains("AquaMaps SuitableRange2050 algorithm")){ - algoritm = "SUITABLE 2050"; - } - else if (abstractS.contains("AquaMaps NativeRange algorithm")){ - algoritm = "NATIVE"; - } - - String outstring = speciesname+",\""+WMS+"\",\""+WFS+"\","+algoritm+",\""+abstractS.replace("\"", "")+"\""; -// System.out.println(abstractS); - System.out.println(outstring); - bw.write(outstring+"\n"); - //System.out.println("WFS = "+gnInspector.getWFSLink(meta)); - //System.out.println("ABSTRACT = "+meta.getIdentificationInfo().iterator().next().getAbstract()); - - } - - line = br.readLine(); - } - - bw.close(); - br.close(); - } - - -} diff --git a/src/main/java/org/gcube/dataanalysis/geo/test/infra/TestESRIGRIDExtraction.java b/src/main/java/org/gcube/dataanalysis/geo/test/infra/TestESRIGRIDExtraction.java deleted file mode 100644 index f492d95..0000000 --- a/src/main/java/org/gcube/dataanalysis/geo/test/infra/TestESRIGRIDExtraction.java +++ /dev/null @@ -1,69 +0,0 @@ -package org.gcube.dataanalysis.geo.test.infra; - -import java.util.List; - -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; -import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType; -import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent; -import org.gcube.dataanalysis.ecoengine.processing.factories.TransducerersFactory; -import org.gcube.dataanalysis.ecoengine.test.regression.Regressor; -import org.gcube.dataanalysis.geo.connectors.table.TableMatrixRepresentation; - -public class TestESRIGRIDExtraction { - -// static AlgorithmConfiguration[] configs = { testXYExtractionNetCDF(),testXYExtractionAquaMaps(),testXYExtractionTable(),testXYExtractionTable2(),testDirectExtraction()}; -// static AlgorithmConfiguration[] configs = { testXYExtractionTable2()}; -// static AlgorithmConfiguration[] configs = { testDirectExtraction()}; -// static AlgorithmConfiguration[] configs = { testXYExtractionAquaMaps()}; -// static AlgorithmConfiguration[] configs = { testXYExtractionGeotermia()}; -// static AlgorithmConfiguration[] configs = { testXYExtractionFAO()}; - static AlgorithmConfiguration[] configs = { testXYExtractionNetCDF()}; - public static void main(String[] args) throws Exception { - - System.out.println("TEST 1"); - - for (int i = 0; i < configs.length; i++) { - AnalysisLogger.getLogger().debug("Executing: "+configs[i].getAgent()); - List trans = null; - trans = TransducerersFactory.getTransducerers(configs[i]); - trans.get(0).init(); - Regressor.process(trans.get(0)); - StatisticalType st = trans.get(0).getOutput(); - AnalysisLogger.getLogger().debug("ST:" + st); - trans = null; - } - } - - - - private static AlgorithmConfiguration testXYExtractionNetCDF() { - - AlgorithmConfiguration config = new AlgorithmConfiguration(); - - config.setAgent("ESRI_GRID_EXTRACTION"); - 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("/d4science.research-infrastructures.eu/gCubeApps/BiodiversityLab"); - config.setGcubeScope("/gcube/devsec/devVRE"); - - config.setParam("Layer","fc9ac2f4-a2bd-43d1-a361-ac67c5ceac31"); - config.setParam("Z","0"); - config.setParam("TimeIndex","0"); - config.setParam("BBox_LowerLeftLat","-60"); - config.setParam("BBox_LowerLeftLong","-50"); - config.setParam("BBox_UpperRightLat","60"); - config.setParam("BBox_UpperRightLong","50"); - config.setParam("XResolution","1"); - config.setParam("YResolution","1"); - - return config; - } - - - -} diff --git a/src/main/java/org/gcube/dataanalysis/geo/test/infra/TestEstimateFishingActivity.java b/src/main/java/org/gcube/dataanalysis/geo/test/infra/TestEstimateFishingActivity.java deleted file mode 100644 index 5b34329..0000000 --- a/src/main/java/org/gcube/dataanalysis/geo/test/infra/TestEstimateFishingActivity.java +++ /dev/null @@ -1,57 +0,0 @@ -package org.gcube.dataanalysis.geo.test.infra; - -import java.util.List; - -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; -import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType; -import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent; -import org.gcube.dataanalysis.ecoengine.processing.factories.TransducerersFactory; -import org.gcube.dataanalysis.ecoengine.test.regression.Regressor; -import org.gcube.dataanalysis.geo.connectors.table.TableMatrixRepresentation; - -public class TestEstimateFishingActivity { - - static AlgorithmConfiguration[] configs = { testGridConversion()}; - public static void main(String[] args) throws Exception { - - System.out.println("TEST 1"); - - for (int i = 0; i < configs.length; i++) { - AnalysisLogger.getLogger().debug("Executing: "+configs[i].getAgent()); - List trans = null; - trans = TransducerersFactory.getTransducerers(configs[i]); - trans.get(0).init(); - Regressor.process(trans.get(0)); - StatisticalType st = trans.get(0).getOutput(); - AnalysisLogger.getLogger().debug("ST:" + st); - trans = null; - } - } - - - private static AlgorithmConfiguration testGridConversion() { - - AlgorithmConfiguration config = new AlgorithmConfiguration(); - - config.setAgent("ESTIMATE_FISHING_ACTIVITY"); - config.setConfigPath("./cfg/"); - config.setPersistencePath("./"); - config.setParam("DatabaseUserName","utente"); - config.setParam("DatabasePassword","d4science"); - config.setParam("DatabaseURL","jdbc:postgresql://statistical-manager.d.d4science.org/testdb"); - config.setParam("DatabaseDriver","org.postgresql.Driver"); - config.setGcubeScope("/gcube/devsec/devVRE"); - - config.setParam("InputTable", "generic_idb7822ad1_f66c_444c_9c07_2698b824bab3"); - config.setParam("VesselsIDColumn", "vessel_id"); - config.setParam("VesselsSpeedsColumn", "speed"); - config.setParam("VesselsTimestampsColumn", "datetime"); - config.setParam("VesselsLatitudesColumn", "y"); - config.setParam("VesselsLongitudesColumn", "x"); - - return config; - } - - -} diff --git a/src/main/java/org/gcube/dataanalysis/geo/test/infra/TestEstimateMonthlyFishingEffort.java b/src/main/java/org/gcube/dataanalysis/geo/test/infra/TestEstimateMonthlyFishingEffort.java deleted file mode 100644 index fb7f9a2..0000000 --- a/src/main/java/org/gcube/dataanalysis/geo/test/infra/TestEstimateMonthlyFishingEffort.java +++ /dev/null @@ -1,58 +0,0 @@ -package org.gcube.dataanalysis.geo.test.infra; - -import java.util.List; - -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; -import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType; -import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent; -import org.gcube.dataanalysis.ecoengine.processing.factories.TransducerersFactory; -import org.gcube.dataanalysis.ecoengine.test.regression.Regressor; -import org.gcube.dataanalysis.geo.connectors.table.TableMatrixRepresentation; - -public class TestEstimateMonthlyFishingEffort { - - static AlgorithmConfiguration[] configs = { testGridConversion()}; - public static void main(String[] args) throws Exception { - - System.out.println("TEST 1"); - - for (int i = 0; i < configs.length; i++) { - AnalysisLogger.getLogger().debug("Executing: "+configs[i].getAgent()); - List trans = null; - trans = TransducerersFactory.getTransducerers(configs[i]); - trans.get(0).init(); - Regressor.process(trans.get(0)); - StatisticalType st = trans.get(0).getOutput(); - AnalysisLogger.getLogger().debug("ST:" + st); - trans = null; - } - } - - - private static AlgorithmConfiguration testGridConversion() { - - AlgorithmConfiguration config = new AlgorithmConfiguration(); - - config.setAgent("ESTIMATE_MONTHLY_FISHING_EFFORT"); - config.setConfigPath("./cfg/"); - config.setPersistencePath("./"); - config.setParam("DatabaseUserName","utente"); - config.setParam("DatabasePassword","d4science"); - config.setParam("DatabaseURL","jdbc:postgresql://statistical-manager.d.d4science.org/testdb"); - config.setParam("DatabaseDriver","org.postgresql.Driver"); - config.setGcubeScope("/gcube/devsec/devVRE"); - - config.setParam("InputTable", "code_0b7c500bfaca49f2a0ab4fd3c1647074"); - config.setParam("VesselsIDColumn", "vessel_id"); - config.setParam("VesselsTimestampsColumn", "datetime"); - config.setParam("VesselsLatitudesColumn", "y"); - config.setParam("VesselsLongitudesColumn", "x"); - config.setParam("VesselsActivityHoursColumn", "activity_hours"); - config.setParam("VesselsActivityClassificationColumn", "activity_class_speed"); - - return config; - } - - -} diff --git a/src/main/java/org/gcube/dataanalysis/geo/test/infra/TestExtraction.java b/src/main/java/org/gcube/dataanalysis/geo/test/infra/TestExtraction.java deleted file mode 100644 index 8fe0529..0000000 --- a/src/main/java/org/gcube/dataanalysis/geo/test/infra/TestExtraction.java +++ /dev/null @@ -1,249 +0,0 @@ -package org.gcube.dataanalysis.geo.test.infra; - -import java.util.List; - -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; -import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType; -import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent; -import org.gcube.dataanalysis.ecoengine.processing.factories.TransducerersFactory; -import org.gcube.dataanalysis.ecoengine.test.regression.Regressor; -import org.gcube.dataanalysis.geo.connectors.table.TableMatrixRepresentation; - -public class TestExtraction { - -// static AlgorithmConfiguration[] configs = { testXYExtractionNetCDF(),testXYExtractionAquaMaps(),testXYExtractionTable(),testXYExtractionTable2(),testDirectExtraction()}; -// static AlgorithmConfiguration[] configs = { testXYExtractionTable2()}; -// static AlgorithmConfiguration[] configs = { testDirectExtraction()}; -// static AlgorithmConfiguration[] configs = { testXYExtractionAquaMaps()}; -// static AlgorithmConfiguration[] configs = { testXYExtractionGeotermia()}; -// static AlgorithmConfiguration[] configs = { testXYExtractionFAO()}; - static AlgorithmConfiguration[] configs = { testXYExtractionNetCDF()}; - public static void main(String[] args) throws Exception { - - System.out.println("TEST 1"); - - for (int i = 0; i < configs.length; i++) { - AnalysisLogger.getLogger().debug("Executing: "+configs[i].getAgent()); - List trans = null; - trans = TransducerersFactory.getTransducerers(configs[i]); - trans.get(0).init(); - Regressor.process(trans.get(0)); - StatisticalType st = trans.get(0).getOutput(); - AnalysisLogger.getLogger().debug("ST:" + st); - trans = null; - } - } - - private static AlgorithmConfiguration testXYExtractionProd() { - - AlgorithmConfiguration config = new AlgorithmConfiguration(); - - config.setAgent("XYEXTRACTOR"); - 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("/d4science.research-infrastructures.eu/gCubeApps/BiodiversityLab"); - - config.setParam("Layer","0aac424b-5f5b-4fa6-97d6-4b4deee62b97"); - config.setParam("Z","0"); - config.setParam("TimeIndex","0"); - config.setParam("BBox_LowerLeftLat","-60"); - config.setParam("BBox_LowerLeftLong","-50"); - config.setParam("BBox_UpperRightLat","60"); - config.setParam("BBox_UpperRightLong","50"); - config.setParam("XResolution","0.5"); - config.setParam("YResolution","0.5"); - config.setParam("OutputTableName","testextractionprod"); - config.setParam("OutputTableLabel","testextractionprod"); - - return config; - } - - private static AlgorithmConfiguration testXYExtractionGeotermia() { - - AlgorithmConfiguration config = new AlgorithmConfiguration(); - - config.setAgent("XYEXTRACTOR"); - 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("/d4science.research-infrastructures.eu/gCubeApps/BiodiversityLab"); - - config.setParam("Layer","http://repoigg.services.iit.cnr.it:8080/geoserver/IGG/ows?service=WFS&version=1.0.0&request=GetFeature&typeName=IGG:area_temp_1000&maxFeatures=50"); - config.setParam("Z","-1000"); - config.setParam("TimeIndex","0"); - config.setParam("BBox_LowerLeftLat","34.46"); - config.setParam("BBox_LowerLeftLong","5.85"); - config.setParam("BBox_UpperRightLat","49"); - config.setParam("BBox_UpperRightLong","21.41"); - config.setParam("XResolution","0.01"); - config.setParam("YResolution","0.01"); - config.setParam("OutputTableName","testextractiongeotermia"); - config.setParam("OutputTableLabel","testextractiongeotermia"); - - return config; - } - - private static AlgorithmConfiguration testXYExtractionFAO() { - - AlgorithmConfiguration config = new AlgorithmConfiguration(); - - config.setAgent("XYEXTRACTOR"); - 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","20c06241-f00f-4cb0-82a3-4e5ec97a0d0a"); - config.setParam("Z","0"); - config.setParam("TimeIndex","0"); - config.setParam("BBox_LowerLeftLat","-90"); - config.setParam("BBox_LowerLeftLong","-180"); - config.setParam("BBox_UpperRightLat","90"); - config.setParam("BBox_UpperRightLong","180"); - config.setParam("XResolution","0.2"); - config.setParam("YResolution","0.2"); - config.setParam("OutputTableName","testextractionfao"); - config.setParam("OutputTableLabel","testextractionfao"); - - return config; - } - - private static AlgorithmConfiguration testXYExtractionNetCDF() { - - AlgorithmConfiguration config = new AlgorithmConfiguration(); - - config.setAgent("XYEXTRACTOR"); - 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("/d4science.research-infrastructures.eu/gCubeApps/BiodiversityLab"); - - config.setParam("Layer","c565e32c-c5b3-4964-b44f-06dc620563e9"); - config.setParam("Z","0"); - config.setParam("TimeIndex","0"); - config.setParam("BBox_LowerLeftLat","-60"); - config.setParam("BBox_LowerLeftLong","-50"); - config.setParam("BBox_UpperRightLat","60"); - config.setParam("BBox_UpperRightLong","50"); - config.setParam("XResolution","0.5"); - config.setParam("YResolution","0.5"); - config.setParam("OutputTableName","testextraction2"); - config.setParam("OutputTableLabel","testextraction2"); - - return config; - } - - private static AlgorithmConfiguration testDirectExtraction() { - - AlgorithmConfiguration config = new AlgorithmConfiguration(); - - config.setAgent("XYEXTRACTOR"); - 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("/d4science.research-infrastructures.eu/gCubeApps/BiodiversityLab"); - - config.setParam("Layer","https://dl.dropboxusercontent.com/u/12809149/geoserver-GetCoverage.image.asc"); - config.setParam("Z","0"); - config.setParam("TimeIndex","0"); - config.setParam("BBox_LowerLeftLat","-60"); - config.setParam("BBox_LowerLeftLong","-50"); - config.setParam("BBox_UpperRightLat","60"); - config.setParam("BBox_UpperRightLong","50"); - config.setParam("XResolution","0.5"); - config.setParam("YResolution","0.5"); - config.setParam("OutputTableName","testextractiondirect"); - config.setParam("OutputTableLabel","testextractiondirect"); - - return config; - } - - - private static AlgorithmConfiguration testXYExtractionAquaMaps() { - - AlgorithmConfiguration config = testXYExtractionNetCDF(); - config.setParam("Layer","04e61cb8-3c32-47fe-823c-80ac3d417a0b"); - config.setParam("OutputTableName","testextractionaquamaps"); - - return config; - } - - - private static AlgorithmConfiguration testXYExtractionTable() { - - AlgorithmConfiguration config = testXYExtractionNetCDF(); - config.setAgent("XYEXTRACTOR_TABLE"); - - config.setParam("OutputTableName","testextractiontable"); - 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"); - // vessels - /* - config.setParam(TableMatrixRepresentation.tableNameParameter, "generic_id037d302d_2ba0_4e43_b6e4_1a797bb91728"); - config.setParam(TableMatrixRepresentation.xDimensionColumnParameter, "x"); - config.setParam(TableMatrixRepresentation.yDimensionColumnParameter, "y"); - config.setParam(TableMatrixRepresentation.timeDimensionColumnParameter, "datetime"); - config.setParam(TableMatrixRepresentation.valueDimensionColumnParameter, "speed"); - config.setParam(TableMatrixRepresentation.filterParameter, "speed<2"); - */ - config.setParam(TableMatrixRepresentation.tableNameParameter, "occurrence_species_id0045886b_2a7c_4ede_afc4_3157c694b893"); - config.setParam(TableMatrixRepresentation.xDimensionColumnParameter, "decimallongitude"); - config.setParam(TableMatrixRepresentation.yDimensionColumnParameter, "decimallatitude"); - config.setParam(TableMatrixRepresentation.timeDimensionColumnParameter, " "); - config.setParam(TableMatrixRepresentation.valueDimensionColumnParameter, "decimallatitude"); - config.setParam(TableMatrixRepresentation.filterParameter, " "); - - return config; - } - - private static AlgorithmConfiguration testXYExtractionTable2() { - - AlgorithmConfiguration config = testXYExtractionNetCDF(); - config.setAgent("XYEXTRACTOR_TABLE"); - - 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"); - config.setParam("DatabaseDriver", "org.postgresql.Driver"); - // vessels - /* - config.setParam(TableMatrixRepresentation.tableNameParameter, "generic_id037d302d_2ba0_4e43_b6e4_1a797bb91728"); - config.setParam(TableMatrixRepresentation.xDimensionColumnParameter, "x"); - config.setParam(TableMatrixRepresentation.yDimensionColumnParameter, "y"); - config.setParam(TableMatrixRepresentation.timeDimensionColumnParameter, "datetime"); - config.setParam(TableMatrixRepresentation.valueDimensionColumnParameter, "speed"); - config.setParam(TableMatrixRepresentation.filterParameter, "speed<2"); - */ - config.setParam(TableMatrixRepresentation.tableNameParameter, "occurrence_species_id0045886b_2a7c_4ede_afc4_3157c694b893"); - config.setParam(TableMatrixRepresentation.xDimensionColumnParameter, "decimallongitude"); - config.setParam(TableMatrixRepresentation.yDimensionColumnParameter, "decimallatitude"); - config.setParam(TableMatrixRepresentation.timeDimensionColumnParameter, "modified"); - config.setParam(TableMatrixRepresentation.valueDimensionColumnParameter, "decimallatitude"); - config.setParam(TableMatrixRepresentation.filterParameter, " "); - config.setParam("Z","0"); - config.setParam("TimeIndex","1"); - - return config; - } - -} diff --git a/src/main/java/org/gcube/dataanalysis/geo/test/infra/TestGridCWPConversion.java b/src/main/java/org/gcube/dataanalysis/geo/test/infra/TestGridCWPConversion.java deleted file mode 100644 index 5240a9b..0000000 --- a/src/main/java/org/gcube/dataanalysis/geo/test/infra/TestGridCWPConversion.java +++ /dev/null @@ -1,54 +0,0 @@ -package org.gcube.dataanalysis.geo.test.infra; - -import java.util.List; - -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; -import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType; -import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent; -import org.gcube.dataanalysis.ecoengine.processing.factories.TransducerersFactory; -import org.gcube.dataanalysis.ecoengine.test.regression.Regressor; -import org.gcube.dataanalysis.geo.connectors.table.TableMatrixRepresentation; - -public class TestGridCWPConversion { - - static AlgorithmConfiguration[] configs = { testGridConversion()}; - public static void main(String[] args) throws Exception { - - System.out.println("TEST 1"); - - for (int i = 0; i < configs.length; i++) { - AnalysisLogger.getLogger().debug("Executing: "+configs[i].getAgent()); - List trans = null; - trans = TransducerersFactory.getTransducerers(configs[i]); - trans.get(0).init(); - Regressor.process(trans.get(0)); - StatisticalType st = trans.get(0).getOutput(); - AnalysisLogger.getLogger().debug("ST:" + st); - trans = null; - } - } - - - private static AlgorithmConfiguration testGridConversion() { - - AlgorithmConfiguration config = new AlgorithmConfiguration(); - - config.setAgent("GRID_CWP_TO_COORDINATES"); - config.setConfigPath("./cfg/"); - config.setPersistencePath("./"); - config.setParam("DatabaseUserName","utente"); - config.setParam("DatabasePassword","d4science"); - config.setParam("DatabaseURL","jdbc:postgresql://statistical-manager.d.d4science.org/testdb"); - config.setParam("DatabaseDriver","org.postgresql.Driver"); - config.setGcubeScope("/gcube/devsec/devVRE"); - - config.setParam("InputTable", "timeseries_idc9450f74_7791_4077_a0a7_9cba4da0c93f"); - config.setParam("ColumnWithCodes", "grid"); - config.setParam("OutputTableName", "cwp_t2"); - - return config; - } - - -} diff --git a/src/main/java/org/gcube/dataanalysis/geo/test/infra/TestMaxEnt.java b/src/main/java/org/gcube/dataanalysis/geo/test/infra/TestMaxEnt.java deleted file mode 100644 index d255cda..0000000 --- a/src/main/java/org/gcube/dataanalysis/geo/test/infra/TestMaxEnt.java +++ /dev/null @@ -1,92 +0,0 @@ -package org.gcube.dataanalysis.geo.test.infra; - -import java.util.List; - -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; -import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType; -import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent; -import org.gcube.dataanalysis.ecoengine.processing.factories.TransducerersFactory; -import org.gcube.dataanalysis.ecoengine.test.regression.Regressor; -import org.gcube.dataanalysis.geo.connectors.table.TableMatrixRepresentation; - -public class TestMaxEnt { - - static AlgorithmConfiguration[] configs = { testMaxentTemperature()}; - - public static void main(String[] args) throws Exception { - - System.out.println("TEST 1"); - - for (int i = 0; i < configs.length; i++) { - AnalysisLogger.getLogger().debug("Executing: "+configs[i].getAgent()); - List trans = null; - trans = TransducerersFactory.getTransducerers(configs[i]); - trans.get(0).init(); - Regressor.process(trans.get(0)); - StatisticalType st = trans.get(0).getOutput(); - AnalysisLogger.getLogger().debug("ST:" + st); - trans = null; - } - } - - private static AlgorithmConfiguration testMaxentTemperature() { - - AlgorithmConfiguration config = new AlgorithmConfiguration(); - - config.setAgent("MAX_ENT_NICHE_MODELLING"); - 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("OutputTableName","maxenttest"); - config.setParam("OutputTableLabel","maxenttest"); - config.setParam("SpeciesName","testsspecies"); - - config.setParam("OccurrencesTable","occurrence_species_id0045886b_2a7c_4ede_afc4_3157c694b893"); - config.setParam("LongitudeColumn","decimallongitude"); - config.setParam("LatitudeColumn","decimallatitude"); - config.setParam("ScientificNameColumn","scientificname"); - - String sep=AlgorithmConfiguration.getListSeparator(); -// config.setParam("Layers","dfd1bad2-ab00-42ac-8bb2-46a17162f509"+sep+"23646f93-23a8-4be4-974e-aee6bebe1707"); - //config.setParam("Layers","94ea5767-ae76-41dc-be87-f9a0bdc96419");//temperature 99-09 2D -// config.setParam("Layers","23646f93-23a8-4be4-974e-aee6bebe1707");//ph -// config.setParam("Layers","fc9ac2f4-a2bd-43d1-a361-ac67c5ceac31");//temperature - - config.setParam("Layers","http://geoserver-dev.d4science-ii.research-infrastructures.eu/geoserver/ows?service=wfs&version=1.0.0&request=GetFeature&srsName=urn:x-ogc:def:crs:EPSG:4326&TYPENAME=aquamaps:worldborders"); - - config.setParam("MaxIterations","10000"); - config.setParam("DefaultPrevalence","1"); - - config.setParam("Z","0"); - config.setParam("TimeIndex","0"); - - config.setParam("BBox_LowerLeftLong","-180"); - config.setParam("BBox_UpperRightLong","180"); - config.setParam("BBox_LowerLeftLat","-90"); - config.setParam("BBox_UpperRightLat","90"); - - /* - config.setParam("BBox_LowerLeftLong","-60"); - config.setParam("BBox_UpperRightLong","60"); - config.setParam("BBox_LowerLeftLat","-10"); - config.setParam("BBox_UpperRightLat","10"); - */ - -// config.setParam("XResolution","0.5"); -// config.setParam("YResolution","0.5"); - - config.setParam("XResolution","1"); - config.setParam("YResolution","1"); - - - return config; - } - - -} diff --git a/src/main/java/org/gcube/dataanalysis/geo/test/infra/TestOccurrenceEnrichment.java b/src/main/java/org/gcube/dataanalysis/geo/test/infra/TestOccurrenceEnrichment.java deleted file mode 100644 index cdf1ae7..0000000 --- a/src/main/java/org/gcube/dataanalysis/geo/test/infra/TestOccurrenceEnrichment.java +++ /dev/null @@ -1,149 +0,0 @@ -package org.gcube.dataanalysis.geo.test.infra; - -import java.util.ArrayList; -import java.util.List; - -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; -import org.gcube.dataanalysis.ecoengine.datatypes.ColumnType; -import org.gcube.dataanalysis.ecoengine.datatypes.InputTable; -import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveTypesList; -import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType; -import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.PrimitiveTypes; -import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.TableTemplates; -import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent; -import org.gcube.dataanalysis.ecoengine.processing.factories.TransducerersFactory; -import org.gcube.dataanalysis.ecoengine.test.regression.Regressor; -import org.gcube.dataanalysis.ecoengine.utils.IOHelper; - -public class TestOccurrenceEnrichment { - -// static AlgorithmConfiguration[] configs = { testOccEnrichment(), testOccEnrichmentWFS()}; - static AlgorithmConfiguration[] configs = { testOccEnrichmentWFSFAO()}; - public static void main(String[] args) throws Exception { - - System.out.println("TEST 1"); - - for (int i = 0; i < configs.length; i++) { - AnalysisLogger.getLogger().debug("Executing: "+configs[i].getAgent()); - List trans = null; - trans = TransducerersFactory.getTransducerers(configs[i]); - trans.get(0).init(); - Regressor.process(trans.get(0)); - StatisticalType st = trans.get(0).getOutput(); - AnalysisLogger.getLogger().debug("ST:" + st); - trans = null; - } - } - - - private static AlgorithmConfiguration testOccEnrichment() { - - 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("/d4science.research-infrastructures.eu/gCubeApps/BiodiversityLab"); - - config.setParam("OccurrenceTable","occurrence_species_id0045886b_2a7c_4ede_afc4_3157c694b893"); - 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","testenrichment"); - config.setParam("OutputTableName","testenrichment"); - String sep=AlgorithmConfiguration.getListSeparator(); -// config.setParam("Layers","http://thredds.research-infrastructures.eu/thredds/dodsC/public/netcdf/global-reanalysis-phys-001-004-b-ref-fr-mjm95-gridt__ENVIRONMENT_OCEANS_ELEVATION_1366210702774.nc"+sep+"4d597da9-dbfa-4a65-9de6-9bbff69eac19"+sep+"2c2304d1-681a-4f3a-8409-e8cdb5ed447f"); - //ASC file - config.setParam("Layers","http://goo.gl/s6fOfS"); - config.setParam("Layers","https://dl.dropboxusercontent.com/u/12809149/test1.tiff"); - - -// config.setParam("Layers","https://dl.dropboxusercontent.com/u/12809149/geoserver-GetCoverage.image.asc"); - //NETCDF http - cannot work -// config.setParam("Layers","http://goo.gl/qXtqiY"); -// config.setParam("Layers","https://dl.dropboxusercontent.com/u/12809149/geoserver-GetCoverage.image.tiff"); -// config.setParam("Layers","https://dl.dropboxusercontent.com/u/12809149/TrueMarble.tif"); -// config.setParam("Layers","http://goo.gl/l4tEmd"); - - -// config.setParam("Layers","8f5d883f-95bf-4b7c-8252-aaf0b2e6fd81"+sep+"4d597da9-dbfa-4a65-9de6-9bbff69eac19"+sep+"2c2304d1-681a-4f3a-8409-e8cdb5ed447f"); - config.setParam("FeaturesNames","temperature"+sep+"chlorophyll"+sep+"ph"); -// config.setParam("Layers","4d597da9-dbfa-4a65-9de6-9bbff69eac19"+sep+"2c2304d1-681a-4f3a-8409-e8cdb5ed447f"); -// config.setParam("FeaturesNames","chlorophyll"+sep+"ph"); - return config; - } - - private static AlgorithmConfiguration testOccEnrichmentWFSFAO() { - - 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","testenrichmentwpsfao"); - config.setParam("OutputTableName","testenrichmentwpsfao"); - String sep=AlgorithmConfiguration.getListSeparator(); - - //WFS: carcharodon - config.setParam("Layers"," fao-species-map-wsh"); - - - return config; - } - - private static AlgorithmConfiguration testOccEnrichmentWFS() { - - 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; - } - -} diff --git a/src/main/java/org/gcube/dataanalysis/geo/test/infra/TestSHAPEFILEPUBLISHER.java b/src/main/java/org/gcube/dataanalysis/geo/test/infra/TestSHAPEFILEPUBLISHER.java deleted file mode 100644 index fbc4f69..0000000 --- a/src/main/java/org/gcube/dataanalysis/geo/test/infra/TestSHAPEFILEPUBLISHER.java +++ /dev/null @@ -1,62 +0,0 @@ -package org.gcube.dataanalysis.geo.test.infra; - -import java.util.List; - -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; -import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType; -import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent; -import org.gcube.dataanalysis.ecoengine.processing.factories.TransducerersFactory; -import org.gcube.dataanalysis.ecoengine.test.regression.Regressor; -import org.gcube.dataanalysis.geo.connectors.table.TableMatrixRepresentation; - -public class TestSHAPEFILEPUBLISHER { - - static AlgorithmConfiguration[] configs = { testSFImporter()}; - public static void main(String[] args) throws Exception { - - System.out.println("TEST 1"); - - for (int i = 0; i < configs.length; i++) { - AnalysisLogger.getLogger().debug("Executing: "+configs[i].getAgent()); - List trans = null; - trans = TransducerersFactory.getTransducerers(configs[i]); - trans.get(0).init(); - Regressor.process(trans.get(0)); - StatisticalType st = trans.get(0).getOutput(); - AnalysisLogger.getLogger().debug("ST:" + st); - trans = null; - } - } - - - - private static AlgorithmConfiguration testSFImporter() { - - AlgorithmConfiguration config = new AlgorithmConfiguration(); - - config.setAgent("SHAPEFILE_PUBLISHER"); - config.setConfigPath("./cfg/"); - config.setPersistencePath("./"); - config.setParam("DBUser","postgres"); - config.setParam("DBPassword","d4science2"); - config.setParam("DBUrl","jdbc:postgresql://geoserver-test.d4science-ii.research-infrastructures.eu:5432/timeseriesgisdb"); - config.setParam("driver","org.postgresql.Driver"); -// config.setGcubeScope("/d4science.research-infrastructures.eu/gCubeApps/BiodiversityLab"); - config.setGcubeScope("/gcube/devsec/devVRE"); - - config.setParam("MapTitle","Test local shapefile"); - config.setParam("MapAbstract","A local test"); - config.setParam("ShapeFileZip","shapefiletest.zip"); - config.setParam("ShapeFileName","shapefile2.shp"); - config.setParam("Topics","test|shapefile"); - config.setParam("PublicationLevel","PUBLIC"); - config.setParam("ServiceUserName","gianpaolo.coro"); - - - return config; - } - - - -} diff --git a/src/main/java/org/gcube/dataanalysis/geo/test/infra/TestTimeExtraction.java b/src/main/java/org/gcube/dataanalysis/geo/test/infra/TestTimeExtraction.java deleted file mode 100644 index ae5c385..0000000 --- a/src/main/java/org/gcube/dataanalysis/geo/test/infra/TestTimeExtraction.java +++ /dev/null @@ -1,211 +0,0 @@ -package org.gcube.dataanalysis.geo.test.infra; - -import java.util.List; - -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; -import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType; -import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent; -import org.gcube.dataanalysis.ecoengine.processing.factories.TransducerersFactory; -import org.gcube.dataanalysis.ecoengine.test.regression.Regressor; -import org.gcube.dataanalysis.ecoengine.transducers.TimeSeriesAnalysis; -import org.gcube.dataanalysis.ecoengine.utils.IOHelper; -import org.gcube.dataanalysis.geo.connectors.table.TableMatrixRepresentation; - -public class TestTimeExtraction { - -// static AlgorithmConfiguration[] configs = { testTimeExtractionTable(), testTimeExtractionNetCDF(),testTimeExtractionTable2()}; -// static AlgorithmConfiguration[] configs = { testTimeExtractionNetCDF()}; -// static AlgorithmConfiguration[] configs = { testTExtractionAquamaps()}; - static AlgorithmConfiguration[] configs = { testTExtractionTemperature()}; - - public static void main(String[] args) throws Exception { - - System.out.println("TEST 1"); - TimeSeriesAnalysis.display=true; - for (int i = 0; i < configs.length; i++) { - AnalysisLogger.getLogger().debug("Executing: "+configs[i].getAgent()); - List trans = null; - trans = TransducerersFactory.getTransducerers(configs[i]); - trans.get(0).init(); - Regressor.process(trans.get(0)); - StatisticalType st = trans.get(0).getOutput(); - AnalysisLogger.getLogger().debug("ST:" + st); - trans = null; - } - } - - - - - private static AlgorithmConfiguration testTExtractionTemperature() { - - 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","b875403f-1e63-44e1-a1c0-2296d3e147a6"); - - config.setParam("OutputTableName","testtextractiontemp2"); - config.setParam("OutputTableLabel","testtextractiontemp2"); - - config.setParam("X","0"); - config.setParam("Y","0"); - config.setParam("Resolution","0.5"); - config.setParam("Z","0"); - config.setParam("SamplingFreq","-1"); -// config.setParam("MinFrequency","-1"); -// config.setParam("MaxFrequency","-1"); -// config.setParam("FFTSamples","100"); - - return config; - } - - 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(); - - 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("/d4science.research-infrastructures.eu/gCubeApps/BiodiversityLab"); - config.setGcubeScope("/gcube/devsec/devVRE"); -// config.setParam("Layer","c565e32c-c5b3-4964-b44f-06dc620563e9"); - -// config.setParam("Layer","dffa504b-dbc8-4553-896e-002549f8f5d3"); - //wind - config.setParam("Layer","21715b2e-28de-4646-acce-d4f16b59d6d0"); - config.setParam("OutputTableName","testtimeextraction"); - config.setParam("OutputTableLabel","testtimeextraction"); - - config.setParam("Z","0"); - config.setParam("X","0"); - config.setParam("Y","0"); - config.setParam("Resolution","0.5"); - config.setParam("SamplingFreq","-1"); - config.setParam("MinFrequency","-1"); - config.setParam("MaxFrequency","-1"); - config.setParam("FrequencyError","-1"); - - return config; - } - - - private static AlgorithmConfiguration testTimeExtractionTable() { - - AlgorithmConfiguration config = new AlgorithmConfiguration(); - - config.setAgent("TIMEEXTRACTION"); - 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("/d4science.research-infrastructures.eu/gCubeApps/BiodiversityLab"); - - config.setParam("Layer","c565e32c-c5b3-4964-b44f-06dc620563e9"); - - config.setParam("OutputTableName","testtimeextraction2"); - config.setParam("OutputTableLabel","testtimeextraction2"); - - config.setParam("Z","0"); - config.setParam("X","-47.97"); - config.setParam("Y","43.42"); - config.setParam("Resolution","0.5"); - config.setParam("SamplingFreq","-1"); - config.setParam("MinFrequency","-1"); - config.setParam("MaxFrequency","-1"); - config.setParam("FrequencyError","-1"); - - config.setParam(TableMatrixRepresentation.tableNameParameter, "generic_id037d302d_2ba0_4e43_b6e4_1a797bb91728"); - config.setParam(TableMatrixRepresentation.xDimensionColumnParameter, "x"); - config.setParam(TableMatrixRepresentation.yDimensionColumnParameter, "y"); - - config.setParam(TableMatrixRepresentation.timeDimensionColumnParameter, "datetime"); - config.setParam(TableMatrixRepresentation.valueDimensionColumnParameter, "speed"); - config.setParam(TableMatrixRepresentation.filterParameter, "speed<2"); - - return config; - } - - - private static AlgorithmConfiguration testTimeExtractionTable2() { - - AlgorithmConfiguration config = new AlgorithmConfiguration(); - - config.setAgent("TIMEEXTRACTION"); - 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("/d4science.research-infrastructures.eu/gCubeApps/BiodiversityLab"); - - config.setParam("OutputTableName","testtimeextraction2"); - config.setParam("OutputTableLabel","testtimeextraction2"); - - config.setParam("Z","0"); - config.setParam("X","18.61669921875"); - config.setParam("Y","-34.1833000183105"); - config.setParam("Resolution","10"); - config.setParam("SamplingFreq","-1"); - config.setParam("MinFrequency","-1"); - config.setParam("MaxFrequency","-1"); - config.setParam("FrequencyError","-1"); - - config.setParam(TableMatrixRepresentation.tableNameParameter, "occurrence_species_id0045886b_2a7c_4ede_afc4_3157c694b893"); - config.setParam(TableMatrixRepresentation.xDimensionColumnParameter, "decimallongitude"); - config.setParam(TableMatrixRepresentation.yDimensionColumnParameter, "decimallatitude"); - - config.setParam(TableMatrixRepresentation.timeDimensionColumnParameter, "eventdate"); - config.setParam(TableMatrixRepresentation.valueDimensionColumnParameter, "decimallongitude"); - config.setParam(TableMatrixRepresentation.filterParameter, " "); - - return config; - } - - -} diff --git a/src/main/java/org/gcube/dataanalysis/geo/test/infra/TestZExtraction.java b/src/main/java/org/gcube/dataanalysis/geo/test/infra/TestZExtraction.java deleted file mode 100644 index a39426c..0000000 --- a/src/main/java/org/gcube/dataanalysis/geo/test/infra/TestZExtraction.java +++ /dev/null @@ -1,190 +0,0 @@ -package org.gcube.dataanalysis.geo.test.infra; - -import java.util.List; - -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; -import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType; -import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent; -import org.gcube.dataanalysis.ecoengine.processing.factories.TransducerersFactory; -import org.gcube.dataanalysis.ecoengine.test.regression.Regressor; -import org.gcube.dataanalysis.ecoengine.utils.IOHelper; -import org.gcube.dataanalysis.geo.connectors.table.TableMatrixRepresentation; - -public class TestZExtraction { - -// static AlgorithmConfiguration[] configs = { testTimeExtractionTable(), testZExtractionLongNetCDF(),testZExtractionNetCDF(),testTimeExtractionTable2()}; - static AlgorithmConfiguration[] configs = { testZExtractionAquamaps()}; - - public static void main(String[] args) throws Exception { - - System.out.println("TEST 1"); - - for (int i = 0; i < configs.length; i++) { - AnalysisLogger.getLogger().debug("Executing: "+configs[i].getAgent()); - List trans = null; - trans = TransducerersFactory.getTransducerers(configs[i]); - trans.get(0).init(); - Regressor.process(trans.get(0)); - StatisticalType st = trans.get(0).getOutput(); - AnalysisLogger.getLogger().debug("ST:" + st); - trans = null; - } - } - - 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() { - - 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("/d4science.research-infrastructures.eu/gCubeApps/BiodiversityLab"); - - config.setParam("Layer","6411b110-7572-457a-a662-a16e4ff09e4e"); -// config.setParam("Layer","dffa504b-dbc8-4553-896e-002549f8f5d3"); - - config.setParam("OutputTableName","testzextractionlong"); - config.setParam("OutputTableLabel","testzextractionlong"); - - config.setParam("TimeIndex","0"); - config.setParam("X","0"); - config.setParam("Y","0"); - config.setParam("Resolution","0.5"); - - return config; - } - - private static AlgorithmConfiguration testZExtractionNetCDF() { - - 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"); - - config.setParam("Layer","7f90e153-0c5c-4d45-a498-a6374593e68d"); - - config.setParam("OutputTableName","testzextractionstandard"); - config.setParam("OutputTableLabel","testzextractionstandard"); - - config.setParam("TimeIndex","0"); - config.setParam("X","0"); - config.setParam("Y","0"); - config.setParam("Resolution","100"); - - return config; - } - - private static AlgorithmConfiguration testTimeExtractionTable() { - - AlgorithmConfiguration config = new AlgorithmConfiguration(); - - config.setAgent("TIMEEXTRACTION"); - 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("/d4science.research-infrastructures.eu/gCubeApps/BiodiversityLab"); - - config.setParam("Layer","c565e32c-c5b3-4964-b44f-06dc620563e9"); - - config.setParam("OutputTableName","testtimeextraction"); - config.setParam("OutputTableLabel","testtimeextraction"); - - config.setParam("Z","0"); - config.setParam("X","-47.97"); - config.setParam("Y","43.42"); - config.setParam("Resolution","0.5"); - config.setParam("SamplingFreq","-1"); - config.setParam("MinFrequency","-1"); - config.setParam("MaxFrequency","-1"); - config.setParam("FrequencyError","-1"); - - config.setParam(TableMatrixRepresentation.tableNameParameter, "generic_id037d302d_2ba0_4e43_b6e4_1a797bb91728"); - config.setParam(TableMatrixRepresentation.xDimensionColumnParameter, "x"); - config.setParam(TableMatrixRepresentation.yDimensionColumnParameter, "y"); - - config.setParam(TableMatrixRepresentation.timeDimensionColumnParameter, "datetime"); - config.setParam(TableMatrixRepresentation.valueDimensionColumnParameter, "speed"); - config.setParam(TableMatrixRepresentation.filterParameter, "speed<2"); - - return config; - } - - - private static AlgorithmConfiguration testTimeExtractionTable2() { - - AlgorithmConfiguration config = new AlgorithmConfiguration(); - - config.setAgent("TIMEEXTRACTION"); - 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("/d4science.research-infrastructures.eu/gCubeApps/BiodiversityLab"); - - config.setParam("OutputTableName","testtimeextraction2"); - config.setParam("OutputTableLabel","testtimeextraction2"); - - config.setParam("Z","0"); - config.setParam("X","18.61669921875"); - config.setParam("Y","-34.1833000183105"); - config.setParam("Resolution","10"); - config.setParam("SamplingFreq","-1"); - config.setParam("MinFrequency","-1"); - config.setParam("MaxFrequency","-1"); - config.setParam("FrequencyError","-1"); - - config.setParam(TableMatrixRepresentation.tableNameParameter, "occurrence_species_id0045886b_2a7c_4ede_afc4_3157c694b893"); - config.setParam(TableMatrixRepresentation.xDimensionColumnParameter, "decimallongitude"); - config.setParam(TableMatrixRepresentation.yDimensionColumnParameter, "decimallatitude"); - - config.setParam(TableMatrixRepresentation.timeDimensionColumnParameter, "eventdate"); - config.setParam(TableMatrixRepresentation.valueDimensionColumnParameter, "decimallongitude"); - config.setParam(TableMatrixRepresentation.filterParameter, " "); - - return config; - } - - -} diff --git a/src/main/java/org/gcube/dataanalysis/geo/test/maps/TestMapCreation.java b/src/main/java/org/gcube/dataanalysis/geo/test/maps/TestMapCreation.java deleted file mode 100644 index d24ab89..0000000 --- a/src/main/java/org/gcube/dataanalysis/geo/test/maps/TestMapCreation.java +++ /dev/null @@ -1,119 +0,0 @@ -package org.gcube.dataanalysis.geo.test.maps; - -import org.gcube.common.scope.api.ScopeProvider; -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; -import org.gcube.dataanalysis.geo.algorithms.PointsMapsCreator; -import org.gcube.dataanalysis.geo.algorithms.PolygonMapsCreator; - -public class TestMapCreation { - - - static String cfg = "./cfg/"; - public static void main1(String[] args) throws Exception{ - - AnalysisLogger.setLogger(cfg+AlgorithmConfiguration.defaultLoggerFile); - AlgorithmConfiguration config = new