diff --git a/.classpath b/.classpath deleted file mode 100644 index f38b7ff..0000000 --- a/.classpath +++ /dev/null @@ -1,8 +0,0 @@ - - - - - - - - diff --git a/.project b/.project deleted file mode 100644 index cdb59e9..0000000 --- a/.project +++ /dev/null @@ -1,23 +0,0 @@ - - - EcologicalEngineGeoSpatialExtension - - - - - - org.eclipse.jdt.core.javabuilder - - - - - org.eclipse.m2e.core.maven2Builder - - - - - - org.eclipse.m2e.core.maven2Nature - org.eclipse.jdt.core.javanature - - diff --git a/.settings/org.eclipse.core.resources.prefs b/.settings/org.eclipse.core.resources.prefs deleted file mode 100644 index 11ad4d0..0000000 --- a/.settings/org.eclipse.core.resources.prefs +++ /dev/null @@ -1,4 +0,0 @@ -#Mon Apr 08 18:49:41 CEST 2013 -eclipse.preferences.version=1 -encoding//src/main/java=UTF-8 -encoding/=UTF-8 diff --git a/.settings/org.eclipse.jdt.core.prefs b/.settings/org.eclipse.jdt.core.prefs deleted file mode 100644 index 30b5aca..0000000 --- a/.settings/org.eclipse.jdt.core.prefs +++ /dev/null @@ -1,13 +0,0 @@ -#Mon Apr 08 18:49:41 CEST 2013 -eclipse.preferences.version=1 -org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled -org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.6 -org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve -org.eclipse.jdt.core.compiler.compliance=1.6 -org.eclipse.jdt.core.compiler.debug.lineNumber=generate -org.eclipse.jdt.core.compiler.debug.localVariable=generate -org.eclipse.jdt.core.compiler.debug.sourceFile=generate -org.eclipse.jdt.core.compiler.problem.assertIdentifier=error -org.eclipse.jdt.core.compiler.problem.enumIdentifier=error -org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning -org.eclipse.jdt.core.compiler.source=1.6 diff --git a/.settings/org.eclipse.m2e.core.prefs b/.settings/org.eclipse.m2e.core.prefs deleted file mode 100644 index dd42b7f..0000000 --- a/.settings/org.eclipse.m2e.core.prefs +++ /dev/null @@ -1,5 +0,0 @@ -#Mon Apr 08 18:15:49 CEST 2013 -activeProfiles= -eclipse.preferences.version=1 -resolveWorkspaceProjects=true -version=1 diff --git a/netcdf_data.html b/netcdf_data.html deleted file mode 100644 index 91cbdee..0000000 --- a/netcdf_data.html +++ /dev/null @@ -1,411 +0,0 @@ - - - - - - - - - - - - - - - - World Ocean Atlas 2009 data in NetCDF format - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
National Oceanic and Atmospheric AdministrationNODC, National Oceanographic Data CenterDepartment of Commerce
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You are here: NODC Home > -Ocean Climate Laboratory > -OCL Products > -WOA09 > -WOA09 data in NetCDF format -
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World Ocean Atlas 2009 Data in NetCDF format -
Data are available courtesy of Upendra Dadi. -For any questions about this product, please e-mail OCLhelp desk. -
-The data can be accessed by using OpenDAP or -you can do simple analysis and visualization of the data using the NODC Live Access Server. - -The THREDDS page below have an OpenDAP link to the netCDF files. -
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Grid SizeVariableTime PeriodFTP Link to NetCDF fileTHREDDS LinkOpenDAP Metadata Link
1 DEGREETemperatureAnnualtemperature_annual_1deg.nctemperature_annual_1deg.nctemperature_annual_1deg.nc.info
Seasonaltemperature_seasonal_1deg.nctemperature_seasonal_1deg.nctemperature_seasonal_1deg.nc.info
Monthlytemperature_monthly_1deg.nctemperature_monthly_1deg.nctemperature_monthly_1deg.nc.info
SalinityAnnualsalinity_annual_1deg.ncsalinity_annual_1deg.ncsalinity_annual_1deg.nc.info
Seasonalsalinity_seasonal_1deg.ncsalinity_seasonal_1deg.ncsalinity_seasonal_1deg.nc.info
Monthlysalinity_monthly_1deg.ncsalinity_monthly_1deg.ncsalinity_monthly_1deg.nc.info
Dissolved OxygenAnnualdissolved_oxygen_annual_1deg.ncdissolved_oxygen_annual_1deg.ncdissolved_oxygen_annual_1deg.nc.info
Seasonaldissolved_oxygen_seasonal_1deg.ncdissolved_oxygen_seasonal_1deg.ncdissolved_oxygen_seasonal_1deg.nc.info
Monthlydissolved_oxygen_monthly_1deg.ncdissolved_oxygen_monthly_1deg.ncdissolved_oxygen_monthly_1deg.nc.info
Oxygen SaturationAnnualoxygen_saturation_annual_1deg.ncoxygen_saturation_annual_1deg.ncoxygen_saturation_annual_1deg.nc.info
Seasonaloxygen_saturation_seasonal_1deg.ncoxygen_saturation_seasonal_1deg.ncoxygen_saturation_seasonal_1deg.nc.info
Monthlyoxygen_saturation_monthly_1deg.ncoxygen_saturation_monthly_1deg.ncoxygen_saturation_monthly_1deg.nc.info
Apparent Oxygen
Utilization		Annualapparent_oxygen_utilization_annual_1deg.ncapparent_oxygen_utilization_annual_1deg.ncapparent_oxygen_utilization_annual_1deg.nc.info
Seasonalapparent_oxygen_utilization_seasonal_1deg.ncapparent_oxygen_utilization_seasonal_1deg.ncapparent_oxygen_utilization_seasonal_1deg.nc.info
Monthlyapparent_oxygen_utilization_monthly_1deg.ncapparent_oxygen_utilization_monthly_1deg.ncapparent_oxygen_utilization_monthly_1deg.nc.info
PhosphateAnnualphosphate_annual_1deg.ncphosphate_annual_1deg.ncphosphate_annual_1deg.nc.info
Seasonalphosphate_seasonal_1deg.ncphosphate_seasonal_1deg.ncphosphate_seasonal_1deg.nc.info
Monthlyphosphate_monthly_1deg.ncphosphate_monthly_1deg.ncphosphate_monthly_1deg.nc.info
SilicateAnnualsilicate_annual_1deg.ncsilicate_annual_1deg.ncsilicate_annual_1deg.nc.info
Seasonalsilicate_seasonal_1deg.ncsilicate_seasonal_1deg.ncsilicate_seasonal_1deg.nc.info
Monthlysilicate_monthly_1deg.ncsilicate_monthly_1deg.ncsilicate_monthly_1deg.nc.info
NitrateAnnualnitrate_annual_1deg.ncnitrate_annual_1deg.ncnitrate_annual_1deg.nc.info
Seasonalnitrate_seasonal_1deg.ncnitrate_seasonal_1deg.ncnitrate_seasonal_1deg.nc.info
Monthlynitrate_monthly_1deg.ncnitrate_monthly_1deg.ncnitrate_monthly_1deg.nc.info
5 DEGREETemperatureAnnualtemperature_annual_5deg.nctemperature_annual_5deg.nctemperature_annual_5deg.nc.info
Seasonaltemperature_seasonal_5deg.nctemperature_seasonal_5deg.nctemperature_seasonal_5deg.nc.info
Monthlytemperature_monthly_5deg.nctemperature_monthly_5deg.nctemperature_monthly_5deg.nc.info
SalinityAnnualsalinity_annual_5deg.ncsalinity_annual_5deg.ncsalinity_annual_5deg.nc.info
Seasonalsalinity_seasonal_5deg.ncsalinity_seasonal_5deg.ncsalinity_seasonal_5deg.nc.info
Monthlysalinity_monthly_5deg.ncsalinity_monthly_5deg.ncsalinity_monthly_5deg.nc.info
Dissolved OxygenAnnualdissolved_oxygen_annual_5deg.ncdissolved_oxygen_annual_5deg.ncdissolved_oxygen_annual_5deg.nc.info
Seasonaldissolved_oxygen_seasonal_5deg.ncdissolved_oxygen_seasonal_5deg.ncdissolved_oxygen_seasonal_5deg.nc.info
Monthlydissolved_oxygen_monthly_5deg.ncdissolved_oxygen_monthly_5deg.ncdissolved_oxygen_monthly_5deg.nc.info
Oxygen SaturationAnnualoxygen_saturation_annual_5deg.ncoxygen_saturation_annual_5deg.ncoxygen_saturation_annual_5deg.nc.info
Seasonaloxygen_saturation_seasonal_5deg.ncoxygen_saturation_seasonal_5deg.ncoxygen_saturation_seasonal_5deg.nc.info
Monthlyoxygen_saturation_monthly_5deg.ncoxygen_saturation_monthly_5deg.ncoxygen_saturation_monthly_5deg.nc.info
Apparent Oxygen
Utilization		Annualapparent_oxygen_utilization_annual_5deg.ncapparent_oxygen_utilization_annual_5deg.ncapparent_oxygen_utilization_annual_5deg.nc.info
Seasonalapparent_oxygen_utilization_seasonal_5deg.ncapparent_oxygen_utilization_seasonal_5deg.ncapparent_oxygen_utilization_seasonal_5deg.nc.info
Monthlyapparent_oxygen_utilization_monthly_5deg.ncapparent_oxygen_utilization_monthly_5deg.ncapparent_oxygen_utilization_monthly_5deg.nc.info
PhosphateAnnualphosphate_annual_5deg.ncphosphate_annual_5deg.ncphosphate_annual_5deg.nc.info
Seasonalphosphate_seasonal_5deg.ncphosphate_seasonal_5deg.ncphosphate_seasonal_5deg.nc.info
Monthlyphosphate_monthly_5deg.ncphosphate_monthly_5deg.ncphosphate_monthly_5deg.nc.info
SilicateAnnualsilicate_annual_5deg.ncsilicate_annual_5deg.ncsilicate_annual_5deg.nc.info
Seasonalsilicate_seasonal_5deg.ncsilicate_seasonal_5deg.ncsilicate_seasonal_5deg.nc.info
Monthlysilicate_monthly_5deg.ncsilicate_monthly_5deg.ncsilicate_monthly_5deg.nc.info
NitrateAnnualnitrate_annual_5deg.ncnitrate_annual_5deg.ncnitrate_annual_5deg.nc.info
Seasonalnitrate_seasonal_5deg.ncnitrate_seasonal_5deg.ncnitrate_seasonal_5deg.nc.info
Monthlynitrate_monthly_5deg.ncnitrate_monthly_5deg.ncnitrate_monthly_5deg.nc.info
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- - - - - - - diff --git a/pom.xml b/pom.xml deleted file mode 100644 index 5ce3f60..0000000 --- a/pom.xml +++ /dev/null @@ -1,183 +0,0 @@ - - 4.0.0 - - maven-parent - org.gcube.tools - 1.0.0 - - - org.gcube.dataanalysis - ecological-engine-geospatial-extensions - 1.0.0-SNAPSHOT - ecological-engine-geospatial-extension - ecological-engine-geospatial-extension - - ${project.basedir}/distro - - - - org.gcube.dataanalysis - ecological-engine - 1.7.0-SNAPSHOT - - - org.gcube.spatial.data - geonetwork - 1.0.0-SNAPSHOT - - - org.jdom - jdom - 1.1 - - - org.gcube.externals - geo-utils-custom-opendap - 2.2.0 - - - org.gcube.externals - geo-utils-custom-netcdfui - 4.2.0 - - - org.gcube.externals - geo-utils-custom-netcdf - 4.2.0 - - - org.gcube.externals - geo-utils-custom-bounce - 0.14.0 - - - commons-codec - commons-codec - 20041127.091804 - - - commons-httpclient - commons-httpclient - 3.1 - - - commons-logging - commons-logging - 1.1.1 - - - com.google.code.gson - gson - 1.7.1 - - - org.slf4j - slf4j-log4j12 - 1.6.4 - - - org.gcube.core - common-utils-encryption - [1.0.2-SNAPSHOT,2.0.0-SNAPSHOT) - - - org.gcube.externals - geo-utils-custom-opendap - 2.2.0 - - - org.gcube.externals - geo-utils-custom-netcdfui - 4.2.0 - - - org.gcube.externals - geo-utils-custom-netcdf - 4.2.0 - - - org.gcube.externals - geo-utils-custom-bounce - 0.14.0 - - - org.gcube.externals - geo-utils-custom-geopeo - 1.0.2-min - - - - - - osgeo - Open Source Geospatial Foundation Repository Mirror - http://maven.research-infrastructures.eu/nexus/content/repositories/osgeo// - - - - - - maven-compiler-plugin - - 1.6 - 1.6 - - - - org.apache.maven.plugins - maven-surefire-plugin - 2.12 - - true - - - - org.apache.maven.plugins - maven-resources-plugin - 2.5 - - - copy-profile - install - - copy-resources - - - target - - - ${distroDirectory} - true - - profile.xml - - - - - - - - - org.apache.maven.plugins - maven-assembly-plugin - 2.2 - - - ${distroDirectory}/descriptor.xml - - - - - servicearchive - install - - single - - - - - - - \ No newline at end of file diff --git a/src/main/java/org/gcube/dataanalysis/geo/algorithms/MapsComparator.java b/src/main/java/org/gcube/dataanalysis/geo/algorithms/MapsComparator.java deleted file mode 100644 index 9b2e75d..0000000 --- a/src/main/java/org/gcube/dataanalysis/geo/algorithms/MapsComparator.java +++ /dev/null @@ -1,285 +0,0 @@ -package org.gcube.dataanalysis.geo.algorithms; - -import java.awt.Image; -import java.io.File; -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.data.conversions.ImageTools; -import org.gcube.contentmanagement.graphtools.plotting.graphs.GaussianDistributionGraph; -import org.gcube.contentmanagement.graphtools.utils.MathFunctions; -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.gcube.contentmanagement.lexicalmatcher.utils.DatabaseFactory; -import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; -import org.gcube.dataanalysis.ecoengine.datatypes.DatabaseType; -import org.gcube.dataanalysis.ecoengine.datatypes.OutputTable; -import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveType; -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.evaluation.DiscrepancyAnalysis; -import org.gcube.dataanalysis.ecoengine.interfaces.DataAnalysis; -import org.gcube.dataanalysis.ecoengine.utils.DatabaseUtils; -import org.gcube.dataanalysis.ecoengine.utils.IOHelper; -import org.gcube.dataanalysis.geo.insertion.RasterTable; -import org.gcube.dataanalysis.geo.meta.features.FeaturesManager; -import org.gcube.dataanalysis.geo.retrieval.GeoIntersector; -import org.jfree.chart.JFreeChart; -import org.jfree.data.function.NormalDistributionFunction2D; -import org.jfree.data.general.DatasetUtilities; -import org.jfree.data.xy.XYSeriesCollection; -import org.opengis.metadata.Metadata; - -public class MapsComparator extends DataAnalysis { - - static String layer1 = "Layer_1"; - static String layer2 = "Layer_2"; - static String zString = "Z"; - static String t1 = "TimeIndex_1"; - static String t2 = "TimeIndex_2"; - static String valuesThr = "ValuesComparisonThreshold"; - float status = 0; - - public List inputs = new ArrayList(); - public LinkedHashMap outputParameters = new LinkedHashMap(); - - @Override - public void init() throws Exception { - AnalysisLogger.getLogger().debug("Initialization"); - } - - @Override - public String getDescription() { - return "An algorithm for comparing two OGC/NetCDF maps in seamless way to the user"; - } - - @Override - public void compute() throws Exception{ - status = 0; - AnalysisLogger.setLogger(config.getConfigPath() + AlgorithmConfiguration.defaultLoggerFile); - long t0 = System.currentTimeMillis(); - String layerT1 = IOHelper.getInputParameter(config,layer1); - String layerT2 = IOHelper.getInputParameter(config,layer2); - String z$ = IOHelper.getInputParameter(config,zString); - String valuesthr$ = IOHelper.getInputParameter(config,valuesThr); - String time1$ = IOHelper.getInputParameter(config,t1); - String time2$ = IOHelper.getInputParameter(config,t2); - int time1 = ((time1$ != null) && (time1$.trim().length() > 0)) ? Integer.parseInt(time1$) : 0; - int time2 = ((time2$ != null) && (time2$.trim().length() > 0)) ? Integer.parseInt(time2$) : 0; - - if (time1 < 0) - time1 = 0; - - if (time2 < 0) - time2 = 0; - - double valuesthreshold = 0.1; - if ((valuesthr$ != null) && (valuesthr$.trim().length() > 0)) - try { - valuesthreshold = Double.parseDouble(valuesthr$); - } catch (Exception ee) { - } - - double z = 0; - if ((z$ != null) && (z$.trim().length() > 0)) - try { - z = Double.parseDouble(z$); - } catch (Exception ee) { - } - try { - - //TODO : delete this force -// String scope = config.getGcubeScope(); - String scope = null; - AnalysisLogger.getLogger().debug("MapsComparator: Using Scope: " + scope + " Z: " + z + " Values Threshold: " + valuesthreshold + " Layer1: " + layerT1 + " vs " + layerT2); - GeoIntersector intersector = new GeoIntersector(scope, config.getConfigPath()); - AnalysisLogger.getLogger().debug("MapsComparator: GeoIntersector initialized"); - - double x1 = -180; - double x2 = 180; - double y1 = -90; - double y2 = 90; - status = 10; - FeaturesManager fm = intersector.getFeaturer(); - AnalysisLogger.getLogger().debug("MapsComparator: Taking info for the layer: " + layerT1); - Metadata meta1 = fm.getGNInfobyUUIDorName(layerT1); - if (meta1==null) throw new Exception("No Correspondence with Layer 1"); - double resolution1 = 0; - try { - resolution1 = FeaturesManager.getResolution(meta1); - } catch (Exception e) { - AnalysisLogger.getLogger().debug("MapsComparator: Undefined resolution"); - } - AnalysisLogger.getLogger().debug("MapsComparator: Resolution: " + resolution1); - status = 15; - AnalysisLogger.getLogger().debug("MapsComparator: Taking info for the layer: " + layerT2); - AnalysisLogger.getLogger().debug("MapsComparator: Trying with UUID..." + layerT2); - Metadata meta2 = fm.getGNInfobyUUIDorName(layerT2); - if (meta2==null) throw new Exception("No Correspondence with Layer 2"); - - double resolution2 = 0; - try { - resolution2 = FeaturesManager.getResolution(meta2); - } catch (Exception e) { - AnalysisLogger.getLogger().debug("MapsComparator: Undefined resolution"); - } - AnalysisLogger.getLogger().debug("MapsComparator: Resolution: " + resolution2); - status = 20; - // take the lowest resolution to perform the comparison - double resolution = Math.max(resolution1, resolution2); - if (resolution == 0) - resolution = 0.5d; - AnalysisLogger.getLogger().debug("MapsComparator: Evaluation Resolution: " + resolution); - - AnalysisLogger.getLogger().debug("MapsComparator: ****Rasterizing map 1****"); - double[][] slice1 = intersector.takeTimeSlice(layerT1, time1, x1, x2, y1, y2, z, resolution, resolution); - AnalysisLogger.getLogger().debug("MapsComparator: Dumping map 1"); - status = 30; - RasterTable raster1 = new RasterTable(x1, x2, y1, y2, z, resolution, resolution, slice1, config); - raster1.dumpGeoTable(); - String rastertable1 = raster1.getTablename(); - AnalysisLogger.getLogger().debug("MapsComparator: Map 1 was dumped in table: " + rastertable1); - status = 40; - AnalysisLogger.getLogger().debug("MapsComparator: ****Rasterizing map 2****"); - double[][] slice2 = intersector.takeTimeSlice(layerT2, time2, x1, x2, y1, y2, z, resolution, resolution); - AnalysisLogger.getLogger().debug("MapsComparator: Dumping map 2"); - status = 50; - RasterTable raster2 = new RasterTable(x1, x2, y1, y2, z, resolution, resolution, slice2, config); - raster2.dumpGeoTable(); - String rastertable2 = raster2.getTablename(); - AnalysisLogger.getLogger().debug("MapsComparator: Map 2 was dumped in table: " + rastertable2); - status = 60; - /* - * String rastertable1 = "rstr909f60c1d3f1472e9de998e844990724"; String rastertable2 = "rstre52e744c99224de3a1c5354263c6c8d8"; String resolution = "0.5"; - */ - config.setNumberOfResources(1); - config.setParam("FirstTable", rastertable1); - config.setParam("SecondTable", rastertable2); - config.setParam("FirstTableCsquareColumn", RasterTable.csquareColumn); - config.setParam("SecondTableCsquareColumn", RasterTable.csquareColumn); - config.setParam("FirstTableProbabilityColumn", RasterTable.probabilityColumn); - config.setParam("SecondTableProbabilityColumn", RasterTable.probabilityColumn); - config.setParam("ComparisonThreshold", "" + valuesthreshold); - AnalysisLogger.getLogger().debug("MapsComparator: Analyzing discrepancy between maps: " + rastertable1 + " and " + rastertable2); - DiscrepancyAnalysis da = new DiscrepancyAnalysis(); - da.setConfiguration(config); - da.init(false); - outputParameters = da.analyze(); - outputParameters.put("RESOLUTION", "" + MathFunctions.roundDecimal(resolution,4)); - status = 80; - AnalysisLogger.getLogger().debug("MapsComparator: Output: " + outputParameters); - - // delete the tables - - connection = DatabaseUtils.initDBSession(config); - AnalysisLogger.getLogger().debug("MapsComparator: Deleting table " + rastertable1); - DatabaseFactory.executeSQLUpdate(DatabaseUtils.dropTableStatement(rastertable1), connection); - status = 90; - AnalysisLogger.getLogger().debug("MapsComparator: Deleting table " + rastertable2); - DatabaseFactory.executeSQLUpdate(DatabaseUtils.dropTableStatement(rastertable2), connection); - AnalysisLogger.getLogger().debug("MapsComparator: Elapsed: Whole operation completed in " + ((double) (System.currentTimeMillis() - t0) / 1000d) + "s"); - } catch (Exception e) { - e.printStackTrace(); - AnalysisLogger.getLogger().debug("MapsComparator: ERROR!: " + e.getLocalizedMessage()); - } finally { - DatabaseUtils.closeDBConnection(connection); - status = 100; - - } - - } - - @Override - public List getInputParameters(){ - - IOHelper.addStringInput(inputs,layer1, "First Layer Title or UUID: The title or the UUID (preferred) of a layer indexed in the e-Infrastructure on GeoNetwork - You can retrieve it from GeoExplorer", "86a7ac79-866a-49c6-b5d5-602fc2d87ddd");//"Sarda australis"); - IOHelper.addStringInput(inputs, layer2, "Second Layer Title or UUID: The title or the UUID (preferred) of a second layer indexed in the e-Infrastructure on GeoNetwork - You can retrieve it from GeoExplorer", "0e03d0fa-9c44-4a0c-a7e3-9f6d48710d00");//"Sarda orientalis"); - IOHelper.addIntegerInput(inputs, zString, "value of Z. Default is 0, that means comparison will be at surface level", "0"); - IOHelper.addDoubleInput(inputs, valuesThr, "A comparison threshold for the values in the map. Null equals to 0.1", "0.1"); - IOHelper.addIntegerInput(inputs, t1, "First Layer Time Index. The default is the first", "0"); - IOHelper.addIntegerInput(inputs, t2, "Second Layer Time Index. The default is the first", "0"); - IOHelper.addDoubleInput(inputs, "KThreshold", "Threshold for K-Statistic: over this threshold values will be considered 1 for agreement calculation. Default is 0.5","0.5"); - - DatabaseType.addDefaultDBPars(inputs); - - return inputs; - } - - @Override - public void shutdown() { - AnalysisLogger.getLogger().debug("Shutdown"); - - } - - - - - - - protected Image generateGaussian(double mean, double variance){ - // gaussian - XYSeriesCollection xyseriescollection = new XYSeriesCollection(); - if (variance == 0) - variance = 0.01; - AnalysisLogger.getLogger().debug("MapsComparator: Adopting mean:" + mean + " and variance:" + variance); - NormalDistributionFunction2D normaldistributionfunction2d = new NormalDistributionFunction2D(mean, variance); - org.jfree.data.xy.XYSeries xyseries = DatasetUtilities.sampleFunction2DToSeries(normaldistributionfunction2d, (mean - (2 * variance)), (mean + (2 * variance)), 121, "Distribution of the Error"); - xyseriescollection.addSeries(xyseries); - // end gaussian - - JFreeChart chart = GaussianDistributionGraph.createStaticChart(xyseriescollection, mean, variance); - Image image = ImageTools.toImage(chart.createBufferedImage(680, 420)); - /* - * GaussianDistributionGraph graph = new GaussianDistributionGraph("Error Distribution"); graph.mean=mean;graph.variance=variance; graph.render(xyseriescollection); - */ - // end build image - AnalysisLogger.getLogger().debug("MapsComparator: Gaussian Distribution Produced"); - return image; - } - - @Override - public StatisticalType getOutput() { - - // set the output map containing values - AnalysisLogger.getLogger().debug("MapsComparator: Producing Gaussian Distribution for the errors"); - - // build image: - HashMap producedImages = new HashMap(); - double mean = Double.parseDouble(outputParameters.get("MEAN")); - double variance = Double.parseDouble(outputParameters.get("VARIANCE")); - producedImages.put("Error Distribution", generateGaussian(mean, variance)); - PrimitiveType images = new PrimitiveType("Images", producedImages, PrimitiveTypes.IMAGES, "Distribution of the Error", "The distribution of the error along with variance"); - - LinkedHashMap map = new LinkedHashMap(); - - for (String key:outputParameters.keySet()){ - String value = outputParameters.get(key); - PrimitiveType val = new PrimitiveType(String.class.getName(), "" + value, PrimitiveTypes.STRING, key, key); - map.put(key, val); - } - - // collect all the outputs - map.put("Images", images); - - // generate a primitive type for the collection - PrimitiveType output = new PrimitiveType(HashMap.class.getName(), map, PrimitiveTypes.MAP, "ResultsMap", "Results Map"); - - return output; - } - - @Override - public float getStatus() { - return status; - } - - @Override - public LinkedHashMap analyze() throws Exception { - // TODO Auto-generated method stub - return null; - } - - -} diff --git a/src/main/java/org/gcube/dataanalysis/geo/batch/BaseLayerMetadataInsertDev.java b/src/main/java/org/gcube/dataanalysis/geo/batch/BaseLayerMetadataInsertDev.java deleted file mode 100644 index 82a6f90..0000000 --- a/src/main/java/org/gcube/dataanalysis/geo/batch/BaseLayerMetadataInsertDev.java +++ /dev/null @@ -1,227 +0,0 @@ -package org.gcube.dataanalysis.geo.batch; - -import org.gcube.dataanalysis.geo.meta.GenericLayerMetadata; -import org.gcube.dataanalysis.geo.meta.NetCDFMetadata; -import org.opengis.metadata.identification.TopicCategory; - -public class BaseLayerMetadataInsertDev { - - static String geonetworkurl = "http://geoserver-dev.d4science-ii.research-infrastructures.eu/geonetwork/"; - static String geoserverurl = "http://geoserver-dev.d4science-ii.research-infrastructures.eu/geoserver"; - static String user = "admin"; - static String password = "admin"; - - public static void main(String[] args) throws Exception{ - GenericLayerMetadata metadataInserter = new GenericLayerMetadata(); - metadataInserter.setGeonetworkUrl(geonetworkurl); - metadataInserter.setGeonetworkUser(user); - metadataInserter.setGeonetworkPwd(password); - metadataInserter.setGeoserverUrl(geoserverurl); - metadataInserter.setResolution(0.5); - metadataInserter.setXLeftLow(-180); - metadataInserter.setYLeftLow(-85.5); - metadataInserter.setXRightUpper(180); - metadataInserter.setYRightUpper(85.5); - /* - faoarea(metadataInserter); - metadataInserter.insertMetaData(); - eezall(metadataInserter); - metadataInserter.insertMetaData(); - - lme(metadataInserter); - metadataInserter.insertMetaData(); - gebco(); - - meow(metadataInserter); - metadataInserter.insertMetaData(); - - ices(metadataInserter); - metadataInserter.insertMetaData(); - - longhurst(metadataInserter); - metadataInserter.insertMetaData(); - - ihovseez(metadataInserter); - metadataInserter.insertMetaData(); - - iho(metadataInserter); - metadataInserter.insertMetaData(); - */ - - - /* - DepthMeanAnnual(metadataInserter); - metadataInserter.insertMetaData(); - - SSTAnMean(metadataInserter); - metadataInserter.insertMetaData(); - SalinityMean(metadataInserter); - metadataInserter.insertMetaData(); - PrimProdMean(metadataInserter); - metadataInserter.insertMetaData(); - environments(metadataInserter); - metadataInserter.insertMetaData(); - IceConAnn(metadataInserter); - metadataInserter.insertMetaData(); - */ - - - } - - // eezall - private static void eezall(GenericLayerMetadata metadataInserter ){ - metadataInserter.setTitle("Exclusive Economic Zones Boundaries (EEZ)"); - metadataInserter.setLayerName("aquamaps:WorldEEZv72012HR"); - metadataInserter.setResolution(0); - metadataInserter.setCategoryTypes("_"+TopicCategory.OCEANS.name()+"_"); - metadataInserter.setAbstractField("VLIZ (2012). Maritime Boundaries Geodatabase, version 7. Available online at http://www.marineregions.org/. Consulted on 2013-06-05. This dataset represents Exclusive Economic Zones (EEZ) of the world. Up to now, there was no global public domain cover available. Therefore, the Flanders Marine Institute decided to develop its own database. The database includes two global GIS-layers: one contains polylines that represent the maritime boundaries of the world countries, the other one is a polygon layer representing the Exclusive Economic Zone of countries. The database also contains digital information about treaties. Please note that the EEZ shapefile also includes the internal waters of each country"); - metadataInserter.setCustomTopics("i-Marine","Exclusive Economic Zones","VLIZ"); - - } - - // lme - private static void lme(GenericLayerMetadata metadataInserter ){ - metadataInserter.setTitle("Large Marine Ecosystems of the World"); - metadataInserter.setLayerName("aquamaps:lmes64"); - metadataInserter.setResolution(0); - metadataInserter.setCategoryTypes("_"+TopicCategory.OCEANS.name()+"_"); - metadataInserter.setAbstractField("This dataset represents the Large Marine Ecosystems of the world. It was composed by the National Oceanic and Atmospheric Administration (NOAA). The dataset exists as a polygon and as a polyline layer. The dataset can be downloaded from http://www.edc.uri.edu/lme/gisdata.htm."); - metadataInserter.setCustomTopics("i-Marine","Large Marine Ecosystems","NOAA"); - } - - //meow - private static void meow(GenericLayerMetadata metadataInserter ){ - metadataInserter.setTitle("Marine Ecoregions of the World, MEOW (Spalding et al., 2007)"); - metadataInserter.setLayerName("aquamaps:meowecos"); - metadataInserter.setResolution(0); - metadataInserter.setCategoryTypes("_"+TopicCategory.OCEANS.name()+"_"); - metadataInserter.setAbstractField("MEOW is a biogeographic classification of the world's coasts and shelves. It is the first ever comprehensive marine classification system with clearly defined boundaries and definitions and was developed to closely link to existing regional systems. The ecoregions nest within the broader biogeographic tiers of Realms and Provinces. MEOW represents broad-scale patterns of species and communities in the ocean, and was designed as a tool for planning conservation across a range of scales and assessing conservation efforts and gaps worldwide. The current system focuses on coast and shelf areas (as this is where the majority of human activity and conservation action is focused) and does not consider realms in pelagic or deep benthic environment. It is hoped that parallel but distinct systems for pelagic and deep benthic biotas will be devised in the near future. The project was led by The Nature Conservancy (TNC) and the World Wildlife Fund (WWF), with broad input from a working group representing key NGO, academic and intergovernmental conservation partners. (source: http://www.worldwildlife.org/science/ecoregions/marine/item1266.html). Reference: Spalding, M. D. Fox, H. E. Allen, G. R. Davidson, N. Ferdana, Z. A. Finlayson, M. Halpern, B. S. Jorge, M. A. Lombana, A. Lourie, S. A., (2007). Marine Ecoregions of the World: A Bioregionalization of Coastal and Shelf Areas. Bioscience 2007, VOL 57; numb 7, pages 573-584."); - metadataInserter.setCustomTopics("i-Marine","Marine Ecoregions of the World","MEOW","Spalding"); - } - - //ICES - private static void ices(GenericLayerMetadata metadataInserter ){ - metadataInserter.setTitle("ICES Ecoregions"); - metadataInserter.setLayerName("aquamaps:Ecoregions20090430"); - metadataInserter.setResolution(0); - metadataInserter.setCategoryTypes("_"+TopicCategory.OCEANS.name()+"_"); - metadataInserter.setAbstractField("ICES EcoRegions are large-scale management units for the ICES regional seas and are used in advisory reports to segment advice into the different sea areas. The EcoRegions were first referenced by the predecessor to ACOM (Advisory Committee) in 2004 (source: http://www.ices.dk/InSideOut/mayjun09/j.html)"); - metadataInserter.setCustomTopics("i-Marine","ICES Ecoregions","ICES"); - } - - //longhurst - private static void longhurst(GenericLayerMetadata metadataInserter ){ - metadataInserter.setTitle("Longhurst Biogeographical Provinces"); - metadataInserter.setLayerName("aquamaps:Longhurstworldv42010"); - metadataInserter.setResolution(0); - metadataInserter.setCategoryTypes("_"+TopicCategory.OCEANS.name()+"_"); - metadataInserter.setAbstractField("VLIZ (2009). Longhurst Biogeographical Provinces. Available online at http://www.marineregions.org/. This dataset represents a partition of the world oceans into provinces as defined by Longhurst (1995; 1998; 2006), and are based on the prevailing role of physical forcing as a regulator of phytoplankton distribution. The dataset represents the initial static boundaries developed at the Bedford Institute of Oceanography, Canada. Note that the boundaries of these provinces are not fixed in time and space, but are dynamic and move under seasonal and interannual changes in physical forcing. At the first level of reduction, Longhurst recognised four principal biomes (also referred to as domains in earlier publications): the Polar Biome, the Westerlies Biome, the Trade-Winds Biome, and the Coastal Boundary Zone Biome. These four Biomes are recognisable in every major ocean basin. At the next level of reduction, the ocean basins are partitioned into provinces, roughly ten for each basin. These partitions provide a template for data analysis or for making parameter assignments on a global scale. Please refer to Longhurst's publications when using these shapefiles. Consulted on 2013-06-05. Reference: References: Longhurst, A.R et al. (1995). An estimate of global primary production in the ocean from satellite radiometer data. J. Plankton Res. 17, 1245-1271. Longhurst, A.R. (1995). Seasonal cycles of pelagic production and consumption. Prog. Oceanogr. 36, 77-167. Longhurst, A.R. (1998). Ecological Geography of the Sea. Academic Press, San Diego. 397p. (IMIS). Longhurst, A.R. (2006). Ecological Geography of the Sea. 2nd Edition. Academic Press, San Diego, 560p."); - metadataInserter.setCustomTopics("i-Marine","Longhurst Biogeographical Provinces","Longhurst","VLIZ"); - } - - - //longhurst - private static void ihovseez(GenericLayerMetadata metadataInserter ){ - metadataInserter.setTitle("Marineregions: the intersect of the Exclusive Economic Zones and IHO areas"); - metadataInserter.setLayerName("aquamaps:EEZIHOunionv2"); - metadataInserter.setResolution(0); - metadataInserter.setCategoryTypes("_"+TopicCategory.OCEANS.name()+"_"); - metadataInserter.setAbstractField("VLIZ (2010). Intersect of IHO Sea Areas and Exclusive Economic Zones (version 1). Available online at http://www.marineregions.org/. Consulted on 2013-06-05. VLIZ (2012). Intersect of IHO Sea Areas and Exclusive Economic Zones (version 2). Available online at http://www.marineregions.org/. Consulted on 2013-06-05. The maritime boundaries provide a useful tool to limit national marine areas, but do not include information on marine regional and sub regional seas. This hampers the usage of these boundaries for implementing nature conservation strategies or analyzing marine biogeographic patterns. For example, a species occurring in the German EEZ can live in the North Sea, the Baltic Sea or Kattegat area. Each of these different marine areas has very distinct hydrological, oceanographic and ecological conditions. Therefore, by combining the information on regional seas and national maritime boundaries, we can include both a environmental and managerial factor. We propose to overlay the information from the maritime boundaries (the Exclusive Economic Zones) with the IHO Sea Areas (IHO, 1953). This map including the global oceans and seas, has been drafted for hydrographic purposes, but also gives an unequivocal and acceptable distinction of the regional seas and oceans from an oceanographic point of view. The combination of these two boundaries allows us for example to create national regional sea areas for the global ocean."); - metadataInserter.setCustomTopics("i-Marine","Marineregions: the intersect of the Exclusive Economic Zones and IHO areas","Marineregions","VLIZ","EEZ","IHO"); - } - - - //iho - private static void iho(GenericLayerMetadata metadataInserter ){ - metadataInserter.setTitle("IHO Sea Areas"); - metadataInserter.setLayerName("aquamaps:WorldSeas"); - metadataInserter.setResolution(0); - metadataInserter.setCategoryTypes("_"+TopicCategory.OCEANS.name()+"_"); - metadataInserter.setAbstractField("VLIZ (2005). IHO Sea Areas. Available online at http://www.marineregions.org/. Consulted on 2013-06-05. This dataset represents the boundaries of the major oceans and seas of the world. The source for the boundaries is the publication 'Limits of Oceans & Seas, Special Publication No. 23' published by the IHO in 1953. The dataset was composed by the Flanders Marine Data and Information Centre. NB: The Southern Ocean is not included in the IHO publication and its limits are subject of discussion among the scientific community. The Flanders Marine Institute acknowledges the controversy around this subject but decided to include the Southern Ocean in the dataset as this term is often used by scientists working in this area."); - metadataInserter.setCustomTopics("i-Marine","IHO Sea Areas","Marineregions","VLIZ","IHO"); - } - - - //gebco - private static void gebco() throws Exception{ - NetCDFMetadata metadataInserter = new NetCDFMetadata(); - metadataInserter.setGeonetworkUrl(geonetworkurl); - metadataInserter.setGeonetworkUser(user); - metadataInserter.setGeonetworkPwd(password); - metadataInserter.setThreddsCatalogUrl("http://thredds.research-infrastructures.eu/thredds/catalog/public/netcdf/catalog.xml"); - metadataInserter.setTitle("General Bathymetric Chart of the Oceans (GEBCO) 3D"); - metadataInserter.setLayerName("z"); - metadataInserter.setLayerUrl("http://thredds.research-infrastructures.eu/thredds/dodsC/public/netcdf/gebco_08_OCEANS_CLIMATOLOGY_METEOROLOGY_ATMOSPHERE_.nc"); - metadataInserter.setSourceFileName("gebco_08_OCEANS_CLIMATOLOGY_METEOROLOGY_ATMOSPHERE_.nc"); - metadataInserter.setResolution(0.0083); - metadataInserter.setAbstractField("The GEBCO_08 Grid: a global 30 arc-second grid. The General Bathymetric Chart of the Oceans (GEBCO) consists of an international group of experts who work on the development of a range of bathymetric data sets and data products, including gridded bathymetric data sets, the GEBCO Digital Atlas, the GEBCO world map and the GEBCO Gazetteer of Undersea Feature Names."); - metadataInserter.setCustomTopics("i-Marine","General Bathymetric Chart of the Oceans","GEBCO","3D"); - metadataInserter.insertMetaData(); - } - - // IceConAnn - private static void IceConAnn(GenericLayerMetadata metadataInserter ){ - metadataInserter.setTitle("IceConAnn"); - metadataInserter.setLayerName("aquamaps:iceConAnn"); - metadataInserter.setCategoryTypes("_"+TopicCategory.ENVIRONMENT.name()+"_"); - metadataInserter.setAbstractField("Mean Annual Ice Concentration"); - metadataInserter.setCustomTopics("i-Marine","Mean Annual Ice Concentration"); - } - //DepthMeanAnnual - private static void DepthMeanAnnual(GenericLayerMetadata metadataInserter ){ - metadataInserter.setTitle("DepthMeanAnnual"); - metadataInserter.setLayerName("aquamaps:DepthMeanAnnual"); - metadataInserter.setCategoryTypes("_"+TopicCategory.ENVIRONMENT.name()+"_"); - metadataInserter.setAbstractField("Mean Depth at half-degree resolution"); - metadataInserter.setCustomTopics("i-Marine","Mean Depth"); - } - - //faoarea - private static void faoarea(GenericLayerMetadata metadataInserter ){ - metadataInserter.setTitle("FAO Fishing Areas"); - metadataInserter.setResolution(0); - metadataInserter.setLayerName("aquamaps:WorldFaoZones"); - metadataInserter.setCategoryTypes("_"+TopicCategory.OCEANS.name()+"_"); - metadataInserter.setAbstractField("The dataset represents the boundaries of the FAO Fishing Areas. The source for the boundaries is the description that can be found on the FAO website. The dataset was composed by the Flanders Marine Data and Information Centre."); - metadataInserter.setCustomTopics("i-Marine","FAO Areas"); - } - - //SSTANMean - private static void SSTAnMean(GenericLayerMetadata metadataInserter ){ - metadataInserter.setTitle("SSTAnMean"); - metadataInserter.setLayerName("aquamaps:sstAnMean"); - metadataInserter.setCategoryTypes("_"+TopicCategory.ENVIRONMENT.name()+"_"); - metadataInserter.setAbstractField("Mean Annual Sea Surface Temperature at half-degree resolution"); - metadataInserter.setCustomTopics("i-Marine","Mean Annual Sea Surface Temperature"); - } - - //SalinityMean - private static void SalinityMean(GenericLayerMetadata metadataInserter ){ - metadataInserter.setTitle("SalinityMean"); - metadataInserter.setLayerName("aquamaps:salinityMean"); - metadataInserter.setCategoryTypes("_"+TopicCategory.ENVIRONMENT.name()+"_"); - metadataInserter.setAbstractField("Mean Annual Salinity at half-degree resolution"); - metadataInserter.setCustomTopics("i-Marine","Mean Annual Salinity"); - } - - // PrimProdMean - private static void PrimProdMean(GenericLayerMetadata metadataInserter ){ - metadataInserter.setTitle("PrimProdMean"); - metadataInserter.setLayerName("aquamaps:primProdMean"); - metadataInserter.setCategoryTypes("_"+TopicCategory.ENVIRONMENT.name()+"_"+TopicCategory.BIOTA.name()+"_"); - metadataInserter.setAbstractField("Mean Annual Primary Production at half-degree resolution"); - metadataInserter.setCustomTopics("i-Marine","Mean Annual Primary Production"); - } - - //environments - private static void environments(GenericLayerMetadata metadataInserter ){ - metadataInserter.setTitle("environments"); - metadataInserter.setLayerName("aquamaps:environments"); - metadataInserter.setCategoryTypes("_"+TopicCategory.ENVIRONMENT.name()+"_"+TopicCategory.BIOTA.name()+"_"); - metadataInserter.setAbstractField("Aggregated environmental and biota data at half-degree resolution"); - metadataInserter.setCustomTopics("i-Marine","Aggregated environmental and biota data"); - } - - - -} diff --git a/src/main/java/org/gcube/dataanalysis/geo/batch/ThreddsMetadataBatchInserter.java b/src/main/java/org/gcube/dataanalysis/geo/batch/ThreddsMetadataBatchInserter.java deleted file mode 100644 index 59af307..0000000 --- a/src/main/java/org/gcube/dataanalysis/geo/batch/ThreddsMetadataBatchInserter.java +++ /dev/null @@ -1,14 +0,0 @@ -package org.gcube.dataanalysis.geo.batch; - -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; -import org.gcube.dataanalysis.geo.insertion.ThreddsFetcher; - -public class ThreddsMetadataBatchInserter { - - public static void main(String[] args) throws Exception{ - AnalysisLogger.setLogger("./cfg/"+AlgorithmConfiguration.defaultLoggerFile); - ThreddsFetcher tf = new ThreddsFetcher(null); - tf.fetch("http://thredds.research-infrastructures.eu/thredds/catalog/public/netcdf/catalog.xml"); - } -} diff --git a/src/main/java/org/gcube/dataanalysis/geo/insertion/RasterTable.java b/src/main/java/org/gcube/dataanalysis/geo/insertion/RasterTable.java deleted file mode 100644 index 3565291..0000000 --- a/src/main/java/org/gcube/dataanalysis/geo/insertion/RasterTable.java +++ /dev/null @@ -1,128 +0,0 @@ -package org.gcube.dataanalysis.geo.insertion; - -import java.util.List; -import java.util.UUID; - -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.gcube.contentmanagement.lexicalmatcher.utils.DatabaseFactory; -import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; -import org.gcube.dataanalysis.ecoengine.utils.DatabaseUtils; -import org.gcube.dataanalysis.ecoengine.utils.Tuple; -import org.gcube.dataanalysis.geo.retrieval.GeoIntersector; -import org.gcube.dataanalysis.geo.utils.CSquareCodesConverter; -import org.hibernate.SessionFactory; - -/** - * transforms a raster map into a table - * - * @author coro - * - */ -public class RasterTable { - - private double valuesMatrix[][]; - double x1; - double x2; - double y1; - double y2; - double z; - double xResolution; - double yResolution; - - private AlgorithmConfiguration configuration; - private String tablename = "rstr" + ("" + UUID.randomUUID()).replace("-", ""); - static String createTableStatement = "CREATE TABLE %1$s (id serial, csquarecode character varying, x real, y real, z real, probability real)"; - static String columnsnames = "csquarecode, x , y , z , probability"; - public static String csquareColumn = "csquarecode"; - public static String probabilityColumn = "probability"; - public static String idColumn = "id"; - - public String getTablename() { - return tablename; - } - - public void setTablename(String tablename) { - this.tablename = tablename; - } - - public RasterTable(double x1, double x2, double y1, double y2, double z, double xResolution, double yResolution, double[][] values, AlgorithmConfiguration configuration) { - this.valuesMatrix = values; - this.configuration = configuration; - this.x1 = x1; - this.x2 = x2; - this.y1 = y1; - this.y2 = y2; - this.z = z; - this.xResolution = xResolution; - this.yResolution = yResolution; - } - - public void dumpGeoTable() { - - // open the connection to the db - SessionFactory dbconnection = DatabaseUtils.initDBSession(configuration); - try { - AnalysisLogger.getLogger().debug("Database Initialized"); - // create a table - DatabaseFactory.executeSQLUpdate(String.format(createTableStatement, tablename), dbconnection); - AnalysisLogger.getLogger().debug("Table " + tablename + " created"); - List> coordinates = GeoIntersector.generateCoordinateTriplets(x1, x2, y1, y2, z, xResolution, yResolution); - int triplets = coordinates.size(); - AnalysisLogger.getLogger().debug("Generated " + triplets + " coordinates triples"); - List values = GeoIntersector.associateValueToCoordinates(coordinates, valuesMatrix); - AnalysisLogger.getLogger().debug("Association to values completed - fulfilling buffer"); - // for each element in the matrix, build the corresponding csquare code - StringBuffer sb = new StringBuffer(); - for (int i = 0; i < triplets; i++) { - // save the string in a buffer - Tuple cset = coordinates.get(i); - double x = cset.getElements().get(0); - double y = cset.getElements().get(1); - String csquare = CSquareCodesConverter.convertAtResolution(y,x, xResolution); - Double value = values.get(i); - //we do not use NaNs in this case every value will be filled - if (value.isNaN()) - value = 0d; - - sb.append("('" + csquare + "'," + x + "," + y + "," + z + ",'" + value + "')"); - - if (i % 5000 == 0) { -// AnalysisLogger.getLogger().debug("Partial Inserting Buffer of " + sb.length() + " Values"); - String insertStatement = DatabaseUtils.insertFromBuffer(tablename, columnsnames, sb); - DatabaseFactory.executeSQLUpdate(insertStatement, dbconnection); -// AnalysisLogger.getLogger().debug("Partial Insertion completed with Success!"); - sb = new StringBuffer(); - } else if (i < triplets - 1) - sb.append(","); - } - - AnalysisLogger.getLogger().debug("Inserting Final Buffer of " + sb.length() + " Values"); - // save all the strings on the table - if (sb.length() > 0) { - String insertStatement = DatabaseUtils.insertFromBuffer(tablename, columnsnames, sb); - DatabaseFactory.executeSQLUpdate(insertStatement, dbconnection); - AnalysisLogger.getLogger().debug("Insertion completed with Success!"); - } - } catch (Exception e) { - e.printStackTrace(); - AnalysisLogger.getLogger().debug("Error in dumping table: " + e.getLocalizedMessage()); - } finally { - // close the connection - DatabaseUtils.closeDBConnection(dbconnection); - AnalysisLogger.getLogger().debug("Raster Geo Table DB closed!"); - } - } - - public void deleteTable() { - SessionFactory dbconnection = null; - try { - dbconnection = DatabaseUtils.initDBSession(configuration); - DatabaseFactory.executeSQLUpdate(DatabaseUtils.dropTableStatement(tablename), dbconnection); - } catch (Exception e) { - e.printStackTrace(); - } finally { - DatabaseUtils.closeDBConnection(dbconnection); - } - } - -} diff --git a/src/main/java/org/gcube/dataanalysis/geo/insertion/ThreddsFetcher.java b/src/main/java/org/gcube/dataanalysis/geo/insertion/ThreddsFetcher.java deleted file mode 100644 index d2150c7..0000000 --- a/src/main/java/org/gcube/dataanalysis/geo/insertion/ThreddsFetcher.java +++ /dev/null @@ -1,198 +0,0 @@ -package org.gcube.dataanalysis.geo.insertion; - -import java.util.List; -import java.util.Locale; - -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; -import org.gcube.dataanalysis.geo.meta.NetCDFMetadata; -import org.gcube.dataanalysis.geo.meta.OGCFormatter; -import org.gcube.dataanalysis.geo.meta.features.FeaturesManager; -import org.gcube.dataanalysis.geo.utils.ThreddsDataExplorer; -import org.opengis.metadata.Metadata; - -import ucar.nc2.dataset.CoordinateAxis; -import ucar.nc2.dt.GridDatatype; -import ucar.nc2.dt.grid.GridDataset; -import ucar.nc2.units.DateRange; - -import com.ibm.icu.text.SimpleDateFormat; - -public class ThreddsFetcher { - - private FeaturesManager featurer; - public static String NetCDFDateFormat = "time: E MMM dd HH:mm:ss zzz yyyy"; - public static String HumanDateFormat = "MM-dd-yy HH:mm"; - - public ThreddsFetcher(String scope) { - featurer = new FeaturesManager(); - featurer.setScope(scope); - } - - public void fetch(String threddsCatalogURL) throws Exception { - - List filesURL = ThreddsDataExplorer.getFiles(threddsCatalogURL); - for (String filename : filesURL) { -// if (!filename.equalsIgnoreCase("cami_0000-09-01_64x128_L26_c030918.nc")) -// continue; - - String url = OGCFormatter.getOpenDapURL(threddsCatalogURL, filename); - if (ThreddsDataExplorer.isGridDataset(url)) { - // retrieve information - GridDataset gds = ucar.nc2.dt.grid.GridDataset.open(url); - - List gridTypes = gds.getGrids(); - for (GridDatatype gdt : gridTypes) { - String description = gdt.getDescription(); - if ((description==null) || (description.length()==0)) - description = gdt.getFullName(); - // get date range - DateRange dr = gdt.getCoordinateSystem().getDateRange(); -// SimpleDateFormat netcdfDF = new SimpleDateFormat(NetCDFDateFormat, Locale.ENGLISH); - SimpleDateFormat humanDF = new SimpleDateFormat(HumanDateFormat, Locale.ROOT); - String hStartDate = null; - String hEndDate = null; - String duration = null; - String resolution = gdt.getTimeDimension()==null?null:""+gdt.getTimeDimension().getLength(); - - int numberOfDimensions = 2; - if ((gdt.getZDimension()!