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Merged
euskalhenriko merged 18 commits into from
Mar 25, 2026
Merged

Feature/upgrade hm #296

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b11f9c9
Modify POM
euskalhenriko Feb 5, 2026
1a5a112
Correct previous HM version
euskalhenriko Feb 10, 2026
1f6d6bb
Remove apache.common.login
euskalhenriko Feb 10, 2026
c3c3ac2
Move to 17
euskalhenriko Feb 10, 2026
6ab0d4f
First step running ant file to upgrade GT, still not compiling
euskalhenriko Feb 10, 2026
4e728d3
Remove singleton annotation as component IS a singleton
euskalhenriko Feb 12, 2026
577ea89
Revert automatic modification as Envelope is a klab custom class
euskalhenriko Feb 12, 2026
af97085
More import arrangements
euskalhenriko Feb 12, 2026
da81300
Solved but need to check why the FileUtils class is not the last version
euskalhenriko Feb 13, 2026
cead232
Apply JAI to ImageM update ant file
euskalhenriko Feb 13, 2026
70d730e
Add jaitools disappeared classes
euskalhenriko Feb 13, 2026
4ab0b10
Remove code with DiskMemImage and the dependencies
euskalhenriko Feb 16, 2026
6b9d2b9
Merge branch 'feature/observation-from-10' into feature/upgrade-hm
euskalhenriko Mar 3, 2026
c4c50f7
Merge branch 'develop' into feature/upgrade-hm
euskalhenriko Mar 6, 2026
c9bd14b
Add exclusion to HM to avoid poi NoSuchMethodException
euskalhenriko Mar 17, 2026
6bd647f
Clean poms
euskalhenriko Mar 20, 2026
f478bcd
[docker build] Add maven plugin to remove offensive library to jar
euskalhenriko Mar 20, 2026
5793d03
[docker build] Use Ant’s built-in zip on archive tasks in plugin
euskalhenriko Mar 20, 2026
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6 changes: 2 additions & 4 deletions ...ube/src/main/java/org/integratedmodelling/adapter/datacube/ChunkedDatacubeRepository.java
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Expand Up @@ -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;
Expand All @@ -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;
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4 changes: 4 additions & 0 deletions adapters/klab.ogc/pom.xml
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Expand Up @@ -60,6 +60,10 @@
<groupId>org.mongodb</groupId>
<artifactId>mongo-java-driver</artifactId>
</exclusion>
<exclusion>
<groupId>edu.colostate.omslab</groupId>
<artifactId>oms</artifactId>
</exclusion>
</exclusions>
</dependency>
<!--- S3 dependencies-->
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2 changes: 1 addition & 1 deletion adapters/klab.ogc/src/main/java/org/integratedmodelling/klab/ogc/RasterAdapter.java
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Expand Up @@ -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" };

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6 changes: 3 additions & 3 deletions adapters/klab.ogc/src/main/java/org/integratedmodelling/klab/ogc/integration/Geoserver.java
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Expand Up @@ -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;
Expand All @@ -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;
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16 changes: 8 additions & 8 deletions adapters/klab.ogc/src/main/java/org/integratedmodelling/klab/ogc/integration/Postgis.java
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Expand Up @@ -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;
Expand All @@ -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 {
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22 changes: 11 additions & 11 deletions ...s/klab.ogc/src/main/java/org/integratedmodelling/klab/ogc/vector/files/VectorEncoder.java
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Expand Up @@ -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;
Expand Down Expand Up @@ -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.
Expand Down Expand Up @@ -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);

/*
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10 changes: 5 additions & 5 deletions .../klab.ogc/src/main/java/org/integratedmodelling/klab/ogc/vector/files/VectorImporter.java
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Expand Up @@ -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;
Expand Down Expand Up @@ -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 {

