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ecological-engine-geospatial-extensions
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git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/EcologicalEngineGeoSpatialExtension@129111 82a268e6-3cf1-43bd-a215-b396298e98cf

This commit is contained in:
Gianpaolo Coro 2016-06-14 10:47:46 +00:00
parent 63c5343544
commit 6407ad45f3
17 changed files with 175 additions and 73 deletions
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13
src/main/java/org/gcube/dataanalysis/geo/algorithms/MapsCreator.java
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@ -8,10 +8,13 @@ import java.util.UUID;
import org.gcube.common.scope.api.ScopeProvider;
import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveType;
import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.PrimitiveTypes;
import org.gcube.dataanalysis.ecoengine.interfaces.StandardLocalExternalAlgorithm;
import org.gcube.dataanalysis.ecoengine.utils.DatabaseFactory;
import org.gcube.dataanalysis.ecoengine.utils.DatabaseUtils;
import org.gcube.dataanalysis.geo.meta.PolyMapMetadata;
import org.gcube.dataanalysis.geo.utils.GeospatialDataPublicationLevel;
import org.gcube.spatial.data.gis.model.report.PublishResponse;
import org.hibernate.SessionFactory;
@ -34,6 +37,7 @@ public abstract class MapsCreator extends StandardLocalExternalAlgorithm {
static String infoParameter = "Info";
static String resolutionParameter = "Resolution";
static String layerNameParameter = "MapName";
static String publicationLevel= "PublicationLevel";
static int maxNPoints = 259000;
SessionFactory gisdbconnection = null;
SessionFactory smdbconnection = null;
@ -77,6 +81,13 @@ public abstract class MapsCreator extends StandardLocalExternalAlgorithm {
if (scope == null)
scope = ScopeProvider.instance.get();
log("Using scope:"+scope);
String publicationLevelValue = getInputParameter(publicationLevel);
log("Publication Level:"+publicationLevelValue);
boolean isprivate = false;
if (GeospatialDataPublicationLevel.valueOf(publicationLevelValue)==GeospatialDataPublicationLevel.PRIVATE)
isprivate=true;
//initialize Gis DB parameters
String databaseJdbc = getInputParameter(dburlParameterName);
String databaseUser = getInputParameter(dbuserParameterName);
@ -202,7 +213,7 @@ public abstract class MapsCreator extends StandardLocalExternalAlgorithm {
username = usernameP;
String layerName = config.getParam(layerNameParameter);
PublishResponse response = PolyMapMetadata.publishTable(scope, gisTableName, resolution, username, layerName, defaultStyle, workspace, datastore, purpose, credits, keyword);
PublishResponse response = PolyMapMetadata.publishTable(scope, gisTableName, resolution, username, layerName, defaultStyle, workspace, datastore, purpose, credits, keyword,isprivate);
status = 80;
//analyzing response
if (response == null) {

6
src/main/java/org/gcube/dataanalysis/geo/algorithms/PointsMapsCreator.java
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@ -7,7 +7,10 @@ import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
import org.gcube.dataanalysis.ecoengine.datatypes.ColumnType;
import org.gcube.dataanalysis.ecoengine.datatypes.DatabaseType;
import org.gcube.dataanalysis.ecoengine.datatypes.InputTable;
import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveType;
import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.PrimitiveTypes;
import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.TableTemplates;
import org.gcube.dataanalysis.geo.utils.GeospatialDataPublicationLevel;
public class PointsMapsCreator extends MapsCreator {
@ -31,6 +34,9 @@ public class PointsMapsCreator extends MapsCreator {
@Override
protected void setInputParameters() {
try {
PrimitiveType e = new PrimitiveType(Enum.class.getName(), GeospatialDataPublicationLevel.values(), PrimitiveTypes.ENUMERATED, publicationLevel, "The visibility level of the produced map",""+GeospatialDataPublicationLevel.PRIVATE);
inputs.add(e);
List<TableTemplates> templates = new ArrayList<TableTemplates>();
addRemoteDatabaseInput(databaseParameterName, dburlParameterName, dbuserParameterName, dbpasswordParameterName, "driver", "dialect");
templates.add(TableTemplates.GENERIC);

6
src/main/java/org/gcube/dataanalysis/geo/algorithms/PolygonMapsCreator.java
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@ -7,7 +7,10 @@ import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
import org.gcube.dataanalysis.ecoengine.datatypes.ColumnType;
import org.gcube.dataanalysis.ecoengine.datatypes.DatabaseType;
import org.gcube.dataanalysis.ecoengine.datatypes.InputTable;
import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveType;
import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.PrimitiveTypes;
import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.TableTemplates;
import org.gcube.dataanalysis.geo.utils.GeospatialDataPublicationLevel;
public class PolygonMapsCreator extends MapsCreator {
@ -32,6 +35,9 @@ return "A transducer algorithm to produce a GIS map of filled polygons associate
@Override
protected void setInputParameters() {
try {
PrimitiveType e = new PrimitiveType(Enum.class.getName(), GeospatialDataPublicationLevel.values(), PrimitiveTypes.ENUMERATED, publicationLevel, "The visibility level of the produced map",""+GeospatialDataPublicationLevel.PRIVATE);
inputs.add(e);
List<TableTemplates> templates = new ArrayList<TableTemplates>();
addRemoteDatabaseInput(databaseParameterName, dburlParameterName, dbuserParameterName, dbpasswordParameterName, "driver", "dialect");
templates.add(TableTemplates.GENERIC);

