git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/EcologicalEngineGeoSpatialExtension@73360 82a268e6-3cf1-43bd-a215-b396298e98cf
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package org.gcube.dataanalysis.geo.meta.features;
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import it.geosolutions.geonetwork.util.GNSearchRequest;
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import it.geosolutions.geonetwork.util.GNSearchResponse;
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import org.gcube.common.scope.api.ScopeProvider;
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import org.gcube.spatial.data.geonetwork.GeoNetwork;
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import org.gcube.spatial.data.geonetwork.GeoNetworkReader;
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import org.opengis.metadata.Metadata;
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import org.opengis.metadata.citation.OnlineResource;
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import org.opengis.metadata.distribution.DigitalTransferOptions;
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public class FeaturesManager {
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private String geonetworkUrl = "http://geoserver-dev.d4science-ii.research-infrastructures.eu/geonetwork/";
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private String geonetworkUser = "admin";
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private String geonetworkPwd = "admin";
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private String scope = "/gcube/devsec";
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public String getScope() {
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return scope;
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}
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public void setScope(String scope) {
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this.scope = scope;
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}
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private String searchInUrl(Metadata meta, String criterion) {
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String link = null;
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for (DigitalTransferOptions option : meta.getDistributionInfo().getTransferOptions()) {
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for (OnlineResource resource : option.getOnLines()) {
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String tlink = resource.getLinkage().toString();
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if (tlink.toLowerCase().contains(criterion.toLowerCase())) {
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link = tlink;
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break;
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}
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}
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}
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if (link == null)
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System.out.println("NO ONLINE LINK WAS FOUND ACCORDING TO THE CRITERION :" + criterion);
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return link;
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}
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public String getWFSLink(Metadata meta) {
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return searchInUrl(meta, "service=wfs");
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}
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// retrieves the wms link
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public String getWMSLink(Metadata meta) {
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return searchInUrl(meta, "service=wms");
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}
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public String getWCSLink(Metadata meta) {
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return searchInUrl(meta, "service=wcs");
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}
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public String getOpenDapLink(Metadata meta) {
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return searchInUrl(meta, "/dodsC");
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}
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public String getThreddsLink(Metadata meta) {
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return searchInUrl(meta, "catalog.xml");
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}
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public String getLayerName(Metadata meta) {
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String wmslink = getWMSLink(meta);
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String layer = null;
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String finder = "layers=";
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if (wmslink != null) {
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int idxfinder = wmslink.indexOf(finder);
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if (idxfinder > 0) {
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wmslink = wmslink.substring(idxfinder);
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int andIdx = wmslink.indexOf("&");
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if (andIdx < 0)
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andIdx = wmslink.length();
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layer = wmslink.substring(finder.length(), andIdx).trim();
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}
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}
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return layer;
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}
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public boolean isThreddsFile(Metadata meta) {
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return (getOpenDapLink(meta) != null);
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}
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public Metadata getGNInfobyTitle(String info) throws Exception {
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ScopeProvider.instance.set(scope);
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GeoNetworkReader gn = GeoNetwork.get();
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// Form query object
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gn.login();
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GNSearchRequest req = new GNSearchRequest();
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req.addParam(GNSearchRequest.Param.title, info);
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GNSearchResponse resp = gn.query(req);
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Metadata meta = null;
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if (resp.getCount() != 0)
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for (GNSearchResponse.GNMetadata metadata : resp) {
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meta = gn.getById(metadata.getUUID());
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break;
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}
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return meta;
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}
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public String getGeonetworkUrl() {
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return geonetworkUrl;
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}
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public void setGeonetworkUrl(String geonetworkUrl) {
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this.geonetworkUrl = geonetworkUrl;
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}
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public String getGeonetworkUser() {
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return geonetworkUser;
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}
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public void setGeonetworkUser(String geonetworkUser) {
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this.geonetworkUser = geonetworkUser;
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}
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public String getGeonetworkPwd() {
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return geonetworkPwd;
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}