AlgorithmConfiguration(); - config.setConfigPath(cfg); -// config.setGcubeScope("/gcube/devsec/statVRE"); - config.setGcubeScope("/gcube/devsec/devVRE"); - config.setPersistencePath("./"); - - config.setParam("MapName","Test Polygonal Map Ph 6"); - /* - config.setParam("InputTable","occurrence_species_id0045886b_2a7c_4ede_afc4_3157c694b893"); - config.setParam("xDimension","decimallongitude"); - config.setParam("yDimension","decimallatitude"); - config.setParam("Info","recordedby") ; - config.setParam("Resolution","0.5"); - */ - config.setParam("InputTable","generic_idbc699da3_a4d5_40fb_80ff_666dbf1316d5"); - config.setParam("xDimension","x"); - config.setParam("yDimension","y"); - config.setParam("Info","fvalue") ; - - - - config.setParam("DatabaseUserName","utente"); - config.setParam("DatabasePassword","d4science"); - config.setParam("DatabaseURL","jdbc:postgresql://statistical-manager.d.d4science.org/testdb"); - config.setParam("DatabaseDriver","org.postgresql.Driver"); - - config.setParam("Z","0"); - - config.setParam("user", "postgres"); - config.setParam("password", "d4science2"); - config.setParam("STOREURL","jdbc:postgresql://geoserver-test.d4science-ii.research-infrastructures.eu/timeseriesgisdb"); - config.setParam("driver", "org.postgresql.Driver"); - config.setParam("dialect", "org.hibernatespatial.postgis.PostgisDialect"); - /* - PolygonMapsCreator mc = new PolygonMapsCreator(); - */ - PointsMapsCreator mc = new PointsMapsCreator(); - mc.setConfiguration(config); - mc.init(); - mc.compute(); - - } - - -public static void main(String[] args) throws Exception{ - - AnalysisLogger.setLogger(cfg+AlgorithmConfiguration.defaultLoggerFile); - AlgorithmConfiguration config = new AlgorithmConfiguration(); - config.setConfigPath(cfg); -// config.setGcubeScope("/gcube/devsec/statVRE"); - config.setGcubeScope("/gcube/devsec/devVRE"); - ScopeProvider.instance.set("/gcube/devsec/devVRE"); - - config.setPersistencePath("./"); - - config.setParam("MapName","Test Polygonal Map Ph 10"); - config.setParam("PublicationLevel","PRIVATE"); - /* - config.setParam("InputTable","occurrence_species_id0045886b_2a7c_4ede_afc4_3157c694b893"); - config.setParam("xDimension","decimallongitude"); - config.setParam("yDimension","decimallatitude"); - config.setParam("Info","recordedby") ; - config.setParam("Resolution","0.5"); - */ - /* - config.setParam("InputTable","testextraction2"); - config.setParam("xDimension","x"); - config.setParam("yDimension","y"); - config.setParam("Info","fvalue") ; - */ - - config.setParam("InputTable","code_85e5d927f7094a3ca677a53f4433fed4"); - config.setParam("xDimension","longitude"); - config.setParam("yDimension","latitude"); - config.setParam("Info","longitude") ; - - config.setParam("DatabaseUserName","utente"); - config.setParam("DatabasePassword","d4science"); - config.setParam("DatabaseURL","jdbc:postgresql://statistical-manager.d.d4science.org/testdb"); - config.setParam("DatabaseDriver","org.postgresql.Driver"); -/* - config.setParam("DatabaseUserName","gcube"); - config.setParam("DatabasePassword","d4science2"); - config.setParam("DatabaseURL","jdbc:postgresql://localhost/testdb"); - config.setParam("DatabaseDriver","org.postgresql.Driver"); -*/ - config.setParam("Z","0"); - - config.setParam("user", "postgres"); - config.setParam("password", "d4science2"); - config.setParam("STOREURL","jdbc:postgresql://geoserver-test.d4science-ii.research-infrastructures.eu/timeseriesgisdb"); - config.setParam("driver", "org.postgresql.Driver"); - config.setParam("dialect", "org.hibernatespatial.postgis.PostgisDialect"); - /* - PolygonMapsCreator mc = new PolygonMapsCreator(); - */ - PointsMapsCreator mc = new PointsMapsCreator(); - mc.setConfiguration(config); - mc.init(); - mc.compute(); - - } - -} diff --git a/src/main/java/org/gcube/dataanalysis/geo/test/maps/TestMapsComparison.java b/src/main/java/org/gcube/dataanalysis/geo/test/maps/TestMapsComparison.java deleted file mode 100644 index 53cb29f..0000000 --- a/src/main/java/org/gcube/dataanalysis/geo/test/maps/TestMapsComparison.java +++ /dev/null @@ -1,66 +0,0 @@ -package org.gcube.dataanalysis.geo.test.maps; - -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; -import org.gcube.dataanalysis.geo.algorithms.MapsComparator; -import org.gcube.dataanalysis.geo.matrixmodel.MatrixExtractor; -import org.gcube.dataanalysis.geo.matrixmodel.RasterTable; - -public class TestMapsComparison { - - static String cfg = "./cfg/"; - public static void main(String[] args) throws Exception{ -// String layertitle = "Ice velocity u from [12-15-02 01:00] to [12-15-09 01:00] (2D) {Native grid ORCA025.L75 monthly average: Data extracted from dataset http://atoll-mercator.vlandata.cls.fr:44080/thredds/dodsC/global-reanalysis-phys-001-004-b-ref-fr-mjm95-icemod}"; -// String layertitle2 = "Ice velocity v from [12-15-02 01:00] to [12-15-09 01:00] (2D) {Native grid ORCA025.L75 monthly average: Data extracted from dataset http://atoll-mercator.vlandata.cls.fr:44080/thredds/dodsC/global-reanalysis-phys-001-004-b-ref-fr-mjm95-icemod}"; -// String layertitle = "Number of Observations in [07-01-01 01:00] (3D) {World Ocean Atlas 09: Apparent Oxygen Utilization - annual: dods://thredds.research-infrastructures.eu/thredds/dodsC/public/netcdf/apparent_oxygen_utilization_annual_1deg_ENVIRONMENT_BIOTA_.nc}"; -// String layertitle2 = "Seasonal or Monthly Climatology minus Annual Climatology in [07-01-01 01:00] (3D) {World Ocean Atlas 09: Apparent Oxygen Utilization - annual: dods://thredds.research-infrastructures.eu/thredds/dodsC/public/netcdf/apparent_oxygen_utilization_annual_1deg_ENVIRONMENT_BIOTA_.nc}"; -// String layertitle2 = "Number of Mean Values within Radius of Influence in [07-01-01 01:00] (3D) {World Ocean Atlas 09: Apparent Oxygen Utilization - annual: dods://thredds.research-infrastructures.eu/thredds/dodsC/public/netcdf/apparent_oxygen_utilization_annual_1deg_ENVIRONMENT_BIOTA_.nc}"; -// String layertitle = "Ice velocity u from [12-15-02 01:00] to [12-15-09 01:00] (2D) {Native grid ORCA025.L75 monthly average: Data extracted from dataset http://atoll-mercator.vlandata.cls.fr:44080/thredds/dodsC/global-reanalysis-phys-001-004-b-ref-fr-mjm95-icemod}"; -// String layertitle2 = "Ice velocity v from [12-15-02 01:00] to [12-15-09 01:00] (2D) {Native grid ORCA025.L75 monthly average: Data extracted from dataset http://atoll-mercator.vlandata.cls.fr:44080/thredds/dodsC/global-reanalysis-phys-001-004-b-ref-fr-mjm95-icemod}"; - - //String layertitle = "wind stress from [05-01-07 14:00] to [04-01-12 14:00] (2D) {Monthly ASCAT global wind field: Data extracted from dataset http://tds0.ifremer.fr/thredds/dodsC/CERSAT-GLO-CLIM_WIND_L4-OBS_FULL_TIME_SERIE}"; - //String layertitle2 = "wind speed from [05-01-07 14:00] to [04-01-12 14:00] (2D) {Monthly ASCAT global wind field: Data extracted from dataset http://tds0.ifremer.fr/thredds/dodsC/CERSAT-GLO-CLIM_WIND_L4-OBS_FULL_TIME_SERIE}"; - - //String layertitle = "Objectively Analyzed Climatology from [02-16-01 01:00] to [11-16-01 01:00] (3D) {World Ocean Atlas 09: Sea Water Salinity - seasonal: dods://thredds.research-infrastructures.eu/thredds/dodsC/public/netcdf/salinity_seasonal_1deg_ENVIRONMENT_OCEANS_.nc}"; - //String layertitle2 = "Objectively Analyzed Climatology from [01-16-01 01:00] to [12-16-01 01:00] (3D) {World Ocean Atlas 09: Apparent Oxygen Utilization - monthly: dods://thredds.research-infrastructures.eu/thredds/dodsC/public/netcdf/apparent_oxygen_utilization_monthly_1deg_ENVIRONMENT_BIOTA_.nc}"; - - -// String layertitle = "FAO aquatic species distribution map of Istiophorus platypterus"; -// String layertitle2 = "FAO aquatic species distribution map of Teuthowenia megalops"; - //{MEAN=1.0, VARIANCE=0.0, NUMBER_OF_ERRORS=38596, NUMBER_OF_COMPARISONS=260281, ACCURACY=85.17, MAXIMUM_ERROR=1.0, MAXIMUM_ERROR_POINT=3207:219:1, TREND=CONTRACTION, Resolution=0.5} - - //String layertitle = "Sarda orientalis"; - //String layertitle2 = "FAO aquatic species distribution map of Sarda chiliensis"; - -// String layertitle2 = "4e5c1bbf-f5ce-4b66-a67c-14d7d9920aa0"; -// String layertitle = "38b2eb74-1c07-4569-8a81-36ac2f973146"; - - //String layertitle = "http://geoserver.d4science-ii.research-infrastructures.eu/geoserver/ows?service=WFS&version=1.0.0&request=GetFeature&typeName=lluidiamaculata20121218223748535cet&format=json&maxfeatures=1"; - //String layertitle2 = "http://geoserver.d4science-ii.research-infrastructures.eu/geoserver/ows?service=WFS&version=1.0.0&request=GetFeature&typeName=lluidiamaculata20121218223748535cet&format=json&maxfeatures=1"; - - String layertitle = "http://geoserver-dev4.d4science.org/geoserver/aquamaps/ows?service=wfs&version=1.1.0&REQUEST=GetFeature&srsName=urn:x-ogc:def:crs:EPSG:4326&TYPENAME=aquamaps:llatimeriachalumnae20130717140243002cest&format=json&maxfeatures=1"; - String layertitle2 = "http://geoserver-dev4.d4science.org/geoserver/aquamaps/ows?service=wfs&version=1.1.0&REQUEST=GetFeature&srsName=urn:x-ogc:def:crs:EPSG:4326&TYPENAME=aquamaps:llatimeriachalumnae20130717140243002cest&format=json&maxfeatures=1"; - - AnalysisLogger.setLogger(cfg+AlgorithmConfiguration.defaultLoggerFile); - AlgorithmConfiguration config = new AlgorithmConfiguration(); - config.setConfigPath(cfg); - config.setGcubeScope("/gcube/devsec"); - config.setPersistencePath("./"); - - config.setParam("DatabaseUserName","gcube"); - config.setParam("DatabasePassword","d4science2"); - config.setParam("DatabaseURL","jdbc:postgresql://localhost/testdb"); - config.setParam("DatabaseDriver","org.postgresql.Driver"); - config.setParam("Layer_1",layertitle); - config.setParam("Layer_2",layertitle2); - config.setParam("ValuesComparisonThreshold","0.1"); - config.setParam("Z","0"); - - - MapsComparator mc = new MapsComparator(); - mc.setConfiguration(config); - mc.init(); - mc.compute(); - mc.getOutput(); - } -} diff --git a/src/main/java/org/gcube/dataanalysis/geo/test/maps/TestMapsComparisonASCFiles.java b/src/main/java/org/gcube/dataanalysis/geo/test/maps/TestMapsComparisonASCFiles.java deleted file mode 100644 index d3d6705..0000000 --- a/src/main/java/org/gcube/dataanalysis/geo/test/maps/TestMapsComparisonASCFiles.java +++ /dev/null @@ -1,46 +0,0 @@ -package org.gcube.dataanalysis.geo.test.maps; - -import java.util.List; - -import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; -import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent; -import org.gcube.dataanalysis.ecoengine.interfaces.Evaluator; -import org.gcube.dataanalysis.ecoengine.processing.factories.EvaluatorsFactory; -import org.gcube.dataanalysis.ecoengine.test.regression.Regressor; - -public class TestMapsComparisonASCFiles { - /** - * example of parallel processing on a single machine the procedure will generate a new table for a distribution on suitable species - * - */ - - public static void main(String[] args) throws Exception { - - List evaluators = EvaluatorsFactory.getEvaluators(testConfig1()); - evaluators.get(0).init(); - Regressor.process(evaluators.get(0)); - evaluators = null; - } - - private static AlgorithmConfiguration testConfig1() { - - AlgorithmConfiguration config = Regressor.getConfig(); - config.setNumberOfResources(1); - config.setConfigPath("./cfg"); - config.setPersistencePath("./"); - config.setAgent("MAPS_COMPARISON"); - config.setParam("DatabaseUserName","gcube"); - config.setParam("DatabasePassword","d4science2"); - config.setParam("DatabaseURL","jdbc:postgresql://localhost/testdb"); - config.setParam("DatabaseDriver","org.postgresql.Driver"); - - config.setParam("Layer_1","Bio-Oracle Chlorophyll A Concentration (Mean)"); - config.setParam("Layer_2","Bio-Oracle Chlorophyll A Concentration (Max)"); - - config.setParam("ValuesComparisonThreshold",""+0.1); - config.setParam("Z","0"); - config.setGcubeScope("/gcube"); - - return config; - } -} diff --git a/src/main/java/org/gcube/dataanalysis/geo/test/maps/TestMapsComparisonAquaMapsvsFAO.java b/src/main/java/org/gcube/dataanalysis/geo/test/maps/TestMapsComparisonAquaMapsvsFAO.java deleted file mode 100644 index 06d951c..0000000 --- a/src/main/java/org/gcube/dataanalysis/geo/test/maps/TestMapsComparisonAquaMapsvsFAO.java +++ /dev/null @@ -1,50 +0,0 @@ -package org.gcube.dataanalysis.geo.test.maps; - -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; -import org.gcube.dataanalysis.geo.algorithms.MapsComparator; -import org.gcube.dataanalysis.geo.matrixmodel.MatrixExtractor; -import org.gcube.dataanalysis.geo.matrixmodel.RasterTable; - -public class TestMapsComparisonAquaMapsvsFAO { - - static String cfg = "./cfg/"; - public static void main(String[] args) throws Exception{ - String layertitle = "FAO aquatic species distribution map of Eleutheronema tetradactylum"; - String layertitle2 = "Eleutheronema tetradactylum"; - - /* - * {MEAN=0.81, VARIANCE=0.02, NUMBER_OF_ERRORS=6691, NUMBER_OF_COMPARISONS=259200, - * ACCURACY=97.42, - * MAXIMUM_ERROR=1.0, MAXIMUM_ERROR_POINT=3005:363:1, - * COHENS_KAPPA=0.218, - * COHENS_KAPPA_CLASSIFICATION_LANDIS_KOCH=Fair, - * COHENS_KAPPA_CLASSIFICATION_FLEISS=Marginal, - * TREND=EXPANSION, - * Resolution=0.5} - */ - - AnalysisLogger.setLogger(cfg+AlgorithmConfiguration.defaultLoggerFile); - AlgorithmConfiguration config = new AlgorithmConfiguration(); - 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.setParam("Layer_1",layertitle); - config.setParam("Layer_2",layertitle2); - config.setParam("ValuesComparisonThreshold","0.5"); - config.setParam("KThreshold","0.5"); - - config.setParam("Z","0"); - config.setGcubeScope("/gcube/devsec/devVRE"); - - - MapsComparator mc = new MapsComparator(); - mc.setConfiguration(config); - mc.init(); - mc.compute(); - mc.getOutput(); - } -} diff --git a/src/main/java/org/gcube/dataanalysis/geo/test/maps/TestMapsComparisonArchiteuthis.java b/src/main/java/org/gcube/dataanalysis/geo/test/maps/TestMapsComparisonArchiteuthis.java deleted file mode 100644 index 88ff7d7..0000000 --- a/src/main/java/org/gcube/dataanalysis/geo/test/maps/TestMapsComparisonArchiteuthis.java +++ /dev/null @@ -1,39 +0,0 @@ -package org.gcube.dataanalysis.geo.test.maps; - -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; -import org.gcube.dataanalysis.geo.algorithms.MapsComparator; -import org.gcube.dataanalysis.geo.matrixmodel.MatrixExtractor; -import org.gcube.dataanalysis.geo.matrixmodel.RasterTable; - -public class TestMapsComparisonArchiteuthis { - - static String cfg = "./cfg/"; - public static void main(String[] args) throws Exception{ - String layertitle = "96575f38-583c-4b6c-926f-e804156c7baa"; - String layertitle2 = "f9a831c0-143f-4792-a5d9-896d72db73f6"; - - AnalysisLogger.setLogger(cfg+AlgorithmConfiguration.defaultLoggerFile); - AlgorithmConfiguration config = new AlgorithmConfiguration(); - config.setConfigPath(cfg); - config.setPersistencePath("./"); - config.setParam("DatabaseUserName","utente"); - config.setParam("DatabasePassword","d4science"); - config.setParam("DatabaseURL","jdbc:postgresql://statistical-manager.d.d4science.org/testdb"); - config.setParam("DatabaseDriver","org.postgresql.Driver"); - config.setParam("Layer_1",layertitle); - config.setParam("Layer_2",layertitle2); - config.setParam("ValuesComparisonThreshold","0.5"); - config.setParam("KThreshold","0.5"); - - config.setParam("Z","0"); - config.setGcubeScope("/gcube/devsec/devVRE"); - - - MapsComparator mc = new MapsComparator(); - mc.setConfiguration(config); - mc.init(); - mc.compute(); - mc.getOutput(); - } -} diff --git a/src/main/java/org/gcube/dataanalysis/geo/test/maps/TestMapsComparisonExampleTCOM.java b/src/main/java/org/gcube/dataanalysis/geo/test/maps/TestMapsComparisonExampleTCOM.java deleted file mode 100644 index 24c17f3..0000000 --- a/src/main/java/org/gcube/dataanalysis/geo/test/maps/TestMapsComparisonExampleTCOM.java +++ /dev/null @@ -1,36 +0,0 @@ -package org.gcube.dataanalysis.geo.test.maps; - -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; -import org.gcube.dataanalysis.geo.algorithms.MapsComparator; -import org.gcube.dataanalysis.geo.matrixmodel.MatrixExtractor; -import org.gcube.dataanalysis.geo.matrixmodel.RasterTable; - -public class TestMapsComparisonExampleTCOM { - - static String cfg = "./cfg/"; - public static void main(String[] args) throws Exception{ - String layertitle2 = "FAO aquatic species distribution map of Eleutheronema tetradactylum"; - String layertitle = "FAO aquatic species distribution map of Leptomelanosoma indicum"; - - //{MEAN=1.0, VARIANCE=0.0, NUMBER_OF_ERRORS=1823, NUMBER_OF_COMPARISONS=260281, ACCURACY=99.3, MAXIMUM_ERROR=1.0, MAXIMUM_ERROR_POINT=1008:390:1, TREND=EXPANSION, Resolution=0.5} - - AnalysisLogger.setLogger(cfg+AlgorithmConfiguration.defaultLoggerFile); - AlgorithmConfiguration config = new AlgorithmConfiguration(); - 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.setParam("Layer_1",layertitle); - config.setParam("Layer_2",layertitle2); - config.setParam("Z","0"); - config.setGcubeScope(null); - - MapsComparator mc = new MapsComparator(); - mc.setConfiguration(config); - mc.init(); - mc.compute(); - } -} diff --git a/src/main/java/org/gcube/dataanalysis/geo/test/maps/TestMapsComparisonGeothermal.java b/src/main/java/org/gcube/dataanalysis/geo/test/maps/TestMapsComparisonGeothermal.java deleted file mode 100644 index e1dd5d6..0000000 --- a/src/main/java/org/gcube/dataanalysis/geo/test/maps/TestMapsComparisonGeothermal.java +++ /dev/null @@ -1,50 +0,0 @@ -package org.gcube.dataanalysis.geo.test.maps; - -import org.gcube.common.scope.api.ScopeProvider; -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; -import org.gcube.dataanalysis.geo.algorithms.MapsComparator; -import org.gcube.dataanalysis.geo.matrixmodel.MatrixExtractor; -import org.gcube.dataanalysis.geo.matrixmodel.RasterTable; - -public class TestMapsComparisonGeothermal { - - static String cfg = "./cfg/"; - public static void main(String[] args) throws Exception{ -// String layertitle = "Temperature in [12-15-09 01:00] (3D) {Native grid ORCA025.L75 monthly average: Data extracted from dataset http://atoll-mercator.vlandata.cls.fr:44080/thredds/dodsC/global-reanalysis-phys-001-004-b-ref-fr-mjm95-gridt}"; -// String layertitle = "Standard Deviation from Statistical Mean from [01-16-01 01:00] to [12-16-01 01:00] (3D) {World Ocean Atlas 09: Sea Water Temperature - monthly: dods://thredds.research-infrastructures.eu/thredds/dodsC/public/netcdf/temperature_monthly_1deg_ENVIRONMENT_OCEANS_.nc}"; -// String layertitle = "86a7ac79-866a-49c6-b5d5-602fc2d87ddd"; - String layertitle = "821b1753-a52c-45ff-9a39-14af88833a0f"; - -// String layertitle2 = "Statistical Mean in [07-01-01 01:00] (3D) {World Ocean Atlas 09: Sea Water Temperature - annual: dods://thredds.research-infrastructures.eu/thredds/dodsC/public/netcdf/temperature_annual_1deg_ENVIRONMENT_OCEANS_.nc}"; -// String layertitle2 = "0e03d0fa-9c44-4a0c-a7e3-9f6d48710d00"; -// String layertitle2 = layertitle; - String layertitle2 = "821b1753-a52c-45ff-9a39-14af88833a0f"; -// {MEAN=224.49, VARIANCE=10337.11, NUMBER_OF_ERRORS=47054, NUMBER_OF_COMPARISONS=65522, ACCURACY=28.19, MAXIMUM_ERROR=303.6, MAXIMUM_ERROR_POINT=5006:104, Resolution=0.9972222222222222} - -// layertitle = "3fb7fd88-33d4-492d-b241-4e61299c44bb"; -// layertitle2 = "3fb7fd88-33d4-492d-b241-4e61299c44bb"; - - AnalysisLogger.setLogger(cfg+AlgorithmConfiguration.defaultLoggerFile); - AlgorithmConfiguration config = new AlgorithmConfiguration(); - 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.setParam("Layer_1",layertitle); - config.setParam("Layer_2",layertitle2); - config.setParam("ValuesComparisonThreshold",""+0.1); - config.setParam("Z","0"); - config.setGcubeScope(null); -// ScopeProvider.instance.set("/gcube/devNext/NextNext"); - ScopeProvider.instance.set("/d4science.research-infrastructures.eu/gCubeApps/EGIP"); -// ScopeProvider.instance.set("/gcube/devsec"); - MapsComparator mc = new MapsComparator(); - mc.setConfiguration(config); - mc.init(); - mc.compute(); - mc.getOutput(); - } -} diff --git a/src/main/java/org/gcube/dataanalysis/geo/test/maps/TestMapsComparisonTemperature.java b/src/main/java/org/gcube/dataanalysis/geo/test/maps/TestMapsComparisonTemperature.java deleted file mode 100644 index 511b89b..0000000 --- a/src/main/java/org/gcube/dataanalysis/geo/test/maps/TestMapsComparisonTemperature.java +++ /dev/null @@ -1,41 +0,0 @@ -package org.gcube.dataanalysis.geo.test.maps; - -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; -import org.gcube.dataanalysis.geo.algorithms.MapsComparator; -import org.gcube.dataanalysis.geo.matrixmodel.MatrixExtractor; -import org.gcube.dataanalysis.geo.matrixmodel.RasterTable; - -public class TestMapsComparisonTemperature { - - static String cfg = "./cfg/"; - public static void main(String[] args) throws Exception{ -// String layertitle = "MyDistributionMap"; -// String layertitle = "Mass Concentration of Chlorophyll in Sea Water in [03-30-13 01:00] (3D) {Mercator Ocean BIOMER1V1R1: Data extracted from dataset http://atoll-mercator.vlandata.cls.fr:44080/thredds/dodsC/global-analysis-bio-001-008-a}"; - String layertitle = "Temperature in [12-15-09 01:00] (3D) {Native grid ORCA025.L75 monthly average: Data extracted from dataset