24
src/main/java/org/gcube/dataanalysis/geo/algorithms/RasterDataPublisher.java
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@ -4,6 +4,7 @@ import java.io.File;
import java.util.ArrayList;
import java.util.Arrays;
import org.apache.commons.io.FileDeleteStrategy;
import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveType;
@ -11,7 +12,10 @@ import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveTypesList;
import org.gcube.dataanalysis.ecoengine.datatypes.ServiceType;
import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.PrimitiveTypes;
import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.ServiceParameters;
import org.gcube.dataanalysis.ecoengine.evaluation.bioclimate.InterpolateTables;
import org.gcube.dataanalysis.ecoengine.interfaces.StandardLocalExternalAlgorithm;
import org.gcube.dataanalysis.executor.scripts.OSCommand;
import org.gcube.dataanalysis.geo.utils.GeospatialDataPublicationLevel;
import org.gcube.dataanalysis.geo.utils.ThreddsPublisher;
public class RasterDataPublisher extends StandardLocalExternalAlgorithm{
@ -44,6 +48,11 @@ public class RasterDataPublisher extends StandardLocalExternalAlgorithm{
String abstractField = config.getParam(layerAbstractParam);
String[] topics = config.getParam(TopicsParam).split(AlgorithmConfiguration.listSeparator);
String publicationLevelValue = getInputParameter("PublicationLevel");
log("Publication Level:"+publicationLevelValue);
boolean isprivate = false;
if (GeospatialDataPublicationLevel.valueOf(publicationLevelValue)==GeospatialDataPublicationLevel.PRIVATE)
isprivate=true;
AnalysisLogger.getLogger().debug("scope: "+scope);
AnalysisLogger.getLogger().debug("username: "+username);
@ -53,7 +62,7 @@ public class RasterDataPublisher extends StandardLocalExternalAlgorithm{
AnalysisLogger.getLogger().debug("abstractField: "+abstractField);
AnalysisLogger.getLogger().debug("topics: "+topics);
AnalysisLogger.getLogger().debug("filename: "+fileName);
AnalysisLogger.getLogger().debug("is private: "+isprivate);
if (scope==null || username==null)
throw new Exception ("Service parameters are not set - please contact the Administrators");
@ -94,7 +103,7 @@ public class RasterDataPublisher extends StandardLocalExternalAlgorithm{
String [] topicsListArr = new String[listTopics.size()];
topics = listTopics.toArray(topicsListArr);
boolean result = ThreddsPublisher.publishOnThredds(scope, username, newf.getAbsolutePath(), layerTitle, layerName, abstractField, topics, resolution);
boolean result = ThreddsPublisher.publishOnThredds(scope, username, newf.getAbsolutePath(), layerTitle, layerName, abstractField, topics, resolution,isprivate);
if (result) {
addOutputString("Created map name", layerTitle);
@ -105,13 +114,22 @@ public class RasterDataPublisher extends StandardLocalExternalAlgorithm{
addOutputString("Map creator", username);
}
AnalysisLogger.getLogger().debug("Deleting raster file "+newf.getAbsolutePath());
newf.delete();
try{OSCommand.ExecuteGetLine("rm "+newf.getAbsolutePath(), null);}catch(Exception e){}
FileDeleteStrategy.FORCE.deleteQuietly(newf);
System.gc();
// newf.delete();
status = 100;
}
@Override
protected void setInputParameters() {
try {
PrimitiveType e = new PrimitiveType(Enum.class.getName(), GeospatialDataPublicationLevel.values(), PrimitiveTypes.ENUMERATED, "PublicationLevel", "The visibility level of the produced map",""+GeospatialDataPublicationLevel.PRIVATE);
inputs.add(e);
addStringInput(layerTitleParam, "Title of the geospatial dataset to be shown on GeoExplorer", "Generic Raster Layer");
addStringInput(layerAbstractParam, "Abstract defining the content, the references and usage policies", "Abstract");
addStringInput(layerInnerNameParam, "Name of the inner layer or band to be published as a Map (ignored for non-NetCDF files)", "band_1");

