Merge to master

adapters/klab.adapter.datacube/pom.xml

@@ -1,6 +1,6 @@
 <project xmlns="http://maven.apache.org/POM/4.0.0"
 	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 https://maven.apache.org/xsd/maven-4.0.0.xsd">
+	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
 	<modelVersion>4.0.0</modelVersion>
 	<parent>
 		<groupId>org.integratedmodelling</groupId>

adapters/klab.adapter.datacube/src/main/java/org/integratedmodelling/adapter/datacube/ChunkedDatacubeRepository.java

@@ -24,10 +24,10 @@
 import java.util.logging.Level;
 
 import javax.annotation.Nullable;
-import javax.media.jai.iterator.RandomIter;
-import javax.media.jai.iterator.RandomIterFactory;
 
 import org.apache.commons.io.FileUtils;
+import org.eclipse.imagen.iterator.RandomIter;
+import org.eclipse.imagen.iterator.RandomIterFactory;
 import org.geotools.coverage.grid.GridCoverage2D;
 import org.integratedmodelling.adapter.datacube.api.IDatacube;
 import org.integratedmodelling.klab.Configuration;
@@ -40,8 +40,6 @@
 import org.integratedmodelling.klab.api.data.IResource.Availability;
 import org.integratedmodelling.klab.api.data.adapters.IKlabData.Builder;
 import org.integratedmodelling.klab.api.data.mediation.IUnit;
-import org.integratedmodelling.klab.api.observations.IState;
-import org.integratedmodelling.klab.api.observations.scale.IExtent;
 import org.integratedmodelling.klab.api.observations.scale.IScale;
 import org.integratedmodelling.klab.api.observations.scale.space.IGrid;
 import org.integratedmodelling.klab.api.observations.scale.space.ISpace;

adapters/klab.ogc/pom.xml

@@ -47,6 +47,22 @@
 			<version>1.68</version>
 		</dependency>
 
+		<dependency>
+	        <groupId>com.fasterxml.jackson.core</groupId>
+	        <artifactId>jackson-core</artifactId>
+	    </dependency>
+
+	    <dependency>
+	        <groupId>com.fasterxml.jackson.core</groupId>
+	        <artifactId>jackson-databind</artifactId>
+
+	    </dependency>
+
+	    <dependency>
+	        <groupId>com.fasterxml.jackson.core</groupId>
+	        <artifactId>jackson-annotations</artifactId>
+	    </dependency>
+
        <dependency>
             <groupId>org.hortonmachine</groupId>
             <artifactId>hm-gears</artifactId>
@@ -56,10 +72,15 @@
                     <groupId>javax.measure</groupId>
                     <artifactId>jsr-275</artifactId>
                 </exclusion>
+
                 <exclusion>
                     <groupId>org.mongodb</groupId>
                     <artifactId>mongo-java-driver</artifactId>
                 </exclusion>
+                <exclusion>
+		            <groupId>edu.colostate.omslab</groupId>
+		            <artifactId>oms</artifactId>
+		        </exclusion>
             </exclusions>
         </dependency>
         <!--- S3 dependencies-->
@@ -68,7 +89,6 @@
             <artifactId>aws-lightweight-client-java</artifactId>
             <version>${s3.version}</version>
         </dependency>
-
 		<!-- <dependency> <groupId>org.geotools.xsd</groupId> <artifactId>gt-xsd-core</artifactId> 
 			<version>${geotools.version}</version> </dependency>
 		<dependency>

adapters/klab.ogc/src/main/java/org/integratedmodelling/klab/ogc/RasterAdapter.java

@@ -75,7 +75,7 @@ public class RasterAdapter implements IResourceAdapter {
 	public static final String INTERPOLATION_TYPE_FIELD = "interpolation";
 
 	/**
-	 * Possible values of interpolation type (JAI classes)
+	 * Possible values of interpolation type (ImageN classes)
 	 */
 	public static final String[] INTERPOLATION_TYPE_VALUES = { "bilinear", "nearest", "bicubic", "bicubic2" };
 

adapters/klab.ogc/src/main/java/org/integratedmodelling/klab/ogc/integration/Geoserver.java