=null)&&(gdt.getZDimension().getLength()>1)){ - numberOfDimensions = 3; - AnalysisLogger.getLogger().debug("Length of Z Dimension: "+gdt.getZDimension().getLength()); - } - else - AnalysisLogger.getLogger().debug("Bidimensional Layer "); - - if (dr != null) { - hStartDate = dr.getStart() == null ? null : humanDF.format(dr.getStart().getDate()); - hEndDate = dr.getEnd() == null ? null : humanDF.format(dr.getEnd().getDate()); - duration = dr.getDuration() == null ? null : "" + dr.getDuration(); - } - - // control if the file is yet on GN -// String generatedTitle = generateTitle(filename, description, hStartDate, hEndDate, numberOfDimensions); - String generatedTitle = generateTitle(gds.getTitle()+": "+gds.getDescription(), description, hStartDate, hEndDate, numberOfDimensions); - - CoordinateAxis xAxis = gdt.getCoordinateSystem().getXHorizAxis(); - CoordinateAxis yAxis = gdt.getCoordinateSystem().getYHorizAxis(); - AnalysisLogger.getLogger().debug("Bounds:"+xAxis.getMinValue()+","+yAxis.getMinValue()+","+xAxis.getMaxValue()+","+yAxis.getMaxValue()); - - Metadata previousmeta = featurer.getGNInfobyUUIDorName(generatedTitle); - if (previousmeta!=null){ - AnalysisLogger.getLogger().debug("***WARNING: layer yet found on GeoNetwork***"); - continue; - } - /*Layers check - for testing only - else { - AnalysisLogger.getLogger().debug("***layer retrieval failed***"); - if (true) System.exit(0); - } - */ - - // get resolution - take the maximum regular step - double resolutionX = Math.abs((double) (xAxis.getMaxValue() - xAxis.getMinValue()) / (double) xAxis.getShape()[0]); - double resolutionY = Math.abs((double) (yAxis.getMaxValue() - yAxis.getMinValue()) / (double) yAxis.getShape()[0]); - - //build metadata - NetCDFMetadata metadataInserter = new NetCDFMetadata(); - metadataInserter.setGeonetworkUrl(featurer.getGeonetworkURLFromScope()); - metadataInserter.setGeonetworkUser(featurer.getGeonetworkUserFromScope()); - metadataInserter.setGeonetworkPwd(featurer.getGeonetworkPasswordFromScope()); - - // Build standard info: - metadataInserter.setThreddsCatalogUrl(threddsCatalogURL); - metadataInserter.setLayerUrl(url); - metadataInserter.setLayerName(gdt.getFullName()); - metadataInserter.setSourceFileName(filename); - // insert ranges and sampling - metadataInserter.setTitle(generatedTitle); - metadataInserter.setAbstractField(generateAbstractField(gdt.getFullName(), filename, description, gdt.getUnitsString().trim(), hStartDate, hEndDate, duration, resolution, numberOfDimensions, gds.getTitle(), gds.getDescription())); - metadataInserter.setResolution(Math.max(resolutionX, resolutionY)); - // set Bounding box - double minX = ThreddsDataExplorer.getMinX(gdt.getCoordinateSystem()); - double maxX = ThreddsDataExplorer.getMaxX(gdt.getCoordinateSystem()); - double minY = ThreddsDataExplorer.getMinY(gdt.getCoordinateSystem()); - double maxY = ThreddsDataExplorer.getMaxY(gdt.getCoordinateSystem()); - - if (gds.getTitle().toUpperCase().contains("WORLD OCEAN ATLAS")) - { - AnalysisLogger.getLogger().debug("Managing WoA Layer"); - minX = minX-180; - maxX = maxX-180; - } - - metadataInserter.setXLeftLow(minX); - metadataInserter.setYLeftLow(minY); - metadataInserter.setXRightUpper(maxX); - metadataInserter.setYRightUpper(maxY); - - //set keywords - metadataInserter.setCustomTopics(filename, description,numberOfDimensions+"D",gds.getTitle(),gds.getDescription(),"unit:"+gdt.getUnitsString().trim()); - //set Temporal Extent - if (hStartDate!=null){ - metadataInserter.setStartDate(dr.getStart().getDate()); - metadataInserter.setEndDate(dr.getEnd().getDate()); - } - - AnalysisLogger.getLogger().debug("title: " + metadataInserter.getTitle()); - AnalysisLogger.getLogger().debug("abstract: " + metadataInserter.getAbstractField()); - - metadataInserter.insertMetaData(); -// break; - } - - } -// break; - } - } - - public static String generateTitle(String filename, String description, String startDate, String endDate, int numberOfDimensions) { - String dateString = ""; - if (startDate != null){ - if (startDate.equals(endDate)) - dateString = " in [" + startDate + "]"; - else - dateString = " from [" + startDate + "] to [" + endDate + "]"; - } - - description = description + " "+dateString+" (" + numberOfDimensions+ "D) {" + filename + "}"; - - return description.replaceAll("( )+", " "); - } - - public static String generateAbstractField(String layername, String filename, String description, String unit, String startDate, String endDate, String duration, String timeInstants, int numberOfDimensions, String netcdftitle, String netcdfdescription) { - String timeresolutionString = ""; - String durationString = ""; - if ((timeInstants != null) && (timeInstants.length() > 0)) - timeresolutionString = " Number of time instants: " + timeInstants+"."; - - if ((duration != null) && (duration.length() > 0)) - durationString = " Time interval lenght: " + duration+"."; - - String dateString = ""; - if (startDate != null) - dateString = " in the time range between [" + startDate + "] and [" + endDate + "]."; - - String unitString = ""; - if ((unit != null) && (unit.length()>0)) - unitString= " (" + unit + ")"; - - String numberOfDimensionsString = ""; - if (numberOfDimensions>0) - numberOfDimensionsString = " Number of Dimensions: "+numberOfDimensions+"."; - - String netcdfinfo = ""; - if (netcdftitle!=null) - netcdfinfo = " "+netcdftitle+": "+netcdfdescription+"."; - - return layername + ": " + description + unitString+dateString + durationString + timeresolutionString + numberOfDimensionsString+netcdfinfo+" Local file in iMarine: " + filename + "."; - } - - public static void main(String[] args) throws Exception { - AnalysisLogger.setLogger("./cfg/"+AlgorithmConfiguration.defaultLoggerFile); -// ThreddsFetcher tf = new ThreddsFetcher("/gcube/devsec"); - ThreddsFetcher tf = new ThreddsFetcher(null); - tf.fetch("http://thredds.research-infrastructures.eu/thredds/catalog/public/netcdf/catalog.xml"); - } - -} diff --git a/src/main/java/org/gcube/dataanalysis/geo/meta/GenericLayerMetadata.java b/src/main/java/org/gcube/dataanalysis/geo/meta/GenericLayerMetadata.java deleted file mode 100644 index 1fc18e8..0000000 --- a/src/main/java/org/gcube/dataanalysis/geo/meta/GenericLayerMetadata.java +++ /dev/null @@ -1,475 +0,0 @@ -package org.gcube.dataanalysis.geo.meta; - -import it.geosolutions.geonetwork.GNClient; -import it.geosolutions.geonetwork.util.GNInsertConfiguration; - -import java.io.File; -import java.io.FileWriter; -import java.io.IOException; -import java.net.URI; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.Collections; -import java.util.Date; -import java.util.HashMap; -import java.util.HashSet; -import java.util.List; -import java.util.Locale; -import java.util.Map.Entry; - -import javax.xml.bind.JAXBException; - -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.geotoolkit.metadata.iso.DefaultIdentifier; -import org.geotoolkit.metadata.iso.DefaultMetadata; -import org.geotoolkit.metadata.iso.citation.DefaultCitation; -import org.geotoolkit.metadata.iso.citation.DefaultCitationDate; -import org.geotoolkit.metadata.iso.citation.DefaultContact; -import org.geotoolkit.metadata.iso.citation.DefaultOnlineResource; -import org.geotoolkit.metadata.iso.citation.DefaultResponsibleParty; -import org.geotoolkit.metadata.iso.constraint.DefaultLegalConstraints; -import org.geotoolkit.metadata.iso.distribution.DefaultDigitalTransferOptions; -import org.geotoolkit.metadata.iso.distribution.DefaultDistribution; -import org.geotoolkit.metadata.iso.distribution.DefaultFormat; -import org.geotoolkit.metadata.iso.extent.DefaultExtent; -import org.geotoolkit.metadata.iso.extent.DefaultGeographicBoundingBox; -import org.geotoolkit.metadata.iso.identification.DefaultDataIdentification; -import org.geotoolkit.metadata.iso.identification.DefaultKeywords; -import org.geotoolkit.metadata.iso.identification.DefaultResolution; -import org.geotoolkit.metadata.iso.identification.DefaultUsage; -import org.geotoolkit.metadata.iso.lineage.DefaultLineage; -import org.geotoolkit.metadata.iso.lineage.DefaultNominalResolution; -import org.geotoolkit.metadata.iso.lineage.DefaultProcessStep; -import org.geotoolkit.metadata.iso.lineage.DefaultProcessing; -import org.geotoolkit.metadata.iso.lineage.DefaultSource; -import org.geotoolkit.metadata.iso.maintenance.DefaultMaintenanceInformation; -import org.geotoolkit.metadata.iso.quality.DefaultDataQuality; -import org.geotoolkit.metadata.iso.quality.DefaultScope; -import org.geotoolkit.metadata.iso.spatial.DefaultGeometricObjects; -import org.geotoolkit.metadata.iso.spatial.DefaultVectorSpatialRepresentation; -import org.geotoolkit.util.DefaultInternationalString; -import org.geotoolkit.xml.XML; -import org.opengis.metadata.Metadata; -import org.opengis.metadata.citation.DateType; -import org.opengis.metadata.citation.PresentationForm; -import org.opengis.metadata.citation.ResponsibleParty; -import org.opengis.metadata.citation.Role; -import org.opengis.metadata.constraint.Restriction; -import org.opengis.metadata.identification.KeywordType; -import org.opengis.metadata.identification.TopicCategory; -import org.opengis.metadata.lineage.ProcessStep; -import org.opengis.metadata.maintenance.MaintenanceFrequency; -import org.opengis.metadata.maintenance.ScopeCode; -import org.opengis.metadata.spatial.GeometricObjectType; -import org.opengis.metadata.spatial.SpatialRepresentationType; -import org.opengis.metadata.spatial.TopologyLevel; -import org.opengis.util.InternationalString; - -public class GenericLayerMetadata { - - private String geonetworkUrl = "http://geoserver-dev.d4science-ii.research-infrastructures.eu/geonetwork/"; - private String geoserverUrl = "http://geoserver-dev.d4science-ii.research-infrastructures.eu/geonetwork/"; - private String geonetworkUser = "admin"; - private String geonetworkPwd = "admin"; - private String title = "temperature 04091217ruc.nc"; - private String layerName = "T"; - private String usageField = "Environmental enrichment"; - private String processdescription = "Maps publication"; - private String usageLimitations = "Not for commercial scopes"; - private Date sourceGenerationDate = new Date(System.currentTimeMillis()); - private String categoryTypes = "_BIOTA_"; - private String contactInfo = "support@d4science.research-infrastructures.eu"; - private String abstractField = ""; - private String purpose = "Maps publication"; - private String author = "i-Marine"; - private double res = 0.5d; - private double xLL = -180; - private double xRU = 180; - private double yLL = -85.5; - private double yRU = 85.5; - private HashSet customTopics; - private Date startDate; - private Date endDate; - - public void setCustomTopics(String... topics){ - customTopics = new HashSet(); - for (String topic:topics) - customTopics.add(topic); - } - - public HashSet getCustomTopics(){ - return customTopics; - } - - public void setStartDate(Date date){ - startDate=date; - } - - public void setEndDate(Date date){ - endDate=date; - } - - public Date getStartDate(){ - return startDate; - } - - public Date getEndDate(){ - return endDate; - } - - public String getGeonetworkUrl() { - return geonetworkUrl; - } - - public void setGeonetworkUrl(String geonetworkUrl) { - this.geonetworkUrl = geonetworkUrl; - } - - public String getGeonetworkUser() { - return geonetworkUser; - } - - public void setGeonetworkUser(String geonetworkUser) { - this.geonetworkUser = geonetworkUser; - } - - public String getGeonetworkPwd() { - return geonetworkPwd; - } - - public void setGeonetworkPwd(String geonetworkPwd) { - this.geonetworkPwd = geonetworkPwd; - } - - public String getTitle() { - return title; - } - - public void setTitle(String title) { - this.title = title; - } - - public String getLayerName() { - return layerName; - } - - public void setLayerName(String layerName) { - this.layerName = layerName; - } - - public String getUsageField() { - return usageField; - } - - public void setUsageField(String usageField) { - this.usageField = usageField; - } - - public String getProcessdescription() { - return processdescription; - } - - public void setProcessdescription(String processdescription) { - this.processdescription = processdescription; - } - - public String getUsageLimitations() { - return usageLimitations; - } - - public void setUsageLimitations(String usageLimitations) { - this.usageLimitations = usageLimitations; - } - - public Date getSourceGenerationDate() { - return sourceGenerationDate; - } - - public void setSourceGenerationDate(Date sourceGenerationDate) { - this.sourceGenerationDate = sourceGenerationDate; - } - - public String getCategoryTypes() { - return categoryTypes; - } - - public void setCategoryTypes(String categoryTypes) { - this.categoryTypes = categoryTypes; - } - - public String getContactInfo() { - return contactInfo; - } - - public void setContactInfo(String contactInfo) { - this.contactInfo = contactInfo; - } - - public String getAbstractField() { - return abstractField; - } - - public void setAbstractField(String abstractField) { - this.abstractField = abstractField; - } - - public String getPurpose() { - return purpose; - } - - public void setPurpose(String purpose) { - this.purpose = purpose; - } - - public String getAuthor() { - return author; - } - - public void setAuthor(String author) { - this.author = author; - } - - public double getResolution() { - return res; - } - - public void setResolution(double res) { - this.res = res; - } - - public double getXLeftLow() { - return xLL; - } - - public void setXLeftLow(double xLL) { - this.xLL = xLL; - } - - public double getXRightUpper() { - return xRU; - } - - public void setXRightUpper(double xRU) { - this.xRU = xRU; - } - - public double getYLeftLow() { - return yLL; - } - - public void setYLeftLow(double yLL) { - this.yLL = yLL; - } - - public double getYRightUpper() { - return yRU; - } - - public void setYRightUpper(double yRU) { - this.yRU = yRU; - } - - public String getGeoserverUrl() { - return geoserverUrl; - } - - public void setGeoserverUrl(String geoserverUrl) { - this.geoserverUrl = geoserverUrl; - } - - static File meta2File(Metadata meta) throws IOException, JAXBException { - File temp = File.createTempFile("meta", ".xml"); - FileWriter writer = new FileWriter(temp); - writer.write(XML.marshal(meta)); - writer.close(); - return temp; - } - - public void insertMetaData() throws Exception { - - // layer uri: wms, wfs wcs - List layerUris = new ArrayList(); - layerUris.add(OGCFormatter.getWmsUrl(geoserverUrl, layerName, null, OGCFormatter.buildBoundingBox(xLL, yLL, xRU, yRU))); - layerUris.add(OGCFormatter.getWfsUrl(geoserverUrl, layerName, OGCFormatter.buildBoundingBox(xLL, yLL, xRU, yRU), 0, "json")); - layerUris.add(OGCFormatter.getWcsUrl(geoserverUrl, layerName, OGCFormatter.buildBoundingBox(xLL, yLL, xRU, yRU))); - - // layer keywords - HashMap> descriptiveKeyWords = new HashMap>(); - HashSet keySet = new HashSet(); - keySet.add("i-Marine"); - if (customTopics!=null) - keySet.addAll(customTopics); - - descriptiveKeyWords.put(KeywordType.THEME, keySet); - - if (startDate!=null){ - HashSet temporalkeySet = new HashSet(); - temporalkeySet.add(startDate.toString()); - if (!endDate.equals(startDate)) - temporalkeySet.add(endDate.toString()); - descriptiveKeyWords.put(KeywordType.TEMPORAL, temporalkeySet); - } - - // author: - DefaultResponsibleParty party = new DefaultResponsibleParty(); - party.setIndividualName(author); - DefaultContact contact = new DefaultContact(); - contact.setContactInstructions(new DefaultInternationalString(contactInfo)); - party.setContactInfo(contact); - party.setRole(Role.ORIGINATOR); - - // citation: - DefaultCitation citation = new DefaultCitation(); - citation.setTitle(new DefaultInternationalString(title)); - ArrayList citDates = new ArrayList(); - citDates.add(new DefaultCitationDate(sourceGenerationDate, DateType.CREATION)); - citDates.add(new DefaultCitationDate(sourceGenerationDate, DateType.PUBLICATION)); - citDates.add(new DefaultCitationDate(sourceGenerationDate, DateType.REVISION)); - citation.setDates(citDates); - ArrayList citAltTitle = new ArrayList(); - citAltTitle.add(new DefaultInternationalString(title)); - citation.setAlternateTitles(citAltTitle); - citation.setEditionDate(sourceGenerationDate); - citation.getPresentationForms().add(PresentationForm.MAP_DIGITAL); - ArrayList keywordslist = new ArrayList(); - for (Entry> entry : descriptiveKeyWords.entrySet()) { - DefaultKeywords keywords = new DefaultKeywords(); - for (String key : entry.getValue()) - keywords.getKeywords().add(new DefaultInternationalString(key)); - - keywords.setType(entry.getKey()); - DefaultCitation thesaurus = new DefaultCitation(); - thesaurus.setTitle(new DefaultInternationalString("General")); - thesaurus.setDates(citDates); - keywords.setThesaurusName(thesaurus); - keywordslist.add(keywords); - } - - // usage: - DefaultUsage usage = new DefaultUsage(); - usage.setSpecificUsage(new DefaultInternationalString(usageField)); - usage.setUsageDate(sourceGenerationDate); - usage.setUserDeterminedLimitations(new DefaultInternationalString(usageLimitations)); - usage.setUserContactInfo(new ArrayList(Arrays.asList(party))); - ArrayList usages = new ArrayList(Arrays.asList(usage)); - //build categories by guessing on the filename - List categories = guessTopicCategory(categoryTypes); - AnalysisLogger.getLogger().debug("Guessed Topics: "+categories); - // Spatial Rapresentation Info - DefaultGeometricObjects geoObjs = new DefaultGeometricObjects(); - geoObjs.setGeometricObjectType(GeometricObjectType.COMPLEX); - DefaultVectorSpatialRepresentation spatial = new DefaultVectorSpatialRepresentation(); - spatial.setTopologyLevel(TopologyLevel.GEOMETRY_ONLY); - spatial.getGeometricObjects().add(geoObjs); - - // Extent: - DefaultExtent extent = new DefaultExtent(); - extent.setGeographicElements(Collections.singleton(new DefaultGeographicBoundingBox(xLL, xRU, yLL, yRU))); - extent.setDescription(new DefaultInternationalString("Bounding box")); - - /*Only with Geotoolkit 4.x - DefaultTemporalExtent stext = new DefaultTemporalExtent(startDate,endDate); - stext.setStartTime(startDate); - stext.setEndTime(endDate); - extent.setTemporalElements(Arrays.asList(stext)); - */ - extent.freeze(); - - //resolution - DefaultNominalResolution resolution = new DefaultNominalResolution(); - resolution.setGroundResolution(res); - resolution.setScanningResolution(res); - DefaultResolution dres = new DefaultResolution(); - dres.setDistance(res); - - // layers access: - DefaultDistribution distribution = new DefaultDistribution(); - DefaultDigitalTransferOptions transferOptions = new DefaultDigitalTransferOptions(); - for (String uri : layerUris) - transferOptions.getOnLines().add(new DefaultOnlineResource(new URI(uri))); - distribution.getTransferOptions().add(transferOptions); - DefaultFormat format1 = new DefaultFormat(); - format1.setName(new DefaultInternationalString("WMS")); - format1.setVersion(new DefaultInternationalString("1.1.0")); - DefaultFormat format2 = new DefaultFormat(); - format2.setName(new DefaultInternationalString("WFS")); - format2.setVersion(new DefaultInternationalString("1.1.0")); - DefaultFormat format3 = new DefaultFormat(); - format3.setName(new DefaultInternationalString("WCS")); - format3.setVersion(new DefaultInternationalString("1.0.0")); - - distribution.setDistributionFormats(new ArrayList(Arrays.asList(format1, format2, format3))); - - // legal constraints - DefaultLegalConstraints constraints = new DefaultLegalConstraints(); - constraints.getUseLimitations().add(new DefaultInternationalString("Licensed")); - constraints.getAccessConstraints().add(Restriction.LICENSE); - constraints.getUseConstraints().add(Restriction.LICENSE); - - // quality declaration: - DefaultDataQuality processQuality = new DefaultDataQuality(); - - //citation - DefaultCitation sourceCitation = new DefaultCitation(); - sourceCitation.setTitle(new DefaultInternationalString(title)); - sourceCitation.getDates().add(new DefaultCitationDate(sourceGenerationDate, DateType.CREATION)); - sourceCitation.getIdentifiers().add(new DefaultIdentifier(categoryTypes)); - - //source - DefaultSource source = new DefaultSource(); - source.setResolution(resolution); - source.setDescription(new DefaultInternationalString(title)); - source.setSourceCitation(sourceCitation); - - // provenance - DefaultProcessStep preprocessStep = new DefaultProcessStep(); - DefaultProcessStep processStep = new DefaultProcessStep(preprocessStep); - DefaultProcessing processing = new DefaultProcessing(); - processing.setSoftwareReferences(new ArrayList(Arrays.asList(sourceCitation))); - processStep.setDescription(new DefaultInternationalString(processdescription)); - DefaultLineage processLineage = new DefaultLineage(); - processLineage.setProcessSteps(new ArrayList(Arrays.asList(processStep))); - processQuality.setLineage(processLineage); - processQuality.setScope(new DefaultScope(ScopeCode.DATASET)); - - // fulfill identification - DefaultDataIdentification ident = new DefaultDataIdentification(); - ident.setCitation(citation); - ident.setAbstract(new DefaultInternationalString(abstractField)); - ident.setPurpose(new DefaultInternationalString(purpose)); - ident.getResourceMaintenances().add(new DefaultMaintenanceInformation(MaintenanceFrequency.AS_NEEDED)); - ident.setDescriptiveKeywords(keywordslist); - ident.setTopicCategories(categories); - ident.setResourceSpecificUsages(usages); - ident.setExtents(new ArrayList(Arrays.asList(extent))); - ident.setSpatialRepresentationTypes(new ArrayList(Arrays.asList(SpatialRepresentationType.GRID))); - ident.setSpatialResolutions(new ArrayList(Arrays.asList(dres))); - ident.setLanguages(new ArrayList(Arrays.asList(Locale.ENGLISH))); - - // Metadata Obj: - DefaultMetadata meta = new DefaultMetadata(party, sourceGenerationDate, ident); - meta.getSpatialRepresentationInfo().add(spatial); - meta.setDistributionInfo(distribution); - meta.getMetadataConstraints().add(constraints); - meta.getDataQualityInfo().add(processQuality); - meta.setLanguage(Locale.ENGLISH); -// System.out.println(meta); - GNClient client = new GNClient(geonetworkUrl); - client.login(geonetworkUser, geonetworkPwd); - File tmetafile = meta2File(meta); - client.insertMetadata(new GNInsertConfiguration("3", "datasets", "_none_", true), tmetafile); - tmetafile.delete(); - - } - - public static List guessTopicCategory(String refString){ - String searcher = refString.toLowerCase(); - List categories = new ArrayList(); - for (TopicCategory topic:TopicCategory.values()){ - if (searcher.contains("_"+topic.name().toLowerCase()+"_")){ - categories.add(topic); - } - } - return categories; - } -} diff --git a/src/main/java/org/gcube/dataanalysis/geo/meta/NetCDFMetadata.java b/src/main/java/org/gcube/dataanalysis/geo/meta/NetCDFMetadata.java deleted file mode 100644 index dd35549..0000000 --- a/src/main/java/org/gcube/dataanalysis/geo/meta/NetCDFMetadata.java +++ /dev/null @@ -1,492 +0,0 @@ -package org.gcube.dataanalysis.geo.meta; - -import it.geosolutions.geonetwork.GNClient; -import it.geosolutions.geonetwork.util.GNInsertConfiguration; - -import java.io.File; -import java.io.FileWriter; -import java.io.IOException; -import java.net.URI; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.Collections; -import java.util.Date; -import java.util.HashMap; -import java.util.HashSet; -import java.util.List; -import java.util.Locale; -import java.util.Map.Entry; - -import javax.xml.bind.JAXBException; - -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.geotoolkit.metadata.iso.DefaultIdentifier; -import org.geotoolkit.metadata.iso.DefaultMetadata; -import org.geotoolkit.metadata.iso.citation.DefaultCitation; -import org.geotoolkit.metadata.iso.citation.DefaultCitationDate; -import org.geotoolkit.metadata.iso.citation.DefaultContact; -import org.geotoolkit.metadata.iso.citation.DefaultOnlineResource; -import org.geotoolkit.metadata.iso.citation.DefaultResponsibleParty; -import org.geotoolkit.metadata.iso.constraint.DefaultLegalConstraints; -import org.geotoolkit.metadata.iso.distribution.DefaultDigitalTransferOptions; -import org.geotoolkit.metadata.iso.distribution.DefaultDistribution; -import org.geotoolkit.metadata.iso.distribution.DefaultFormat; -import org.geotoolkit.metadata.iso.extent.DefaultExtent; -import org.geotoolkit.metadata.iso.extent.DefaultGeographicBoundingBox; -import org.geotoolkit.metadata.iso.identification.DefaultDataIdentification; -import org.geotoolkit.metadata.iso.identification.DefaultKeywords; -import org.geotoolkit.metadata.iso.identification.DefaultResolution; -import org.geotoolkit.metadata.iso.identification.DefaultUsage; -import org.geotoolkit.metadata.iso.lineage.DefaultLineage; -import org.geotoolkit.metadata.iso.lineage.DefaultNominalResolution; -import org.geotoolkit.metadata.iso.lineage.DefaultProcessStep; -import org.geotoolkit.metadata.iso.lineage.DefaultProcessing; -import org.geotoolkit.metadata.iso.lineage.DefaultSource; -import org.geotoolkit.metadata.iso.maintenance.DefaultMaintenanceInformation; -import org.geotoolkit.metadata.iso.quality.DefaultDataQuality; -import org.geotoolkit.metadata.iso.quality.DefaultScope; -import org.geotoolkit.metadata.iso.spatial.DefaultGeometricObjects; -import org.geotoolkit.metadata.iso.spatial.DefaultVectorSpatialRepresentation; -import org.geotoolkit.util.DefaultInternationalString; -import org.geotoolkit.xml.XML; -import org.opengis.metadata.Metadata; -import org.opengis.metadata.citation.DateType; -import org.opengis.metadata.citation.PresentationForm; -import org.opengis.metadata.citation.ResponsibleParty; -import org.opengis.metadata.citation.Role; -import org.opengis.metadata.constraint.Restriction; -import org.opengis.metadata.identification.KeywordType; -import org.opengis.metadata.identification.TopicCategory; -import org.opengis.metadata.lineage.ProcessStep; -import org.opengis.metadata.maintenance.MaintenanceFrequency; -import org.opengis.metadata.maintenance.ScopeCode; -import org.opengis.metadata.spatial.GeometricObjectType; -import org.opengis.metadata.spatial.SpatialRepresentationType; -import org.opengis.metadata.spatial.TopologyLevel; -import org.opengis.util.InternationalString; - -public class NetCDFMetadata { - - private String geonetworkUrl = "http://geoserver-dev.d4science-ii.research-infrastructures.eu/geonetwork/"; - private String geonetworkUser = "admin"; - private String geonetworkPwd = "admin"; - private String threddsCatalogUrl = "http://thredds.research-infrastructures.eu/thredds/catalog/public/netcdf/catalog.xml"; - private String title = "temperature 04091217ruc.nc"; - private String layerName = "T"; - private String usageField = "Environmental enrichment"; - private String processdescription = "Maps publication"; - private String usageLimitations = "Not for commercial scopes"; - private Date sourceGenerationDate = new Date(System.currentTimeMillis()); - private String sourceFileName = "04091217_ruc.nc"; - private String contactInfo = "support@d4science.research-infrastructures.eu"; - private String abstractField = "T: temperature (degK) from 04091217ruc.nc resident on the THREDDS instance " + threddsCatalogUrl; - private String purpose = "Maps publication"; - private String author = "i-Marine"; - private double res = 0.5d; - private double xLL = -180; - private double xRU = 180; - private double yLL = -85.5; - private double yRU = 85.5; - private String layerUrl = "http://thredds.research-infrastructures.eu:8080/thredds/dodsC/public/netcdf/04091217_ruc.nc"; - private HashSet customTopics; - private Date startDate; - private Date endDate; - - public void setCustomTopics(String... topics){ - customTopics = new HashSet(); - for (String topic:topics) - customTopics.add(topic); - } - - public HashSet getCustomTopics(){ - return customTopics; - } - - public void setStartDate(Date date){ - startDate=date; - } - - public void setEndDate(Date date){ - endDate=date; - } - - public Date getStartDate(){ - return startDate; - } - - public Date getEndDate(){ - return endDate; - } - - public String getGeonetworkUrl() { - return geonetworkUrl; - } - - public void setGeonetworkUrl(String geonetworkUrl) { - this.geonetworkUrl = geonetworkUrl; - } - - public String getGeonetworkUser() { - return geonetworkUser; - } - - public void setGeonetworkUser(String geonetworkUser) { - this.geonetworkUser = geonetworkUser; - } - - public String getGeonetworkPwd() { - return geonetworkPwd; - } - - public void setGeonetworkPwd(String geonetworkPwd) { - this.geonetworkPwd = geonetworkPwd; - } - - public String getThreddsCatalogUrl() { - return threddsCatalogUrl; - } - - public void setThreddsCatalogUrl(String threddsCatalogUrl) { - this.threddsCatalogUrl = threddsCatalogUrl; - } - - public String getTitle() { - return title; - } - - public void setTitle(String title) { - this.title = title; - } - - public String getLayerName() { - return layerName; - } - - public void setLayerName(String layerName) { - this.layerName = layerName; - } - - public String getUsageField() { - return usageField; - } - - public void setUsageField(String usageField) { - this.usageField = usageField; - } - - public String getProcessdescription() { - return processdescription; - } - - public void setProcessdescription(String processdescription) { - this.processdescription = processdescription; - } - - public String getUsageLimitations() { - return usageLimitations; - } - - public void setUsageLimitations(String usageLimitations) { - this.usageLimitations = usageLimitations; - } - - public Date getSourceGenerationDate() { - return sourceGenerationDate; - } - - public void setSourceGenerationDate(Date sourceGenerationDate) { - this.sourceGenerationDate = sourceGenerationDate; - } - - public String getSourceFileName() { - return sourceFileName; - } - - public void setSourceFileName(String sourceTableName) { - this.sourceFileName = sourceTableName; - } - - public String getContactInfo() { - return contactInfo; - } - - public void setContactInfo(String contactInfo) { - this.contactInfo = contactInfo; - } - - public String getAbstractField() { - return abstractField; - } - - public void setAbstractField(String abstractField) { - this.abstractField = abstractField; - } - - public String getPurpose() { - return purpose; - } - - public void setPurpose(String purpose) { - this.purpose = purpose; - } - - public String getAuthor() { - return author; - } - - public void setAuthor(String author) { - this.author = author; - } - - public double getResolution() { - return res; - } - - public void setResolution(double res) { - this.res = res; - } - - public double getXLeftLow() { - return xLL; - } - - public void setXLeftLow(double xLL) { - this.xLL = xLL; - } - - public double getXRightUpper() { - return xRU; - } - - public void setXRightUpper(double xRU) { - this.xRU = xRU; - } - - public double getYLeftLow() { - return yLL; - } - - public void setYLeftLow(double yLL) { - this.yLL = yLL; - } - - public double getYRightUpper() { - return yRU; - } - - public void setYRightUpper(double yRU) { - this.yRU = yRU; - } - - public String getLayerUrl() { - return layerUrl; - } - - public void setLayerUrl(String layerUrl) { - this.layerUrl = layerUrl; - } - - static File meta2File(Metadata meta) throws IOException, JAXBException { - File temp = File.createTempFile("meta", ".xml"); - FileWriter writer = new FileWriter(temp); - writer.write(XML.marshal(meta)); - writer.close(); - return temp; - } - - public void insertMetaData() throws Exception{ - insertMetaData("3", "datasets", "_none_", true); - } - - public void insertMetaData(String group, String category, String stylesheet, boolean validate) throws Exception { - - // layer uri: wms, wfs wcs - List layerUris = new ArrayList(); - layerUris.add(OGCFormatter.getWmsNetCDFUrl(layerUrl, layerName, OGCFormatter.buildBoundingBox(xLL, yLL, xRU, yRU))); - layerUris.add(layerUrl); - layerUris.add(OGCFormatter.getWcsNetCDFUrl(layerUrl, layerName, OGCFormatter.buildBoundingBox(xLL, yLL, xRU, yRU))); - layerUris.add(threddsCatalogUrl); - - // layer keywords - HashMap> descriptiveKeyWords = new HashMap>(); - HashSet keySet = new HashSet(); - keySet.add("THREDDS"); - keySet.add("i-Marine"); - keySet.add("NetCDF"); - if (customTopics!=null) - keySet.addAll(customTopics); - - descriptiveKeyWords.put(KeywordType.THEME, keySet); - - if (startDate!=null){ - HashSet temporalkeySet = new HashSet(); - temporalkeySet.add(startDate.toString()); - if (!endDate.equals(startDate)) - temporalkeySet.add(endDate.toString()); - descriptiveKeyWords.put(KeywordType.TEMPORAL, temporalkeySet); - } - - - // author: - DefaultResponsibleParty party = new DefaultResponsibleParty(); - party.setIndividualName(author); - DefaultContact contact = new DefaultContact(); - contact.setContactInstructions(new DefaultInternationalString(contactInfo)); - party.setContactInfo(contact); - party.setRole(Role.ORIGINATOR); - - // citation: - DefaultCitation citation = new DefaultCitation(); - citation.setTitle(new DefaultInternationalString(title)); - ArrayList citDates = new ArrayList(); - citDates.add(new DefaultCitationDate(sourceGenerationDate, DateType.CREATION)); - citDates.add(new DefaultCitationDate(sourceGenerationDate, DateType.PUBLICATION)); - citDates.add(new DefaultCitationDate(sourceGenerationDate, DateType.REVISION)); - citation.setDates(citDates); - ArrayList citAltTitle = new ArrayList(); - citAltTitle.add(new DefaultInternationalString(title)); - citation.setAlternateTitles(citAltTitle); - citation.setEditionDate(sourceGenerationDate); - citation.getPresentationForms().add(PresentationForm.MAP_DIGITAL); - ArrayList keywordslist = new ArrayList(); - for (Entry> entry : descriptiveKeyWords.entrySet()) { - DefaultKeywords keywords = new DefaultKeywords(); - for (String key : entry.getValue()) - keywords.getKeywords().add(new DefaultInternationalString(key)); - - keywords.setType(entry.getKey()); - DefaultCitation thesaurus = new DefaultCitation(); - thesaurus.setTitle(new DefaultInternationalString("General")); - thesaurus.setDates(citDates); - keywords.setThesaurusName(thesaurus); - keywordslist.add(keywords); - } - - // usage: - DefaultUsage usage = new DefaultUsage(); - usage.setSpecificUsage(new DefaultInternationalString(usageField)); - usage.setUsageDate(sourceGenerationDate); - usage.setUserDeterminedLimitations(new DefaultInternationalString(usageLimitations)); - usage.setUserContactInfo(new ArrayList(Arrays.asList(party))); - ArrayList usages = new ArrayList(Arrays.asList(usage)); - //build categories by guessing on the filename - List categories = guessTopicCategory(sourceFileName); - AnalysisLogger.getLogger().debug("Guessed Topics: "+categories); - // Spatial Rapresentation Info - DefaultGeometricObjects geoObjs = new DefaultGeometricObjects(); - geoObjs.setGeometricObjectType(GeometricObjectType.COMPLEX); - DefaultVectorSpatialRepresentation spatial = new DefaultVectorSpatialRepresentation(); - spatial.setTopologyLevel(TopologyLevel.GEOMETRY_ONLY); - spatial.getGeometricObjects().add(geoObjs); - - // Extent: - DefaultExtent extent = new DefaultExtent(); - extent.setGeographicElements(Collections.singleton(new DefaultGeographicBoundingBox(xLL, xRU, yLL, yRU))); - extent.setDescription(new DefaultInternationalString("Bounding box")); - - /*Only with Geotoolkit 4.x - DefaultTemporalExtent stext = new DefaultTemporalExtent(startDate,endDate); - stext.setStartTime(startDate); - stext.setEndTime(endDate); - extent.setTemporalElements(Arrays.asList(stext)); - */ - extent.freeze(); - - //resolution - DefaultNominalResolution resolution = new DefaultNominalResolution(); - resolution.setGroundResolution(res); - resolution.setScanningResolution(res); - DefaultResolution dres = new DefaultResolution(); - dres.setDistance(res); - - // layers access: - DefaultDistribution distribution = new DefaultDistribution(); - DefaultDigitalTransferOptions transferOptions = new DefaultDigitalTransferOptions(); - for (String uri : layerUris) - transferOptions.getOnLines().add(new DefaultOnlineResource(new URI(uri))); - distribution.getTransferOptions().add(transferOptions); - DefaultFormat format1 = new DefaultFormat(); - format1.setName(new DefaultInternationalString("WMS")); - format1.setVersion(new DefaultInternationalString("1.1.0")); - DefaultFormat format2 = new DefaultFormat(); - format2.setName(new DefaultInternationalString("OPeNDAP")); - format2.setVersion(new DefaultInternationalString("2.0.0")); - DefaultFormat format3 = new DefaultFormat(); - format3.setName(new DefaultInternationalString("WCS")); - format3.setVersion(new DefaultInternationalString("1.0.0")); - - distribution.setDistributionFormats(new ArrayList(Arrays.asList(format1, format2, format3))); - - // legal constraints - DefaultLegalConstraints constraints = new DefaultLegalConstraints(); - constraints.getUseLimitations().add(new DefaultInternationalString("Licensed")); - constraints.getAccessConstraints().add(Restriction.LICENSE); - constraints.getUseConstraints().add(Restriction.LICENSE); - - // quality declaration: - DefaultDataQuality processQuality = new DefaultDataQuality(); - - //citation - DefaultCitation sourceCitation = new DefaultCitation(); - sourceCitation.setTitle(new DefaultInternationalString(title)); - sourceCitation.getDates().add(new DefaultCitationDate(sourceGenerationDate, DateType.CREATION)); - sourceCitation.getIdentifiers().add(new DefaultIdentifier(sourceFileName)); - - //source - DefaultSource source = new DefaultSource(); - source.setResolution(resolution); - source.setDescription(new DefaultInternationalString(title)); - source.setSourceCitation(sourceCitation); - - // provenance - DefaultProcessStep preprocessStep = new DefaultProcessStep(); - DefaultProcessStep processStep = new DefaultProcessStep(preprocessStep); - DefaultProcessing processing = new DefaultProcessing(); - processing.setSoftwareReferences(new ArrayList(Arrays.asList(sourceCitation))); - processStep.setDescription(new DefaultInternationalString(processdescription)); - DefaultLineage processLineage = new DefaultLineage(); - processLineage.setProcessSteps(new ArrayList(Arrays.asList(processStep))); - processQuality.setLineage(processLineage); - processQuality.setScope(new DefaultScope(ScopeCode.DATASET)); - - // fulfill identification - DefaultDataIdentification ident = new DefaultDataIdentification(); - ident.setCitation(citation); - ident.setAbstract(new DefaultInternationalString(abstractField)); - ident.setPurpose(new DefaultInternationalString(purpose)); - ident.getResourceMaintenances().add(new DefaultMaintenanceInformation(MaintenanceFrequency.AS_NEEDED)); - ident.setDescriptiveKeywords(keywordslist); - ident.setTopicCategories(categories); - ident.setResourceSpecificUsages(usages); - ident.setExtents(new ArrayList(Arrays.asList(extent))); - ident.setSpatialRepresentationTypes(new ArrayList(Arrays.asList(SpatialRepresentationType.GRID))); - ident.setSpatialResolutions(new ArrayList(Arrays.asList(dres))); - ident.setLanguages(new ArrayList(Arrays.asList(Locale.ENGLISH))); - - // Metadata Obj: - DefaultMetadata meta = new DefaultMetadata(party, sourceGenerationDate, ident); - meta.getSpatialRepresentationInfo().add(spatial); - meta.setDistributionInfo(distribution); - meta.getMetadataConstraints().add(constraints); - meta.getDataQualityInfo().add(processQuality); - meta.setLanguage(Locale.ENGLISH); -// System.out.println(meta); - GNClient client = new GNClient(geonetworkUrl); - client.login(geonetworkUser, geonetworkPwd); - File tmetafile = meta2File(meta); - client.insertMetadata(new GNInsertConfiguration(group, category, stylesheet,validate), tmetafile); - tmetafile.delete(); - - } - - public static List guessTopicCategory(String refString){ - String searcher = refString.toLowerCase(); - List categories = new ArrayList(); - for (TopicCategory topic:TopicCategory.values()){ - if (searcher.contains("_"+topic.name().toLowerCase()+"_")){ - categories.add(topic); - } - } - return categories; - } -} diff --git a/src/main/java/org/gcube/dataanalysis/geo/meta/OGCFormatter.java b/src/main/java/org/gcube/dataanalysis/geo/meta/OGCFormatter.java deleted file mode 100644 index 40f62f9..0000000 --- a/src/main/java/org/gcube/dataanalysis/geo/meta/OGCFormatter.java +++ /dev/null @@ -1,48 +0,0 @@ -package org.gcube.dataanalysis.geo.meta; - -public class OGCFormatter { - public static String getWfsUrl(String geoServerUrl, String layerName, String bbox, int limit, String format) { - return geoServerUrl + "/wfs?service=wfs&version=1.1.0&REQUEST=GetFeature" + "&TYPENAME=" + layerName + (bbox==null? "":"&BBOX=" + bbox) + (limit == 0 ? "" : "&MAXFEATURES=" + limit) + (format == null ? "" : "&OUTPUTFORMAT=" + format); - } - - public static String getWmsUrl(String geoServerUrl, String layerName, String style, String bbox) { - return geoServerUrl + "/wms?service=wms&version=1.1.0" + "&request=GetMap&layers=" + layerName + "&styles=" + (style == null ? "" : style) + "&bbox=" + bbox + "&width=676&height=330&srs=EPSG:4326&format=application/openlayers"; - } - - public static String getWcsUrl(String geoServerUrl, String layerName, String bbox) { - return geoServerUrl + "/wcs?service=wcs&version=1.0.0" + "&request=GetCoverage&coverage=" + layerName + "&CRS=EPSG:4326" + "&bbox=" + bbox + "&width=676&height=330&format=geotiff"; - } - - public static String getWmsNetCDFUrl(String fileUrl, String layerName, String bbox) { - return fileUrl.replace("dodsC", "wms") + "?service=wms&version=1.3.0" + "&request=GetMap&layers=" + layerName + "&bbox=" + bbox + "&styles=&width=676&height=330&srs=EPSG:4326&CRS=EPSG:4326&format=image/png"; - } - - public static String getWcsNetCDFUrl(String fileUrl, String layerName, String bbox) { - return fileUrl.replace("dodsC", "wcs") + "?service=wcs&version=1.0.0" + "&request=GetCoverage&coverage=" + layerName + "&CRS=EPSG:4326" + "&bbox=" + bbox + "&width=676&height=330&format=geotiff"; - } - - public static String getOpenDapURL(String threddsCatalog, String filename) { - return threddsCatalog.replace("catalog.xml",filename).replace("catalog","dodsC"); - } - - public static String buildBoundingBox(double x1, double y1, double x2, double y2) { - // note: the bounding box is left,lower,right,upper - return (x1 + "," + y1 + "," + x2 + "," + y2); - } - - public static String pointToBoundingBox(double x1, double y1, double tolerance) { - // note: the bounding box is left,lower,right,upper - double x11 = x1 - tolerance; - double y11 = y1 - tolerance; - double x22 = x1 + tolerance; - double y22 = y1 + tolerance; - return OGCFormatter.buildBoundingBox(x11, y11, x22, y22); - } - - - public static void main(String [] args){ - //http://geoserver-dev.d4science-ii.research-infrastructures.eu/geoserver/wcs?service=WCS&version=1.0.0&request=GetCoverage&COVERAGE=aquamaps:WorldClimBio2&CRS=EPSG:4326&BBOX=-180,-90,180,90&WIDTH=640&HEIGHT=480&FORMAT=geotiff - String wcs = getWcsUrl("http://geoserver-dev.d4science-ii.research-infrastructures.eu/geoserver", "aquamaps:WorldClimBio2", buildBoundingBox(-180, -85.5,180, 90)); - System.out.println(wcs); - } -} diff --git a/src/main/java/org/gcube/dataanalysis/geo/meta/features/FeaturesManager.java b/src/main/java/org/gcube/dataanalysis/geo/meta/features/FeaturesManager.java deleted file mode 100644 index 6b34bd5..0000000 --- a/src/main/java/org/gcube/dataanalysis/geo/meta/features/FeaturesManager.java +++ /dev/null @@ -1,477 +0,0 @@ -package org.gcube.dataanalysis.geo.meta.features; - -import it.geosolutions.geonetwork.util.GNSearchRequest; -import it.geosolutions.geonetwork.util.GNSearchResponse; - -import java.util.ArrayList; -import java.util.List; - -import org.gcube.common.scope.api.ScopeProvider; -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.gcube.spatial.data.geonetwork.GeoNetwork; -import org.gcube.spatial.data.geonetwork.GeoNetworkReader; -import org.gcube.spatial.data.geonetwork.configuration.Configuration; -import org.gcube.spatial.data.geonetwork.configuration.ConfigurationManager; -import org.geotoolkit.metadata.iso.identification.DefaultDataIdentification; -import org.opengis.metadata.Metadata; -import org.opengis.metadata.citation.OnlineResource; -import org.opengis.metadata.distribution.DigitalTransferOptions; -import org.opengis.metadata.identification.Identification; -import org.opengis.metadata.identification.Resolution; - -public class FeaturesManager { -// private String geonetworkUrl = "http://geoserver-dev.d4science-ii.research-infrastructures.eu/geonetwork/"; - private String geonetworkUrl = "http://geoserver-last.d4science-ii.research-infrastructures.eu/geonetwork/"; -// private String geonetworkUrl = "http://geoserver.d4science-ii.research-infrastructures.eu/geonetwork/"; - private String geonetworkUser = "admin"; - private String geonetworkPwd = "admin"; - private String scope = "/gcube/devsec"; - - public String getScope() { - return scope; - } - - public void setScope(String scope) { - this.scope = scope; - } - - public static double getResolution(Metadata meta){ - double res = 0; - try{ - DefaultDataIdentification ddi = (DefaultDataIdentification) meta.getIdentificationInfo().iterator().next(); - //take the lowest resolution - for (Resolution r:ddi.getSpatialResolutions()){ - Double rr = r.getDistance(); - if (rr ==null) - rr=r.getEquivalentScale().doubleValue(); - - if (rr!