6
src/main/java/org/gcube/dataanalysis/geo/algorithms/SpeciesDistributionsMapsCreatorFromCsquares.java
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@ -7,7 +7,10 @@ import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
import org.gcube.dataanalysis.ecoengine.datatypes.ColumnType;
import org.gcube.dataanalysis.ecoengine.datatypes.DatabaseType;
import org.gcube.dataanalysis.ecoengine.datatypes.InputTable;
import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveType;
import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.PrimitiveTypes;
import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.TableTemplates;
import org.gcube.dataanalysis.geo.utils.GeospatialDataPublicationLevel;
public class SpeciesDistributionsMapsCreatorFromCsquares extends MapsCreator {
@ -31,6 +34,9 @@ public class SpeciesDistributionsMapsCreatorFromCsquares extends MapsCreator {
@Override
protected void setInputParameters() {
try {
PrimitiveType e = new PrimitiveType(Enum.class.getName(), GeospatialDataPublicationLevel.values(), PrimitiveTypes.ENUMERATED, publicationLevel, "The visibility level of the produced map",""+GeospatialDataPublicationLevel.PRIVATE);
inputs.add(e);
List<TableTemplates> templates = new ArrayList<TableTemplates>();
addRemoteDatabaseInput(databaseParameterName, dburlParameterName, dbuserParameterName, dbpasswordParameterName, "driver", "dialect");
templates.add(TableTemplates.GENERIC);

6
src/main/java/org/gcube/dataanalysis/geo/algorithms/SpeciesDistributionsMapsCreatorFromPoints.java
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@ -7,7 +7,10 @@ import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
import org.gcube.dataanalysis.ecoengine.datatypes.ColumnType;
import org.gcube.dataanalysis.ecoengine.datatypes.DatabaseType;
import org.gcube.dataanalysis.ecoengine.datatypes.InputTable;
import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveType;
import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.PrimitiveTypes;
import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.TableTemplates;
import org.gcube.dataanalysis.geo.utils.GeospatialDataPublicationLevel;
public class SpeciesDistributionsMapsCreatorFromPoints extends MapsCreator {
@ -31,6 +34,9 @@ public class SpeciesDistributionsMapsCreatorFromPoints extends MapsCreator {
@Override
protected void setInputParameters() {
try {
PrimitiveType e = new PrimitiveType(Enum.class.getName(), GeospatialDataPublicationLevel.values(), PrimitiveTypes.ENUMERATED, publicationLevel, "The visibility level of the produced map",""+GeospatialDataPublicationLevel.PRIVATE);
inputs.add(e);
List<TableTemplates> templates = new ArrayList<TableTemplates>();
addRemoteDatabaseInput(databaseParameterName, dburlParameterName, dbuserParameterName, dbpasswordParameterName, "driver", "dialect");
templates.add(TableTemplates.GENERIC);

8
src/main/java/org/gcube/dataanalysis/geo/batch/BaseLayerAddonMetadataInsertDev.java
View File

@ -1,5 +1,6 @@
package org.gcube.dataanalysis.geo.batch;
import org.gcube.common.scope.api.ScopeProvider;
import org.gcube.dataanalysis.geo.meta.GenericLayerMetadata;
import org.gcube.dataanalysis.geo.meta.NetCDFMetadata;
import org.opengis.metadata.identification.TopicCategory;
@ -15,11 +16,12 @@ public class BaseLayerAddonMetadataInsertDev {
//static String geoserverurl = "http://geoserver-dev.d4science-ii.research-infrastructures.eu/geoserver";
static String user = "admin";
static String password = "admin";
static String password = "Geey6ohz";
static String workspace= "aquamaps";
// static String workspace= "timeseriesgisdb";
public static void main(String[] args) throws Exception{
ScopeProvider.instance.set("/gcube/devsec");
GenericLayerMetadata metadataInserter = new GenericLayerMetadata();
metadataInserter.setGeonetworkUrl(geonetworkurl);
metadataInserter.setGeonetworkUser(user);
@ -34,7 +36,7 @@ public class BaseLayerAddonMetadataInsertDev {
terrestrialecoregions(metadataInserter);
metadataInserter.insertMetaData();
/*
nafo(metadataInserter);
metadataInserter.insertMetaData();
tdwg(metadataInserter);
@ -43,7 +45,7 @@ public class BaseLayerAddonMetadataInsertDev {
metadataInserter.insertMetaData();
continental(metadataInserter);
metadataInserter.insertMetaData();
*/
}

4
src/main/java/org/gcube/dataanalysis/geo/batch/MetadataInsertDevExample.java
View File

@ -18,8 +18,8 @@ public class MetadataInsertDevExample {
static String geonetworkurl = "http://geoserver-dev2.d4science-ii.research-infrastructures.eu/geonetwork/";
//
static String user = "...";
static String password = "..";
static String user = "admin";
static String password = "Geey6ohz";
static String threddsbaseURL= "thredds-d-d4s.d4science.org";
static String threddsURL = "http://"+threddsbaseURL+"/thredds/catalog/public/netcdf/catalog.xml";

69
src/main/java/org/gcube/dataanalysis/geo/infrastructure/GeoNetworkInspector.java
View File