@@ -15,9 +15,10 @@
 import java.util.function.Function;
 
 import javax.annotation.Nullable;
-import javax.media.jai.iterator.RandomIter;
-import javax.media.jai.iterator.RandomIterFactory;
 
+import org.eclipse.imagen.iterator.RandomIter;
+import org.eclipse.imagen.iterator.RandomIterFactory;
+import org.geotools.api.coverage.grid.GridCoverage;
 import org.geotools.coverage.grid.GridCoverage2D;
 import org.geotools.gce.geotiff.GeoTiffReader;
 import org.integratedmodelling.klab.Configuration;
@@ -39,7 +40,6 @@
 import org.integratedmodelling.klab.utils.FileUtils;
 import org.integratedmodelling.klab.utils.MiscUtilities;
 import org.integratedmodelling.klab.utils.NumberUtils;
-import org.opengis.coverage.grid.GridCoverage;
 
 import kong.unirest.GetRequest;
 import kong.unirest.HttpRequestWithBody;

adapters/klab.ogc/src/main/java/org/integratedmodelling/klab/ogc/integration/Postgis.java

@@ -12,16 +12,16 @@
 import java.util.List;
 import java.util.Map;
 
-import org.geotools.data.DataStore;
-import org.geotools.data.DataStoreFinder;
+import org.geotools.api.data.DataStore;
+import org.geotools.api.data.DataStoreFinder;
 import org.geotools.data.DataUtilities;
-import org.geotools.data.FeatureWriter;
-import org.geotools.data.Transaction;
+import org.geotools.api.data.FeatureWriter;
+import org.geotools.api.data.Transaction;
 import org.geotools.data.postgis.PostgisNGDataStoreFactory;
 import org.geotools.data.shapefile.ShapefileDataStore;
 import org.geotools.data.simple.SimpleFeatureCollection;
 import org.geotools.data.simple.SimpleFeatureIterator;
-import org.geotools.data.simple.SimpleFeatureSource;
+import org.geotools.api.data.SimpleFeatureSource;
 import org.geotools.jdbc.JDBCDataStore;
 import org.geotools.util.factory.Hints;
 import org.integratedmodelling.klab.Configuration;
@@ -46,9 +46,9 @@
 import org.integratedmodelling.klab.utils.Parameters;
 import  org.locationtech.jts.geom.Geometry;
 import  org.locationtech.jts.io.WKBReader;
-import org.opengis.feature.simple.SimpleFeature;
-import org.opengis.feature.simple.SimpleFeatureType;
-import org.opengis.feature.type.AttributeDescriptor;
+import org.geotools.api.feature.simple.SimpleFeature;
+import org.geotools.api.feature.simple.SimpleFeatureType;
+import org.geotools.api.feature.type.AttributeDescriptor;
 import org.postgresql.util.PGobject;
 
 public class Postgis extends org.integratedmodelling.klab.persistence.postgis.Postgis {

adapters/klab.ogc/src/main/java/org/integratedmodelling/klab/ogc/vector/files/VectorEncoder.java

@@ -19,11 +19,11 @@
 import java.util.HashMap;
 import java.util.Map;
 
-import org.geotools.data.DataStore;
-import org.geotools.data.DataStoreFinder;
-import org.geotools.data.FeatureSource;
+import org.geotools.api.data.DataStore;
+import org.geotools.api.data.DataStoreFinder;
+import org.geotools.api.data.FeatureSource;
 import org.geotools.data.shapefile.ShapefileDataStoreFactory;
-import org.geotools.data.simple.SimpleFeatureSource;
+import org.geotools.api.data.SimpleFeatureSource;
 import org.geotools.factory.CommonFactoryFinder;
 import org.geotools.feature.FeatureCollection;
 import org.geotools.feature.FeatureIterator;
@@ -68,12 +68,12 @@
 import org.locationtech.jts.geom.MultiPoint;
 import org.locationtech.jts.geom.Point;
 import org.locationtech.jts.geom.Polygon;
-import org.opengis.feature.simple.SimpleFeature;
-import org.opengis.feature.simple.SimpleFeatureType;
-import org.opengis.feature.type.AttributeDescriptor;
-import org.opengis.filter.Filter;
-import org.opengis.filter.FilterFactory2;
-import org.opengis.referencing.crs.CoordinateReferenceSystem;
+import org.geotools.api.feature.simple.SimpleFeature;
+import org.geotools.api.feature.simple.SimpleFeatureType;
+import org.geotools.api.feature.type.AttributeDescriptor;
+import org.geotools.api.filter.Filter;
+import org.geotools.api.filter.FilterFactory;
+import org.geotools.api.referencing.crs.CoordinateReferenceSystem;
 