http://atoll-mercator.vlandata.cls.fr:44080/thredds/dodsC/global-reanalysis-phys-001-004-b-ref-fr-mjm95-gridt}"; - String layertitle2 = "Statistical Mean in [07-01-01 01:00] (3D) {World Ocean Atlas 09: Sea Water Temperature - annual: dods://thredds.research-infrastructures.eu/thredds/dodsC/public/netcdf/temperature_annual_1deg_ENVIRONMENT_OCEANS_.nc}"; -// String layertitle2 = "Objectively Analyzed Climatology in [07-01-01 01:00] (3D) {World Ocean Atlas 09: Sea Water Temperature - annual: dods://thredds.research-infrastructures.eu/thredds/dodsC/public/netcdf/temperature_annual_1deg_ENVIRONMENT_OCEANS_.nc}"; -// String layertitle2 = "FAO AQUATIC SPECIES DISTRIBUTION MAP OF MEGALASPIS CORDYLA"; -// {MEAN=224.49, VARIANCE=10337.11, NUMBER_OF_ERRORS=47054, NUMBER_OF_COMPARISONS=65522, ACCURACY=28.19, MAXIMUM_ERROR=303.6, MAXIMUM_ERROR_POINT=5006:104, Resolution=0.9972222222222222} - - AnalysisLogger.setLogger(cfg+AlgorithmConfiguration.defaultLoggerFile); - AlgorithmConfiguration config = new AlgorithmConfiguration(); - 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.setParam("Layer_1",layertitle); - config.setParam("Layer_2",layertitle2); - config.setParam("ValuesComparisonThreshold",""+0.1); - config.setParam("Z","0"); - config.setGcubeScope(null); - - MapsComparator mc = new MapsComparator(); - mc.setConfiguration(config); - mc.init(); - mc.compute(); - mc.getOutput(); - } -} diff --git a/src/main/java/org/gcube/dataanalysis/geo/test/maps/TestMapsComparisonTemperatureUUID.java b/src/main/java/org/gcube/dataanalysis/geo/test/maps/TestMapsComparisonTemperatureUUID.java deleted file mode 100644 index 4f23a7d..0000000 --- a/src/main/java/org/gcube/dataanalysis/geo/test/maps/TestMapsComparisonTemperatureUUID.java +++ /dev/null @@ -1,45 +0,0 @@ -package org.gcube.dataanalysis.geo.test.maps; - -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; -import org.gcube.dataanalysis.geo.algorithms.MapsComparator; -import org.gcube.dataanalysis.geo.matrixmodel.MatrixExtractor; -import org.gcube.dataanalysis.geo.matrixmodel.RasterTable; - -public class TestMapsComparisonTemperatureUUID { - - static String cfg = "./cfg/"; - public static void main(String[] args) throws Exception{ -// String layertitle = "Temperature in [12-15-09 01:00] (3D) {Native grid ORCA025.L75 monthly average: Data extracted from dataset http://atoll-mercator.vlandata.cls.fr:44080/thredds/dodsC/global-reanalysis-phys-001-004-b-ref-fr-mjm95-gridt}"; -// String layertitle = "Standard Deviation from Statistical Mean from [01-16-01 01:00] to [12-16-01 01:00] (3D) {World Ocean Atlas 09: Sea Water Temperature - monthly: dods://thredds.research-infrastructures.eu/thredds/dodsC/public/netcdf/temperature_monthly_1deg_ENVIRONMENT_OCEANS_.nc}"; -// String layertitle = "86a7ac79-866a-49c6-b5d5-602fc2d87ddd"; - String layertitle = "35412bde-aa6e-49f6-b9ad-e99458882f92"; - -// String layertitle2 = "Statistical Mean in [07-01-01 01:00] (3D) {World Ocean Atlas 09: Sea Water Temperature - annual: dods://thredds.research-infrastructures.eu/thredds/dodsC/public/netcdf/temperature_annual_1deg_ENVIRONMENT_OCEANS_.nc}"; -// String layertitle2 = "0e03d0fa-9c44-4a0c-a7e3-9f6d48710d00"; -// String layertitle2 = layertitle; - String layertitle2 = "625ba45b-c19f-4a9d-b3f7-be13e8f73101"; -// {MEAN=224.49, VARIANCE=10337.11, NUMBER_OF_ERRORS=47054, NUMBER_OF_COMPARISONS=65522, ACCURACY=28.19, MAXIMUM_ERROR=303.6, MAXIMUM_ERROR_POINT=5006:104, Resolution=0.9972222222222222} - - - AnalysisLogger.setLogger(cfg+AlgorithmConfiguration.defaultLoggerFile); - AlgorithmConfiguration config = new AlgorithmConfiguration(); - 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.setParam("Layer_1",layertitle); - config.setParam("Layer_2",layertitle2); - config.setParam("ValuesComparisonThreshold",""+0.1); - config.setParam("Z","0"); - config.setGcubeScope(null); - - MapsComparator mc = new MapsComparator(); - mc.setConfiguration(config); - mc.init(); - mc.compute(); - mc.getOutput(); - } -} diff --git a/src/main/java/org/gcube/dataanalysis/geo/test/maps/TestMapsComparisonTemperatureWOA.java b/src/main/java/org/gcube/dataanalysis/geo/test/maps/TestMapsComparisonTemperatureWOA.java deleted file mode 100644 index 3bec98c..0000000 --- a/src/main/java/org/gcube/dataanalysis/geo/test/maps/TestMapsComparisonTemperatureWOA.java +++ /dev/null @@ -1,35 +0,0 @@ -package org.gcube.dataanalysis.geo.test.maps; - -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; -import org.gcube.dataanalysis.geo.algorithms.MapsComparator; - -public class TestMapsComparisonTemperatureWOA { - - static String cfg = "./cfg/"; - public static void main(String[] args) throws Exception{ - String layertitle = "Temperature in [07-01-01 13:00] (3D) {World Ocean Atlas 2005: Tcl version: 8.4.13, NAP version: 6.2.2}"; - String layertitle2 = "Statistical Mean in [07-01-01 01:00] (3D) {World Ocean Atlas 09: Sea Water Temperature - annual: dods://thredds.research-infrastructures.eu/thredds/dodsC/public/netcdf/temperature_annual_1deg_ENVIRONMENT_OCEANS_.nc}"; - //{MEAN=0.0, VARIANCE=0.0, NUMBER_OF_ERRORS=0, NUMBER_OF_COMPARISONS=65522, ACCURACY=100.0, MAXIMUM_ERROR=0.0, MAXIMUM_ERROR_POINT=null, TREND=STATIONARY, Resolution=0.9972222222222222} - - AnalysisLogger.setLogger(cfg+AlgorithmConfiguration.defaultLoggerFile); - AlgorithmConfiguration config = new AlgorithmConfiguration(); - 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.setParam("Layer_1",layertitle); - config.setParam("Layer_2",layertitle2); - config.setParam("ValuesComparisonThreshold",""+0.1); - config.setParam("Z","0"); - config.setGcubeScope("/gcube/devsec/devVRE"); - - MapsComparator mc = new MapsComparator(); - mc.setConfiguration(config); - mc.init(); - mc.compute(); - mc.getOutput(); - } -} diff --git a/src/main/java/org/gcube/dataanalysis/geo/test/maps/TestMapsComparisoninTime.java b/src/main/java/org/gcube/dataanalysis/geo/test/maps/TestMapsComparisoninTime.java deleted file mode 100644 index 5e8aacc..0000000 --- a/src/main/java/org/gcube/dataanalysis/geo/test/maps/TestMapsComparisoninTime.java +++ /dev/null @@ -1,65 +0,0 @@ -package org.gcube.dataanalysis.geo.test.maps; - -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; -import org.gcube.dataanalysis.geo.algorithms.MapsComparator; - -public class TestMapsComparisoninTime { - - static String cfg = "./cfg/"; - - public static void main(String[] args) throws Exception{ - - int[] timeIdx = {0,12,24,36,48,60,72,84,96,108,120}; - - for (int i=1;i0) {MEAN=0.53, VARIANCE=0.28, NUMBER_OF_ERRORS=36075, NUMBER_OF_COMPARISONS=522242, ACCURACY=93.09, MAXIMUM_ERROR=6.0, MAXIMUM_ERROR_POINT=7309:456, TREND=EXPANSION, Resolution=0.3525954946131244} ELAPSED: 1370363639187 -**********(24->12) {MEAN=0.56, VARIANCE=0.3, NUMBER_OF_ERRORS=36053, NUMBER_OF_COMPARISONS=522242, ACCURACY=93.1, MAXIMUM_ERROR=6.95, MAXIMUM_ERROR_POINT=1313:143, TREND=EXPANSION, Resolution=0.3525954946131244} ELAPSED: 1370363722843 Japan -**********(36->24) {MEAN=0.62, VARIANCE=0.33, NUMBER_OF_ERRORS=35744, NUMBER_OF_COMPARISONS=522242, ACCURACY=93.16, MAXIMUM_ERROR=6.87, MAXIMUM_ERROR_POINT=1314:465, TREND=EXPANSION, Resolution=0.3525954946131244} ELAPSED: 1370363798387 -**********(48->36) {MEAN=0.49, VARIANCE=0.22, NUMBER_OF_ERRORS=35664, NUMBER_OF_COMPARISONS=522242, ACCURACY=93.17, MAXIMUM_ERROR=7.54, MAXIMUM_ERROR_POINT=7307:456, TREND=CONTRACTION, Resolution=0.3525954946131244} ELAPSED: 1370363875063 North Carolina -**********(60->48) {MEAN=0.46, VARIANCE=0.23, NUMBER_OF_ERRORS=36133, NUMBER_OF_COMPARISONS=522242, ACCURACY=93.08, MAXIMUM_ERROR=5.42, MAXIMUM_ERROR_POINT=7307:456, TREND=EXPANSION, Resolution=0.3525954946131244} ELAPSED: 1370363953390 -**********(72->60) {MEAN=0.56, VARIANCE=0.31, NUMBER_OF_ERRORS=35970, NUMBER_OF_COMPARISONS=522242, ACCURACY=93.11, MAXIMUM_ERROR=7.01, MAXIMUM_ERROR_POINT=7307:236, TREND=EXPANSION, Resolution=0.3525954946131244} ELAPSED: 1370364033154 -**********(84->72) {MEAN=0.57, VARIANCE=0.31, NUMBER_OF_ERRORS=36148, NUMBER_OF_COMPARISONS=522242, ACCURACY=93.08, MAXIMUM_ERROR=7.02, MAXIMUM_ERROR_POINT=7307:247, TREND=CONTRACTION, Resolution=0.3525954946131244} ELAPSED: 1370364110444 -**********(96->84) {MEAN=0.59, VARIANCE=0.32, NUMBER_OF_ERRORS=35873, NUMBER_OF_COMPARISONS=522242, ACCURACY=93.13, MAXIMUM_ERROR=5.23, MAXIMUM_ERROR_POINT=7306:249, TREND=CONTRACTION, Resolution=0.3525954946131244} ELAPSED: 1370364190900 -**********(108->96) {MEAN=0.53, VARIANCE=0.27, NUMBER_OF_ERRORS=35789, NUMBER_OF_COMPARISONS=522242, ACCURACY=93.15, MAXIMUM_ERROR=4.96, MAXIMUM_ERROR_POINT=7306:249, TREND=EXPANSION, Resolution=0.3525954946131244} ELAPSED: 1370364272133 -**********(120->108) {MEAN=0.62, VARIANCE=0.37, NUMBER_OF_ERRORS=36194, NUMBER_OF_COMPARISONS=522242, ACCURACY=93.07, MAXIMUM_ERROR=5.51, MAXIMUM_ERROR_POINT=1316:352, TREND=EXPANSION, Resolution=0.3525954946131244} pacific ocean - - */ - long t0=0; - AnalysisLogger.setLogger(cfg+AlgorithmConfiguration.defaultLoggerFile); - AlgorithmConfiguration config = new AlgorithmConfiguration(); - 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.setParam("Layer_1",layertitle); - config.setParam("Layer_2",layertitle); - config.setParam("TimeIndex_1",""+t1); - config.setParam("TimeIndex_2",""+t2); - config.setParam("ValuesComparisonThreshold","0.01"); - config.setParam("Z","0"); - config.setGcubeScope(null); - - MapsComparator mc = new MapsComparator(); - mc.setConfiguration(config); - mc.init(); - mc.compute(); - mc.getOutput(); - System.out.println("*********("+t2+"->"+t1+") "+mc.outputParameters +" ELAPSED: "+(System.currentTimeMillis()-t0)); - - } -} diff --git a/src/main/java/org/gcube/dataanalysis/geo/test/projections/GeolocateCountry.java b/src/main/java/org/gcube/dataanalysis/geo/test/projections/GeolocateCountry.java deleted file mode 100644 index da1459e..0000000 --- a/src/main/java/org/gcube/dataanalysis/geo/test/projections/GeolocateCountry.java +++ /dev/null @@ -1,218 +0,0 @@ -package org.gcube.dataanalysis.geo.test.projections; - -import java.io.BufferedReader; -import java.io.BufferedWriter; -import java.io.File; -import java.io.FileReader; -import java.io.FileWriter; -import java.util.ArrayList; -import java.util.HashMap; -import java.util.LinkedHashMap; -import java.util.List; -import java.util.Map; - -import org.gcube.contentmanagement.graphtools.utils.MathFunctions; -import org.gcube.contentmanagement.lexicalmatcher.utils.DistanceCalculator; -import org.gcube.dataanalysis.ecoengine.utils.Transformations; - -public class GeolocateCountry { - - static String faoreport = "FAO data.csv"; - - // static String faoreport = "C:\\Users\\coro\\Desktop\\allCountries.txt"; - - public static void main1(String[] args) throws Exception { - BufferedReader fr = new BufferedReader(new FileReader(new File(faoreport))); - String line = fr.readLine(); - long counter = 0; - while (line != null) { - // System.out.println(line); - String[] split = line.split("\t"); - String country = split[17]; - String x = split[5]; - String y = split[4]; - if (country.contains("Russia")) - break; - // else - // System.out.println("Country:"+country+" "+x+","+y); - - counter++; - if (counter % 500000 == 0) - System.out.println("Country:" + country + " " + x + "," + y); - line = fr.readLine(); - } - - fr.close(); - } - - public static void main2(String[] args) throws Exception { - BufferedReader fr = new BufferedReader(new FileReader(new File(faoreport))); - String line = fr.readLine(); - parseCentroidsFile(); - parseWorldCapitalsFile(); - line = fr.readLine(); - HashMap yetDone = new HashMap(); - while (line != null) { - List p = Transformations.parseCVSString(line, ","); - String country = p.get(1); - // TO DO rebuild the original CSV file - String suggestion = yetDone.get(country); - if (suggestion == null) { - suggestion = getCentroid(country, capitals, 0.6); - if (suggestion.length() == 0) - suggestion = getCentroid(country, centroids, 0.3); - - yetDone.put(country, suggestion); - } - - System.out.println(line + "," + suggestion); - - line = fr.readLine(); - } - - fr.close(); - } - - public static void main(String[] args) throws Exception { - String file = "LargeTS.csv"; - System.out.println("Processing"); - List countries = GeolocateCountry.geoLocateCountries(1, file); - System.out.println("Dumping"); - BufferedWriter bw = new BufferedWriter(new FileWriter(new File("LargeTsGeo.csv"))); - for (String country:countries){ - bw.write(country+"\n"); - } - bw.close(); - System.out.println("Done"); - } - - public static List geoLocateCountries(int idxCountryColumn, String file) throws Exception { - BufferedReader fr = new BufferedReader(new FileReader(new File(file))); - String line = fr.readLine(); - parseCentroidsFile(); - parseWorldCapitalsFile(); - line = fr.readLine(); - List yetDone = new ArrayList(); - - while (line != null) { - List p = Transformations.parseCVSString(line, ","); - String country = p.get(idxCountryColumn); - String suggestion = null; - suggestion = getCentroid(country, capitals, 0.6); - if (suggestion.length() == 0) - suggestion = getCentroid(country, centroids, 0.3); - if (suggestion==null || suggestion.length()==0) - suggestion = ",,,,"; - String outstring = country + "," + suggestion; - yetDone.add(outstring); -// System.out.println(outstring); - line = fr.readLine(); - } - - fr.close(); - return yetDone; - } - - public static Map geoLocateCountriesWithNoDuplicates(int idxCountryColumn, String file) throws Exception { - BufferedReader fr = new BufferedReader(new FileReader(new File(file))); - String line = fr.readLine(); - parseCentroidsFile(); - parseWorldCapitalsFile(); - line = fr.readLine(); - LinkedHashMap yetDone = new LinkedHashMap(); - - while (line != null) { - List p = Transformations.parseCVSString(line, ","); - String country = p.get(idxCountryColumn); - String suggestion = yetDone.get(country); - if (suggestion == null) { - suggestion = getCentroid(country, capitals, 0.6); - if (suggestion.length() == 0) - suggestion = getCentroid(country, centroids, 0.3); - - yetDone.put(country, suggestion); - } - - System.out.println(line + "," + suggestion); - - line = fr.readLine(); - } - - fr.close(); - return yetDone; - } - - static HashMap centroids = new HashMap(); - static HashMap capitals = new HashMap(); - - public static void parseCentroidsFile() throws Exception { - BufferedReader fr = new BufferedReader(new FileReader(new File("countriescentroids.txt"))); - String line = fr.readLine(); - - while (line != null) { - String[] elems = line.split(","); - String x = elems[0]; - String y = elems[1]; - String cntry_name = elems[2]; - centroids.put(cntry_name, x + "," + y); - line = fr.readLine(); - } - - fr.close(); - } - - public static void parseWorldCapitalsFile() throws Exception { - BufferedReader fr = new BufferedReader(new FileReader(new File("country-capitals.csv"))); - String line = fr.readLine(); - - while (line != null) { - String[] elems = line.split(","); - String x = elems[3]; - String y = elems[2]; - String cntry_name = elems[0]; - capitals.put(cntry_name, x + "," + y); - line = fr.readLine(); - } - - fr.close(); - } - - public static String getCentroid(String country, HashMap centroids, double threshold) { - - String c = centroids.get(country); - List sb = new ArrayList(); - List scores = new ArrayList(); - DistanceCalculator dc = new DistanceCalculator(); - if (c == null) { - for (String key : centroids.keySet()) { - if (key.length() > 0) { - /* - * if (key.contains(country) || country.contains(key)) { if (sb.length() > 0) sb.append("/"); - * - * sb.append(key + "," + centroids.get(key) + "("+0.8+")"+" "); } else { - */ - double score = dc.CD(false, country, key, true, false); - if (score > threshold) { - int i = 0; - for (Double cscore : scores) { - if (cscore < score) - break; - i++; - } - - sb.add(i, key + "," + centroids.get(key) + "," + MathFunctions.roundDecimal(score, 2)); - scores.add(i, score); - } - - // } - } - } - if (sb.size() > 0) - return sb.get(0).toString(); - else - return ""; - } else - return country + "," + c + "," + 1; - } - -} diff --git a/src/main/java/org/gcube/dataanalysis/geo/test/projections/ProduceASCFile.java b/src/main/java/org/gcube/dataanalysis/geo/test/projections/ProduceASCFile.java deleted file mode 100644 index dec058a..0000000 --- a/src/main/java/org/gcube/dataanalysis/geo/test/projections/ProduceASCFile.java +++ /dev/null @@ -1,143 +0,0 @@ -package org.gcube.dataanalysis.geo.test.projections; - -import java.io.File; -import java.io.FileWriter; -import java.util.List; - -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; -import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType; -import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent; -import org.gcube.dataanalysis.ecoengine.processing.factories.TransducerersFactory; -import org.gcube.dataanalysis.ecoengine.test.regression.Regressor; -import org.gcube.dataanalysis.ecoengine.utils.Tuple; -import org.gcube.dataanalysis.geo.connectors.asc.AscRasterWriter; -import org.gcube.dataanalysis.geo.connectors.table.Table; -import org.gcube.dataanalysis.geo.connectors.table.TableMatrixRepresentation; -import org.gcube.dataanalysis.geo.utils.MapUtils; -import org.gcube.dataanalysis.geo.utils.VectorOperations; - -public class ProduceASCFile { - - static String layer = "http://geoserver-dev.d4science-ii.research-infrastructures.eu/geoserver/ows?service=wfs&version=1.0.0&request=GetFeature&srsName=urn:x-ogc:def:crs:EPSG:4326&TYPENAME=aquamaps:worldborders"; - -// static String layer = "ed8f77bd-2423-4036-b34d-2f1cb5fcaffc"; -// static String layer = "http://geoserver-dev.d4science-ii.research-infrastructures.eu/geoserver/ows?service=wfs&version=1.0.0&request=GetFeature&srsName=urn:x-ogc:def:crs:EPSG:4326&TYPENAME=aquamaps:eezall"; -// static String layer = "http://geo.vliz.be/geoserver/MarineRegions/ows?service=wfs&version=1.0.0&request=GetFeature&srsName=urn:x-ogc:def:crs:EPSG:4326&typename=MarineRegions:eez"; -// static String layer = "aeabfdb5-9ddb-495e-b628-5b7d2cf1d8a2"; - - static String field = "f_cat"; -// static String field = "eez_id"; -// static String field = "f_eezall"; -// static String field = "f_eez_id"; -// static String field = "f_zone"; - - static double res = 0.3; - static String table = "testextraction4"; - static String scope = "/gcube/devsec/devVRE"; - static String databaseUser = "gcube"; - static String databasePwd = "d4science2"; - static String databaseURL = "jdbc:postgresql://localhost/testdb"; - static String databaseDriver = "org.postgresql.Driver"; - static double xll = -180; - static double yll=-90; - static double xur=180; - static double yur=90; - - static String outASCIIMAP = "producedmap.txt"; - static String outASCFile = "produced.asc"; - - private static AlgorithmConfiguration XYExtractionConfig() { - - AlgorithmConfiguration config = new AlgorithmConfiguration(); - - config.setAgent("XYEXTRACTOR"); - config.setConfigPath("./cfg/"); - config.setPersistencePath("./"); - config.setParam("DatabaseUserName", databaseUser); - config.setParam("DatabasePassword", databasePwd); - config.setParam("DatabaseURL", databaseURL); - config.setParam("DatabaseDriver", databaseDriver); - config.setGcubeScope(scope); - - config.setParam("Layer", layer); - - config.setParam("Z", "0"); - config.setParam("TimeIndex", "0"); - config.setParam("BBox_LowerLeftLat", ""+yll); - config.setParam("BBox_LowerLeftLong", ""+xll); - config.setParam("BBox_UpperRightLat", ""+yur); - config.setParam("BBox_UpperRightLong", ""+xur); - config.setParam("XResolution", ""+res); - config.setParam("YResolution", ""+res); - config.setParam("OutputTableName", table); - config.setParam("OutputTableLabel", table); - - return config; - } - - private static AlgorithmConfiguration TableExtractionConfig() { - - AlgorithmConfiguration config = new AlgorithmConfiguration(); - - config.setConfigPath("./cfg/"); - config.setPersistencePath("./"); - config.setParam("DatabaseUserName", databaseUser); - config.setParam("DatabasePassword", databasePwd); - config.setParam("DatabaseURL", databaseURL); - config.setParam("DatabaseDriver", databaseDriver); - config.setGcubeScope(scope); - config.setParam("BBox_LowerLeftLat", ""+yll); - config.setParam("BBox_LowerLeftLong", ""+xll); - config.setParam("BBox_UpperRightLat", ""+xur); - config.setParam("BBox_UpperRightLong", ""+yur); - config.setParam("XResolution", ""+res); - config.setParam("YResolution", ""+res); - config.setParam("OutputTableName", table); - config.setParam("OutputTableLabel", table); - - config.setParam(TableMatrixRepresentation.tableNameParameter, table); - config.setParam(TableMatrixRepresentation.xDimensionColumnParameter, "approx_x"); - config.setParam(TableMatrixRepresentation.yDimensionColumnParameter, "approx_y"); - config.setParam(TableMatrixRepresentation.timeDimensionColumnParameter, "time"); - config.setParam(TableMatrixRepresentation.valueDimensionColumnParameter, field); - config.setParam(TableMatrixRepresentation.filterParameter, " "); - - return config; - } - - public static void main(String[] args) throws Exception{ - -// produce(XYExtractionConfig()); - AnalysisLogger.setLogger("./cfg/"+AlgorithmConfiguration.defaultLoggerFile); - List> tuples = VectorOperations.generateCoordinateTripletsInBoundingBox(xll,xur,yll,yur, 0, res, res); - Table connector = new Table(TableExtractionConfig(), res); - List values = connector.getFeaturesInTimeInstantAndArea(null, null, 0, tuples, xll,xur,yll,yur); - double[][] matrix = VectorOperations.vectorToMatix(values, xll,xur,yll,yur,res, res); - System.out.println(MapUtils.globalASCIIMap(matrix)); - FileWriter fw = new FileWriter(new File(outASCIIMAP)); - fw.write(MapUtils.globalASCIIMap(matrix)); - fw.close(); - - AscRasterWriter writer = new AscRasterWriter(); - writer.writeRasterInvertYAxis(outASCFile, matrix, xll,yll, res, "-9999"); - } - - - public static void produce(AlgorithmConfiguration config) throws Exception { - - System.out.println("TEST 1"); - - - AnalysisLogger.getLogger().debug("Executing: "+config.getAgent()); - List trans = null; - trans = TransducerersFactory.getTransducerers(config); - trans.get(0).init(); - Regressor.process(trans.get(0)); - StatisticalType st = trans.get(0).getOutput(); - AnalysisLogger.getLogger().debug("ST:" + st); - trans = null; - - } - -} diff --git a/src/main/java/org/gcube/dataanalysis/geo/test/projections/ProduceCentroids.java b/src/main/java/org/gcube/dataanalysis/geo/test/projections/ProduceCentroids.java deleted file mode 100644 index 7b30a2a..0000000 --- a/src/main/java/org/gcube/dataanalysis/geo/test/projections/ProduceCentroids.java +++ /dev/null @@ -1,48 +0,0 @@ -package org.gcube.dataanalysis.geo.test.projections; - -import java.util.ArrayList; -import java.util.HashMap; -import java.util.List; - -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.gcube.dataanalysis.geo.connectors.wfs.FeaturedPolygon; -import org.gcube.dataanalysis.geo.connectors.wfs.WFSDataExplorer; - -import com.vividsolutions.jts.geom.Geometry; -import com.vividsolutions.jts.geom.Point; -import com.vividsolutions.jts.geom.Polygon; - -public class ProduceCentroids { - static String layer = "http://geoserver-dev.d4science-ii.research-infrastructures.eu/geoserver/ows?service=wfs&version=1.0.0&request=GetFeature&srsName=urn:x-ogc:def:crs:EPSG:4326&TYPENAME=aquamaps:worldborders"; - static String layername = "aquamaps:worldborders"; - - public static void main(String[] args) throws Exception{ - - List featuresInTime = new ArrayList(); - AnalysisLogger.getLogger().debug("taking WFS features from layer: "+layer); - featuresInTime = WFSDataExplorer.getFeatures(layer, layername, -180, -90, 180, 90); - HashMap centroidsmap = new HashMap(); - HashMap polymap = new HashMap(); - for (FeaturedPolygon fpoly:featuresInTime){ -// Point centroid = fpoly.p.getCentroid(); - Geometry prevPoly = polymap.get(fpoly.features.get("cntry_name")); - - if (prevPoly!