@ -17,6 +17,7 @@ import org.gcube.spatial.data.geonetwork.GeoNetworkReader;
import org.gcube.spatial.data.geonetwork.LoginLevel;
import org.gcube.spatial.data.geonetwork.configuration.Configuration;
import org.gcube.spatial.data.geonetwork.configuration.ConfigurationManager;
import org.gcube.spatial.data.geonetwork.model.Account;
import org.geotoolkit.metadata.iso.identification.DefaultDataIdentification;
import org.opengis.metadata.Metadata;
import org.opengis.metadata.citation.OnlineResource;
@ -311,36 +312,6 @@ public class GeoNetworkInspector {
AnalysisLogger.getLogger().debug("Features Manager: configuring GeoNetwork");
if (scope != null)
ScopeProvider.instance.set(scope);
else {
AnalysisLogger.getLogger().debug("Features Manager: Using manual configuration of GeoNetwork");
class CustomConfiguration implements Configuration {
@Override
public String getGeoNetworkEndpoint() {
return geonetworkUrl;
}
@Override
public Map<LoginLevel, String> getGeoNetworkPasswords() {
HashMap<LoginLevel, String> map = new HashMap<LoginLevel, String>();
map.put(LoginLevel.DEFAULT, geonetworkPwd);
return map;
}
@Override
public Map<LoginLevel, String> getGeoNetworkUsers() {
HashMap<LoginLevel, String> map = new HashMap<LoginLevel, String>();
map.put(LoginLevel.DEFAULT, geonetworkUser);
return map;
}
@Override
public int getScopeGroup() {
return 0;
}
}
ConfigurationManager.setConfiguration(CustomConfiguration.class);
}
AnalysisLogger.getLogger().debug("Initializing GeoNetwork");
@ -358,19 +329,29 @@ public class GeoNetworkInspector {
public String getGeonetworkUserFromScope() throws Exception {
GeoNetworkReader gn = initGeoNetworkReader();
return gn.getConfiguration().getGeoNetworkUsers().get(LoginLevel.DEFAULT);
return gn.getConfiguration().getScopeConfiguration().getAccounts().get(Account.Type.SCOPE).getUser();
}
public String getGeonetworkPrivateGroup() throws Exception {
GeoNetworkReader gn = initGeoNetworkReader();
return ""+gn.getConfiguration().getScopeConfiguration().getPrivateGroup();
}
public String getGeonetworkPublicGroup() throws Exception {
GeoNetworkReader gn = initGeoNetworkReader();
return ""+gn.getConfiguration().getScopeConfiguration().getPublicGroup();
}
public String getGeonetworkPasswordFromScope() throws Exception {
GeoNetworkReader gn = initGeoNetworkReader();
return gn.getConfiguration().getGeoNetworkPasswords().get(LoginLevel.DEFAULT);
return gn.getConfiguration().getScopeConfiguration().getAccounts().get(Account.Type.SCOPE).getPassword();
}
private Metadata getGNInfobyTitle(String info) throws Exception {
GeoNetworkReader gn = initGeoNetworkReader();
// Form query object
gn.login(LoginLevel.DEFAULT);
gn.login(LoginLevel.ADMIN);
GNSearchRequest req = new GNSearchRequest();
req.addParam(GNSearchRequest.Param.title, info);
// req.addConfig(GNSearchRequest.Config.similarity, "1");
@ -393,7 +374,7 @@ public class GeoNetworkInspector {
GeoNetworkReader gn = initGeoNetworkReader();
// Form query object
gn.login(LoginLevel.DEFAULT);
gn.login(LoginLevel.ADMIN);
GNSearchRequest req = new GNSearchRequest();
req.addParam(GNSearchRequest.Param.title, info);
req.addConfig(GNSearchRequest.Config.similarity, tolerance);
@ -417,7 +398,7 @@ public class GeoNetworkInspector {
GeoNetworkReader gn = initGeoNetworkReader();
// Form query object
gn.login(LoginLevel.DEFAULT);
gn.login(LoginLevel.ADMIN);
GNSearchRequest req = new GNSearchRequest();
req.addParam(GNSearchRequest.Param.any, info);
req.addConfig(GNSearchRequest.Config.similarity, tolerance);
@ -441,7 +422,7 @@ public class GeoNetworkInspector {
GeoNetworkReader gn = initGeoNetworkReader();
// Form query object
gn.login(LoginLevel.DEFAULT);
gn.login(LoginLevel.ADMIN);
GNSearchRequest req = new GNSearchRequest();
req.addParam(GNSearchRequest.Param.title, info);
req.addConfig(GNSearchRequest.Config.similarity, tolerance);
@ -476,7 +457,7 @@ public class GeoNetworkInspector {
GeoNetworkReader gn = initGeoNetworkReader();
AnalysisLogger.getLogger().debug("Initialized GeoNetwork!");
// Form query object
gn.login(LoginLevel.DEFAULT);
gn.login(LoginLevel.ADMIN);
Metadata meta = gn.getById(UUID);
AnalysisLogger.getLogger().debug("Layer with UUID: " + UUID + " successfully Retrieved!");
@ -583,14 +564,22 @@ public class GeoNetworkInspector {
return layerTitle2.replaceAll(punct, " ").replaceAll("( )+", " ");
}
public static void main1(String args[]) throws Exception {
public static void main(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";
GeoNetworkInspector fm = new GeoNetworkInspector();
Metadata meta = fm.getGNInfobyTitle(title);
// Metadata meta = fm.getGNInfobyTitle(title);
// fm.setScope("/gcube/devsec/devVRE");
// fm.setScope("/gcube/devsec/devVRE");
fm.setScope("/gcube/devsec");
// Metadata meta = fm.getGNInfobyUUID("ffd86c4b-e624-493b-b279-2cd20d6b267f");
// Metadata meta = fm.getGNInfobyUUID("0815e357-ebd7-4c02-8dc8-f945eceb870c"); //public
// Metadata meta = fm.getGNInfobyUUID("d57e7f27-9763-4216-a72f-48289f35779f"); //private
Metadata meta = fm.getGNInfobyUUID("c286077b-53e9-4389-aaf8-85fb3cb480a2"); //public
System.out.println("is file? " + fm.isNetCDFFile(meta));
System.out.println("opendap: " + fm.getOpenDapLink(meta));
System.out.println("wcs:" + fm.getWCSLink(meta));
@ -598,7 +587,7 @@ public class GeoNetworkInspector {
System.out.println("thredds:" + fm.getThreddsLink(meta));
}
public static void main(String args[]) throws Exception {
public static void main2(String args[]) throws Exception {
System.out.println(treatTitleForGN("sea/land/lake/ice field composite mask from"));
}
}