=null && rr>res){ - res = rr; - } - } - }catch(Exception e){ - e.printStackTrace(); - AnalysisLogger.getLogger().debug("Could not get Data Identification"); - } - - AnalysisLogger.getLogger().debug("Calculated Resolution is:"+res); - - return res; - } - - - public String getGeoserverLink(Metadata meta) { - String link = null; - String geoserverString = "/geoserver/"; - String geoserverEndString = "/geoserver?"; - String wmslink = getWMSLink(meta); - if (wmslink!=null){ - int idx = wmslink.indexOf(geoserverString); - if (idx<0) - idx = wmslink.indexOf(geoserverEndString); - if (idx>0){ - link = wmslink.substring(0,idx+geoserverString.length()-1); - return link; - } - } - String wfslink = getWFSLink(meta); - if (wfslink!=null){ - int idx = wfslink.indexOf(geoserverString); - if (idx<0) - idx = wfslink.indexOf(geoserverEndString); - - if (idx>0){ - link = wfslink.substring(0,idx+geoserverString.length()-1); - return link; - } - } - String wcslink = getWCSLink(meta); - if (wcslink!=null){ - int idx = wcslink.indexOf(geoserverString); - if (idx<0) - idx = wcslink.indexOf(geoserverEndString); - - if (idx>0){ - link = wcslink.substring(0,idx+geoserverString.length()-1); - return link; - } - } - - if (link == null) - System.out.println("NO GEOSERVER LINK WAS FOUND ACCORDING TO THE CRITERION"); - - return link; - } - - private String searchInUrl(Metadata meta, String criterion) { - String link = null; - for (DigitalTransferOptions option : meta.getDistributionInfo().getTransferOptions()) { - for (OnlineResource resource : option.getOnLines()) { - String tlink = resource.getLinkage().toString(); - if (tlink.toLowerCase().contains(criterion.toLowerCase())) { - link = tlink; - break; - } - } - - } - if (link == null) - System.out.println("NO ONLINE LINK WAS FOUND ACCORDING TO THE CRITERION :" + criterion); - return link; - } - - - private String searchLayerNameInMeta(Metadata meta) { - String innerlayername = null; - for (DigitalTransferOptions option : meta.getDistributionInfo().getTransferOptions()) { - for (OnlineResource resource : option.getOnLines()) { - String layername = resource.getName(); - if (layername!=null) { - innerlayername = layername; - break; - } - } - - } - if (innerlayername == null) - System.out.println("NO LAYER NAME WAS FOUND IN TRANSFER OPTIONS"); - return innerlayername; - } - - public String getWFSLink(Metadata meta) { - return searchInUrl(meta, "service=wfs"); - } - - // retrieves the wms link - public String getWMSLink(Metadata meta) { - return searchInUrl(meta, "service=wms"); - } - - public String getWCSLink(Metadata meta) { - return searchInUrl(meta, "service=wcs"); - } - - public String getOpenDapLink(Metadata meta) { - return searchInUrl(meta, "/dodsC"); - } - - public String getThreddsLink(Metadata meta) { - return searchInUrl(meta, "catalog.xml"); - } - - public String getLayerName(Metadata meta) { - AnalysisLogger.getLogger().debug("Retrieving Layer Name"); - String wmslink = getWMSLink(meta); - String layer = null; - String finder = "layers="; - if (wmslink != null) { - AnalysisLogger.getLogger().debug("WMS layer found!"); - int idxfinder = wmslink.indexOf(finder); - if (idxfinder > 0) { - AnalysisLogger.getLogger().debug("Searching for Layer Name inside the WMS Link"); - wmslink = wmslink.substring(idxfinder); - int andIdx = wmslink.indexOf("&"); - if (andIdx < 0) - andIdx = wmslink.length(); - - layer = wmslink.substring(finder.length(), andIdx).trim(); - } - //if the layer is not inside the wmslink - else{ - AnalysisLogger.getLogger().debug("Searching for Layer Name inside the file"); - layer = searchLayerNameInMeta(meta); - } - } - return layer; - } - - public boolean isThreddsFile(Metadata meta) { - return (getOpenDapLink(meta) != null); - } - - public GeoNetworkReader initGeoNetworkReader() throws Exception { - if (scope!=null) - ScopeProvider.instance.set(scope); - else{ - AnalysisLogger.getLogger().debug("Features Manager: Using manual configuration of GeoNetwork"); - ConfigurationManager.setConfiguration(new Configuration() { - @Override - public String getGeoNetworkUser() { - return geonetworkUser; - } - @Override - public String getGeoNetworkPassword() { - return geonetworkPwd; - } - @Override - public String getGeoNetworkEndpoint() { - return geonetworkUrl; - } - }); - } - GeoNetworkReader gn = GeoNetwork.get(); - return gn; - } - - public String getGeonetworkURLFromScope() throws Exception { - GeoNetworkReader gn = initGeoNetworkReader(); - return gn.getConfiguration().getGeoNetworkEndpoint(); - } - - public String getGeonetworkUserFromScope() throws Exception { - GeoNetworkReader gn = initGeoNetworkReader(); - return gn.getConfiguration().getGeoNetworkUser(); - } - - public String getGeonetworkPasswordFromScope() throws Exception { - GeoNetworkReader gn = initGeoNetworkReader(); - return gn.getConfiguration().getGeoNetworkPassword(); - } - - private Metadata getGNInfobyTitle(String info) throws Exception { - - GeoNetworkReader gn = initGeoNetworkReader(); - // Form query object - gn.login(); - GNSearchRequest req = new GNSearchRequest(); - req.addParam(GNSearchRequest.Param.title, info); - // req.addConfig(GNSearchRequest.Config.similarity, "1"); - GNSearchResponse resp = gn.query(req); - Metadata meta = null; - if (resp.getCount() != 0) - for (GNSearchResponse.GNMetadata metadata : resp) { - try { - meta = gn.getById(metadata.getUUID()); - break; - } catch (Exception e) { - AnalysisLogger.getLogger().debug("Error retrieving information for some metadata"); - } - } - - return meta; - } - - public List getAllGNInfobyTitle(String info, String tolerance) throws Exception { - - GeoNetworkReader gn = initGeoNetworkReader(); - // Form query object - gn.login(); - GNSearchRequest req = new GNSearchRequest(); - req.addParam(GNSearchRequest.Param.title, info); - req.addConfig(GNSearchRequest.Config.similarity, tolerance); - GNSearchResponse resp = gn.query(req); - Metadata meta = null; - List metadatalist = new ArrayList(); - if (resp.getCount() != 0) - for (GNSearchResponse.GNMetadata metadata : resp) { - try { - meta = gn.getById(metadata.getUUID()); - metadatalist.add(meta); - } catch (Exception e) { - AnalysisLogger.getLogger().debug("Error retrieving information for some metadata"); - } - } - - return metadatalist; - } - - public List getAllGNInfobyText(String info, String tolerance) throws Exception { - - GeoNetworkReader gn = initGeoNetworkReader(); - // Form query object - gn.login(); - GNSearchRequest req = new GNSearchRequest(); - req.addParam(GNSearchRequest.Param.any, info); - req.addConfig(GNSearchRequest.Config.similarity, tolerance); - GNSearchResponse resp = gn.query(req); - Metadata meta = null; - List metadatalist = new ArrayList(); - if (resp.getCount() != 0) - for (GNSearchResponse.GNMetadata metadata : resp) { - try { - meta = gn.getById(metadata.getUUID()); - metadatalist.add(meta); - } catch (Exception e) { - AnalysisLogger.getLogger().debug("Error retrieving information for some metadata"); - } - } - - return metadatalist; - } - - private List getFastGNInfobyTitle(String info, String completeTitle, String tolerance) throws Exception { - - GeoNetworkReader gn = initGeoNetworkReader(); - // Form query object - gn.login(); - GNSearchRequest req = new GNSearchRequest(); - req.addParam(GNSearchRequest.Param.title, info); - req.addConfig(GNSearchRequest.Config.similarity, tolerance); - GNSearchResponse resp = gn.query(req); - - Metadata meta = null; - List metadatalist = new ArrayList(); - if (resp.getCount() != 0){ - AnalysisLogger.getLogger().debug("Retrieving information ..."); - for (GNSearchResponse.GNMetadata metadata : resp) { - try { - meta = gn.getById(metadata.getUUID()); - Identification id = meta.getIdentificationInfo().iterator().next(); - String title = id.getCitation().getTitle().toString(); - if (title.equalsIgnoreCase(completeTitle)){ - AnalysisLogger.getLogger().debug("Found UUID:"+metadata.getUUID()); - metadatalist.add(meta); - break; - } - } catch (Exception e) { - AnalysisLogger.getLogger().debug("Error retrieving information for some metadata"); - } - } - AnalysisLogger.getLogger().debug("Information Successfully Retrieved"); - } - return metadatalist; - } - - - private Metadata getGNInfobyUUID(String UUID) throws Exception { - - GeoNetworkReader gn = initGeoNetworkReader(); - // Form query object - gn.login(); - Metadata meta = gn.getById(UUID); - AnalysisLogger.getLogger().debug("Layer with UUID: "+UUID+" successfully Retrieved!"); - - return meta; - } - - public Metadata getGNInfobyUUIDorName(String layerUUIDorTitle) throws Exception { - - AnalysisLogger.getLogger().debug("MapsComparator: Getting layer with UUID..."+layerUUIDorTitle); - Metadata meta = null; - try{ - meta = getGNInfobyUUID(layerUUIDorTitle); - }catch(Exception e){ - AnalysisLogger.getLogger().debug("MapsComparator: Impossible to get layer as UUID"); - } - - if (meta==null){ - AnalysisLogger.getLogger().debug("MapsComparator: NO UUID Available - Trying with NAME..."+layerUUIDorTitle); - try{ - meta = checkForMetadatabyTitle(FeaturesManager.treatTitleForGN(layerUUIDorTitle), layerUUIDorTitle); - }catch(Exception e){ - throw new Exception("Layer does not exist"); - } - } - - return meta; - } - - private Metadata checkForMetadatabyTitle(String searchString, String completetitle) throws Exception { - return checkForMetadatabyTitle(searchString, completetitle, ""); - } - - private Metadata checkForMetadatabyTitle(String searchString, String completetitle, String filename) throws Exception { - AnalysisLogger.getLogger().debug("Searching for: "+searchString); - List mlist = getFastGNInfobyTitle(searchString, completetitle,"1"); - AnalysisLogger.getLogger().debug("Found:"+mlist.size()+" results"); - Metadata mfound = null; -// DefaultInternationalString intfilename = new DefaultInternationalString(filename); - for (Metadata m : mlist) { - Identification id = m.getIdentificationInfo().iterator().next(); - String title = id.getCitation().getTitle().toString(); - if (completetitle.equalsIgnoreCase(title)) { - /* - Iterator it = id.getDescriptiveKeywords().iterator(); - while (it.hasNext()){ - Keywords keys = (Keywords)it.next(); - for (InternationalString is :keys.getKeywords()){ -// System.out.println(is); - if (is.toString().equals(filename)){ - mfound = m; - break; - } - } - if (mfound!=null) - break; - } - } - if (mfound!=null) - break; - */ - mfound = m; - break; - } - } - - return mfound; - } - - public String getGeonetworkUrl() { - return geonetworkUrl; - } - - public void setGeonetworkUrl(String geonetworkUrl) { - this.geonetworkUrl = geonetworkUrl; - } - - public String getGeonetworkUser() { - return geonetworkUser; - } - - public void setGeonetworkUser(String geonetworkUser) { - this.geonetworkUser = geonetworkUser; - } - - public String getGeonetworkPwd() { - return geonetworkPwd; - } - - public void setGeonetworkPwd(String geonetworkPwd) { - this.geonetworkPwd = geonetworkPwd; - } - - public static String treatTitleForGN(String origLayerTitle) { - String layerTitle = origLayerTitle.toLowerCase(); - int idx = layerTitle.indexOf(" from ["); - String layerTitle2 = layerTitle; - if (idx>0) - layerTitle2 = layerTitle.toLowerCase().substring(0, idx).trim(); - else { - idx = layerTitle.indexOf(" in ["); - if (idx>0) - layerTitle2 = layerTitle.toLowerCase().substring(0, idx).trim(); - else{ - idx = layerTitle.indexOf("("); - if (idx>0) - layerTitle2 = layerTitle.toLowerCase().substring(0, idx).trim(); - } - } - layerTitle2 = layerTitle2.replaceAll("(\\(.*\\))", " "); - - layerTitle2 = layerTitle2.replace("_", " ").replace("-", " ").replace("(", " ").replace(")", " "); - String punct = "[!\"#$%&'*+,./:;<=>?@\\^_`{|}~-]"; - - layerTitle2 = layerTitle2.replaceAll("( |^)+[^A-Za-z]+("+punct+")*[^A-Za-z]*", " ").trim(); - - return layerTitle2.replaceAll(punct, " ").replaceAll("( )+", " "); - } - - public static void main1(String args[]) throws Exception { - // String title = "temperature (04091217ruc.nc)"; - // String title = "Bathymetry"; - // String title = "FAO aquatic species distribution map of Melanogrammus aeglefinus"; - // String title = "geopotential height from [12/09/2004 19:00] to [12/09/2004 22:00] (04091217_ruc.nc)"; - String title = "geopotential height"; - FeaturesManager fm = new FeaturesManager(); - Metadata meta = fm.getGNInfobyTitle(title); - System.out.println("is file? " + fm.isThreddsFile(meta)); - System.out.println("opendap: " + fm.getOpenDapLink(meta)); - System.out.println("wcs:" + fm.getWCSLink(meta)); - System.out.println("wms:" + fm.getWMSLink(meta)); - System.out.println("thredds:" + fm.getThreddsLink(meta)); - } - - public static void main(String args[]) throws Exception { - System.out.println(treatTitleForGN("sea/land/lake/ice field composite mask from")); - } -} diff --git a/src/main/java/org/gcube/dataanalysis/geo/retrieval/GeoIntersector.java b/src/main/java/org/gcube/dataanalysis/geo/retrieval/GeoIntersector.java deleted file mode 100644 index 22fccea..0000000 --- a/src/main/java/org/gcube/dataanalysis/geo/retrieval/GeoIntersector.java +++ /dev/null @@ -1,326 +0,0 @@ -package org.gcube.dataanalysis.geo.retrieval; - -import java.util.ArrayList; -import java.util.Arrays; -import java.util.Collection; -import java.util.LinkedHashMap; -import java.util.List; - -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.meta.features.FeaturesManager; -import org.gcube.dataanalysis.geo.utils.EnvDataExplorer; -import org.gcube.dataanalysis.geo.utils.FeaturedPolygon; -import org.gcube.dataanalysis.geo.utils.ThreddsDataExplorer; -import org.opengis.metadata.Metadata; -import org.opengis.metadata.identification.Identification; - -import com.vividsolutions.jts.geom.Coordinate; -import com.vividsolutions.jts.geom.GeometryFactory; -import com.vividsolutions.jts.geom.Point; -import com.vividsolutions.jts.geom.PrecisionModel; -import com.vividsolutions.jts.geom.impl.CoordinateArraySequence; - -public class GeoIntersector { - - private FeaturesManager featurer; - private String configDir; - public GeoIntersector(String scope, String cfgDir) { - featurer = new FeaturesManager(); - featurer.setScope(scope); - this.configDir=cfgDir; - } - - public FeaturesManager getFeaturer(){ - return featurer; - } - - public LinkedHashMap getFeaturesInTime(String layerTitle, double x, double y) throws Exception { - return getFeaturesInAllTimes(layerTitle, x, y, 0); - } - - public LinkedHashMap getFeaturesInAllTimes(String layerTitle, double x, double y, double z) throws Exception { - LinkedHashMap features = new LinkedHashMap(); - // get the layer - // Metadata meta = featurer.getGNInfobyTitle(layerTitle); - Metadata meta = featurer.getGNInfobyUUIDorName(layerTitle); - // if the layer is good - if (meta != null) { - String layer = featurer.getLayerName(meta); - - if (layer == null) - layer = layerTitle; - - // check if it is a NetCDF - if (featurer.isThreddsFile(meta)) { - Identification id = meta.getIdentificationInfo().iterator().next(); - String title = id.getCitation().getTitle().toString(); - - AnalysisLogger.getLogger().debug("found a netCDF file with title " + title + " and layer name " + layer); - features = getFeaturesFromNetCDF(featurer.getOpenDapLink(meta), layer, x, y, z); - } else { - AnalysisLogger.getLogger().debug("found a Geo Layer with title " + layerTitle + " and layer name " + layer); - features = getFeaturesFromWFS(featurer.getWFSLink(meta), layer, x, y); - } - } - - return features; - } - - public List getFeaturesInTimeInstant(String layerTitle, int time, List> triplets, double xL,double xR, double yL, double yR) throws Exception { - List features = new ArrayList(); - // get the layer - Metadata meta = featurer.getGNInfobyUUIDorName(layerTitle); - // if the layer is good - if (meta != null) { - String layer = featurer.getLayerName(meta); - if (layer == null) - layer = layerTitle; - // check if it is a NetCDF - if (featurer.isThreddsFile(meta)) { - Identification id = meta.getIdentificationInfo().iterator().next(); - String title = id.getCitation().getTitle().toString(); - AnalysisLogger.getLogger().debug("found a netCDF file with title " + title + " and layer name " + layer); - features = getFeaturesFromNetCDF(featurer.getOpenDapLink(meta), layer, time, triplets, xL,xR, yL, yR); - /* - for (Tuple triplet : triplets) { - double x = triplet.getElements().get(0); - double y = triplet.getElements().get(1); - double z = 0; - if (triplet.getElements().size() > 2) - z = triplet.getElements().get(2); - AnalysisLogger.getLogger().debug("Taking point: (" + x + "," + y + "," + z + ")"); - LinkedHashMap features = new LinkedHashMap(); - features = getFeaturesFromNetCDF(featurer.getOpenDapLink(meta), layer, x, y, z); - AnalysisLogger.getLogger().debug("Got: (" + features + ")"); - featuresSets.add(features); - } - */ - } else { - AnalysisLogger.getLogger().debug("found a Geo Layer with reference " + layerTitle + " and layer name " + layer); -// AnalysisLogger.getLogger().debug("Taking point: (" + x + "," + y + ")"); - List featuresInTime = new ArrayList(); - AnalysisLogger.getLogger().debug("taking WFS features"); - featuresInTime = getFeaturesFromWFS(featurer.getGeoserverLink(meta), layer, xL,yL, xR, yR); - int tsize = triplets.size(); - AnalysisLogger.getLogger().debug("Intersecting "+tsize+" vs "+featuresInTime.size() +" elements"); - int ttc= 0; - Double[] featuresarray = new Double[tsize]; - int k=0; - long t0=0; - GeometryFactory factory = new GeometryFactory(new PrecisionModel(), 4326); -// Tuple[] tripletss = new Tuple[tsize]; -// tripletss = triplets.toArray(tripletss); -// for (Tuple triplet:triplets){ - for (Tuple triplet:triplets){ - ArrayList elements = triplet.getElements(); - CoordinateArraySequence pcoords = new CoordinateArraySequence(new Coordinate[] { new Coordinate(elements.get(0),elements.get(1)),}); - Point po = new Point(pcoords, factory); - boolean found = false; - - for (FeaturedPolygon poly:featuresInTime){ - if (poly!=null && poly.p!=null && poly.p.covers(po)){ -// System.out.println(po+" intersected by "+poly.p+ " assigning value "+poly.value); -// features.add(poly.value); - featuresarray[k] = poly.value; - found = true; - break; - } - - - } - po = null; - if (!found){ -// features.add(Double.NaN); - featuresarray[k] = Double.NaN; - } - - - if (ttc%10000==0){ - AnalysisLogger.getLogger().debug("Status: "+((double)ttc*100d/(double)tsize)); -// System.out.println("::"+((System.currentTimeMillis()-t0)/1000)); - } - ttc++; - k++; - -// if (ttc%1000==0) -// t0 = System.currentTimeMillis(); - } - - - features = Arrays.asList(featuresarray); - - } - } - return features; - } - - private List getFeaturesFromNetCDF(String opendapURL, String layer, int time, List> triplets, double xL,double xR, double yL, double yR) { - if (opendapURL == null) - return null; - - return ThreddsDataExplorer.retrieveDataFromNetCDF(opendapURL, layer, time, triplets, xL,xR, yL, yR); - } - - private LinkedHashMap getFeaturesFromNetCDF(String opendapURL, String layer, double x, double y, double z) { - if (opendapURL == null) - return null; - - return ThreddsDataExplorer.retrieveDataFromNetCDF(opendapURL, layer, x, y, z); - } - - private LinkedHashMap getFeaturesFromWFS(String geoserverUrl, String layer, double x, double y) { - if (geoserverUrl == null) - return null; - - return EnvDataExplorer.getFeatures(geoserverUrl, layer, x, y); - } - - private List getFeaturesFromWFS(String geoserverUrl, String layer, double xL,double yL,double xR, double yR) { - if (geoserverUrl == null) - return null; - - return EnvDataExplorer.getFeatures(geoserverUrl, layer, xL,yL,xR, yR); - } - - - public static List> generateCoordinateTriplets(double x1, double x2, double y1, double y2, double z, double xResolution, double yResolution){ - - int ysteps = (int) ((y2 - y1) / yResolution); - int xsteps = (int) ((x2 - x1) / xResolution); - List> tuples = new ArrayList>(); - AnalysisLogger.getLogger().debug("Building the points grid according to YRes:" + yResolution + " and XRes:" + xResolution); - // build the tuples according to the desired resolution - for (int i = 0; i < ysteps + 1; i++) { - double y = (i * yResolution) + y1; - if (i == ysteps) - y = y2; - for (int j = 0; j < xsteps + 1; j++) { - double x = (j * xResolution) + x1; - if (j == xsteps) - x = x2; - tuples.add(new Tuple(x, y, z)); - } - } - - return tuples; - } - - public static List associateValueToCoordinates(List> coordinates, double[][] data){ - List values = new ArrayList(); - - int k = 0; - int g = 0; - int ntriplets = coordinates.size(); - int xsteps = data[0].length-1; - for (int t = 0; t < ntriplets; t++) { - values.add(data[k][g]); - if (g == xsteps) { - g = 0; - k++; - } - else - g++; - } - - return values; - } - - public double[][] takeTimeSlice(String layerTitle, int timeInstant, double x1, double x2, double y1, double y2, double z, double xResolution, double yResolution) throws Exception { - AnalysisLogger.getLogger().debug("Bounding box: (" + x1 + "," + x2 + ";" + y1 + "," + y2 + ")"); - boolean faolayer = false; - if (layerTitle.toLowerCase().contains("fao aquatic species distribution map") ) - { - AnalysisLogger.getLogger().debug("FAO DISTRIBUTION LAYER ... TO APPY PATCH!"); - faolayer=true; - } - if ((x2 < x1) || (y2 < y1)) { - AnalysisLogger.getLogger().debug("ERROR: BAD BOUNDING BOX!!!"); - return new double[0][0]; - } - - int ysteps = (int) ((y2 - y1) / yResolution); - int xsteps = (int) ((x2 - x1) / xResolution); - double[][] slice = new double[ysteps + 1][xsteps + 1]; - List> tuples = new ArrayList>(); - AnalysisLogger.getLogger().debug("Building the points grid according to YRes:" + yResolution + " and XRes:" + xResolution); - // build the tuples according to the desired resolution - for (int i = 0; i < ysteps + 