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public void setGeonetworkPwd(String geonetworkPwd) {
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this.geonetworkPwd = geonetworkPwd;
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}
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public static void main(String args[]) throws Exception {
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// String title = "temperature (04091217ruc.nc)";
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// String title = "Bathymetry";
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String title = "FAO aquatic species distribution map of Melanogrammus aeglefinus";
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FeaturesManager fm = new FeaturesManager();
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Metadata meta = fm.getGNInfobyTitle(title);
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System.out.println("is file? " + fm.isThreddsFile(meta));
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System.out.println("opendap: " + fm.getOpenDapLink(meta));
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System.out.println("wcs:" + fm.getWCSLink(meta));
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System.out.println("wms:" + fm.getWMSLink(meta));
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System.out.println("thredds:" + fm.getThreddsLink(meta));
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}
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}
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package org.gcube.dataanalysis.geo.meta.test;
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import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
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import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
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import org.gcube.dataanalysis.geo.retrieval.GeoIntersector;
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public class TestIntersectionNetCDF {
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public static void main(String args[] ) throws Exception{
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AnalysisLogger.setLogger("./cfg/"+AlgorithmConfiguration.defaultLoggerFile);
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GeoIntersector inters = new GeoIntersector("/gcube/devsec");
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System.out.println(inters.getFeaturesInTime("temperature (04091217ruc.nc)", 0.1, 0.1));
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}
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}
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package org.gcube.dataanalysis.geo.retrieval;
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import java.util.LinkedHashMap;
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import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
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import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
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import org.gcube.dataanalysis.geo.meta.features.FeaturesManager;
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import org.gcube.dataanalysis.geo.utils.EnvDataExplorer;
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import org.gcube.dataanalysis.geo.utils.ThreddsDataExplorer;
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import org.opengis.metadata.Metadata;
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public class GeoIntersector {
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private FeaturesManager featurer;
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public GeoIntersector(String scope) {
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featurer = new FeaturesManager();
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featurer.setScope(scope);
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}
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public LinkedHashMap<String, Double> getFeaturesInTime(String layerTitle, double x, double y) throws Exception {
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LinkedHashMap<String, Double> features = new LinkedHashMap<String, Double>();
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// get the layer
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Metadata meta = featurer.getGNInfobyTitle(layerTitle);
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// if the layer is good
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if (meta != null) {
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String layer = featurer.getLayerName(meta);
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if (layer == null)
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layer = layerTitle;
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// check if it is a NetCDF
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if (featurer.isThreddsFile(meta)) {
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System.out.println("found a netCDF file with title " + layerTitle+" and layer name "+layer);
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features = getFeaturesFromNetCDF(featurer.getOpenDapLink(meta), layer, x, y);
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} else {
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System.out.println("found a Geo Layer with title " + layerTitle+" and layer name "+layer);
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features = getFeaturesFromWFS(featurer.getWFSLink(meta), layer, x, y);
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}
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}
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return features;
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}
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private LinkedHashMap<String, Double> getFeaturesFromNetCDF(String opendapURL, String layer, double x, double y) {
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if (opendapURL == null)
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return null;
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return ThreddsDataExplorer.retrieveDataFromNetCDF(opendapURL, layer, x, y);
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}
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private LinkedHashMap<String, Double> getFeaturesFromWFS(String wfsUrl, String layer, double x, double y) {
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if (wfsUrl == null)
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return null;
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return EnvDataExplorer.getFeatures(wfsUrl, layer, x, y);
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}
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public static void main(String args[] ) throws Exception{
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AnalysisLogger.setLogger("./cfg/"+AlgorithmConfiguration.defaultLoggerFile);
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GeoIntersector inters = new GeoIntersector("/gcube/devsec");
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// System.out.println(inters.getFeaturesInTime("temperature (04091217ruc.nc)", 0.1, 0.1));
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System.out.println(inters.getFeaturesInTime("occpoints_occ50f01212e04247c288b603c93c4325cd", 0.1, 0.1));
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}
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}
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package org.gcube.dataanalysis.geo.utils;
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import java.util.HashMap;
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import java.util.LinkedHashMap;
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import org.gcube.contentmanagement.graphtools.utils.HttpRequest;
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import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
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import org.gcube.dataanalysis.geo.meta.OGCFormatter;
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public class EnvDataExplorer {
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private static String callWFS(String geoServer, String layer, double x, double y) {
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float tolerance = 0.25f;
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String wfsURL = OGCFormatter.getWfsUrl(geoServer, layer, OGCFormatter.pointToBoundingBox(x, y, tolerance), 1, "json");