15
src/main/java/org/gcube/dataanalysis/geo/meta/GenericLayerMetadata.java
View File

@ -72,6 +72,8 @@ public class GenericLayerMetadata {
private String geoserverUrl = "http://geoserver-dev.d4science-ii.research-infrastructures.eu/geonetwork/";
private String geonetworkUser = "admin";
private String geonetworkPwd = "admin";
private String geonetworkGroup = "3";
private String title = "temperature 04091217ruc.nc";
private String layerName = "T";
private String usageField = "Environmental enrichment";
@ -278,6 +280,14 @@ public class GenericLayerMetadata {
this.geoserverUrl = geoserverUrl;
}
public String getGeonetworkGroup() {
return geonetworkGroup;
}
public void setGeonetworkGroup(String geonetworkGroup) {
this.geonetworkGroup = geonetworkGroup;
}
static File meta2File(Metadata meta) throws IOException, JAXBException {
File temp = File.createTempFile("meta", ".xml");
FileWriter writer = new FileWriter(temp);
@ -458,7 +468,7 @@ public class GenericLayerMetadata {
GNClient client = new GNClient(geonetworkUrl);
client.login(geonetworkUser, geonetworkPwd);
File tmetafile = meta2File(meta);
client.insertMetadata(new GNInsertConfiguration("3", "datasets", "_none_", true), tmetafile);
client.insertMetadata(new GNInsertConfiguration(geonetworkGroup, "datasets", "_none_", true), tmetafile);
tmetafile.delete();
}
@ -635,7 +645,8 @@ public class GenericLayerMetadata {
GNClient client = new GNClient(geonetworkUrl);
client.login(geonetworkUser, geonetworkPwd);
File tmetafile = meta2File(meta);
client.insertMetadata(new GNInsertConfiguration("3", "datasets", "_none_", true), tmetafile);
client.insertMetadata(new GNInsertConfiguration(geonetworkGroup, "datasets", "_none_", true), tmetafile);
tmetafile.delete();
}