Expand Down
18 changes: 9 additions & 9 deletions ...klab.ogc/src/main/java/org/integratedmodelling/klab/ogc/vector/files/VectorValidator.java
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Expand Up @@ -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;
Expand Down Expand Up @@ -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;
Expand Down
6 changes: 3 additions & 3 deletions adapters/klab.ogc/src/main/java/org/integratedmodelling/klab/ogc/vector/wfs/WfsEncoder.java
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Expand Up @@ -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;
Expand All @@ -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
Expand Down
6 changes: 3 additions & 3 deletions ...ters/klab.ogc/src/main/java/org/integratedmodelling/klab/ogc/vector/wfs/WfsValidator.java
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Expand Up @@ -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;
Expand All @@ -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.
Expand Down
23 changes: 11 additions & 12 deletions adapters/klab.ogc/src/main/java/org/integratedmodelling/klab/raster/files/RasterEncoder.java
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Expand Up @@ -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;
Expand Down Expand Up @@ -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;
Expand Down
10 changes: 5 additions & 5 deletions ...ters/klab.ogc/src/main/java/org/integratedmodelling/klab/raster/files/RasterImporter.java
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Expand Up @@ -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;
Expand All @@ -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 {
Expand Down
8 changes: 4 additions & 4 deletions ...ers/klab.ogc/src/main/java/org/integratedmodelling/klab/raster/files/RasterValidator.java
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Expand Up @@ -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.
Expand All @@ -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
Expand Down
12 changes: 6 additions & 6 deletions adapters/klab.ogc/src/main/java/org/integratedmodelling/klab/raster/wcs/WcsEncoder.java
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Expand Up @@ -44,9 +44,9 @@
import org.integratedmodelling.klab.raster.files.RasterEncoder;
import org.integratedmodelling.klab.raster.wcs.WCSService.WCSLayer;
import org.integratedmodelling.klab.utils.FileUtils;
import org.opengis.coverage.grid.GridCoverage;
import org.opengis.geometry.DirectPosition;
import org.opengis.geometry.Envelope;
import org.geotools.api.coverage.grid.GridCoverage;
import org.geotools.api.geometry.Position;
import org.geotools.api.geometry.Bounds;

/**
* The Class WcsEncoder.
Expand Down Expand Up @@ -136,10 +136,10 @@ public static File getAdjustedCoverage(InputStream input, IGeometry geometry) {
double[] extent = space.getParameters().get(Geometry.PARAMETER_SPACE_BOUNDINGBOX, double[].class);

GridCoverage2D coverage = OmsRasterReader.readRaster(coverageFile.getAbsolutePath());
Envelope envelope = coverage.getEnvelope();
DirectPosition lowerCorner = envelope.getLowerCorner();
Bounds envelope = coverage.getEnvelope();
Position lowerCorner = envelope.getLowerCorner();
double[] westSouth = lowerCorner.getCoordinate();
DirectPosition upperCorner = envelope.getUpperCorner();
Position upperCorner = envelope.getUpperCorner();
double[] eastNorth = upperCorner.getCoordinate();

org.locationtech.jts.geom.Envelope requestedExtend = new org.locationtech.jts.geom.Envelope(extent[0],
Expand Down
12 changes: 6 additions & 6 deletions adapters/klab.ogc/src/main/java/org/integratedmodelling/klab/stac/STACEncoder.java
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Expand Up @@ -9,7 +9,7 @@
import java.util.stream.Collectors;

import org.geotools.coverage.grid.GridCoverage2D;
import org.geotools.data.FeatureSource;
import org.geotools.api.data.FeatureSource;
import org.geotools.geometry.jts.ReferencedEnvelope;
import org.hortonmachine.gears.io.stac.HMStacCollection;
import org.hortonmachine.gears.io.stac.HMStacItem;
Expand Down Expand Up @@ -60,12 +60,12 @@
import org.locationtech.jts.geom.Envelope;
import org.locationtech.jts.geom.Geometry;
import org.locationtech.jts.geom.Polygon;
import org.opengis.feature.simple.SimpleFeature;
import org.opengis.feature.simple.SimpleFeatureType;
import org.opengis.geometry.DirectPosition;
import org.geotools.api.feature.simple.SimpleFeature;
import org.geotools.api.feature.simple.SimpleFeatureType;
import org.geotools.api.geometry.Position;
import org.geotools.referencing.CRS;
import org.opengis.referencing.FactoryException;
import org.opengis.referencing.crs.CoordinateReferenceSystem;
import org.geotools.api.referencing.FactoryException;
import org.geotools.api.referencing.crs.CoordinateReferenceSystem;

import com.github.davidmoten.aws.lw.client.Client;
import com.github.davidmoten.aws.lw.client.Credentials;
Expand Down
2 changes: 1 addition & 1 deletion adapters/klab.ogc/src/main/java/org/integratedmodelling/klab/stac/STACUtils.java
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Expand Up @@ -11,7 +11,7 @@
import org.integratedmodelling.klab.api.provenance.IArtifact.Type;
import org.integratedmodelling.klab.exceptions.KlabResourceAccessException;
import org.integratedmodelling.klab.utils.DOIReader;
import org.opengis.feature.simple.SimpleFeature;
import org.geotools.api.feature.simple.SimpleFeature;

import com.fasterxml.jackson.core.JsonParseException;

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