 /**
  * The Class RasterEncoder.
@@ -139,7 +139,7 @@ public void encodeFromFeatures(FeatureSource<SimpleFeatureType, SimpleFeature> s
             Map<String, String> urnParameters, IGeometry geometry, Builder builder, IContextualizationScope scope) {
 
         Filter filter = null;
-        FilterFactory2 ff = CommonFactoryFinder.getFilterFactory2(GeoTools.getDefaultHints());
+        FilterFactory ff = CommonFactoryFinder.getFilterFactory(GeoTools.getDefaultHints());
         Scale requestScale = geometry instanceof Scale ? (Scale) geometry : Scale.create(geometry);
 
         /*

adapters/klab.ogc/src/main/java/org/integratedmodelling/klab/ogc/vector/files/VectorImporter.java

@@ -13,11 +13,11 @@
 import java.util.Map;
 
 import org.geotools.data.DefaultTransaction;
-import org.geotools.data.Transaction;
+import org.geotools.api.data.Transaction;
 import org.geotools.data.shapefile.ShapefileDataStore;
 import org.geotools.data.shapefile.ShapefileDataStoreFactory;
-import org.geotools.data.simple.SimpleFeatureSource;
-import org.geotools.data.simple.SimpleFeatureStore;
+import org.geotools.api.data.SimpleFeatureSource;
+import org.geotools.api.data.SimpleFeatureStore;
 import org.geotools.feature.DefaultFeatureCollection;
 import org.geotools.feature.FeatureCollection;
 import org.geotools.feature.simple.SimpleFeatureBuilder;
@@ -48,8 +48,8 @@
 import org.locationtech.jts.geom.MultiLineString;
 import org.locationtech.jts.geom.MultiPolygon;
 import org.locationtech.jts.geom.Point;
-import org.opengis.feature.simple.SimpleFeature;
-import org.opengis.feature.simple.SimpleFeatureType;
+import org.geotools.api.feature.simple.SimpleFeature;
+import org.geotools.api.feature.simple.SimpleFeatureType;
 
 public class VectorImporter extends AbstractFilesetImporter {
 

adapters/klab.ogc/src/main/java/org/integratedmodelling/klab/ogc/vector/files/VectorValidator.java

@@ -26,10 +26,10 @@
 import java.util.Map;
 
 import org.eclipse.xtext.util.Arrays;
-import org.geotools.data.DataAccessFactory;
-import org.geotools.data.DataStore;
-import org.geotools.data.DataStoreFinder;
-import org.geotools.data.FeatureSource;
+import org.geotools.api.data.DataAccessFactory;
+import org.geotools.api.data.DataStore;
+import org.geotools.api.data.DataStoreFinder;
+import org.geotools.api.data.FeatureSource;
 import org.geotools.data.shapefile.ShapefileDataStoreFactory;
 import org.geotools.feature.FeatureCollection;
 import org.geotools.feature.FeatureIterator;
@@ -60,11 +60,11 @@
 import org.integratedmodelling.klab.utils.MiscUtilities;
 import org.integratedmodelling.klab.utils.StringUtils;
 import org.integratedmodelling.klab.utils.Utils;
-import org.opengis.feature.simple.SimpleFeature;
-import org.opengis.feature.simple.SimpleFeatureType;
-import org.opengis.feature.type.AttributeDescriptor;
-import org.opengis.filter.Filter;
-import org.opengis.referencing.crs.CoordinateReferenceSystem;
+import org.geotools.api.feature.simple.SimpleFeature;
+import org.geotools.api.feature.simple.SimpleFeatureType;
+import org.geotools.api.feature.type.AttributeDescriptor;
+import org.geotools.api.filter.Filter;
+import org.geotools.api.referencing.crs.CoordinateReferenceSystem;
 