10
src/main/java/org/gcube/dataanalysis/geo/meta/PolyMapMetadata.java
View File

@ -1,6 +1,5 @@
package org.gcube.dataanalysis.geo.meta;
import it.geosolutions.geonetwork.util.GNInsertConfiguration;
import it.geosolutions.geoserver.rest.encoder.GSLayerEncoder;
import it.geosolutions.geoserver.rest.encoder.feature.GSFeatureTypeEncoder;
@ -24,7 +23,7 @@ public class PolyMapMetadata {
private static final String crs = "GEOGCS[\"WGS 84\", DATUM[\"World Geodetic System 1984\", SPHEROID[\"WGS 84\", 6378137.0, 298.257223563, AUTHORITY[\"EPSG\",\"7030\"]]," + "AUTHORITY[\"EPSG\",\"6326\"]], PRIMEM[\"Greenwich\", 0.0, AUTHORITY[\"EPSG\",\"8901\"]], UNIT[\"degree\", 0.017453292519943295]," + "AXIS[\"Geodetic longitude\", EAST], AXIS[\"Geodetic latitude\", NORTH], AUTHORITY[\"EPSG\",\"4326\"]]";
public static PublishResponse publishTable(String scope, String tableName, double resolution, String username, String layerName, String defaultStyle, String workspace, String datastore, String purpose, String credits, String keyword) throws Exception {
public static PublishResponse publishTable(String scope, String tableName, double resolution, String username, String layerName, String defaultStyle, String workspace, String datastore, String purpose, String credits, String keyword, boolean isprivate) throws Exception {
GSFeatureTypeEncoder fte = new GSFeatureTypeEncoder();
fte.setEnabled(true);
@ -40,7 +39,12 @@ public class PolyMapMetadata {
GISInterface gis = GISInterface.get();
Configuration gnConfig = gis.getGeoNetworkReader().getConfiguration();
AnalysisLogger.getLogger().debug("Using the following GNetwork:" + gnConfig.getGeoNetworkEndpoint());
PublishResponse resp = gis.publishDBTable(workspace, datastore, fte, le, meta.getMetadata(), new GNInsertConfiguration(gnConfig.getScopeGroup() + "", "datasets", "_none_", true), LoginLevel.DEFAULT);
LoginLevel level = LoginLevel.SCOPE;
if (isprivate)
level = LoginLevel.PRIVATE;
//PublishResponse resp = gis.publishDBTable(workspace, datastore, fte, le, meta.getMetadata(), new GNInsertConfiguration(gnConfig.getScopeGroup() + "", "datasets", "_none_", true), LoginLevel.DEFAULT);
PublishResponse resp = gis.publishDBTable(workspace, datastore, fte, le, meta.getMetadata(), "datasets","_none_", level);
AnalysisLogger.getLogger().debug(resp);
AnalysisLogger.getLogger().debug("ID:" + resp.getReturnedMetaId());
AnalysisLogger.getLogger().debug("Result:" + resp.getMetaOperationResult());

10
src/main/java/org/gcube/dataanalysis/geo/test/TestRasterPublisher.java
View File

@ -2,6 +2,7 @@ package org.gcube.dataanalysis.geo.test;
import java.util.List;
import org.gcube.common.scope.api.ScopeProvider;
import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType;
@ -17,22 +18,25 @@ public class TestRasterPublisher {
public static void main(String[] args) throws Exception {
AlgorithmConfiguration config = new AlgorithmConfiguration();
ScopeProvider.instance.set("/gcube/devsec");
config.setConfigPath("./cfg/");
config.setPersistencePath("./");
config.setAgent("RASTER_DATA_PUBLISHER");
config.setGcubeScope("/gcube/devsec");
config.setParam("ServiceUserName","gianpaolo.coro");
config.setParam("PublicationLevel","PRIVATE");
config.setParam("DatasetTitle", "test raster dataset production");
config.setParam("DatasetAbstract", "test raster dataset production abstract");
config.setParam("InnerLayerName", "adux_pres_1");
config.setParam("RasterFile", "C:/Users/coro/Downloads/adux_pres_portale_test.nc");
config.setParam("Topics", "adux"+AlgorithmConfiguration.listSeparator+"gianpaolo");
config.setParam("SpatialResolution", "-1");
config.setParam("FileNameOnInfra", "adux_pres_portale_test_10.nc");
AnalysisLogger.setLogger(config.getConfigPath() + AlgorithmConfiguration.defaultLoggerFile);
AnalysisLogger.getLogger().debug("Executing: " + config.getAgent());

2
src/main/java/org/gcube/dataanalysis/geo/test/TestStandardLayerMetadataInsert.java
View File

@ -23,6 +23,6 @@ public class TestStandardLayerMetadataInsert {
metadataInserter.setXRightUpper(180);
metadataInserter.setYRightUpper(85.5);
metadataInserter.insertMetaData();
//metadataInserter.insertMetaData("");
}
}

20
src/main/java/org/gcube/dataanalysis/geo/test/maps/TestMapCreation.java
View File

@ -1,5 +1,6 @@
package org.gcube.dataanalysis.geo.test.maps;
import org.gcube.common.scope.api.ScopeProvider;
import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
import org.gcube.dataanalysis.geo.algorithms.PointsMapsCreator;
@ -63,9 +64,12 @@ public static void main(String[] args) throws Exception{
config.setConfigPath(cfg);
// config.setGcubeScope("/gcube/devsec/statVRE");
config.setGcubeScope("/gcube/devsec/devVRE");
ScopeProvider.instance.set("/gcube/devsec/devVRE");
config.setPersistencePath("./");
config.setParam("MapName","Test Polygonal Map Ph 7");
config.setParam("MapName","Test Polygonal Map Ph 10");
config.setParam("PublicationLevel","PRIVATE");
/*
config.setParam("InputTable","occurrence_species_id0045886b_2a7c_4ede_afc4_3157c694b893");
config.setParam("xDimension","decimallongitude");
@ -73,18 +77,28 @@ public static void main(String[] args) throws Exception{
config.setParam("Info","recordedby") ;
config.setParam("Resolution","0.5");
*/
/*
config.setParam("InputTable","testextraction2");
config.setParam("xDimension","x");
config.setParam("yDimension","y");
config.setParam("Info","fvalue") ;
*/
config.setParam("InputTable","code_85e5d927f7094a3ca677a53f4433fed4");
config.setParam("xDimension","longitude");
config.setParam("yDimension","latitude");
config.setParam("Info","longitude") ;
config.setParam("DatabaseUserName","utente");
config.setParam("DatabasePassword","d4science");
config.setParam("DatabaseURL","jdbc:postgresql://statistical-manager.d.d4science.org/testdb");
config.setParam("DatabaseDriver","org.postgresql.Driver");
/*
config.setParam("DatabaseUserName","gcube");
config.setParam("DatabasePassword","d4science2");
config.setParam("DatabaseURL","jdbc:postgresql://localhost/testdb");
config.setParam("DatabaseDriver","org.postgresql.Driver");
*/
config.setParam("Z","0");
config.setParam("user", "postgres");