=null){ - prevPoly = prevPoly.union(fpoly.p); - } - else - prevPoly = fpoly.p; - -// if ((""+fpoly.features).contains("United States")) -// System.out.println("centroid:"+fpoly.p.getCentroid()+" now "+prevPoly.getCentroid()); - - polymap.put(fpoly.features.get("cntry_name"),prevPoly); - } - - for (String key:polymap.keySet()){ - Point centroid = polymap.get(key).getCentroid(); - System.out.println(centroid.getX()+","+centroid.getY()+","+key); - } - } - -} diff --git a/src/main/java/org/gcube/dataanalysis/geo/test/projections/TestExtractionXYMatrixFromTable.java b/src/main/java/org/gcube/dataanalysis/geo/test/projections/TestExtractionXYMatrixFromTable.java deleted file mode 100644 index f93c4f7..0000000 --- a/src/main/java/org/gcube/dataanalysis/geo/test/projections/TestExtractionXYMatrixFromTable.java +++ /dev/null @@ -1,114 +0,0 @@ -package org.gcube.dataanalysis.geo.test.projections; - -import java.io.File; -import java.io.FileWriter; - -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; -import org.gcube.dataanalysis.geo.connectors.table.TableMatrixRepresentation; -import org.gcube.dataanalysis.geo.matrixmodel.XYExtractor; -import org.gcube.dataanalysis.geo.utils.MapUtils; - -public class TestExtractionXYMatrixFromTable { - - public static void sliceTableAquaMaps(AlgorithmConfiguration config) throws Exception { - // latimeria chalumnae - config.setParam(TableMatrixRepresentation.tableNameParameter, "testextractionaquamaps"); - config.setParam(TableMatrixRepresentation.xDimensionColumnParameter, "approx_x"); - config.setParam(TableMatrixRepresentation.yDimensionColumnParameter, "approx_y"); - config.setParam(TableMatrixRepresentation.timeDimensionColumnParameter, "time"); - config.setParam(TableMatrixRepresentation.valueDimensionColumnParameter, "f_probability"); - config.setParam(TableMatrixRepresentation.filterParameter, ""); - } - - public static void sliceTablePhImported(AlgorithmConfiguration config) throws Exception { - // ph - config.setParam("DatabaseUserName", "utente"); - config.setParam("DatabasePassword", "d4science"); - config.setParam("DatabaseURL", "jdbc:postgresql://statistical-manager.d.d4science.org/testdb"); - config.setParam(TableMatrixRepresentation.tableNameParameter, "generic_idbc699da3_a4d5_40fb_80ff_666dbf1316d5"); - config.setParam(TableMatrixRepresentation.xDimensionColumnParameter, "x"); - config.setParam(TableMatrixRepresentation.yDimensionColumnParameter, "y"); - config.setParam(TableMatrixRepresentation.timeDimensionColumnParameter, "time"); - config.setParam(TableMatrixRepresentation.valueDimensionColumnParameter, "fvalue"); - config.setParam(TableMatrixRepresentation.filterParameter, ""); - } - - - public static void sliceTablePh(AlgorithmConfiguration config) throws Exception { - // ph - config.setParam(TableMatrixRepresentation.tableNameParameter, "testextraction"); - config.setParam(TableMatrixRepresentation.xDimensionColumnParameter, "x"); - config.setParam(TableMatrixRepresentation.yDimensionColumnParameter, "y"); - config.setParam(TableMatrixRepresentation.timeDimensionColumnParameter, "time"); - config.setParam(TableMatrixRepresentation.valueDimensionColumnParameter, "fvalue"); - config.setParam(TableMatrixRepresentation.filterParameter, ""); - } - - public static void sliceMapCreated(AlgorithmConfiguration config) throws Exception { - - config.setParam(TableMatrixRepresentation.tableNameParameter, "testextraction2"); - config.setParam(TableMatrixRepresentation.xDimensionColumnParameter, "x"); - config.setParam(TableMatrixRepresentation.yDimensionColumnParameter, "y"); - config.setParam(TableMatrixRepresentation.timeDimensionColumnParameter, "time"); - config.setParam(TableMatrixRepresentation.valueDimensionColumnParameter, "fvalue"); - config.setParam(TableMatrixRepresentation.filterParameter, ""); - } - - public static void sliceMapCreated2(AlgorithmConfiguration config) throws Exception { - - config.setParam(TableMatrixRepresentation.tableNameParameter, "testextraction2"); - config.setParam(TableMatrixRepresentation.xDimensionColumnParameter, "approx_x"); - config.setParam(TableMatrixRepresentation.yDimensionColumnParameter, "approx_y"); - config.setParam(TableMatrixRepresentation.timeDimensionColumnParameter, "time"); - config.setParam(TableMatrixRepresentation.valueDimensionColumnParameter, "f_temp"); - config.setParam(TableMatrixRepresentation.filterParameter, ""); - } - - public static void sliceMaxEnt(AlgorithmConfiguration config) throws Exception { - - config.setParam(TableMatrixRepresentation.tableNameParameter, "rstrf31af9ff13de42e583327e4ca51c38ef"); - config.setParam(TableMatrixRepresentation.xDimensionColumnParameter, "x"); - config.setParam(TableMatrixRepresentation.yDimensionColumnParameter, "y"); - config.setParam(TableMatrixRepresentation.timeDimensionColumnParameter, "time"); - config.setParam(TableMatrixRepresentation.valueDimensionColumnParameter, "fvalue"); - config.setParam(TableMatrixRepresentation.filterParameter, ""); - } - - public static void sliceTableMapServer(AlgorithmConfiguration config) throws Exception { - - config.setParam(TableMatrixRepresentation.tableNameParameter, "testextraction3"); - config.setParam(TableMatrixRepresentation.xDimensionColumnParameter, "approx_x"); - config.setParam(TableMatrixRepresentation.yDimensionColumnParameter, "approx_y"); - config.setParam(TableMatrixRepresentation.timeDimensionColumnParameter, "time"); - config.setParam(TableMatrixRepresentation.valueDimensionColumnParameter, "f_depth"); - config.setParam(TableMatrixRepresentation.filterParameter, ""); - } - - - public static void main(String[] args) throws Exception { - AnalysisLogger.setLogger("./cfg/" + AlgorithmConfiguration.defaultLoggerFile); - AlgorithmConfiguration config = new AlgorithmConfiguration(); - - 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"); - sliceTableMapServer(config); - - double resolution = 1; - FileWriter fw = new FileWriter(new File("maps.txt")); - - XYExtractor extractor = new XYExtractor(config); - double[][] matrix = extractor.extractXYGrid(null, 0, -180, 180, -90, 90, 0, resolution, resolution); - String map = MapUtils.globalASCIIMap(matrix); - fw.write(map); - - fw.close(); - System.out.println("DONE!"); - } - -} diff --git a/src/main/java/org/gcube/dataanalysis/geo/test/projections/TestMapCreation.java b/src/main/java/org/gcube/dataanalysis/geo/test/projections/TestMapCreation.java deleted file mode 100644 index a83f54e..0000000 --- a/src/main/java/org/gcube/dataanalysis/geo/test/projections/TestMapCreation.java +++ /dev/null @@ -1,60 +0,0 @@ -package org.gcube.dataanalysis.geo.test.projections; - -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; -import org.gcube.dataanalysis.geo.algorithms.PointsMapsCreator; -import org.gcube.dataanalysis.geo.algorithms.PolygonMapsCreator; - -public class TestMapCreation { - - - static String cfg = "./cfg/"; - - -public static void main(String[] args) throws Exception{ - - AnalysisLogger.setLogger(cfg+AlgorithmConfiguration.defaultLoggerFile); - AlgorithmConfiguration config = new AlgorithmConfiguration(); - config.setConfigPath(cfg); -// config.setGcubeScope("/gcube/devsec/statVRE"); - config.setGcubeScope("/gcube/devsec/devVRE"); - config.setPersistencePath("./"); - - config.setParam("MapName","Test Polygonal Map Ph 8"); - /* - config.setParam("InputTable","occurrence_species_id0045886b_2a7c_4ede_afc4_3157c694b893"); - config.setParam("xDimension","decimallongitude"); - config.setParam("yDimension","decimallatitude"); - config.setParam("Info","recordedby") ; - config.setParam("Resolution","0.5"); - */ - - config.setParam("InputTable","testextraction2"); - config.setParam("xDimension","x"); - config.setParam("yDimension","y"); - config.setParam("Info","fvalue") ; - - - config.setParam("DatabaseUserName","gcube"); - config.setParam("DatabasePassword","d4science2"); - config.setParam("DatabaseURL","jdbc:postgresql://localhost/testdb"); - config.setParam("DatabaseDriver","org.postgresql.Driver"); - - config.setParam("Z","0"); - - config.setParam("user", "postgres"); - config.setParam("password", "d4science2"); - config.setParam("STOREURL","jdbc:postgresql://geoserver-test.d4science-ii.research-infrastructures.eu/timeseriesgisdb"); - config.setParam("driver", "org.postgresql.Driver"); - config.setParam("dialect", "org.hibernatespatial.postgis.PostgisDialect"); - /* - PolygonMapsCreator mc = new PolygonMapsCreator(); - */ - PointsMapsCreator mc = new PointsMapsCreator(); - mc.setConfiguration(config); - mc.init(); - mc.compute(); - - } - -} diff --git a/src/main/java/org/gcube/dataanalysis/geo/test/projections/TestXYExtractionAlgorithm.java b/src/main/java/org/gcube/dataanalysis/geo/test/projections/TestXYExtractionAlgorithm.java deleted file mode 100644 index 2639886..0000000 --- a/src/main/java/org/gcube/dataanalysis/geo/test/projections/TestXYExtractionAlgorithm.java +++ /dev/null @@ -1,316 +0,0 @@ -package org.gcube.dataanalysis.geo.test.projections; - -import java.util.List; - -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; -import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType; -import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent; -import org.gcube.dataanalysis.ecoengine.processing.factories.TransducerersFactory; -import org.gcube.dataanalysis.ecoengine.test.regression.Regressor; -import org.gcube.dataanalysis.geo.connectors.table.TableMatrixRepresentation; - -public class TestXYExtractionAlgorithm { - -// static AlgorithmConfiguration[] configs = { testXYExtractionNetCDF(),testXYExtractionAquaMaps(),testXYExtractionTable(),testXYExtractionTable2(),testDirectExtraction()}; -// static AlgorithmConfiguration[] configs = { testXYExtractionTable2()}; -// static AlgorithmConfiguration[] configs = { testDirectExtraction()}; -// static AlgorithmConfiguration[] configs = { testXYExtractionAquaMaps()}; -// static AlgorithmConfiguration[] configs = { testXYExtractionGeotermia()}; -// static AlgorithmConfiguration[] configs = { testXYExtractionFAO()}; -// static AlgorithmConfiguration[] configs = { testXYExtractionNetCDF()}; -// static AlgorithmConfiguration[] configs = { testXYExtractionWFS11()}; - static AlgorithmConfiguration[] configs = { testXYExtractionWFSDirect()}; - - public static void main(String[] args) throws Exception { - - System.out.println("TEST 1"); - - for (int i = 0; i < configs.length; i++) { - AnalysisLogger.getLogger().debug("Executing: "+configs[i].getAgent()); - List trans = null; - trans = TransducerersFactory.getTransducerers(configs[i]); - trans.get(0).init(); - Regressor.process(trans.get(0)); - StatisticalType st = trans.get(0).getOutput(); - AnalysisLogger.getLogger().debug("ST:" + st); - trans = null; - } - } - - private static AlgorithmConfiguration testXYExtractionProd() { - - AlgorithmConfiguration config = new AlgorithmConfiguration(); - - config.setAgent("XYEXTRACTOR"); - 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("/d4science.research-infrastructures.eu/gCubeApps/BiodiversityLab"); - - config.setParam("Layer","0aac424b-5f5b-4fa6-97d6-4b4deee62b97"); - config.setParam("Z","0"); - config.setParam("TimeIndex","0"); - config.setParam("BBox_LowerLeftLat","-60"); - config.setParam("BBox_LowerLeftLong","-50"); - config.setParam("BBox_UpperRightLat","60"); - config.setParam("BBox_UpperRightLong","50"); - config.setParam("XResolution","0.5"); - config.setParam("YResolution","0.5"); - config.setParam("OutputTableName","testextractionprod"); - config.setParam("OutputTableLabel","testextractionprod"); - - return config; - } - - private static AlgorithmConfiguration testXYExtractionGeotermia() { - - AlgorithmConfiguration config = new AlgorithmConfiguration(); - - config.setAgent("XYEXTRACTOR"); - 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("/d4science.research-infrastructures.eu/gCubeApps/BiodiversityLab"); - - config.setParam("Layer","http://repoigg.services.iit.cnr.it:8080/geoserver/IGG/ows?service=WFS&version=1.0.0&request=GetFeature&typeName=IGG:area_temp_1000&maxFeatures=50"); - config.setParam("Z","-1000"); - config.setParam("TimeIndex","0"); - config.setParam("BBox_LowerLeftLat","34.46"); - config.setParam("BBox_LowerLeftLong","5.85"); - config.setParam("BBox_UpperRightLat","49"); - config.setParam("BBox_UpperRightLong","21.41"); - config.setParam("XResolution","0.01"); - config.setParam("YResolution","0.01"); - config.setParam("OutputTableName","testextractiongeotermia"); - config.setParam("OutputTableLabel","testextractiongeotermia"); - - return config; - } - - private static AlgorithmConfiguration testXYExtractionFAO() { - - AlgorithmConfiguration config = new AlgorithmConfiguration(); - - config.setAgent("XYEXTRACTOR"); - 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","20c06241-f00f-4cb0-82a3-4e5ec97a0d0a"); - config.setParam("Z","0"); - config.setParam("TimeIndex","0"); - config.setParam("BBox_LowerLeftLat","-90"); - config.setParam("BBox_LowerLeftLong","-180"); - config.setParam("BBox_UpperRightLat","90"); - config.setParam("BBox_UpperRightLong","180"); - config.setParam("XResolution","0.2"); - config.setParam("YResolution","0.2"); - config.setParam("OutputTableName","testextractionfao"); - config.setParam("OutputTableLabel","testextractionfao"); - - return config; - } - - private static AlgorithmConfiguration testXYExtractionNetCDF() { - - AlgorithmConfiguration config = new AlgorithmConfiguration(); - - config.setAgent("XYEXTRACTOR"); - 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("/d4science.research-infrastructures.eu/gCubeApps/BiodiversityLab"); - - config.setParam("Layer","c565e32c-c5b3-4964-b44f-06dc620563e9"); - config.setParam("Z","0"); - config.setParam("TimeIndex","0"); - config.setParam("BBox_LowerLeftLat","-60"); - config.setParam("BBox_LowerLeftLong","-50"); - config.setParam("BBox_UpperRightLat","60"); - config.setParam("BBox_UpperRightLong","50"); - config.setParam("XResolution","0.5"); - config.setParam("YResolution","0.5"); - config.setParam("OutputTableName","testextraction2"); - config.setParam("OutputTableLabel","testextraction2"); - - return config; - } - - - private static AlgorithmConfiguration testXYExtractionWFS11() { - - AlgorithmConfiguration config = new AlgorithmConfiguration(); - - config.setAgent("XYEXTRACTOR"); - 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("/d4science.research-infrastructures.eu/gCubeApps/EGIP"); - - config.setParam("Layer","3f16f87a-68db-49ca-bfc7-affcd83ae274"); - config.setParam("Z","0"); - config.setParam("TimeIndex","0"); - config.setParam("BBox_LowerLeftLat","-60"); - config.setParam("BBox_LowerLeftLong","-70"); - config.setParam("BBox_UpperRightLat","60"); - config.setParam("BBox_UpperRightLong","70"); - config.setParam("XResolution","0.5"); - config.setParam("YResolution","0.5"); - config.setParam("OutputTableName","testextraction2"); - config.setParam("OutputTableLabel","testextraction2"); - - return config; - } - - - private static AlgorithmConfiguration testXYExtractionWFSDirect() { - - AlgorithmConfiguration config = new AlgorithmConfiguration(); - - config.setAgent("XYEXTRACTOR"); - 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("/d4science.research-infrastructures.eu/gCubeApps/EGIP"); - - //config.setParam("Layer","http://repoigg.services.iit.cnr.it/geoserver/IGG/ows?service=WFS&version=1.1.0&request=GetFeature&srsName=urn:x-ogc:def:crs:EPSG:4326&TYPENAME=IGG:HeatFlowUnit"); -// config.setParam("Layer","http://egip.brgm-rec.fr/wxs/?service=WFS&version=1.1.0&request=GetFeature&typeName=TemperatureUnit&srsName=EPSG:4326"); - config.setParam("Layer","http://geoserver-dev.d4science-ii.research-infrastructures.eu/geoserver/ows?service=wfs&version=1.0.0&request=GetFeature&srsName=urn:x-ogc:def:crs:EPSG:4326&TYPENAME=aquamaps:worldborders"); - - https://issue.imarine.research-infrastructures.eu/raw-attachment/ticket/3082/gifgeomap.gif - config.setParam("Z","0"); - config.setParam("TimeIndex","0"); - config.setParam("BBox_LowerLeftLat","-90"); - config.setParam("BBox_LowerLeftLong","-180"); - config.setParam("BBox_UpperRightLat","90"); - config.setParam("BBox_UpperRightLong","180"); -// config.setParam("XResolution","0.3"); -// config.setParam("YResolution","0.3"); - config.setParam("XResolution","0.5"); - config.setParam("YResolution","0.5"); - config.setParam("OutputTableName","testextraction4"); - config.setParam("OutputTableLabel","testextraction4"); - - return config; - } - - private static AlgorithmConfiguration testDirectExtraction() { - - AlgorithmConfiguration config = new AlgorithmConfiguration(); - - config.setAgent("XYEXTRACTOR"); - 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("/d4science.research-infrastructures.eu/gCubeApps/BiodiversityLab"); - - config.setParam("Layer","https://dl.dropboxusercontent.com/u/12809149/geoserver-GetCoverage.image.asc"); - config.setParam("Z","0"); - config.setParam("TimeIndex","0"); - config.setParam("BBox_LowerLeftLat","-60"); - config.setParam("BBox_LowerLeftLong","-50"); - config.setParam("BBox_UpperRightLat","60"); - config.setParam("BBox_UpperRightLong","50"); - config.setParam("XResolution","0.5"); - config.setParam("YResolution","0.5"); - config.setParam("OutputTableName","testextractiondirect"); - config.setParam("OutputTableLabel","testextractiondirect"); - - return config; - } - - - private static AlgorithmConfiguration testXYExtractionAquaMaps() { - - AlgorithmConfiguration config = testXYExtractionNetCDF(); - config.setParam("Layer","04e61cb8-3c32-47fe-823c-80ac3d417a0b"); - config.setParam("OutputTableName","testextractionaquamaps"); - - return config; - } - - - private static AlgorithmConfiguration testXYExtractionTable() { - - AlgorithmConfiguration config = testXYExtractionNetCDF(); - config.setAgent("XYEXTRACTOR_TABLE"); - - config.setParam("OutputTableName","testextractiontable"); - 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"); - // vessels - /* - config.setParam(TableMatrixRepresentation.tableNameParameter, "generic_id037d302d_2ba0_4e43_b6e4_1a797bb91728"); - config.setParam(TableMatrixRepresentation.xDimensionColumnParameter, "x"); - config.setParam(TableMatrixRepresentation.yDimensionColumnParameter, "y"); - config.setParam(TableMatrixRepresentation.timeDimensionColumnParameter, "datetime"); - config.setParam(TableMatrixRepresentation.valueDimensionColumnParameter, "speed"); - config.setParam(TableMatrixRepresentation.filterParameter, "speed<2"); - */ - config.setParam(TableMatrixRepresentation.tableNameParameter, "occurrence_species_id0045886b_2a7c_4ede_afc4_3157c694b893"); - config.setParam(TableMatrixRepresentation.xDimensionColumnParameter, "decimallongitude"); - config.setParam(TableMatrixRepresentation.yDimensionColumnParameter, "decimallatitude"); - config.setParam(TableMatrixRepresentation.timeDimensionColumnParameter, " "); - config.setParam(TableMatrixRepresentation.valueDimensionColumnParameter, "decimallatitude"); - config.setParam(TableMatrixRepresentation.filterParameter, " "); - - return config; - } - - private static AlgorithmConfiguration testXYExtractionTable2() { - - AlgorithmConfiguration config = testXYExtractionNetCDF(); - config.setAgent("XYEXTRACTOR_TABLE"); - - 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"); - config.setParam("DatabaseDriver", "org.postgresql.Driver"); - // vessels - /* - config.setParam(TableMatrixRepresentation.tableNameParameter, "generic_id037d302d_2ba0_4e43_b6e4_1a797bb91728"); - config.setParam(TableMatrixRepresentation.xDimensionColumnParameter, "x"); - config.setParam(TableMatrixRepresentation.yDimensionColumnParameter, "y"); - config.setParam(TableMatrixRepresentation.timeDimensionColumnParameter, "datetime"); - config.setParam(TableMatrixRepresentation.valueDimensionColumnParameter, "speed"); - config.setParam(TableMatrixRepresentation.filterParameter, "speed<2"); - */ - config.setParam(TableMatrixRepresentation.tableNameParameter, "occurrence_species_id0045886b_2a7c_4ede_afc4_3157c694b893"); - config.setParam(TableMatrixRepresentation.xDimensionColumnParameter, "decimallongitude"); - config.setParam(TableMatrixRepresentation.yDimensionColumnParameter, "decimallatitude"); - config.setParam(TableMatrixRepresentation.timeDimensionColumnParameter, "modified"); - config.setParam(TableMatrixRepresentation.valueDimensionColumnParameter, "decimallatitude"); - config.setParam(TableMatrixRepresentation.filterParameter, " "); - config.setParam("Z","0"); - config.setParam("TimeIndex","1"); - - return config; - } - -} diff --git a/src/main/java/org/gcube/dataanalysis/geo/test/projections/TestXYExtractionConnectors.java b/src/main/java/org/gcube/dataanalysis/geo/test/projections/TestXYExtractionConnectors.java deleted file mode 100644 index 0c9dfef..0000000 --- a/src/main/java/org/gcube/dataanalysis/geo/test/projections/TestXYExtractionConnectors.java +++ /dev/null @@ -1,142 +0,0 @@ -package org.gcube.dataanalysis.geo.test.projections; - -import java.io.File; -import java.io.FileWriter; -import java.util.List; - -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; -import org.gcube.dataanalysis.ecoengine.utils.Tuple; -import org.gcube.dataanalysis.geo.connectors.asc.AscDataExplorer; -import org.gcube.dataanalysis.geo.connectors.asc.AscRasterWriter; -import org.gcube.dataanalysis.geo.connectors.geotiff.GeoTiff; -import org.gcube.dataanalysis.geo.connectors.netcdf.NetCDF; -import org.gcube.dataanalysis.geo.connectors.table.Table; -import org.gcube.dataanalysis.geo.connectors.table.TableMatrixRepresentation; -import org.gcube.dataanalysis.geo.connectors.wcs.WCS; -import org.gcube.dataanalysis.geo.connectors.wfs.WFS; -import org.gcube.dataanalysis.geo.utils.MapUtils; -import org.gcube.dataanalysis.geo.utils.VectorOperations; - -public class TestXYExtractionConnectors { - - static String[] urlToTest3 = { - // "http://geoserver3.d4science.research-infrastructures.eu/geoserver" - // "http://geoserver2.d4science.research-infrastructures.eu/geoserver" - "http://www.fao.org/figis/geoserver/species/ows" }; - - static String[] layernamesTest3 = { - // "lsoleasolea20121217184934494cet" - // "lcarcharodoncarcharias20121217173706733cet" - // "lxiphiasgladius20130410182141778cest" - // "SPECIES_DIST_BIB" - - "SPECIES_DIST_SWO" }; - - static String[] urlToTest1 = { "http://thredds.research-infrastructures.eu/thredds/dodsC/public/netcdf/global-reanalysis-phys-001-004-b-ref-fr-mjm95-gridv_OCEANS_CLIMATOLOGY_METEOROLOGY_ATMOSPHERE_1366211498692.nc", }; - - static String[] layernamesTest1 = { "vomecrty" }; - - static String[] urlToTest2 = { "http://thredds.research-infrastructures.eu/thredds/dodsC/public/netcdf/WOA2005TemperatureAnnual_CLIMATOLOGY_METEOROLOGY_ATMOSPHERE_.nc" }; - - static String[] layernamesTest2 = { "t00an1" }; - - static String[] urlToTest5 = { "./maxent3719990c-7998-4859-9dca-4b0a792f9d2f/layer1.asc" }; - - static String[] layernamesTest5 = { "layer1" }; - - static String[] urlToTest6 = { "table" }; - - static String[] layernamesTest6 = { "table" }; - - static String[] urlToTest = { "tableeez" }; - - static String[] layernamesTest = { "tableeez" }; - - static String[] urlToTest_ = { "https://dl.dropboxusercontent.com/u/12809149/layer1.asc", "http://thredds.research-infrastructures.eu/thredds/fileServer/public/netcdf/ph.asc", "http://thredds.research-infrastructures.eu/thredds/fileServer/public/netcdf/calcite.asc", - "https://dl.dropboxusercontent.com/u/12809149/wind1.tif", - "http://thredds.research-infrastructures.eu/thredds/dodsC/public/netcdf/WOA2005TemperatureAnnual_CLIMATOLOGY_METEOROLOGY_ATMOSPHERE_.nc", "http://thredds.research-infrastructures.eu/thredds/dodsC/public/netcdf/salinity_annual_1deg_ENVIRONMENT_OCEANS_.nc", "http://thredds.d4science.org/thredds/fileServer/public/netcdf/global-reanalysis-phys-001-004-b-ref-fr-mjm95-icemod_ENVIRONMENT_OCEANS_CLIMATOLOGY_METEOROLOGY_ATMOSPHERE_1366211441189.nc", "http://thredds.research-infrastructures.eu/thredds/dodsC/public/netcdf/CERSAT-GLO-CLIM_WIND_L4-OBS_FULL_TIME_SERIE_CLIMATOLOGY_METEOROLOGY_ATMOSPHERE_1366217956317.nc", "http://thredds.research-infrastructures.eu/thredds/dodsC/public/netcdf/phosphate_seasonal_5deg_ENVIRONMENT_BIOTA_.nc", "http://thredds.research-infrastructures.eu/thredds/dodsC/public/netcdf/global-analysis-bio-001-008-_a_BIOTA_ENVIRONMENT_1366217546908.nc", "http://thredds.research-infrastructures.eu/thredds/dodsC/public/netcdf/dissolved_oxygen_annual_1deg_ENVIRONMENT_BIOTA_.nc", "http://thredds.research-infrastructures.eu/thredds/dodsC/public/netcdf/global-reanalysis-phys-001-004-b-ref-fr-mjm95-gridv_OCEANS_CLIMATOLOGY_METEOROLOGY_ATMOSPHERE_1366211498692.nc", "http://thredds.research-infrastructures.eu/thredds/dodsC/public/netcdf/nitrate_seasonal_5deg_ENVIRONMENT_BIOTA_.nc", "http://thredds.research-infrastructures.eu/thredds/dodsC/public/netcdf/global-analysis-bio-001-008-a_BIOTA_ENVIRONMENT_1366217608283.nc", "http://thredds.research-infrastructures.eu/thredds/fileServer/public/netcdf/cloudmean.asc", - "http://geoserver-dev.d4science-ii.research-infrastructures.eu/geoserver/wcs/wcs?service=wcs&version=1.0.0&request=GetCoverage&coverage=aquamaps:WorldClimBio2&CRS=EPSG:4326&bbox=-180,0,180,90&width=1&height=1&format=geotiff&RESPONSE_CRS=EPSG:4326", - "http://geoserver2.d4science.research-infrastructures.eu/geoserver" - - }; - - static String[] layernamesTest_ = { "layer1", "ph", "calcite", "wind", "t00an1", "s_sd", "iicevelu", "wind_speed", "p_mn", "CHL", "o_mn", "vomecrty", "n_mn", "PHYC", "cloud", "aquamaps:WorldClimBio2", "lxiphiasgladius20130410182141778cest" }; - - public static void main(String[] args) throws Exception { - AnalysisLogger.setLogger("./cfg/" + AlgorithmConfiguration.defaultLoggerFile); - AlgorithmConfiguration config = new AlgorithmConfiguration(); - - 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"); - - FileWriter fw = new FileWriter(new File("mapsconnectors.txt")); - for (int t = 0; t < urlToTest.length; t++) { - - String layerURL = urlToTest[t]; - String layerName = layernamesTest[t]; - AnalysisLogger.getLogger().debug("Processing Layer: " + layerURL); - List values = null; - double res = 0.5d; - List> tuples = VectorOperations.generateCoordinateTripletsInBoundingBox(-180, 180, -90, 90, 0, res, res); - - if (layerURL.endsWith(".nc")) { - NetCDF geotiff = new NetCDF(layerURL, layerName); - values = geotiff.getFeaturesInTimeInstantAndArea(layerURL, layerName, 0, tuples, -180, 180, -90, 90); - } else if (layerURL.endsWith(".asc")) { - AscDataExplorer asc = new AscDataExplorer(layerURL); - values = asc.retrieveDataFromAsc(tuples, 0); - } else if (layerURL.endsWith("tif")) { - GeoTiff geotiff = new GeoTiff(config); - values = geotiff.getFeaturesInTimeInstantAndArea(layerURL, layerName, 0, tuples, -180, 180, -90, 90); - } else if (layerURL.contains("wcs")) { - WCS wcs = new WCS(config, layerURL); - values = wcs.getFeaturesInTimeInstantAndArea(layerURL, layerName, 0, tuples, -180, 180, -90, 90); - } else if (layerURL.contains("geoserver")) { - WFS wfs = new WFS(); - values = wfs.getFeaturesInTimeInstantAndArea(layerURL, layerName, 0, tuples, -180, 180, -90, 90); - } else if (layerURL.equals("table")) { - config.setParam(TableMatrixRepresentation.tableNameParameter, "testextraction4"); - config.setParam(TableMatrixRepresentation.xDimensionColumnParameter, "approx_x"); - config.setParam(TableMatrixRepresentation.yDimensionColumnParameter, "approx_y"); - config.setParam(TableMatrixRepresentation.timeDimensionColumnParameter, "time"); - config.setParam(TableMatrixRepresentation.valueDimensionColumnParameter, "f_cat"); - config.setParam(TableMatrixRepresentation.filterParameter, " "); - - Table connector = new Table(config, res); - values = connector.getFeaturesInTimeInstantAndArea(null, null, 0, tuples, -180, 180, -90, 90); - } else if (layerURL.contains("tableeez")) { - config.setParam("DatabaseUserName", "postgres"); - config.setParam("DatabasePassword", "d4science2"); - config.setParam("DatabaseURL", "jdbc:postgresql://geoserver-dev.d4science-ii.research-infrastructures.eu/aquamapsdb"); - config.setParam(TableMatrixRepresentation.tableNameParameter, "\"WorldEEZv72012HR\""); - config.setParam(TableMatrixRepresentation.xDimensionColumnParameter, "longitude"); - config.setParam(TableMatrixRepresentation.yDimensionColumnParameter, "latitude"); - config.setParam(TableMatrixRepresentation.timeDimensionColumnParameter, ""); - config.setParam(TableMatrixRepresentation.valueDimensionColumnParameter, "eez_id"); - config.setParam(TableMatrixRepresentation.filterParameter, " "); - - Table connector = new Table(config, res); - values = connector.getFeaturesInTimeInstantAndArea(null, null, 0, tuples, -180, 180, -90, 90); - } - double[][] matrix = VectorOperations.vectorToMatix(values, -180, 180, -90, 90, res, res); - - // System.out.println(MapUtils.globalASCIIMap(values,step,step)); - System.out.println(MapUtils.globalASCIIMap(matrix)); - fw.write(MapUtils.globalASCIIMap(matrix)); - - AscRasterWriter writer = new AscRasterWriter(); - writer.writeRasterInvertYAxis("testraster.asc", matrix, -180, -90, res, "-9999"); - - } - - fw.close(); - - } - -} diff --git a/src/main/java/org/gcube/dataanalysis/geo/test/regression/RegressionGeoTiff.java b/src/main/java/org/gcube/dataanalysis/geo/test/regression/RegressionGeoTiff.java deleted file mode 100644 index fb484ca..0000000 --- a/src/main/java/org/gcube/dataanalysis/geo/test/regression/RegressionGeoTiff.java +++ /dev/null @@ -1,75 +0,0 @@ -package org.gcube.dataanalysis.geo.test.regression; - -import java.io.BufferedReader; -import java.io.BufferedWriter; -import java.io.File; -import java.io.FileReader; -import java.io.FileWriter; - -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; -import org.gcube.dataanalysis.ecoengine.signals.PeriodicityDetector; -import org.gcube.dataanalysis.ecoengine.signals.SignalProcessing; -import org.gcube.dataanalysis.geo.matrixmodel.MatrixExtractor; -import org.gcube.dataanalysis.geo.matrixmodel.TimeSeriesExtractor; - -public class RegressionGeoTiff { - - static String cfg = "./cfg/"; - public static void main(String[] args) throws Exception{ - String layertitle = "WorldClimBioGeoTiffTest2"; - - long t0 = System.currentTimeMillis(); - AnalysisLogger.setLogger(cfg+AlgorithmConfiguration.defaultLoggerFile); - - AlgorithmConfiguration config = new AlgorithmConfiguration(); - config.setGcubeScope("/d4science.research-infrastructures.eu/gCubeApps/BiodiversityLab"); - config.setConfigPath(cfg); - TimeSeriesExtractor intersector = new TimeSeriesExtractor(config); - - double signal[] = intersector.extractT(layertitle, 0d, 0d,0d,0.5); - - SignalProcessing.displaySignalWithGenericTime(signal, 0, 1, "signal"); - - System.out.println("ELAPSED TIME: "+(System.currentTimeMillis()-t0)); - - } - - public static void main1(String[] args) throws Exception{ - takeSignal(); - } - public static void takeSignal() throws Exception{ - BufferedReader br = new BufferedReader(new FileReader(new File("signal.txt"))); - String line = br.readLine(); - double[] signal = null; - - while (line!=null){ - String [] el = line.split(","); - signal=new double[el.length]; - int i=0; - for (String e:el){ - signal[i]=Double.parseDouble(e); - i++; - } - line = null; - } - br.close(); - - -// SignalProcessing.displaySignalWithGenericTime(signal, 0, 1, "signal"); - PeriodicityDetector pd = new PeriodicityDetector(); - -// signal = pd.produceNoisySignal(2000, 1, 0.1f, 0f); - - //float freq=1;//signal.length; - -// double F = pd.detectFrequency(signal, (int)freq, 0, freq, 1f,true); - double F = pd.detectFrequency(signal,true); - - System.out.println("Detected Frequency:"+F+" indecision ["+pd.lowermeanF+" , "+pd.uppermeanF+"]"); - System.out.println("Detected Period:"+pd.meanPeriod+" indecision ["+pd.lowermeanPeriod+" , "+pd.uppermeanPeriod+"]"); - System.out.println("Detected Periodicity Strength:"+pd.periodicityStrength); - - } - -} diff --git a/src/main/java/org/gcube/dataanalysis/geo/test/regression/RegressionLowPeriodicity.java b/src/main/java/org/gcube/dataanalysis/geo/test/regression/RegressionLowPeriodicity.java deleted file mode 100644 index cd044d9..0000000 --- a/src/main/java/org/gcube/dataanalysis/geo/test/regression/RegressionLowPeriodicity.java +++ /dev/null @@ -1,33 +0,0 @@ -package org.gcube.dataanalysis.geo.test.regression; - -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; -import org.gcube.dataanalysis.ecoengine.signals.PeriodicityDetector; -import org.gcube.dataanalysis.geo.matrixmodel.TimeSeriesExtractor; - -public class RegressionLowPeriodicity { - - static String cfg = "./cfg/"; - public static void main(String[] args) throws Exception{ - String layertitle = "c565e32c-c5b3-4964-b44f-06dc620563e9"; - long t0 = System.currentTimeMillis(); - AnalysisLogger.setLogger(cfg+AlgorithmConfiguration.defaultLoggerFile); - - AlgorithmConfiguration config = new AlgorithmConfiguration(); - config.setGcubeScope("/d4science.research-infrastructures.eu/gCubeApps/BiodiversityLab"); - config.setConfigPath(cfg); - TimeSeriesExtractor intersector = new TimeSeriesExtractor(config); - double signal[] = intersector.extractT(layertitle, 0d, 0d,0d,0.5); - System.out.println("ELAPSED TIME: "+(System.currentTimeMillis()-t0)); - - System.out.println("Signal: "+signal.length); - - PeriodicityDetector pd = new PeriodicityDetector(); - double F = pd.detectFrequency(signal,true); - - System.out.println("Detected Frequency:"+F+" indecision ["+pd.lowermeanF+" , "+pd.uppermeanF+"]"); - System.out.println("Detected Period:"+pd.meanPeriod+" indecision ["+pd.lowermeanPeriod+" , "+pd.uppermeanPeriod+"]"); - System.out.println("Detected Periodicity Strength:"+pd.periodicityStrength+":"+pd.getPeriodicityStregthInterpretation()); - } - -} diff --git a/src/main/java/org/gcube/dataanalysis/geo/test/regression/RegressionOccurrenceEnrichment.java b/src/main/java/org/gcube/dataanalysis/geo/test/regression/RegressionOccurrenceEnrichment.java deleted file mode 100644 index 3817051..0000000 --- a/src/main/java/org/gcube/dataanalysis/geo/test/regression/RegressionOccurrenceEnrichment.java +++ /dev/null @@ -1,70 +0,0 @@ -package org.gcube.dataanalysis.geo.test.regression; - -import java.util.ArrayList; -import java.util.List; - -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; -import org.gcube.dataanalysis.ecoengine.datatypes.ColumnType; -import org.gcube.dataanalysis.ecoengine.datatypes.InputTable; -import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveTypesList; -import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType; -import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.PrimitiveTypes; -import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.TableTemplates; -import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent; -import org.gcube.dataanalysis.ecoengine.processing.factories.TransducerersFactory; -import org.gcube.dataanalysis.ecoengine.test.regression.Regressor; -import org.gcube.dataanalysis.ecoengine.utils.IOHelper; - -public class RegressionOccurrenceEnrichment { - - static AlgorithmConfiguration[] configs = { testOccEnrichment()}; - public static void main(String[] args) throws Exception { - - System.out.println("TEST 1"); - - for (int i = 0; i < configs.length; i++) { - AnalysisLogger.getLogger().debug("Executing: "+configs[i].getAgent()); - List trans = null; - trans = TransducerersFactory.getTransducerers(configs[i]); - trans.get(0).init(); - Regressor.process(trans.get(0)); - StatisticalType st = trans.get(0).getOutput(); - AnalysisLogger.getLogger().debug("ST:" + st); - trans = null; - } - } - - - private static AlgorithmConfiguration testOccEnrichment() { - - 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("/d4science.research-infrastructures.eu/gCubeApps/BiodiversityLab"); - - config.setParam("OccurrenceTable","occurrence_species_id0045886b_2a7c_4ede_afc4_3157c694b893"); - 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","testenrichment"); - config.setParam("OutputTableName","testenrichment"); - String sep=AlgorithmConfiguration.getListSeparator(); - config.setParam("Layers","8f5d883f-95bf-4b7c-8252-aaf0b2e6fd81"+sep+"4d597da9-dbfa-4a65-9de6-9bbff69eac19"+sep+"2c2304d1-681a-4f3a-8409-e8cdb5ed447f"); - config.setParam("FeaturesNames","temperature"+sep+"chlorophyll"+sep+"ph"); -// config.setParam("Layers","4d597da9-dbfa-4a65-9de6-9bbff69eac19"+sep+"2c2304d1-681a-4f3a-8409-e8cdb5ed447f"); -// config.setParam("FeaturesNames","chlorophyll"+sep+"ph"); - return config; - } - -} diff --git a/src/main/java/org/gcube/dataanalysis/geo/test/regression/RegressionPeriodicity.java b/src/main/java/org/gcube/dataanalysis/geo/test/regression/RegressionPeriodicity.java deleted file mode 100644 index 34de1cf..0000000 --- a/src/main/java/org/gcube/dataanalysis/geo/test/regression/RegressionPeriodicity.java +++ /dev/null @@ -1,40 +0,0 @@ -package org.gcube.dataanalysis.geo.test.regression; - -import java.io.BufferedReader; -import java.io.File; -import java.io.FileReader; - -import org.gcube.dataanalysis.ecoengine.signals.PeriodicityDetector; - -public class RegressionPeriodicity { - - static String cfg = "./cfg/"; - public static void main(String[] args) throws Exception{ - takeSignal(); - } - public static void takeSignal() throws Exception{ - BufferedReader br = new BufferedReader(new FileReader(new File("signalPeriodic.txt"))); - String line = br.readLine(); - double[] signal = null; - - while (line!