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
-
-
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