1; i++) { - double y = (i * yResolution) + y1; - if (i == ysteps) - y = y2; - for (int j = 0; j < xsteps + 1; j++) { - double x = (j * xResolution) + x1; - if (j == xsteps) - x = x2; - tuples.add(new Tuple(x, y, z)); - } - } - - AnalysisLogger.getLogger().debug("Taking " + ysteps + " values per "+xsteps+"="+(ysteps*xsteps)+ "..."); - List timeValues = getFeaturesInTimeInstant(layerTitle, timeInstant, tuples, x1, x2, y1,y2); - AnalysisLogger.getLogger().debug("Taken " + timeValues.size() + " values"); - - // build back the values matrix - int k = 0; - int g = 0; - int ntriplets = timeValues.size(); - //cycle on all the triplets to recontruct the matrix - for (int t = 0; t < ntriplets; t++) { - //take the corresponding (time,value) pair - Double value = timeValues.get(t); - //if there is value, then set it, otherwise set NaN - //the layer is undefined in that point and a value must be generated - //assign a value to the matrix - - //WARNING: PATCH FOR FAO LAYERS:. Probability can be equal to 2 for uncertainty (Kolmogorov, forgive them for they know not what they do) - if (faolayer && (value>1)){ - AnalysisLogger.getLogger().debug("APPLYING FAO PATCH!"); - slice[k][g] = 0.5; - } - else - slice[k][g] = value; - //increase the x step according to the matrix - if (g == xsteps) { - g = 0; - k++; - } - else - g++; - } - - /* - AnalysisLogger.getLogger().debug("Applying nearest Neighbor to all the rows"); - //apply nearest neighbor to each row - AlgorithmConfiguration config = new AlgorithmConfiguration(); - config.setConfigPath(configDir); - boolean rapidinit = false; - - - for (int i=0;i metae = featurer.getAllGNInfobyText("thredds", "1"); - System.out.println("ELAPSED TIME: "+(System.currentTimeMillis()-t0)); - String d = "#"; - System.out.println("Parameter Name"+d+"Time Range"+d+"Dimensions"+d+"Unit of Measure"+d+"Resolution (decimal degrees)"+d+"Details"); - List table = new ArrayList(); - for (Metadata meta:metae){ - Identification id = meta.getIdentificationInfo().iterator().next(); - String title = id.getCitation().getTitle().toString(); - - DefaultDataIdentification did = (DefaultDataIdentification) id; - double resolution = MathFunctions.roundDecimal(did.getSpatialResolutions().iterator().next().getDistance(),3); - Collection keys = id.getDescriptiveKeywords(); - String unit = ""; - for (Keywords key:keys){ - for(InternationalString string:key.getKeywords()) { - String ss = string.toString(); - if (ss.startsWith("unit:")) - unit = ss.substring(ss.indexOf(":")+1); - } - } - String[] elements = parseTitle(title); - String entry = elements[0]+d+elements[1]+d+elements[2]+d+unit+d+resolution+d+elements[3]; - if (!table.contains(entry)){ - table.add(entry); -// System.out.println(elements[0]+d+elements[1]+d+elements[2]+d+resolution+d+elements[3]); - } - } - Collections.sort(table); - for (String element:table){ - System.out.println(element); - } -// System.out.println("ELAPSED TIME: "+(System.currentTimeMillis()-t0)); - } - - - public static void main1(String[] args) throws Exception{ -// String example = "Standard Deviation from 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 example = "Salinity from [12-15-99 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-grids}"; - String example = "Salinity from [12-15-99 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-grids}"; - parseTitle(example); - } - - public static String[] parseTitle(String title){ - String timerange = title.substring(title.indexOf("["),title.lastIndexOf("]")+1); -// timerange = timerange.replace("] to [", " ; "); -// System.out.println(timerange); - String realtitle = title.substring(0,title.indexOf("[")).trim(); - realtitle = realtitle.substring(0,realtitle.lastIndexOf(" ")).trim(); -// System.out.println(realtitle); - String dimensions = title.substring(title.indexOf("] (")+3); - dimensions = dimensions.substring(0,dimensions.indexOf(")")).trim(); -// System.out.println(dimensions); - String notes = title.substring(title.indexOf("{")+1,title.lastIndexOf("}")); - String woa = "World Ocean Atlas 09:"; - String prefixnote = ""; - if (notes.startsWith(woa)){ - prefixnote = notes.substring(woa.length()+1); - prefixnote = prefixnote.substring(0,prefixnote.indexOf(":")).trim()+": "; - } -// System.out.println(notes); - String[] elements = new String[]{prefixnote+realtitle, timerange, dimensions,notes}; - return elements; - } - -} diff --git a/src/main/java/org/gcube/dataanalysis/geo/test/TestNetCDFMetadataInsert.java b/src/main/java/org/gcube/dataanalysis/geo/test/TestNetCDFMetadataInsert.java deleted file mode 100644 index d9f95f9..0000000 --- a/src/main/java/org/gcube/dataanalysis/geo/test/TestNetCDFMetadataInsert.java +++ /dev/null @@ -1,26 +0,0 @@ -package org.gcube.dataanalysis.geo.test; - -import org.gcube.dataanalysis.geo.meta.NetCDFMetadata; - -public class TestNetCDFMetadataInsert { - - public static void main(String[] args) throws Exception{ - NetCDFMetadata metadataInserter = new NetCDFMetadata(); - metadataInserter.setGeonetworkUrl("http://geoserver-dev.d4science-ii.research-infrastructures.eu/geonetwork/"); - metadataInserter.setGeonetworkUser("admin"); - metadataInserter.setGeonetworkPwd("admin"); - metadataInserter.setThreddsCatalogUrl("http://thredds.research-infrastructures.eu/thredds/catalog/public/netcdf/catalog.xml"); - metadataInserter.setLayerUrl("http://thredds.research-infrastructures.eu/thredds/dodsC/public/netcdf/04091217_ruc.nc"); - metadataInserter.setTitle("temperature (04091217ruc.nc)"); - metadataInserter.setLayerName("T"); - metadataInserter.setSourceFileName("04091217_ruc.nc"); - metadataInserter.setAbstractField("T: temperature (degK) from 04091217ruc.nc resident on a THREDDS instance"); - metadataInserter.setResolution(0.5); - metadataInserter.setXLeftLow(-180); - metadataInserter.setYLeftLow(-85.5); - metadataInserter.setXRightUpper(180); - metadataInserter.setYRightUpper(85.5); - - metadataInserter.insertMetaData(); - } -} diff --git a/src/main/java/org/gcube/dataanalysis/geo/test/TestRasterTable.java b/src/main/java/org/gcube/dataanalysis/geo/test/TestRasterTable.java deleted file mode 100644 index 8b5e00a..0000000 --- a/src/main/java/org/gcube/dataanalysis/geo/test/TestRasterTable.java +++ /dev/null @@ -1,51 +0,0 @@ -package org.gcube.dataanalysis.geo.test; - -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; -import org.gcube.dataanalysis.geo.insertion.RasterTable; -import org.gcube.dataanalysis.geo.retrieval.GeoIntersector; - -public class TestRasterTable { - - 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 = "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 layertitle = "FAO AQUATIC SPECIES DISTRIBUTION MAP OF MEGALASPIS CORDYLA"; - long t0 = System.currentTimeMillis(); - 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://dbtest.next.research-infrastructures.eu/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"); - - GeoIntersector intersector = new GeoIntersector(null, cfg); - int t = 0; - double x1 = -180; - double x2 = 180; - double y1 = -90; - double y2 = 90; - double z = 0; - double xResolution = 0.5; - double yResolution = 0.5; - - double[][] slice = intersector.takeTimeSlice(layertitle, t, x1, x2, y1,y2,z,xResolution,yResolution); - - RasterTable raster = new RasterTable(x1, x2, y1, y2, z, xResolution, yResolution, slice, config); - raster.dumpGeoTable(); - - System.out.println("ELAPSED TIME: "+(System.currentTimeMillis()-t0)); - } -} diff --git a/src/main/java/org/gcube/dataanalysis/geo/test/TestStandardLayerMetadataInsert.java b/src/main/java/org/gcube/dataanalysis/geo/test/TestStandardLayerMetadataInsert.java deleted file mode 100644 index 9bd059d..0000000 --- a/src/main/java/org/gcube/dataanalysis/geo/test/TestStandardLayerMetadataInsert.java +++ /dev/null @@ -1,28 +0,0 @@ -package org.gcube.dataanalysis.geo.test; - -import org.gcube.dataanalysis.geo.meta.GenericLayerMetadata; - -public class TestStandardLayerMetadataInsert { - - public static void main(String[] args) throws Exception{ - GenericLayerMetadata metadataInserter = new GenericLayerMetadata(); - - metadataInserter.setGeonetworkUrl("http://geoserver-dev.d4science-ii.research-infrastructures.eu/geonetwork/"); -// metadataInserter.setGeonetworkUrl("http://geoserver.d4science-ii.research-infrastructures.eu/geonetwork/"); - metadataInserter.setGeonetworkUser("admin"); - metadataInserter.setGeonetworkPwd("admin"); - metadataInserter.setGeoserverUrl("http://geoserver-dev.d4science-ii.research-infrastructures.eu/geoserver"); - metadataInserter.setTitle("Biodiversity according to LME - Obis"); - metadataInserter.setLayerName("aquamaps:biodiversity_lme_geo"); - metadataInserter.setCategoryTypes("_BIOTA_"); - metadataInserter.setAbstractField("Biodiversity according to LME - Obis"); - metadataInserter.setCustomTopics("Obis","Large Marine Ecosystems"); - metadataInserter.setResolution(0.5); - metadataInserter.setXLeftLow(-180); - metadataInserter.setYLeftLow(-85.5); - metadataInserter.setXRightUpper(180); - metadataInserter.setYRightUpper(85.5); - - metadataInserter.insertMetaData(); - } -} diff --git a/src/main/java/org/gcube/dataanalysis/geo/test/maps/RegressionTestMapsComparison.java b/src/main/java/org/gcube/dataanalysis/geo/test/maps/RegressionTestMapsComparison.java deleted file mode 100644 index c197106..0000000 --- a/src/main/java/org/gcube/dataanalysis/geo/test/maps/RegressionTestMapsComparison.java +++ /dev/null @@ -1,44 +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 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"); - config.setParam("ValuesComparisonThreshold",""+0.1); - config.setParam("Z","0"); - config.setGcubeScope(null); - - return config; - } -} 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 7ef8395..0000000 --- a/src/main/java/org/gcube/dataanalysis/geo/test/maps/TestMapsComparison.java +++ /dev/null @@ -1,56 +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.insertion.RasterTable; -import org.gcube.dataanalysis.geo.retrieval.GeoIntersector; - -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"; - - - 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","0.01"); - 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/TestMapsComparisonAquaMapsvsFAO.java b/src/main/java/org/gcube/dataanalysis/geo/test/maps/TestMapsComparisonAquaMapsvsFAO.java deleted file mode 100644 index 6f6c97c..0000000 --- a/src/main/java/org/gcube/dataanalysis/geo/test/maps/TestMapsComparisonAquaMapsvsFAO.java +++ /dev/null @@ -1,49 +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.insertion.RasterTable; -import org.gcube.dataanalysis.geo.retrieval.GeoIntersector; - -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(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/TestMapsComparisonExampleTCOM.java b/src/main/java/org/gcube/dataanalysis/geo/test/maps/TestMapsComparisonExampleTCOM.java deleted file mode 100644 index 6106e9d..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.insertion.RasterTable; -import org.gcube.dataanalysis.geo.retrieval.GeoIntersector; - -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/TestMapsComparisonTemperature.java b/src/main/java/org/gcube/dataanalysis/geo/test/maps/TestMapsComparisonTemperature.java deleted file mode 100644 index 9a4ede3..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.insertion.RasterTable; -import org.gcube.dataanalysis.geo.retrieval.GeoIntersector; - -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",""+100); - 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 5a4e64e..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.insertion.RasterTable; -import org.gcube.dataanalysis.geo.retrieval.GeoIntersector; - -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 2fec83c..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",""+100); - 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/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/utils/CSquareCodesConverter.java b/src/main/java/org/gcube/dataanalysis/geo/utils/CSquareCodesConverter.java deleted file mode 100644 index 06fcdf0..0000000 --- a/src/main/java/org/gcube/dataanalysis/geo/utils/CSquareCodesConverter.java +++ /dev/null @@ -1,38 +0,0 @@ -package org.gcube.dataanalysis.geo.utils; - -public class CSquareCodesConverter { - - - public static String convertHalfDegree(double x, double y){ - - if (x ==0) - x = 0.25; - if (y ==0) - y = 0.25; - - String csquare = it.cnr.aquamaps.CSquare.centroidToCode(x,y, 0.5); - return csquare; - } - - - public static String convertAtResolution(double x, double y, double resolution){ - if (resolution==0) - resolution=0.1; - if (x ==0) - x = resolution; - if (y ==0) - y = resolution; - - String csquare = it.cnr.aquamaps.CSquare.centroidToCode(x,y, resolution); - return csquare; - } - - public static void main(String[] args){ - //System.out.println(it.cnr.aquamaps.CSquare.centroidToCode(0.5,0.5, 0.0001)); -// System.out.println(it.cnr.aquamaps.CSquare.centroidToCode(-49.99999999999994,35.75000000000006, 1)); -// System.out.println(it.cnr.aquamaps.CSquare.centroidToCode(35.75000000000006,-49.99999999999994, 0.5)); -// System.out.println(it.cnr.aquamaps.CSquare.centroidToCode(35.75,-50, 0.5)); - System.out.println(it.cnr.aquamaps.CSquare.centroidToCode(35.7500,-49.9999, 0.5)); - - } -} diff --git a/src/main/java/org/gcube/dataanalysis/geo/utils/CrsHelper.java b/src/main/java/org/gcube/dataanalysis/geo/utils/CrsHelper.java deleted file mode 100644 index 62288ff..0000000 --- a/src/main/java/org/gcube/dataanalysis/geo/utils/CrsHelper.java +++ /dev/null @@ -1,191 +0,0 @@ -/* - * Copyright (c) 2009 The University of Reading - * All rights reserved. - * - * Redistribution and use in source and binary forms, with or without - * modification, are permitted provided that the following conditions - * are met: - * 1. Redistributions of source code must retain the above copyright - * notice, this list of conditions and the following disclaimer. - * 2. Redistributions in binary form must reproduce the above copyright - * notice, this list of conditions and the following disclaimer in the - * documentation and/or other materials provided with the distribution. - * 3. Neither the name of the University of Reading, nor the names of the - * authors or contributors may be used to endorse or promote products - * derived from this software without specific prior written permission. - * - * THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR - * IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES - * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. - * IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, - * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT - * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, - * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY - * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT - * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF - * THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - */ - -package org.gcube.dataanalysis.geo.utils; - -import java.util.ArrayList; -import java.util.List; - -import org.geotoolkit.referencing.CRS; -import org.geotoolkit.referencing.crs.DefaultGeographicCRS; -import org.opengis.referencing.crs.CoordinateReferenceSystem; -import org.opengis.referencing.cs.CoordinateSystemAxis; -import org.opengis.referencing.operation.MathTransform; -import org.opengis.referencing.operation.TransformException; - -import ucar.unidata.geoloc.LatLonPoint; -import ucar.unidata.geoloc.LatLonPointImpl; -import ucar.unidata.geoloc.ProjectionPoint; -import ucar.unidata.geoloc.ProjectionPointImpl; - -/** - * This class wraps the GeoTools/GeoAPI coordinate reference system methods, providing a set of convenience methods such as transformations and validity checks. - * - * @todo this object is immutable and could be re-used. - * @author Jon - */ -public final class CrsHelper { - - public static final String PLATE_CARREE_CRS_CODE = "CRS:84"; - public static final List SUPPORTED_CRS_CODES = new ArrayList(); - - private CoordinateReferenceSystem crs; - private MathTransform crsToLatLon; - private MathTransform latLonToCrs; - private boolean isLatLon; - - static { - // Find the supported CRS codes - // I think this is the appropriate method to get all the CRS codes - // that we can support - for (Object codeObj : CRS.getSupportedCodes("urn:ogc:def")) { - SUPPORTED_CRS_CODES.add((String) codeObj); - } - System.out.println("Supported Codes:"+SUPPORTED_CRS_CODES); - } - - /** Private constructor to prevent direct instantiation */ - private CrsHelper() { - } - - public static CrsHelper fromCrsCode(String crsCode) throws Exception { - // TODO: could cache CrsHelpers with the same code - CrsHelper crsHelper = new CrsHelper(); - try { - // The "true" means "force longitude first" axis order - crsHelper.crs = CRS.decode(crsCode, true); - // Get transformations to and from lat-lon. - // The "true" means "lenient", i.e. ignore datum shifts. This - // is necessary to prevent "Bursa wolf parameters required" - // errors (Some CRSs, including British National Grid, fail if - // we are not "lenient".) - crsHelper.crsToLatLon = CRS.findMathTransform(crsHelper.crs, DefaultGeographicCRS.WGS84, true); - crsHelper.latLonToCrs = CRS.findMathTransform(DefaultGeographicCRS.WGS84, crsHelper.crs, true); - crsHelper.isLatLon = crsHelper.crsToLatLon.isIdentity(); - return crsHelper; - } catch (Exception e) { - throw new Exception("Error creating CrsHelper from code " + crsCode); - } - } - - public CoordinateReferenceSystem getCoordinateReferenceSystem() { - return this.crs; - } - - /** - * @return true if the given coordinate pair is within the valid range of both the x and y axis of this coordinate reference system. - */ - public boolean isPointValidForCrs(ProjectionPoint point) { - return this.isPointValidForCrs(point.getX(), point.getY()); - } - - /** - * @return true if the given coordinate pair is within the valid range of both the x and y axis of this coordinate reference system. - */ - public boolean isPointValidForCrs(double x, double y) { - CoordinateSystemAxis xAxis = this.crs.getCoordinateSystem().getAxis(0); - CoordinateSystemAxis yAxis = this.crs.getCoordinateSystem().getAxis(1); - return x >= xAxis.getMinimumValue() && x <= xAxis.getMaximumValue() && y >= yAxis.getMinimumValue() && y <= yAxis.getMaximumValue(); - } - - /** - * Transforms the given x-y point in this {@link #getCoordinateReferenceSystem() CRS} to a LatLonPoint. - * - * @throws TransformException - * if the required transformation could not be performed - */ - public LatLonPoint crsToLatLon(double x, double y) throws TransformException { - if (this.isLatLon) { - // We don't need to do the transformation - return new LatLonPointImpl(y, x); - } - // We know x must go first in this array because we selected - // "force longitude-first" when creating the CRS for this grid - double[] point = new double[] { x, y }; - // Transform to lat-lon in-place - this.crsToLatLon.transform(point, 0, point, 0, 1); - return new LatLonPointImpl(point[1], point[0]); - } - - /** - * Transforms the given x-y point in this {@link #getCoordinateReferenceSystem() CRS} to a LatLonPoint. - * - * @throws TransformException - * if the required transformation could not be performed - */ - public LatLonPoint crsToLatLon(ProjectionPoint point) throws TransformException { - return this.crsToLatLon(point.getX(), point.getY()); - } - - /** - * Transforms the given LatLonPoint to an x-y point in this {@link #getCoordinateReferenceSystem() CRS}. - * - * @throws TransformException - * if the required transformation could not be performed - */ - public ProjectionPoint latLonToCrs(LatLonPoint latLonPoint) throws TransformException { - return this.latLonToCrs(latLonPoint.getLongitude(), latLonPoint.getLatitude()); - } - - /** - * Transforms the given longitude-latitude point to an x-y point in this {@link #getCoordinateReferenceSystem() CRS}. - * - * @throws TransformException - * if the required transformation could not be performed - */ - public ProjectionPoint latLonToCrs(double longitude, double latitude) throws TransformException { - if (this.isLatLon) { - // We don't need to do the transformation - return new ProjectionPointImpl(longitude, latitude); - } - // We know x must go first in this array because we selected - // "force longitude-first" when creating the CRS for this grid - double[] point = new double[] { longitude, latitude }; - // Transform to lat-lon in-place - this.latLonToCrs.transform(point, 0, point, 0, 1); - return new ProjectionPointImpl(point[0], point[1]); - } - - /** - * @return true if this crs is lat-lon - */ - public boolean isLatLon() { - return this.isLatLon; - } - - public static void main(String[] args) throws Exception{ - CrsHelper helper = fromCrsCode("CRS:84"); -// boolean valid = helper.isPointValidForCrs(180, 0); -// System.out.println(valid); - LatLonPoint point = helper.crsToLatLon(190,10); - double x = point.getLongitude(); - double y = point.getLatitude(); - System.out.println(point+" ("+x+","+y+")"); - } - -} diff --git a/src/main/java/org/gcube/dataanalysis/geo/utils/Downloader.java b/src/main/java/org/gcube/dataanalysis/geo/utils/Downloader.java deleted file mode 100644 index a2ccdea..0000000 --- a/src/main/java/org/gcube/dataanalysis/geo/utils/Downloader.java +++ /dev/null @@ -1,117 +0,0 @@ -package org.gcube.dataanalysis.geo.utils; - -import java.io.BufferedReader; -import java.io.BufferedWriter; -import java.io.File; -import java.io.FileReader; -import java.io.FileWriter; -import java.io.IOException; -import java.io.InputStreamReader; -import java.io.Reader; -import java.io.Writer; -import java.net.URL; -import java.net.URLConnection; -import java.util.ArrayList; -import java.util.List; - -public class Downloader { - - public static void main(String[] args) throws Exception { - List hfiles = getfiles("netcdf_data.html", "fileServer","http", ".nc"); - System.out.println(hfiles); - System.out.println("Number of links:"+hfiles.size()); - List files = enrichfiles(hfiles); - System.out.println(files); - buildwgetFile("wgetfiles.sh", hfiles, files); - } - - public static void buildwgetFile(String filename, List hfiles, List files) throws Exception{ - int size = hfiles.size(); - BufferedWriter bw = new BufferedWriter(new FileWriter(new File(filename))); - for (int i=0;i enrichfiles(List files) throws Exception{ - List arrayfile = new ArrayList(); - for (String fileh:files){ - String file = fileh.substring(fileh.lastIndexOf("/")+1); - if (file.contains("temperature")) - file = buildTopicString(file,"ENVIRONMENT", "OCEANS"); - else if (file.contains("salinity")) - file = buildTopicString(file,"ENVIRONMENT", "OCEANS"); - else if (file.contains("oxygen")) - file = buildTopicString(file,"ENVIRONMENT", "BIOTA"); - else if (file.contains("phosphate")) - file = buildTopicString(file,"ENVIRONMENT", "BIOTA"); - else if (file.contains("nitrate")) - file = buildTopicString(file,"ENVIRONMENT", "BIOTA"); - else if (file.contains("silicate")) - file = buildTopicString(file,"ENVIRONMENT", "BIOTA"); - else - file = buildTopicString(file,"ENVIRONMENT", "OCEANS"); - arrayfile.add(file); - } - return arrayfile; - } - - public static List getfiles(String filename,String criterion,String initselection, String endselection) throws Exception{ - List files = new ArrayList(); - BufferedReader br = new BufferedReader(new FileReader(new File(filename))); - String line = br.readLine(); - while (line!