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AnalysisLogger.getLogger().debug("EnvDataExplorer-> Requesting URL: " + wfsURL);
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String returned = null;
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try {
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returned = HttpRequest.sendGetRequest(wfsURL, null);
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} catch (Exception e) {
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AnalysisLogger.getLogger().debug("EnvDataExplorer-> ERROR " + e.getLocalizedMessage());
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}
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if (returned != null)
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AnalysisLogger.getLogger().debug("EnvDataExplorer-> Found Intersection: " + returned);
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else
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AnalysisLogger.getLogger().debug("EnvDataExplorer-> Found Nothing!");
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return returned;
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}
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public static LinkedHashMap<String, Double> getFeatures(String geoserver, String layer, double x, double y) {
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try {
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String jsonString = callWFS(geoserver, layer, x, y);
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LinkedHashMap<String, Object> map = JsonMapper.parse(jsonString);
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LinkedHashMap<String, String> mapout = (LinkedHashMap<String, String>) ((HashMap<String, Object>) map.get("features")).get("properties");
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LinkedHashMap<String, Double> values = new LinkedHashMap<String, Double>();
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for (String key:mapout.keySet()){
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values.put(key, Double.parseDouble(mapout.get(key)));
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}
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return values;
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} catch (Exception e) {
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AnalysisLogger.getLogger().debug("EnvDataExplorer-> Error in getting properties");
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return null;
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}
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}
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}
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package org.gcube.dataanalysis.geo.utils;
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import java.util.Iterator;
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import java.util.LinkedHashMap;
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import java.util.Map;
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import java.util.Set;
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import com.google.gson.JsonArray;
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import com.google.gson.JsonElement;
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import com.google.gson.JsonObject;
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public class JsonMapper {
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public static LinkedHashMap<String, Object> parse(String json) {
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Object genericobject = new com.google.gson.JsonParser().parse(json);
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com.google.gson.JsonObject object = null;
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LinkedHashMap<String, Object> map = new LinkedHashMap<String, Object>();
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if (genericobject instanceof com.google.gson.JsonObject){
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object = (JsonObject) genericobject;
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parseMap(map,object);
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}
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else if (genericobject instanceof com.google.gson.JsonArray){
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JsonArray ArrObject = (JsonArray) new com.google.gson.JsonParser().parse(json);
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Iterator<JsonElement> iterator = ArrObject.iterator();
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while (iterator.hasNext()) {
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JsonElement element = iterator.next();
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if (element instanceof JsonObject){
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if (!element.isJsonPrimitive()) {
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parseMap(map, (JsonObject) element);
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}
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}
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}
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}
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return map;
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}
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private static void parseMap(LinkedHashMap<String, Object> map, JsonObject object ){
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Set<Map.Entry<String, JsonElement>> set = object.entrySet();
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Iterator<Map.Entry<String, JsonElement>> iterator = set.iterator();
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while (iterator.hasNext()) {
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Map.Entry<String, JsonElement> entry = iterator.next();
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String key = entry.getKey();
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JsonElement value = entry.getValue();
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if (!value.isJsonPrimitive()) {
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map.put(key, parse(value.toString()));
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} else {
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map.put(key, value.getAsString());
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}
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}
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}
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}
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package org.gcube.dataanalysis.geo.utils;
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import java.io.ByteArrayInputStream;
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import java.util.ArrayList;
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import java.util.Formatter;
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import java.util.LinkedHashMap;
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import java.util.List;
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import javax.xml.xpath.XPath;
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import javax.xml.xpath.XPathConstants;
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import javax.xml.xpath.XPathExpression;
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import javax.xml.xpath.XPathFactory;
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import org.gcube.contentmanagement.graphtools.utils.HttpRequest;
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import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
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import org.w3c.dom.Node;
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import org.w3c.dom.NodeList;
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import org.xml.sax.InputSource;
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import ucar.ma2.Array;
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import ucar.ma2.StructureData;
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import ucar.ma2.StructureMembers.Member;
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import ucar.nc2.constants.FeatureType;
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import ucar.nc2.dataset.CoordinateAxis;
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import ucar.nc2.dataset.CoordinateAxis1DTime;