6
src/main/java/org/gcube/dataanalysis/geo/utils/GeospatialDataPublicationLevel.java Normal file
View File

@ -0,0 +1,6 @@
package org.gcube.dataanalysis.geo.utils;
public enum GeospatialDataPublicationLevel {
PUBLIC,
PRIVATE
}

34
src/main/java/org/gcube/dataanalysis/geo/utils/ThreddsPublisher.java
View File

@ -30,10 +30,10 @@ public class ThreddsPublisher {
String[] topics = {"adux","D4Science"};
double resolution = -1;
AnalysisLogger.setLogger("./cfg/"+AlgorithmConfiguration.defaultLoggerFile);
publishOnThredds(scope, username, fileAbsolutePath, layerTitle, layerName, abstractField, topics, resolution);
publishOnThredds(scope, username, fileAbsolutePath, layerTitle, layerName, abstractField, topics, resolution,false);
}
public static boolean publishOnThredds(String scope,String username, String fileAbsolutePath, String layerTitle, String layerName, String abstractField, String[] topics, double resolution) throws Exception{
public static boolean publishOnThredds(String scope,String username, String fileAbsolutePath, String layerTitle, String layerName, String abstractField, String[] topics, double resolution, boolean isprivate) throws Exception{
//TODO manage faults
String remoteFolder = "/data/content/thredds/public/netcdf/";
List<String> threddsAddress = InfraRetrieval.retrieveServiceAddress("Gis", "THREDDS", scope, "Geoserver");
@ -90,11 +90,11 @@ public class ThreddsPublisher {
AnalysisLogger.getLogger().debug("Adding metadata on GeoNetwork");
if (fileAbsolutePath.endsWith(".nc") && gridded)
publishNetCDFMeta(scope, layerTitle, abstractField, new File(fileAbsolutePath).getName(),layerName,threddServiceAddress,username,topics);
publishNetCDFMeta(scope, layerTitle, abstractField, new File(fileAbsolutePath).getName(),layerName,threddServiceAddress,username,topics,isprivate);
else{
if (resolution==-1 && gridded)
throw new Exception ("Specify valid resolution parameter for non-NetCDF raster datasets");
publishOtherFileMeta(scope, layerTitle, resolution, abstractField, new File(fileAbsolutePath).getName(), threddServiceAddress,username,topics);
publishOtherFileMeta(scope, layerTitle, resolution, abstractField, new File(fileAbsolutePath).getName(), threddServiceAddress,username,topics,isprivate);
}
@ -102,7 +102,7 @@ public class ThreddsPublisher {
return true;
}
private static void publishOtherFileMeta(String scope, String layerTitle, double resolution, String abstractField, String filename, String threddsURL, String username, String [] topics) throws Exception{
private static void publishOtherFileMeta(String scope, String layerTitle, double resolution, String abstractField, String filename, String threddsURL, String username, String [] topics, boolean isprivate) throws Exception{
GenericLayerMetadata metadataInserter = new GenericLayerMetadata();
GeoNetworkInspector gninspector =new GeoNetworkInspector();
@ -110,12 +110,18 @@ public class ThreddsPublisher {
String geonetworkURL = gninspector.getGeonetworkURLFromScope();
String geonetworkUser = gninspector.getGeonetworkUserFromScope();
String geonetworkPassword = gninspector.getGeonetworkPasswordFromScope();
AnalysisLogger.getLogger().debug("GeoNetwork Info: "+geonetworkURL+" "+geonetworkUser);
String geonetworkGroup = "";
if (isprivate)
geonetworkGroup = gninspector.getGeonetworkPrivateGroup();
else
geonetworkGroup = gninspector.getGeonetworkPublicGroup();
AnalysisLogger.getLogger().debug("GeoNetwork Info: "+geonetworkURL+" "+geonetworkUser+" "+geonetworkGroup);
metadataInserter.setGeonetworkUrl(geonetworkURL);
metadataInserter.setGeonetworkPwd(geonetworkPassword);
metadataInserter.setGeonetworkUser(geonetworkUser);
metadataInserter.setGeonetworkGroup(geonetworkGroup);
metadataInserter.setTitle(layerTitle);
metadataInserter.setCategoryTypes("_"+TopicCategory.ENVIRONMENT.name()+"_");
@ -132,11 +138,13 @@ public class ThreddsPublisher {
String [] protocols = {"HTTP"};
AnalysisLogger.getLogger().debug("Publishing in group: "+metadataInserter.getGeonetworkGroup());
AnalysisLogger.getLogger().debug("Inserting custom metadata ");
metadataInserter.customMetaDataInsert(urls,protocols);
}
private static void publishNetCDFMeta(String scope, String layerTitle,String abstractField, String filename, String netCDFLayerName, String threddsURL, String username, String [] topics) throws Exception{
private static void publishNetCDFMeta(String scope, String layerTitle,String abstractField, String filename, String netCDFLayerName, String threddsURL, String username, String [] topics, boolean isprivate) throws Exception{
AnalysisLogger.getLogger().debug("Getting GeoNetwork Info");
GenericLayerMetadata metadataInserter = new GenericLayerMetadata();
@ -145,12 +153,18 @@ public class ThreddsPublisher {
String geonetworkURL = gninspector.getGeonetworkURLFromScope();
String geonetworkUser = gninspector.getGeonetworkUserFromScope();
String geonetworkPassword = gninspector.getGeonetworkPasswordFromScope();
String geonetworkGroup = "";
if (isprivate)
geonetworkGroup = gninspector.getGeonetworkPrivateGroup();
else
geonetworkGroup = gninspector.getGeonetworkPublicGroup();
AnalysisLogger.getLogger().debug("GeoNetwork Info: "+geonetworkURL+" "+geonetworkUser);
AnalysisLogger.getLogger().debug("GeoNetwork Info: "+geonetworkURL+" "+geonetworkUser+" "+geonetworkGroup);
metadataInserter.setGeonetworkUrl(geonetworkURL);
metadataInserter.setGeonetworkPwd(geonetworkPassword);
metadataInserter.setGeonetworkUser(geonetworkUser);
metadataInserter.setGeonetworkGroup(geonetworkGroup);
metadataInserter.setTitle(layerTitle);
metadataInserter.setCategoryTypes("_"+TopicCategory.ENVIRONMENT.name()+"_");
@ -189,7 +203,7 @@ public class ThreddsPublisher {
metadataInserter.setYLeftLow(minY);
metadataInserter.setXRightUpper(maxX);
metadataInserter.setYRightUpper(maxY);
AnalysisLogger.getLogger().debug("Publishing in group: "+metadataInserter.getGeonetworkGroup());
AnalysisLogger.getLogger().debug("Inserting metadata ");
metadataInserter.customMetaDataInsert(urls,protocols);
}