=null){ - if (line.contains(criterion)){ - String cut = line.substring(line.indexOf(initselection),line.indexOf(endselection)+endselection.length()); - files.add(cut); - } - line = br.readLine(); - } - br.close(); - return files; - } - public static String buildGetterString(String httpstring,String filename){ - return String.format("wget --output-document=%1$s %2$s",filename,httpstring); - } - - public static String buildTopicString(String filename, String... topics){ - int idx = filename.indexOf(".n"); - String file = filename.substring(0,idx); - String ext = filename.substring(idx); - for (String topic:topics){ - file=file+"_"+topic; - } - return file+"_"+ext; - } - - public static void downloadData(String endpoint, String file) throws Exception { - // Send data - String urlStr = endpoint; - URL url = new URL(urlStr); - URLConnection conn = url.openConnection(); - InputStreamReader isr = new InputStreamReader(conn.getInputStream()); - FileWriter fw = new FileWriter(new File(file)); - pipe(isr, fw); - fw.close(); - isr.close(); - } - - private static void pipe(Reader reader, Writer writer) throws IOException { - char[] buf = new char[1024]; - int read = 0; - double bytes = 0; - long i = 0; - while ((read = reader.read(buf)) >= 0) { - writer.write(buf, 0, read); - bytes=(bytes+read); - if (i%1000==0) - System.out.println("B:"+bytes); - i++; - } - - writer.flush(); - } - -} diff --git a/src/main/java/org/gcube/dataanalysis/geo/utils/EnvDataExplorer.java b/src/main/java/org/gcube/dataanalysis/geo/utils/EnvDataExplorer.java deleted file mode 100644 index aaf2903..0000000 --- a/src/main/java/org/gcube/dataanalysis/geo/utils/EnvDataExplorer.java +++ /dev/null @@ -1,317 +0,0 @@ -package org.gcube.dataanalysis.geo.utils; - -import java.util.ArrayList; -import java.util.Arrays; -import java.util.HashMap; -import java.util.LinkedHashMap; -import java.util.List; - -import org.gcube.contentmanagement.graphtools.utils.HttpRequest; -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.gcube.dataanalysis.geo.meta.OGCFormatter; - -import com.vividsolutions.jts.geom.Coordinate; -import com.vividsolutions.jts.geom.Geometry; -import com.vividsolutions.jts.geom.GeometryFactory; -import com.vividsolutions.jts.geom.LinearRing; -import com.vividsolutions.jts.geom.MultiPolygon; -import com.vividsolutions.jts.geom.Point; -import com.vividsolutions.jts.geom.Polygon; -import com.vividsolutions.jts.geom.PrecisionModel; -import com.vividsolutions.jts.geom.impl.CoordinateArraySequence; - -public class EnvDataExplorer { - - private static String callWFS(String geoServer, String layer, double x, double y) { - - float tolerance = 0.25f; - String wfsURL = OGCFormatter.getWfsUrl(geoServer, layer, OGCFormatter.pointToBoundingBox(x, y, tolerance), 1, "json"); - AnalysisLogger.getLogger().debug("EnvDataExplorer-> Requesting URL: " + wfsURL); - String returned = null; - try { - returned = HttpRequest.sendGetRequest(wfsURL, null); - } catch (Exception e) { - AnalysisLogger.getLogger().debug("EnvDataExplorer-> ERROR " + e.getLocalizedMessage()); - } - if (returned != null) - // AnalysisLogger.getLogger().debug("EnvDataExplorer-> Found Intersection: " + returned); - AnalysisLogger.getLogger().debug("EnvDataExplorer-> Found Intersection"); - else - AnalysisLogger.getLogger().debug("EnvDataExplorer-> Found Nothing!"); - - return returned; - } - - private static String callWFS(String geoServer, String layer, double xL, double yL, double xR, double yR) { - - // String wfsURL = OGCFormatter.getWfsUrl(geoServer, layer, OGCFormatter.buildBoundingBox(xL, yL, xR, yR), 0, "json"); - // there is a bug in WFS in the retrieval according to a bounding box: y must be in the range -180;180. then I preferred to take all the features - String wfsURL = OGCFormatter.getWfsUrl(geoServer, layer, null, 0, "json"); - AnalysisLogger.getLogger().debug("EnvDataExplorer-> Requesting URL: " + wfsURL); - String returned = null; - try { - returned = HttpRequest.sendGetRequest(wfsURL, null); - } catch (Exception e) { - AnalysisLogger.getLogger().debug("EnvDataExplorer-> ERROR " + e.getLocalizedMessage()); - } - if (returned != null) - // AnalysisLogger.getLogger().debug("EnvDataExplorer-> Found Intersection: " + returned); - AnalysisLogger.getLogger().debug("EnvDataExplorer-> Found Intersection"); - else - AnalysisLogger.getLogger().debug("EnvDataExplorer-> Found Nothing!"); - - return returned; - } - - public static LinkedHashMap getFeatures(String geoserver, String layer, double x, double y) { - try { - AnalysisLogger.getLogger().debug("Calling WFS towards Geoserver:" + geoserver + " and layer:" + layer); - String jsonString = callWFS(geoserver, layer, x, y); - LinkedHashMap map = JsonMapper.parse(jsonString); - LinkedHashMap mapout = (LinkedHashMap) ((HashMap) map.get("features")).get("properties"); - LinkedHashMap values = new LinkedHashMap(); - for (String key : mapout.keySet()) { - values.put(key, Double.parseDouble(mapout.get(key))); - } - return values; - } catch (Exception e) { - AnalysisLogger.getLogger().debug("EnvDataExplorer-> Error in getting properties"); - return null; - } - } - - public static List getFeatures(String geoserver, String layer, double xL, double yL, double xR, double yR) { - try { - AnalysisLogger.getLogger().debug("Calling WFS towards Geoserver:" + geoserver + " and layer:" + layer); - String jsonString = callWFS(geoserver, layer, xL, yL, xR, yR); - // System.out.println("JSON:"+jsonString); - LinkedHashMap map = JsonMapper.parse(jsonString); - List fpolygons = new ArrayList(); - FeaturedPolygon poly = null; - for (String key : map.keySet()) { - if (key.contains("features")) { - HashMap propertiesMap = (HashMap) map.get(key); - - // cycle on all the properties - for (String properties : propertiesMap.keySet()) { - if (properties.contains("properties")) { - if (poly == null) - poly = new FeaturedPolygon(); - - LinkedHashMap props = (LinkedHashMap) propertiesMap.get(properties); - // fill the properties of the fpolygon - for (String keyprop : props.keySet()) { - try { - // fulfill the FeaturedPolygon - String value = props.get(keyprop); - try { - String lowcaseprop = keyprop.toLowerCase(); - if ((poly.value == null) && !lowcaseprop.startsWith("id") && !lowcaseprop.endsWith("id")) - poly.setValue(Double.parseDouble(value)); - else - poly.addFeature(keyprop, value); - } catch (Exception e2) { - poly.addFeature(keyprop, value); - } - } catch (Exception e) { - } - } - } else if (properties.contains("geometry") && !properties.contains("geometry_")) { - - if (poly == null) - poly = new FeaturedPolygon(); - else if (poly.p != null) { - if (poly.value == null) - poly.value = Double.NaN; - fpolygons.add(poly); - poly = new FeaturedPolygon(); - } - - LinkedHashMap props = (LinkedHashMap) propertiesMap.get(properties); - List coords = WFS2Coordinates(props.toString()); - Geometry p = buildGeometryFromCoordinates(coords); - - if (p != null) { - poly.setPolygon(p); - AnalysisLogger.getLogger().trace(p); - } - /* - * GeometryFactory factory = new GeometryFactory(new PrecisionModel(), 4326); Polygon p = null; if (coords != null) { - * - * Coordinate[] coordarray = new Coordinate[coords.size()]; int i = 0; for (double[] pair : coords) { coordarray[i] = new Coordinate(pair[0], pair[1]); - * - * i++; } // TODO: build a multipoly if the ring is not closed! CoordinateArraySequence coordseq = new CoordinateArraySequence(coordarray); LinearRing ring = new LinearRing(coordseq, factory); p = new Polygon(ring, new LinearRing[] {}, factory); } poly.setPolygon(p); - */ - } - - } - } - }// end for on all the wfs - - if (poly != null) { - if (poly.value == null) - poly.value = Double.NaN; - fpolygons.add(poly); - } - return fpolygons; - } catch (Exception e) { - AnalysisLogger.getLogger().debug("EnvDataExplorer-> Error in getting properties"); - e.printStackTrace(); - return null; - } - } - - public static Geometry buildGeometryFromCoordinates(List coords) { - Geometry p = null; - GeometryFactory factory = new GeometryFactory(new PrecisionModel(), 4326); - - int idx = -1; - List coordinatesArray = new ArrayList(); - List polys = new ArrayList(); - List holespolys = new ArrayList(); - int j = 1; - int i = 1; - - for (double[] pair : coords) { - Coordinate coordPair = new Coordinate(pair[0], pair[1]); - if ((idx = coordinatesArray.indexOf(coordPair)) >= 0) { - // System.out.println("List Contains: "+coordinatesArray.get(idx)); - coordinatesArray.add(coordPair); - if (idx == 0) { - // System.out.println("Switching polygon: "+j+" "+coordinatesArray.get(idx)); - j++; - i = 1; - Polygon pp = sequence2Polygon(factory, coordinatesArray.subList(idx, coordinatesArray.size()), holespolys); - - // System.out.println(pp); - polys.add(pp); - coordinatesArray = new ArrayList(); - } else { - // System.out.println("Linear Ring "+i + " "+coordinatesArray.get(idx)); - i++; - LinearRing ring = sequence2Ring(factory, coordinatesArray.subList(idx, coordinatesArray.size())); - holespolys.add(ring); - coordinatesArray = coordinatesArray.subList(0, idx); - } - } else - coordinatesArray.add(coordPair); - - } - - // build a multipoly if the ring is not closed! - - if (polys.size() > 0) { - // cut the holes - List polysnoholes = new ArrayList(); - for (Polygon pp : polys) { - boolean found = false; - int h = 0; - for (Polygon polnh : polysnoholes) { - if (polnh.covers(pp)) { - // System.out.println("found hole! "+pp+" vs "+polnh); - polysnoholes.set(h, (Polygon) polnh.difference(pp)); - found = true; - } else if (pp.covers(polnh)) { - polysnoholes.set(h, (Polygon) pp.difference(polnh)); - found = true; - } - h++; - } - if (!found) - polysnoholes.add(pp); - } - Polygon[] polyrawarray = polysnoholes.toArray(new Polygon[polysnoholes.size()]); - p = new MultiPolygon(polyrawarray, factory); - } - - return p; - } - - private static LinearRing sequence2Ring(GeometryFactory factory, List coordinatesArray) { - // System.out.println(coordinatesArray); - Coordinate[] coordrawarray = coordinatesArray.toArray(new Coordinate[coordinatesArray.size()]); - CoordinateArraySequence coordseq = new CoordinateArraySequence(coordrawarray); - LinearRing ring = new LinearRing(coordseq, factory); - - return ring; - } - - private static Polygon sequence2Polygon(GeometryFactory factory, List coordinatesArray, List holespolys) { - // System.out.println(coordinatesArray); - Coordinate[] coordrawarray = coordinatesArray.toArray(new Coordinate[coordinatesArray.size()]); - LinearRing[] holes = holespolys.toArray(new LinearRing[holespolys.size()]); - - CoordinateArraySequence coordseq = new CoordinateArraySequence(coordrawarray); - LinearRing ring = new LinearRing(coordseq, factory); - - Polygon p = new Polygon(ring, holes, factory); - return p; - } - - public static List WFS2Coordinates(String wfsgeometry) { - - // geometry935133b1-ba3c-493d-8e18-6fb496ced995={type=MultiPolygon, coordinates={966a275c-23aa-4a43-a943-7e1c7eaf5d65=[[[1.5,125.00000000000011],[1.5,124.5],[2.000000000000057,124.5],[2.000000000000057,125.00000000000011],[1.5,125.00000000000011]]]}}, - String[] coordinatePairs = null; - List dpairs = new ArrayList(); - if (wfsgeometry.toLowerCase().contains("multipolygon")) { - String coordString = "coordinates="; - String coordinates = wfsgeometry.substring(wfsgeometry.indexOf(coordString) + coordString.length()); - coordinates = coordinates.substring(coordinates.indexOf("=") + 1); - if (coordinates.contains("=")) { - coordinates = coordinates.replaceAll("([A-Za-z0-9]|-|_)+=", ""); - coordinates = coordinates.replaceAll("\\],( )+\\[", "],["); - } - coordinatePairs = coordinates.split("\\],\\["); - for (String coord : coordinatePairs) { - coord = coord.replaceAll("(\\[|\\]|\\}|\\{|)", ""); - String[] coordpair = coord.split(","); - double[] dd = new double[2]; - // invert the coordinates as the final must be are long,lat - dd[1] = Double.parseDouble(coordpair[0]); - dd[0] = Double.parseDouble(coordpair[1]); - dpairs.add(dd); - } - } - return dpairs; - } - - public static void main1(String[] args) { - - String geom = "{type=MultiPolygon, coordinates={cce4daf3-966e-4b5f-adea-f88ea2b93d03=[[[-16,-146.49999999999997],[-16,-146.99999999999994],[-15.5,-146.99999999999994],[-15.5,-146.49999999999997],[-16,-146.49999999999997]]]}}"; - List coords = WFS2Coordinates(geom); - - GeometryFactory factory = new GeometryFactory(new PrecisionModel(), 4326); - // GeometryFactory factory = new GeometryFactory(new PrecisionModel(), 0); - /* - * CoordinateArraySequence coords = new CoordinateArraySequence(new Coordinate[] { new Coordinate(12.0, 34.23), new Coordinate(12.000, 54.555), new Coordinate(7, 8), new Coordinate(12.0, 34.23) }); LinearRing ring = new LinearRing(coords, factory); Polygon p = new Polygon(ring, null, factory); CoordinateArraySequence pcoords = new CoordinateArraySequence(new Coordinate[] { new Coordinate(12.0, 34.23),}); - */ - // CoordinateArraySequence coords = new CoordinateArraySequence(new Coordinate[] { new Coordinate(1.5, 125.00000000000011), new Coordinate(1.5, 124.5), new Coordinate(2.000000000000057, 124.5), new Coordinate(2.000000000000057, 125.00000000000011), new Coordinate(1.5, 125.00000000000011) }); - - if (coords != null) { - Coordinate[] coordarray = new Coordinate[coords.size()]; - int i = 0; - for (double[] pair : coords) { - coordarray[i] = new Coordinate(pair[0], pair[1]); - i++; - } - CoordinateArraySequence coordseq = new CoordinateArraySequence(coordarray); - LinearRing ring = new LinearRing(coordseq, factory); - Polygon p = new Polygon(ring, new LinearRing[] {}, factory); - // CoordinateArraySequence pcoords = new CoordinateArraySequence(new Coordinate[] { new Coordinate(-16,-146.49999999999997), }); - CoordinateArraySequence pcoords = new CoordinateArraySequence(new Coordinate[] { new Coordinate(-150, -16), }); - Point po = new Point(pcoords, factory); - // po = p.getCentroid(); - System.out.println("contains: " + p.contains(po) + " boundary: " + p.covers(po)); - } - } - - public static void main(String[] args) { - - String q = "[[[-10.0011869534696,151.288335840039],[-10.0353384533966,151.27859643813],[-10.0228061679999,151.308700562],[-10.0011869534696,151.288335840039]]], e3c47901-3de5-45d2-a272-c6f7d5df1dec=[[[-8.54674625399991,150.53036499],[-8.83403205899992,150.287445068],[-9.20889866086486,150.195933942647],[-9.20555999999993,150.21039],[-9.20777999999995,150.23218],[-9.27360999999991,150.33095],[-9.38638999999995,150.37717],[-9.39873372345699,150.375441317138],[-9.37888717699991,150.41633606],[-9.64140796699991,150.411376953],[-9.68103313399996,150.684051514],[-9.79481071047286,150.758883440934],[-9.74832999999995,150.75027],[-9.73082999999991,150.74884],[-9.70784999999995,150.76262],[-9.7194399999999,150.78802],[-9.73138999999991,150.80304],[-9.74693999999994,150.82163],[-9.81916999999993,150.90026],[-9.85235999999992,150.93539],[-9.89360999999991,150.96274],[-9.98527999999993,151.03055],[-9.99693999999994,151.03943],[-10.0169399999999,151.05996],[-10.0244399999999,151.07303],[-10.0466,151.11809],[-10.0413899999999,151.13666],[-10.03014,151.14818],[-10.0194499999999,151.14875],[-10.0033999999999,151.13893],[-9.98916999999994,151.13637],[-9.94207999999991,151.18817],[-9.93666999999993,151.20053],[-9.93091343037411,151.222140060489],[-9.68598556499995,150.991424561],[-9.45813846599992,150.936889648],[-9.30954170199993,151.03604126],[-9.13122558599991,150.961669922],[-8.80926608999994,151.055862427],[-8.66848054747773,151.099704833311],[-8.63888999999995,151.10107],[-8.56673125859819,151.063276911059],[-8.52198028599992,150.922012329],[-8.54674625399991,150.53036499]],[[-9.43832999999995,150.66666],[-9.44124999999991,150.67997],[-9.42805999999996,150.73191],[-9.42055999999991,150.7462],[-9.40541999999993,150.7615],[-9.41471999999993,150.77777],[-9.43277999999992,150.80442],[-9.45638999999994,150.8283],[-9.52319999999992,150.88692],[-9.64471999999995,150.93219],[-9.65916999999996,150.93055],[-9.67082999999991,150.92163],[-9.68207999999993,150.90387],[-9.67221999999992,150.89177],[-9.67916999999994,150.87523],[-9.71805999999992,150.84692],[-9.68555999999995,150.84412],[-9.65860999999995,150.80163],[-9.66249999999991,150.76331],[-9.66332999999991,150.69135],[-9.66291999999993,150.65804],[-9.65388999999993,150.62274],[-9.62332999999995,150.51443],[-9.5836099999999,150.4905],[-9.44082999999995,150.42746],[-9.4313899999999,150.42331],[-9.41471999999993,150.41999],[-9.40110999999996,150.41999],[-9.38943999999992,150.4219],[-9.37666999999993,150.42609],[-9.35707999999994,150.43913],[-9.33770999999996,150.48044],[-9.34124999999994,150.5022],[-9.35166999999995,150.53028],[-9.37054999999992,150.57135],[-9.38499999999993,150.59802],[-9.40110999999996,150.62149],[-9.4233299999999,150.63734],[-9.43832999999995,150.66666]]], c905ab63-23c2-4587-bdd6-d6d37a56be51=[[[-8.58588343092737,151.123734225448],[-8.59127089890423,151.123748898655],[-8.58637142199996,151.125274658],[-8.58588343092737,151.123734225448]]], 8471299d-4904-4a10-ab00-c6cc5605bf3b=[[[-10.1228941076499,151.06827675758],[-10.1141699999999,151.02582],[-10.1108299999999,150.99831],[-10.1127799999999,150.98331],[-10.1127665622499,150.982996372512],[-10.1466360089999,151.011245728],[-10.1228941076499,151.06827675758]]], d0a0b923-b401-4cec-ac35-c3d8c837bffc=[[[-10.0506772730004,150.931209804608],[-10.0041699999999,150.91553],[-9.92666999999994,150.87774],[-9.83888999999993,150.8269],[-9.80718113528387,150.767019514441],[-10.0277585979999,150.912094116],[-10.0506772730004,150.931209804608]]]}}"; - q = q.replaceAll("([A-Za-z0-9]|-|_)+=", ""); - // q = q.replaceAll("\\], .*=\\[", "],["); - System.out.println(q); - q = q.replaceAll("\\],( )+\\[", "],["); - System.out.println(q); - } -} diff --git a/src/main/java/org/gcube/dataanalysis/geo/utils/FeaturedPolygon.java b/src/main/java/org/gcube/dataanalysis/geo/utils/FeaturedPolygon.java deleted file mode 100644 index 4d0cd3b..0000000 --- a/src/main/java/org/gcube/dataanalysis/geo/utils/FeaturedPolygon.java +++ /dev/null @@ -1,28 +0,0 @@ -package org.gcube.dataanalysis.geo.utils; - -import java.util.LinkedHashMap; - -import com.vividsolutions.jts.geom.Geometry; - -public class FeaturedPolygon { - public Geometry p; - public LinkedHashMap features; - public Double value; - public FeaturedPolygon(){ - - } - - public void setPolygon(Geometry p){ - this.p=p; - } - - public void setValue(Double v){ - this.value=v; - } - - public void addFeature(String key,String value){ - if (features==null) - features = new LinkedHashMap(); - features.put(key,value); - } -} diff --git a/src/main/java/org/gcube/dataanalysis/geo/utils/JsonMapper.java b/src/main/java/org/gcube/dataanalysis/geo/utils/JsonMapper.java deleted file mode 100644 index 81a5a7b..0000000 --- a/src/main/java/org/gcube/dataanalysis/geo/utils/JsonMapper.java +++ /dev/null @@ -1,67 +0,0 @@ -package org.gcube.dataanalysis.geo.utils; - -import java.util.Iterator; -import java.util.LinkedHashMap; -import java.util.Map; -import java.util.Set; -import java.util.UUID; - -import com.google.gson.JsonArray; -import com.google.gson.JsonElement; -import com.google.gson.JsonObject; - -public class JsonMapper { - - - public static LinkedHashMap parse(String json) { - - Object genericobject = new com.google.gson.JsonParser().parse(json); - com.google.gson.JsonObject object = null; - LinkedHashMap map = new LinkedHashMap(); - - if (genericobject instanceof com.google.gson.JsonObject){ - object = (JsonObject) genericobject; - parseMap(map,object); - } - else if (genericobject instanceof com.google.gson.JsonArray){ - JsonArray ArrObject = (JsonArray) new com.google.gson.JsonParser().parse(json); - Iterator iterator = ArrObject.iterator(); - while (iterator.hasNext()) { - JsonElement element = iterator.next(); - if (element instanceof JsonObject){ - if (!element.isJsonPrimitive()) { - parseMap(map, (JsonObject) element); - } - } - else{ - map.put(UUID.randomUUID().toString(), element.toString()); - } - } - } - - return map; - } - - private static void parseMap(LinkedHashMap map, JsonObject object ){ - - Set> set = object.entrySet(); - Iterator> iterator = set.iterator(); - - while (iterator.hasNext()) { - Map.Entry entry = iterator.next(); - String key = entry.getKey(); - JsonElement value = entry.getValue(); - if (map.get(key)!