 import org.locationtech.jts.geom.Lineal;
 import org.locationtech.jts.geom.Polygonal;

adapters/klab.ogc/src/main/java/org/integratedmodelling/klab/ogc/vector/wfs/WfsEncoder.java

@@ -17,7 +17,7 @@
 
 import java.io.IOException;
 
-import org.geotools.data.FeatureSource;
+import org.geotools.api.data.FeatureSource;
 import org.geotools.data.wfs.WFSDataStore;
 import org.integratedmodelling.klab.Version;
 import org.integratedmodelling.klab.api.data.IGeometry;
@@ -26,8 +26,8 @@
 import org.integratedmodelling.klab.exceptions.KlabIOException;
 import org.integratedmodelling.klab.ogc.WfsAdapter;
 import org.integratedmodelling.klab.ogc.vector.files.VectorEncoder;
-import org.opengis.feature.simple.SimpleFeature;
-import org.opengis.feature.simple.SimpleFeatureType;
+import org.geotools.api.feature.simple.SimpleFeature;
+import org.geotools.api.feature.simple.SimpleFeatureType;
 
 /**
  * The WFS encoder simply redefines the getFeatureSource method within a vector

adapters/klab.ogc/src/main/java/org/integratedmodelling/klab/ogc/vector/wfs/WfsValidator.java

@@ -19,7 +19,7 @@
 import java.net.URL;
 import java.util.Collection;
 
-import org.geotools.data.FeatureSource;
+import org.geotools.api.data.FeatureSource;
 import org.geotools.data.wfs.WFSDataStore;
 import org.geotools.filter.text.cql2.CQLException;
 import org.geotools.filter.text.ecql.ECQL;
@@ -30,8 +30,8 @@
 import org.integratedmodelling.klab.api.runtime.monitoring.IMonitor;
 import org.integratedmodelling.klab.ogc.WfsAdapter;
 import org.integratedmodelling.klab.ogc.vector.files.VectorValidator;
-import org.opengis.feature.simple.SimpleFeature;
-import org.opengis.feature.simple.SimpleFeatureType;
+import org.geotools.api.feature.simple.SimpleFeature;
+import org.geotools.api.feature.simple.SimpleFeatureType;
 
 /**
  * The Class WcsValidator.

adapters/klab.ogc/src/main/java/org/integratedmodelling/klab/raster/files/RasterEncoder.java

@@ -21,21 +21,24 @@
 import java.util.Map;
 import java.util.Set;
 
-import javax.media.jai.Interpolation;
-import javax.media.jai.InterpolationBicubic;
-import javax.media.jai.InterpolationBicubic2;
-import javax.media.jai.InterpolationBilinear;
-import javax.media.jai.InterpolationNearest;
-import javax.media.jai.iterator.RandomIter;
-import javax.media.jai.iterator.RandomIterFactory;
-
+import org.eclipse.imagen.Interpolation;
+import org.eclipse.imagen.InterpolationBicubic;
+import org.eclipse.imagen.InterpolationBicubic2;
+import org.eclipse.imagen.InterpolationBilinear;
+import org.eclipse.imagen.InterpolationNearest;
+import org.eclipse.imagen.iterator.RandomIter;
+import org.eclipse.imagen.iterator.RandomIterFactory;
+import org.eclipse.imagen.media.range.NoDataContainer;
+import org.geotools.api.coverage.grid.GridCoverage;
+import org.geotools.api.referencing.crs.CoordinateReferenceSystem;
 import org.geotools.coverage.grid.GeneralGridEnvelope;
 import org.geotools.coverage.grid.GridCoverage2D;
 import org.geotools.coverage.grid.GridGeometry2D;
 import org.geotools.coverage.grid.io.AbstractGridFormat;
 import org.geotools.coverage.grid.io.GridCoverage2DReader;
 import org.geotools.coverage.grid.io.GridFormatFinder;
 import org.geotools.coverage.processing.Operations;
+import org.geotools.coverage.util.CoverageUtilities;
 import org.geotools.gce.geotiff.GeoTiffFormat;
 import org.geotools.geometry.jts.ReferencedEnvelope;
 import org.geotools.referencing.CRS;
@@ -67,10 +70,6 @@
 import org.integratedmodelling.klab.scale.Scale;
 import org.integratedmodelling.klab.utils.MiscUtilities;
 import org.integratedmodelling.klab.utils.NumberUtils;
-import org.opengis.coverage.grid.GridCoverage;
-import org.opengis.referencing.crs.CoordinateReferenceSystem;
-import org.geotools.coverage.util.CoverageUtilities;
-import it.geosolutions.jaiext.range.NoDataContainer;
 