9
src/main/java/org/gcube/dataanalysis/geo/vti/EstimateFishingActivity.java
View File

@ -1,5 +1,6 @@
package org.gcube.dataanalysis.geo.vti;
import java.io.File;
import java.util.ArrayList;
import java.util.Date;
import java.util.List;
@ -140,8 +141,10 @@ public class EstimateFishingActivity extends GridCWP2Coordinates{
"\""+config.getParam(VesselsLongitudesColumn)+"\""+" as fhv04,"+
"\""+config.getParam(VesselsLatitudesColumn)+"\""+" as fhv05 "+
" from "+table+
" where "+"\""+config.getParam(VesselsIDColumn)+"\""+" ="+vesselID+" order by CAST("+"\""+config.getParam(VesselsTimestampsColumn)+"\""+" as timestamp)";
" where "+"CAST(\""+config.getParam(VesselsIDColumn)+"\" as integer)"+" ="+vesselID+" order by CAST("+"\""+config.getParam(VesselsTimestampsColumn)+"\""+" as timestamp)";
AnalysisLogger.getLogger().debug("EstimateFishingActivity: EstimateFishingActivity: Select trajectory: "+selectTrajectory);
List<Object> vesselTrajectory = DatabaseFactory.executeSQLQuery(selectTrajectory, connection);
@ -180,7 +183,9 @@ public class EstimateFishingActivity extends GridCWP2Coordinates{
short [] bathymetry = null;
try{
Bathymetry bathymetryprocessor = new Bathymetry(config.getConfigPath()+"gebco_08.nc");
String bathpath=new File(config.getConfigPath(),"gebco_08.nc").getAbsolutePath();
AnalysisLogger.getLogger().debug("EstimateFishingActivity: searching bathymetry in "+bathpath);
Bathymetry bathymetryprocessor = new Bathymetry(bathpath);
bathymetry = bathymetryprocessor.compute(coordinates);
}catch(Exception e){
AnalysisLogger.getLogger().debug("EstimateFishingActivity: Error - Bathymetry resource not available for the service "+e.getLocalizedMessage());