=null){ - key+=UUID.randomUUID(); - } - - if (!value.isJsonPrimitive()) { - map.put(key, parse(value.toString())); - } else { - map.put(key, value.getAsString()); - } - } - - } - -} diff --git a/src/main/java/org/gcube/dataanalysis/geo/utils/NetCDFTemporalPrimitive.java b/src/main/java/org/gcube/dataanalysis/geo/utils/NetCDFTemporalPrimitive.java deleted file mode 100644 index d89dd14..0000000 --- a/src/main/java/org/gcube/dataanalysis/geo/utils/NetCDFTemporalPrimitive.java +++ /dev/null @@ -1,32 +0,0 @@ -package org.gcube.dataanalysis.geo.utils; - -import org.opengis.temporal.TemporalPrimitive; - -public class NetCDFTemporalPrimitive implements TemporalPrimitive{ - - @Override - protected Object clone() throws CloneNotSupportedException { - return super.clone(); - } - - @Override - public boolean equals(Object obj) { - return super.equals(obj); - } - - @Override - protected void finalize() throws Throwable { - super.finalize(); - } - - @Override - public int hashCode() { - return 1; - } - - @Override - public String toString() { - return ""; - } - -} diff --git a/src/main/java/org/gcube/dataanalysis/geo/utils/ThreddsDataExplorer.java b/src/main/java/org/gcube/dataanalysis/geo/utils/ThreddsDataExplorer.java deleted file mode 100644 index a46f178..0000000 --- a/src/main/java/org/gcube/dataanalysis/geo/utils/ThreddsDataExplorer.java +++ /dev/null @@ -1,480 +0,0 @@ -package org.gcube.dataanalysis.geo.utils; - -import java.io.ByteArrayInputStream; -import java.util.ArrayList; -import java.util.Formatter; -import java.util.LinkedHashMap; -import java.util.List; - -import javax.xml.xpath.XPath; -import javax.xml.xpath.XPathConstants; -import javax.xml.xpath.XPathExpression; -import javax.xml.xpath.XPathFactory; - -import org.gcube.contentmanagement.graphtools.utils.HttpRequest; -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.gcube.dataanalysis.ecoengine.utils.Tuple; -import org.w3c.dom.Node; -import org.w3c.dom.NodeList; -import org.xml.sax.InputSource; - -import ucar.ma2.Array; -import ucar.ma2.ArrayDouble; -import ucar.ma2.ArrayFloat; -import ucar.ma2.ArrayInt; -import ucar.ma2.ArrayLong; -import ucar.ma2.Range; -import ucar.ma2.StructureData; -import ucar.ma2.StructureMembers.Member; -import ucar.nc2.constants.FeatureType; -import ucar.nc2.dataset.CoordinateAxis; -import ucar.nc2.dataset.CoordinateAxis1DTime; -import ucar.nc2.dt.GridCoordSystem; -import ucar.nc2.dt.GridDatatype; -import ucar.nc2.dt.grid.GridDataset; -import ucar.nc2.ft.FeatureCollection; -import ucar.nc2.ft.FeatureDataset; -import ucar.nc2.ft.FeatureDatasetFactoryManager; -import ucar.nc2.ft.PointFeatureCollection; -import ucar.nc2.ft.PointFeatureIterator; -import ucar.nc2.ft.point.PointDatasetImpl; -import ucar.nc2.ft.point.standard.StandardPointCollectionImpl; -import ucar.unidata.geoloc.LatLonPointImpl; -import ucar.unidata.geoloc.LatLonRect; - -public class ThreddsDataExplorer { - - // http://thredds.research-infrastructures.eu:8080/thredds/catalog/public/netcdf/catalog.xml - public static String timePrefix = "time:"; - - public static List getFiles(String catalogURL) throws Exception { - - String xml = HttpRequest.sendGetRequest(catalogURL, null); - XPath xpath = XPathFactory.newInstance().newXPath(); - XPathExpression xPathExpression = xpath.compile("//child::*[local-name()='catalog']/child::*[local-name()='dataset']/child::*[local-name()='dataset']"); - InputSource inputSource = new InputSource(new ByteArrayInputStream(xml.getBytes("UTF-8"))); - NodeList nodes = (NodeList) xPathExpression.evaluate(inputSource, XPathConstants.NODESET); - List fileNames = new ArrayList(); - for (int i = 0; i < nodes.getLength(); i++) { - Node node = nodes.item(i); - String name = node.getAttributes().getNamedItem("name").getNodeValue(); - if (name != null) - fileNames.add(name); - } - - return fileNames; - } - - public static LinkedHashMap retrieveDataFromNetCDF(String openDapLink, String layer, double x, double y, double z) { - try { - LinkedHashMap map = new LinkedHashMap(); - if (isGridDataset(openDapLink)) { - AnalysisLogger.getLogger().debug("Managing Grid File"); - return manageGridDataset(layer, openDapLink, x, y, z); - } - /* - * else if (isPointDataset(openDapLink)) { AnalysisLogger.getLogger().debug("Managing Points File"); } - */ - else - AnalysisLogger.getLogger().debug("Warning: the NETCDF file is of an unknown type"); - return map; - } catch (Exception e) { - AnalysisLogger.getLogger().debug("ERROR: " + e.getMessage()); - AnalysisLogger.getLogger().debug(e); - e.printStackTrace(); - return null; - } - } - - public static List retrieveDataFromNetCDF(String openDapLink, String layer, int time, List> triplets, double xL, double xR, double yL, double yR) { - try { - List values = new ArrayList(); - if (isGridDataset(openDapLink)) { - AnalysisLogger.getLogger().debug("Managing Grid File"); - return manageGridDataset(layer, openDapLink, time, triplets, xL, xR, yL, yR); - } - /* - * else if (isPointDataset(openDapLink)) { AnalysisLogger.getLogger().debug("Managing Points File"); } - */ - else - AnalysisLogger.getLogger().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(); - return null; - } - } - - // A GridDatatype is like a specialized Variable that explicitly handles X,Y,Z,T dimensions - public static List manageGridDataset(String layer, String filename, int time, List> triplets, double xL, double xR, double yL, double yR) throws Exception { - List values = new ArrayList(); - 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.getFullName()); - if (layer.equalsIgnoreCase(gdt.getFullName())) { - AnalysisLogger.getLogger().debug("Found layer " + layer + " inside file"); - GridDatatype grid = gds.findGridDatatype(gdt.getName()); - CoordinateAxis zAxis = gdt.getCoordinateSystem().getVerticalAxis(); - CoordinateAxis xAxis = gdt.getCoordinateSystem().getXHorizAxis(); - CoordinateAxis yAxis = gdt.getCoordinateSystem().getYHorizAxis(); - 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()); - }catch(Exception e){}; - double resolutionX = Math.abs((double) (xAxis.getMaxValue() - xAxis.getMinValue()) / (double) xAxis.getShape()[0]); - double resolutionY = Math.abs((double) (yAxis.getMaxValue() - yAxis.getMinValue()) / (double) yAxis.getShape()[0]); - - int tsize = triplets.size(); - long t01 = System.currentTimeMillis(); - LatLonRect llr = null; - AnalysisLogger.getLogger().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(); - int zD = 0; - int xD = 0; - int yD = 0; - if (shapeD.length>2) - { - zD=shapeD[0]; - yD=shapeD[1]; - xD=shapeD[2]; - } - - else if (shapeD.length>1) - { - yD=shapeD[0]; - xD=shapeD[1]; - } - - AnalysisLogger.getLogger().debug("Shape: Z:"+zD+" X:"+ xD+" Y:"+yD); - - AnalysisLogger.getLogger().debug("Layer Information Retrieval ELAPSED Time: " + (System.currentTimeMillis() - t01)); - int rank = data.getRank(); - AnalysisLogger.getLogger().debug("Rank of the layer: " + rank); - - ArrayFloat.D3 data3Float = null; - ArrayDouble.D3 data3Double = null; - ArrayInt.D3 data3Int = null; - ArrayLong.D3 data3Long = null; - ArrayFloat.D2 data2Float = null; - ArrayDouble.D2 data2Double= null; - ArrayInt.D2 data2Int = null; - ArrayLong.D2 data2Long = null; - - if (data.getRank() == 3){ - if (data instanceof ArrayFloat.D3) - data3Float = (ArrayFloat.D3) data; - else if (data instanceof ArrayInt.D3) - data3Int = (ArrayInt.D3) data; - else if (data instanceof ArrayDouble.D3) - data3Double = (ArrayDouble.D3) data; - else if (data instanceof ArrayDouble.D3) - data3Double = (ArrayDouble.D3) data; - else if (data instanceof ArrayLong.D3) - data3Long = (ArrayLong.D3) data; - else - throw new Exception("Layer data format not supported"); - } - else{ - if (data instanceof ArrayFloat.D2) - data2Float = (ArrayFloat.D2) data; - else if (data instanceof ArrayInt.D2) - data2Int = (ArrayInt.D2) data; - else if (data instanceof ArrayDouble.D2) - data2Double = (ArrayDouble.D2) data; - else if (data instanceof ArrayLong.D2) - data2Long = (ArrayLong.D2) data; - else - throw new Exception("Layer data format not supported"); - } - - - double xmin = xAxis.getMinValue(); - double xmax = xAxis.getMaxValue(); - if (((xmax==360) && (xmin==0)) || ((xmax==359.5) && (xmin==0.5))){ - xmax = 180; - xmin=-180; - } - AnalysisLogger.getLogger().debug("X dimension: "+xD+" Xmin:"+ xmax+" Xmax:"+xmin); - - for (int i = 0; i < tsize; i++) { - int zint = 0; - int xint = 0; - int yint = 0; - Tuple triplet = triplets.get(i); - double x = triplet.getElements().get(0); - double y = triplet.getElements().get(1); - if (x == 180) - x = -180; - if (y == 90) - y = -90; - double z = 0; - if (triplet.getElements().size() > 1) - z = triplet.getElements().get(2); - if (resolutionZ > 0) { - if ((zAxis.getMinValue() <= z) && (zAxis.getMaxValue() >= z)) - zint = Math.abs((int) Math.round((z - zAxis.getMinValue()) / resolutionZ)); - } - -// AnalysisLogger.getLogger().debug("Z Index: "+zint); - /* - GridCoordSystem gcs = grid.getCoordinateSystem(); - int[] xy = gcs.findXYindexFromLatLon(x, y, null); - Array datas=grid.readDataSlice(time, zint, xy[1], xy[0]); - */ - if ((xmin <= x) && (xmax >= x)) - xint = (int) Math.round((x - xmin) / resolutionX); - if ((yAxis.getMinValue() <= y) && (yAxis.getMaxValue() >= y)) - yint = (int) Math.round((y - yAxis.getMinValue()) / resolutionY); - Double val = Double.NaN; - if (xint > xD-1) - xint = xD-1; - if (yint > yD-1) - yint = yD-1; - if (zint>zD-1) - zint = zD-1; - if (data3Float != null) - val = Double.valueOf(data3Float.get(zint, yint, xint)); - else if (data3Int != null) - val = Double.valueOf(data3Int.get(zint, yint, xint)); - else if (data3Double != null) - val = Double.valueOf(data3Double.get(zint, yint, xint)); - else if (data3Long != null) - val = Double.valueOf(data3Long.get(zint, yint, xint)); - - else if (data2Float != null) - val = Double.valueOf(data2Float.get(yint, xint)); - else if (data2Int != null) - val = Double.valueOf(data2Int.get(yint, xint)); - else if (data2Double != null) - val = Double.valueOf(data2Double.get(yint, xint)); - else if (data2Long != null) - val = Double.valueOf(data2Long.get(yint, xint)); - - values.add(val); - } - break; - } - } - return values; - } - - // A GridDatatype is like a specialized Variable that explicitly handles X,Y,Z,T dimensions - public static LinkedHashMap manageGridDataset(String layer, String filename, double x, double y, double z) throws Exception { - LinkedHashMap valuesMap = new LinkedHashMap(); - 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.getFullName()); - if (layer.equalsIgnoreCase(gdt.getFullName())) { - AnalysisLogger.getLogger().debug("Found layer " + layer + " inside file"); - GridDatatype grid = gds.findGridDatatype(gdt.getName()); - GridCoordSystem gcs = grid.getCoordinateSystem(); - long timeSteps = 0; - java.util.Date[] dates = null; - if (gcs.hasTimeAxis1D()) { - CoordinateAxis1DTime tAxis1D = gcs.getTimeAxis1D(); - dates = tAxis1D.getTimeDates(); - timeSteps = dates.length; - } else if (gcs.hasTimeAxis()) { - CoordinateAxis tAxis = gcs.getTimeAxis(); - timeSteps = tAxis.getSize(); - } - - CoordinateAxis zAxis = gdt.getCoordinateSystem().getVerticalAxis(); - double resolutionZ = Math.abs((double) (zAxis.getMaxValue() - zAxis.getMinValue()) / (double) zAxis.getShape()[0]); - int zint = 0; - if (resolutionZ > 0) { - if ((zAxis.getMinValue() <= z) && (zAxis.getMaxValue() >= z)) - zint = Math.abs((int) Math.round((z - zAxis.getMinValue()) / resolutionZ)); - } - - AnalysisLogger.getLogger().debug("Z index to take: " + zint); - - int[] xy = gcs.findXYindexFromLatLon(x, y, null); - for (int j = 0; j < timeSteps; j++) { - try { - Array data = grid.readDataSlice(j, zint, xy[1], xy[0]); // note order is t, z, y, x - Double val = takeFirstDouble(data); - if (!val.isNaN()) { - String date = "" + j; - if (dates != null) - date = dates[j].toString(); - 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]); - } - } - break; - } - } - return valuesMap; - } - - public static Double takeFirstDouble(Array data) { - long datal = data.getSize(); - Double val = Double.NaN; - try { - for (int k = 0; k < datal; k++) { - Double testVal = data.getDouble(k); - if (!testVal.isNaN()) { - val = testVal; - break; - } - } - } catch (Exception ee) { - AnalysisLogger.getLogger().debug("ThreddsDataExplorer-> WARNING: Error in getting value: " + ee.getLocalizedMessage()); - } - return val; - } - - // A GridDatatype is like a specialized Variable that explicitly handles X,Y,Z,T dimensions - public LinkedHashMap managePointsDataset(String layer, String filename, double x, double y) throws Exception { - LinkedHashMap valuesMap = new LinkedHashMap(); - float tolerance = 0.25f; - Formatter errlog = new Formatter(); - FeatureDataset fdataset = FeatureDatasetFactoryManager.open(FeatureType.POINT, filename, null, errlog); - PointDatasetImpl ds = (PointDatasetImpl) fdataset; - List lfc = ds.getPointFeatureCollectionList(); - - for (FeatureCollection fc : lfc) { - - StandardPointCollectionImpl spf = (StandardPointCollectionImpl) fc; - PointFeatureIterator iter = null; - while ((y - tolerance > -90) && (x - tolerance > -180) && (y + tolerance < 90) && (x + tolerance < 180)) { - LatLonRect rect = new LatLonRect(new LatLonPointImpl(y - tolerance, x - tolerance), new LatLonPointImpl(y + tolerance, x + tolerance)); - PointFeatureCollection coll = spf.subset(rect, null); - iter = coll.getPointFeatureIterator(100 * 1000); // 100Kb buffer - if (iter.getCount() == 0) - iter.finish(); - else - break; - tolerance = tolerance + 0.25f; - AnalysisLogger.getLogger().debug("ThreddsDataExplorer-> tolerance = " + tolerance); - } - - if (iter != null) { - try { - while (iter.hasNext()) { - ucar.nc2.ft.PointFeature pf = iter.next(); - AnalysisLogger.getLogger().debug("ThreddsDataExplorer-> EarthLoc: " + pf.getLocation()); - AnalysisLogger.getLogger().debug("ThreddsDataExplorer-> 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("ThreddsDataExplorer-> description: " + m.getDescription()); - AnalysisLogger.getLogger().debug("ThreddsDataExplorer-> data param: " + m.getDataParam()); - AnalysisLogger.getLogger().debug("ThreddsDataExplorer-> name: " + m.getName()); - AnalysisLogger.getLogger().debug("ThreddsDataExplorer-> unit: " + m.getUnitsString()); - AnalysisLogger.getLogger().debug("ThreddsDataExplorer-> type: " + m.getDataType()); - Array arr = sd.getArray(m.getName()); - AnalysisLogger.getLogger().debug("ThreddsDataExplorer-> is Time: " + m.getDataType()); - Double val = takeFirstDouble(arr); - - AnalysisLogger.getLogger().debug("ThreddsDataExplorer-> extracted value: " + val); - } - } - AnalysisLogger.getLogger().debug("ThreddsDataExplorer-> EarthTime: "); - } - } finally { - iter.finish(); - } - } - break; - } - return valuesMap; - } - - // 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); - 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("ThreddsDataExplorer-> NOT GRID"); - return false; - } else - return true; - } catch (Throwable e) { - return false; - } - } - - // A GridDatatype is like a specialized Variable that explicitly handles X,Y,Z,T dimensions - public static boolean isPointDataset(String filename) { - try { - Formatter errlog = new Formatter(); - FeatureDataset fdataset = FeatureDatasetFactoryManager.open(FeatureType.POINT, filename, null, errlog); - if (fdataset == null) { - AnalysisLogger.getLogger().debug("ThreddsDataExplorer-> NOT POINT"); - return false; - } else - return true; - } catch (Exception e) { - return false; - } - } - - public static boolean isDataset(String filename) throws Exception { - boolean isdataset = false; - try { - Formatter errlog = new Formatter(); - FeatureType[] fts = FeatureType.values(); - for (int i = 0; i < fts.length; i++) { - FeatureDataset fdataset = FeatureDatasetFactoryManager.open(fts[i], filename, null, errlog); - if (fdataset == null) { - // System.out.printf(fts[i]+": Parse failed --> %s\n",errlog); - } else { - AnalysisLogger.getLogger().debug("ThreddsDataExplorer-> " + fts[i] + " OK!"); - isdataset = true; - } - } - } catch (Exception e) { - } - return isdataset; - } - - public static double adjX(double x) { - /* - * if (x < -180) x = -180; if (x > 180) x = 180; - */ - return x; - } - - public static double adjY(double y) { - /* - * if (y < -90) y = -90; if (y > 90) y = 90; - */ - return y; - } - - public static double getMinX(GridCoordSystem gcs) { - CoordinateAxis xAxis = gcs.getXHorizAxis(); - return adjX(xAxis.getMinValue()); - } - - public static double getMaxX(GridCoordSystem gcs) { - CoordinateAxis xAxis = gcs.getXHorizAxis(); - return adjX(xAxis.getMaxValue()); - } - - public static double getMinY(GridCoordSystem gcs) { - CoordinateAxis yAxis = gcs.getYHorizAxis(); - return adjY(yAxis.getMinValue()); - } - - public static double getMaxY(GridCoordSystem gcs) { - CoordinateAxis yAxis = gcs.getYHorizAxis(); - return adjY(yAxis.getMaxValue()); - } -} diff --git a/src/main/resources/symm.key b/src/main/resources/symm.key deleted file mode 100644 index b113201..0000000 --- a/src/main/resources/symm.key +++ /dev/null @@ -1 +0,0 @@ -< ¬@Qaj¤F€g¸ðQ \ No newline at end of file diff --git a/temperature_annual_1deg.nc b/temperature_annual_1deg.nc deleted file mode 100644 index e946858..0000000 Binary files a/temperature_annual_1deg.nc and /dev/null differ diff --git a/wgetfiles.sh b/wgetfiles.sh deleted file mode 100644 index a944bcb..0000000 --- a/wgetfiles.sh +++ /dev/null @@ -1,48 +0,0 @@ -wget --output-document=temperature_annual_1deg_ENVIRONMENT_OCEANS_.nc http://data.nodc.noaa.gov/thredds/fileServer/woa/WOA09/NetCDFdata/temperature_annual_1deg.nc -wget --output-document=temperature_seasonal_1deg_ENVIRONMENT_OCEANS_.nc http://data.nodc.noaa.gov/thredds/fileServer/woa/WOA09/NetCDFdata/temperature_seasonal_1deg.nc -wget --output-document=temperature_monthly_1deg_ENVIRONMENT_OCEANS_.nc http://data.nodc.noaa.gov/thredds/fileServer/woa/WOA09/NetCDFdata/temperature_monthly_1deg.nc -wget --output-document=salinity_annual_1deg_ENVIRONMENT_OCEANS_.nc http://data.nodc.noaa.gov/thredds/fileServer/woa/WOA09/NetCDFdata/salinity_annual_1deg.nc -wget --output-document=salinity_seasonal_1deg_ENVIRONMENT_OCEANS_.nc http://data.nodc.noaa.gov/thredds/fileServer/woa/WOA09/NetCDFdata/salinity_seasonal_1deg.nc -wget --output-document=salinity_monthly_1deg_ENVIRONMENT_OCEANS_.nc http://data.nodc.noaa.gov/thredds/fileServer/woa/WOA09/NetCDFdata/salinity_monthly_1deg.nc -wget --output-document=dissolved_oxygen_annual_1deg_ENVIRONMENT_BIOTA_.nc http://data.nodc.noaa.gov/thredds/fileServer/woa/WOA09/NetCDFdata/dissolved_oxygen_annual_1deg.nc -wget --output-document=dissolved_oxygen_seasonal_1deg_ENVIRONMENT_BIOTA_.nc http://data.nodc.noaa.gov/thredds/fileServer/woa/WOA09/NetCDFdata/dissolved_oxygen_seasonal_1deg.nc -wget --output-document=dissolved_oxygen_monthly_1deg_ENVIRONMENT_BIOTA_.nc http://data.nodc.noaa.gov/thredds/fileServer/woa/WOA09/NetCDFdata/dissolved_oxygen_monthly_1deg.nc -wget --output-document=oxygen_saturation_annual_1deg_ENVIRONMENT_BIOTA_.nc http://data.nodc.noaa.gov/thredds/fileServer/woa/WOA09/NetCDFdata/oxygen_saturation_annual_1deg.nc -wget --output-document=oxygen_saturation_seasonal_1deg_ENVIRONMENT_BIOTA_.nc http://data.nodc.noaa.gov/thredds/fileServer/woa/WOA09/NetCDFdata/oxygen_saturation_seasonal_1deg.nc -wget --output-document=oxygen_saturation_monthly_1deg_ENVIRONMENT_BIOTA_.nc http://data.nodc.noaa.gov/thredds/fileServer/woa/WOA09/NetCDFdata/oxygen_saturation_monthly_1deg.nc -wget --output-document=apparent_oxygen_utilization_annual_1deg_ENVIRONMENT_BIOTA_.nc http://data.nodc.noaa.gov/thredds/fileServer/woa/WOA09/NetCDFdata/apparent_oxygen_utilization_annual_1deg.nc -wget --output-document=apparent_oxygen_utilization_seasonal_1deg_ENVIRONMENT_BIOTA_.nc http://data.nodc.noaa.gov/thredds/fileServer/woa/WOA09/NetCDFdata/apparent_oxygen_utilization_seasonal_1deg.nc -wget --output-document=apparent_oxygen_utilization_monthly_1deg_ENVIRONMENT_BIOTA_.nc http://data.nodc.noaa.gov/thredds/fileServer/woa/WOA09/NetCDFdata/apparent_oxygen_utilization_monthly_1deg.nc -wget --output-document=phosphate_annual_1deg_ENVIRONMENT_BIOTA_.nc http://data.nodc.noaa.gov/thredds/fileServer/woa/WOA09/NetCDFdata/phosphate_annual_1deg.nc -wget --output-document=phosphate_seasonal_1deg_ENVIRONMENT_BIOTA_.nc http://data.nodc.noaa.gov/thredds/fileServer/woa/WOA09/NetCDFdata/phosphate_seasonal_1deg.nc -wget --output-document=phosphate_monthly_1deg_ENVIRONMENT_BIOTA_.nc http://data.nodc.noaa.gov/thredds/fileServer/woa/WOA09/NetCDFdata/phosphate_monthly_1deg.nc -wget --output-document=silicate_annual_1deg_ENVIRONMENT_BIOTA_.nc http://data.nodc.noaa.gov/thredds/fileServer/woa/WOA09/NetCDFdata/silicate_annual_1deg.nc -wget --output-document=silicate_seasonal_1deg_ENVIRONMENT_BIOTA_.nc http://data.nodc.noaa.gov/thredds/fileServer/woa/WOA09/NetCDFdata/silicate_seasonal_1deg.nc -wget --output-document=silicate_monthly_1deg_ENVIRONMENT_BIOTA_.nc http://data.nodc.noaa.gov/thredds/fileServer/woa/WOA09/NetCDFdata/silicate_monthly_1deg.nc -wget --output-document=nitrate_annual_1deg_ENVIRONMENT_BIOTA_.nc http://data.nodc.noaa.gov/thredds/fileServer/woa/WOA09/NetCDFdata/nitrate_annual_1deg.nc -wget --output-document=nitrate_seasonal_1deg_ENVIRONMENT_BIOTA_.nc http://data.nodc.noaa.gov/thredds/fileServer/woa/WOA09/NetCDFdata/nitrate_seasonal_1deg.nc -wget --output-document=nitrate_monthly_1deg_ENVIRONMENT_BIOTA_.nc http://data.nodc.noaa.gov/thredds/fileServer/woa/WOA09/NetCDFdata/nitrate_monthly_1deg.nc -wget --output-document=temperature_annual_5deg_ENVIRONMENT_OCEANS_.nc http://data.nodc.noaa.gov/thredds/fileServer/woa/WOA09/NetCDFdata/temperature_annual_5deg.nc -wget --output-document=temperature_seasonal_5deg_ENVIRONMENT_OCEANS_.nc http://data.nodc.noaa.gov/thredds/fileServer/woa/WOA09/NetCDFdata/temperature_seasonal_5deg.nc -wget --output-document=temperature_monthly_5deg_ENVIRONMENT_OCEANS_.nc http://data.nodc.noaa.gov/thredds/fileServer/woa/WOA09/NetCDFdata/temperature_monthly_5deg.nc -wget --output-document=salinity_annual_5deg_ENVIRONMENT_OCEANS_.nc http://data.nodc.noaa.gov/thredds/fileServer/woa/WOA09/NetCDFdata/salinity_annual_5deg.nc -wget --output-document=salinity_seasonal_5deg_ENVIRONMENT_OCEANS_.nc http://data.nodc.noaa.gov/thredds/fileServer/woa/WOA09/NetCDFdata/salinity_seasonal_5deg.nc -wget --output-document=salinity_monthly_5deg_ENVIRONMENT_OCEANS_.nc http://data.nodc.noaa.gov/thredds/fileServer/woa/WOA09/NetCDFdata/salinity_monthly_5deg.nc -wget --output-document=dissolved_oxygen_annual_5deg_ENVIRONMENT_BIOTA_.nc http://data.nodc.noaa.gov/thredds/fileServer/woa/WOA09/NetCDFdata/dissolved_oxygen_annual_5deg.nc -wget --output-document=dissolved_oxygen_seasonal_5deg_ENVIRONMENT_BIOTA_.nc http://data.nodc.noaa.gov/thredds/fileServer/woa/WOA09/NetCDFdata/dissolved_oxygen_seasonal_5deg.nc -wget --output-document=dissolved_oxygen_monthly_5deg_ENVIRONMENT_BIOTA_.nc http://data.nodc.noaa.gov/thredds/fileServer/woa/WOA09/NetCDFdata/dissolved_oxygen_monthly_5deg.nc -wget --output-document=oxygen_saturation_annual_5deg_ENVIRONMENT_BIOTA_.nc http://data.nodc.noaa.gov/thredds/fileServer/woa/WOA09/NetCDFdata/oxygen_saturation_annual_5deg.nc -wget --output-document=oxygen_saturation_seasonal_5deg_ENVIRONMENT_BIOTA_.nc http://data.nodc.noaa.gov/thredds/fileServer/woa/WOA09/NetCDFdata/oxygen_saturation_seasonal_5deg.nc -wget --output-document=oxygen_saturation_monthly_5deg_ENVIRONMENT_BIOTA_.nc http://data.nodc.noaa.gov/thredds/fileServer/woa/WOA09/NetCDFdata/oxygen_saturation_monthly_5deg.nc -wget --output-document=apparent_oxygen_utilization_annual_5deg_ENVIRONMENT_BIOTA_.nc http://data.nodc.noaa.gov/thredds/fileServer/woa/WOA09/NetCDFdata/apparent_oxygen_utilization_annual_5deg.nc -wget --output-document=apparent_oxygen_utilization_seasonal_5deg_ENVIRONMENT_BIOTA_.nc http://data.nodc.noaa.gov/thredds/fileServer/woa/WOA09/NetCDFdata/apparent_oxygen_utilization_seasonal_5deg.nc -wget --output-document=apparent_oxygen_utilization_monthly_5deg_ENVIRONMENT_BIOTA_.nc http://data.nodc.noaa.gov/thredds/fileServer/woa/WOA09/NetCDFdata/apparent_oxygen_utilization_monthly_5deg.nc -wget --output-document=phosphate_annual_5deg_ENVIRONMENT_BIOTA_.nc http://data.nodc.noaa.gov/thredds/fileServer/woa/WOA09/NetCDFdata/phosphate_annual_5deg.nc -wget --output-document=phosphate_seasonal_5deg_ENVIRONMENT_BIOTA_.nc http://data.nodc.noaa.gov/thredds/fileServer/woa/WOA09/NetCDFdata/phosphate_seasonal_5deg.nc -wget --output-document=phosphate_monthly_5deg_ENVIRONMENT_BIOTA_.nc http://data.nodc.noaa.gov/thredds/fileServer/woa/WOA09/NetCDFdata/phosphate_monthly_5deg.nc -wget --output-document=silicate_annual_5deg_ENVIRONMENT_BIOTA_.nc http://data.nodc.noaa.gov/thredds/fileServer/woa/WOA09/NetCDFdata/silicate_annual_5deg.nc -wget --output-document=silicate_seasonal_5deg_ENVIRONMENT_BIOTA_.nc http://data.nodc.noaa.gov/thredds/fileServer/woa/WOA09/NetCDFdata/silicate_seasonal_5deg.nc -wget --output-document=silicate_monthly_5deg_ENVIRONMENT_BIOTA_.nc http://data.nodc.noaa.gov/thredds/fileServer/woa/WOA09/NetCDFdata/silicate_monthly_5deg.nc -wget --output-document=nitrate_annual_5deg_ENVIRONMENT_BIOTA_.nc http://data.nodc.noaa.gov/thredds/fileServer/woa/WOA09/NetCDFdata/nitrate_annual_5deg.nc -wget --output-document=nitrate_seasonal_5deg_ENVIRONMENT_BIOTA_.nc http://data.nodc.noaa.gov/thredds/fileServer/woa/WOA09/NetCDFdata/nitrate_seasonal_5deg.nc -wget --output-document=nitrate_monthly_5deg_ENVIRONMENT_BIOTA_.nc http://data.nodc.noaa.gov/thredds/fileServer/woa/WOA09/NetCDFdata/nitrate_monthly_5deg.nc