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import ucar.nc2.dt.GridCoordSystem;
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import ucar.nc2.dt.GridDatatype;
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import ucar.nc2.dt.grid.GridDataset;
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import ucar.nc2.ft.FeatureCollection;
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import ucar.nc2.ft.FeatureDataset;
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import ucar.nc2.ft.FeatureDatasetFactoryManager;
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import ucar.nc2.ft.PointFeatureCollection;
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import ucar.nc2.ft.PointFeatureIterator;
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import ucar.nc2.ft.point.PointDatasetImpl;
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import ucar.nc2.ft.point.standard.StandardPointCollectionImpl;
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import ucar.unidata.geoloc.LatLonPointImpl;
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import ucar.unidata.geoloc.LatLonRect;
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public class ThreddsDataExplorer {
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// http://thredds.research-infrastructures.eu:8080/thredds/catalog/public/netcdf/catalog.xml
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public static String timePrefix = "time:";
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public static List<String> getFiles(String catalogURL) throws Exception {
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String xml = HttpRequest.sendGetRequest(catalogURL, null);
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XPath xpath = XPathFactory.newInstance().newXPath();
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XPathExpression xPathExpression = xpath.compile("//child::*[local-name()='catalog']/child::*[local-name()='dataset']/child::*[local-name()='dataset']");
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InputSource inputSource = new InputSource(new ByteArrayInputStream(xml.getBytes("UTF-8")));
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NodeList nodes = (NodeList) xPathExpression.evaluate(inputSource, XPathConstants.NODESET);
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List<String> fileNames = new ArrayList<String>();
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for (int i = 0; i < nodes.getLength(); i++) {
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Node node = nodes.item(i);
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String name = node.getAttributes().getNamedItem("name").getNodeValue();
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if (name != null)
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fileNames.add(name);
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}
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return fileNames;
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}
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public static LinkedHashMap<String, Double> retrieveDataFromNetCDF(String openDapLink, String layer, double x, double y) {
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try {
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LinkedHashMap<String, Double> map = new LinkedHashMap<String, Double>();
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if (isGridDataset(openDapLink)) {
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AnalysisLogger.getLogger().debug("Managing Grid File");
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return manageGridDataset(layer, openDapLink, x, y);
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}
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/*
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* else if (isPointDataset(openDapLink)) { AnalysisLogger.getLogger().debug("Managing Points File"); }
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*/
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else
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AnalysisLogger.getLogger().debug("Warning: the NETCDF file is of an unknown type");
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return map;
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} catch (Exception e) {
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AnalysisLogger.getLogger().debug("ERROR: " + e.getMessage());
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AnalysisLogger.getLogger().debug(e);
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e.printStackTrace();
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return null;
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}
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}
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// A GridDatatype is like a specialized Variable that explicitly handles X,Y,Z,T dimensions
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public static LinkedHashMap<String, Double> manageGridDataset(String layer, String filename, double x, double y) throws Exception {
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LinkedHashMap<String, Double> valuesMap = new LinkedHashMap<String, Double>();
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GridDataset gds = ucar.nc2.dt.grid.GridDataset.open(filename);
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List<GridDatatype> gridTypes = gds.getGrids();
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for (GridDatatype gdt : gridTypes) {
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AnalysisLogger.getLogger().debug("Inside File - layer name: "+gdt.getFullName());
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if (layer.equalsIgnoreCase(gdt.getFullName())) {
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AnalysisLogger.getLogger().debug("Found layer "+layer +" inside file");
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GridDatatype grid = gds.findGridDatatype(gdt.getName());
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GridCoordSystem gcs = grid.getCoordinateSystem();
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long timeSteps = 0;
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java.util.Date[] dates = null;
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if (gcs.hasTimeAxis1D()) {
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CoordinateAxis1DTime tAxis1D = gcs.getTimeAxis1D();
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dates = tAxis1D.getTimeDates();
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timeSteps = dates.length;
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} else if (gcs.hasTimeAxis()) {
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CoordinateAxis tAxis = gcs.getTimeAxis();
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timeSteps = tAxis.getSize();
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}
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int[] xy = gcs.findXYindexFromLatLon(y, x, null);
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for (int j = 0; j < timeSteps; j++) {
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Array data = grid.readDataSlice(j, 0, xy[1], xy[0]); // note order is t, z, y, x
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Double val = takeFirstDouble(data);
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if (!val.isNaN()) {
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String date = "" + j;
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if (dates != null)
|
||||
date = dates[j].toString();
|
||||
valuesMap.put(timePrefix + date, Double.parseDouble("" + val));
|
||||
}
|
||||
}
|
||||
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<String, String> managePointsDataset(String layer, String filename, double x, double y) throws Exception {
|
||||
LinkedHashMap<String, String> valuesMap = new LinkedHashMap<String, String>();
|
||||
float tolerance = 0.25f;
|
||||
Formatter errlog = new Formatter();
|
||||
FeatureDataset fdataset = FeatureDatasetFactoryManager.open(FeatureType.POINT, filename, null, errlog);
|
||||
PointDatasetImpl ds = (PointDatasetImpl) fdataset;
|
||||
List<FeatureCollection> 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<Member> 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 {
|
||||
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 (Exception 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;
|
||||
}
|
||||
|
||||
}
|
||||
Loading…
Reference in New Issue