=null){ - String [] el = line.split(","); - signal=new double[el.length]; - int i=0; - for (String e:el){ - signal[i]=Double.parseDouble(e); - i++; - } - line = null; - } - br.close(); - - PeriodicityDetector pd = new PeriodicityDetector(); - double F = pd.detectFrequency(signal,true); - - System.out.println("Detected Frequency:"+F+" indecision ["+pd.lowermeanF+" , "+pd.uppermeanF+"]"); - System.out.println("Detected Period:"+pd.meanPeriod+" indecision ["+pd.lowermeanPeriod+" , "+pd.uppermeanPeriod+"]"); - System.out.println("Detected Periodicity Strength:"+pd.periodicityStrength+":"+pd.getPeriodicityStregthInterpretation()); - } - -} diff --git a/src/main/java/org/gcube/dataanalysis/geo/test/regression/RegressionPeriodicityAutomatic.java b/src/main/java/org/gcube/dataanalysis/geo/test/regression/RegressionPeriodicityAutomatic.java deleted file mode 100644 index 74c2266..0000000 --- a/src/main/java/org/gcube/dataanalysis/geo/test/regression/RegressionPeriodicityAutomatic.java +++ /dev/null @@ -1,25 +0,0 @@ -package org.gcube.dataanalysis.geo.test.regression; - -import org.gcube.dataanalysis.ecoengine.signals.PeriodicityDetector; - -public class RegressionPeriodicityAutomatic { - - static String cfg = "./cfg/"; - public static void main(String[] args) throws Exception{ - takeSignal(); - } - public static void takeSignal() throws Exception{ - - - PeriodicityDetector pd = new PeriodicityDetector(); - - double[] signal = pd.produceNoisySignal(2000, 1, 0.1f, 0f); - - double F = pd.detectFrequency(signal,true); - - System.out.println("Detected Frequency:"+F+" indecision ["+pd.lowermeanF+" , "+pd.uppermeanF+"]"); - System.out.println("Detected Period:"+pd.meanPeriod+" indecision ["+pd.lowermeanPeriod+" , "+pd.uppermeanPeriod+"]"); - System.out.println("Detected Periodicity Strength:"+pd.periodicityStrength+":"+pd.getPeriodicityStregthInterpretation()); - } - -} diff --git a/src/main/java/org/gcube/dataanalysis/geo/test/regression/RegressionPointExtraction.java b/src/main/java/org/gcube/dataanalysis/geo/test/regression/RegressionPointExtraction.java deleted file mode 100644 index 8bb1e22..0000000 --- a/src/main/java/org/gcube/dataanalysis/geo/test/regression/RegressionPointExtraction.java +++ /dev/null @@ -1,39 +0,0 @@ -package org.gcube.dataanalysis.geo.test.regression; - -import java.io.BufferedWriter; -import java.io.File; -import java.io.FileWriter; - -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; -import org.gcube.dataanalysis.ecoengine.signals.PeriodicityDetector; -import org.gcube.dataanalysis.geo.matrixmodel.PointsExtractor; -import org.gcube.dataanalysis.geo.matrixmodel.TimeSeriesExtractor; - -import com.vividsolutions.jts.geom.util.PointExtracter; - -public class RegressionPointExtraction { - - static String cfg = "./cfg/"; - - public static void main(String[] args) throws Exception{ - String layertitle = "afd54b39-30f7-403a-815c-4f91c6c74c26"; - long t0 = System.currentTimeMillis(); - AnalysisLogger.setLogger(cfg+AlgorithmConfiguration.defaultLoggerFile); - AlgorithmConfiguration config = new AlgorithmConfiguration(); - config.setGcubeScope("/d4science.research-infrastructures.eu/gCubeApps/BiodiversityLab"); - config.setConfigPath(cfg); - - PointsExtractor pe = new PointsExtractor(config); - - double value = pe.extractXYZT(layertitle, 0,0,0,0, 0); - - System.out.println("Point value: "+value); - - - System.out.println("ELAPSED TIME: "+(System.currentTimeMillis()-t0)); - - - } - -} diff --git a/src/main/java/org/gcube/dataanalysis/geo/test/regression/RegressionSignalFromTable.java b/src/main/java/org/gcube/dataanalysis/geo/test/regression/RegressionSignalFromTable.java deleted file mode 100644 index 7a5d118..0000000 --- a/src/main/java/org/gcube/dataanalysis/geo/test/regression/RegressionSignalFromTable.java +++ /dev/null @@ -1,51 +0,0 @@ -package org.gcube.dataanalysis.geo.test.regression; - -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; -import org.gcube.dataanalysis.ecoengine.signals.PeriodicityDetector; -import org.gcube.dataanalysis.geo.connectors.table.TableMatrixRepresentation; -import org.gcube.dataanalysis.geo.matrixmodel.TimeSeriesExtractor; - -public class RegressionSignalFromTable { - - static String cfg = "./cfg/"; - public static void main(String[] args) throws Exception{ - AlgorithmConfiguration config = new AlgorithmConfiguration(); - - 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"); - // vessels - config.setParam(TableMatrixRepresentation.tableNameParameter, "generic_id037d302d_2ba0_4e43_b6e4_1a797bb91728"); - config.setParam(TableMatrixRepresentation.xDimensionColumnParameter, "x"); - config.setParam(TableMatrixRepresentation.yDimensionColumnParameter, "y"); - - config.setParam(TableMatrixRepresentation.timeDimensionColumnParameter, "datetime"); - config.setParam(TableMatrixRepresentation.valueDimensionColumnParameter, "speed"); - config.setParam(TableMatrixRepresentation.filterParameter, "speed<2"); - - AnalysisLogger.setLogger(config.getConfigPath() + AlgorithmConfiguration.defaultLoggerFile); - - config.setGcubeScope("/d4science.research-infrastructures.eu/gCubeApps/BiodiversityLab"); - config.setConfigPath(cfg); - - TimeSeriesExtractor intersector = new TimeSeriesExtractor(config); - long t0 = System.currentTimeMillis(); - - double signal[] = intersector.extractT("table", -47.97,43.42, 0d, 0.5); - - System.out.println("ELAPSED TIME: "+(System.currentTimeMillis()-t0)); - System.out.println("Signal: "+signal.length); - - PeriodicityDetector pd = new PeriodicityDetector(); - double F = pd.detectFrequency(signal,true); - - System.out.println("Detected Frequency:"+F+" indecision ["+pd.lowermeanF+" , "+pd.uppermeanF+"]"); - System.out.println("Detected Period:"+pd.meanPeriod+" indecision ["+pd.lowermeanPeriod+" , "+pd.uppermeanPeriod+"]"); - System.out.println("Detected Periodicity Strength:"+pd.periodicityStrength); - } - -} diff --git a/src/main/java/org/gcube/dataanalysis/geo/test/regression/RegressionTestMapsComparison.java b/src/main/java/org/gcube/dataanalysis/geo/test/regression/RegressionTestMapsComparison.java deleted file mode 100644 index 8abc4b0..0000000 --- a/src/main/java/org/gcube/dataanalysis/geo/test/regression/RegressionTestMapsComparison.java +++ /dev/null @@ -1,88 +0,0 @@ -package org.gcube.dataanalysis.geo.test.regression; - -import java.util.List; - -import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; -import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent; -import org.gcube.dataanalysis.ecoengine.interfaces.Evaluator; -import org.gcube.dataanalysis.ecoengine.processing.factories.EvaluatorsFactory; -import org.gcube.dataanalysis.ecoengine.test.regression.Regressor; - -public class RegressionTestMapsComparison { - /** - * example of parallel processing on a single machine the procedure will generate a new table for a distribution on suitable species - * - */ - - public static void main(String[] args) throws Exception { - - List evaluators = EvaluatorsFactory.getEvaluators(testConfig1()); - evaluators.get(0).init(); - Regressor.process(evaluators.get(0)); - evaluators = null; - } - - private static AlgorithmConfiguration testConfig1() { - - AlgorithmConfiguration config = Regressor.getConfig(); - config.setNumberOfResources(1); - config.setConfigPath("./cfg"); - config.setPersistencePath("./"); - config.setAgent("MAPS_COMPARISON"); - config.setParam("DatabaseUserName","gcube"); - config.setParam("DatabasePassword","d4science2"); - config.setParam("DatabaseURL","jdbc:postgresql://localhost/testdb"); - config.setParam("DatabaseDriver","org.postgresql.Driver"); - -// config.setParam("Layer_1","86a7ac79-866a-49c6-b5d5-602fc2d87ddd"); -// config.setParam("Layer_2","86a7ac79-866a-49c6-b5d5-602fc2d87ddd"); - - //World seas : IHO vs Marine regions -// config.setParam("Layer_2","70a6d757-e607-46f7-b643-e21749f45a42"); -// config.setParam("Layer_1","a2a8c130-124f-45b5-973f-c9358028a2a6"); - - //FAO vs FAO: -// config.setParam("Layer_1","b040894b-c5db-47fc-ba9c-d4fafcdcf620"); //goblin shark -// config.setParam("Layer_2","c9a31223-cc00-4acd-bc5b-a0c76a7f79c7"); //humbolt squid - - //FAO vs AquaMaps -// config.setParam("Layer_1","b040894b-c5db-47fc-ba9c-d4fafcdcf620"); -// config.setParam("Layer_2","c9a31223-cc00-4acd-bc5b-a0c76a7f79c7"); - - //NetCDF vs NETCDF WOA -// config.setParam("Layer_1","e0dbbcc0-8364-4087-8bcb-c7d95b2f55c8"); //statistical mean oxygen -// config.setParam("Layer_2","49f5a5a1-80ff-4a00-8c84-dac29bda1a23");//statistical mean phosphate - - //Eleutheronema tetradactylum - config.setParam("Layer_1","fao-species-map-fot"); - config.setParam("Layer_2","c492f5d3-1cfc-44e3-b8d2-8530fec3e7e7"); - - - - //NetCDF vs NetCDF MyOcean -// config.setParam("Layer_1","e0dbbcc0-8364-4087-8bcb-c7d95b2f55c8"); //statistical mean oxygen -// config.setParam("Layer_2","fc9ac2f4-a2bd-43d1-a361-ac67c5ceac31");//temperature - - //NetCDF vs IHO -// config.setParam("Layer_1","70a6d757-e607-46f7-b643-e21749f45a42");//IHO -// config.setParam("Layer_2","fc9ac2f4-a2bd-43d1-a361-ac67c5ceac31");//temperature - - //NetCDF vs NetCDF MyOcean only -// config.setParam("Layer_1","fc9ac2f4-a2bd-43d1-a361-ac67c5ceac31"); //statistical mean oxygen -// config.setParam("Layer_2","fc9ac2f4-a2bd-43d1-a361-ac67c5ceac31");//temperature - - //NetCDF vs NetCDF Envri -// config.setParam("Layer_1","Etna Volcano SAR Analysis 1"); // -// config.setParam("Layer_2","Etna Volcano SAR Analysis 7");// - - - - config.setParam("ValuesComparisonThreshold",""+0.1); - config.setParam("Z","0"); - config.setGcubeScope("/gcube"); -// config.setGcubeScope(null); -// config.setGcubeScope("/d4science.research-infrastructures.eu/gCubeApps"); - - return config; - } -} diff --git a/src/main/java/org/gcube/dataanalysis/geo/test/regression/RegressionWCS.java b/src/main/java/org/gcube/dataanalysis/geo/test/regression/RegressionWCS.java deleted file mode 100644 index 108365e..0000000 --- a/src/main/java/org/gcube/dataanalysis/geo/test/regression/RegressionWCS.java +++ /dev/null @@ -1,75 +0,0 @@ -package org.gcube.dataanalysis.geo.test.regression; - -import java.io.BufferedReader; -import java.io.BufferedWriter; -import java.io.File; -import java.io.FileReader; -import java.io.FileWriter; - -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; -import org.gcube.dataanalysis.ecoengine.signals.PeriodicityDetector; -import org.gcube.dataanalysis.ecoengine.signals.SignalProcessing; -import org.gcube.dataanalysis.geo.matrixmodel.MatrixExtractor; -import org.gcube.dataanalysis.geo.matrixmodel.TimeSeriesExtractor; - -public class RegressionWCS { - - static String cfg = "./cfg/"; - public static void main(String[] args) throws Exception{ - String layertitle = "WorldClimBioWCS2"; - - long t0 = System.currentTimeMillis(); - AnalysisLogger.setLogger(cfg+AlgorithmConfiguration.defaultLoggerFile); - - AlgorithmConfiguration config = new AlgorithmConfiguration(); - config.setGcubeScope("/d4science.research-infrastructures.eu/gCubeApps/BiodiversityLab"); - config.setConfigPath(cfg); - TimeSeriesExtractor intersector = new TimeSeriesExtractor(config); - - double signal[] = intersector.extractT(layertitle, 0d, 0d,0d,0.5); - - SignalProcessing.displaySignalWithGenericTime(signal, 0, 1, "signal"); - - System.out.println("ELAPSED TIME: "+(System.currentTimeMillis()-t0)); - - } - - public static void main1(String[] args) throws Exception{ - takeSignal(); - } - public static void takeSignal() throws Exception{ - BufferedReader br = new BufferedReader(new FileReader(new File("signal.txt"))); - String line = br.readLine(); - double[] signal = null; - - while (line!=null){ - String [] el = line.split(","); - signal=new double[el.length]; - int i=0; - for (String e:el){ - signal[i]=Double.parseDouble(e); - i++; - } - line = null; - } - br.close(); - - -// SignalProcessing.displaySignalWithGenericTime(signal, 0, 1, "signal"); - PeriodicityDetector pd = new PeriodicityDetector(); - -// signal = pd.produceNoisySignal(2000, 1, 0.1f, 0f); - - //float freq=1;//signal.length; - -// double F = pd.detectFrequency(signal, (int)freq, 0, freq, 1f,true); - double F = pd.detectFrequency(signal,true); - - System.out.println("Detected Frequency:"+F+" indecision ["+pd.lowermeanF+" , "+pd.uppermeanF+"]"); - System.out.println("Detected Period:"+pd.meanPeriod+" indecision ["+pd.lowermeanPeriod+" , "+pd.uppermeanPeriod+"]"); - System.out.println("Detected Periodicity Strength:"+pd.periodicityStrength); - - } - -} diff --git a/src/main/java/org/gcube/dataanalysis/geo/test/regression/RegressionWaterColumnGeoTiff.java b/src/main/java/org/gcube/dataanalysis/geo/test/regression/RegressionWaterColumnGeoTiff.java deleted file mode 100644 index b509a4d..0000000 --- a/src/main/java/org/gcube/dataanalysis/geo/test/regression/RegressionWaterColumnGeoTiff.java +++ /dev/null @@ -1,52 +0,0 @@ -package org.gcube.dataanalysis.geo.test.regression; - -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; -import org.gcube.dataanalysis.ecoengine.signals.SignalProcessing; -import org.gcube.dataanalysis.ecoengine.utils.Tuple; -import org.gcube.dataanalysis.geo.connectors.table.TableMatrixRepresentation; -import org.gcube.dataanalysis.geo.matrixmodel.ZExtractor; - -public class RegressionWaterColumnGeoTiff { - - public static void main(String[] args) throws Exception{ - AlgorithmConfiguration config = new AlgorithmConfiguration(); - - config.setConfigPath("./cfg/"); - config.setPersistencePath("./"); - - String layertitle = "WorldClimBioGeoTiffTest2"; -// layertitle = "WorldClimBioWCS2"; - - AnalysisLogger.setLogger(config.getConfigPath() + AlgorithmConfiguration.defaultLoggerFile); - config.setGcubeScope("/d4science.research-infrastructures.eu/gCubeApps/BiodiversityLab"); - - ZExtractor extractor = new ZExtractor(config); - long t0 = System.currentTimeMillis(); - - double watercolumn[] = extractor.extractZ(layertitle, 18.620429d,20.836419d,0, 0); - - System.out.println("ELAPSED TIME: "+(System.currentTimeMillis()-t0)); - System.out.println("Signal: "+watercolumn.length); - System.out.println("Signal first element: "+watercolumn[0]); - SignalProcessing.displaySignalWithGenericTime(watercolumn, 0, 1, "signal"); - - layertitle = "WorldClimBioWCS2"; - - AnalysisLogger.setLogger(config.getConfigPath() + AlgorithmConfiguration.defaultLoggerFile); - config.setGcubeScope("/d4science.research-infrastructures.eu/gCubeApps/BiodiversityLab"); - - extractor = new ZExtractor(config); - t0 = System.currentTimeMillis(); - - watercolumn = extractor.extractZ(layertitle, 18.620429d,20.836419d,0, 0); - - System.out.println("ELAPSED TIME: "+(System.currentTimeMillis()-t0)); - System.out.println("Signal: "+watercolumn.length); - System.out.println("Signal first element: "+watercolumn[0]); - SignalProcessing.displaySignalWithGenericTime(watercolumn, 0, 1, "signal"); - - - } - -} diff --git a/src/main/java/org/gcube/dataanalysis/geo/test/regression/RegressionWaterColumnTable.java b/src/main/java/org/gcube/dataanalysis/geo/test/regression/RegressionWaterColumnTable.java deleted file mode 100644 index 8144b68..0000000 --- a/src/main/java/org/gcube/dataanalysis/geo/test/regression/RegressionWaterColumnTable.java +++ /dev/null @@ -1,45 +0,0 @@ -package org.gcube.dataanalysis.geo.test.regression; - -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; -import org.gcube.dataanalysis.ecoengine.signals.SignalProcessing; -import org.gcube.dataanalysis.geo.connectors.table.TableMatrixRepresentation; -import org.gcube.dataanalysis.geo.matrixmodel.ZExtractor; - -public class RegressionWaterColumnTable { - - static String cfg = "./cfg/"; - public static void main(String[] args) throws Exception{ - AlgorithmConfiguration config = new AlgorithmConfiguration(); - - 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"); - // vessels - config.setParam(TableMatrixRepresentation.tableNameParameter, "generic_id037d302d_2ba0_4e43_b6e4_1a797bb91728"); - config.setParam(TableMatrixRepresentation.xDimensionColumnParameter, "x"); - config.setParam(TableMatrixRepresentation.yDimensionColumnParameter, "y"); - config.setParam(TableMatrixRepresentation.zDimensionColumnParameter, "x"); - config.setParam(TableMatrixRepresentation.timeDimensionColumnParameter, "datetime"); - config.setParam(TableMatrixRepresentation.valueDimensionColumnParameter, "speed"); - config.setParam(TableMatrixRepresentation.filterParameter, "speed<2"); - - AnalysisLogger.setLogger(config.getConfigPath() + AlgorithmConfiguration.defaultLoggerFile); - - config.setGcubeScope("/d4science.research-infrastructures.eu/gCubeApps/BiodiversityLab"); - config.setConfigPath(cfg); - - ZExtractor extractor = new ZExtractor(config); - long t0 = System.currentTimeMillis(); - - double watercolumn[] = extractor.extractZ("table", -47.97,43.42, 0, 0.5); - - System.out.println("ELAPSED TIME: "+(System.currentTimeMillis()-t0)); - System.out.println("Signal: "+watercolumn.length); - SignalProcessing.displaySignalWithGenericTime(watercolumn, 0, 1, "signal"); - } - -} diff --git a/src/main/java/org/gcube/dataanalysis/geo/test/regression/RegressionWaterColumnTemperature.java b/src/main/java/org/gcube/dataanalysis/geo/test/regression/RegressionWaterColumnTemperature.java deleted file mode 100644 index 664fbcb..0000000 --- a/src/main/java/org/gcube/dataanalysis/geo/test/regression/RegressionWaterColumnTemperature.java +++ /dev/null @@ -1,32 +0,0 @@ -package org.gcube.dataanalysis.geo.test.regression; - -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; -import org.gcube.dataanalysis.ecoengine.signals.SignalProcessing; -import org.gcube.dataanalysis.geo.connectors.table.TableMatrixRepresentation; -import org.gcube.dataanalysis.geo.matrixmodel.ZExtractor; - -public class RegressionWaterColumnTemperature { - - public static void main(String[] args) throws Exception{ - AlgorithmConfiguration config = new AlgorithmConfiguration(); - - config.setConfigPath("./cfg/"); - config.setPersistencePath("./"); - - String layertitle = "6411b110-7572-457a-a662-a16e4ff09e4e"; - AnalysisLogger.setLogger(config.getConfigPath() + AlgorithmConfiguration.defaultLoggerFile); - config.setGcubeScope("/d4science.research-infrastructures.eu/gCubeApps/BiodiversityLab"); - - ZExtractor extractor = new ZExtractor(config); - long t0 = System.currentTimeMillis(); - - double watercolumn[] = extractor.extractZ(layertitle, 0,0, 0, 100); - - System.out.println("ELAPSED TIME: "+(System.currentTimeMillis()-t0)); - System.out.println("Signal: "+watercolumn.length); - SignalProcessing.displaySignalWithGenericTime(watercolumn, 0, 1, "signal"); - - } - -} diff --git a/src/main/java/org/gcube/dataanalysis/geo/test/regression/RegressionXYSlice.java b/src/main/java/org/gcube/dataanalysis/geo/test/regression/RegressionXYSlice.java deleted file mode 100644 index 258eaa4..0000000 --- a/src/main/java/org/gcube/dataanalysis/geo/test/regression/RegressionXYSlice.java +++ /dev/null @@ -1,71 +0,0 @@ -package org.gcube.dataanalysis.geo.test.regression; - -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; -import org.gcube.dataanalysis.geo.connectors.table.TableMatrixRepresentation; -import org.gcube.dataanalysis.geo.matrixmodel.XYExtractor; - -public class RegressionXYSlice { - - static String cfg = "./cfg/"; - static String layertitle = "120313e1-c0cb-4b3c-9779-ed651c490cdb"; - static AlgorithmConfiguration config = new AlgorithmConfiguration(); - public static void main(String[] args) throws Exception { - config.setConfigPath(cfg); - config.setGcubeScope("/d4science.research-infrastructures.eu/gCubeApps/BiodiversityLab"); - AnalysisLogger.setLogger(cfg + AlgorithmConfiguration.defaultLoggerFile); - config.setPersistencePath("./"); - -// sliceWFS(); -// sliceNetCDF(); - sliceASC(); -// sliceTable(); - } - - public static void sliceWFS() throws Exception{ - AnalysisLogger.getLogger().debug("WFS"); - // latimeria chalumnae - layertitle = "120313e1-c0cb-4b3c-9779-ed651c490cdb"; - execute(); - } - - public static void sliceNetCDF() throws Exception{ - AnalysisLogger.getLogger().debug("NetCDF"); - // Chlorophyll - layertitle = "c565e32c-c5b3-4964-b44f-06dc620563e9"; - execute(); - } - - public static void sliceASC() throws Exception{ - AnalysisLogger.getLogger().debug("ASC"); - // - layertitle = "2c2304d1-681a-4f3a-8409-e8cdb5ed447f"; - execute(); - } - - public static void sliceTable() throws Exception{ - AnalysisLogger.getLogger().debug("Table"); - // latimeria chalumnae - 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"); - // vessels - config.setParam(TableMatrixRepresentation.tableNameParameter, "generic_id037d302d_2ba0_4e43_b6e4_1a797bb91728"); - config.setParam(TableMatrixRepresentation.xDimensionColumnParameter, "x"); - config.setParam(TableMatrixRepresentation.yDimensionColumnParameter, "y"); -// config.setParam(TableMatrixRepresentation.zDimensionColumnParameter, "x"); - config.setParam(TableMatrixRepresentation.timeDimensionColumnParameter, "datetime"); - config.setParam(TableMatrixRepresentation.valueDimensionColumnParameter, "speed"); - config.setParam(TableMatrixRepresentation.filterParameter, "speed<2"); - - execute(); - } - - public static void execute() throws Exception{ - long t0 = System.currentTimeMillis(); - XYExtractor intersector = new XYExtractor(config); - intersector.extractXYGrid(layertitle, 0, -180, 180, -90, 90, 0, 0.5, 0.5); - System.out.println("ELAPSED TIME: " + (System.currentTimeMillis() - t0)); - } -} diff --git a/src/main/java/org/gcube/dataanalysis/geo/utils/ThreddsPublisher.java b/src/main/java/org/gcube/dataanalysis/geo/utils/ThreddsPublisher.java index 64a6327..28ab2ba 100644 --- a/src/main/java/org/gcube/dataanalysis/geo/utils/ThreddsPublisher.java +++ b/src/main/java/org/gcube/dataanalysis/geo/utils/ThreddsPublisher.java @@ -1,104 +1,121 @@ package org.gcube.dataanalysis.geo.utils; -import java.io.File; import java.util.List; +import java.util.regex.Matcher; +import java.util.regex.Pattern; -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; +import org.gcube.common.resources.gcore.GCoreEndpoint; +import org.gcube.common.scope.api.ScopeProvider; +import org.gcube.data.transfer.library.TransferResult; import org.gcube.dataanalysis.executor.util.DataTransferer; -import org.gcube.dataanalysis.executor.util.InfraRetrieval; import org.gcube.dataanalysis.geo.connectors.netcdf.NetCDFDataExplorer; import org.gcube.dataanalysis.geo.infrastructure.GeoNetworkInspector; import org.gcube.dataanalysis.geo.meta.GenericLayerMetadata; import org.gcube.dataanalysis.geo.meta.OGCFormatter; +import org.gcube.resources.discovery.client.api.DiscoveryClient; +import org.gcube.resources.discovery.client.queries.api.SimpleQuery; +import org.gcube.resources.discovery.icclient.ICFactory; import org.opengis.metadata.identification.TopicCategory; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; import ucar.nc2.dt.GridDatatype; public class ThreddsPublisher { - public static void main (String[] args) throws Exception{ -// String scope = "/d4science.research-infrastructures.eu/gCubeApps"; - String scope = "/gcube/devsec"; - String username = "gianpaolo.coro"; - //String fileAbsolutePath = "C:/Users/coro/Dropbox/Public/wind1.tif"; - String fileAbsolutePath = "C:/Users/coro/Downloads/adux_pres_portale_test.nc"; - - String layerTitle = "architeuthis dux distribution file - test"; - String layerName = "adux_pres_2"; - String abstractField = "abstract architeuthis dux distribution file - test"; - String[] topics = {"adux","D4Science"}; - double resolution = -1; - AnalysisLogger.setLogger("./cfg/"+AlgorithmConfiguration.defaultLoggerFile); - publishOnThredds(scope, username, fileAbsolutePath, layerTitle, layerName, abstractField, topics, resolution,false); - } + private static final String threddsServiceName = "Thredds"; + private static final String threddsServiceClass = "SDI"; - public static boolean publishOnThredds(String scope,String username, String fileAbsolutePath, String layerTitle, String layerName, String abstractField, String[] topics, double resolution, boolean isprivate) throws Exception{ + private static final String dataTransferName = "data-transfer-service"; + private static final String dataTransferClass = "DataTransfer"; + private static final String dataTransferEndpoint = "org.gcube.data.transfer.service.DTService"; + + private static final String threddsPersistenceID = "thredds"; + private static final String threddsRemoteFolder = "/public/netcdf"; + + private static final String threddsFileServerPath = "/thredds/fileServer/public/netcdf/"; + private static final String threddsCatalogPath = "/thredds/catalog/public/netcdf/catalog.xml"; + + private static final String netCDFExtension = ".nc"; + + private static final Logger log = LoggerFactory.getLogger(ThreddsPublisher.class); + + public static boolean publishOnThredds(String username, String fileAbsolutePath, String layerTitle, String layerName, String abstractField, String[] topics, double resolution, boolean isprivate) throws Exception{ //TODO manage faults - String remoteFolder = "/data/content/thredds/public/netcdf/"; - List threddsAddress = InfraRetrieval.retrieveServiceAddress("Gis", "THREDDS", scope, "Geoserver"); - if (threddsAddress.size()==0) - threddsAddress = InfraRetrieval.retrieveServiceAddress("Gis", "Thredds", scope, "Geoserver"); + + DiscoveryClient threddsClient = ICFactory.client(); + + SimpleQuery thrredsQuery = ICFactory.queryFor(GCoreEndpoint.class); + thrredsQuery.addCondition(String.format("$resource/Profile/ServiceName eq '%s'",threddsServiceName)); + thrredsQuery.addCondition(String.format("$resource/Profile/ServiceClass eq '%s'",threddsServiceClass)); + thrredsQuery.setResult("$resource/Profile/GHN/@UniqueID/string()"); + List threddsAddress = threddsClient.submit(thrredsQuery); if (threddsAddress.size()==0) - throw new Exception("Thredds resource is not available in scope "+scope); + throw new Exception("Thredds Endpoint not found in scope "+ScopeProvider.instance.get()); - String threddServiceAddress = threddsAddress.get(0); - threddServiceAddress = threddServiceAddress.substring(threddServiceAddress.indexOf("http://")+7); - threddServiceAddress = threddServiceAddress.substring(0,threddServiceAddress.indexOf("/")); + String threddsWhnId = threddsAddress.get(0); - AnalysisLogger.getLogger().debug("Found "+threddsAddress.size()+" thredds services"); - AnalysisLogger.getLogger().debug("THREDDS: "+threddServiceAddress); - List dataTransferAddress = InfraRetrieval.retrieveService("agent-service", scope); + DiscoveryClient dataTransferClient = ICFactory.client(); + SimpleQuery dataTransferQuery = ICFactory.queryFor(GCoreEndpoint.class); + dataTransferQuery.addCondition(String.format("$resource/Profile/ServiceName/string() eq '%s'",dataTransferName)); + dataTransferQuery.addCondition(String.format("$resource/Profile/ServiceClass/string() eq '%s'",dataTransferClass)); + dataTransferQuery.addCondition(String.format("$resource/Profile/GHN/@UniqueID/string() eq '%s'",threddsWhnId)); + dataTransferQuery.setResult(String.format("$resource/Profile/AccessPoint/RunningInstanceInterfaces/Endpoint[@EntryName/string() eq \"%s\"]/string()",dataTransferEndpoint)); + + List dataTransferAddress = dataTransferClient.submit(dataTransferQuery); + if (dataTransferAddress.size()==0) - throw new Exception("Data Transfer services are not available in scope "+scope); + throw new Exception("Data Transfer services is not available in scope "+ScopeProvider.instance.get()); + - AnalysisLogger.getLogger().debug("Found "+dataTransferAddress.size()+" transfer services"); - String threddsDTService = threddServiceAddress; - int threddsDTPort = 9090; - boolean found = false; - for (String datatransferservice:dataTransferAddress){ - AnalysisLogger.getLogger().debug("Transfer service found"); - datatransferservice = datatransferservice.substring(datatransferservice.indexOf("http://")+7); - String servicehost = datatransferservice.substring(0,datatransferservice.indexOf(":")); - String serviceport = datatransferservice.substring(datatransferservice.indexOf(":")+1,datatransferservice.indexOf("/")); - AnalysisLogger.getLogger().debug("Transfer service: "+servicehost+":"+serviceport); - if (threddServiceAddress.equals(servicehost)){ - threddsDTPort = Integer.parseInt(serviceport); - found = true; - break; - } - } + String threddsDTService = dataTransferAddress.get(0); + log.debug("data transfer found is {}",threddsDTService); + + Pattern pattern = Pattern.compile("(https?)://([^:/]*)(:(\\d{2,5}))?.*"); + Matcher matcher = pattern.matcher(threddsDTService); + + if (!matcher.find()) + throw new Exception("wrong address found "+threddsDTService); + + String dataTransferProtocol = matcher.group(1); + String dataTransferHost = matcher.group(2); + String portAsString = matcher.group(4); + Integer dataTransferPort = portAsString==null?null:Integer.parseInt(portAsString); + + StringBuilder threedsBaseURL = new StringBuilder(dataTransferProtocol).append("://").append(dataTransferHost); + if (portAsString!=null) + threedsBaseURL.append(":").append(portAsString); - if (!found) - throw new Exception("Thredds data transfer has not been found in the same scope of the catalog: "+scope); boolean gridded=true; if (fileAbsolutePath.endsWith(".nc")){ - AnalysisLogger.getLogger().debug("checking NetCDF file coherence"+fileAbsolutePath); + log.debug("checking NetCDF file coherence {}",fileAbsolutePath); //let's publish also if the netCDF is not gridded try{ NetCDFDataExplorer.getGrid(layerName, fileAbsolutePath); }catch(Exception e){ gridded=false; - AnalysisLogger.getLogger().debug("NetCDF is not gridded"+fileAbsolutePath); + log.debug("NetCDF is not gridded {}",fileAbsolutePath); } } - AnalysisLogger.getLogger().debug("Transferring via DT to "+threddServiceAddress); - DataTransferer.transferFileToService(scope, username, threddsDTService, threddsDTPort, fileAbsolutePath, remoteFolder); + log.debug("Transferring via DT to {} with parameters {} {} {} {} ",threddsDTService, dataTransferHost, dataTransferPort, fileAbsolutePath, threddsRemoteFolder); + TransferResult transferResult = DataTransferer.transferFileToService(ScopeProvider.instance.get(), username, dataTransferHost, dataTransferPort, fileAbsolutePath, threddsRemoteFolder, threddsPersistenceID); - AnalysisLogger.getLogger().debug("Adding metadata on GeoNetwork"); + String realFileName = transferResult.getRemotePath().substring(transferResult.getRemotePath().lastIndexOf("/")+1); - if (fileAbsolutePath.endsWith(".nc") && gridded) - publishNetCDFMeta(scope, layerTitle, abstractField, new File(fileAbsolutePath).getName(),layerName,threddServiceAddress,username,topics,isprivate); + log.debug("Adding metadata on GeoNetwork, real file name on threadds is {} ",realFileName); + + if (fileAbsolutePath.endsWith(netCDFExtension) && gridded) + publishNetCDFMeta(ScopeProvider.instance.get(), layerTitle, abstractField, realFileName,layerName,threedsBaseURL.toString(),username,topics,isprivate); else{ if (resolution==-1 && gridded) throw new Exception ("Specify valid resolution parameter for non-NetCDF raster datasets"); - publishOtherFileMeta(scope, layerTitle, resolution, abstractField, new File(fileAbsolutePath).getName(), threddServiceAddress,username,topics,isprivate); + publishOtherFileMeta(ScopeProvider.instance.get(), layerTitle, resolution, abstractField, realFileName, threedsBaseURL.toString(),username,topics,isprivate); } - AnalysisLogger.getLogger().debug("Finished"); + log.debug("Finished"); return true; } @@ -116,7 +133,7 @@ public class ThreddsPublisher { else geonetworkGroup = gninspector.getGeonetworkPublicGroup(); - AnalysisLogger.getLogger().debug("GeoNetwork Info: "+geonetworkURL+" "+geonetworkUser+" "+geonetworkGroup); + log.debug("GeoNetwork Info: "+geonetworkURL+" "+geonetworkUser+" "+geonetworkGroup); metadataInserter.setGeonetworkUrl(geonetworkURL); metadataInserter.setGeonetworkPwd(geonetworkPassword); @@ -132,20 +149,20 @@ public class ThreddsPublisher { metadataInserter.setResolution(resolution); - AnalysisLogger.getLogger().debug("Res:"+resolution); + log.debug("Res:"+resolution); - String [] urls = {"http://"+threddsURL+"/thredds/fileServer/public/netcdf/"+filename}; + String [] urls = {threddsURL+threddsFileServerPath+filename}; String [] protocols = {"HTTP"}; - AnalysisLogger.getLogger().debug("Publishing in group: "+metadataInserter.getGeonetworkGroup()); - AnalysisLogger.getLogger().debug("Inserting custom metadata "); + log.debug("Publishing in group: "+metadataInserter.getGeonetworkGroup()); + log.debug("Inserting custom metadata "); metadataInserter.customMetaDataInsert(urls,protocols,isprivate); } - private static void publishNetCDFMeta(String scope, String layerTitle,String abstractField, String filename, String netCDFLayerName, String threddsURL, String username, String [] topics, boolean isprivate) throws Exception{ - AnalysisLogger.getLogger().debug("Getting GeoNetwork Info"); + private static void publishNetCDFMeta(String scope, String layerTitle,String abstractField, String filename, String netCDFLayerName, String threddsURL, String username, String [] topics, boolean isprivate) throws Exception{ + log.debug("Getting GeoNetwork Info"); GenericLayerMetadata metadataInserter = new GenericLayerMetadata(); GeoNetworkInspector gninspector =new GeoNetworkInspector(); @@ -159,7 +176,7 @@ public class ThreddsPublisher { else geonetworkGroup = gninspector.getGeonetworkPublicGroup(); - AnalysisLogger.getLogger().debug("GeoNetwork Info: "+geonetworkURL+" "+geonetworkUser+" "+geonetworkGroup); + log.debug("GeoNetwork Info: "+geonetworkURL+" "+geonetworkUser+" "+geonetworkGroup); metadataInserter.setGeonetworkUrl(geonetworkURL); metadataInserter.setGeonetworkPwd(geonetworkPassword); @@ -172,9 +189,9 @@ public class ThreddsPublisher { metadataInserter.setAbstractField(abstractField+" Hosted on the D4Science Thredds Catalog: "+threddsURL); metadataInserter.setCustomTopics(topics); metadataInserter.setAuthor(username); - String Threddscatalog = "http://"+threddsURL+"/thredds/catalog/public/netcdf/catalog.xml"; - String url = OGCFormatter.getOpenDapURL(Threddscatalog, filename); - AnalysisLogger.getLogger().debug("OpenDAP URL: "+url); + String threddscatalog = threddsURL+threddsCatalogPath; + String url = OGCFormatter.getOpenDapURL(threddscatalog, filename); + log.debug("OpenDAP URL: {} ",url); GridDatatype gdt = NetCDFDataExplorer.getGrid(netCDFLayerName, url); @@ -187,15 +204,16 @@ public class ThreddsPublisher { metadataInserter.setResolution(resolutionY); - AnalysisLogger.getLogger().debug("minX: "+minX+" minY: "+minY+" maxX:"+maxX+" maxY:"+maxY+" Res:"+resolutionY); + log.debug("minX: "+minX+" minY: "+minY+" maxX:"+maxX+" maxY:"+maxY+" Res:"+resolutionY); String wms = OGCFormatter.getWmsNetCDFUrl(url, netCDFLayerName, OGCFormatter.buildBoundingBox(minX, minY, maxX, maxY)).replace("width=676", "width=640").replace("height=330", "height=480"); - AnalysisLogger.getLogger().debug("WMS URL: "+wms); + log.debug("WMS URL: {}",wms); String wcs = OGCFormatter.getWcsNetCDFUrl(url, netCDFLayerName, OGCFormatter.buildBoundingBox(minX, minY, maxX, maxY)).replace("width=676", "width=640").replace("height=330", "height=480"); - AnalysisLogger.getLogger().debug("WCS URL: "+wcs); - AnalysisLogger.getLogger().debug("HTTP URL: "+"http://"+threddsURL+"/thredds/fileServer/public/netcdf/"+filename); - String [] urls = {"http://"+threddsURL+"/thredds/fileServer/public/netcdf/"+filename,wms,wcs,url}; + log.debug("WCS URL: {}",wcs); + String fileServerUrl = threddsURL+threddsFileServerPath+filename; + log.debug("HTTP URL: {} ",fileServerUrl); + String [] urls = {fileServerUrl,wms,wcs,url}; String [] protocols = {"HTTP","WMS","WCS","OPeNDAP"}; @@ -203,8 +221,8 @@ public class ThreddsPublisher { metadataInserter.setYLeftLow(minY); metadataInserter.setXRightUpper(maxX); metadataInserter.setYRightUpper(maxY); - AnalysisLogger.getLogger().debug("Publishing in group: "+metadataInserter.getGeonetworkGroup()); - AnalysisLogger.getLogger().debug("Inserting metadata "); + log.debug("Publishing in group: {} ",metadataInserter.getGeonetworkGroup()); + log.debug("Inserting metadata "); metadataInserter.customMetaDataInsert(urls,protocols,isprivate); } diff --git a/src/main/java/org/gcube/dataanalysis/geo/test/TestCSquareCodesCreator.java b/src/test/java/org/gcube/dataanalysis/geo/test/TestCSquareCodesCreator.java similarity index 100% rename from src/main/java/org/gcube/dataanalysis/geo/test/TestCSquareCodesCreator.java rename to src/test/java/org/gcube/dataanalysis/geo/test/TestCSquareCodesCreator.java diff --git a/src/main/java/org/gcube/dataanalysis/geo/test/TestChunkization.java b/src/test/java/org/gcube/dataanalysis/geo/test/TestChunkization.java similarity index 100% rename from src/main/java/org/gcube/dataanalysis/geo/test/TestChunkization.java rename to src/test/java/org/gcube/dataanalysis/geo/test/TestChunkization.java diff --git a/src/main/java/org/gcube/dataanalysis/geo/test/TestChunkizationLayer.java b/src/test/java/org/gcube/dataanalysis/geo/test/TestChunkizationLayer.java similarity index 100% rename from src/main/java/org/gcube/dataanalysis/geo/test/TestChunkizationLayer.java rename to src/test/java/org/gcube/dataanalysis/geo/test/TestChunkizationLayer.java diff --git a/src/main/java/org/gcube/dataanalysis/geo/test/TestExtractionXYMatrix.java b/src/test/java/org/gcube/dataanalysis/geo/test/TestExtractionXYMatrix.java similarity index 100% rename from src/main/java/org/gcube/dataanalysis/geo/test/TestExtractionXYMatrix.java rename to src/test/java/org/gcube/dataanalysis/geo/test/TestExtractionXYMatrix.java diff --git a/src/main/java/org/gcube/dataanalysis/geo/test/TestFAOAreaCodesCreator.java b/src/test/java/org/gcube/dataanalysis/geo/test/TestFAOAreaCodesCreator.java similarity index 100% rename from src/main/java/org/gcube/dataanalysis/geo/test/TestFAOAreaCodesCreator.java rename to src/test/java/org/gcube/dataanalysis/geo/test/TestFAOAreaCodesCreator.java diff --git a/src/main/java/org/gcube/dataanalysis/geo/test/TestFAOAreaCodesQuadrantCreator.java b/src/test/java/org/gcube/dataanalysis/geo/test/TestFAOAreaCodesQuadrantCreator.java similarity index 100% rename from src/main/java/org/gcube/dataanalysis/geo/test/TestFAOAreaCodesQuadrantCreator.java rename to src/test/java/org/gcube/dataanalysis/geo/test/TestFAOAreaCodesQuadrantCreator.java diff --git a/src/main/java/org/gcube/dataanalysis/geo/test/TestGeoCharts.java b/src/test/java/org/gcube/dataanalysis/geo/test/TestGeoCharts.java similarity index 100% rename from src/main/java/org/gcube/dataanalysis/geo/test/TestGeoCharts.java rename to src/test/java/org/gcube/dataanalysis/geo/test/TestGeoCharts.java diff --git a/src/main/java/org/gcube/dataanalysis/geo/test/TestGeoTiff.java b/src/test/java/org/gcube/dataanalysis/geo/test/TestGeoTiff.java similarity index 100% rename from src/main/java/org/gcube/dataanalysis/geo/test/TestGeoTiff.java rename to src/test/java/org/gcube/dataanalysis/geo/test/TestGeoTiff.java diff --git a/src/main/java/org/gcube/dataanalysis/geo/test/TestLayersRetrieval.java b/src/test/java/org/gcube/dataanalysis/geo/test/TestLayersRetrieval.java similarity index 100% rename from src/main/java/org/gcube/dataanalysis/geo/test/TestLayersRetrieval.java rename to src/test/java/org/gcube/dataanalysis/geo/test/TestLayersRetrieval.java diff --git a/src/main/java/org/gcube/dataanalysis/geo/test/TestNetCDFMetadataInsert.java b/src/test/java/org/gcube/dataanalysis/geo/test/TestNetCDFMetadataInsert.java similarity index 100% rename from src/main/java/org/gcube/dataanalysis/geo/test/TestNetCDFMetadataInsert.java rename to src/test/java/org/gcube/dataanalysis/geo/test/TestNetCDFMetadataInsert.java diff --git a/src/main/java/org/gcube/dataanalysis/geo/test/TestPointslice.java b/src/test/java/org/gcube/dataanalysis/geo/test/TestPointslice.java similarity index 100% rename from src/main/java/org/gcube/dataanalysis/geo/test/TestPointslice.java rename to src/test/java/org/gcube/dataanalysis/geo/test/TestPointslice.java diff --git a/src/main/java/org/gcube/dataanalysis/geo/test/TestRasterPublisher.java b/src/test/java/org/gcube/dataanalysis/geo/test/TestRasterPublisher.java similarity index 86% rename from src/main/java/org/gcube/dataanalysis/geo/test/TestRasterPublisher.java rename to src/test/java/org/gcube/dataanalysis/geo/test/TestRasterPublisher.java index 6d4243e..1145fd1 100644 --- a/src/main/java/org/gcube/dataanalysis/geo/test/TestRasterPublisher.java +++ b/src/test/java/org/gcube/dataanalysis/geo/test/TestRasterPublisher.java @@ -8,9 +8,6 @@ import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType; import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent; import org.gcube.dataanalysis.ecoengine.processing.factories.TransducerersFactory; -import org.gcube.dataanalysis.ecoengine.test.regression.Regressor; -import org.gcube.dataanalysis.geo.connectors.table.TableMatrixRepresentation; -import org.gcube.dataanalysis.geo.matrixmodel.ZExtractor; public class TestRasterPublisher { @@ -43,7 +40,8 @@ public class TestRasterPublisher { List trans = null; trans = TransducerersFactory.getTransducerers(config); trans.get(0).init(); - Regressor.process(trans.get(0)); + //TODO: check the next line + //Regressor.process(trans.get(0)); StatisticalType st = trans.get(0).getOutput(); AnalysisLogger.getLogger().debug("ST:" + st); trans = null; diff --git a/src/main/java/org/gcube/dataanalysis/geo/test/TestRasterTable.java b/src/test/java/org/gcube/dataanalysis/geo/test/TestRasterTable.java similarity index 100% rename from src/main/java/org/gcube/dataanalysis/geo/test/TestRasterTable.java rename to src/test/java/org/gcube/dataanalysis/geo/test/TestRasterTable.java diff --git a/src/main/java/org/gcube/dataanalysis/geo/test/TestResourcesRetrieval.java b/src/test/java/org/gcube/dataanalysis/geo/test/TestResourcesRetrieval.java similarity index 100% rename from src/main/java/org/gcube/dataanalysis/geo/test/TestResourcesRetrieval.java rename to src/test/java/org/gcube/dataanalysis/geo/test/TestResourcesRetrieval.java diff --git a/src/main/java/org/gcube/dataanalysis/geo/test/TestSignal.java b/src/test/java/org/gcube/dataanalysis/geo/test/TestSignal.java similarity index 100% rename from src/main/java/org/gcube/dataanalysis/geo/test/TestSignal.java rename to src/test/java/org/gcube/dataanalysis/geo/test/TestSignal.java diff --git a/src/main/java/org/gcube/dataanalysis/geo/test/TestSignalTable.java b/src/test/java/org/gcube/dataanalysis/geo/test/TestSignalTable.java similarity index 100% rename from src/main/java/org/gcube/dataanalysis/geo/test/TestSignalTable.java rename to src/test/java/org/gcube/dataanalysis/geo/test/TestSignalTable.java diff --git a/src/main/java/org/gcube/dataanalysis/geo/test/TestStandardLayerMetadataInsert.java b/src/test/java/org/gcube/dataanalysis/geo/test/TestStandardLayerMetadataInsert.java similarity index 100% rename from src/main/java/org/gcube/dataanalysis/geo/test/TestStandardLayerMetadataInsert.java rename to src/test/java/org/gcube/dataanalysis/geo/test/TestStandardLayerMetadataInsert.java diff --git a/src/main/java/org/gcube/dataanalysis/geo/test/TestWaterColumn.java b/src/test/java/org/gcube/dataanalysis/geo/test/TestWaterColumn.java similarity index 100% rename from src/main/java/org/gcube/dataanalysis/geo/test/TestWaterColumn.java rename to src/test/java/org/gcube/dataanalysis/geo/test/TestWaterColumn.java diff --git a/src/main/java/org/gcube/dataanalysis/geo/test/TestWaterColumnGeoTiff.java b/src/test/java/org/gcube/dataanalysis/geo/test/TestWaterColumnGeoTiff.java similarity index 100% rename from src/main/java/org/gcube/dataanalysis/geo/test/TestWaterColumnGeoTiff.java rename to src/test/java/org/gcube/dataanalysis/geo/test/TestWaterColumnGeoTiff.java diff --git a/src/main/java/org/gcube/dataanalysis/geo/test/TestWaterColumnTemperature.java b/src/test/java/org/gcube/dataanalysis/geo/test/TestWaterColumnTemperature.java similarity index 100% rename from src/main/java/org/gcube/dataanalysis/geo/test/TestWaterColumnTemperature.java rename to src/test/java/org/gcube/dataanalysis/geo/test/TestWaterColumnTemperature.java diff --git a/src/test/resources/logback-test.xml b/src/test/resources/logback-test.xml new file mode 100644 index 0000000..4f36cc8 --- /dev/null +++ b/src/test/resources/logback-test.xml @@ -0,0 +1,16 @@ + + + + + %d{HH:mm:ss.SSS} [%thread] %-5level %logger{0}: %msg%n + + + + + + + + + + + \ No newline at end of file