 import groovy.lang.Binding;
 import groovy.lang.GroovyShell;

adapters/klab.ogc/src/main/java/org/integratedmodelling/klab/raster/files/RasterImporter.java

@@ -24,9 +24,9 @@
 import org.geotools.data.shapefile.dbf.DbaseFileWriter;
 import org.geotools.gce.geotiff.GeoTiffWriteParams;
 import org.geotools.gce.geotiff.GeoTiffWriter;
-import org.geotools.styling.ColorMap;
-import org.geotools.styling.ColorMapEntry;
-import org.geotools.styling.RasterSymbolizer;
+import org.geotools.api.style.ColorMap;
+import org.geotools.api.style.ColorMapEntry;
+import org.geotools.api.style.RasterSymbolizer;
 import org.integratedmodelling.kim.api.IParameters;
 import org.integratedmodelling.klab.Logging;
 import org.integratedmodelling.klab.Observations;
@@ -51,8 +51,8 @@
 import org.integratedmodelling.klab.utils.Parameters;
 import org.integratedmodelling.klab.utils.Triple;
 import org.integratedmodelling.klab.utils.ZipUtils;
-import org.opengis.parameter.GeneralParameterValue;
-import org.opengis.parameter.ParameterValue;
+import org.geotools.api.parameter.GeneralParameterValue;
+import org.geotools.api.parameter.ParameterValue;
 import it.geosolutions.imageio.plugins.tiff.BaselineTIFFTagSet;
 
 public class RasterImporter extends AbstractFilesetImporter {

adapters/klab.ogc/src/main/java/org/integratedmodelling/klab/raster/files/RasterValidator.java

@@ -45,9 +45,9 @@
 import org.integratedmodelling.klab.utils.FileUtils;
 import org.integratedmodelling.klab.utils.MiscUtilities;
 import org.integratedmodelling.klab.utils.URLUtils;
-import org.opengis.coverage.SampleDimension;
-import org.opengis.geometry.Envelope;
-import org.opengis.referencing.crs.CoordinateReferenceSystem;
+import org.geotools.api.coverage.SampleDimension;
+import org.geotools.api.geometry.Bounds;
+import org.geotools.api.referencing.crs.CoordinateReferenceSystem;
 
 /**
  * The Class RasterValidator.
@@ -72,7 +72,7 @@ public IResource.Builder validate(String urn, URL url, IParameters<String> userD
             AbstractGridFormat format = GridFormatFinder.findFormat(file);
             AbstractGridCoverage2DReader reader = format.getReader(file);
             GridCoverage2D coverage = reader.read(null);
-            Envelope envelope = coverage.getEnvelope();
+            Bounds envelope = coverage.getEnvelope();
             CoordinateReferenceSystem crs = coverage.getCoordinateReferenceSystem();
             GridGeometry2D grid = coverage.getGridGeometry();
             org.integratedmodelling.klab.components.geospace.extents.Envelope refenv = org.integratedmodelling.klab.components.geospace.extents.Envelope